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Pearce SC, Weber GJ, Doherty LA, Soares JW. Human iPSC colon organoid function is improved by exposure to fecal fermentates. FASEB Bioadv 2022; 4:468-484. [PMID: 35812075 PMCID: PMC9254220 DOI: 10.1096/fba.2021-00166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 03/01/2022] [Accepted: 03/18/2022] [Indexed: 11/11/2022] Open
Abstract
The host-microbe interaction is critical for intestinal homeostasis. By-products from microbial metabolism of unabsorbed dietary components have been studied increasingly as potential contributors to health and disease. In vitro fermentation systems provide a way to simulate microbial activity and by-product production of the colon using human fecal samples. Objectives of the study were to determine how clarified supernatants from two different fermentation conditions affect markers of cell proliferation, differentiation, barrier function, and immune function in a human-induced pluripotent (iPSC) colon organoid model. SCFA and BCFA's of the supernatants were analyzed and were similar to known in vivo concentrations. Molecular results showed 25% of the clarified supernatant from batch fermentation led to a more physiological intestinal phenotype including increased markers of differentiation, including alkaline phosphatase, chromogranin A, SCFA transport monocarboxylate transporter-1, (6.2-fold, 2.1-fold, and 1.8-fold, respectively; p < 0.05). Mucin production (mucin-2, mucin-4) was increased in cells treated with 25% supernatant, as observed by confocal microscopy. In addition, increased tight junction expression (claudin-3) was noted by immunofluorescence in 25% supernatant- treated cells. A dose-response increase in barrier function was observed over the 72-h time course, with a twofold increase in transepithelial electrical resistance (TER) in the 25% group compared to the control group (p < 0.05). To further investigate host effects, clarified supernatants from a continuous multistage fermentation representing the ascending (AC), transverse (TC), and descending (DC) colonic domains were utilized and some regional differences were observed including increased markers of inflammation (IL-1β, 6.15 pg/ml; IL-6, 27.58 pg/ml; TNFα, 4.49 pg/ml; p < 0.05) in DC-treated samples only. Overall, clarified supernatants represent a valuable model to examine effects of microbial by-products on host intestinal development and function and future efforts will be designed to further understand microbial communities and metabolites, along with additional host response measures.
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Affiliation(s)
- Sarah C. Pearce
- Soldier Sustainment Directorate, Combat Capabilities Development Command Soldier CenterNatickMassachusettsUSA
- USDA‐ARS National Laboratory for Agriculture and the EnvironmentAmesIowaUSA
| | - Gregory J. Weber
- Soldier Sustainment Directorate, Combat Capabilities Development Command Soldier CenterNatickMassachusettsUSA
| | - Laurel A. Doherty
- Soldier Effectiveness Directorate, Combat Capabilities Development Command Soldier CenterNatickMassachusettsUSA
| | - Jason W. Soares
- Soldier Effectiveness Directorate, Combat Capabilities Development Command Soldier CenterNatickMassachusettsUSA
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2
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Early Pregnancy Exposure to Ambient Air Pollution among Late-Onset Preeclamptic Cases Is Associated with Placental DNA Hypomethylation of Specific Genes and Slower Placental Maturation. TOXICS 2021; 9:toxics9120338. [PMID: 34941772 PMCID: PMC8708250 DOI: 10.3390/toxics9120338] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 11/25/2021] [Accepted: 11/29/2021] [Indexed: 01/19/2023]
Abstract
Exposure to ambient air pollution during pregnancy has been associated with an increased risk of preeclampsia (PE). Some suggested mechanisms behind this association are changes in placental DNA methylation and gene expression. The objective of this study was to identify how early pregnancy exposure to ambient nitrogen oxides (NOx) among PE cases and normotensive controls influence DNA methylation (EPIC array) and gene expression (RNA-seq). The study included placentas from 111 women (29 PE cases/82 controls) in Scania, Sweden. First-trimester NOx exposure was assessed at the participants’ residence using a dispersion model and categorized via median split into high or low NOx. Placental gestational epigenetic age was derived from the DNA methylation data. We identified six differentially methylated positions (DMPs, q < 0.05) comparing controls with low NOx vs. cases with high NOx and 14 DMPs comparing cases and controls with high NOx. Placentas with female fetuses showed more DMPs (N = 309) than male-derived placentas (N = 1). Placentas from PE cases with high NOx demonstrated gestational age deceleration compared to controls with low NOx (p = 0.034). No differentially expressed genes (DEGs, q < 0.05) were found. In conclusion, early pregnancy exposure to NOx affected placental DNA methylation in PE, resulting in placental immaturity and showing sexual dimorphism.
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Jiang Y, Yan X, Liu K, Shi Y, Wang C, Hu J, Li Y, Wu Q, Xiang M, Zhao R. Discovering the molecular differences between right- and left-sided colon cancer using machine learning methods. BMC Cancer 2020; 20:1012. [PMID: 33076847 PMCID: PMC7574488 DOI: 10.1186/s12885-020-07507-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 10/07/2020] [Indexed: 12/24/2022] Open
Abstract
Background In recent years, the differences between left-sided colon cancer (LCC) and right-sided colon cancer (RCC) have received increasing attention due to the clinicopathological variation between them. However, some of these differences have remained unclear and conflicting results have been reported. Methods From The Cancer Genome Atlas (TCGA), we obtained RNA sequencing data and gene mutation data on 323 and 283 colon cancer patients, respectively. Differential analysis was firstly done on gene expression data and mutation data between LCC and RCC, separately. Machine learning (ML) methods were then used to select key genes or mutations as features to construct models to classify LCC and RCC patients. Finally, we conducted correlation analysis to identify the correlations between differentially expressed genes (DEGs) and mutations using logistic regression (LR) models. Results We found distinct gene mutation and expression patterns between LCC and RCC patients and further selected the 30 most important mutations and 17 most important gene expression features using ML methods. The classification models created using these features classified LCC and RCC patients with high accuracy (areas under the curve (AUC) of 0.8 and 0.96 for mutation and gene expression data, respectively). The expression of PRAC1 and BRAF V600E mutation (rs113488022) were the most important feature for each model. Correlations of mutations and gene expression data were also identified using LR models. Among them, rs113488022 was found to have significance relevance to the expression of four genes, and thus should be focused on in further study. Conclusions On the basis of ML methods, we found some key molecular differences between LCC and RCC, which could differentiate these two groups of patients with high accuracy. These differences might be key factors behind the variation in clinical features between LCC and RCC and thus help to improve treatment, such as determining the appropriate therapy for patients.
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Affiliation(s)
- Yimei Jiang
- Department of General Surgery, Ruijin Hospital North, Shanghai Jiaotong University School of Medicine, Shanghai, 201801, China
| | - Xiaowei Yan
- Department of General Surgery, Ruijin Hospital North, Shanghai Jiaotong University School of Medicine, Shanghai, 201801, China
| | - Kun Liu
- Department of General Surgery, Ruijin Hospital North, Shanghai Jiaotong University School of Medicine, Shanghai, 201801, China
| | - Yiqing Shi
- Department of General Surgery, Ruijin Hospital North, Shanghai Jiaotong University School of Medicine, Shanghai, 201801, China
| | - Changgang Wang
- Department of General Surgery, Ruijin Hospital North, Shanghai Jiaotong University School of Medicine, Shanghai, 201801, China
| | - Jiele Hu
- Department of General Surgery, Ruijin Hospital North, Shanghai Jiaotong University School of Medicine, Shanghai, 201801, China
| | - You Li
- Department of General Surgery, Ruijin Hospital North, Shanghai Jiaotong University School of Medicine, Shanghai, 201801, China
| | - Qinghua Wu
- Department of General Surgery, Ruijin Hospital North, Shanghai Jiaotong University School of Medicine, Shanghai, 201801, China
| | - Ming Xiang
- Department of General Surgery, Ruijin Hospital North, Shanghai Jiaotong University School of Medicine, Shanghai, 201801, China.
| | - Ren Zhao
- Department of General Surgery, Ruijin Hospital North, Shanghai Jiaotong University School of Medicine, Shanghai, 201801, China.
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4
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Eskra JN, Rabizadeh D, Mangold L, Fabian E, Brennen WN, Yeater DB, Pienta KJ, Partin AW, Isaacs WB, Pavlovich CP, Luo J. A novel method for detection of exfoliated prostate cancer cells in urine by RNA in situ hybridization. Prostate Cancer Prostatic Dis 2020; 24:220-232. [PMID: 32820256 DOI: 10.1038/s41391-020-00272-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 08/03/2020] [Accepted: 08/10/2020] [Indexed: 11/09/2022]
Abstract
BACKGROUND In the current study, we explore the feasibility of detecting exfoliated prostate cancer cells in urine using an RNA in situ hybridization (RISH) assay. We hypothesized that robust and specific labeling of prostate cancer cells could be achieved in post-digital rectal examination (DRE) urine samples using RISH. METHODS We focused on method development, optimization, and analytical evaluation of RISH-based detection of prostate cancer in urine. We optimized a sample collection, processing, and target detection workflow for urine cytology specimens in conjunction with RNA target detection by RISH. We screened a panel of 11 prostate-specific RNA targets, and selected NKX3-1 and PRAC1 as markers for cells of prostate origin and PCA3 as a marker of prostate malignancy. Following analytical validation of a multiplexed NKX3-1/PRAC1/PCA3 assay, we evaluated whether prostate cancer cells can be detected in a pilot cohort of 19 post-DRE specimens obtained from men diagnosed with prostate cancer. RESULTS Using cytology specimens prepared from spiked urine samples, we established the analytical validity of the RISH assay for detection and visualization of prostate cells in urine. Cells of prostate origin could be readily and specifically identified and separated into benign and malignant cell populations based on the multiplex test that consisted of markers specific for prostate cells (NKX3-1, PRAC1) and prostate cancer cells (PCA3). Upon evaluation of post-DRE urine from a pilot cohort of prostate cancer patients, we identified 11 samples in which prostate cells were present, 6 of which were also positive for prostate cancer cells. CONCLUSIONS Multiplex RISH enables the direct visualization and molecular characterization of individual exfoliated prostate cells in urine. This proof-of-principle study provides evidence supporting the application of RISH as a potential noninvasive tool for prostate cancer detection.
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Affiliation(s)
- Jillian N Eskra
- Department of Urology, The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Daniel Rabizadeh
- Department of Urology, The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Leslie Mangold
- Department of Urology, The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Elizabeth Fabian
- Department of Urology, The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - W Nathaniel Brennen
- Department of Urology, The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David B Yeater
- Department of Urology, The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Kenneth J Pienta
- Department of Urology, The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alan W Partin
- Department of Urology, The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - William B Isaacs
- Department of Urology, The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christian P Pavlovich
- Department of Urology, The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jun Luo
- Department of Urology, The James Buchanan Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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Mukund K, Syulyukina N, Ramamoorthy S, Subramaniam S. Right and left-sided colon cancers - specificity of molecular mechanisms in tumorigenesis and progression. BMC Cancer 2020; 20:317. [PMID: 32293332 PMCID: PMC7161305 DOI: 10.1186/s12885-020-06784-7] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Accepted: 03/24/2020] [Indexed: 12/13/2022] Open
Abstract
Background Given the differences in embryonic origin, vascular and nervous supplies, microbiotic burden, and main physiological functions of left and right colons, tumor location is increasingly suggested to dictate tumor behavior affecting pathology, progression and prognosis. Right-sided colon cancers arise in the cecum, ascending colon, hepatic flexure and/or transverse colon, while left-sided colon cancers arise in the splenic flexure, descending, and/or sigmoid colon. In contrast to prior reports, we attempt to delineate programs of tumorigenesis independently for each side. Methods Four hundred and eleven samples were extracted from The Cancer Genome Atlas-COAD cohort, based on a conservative sample inclusion criterion. Each side was independently analyzed with respect to their respective normal tissue, at the level of transcription, post-transcription, miRNA control and methylation in both a stage specific and stage-agnostic manner. Results Our results indicate a suppression of enzymes involved in various stages of carcinogen breakdown including CYP2C8, CYP4F12, GSTA1, and UGT1A within right colon tumors. This implies its reduced capacity to detoxify carcinogens, contributing to a genotoxic tumor environment, and subsequently a more aggressive phenotype. Additionally, we highlight a crucial nexus between calcium homeostasis (sensing, mobilization and absorption) and immune/GPCR signaling within left-sided tumors, possibly contributing to its reduced proliferative and metastatic potential. Interestingly, two genes SLC6A4 and HOXB13 show opposing regulatory trends within right and left tumors. Post-transcriptional regulation mediated by both RNA-binding proteins (e.g. NKRF (in left) and MSI2 (in right)) and miRNAs (e.g. miR-29a (in left); miR-155, miR181-d, miR-576 and miR23a (in right)) appear to exhibit side-specificity in control of their target transcripts and is pronounced in right colon tumors. Additionally, methylation results depict location-specific differences, with increased hypomethylation in open seas within left tumors, and increased hypermethylation of CpG islands within right tumors. Conclusions Differences in molecular mechanisms captured here highlight distinctions in tumorigenesis and progression between left and right colon tumors, which will serve as the basis for future studies, influencing the efficacies of existing and future diagnostic, prognostic and therapeutic interventions.
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Affiliation(s)
- Kavitha Mukund
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Natalia Syulyukina
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA
| | - Sonia Ramamoorthy
- Division of Colon and Rectal Surgery, Moores Cancer Center, University of California San Diego Health System, La Jolla, CA, USA
| | - Shankar Subramaniam
- Department of Bioengineering, University of California, San Diego, La Jolla, CA, USA. .,Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, CA, USA. .,Department of Computer Science and Engineering, University of California, San Diego, La Jolla, CA, USA.
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Paralogous HOX13 Genes in Human Cancers. Cancers (Basel) 2019; 11:cancers11050699. [PMID: 31137568 PMCID: PMC6562813 DOI: 10.3390/cancers11050699] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 04/17/2019] [Accepted: 05/16/2019] [Indexed: 12/12/2022] Open
Abstract
Hox genes (HOX in humans), an evolutionary preserved gene family, are key determinants of embryonic development and cell memory gene program. Hox genes are organized in four clusters on four chromosomal loci aligned in 13 paralogous groups based on sequence homology (Hox gene network). During development Hox genes are transcribed, according to the rule of “spatio-temporal collinearity”, with early regulators of anterior body regions located at the 3’ end of each Hox cluster and the later regulators of posterior body regions placed at the distal 5’ end. The onset of 3’ Hox gene activation is determined by Wingless-type MMTV integration site family (Wnt) signaling, whereas 5’ Hox activation is due to paralogous group 13 genes, which act as posterior-inhibitors of more anterior Hox proteins (posterior prevalence). Deregulation of HOX genes is associated with developmental abnormalities and different human diseases. Paralogous HOX13 genes (HOX A13, HOX B13, HOX C13 and HOX D13) also play a relevant role in tumor development and progression. In this review, we will discuss the role of paralogous HOX13 genes regarding their regulatory mechanisms during carcinogenesis and tumor progression and their use as biomarkers for cancer diagnosis and treatment.
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Miyahira AK, Den RB, Carlo MI, de Leeuw R, Hope TA, Karzai F, McKay RR, Salami SS, Simons JW, Pienta KJ, Soule HR. Tumor cell heterogeneity and resistance; report from the 2018 Coffey-Holden Prostate Cancer Academy Meeting. Prostate 2019; 79:244-258. [PMID: 30381857 DOI: 10.1002/pros.23729] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 10/05/2018] [Indexed: 12/18/2022]
Abstract
INTRODUCTION The 2018 Coffey-Holden Prostate Cancer Academy (CHPCA) Meeting, "Tumor Cell Heterogeneity and Resistance," was held in Los Angeles, California from June 21 to 24, 2018. METHODS The CHPCA Meeting is a unique, discussion-oriented scientific conference convened annually by the Prostate Cancer Foundation (PCF), which focuses on the most critical topics in need of further study to advance the treatment of lethal prostate cancer. The 6th Annual CHPCA Meeting was attended by 70 investigators and concentrated on prostate cancer heterogeneity and treatment resistance. RESULTS The meeting focused on topics including: recognition of tumor heterogeneity, molecular drivers of heterogeneity, the role of the tumor microenvironment, the role of heterogeneity in disease progression, metastasis and treatment resistance, clinical trials designed to target resistance and tumor heterogeneity, and immunotherapeutic approaches to target and overcome tumor heterogeneity. DISCUSSION This review article summarizes the presentations and discussions from the 2018 CHPCA Meeting in order to share this knowledge with the scientific community and encourage new studies that will lead to improved treatments and outcomes for men with prostate cancer.
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Affiliation(s)
| | - Robert B Den
- Department of Radiation Oncology, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Maria I Carlo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Renée de Leeuw
- Department of Pathology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois
| | - Thomas A Hope
- Department of Radiology and Biomedical Imaging, University of California San Francisco, San Francisco, California
- Department of Radiology, San Francisco VA Medical Center, San Francisco, California
- UCSF Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, California
| | - Fatima Karzai
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Rana R McKay
- Department of Medicine, Division of Hematology/Oncology, University of California San Diego, San Diego, California
| | - Simpa S Salami
- Department of Urology, University of Michigan Health System, Ann Arbor, Michigan
- University of Michigan Rogel Cancer Center, Ann Arbor, Michigan
| | | | - Kenneth J Pienta
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins School of Medicine, Baltimore, Maryland
- Department of Urology, The James Buchanan Brady Urological Institute, Baltimore, Maryland
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins School of Medicine, Baltimore, Maryland
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Xiong Y, Kuang W, Lu S, Guo H, Wu M, Ye M, Wu L. Long noncoding RNA HOXB13-AS1 regulates HOXB13 gene methylation by interacting with EZH2 in glioma. Cancer Med 2018; 7:4718-4728. [PMID: 30105866 PMCID: PMC6144250 DOI: 10.1002/cam4.1718] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 07/11/2018] [Accepted: 07/14/2018] [Indexed: 12/30/2022] Open
Abstract
Dysregulation of long noncoding RNAs (lncRNAs) has been implicated in human diseases, in particular, cancers. In this study, we determined the expression of an lncRNA, HOXB13‐AS1, involving in glioma. We showed that HOXB13‐AS1 was significantly upregulated in glioma tissues and cells and was negatively correlated with its surrounding gene HOXB13 levels. Functional experiments in vitro and in vivo revealed that high level of HOXB13‐AS1 increased cell proliferation and tumor growth by promoting cell cycle progression. Conversely, knockdown of HOXB13‐AS1 resulted in decreased cell proliferation and tumor growth. Mechanistically, we showed that HOXB13‐AS1 overexpression increased DNMT3B‐mediated methylation of adjacent gene HOXB13 promoter by binding with the enhancer of zeste homolog 2 (EZH2) using bisulfite sequencing PCR (BSP), epigenetically suppressing HOXB13 expression. Additionally, the interaction between HOXB13‐AS1 and HOXB13 was validated by RNA immunoprecipitation (RIP) and chromatin immunoprecipitation (ChIP) assays using antibody against to EZH2. Taken together, our study indicated that HOXB13‐AS1 could regulate HOXB13 gene expression by methylation HOXB13 promoter and acts as an epigenetic oncogenic in glioma.
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Affiliation(s)
- Yu Xiong
- Department of Ophthalmology, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Wei Kuang
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Shigang Lu
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Hua Guo
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Miaojing Wu
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Minhua Ye
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
| | - Lei Wu
- Department of Neurosurgery, The Second Affiliated Hospital of Nanchang University, Nanchang, China
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Schroll MM, Ludwig KR, Bauer KM, Hummon AB. Calcitriol Supplementation Causes Decreases in Tumorigenic Proteins and Different Proteomic and Metabolomic Signatures in Right versus Left-Sided Colon Cancer. Metabolites 2018; 8:E5. [PMID: 29324674 PMCID: PMC5875995 DOI: 10.3390/metabo8010005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 01/05/2018] [Accepted: 01/09/2018] [Indexed: 12/20/2022] Open
Abstract
Vitamin D deficiency is a common problem worldwide. In particular, it is an issue in the Northern Hemisphere where UVB radiation does not penetrate the atmosphere as readily. There is a correlation between vitamin D deficiency and colorectal cancer incidence and mortality. Furthermore, there is strong evidence that cancer of the ascending (right side) colon is different from cancer of the descending (left side) colon in terms of prognosis, tumor differentiation, and polyp type, as well as at the molecular level. Right-side tumors have elevated Wnt signaling and are more likely to relapse, whereas left-side tumors have reduced expression of tumor suppressor genes. This study seeks to understand both the proteomic and metabolomic changes resulting from treatment of the active metabolite of vitamin D, calcitriol, in right-sided and left-sided colon cancer. Our results show that left-sided colon cancer treated with calcitriol has a substantially greater number of changes in both the proteome and the metabolome than right-sided colon cancer. We found that calcitriol treatment in both right-sided and left-sided colon cancer causes a downregulation of ribosomal protein L37 and protein S100A10. Both of these proteins are heavily involved in tumorigenesis, suggesting a possible mechanism for the correlation between low vitamin D levels and colon cancer.
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Affiliation(s)
- Monica M Schroll
- Department of Chemistry and Biochemistry, Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Katelyn R Ludwig
- Department of Chemistry and Biochemistry, Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Kerry M Bauer
- Department of Chemistry and Biochemistry, Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Amanda B Hummon
- Department of Chemistry and Biochemistry, Harper Cancer Research Institute, University of Notre Dame, Notre Dame, IN 46556, USA.
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10
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Hu W, Yang Y, Li X, Huang M, Xu F, Ge W, Zhang S, Zheng S. Multi-omics Approach Reveals Distinct Differences in Left- and Right-Sided Colon Cancer. Mol Cancer Res 2017; 16:476-485. [PMID: 29187560 DOI: 10.1158/1541-7786.mcr-17-0483] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/26/2017] [Accepted: 11/27/2017] [Indexed: 02/05/2023]
Abstract
Increasing evidence suggests that left-sided colon cancer (LCC) and right-sided colon cancer (RCC) are emerging as two different colorectal cancer types with distinct clinical characteristics. However, the discrepancy in the underlying molecular event between these types of cancer has not been thoroughly elucidated to date and warrants comprehensive investigation. To this end, an integrated dataset from The Cancer Genome Atlas was used to compare and contrast LCC and RCC, covering mutation, DNA methylation, gene expression, and miRNA. Briefly, the signaling pathway cross-talk is more prevalent in RCC than LCC, such as RCC-specific PI3K pathway, which often exhibits cross-talk with the RAS and P53 pathways. Meanwhile, methylation signatures revealed that RCC was hypermethylated relative to LCC. In addition, differentially expressed genes (n = 253) and differentially expressed miRNAs (n = 16) were determined between LCC and RCC. Especially for Prostate Cancer Susceptibility Candidate 1 (PRAC1), a gene that was closely associated with hypermethylation, was the top significantly downregulated gene in RCC. Multi-omics comparison of LCC and RCC suggests that there are more aggressive markers in RCC and that tumor heterogeneity occurs within the location-based subtypes of colon cancer. These results clarify the debate regarding the conflicting prognosis between LCC and RCC, as proposed by different studies.Implications: The underlying molecular features present in LCC and RCC identified in this study are beneficial for adopting reasonable therapeutic approaches to prolong overall survival and progression-free survival in colorectal cancer patients. Mol Cancer Res; 16(3); 476-85. ©2017 AACR.
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Affiliation(s)
- Wangxiong Hu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| | - Yanmei Yang
- Key Laboratory of Reproductive and Genetics, Ministry of Education, Women's Hospital, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaofen Li
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.,Department of Abdominal Oncology, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Minran Huang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Fei Xu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Weiting Ge
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China.
| | - Suzhan Zhang
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China. .,Research Center for Air Pollution and Health, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Shu Zheng
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education), The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China. .,Research Center for Air Pollution and Health, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
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Barnicle A, Seoighe C, Greally JM, Golden A, Egan LJ. Inflammation-associated DNA methylation patterns in epithelium of ulcerative colitis. Epigenetics 2017; 12:591-606. [PMID: 28557546 DOI: 10.1080/15592294.2017.1334023] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Aberrant DNA methylation patterns have been reported in inflamed tissues and may play a role in disease. We studied DNA methylation and gene expression profiles of purified intestinal epithelial cells from ulcerative colitis patients, comparing inflamed and non-inflamed areas of the colon. We identified 577 differentially methylated sites (false discovery rate <0.2) mapping to 210 genes. From gene expression data from the same epithelial cells, we identified 62 differentially expressed genes with increased expression in the presence of inflammation at prostate cancer susceptibility genes PRAC1 and PRAC2. Four genes showed inverse correlation between methylation and gene expression; ROR1, GXYLT2, FOXA2, and, notably, RARB, a gene previously identified as a tumor suppressor in colorectal adenocarcinoma as well as breast, lung and prostate cancer. We highlight targeted and specific patterns of DNA methylation and gene expression in epithelial cells from inflamed colon, while challenging the importance of epithelial cells in the pathogenesis of chronic inflammation.
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Affiliation(s)
- Alan Barnicle
- a Clinical Pharmacology, School of Medicine, National University of Ireland , Galway , Ireland.,b School of Mathematics, Statistics and Applied Mathematics, National University of Ireland , Galway , Ireland
| | - Cathal Seoighe
- b School of Mathematics, Statistics and Applied Mathematics, National University of Ireland , Galway , Ireland
| | - John M Greally
- c Center of Epigenomics and Department of Genetics (Division of Computational Genetics) , Albert Einstein College of Medicine, Morris Park Avenue , Bronx , NY , USA
| | - Aaron Golden
- b School of Mathematics, Statistics and Applied Mathematics, National University of Ireland , Galway , Ireland.,c Center of Epigenomics and Department of Genetics (Division of Computational Genetics) , Albert Einstein College of Medicine, Morris Park Avenue , Bronx , NY , USA.,d Department of Mathematical Sciences , Yeshiva University , 2495 Amsterdam Avenue, New York , NY , USA
| | - Laurence J Egan
- a Clinical Pharmacology, School of Medicine, National University of Ireland , Galway , Ireland
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12
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Taherian Fard A, Ragan MA. Modeling the Attractor Landscape of Disease Progression: a Network-Based Approach. Front Genet 2017; 8:48. [PMID: 28458684 PMCID: PMC5394169 DOI: 10.3389/fgene.2017.00048] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 03/31/2017] [Indexed: 12/25/2022] Open
Abstract
Genome-wide regulatory networks enable cells to function, develop, and survive. Perturbation of these networks can lead to appearance of a disease phenotype. Inspired by Conrad Waddington's epigenetic landscape of cell development, we use a Hopfield network formalism to construct an attractor landscape model of disease progression based on protein- or gene-correlation networks of Parkinson's disease, glioma, and colorectal cancer. Attractors in this landscape correspond to normal and disease states of the cell. We introduce approaches to estimate the size and robustness of these attractors, and take a network-based approach to study their biological features such as the key genes and their functions associated with the attractors. Our results show that the attractor of cancer cells is wider than the attractor of normal cells, suggesting a heterogeneous nature of cancer. Perturbation analysis shows that robustness depends on characteristics of the input data (number of samples per time-point, and the fraction which converge to an attractor). We identify unique gene interactions at each stage, which reflect the temporal rewiring of the gene regulatory network (GRN) with disease progression. Our model of the attractor landscape, constructed from large-scale gene expression profiles of individual patients, captures snapshots of disease progression and identifies gene interactions specific to different stages, opening the way for development of stage-specific therapeutic strategies.
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Affiliation(s)
- Atefeh Taherian Fard
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, QLD, Australia
| | - Mark A Ragan
- Institute for Molecular Bioscience, University of Queensland, St. Lucia, QLD, Australia
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13
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Clinical Implications and Prognostic Values of Prostate Cancer Susceptibility Candidate Methylation in Primary Nonmuscle Invasive Bladder Cancer. DISEASE MARKERS 2015; 2015:402963. [PMID: 26074659 PMCID: PMC4444592 DOI: 10.1155/2015/402963] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Accepted: 03/30/2015] [Indexed: 12/20/2022]
Abstract
DNA methylation is the most common and well-characterized epigenetic change in human cancer. Recently, an association between prostate cancer susceptibility candidate (PRAC) methylation and genitourinary cancer was proposed. The aim of the present study was to evaluate the association between PRAC methylation status and clinicopathological parameters and prognosis in long-term follow-up primary nonmuscle invasive bladder cancer (NMIBC). The clinical relevance of PRAC methylation was determined in 136 human bladder specimens (eight normal controls [NCs] and 128 primary NMIBCs) using quantitative pyrosequencing analysis. PRAC methylation was significantly higher in NMIBC patients than in NCs and was significantly associated with higher grade and more advanced stage of cancer. Kaplan-Meier estimates revealed significant difference in tumor recurrence and progression according to PRAC methylation status (both p < 0.05). Multivariate Cox regression analysis revealed that the PRAC methylation status was a strong predictor of recurrence (hazard ratio [HR], 2.652; p = 0.012) and progression (HR, 9.531; p = 0.035) of NMIBC. Enhanced methylation status of PRAC was positively associated with a high rate of recurrence and progression in NMIBC patients, suggesting that PRAC methylation may be a promising prognostic marker of NMIBC.
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14
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Wei IH, Shi Y, Jiang H, Kumar-Sinha C, Chinnaiyan AM. RNA-Seq accurately identifies cancer biomarker signatures to distinguish tissue of origin. Neoplasia 2014; 16:918-27. [PMID: 25425966 PMCID: PMC4240918 DOI: 10.1016/j.neo.2014.09.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Revised: 09/23/2014] [Accepted: 09/23/2014] [Indexed: 12/27/2022] Open
Abstract
Metastatic cancer of unknown primary (CUP) accounts for up to 5% of all new cancer cases, with a 5-year survival rate of only 10%. Accurate identification of tissue of origin would allow for directed, personalized therapies to improve clinical outcomes. Our objective was to use transcriptome sequencing (RNA-Seq) to identify lineage-specific biomarker signatures for the cancer types that most commonly metastasize as CUP (colorectum, kidney, liver, lung, ovary, pancreas, prostate, and stomach). RNA-Seq data of 17,471 transcripts from a total of 3,244 cancer samples across 26 different tissue types were compiled from in-house sequencing data and publically available International Cancer Genome Consortium and The Cancer Genome Atlas datasets. Robust cancer biomarker signatures were extracted using a 10-fold cross-validation method of log transformation, quantile normalization, transcript ranking by area under the receiver operating characteristic curve, and stepwise logistic regression. The entire algorithm was then repeated with a new set of randomly generated training and test sets, yielding highly concordant biomarker signatures. External validation of the cancer-specific signatures yielded high sensitivity (92.0% ± 3.15%; mean ± standard deviation) and specificity (97.7% ± 2.99%) for each cancer biomarker signature. The overall performance of this RNA-Seq biomarker-generating algorithm yielded an accuracy of 90.5%. In conclusion, we demonstrate a computational model for producing highly sensitive and specific cancer biomarker signatures from RNA-Seq data, generating signatures for the top eight cancer types responsible for CUP to accurately identify tumor origin.
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Affiliation(s)
- Iris H Wei
- University of Michigan Department of Surgery, University of Michigan Medical School, Ann Arbor, MI, USA 48109
| | - Yang Shi
- University of Michigan Department of Biostatistics, University of Michigan Medical School, Ann Arbor, MI, USA 48109
| | - Hui Jiang
- University of Michigan Department of Biostatistics, University of Michigan Medical School, Ann Arbor, MI, USA 48109
| | - Chandan Kumar-Sinha
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA 48109 ; University of Michigan Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA 48109
| | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, University of Michigan Medical School, Ann Arbor, MI, USA 48109 ; University of Michigan Department of Pathology, University of Michigan Medical School, Ann Arbor, MI, USA 48109 ; Comprehensive Cancer Center, University of Michigan Medical School, Ann Arbor, MI, USA 48109 ; University of Michigan Department of Urology, University of Michigan Medical School, Ann Arbor, MI, USA 48109 ; Howard Hughes Medical Institute, University of Michigan Medical School, Ann Arbor, MI, USA 48109
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15
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Lenka G, Weng WH, Chuang CK, Ng KF, Pang ST. Aberrant expression of the PRAC gene in prostate cancer. Int J Oncol 2013; 43:1960-6. [PMID: 24100630 DOI: 10.3892/ijo.2013.2117] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2013] [Accepted: 08/23/2013] [Indexed: 11/06/2022] Open
Abstract
Identification of aberrant expression patterns of genes in prostate cancer (PCa) is a key step towards the development of effective therapies. Prostate-specific antigen (PSA) levels are commonly measured for the early detection of PCa, but which itself is still not an ideal biomarker. We analysed the expression patterns of prostate cancer susceptibility candidate (PRAC) in prostate cancer. The PRAC gene is known to be commonly expressed in prostate tissue, rectum and colon. To provide clear insights into the expression patterns of PRAC in PCa, we examined the gene expression by quantitative real-time PCR (qRT-PCR), western blot analysis and immunohistochemistry (IHC). The results showed that PRAC expression levels in androgen‑insensitive cells (DU145 and PC3) are lower than those in androgen-sensitive cell lines (LNCaP, LNCaP-R and CW22R). However, treatment of the LNCaP cell line with androgen and anti-androgen demonstrated that PRAC is expressed in an androgen-independent manner. Further, PRAC expression was restored upon treatment of DU145 and PC3 cells with the methyltransferase inhibitor, 5-aza-2'-deoxycytidine (5-aza-CdR), which indicates the effect of methylation in the control of PRAC expression. In addition, IHC analysis revealed a significantly decreased immunoreactivity of PRAC protein in PCa tissues compared to benign prostatic hyperplasia (BPH) (p<0.0001). Thus, our findings suggest that the pathogenesis of PCa may be due to the expression levels of PRAC protein, and this protein can serve as a potential biomarker for the management of PCa.
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Affiliation(s)
- Govinda Lenka
- Department of Chemical Engineering and Biotechnology, Institute of Biochemical and Biomedical Engineering, National Taipei University of Technology, Taipei, Taiwan, R.O.C
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16
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Bauer KM, Hummon AB, Buechler S. Right-side and left-side colon cancer follow different pathways to relapse. Mol Carcinog 2011; 51:411-21. [PMID: 21656576 DOI: 10.1002/mc.20804] [Citation(s) in RCA: 48] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Revised: 04/27/2011] [Accepted: 05/03/2011] [Indexed: 12/18/2022]
Abstract
There is growing evidence that cancer of the ascending (right-side) colon is different from cancer of the descending (left-side) colon at the molecular level. Using microarray data from 102 right-side colon carcinomas and 95 left-side colon carcinomas we show that different pathways dominate progression to relapse in right-side and left-side colon cancer. Right-side tumors at a high risk for relapse exhibit elevated expression of cell cycle control genes and elevated Wnt signaling. On the other hand, relapse-prone left-side tumors show elevated expression of genes that promote stromal expansion and reduced expression of tumor suppressor genes that initiate Wnt signaling. Single gene prognostic biomarkers are found separately for right-side and left-side disease. In left-side tumors with low expression levels of NADPH oxidase 4 (NOX4) the 5-yr relapse-free survival probability is 0.89 95% CI (0.80-0.99), and in tumors with elevated NOX4 expression the probability is 0.51 95% CI (0.37-0.70). Right-side tumors with elevated expression levels of caudal type homeobox 2 (CDX2) have a 5-yr relapse-free survival probability of 0.88 95% CI (0.80-0.96), and those with low CDX2 expression have a corresponding probability of 0.39 95% CI (0.15-0.78). Both NOX4 and CDX2 are much less prognostic on the opposite sides. This newly identified role of NOX4 in colon cancer is further investigated using the SW620 lymph node metastasis colon adenocarcinoma cell line and RNA interference. We show that NOX4 is expressed in the SW620 cell line and that application of NOX4 siRNA causes a significant reduction in reactive oxidative species production.
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Affiliation(s)
- Kerry M Bauer
- Department of Chemistry & Biochemistry, University of Notre Dame, Notre Dame, Indiana 46556, USA
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17
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Bera T, Lee B. Mining of Genome Sequence Databases to Identify New Targets for Prostate and Breast Cancer Therapy. Genomics 2008. [DOI: 10.3109/9781420067064-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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18
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Vasanthi D, Mishra RK. Epigenetic regulation of genes during development: A conserved theme from flies to mammals. J Genet Genomics 2008; 35:413-29. [DOI: 10.1016/s1673-8527(08)60059-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2008] [Revised: 06/04/2008] [Accepted: 06/05/2008] [Indexed: 01/16/2023]
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19
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LaPointe LC, Dunne R, Brown GS, Worthley DL, Molloy PL, Wattchow D, Young GP. Map of differential transcript expression in the normal human large intestine. Physiol Genomics 2007; 33:50-64. [PMID: 18056783 DOI: 10.1152/physiolgenomics.00185.2006] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
While there is considerable research related to using differential gene expression to predict disease phenotype classification, e.g., neoplastic tissue from nonneoplastic controls, there is little understanding of the range of expression in normal tissues. Understanding patterns of gene expression in nonneoplastic tissue, including regional anatomic expression changes within an organ, is vital to understanding gene expression changes in diseased tissue. To explore the gene expression change along the proximal-distal axis of the large intestine, we analyzed microarray data in 184 normal human specimens using univariate and multivariate techniques. We found 219 probe sets that were differentially expressed between the proximal and distal colorectal regions and 115 probe sets that were differentially expressed between the terminal segments, i.e., the cecum and rectum. We did not observe any probe sets that were statistically different between any two contiguous colorectal segments. The dominant expression pattern (65 probe sets) follows a dichotomous expression pattern consistent with the midgut-hindgut embryonic origins of the gut while a second pattern (50 probe sets) depicts a gradual change in transcript levels from the cecum to the rectum. While the dichotomous pattern includes roughly equal numbers of probe sets that are elevated proximally and distally, nearly all probe sets that show a gradual change demonstrate increasing expression levels moving from proximal to distal segments. These patterns describe an expression map of individual transcript variation as well as multigene expression patterns along the large intestine. This is the first gene expression map of an entire human organ.
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Affiliation(s)
- Lawrence C LaPointe
- Department of Medicine, Flinders University of South Australia, Adelaide, Australia.
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20
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Cooper CS, Campbell C, Jhavar S. Mechanisms of Disease: biomarkers and molecular targets from microarray gene expression studies in prostate cancer. ACTA ACUST UNITED AC 2007; 4:677-87. [DOI: 10.1038/ncpuro0946] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2007] [Accepted: 08/24/2007] [Indexed: 11/09/2022]
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21
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Edwards S, Campbell C, Flohr P, Shipley J, Giddings I, te-Poele R, Dodson A, Foster C, Clark J, Jhavar S, Kovacs G, Cooper CS. Expression analysis onto microarrays of randomly selected cDNA clones highlights HOXB13 as a marker of human prostate cancer. Br J Cancer 2005; 92:376-81. [PMID: 15583692 PMCID: PMC2361840 DOI: 10.1038/sj.bjc.6602261] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
In a strategy aimed at identifying novel markers of human prostate cancer, we performed expression analysis using microarrays of clones randomly selected from a cDNA library prepared from the LNCaP prostate cancer cell line. Comparisons of expression profiles in primary human prostate cancer, adjacent normal prostate tissue, and a selection of other (nonprostate) normal human tissues, led to the identification of a set of clones that were judged as the best candidate markers of normal and/or malignant prostate tissue. DNA sequencing of the selected clones revealed that they included 10 genes that had previously been established as prostate markers: NKX3.1, KLK2, KLK3 (PSA), FOLH1 (PSMA), STEAP2, PSGR, PRAC, RDH11, Prostein and FASN. Following analysis of the expression patterns of all selected and sequenced genes through interrogation of SAGE databases, a further three genes from our clone set, HOXB13, SPON2 and NCAM2, emerged as additional candidate markers of human prostate cancer. Quantitative RT-PCR demonstrated the specificity of expression of HOXB13 in prostate tissue and revealed its ubiquitous expression in a series of 37 primary prostate cancers and 20 normal prostates. These results demonstrate the utility of this expression-microarray approach in hunting for new markers of individual human cancer types.
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Affiliation(s)
- S Edwards
- Section of Molecular Carcinogenesis, Male Urological Cancer Research Centre, Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - C Campbell
- Department of Engineering Mathematics, University of Bristol, Bristol BS8 1TR, UK
| | - P Flohr
- Section of Molecular Carcinogenesis, Male Urological Cancer Research Centre, Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - J Shipley
- Section of Molecular Carcinogenesis, Male Urological Cancer Research Centre, Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - I Giddings
- Section of Molecular Carcinogenesis, Male Urological Cancer Research Centre, Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - R te-Poele
- CRUK Centre for Cancer Therapeutics, Male Urological Cancer Research Centre, Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - A Dodson
- Department of Pathology & Molecular Genetics, University of Liverpool, Duncan Building, Daulby Street, Liverpool L69 3GA, UK
| | - C Foster
- Department of Pathology & Molecular Genetics, University of Liverpool, Duncan Building, Daulby Street, Liverpool L69 3GA, UK
| | - J Clark
- Section of Molecular Carcinogenesis, Male Urological Cancer Research Centre, Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - S Jhavar
- Section of Cancer Genetics, Male Urological Cancer Research Centre, Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
| | - G Kovacs
- Laboratory of Molecular Oncology, University Surgical Hospital, Im Neuenheimer Feld 365, Heidelberg 69120, Germany
| | - C S Cooper
- Section of Molecular Carcinogenesis, Male Urological Cancer Research Centre, Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK
- Section of Molecular Carcinogenesis, Male Urological Cancer Research Centre, Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey SM2 5NG, UK. E-mail:
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22
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Clegg N, Abbott D, Ferguson C, Coleman R, Nelson PS. Characterization and comparative analyses of transcriptomes from the normal and neoplastic human prostate. Prostate 2004; 60:227-39. [PMID: 15176052 DOI: 10.1002/pros.20055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND The prostate gland is a highly specialized organ with functional attributes that serve to enhance the fertility of mammalian species. Pathological processes affecting the prostate include benign prostate hypertrophy and prostate carcinoma; diseases that account for major morbidity and mortality in middle-aged and elderly men. To facilitate studies of biological processes uniquely represented in the prostate and assess molecular alterations associated with prostate carcinoma, we sought to establish the diversity of gene expression in the normal and neoplastic prostate through the compilation and analysis of a prostate transcriptome. METHODS We assembled and annotated ESTs derived from prostate cDNA libraries that were either produced in our laboratory or available from public sequence repositories such as CGAP, dbEST, and Unigene. Determinations of differential gene expression between the normal prostate, other normal tissues, and neoplastic prostate tissues was performed using statistical algorithms. Confirmation of differential expression was performed by quantitative PCR and Northern analysis. RESULTS A total of 99,448 high-quality ESTs were assembled and annotated to produce a prostate transcriptome comprised of 24,580 distinct TUs. Comparative analyses of gene expression levels identified 61 TUs with exclusive expression in the prostate and 45 TUs with high levels of expression in the prostate relative to at least 25 other normal tissues (P > 0.99). Comparative analyses of ESTs derived from neoplastic prostate tissues identified 75 genes with dysregulated expression in cancer (P > 0.99). CONCLUSIONS The human prostate expresses a diverse repertoire of genes that reflect a functionally complex organ. The identification of genes with prostate-restricted or enhanced expression may provide additional insights into the biochemical processes that interact to form the developmental, signaling, and metabolic pathways of the normal and neoplastic gland.
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Affiliation(s)
- Nigel Clegg
- Division of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
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Bera TK, Hahn Y, Lee B, Pastan IH. TEPP, a new gene specifically expressed in testis, prostate, and placenta and well conserved in chordates. Biochem Biophys Res Commun 2003; 312:1209-15. [PMID: 14652002 DOI: 10.1016/j.bbrc.2003.11.031] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We have combined computer-based screening and experimental expression analysis to identify genes that are expressed in normal prostate and/or prostate cancer but not in essential human tissues. Using this approach we identified a new gene that is specifically expressed in testis, prostate, and placenta. The gene has one major transcript of 1.0kb in size and encodes for a protein of 30.7kDa molecular weight. We named this gene TEPP (expressed in testis, prostate, and placenta). The amino acid sequence analysis of TEPP using SignalP program shows that it has a signal peptide with a predicted cleavage site between amino acids 19 and 20, indicating that it might be a secreted protein. Analysis of the predicted TEPP orthologs from different species shows that these proteins are highly conserved in chordates. In addition we have identified a splice variant of TEPP, which encodes a 37kDa protein. In conclusion, a combination of bioinformatic and molecular approaches is useful in the identification of genes expressed in specific tissues. Selective expression of TEPP in testis, prostate, and in placenta and its high conservation among different species indicate that TEPP might have a role in reproductive biology.
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Affiliation(s)
- Tapan Kumar Bera
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
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24
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Olsson P, Motegi A, Bera TK, Lee B, Pastan I. PRAC2: a new gene expressed in human prostate and prostate cancer. Prostate 2003; 56:123-30. [PMID: 12746837 DOI: 10.1002/pros.10185] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
BACKGROUND The database of human Expressed Sequence Tags was previously used to identify PRAC (Prostate 47:125-131, 2001), a novel gene specifically expressed in human prostate, prostate cancer, rectum, and distal colon. In this report, we have identified PRAC2, another gene with a similar expression pattern that is located adjacent to the original PRAC gene on chromosome 17q21.3. METHODS Using a computer-based analysis, a cluster of sequence homologous ESTs was identified that is mainly derived from human prostate cDNA libraries. The tissue specificity was examined by multiple tissue RNA dot blots and RT-PCR. The PRAC2 transcript and protein were identified using Northern blot analysis, RACE-PCR, primer extension, and Western blots. RESULTS PRAC2 encodes a 564 nucleotide RNA found in prostate, rectum, distal colon, and testis. Weak expression was also found in placenta, peripheral blood leukocytes, skin, and in two prostate cancer cell lines: LNCaP and PC-3. The transcript seems to encode a 10.5-kDa nuclear protein. The PRAC2 gene is located on chromosome 17 at position 17q21, between the Hoxb-13 gene and the recently discovered PRAC gene. CONCLUSIONS Because of the higher expression of PRAC2 in prostate and its proximity to Hoxb-13, PRAC2 may have a function in prostate growth and development.
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Affiliation(s)
- Pär Olsson
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
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25
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Maitra R, Grigoryev DN, Bera TK, Pastan IH, Lee B. Cloning, molecular characterization, and expression analysis of Copine 8. Biochem Biophys Res Commun 2003; 303:842-7. [PMID: 12670487 DOI: 10.1016/s0006-291x(03)00445-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Copines are ubiquitously expressed, phospholipid-binding proteins that have been conserved through evolution. In this paper, we report the cloning and molecular characterization of a new member of the Copine family, Copine 8. This gene has been isolated and characterized using a combination of bioinformatic and experimental approaches. Using an algorithm to cluster ESTs (expressed sequence tags) that are available through the public "GoldenPath" database, Copine 8 was initially identified as a gene predominantly expressed in prostate and testis. Cloning and molecular analysis revealed that this gene is expressed in low-levels in most tissues examined. Two different isoforms of this gene have been isolated. Strongest expression of Copine 8 mRNA is seen in the prostate, heart, and brain. Taken together, this data suggest that Copine 8 may have an important role to play in prostate regulation and development.
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Affiliation(s)
- Rangan Maitra
- Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, 37 Convent Drive Room 5120 MSC 4262, Bethesda, MD 20892-4264, USA
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26
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Mydlo JH, Karlovsky M. Prostate Cancer with Other Primary Malignancies. Prostate Cancer 2003. [DOI: 10.1016/b978-012286981-5/50008-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
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27
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Nelson PS. Identifying immunotherapeutic targets for prostate carcinoma through the analysis of gene expression profiles. Ann N Y Acad Sci 2002; 975:232-46. [PMID: 12538168 DOI: 10.1111/j.1749-6632.2002.tb05955.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Carcinoma of the prostate represents one of the most frequently diagnosed cancers in men. If detected at an early stage, prostate cancer is highly treatable. However, cancers identified at a late stage are rarely cured with contemporary medical therapies. Early detection strategies presently center on the identification of prostate-specific proteins in the serum, and emerging therapeutics have utilized genes and proteins with prostate-restricted expression for tissue-selective immunological regimens incorporating vaccines, dendritic cell therapy, gene therapy, and antibody-based cell targeting. In order to develop improved therapeutic procedures, efforts have been directed toward the identification of genes exhibiting prostate-restricted expression profiles, or altered expression levels in neoplastic cells relative to their normal counterparts. Comprehensive expression profiling approaches such as the analysis of oligonucleotide- or complementary DNA (cDNA)-microarrays have greatly enhanced these efforts. Genes and their cognate proteins identified using such methods offer additional diagnostic and therapeutic targets that may aid in the understanding and treatment of prostate carcinoma.
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Affiliation(s)
- Peter S Nelson
- The Divisions of Human Biology and Clinical Research Fred Hutchinson Cancer Research Center Seattle, Washington 98109-1024, USA.
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28
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Bera TK, Maitra R, Iavarone C, Salvatore G, Kumar V, Vincent JJ, Sathyanarayana BK, Duray P, Lee BK, Pastan I. PATE, a gene expressed in prostate cancer, normal prostate, and testis, identified by a functional genomic approach. Proc Natl Acad Sci U S A 2002; 99:3058-63. [PMID: 11880645 PMCID: PMC122472 DOI: 10.1073/pnas.052713699] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
To identify target antigens for prostate cancer therapy, we have combined computer-based screening of the human expressed sequence tag database and experimental expression analysis to identify genes that are expressed in normal prostate and prostate cancer but not in essential human tissues. Using this approach, we identified a gene that is expressed specifically in prostate cancer, normal prostate, and testis. The gene has a 1.5-kb transcript that encodes a protein of 14 kDa. We named this gene PATE (expressed in prostate and testis). In situ hybridization shows that PATE mRNA is expressed in the epithelial cells of prostate cancers and in normal prostate. Transfection of the PATE cDNA with a Myc epitope tag into NIH 3T3 cells and subsequent cell fractionation analysis shows that the PATE protein is localized in the membrane fraction of the cell. Analysis of the amino acid sequence of PATE shows that it has structural similarities to a group of proteins known as three-finger toxins, which includes the extracellular domain of the type beta transforming growth factor receptor. Restricted expression of PATE makes it a potential candidate for the immunotherapy of prostate cancer.
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Affiliation(s)
- Tapan K Bera
- Laboratory of Molecular Biology and Laboratory of Pathology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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Mydlo JH, Gerstein M. Patients with urologic cancer and other nonurologic malignancies: analysis of a sample and review of the literature. Urology 2001; 58:864-9. [PMID: 11744447 DOI: 10.1016/s0090-4295(01)01394-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
OBJECTIVES To describe our experience with patients with urologic cancers who also have malignancies of nonurologic origin, before, after, or simultaneously, to review the literature, and to suggest treatment options. METHODS We reviewed our institutions' tumor registry from 1995 to 2000 to discover how many patients had a urologic malignancy and another nonurologic cancer (antecedent, subsequent, or synchronous). We reviewed Medline from 1966 to 2000 and also questioned several urologists at major centers in the United States concerning this clinical dilemma. RESULTS We encountered 18 patients during a 6-year period with a urologic cancer and another primary malignancy. Thirteen patients had their second cancer detected during the workup of their primary urologic tumor. Two patients developed a second tumor within 1 year of treatment of the primary urologic tumor. Another patient was referred with two primaries already diagnosed, and another had renal carcinoma detected during her colon cancer workup. We found that multiple tumors, although very rare, are usually detected during the preoperative workup of the primary tumor, usually by physical examination and improved radiologic imaging, or during the follow-up examinations. Most reports suggest that treatment should be performed simultaneously, especially if the lesions are relatively small and require a single incision, and the patient's medical condition allows longer anesthesia exposure. If these prerequisites are not met, most investigators agree that treatment should be directed at the more aggressive lesion first, which may improve the condition and/or survival, and thus, if a second operation is warranted, it will be possible. CONCLUSIONS Although patients with multiple malignancies are rare, the urologist and/or other specialist should be alerted to this possibility when evaluating patients for the initially presenting symptoms and/or detected tumor, as well as during the follow-up evaluations.
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Affiliation(s)
- J H Mydlo
- Department of Urology, Temple University School of Medicine, Philadelphia, Pennsylvania, USA
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