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Masqué-Soler N, Gehrung M, Kosmidou C, Li X, Diwan I, Rafferty C, Atabakhsh E, Markowetz F, Fitzgerald RC. Computational pathology aids derivation of microRNA biomarker signals from Cytosponge samples. EBioMedicine 2022; 76:103814. [PMID: 35051729 PMCID: PMC8883000 DOI: 10.1016/j.ebiom.2022.103814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 12/22/2021] [Accepted: 01/04/2022] [Indexed: 10/27/2022] Open
Abstract
BACKGROUND Non-endoscopic cell collection devices combined with biomarkers can detect Barrett's intestinal metaplasia and early oesophageal cancer. However, assays performed on multi-cellular samples lose information about the cell source of the biomarker signal. This cross-sectional study examines whether a bespoke artificial intelligence-based computational pathology tool could ascertain the cellular origin of microRNA biomarkers, to inform interpretation of the disease pathology, and confirm biomarker validity. METHODS The microRNA expression profiles of 110 targets were assessed with a custom multiplexed panel in a cohort of 117 individuals with reflux that took a Cytosponge test. A computational pathology tool quantified the amount of columnar epithelium present in pathology slides, and results were correlated with microRNA signals. An independent cohort of 139 Cytosponges, each from an individual patient, was used to validate the findings via qPCR. FINDINGS Seventeen microRNAs are upregulated in BE compared to healthy squamous epithelia, of which 13 remain upregulated in dysplasia. A pathway enrichment analysis confirmed association to neoplastic and cell cycle regulation processes. Ten microRNAs positively correlated with columnar epithelium content, with miRNA-192-5p and -194-5p accurately detecting the presence of gastric cells (AUC 0.97 and 0.95). In contrast, miR-196a-5p is confirmed as a specific BE marker. INTERPRETATION Computational pathology tools aid accurate cellular attribution of molecular signals. This innovative design with multiplex microRNA coupled with artificial intelligence has led to discovery of a quality control metric suitable for large scale application of the Cytosponge. Similar approaches could aid optimal interpretation of biomarkers for clinical use. FUNDING Funded by the NIHR Cambridge Biomedical Research Centre, the Medical Research Council, the Rosetrees and Stoneygate Trusts, and CRUK core grants.
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Affiliation(s)
- Neus Masqué-Soler
- MRC Cancer Unit, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK.
| | - Marcel Gehrung
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
| | - Cassandra Kosmidou
- MRC Cancer Unit, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Xiaodun Li
- MRC Cancer Unit, Box 197, Cambridge Biomedical Campus, Cambridge, CB2 0XZ, UK
| | - Izzuddin Diwan
- Abcam Inc., 1 Kendall Sq B2304, Cambridge, MA, 02139, United States
| | - Conor Rafferty
- Abcam Inc., 1 Kendall Sq B2304, Cambridge, MA, 02139, United States
| | - Elnaz Atabakhsh
- Abcam Inc., 1 Kendall Sq B2304, Cambridge, MA, 02139, United States
| | - Florian Markowetz
- Cancer Research UK Cambridge Institute, Li Ka Shing Centre, Robinson Way, Cambridge, CB2 0RE, UK
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Zhu H, Lin Y, Liu Y. miR‑34a increases inflammation and oxidative stress levels in patients with necrotizing enterocolitis by downregulating SIRT1 expression. Mol Med Rep 2021; 24:664. [PMID: 34296298 DOI: 10.3892/mmr.2021.12303] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 05/24/2021] [Indexed: 11/06/2022] Open
Abstract
The miR‑34a/SIRT1 signaling axis is an important signaling axis in tumors and diseases. Notably, low SIRT1 expression in the intestinal tissues of patients with necrotizing enterocolitis (NEC) has been reported. However, whether miR‑34a/SIRT1 signaling as a target to protect the intestines during the NEC process is unclear and remains to be elucidated. Blood samples were collected from 30 patients with NEC, and an NEC rat model was used. The miR‑34a and SIRT1 gene and protein expression levels were assayed by qPCR and Western blotting method. The inflammatory cytokine levels and oxidative stress levels were detected using the ELISA method. The results demonstrated that birth weight, albumin and glucose concentrations were significantly decreased in the NEC patient group compared with the control group, but the C‑reactive protein (CRP) and procalcitonin (PCT) concentrations were significantly increased. The miR‑34a expression level was notably increased in the NEC group, but the SIRT1 expression level was markedly decreased. Notably, the miR‑34a was significantly correlated with NEC severity and the concentrations of CRP, PCT, IL‑6, TNF‑α, IL‑1β, IL‑8, MCP‑1, VCAM1 and malondialdehyde (MDA), but was significantly negatively correlated with SIRT1 gene expression and the concentration of IL‑10. Intestinal villi damage in NEC rats was decreased with miR‑34a inhibition and SIRT1 activation treatment by decreasing the levels of inflammatory cytokines, including IL‑6, TNF‑α, IL‑1β and IL‑8, and oxidative stress proteins, including MCP‑1, VCAM1, and MDA, as well as increasing the level of the anti‑inflammatory cytokine IL‑10. In addition, the results indicated that miR‑34a inhibition and SIRT1 activation strongly protected the intestine and decreased the damage caused by NEC, not only by decreasing the protein levels of SIRT1, TNF‑α, IL‑1β, IL‑6 and IL‑8, but also by increasing the IL‑10 protein levels. The miR‑34a inhibition and SIRT1 activation may decrease the damage caused by NEC by decreasing proinflammatory cytokines and oxidative stress proteins and by increasing the anti‑inflammatory cytokine pathway. Based on the aforementioned analysis, the miR‑34a and SIRT1 proteins may be potential novel therapeutic targets in NEC.
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Affiliation(s)
- Hui Zhu
- Department of NICU, Fujian Provincial Hospital, Provincial Clinical College of Fujian Medical University, Fuzhou, Fujian 350001, P.R. China
| | - Yan Lin
- Department of NICU, Fujian Provincial Hospital, Provincial Clinical College of Fujian Medical University, Fuzhou, Fujian 350001, P.R. China
| | - Yongle Liu
- Department of NICU, Fujian Provincial Hospital, Provincial Clinical College of Fujian Medical University, Fuzhou, Fujian 350001, P.R. China
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MiRNAs and Cancer: Key Link in Diagnosis and Therapy. Genes (Basel) 2021; 12:genes12081289. [PMID: 34440464 PMCID: PMC8395027 DOI: 10.3390/genes12081289] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 08/18/2021] [Accepted: 08/20/2021] [Indexed: 02/07/2023] Open
Abstract
Since the discovery of the first microRNA (miRNA), the exploration of miRNA biology has come to a new era in recent decades. Monumental studies have proven that miRNAs can be dysregulated in different types of cancers and the roles of miRNAs turn out to function to either tumor promoters or tumor suppressors. The interplay between miRNAs and the development of cancers has grabbed attention of miRNAs as novel tools and targets for therapeutic attempts. Moreover, the development of miRNA delivery system accelerates miRNA preclinical implications. In this review, we depict recent advances of miRNAs in cancer and discuss the potential diagnostic or therapeutic approaches of miRNAs.
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De A, Zhou J, Liu P, Huang M, Gunewardena S, Mathur SC, Christenson LK, Sharma M, Zhang Q, Bansal A. Forkhead box F1 induces columnar phenotype and epithelial-to-mesenchymal transition in esophageal squamous cells to initiate Barrett's like metaplasia. J Transl Med 2021; 101:745-759. [PMID: 33495575 PMCID: PMC9296259 DOI: 10.1038/s41374-021-00534-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Revised: 12/22/2020] [Accepted: 12/28/2020] [Indexed: 11/08/2022] Open
Abstract
Multiple genome-wide association studies (GWAS) have linked Forkhead Box F1 (FOXF1) to Barrett's esophagus (BE). Understanding whether FOXF1 is involved in initiation of Barrett's metaplasia could allow FOXF1 to be used for risk stratification and for therapy. Two-dimensional cell cultures and three-dimensional organoid cultures and well-annotated human biopsies were used to determine the role of FOXF1 in BE pathogenesis. Multiple established esophageal squamous and BE cell lines were tested in gain- and loss-of-function studies. Initiation of a BE-like metaplastic change was evaluated by measuring characteristic cytokeratins and global gene expression profiling and by culturing organoids. Epithelial-mesenchymal transition (EMT) was evaluated by immunostaining for E-cadherin, vimentin and Snail, and by cell motility assay. Columnar esophageal epithelium of BE patients exhibited higher expression of FOXF1 compared to normal squamous esophageal epithelium of GERD patients (P < 0.001). Acidic bile salts induced nuclear FOXF1 in esophageal squamous cells. FOXF1 overexpression in normal esophageal squamous cells: (a) increased columnar cytokeratins and decreased squamous cytokeratins, (b) converted squamous organoids to glandular organoids, and (c) switched global gene profiles to resemble that of human BE epithelium (P = 2.1685e - 06 for upregulated genes and P = 8.3378e - 09 for downregulated genes). FOXF1 inhibition in BE cell lines led to loss of BE differentiation markers, CK7, and mucin 2. Also, FOXF1 induced EMT and promoted cell motility in normal esophageal squamous epithelial cells. FOXF1-induced genes mapped to pathways such as Cancer, Cellular Assembly and Organization, DNA Replication, Recombination, and Repair. In conclusion, FOXF1 promotes a BE-like columnar phenotype and cell motility in esophageal squamous epithelial cells, which may have a critical role in BE development. FOXF1 should be studied further as a biomarker for BE and as a target for BE treatment.
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Affiliation(s)
- Alok De
- Midwest Veterans' Biomedical Research Foundation (MVBRF), Kansas City, MO, USA
- Kansas City VA Medical Center, Kansas City, MO, USA
| | - Jianping Zhou
- Midwest Veterans' Biomedical Research Foundation (MVBRF), Kansas City, MO, USA
- Kansas City VA Medical Center, Kansas City, MO, USA
| | - Pi Liu
- Department of Medicine, Center for Esophageal Diseases, Baylor University Medical Center and Center for Esophageal Research, Baylor Scott & White Research Institute, Dallas, TX, 75246, USA
| | - Manling Huang
- Department of Medicine, Center for Esophageal Diseases, Baylor University Medical Center and Center for Esophageal Research, Baylor Scott & White Research Institute, Dallas, TX, 75246, USA
| | - Sumedha Gunewardena
- Department of Molecular and Integrative Physiology, The University of Kansas Medical Center, Kansas City, KS, USA
| | - Sharad C Mathur
- Department of Pathology and Laboratory Medicine, Veterans Affairs Medical Center, Kansas City, MO, USA
- The University of Kansas Medical Center, Kansas City, KS, USA
| | - Lane K Christenson
- Department of Molecular and Integrative Physiology, The University of Kansas Medical Center, Kansas City, KS, USA
| | - Mukut Sharma
- Midwest Veterans' Biomedical Research Foundation (MVBRF), Kansas City, MO, USA
- Research and Development Service, Kansas City Veterans Affairs Medical Center, Kansas City, MO, USA
| | - Qiuyang Zhang
- Department of Medicine, Center for Esophageal Diseases, Baylor University Medical Center and Center for Esophageal Research, Baylor Scott & White Research Institute, Dallas, TX, 75246, USA.
| | - Ajay Bansal
- Division of Gastroenterology and Hepatology, The University of Kansas Medical Center, Kansas City, KS, USA.
- Division of Gastroenterology and Hepatology, Veterans Affairs Medical Center, Kansas City, MO, USA.
- The University of Kansas Cancer Center, Kansas City, KS, USA.
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Role of Extracellular Vesicles in the Diagnosis and Pathogenesis of Barrett's Esophagus: A Mini-Review. Dig Dis Sci 2021; 66:705-713. [PMID: 32277372 DOI: 10.1007/s10620-020-06250-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/15/2020] [Accepted: 04/02/2020] [Indexed: 12/14/2022]
Abstract
Esophageal adenocarcinoma (EAC) continues to be a significant public health problem with survival rates that have remained stagnant. Although the population at the highest risk for EAC, i.e., patients with Barrett's esophagus (BE) has been clearly defined, patients with EAC continue to do poorly due to advanced stage at diagnosis. The field of extracellular vesicles (EV) could have huge application for the management of patients with BE and EAC by allowing timely diagnosis, serial monitoring, and improved understanding of disease biology. EV are actively packaged and actively secreted vesicles and contain microRNAs, proteins, lipids, and DNA. The contents of EV have been shown to provide useful insights into cellular transformation and pro-oncogenic processes. Early work shows promise but suffers from a high degree of technical and biological variation. The current review not only summarizes the current knowledge about EV as diagnostic biomarkers and their role in disease progression of BE and EAC but also provides the reader practical guidance to devise future experiments to perform well-designed studies.
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Ren FJ, Yao Y, Cai XY, Fang GY. Emerging Role of MiR-192-5p in Human Diseases. Front Pharmacol 2021; 12:614068. [PMID: 33708127 PMCID: PMC7940509 DOI: 10.3389/fphar.2021.614068] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/19/2021] [Indexed: 12/24/2022] Open
Abstract
MicroRNAs (miRNAs) are a type of small non-coding RNAs that play an essential role in numerous biological processes by regulating the post-transcriptional expression of target genes. Recent studies have demonstrated that miR-192-5p, a member of the miR-192 family, partakes in several human diseases, especially various cancers, including cancers of the lung, liver, and breast. Importantly, the levels of miR-192-5p are abundant in biofluids, including the serum and urine, and the exosomal levels of miR-192-5p in circulation can aid in the diagnosis and prognosis of various diseases, such as chronic hepatitis B (CHB) infection disease. Notably, recent studies suggest that miR-192-5p is regulated by long noncoding RNAs (lncRNAs) and circular RNAs (circRNAs). However, there are no comprehensive overviews on the role of miR-192-5p in human diseases. This review discusses the significant studies on the role of miR-192-5p in various human diseases, with special emphasis on the diseases of the respiratory and digestive systems.
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Affiliation(s)
- Fu-Jia Ren
- Department of Pharmacy, Hangzhou Women's Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, China
| | - Yao Yao
- Department of Pharmacy, Women's Hospital School of Medicine, Zhejiang University, Hangzhou, China
| | - Xiao-Yu Cai
- Department of Pharmacy, Hangzhou First People's Hospital, Hangzhou, China
| | - Guo-Ying Fang
- Department of Pharmacy, Hangzhou Women's Hospital (Hangzhou Maternity and Child Health Care Hospital), Hangzhou, China
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Saller J, Al Diffalha S, Neill K, Bhaskar RA, Oliveri C, Boulware D, Levine H, Kalvaria I, Corbett FS, Khazanchi A, Klapman J, Coppola D. CDX-2 Expression in Esophageal Biopsies Without Goblet Cell Intestinal Metaplasia May Be Predictive of Barrett's Esophagus. Dig Dis Sci 2020; 65:1992-1998. [PMID: 31691172 PMCID: PMC7771382 DOI: 10.1007/s10620-019-05914-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 10/20/2019] [Indexed: 12/17/2022]
Abstract
BACKGROUND CDX-2 is a nuclear homeobox transcription factor not normally expressed in esophageal and gastric epithelia, reported to highlight intestinal metaplasia (IM) in the esophagus. Pathological absence of goblet cells at initial screening via hematoxylin and eosin (HE) and alcian blue (AB) staining results in patient exclusion from surveillance programs. AIMS This study aimed to determine whether non-goblet cell IM, as defined by CDX-2 positivity, can be considered to be a precursor to Barrett's esophagus (BE). METHODS This study received IRB approval (17,284). Patients with gastroesophageal reflux disease (n = 181) who underwent upper-gastrointestinal endoscopy with biopsies of the distal esophagus to rule out BE using HE/AB staining and CDX-2 immunostaining were followed for 3 years. Initial and follow-up staining results were evaluated for age/sex. RESULTS Differences between development of goblet cell IM in CDX-2-negative and CDX-2-positive groups were evaluated. A Kaplan-Meier curve showed that, out of the 134 patients initially positive for CDX-2, 25 (18.7%) had developed goblet cell IM after 2 years and 106 (79.1%) after 3 years. Conversely, of the 47 patients initially negative for CDX-2, 8 (17.9%) developed goblet cell IM after 24 months and only 11 (23.8%) after 40 to 45 months (P = .049; age-adjusted Cox proportional hazard regression model). CONCLUSION In cases that are initially AB negative and CDX-2 positive, CDX-2 was demonstrated to have a potential prognostic utility for early detection of progression to BE. CDX-2 expression is significantly predictive for risk of goblet cell IM development 40 to 45 months after initial biopsy.
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Affiliation(s)
- James Saller
- Departments of Anatomic Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Sameer Al Diffalha
- Departments of Anatomic Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Kevin Neill
- Departments of Anatomic Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Rahill A Bhaskar
- Departments of Anatomic Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | | | - David Boulware
- Biostatistics, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | | | - Isaac Kalvaria
- Florida Digestive Health Specialists, Lakewood Ranch, FL, USA
| | - F Scott Corbett
- Florida Digestive Health Specialists, Lakewood Ranch, FL, USA
| | - Arun Khazanchi
- Florida Digestive Health Specialists, Lakewood Ranch, FL, USA
| | - Jason Klapman
- Endoscopy, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA
| | - Domenico Coppola
- Departments of Anatomic Pathology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, FL, USA.
- Tumor Biology, H. Lee Moffitt Cancer Center and Research Institute, 12902 USF Magnolia Drive, Tampa, FL, 33612, USA.
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Lv J, Zhao HP, Dai K, Cheng Y, Zhang J, Guo L. Circulating exosomal miRNAs as potential biomarkers for Barrett's esophagus and esophageal adenocarcinoma. World J Gastroenterol 2020; 26:2889-2901. [PMID: 32587437 PMCID: PMC7304109 DOI: 10.3748/wjg.v26.i22.2889] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2019] [Revised: 03/26/2020] [Accepted: 05/26/2020] [Indexed: 02/06/2023] Open
Abstract
Exosomes, a class of extracellular vesicles, are small membrane-bound vesicles derived from almost all cell types that can play important roles in intercellular communication. Exosomes contain proteins, lipids, and nucleic acids that are obtained from the parental cells and participate in various pathophysiological processes, including cell growth, migration, inflammation, immune regulation, and tumor pathogenesis. Moreover, exosomes might be applied in clinical settings, such as diagnosis, treatment, and outcome prediction of diseases, including various cancers. The incidence rates of Barrett's esophagus (BE) and esophageal adenocarcinoma (EAC) have increased in recent decades, and studies have proposed specific factors that may contribute to the development and progression of these diseases. However, how exosomes play a role in this pathological process needs to be clarified. Studies have identified candidate microRNAs (miRNAs) that might be related to BE/EAC. Further studies are needed to ascertain whether circulating exosomal miRNAs are altered before or after disease onset, which could also help understand the pathophysiology of and find potential targets for prevention, diagnosis, and therapy in BE/EAC. This review summarizes recent findings on the features of circulating exosomal miRNAs in BE/EAC, which could be valuable for the early diagnosis, therapeutic approaches, and outcome prediction of BE/EAC.
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Affiliation(s)
- Jing Lv
- Department of Clinical Laboratory, Honghui Hospital, Xi'an Jiaotong University, Xi'an 710054, Shaanxi Province, China
| | - He-Ping Zhao
- Department of Clinical Laboratory, Honghui Hospital, Xi'an Jiaotong University, Xi'an 710054, Shaanxi Province, China
| | - Kun Dai
- Department of Clinical Laboratory, Yanliang Railway Hospital of Xi’an, Xi'an 710089, Shaanxi Province, China
| | - Yan Cheng
- Department of Gastroenterology, Second Affiliated Hospital of Xi’an Jiaotong University, Xi'an 710004, Shaanxi Province, China
| | - Jun Zhang
- Department of Gastroenterology, Second Affiliated Hospital of Xi’an Jiaotong University, Xi'an 710004, Shaanxi Province, China
| | - Lei Guo
- Department of Spinal Surgery, Honghui Hospital, Xi'an Jiaotong University, Xi'an 710054, Shaanxi Province, China
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Profile analysis reveals endogenous RNAs regulate necrotizing enterocolitis progression. Biomed Pharmacother 2020; 125:109975. [PMID: 32036223 DOI: 10.1016/j.biopha.2020.109975] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 01/24/2020] [Accepted: 01/27/2020] [Indexed: 12/31/2022] Open
Abstract
Necrotizing enterocolitis (NEC) is one of the most common and devastating gastrointestinal diseases in preterm newborns, and its underlying mechanisms remain unclear. Non-coding RNAs (ncRNAs) play critical roles in intestinal diseases; however, little is known about their roles in the development of NEC. To gain a deeper understanding of the pathophysiological mechanism of NEC, long non-coding RNAs (lncRNAs), microRNAs (miRNAs) and mRNAs were detected in an NEC rat model. In total, 1820 lncRNAs, 118 miRNAs and 929 mRNAs were differentially expressed in NEC group. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that these molecules were enriched in apoptosis, autophagic cell death, TLR4 signaling pathway, Notch signaling pathway, and mTOR signaling pathway. These pathways are thought to be closely associated with NEC. Furthermore, a lncRNA-miRNA interaction network was constructed, and four of the novel, differentially expressed lncRNAs with large changes were randomly verified using quantitative polymerase chain reaction (qPCR). The GO and KEGG pathway analysis of these four lncRNAs showed that they were associated with the negative regulation of TLR4 signaling pathway and Notch signaling pathway. In conclusion, our study revealed that these differentially expressed lncRNAs may participate in the development of NEC via interactions with miRNAs and may serve as possible biomarkers and target genes in NEC.
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Vychytilova-Faltejskova P, Slaby O. MicroRNA-215: From biology to theranostic applications. Mol Aspects Med 2019; 70:72-89. [DOI: 10.1016/j.mam.2019.03.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 03/10/2019] [Accepted: 03/17/2019] [Indexed: 02/07/2023]
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Clark RJ, Craig MP, Agrawal S, Kadakia M. microRNA involvement in the onset and progression of Barrett's esophagus: a systematic review. Oncotarget 2018; 9:8179-8196. [PMID: 29487725 PMCID: PMC5814292 DOI: 10.18632/oncotarget.24145] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 12/22/2017] [Indexed: 12/13/2022] Open
Abstract
Esophageal adenocarcinoma (EAC) is a highly aggressive malignancy that develops from Barrett's esophagus (BE), an intestinal metaplasia of the distal esophagus. microRNAs (miRNAs), short non-coding regulatory RNAs, are frequently dysregulated in BE and are thought to play key roles in the onset of BE and its progression to EAC. miRNAs thus have potential diagnostic and prognostic value and are increasingly being used as cancer biomarkers. This review summarizes the current literature related to miRNAs that are dysregulated in BE within the context of Hedgehog, Notch, MAPK, NF kappa-B, Wnt and epithelial-mesenchymal transition (EMT) signaling which are thought to drive BE onset and progression. This comprehensive analysis of miRNAs and their associated signaling in the regulation of BE provides an overview of vital discoveries in this field and highlights gaps in our understanding of BE pathophysiology that warrant further investigation.
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Affiliation(s)
- Reilly J Clark
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, OH, USA
| | - Michael P Craig
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, OH, USA
| | | | - Madhavi Kadakia
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, OH, USA
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12
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Nwachokor J, Tawfik O, Danley M, Mathur S, House J, Sharma P, Christenson LK, Bansal A. Quantitation of spatial and temporal variability of biomarkers for Barrett's Esophagus. Dis Esophagus 2017; 30:1-8. [PMID: 28859356 PMCID: PMC6036660 DOI: 10.1093/dote/dox023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Accepted: 03/03/2017] [Indexed: 12/11/2022]
Abstract
Chemoprevention and risk-stratification studies in Barrett's esophagus (BE) rely on biomarkers but the variability in their temporal and spatial expression is unknown. If such variability exists, it will impact sampling techniques and sample size calculations. Specimens from three levels of biopsies over two serial endoscopies in nondysplastic BE patients were analyzed for aneuploidy, proliferation markers (Ki67, Mcm2), and cell cycle markers (cyclin A and cyclin D1). A modification of the image cytometry technique, where cytokeratin staining automatically distinguished epithelial and stromal cells, measured aneuploidy on whole tissue sections. Other biomarkers were studied by immunohistochemistry. Coefficient of variability (SD/mean) was calculated; a value <10% indicated low variability. A total of 120 specimens (20 subjects each with three biopsy levels at two time points) from nondysplastic BE patients (71 ± 8.8 years, all Caucasian, 90% males, C5.1M7.5 ± 3.4 cm) were analyzed. The mean interval between endoscopies was 32.8 ± 8.4 months. Aneuploidy had a spatial variability of 6.8% at visit 1 (mean diploid index: 1.1 ± 0.09) and 7.9% at visit 2 (mean diploid index: 1.1 ± 0.06) and a temporal variability of 7.0-8.1% for the three levels. For other biomarkers, the spatial variability ranged from ∼5 to 30% at visit 1 and 11-92% at visit 2 and the temporal variability ranged from 0 to 77%. To conclude, of all the biomarkers, only aneuploidy had both spatial and temporal variability of <10%. Spatial and temporal variability were biomarker dependent and could be as high as 90% even without progression. These data will be useful to design chemoprevention and risk-stratification studies in BE.
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Affiliation(s)
| | - O. Tawfik
- Pathology and Laboratory Medicine, the University of Kansas School of Medicine,The Kansas Cancer Institute, Kansas City, KS
| | - M. Danley
- Pathology and Laboratory Medicine, the University of Kansas School of Medicine
| | - S. Mathur
- Pathology and Laboratory Medicine, the University of Kansas School of Medicine,Department of Pathology and Laboratory Medicine, the Veterans Affairs Medical Center
| | - J. House
- Department of Biostatistics, Saint Lukes Mid-America Heart Institute
| | - P. Sharma
- The Kansas Cancer Institute, Kansas City, KS,Department of Gastroenterology and Hepatology, the Veterans Affairs Medical Center, Kansas City, MO,Departments of Gastroenterology and Hepatology
| | - L. K. Christenson
- Molecular and Integrative Physiology, the University of Kansas Medical Center, Kansas City, KS
| | - A. Bansal
- The Kansas Cancer Institute, Kansas City, KS,Department of Gastroenterology and Hepatology, the Veterans Affairs Medical Center, Kansas City, MO,Departments of Gastroenterology and Hepatology
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Chen Q, Tong C, Ma S, Zhou L, Zhao L, Zhao X. Involvement of MicroRNAs in Probiotics-Induced Reduction of the Cecal Inflammation by Salmonella Typhimurium. Front Immunol 2017; 8:704. [PMID: 28659929 PMCID: PMC5468434 DOI: 10.3389/fimmu.2017.00704] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Accepted: 05/31/2017] [Indexed: 12/20/2022] Open
Abstract
The microRNAs (miRNAs) have been shown to play important roles in the development of the immune system and in regulation of host inflammation responses. Probiotics can effectively alleviate the inflammation caused by Salmonella in chickens. However, whether and how miRNAs are involved in modulation of the inflammation response in the gut of chickens have not been reported. In this study, the impact of a probiotics, Lactobacillus plantarum Z01 (LPZ01), was investigated on the cecal miRNAs and cytokine secretions in Salmonella Typhimurium (S. Typhimurium)-infected chickens at the age of 3 days. Newly hatched chicks were assigned to four groups (1): NC (basal diet) (2): S (basal diet + S. Typhimurium challenged) (3): SP (basal diet + S. Typhimurium challenged + LPZ01) (4): P (basal diet + LPZ01). In comparison with the S group, chicks in the SP group reduced the number of S. Typhimurium and had lower levels of interferon-γ and lipopolysaccharide-induced tumor necrosis factor alpha factor (LITAF) in ceca post challenge. Expression of 14 miRNAs was significantly affected by the presence of S. Typhimurium and/or lactobacillus. Five differential expression miRNAs (gga-miR-215-5p, gga-miR-3525, gga-miR-193a-5p, gga-miR-122-5p, and gga-miR-375) were randomly selected for confirmation by the RT-PCR. Predicted target genes of differentially expressed miRNAs were enriched in regulation of cAMP-dependent protein kinase activity, stress-activated MAPK cascade, immune system development and regulation of immune system process as well as in immune related pathways such as MAPK and Wnt signaling pathways. The relationship between changes of miRNAs and changes of cytokines was explored. Finally, 119 novel miRNAs were identified in 36 libraries totally. Identification of novel miRNAs significantly expanded the repertoire of chicken miRNAs and provided the basis for understanding the function of miRNAs in the host. Our results suggest that the probiotics reduce the inflammation of the S. Typhimurium infection in neonatal broiler chicks, at least partially, through regulation of miRNAs expression.
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Affiliation(s)
- Qiaoling Chen
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chao Tong
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Shaoyang Ma
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Luoxiong Zhou
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Lili Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xin Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.,Department of Animal Science, McGill University, Montreal, QC, Canada
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14
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Abstract
Tumor suppresser gene TP53 is one of the most frequently deleted
or mutated genes in gastrointestinal cancers. As a transcription factor, p53
regulates a number of important protein coding genes to control cell cycle, cell
death, DNA damage/repair, stemness, differentiation and other key cellular
functions. In addition, p53 is also able to activate the expression of a number
of small non-coding microRNAs (miRNAs) through direct binding to the promoter
region of these miRNAs. Many miRNAs have been identified to be potential tumor
suppressors by regulating key effecter target mRNAs. Our understanding of the
regulatory network of p53 has recently expanded to include long non-coding RNAs
(lncRNAs). Like miRNA, lncRNAs have been found to play important roles in cancer
biology. With our increased understanding of the important functions of these
non-coding RNAs and their relationship with p53, we are gaining exciting new
insights into the biology and function of cells in response to various growth
environment changes. In this review we summarize the current understanding of
the ever expanding involvement of non-coding RNAs in the p53 regulatory network
and its implications for our understanding of gastrointestinal cancer.
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Affiliation(s)
- Andrew Fesler
- Translational Research Laboratory, Department of Pathology, Stony Brook University, Stony Brook, USA
| | - Ning Zhang
- Department of Pharmacy, Dalian Medical University, Dalian, China
| | - Jingfang Ju
- Translational Research Laboratory, Department of Pathology, Stony Brook University, Stony Brook, USA
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15
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Profiling of circulating microRNAs in patients with Barrett's esophagus and esophageal adenocarcinoma. J Gastroenterol 2016; 51:560-70. [PMID: 26585599 PMCID: PMC4880635 DOI: 10.1007/s00535-015-1133-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/13/2015] [Accepted: 10/06/2015] [Indexed: 02/04/2023]
Abstract
BACKGROUND Circulating microRNAs (miRNAs) have been suggested as novel markers for various diseases. The goal of this pilot study was to identify circulating miRNAs differentially expressed comparing Barrett's esophagus (BE), esophageal adenocarcinoma (EAC), and controls. METHODS MicroRNA expression profiling was performed by qPCR array using plasma from six controls and eight BE and eight EAC patients. Validation was performed by analyzing the expression of six selected miRNAs, by qRT-PCR in 115 plasma samples of controls, BE, and EAC patients. Diagnostic accuracy was evaluated by area under the curve (AUC) analysis. RESULTS We identified three miRNAs that were elevated in EAC and four miRNAs that were elevated in BE. Further validation showed that miRNA-382-5p was significantly increased and miRNA-133a-3p significantly decreased in EAC. miRNA-194-5p and miRNA-451a were significantly increased and miRNA-136-5p significantly decreased in BE versus controls. A combination of three or more miRNAs was found to have a good diagnostic performance in discriminating BE from controls (AUC: 0.832), EAC from controls (AUC: 0.846), and BE from EAC (AUC: 0.797). CONCLUSION Our data suggest that circulating miRNAs are differentially expressed in BE and EAC. The miRNAs identified may be used for future non-invasive screening of BE and EAC.
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16
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Vychytilova-Faltejskova P, Slaby O. Circulating Blood-Borne microRNAs as Biomarkers in Solid Tumors. ACTA ACUST UNITED AC 2015; 106:75-122. [PMID: 26608200 DOI: 10.1007/978-3-0348-0955-9_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
One of the major challenges in cancer research is the identification of stable biomarkers that could be routinely measured in easily accessible samples. Human blood and other body fluids represent rich sources for the identification of novel biomarkers. It is apparent that the availability of these biomarkers would improve an early detection of asymptomatic disease and the clinical management of cancer. MicroRNAs have been described to be present in various types of body fluids including cell-free serum and plasma. These days, the involvement of microRNAs in molecular pathology of cancer is well established. Moreover, it seems that these molecules could be optimal noninvasive biomarkers owing to their high stability under storage and handling conditions and high sensitivity and specificity in various diseases. To date, more than 100 circulating microRNAs with the potential to serve as novel diagnostic, prognostic, or predictive biomarkers for different types of cancers have been identified, and this number is still increasing. However, there are major discrepancies in the findings by different research groups, and few commonly altered microRNAs have been reported in these studies. Further studies on large cohorts using uniform methodology are warranted to establish the clinical applicability of circulating microRNAs for solid tumors. Here, we summarize the tumor-specific profiles of blood-borne microRNAs and discuss their potential utility for personalized medicine of solid tumors.
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Affiliation(s)
| | - Ondrej Slaby
- Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00, Brno, Czech Republic.
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17
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Buas MF, Onstad L, Levine DM, Risch HA, Chow WH, Liu G, Fitzgerald RC, Bernstein L, Ye W, Bird NC, Romero Y, Casson AG, Corley DA, Shaheen NJ, Wu AH, Gammon MD, Reid BJ, Hardie LJ, Peters U, Whiteman DC, Vaughan TL. MiRNA-Related SNPs and Risk of Esophageal Adenocarcinoma and Barrett's Esophagus: Post Genome-Wide Association Analysis in the BEACON Consortium. PLoS One 2015; 10:e0128617. [PMID: 26039359 PMCID: PMC4454432 DOI: 10.1371/journal.pone.0128617] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 04/30/2015] [Indexed: 01/09/2023] Open
Abstract
Incidence of esophageal adenocarcinoma (EA) has increased substantially in recent decades. Multiple risk factors have been identified for EA and its precursor, Barrett’s esophagus (BE), such as reflux, European ancestry, male sex, obesity, and tobacco smoking, and several germline genetic variants were recently associated with disease risk. Using data from the Barrett’s and Esophageal Adenocarcinoma Consortium (BEACON) genome-wide association study (GWAS) of 2,515 EA cases, 3,295 BE cases, and 3,207 controls, we examined single nucleotide polymorphisms (SNPs) that potentially affect the biogenesis or biological activity of microRNAs (miRNAs), small non-coding RNAs implicated in post-transcriptional gene regulation, and deregulated in many cancers, including EA. Polymorphisms in three classes of genes were examined for association with risk of EA or BE: miRNA biogenesis genes (157 SNPs, 21 genes); miRNA gene loci (234 SNPs, 210 genes); and miRNA-targeted mRNAs (177 SNPs, 158 genes). Nominal associations (P<0.05) of 29 SNPs with EA risk, and 25 SNPs with BE risk, were observed. None remained significant after correction for multiple comparisons (FDR q>0.50), and we did not find evidence for interactions between variants analyzed and two risk factors for EA/BE (smoking and obesity). This analysis provides the most extensive assessment to date of miRNA-related SNPs in relation to risk of EA and BE. While common genetic variants within components of the miRNA biogenesis core pathway appear unlikely to modulate susceptibility to EA or BE, further studies may be warranted to examine potential associations between unassessed variants in miRNA genes and targets with disease risk.
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Affiliation(s)
- Matthew F. Buas
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- * E-mail: (MFB); (TLV)
| | - Lynn Onstad
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - David M. Levine
- Department of Biostatistics, University of Washington, School of Public Health, Seattle, Washington, United States of America
| | - Harvey A. Risch
- Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT, United States of America
| | - Wong-Ho Chow
- Department of Epidemiology, MD Anderson Cancer Center, Houston, TX, United States of America
| | - Geoffrey Liu
- Pharmacogenomic Epidemiology, Ontario Cancer Institute, Toronto, Ontario, Canada, M5G 2M9
| | - Rebecca C. Fitzgerald
- Medical Research Council (MRC) Cancer Cell Unit, Hutchison-MRC Research Centre and University of Cambridge, Cambridge, United Kingdom
| | - Leslie Bernstein
- Department of Populations Sciences, Beckman Research Institute and City of Hope Comprehensive Cancer Center, Duarte, California, United States of America
| | - Weimin Ye
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Nigel C. Bird
- Department of Oncology, Medical School, University of Sheffield, Sheffield, United Kingdom
| | - Yvonne Romero
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, Minnesota, United States of America
- The Romero Registry, Mayo Clinic, Rochester, Minnesota, United States of America
| | - Alan G. Casson
- Department of Surgery, University of Saskatchewan, Saskatoon, SK, Canada
| | - Douglas A. Corley
- Division of Research, Kaiser Permanente Northern California, Oakland, California, United States of America
- San Francisco Medical Center, Kaiser Permanente Northern California, San Francisco, California, United States of America
| | - Nicholas J. Shaheen
- Division of Gastroenterology and Hepatology, University of North Carolina School of Medicine, University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Anna H. Wu
- Department of Preventive Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, California, United States of America
| | - Marilie D. Gammon
- Department of Epidemiology, University of North Carolina School of Public Health, Chapel Hill, North Carolina, United States of America
| | - Brian J. Reid
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Laura J. Hardie
- Division of Epidemiology, University of Leeds, Leeds, United Kingdom
| | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington, School of Public Health, Seattle, Washington, United States of America
| | - David C. Whiteman
- Cancer Control, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Thomas L. Vaughan
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
- Department of Epidemiology, University of Washington, School of Public Health, Seattle, Washington, United States of America
- * E-mail: (MFB); (TLV)
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18
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Bansal A, Fitzgerald RC. Biomarkers in Barrett's Esophagus: Role in Diagnosis, Risk Stratification, and Prediction of Response to Therapy. Gastroenterol Clin North Am 2015; 44:373-90. [PMID: 26021200 DOI: 10.1016/j.gtc.2015.02.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Esophageal adenocarcinoma (EAC) has increased dramatically in the past 3 decades, making its precursor lesion Barrett's esophagus (BE) an important clinical problem. Effective interventions are available, but overall outcomes remain unchanged. Most of the BE population remains undiagnosed; most EACs are diagnosed late, and most BE patients will never progress to cancer. These epidemiologic factors make upper endoscopy an inefficient and ineffective strategy for BE diagnosis and risk stratification. In the current review, biomarkers for diagnosis, risk stratification, and predictors of response to therapy in BE are discussed.
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Affiliation(s)
- Ajay Bansal
- Division of Gastroenterology and Hepatology, Department of Veterans Affairs Medical Center and the University of Kansas Medical Center, 4801 East Linwood Boulevard, Kansas City, MO 64128-2295, USA.
| | - Rebecca C Fitzgerald
- MRC Cancer Unit, Hutchison-MRC Research Centre, University of Cambridge, Hills Road, Cambridge CB2 0XZ, UK
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