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Hasnain AC, Stark A, Trick AY, Ma K, Hsieh K, Cheng Y, Meltzer SJ, Wang TH. Cancer Methylation Biomarker Detection in an Automated, Portable, Multichannel Magnetofluidic Platform. ACS Nano 2024. [PMID: 38669469 DOI: 10.1021/acsnano.3c10070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/28/2024]
Abstract
Early detection of cancer is critical to improving clinical outcomes, especially in territories with limited healthcare resources. DNA methylation biomarkers have shown promise in early cancer detection, but typical workflows require highly trained personnel and specialized equipment for manual and lengthy processing, limiting use in resource-constrained areas. As a potential solution, we introduce the Automated Cartridge-based Cancer Early Screening System (ACCESS), a compact, portable, multiplexed, automated platform that performs droplet magnetofluidic- and methylation-specific qPCR-based assays for the detection of DNA methylation cancer biomarkers. Development of ACCESS focuses on esophageal cancer, which is among the most prevalent cancers in low- and middle-income countries with extremely low survival rates. Upon implementing detection assays for two esophageal cancer methylation biomarkers within ACCESS, we demonstrated successful detection of both biomarkers from esophageal tumor tissue samples from eight esophageal cancer patients while showing specificity in paired normal esophageal tissue samples. These results illustrate ACCESS's potential as an amenable epigenetic diagnostic tool for resource-constrained areas toward early detection of esophageal cancer and potentially other malignancies.
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Affiliation(s)
- Alexander C Hasnain
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Alejandro Stark
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Alexander Y Trick
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Ke Ma
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, United States
| | - Kuangwen Hsieh
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Yulan Cheng
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, United States
| | - Stephen J Meltzer
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland 21287, United States
| | - Tza-Huei Wang
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Department of Mechanical Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
- Institute for NanoBiotechnology, Johns Hopkins University, Baltimore, Maryland 21218, United States
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2
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Jiang Y, Zhao H, Kong S, Zhou D, Dong J, Cheng Y, Zhang S, Wang F, Kalra A, Yang N, Wei DD, Chen J, Zhang YW, Lin DC, Meltzer SJ, Jiang YY. Establishing mouse and human oral esophageal organoids to investigate the tumor immune response. Dis Model Mech 2024; 17:dmm050319. [PMID: 38258518 PMCID: PMC10846528 DOI: 10.1242/dmm.050319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 05/24/2023] [Accepted: 11/24/2023] [Indexed: 01/24/2024] Open
Abstract
Organoid culture systems are very powerful models that recapitulate in vivo organ development and disease pathogenesis, offering great promise in basic research, drug screening and precision medicine. However, the application of organoids derived from patients with cancer to immunotherapeutic research is a relatively untapped area. Esophageal cancer is one of the most lethal malignancies worldwide, including two major pathological subtypes: esophageal squamous cell carcinoma (ESCC) and esophageal adenocarcinoma. ESCC shares many biological and genomic features with oral squamous cell cancers. Herein, we provide a versatile protocol for the establishment and maintenance of oral and esophageal organoid cultures derived from both murine and human samples. We describe culture conditions for organoids derived from normal tongue, esophagus and gastroesophageal junction, esophageal cancer and Barrett's esophagus. In addition, we establish an ex vivo model by co-culturing patient tumor-derived organoids and autologous CD8+ T lymphocytes to assess CD8+ T cell-mediated tumor killing. Our protocol can also be modified for organoid establishment from other squamous epithelia and carcinomas. The co-culture model can serve as a template for studies of other tumor-immune cell interactions and the efficacy of immune checkpoint blockade therapy.
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Affiliation(s)
- Yuan Jiang
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Hua Zhao
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Shuai Kong
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Dan Zhou
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- Institutes of Physical Science and Technology, Anhui University, Hefei 230601, China
| | - Jinxiu Dong
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - Yulan Cheng
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Shuo Zhang
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Fei Wang
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
| | - Andrew Kalra
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Nina Yang
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Dan-Dan Wei
- University of Science and Technology of China, Hefei 230026, China
- Hefei Cancer Hospital, Chinese Academy of Sciences, Hefei 230031, China
| | - Jian Chen
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - Yuan-Wei Zhang
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
| | - De-Chen Lin
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Stephen J. Meltzer
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Yan-Yi Jiang
- Institute of Health and Medical Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei 230031, China
- University of Science and Technology of China, Hefei 230026, China
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3
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Zhao H, Cheng Y, Kalra A, Ma K, Zheng Y, Ziman B, Tressler C, Glunde K, Shin EJ, Ngamruengphong S, Khashab M, Singh V, Anders RA, Jit S, Wyhs N, Chen W, Li X, Lin DC, Meltzer SJ. Generation and multiomic profiling of a TP53/CDKN2A double-knockout gastroesophageal junction organoid model. Sci Transl Med 2022; 14:eabq6146. [PMID: 36449602 PMCID: PMC10026384 DOI: 10.1126/scitranslmed.abq6146] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [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: 12/02/2022]
Abstract
Inactivation of the tumor suppressor genes tumor protein p53 (TP53) and cyclin-dependent kinase inhibitor 2A (CDKN2A) occurs early during gastroesophageal junction (GEJ) tumorigenesis. However, because of a paucity of GEJ-specific disease models, cancer-promoting consequences of TP53 and CDKN2A inactivation at the GEJ have not been characterized. Here, we report the development of a wild-type primary human GEJ organoid model and a CRISPR-edited transformed GEJ organoid model. CRISPR-Cas9-mediated TP53 and CDKN2A knockout (TP53/CDKN2AKO) in GEJ organoids induced morphologic dysplasia and proneoplastic features in vitro and tumor formation in vivo. Lipidomic profiling identified several platelet-activating factors (PTAFs) among the most up-regulated lipids in CRISPR-edited organoids. PTAF/PTAF receptor (PTAFR) abrogation by siRNA knockdown or a pharmacologic inhibitor (WEB2086) reduced proliferation and other proneoplastic features of TP53/CDKN2AKO GEJ organoids in vitro and tumor formation in vivo. In addition, murine xenografts of Eso26, an established human esophageal adenocarcinoma cell line, were suppressed by WEB2086. Mechanistically, TP53/CDKN2A dual inactivation disrupted both the transcriptome and the DNA methylome, likely mediated by key transcription factors, particularly forkhead box M1 (FOXM1). FOXM1 activated PTAFR transcription by binding to the PTAFR promoter, further amplifying the PTAF-PTAFR pathway. Together, these studies established a robust model system for investigating early GEJ neoplastic events, identified crucial metabolic and epigenomic changes occurring during GEJ model tumorigenesis, and revealed a potential cancer therapeutic strategy. This work provides insights into proneoplastic mechanisms associated with TP53/CDKN2A inactivation in early GEJ neoplasia, which may facilitate early diagnosis and prevention of GEJ neoplasms.
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Affiliation(s)
- Hua Zhao
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Clinical Laboratory, The First Affiliated Hospital of Xi’an Jiaotong University, No. 277 Yanta West Road, Xi’an 710061, Shaanxi, China
| | - Yulan Cheng
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Andrew Kalra
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Ke Ma
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Einstein Healthcare Network, Philadelphia, PA 19136, USA
| | - Yueyuan Zheng
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Benjamin Ziman
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Caitlin Tressler
- Russell H. Morgan Department of Radiology and Radiological Science, Division of Cancer Imaging Research, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Kristine Glunde
- Russell H. Morgan Department of Radiology and Radiological Science, Division of Cancer Imaging Research, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Eun Ji Shin
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Saowanee Ngamruengphong
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Mouen Khashab
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Vikesh Singh
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Robert A. Anders
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Simran Jit
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Nicolas Wyhs
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Wei Chen
- Clinical Laboratory, The First Affiliated Hospital of Xi’an Jiaotong University, No. 277 Yanta West Road, Xi’an 710061, Shaanxi, China
| | - Xu Li
- Center for Translational Medicine, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an 710061, Shaanxi, China
| | - De-Chen Lin
- Center for Craniofacial Molecular Biology, Herman Ostrow School of Dentistry, and Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 90033, USA
| | - Stephen J. Meltzer
- Division of Gastroenterology and Hepatology, Department of Medicine and Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
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Luo X, Chang S, Xiao S, Peng Y, Gao Y, Hu F, Liang J, Xu Y, Du K, Chen Y, Qin J, Meltzer SJ, Deng S, Feng X, Fan X, Hou G, Jin Z, Zhang X. PAD4-dependent citrullination of nuclear translocation of GSK3β promotes colorectal cancer progression via the degradation of nuclear CDKN1A. Neoplasia 2022; 33:100835. [PMID: 36113195 PMCID: PMC9483803 DOI: 10.1016/j.neo.2022.100835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 07/01/2022] [Revised: 08/15/2022] [Accepted: 08/23/2022] [Indexed: 11/06/2022]
Abstract
Peptidylarginine deiminase 4 (PAD4), a Ca2+-dependent enzyme, catalyzes the conversion of arginine to citrulline and has been strongly associated with many malignant tumors. However, the molecular mechanisms of PAD4 in the development and progression of colorectal cancer (CRC) remain unclearly defined. In our study, PAD4 expression was increased in CRC tissues and cells, and was closely related to tumor size, lymph node metastasis. Moreover, the transcription factor KLF9 directly bound to PADI4 gene promoter, leading to overexpression of PAD4 in CRC cells, which augmented cell growth and migration. We revealed that PAD4 interacted with and citrullinated glycogen synthase kinase-3β (GSK3β) in CRC cells, and GSK3β Arg-344 was the dominating PAD4-citrullination site. Furthermore, IgL2 and catalytic domains of PAD4 directly bound to the kinase domain of GSK3β in CRC cells. Mechanistically, PAD4 promoted the transport of GSK3β from the cytoplasm to the nucleus, thereby increasing the ubiquitin-dependent proteasome degradation of nuclear cyclin-dependent kinase inhibitor 1 (CDKN1A). Our study is the first to reveal the details of a critical PAD4/GSK3β/CDKN1A signaling axis for CRC progression, and provides evidence that PAD4 is a potential diagnosis biomarker and therapeutic target in CRC.
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Affiliation(s)
- Xiaonuan Luo
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, People's Republic of China
| | - Shanshan Chang
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, People's Republic of China
| | - Siyu Xiao
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, People's Republic of China
| | - Yin Peng
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, People's Republic of China
| | - Yuli Gao
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, People's Republic of China
| | - Fan Hu
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, People's Republic of China
| | - Jianxue Liang
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, People's Republic of China
| | - Yidan Xu
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, People's Republic of China
| | - Kaining Du
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, People's Republic of China
| | - Yang Chen
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, People's Republic of China
| | - Jiequan Qin
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, People's Republic of China
| | - Stephen J Meltzer
- Department of Medicine/GI Division, Johns Hopkins University School of Medicine and Sidney Ki-mmel Comprehensive Cancer Center, Baltimore, MD, USA
| | - Shiqi Deng
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, People's Republic of China
| | - Xianling Feng
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, People's Republic of China
| | - Xinmin Fan
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, People's Republic of China
| | - Gangqiang Hou
- Department of Medical Image Center, Kangning Hospital of Shenzhen, Shenzhen, Guangdong Province, People's Republic of China
| | - Zhe Jin
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, People's Republic of China
| | - Xiaojing Zhang
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, People's Republic of China.
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Gong D, Lunz D, Stover JS, Meltzer SJ. The utility of a genetic progression risk test for Barrett esophagus. Medicine (Baltimore) 2022; 101:e30503. [PMID: 36123898 PMCID: PMC10662832 DOI: 10.1097/md.0000000000030503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 08/04/2022] [Indexed: 11/26/2022] Open
Abstract
This study sought to characterize the utility of a gene methylation-based biomarker test that has been validated to predict progression towards esophageal adenocarcinoma. Barrett esophagus (BE) is a precursor condition for esophageal adenocarcinoma (EAC) with somewhat variable approaches among gastroenterologists toward managing neoplastic progression risk. Capsulomics has developed a validated multigene DNA methylation-based biomarker assay performed on BE biopsies designed to address this variability by classifying BE patients into progression risk groups. In the current study, a survey was administered to practicing gastroenterologists in order to assess the potential impact of this assay on clinical practice. In this context, 89% (95% Cl: 85.4-92.6%) of surveyed physicians felt strongly that the multigene Barrett Esophagus test helped resolve uncertainties and optimize care of patients with BE by impacting their decisions on surveillance intervals and use of active treatments, such as ablation. The assay significantly impacted surveillance intervals for both high-risk (22.0 no assay vs 12.3 months with assay; P = 1.7E-8) and low-risk (7.9 no assay vs 11.4 months with assay, P = 8.8E-4) stratified case results. Finally, the assay also significantly impacted decisions to pursue active ablation treatments in both high-risk (5% recommending ablation without assay vs 42% with assay; P = 3.7E-11) and low-risk (42% recommending ablation without assay vs 29% with assay; P = .049) stratified case results. Results demonstrated a strong effect of the assay on clinical decision making, even in conjunction with established clinical guidelines.
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Affiliation(s)
- Dennis Gong
- Capsulomics, Baltimore, MD
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD
| | | | | | - Stephen J. Meltzer
- Capsulomics, Baltimore, MD
- Division of Gastroenterology, Johns Hopkins Hospital, Baltimore, MD
- Johns Hopkins Sidney Kimmel Cancer Center, Baltimore, MD
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Ma K, Kalra A, Tsai HL, Okello S, Cheng Y, Meltzer SJ. Accurate Nonendoscopic Detection of Esophageal Squamous Cell Carcinoma Using Methylated DNA Biomarkers. Gastroenterology 2022; 163:507-509.e2. [PMID: 35483446 PMCID: PMC9555873 DOI: 10.1053/j.gastro.2022.04.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/18/2022] [Accepted: 04/20/2022] [Indexed: 12/02/2022]
Affiliation(s)
- Ke Ma
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Andrew Kalra
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hua-Ling Tsai
- Division of Biostatistics, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Samson Okello
- Department of Internal Medicine, Mbarara University of Science and Technology, Mbarara, Uganda
| | - Yulan Cheng
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Stephen J Meltzer
- Division of Gastroenterology and Hepatology, Department of Medicine and, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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7
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Hu F, Peng Y, Chang S, Luo X, Yuan Y, Zhu X, Xu Y, Du K, Chen Y, Deng S, Yu F, Feng X, Fan X, Ashktorab H, Smoot D, Meltzer SJ, Li S, Wei Y, Zhang X, Jin Z. Vimentin binds to a novel tumor suppressor protein, GSPT1-238aa, encoded by circGSPT1 with a selective encoding priority to halt autophagy in gastric carcinoma. Cancer Lett 2022; 545:215826. [PMID: 35839920 DOI: 10.1016/j.canlet.2022.215826] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/20/2022] [Accepted: 07/09/2022] [Indexed: 12/24/2022]
Abstract
Circular RNAs (circRNAs) are covalently closed, endogenous molecules that are widespread in eukaryotes. Recent evidence indicates that circRNAs play important roles in carcinogenesis. Several circRNAs have been reported to comprise translatable RNA; however, whether circRNAs encode functional proteins remains unknown. In our study, circRNA sequencing was carried out using five pathologically diagnosed gastric carcinoma (GC) samples and their paired adjacent normal tissues, we characterized the circRNA GSPT1 (circGSPT1), which is expressed at low levels in GC. Antibody detections, and mass spectrometry were used to validate active circRNA translation. The spanning junction open reading frame in circGSPT1, driven by an internal ribosome entry site (IRES), encodes a functional peptide, termed GSPT1-238aa. Interestingly, GSPT1-238aa tends to select the start codon used to initiate translation. This is the first finding of selective translation driven by IRES. CircGSPT1 and GSPT1-238aa halted the proliferation, migration, and invasion in GC cells in vitro. We also confirmed that the vimentin/Beclin1/14-3-3 complex interacts with GSPT1-238aa and modulates autophagy via the PI3K/AKT/mTOR signaling pathway in GC cells. Our study reveals that GSPT1-238aa, a novel protein encoded by circGSPT1, halts GC tumorigenesis. We also provide insights into the function and underlying molecular mechanisms of GSPT1-238aa in GC and suggest that this protein represents a novel target for GC treatment.
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Affiliation(s)
- Fan Hu
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, 518060, PR China
| | - Yin Peng
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, 518060, PR China
| | - Shanshan Chang
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, 518060, PR China
| | - Xiaonuan Luo
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, 518060, PR China
| | - Yuan Yuan
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, 518060, PR China
| | - Xiaohui Zhu
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, 518060, PR China
| | - Yidan Xu
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, 518060, PR China
| | - Kaining Du
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, 518060, PR China
| | - Yang Chen
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, 518060, PR China
| | - Shiqi Deng
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, 518060, PR China
| | - Fan Yu
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, 518060, PR China
| | - Xianling Feng
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, 518060, PR China
| | - Xinmin Fan
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, 518060, PR China
| | - Hassan Ashktorab
- Department of Medicine and Cancer Center, Howard University, College of Medicine, Washington, DC, 20060, USA
| | - Duane Smoot
- Department of Medicine, Meharry Medical Center, Nashville, TN, 37208, USA
| | - Stephen J Meltzer
- Department of Medicine/GI Division, Johns Hopkins University School of Medicine and Sidney Ki-mel Comprehensive Cancer Center, Baltimore, MD, 21287, USA
| | - Song Li
- Shenzhen Science & Technology Development Exchange Center, Shenzhen Science and Technology Building, Shenzhen, Guangdong, 518055, PR China
| | - Yanjie Wei
- Center for High Performance Computing, Shenzhen Institutes of Advanced Technology, Shenzhen, Guangdong, 518000, PR China
| | - Xiaojing Zhang
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, 518060, PR China.
| | - Zhe Jin
- Guangdong Provincial Key Laboratory of Genome Stability and Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, 518060, PR China.
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8
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Peng Y, Xu Y, Zhang X, Deng S, Yuan Y, Luo X, Hossain MT, Zhu X, Du K, Hu F, Chen Y, Chang S, Feng X, Fan X, Ashktorab H, Smoot D, Meltzer SJ, Hou G, Wei Y, Li S, Qin Y, Jin Z. A novel protein AXIN1-295aa encoded by circAXIN1 activates the Wnt/β-catenin signaling pathway to promote gastric cancer progression. Mol Cancer 2021; 20:158. [PMID: 34863211 PMCID: PMC8642992 DOI: 10.1186/s12943-021-01457-w] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [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: 04/12/2021] [Accepted: 11/05/2021] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Circular RNA (circRNA), a subclass of non-coding RNA, plays a critical role in cancer tumorigenesis and metastasis. It has been suggested that circRNA acts as a microRNA sponge or a scaffold to interact with protein complexes; however, its full range of functions remains elusive. Recently, some circRNAs have been found to have coding potential. METHODS To investigate the role of circRNAs in gastric cancer (GC), parallel sequencing was performed using five paired GC samples. Differentially expressed circAXIN1 was proposed to encode a novel protein. FLAG-tagged circRNA overexpression plasmid construction, immunoblotting, mass spectrometry, and luciferase reporter analyses were applied to confirm the coding potential of circAXIN1. Gain- and loss-of-function studies were conducted to study the oncogenic role of circAXIN1 and AXIN1-295aa on the proliferation, migration, invasion, and metastasis of GC cells in vitro and in vivo. The competitive interaction between AXIN1-295aa and adenomatous polyposis coli (APC) was investigated by immunoprecipitation analyses. Wnt signaling activity was observed using a Top/Fopflash assay, real-time quantitative RT-PCR, immunoblotting, immunofluorescence staining, and chromatin immunoprecipitation. RESULTS CircAXIN1 is highly expressed in GC tissues compared with its expression in paired adjacent normal gastric tissues. CircAXIN1 encodes a 295 amino acid (aa) novel protein, which was named AXIN1-295aa. CircAXIN1 overexpression enhances the cell proliferation, migration, and invasion of GC cells, while the knockdown of circAXIN1 inhibits the malignant behaviors of GC cells in vitro and in vivo. Mechanistically, AXIN1-295aa competitively interacts with APC, leading to dysfunction of the "destruction complex" of the Wnt pathway. Released β-catenin translocates to the nucleus and binds to the TCF consensus site on the promoter, inducing downstream gene expression. CONCLUSION CircAXIN1 encodes a novel protein, AXIN1-295aa. AXIN1-295aa functions as an oncogenic protein, activating the Wnt signaling pathway to promote GC tumorigenesis and progression, suggesting a potential therapeutic target for GC.
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Affiliation(s)
- Yin Peng
- grid.263488.30000 0001 0472 9649Guangdong Provincial Key Laboratory for Genome Stability & Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, 3688 Nanhai Avenue, Nanshan, Shenzhen, Guangdong 518060 People’s Republic of China
| | - Yidan Xu
- grid.263488.30000 0001 0472 9649Guangdong Provincial Key Laboratory for Genome Stability & Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, 3688 Nanhai Avenue, Nanshan, Shenzhen, Guangdong 518060 People’s Republic of China
| | - Xiaojing Zhang
- grid.263488.30000 0001 0472 9649Guangdong Provincial Key Laboratory for Genome Stability & Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, 3688 Nanhai Avenue, Nanshan, Shenzhen, Guangdong 518060 People’s Republic of China
| | - Shiqi Deng
- grid.263488.30000 0001 0472 9649Guangdong Provincial Key Laboratory for Genome Stability & Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, 3688 Nanhai Avenue, Nanshan, Shenzhen, Guangdong 518060 People’s Republic of China
| | - Yuan Yuan
- grid.263488.30000 0001 0472 9649Guangdong Provincial Key Laboratory for Genome Stability & Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, 3688 Nanhai Avenue, Nanshan, Shenzhen, Guangdong 518060 People’s Republic of China
| | - Xiaonuan Luo
- grid.263488.30000 0001 0472 9649Guangdong Provincial Key Laboratory for Genome Stability & Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, 3688 Nanhai Avenue, Nanshan, Shenzhen, Guangdong 518060 People’s Republic of China
| | - Md Tofazzal Hossain
- grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District Beijing, 100049 People’s Republic of China ,grid.458489.c0000 0001 0483 7922Center for High Performance Computing, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong 518000 People’s Republic of China , Department of Statistics, Bangabandhu Sheikh Mujibur Rahaman Science and Technology University, Gopalganj, 8100 Bangladesh
| | - Xiaohui Zhu
- grid.263488.30000 0001 0472 9649Guangdong Provincial Key Laboratory for Genome Stability & Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, 3688 Nanhai Avenue, Nanshan, Shenzhen, Guangdong 518060 People’s Republic of China
| | - Kaining Du
- grid.263488.30000 0001 0472 9649Guangdong Provincial Key Laboratory for Genome Stability & Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, 3688 Nanhai Avenue, Nanshan, Shenzhen, Guangdong 518060 People’s Republic of China
| | - Fan Hu
- grid.263488.30000 0001 0472 9649Guangdong Provincial Key Laboratory for Genome Stability & Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, 3688 Nanhai Avenue, Nanshan, Shenzhen, Guangdong 518060 People’s Republic of China
| | - Yang Chen
- grid.263488.30000 0001 0472 9649Guangdong Provincial Key Laboratory for Genome Stability & Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, 3688 Nanhai Avenue, Nanshan, Shenzhen, Guangdong 518060 People’s Republic of China
| | - Shanshan Chang
- grid.263488.30000 0001 0472 9649Guangdong Provincial Key Laboratory for Genome Stability & Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, 3688 Nanhai Avenue, Nanshan, Shenzhen, Guangdong 518060 People’s Republic of China
| | - Xianling Feng
- grid.263488.30000 0001 0472 9649Guangdong Provincial Key Laboratory for Genome Stability & Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, 3688 Nanhai Avenue, Nanshan, Shenzhen, Guangdong 518060 People’s Republic of China
| | - Xinmin Fan
- grid.263488.30000 0001 0472 9649Guangdong Provincial Key Laboratory for Genome Stability & Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, 3688 Nanhai Avenue, Nanshan, Shenzhen, Guangdong 518060 People’s Republic of China
| | - Hassan Ashktorab
- grid.257127.40000 0001 0547 4545Department of Medicine and Cancer Center, Howard University, College of Medicine, Washington, DC, 20060 USA
| | - Duane Smoot
- Department of Medicine, Meharry Medical Center, Nashville, TN 37208 USA
| | - Stephen J. Meltzer
- grid.21107.350000 0001 2171 9311Department of Medicine/GI Division, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287 USA
| | - Gangqiang Hou
- grid.440238.9Department of Medical Image Center, Kangning Hospital, Shenzhen, Guangdong 518000 People’s Republic of China
| | - Yanjie Wei
- grid.410726.60000 0004 1797 8419University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District Beijing, 100049 People’s Republic of China
| | - Song Li
- Shenzhen Science & Technology Development Exchange Center, Shenzhen Science and Technology Building, Shenzhen, Guangdong, 518055, People's Republic of China.
| | - Ying Qin
- Department of Gastrointestinal Surgery, Shenzhen Second People's Hospital, Shenzhen, Guangdong, 518000, People's Republic of China.
| | - Zhe Jin
- Guangdong Provincial Key Laboratory for Genome Stability & Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, 3688 Nanhai Avenue, Nanshan, Shenzhen, Guangdong, 518060, People's Republic of China.
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9
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Kandimalla R, Xu J, Link A, Matsuyama T, Yamamura K, Parker MI, Uetake H, Balaguer F, Borazanci E, Tsai S, Evans D, Meltzer SJ, Baba H, Brand R, Von Hoff D, Li W, Goel A. EpiPanGI Dx: A Cell-free DNA Methylation Fingerprint for the Early Detection of Gastrointestinal Cancers. Clin Cancer Res 2021; 27:6135-6144. [PMID: 34465601 DOI: 10.1158/1078-0432.ccr-21-1982] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2021] [Revised: 07/24/2021] [Accepted: 08/26/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE DNA methylation alterations have emerged as front-runners in cell-free DNA (cfDNA) biomarker development. However, much effort to date has focused on single cancers. In this context, gastrointestinal (GI) cancers constitute the second leading cause of cancer-related deaths worldwide; yet there is no blood-based assay for the early detection and population screening of GI cancers. EXPERIMENTAL DESIGN Herein, we performed a genome-wide DNA methylation analysis of multiple GI cancers to develop a pan-GI diagnostic assay. By analyzing DNA methylation data from 1,781 tumor and adjacent normal tissues, we first identified differentially methylated regions (DMR) between individual GI cancers and adjacent normal, as well as across GI cancers. We next prioritized a list of 67,832 tissue DMRs by incorporating all significant DMRs across various GI cancers to design a custom, targeted bisulfite sequencing platform. We subsequently validated these tissue-specific DMRs in 300 cfDNA specimens and applied machine learning algorithms to develop three distinct categories of DMR panels RESULTS: We identified three distinct DMR panels: (i) cancer-specific biomarker panels with AUC values of 0.98 (colorectal cancer), 0.98 (hepatocellular carcinoma), 0.94 (esophageal squamous cell carcinoma), 0.90 (gastric cancer), 0.90 (esophageal adenocarcinoma), and 0.85 (pancreatic ductal adenocarcinoma); (ii) a pan-GI panel that detected all GI cancers with an AUC of 0.88; and (iii) a multi-cancer (tissue of origin) prediction panel, EpiPanGI Dx, with a prediction accuracy of 0.85-0.95 for most GI cancers. CONCLUSIONS Using a novel biomarker discovery approach, we provide the first evidence for a cfDNA methylation assay that offers robust diagnostic accuracy for GI cancers.
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Affiliation(s)
- Raju Kandimalla
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute, Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas
| | - Jianfeng Xu
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas.,Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, California
| | - Alexander Link
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University Hospital, Magdeburg, Germany
| | - Takatoshi Matsuyama
- Department of Gastrointestinal Surgery, Tokyo Medical and Dental University Graduate School of Medicine, Tokyo, Japan
| | - Kensuke Yamamura
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - M Iqbal Parker
- Division of Medical Biochemistry and Structural Biology, Institute for Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Hiroyuki Uetake
- Department of Specialized Surgery, Tokyo Medical and Dental University Graduate School of Medicine, Tokyo, Japan
| | - Francesc Balaguer
- Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, University of Barcelona, Barcelona, Spain
| | | | - Susan Tsai
- Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Douglas Evans
- Department of Surgery, Medical College of Wisconsin, Milwaukee, Wisconsin
| | - Stephen J Meltzer
- Department of Medicine, Division of Gastroenterology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hideo Baba
- Department of Gastroenterological Surgery, Graduate School of Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - Randall Brand
- Department of Medicine, Division of Gastroenterology, Hepatology, and Nutrition, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Daniel Von Hoff
- HonorHealth Research Institute, Scottsdale, Arizona.,Translational Genomics Research Institute, an Affiliate of City of Hope, Phoenix, Arizona
| | - Wei Li
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, Texas. .,Department of Biological Chemistry, School of Medicine, University of California, Irvine, Irvine, California
| | - Ajay Goel
- Center for Gastrointestinal Research, Center for Translational Genomics and Oncology, Baylor Scott & White Research Institute, Charles A Sammons Cancer Center, Baylor University Medical Center, Dallas, Texas. .,Department of Molecular Diagnostics and Experimental Therapeutics, Beckman Research Institute of City of Hope, Monrovia, California.,City of Hope Comprehensive Cancer Center, Duarte, California
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10
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Li LY, Yang Q, Jiang YY, Yang W, Jiang Y, Li X, Hazawa M, Zhou B, Huang GW, Xu XE, Gery S, Zhang Y, Ding LW, Ho AS, Zumsteg ZS, Wang MR, Fullwood MJ, Freedland SJ, Meltzer SJ, Xu LY, Li EM, Koeffler HP, Lin DC. Interplay and cooperation between SREBF1 and master transcription factors regulate lipid metabolism and tumor-promoting pathways in squamous cancer. Nat Commun 2021; 12:4362. [PMID: 34272396 PMCID: PMC8285542 DOI: 10.1038/s41467-021-24656-x] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [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: 02/11/2020] [Accepted: 06/29/2021] [Indexed: 02/05/2023] Open
Abstract
Squamous cell carcinomas (SCCs) comprise one of the most common histologic types of human cancer. Transcriptional dysregulation of SCC cells is orchestrated by tumor protein p63 (TP63), a master transcription factor (TF) and a well-researched SCC-specific oncogene. In the present study, both Gene Set Enrichment Analysis (GSEA) of SCC patient samples and in vitro loss-of-function assays establish fatty-acid metabolism as a key pathway downstream of TP63. Further studies identify sterol regulatory element binding transcription factor 1 (SREBF1) as a central mediator linking TP63 with fatty-acid metabolism, which regulates the biosynthesis of fatty-acids, sphingolipids (SL), and glycerophospholipids (GPL), as revealed by liquid chromatography tandem mass spectrometry (LC-MS/MS)-based lipidomics. Moreover, a feedback co-regulatory loop consisting of SREBF1/TP63/Kruppel like factor 5 (KLF5) is identified, which promotes overexpression of all three TFs in SCCs. Downstream of SREBF1, a non-canonical, SCC-specific function is elucidated: SREBF1 cooperates with TP63/KLF5 to regulate hundreds of cis-regulatory elements across the SCC epigenome, which converge on activating cancer-promoting pathways. Indeed, SREBF1 is essential for SCC viability and migration, and its overexpression is associated with poor survival in SCC patients. Taken together, these data shed light on mechanisms of transcriptional dysregulation in cancer, identify specific epigenetic regulators of lipid metabolism, and uncover SREBF1 as a potential therapeutic target and prognostic marker in SCC.
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Affiliation(s)
- Li-Yan Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China.
- Department of Medicine, Samuel Oschin Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
| | - Qian Yang
- Department of Medicine, Samuel Oschin Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Yan-Yi Jiang
- Department of Medicine, Samuel Oschin Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Wei Yang
- Departments of Surgery and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Yuan Jiang
- Department of Medicine, Samuel Oschin Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Xiang Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China
| | - Masaharu Hazawa
- Cell-Bionomics Research Unit, Innovative Integrated Bio-Research Core, Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan
| | - Bo Zhou
- Departments of Surgery and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Guo-Wei Huang
- Department of Medicine, Samuel Oschin Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Xiu-E Xu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China
| | - Sigal Gery
- Department of Medicine, Samuel Oschin Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ying Zhang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Ling-Wen Ding
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Allen S Ho
- Division of Otolaryngology-Head and Neck Surgery, Department of Surgery, Samuel Oschin Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Zachary S Zumsteg
- Department of Radiation Oncology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Ming-Rong Wang
- State Key Laboratory of Molecular Oncology, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Melissa J Fullwood
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
| | - Stephen J Freedland
- Division of Urology, Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, USA and the Durham VA Medical Center, Durham, NC, USA
| | - Stephen J Meltzer
- Departments of Medicine and Oncology, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
| | - Li-Yan Xu
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China.
| | - En-Min Li
- The Key Laboratory of Molecular Biology for High Cancer Incidence Coastal Chaoshan Area, Shantou University Medical College, Shantou, China.
| | - H Phillip Koeffler
- Department of Medicine, Samuel Oschin Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - De-Chen Lin
- Department of Medicine, Samuel Oschin Cancer Center, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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11
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Tan X, Ren S, Fu MZ, Ren S, Yang C, Wu X, Chen T, Latham PS, Meltzer SJ, Fu SW. microRNA-196b promotes esophageal squamous cell carcinogenesis and chemoradioresistance by inhibiting EPHA7, thereby restoring EPHA2 activity. Am J Cancer Res 2021; 11:3594-3610. [PMID: 34354862 PMCID: PMC8332861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/17/2021] [Indexed: 06/13/2023] Open
Abstract
Esophageal cancer (EC) is extremely aggressive and has a very poor survival rate. Esophageal squamous cell carcinoma (ESCC) accounts for 80% of all ECs worldwide, with the majority of the remaining 20% being esophageal adenocarcinoma (EAC). Due to its occult and insidious presentation, ESCC is typically diagnosed and treated in its advanced stages, thereby limiting the success of present therapeutic modalities. microRNAs (miRNAs) can function as tumor suppressors or oncogenes, playing critical roles in cancer initiation and progression by regulating target genes in oncogenic pathways. In the current study, we demonstrated that microRNA-196b (miR-196b) is one of the most upregulated miRNAs in both ESCC and EAC. miR-196b was overexpressed in ESCC and EAC cell lines, cellular exosomal RNAs, and ESCC tissue samples. Functional studies revealed that miR-196b acted as an oncomiR by directly targeting a tumor suppressor, ephrin type-A receptor 7 (EPHA7). EPHA7 abrogates the activity of ephrin type-A receptor 2 (EPHA2), a key molecule involved in the epithelial-to-mesenchymal transition (EMT) and MAPK/ERK pathways, mediating resistance to UV and chemoradiotherapy in both ESCC and EAC. Taken together, these findings suggest that miR-196b is a strong candidate molecular target for EC treatment.
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Affiliation(s)
- Xiaohui Tan
- Department of Medicine, Division of Genomic Medicine, Department of Microbiology, Immunology and Tropical Medicine, The George Washington University School of Medicine and Health SciencesWashington, DC, USA
| | - Shuchang Ren
- Department of Medicine, Division of Genomic Medicine, Department of Microbiology, Immunology and Tropical Medicine, The George Washington University School of Medicine and Health SciencesWashington, DC, USA
| | - Melinda Z Fu
- Department of Medicine, Division of Genomic Medicine, Department of Microbiology, Immunology and Tropical Medicine, The George Washington University School of Medicine and Health SciencesWashington, DC, USA
| | - Shuyang Ren
- Department of Medicine, Division of Genomic Medicine, Department of Microbiology, Immunology and Tropical Medicine, The George Washington University School of Medicine and Health SciencesWashington, DC, USA
| | - Canyuan Yang
- Department of Medicine, Division of Genomic Medicine, Department of Microbiology, Immunology and Tropical Medicine, The George Washington University School of Medicine and Health SciencesWashington, DC, USA
| | - Xiaoling Wu
- Department of Medicine, Chengdu Military General HospitalChengdu, Sichuan, China
| | - Tao Chen
- Department of Medicine, Chengdu Military General HospitalChengdu, Sichuan, China
| | - Patricia S Latham
- Department of Pathology, The George Washington University School of Medicine and Health SciencesWashington, DC, USA
| | - Stephen J Meltzer
- Departments of Medicine and Oncology, The Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer CenterBaltimore, MD, USA
| | - Sidney W Fu
- Department of Medicine, Division of Genomic Medicine, Department of Microbiology, Immunology and Tropical Medicine, The George Washington University School of Medicine and Health SciencesWashington, DC, USA
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12
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Li L, Halpert G, Lerner MG, Hu H, Dimitrion P, Weiss MJ, He J, Philosophe B, Burkhart R, Burns WR, Wesson RN, MacGregor Cameron A, Wolfgang CL, Georgiades C, Kawamoto S, Azad NS, Yarchoan M, Meltzer SJ, Oshima K, Ensign LM, Bader JS, Selaru FM. Protein synthesis inhibitor omacetaxine is effective against hepatocellular carcinoma. JCI Insight 2021; 6:138197. [PMID: 34003798 PMCID: PMC8262474 DOI: 10.1172/jci.insight.138197] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 03/16/2020] [Accepted: 05/12/2021] [Indexed: 12/24/2022] Open
Abstract
Hepatocellular carcinoma (HCC) is the sixth most common and the fourth most deadly cancer worldwide. The development cost of new therapeutics is a major limitation in patient outcomes. Importantly, there is a paucity of preclinical HCC models in which to test new small molecules. Herein, we implemented potentially novel patient-derived organoid (PDO) and patient-derived xenografts (PDX) strategies for high-throughput drug screening. Omacetaxine, an FDA-approved drug for chronic myelogenous leukemia (CML), was found to be a top effective small molecule in HCC PDOs. Next, omacetaxine was tested against a larger cohort of 40 human HCC PDOs. Serial dilution experiments demonstrated that omacetaxine is effective at low (nanomolar) concentrations. Mechanistic studies established that omacetaxine inhibits global protein synthesis, with a disproportionate effect on short–half-life proteins. High-throughput expression screening identified molecular targets for omacetaxine, including key oncogenes, such as PLK1. In conclusion, by using an innovative strategy, we report — for the first time to our knowledge — the effectiveness of omacetaxine in HCC. In addition, we elucidate key mechanisms of omacetaxine action. Finally, we provide a proof-of-principle basis for future studies applying drug screening PDOs sequenced with candidate validation in PDX models. Clinical trials could be considered to evaluate omacetaxine in patients with HCC.
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Affiliation(s)
- Ling Li
- Division of Gastroenterology and Hepatology and
| | - Gilad Halpert
- Center for Nanomedicine at the Wilmer Eye Institute, Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Michael G Lerner
- Department of Physics and Astronomy, Earlham College, Richmond, Indiana, USA
| | - Haijie Hu
- Division of Gastroenterology and Hepatology and
| | - Peter Dimitrion
- Center for Nanomedicine at the Wilmer Eye Institute, Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Matthew J Weiss
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jin He
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Benjamin Philosophe
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Richard Burkhart
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - William R Burns
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Russell N Wesson
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | | | | | - Nilofer S Azad
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Mark Yarchoan
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Stephen J Meltzer
- Division of Gastroenterology and Hepatology and.,Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | - Laura M Ensign
- Center for Nanomedicine at the Wilmer Eye Institute, Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Joel S Bader
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, Maryland, USA
| | - Florin M Selaru
- Division of Gastroenterology and Hepatology and.,Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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13
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Chang KH, Shoureshi P, Lay F, Sebastian R, Alikhassy Habibabady Z, Born LJ, Marti GP, Meltzer SJ, Abraham JM, Harmon JW. Preconditioning of surgical pedicle flaps with DNA plasmid expressing hypoxia-inducible factor-1α (HIF-1α) promotes tissue viability. Gene Ther 2021; 28:319-328. [PMID: 33024315 DOI: 10.1038/s41434-020-00199-6] [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] [Received: 05/23/2020] [Revised: 09/05/2020] [Accepted: 09/24/2020] [Indexed: 01/29/2023]
Abstract
Ischemic necrosis of surgical flaps after reconstruction is a major clinical problem. Hypoxia-inducible factor-1α (HIF-1α) is considered the master regulator of the adaptive response to hypoxia. Among its many properties, it regulates the expression of genes encoding angiogenic growth factors, which have a short half-life in vivo. To achieve a continuous application of the therapeutic, we utilized DNA plasmid delivery. Transcription of the DNA plasmid confirmed by qRT-PCR showed significantly increased mRNA for HIF-1α in the transfected tissue compared to saline control tissue. Rats were preconditioned by injecting with either HIF-1α DNA plasmid or saline intradermally in the designated flap region on each flank. Seven days after preconditioning, each rat had two isolated pedicle flaps raised with a sterile silicone sheet implanted between the skin flap and muscle layer. The flaps preconditioned with HIF-1α DNA plasmid had significantly less necrotic area. Angiogenesis measured by CD31 staining showed a significant increase in the number of vessels per high powered field in the HIF-1α group (p < 0.05). Our findings offer a potential therapeutic strategy for significantly promoting the viability of surgical pedicle flaps by ischemic preconditioning with HIF-1α DNA plasmid.
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Affiliation(s)
- Kai-Hua Chang
- Hendrix burn and Wound Healing Laboratory, Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Pouria Shoureshi
- Hendrix burn and Wound Healing Laboratory, Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Frank Lay
- Hendrix burn and Wound Healing Laboratory, Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Raul Sebastian
- Department of Surgery, George Washington University School of Medicine and Health Science, Washington, DC, USA
| | | | - Louis J Born
- Fischell Department of Bioengineering, University of Maryland, College Park, MD, USA
| | - Guy P Marti
- Hendrix burn and Wound Healing Laboratory, Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Clinique Saint Jean l'Ermitage, Melun, France
| | - Stephen J Meltzer
- Division of Gastroenterology, Department of Medicine and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - John M Abraham
- Hendrix burn and Wound Healing Laboratory, Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Division of Gastroenterology, Department of Medicine and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - John W Harmon
- Hendrix burn and Wound Healing Laboratory, Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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14
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Kelly RJ, Ansari AM, Miyashita T, Zahurak M, Lay F, Ahmed AK, Born LJ, Pezhouh MK, Salimian KJ, Ng C, Matsangos AE, Stricker-Krongrad AH, Mukaisho KI, Marti GP, Chung CH, Canto MI, Rudek MA, Meltzer SJ, Harmon JW. Targeting the Hedgehog Pathway Using Itraconazole to Prevent Progression of Barrett's Esophagus to Invasive Esophageal Adenocarcinoma. Ann Surg 2021; 273:e206-e213. [PMID: 31290765 PMCID: PMC8147663 DOI: 10.1097/sla.0000000000003455] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [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] [Indexed: 01/12/2023]
Abstract
OBJECTIVE The aim of the study was to investigate whether inhibition of Sonic Hedgehog (SHH) pathway would prevent progression of Barrett's Esophagus (BE) to esophageal adenocarcinoma. BACKGROUND The hedgehog signaling pathway is a leading candidate as a molecular mediator of BE and esophageal adenocarcinoma (EAC). Repurposed use of existing off-patent, safe and tolerable drugs that can inhibit hedgehog, such as itraconazole, could prevent progression of BE to EAC. METHODS The efficacy of itraconazole was investigated using a surgical rat reflux model of Barrett's Metaplasia (BM). Weekly intraperitoneal injections of saline (control group) or itraconazole (treatment group; 200 mg/kg) were started at 24 weeks postsurgery. Esophageal tissue was harvested at 40 weeks. The role of the Hh pathway was also evaluated clinically. Esophageal tissue was harvested after 40 weeks for pathological examination and evaluation of the SHH pathway by immunohistochemistry. RESULTS BM was present in control animals 29 of 31 (93%) versus itraconazole 22 of 24 (91%). EAC was significantly lower in itraconazole 2 of 24 (8%) versus control 10 of 31 (32%), respectively (P = 0.033). Esophageal SHH levels were lower in itraconazole vs control (P = 0.12). In esophageal tissue from humans with recurrent or persistent dysplastic BE within 24 months of ablative treatment, strong SHH and Indian Hedgehog expression occurred in distal BE versus proximal squamous epithelium, odds ratio = 6.1 (95% confidence interval: 1.6, 23.4) and odds ratio = 6.4 (95% confidence interval: 1.2, 32.8), respectively. CONCLUSION Itraconazole significantly decreases EAC development and SHH expression in a preclinical animal model of BM. In humans, BE tissue expresses higher SHH, Indian Hedgehog, and bone morphogenic protein levels than normal squamous esophageal epithelium.
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Affiliation(s)
- Ronan J Kelly
- The Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD
- Charles A. Sammons Cancer Center, Baylor University Medical Center, Dallas, TX
| | - Amir M Ansari
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Tomoharu Miyashita
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Marianna Zahurak
- Department of Oncology, Division of Biostatistics and Bioinformatics, Johns Hopkins Sidney Kimmel Cancer Center, Baltimore, MD
| | - Frank Lay
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - A Karim Ahmed
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Louis J Born
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Maryam K Pezhouh
- Department of Pathology, Northwestern University School of Medicine, Chicago, IL
| | - Kevan J Salimian
- Department of Pathology, The Johns Hopkins Hospital, Baltimore, MD
| | - Christopher Ng
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Aerielle E Matsangos
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - Ken-Ichi Mukaisho
- Department of Pathology, Shiga University of Medical Science, Shiga, Japan
| | - Guy P Marti
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD
| | - Christine H Chung
- Department of Head and Neck-Endocrine Oncology, Moffitt Cancer Center, Tampa, FL
| | - Marcia I Canto
- Department of Medicine, Division of gastroenterology, The Johns Hopkins University School of Medicine
| | - Michelle A Rudek
- Analytical Pharmacology Core, Department of Oncology, Department of Medicine/Division of Clinical Pharmacology, The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Stephen J Meltzer
- Department of Medicine, Division of gastroenterology, The Johns Hopkins University School of Medicine
| | - John W Harmon
- Department of Surgery, The Johns Hopkins University School of Medicine, Baltimore, MD
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15
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Peng Y, Qin Y, Zhang X, Deng S, Yuan Y, Feng X, Chen W, Hu F, Gao Y, He J, Cheng Y, Wei Y, Fan X, Ashktorab H, Smoot D, Li S, Meltzer SJ, Zhuang S, Tang N, Jin Z. MiRNA-20b/SUFU/Wnt axis accelerates gastric cancer cell proliferation, migration and EMT. Heliyon 2021; 7:e06695. [PMID: 33912703 PMCID: PMC8065298 DOI: 10.1016/j.heliyon.2021.e06695] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [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: 12/10/2019] [Revised: 08/17/2020] [Accepted: 04/01/2021] [Indexed: 12/25/2022] Open
Abstract
Previous research has found that miRNA-20b is highly expressed in gastric cancer (GC), however, its function and underlying mechanism are not clear. Wnt signaling pathway, implicated in tumorigeneisis, is activated in more than 30% of GC. We would like to characterize the biological behavior of miRNA-20b in terms of modulating Wnt/β-catenin signaling and EMT. We showed that miRNA-20b inhibitors suppressed Topflash/Fopflash dependent luciferase activity and the β-catenin nuclear translocation, resulting in inhibition of Wnt pathway activity and EMT. SUFU, negatively regulating Wnt and Hedgehog signaling pathway, was proved to be targeted by miRNA-20b. Moreover, additional knockdown of SUFU alleviated the inhibitory effect on Wnt pathway activity, EMT, cell proliferation/migration and colony formation caused by miRNA-20b inhibition. In summary, miRNA-20b is an oncogenic miRNA and promoted cell proliferation, migration and EMT in GC partially by activating Wnt pathway via targeting SUFU.
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Affiliation(s)
- Yin Peng
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China,Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathology, Health Science Center, Shenzhen University, Shenzhen, Guangdong, 518055, China,Corresponding author.
| | - Ying Qin
- Department of Gastrointestinal Surgery, Shenzhen Second People's Hospital, Shenzhen, Guangdong 518000, China
| | - Xiaojing Zhang
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China,Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathology, Health Science Center, Shenzhen University, Shenzhen, Guangdong, 518055, China,Department of Pathology, Guangdong Province Key Laboratory of Molecular Oncologic Pathology, China
| | - Shiqi Deng
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China
| | - Yuan Yuan
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China
| | - Xianling Feng
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China
| | - Wangchun Chen
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China
| | - Fan Hu
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China
| | - Yuli Gao
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China
| | - Jieqiong He
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China
| | - Yulan Cheng
- Department of Medicine/GI Division, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
| | - Yanjie Wei
- Center for High Performance Computing, Shenzhen Institutes of Advanced Technology, Shenzhen, Guangdong, 518000, China
| | - Xinmin Fan
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China
| | - Hassan Ashktorab
- Department of Medicine and Cancer Center, Howard University, College of Medicine, Washington, DC 20060, USA
| | - Duane Smoot
- Department of Medicine, Meharry Medical Center, Nashville, TN 37208, USA
| | - Song Li
- Shenzhen Science & Technology Development Exchange Center, Shenzhen Science and Technology Building, Shenzhen, Guangdong, 518055, China
| | - Stephen J. Meltzer
- Department of Medicine/GI Division, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
| | - Shutong Zhuang
- Department of Gastrointestinal Surgery, Shenzhen Second People's Hospital, Shenzhen, Guangdong 518000, China
| | - Na Tang
- Department of Pathology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, Guangdong, China
| | - Zhe Jin
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, China,Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathology, Health Science Center, Shenzhen University, Shenzhen, Guangdong, 518055, China,Corresponding author.
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16
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Peng Y, Zhang X, Lin H, Deng S, Qin Y, He J, Hu F, Zhu X, Feng X, Wang J, Wei Y, Fan X, Lin H, Ashktorab H, Smoot D, Lv Y, Li S, Meltzer SJ, Jin Z. Dual activation of Hedgehog and Wnt/β-catenin signaling pathway caused by downregulation of SUFU targeted by miRNA-150 in human gastric cancer. Aging (Albany NY) 2021; 13:10749-10769. [PMID: 33848981 PMCID: PMC8064165 DOI: 10.18632/aging.202895] [Citation(s) in RCA: 11] [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: 06/26/2020] [Accepted: 10/22/2020] [Indexed: 02/06/2023]
Abstract
Mounting evidence has shown that miRNA-150 expression is upregulated in gastric cancer (GC) and is associated with gastric carcinogenesis, but the underlying oncogenic mechanism remains elusive. Here, we discovered that miRNA-150 targets the tumor suppressor SUFU to promote cell proliferation, migration, and the epithelial-mesenchymal transition (EMT) via the dual activation of Hedgehog (Hh) and Wnt signaling. MiRNA-150 was highly expressed in GC tissues and cell lines, and the level of this miRNA was negatively related to that of SUFU. In addition, both the miRNA-150 and SUFU levels were associated with tumor differentiation. Furthermore, miRNA-150 activated GC cell proliferation and migration in vitro. We found that miRNA-150 inhibitors repressed not only Wnt signaling by promoting cytoplasmic β-catenin localization, but also repressed Hh signaling and EMT. MiRNA-150 inhibition also resulted in significant tumor volume reductions in vivo, suggesting the potential application of miRNA-150 inhibitors in GC therapy. The expression of genes downstream of Hh and Wnt signaling was also reduced in tumors treated with miRNA-150 inhibitors. Notably, anti-SUFU siRNAs rescued the inhibitory effects of miRNA-150 inhibitors on Wnt signaling, Hh activation, EMT, cell proliferation, cell migration, and colony formation. Taken together, these findings indicate that miRNA-150 is oncogenic and promotes GC cell proliferation, migration, and EMT by activating Wnt and Hh signaling via the suppression of SUFU expression.
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Affiliation(s)
- Yin Peng
- Guangdong Key Laboratory for Genome Stability and Disease Prevention, Department of Pathology, Shenzhen University School of Medicine, Shenzhen 518060, Guangdong, P.R. China,Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathology, Health Science Center, Shenzhen University, Shenzhen 518060, Guangdong, P.R. China
| | - Xiaojing Zhang
- Guangdong Key Laboratory for Genome Stability and Disease Prevention, Department of Pathology, Shenzhen University School of Medicine, Shenzhen 518060, Guangdong, P.R. China,Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathology, Health Science Center, Shenzhen University, Shenzhen 518060, Guangdong, P.R. China,Department of Pathology, Guangdong Province Key Laboratory of Molecular Oncologic Pathology, Guangzhou 510515, Guangdong, P.R. China
| | - Huijuan Lin
- Department of Ultrasound, Guangdong Women and Children Hospital, Guangzhou 510000, Guangdong, P.R. China,Department of Pathology and Pathophysiology, Guangzhou Medical University, Guangzhou 510000, Guangdong, P.R. China
| | - Shiqi Deng
- Guangdong Key Laboratory for Genome Stability and Disease Prevention, Department of Pathology, Shenzhen University School of Medicine, Shenzhen 518060, Guangdong, P.R. China
| | - Ying Qin
- Department of Gastrointestinal Surgery, The First Affiliated Hospital of Shenzhen University, Shenzhen 518000, Guangdong, P.R. China
| | - Jieqiong He
- Guangdong Key Laboratory for Genome Stability and Disease Prevention, Department of Pathology, Shenzhen University School of Medicine, Shenzhen 518060, Guangdong, P.R. China
| | - Fan Hu
- Guangdong Key Laboratory for Genome Stability and Disease Prevention, Department of Pathology, Shenzhen University School of Medicine, Shenzhen 518060, Guangdong, P.R. China
| | - Xiaohui Zhu
- Guangdong Key Laboratory for Genome Stability and Disease Prevention, Department of Pathology, Shenzhen University School of Medicine, Shenzhen 518060, Guangdong, P.R. China
| | - Xianling Feng
- Guangdong Key Laboratory for Genome Stability and Disease Prevention, Department of Pathology, Shenzhen University School of Medicine, Shenzhen 518060, Guangdong, P.R. China
| | - Jian Wang
- Department of Pathology and Pathophysiology, Guangzhou Medical University, Guangzhou 510000, Guangdong, P.R. China
| | - Yanjie Wei
- Center for High Performance Computing, Shenzhen Institutes of Advanced Technology, Shenzhen 518000, Guangdong, P.R. China
| | - Xinmin Fan
- Guangdong Key Laboratory for Genome Stability and Disease Prevention, Department of Pathology, Shenzhen University School of Medicine, Shenzhen 518060, Guangdong, P.R. China
| | - Huan Lin
- Department of Vascular Surgery, The First Affiliated Hospital of Shenzhen University, Shenzhen 518060, Guangdong, P.R. China
| | - Hassan Ashktorab
- Department of Medicine and Cancer Center, Howard University, College of Medicine, Washington, DC 20060, USA
| | - Duane Smoot
- Department of Medicine, Meharry Medical Center, Nashville, TN 37208, USA
| | - Yansi Lv
- Guangdong Key Laboratory for Genome Stability and Disease Prevention, Department of Pathology, Shenzhen University School of Medicine, Shenzhen 518060, Guangdong, P.R. China
| | - Song Li
- Shenzhen Science and Technology Development Exchange Center, Shenzhen 518060, Guangdong, P.R. China
| | - Stephen J. Meltzer
- Department of Medicine, GI Division, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
| | - Zhe Jin
- Guangdong Key Laboratory for Genome Stability and Disease Prevention, Department of Pathology, Shenzhen University School of Medicine, Shenzhen 518060, Guangdong, P.R. China,Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathology, Health Science Center, Shenzhen University, Shenzhen 518060, Guangdong, P.R. China
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17
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Song JH, Tieu AH, Cheng Y, Ma K, Akshintala VS, Simsek C, Prasath V, Shin EJ, Ngamruengphong S, Khashab MA, Abraham JM, Meltzer SJ. Novel Long Noncoding RNA miR205HG Functions as an Esophageal Tumor-Suppressive Hedgehog Inhibitor. Cancers (Basel) 2021; 13:cancers13071707. [PMID: 33916875 PMCID: PMC8038513 DOI: 10.3390/cancers13071707] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [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: 03/16/2021] [Accepted: 03/24/2021] [Indexed: 12/12/2022] Open
Abstract
Simple Summary Barrett’s esophagus (BE) is a precursor to esophageal adenocarcinoma (EAC). Long noncoding RNAs (lncRNAs) have been identified as key regulators of biological pathways and we identified lncRNA, miR205HG, as a tumor suppressor in the development of Barrett’s esophagus and esophageal adenocarcinoma, in part through its effect on the Hedgehog signaling pathway. The aims of the current study were: (1) to study involvement of miR205HG in the development of BE and EAC (2) to clarify the role of miR205HG in in vitro and in vivo experiments; and (3) to investigate the mechanism of miR205HG involving the Hedgehog (Hh) signaling pathway Abstract Barrett’s esophagus (BE) is a precursor to esophageal adenocarcinoma (EAC). Recently, long noncoding RNAs (lncRNAs) have been identified as key regulators of biological pathways. However, involvement of lncRNAs in the development of BE and EAC has not been well-studied. The aims of the current study were: (1) to study involvement of the lncRNA, miR205HG, in the development of BE and EAC; (2) to clarify the role of miR205HG in in vitro and in vivo experiments; and (3) to investigate the mechanism of miR205HG involving the Hedgehog (Hh) signaling pathway. These experiments revealed that miR205HG was downregulated in EAC vs. normal esophageal epithelia (NE) as well as in EAC cell lines, and its forced overexpression inhibited EAC cell proliferation and cell cycle progression in vitro. Similarly, overexpression of miR205HG inhibited xenograft tumor growth in mice In vivo. Finally, we show that one mechanism of action of miR205HG involves the Hh signaling pathway: miR205HG and Hh expression levels were inversely correlated in both EAC (r = −0.73) and BE (r = −0.83) tissues, and in vitro studies revealed details of Hh signaling inhibition induced by miR205HG. In conclusion, these findings establish that lncRNA miR205HG functions as a tumor suppressor in the development of BE and EAC, at least in part through its effect on the Hh signaling pathway.
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Affiliation(s)
- Jee Hoon Song
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA; (J.H.S.); (A.H.T.); (Y.C.); (K.M.); (V.S.A.); (C.S.); (V.P.); (E.J.S.); (S.N.); (M.A.K.); (J.M.A.)
- Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21287, USA
| | - Alan H. Tieu
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA; (J.H.S.); (A.H.T.); (Y.C.); (K.M.); (V.S.A.); (C.S.); (V.P.); (E.J.S.); (S.N.); (M.A.K.); (J.M.A.)
- Division of Gastroenterology and Hepatology, Department of Medicine, Eastern Virginia Medical School, Norfolk, VA 23456, USA
| | - Yulan Cheng
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA; (J.H.S.); (A.H.T.); (Y.C.); (K.M.); (V.S.A.); (C.S.); (V.P.); (E.J.S.); (S.N.); (M.A.K.); (J.M.A.)
| | - Ke Ma
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA; (J.H.S.); (A.H.T.); (Y.C.); (K.M.); (V.S.A.); (C.S.); (V.P.); (E.J.S.); (S.N.); (M.A.K.); (J.M.A.)
| | - Venkata S. Akshintala
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA; (J.H.S.); (A.H.T.); (Y.C.); (K.M.); (V.S.A.); (C.S.); (V.P.); (E.J.S.); (S.N.); (M.A.K.); (J.M.A.)
| | - Cem Simsek
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA; (J.H.S.); (A.H.T.); (Y.C.); (K.M.); (V.S.A.); (C.S.); (V.P.); (E.J.S.); (S.N.); (M.A.K.); (J.M.A.)
| | - Vishnu Prasath
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA; (J.H.S.); (A.H.T.); (Y.C.); (K.M.); (V.S.A.); (C.S.); (V.P.); (E.J.S.); (S.N.); (M.A.K.); (J.M.A.)
| | - Eun Ji Shin
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA; (J.H.S.); (A.H.T.); (Y.C.); (K.M.); (V.S.A.); (C.S.); (V.P.); (E.J.S.); (S.N.); (M.A.K.); (J.M.A.)
| | - Saowanee Ngamruengphong
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA; (J.H.S.); (A.H.T.); (Y.C.); (K.M.); (V.S.A.); (C.S.); (V.P.); (E.J.S.); (S.N.); (M.A.K.); (J.M.A.)
| | - Mouen A. Khashab
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA; (J.H.S.); (A.H.T.); (Y.C.); (K.M.); (V.S.A.); (C.S.); (V.P.); (E.J.S.); (S.N.); (M.A.K.); (J.M.A.)
| | - John M. Abraham
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA; (J.H.S.); (A.H.T.); (Y.C.); (K.M.); (V.S.A.); (C.S.); (V.P.); (E.J.S.); (S.N.); (M.A.K.); (J.M.A.)
| | - Stephen J. Meltzer
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins School of Medicine, Baltimore, MD 21287, USA; (J.H.S.); (A.H.T.); (Y.C.); (K.M.); (V.S.A.); (C.S.); (V.P.); (E.J.S.); (S.N.); (M.A.K.); (J.M.A.)
- Correspondence: ; Tel.: +410-502-6071
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18
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Zhang X, Peng Y, Yuan Y, Gao Y, Hu F, Wang J, Zhu X, Feng X, Cheng Y, Wei Y, Fan X, Xie Y, Lv Y, Ashktorab H, Smoot D, Li S, Meltzer SJ, Hou G, Jin Z. Histone methyltransferase SET8 is regulated by miR-192/215 and induces oncogene-induced senescence via p53-dependent DNA damage in human gastric carcinoma cells. Cell Death Dis 2020; 11:937. [PMID: 33127874 PMCID: PMC7599338 DOI: 10.1038/s41419-020-03130-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [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: 03/22/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 12/21/2022]
Abstract
Gastric cancer (GC) is the most common cancer throughout the world. Despite advances of the treatments, detailed oncogenic mechanisms are largely unknown. In our previous study, we investigated microRNA (miR) expression profiles in human GC using miR microarrays. We found miR-192/215 were upregulated in GC tissues. Then gene microarray was implemented to discover the targets of miR-192/215. We compared the expression profile of BGC823 cells transfected with miR-192/215 inhibitors, and HFE145 cells transfected with miR-192/-215 mimics, respectively. SET8 was identified as a proposed target based on the expression change of more than twofold. SET8 belongs to the SET domain-containing methyltransferase family and specifically catalyzes monomethylation of H4K20me. It is involved in diverse functions in tumorigenesis and metastasis. Therefore, we focused on the contributions of miR-192/215/SET8 axis to the development of GC. In this study, we observe that functionally, SET8 regulated by miR-192/215 is involved in GC-related biological activities. SET8 is also found to trigger oncogene-induced senescence (OIS) in GC in vivo and in vitro, which is dependent on the DDR (DNA damage response) and p53. Our findings reveal that SET8 functions as a negative regulator of metastasis via the OIS-signaling pathway. Taken together, we investigated the functional significance, molecular mechanisms, and clinical impact of miR-192/215/SET8/p53 in GC.
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Affiliation(s)
- Xiaojing Zhang
- grid.263488.30000 0001 0472 9649Guangdong Key Laboratory for Genome Stability & Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060 People’s Republic of China
| | - Yin Peng
- grid.263488.30000 0001 0472 9649Guangdong Key Laboratory for Genome Stability & Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060 People’s Republic of China
| | - Yuan Yuan
- grid.263488.30000 0001 0472 9649Guangdong Key Laboratory for Genome Stability & Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060 People’s Republic of China
| | - Yuli Gao
- grid.263488.30000 0001 0472 9649Guangdong Key Laboratory for Genome Stability & Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060 People’s Republic of China
| | - Fan Hu
- grid.263488.30000 0001 0472 9649Guangdong Key Laboratory for Genome Stability & Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060 People’s Republic of China
| | - Jian Wang
- grid.263488.30000 0001 0472 9649Guangdong Key Laboratory for Genome Stability & Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060 People’s Republic of China
| | - Xiaohui Zhu
- grid.263488.30000 0001 0472 9649Guangdong Key Laboratory for Genome Stability & Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060 People’s Republic of China
| | - Xianling Feng
- grid.263488.30000 0001 0472 9649Guangdong Key Laboratory for Genome Stability & Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060 People’s Republic of China
| | - Yulan Cheng
- grid.21107.350000 0001 2171 9311Department of Medicine/GI Division, Johns Hopkins University School of Medicine and Sidney Ki-mmel Comprehensive Cancer Center, Baltimore, MD 21287 USA
| | - Yanjie Wei
- grid.458489.c0000 0001 0483 7922Center for High Performance Computing, Shenzhen Institutes of Advanced Technology, Shenzhen, Guangdong 518000 People’s Republic of China
| | - Xinmin Fan
- grid.263488.30000 0001 0472 9649Guangdong Key Laboratory for Genome Stability & Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060 People’s Republic of China
| | - Yaohong Xie
- grid.263488.30000 0001 0472 9649Guangdong Key Laboratory for Genome Stability & Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060 People’s Republic of China
| | - Yansi Lv
- grid.263488.30000 0001 0472 9649Guangdong Key Laboratory for Genome Stability & Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong 518060 People’s Republic of China
| | - Hassan Ashktorab
- grid.257127.40000 0001 0547 4545Department of Medicine and Cancer Center, Howard University College of Medicine, Washington, DC 20060 USA
| | - Duane Smoot
- Department of Medicine, Meharry Medical Center, Nashville, TN 37208 USA
| | - Song Li
- grid.454883.6Shenzhen Science & Technology Development Exchange Center, Shenzhen Science and Technology Building, Shenzhen, Guangdong 518055 People’s Republic of China
| | - Stephen J. Meltzer
- grid.21107.350000 0001 2171 9311Department of Medicine/GI Division, Johns Hopkins University School of Medicine and Sidney Ki-mmel Comprehensive Cancer Center, Baltimore, MD 21287 USA
| | - Gangqiang Hou
- Department of Medical Image Center, Kangning Hospital, Shenzhen, Guangdong Province, 518000, People's Republic of China.
| | - Zhe Jin
- Guangdong Key Laboratory for Genome Stability & Disease Prevention and Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine, Shenzhen, Guangdong, 518060, People's Republic of China.
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19
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Peng Y, Zhang X, Lin H, Deng S, Qin Y, Yuan Y, Feng X, Wang J, Chen W, Hu F, Yan R, Zhao Y, Cheng Y, Wei Y, Fan X, Ashktorab H, Smoot D, Li S, Meltzer SJ, Jin Z. SUFU mediates EMT and Wnt/β-catenin signaling pathway activation promoted by miRNA-324-5p in human gastric cancer. Cell Cycle 2020; 19:2720-2733. [PMID: 33017570 DOI: 10.1080/15384101.2020.1826632] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 01/20/2023] Open
Abstract
The poor prognosis of late gastric carcinomas (GC) underscores the necessity to identify novel biomarkers for earlier diagnosis and effective therapeutic targets. MiRNA-324-5p has been shown to be over-expressed in GC, however the biological function of miRNA-324-5p implicated in gastric cancer and its downstream targets were not well understood. Wnt/β-catenin signaling pathway is aberrantly regulated in GC. We sought to explore if miRNA-324-5p promotes oncogenesis through modulating Wnt signaling and EMT. MiRNA-324-5p is highly expressed in GC based on qRT-PCR and TCGA data. In addition, in vitro cell proliferation, cell migration assays and in vivo animal exenograft were executed to show that miRNA-324-5p is an oncogenic miRNA in GC. MiRNA-324-5p activates Wnt signaling and induces EMT in GC. Further, SUFU was identified as a target of miRNA-324-5p confirmed by western blotting and luciferase assays. Spearson analysis and TCGA data indicate that the expression of SUFU is negatively associated with the expression of miRNA-324-5p. Rescue experiments were performed to determine if SUFU mediates the Wnt activation, EMT and oncogenic function of miRNA-324-5p. MiRNA-324-5p inhibitors plus SUFU siRNAs rescue partially the inhibitory effect on Wnt signaling and EMT caused by miRNA-324-5p inhibitors. Finally, the suppression of cell proliferation, migration, and colony formation ability induced by miRNA-324-5p inhibitors is alleviated by addition of SUFU siRNAs. In summary, miRNA-324-5p is overexpressed in vivo and exerts cell growth and migration-promoting effects through activating Wnt signaling and EMT by targeting SUFU in GC. It represents a potential miRNA with an oncogenic role in human gastric cancer.
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Affiliation(s)
- Yin Peng
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine , Shenzhen, Guangdong, China
| | - Xiaojing Zhang
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine , Shenzhen, Guangdong, China.,Department of Pathology, Guangdong Province Key Laboratory of Molecular Oncologic Pathology , Guangzhou, Guangdong, China
| | - Huijuan Lin
- Department of Pathology and Pathophysiology, Guangzhou Medical University , Guangzhou, Guangdong, China.,Department of Ultrasound, Guangdong Women and Children Hospital , Guangzhou, Guangdong, China
| | - Shiqi Deng
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine , Shenzhen, Guangdong, China
| | - Ying Qin
- Department of Gastrointestinal Surgery, Shenzhen Second People's Hospital , Shenzhen, Guangdong, China
| | - Yuan Yuan
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine , Shenzhen, Guangdong, China
| | - Xianling Feng
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine , Shenzhen, Guangdong, China
| | - Jian Wang
- Department of Pathology and Pathophysiology, Guangzhou Medical University , Guangzhou, Guangdong, China
| | - Wangchun Chen
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine , Shenzhen, Guangdong, China
| | - Fan Hu
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine , Shenzhen, Guangdong, China
| | - Ruibin Yan
- Laboratory of Chemical Genomics, Shenzhen Graduate School of Peking University , Shenzhen, Guangdong, P.R. China
| | - Yanqiu Zhao
- Laboratory of Chemical Genomics, Shenzhen Graduate School of Peking University , Shenzhen, Guangdong, P.R. China
| | - Yulan Cheng
- Department of Medicine/GI Division, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center , Baltimore, MD, USA
| | - Yanjie Wei
- Center for High Performance Computing, Shenzhen Institutes of Advanced Technology , Shenzhen, Guangdong, P.R. China
| | - Xinmin Fan
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine , Shenzhen, Guangdong, China
| | - Hassan Ashktorab
- Department of Medicine and Cancer Center, Howard University, College of Medicine , Washington, USA
| | - Duane Smoot
- Department of Medicine, Meharry Medical Center , Nashville, TN, USA
| | - Song Li
- Laboratory of Chemical Genomics, Shenzhen Graduate School of Peking University , Shenzhen, Guangdong, P.R. China
| | - Stephen J Meltzer
- Department of Medicine/GI Division, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center , Baltimore, MD, USA
| | - Zhe Jin
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Department of Pathology, Shenzhen University School of Medicine , Shenzhen, Guangdong, China
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20
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Kandimalla R, Xu J, Link A, Matsuyama T, Yamamura K, Parker I, Uetake H, Hernandez-Illan E, Lozano J, Borazanci E, Tsai S, Evans D, Meltzer SJ, Baba H, Brand R, Von Hoff D, Balaguer F, Li W, Goel A. Abstract 1084: EpiPanGI-Dx: A cell-free DNA methylation fingerprint for the early detection of gastrointestinal cancers. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-1084] [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
Purpose: In view of high cancer-specificity, DNA methylation alterations have emerged as front-runners in biomarker development, especially as cell-free DNA (cf-DNA) biomarkers for early detection of cancer. However, much effort to date has focused on developing cancer type-specific biomarkers, but have not explored the possibility of developing a pan-cancer diagnostic assay. In this context, gastrointestinal (GI) cancers, including colorectal (CRC), esophageal squamous cell and adenocarcinoma (ESCC and EAC), gastric (GC), liver (HCC) and pancreatic ductal adenocarcinoma (PDAC) constitute the second leading cause of cancer-related deaths worldwide; yet there is no blood-based assay for the early detection and population screening of GI cancers. Here we undertook a genomewide DNA methylation analysis for multiple GI cancers, followed by development of a novel cf-DNA methylation biomarker panels for the early detection of GI cancers (EpiPanGI Dx).
Experimental design: By analyzing the DNA methylation data from 1940 tumor and adjacent normal tissues from TCGA and GSE72872 datasets, we first identified the differentially methylated regions (DMRs) between individual GI cancers and adjacent normal tissues, as well as across all GI cancers. We next prioritized a list of DMRs encompassing a 25.6 Mb genomic region by incorporating all identified DMRs across various GI cancers to design a custom SeqCap Epi, targeted bisulfite sequencing platform, optimized for analysis of low-abundance cf-DNA derived from plasma specimens. Using this approach, we sequenced 300 plasma specimens from all GI cancers, as well as age-matched healthy controls, with a 40X coverage. Finally, using machine learning algorithms, we identified unique DMR panels for the detection of various GI cancers.
Results: Methylation profiling data from various GI tissues led to the identification of 67,832 DMRs with an adjusted p<0.001 and a delta beta value of 0.2, in all the comparisons across all GI cancers. Subsequent investigation of these tissue-specific DMRs in 300 cf-DNA specimens using our custom SeqCap panel led to the development of three distinct categories of DMR panels: 1) Cancer-specific biomarker panels with an AUC values of 0.98 (CRC), 0.94 (ESCC), 0.90 (EAC), 0.90 (GC), 0.98 (HCC), and 0.85 (PDAC); 2) A pan-GI biomarker panel that detected all GI cancers with an AUC of 0.90; and 3) A multi-cancer prediction panel, EpiPanGI Dx, with a prediction accuracy around 0.85 for most GI cancers. All three groups of DMR panels when trained and tested in the cf-DNA cohorts achieved excellent diagnostic accuracy with AUC values ranging from 0.74-0.98, even for each of the early-stage GI cancers.
Conclusions: Utilizing a novel biomarker discovery approach, we provide first evidence for cell-free DNA methylation biomarkers that offer a robust diagnostic accuracy for the identification of specific cancer types, and demonstrate their potential clinical application as a Pan-cancer panel for the early detection of all gastrointestinal cancers.
Citation Format: Raju Kandimalla, Jianfeng Xu, Alexander Link, Takatoshi Matsuyama, Kensuke Yamamura, Iqbal Parker, Hiroyuki Uetake, Eva Hernandez-Illan, Juanjo Lozano, Erkut Borazanci, Susan Tsai, Douglas Evans, Stephen J. Meltzer, Hideo Baba, Randall Brand, Daniel Von Hoff, Francesc Balaguer, Wei Li, Ajay Goel. EpiPanGI-Dx: A cell-free DNA methylation fingerprint for the early detection of gastrointestinal cancers [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1084.
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Affiliation(s)
| | | | | | | | - Kensuke Yamamura
- 5Graduate School of Medical Sciences, Kumamoto University, Japan
| | - Iqbal Parker
- 6Institute for Infectious Disease and Molecular Medicine, University of Cape Town, South Africa
| | - Hiroyuki Uetake
- 4Tokyo Medical and Dental University Graduate School of Medicine, Japan
| | | | | | | | - Susan Tsai
- 9Medical College of Wisconsin, Milwaukee, WI
| | | | | | - Hideo Baba
- 5Graduate School of Medical Sciences, Kumamoto University, Japan
| | | | | | | | - Wei Li
- 13University of California, CA
| | - Ajay Goel
- 14Beckman Research Institute, City of Hope Comprehensive Cancer Center, Duarte, CA
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21
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Chen L, Huang M, Plummer J, Pan J, Jiang YY, Yang Q, Silva TC, Gull N, Chen S, Ding LW, An O, Yang H, Cheng Y, Said JW, Doan N, Dinjens WN, Waters KM, Tuli R, Gayther SA, Klempner SJ, Berman BP, Meltzer SJ, Lin DC, Koeffler HP. Master transcription factors form interconnected circuitry and orchestrate transcriptional networks in oesophageal adenocarcinoma. Gut 2020; 69:630-640. [PMID: 31409603 PMCID: PMC8108390 DOI: 10.1136/gutjnl-2019-318325] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [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: 01/18/2019] [Revised: 06/25/2019] [Accepted: 07/21/2019] [Indexed: 12/14/2022]
Abstract
OBJECTIVE While oesophageal squamous cell carcinoma remains infrequent in Western populations, the incidence of oesophageal adenocarcinoma (EAC) has increased sixfold to eightfold over the past four decades. We aimed to characterise oesophageal cancer-specific and subtypes-specific gene regulation patterns and their upstream transcription factors (TFs). DESIGN: To identify regulatory elements, we profiled fresh-frozen oesophageal normal samples, tumours and cell lines with chromatin immunoprecipitation sequencing (ChIP-Seq). Mathematical modelling was performed to establish (super)-enhancers landscapes and interconnected transcriptional circuitry formed by master TFs. Coregulation and cooperation between master TFs were investigated by ChIP-Seq, circularised chromosome conformation capture sequencing and luciferase assay. Biological functions of candidate factors were evaluated both in vitro and in vivo. RESULTS We found widespread and pervasive alterations of the (super)-enhancer reservoir in both subtypes of oesophageal cancer, leading to transcriptional activation of a myriad of novel oncogenes and signalling pathways, some of which may be exploited pharmacologically (eg, leukemia inhibitory factor (LIF) pathway). Focusing on EAC, we bioinformatically reconstructed and functionally validated an interconnected circuitry formed by four master TFs-ELF3, KLF5, GATA6 and EHF-which promoted each other's expression by interacting with each super-enhancer. Downstream, these master TFs occupied almost all EAC super-enhancers and cooperatively orchestrated EAC transcriptome. Each TF within the transcriptional circuitry was highly and specifically expressed in EAC and functionally promoted EAC cell proliferation and survival. CONCLUSIONS By establishing cancer-specific and subtype-specific features of the EAC epigenome, our findings promise to transform understanding of the transcriptional dysregulation and addiction of EAC, while providing molecular clues to develop novel therapeutic modalities against this malignancy.
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Affiliation(s)
- Li Chen
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Moli Huang
- School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Jasmine Plummer
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Jian Pan
- Department of Hematology and Oncology, Children's Hospital of Soochow University, Suzhou, China
| | - Yan-Yi Jiang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Qian Yang
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Tiago Chedraoui Silva
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Nicole Gull
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Stephanie Chen
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Ling-Wen Ding
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Omer An
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Yulan Cheng
- Departments of Medicine and Oncology, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, USA
| | - Jonathan W. Said
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, USA
| | - Ngan Doan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, USA
| | - Winand N.M. Dinjens
- Department of Pathology, Erasmus MC, University Medical Center Rotterdam, The Netherlands
| | - Kevin M. Waters
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Richard Tuli
- Department of Radiation Oncology, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Simon A. Gayther
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Samuel J. Klempner
- The Angeles Clinic and Research Institute, Los Angeles, CA, USA,Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Benjamin P. Berman
- Center for Bioinformatics and Functional Genomics, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Stephen J. Meltzer
- Departments of Medicine and Oncology, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, USA
| | - De-Chen Lin
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - H. Phillip Koeffler
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, USA,Cancer Science Institute of Singapore, National University of Singapore, Singapore
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22
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Kambhampati S, Tieu AH, Luber B, Wang H, Meltzer SJ. Risk Factors for Progression of Barrett's Esophagus to High Grade Dysplasia and Esophageal Adenocarcinoma. Sci Rep 2020; 10:4899. [PMID: 32184470 PMCID: PMC7078316 DOI: 10.1038/s41598-020-61874-7] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [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: 07/05/2019] [Accepted: 03/01/2020] [Indexed: 12/17/2022] Open
Abstract
Barrett’s esophagus (BE) is the only known precursor to esophageal adenocarcinoma (EAC). Methods of identifying BE patients at high risk for progression to high-grade dysplasia (HGD) or EAC are needed to improve outcomes and identify who will benefit most from intensive surveillance or ablative therapy. Clinical predictors of BE progression to HGD or EAC are poorly understood, with multiple contradictory studies. We performed a retrospective study which included 460 patients at Johns Hopkins Hospital who underwent at least 2 upper endoscopies 6 months apart showing biopsy-documented BE between 1992 and 2013. Patients with EAC or HGD at the initial endoscopy were excluded. Demographic, clinicopathological, and endoscopic data were collected. Univariate and multivariate Cox proportional hazards analyses with time to progression to HGD and EAC were performed. Among 460 patients included in the study, 132 BE patients developed HGD and 62 developed EAC. Significant EAC risk factors included age, abdominal obesity, caffeine intake, and the presence of HGD. Risk factors for HGD or EAC included age, caffeine intake, and low-grade dysplasia while colonic adenomas trended towards significance. Notably, a history of statin or SSRI usage reduced the risk of EAC or HGD by 49% or 61%, respectively. Our study validated several known and identified several novel risk factors, including a history of colonic adenomas or caffeine usage. Low-grade dysplasia was a risk factor for progression but various endoscopic characteristics were not, suggesting that screening strategies should focus on histology instead. We identified SSRIs as a new potentially chemoprotective medication.
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Affiliation(s)
- Swetha Kambhampati
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Alan H Tieu
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States.,Division of Gastroenterology and Hepatology, Department of Medicine, Eastern Virginia Medical School, Norfolk, VA, United States
| | - Brandon Luber
- Division of Bioinformatics and Biostatistics, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Hao Wang
- Division of Bioinformatics and Biostatistics, Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Stephen J Meltzer
- Division of Gastroenterology and Hepatology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, United States. .,Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States.
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23
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Deng S, Zhang X, Qin Y, Chen W, Fan H, Feng X, Wang J, Yan R, Zhao Y, Cheng Y, Wei Y, Fan X, Ashktorab H, Smoot D, Meltzer SJ, Li S, Li K, Peng Y, Jin Z. miRNA-192 and -215 activate Wnt/β-catenin signaling pathway in gastric cancer via APC. J Cell Physiol 2020; 235:6218-6229. [PMID: 32091625 DOI: 10.1002/jcp.29550] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 01/09/2020] [Indexed: 12/13/2022]
Abstract
Although great progress has been made in surgical techniques, traditional radiotherapy, and chemotherapy, gastric cancer (GC) is still the most common malignant tumor and has a high mortality, which highlights the importance of novel diagnostic markers. Emerging studies suggest that different microRNAs (miRNAs) are involved in tumorigenesis of GC. In this study, we found that miRNA-192 and -215 are significantly upregulated in GC and promote cell proliferation and migration. Adenomatous polyposis coli (APC), a well-known negative regulator in Wnt signaling, has been proved to be a target of miRNA-192 and -215. Inhibition of miRNA-192 or -215 reduced the Topflash activities and repressed the expression of Wnt signaling pathway proteins, while APC small interfering RNAs reversed the inhibitory effects, suggesting that miRNA-192 and -215 activate Wnt signaling via APC. In addition, APC mediates the cell proliferation and migration regulated by miRNA-192 and -215. Furthermore, APC is downregulated in GC tissues and negatively correlated with the expression of miRNA-192 and -215. In summary, miRNA-192 and -215 target APC and function as oncogenic miRNAs by activating Wnt signaling in GC, revealing to be potential therapeutic targets.
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Affiliation(s)
- Shiqi Deng
- Department of Pathology, Guangdong Key Laboratory for Genome Stability & Disease Prevention, The Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Xiaojing Zhang
- Department of Pathology, Guangdong Key Laboratory for Genome Stability & Disease Prevention, The Shenzhen University School of Medicine, Shenzhen, Guangdong, China.,Department of Pathology, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Health Science Center, Shenzhen University, Shenzhen, China.,Department of Pathology, Guangdong Province Key Laboratory of Molecular Oncologic Pathology, Guangdong, China
| | - Ying Qin
- Department of Gastrointestinal Surgery, Shenzhen Second People's Hospital, Shenzhen, Guangdong, China
| | - Wangchun Chen
- Department of Pathology, Guangdong Key Laboratory for Genome Stability & Disease Prevention, The Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Hu Fan
- Department of Pathology, Guangdong Key Laboratory for Genome Stability & Disease Prevention, The Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Xianling Feng
- Department of Pathology, Guangdong Key Laboratory for Genome Stability & Disease Prevention, The Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Jian Wang
- Department of Pathology and Pathophysiology, The Guangzhou Medical University, Guangzhou, China
| | - Ruibin Yan
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, The Shenzhen Graduate School of Peking University, Shenzhen, Guangdong, China
| | - Yanqiu Zhao
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, The Shenzhen Graduate School of Peking University, Shenzhen, Guangdong, China
| | - Yulan Cheng
- Department of Medicine/GI Division, The Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - Yanjie Wei
- Center for High Performance Computing, Shenzhen Institutes of Advanced Technology, Shenzhen, Guangdong, China
| | - Xinmin Fan
- Department of Pathology, Guangdong Key Laboratory for Genome Stability & Disease Prevention, The Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Hassan Ashktorab
- Department of Medicine and Cancer Center, College of Medicine, Howard University, Washington DC
| | - Duane Smoot
- Department of Medicine, Meharry Medical Center, Nashville, Tennessee
| | - Stephen J Meltzer
- Department of Medicine/GI Division, The Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - Song Li
- Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, The Shenzhen Graduate School of Peking University, Shenzhen, Guangdong, China
| | - Kuan Li
- Department of Pathology, Guangdong Key Laboratory for Genome Stability & Disease Prevention, The Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Yin Peng
- Department of Pathology, Guangdong Key Laboratory for Genome Stability & Disease Prevention, The Shenzhen University School of Medicine, Shenzhen, Guangdong, China.,Department of Pathology, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Health Science Center, Shenzhen University, Shenzhen, China
| | - Zhe Jin
- Department of Pathology, Guangdong Key Laboratory for Genome Stability & Disease Prevention, The Shenzhen University School of Medicine, Shenzhen, Guangdong, China.,Department of Pathology, Guangdong Provincial Key Laboratory of Regional Immunity and Diseases, Health Science Center, Shenzhen University, Shenzhen, China
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24
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Tsuge S, Saberi B, Cheng Y, Wang Z, Kim A, Luu H, Abraham JM, Ybanez MD, Hamilton JP, Selaru FM, Villacorta-Martin C, Schlesinger F, Philosophe B, Cameron AM, Zhu Q, Anders R, Gurakar A, Meltzer SJ. Detection of Novel Fusion Transcript VTI1A-CFAP46 in Hepatocellular Carcinoma. Gastrointest Tumors 2019; 6:11-27. [PMID: 31602373 DOI: 10.1159/000496795] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [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: 12/20/2018] [Accepted: 12/23/2018] [Indexed: 11/19/2022] Open
Abstract
Background Hepatocellular carcinoma (HCC) is now the second-highest cause of cancer death worldwide. Recent studies have discovered a wide range of somatic mutations in HCC. These mutations involve various vital signaling pathways such as: Wnt/β-Catenin, p53, telome-rase reverse transcriptase (TERT), chromatin remodeling, RAS/MAPK signaling, and oxidative stress. However, fusion transcripts have not been broadly explored in HCC. Methods To identify novel fusion transcripts in HCC, in the first phase of our study, we performed targeted RNA sequencing (in HCC and paired non-HCC tissues) on 6 patients with a diagnosis of HCC undergoing liver transplantation. Results As a result of these studies, we discovered the novel fusion transcript, VTI1A-CFAP46. In the second phase of our study, we measured the expression of wild-type VTI1A in 21 HCC specimens, which showed that 10 of 21 exhibited upregulation of wild-type VTI1A in their tumors. VTI1A (Vesicle Transport via Interaction with t-SNARE homolog 1A) is a member of the Soluble N-ethylmaleimide-Sensitive Factor (NSF) attachment protein receptor (SNARE) gene family, which is essential for membrane trafficking and function in endocytosis, autophagy, and Golgi transport. Notably, it is known that autophagy is involved in HCC. Conclusions The link between novel fusion transcript VTI1A-CFAP46 and autophagy as a potential therapeutic target in HCC patients deserves further investigation. Moreover, this study shows that fusion transcripts are worthy of additional exploration in HCC.
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Affiliation(s)
- Shunichi Tsuge
- Division of Gastroenterology and Hepatology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Behnam Saberi
- Division of Gastroenterology and Hepatology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Division of Liver Diseases, Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Yulan Cheng
- Division of Gastroenterology and Hepatology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Zhixiong Wang
- Division of Gastroenterology and Hepatology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Gastrointestinal Surgery, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Amy Kim
- Division of Gastroenterology and Hepatology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Harry Luu
- Division of Gastroenterology and Hepatology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - John M Abraham
- Division of Gastroenterology and Hepatology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Maria D Ybanez
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - James P Hamilton
- Division of Gastroenterology and Hepatology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Florin M Selaru
- Division of Gastroenterology and Hepatology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | | | | | - Benjamin Philosophe
- Department of Transplant Surgery, The Johns Hopkins University, Baltimore, Maryland, USA
| | - Andrew M Cameron
- Department of Transplant Surgery, The Johns Hopkins University, Baltimore, Maryland, USA
| | - Qingfeng Zhu
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Robert Anders
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ahmet Gurakar
- Division of Gastroenterology and Hepatology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Stephen J Meltzer
- Division of Gastroenterology and Hepatology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA.,Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
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25
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Ng CK, Ma K, Cheng Y, Miyashita T, Harmon JW, Meltzer SJ. Krüppel-like Factor 5 Promotes Sonic Hedgehog Signaling and Neoplasia in Barrett's Esophagus and Esophageal Adenocarcinoma. Transl Oncol 2019; 12:1432-1441. [PMID: 31401336 PMCID: PMC6700477 DOI: 10.1016/j.tranon.2019.07.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [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: 07/02/2019] [Accepted: 07/08/2019] [Indexed: 02/07/2023] Open
Abstract
Krüppel-like Factor 5 (KLF5) is a zinc-finger transcription factor associated with cell cycle progression and cell survival. KLF5 plays a key role in mammalian intestinal epithelium development and maintenance, expressed at high levels in basal proliferating cells and low levels in terminally differentiated cells. Considering Barrett's esophagus (BE) and esophageal adenocarcinoma's (EAC) histopathological similarities to intestinal epithelium, we sought to determine KLF5's role in BE and EAC, as well as KLF5's possible connection to the sonic hedgehog (SHH) pathway which is highly active in BE and EAC development. Low levels of KLF5 mRNA were found in BE cell lines and tissue- similar to what has been reported in differentiated intestinal epithelium. In contrast, higher KLF5 levels were observed in EAC cells and tissues. KLF5 knockdown in EAC cells caused significant decreases in cell migration, proliferation, and EAC-associated gene expression. Moreover, KLF5 knockdown led to decreased SHH signaling. These results suggest that KLF5 is connected to the SHH pathway in BE and EAC and may represent a potential drug target in EAC; further studies are now indicated to verify these findings and elucidate underlying mechanisms involved.
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Affiliation(s)
- Christopher K Ng
- Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Ke Ma
- Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Yulan Cheng
- Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Tomoharu Miyashita
- Department of Gastroenterological Surgery, Kanazawa University Hospital, Kanazawa, Japan.
| | - John W Harmon
- Department of Surgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
| | - Stephen J Meltzer
- Division of Gastroenterology and Hepatology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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26
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Wang Z, Ma K, Cheng Y, Abraham JM, Liu X, Ke X, Wang Z, Meltzer SJ. Synthetic circular multi-miR sponge simultaneously inhibits miR-21 and miR-93 in esophageal carcinoma. Lab Invest 2019. [PMID: 31217510 DOI: 10.1038/s41374-019-0273-2.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
MicroRNAs (miRs) are post-transcriptional regulators involved in the initiation and progression of many tumors. Recently, naturally occurring circular RNAs (circRNAs) have been described in eukaryotic cells:;they comprise a new class of gene regulators. Naturally occurring circular miR sponges, which induce miR loss-of-function, can prevent endogenous onco-miRs from binding to their cognate mRNA targets. These findings suggest that synthetic (artificial) circular RNAs could be constructed as therapeutic molecular sponges to suppress harmful onco-miRs. Using enzymatic ligation, we designed and constructed a circular RNA containing both miR-21 and miR-93 binding sites. The synthetic circular sponge was resistant to digestion with RNase R. Luciferase assays and functional experiments showed that the circular multi-miR sponge was more stable than its linear counterpart. Moreover, endogenous miR-21 and miR-93 were inhibited by the circular sponge. In addition, the synthetic sponge significantly suppressed cellular proliferation and migration while promoting apoptosis in esophageal carcinoma cells. Finally, in a murine xenograft model, the circular sponge significantly inhibited tumor growth in vivo. Taken together, these findings establish that the design and construction of efficient artificial miR sponges represent a novel strategy to achieve miR loss-of-function in molecular cancer therapeutics.
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Affiliation(s)
- Zhe Wang
- Department of Gastroenterology, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200092, China.,Division of Gastroenterology, Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Ke Ma
- Division of Gastroenterology, Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Yulan Cheng
- Division of Gastroenterology, Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - John M Abraham
- Division of Gastroenterology, Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Xi Liu
- Department of Pathology, The First Affiliated Hospital of Xi' an Jiaotong University, No. 277 Yanta West Road, Xi' an, 710061, Shaanxi, China
| | - Xiquan Ke
- Department of Gastroenterology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233004, Anhui, China
| | - Zhirong Wang
- Department of Gastroenterology, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200092, China
| | - Stephen J Meltzer
- Division of Gastroenterology, Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA.
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27
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Lin Y, Dong H, Deng W, Lin W, Li K, Xiong X, Guo Y, Zhou F, Ma C, Chen Y, Ren H, Yang H, Dai N, Ma L, Meltzer SJ, Yeung SCJ, Zhang H. Evaluation of Salivary Exosomal Chimeric GOLM1-NAA35 RNA as a Potential Biomarker in Esophageal Carcinoma. Clin Cancer Res 2019; 25:3035-3045. [PMID: 30745298 DOI: 10.1158/1078-0432.ccr-18-3169] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 12/03/2018] [Accepted: 02/01/2019] [Indexed: 02/05/2023]
Abstract
PURPOSE Transcriptionally induced chimeric RNAs are an important emerging area of research into molecular signatures for biomarker and therapeutic target development. Salivary exosomes represent a relatively unexplored, but convenient, and noninvasive area of cancer biomarker discovery. However, the potential of cancer-derived exosomal chimeric RNAs in saliva as biomarkers is unknown. Here, we explore the potential clinical utility of salivary exosomal GOLM1-NAA35 chimeric RNA (seG-NchiRNA) in esophageal squamous cell carcinoma (ESCC). EXPERIMENTAL DESIGN In a retrospective study, the prognostic significance of G-NchiRNA was determined in ESCC tissues. The correlation between seG-NchiRNA and circulating exosomal or tumoral G-NchiRNA was ascertained in cultured cells and mice. In multiple prospective cohorts of patients with ESCC, seG-NchiRNA was measured by qRT-PCR and analyzed for diagnostic accuracy, longitudinal monitoring of treatment response, and prediction of progression-free survival (PFS). RESULTS Exosomal G-NchiRNA was readily detectable in ESCC cells and nude mouse ESCC xenografts. SeG-NchiRNA levels reflected tumor burden in vivo and correlated with tumor G-NchiRNA levels. In prospective studies of a training cohort (n = 220) and a validation cohort (n = 102), seG-NchiRNA levels were substantially reduced after ESCC resection. Moreover, seG-NchiRNA was successfully used to evaluate chemoradiation responsiveness, as well as to detect disease progression earlier than imaging studies. Changes in seG-NchiRNA levels also predicted PFS of patients after chemoradiation. CONCLUSIONS SeG-NchiRNA constitutes an effective candidate noninvasive biomarker for the convenient, reliable assessment of therapeutic response, recurrence, and early detection.
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Affiliation(s)
- Yusheng Lin
- Institute of Precision Cancer Medicine and Pathology, Jinan University Medical College, Guangzhou, Guangdong, China
- Department of Immunotherapy and Gastrointestinal Oncology, Affiliated Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Cancer Research Center, Shantou University Medical College, Shantou, Guangdong, China
| | - Hongmei Dong
- Institute of Precision Cancer Medicine and Pathology, Jinan University Medical College, Guangzhou, Guangdong, China
- Cancer Research Center, Shantou University Medical College, Shantou, Guangdong, China
- Department of Pathology, Jinan University Medical College, Guangzhou, Guangdong, China
| | - Weilun Deng
- Cancer Research Center, Shantou University Medical College, Shantou, Guangdong, China
| | - Wan Lin
- Cancer Research Center, Shantou University Medical College, Shantou, Guangdong, China
| | - Kai Li
- Cancer Research Center, Shantou University Medical College, Shantou, Guangdong, China
| | - Xiao Xiong
- Cancer Research Center, Shantou University Medical College, Shantou, Guangdong, China
| | - Yi Guo
- Endoscopy Center, Affiliated Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Fuyou Zhou
- Department of Thoracic Surgery, Anyang Tumor Hospital, Anyang, Henan, China
| | - Changchun Ma
- Department of Radiation Oncology, Affiliated Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Yuping Chen
- Department of Thoracic Surgery, Affiliated Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China
| | - Hongzheng Ren
- Cancer Research Center, Shantou University Medical College, Shantou, Guangdong, China
| | - Haijun Yang
- Department of Pathology, Anyang Tumor Hospital, Anyang, Henan, China
| | - Ningtao Dai
- Department of Pathology, Anyang Tumor Hospital, Anyang, Henan, China
| | - Lang Ma
- Department of Gastroenterology, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stephen J Meltzer
- Division of Gastroenterology, Department of Medicine, Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - Sai-Ching J Yeung
- Department of Emergency Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas
- Department of Endocrine Neoplasia and Hormonal Disorders, University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Hao Zhang
- Institute of Precision Cancer Medicine and Pathology, Jinan University Medical College, Guangzhou, Guangdong, China.
- Department of Immunotherapy and Gastrointestinal Oncology, Affiliated Cancer Hospital of Shantou University Medical College, Shantou, Guangdong, China
- Cancer Research Center, Shantou University Medical College, Shantou, Guangdong, China
- Department of Pathology, Jinan University Medical College, Guangzhou, Guangdong, China
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28
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Wang Z, Ma K, Pitts S, Cheng Y, Liu X, Ke X, Kovaka S, Ashktorab H, Smoot DT, Schatz M, Wang Z, Meltzer SJ. Novel circular RNA circNF1 acts as a molecular sponge, promoting gastric cancer by absorbing miR-16. Endocr Relat Cancer 2019; 26:265-277. [PMID: 30576282 PMCID: PMC6545167 DOI: 10.1530/erc-18-0478] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [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] [Received: 12/14/2018] [Accepted: 12/14/2018] [Indexed: 12/17/2022]
Abstract
Circular RNAs (circRNAs) are a new class of RNA involved in multiple human malignancies. However, limited information exists regarding the involvement of circRNAs in gastric carcinoma (GC). Therefore, we sought to identify novel circRNAs, their functions and mechanisms in gastric carcinogenesis. We analyzed next-generation RNA sequencing data from GC tissues and cell lines, identifying 75,201 candidate circRNAs. Among these, we focused on one novel circRNA, circNF1 , which was upregulated in GC tissues and cell lines. Loss- and gain-of-function studies demonstrated that circNF1 significantly promotes cell proliferation. Furthermore, luciferase reporter assays showed that circNF1 binds to miR-16, thereby derepressing its downstream target mRNAs, MAP7 and AKT3. Targeted silencing or overexpression of circNF1 had no effect on levels of its linear RNA counterpart, NF1. Taken together, these results suggest that circNF1 acts as a novel oncogenic circRNA in GC by functioning as a miR-16 sponge.
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Affiliation(s)
- Zhe Wang
- Department of Gastroenterology, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200092, China
- Division of Gastroenterology, Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Ke Ma
- Division of Gastroenterology, Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Steffie Pitts
- Cellular and Molecular Medicine Graduate Program, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Yulan Cheng
- Division of Gastroenterology, Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - Xi Liu
- Department of Pathology, The First Affiliated Hospital of Xi’ an Jiaotong University, No. 277 Yanta West Road, Xi’ an, 710061, Shaanxi, China
| | - Xiquan Ke
- Department of Gastroenterology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, 233004, Anhui, China
| | - Samuel Kovaka
- Department of Computer Science, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Hassan Ashktorab
- Cancer Center, Howard University School of Medicine, Washington, D.C
| | - Duane T. Smoot
- Department of Medicine, Meharry Medical College, Nashville, TN
| | - Michael Schatz
- Department of Computer Science, Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, 21205, USA
| | - Zhirong Wang
- Department of Gastroenterology, Tongji Hospital, Tongji University School of Medicine, Shanghai, 200092, China
| | - Stephen J. Meltzer
- Division of Gastroenterology, Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
- Correspondence: Stephen J. Meltzer, MD, The Johns Hopkins University School of Medicine, 1503 East Jefferson Street, Room 112, Baltimore, Maryland 21287, , Tel.: (410) 502-6071, Fax: (410) 502-1329
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29
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Wang Z, Kambhampati S, Cheng Y, Ma K, Simsek C, Tieu AH, Abraham JM, Liu X, Prasath V, Duncan M, Stark A, Trick A, Tsai HL, Wang H, He Y, Khashab MA, Ngamruengphong S, Shin EJ, Wang TH, Meltzer SJ. Methylation Biomarker Panel Performance in EsophaCap Cytology Samples for Diagnosing Barrett's Esophagus: A Prospective Validation Study. Clin Cancer Res 2019; 25:2127-2135. [PMID: 30670490 DOI: 10.1158/1078-0432.ccr-18-3696] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 12/28/2018] [Accepted: 01/17/2019] [Indexed: 12/19/2022]
Abstract
PURPOSE Barrett's esophagus is the only known precursor of esophageal adenocarcinoma (EAC). Although endoscopy and biopsy are standard methods for Barrett's esophagus diagnosis, their high cost and risk limit their use as a screening modality. Here, we sought to develop a Barrett's esophagus detection method based on methylation status in cytology samples captured by EsophaCap using a streamlined sensitive technique, methylation on beads (MOB). EXPERIMENTAL DESIGN We conducted a prospective cohort study on 80 patients (52 in the training set; 28 in the test set). We used MOB to extract and bisulfite-convert DNA, followed by quantitative methylation-specific PCR to assess methylation levels of 8 previously selected candidate markers. Lasso regression was applied to establish a prediction model in the training set, which was then tested on the independent test set. RESULTS In the training set, five of eight candidate methylation biomarkers (p16, HPP1, NELL1, TAC1, and AKAP12) were significantly higher in Barrett's esophagus patients than in controls. We built a four-biomarker-plus-age lasso regression model for Barrett's esophagus diagnosis. The AUC was 0.894, with sensitivity 94.4% [95% confidence interval (CI), 71%-99%] and specificity 62.2% (95% CI, 44.6%-77.3%) in the training set. This model also performed with high accuracy for Barrett's esophagus diagnosis in an independent test set: AUC = 0.929 (P < 0.001; 95% CI, 0.810%-1%), with sensitivity=78.6% (95% CI, 48.8%-94.3%) and specificity = 92.8% (95% CI, 64.1%-99.6%). CONCLUSIONS EsophaCap, in combination with an epigenetic biomarker panel and the MOB method, is a promising, well-tolerated, low-cost esophageal sampling strategy for Barrett's esophagus diagnosis. This approach merits further prospective studies in larger populations.
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Affiliation(s)
- Zhixiong Wang
- Gastrointestinal Surgical Center, First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China.,Center of Gastric Cancer, Sun Yat-Sen University, Guangzhou, China
| | - Swetha Kambhampati
- Division of Hematology/Oncology, Department of Medicine, Helen Diller Family Comprehensive Cancer Center, UCSF Medical Center, San Francisco, California.,Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland
| | - Yulan Cheng
- Division of Gastroenterology, Department of Medicine and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Ke Ma
- Division of Gastroenterology, Department of Medicine and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Cem Simsek
- Division of Gastroenterology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Alan H Tieu
- Division of Gastroenterology, Department of Medicine and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - John M Abraham
- Division of Gastroenterology, Department of Medicine and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Xi Liu
- Department of Pathology, the First Affiliated Hospital of Xi' an Jiaotong University, Xi' an, Shaanxi, China
| | - Vishnu Prasath
- Department of Surgery, Johns Hopkins University, Baltimore, Maryland
| | - Mark Duncan
- Department of Surgery, Johns Hopkins University, Baltimore, Maryland
| | - Alejandro Stark
- Departments of Mechanical Engineering and Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Alexander Trick
- Departments of Mechanical Engineering and Biomedical Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland
| | - Hua-Ling Tsai
- Division of Biostatistics, Department of Oncology, Department of Medicine and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hao Wang
- Division of Biostatistics, Department of Oncology, Department of Medicine and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Yulong He
- Gastrointestinal Surgical Center, First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China.,Center of Gastric Cancer, Sun Yat-Sen University, Guangzhou, China.,Gastrointestinal Surgical Center, Seventh Affiliated Hospital of Sun Yat-Sen University, Shenzhen, China
| | - Mouen A Khashab
- Division of Gastroenterology, Department of Medicine and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Saowanee Ngamruengphong
- Division of Gastroenterology, Department of Medicine and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Eun J Shin
- Division of Gastroenterology, Department of Medicine and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Tza-Huei Wang
- Department of Medicine, Johns Hopkins Hospital, Baltimore, Maryland
| | - Stephen J Meltzer
- Division of Gastroenterology, Department of Medicine and Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, Maryland.
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30
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Peng Y, Zhang X, Lin H, Deng S, Huang Y, Qin Y, Feng X, Yan R, Zhao Y, Cheng Y, Wei Y, Wang J, Chen W, Fan X, Ashktorab H, Smoot D, Meltzer SJ, Li S, Zhang Z, Jin Z. Inhibition of miR‑194 suppresses the Wnt/β‑catenin signalling pathway in gastric cancer. Oncol Rep 2018; 40:3323-3334. [PMID: 30542715 PMCID: PMC6196585 DOI: 10.3892/or.2018.6773] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [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: 02/18/2018] [Accepted: 10/01/2018] [Indexed: 01/01/2023] Open
Abstract
A mounting body of evidence has revealed that microRNAs (miRs) serve pivotal roles in various developmental processes, and in tumourigenesis, by binding to target genes and subsequently regulating gene expression. Continued activation of the Wnt/β-catenin signalling is positively associated with human malignancy. In addition, miR-194 dysregulation has been implicated in gastric cancer (GC); however, the molecular mechanisms underlying the effects of miR-194 on GC carcinogenesis remain to be elucidated. The present study demonstrated that miR-194 was upregulated in GC tissues and SUFU negative regulator of Ηedgehog signaling (SUFU) was downregulated in GC cell lines. Subsequently, inhibition of miR-194 attenuated nuclear accumulation of β-catenin, which consequently blocked Wnt/β-catenin signalling. In addition, the cytoplasmic translocation of β-catenin induced by miR-194 inhibition was mediated by SUFU. Furthermore, genes associated with the Wnt/β-catenin signalling pathway were revealed to be downregulated following inhibition of the Wnt signalling pathway by miR-194 suppression. Finally, the results indicated that cell apoptosis was markedly increased in response to miR-194 inhibition, strongly suggesting the carcinogenic effects of miR-194 in GC. Taken together, these findings demonstrated that miR-194 may promote gastric carcinogenesis through activation of the Wnt/β-catenin signalling pathway, making it a potential therapeutic target for GC.
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Affiliation(s)
- Yin Peng
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Department of Pathology, The Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, P.R. China
| | - Xiaojing Zhang
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Department of Pathology, The Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, P.R. China
| | - Huijuan Lin
- Department of Pathology and Pathophysiology, The Guangzhou Medical University, Guangzhou, Guangdong 510000, P.R. China
| | - Shiqi Deng
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Department of Pathology, The Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, P.R. China
| | - Yong Huang
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Department of Pathology, The Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, P.R. China
| | - Ying Qin
- Department of Gastrointestinal Surgery, Shenzhen Second People's Hospital, Shenzhen, Guangdong 518000, P.R. China
| | - Xianling Feng
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Department of Pathology, The Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, P.R. China
| | - Ruibin Yan
- Laboratory of Chemical Genomics, The Shenzhen Graduate School of Peking University, Shenzhen, Guangdong 518055, P.R. China
| | - Yanqiu Zhao
- Laboratory of Chemical Genomics, The Shenzhen Graduate School of Peking University, Shenzhen, Guangdong 518055, P.R. China
| | - Yulan Cheng
- Department of Medicine/GI Division, The Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
| | - Yanjie Wei
- Center for High Performance Computing, Shenzhen Institutes of Advanced Technology, Shenzhen, Guangdong 518000, P.R. China
| | - Jian Wang
- Department of Pathology and Pathophysiology, The Guangzhou Medical University, Guangzhou, Guangdong 510000, P.R. China
| | - Wangchun Chen
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Department of Pathology, The Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, P.R. China
| | - Xinmin Fan
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Department of Pathology, The Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, P.R. China
| | - Hassan Ashktorab
- Department of Medicine and Cancer Center, Howard University, College of Medicine, Washington, DC 20060, USA
| | - Duane Smoot
- Department of Medicine, Meharry Medical Center, Nashville, TN 37208, USA
| | - Stephen J Meltzer
- Department of Medicine/GI Division, The Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD 21287, USA
| | - Song Li
- Laboratory of Chemical Genomics, The Shenzhen Graduate School of Peking University, Shenzhen, Guangdong 518055, P.R. China
| | - Zhong Zhang
- Department of Pathology, College of Basic Medical Sciences, Shenyang Medical College, Shenyang, Liaoning 110034, P.R. China
| | - Zhe Jin
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Department of Pathology, The Shenzhen University School of Medicine, Shenzhen, Guangdong 518060, P.R. China
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31
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Liu X, Abraham JM, Cheng Y, Wang Z, Wang Z, Zhang G, Ashktorab H, Smoot DT, Cole RN, Boronina TN, DeVine LR, Talbot CC, Liu Z, Meltzer SJ. Synthetic Circular RNA Functions as a miR-21 Sponge to Suppress Gastric Carcinoma Cell Proliferation. Mol Ther Nucleic Acids 2018; 13:312-321. [PMID: 30326427 PMCID: PMC6197335 DOI: 10.1016/j.omtn.2018.09.010] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 09/17/2018] [Accepted: 09/18/2018] [Indexed: 12/15/2022]
Abstract
MicroRNA (miR) sponges containing miR binding sequences constitute a potentially powerful molecular therapeutic strategy. Recently, naturally occurring circular RNAs (circRNAs) were shown to function as efficient miR sponges in cancer cells. We hypothesized that synthetic circRNA sponges could achieve therapeutic loss-of-function targeted against specific miRs. Linear RNA molecules containing miR-21 binding sites were transcribed in vitro; after dephosphorylation and phosphorylation, circularization was achieved using 5'-3' end-ligation by T4 RNA ligase 1. circRNA stability was assessed using RNase R and fetal bovine serum. Competitive inhibition of miR-21 activity by a synthetic circRNA sponge was assessed using luciferase reporter, cell proliferation, and cell apoptosis assays in three gastric cancer cell lines. circRNA effects on downstream proteins were also delineated by Tandem Mass Tag (TMT) labeling (data available via ProteomeXchange identifier PRIDE: PXD008584), followed by western blotting. We conclude that artificial circRNA sponges resistant to nuclease digestion can be synthesized using simple enzymatic ligation steps. These sponges inhibit cancer cell proliferation and suppress the activity of miR-21 on downstream protein targets, including the cancer protein DAXX. In summary, synthetic circRNA sponges represent a simple, effective, convenient strategy for achieving targeted loss of miR function in vitro, with potential future therapeutic application in human patients.
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Affiliation(s)
- Xi Liu
- Department of Pathology, The First Affiliated Hospital of Xi'an Jiaotong University, No. 277 Yanta West Road, Xi'an 710061, Shaanxi, China; Division of Gastroenterology, Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; Division of Gastroenterology, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA
| | - John M Abraham
- Division of Gastroenterology, Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; Division of Gastroenterology, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA
| | - Yulan Cheng
- Division of Gastroenterology, Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; Division of Gastroenterology, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA
| | - Zhixiong Wang
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Zhe Wang
- Division of Gastroenterology, Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; Division of Gastroenterology, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA
| | - Guanjun Zhang
- Department of Pathology, The First Affiliated Hospital of Xi'an Jiaotong University, No. 277 Yanta West Road, Xi'an 710061, Shaanxi, China
| | - Hassan Ashktorab
- Department of Medicine and Cancer Center, Howard University, Washington, DC, USA
| | - Duane T Smoot
- Department of Internal Medicine, Meharry Medical College, Nashville, TN, USA
| | - Robert N Cole
- Mass Spectrometry and Proteomics Facility, Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Tatiana N Boronina
- Mass Spectrometry and Proteomics Facility, Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lauren R DeVine
- Mass Spectrometry and Proteomics Facility, Department of Biological Chemistry, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - C Conover Talbot
- Institute for Basic Biomedical Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Zhengwen Liu
- Department of Infectious Diseases, First Affiliated Hospital of Xi'an Jiaotong University, No. 277 Yanta West Road, Xi'an 710061, Shaanxi, China
| | - Stephen J Meltzer
- Division of Gastroenterology, Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; Division of Gastroenterology, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA.
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Xiong JX, Wang YS, Sheng J, Xiang D, Huang TX, Tan BB, Zeng CM, Li HH, Yang J, Meltzer SJ, Mori Y, Qin YR, Guan XY, Fu L. Epigenetic alterations of a novel antioxidant gene SLC22A3 predispose susceptible individuals to increased risk of esophageal cancer. Int J Biol Sci 2018; 14:1658-1668. [PMID: 30416380 PMCID: PMC6216027 DOI: 10.7150/ijbs.28482] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 07/12/2018] [Accepted: 08/24/2018] [Indexed: 01/29/2023] Open
Abstract
Esophageal squamous cell carcinoma (ESCC) occurs with the highest frequency in China, especially in the high-risk Northern Chinese. Recent studies have reported that SLC22A3 is significantly downregulated in non-tumor (NT) esophageal tissues from familial ESCC patients compared with those from sporadic ESCC. However, the mechanism of how SLC22A3 regulates familial ESCC remains unknown. In this study, post hoc genome-wide association studies (GWAS) in 496 cases with a family history of upper gastrointestinal tract cancers and 1056 controls were performed and the results revealed that SLC22A3 is a novel susceptibility gene for familial ESCC. Reduced expression of SLC22A3 in NT esophageal tissues from familial ESCC patients significantly correlates with its promoter hypermethylation. Moreover, case-control study of Chinese descendants from different risk areas of China revealed that the methylation of the SLC22A3 gene in peripheral blood leukocyte (PBL) DNA samples could be a risk factor for developing ESCC in this high-risk population. Functional studies showed that SLC22A3 is a novel antioxidant gene, and deregulation of SLC22A3 facilitates heat stress-induced oxidative DNA damage and formation of γ-H2AX foci in normal esophageal epithelial cells. Collectively, we show that epigenetic alterations of SLC22A3 predispose susceptible individuals to increased risk of esophageal cancer.
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Affiliation(s)
- Ji-Xian Xiong
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Department of Pharmacology and Carson International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518039, China
| | - Yan-Song Wang
- Department of Stomatology, Shenzhen Hospital of Guangzhou University of Chinese Medicine, Shenzhen, 518033, China
| | - Jingyi Sheng
- Department of Medicine and Therapeutics, Li Ka Shing Institute of Health Sciences, Chinese University of Hong Kong
- Shenzhen Huarui Translational Research Institute, Shenzhen, China
| | - Di Xiang
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Department of Pharmacology and Carson International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518039, China
| | - Tu-Xiong Huang
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Department of Pharmacology and Carson International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518039, China
| | - Bin-Bin Tan
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Department of Pharmacology and Carson International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518039, China
| | - Cui-Mian Zeng
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Department of Pharmacology and Carson International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518039, China
| | - Hua-Hui Li
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Department of Pharmacology and Carson International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518039, China
| | - Jiao Yang
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Department of Pharmacology and Carson International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518039, China
| | - Stephen J. Meltzer
- Department of Medicine and Oncology, The Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
| | - Yuriko Mori
- Department of Medicine and Oncology, The Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland, USA
| | - Yan-Ru Qin
- Department of Clinical Oncology, the First Affiliated Hospital, Zhengzhou University, Zhengzhou, China
| | - Xin-Yuan Guan
- Department of Clinical Oncology, University of Hong Kong, Hong Kong
| | - Li Fu
- Guangdong Key Laboratory for Genome Stability & Disease Prevention, Department of Pharmacology and Carson International Cancer Center, Shenzhen University School of Medicine, Shenzhen 518039, China
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Liu X, Cheng Y, Abraham JM, Wang Z, Wang Z, Ke X, Yan R, Shin EJ, Ngamruengphong S, Khashab MA, Zhang G, McNamara G, Ewald AJ, Lin D, Liu Z, Meltzer SJ. Modeling Wnt signaling by CRISPR-Cas9 genome editing recapitulates neoplasia in human Barrett epithelial organoids. Cancer Lett 2018; 436:109-118. [PMID: 30144514 DOI: 10.1016/j.canlet.2018.08.017] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2018] [Revised: 08/15/2018] [Accepted: 08/16/2018] [Indexed: 02/06/2023]
Abstract
Primary organoid cultures generated from patient biopsies comprise a novel improved platform for disease modeling, being genetically stable and closely recapitulating in vivo scenarios. Barrett esophagus (BE) is the major risk factor for esophageal adenocarcinoma. There has been a dearth of long-term in vitro expansion models of BE neoplastic transformation. We generated a long-term virus-free organoid expansion model of BE neoplasia from patient biopsies. Both wild-type and paired APC-knockout (APCKO) BE organoids genome-edited by CRISPR-Cas9 showed characteristic goblet cell differentiation. Autonomous Wnt activation was confirmed in APCKO organoids by overexpression of Wnt target genes and nuclear-translocated β-catenin expression after withdrawal of Wnt-3A and R-spondin-1. Wnt-activated organoids demonstrated histologic atypia, higher proliferative and replicative activity, reduced apoptosis, and prolonged culturability. Wnt-activated organoids also showed sustained protrusive migration ability accompanied by disrupted basement membrane reorganization and integrity. This CRISPR-Cas9 editing human-derived organoid model recapitulates the critical role of aberrant Wnt/β-catenin signaling activation in BE neoplastic transformation. This system can be used to study other 'driver' pathway alterations in BE-associated neoplasia, avoiding signaling noise present in immortalized or cancer-derived cell lines.
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Affiliation(s)
- Xi Liu
- Department of Pathology, The First Affiliated Hospital of Xi' an Jiaotong University, No. 277 Yanta West Road, Xi' an, 710061, Shaanxi, China; Division of Gastroenterology, Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD, 21205, USA; Division of Gastroenterology, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD, 21205, USA
| | - Yulan Cheng
- Division of Gastroenterology, Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD, 21205, USA; Division of Gastroenterology, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD, 21205, USA
| | - John M Abraham
- Division of Gastroenterology, Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD, 21205, USA; Division of Gastroenterology, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD, 21205, USA
| | - Zhixiong Wang
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Zhe Wang
- Division of Gastroenterology, Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD, 21205, USA; Division of Gastroenterology, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD, 21205, USA
| | - Xiquan Ke
- Department of Gastroenterology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China
| | - Rong Yan
- Department of Surgical Oncology, First Affiliated Hospital of Xi' an Jiaotong University, No. 277 Yanta West Road, Xi' an, 710061, Shaanxi, China
| | - Eun Ji Shin
- Division of Gastroenterology, Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD, 21205, USA; Division of Gastroenterology, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD, 21205, USA
| | - Saowanee Ngamruengphong
- Division of Gastroenterology, Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD, 21205, USA; Division of Gastroenterology, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD, 21205, USA
| | - Mouen A Khashab
- Division of Gastroenterology, Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD, 21205, USA; Division of Gastroenterology, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD, 21205, USA
| | - Guanjun Zhang
- Department of Pathology, The First Affiliated Hospital of Xi' an Jiaotong University, No. 277 Yanta West Road, Xi' an, 710061, Shaanxi, China
| | - George McNamara
- Division of Gastroenterology - Ross Fluorescence Imaging Center, Department of Medicine, Johns Hopkins University, School of Medicine, Baltimore, MD, 21205, USA
| | - Andrew J Ewald
- Department of Cell Biology and Oncology, Center for Cell Dynamics, The Johns Hopkins University School of Medicine, Baltimore, MD, 21205, USA
| | - DeChen Lin
- Division of Hematology and Oncology, Cedars-Sinai Medical Center, UCLA School of Medicine, Los Angeles, CA, 90048, USA
| | - Zhengwen Liu
- Department of Infectious Diseases, First Affiliated Hospital of Xi' an Jiaotong University, No. 277 Yanta West Road, Xi' an, 710061, Shaanxi, China
| | - Stephen J Meltzer
- Division of Gastroenterology, Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD, 21205, USA; Division of Gastroenterology, Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, MD, 21205, USA.
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Ng CK, Cheng Y, Abraham JM, Meltzer SJ. Abstract 3077: Krüppel-like factor 5 and its connection to Sonic Hedgehog signaling in Barrett's esophagus and esophageal adenocarcinoma. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-3077] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [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
Aims: We sought to determine whether KLF5 was involved, at either phenotypic or functional levels, in the genesis and progression of Barrett's esophagus (BE) to esophageal adenocarcinoma (EAC), and whether this involvement was related to sonic hedgehog (SHH) signaling. In human adults, KLF5 is expressed in the less differentiated cells of the intestinal crypts, where its activity promotes cell proliferation, contributes to intestinal epithelial homeostasis, and is necessary for villus formation. KLF5 has been found to be highly active in a number of other cancer types, including gastric cancer; moreover, the known role of KLF5 in intestinal epithelial differentiation may contribute to metaplasia and dysplasia in BE and EAC development. We also sought to ascertain whether KLF5 activity was connected to the sonic hedgehog (SHH) pathway, since this pathway is already known to be highly active in BE and EAC.
Methods and results: Quantitative reverse transcriptase PCR (qRT-PCR) performed on RNA obtained from BE cell lines (GhTRT and QhTRT) and EAC cell lines (SKGT4 and OE33) revealed that KLF5 is underexpressed in BE cell lines and overexpressed in EAC cell lines relative to normal primary squamous esophageal epithelial cells (HEEpic). Moreover, qRT-PCR performed on clinical BE and EAC tissue specimens showed the same pattern, with downregulation in BE tissues and upregulation in EAC tissues (relative to matched normal esophageal control tissues). Next, we determined KLF5 functional effects in EAC in vitro. The EAC cell line SKGT4 was transfected with KLF5 siRNA, and WST-1 cell proliferation assays revealed significantly lower cell proliferation at 72 hours (p<0.00005) and 96 hours (p<0.05) after transfection, relative to mock-transfected SKGT4. We then assayed KLF5 downstream effects on esophageal adenocarcinogenesis as well as SHH signaling in vitro. qRT-PCR performed on KLF5-silenced SKGT4 RNA revealed significantly diminished expression (relative to mock-transfected SKGT4) of the following known EAC-related genes: CDX1 (p<0.005), VIL1 (p<0.05), MUC2 (p<0.005), and MUC5ac (p<0.0005); moreover, GLI1, a known SHH pathway target gene, was significantly downregulated by KLF5 inhibition (p<0.005), while PTCH1, a known SHH pathway-inhibitory gene, was significantly upregulated (p<0.05).
Conclusion: These tissue phenotypic and in vitro functional data identify KLF5 as a potential oncogene in esophageal adenocarcinogenesis. KLF5 is a potential therapeutic and/or chemopreventive target that can be evaluated in future studies of EAC or BE, such as with metformin, which is known to inhibit KLF5 activity. We also identify a potential new connection between KLF5 and SHH pathway activity in the development of EAC. This potential connection deserves further exploration in other malignancies, as well as in physiologic functions such as human development or adult stem cell maintenance.
Citation Format: Christopher K. Ng, Yulan Cheng, John M. Abraham, Stephen J. Meltzer. Krüppel-like factor 5 and its connection to Sonic Hedgehog signaling in Barrett's esophagus and esophageal adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3077.
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Affiliation(s)
| | - Yulan Cheng
- Johns Hopkins University School of Medicine, Baltimore, MD
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35
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Xie JJ, Jiang YY, Jiang Y, Li CQ, Lim MC, An O, Mayakonda A, Ding LW, Long L, Sun C, Lin LH, Chen L, Wu JY, Wu ZY, Cao Q, Fang WK, Yang W, Soukiasian H, Meltzer SJ, Yang H, Fullwood M, Xu LY, Li EM, Lin DC, Koeffler HP. Super-Enhancer-Driven Long Non-Coding RNA LINC01503, Regulated by TP63, Is Over-Expressed and Oncogenic in Squamous Cell Carcinoma. Gastroenterology 2018; 154:2137-2151.e1. [PMID: 29454790 DOI: 10.1053/j.gastro.2018.02.018] [Citation(s) in RCA: 145] [Impact Index Per Article: 24.2] [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: 09/05/2017] [Revised: 02/06/2018] [Accepted: 02/08/2018] [Indexed: 12/19/2022]
Abstract
BACKGROUND & AIMS Long non-coding RNAs (lncRNAs) are expressed in tissue-specific pattern, but it is not clear how these are regulated. We aimed to identify squamous cell carcinoma (SCC)-specific lncRNAs and investigate mechanisms that control their expression and function. METHODS We studied expression patterns and functions of 4 SCC-specific lncRNAs. We obtained 113 esophageal SCC (ESCC) and matched non-tumor esophageal tissues from a hospital in Shantou City, China, and performed quantitative reverse transcription polymerase chain reaction assays to measure expression levels of LINC01503. We collected clinical data from patients and compared expression levels with survival times. LINC01503 was knocked down using small interfering RNAs and oligonucleotides in TE7, TE5, and KYSE510 cell lines and overexpressed in KYSE30 cells. Cells were analyzed by chromatin immunoprecipitation sequencing, luciferase reporter assays, colony formation, migration and invasion, and mass spectrometry analyses. Cells were injected into nude mice and growth of xenograft tumors was measured. LINC01503 interaction with proteins was studied using fluorescence in situ hybridization, RNA pulldown, and RNA immunoprecipitation analyses. RESULTS We identified a lncRNA, LINC01503, which is regulated by a super enhancer and is expressed at significantly higher levels in esophageal and head and neck SCCs than in non-tumor tissues. High levels in SCCs correlated with shorter survival times of patients. The transcription factor TP63 bound to the super enhancer at the LINC01503 locus and activated its transcription. Expression of LINC01503 in ESCC cell lines increased their proliferation, colony formation, migration, and invasion. Knockdown of LINC01503 in SCC cells reduced their proliferation, colony formation, migration, and invasion, and the growth of xenograft tumors in nude mice. Expression of LINC01503 in ESCC cell lines reduced ERK2 dephosphorylation by DUSP6, leading to activation of ERK signaling via MAPK. LINC01503 disrupted the interaction between EBP1 and the p85 subunit of PI3K, increasing AKT signaling. CONCLUSIONS We identified an lncRNA, LINC01503, which is increased in SCC cells compared with non-tumor cells. Increased expression of LINC01503 promotes ESCC cell proliferation, migration, invasion, and growth of xenograft tumors. It might be developed as a biomarker of aggressive SCCs in patients.
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Affiliation(s)
- Jian-Jun Xie
- Department of Biochemistry and Molecular Biology, Medical College of Shantou University, Shantou, China; Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California.
| | - Yan-Yi Jiang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Yuan Jiang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Chun-Quan Li
- School of Medical Informatics, Daqing Campus, Harbin Medical University, Daqing, China
| | - Mei-Chee Lim
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Omer An
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Anand Mayakonda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Ling-Wen Ding
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Lin Long
- Department of Biochemistry and Molecular Biology, Medical College of Shantou University, Shantou, China
| | - Chun Sun
- Department of Biochemistry and Molecular Biology, Medical College of Shantou University, Shantou, China
| | - Le-Hang Lin
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Li Chen
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Jian-Yi Wu
- Department of Biochemistry and Molecular Biology, Medical College of Shantou University, Shantou, China
| | - Zhi-Yong Wu
- Department of Oncologic Surgery, Shantou Central Hospital, Affiliated Shantou Hospital of Sun Yat-Sen University, Shantou, China
| | - Qi Cao
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California
| | - Wang-Kai Fang
- Department of Biochemistry and Molecular Biology, Medical College of Shantou University, Shantou, China
| | - Wei Yang
- Departments of Surgery and Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, California
| | - Harmik Soukiasian
- Division of Thoracic Surgery, Cedars-Sinai Medical Center, Los Angeles, California
| | - Stephen J Meltzer
- Departments of Medicine and Oncology, the Johns Hopkins University School of Medicine, Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - Henry Yang
- Cancer Science Institute of Singapore, National University of Singapore, Singapore
| | - Melissa Fullwood
- Cancer Science Institute of Singapore, National University of Singapore, Singapore; School of Biological Sciences, Nanyang Technological University, Singapore
| | - Li-Yan Xu
- Institute of Oncologic Pathology, Medical College of Shantou University, Shantou, China.
| | - En-Min Li
- Department of Biochemistry and Molecular Biology, Medical College of Shantou University, Shantou, China.
| | - De-Chen Lin
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California.
| | - H Phillip Koeffler
- Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, California; Cancer Science Institute of Singapore, National University of Singapore, Singapore; National University Cancer Institute, National University Hospital Singapore, Singapore
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36
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Ansari A, Miyashita T, Lay F, Ahmed AK, Matsangos AE, Born L, Ng C, Cohen RM, Stricker-Krongrad AH, Salimian K, Marti GP, Mukaisho KI, Kherad Pezhouh M, Marrone K, Meltzer SJ, Rudek MA, Chung CH, Canto M, Harmon JW, Kelly RJ. Targeting the hedgehog pathway in esophageal adenocarcinoma (EAC) using Itraconazole. J Clin Oncol 2018. [DOI: 10.1200/jco.2018.36.15_suppl.e13552] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Amir Ansari
- MedStar Union Memorial Hospital, Baltimore, MD, US
| | | | - Frank Lay
- Johns Hopkins University School of Medicine, Baltimore, MD
| | - A. Karim Ahmed
- Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - Louis Born
- Johns Hopkins University School of Medicine, Baltimore, MD
| | - Christopher Ng
- Johns Hopkins University School of Medicine, Baltimore, MD
| | | | | | | | | | | | | | | | | | | | | | | | - John W Harmon
- Johns Hopkins University School of Medicine, Baltimore, MD
| | - Ronan Joseph Kelly
- Sidney Kimmel Comprehensive Cancer Center at Johns Hopkins University, Baltimore, MD
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37
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Yan R, Zhu K, Dang C, Lan K, Wang H, Yuan D, Chen W, Meltzer SJ, Li K. Paf15 expression correlates with rectal cancer prognosis, cell proliferation and radiation response. Oncotarget 2018; 7:38750-38761. [PMID: 27246972 PMCID: PMC5122426 DOI: 10.18632/oncotarget.9606] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 01/10/2016] [Accepted: 04/26/2016] [Indexed: 01/12/2023] Open
Abstract
Paf15, which participates in DNA repair, is overexpressed in numerous solid tumors. Blocking of Paf15 inhibits the growth of many types of cancer cells; while simultaneously enhancing cellular sensitivity to UV radiation. However, its expression and function in rectal cancer (RC) remain unknown. The current study was undertaken to assess the association of Paf15 expression with RC prognosis, as well as to explore the participation of Paf15 in the response of RC cells to irradiation. Increased Paf15 expression was observed in RC tissues and associated with pTNM stage and poor survival. In vitro, Paf15 induced increased RC cell proliferation while accelerating cell cycle progression, inhibiting cell death, and protecting against gamma radiation-induced DNA damage in RC cells. In conclusion, increased Paf15 expression is associated with increased RC proliferation, decreased patient survival, and a worse radiotherapeutic response.
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Affiliation(s)
- Rong Yan
- Department of Surgical Oncology, The First Affiliated Hospital, Xi'an Jiaotong University College of Medicine, Xi'an, Shaanxi, China.,Department of Medicine (GI Division) and Oncology, Johns Hopkins School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
| | - Kun Zhu
- Department of Surgical Oncology, The First Affiliated Hospital, Xi'an Jiaotong University College of Medicine, Xi'an, Shaanxi, China
| | - Chengxue Dang
- Department of Surgical Oncology, The First Affiliated Hospital, Xi'an Jiaotong University College of Medicine, Xi'an, Shaanxi, China
| | - Ke Lan
- Department of Surgical Oncology, The First Affiliated Hospital, Xi'an Jiaotong University College of Medicine, Xi'an, Shaanxi, China
| | - Haonan Wang
- Department of Surgical Oncology, The First Affiliated Hospital, Xi'an Jiaotong University College of Medicine, Xi'an, Shaanxi, China
| | - Dawei Yuan
- Department of Surgical Oncology, The First Affiliated Hospital, Xi'an Jiaotong University College of Medicine, Xi'an, Shaanxi, China
| | - Wei Chen
- Department of Surgical Oncology, The First Affiliated Hospital, Xi'an Jiaotong University College of Medicine, Xi'an, Shaanxi, China
| | - Stephen J Meltzer
- Department of Medicine (GI Division) and Oncology, Johns Hopkins School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
| | - Kang Li
- Department of Surgical Oncology, The First Affiliated Hospital, Xi'an Jiaotong University College of Medicine, Xi'an, Shaanxi, China
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38
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Zhang X, Peng Y, Huang Y, Yang M, Yan R, Zhao Y, Cheng Y, Liu X, Deng S, Feng X, Lin H, Yu H, Chen S, Zhao Z, Li S, Li K, Wang L, Wei Y, He Z, Fan X, Meltzer SJ, Li S, Jin Z. SMG-1 inhibition by miR-192/-215 causes epithelial-mesenchymal transition in gastric carcinogenesis via activation of Wnt signaling. Cancer Med 2017; 7:146-156. [PMID: 29239144 PMCID: PMC5773975 DOI: 10.1002/cam4.1237] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [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: 08/25/2017] [Accepted: 09/20/2017] [Indexed: 12/18/2022] Open
Abstract
SMG‐1,a member of the phosphoinositide kinase‐like kinase family, functioned as a tumor suppressor gene. However, the role of SMG‐1 in GC remain uncharacterized. In this study, regulation of SMG‐1 by miR‐192 and‐215, along with the biological effects of this modulation, were studied in GC. We used gene microarrays to screening and luciferase reporter assays were to verify the potential targets of miR‐192 and‐215. Tissue microarrays analyses were applied to measure the levels of SMG‐1 in GC tissues. Western blot assays were used to assess the signaling pathway of SMG‐1 regulated by miR‐192 and‐215 in GC. SMG‐1 was significantly downregulated in GC tissues.The proliferative and invasive properties of GC cells were decreased by inhibition of miR‐192 and‐215, whereas an SMG‐1siRNA rescued the inhibitory effects. Finally, SMG‐1 inhibition by miR‐192 and‐215 primed Wnt signaling and induced EMT. Wnt signaling pathway proteins were decreased markedly by inhibitors of miR‐192 and‐215, while SMG‐1 siRNA reversed the inhibition apparently. Meanwhile, miR‐192 and‐215 inhitibtors increased E‐cadherin expression and decreased N‐cadherin and cotransfection of SMG‐1 siRNA reversed these effects. In summary, these findings illustrate that SMG‐1 is suppressed by miR‐192 and‐215 and functions as a tumor suppressor in GC by inactivating Wnt signaling and suppressing EMT.
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Affiliation(s)
- Xiaojing Zhang
- Department of Pathology, The Shenzhen University School of Medicine, Shenzhen, Guangdong, 518060, China.,Shenzhen Key Laboratory of Micromolecule Innovatal Drugs, Shenzhen Key Laboratory of translational Medicine of Tumor, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China.,Guangdong Province Key Laboratory of Molecular Oncologic Pathology, Guangzhou, Guangdong, China
| | - Yin Peng
- Department of Pathology, The Shenzhen University School of Medicine, Shenzhen, Guangdong, 518060, China.,Department of Pathology, Wuhan University School of Basic Medical Sciences, Hubei, China
| | - Yong Huang
- Department of Pathology, The Shenzhen University School of Medicine, Shenzhen, Guangdong, 518060, China
| | - Mengting Yang
- Department of Pathology, The Shenzhen University School of Medicine, Shenzhen, Guangdong, 518060, China
| | - Ruibin Yan
- Laboratory of Chemical Genomics, The Shenzhen Graduate School of Peking University, Shenzhen, Guangdong, China
| | - Yanqiu Zhao
- Laboratory of Chemical Genomics, The Shenzhen Graduate School of Peking University, Shenzhen, Guangdong, China
| | - Yulan Cheng
- Department of Medicine/GI Division, Johns Hopkins University, Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - Xi Liu
- Department of Medicine/GI Division, Johns Hopkins University, Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - Shiqi Deng
- Department of Pathology, The Shenzhen University School of Medicine, Shenzhen, Guangdong, 518060, China
| | - Xianling Feng
- Department of Pathology, The Shenzhen University School of Medicine, Shenzhen, Guangdong, 518060, China
| | - Huijuan Lin
- Department of Pathology and Pathophysiology, The Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Huimin Yu
- Department of Pathology, The Shenzhen University School of Medicine, Shenzhen, Guangdong, 518060, China
| | - Si Chen
- Department of Pathology, The Shenzhen University School of Medicine, Shenzhen, Guangdong, 518060, China
| | - Zhenfu Zhao
- Department of Pathology, The Shenzhen University School of Medicine, Shenzhen, Guangdong, 518060, China
| | - Shanni Li
- Department of Pathology, The Shenzhen University School of Medicine, Shenzhen, Guangdong, 518060, China
| | - Kuan Li
- Department of Pathology, The Shenzhen University School of Medicine, Shenzhen, Guangdong, 518060, China
| | - Liang Wang
- Department of Pathology, The Shenzhen University School of Medicine, Shenzhen, Guangdong, 518060, China.,Shenzhen Key Laboratory of Micromolecule Innovatal Drugs, Shenzhen Key Laboratory of translational Medicine of Tumor, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
| | - Yanjie Wei
- Center for High Performance Computing, Shenzhen Institutes of Advanced Technology, Shenzhen, Guangdong, China
| | - Zhendan He
- Guangdong Province Key Laboratory of Molecular Oncologic Pathology, Guangzhou, Guangdong, China
| | - Xinmin Fan
- Department of Pathology, The Shenzhen University School of Medicine, Shenzhen, Guangdong, 518060, China
| | - Stephen J Meltzer
- Department of Medicine/GI Division, Johns Hopkins University, Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland
| | - Song Li
- Laboratory of Chemical Genomics, The Shenzhen Graduate School of Peking University, Shenzhen, Guangdong, China
| | - Zhe Jin
- Department of Pathology, The Shenzhen University School of Medicine, Shenzhen, Guangdong, 518060, China.,Shenzhen Key Laboratory of Micromolecule Innovatal Drugs, Shenzhen Key Laboratory of translational Medicine of Tumor, Guangdong Key Laboratory for Genome Stability & Disease Prevention, Shenzhen University School of Medicine, Shenzhen, Guangdong, China
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Eluri S, Parian AM, Limketkai BN, Ha CY, Brant SR, Dudley-Brown S, Efron JE, Fang SG, Gearhart SL, Marohn MR, Meltzer SJ, Bashar S, Truta B, Montgomery EA, Lazarev MG. Nearly a Third of High-Grade Dysplasia and Colorectal Cancer Is Undetected in Patients with Inflammatory Bowel Disease. Dig Dis Sci 2017. [PMID: 28631086 PMCID: PMC6435268 DOI: 10.1007/s10620-017-4652-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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: 02/07/2023]
Abstract
BACKGROUND It is unclear whether intensive surveillance protocols have resulted in a decreased incidence of colorectal cancer (CRC) in inflammatory bowel disease (IBD). AIMS To determine the prevalence and characteristics of IBD associated high-grade dysplasia (HGD) or CRC that was undetected on prior colonoscopy. METHODS This is a single-center, retrospective study from 1994 to 2013. All participants had a confirmed IBD diagnosis and underwent a colectomy with either HGD or CRC found in the colectomy specimen.The undetected group had no HGD or CRC on prior colonoscopies. The detected group had HGD or CRC identified on previous biopsies. RESULTS Of 70 participants, with ulcerative colitis (UC) (n = 47), Crohn's disease (CD) (n = 21), and indeterminate colitis (n = 2), 29% (n = 20) had undetected HGD/CRC at colectomy (15 HGD and 5 CRC). In the undetected group, 75% had prior LGD, 15% had indefinite dysplasia, and 10% had no dysplasia (HGD was found in colonic strictures). Patients in the undetected group were more likely to have pancolitis (55 vs. 20%) and multifocal dysplasia (35 vs. 8%). The undetected group was less likely to have CRC at colectomy (25 vs. 62%). There was a trend toward right-sided HGD/CRC at colectomy (40 vs. 20%; p = 0.08). In addition, 84% of the lesions found in the rectum at colectomy were not seen on prior colonoscopy in the undetected group. CONCLUSIONS The prevalence of previously undetected HGD/CRC in IBD found at colectomy was 29%. The high proportion of undetected rectal and right-sided HGD/CRC suggests that these areas may need greater attention during surveillance.
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Affiliation(s)
- Swathi Eluri
- Division of Gastroenterology and Hepatology, School of Medicine, University of North Carolina at Chapel Hill, 4119B Bioinformatics Building, 130 Mason Farm Road, Chapel Hill, NC, 27599-7080, USA.
- Johns Hopkins University School of Medicine, 600 N. Wolfe Street, Baltimore, MD, 21287, USA.
| | - Alyssa M Parian
- Division of Gastroenterology and Hepatology, School of Medicine, University of North Carolina at Chapel Hill, 4119B Bioinformatics Building, 130 Mason Farm Road, Chapel Hill, NC, 27599-7080, USA
| | - Berkeley N Limketkai
- Stanford University School of Medicine, Stanford, CA, USA
- Digestive Health Liver Clinic, 900 Blake Wilbur Dr, MC 5355, Palo Alto, CA, 94304, USA
| | - Christina Y Ha
- David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Ronald Reagan UCLA Medical Center, 757 Westwood Plaza, Los Angeles, CA, 90095, USA
| | - Steven R Brant
- Division of Gastroenterology and Hepatology, School of Medicine, University of North Carolina at Chapel Hill, 4119B Bioinformatics Building, 130 Mason Farm Road, Chapel Hill, NC, 27599-7080, USA
| | - Sharon Dudley-Brown
- Division of Gastroenterology and Hepatology, School of Medicine, University of North Carolina at Chapel Hill, 4119B Bioinformatics Building, 130 Mason Farm Road, Chapel Hill, NC, 27599-7080, USA
| | - Jonathan E Efron
- Division of Gastroenterology and Hepatology, School of Medicine, University of North Carolina at Chapel Hill, 4119B Bioinformatics Building, 130 Mason Farm Road, Chapel Hill, NC, 27599-7080, USA
| | - Sandy G Fang
- Division of Gastroenterology and Hepatology, School of Medicine, University of North Carolina at Chapel Hill, 4119B Bioinformatics Building, 130 Mason Farm Road, Chapel Hill, NC, 27599-7080, USA
| | - Susan L Gearhart
- Division of Gastroenterology and Hepatology, School of Medicine, University of North Carolina at Chapel Hill, 4119B Bioinformatics Building, 130 Mason Farm Road, Chapel Hill, NC, 27599-7080, USA
| | - Michael R Marohn
- Division of Gastroenterology and Hepatology, School of Medicine, University of North Carolina at Chapel Hill, 4119B Bioinformatics Building, 130 Mason Farm Road, Chapel Hill, NC, 27599-7080, USA
| | - Stephen J Meltzer
- Division of Gastroenterology and Hepatology, School of Medicine, University of North Carolina at Chapel Hill, 4119B Bioinformatics Building, 130 Mason Farm Road, Chapel Hill, NC, 27599-7080, USA
| | - Safar Bashar
- Division of Gastroenterology and Hepatology, School of Medicine, University of North Carolina at Chapel Hill, 4119B Bioinformatics Building, 130 Mason Farm Road, Chapel Hill, NC, 27599-7080, USA
| | - Brindusa Truta
- Division of Gastroenterology and Hepatology, School of Medicine, University of North Carolina at Chapel Hill, 4119B Bioinformatics Building, 130 Mason Farm Road, Chapel Hill, NC, 27599-7080, USA
| | - Elizabeth A Montgomery
- Division of Gastroenterology and Hepatology, School of Medicine, University of North Carolina at Chapel Hill, 4119B Bioinformatics Building, 130 Mason Farm Road, Chapel Hill, NC, 27599-7080, USA
| | - Mark G Lazarev
- Division of Gastroenterology and Hepatology, School of Medicine, University of North Carolina at Chapel Hill, 4119B Bioinformatics Building, 130 Mason Farm Road, Chapel Hill, NC, 27599-7080, USA
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Ke X, Yan R, Sun Z, Cheng Y, Meltzer A, Lu N, Shu X, Wang Z, Huang B, Liu X, Wang Z, Song JH, Ng CK, Ibrahim S, Abraham JM, Shin EJ, He S, Meltzer SJ. Esophageal Adenocarcinoma-Derived Extracellular Vesicle MicroRNAs Induce a Neoplastic Phenotype in Gastric Organoids. Neoplasia 2017; 19:941-949. [PMID: 28968550 PMCID: PMC5633352 DOI: 10.1016/j.neo.2017.06.007] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [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: 06/04/2017] [Revised: 06/26/2017] [Accepted: 06/27/2017] [Indexed: 12/13/2022]
Abstract
There have been no reports describing the effects of cancer cell-derived extracellular vesicles (EVs) on three-dimensional organoids. In this study, we delineated the proneoplastic effects of esophageal adenocarcinoma (EAC)-derived EVs on gastric organoids (gastroids) and elucidated molecular mechanisms underlying these effects. EVs were identified using PKH-67 staining. Morphologic changes, Ki-67 immunochemistry, cell viability, growth rates, and expression levels of miR-25 and miR-210, as well as of their target mRNAs, were determined in gastroids co-cultured with EAC-derived extracellular vesicles (c-EVs). C-EVs were efficiently taken up by gastroids. Notably, c-EV-treated gastroids were more crowded, compact, and multilayered and contained smaller lumens than did those cultured in organoid medium alone or in EAC-conditioned medium that had been depleted of EVs. Moreover, c-EV-treated gastroids manifested increased proliferation and cellular viability relative to medium-only or EV-depleted controls. Expression levels of miR-25 and miR-210 were significantly higher, and those of PTEN and AIFM3 significantly lower, in c-EV-treated versus medium-only or EV-depleted control groups. Inhibitors of miR-25 and miR-210 reversed the increased cell proliferation induced by c-exosomes in co-cultured gastroids by lowering miR-25 and miR-210 levels. In conclusion, we have constructed a novel model system featuring the co-culture of c-EVs with three-dimensional gastroids. Using this model, we discovered that cancer-derived EVs induce a neoplastic phenotype in gastroids. These changes are due, at least in part, to EV transfer of miR-25 and miR-210.
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Affiliation(s)
- Xiquan Ke
- Department of Gastroenterology, The First Affiliated Hospital of Bengbu Medical College, Bengbu, Anhui, China; Department of Gastroenterology, the First Affiliated Hospital, Xi'an Jiaotong University School of Medicine, Xi'an, Shaanxi, China; Department of Medicine (GI Division), the Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA; Department of Oncology, the Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
| | - Rong Yan
- Department of Medicine (GI Division), the Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA; Department of Oncology, the Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA; Departments of Surgical Oncology, the First Affiliated Hospital, Xi'an Jiaotong University School of Medicine, Xi'an, Shaanxi, China
| | - Zhenguo Sun
- Department of Thoracic Surgery, Shandong University Qilu Hospital, Jinan, Shandong, PR China
| | - Yulan Cheng
- Department of Medicine (GI Division), the Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA; Department of Oncology, the Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
| | - Amy Meltzer
- Department of Biology, Goucher College, Baltimore, MD, USA
| | - Nonghua Lu
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Xu Shu
- Department of Gastroenterology, The First Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, China
| | - Zhe Wang
- Department of Gastroenterology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Binbin Huang
- Department of Gastroenterology, Tongji Hospital, Tongji University School of Medicine, Shanghai, China
| | - Xi Liu
- Department of Medicine (GI Division), the Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA; Department of Oncology, the Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA; Departments of Pathology, the First Affiliated Hospital, Xi'an Jiaotong University School of Medicine, Xi'an, Shaanxi, China
| | - Zhixiong Wang
- Department of Medicine (GI Division), the Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA; Department of Oncology, the Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA; Departments of Gastrointestinal Surgery, First Affiliated Hospital of Sun Yat-Sen University, Guangzhou, China
| | - Jee Hoon Song
- Department of Medicine (GI Division), the Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA; Department of Oncology, the Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
| | - Christopher K Ng
- Department of Medicine (GI Division), the Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA; Department of Oncology, the Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
| | - Sariat Ibrahim
- Department of Medicine (GI Division), the Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA; Department of Oncology, the Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
| | - John M Abraham
- Department of Medicine (GI Division), the Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA; Department of Oncology, the Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
| | - Eun Ji Shin
- Department of Medicine (GI Division), the Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA; Department of Oncology, the Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA
| | - Shuixiang He
- Department of Gastroenterology, the First Affiliated Hospital, Xi'an Jiaotong University School of Medicine, Xi'an, Shaanxi, China.
| | - Stephen J Meltzer
- Department of Medicine (GI Division), the Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA; Department of Oncology, the Johns Hopkins University School of Medicine and Sidney Kimmel Comprehensive Cancer Center, Baltimore, MD, USA.
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Wang Z, Cheng Y, Abraham JM, Yan R, Liu X, Chen W, Ibrahim S, Schroth GP, Ke X, He Y, Meltzer SJ. RNA sequencing of esophageal adenocarcinomas identifies novel fusion transcripts, including NPC1-MELK, arising from a complex chromosomal rearrangement. Cancer 2017; 123:3916-3924. [PMID: 28640357 PMCID: PMC5626593 DOI: 10.1002/cncr.30837] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2017] [Revised: 05/14/2017] [Accepted: 05/18/2017] [Indexed: 11/11/2022]
Abstract
BACKGROUND Studies of chromosomal rearrangements and fusion transcripts have elucidated mechanisms of tumorigenesis and led to targeted cancer therapies. This study was aimed at identifying novel fusion transcripts in esophageal adenocarcinoma (EAC). METHODS To identify new fusion transcripts associated with EAC, targeted RNA sequencing and polymerase chain reaction (PCR) verification were performed in 40 EACs and matched nonmalignant specimens from the same patients. Genomic PCR and Sanger sequencing were performed to find the breakpoint of fusion genes. RESULTS Five novel in-frame fusion transcripts were identified and verified in 40 EACs and in a validation cohort of 15 additional EACs (55 patients in all): fibroblast growth factor receptor 2 (FGFR2)-GRB2-associated binding protein 2 (GAB2) in 2 of 55 or 3.6%, Niemann-Pick C1 (NPC1)-maternal embryonic leucine zipper kinase (MELK) in 2 of 55 or 3.6%, ubiquitin-specific peptidase 54 (USP54)-calcium/calmodulin dependent protein kinase II γ (CAMK2G) in 2 of 55 or 3.6%, megakaryoblastic leukemia (translocation) 1 (MKL1)-fibulin 1 (FBLN1) in 1 of 55 or 1.8%, and CCR4-NOT transcription complex subunit 2 (CNOT2)-chromosome 12 open reading frame 49 (C12orf49) in 1 of 55 or 1.8%. A genomic analysis indicated that NPC1-MELK arose from a complex interchromosomal translocation event involving chromosomes 18, 3, and 9 with 3 rearrangement points, and this was consistent with chromoplexy. CONCLUSIONS These data indicate that fusion transcripts occur at a stable frequency in EAC. Furthermore, our results indicate that chromoplexy is an underlying mechanism that generates fusion transcripts in EAC. These and other fusion transcripts merit further study as diagnostic markers and potential therapeutic targets in EAC. Cancer 2017;123:3916-24. © 2017 American Cancer Society.
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Affiliation(s)
- Zhixiong Wang
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
- Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Yulan Cheng
- Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, USA
- Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, USA
| | - John M. Abraham
- Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, USA
- Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Rong Yan
- Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Xi Liu
- Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Wei Chen
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Sariat Ibrahim
- Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, USA
- Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, USA
| | | | - Xiquan Ke
- Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Yulong He
- Department of Gastrointestinal Surgery, First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Stephen J. Meltzer
- Division of Gastroenterology, Johns Hopkins University School of Medicine, Baltimore, USA
- Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, USA
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42
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Kroep S, Heberle CR, Curtius K, Kong CY, Lansdorp-Vogelaar I, Ali A, Wolf WA, Shaheen NJ, Spechler SJ, Rubenstein JH, Nishioka NS, Meltzer SJ, Hazelton WD, van Ballegooijen M, Tramontano AC, Gazelle GS, Luebeck EG, Inadomi JM, Hur C. Radiofrequency Ablation of Barrett's Esophagus Reduces Esophageal Adenocarcinoma Incidence and Mortality in a Comparative Modeling Analysis. Clin Gastroenterol Hepatol 2017; 15:1471-1474. [PMID: 28089850 PMCID: PMC5507756 DOI: 10.1016/j.cgh.2016.12.034] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Revised: 11/28/2016] [Accepted: 12/28/2016] [Indexed: 02/07/2023]
Affiliation(s)
- Sonja Kroep
- Department of Public Health, Erasmus MC, Rotterdam, The Netherlands
| | - Curtis R Heberle
- Institute for Technology Assessment, Massachusetts General Hospital, Boston, Massachusetts; Gastrointestinal Unit, Massachusetts General Hospital, Boston, Massachusetts
| | - Kit Curtius
- Division of Gastroenterology, Department of Medicine, University of Washington School of Medicine, Seattle, Washington; Centre for Tumour Biology, Barts Cancer Institute, London, United Kingdom
| | - Chung Yin Kong
- Institute for Technology Assessment, Massachusetts General Hospital, Boston, Massachusetts; Harvard Medical School, Boston, Massachusetts
| | | | - Ayman Ali
- Institute for Technology Assessment, Massachusetts General Hospital, Boston, Massachusetts; Gastrointestinal Unit, Massachusetts General Hospital, Boston, Massachusetts
| | - W Asher Wolf
- Center for Esophageal Diseases and Swallowing, Division of Gastroenterology and Hepatology, University of North Carolina, Chapel Hill, North Carolina
| | - Nicholas J Shaheen
- Center for Esophageal Diseases and Swallowing, Division of Gastroenterology and Hepatology, University of North Carolina, Chapel Hill, North Carolina
| | - Stuart J Spechler
- Esophageal Diseases Center, Department of Medicine, Veterans Affairs (VA) North Texas Health Care System, and the University of Texas Southwestern Medical Center, Dallas, Texas
| | - Joel H Rubenstein
- Veterans Affairs Center for Clinical Management Research, Ann Arbor, and Division of Gastroenterology, University of Michigan Medical School, Ann Arbor, Michigan
| | - Norman S Nishioka
- Gastrointestinal Unit, Massachusetts General Hospital, Boston, Massachusetts; Harvard Medical School, Boston, Massachusetts
| | | | - William D Hazelton
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | | | - Angela C Tramontano
- Institute for Technology Assessment, Massachusetts General Hospital, Boston, Massachusetts
| | - G Scott Gazelle
- Institute for Technology Assessment, Massachusetts General Hospital, Boston, Massachusetts; Harvard Medical School, Boston, Massachusetts
| | - E Georg Luebeck
- Program in Computational Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - John M Inadomi
- Division of Gastroenterology, Department of Medicine, University of Washington School of Medicine, Seattle, Washington
| | - Chin Hur
- Institute for Technology Assessment, Massachusetts General Hospital, Boston, Massachusetts; Harvard Medical School, Boston, Massachusetts.
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43
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Song Y, Kilburn D, Song JH, Cheng Y, Saeui CT, Cheung DG, Croce CM, Yarema KJ, Meltzer SJ, Liu KJ, Wang TH. Determination of absolute expression profiles using multiplexed miRNA analysis. PLoS One 2017; 12:e0180988. [PMID: 28704432 PMCID: PMC5509254 DOI: 10.1371/journal.pone.0180988] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [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: 01/20/2017] [Accepted: 06/23/2017] [Indexed: 12/19/2022] Open
Abstract
Accurate measurement of miRNA expression is critical to understanding their role in gene expression as well as their application as disease biomarkers. Correct identification of changes in miRNA expression rests on reliable normalization to account for biological and technological variance between samples. Ligo-miR is a multiplex assay designed to rapidly measure absolute miRNA copy numbers, thus reducing dependence on biological controls. It uses a simple 2-step ligation process to generate length coded products that can be quantified using a variety of DNA sizing methods. We demonstrate Ligo-miR's ability to quantify miRNA expression down to 20 copies per cell sensitivity, accurately discriminate between closely related miRNA, and reliably measure differential changes as small as 1.2-fold. Then, benchmarking studies were performed to show the high correlation between Ligo-miR, microarray, and TaqMan qRT-PCR. Finally, Ligo-miR was used to determine copy number profiles in a number of breast, esophageal, and pancreatic cell lines and to demonstrate the utility of copy number analysis for providing layered insight into expression profile changes.
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Affiliation(s)
- Yunke Song
- Biomedical Engineering Department, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Duncan Kilburn
- Circulomics Inc, Baltimore, Maryland, United States of America
- * E-mail: (DK); (TW)
| | - Jee Hoon Song
- Department of Medicine (GI Division) and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Yulan Cheng
- Department of Medicine (GI Division) and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Christopher T. Saeui
- Biomedical Engineering Department, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Douglas G. Cheung
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, Ohio, United States of America
| | - Carlo M. Croce
- Department of Cancer Biology and Genetics, The Ohio State University, Columbus, Ohio, United States of America
| | - Kevin J. Yarema
- Biomedical Engineering Department, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Stephen J. Meltzer
- Department of Medicine (GI Division) and Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Kelvin J. Liu
- Circulomics Inc, Baltimore, Maryland, United States of America
- Mechanical Engineering Department, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Tza-Huei Wang
- Biomedical Engineering Department, Johns Hopkins University, Baltimore, Maryland, United States of America
- Mechanical Engineering Department, Johns Hopkins University, Baltimore, Maryland, United States of America
- Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, Baltimore, Maryland, United States of America
- Center of Cancer Nanotechnology Excellence, Johns Hopkins University, Baltimore, Maryland, United States of America
- * E-mail: (DK); (TW)
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44
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Abraham JM, Meltzer SJ. Long Noncoding RNAs in the Pathogenesis of Barrett's Esophagus and Esophageal Carcinoma. Gastroenterology 2017; 153:27-34. [PMID: 28528706 PMCID: PMC5515484 DOI: 10.1053/j.gastro.2017.04.046] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 04/26/2017] [Accepted: 04/28/2017] [Indexed: 12/13/2022]
Abstract
For many years, only a small fraction of the human genome was believed to regulate cell function and development. This protein-coding portion composed only 1% to 2% of 3 billion human DNA base pairs-the remaining sequence was classified as junk DNA. Subsequent research has revealed that most of the genome is transcribed into a broad array of noncoding RNAs, ranging in size from microRNA (20-23 nucleotides) to long noncoding RNA (lncRNA, more than 200 nucleotides). These noncoding RNA classes have been shown to use diverse molecular mechanisms to control gene expression and organ system development. As anticipated, alterations in this large control system can contribute to disease pathogenesis and carcinogenesis. We review the involvement of noncoding RNAs, lncRNAs in particular, in development of Barrett's esophagus and esophageal carcinoma.
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45
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Sun Z, Ke X, Salzberg SL, Kim D, Antonescu V, Cheng Y, Huang B, Song JH, Abraham JM, Ibrahim S, Tian H, Meltzer SJ. The novel fusion transcript NR5A2-KLHL29FT is generated by an insertion at the KLHL29 locus. Cancer 2017. [PMID: 28081303 DOI: 10.1002/cncr.30510.] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Novel fusion transcripts (FTs) caused by chromosomal rearrangement are common factors in the development of cancers. In the current study, the authors used massively parallel RNA sequencing to identify new FTs in colon cancers. METHODS RNA sequencing (RNA-Seq) and TopHat-Fusion were used to identify new FTs in colon cancers. The authors then investigated whether the novel FT nuclear receptor subfamily 5, group A, member 2 (NR5A2)-Kelch-like family member 29 FT (KLHL29FT) was transcribed from a genomic chromosomal rearrangement. Next, the expression of NR5A2-KLHL29FT was measured by quantitative real-time polymerase chain reaction in colon cancers and matched corresponding normal epithelia. RESULTS The authors identified the FT NR5A2-KLHL29FT in normal and cancerous epithelia. While investigating this transcript, it was unexpectedly found that it was due to an uncharacterized polymorphic germline insertion of the NR5A2 sequence from chromosome 1 into the KLHL29 locus at chromosome 2, rather than a chromosomal rearrangement. This germline insertion, which occurred at a population frequency of 0.40, appeared to bear no relationship to cancer development. Moreover, expression of NR5A2-KLHL29FT was validated in RNA specimens from samples with insertions of NR5A2 at the KLHL29 gene locus, but not from samples without this insertion. It is interesting to note that NR5A2-KLH29FT expression levels were significantly lower in colon cancers than in matched normal colonic epithelia (P =.029), suggesting the potential participation of NR5A2-KLHL29FT in the origin or progression of this tumor type. CONCLUSIONS NR5A2-KLHL29FT was generated from a polymorphism insertion of the NR5A2 sequence into the KLHL29 locus. NR5A2-KLHL29FT may influence the origin or progression of colon cancer. Moreover, researchers should be aware that similar FTs may occur due to transchromosomal insertions that are not correctly annotated in genome databases, especially with current assembly algorithms. Cancer 2017;123:1507-1515. © 2017 American Cancer Society.
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Affiliation(s)
- Zhenguo Sun
- Department of Thoracic Surgery, Shandong University Qilu Hospital, Jinan, Shandong, China.,Division of Gastroenterology, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Xiquan Ke
- Division of Gastroenterology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Steven L Salzberg
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Biostatistics, Bloomberg School of Public Health, The Johns Hopkins University, Baltimore, Maryland
| | - Daehwan Kim
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Biostatistics, Bloomberg School of Public Health, The Johns Hopkins University, Baltimore, Maryland
| | - Valentin Antonescu
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Biostatistics, Bloomberg School of Public Health, The Johns Hopkins University, Baltimore, Maryland
| | - Yulan Cheng
- Division of Gastroenterology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Binbin Huang
- Division of Gastroenterology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jee Hoon Song
- Division of Gastroenterology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - John M Abraham
- Division of Gastroenterology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sariat Ibrahim
- Division of Gastroenterology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hui Tian
- Department of Thoracic Surgery, Shandong University Qilu Hospital, Jinan, Shandong, China
| | - Stephen J Meltzer
- Division of Gastroenterology, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
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Abstract
Gastric cancer (GC) remains the third most common cause of cancer death worldwide, with limited therapeutic strategies available. With the advent of next-generation sequencing and new preclinical model technologies, our understanding of its pathogenesis and molecular alterations continues to be revolutionized. Recently, the genomic landscape of GC has been delineated. Molecular characterization and novel therapeutic targets of each molecular subtype have been identified. At the same time, patient-derived tumor xenografts and organoids now comprise effective tools for genetic evolution studies, biomarker identification, drug screening, and preclinical evaluation of personalized medicine strategies for GC patients. These advances are making it feasible to integrate clinical, genome-based and phenotype-based diagnostic and therapeutic methods and apply them to individual GC patients in the era of precision medicine.
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Key Words
- CIMP, CpG island methylator phenotype
- CIN, chromosomally unstable/chromosomal instability
- Cancer Genomics
- EBV, Epstein-Barr virus
- GAPPS, gastric adenocarcinoma and proximal polyposis of the stomach
- GC, gastric cancer
- GTPase, guanosine triphosphatase
- Gastric Cancer
- HDGC, hereditary diffuse gastric cancer
- LOH, loss of heterozygosity
- MSI, microsatellite unstable/instability
- MSI-H, high microsatellite instability
- MSS/EMT, microsatellite stable with epithelial-to-mesenchymal transition features
- Molecular Classification
- NGS, next-generation sequencing
- PDX, patient-derived tumor xenografts
- Preclinical Models
- TCGA, The Cancer Genome Atlas
- TGF, transforming growth factor
- hPSC, human pluripotent stem cell
- lncRNA, long noncoding RNA
- miRNA, microRNA
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Affiliation(s)
- Xi Liu
- Department of Pathology, First Affiliated Hospital of Xi’ an Jiaotong University, Xi’ an, Shaanxi, China,Division of Gastroenterology, Department of Medicine, and Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, Maryland
| | - Stephen J. Meltzer
- Division of Gastroenterology, Department of Medicine, and Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University, School of Medicine, Baltimore, Maryland,Correspondence Address correspondence to: Stephen J. Meltzer, MD, Johns Hopkins University School of Medicine, 1503 East Jefferson Street, Room 112, Baltimore, Maryland 21287. fax: (410) 502-1329.Johns Hopkins University School of Medicine1503 East Jefferson Street, Room 112BaltimoreMaryland21287
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Li L, Piontek K, Ishida M, Fausther M, Dranoff JA, Fu R, Mezey E, Gould SJ, Fordjour FK, Meltzer SJ, Sirica AE, Selaru FM. Extracellular vesicles carry microRNA-195 to intrahepatic cholangiocarcinoma and improve survival in a rat model. Hepatology 2017; 65:501-514. [PMID: 27474881 PMCID: PMC5258762 DOI: 10.1002/hep.28735] [Citation(s) in RCA: 89] [Impact Index Per Article: 12.7] [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: 01/11/2016] [Revised: 06/16/2016] [Accepted: 07/14/2016] [Indexed: 12/12/2022]
Abstract
UNLABELLED The cancer microenvironment plays a central role in cancer development, growth, and homeostasis. This paradigm suggests that cancer fibroblasts support cancers, probably in response to stimuli received from the cancer cells. We aimed at investigating whether extracellular vesicles (EVs) can shuttle microRNA (miR) species between cancer-associated fibroblasts (CAFs) and cancer cells. To this end, we extracted EVs according to published protocols. EVs were studied for their miR content by quantitative reverse-transcription polymerase chain reaction. EVs were transfected with select miR species and utilized in vitro as well as in vivo in a rat model of cholangiocarcinoma (CCA). We found that miR-195 is down-regulated in CCA cells, as well as in adjoining fibroblasts. Furthermore, we report that EVs shuttle miR-195 from fibroblasts to cancer cells. Last, we show that fibroblast-derived EVs, loaded with miR-195, can be administered in a rat model of CCA, concentrate within the tumor, decrease the size of cancers, and improve survival of treated rats. CONCLUSION EVs play a salient role in trafficking miR species between cancer cells and CAFs in human CCA. Understanding of these mechanisms may allow devising of novel therapeutics. (Hepatology 2017;65:501-514).
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Affiliation(s)
- Ling Li
- Division of Gastroenterology and Hepatology, School of Medicine, The Johns Hopkins University, Baltimore, Maryland, USA
| | - Klaus Piontek
- Division of Gastroenterology and Hepatology, School of Medicine, The Johns Hopkins University, Baltimore, Maryland, USA
| | - Masaharu Ishida
- Division of Gastroenterology and Hepatology, School of Medicine, The Johns Hopkins University, Baltimore, Maryland, USA,Department of Surgery, Tohoku University, Sendai, Japan
| | - Michel Fausther
- Division of Gastroenterology and Hepatology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Jonathan A. Dranoff
- Division of Gastroenterology and Hepatology, University of Arkansas for Medical Sciences, Little Rock, Arkansas, USA
| | - Rongdang Fu
- Division of Gastroenterology and Hepatology, School of Medicine, The Johns Hopkins University, Baltimore, Maryland, USA
| | - Esteban Mezey
- Division of Gastroenterology and Hepatology, School of Medicine, The Johns Hopkins University, Baltimore, Maryland, USA
| | - Stephen J. Gould
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Francis K. Fordjour
- Department of Biological Chemistry, The Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Stephen J. Meltzer
- Division of Gastroenterology and Hepatology, School of Medicine, The Johns Hopkins University, Baltimore, Maryland, USA
| | - Alphonse E. Sirica
- Division of Cellular and Molecular Pathogenesis, Department of Pathology, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Florin M. Selaru
- Division of Gastroenterology and Hepatology, School of Medicine, The Johns Hopkins University, Baltimore, Maryland, USA,Sidney Kimmel Cancer Center, The Johns Hopkins University, Baltimore, Maryland, USA,The Institute for Nanobiotechnology, The Johns Hopkins University, Baltimore, Maryland, USA
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Sun Z, Ke X, Salzberg SL, Kim D, Antonescu V, Cheng Y, Huang B, Song JH, Abraham JM, Ibrahim S, Tian H, Meltzer SJ. The novel fusion transcript NR5A2-KLHL29FT is generated by an insertion at the KLHL29 locus. Cancer 2017; 123:1507-1515. [PMID: 28081303 DOI: 10.1002/cncr.30510] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2016] [Revised: 11/08/2016] [Accepted: 11/21/2016] [Indexed: 12/27/2022]
Abstract
BACKGROUND Novel fusion transcripts (FTs) caused by chromosomal rearrangement are common factors in the development of cancers. In the current study, the authors used massively parallel RNA sequencing to identify new FTs in colon cancers. METHODS RNA sequencing (RNA-Seq) and TopHat-Fusion were used to identify new FTs in colon cancers. The authors then investigated whether the novel FT nuclear receptor subfamily 5, group A, member 2 (NR5A2)-Kelch-like family member 29 FT (KLHL29FT) was transcribed from a genomic chromosomal rearrangement. Next, the expression of NR5A2-KLHL29FT was measured by quantitative real-time polymerase chain reaction in colon cancers and matched corresponding normal epithelia. RESULTS The authors identified the FT NR5A2-KLHL29FT in normal and cancerous epithelia. While investigating this transcript, it was unexpectedly found that it was due to an uncharacterized polymorphic germline insertion of the NR5A2 sequence from chromosome 1 into the KLHL29 locus at chromosome 2, rather than a chromosomal rearrangement. This germline insertion, which occurred at a population frequency of 0.40, appeared to bear no relationship to cancer development. Moreover, expression of NR5A2-KLHL29FT was validated in RNA specimens from samples with insertions of NR5A2 at the KLHL29 gene locus, but not from samples without this insertion. It is interesting to note that NR5A2-KLH29FT expression levels were significantly lower in colon cancers than in matched normal colonic epithelia (P =.029), suggesting the potential participation of NR5A2-KLHL29FT in the origin or progression of this tumor type. CONCLUSIONS NR5A2-KLHL29FT was generated from a polymorphism insertion of the NR5A2 sequence into the KLHL29 locus. NR5A2-KLHL29FT may influence the origin or progression of colon cancer. Moreover, researchers should be aware that similar FTs may occur due to transchromosomal insertions that are not correctly annotated in genome databases, especially with current assembly algorithms. Cancer 2017;123:1507-1515. © 2017 American Cancer Society.
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Affiliation(s)
- Zhenguo Sun
- Department of Thoracic Surgery, Shandong University Qilu Hospital, Jinan, Shandong, China.,Division of Gastroenterology, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Xiquan Ke
- Division of Gastroenterology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Steven L Salzberg
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Biostatistics, Bloomberg School of Public Health, The Johns Hopkins University, Baltimore, Maryland
| | - Daehwan Kim
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Biostatistics, Bloomberg School of Public Health, The Johns Hopkins University, Baltimore, Maryland
| | - Valentin Antonescu
- Center for Computational Biology, McKusick-Nathans Institute of Genetic Medicine, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Biostatistics, Bloomberg School of Public Health, The Johns Hopkins University, Baltimore, Maryland
| | - Yulan Cheng
- Division of Gastroenterology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Binbin Huang
- Division of Gastroenterology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Jee Hoon Song
- Division of Gastroenterology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - John M Abraham
- Division of Gastroenterology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Sariat Ibrahim
- Division of Gastroenterology, The Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Hui Tian
- Department of Thoracic Surgery, Shandong University Qilu Hospital, Jinan, Shandong, China
| | - Stephen J Meltzer
- Division of Gastroenterology, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Medicine, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland.,Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, Maryland
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Peng Y, Zhang X, Ma Q, Yan R, Qin Y, Zhao Y, Cheng Y, Yang M, Wang Q, Feng X, Huang Y, Huang W, Zhao Z, Wang L, Wei Y, He Z, Fan X, Li S, Jin Z, Meltzer SJ. MiRNA-194 activates the Wnt/β-catenin signaling pathway in gastric cancer by targeting the negative Wnt regulator, SUFU. Cancer Lett 2017; 385:117-127. [DOI: 10.1016/j.canlet.2016.10.035] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 10/20/2016] [Accepted: 10/22/2016] [Indexed: 12/31/2022]
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50
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Affiliation(s)
- Stephen J Meltzer
- The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
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