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Devall M, Eaton S, Yoshida C, Powell SM, Casey G, Li L. Assessment of Colorectal Cancer Risk Factors through the Application of Network-Based Approaches in a Racially Diverse Cohort of Colon Organoid Stem Cells. Cancers (Basel) 2023; 15:3550. [PMID: 37509213 PMCID: PMC10377524 DOI: 10.3390/cancers15143550] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 07/03/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
Numerous demographic factors have been associated with colorectal cancer (CRC) risk. To better define biological mechanisms underlying these associations, we performed RNA sequencing of stem-cell-enriched organoids derived from the healthy colons of seven European Americans and eight African Americans. A weighted gene co-expression network analysis was performed following RNA sequencing. Module-trait relationships were determined through the association testing of each module and five CRC risk factors (age, body mass index, sex, smoking history, and race). Only modules that displayed a significantly positive correlation for gene significance and module membership were considered for further investigation. In total, 16 modules were associated with known CRC risk factors (p < 0.05). To contextualize the role of risk modules in CRC, publicly available RNA-sequencing data from TCGA-COAD were downloaded and re-analyzed. Differentially expressed genes identified between tumors and matched normal-adjacent tissue were overlaid across each module. Loci derived from CRC genome-wide association studies were additionally overlaid across modules to identify robust putative targets of risk. Among them, MYBL2 and RXRA represented strong plausible drivers through which cigarette smoking and BMI potentially modulated CRC risk, respectively. In summary, our findings highlight the potential of the colon organoid system in identifying novel CRC risk mechanisms in an ancestrally diverse and cellularly relevant population.
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Affiliation(s)
- Matthew Devall
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Stephen Eaton
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Cynthia Yoshida
- Digestive Health Center, University of Virginia, Charlottesville, VA 22903, USA
| | - Steven M Powell
- Digestive Health Center, University of Virginia, Charlottesville, VA 22903, USA
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA
| | - Li Li
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
- University of Virginia Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22908, USA
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Devall MA, Eaton S, Hu G, Sun X, Jakum E, Venkatesh S, Powell SM, Yoshida C, Weisenberger DJ, Cooper GS, Willis J, Ebrahim S, Zoellner J, Casey G, Li L. Potential role of fructose on human colon DNA methylation in racial disparities observed for colorectal cancer risk. medRxiv 2023:2023.05.31.23290777. [PMID: 37398462 PMCID: PMC10312841 DOI: 10.1101/2023.05.31.23290777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/04/2023]
Abstract
Background and aims An increasing body of observational studies has linked fructose intake to colorectal cancer (CRC). African Americans (AAs) are significantly more likely than European Americans to consume greater quantities of fructose and to develop right-side colon cancer. Yet, a mechanistic link between these two associations remains poorly defined. We aimed to identify differentially methylated regions (DMRs) associated with dietary fructose consumption measures obtained from food frequency questionnaires in a cohort of normal colon biopsies derived from AA men and women (n=79). Methods DNA methylation data from this study was obtained using the Illumina Infinium MethylationEPIC kit and is housed under accession GSE151732. DMR analysis was carried out using DMRcate in right and matched left colon, separately. Secondary analysis of CRC tumors was carried out using data derived from TCGA-COAD, GSE101764 and GSE193535. Differential expression analysis was carried out on CRC tumors from TCGA-COAD using DESeq2 . Results We identified 4,263 right-side fructose-DMRs. In contrast, only 24 DMRs survived multiple testing corrections (FDR<0.05) in matched, left colon. To identify targets by which dietary fructose drives CRC risk, we overlaid these findings with data from three CRC tumor datasets. Remarkably, almost 50% of right-side fructose-DMRs overlapped regions associated with CRC in at least one of three datasets. TNXB and CDX2 ranked among the most significant fructose risk DMRs in right and left colon respectively that also displayed altered gene expression in CRC tumors. Conclusions Our mechanistic data support the notion that fructose has a greater CRC-related effect in right than left AA colon, alluding to a potential role for fructose in contributing to racial disparities in CRC.
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Devall M, Ali MW, Eaton S, Weisenberger DJ, Reilley MJ, Powell SM, Li L, Casey G. Multi-omic analysis in normal colon organoids highlights MSH4 as a novel marker of defective mismatch repair in Lynch syndrome and microsatellite instability. Cancer Med 2023. [PMID: 37162286 DOI: 10.1002/cam4.6048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 04/14/2023] [Accepted: 04/27/2023] [Indexed: 05/11/2023] Open
Abstract
INTRODUCTION Lynch syndrome (LS) is a hereditary condition that increases the risk of colorectal (CRC) and extracolonic cancers that exhibit microsatellite instability (MSI-H). MSI-H is driven by defective mismatch repair (dMMR), and approximately 15% of nonhereditary CRCs also exhibit MSI-H. Here, we aimed to better define mechanisms underlying tumor initiation in LS and MSI-H cancers through multi-omic analyses of LS normal colon organoids and MSI-H tumors. METHODS Right (n = 35) and left (n = 23) colon organoids generated from normal colon biopsies at routine colonoscopy of LS and healthy individuals were subjected to Illumina EPIC array. Differentially methylated region (DMR) analysis was performed by DMRcate. RNA-sequencing (n = 16) and bisulfite-sequencing (n = 15) were performed on a subset of right colon organoids. CRISPR-cas9-mediated editing of MMR genes in colon organoids of healthy individuals was followed by quantitative PCR of MSH4. The relationship between MSH4 expression and tumor mutational burden was further explored in three independent tumor data sets. RESULTS We identified a hypermethylated region of MSH4 in both the right and left colon organoids of LS versus healthy controls, which we validated using bisulfite-sequencing. DMR analysis in three gastrointestinal and one endometrial data set revealed that this region was also hypermethylated in MSI-H versus microsatellite stable (MSS) tumors. MSH4 expression was increased in colon organoids of LS versus healthy subjects and in publicly available MSI-H versus MSS tumors across four RNA-seq and four microarray data sets. CRISPR-cas9 editing of MLH1 and MSH2, but not MSH6, in normal colon organoids significantly increased MSH4 expression. MSH4 expression was significantly associated with tumor mutational burden in three publicly available data sets. CONCLUSIONS Our findings implicate DNA methylation and gene expression differences of MSH4 as a marker of dMMR and as a potential novel biomarker of LS. Our study of LS colon organoids supports the hypothesis that dMMR exists in the colons of LS subjects prior to CRC.
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Affiliation(s)
- Matthew Devall
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
- Department of Family Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Mourad W Ali
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
| | - Stephen Eaton
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
- Department of Family Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Daniel J Weisenberger
- Department of Biochemistry and Molecular Medicine, University of Southern California, Los Angeles, California, USA
| | - Matthew J Reilley
- University of Virginia Comprehensive Cancer Center, University of Virginia, Charlottesville, Virginia, USA
| | - Steven M Powell
- Digestive Health Center, University of Virginia, Charlottesville, Virginia, USA
| | - Li Li
- Department of Family Medicine, University of Virginia, Charlottesville, Virginia, USA
- University of Virginia Comprehensive Cancer Center, University of Virginia, Charlottesville, Virginia, USA
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, USA
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Holum PJ, Palmer C, Sun X, Venkatesh S, Devall M, Cooper G, Powell SM, Yoshida C, Li L. Adult BMI change over time and risk of colorectal adenoma. J Clin Oncol 2023. [DOI: 10.1200/jco.2023.41.4_suppl.68] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
68 Background: Obesity and adult weigh gain are established risk factors for colorectal cancer (CRC). Few studies have investigated the association between adult body weight change over time and risk of colorectal adenoma. We hypothesize adult BMI change over time is associated with risk in the development of colorectal adenomas. Methods: We tested this hypothesis in 2,993 patients undergoing screening colonoscopy from 2007–2017. Weight at age 20, 30, 40, and 50 were self-reported via computer assisted personal interviews. Height and weight at recruitment were measured at the time of colonoscopy exam. BMI (kg/m2) change was calculated as the difference of BMI at recruitment from the BMI estimate for each of the age periods. Results: Of the 2,993 patients, 984 had pathologically confirmed diagnosis of colon adenoma. Multivariate logistic regression adjusted for potential confounders and BMI at recruitment showed statistically significant increase of risk of adenoma with increase of BMI since age 30, age 40, and age 50. Compared to those with BMI change of less than 5, the ORs for those with BMI gain of 5-10 and ≥10 were: 1) 1.16 (0.92-1.46) and 1.48 (1.08-2.03) respectively for change from age 30 (ptrend = 0.05); 2) 1.11 (0.87-1.43) and 1.60 (1.09-2.35) respectively for change from age 40 (ptrend = 0.05); and 3) 1.36 (0.95-1.94) and 2.95 (1.33-6.90) respectively for change from age 50 (ptrend = 0.01). Stratified analysis did not reveal noticeable gender differences. Conclusions: Large adult weight gain over time is an independent risk factor for colorectal adenoma. Our results suggest maintaining healthy body weight throughout adulthood is an important preventive measure against the development of early colorectal neoplasia. [Table: see text]
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Affiliation(s)
| | - Chelsea Palmer
- University of Virginia School of Medicine, Charlottesville, VA
| | - Xiangqing Sun
- University of Virginia School of Medicine, Charlottesville, VA
| | | | - Matthew Devall
- University of Virginia School of Medicine, Charlottesville, VA
| | | | | | - Cynthia Yoshida
- University of Virginia School of Medicine, Charlottesville, VA
| | - Li Li
- University of Virginia School of Medicine, Charlottesville, VA
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Devall MAM, Dampier CH, Eaton S, Ali MW, Plummer SJ, Bryant J, Gauderman WJ, Peters U, Powell SM, Casey G. Transcriptomic Response to Calcium in Normal Colon Organoids is Impacted by Colon Location and Sex. Cancer Prev Res (Phila) 2022; 15:679-688. [PMID: 36095330 DOI: 10.1158/1940-6207.capr-22-0068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/21/2022] [Accepted: 06/03/2022] [Indexed: 11/16/2022]
Abstract
Observational studies indicate that calcium supplementation may protect against colorectal cancer. Stratified analyses suggest that this protective effect may differ based on anatomic subsite and sex, but these hypotheses have been difficult to test experimentally. Here, we exposed 36 patient-derived organoid lines derived from normal colon biopsies (21 right colons, 15 left colons) of unrelated subjects (18 female, 18 male) to moderate (1.66 mmol/L) or high (5.0 mmol/L) concentrations of calcium for 72 hours. We performed bulk RNA-sequencing to measure gene expression, and cell composition was inferred using single-cell deconvolution in CIBERSORTx. We tested for significant differences in gene expression using generalized linear models in DESeq2. Exposure to higher levels of calcium was associated with changes in cell composition (P < 0.05), most notably increased goblet and reduced stem cell populations, and differential expression of 485 genes (FDR < 0.05). We found that 40 of these differentially expressed genes mapped to genomic loci identified through colorectal cancer genome-wide association studies, suggesting a potential biologic overlap between calcium supplementation and inherited colorectal cancer risk. Stratified analyses identified more differentially expressed genes in colon organoids derived from right sided colon and male subjects than those derived from left sided colon and female subjects. We confirmed the presence of a stronger right-sided effect for one of these genes, HSD17B2 using qPCR in a subset of matched right and left colon organoids (n = 4). By relating our findings to genetic data, we provide new insights into how nutritional and genetic factors may interact to influence colorectal cancer risk. PREVENTION RELEVANCE A chemopreventive role for calcium in colorectal cancer is still unclear. Here, we identify mechanisms through which calcium supplementation may reduce risk. Calcium supplementation increased differentiation and altered expression of colorectal cancer-related genes in a large study of patient-derived colon organoids. These findings were influenced by colon location and sex.
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Affiliation(s)
- Matthew A M Devall
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Christopher H Dampier
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Stephen Eaton
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Mourad Wagdy Ali
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Sarah J Plummer
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - Jennifer Bryant
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
| | - W James Gauderman
- Division of Biostatistics, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, California
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Center Research Institute, Seattle, Washington
| | - Steven M Powell
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, University of Virginia Health System, Charlottesville, Virginia
| | - Graham Casey
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, Virginia
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Devall MA, Eaton S, Ali MW, Powell SM, Li L, Casey G. Insights into Early Onset Colorectal Cancer through Analysis of Normal Colon Organoids of Familial Adenomatous Polyposis Patients. Cancers (Basel) 2022; 14:4138. [PMID: 36077675 PMCID: PMC9454756 DOI: 10.3390/cancers14174138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 08/22/2022] [Accepted: 08/25/2022] [Indexed: 01/07/2023] Open
Abstract
Early onset colorectal cancer (EOCRC) rates have increased in recent decades. While lowering the recommended age for routine colonoscopies to 45 may reduce this burden, such measures do not address those who develop CRC before that age. Additional measures are needed to identify individuals at-risk for CRC. To better define transcriptomic events that precede the development of CRC, we performed RNA-sequencing analysis in colon organoids derived from seven healthy and six familial adenomatous polyposis (FAP) patients. This led to the identification of 2635 significant differentially expressed genes (FDR < 0.05). Through secondary analysis of publicly available datasets, we found that these genes were enriched for significant genes also present in FAP CRC and non-hereditary CRC datasets, including a subset that were unique to EOCRC. By exposing FAP colon organoids to a three-day ethanol treatment, we found that two EOCRC-relevant genes were also targets of CRC related lifestyle factors. Our data provides unique insight into the potential, early mechanisms of CRC development in colon epithelial cells, which may provide biomarkers for patient monitoring. We also show how modifiable lifestyle factors may further alter genes relevant to EOCRC, adding weight to the hypothesis that such factors represent an important contributor to increased EOCRC incidence.
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Affiliation(s)
- Matthew A. Devall
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Stephen Eaton
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
| | - Mourad W. Ali
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Steven M. Powell
- Digestive Health Center, University of Virginia, Charlottesville, VA 22903, USA
| | - Li Li
- Department of Family Medicine, University of Virginia, Charlottesville, VA 22903, USA
- Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22911, USA
| | - Graham Casey
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
- Comprehensive Cancer Center, University of Virginia, Charlottesville, VA 22911, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, VA 22908, USA
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Devall MA, Eaton S, Ali MW, Dampier CH, Weisenberger D, Powell SM, Li L, Casey G. DNA methylation analysis of normal colon organoids from familial adenomatous polyposis patients reveals novel insight into colon cancer development. Clin Epigenetics 2022; 14:104. [PMID: 35999641 PMCID: PMC9396789 DOI: 10.1186/s13148-022-01324-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 08/05/2022] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Familial adenomatous polyposis (FAP) is an inherited colorectal cancer (CRC) syndrome resulting from germ line mutations in the adenomatous polyposis coli (APC) gene. While FAP accounts for less than 1% of all CRC cases, loss of APC expression is seen in > 80% of non-hereditary CRCs. To better understand molecular mechanisms underlying APC-driven CRC, we performed an epigenome-wide analysis of colon organoids derived from normal-appearing colons of FAP patients versus healthy subjects to identify differentially methylated regions (DMRs) that may precede the onset of CRC. RESULTS We identified 358 DMRs when comparing colon organoids of FAP patients to those of healthy subjects (FDR < 0.05, |mean beta difference| = 5%). Of these, nearly 50% of DMRs were also differentially methylated in at least one of three CRC tumor and normal adjacent tissue (NAT) cohorts (TCGA-COAD, GSE193535 and ColoCare). Moreover, 27 of the DMRs mapped to CRC genome-wide association study (GWAS) loci. We provide evidence suggesting that some of these DMRs led to significant differences in gene expression of adjacent genes using quantitative PCR. For example, we identified significantly greater expression of five genes: Kazal-type serine peptidase inhibitor domain 1 (KAZALD1, P = 0.032), F-Box and leucine-rich repeat protein 8 (FBXL8, P = 0.036), TRIM31 antisense RNA 1 (TRIM31-AS1, P = 0.036), Fas apoptotic inhibitory molecule 2 (FAIM2, P = 0.049) and (Collagen beta (1-0)galactosyltransferase 2 (COLGALT2, P = 0.049). Importantly, both FBXL8 and TRIM31-AS1 were also significantly differentially expressed in TCGA-COAD tumor versus matched NAT, supporting a role for these genes in CRC tumor development. CONCLUSIONS We performed the first DNA methylome-wide analysis of normal colon organoids derived from FAP patients compared to those of healthy subjects. Our results reveal that normal colon organoids from FAP patients exhibit extensive epigenetic differences compared to those of healthy subjects that appear similar to those exhibited in CRC tumor. Our analyses therefore identify DMRs and candidate target genes that are potentially important in CRC tumor development in FAP, with potential implications for non-hereditary CRC.
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Affiliation(s)
- Matthew A. Devall
- grid.27755.320000 0000 9136 933XCenter for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | - Stephen Eaton
- grid.27755.320000 0000 9136 933XCenter for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | - Mourad Wagdy Ali
- grid.27755.320000 0000 9136 933XCenter for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | - Christopher H. Dampier
- grid.27755.320000 0000 9136 933XCenter for Public Health Genomics, University of Virginia, Charlottesville, VA USA
| | - Daniel Weisenberger
- grid.42505.360000 0001 2156 6853Department of Biochemistry and Molecular Medicine, University of Southern California, Los Angeles, CA USA
| | - Steven M. Powell
- grid.27755.320000 0000 9136 933XDigestive Health Center, University of Virginia, Charlottesville, VA USA
| | - Li Li
- grid.27755.320000 0000 9136 933XDepartment of Family Medicine, University of Virginia, Charlottesville, VA USA
| | - Graham Casey
- grid.27755.320000 0000 9136 933XCenter for Public Health Genomics, University of Virginia, Charlottesville, VA USA ,grid.27755.320000 0000 9136 933XDepartment of Public Health Sciences, University of Virginia, Charlottesville, VA USA
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Devall MAM, Drew DA, Dampier CH, Plummer SJ, Eaton S, Bryant J, Díez-Obrero V, Mo J, Kedrin D, Zerjav DC, Takacsi-Nagy O, Jennelle LT, Ali MW, Yilmaz ÖH, Moreno V, Powell SM, Chan AT, Peters U, Casey G. Transcriptome-wide In Vitro Effects of Aspirin on Patient-derived Normal Colon Organoids. Cancer Prev Res (Phila) 2021; 14:1089-1100. [PMID: 34389629 PMCID: PMC8639779 DOI: 10.1158/1940-6207.capr-21-0041] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 05/27/2021] [Accepted: 07/27/2021] [Indexed: 11/16/2022]
Abstract
Mechanisms underlying aspirin chemoprevention of colorectal cancer remain unclear. Prior studies have been limited because of the inability of preclinical models to recapitulate human normal colon epithelium or cellular heterogeneity present in mucosal biopsies. To overcome some of these obstacles, we performed in vitro aspirin treatment of colon organoids derived from normal mucosal biopsies to reveal transcriptional networks relevant to aspirin chemoprevention. Colon organoids derived from 38 healthy individuals undergoing endoscopy were treated with 50 μmol/L aspirin or vehicle control for 72 hours and subjected to bulk RNA sequencing. Paired regression analysis using DESeq2 identified differentially expressed genes (DEG) associated with aspirin treatment. Cellular composition was determined using CIBERSORTx. Aspirin treatment was associated with 1,154 significant (q < 0.10) DEGs prior to deconvolution. We provide replication of these findings in an independent population-based RNA-sequencing dataset of mucosal biopsies (BarcUVa-Seq), where a significant enrichment for overlap of DEGs was observed (P < 2.2E-16). Single-cell deconvolution revealed changes in cell composition, including a decrease in transit-amplifying cells following aspirin treatment (P = 0.01). Following deconvolution, DEGs included novel putative targets for aspirin such as TRABD2A (q = 0.055), a negative regulator of Wnt signaling. Weighted gene co-expression network analysis identified 12 significant modules, including two that contained hubs for EGFR and PTGES2, the latter being previously implicated in aspirin chemoprevention. In summary, aspirin treatment of patient-derived colon organoids using physiologically relevant doses resulted in transcriptome-wide changes that reveal altered cell composition and improved understanding of transcriptional pathways, providing novel insight into its chemopreventive properties. PREVENTION RELEVANCE: Numerous studies have highlighted a role for aspirin in colorectal cancer chemoprevention, though the mechanisms driving this association remain unclear. We addressed this by showing that aspirin treatment of normal colon organoids diminished the transit-amplifying cell population, inhibited prostaglandin synthesis, and dysregulated expression of novel genes implicated in colon tumorigenesis.
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Affiliation(s)
- Matthew A M Devall
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia
| | - David A Drew
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Christopher H Dampier
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia
| | - Sarah J Plummer
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia
| | - Stephen Eaton
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia
| | - Jennifer Bryant
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia
| | - Virginia Díez-Obrero
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Jiancheng Mo
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Dmitriy Kedrin
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Division of Gastroenterology, Elliot Hospital, Manchester, New Hampshire
| | - Dylan C Zerjav
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Oliver Takacsi-Nagy
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Lucas T Jennelle
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia
| | - Mourad W Ali
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia
| | - Ömer H Yilmaz
- Koch Institute for Integrative Cancer Research, Department of Biology, MIT Cambridge, Massachusetts
- Department of Pathology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Victor Moreno
- Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Steven M Powell
- Digestive Health Center, University of Virginia, Charlottesville, Virginia
| | - Andrew T Chan
- Clinical & Translational Epidemiology Unit, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Center Research Institute, Seattle, Washington
| | - Graham Casey
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia.
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Dampier CH, Devall M, Bryant J, Eaton SD, Huyghe JR, Kim AE, Diez-Obrero V, van Duijnhoven FJ, Thomas DC, Powell SM, Gauderman WJ, Peters U, Casey G. Abstract 2578: Calcium modulates apoptosis and differentiation in human normal colon 3D organoids irrespective of donor sex and biopsy site. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-2578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Observational studies indicate that calcium, a micronutrient involved in numerous cell-signaling cascades, may protect against colon cancer. Stratified analyses suggest the protective effect of calcium may depend on sex and anatomic subsite, but these hypotheses have been difficult to test experimentally. Here, we employ human-derived normal colon 3D organoids as a model of the healthy colon crypt to interrogate the effect of calcium exposure on gene expression and the effect of donor sex and biopsy anatomic subsite on the response to calcium.
Methods: A total of 39 3D colon organoid lines derived from colon biopsies (22 proximal, 17 distal) obtained from unrelated subjects (21 female, 18 male) during screening colonoscopy were grown under low (1.7 mM) calcium conditions, and a matching set of the same lines were grown under high (5.0 mM) calcium conditions. After 72 hours, total RNA was extracted from organoid lines, libraries were prepared with poly-A selection, and bulk RNA-sequencing was used to measure gene expression. DNA was extracted from the same lines and genotyped using the OncoArray 500K beadchip. Missing genotypes were imputed to the TOPMed reference panel using the TOPMed Imputation Server. Polygenic risk scores for colorectal cancer were calculated for each organoid line using Plink and 135 of 141 genome-wide significant SNPs associated with colorectal cancer in recent genome-wide association studies. Relative expression between low and high calcium conditions was tested using generalized linear models as implemented in DESeq2. Functional enrichment of gene ontologies among differentially expressed genes was performed with ToppFun. The effects of donor sex, biopsy subsite, and organoid polygenic risk score on response to calcium were tested using single and multiple linear regression as implemented in the base R lm function.
Results: Exposure to calcium induced differential expression of 767 genes with a false discovery rate of 5%. Differentially expressed genes were enriched for biological processes including extracellular structure organization (Bonferroni p=1.6E-3) and positive regulation of apoptosis (Bonferroni p=2.2E-2). Although stratified analyses demonstrated more differentially expressed genes in 3D colon organoids derived from male subjects, no statistically significant effect of sex, subsite, or polygenic risk score on response to calcium was observed.
Conclusion: We tested the effect of calcium exposure on gene expression in human-derived normal colon 3D organoids and found that calcium modulated processes related to differentiation and apoptosis, but the response to calcium was not affected by sex, anatomic subsite, or polygenic risk score.
Citation Format: Christopher H. Dampier, Matthew Devall, Jennifer Bryant, Stephen D. Eaton, Jeroen R. Huyghe, Andre E. Kim, Virginia Diez-Obrero, Franzel J. van Duijnhoven, Duncan C. Thomas, Steven M. Powell, W James Gauderman, Ulrike Peters, Graham Casey. Calcium modulates apoptosis and differentiation in human normal colon 3D organoids irrespective of donor sex and biopsy site [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2578.
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Affiliation(s)
| | | | | | | | | | - Andre E. Kim
- 3University of Southern California, Los Angeles, CA
| | | | | | | | | | | | - Ulrike Peters
- 2Fred Hutchinson Cancer Research Center, Seattle, WA
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10
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Devall M, Plummer SJ, Bryant J, Jennelle LT, Eaton S, Dampier CH, Huyghe JR, Peters U, Powell SM, Casey G. Ethanol exposure drives colon location specific cell composition changes in a normal colon crypt 3D organoid model. Sci Rep 2021; 11:432. [PMID: 33432071 PMCID: PMC7801615 DOI: 10.1038/s41598-020-80240-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Accepted: 12/14/2020] [Indexed: 12/15/2022] Open
Abstract
Alcohol is a consistently identified risk factor for colon cancer. However, the molecular mechanism underlying its effect on normal colon crypt cells remains poorly understood. We employed RNA-sequencing to asses transcriptomic response to ethanol exposure (0.2% vol:vol) in 3D organoid lines derived from healthy colon (n = 34). Paired regression analysis identified 2,162 differentially expressed genes in response to ethanol. When stratified by colon location, a far greater number of differentially expressed genes were identified in organoids derived from the left versus right colon, many of which corresponded to cell-type specific markers. To test the hypothesis that the effects of ethanol treatment on colon organoid populations were in part due to differential cell composition, we incorporated external single cell RNA-sequencing data from normal colon biopsies to estimate cellular proportions following single cell deconvolution. We inferred cell-type-specific changes, and observed an increase in transit amplifying cells following ethanol exposure that was greater in organoids from the left than right colon, with a concomitant decrease in more differentiated cells. If this occurs in the colon following alcohol consumption, this would lead to an increased zone of cells in the lower crypt where conditions are optimal for cell division and the potential to develop mutations.
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Affiliation(s)
- Matthew Devall
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Sarah J Plummer
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jennifer Bryant
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Lucas T Jennelle
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Stephen Eaton
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Christopher H Dampier
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA.,Department of Surgery, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Jeroen R Huyghe
- Public Health Sciences Division, Fred Hutchinson Cancer Center Research Institute, Seattle, WA, USA
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Center Research Institute, Seattle, WA, USA
| | - Steven M Powell
- Digestive Health Center, University of Virginia, Charlottesville, VA, USA
| | - Graham Casey
- Department of Public Health Sciences, Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA.
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11
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Mumford KA, Powell SM, Rayner JL, Hince G, Snape I, Stevens GW. Evaluation of a permeable reactive barrier to capture and degrade hydrocarbon contaminants. Environ Sci Pollut Res Int 2015; 22:12298-12308. [PMID: 25899942 DOI: 10.1007/s11356-015-4438-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Accepted: 03/23/2015] [Indexed: 06/04/2023]
Abstract
A permeable reactive barrier (PRB) was installed during 2005/2006 to intercept, capture and degrade a fuel spill at the Main Power House, Casey Station, Antarctica. Here, evaluation of the performance of the PRB is conducted via interpretation of total petroleum hydrocarbon (TPH) concentrations, degradation indices and most probable number (MPN) counts of total heterotroph and fuel degrading microbial populations. Results indicate that locations which contained the lowest TPH concentrations also exhibited the highest levels of degradation and numbers of fuel degrading microbes, based on the degradation indices and MPN methods selected. This provides insights to the most appropriate reactive materials for use in PRB's in cold and nutrient-limited environments.
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Affiliation(s)
- K A Mumford
- Particulate Fluids Processing Centre, Department of Chemical and Biomolecular Engineering, University of Melbourne, Melbourne, Australia,
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12
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Powell SM, Chapman CC, Bermudes M, Tamplin ML. Dynamics of seawater bacterial communities in a shellfish hatchery. Microb Ecol 2013; 66:245-256. [PMID: 23354180 DOI: 10.1007/s00248-013-0183-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Accepted: 01/09/2013] [Indexed: 06/01/2023]
Abstract
Bacterial disease is a significant issue for larviculture of several species of shellfish, including oysters. One source of bacteria is the seawater used throughout the hatchery. In this study carried out at a commercial oyster hatchery in Tasmania, Australia, the diversity of the bacterial community and its relationship with larval production outcomes were studied over a 2-year period using terminal restriction fragment length polymorphism and tag-encoded pyrosequencing. The bacterial communities were very diverse, dominated by the Alphaproteobacteria, Gammaproteobacteria, Flavobacteria and Cyanobacteria. The communities were highly variable on scales of days, weeks and seasons. The difference between the intake seawater and treated clean seawater used in the hatchery was smaller than the observed temporal differences in the seawater throughout the year. No clear correlation was observed between production outcomes and the overall bacterial community structure. However, one group of Cyanobacterial sequences was more abundant when mass mortality events occurred than when healthy spat were produced although they were always present.
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Affiliation(s)
- S M Powell
- Australian Seafood Cooperative Research Centre and Tasmanian Institute of Agriculture, University of Tasmania, Private Bay 54, Hobart, TAS, Australia.
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13
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Abstract
Hereditary diffuse gastric cancer can be caused by epithelial cadherin mutations for which genetic testing is available. Inherited cancer predisposition syndromes including Lynch, Li-Fraumeni, and Peutz-Jeghers syndromes, can be associated with gastric cancer. Chromosomal and microsatellite instability occur in gastric cancers. Several consistent genetic and molecular alterations including chromosomal instability, microsatellite instability, and epigenetic alterations have been identified in gastric cancers. Biomarkers and molecular profiles are being discovered with potential for diagnostic, prognostic, and treatment guidance implications.
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Affiliation(s)
- Dushant S Uppal
- Division of Gastroenterology/Hepatology, Department of Medicine, University of Virginia, Charlottesville, VA 22908-0708, USA
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14
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Abstract
Gastric antral vascular ectasia (GAVE) and its nodular antral gastropathy (NAG) variant is a unique lesion associated with hypergastrinemic hormonal alterations that may be compounded by concurrent proton pump inhibitor (PPI) therapy. The use of octreotide as a somatostatin analogue and its role in the down regulation of variousenteric hormones has been well documented however its use in the management of NAG has not been widely reported. We herein present a case where octreotide induced gastrin down-regulation as well as PPI cessation facilitated NAG resolution.
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Affiliation(s)
- Alan Brijbassie
- Virginia Tech Carilion School of Medicine, Roanoke, Virginia, USA
| | - Abdullah Al Osaimi
- Digestive Center of Excellence, University of Virginia Health System, Charlottesville, Virginia, USA
| | - Steven M Powell
- Digestive Center of Excellence, University of Virginia Health System, Charlottesville, Virginia, USA
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15
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Tito NB, Rodemann T, Powell SM. Use of near infrared spectroscopy to predict microbial numbers on Atlantic salmon. Food Microbiol 2012; 32:431-6. [PMID: 22986211 DOI: 10.1016/j.fm.2012.07.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2011] [Revised: 04/26/2012] [Accepted: 07/17/2012] [Indexed: 11/17/2022]
Abstract
The potential of a near infrared spectroscopy (NIR) method to detect as well as predict microbial spoilage on Atlantic salmon (Salmo salar) was investigated. Principal component analysis (PCA) of the NIR spectra showed clear separation between the fresh salmon fillets and those stored for nine days at 4°C indicating that NIR could detect spoilage. A partial least squares regression (PLS) prediction model for total aerobic plate counts after nine days was established using the NIR spectra collected when the fish was fresh to predict the number of bacteria that would be present nine days later. The calibration equation was good (R(2) = 0.95 and RMSE = 0.12 log cfu/g) although the error of the validation curve was larger (R(2) = 0.64 and RMSE = 0.32 log cfu/g). These results indicate that with further model development, it may be possible to use NIR to predict bacterial numbers, and hence shelf-life, in Atlantic salmon and other seafood.
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Affiliation(s)
- N B Tito
- Australian Seafood Cooperative Research Centre, University of Tasmania, Private Bag 54, Hobart, Tasmania 7001, Australia.
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16
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Willard MD, Lajiness ME, Wulur IH, Feng B, Swearingen ML, Uhlik MT, Kinzler KW, Velculescu VE, Sjöblom T, Markowitz SD, Powell SM, Vogelstein B, Barber TD. Somatic mutations in CCK2R alter receptor activity that promote oncogenic phenotypes. Mol Cancer Res 2012; 10:739-49. [PMID: 22516348 PMCID: PMC3904773 DOI: 10.1158/1541-7786.mcr-11-0483] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The roles of cholecystokinin 2 receptor (CCK2R) in numerous physiologic processes in the gastrointestinal tract and central nervous system are well documented. There has been some evidence that CCK2R alterations play a role in cancers, but the functional significance of these alterations for tumorigenesis is unknown. We have identified six mutations in CCK2R among a panel of 140 colorectal cancers and 44 gastric cancers. We show that these mutations increase receptor activity, activate multiple downstream signaling pathways, increase cell migration, and promote angiogenesis. Our findings suggest that somatic mutations in CCK2R may promote tumorigenesis through deregulated receptor activity and highlight the importance of evaluating CCK2R inhibitors to block both the normal and mutant forms of the receptor.
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MESH Headings
- Animals
- Cell Movement/genetics
- Cell Shape/genetics
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/metabolism
- Cells, Cultured
- Coculture Techniques
- Colorectal Neoplasms/genetics
- Colorectal Neoplasms/metabolism
- Colorectal Neoplasms/pathology
- DNA Mutational Analysis
- Endothelial Cells/metabolism
- Endothelial Cells/physiology
- HEK293 Cells
- Humans
- Immunoblotting
- Mice
- Microscopy, Fluorescence
- Mutation
- NIH 3T3 Cells
- Neovascularization, Pathologic/genetics
- Neovascularization, Pathologic/metabolism
- Neovascularization, Pathologic/physiopathology
- Neovascularization, Physiologic/genetics
- Neovascularization, Physiologic/physiology
- Phenotype
- RNA Interference
- Receptor, Cholecystokinin B/genetics
- Receptor, Cholecystokinin B/metabolism
- Receptor, Cholecystokinin B/physiology
- Stomach Neoplasms/genetics
- Stomach Neoplasms/metabolism
- Stomach Neoplasms/pathology
- Transfection
- Vascular Endothelial Growth Factor A/metabolism
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Affiliation(s)
- Melinda D. Willard
- Department of Translational Science, Lilly Research Laboratories, Indianapolis, Indiana
| | - Mary E. Lajiness
- Department of Translational Science, Lilly Research Laboratories, Indianapolis, Indiana
| | - Isabella H. Wulur
- Department of Translational Science, Lilly Research Laboratories, Indianapolis, Indiana
| | - Bo Feng
- Department of Translational Science, Lilly Research Laboratories, Indianapolis, Indiana
| | | | - Mark T. Uhlik
- Department of Cancer Angiogenesis, Lilly Research Laboratories, Indianapolis, Indiana
| | - Kenneth W. Kinzler
- Ludwig Center for Cancer Genetics and Therapeutics and Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland
| | - Victor E. Velculescu
- Ludwig Center for Cancer Genetics and Therapeutics and Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland
| | - Tobias Sjöblom
- Ludwig Center for Cancer Genetics and Therapeutics and Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland
| | - Sanford D. Markowitz
- Department of Medicine and Comprehensive Cancer Center, Case Western Reserve University School of Medicine and Case Medical Center, Cleveland, Ohio
| | - Steven M. Powell
- Division of Gastroenterology/Hepatology, University of Virginia Health System, Charlottesville, Virginia
| | - Bert Vogelstein
- Ludwig Center for Cancer Genetics and Therapeutics and Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, Maryland
| | - Thomas D. Barber
- Department of Translational Science, Lilly Research Laboratories, Indianapolis, Indiana
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17
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Woolfenden ENM, Hince G, Powell SM, Stark SC, Snape I, Stark JS, George SC. The rate of removal and the compositional changes of diesel in Antarctic marine sediment. Sci Total Environ 2011; 410-411:205-216. [PMID: 22018965 DOI: 10.1016/j.scitotenv.2011.09.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Revised: 09/07/2011] [Accepted: 09/07/2011] [Indexed: 05/31/2023]
Abstract
Diesels and lubricants used at research stations can persist in terrestrial and marine sediments for decades, but knowledge of their effects on the surrounding environments is limited. In a 5 year in situ investigation, marine sediment spiked with Special Antarctic Blend (SAB) diesel was placed on the seabed of O'Brien Bay near Casey Station, Antarctica and sampled after 5, 56, 65, 104 and 260 weeks. The rates and possible mechanisms of removal of the diesel from the marine sediments are presented here. The hydrocarbons within the spiked sediment were removed at an overall rate of 4.7mg total petroleum hydrocarbons kg(-1) sediment week(-1), or 245mgkg(-1)year(-1), although seasonal variation was evident. The concentration of total petroleum hydrocarbons fell markedly from 2020±340mgkg(-1) to 800±190mgkg(-1), but after 5 years the spiked sediment was still contaminated relative to natural organic matter (160±170mgkg(-1)). Specific compounds in SAB diesel preferentially decreased in concentration, but not as would be expected if biodegradation was the sole mechanism responsible. Naphthalene was removed more readily than n-alkanes, suggesting that aqueous dissolution played a major role in the reduction of SAB diesel. 1,3,5,7-Teramethyladamantane and 1,3-dimethyladamantane were the most recalcitrant isomers in the spiked marine sediment. Dissolution of aromatic compounds from marine sediment increases the availability of more soluble, aromatic compounds in the water column. This could increase the area of contamination and potentially broaden the region impacted by ecotoxicological effects from shallow sediment dwelling fauna, as noted during biodegradation, to shallow (<19m) water dwelling fauna.
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Affiliation(s)
- E N M Woolfenden
- Department of Earth and Planetary Sciences, Macquarie University, North Ryde, Sydney, NSW 2109, Australia.
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18
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Peng D, Sheta EA, Powell SM, Moskaluk CA, Washington K, Goldknopf IL, El-Rifai W. Alterations in Barrett's-related adenocarcinomas: a proteomic approach. Int J Cancer 2008; 122:1303-10. [PMID: 18000824 DOI: 10.1002/ijc.23258] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In this study, we applied high-resolution, two-dimensional, gel electrophoresis and matrix-assisted laser desorption/ionization, time-of-flight and tandem mass spectrometry analysis (MALDI TOF MS) to identify novel proteins that are involved in Barrett's tumorigenesis. We analyzed 12 primary tissue samples that included 8 Barrett's-related adenocarcinomas (BA) and 4 normal mucosae samples. Twenty-three spots were consistently altered (>or=2-fold) in at least half of the tumors when compared with all normal samples and thus subjected to further analysis. The MALDI TOF MS analysis demonstrated biologically interesting upregulated proteins such as ErbB3, Dr5 and Cyclin D1 as well as several members of the zinc finger proteins (Znf146, Znf212 and Znf363). Examples of downregulated proteins included Lgi1 and Klf6. We selected four proteins (ErbB3, Dr5, Znf146 and Lgi1) that are novel for BAs for validation using quantitative real-time reverse-transcription PCR on 39 BA tissue samples when compared with normal samples. We demonstrated mRNA upregulation of ERBB3 (51.3%), DR5 (41%) and ZNF146 (30.7%) and downregulation of LGI1 (100%) in BA. We have further validated the protein overexpression of ErbB3, Dr5 and Znf146, using immunohistochemical (IHC) analysis on a tissue microarray that contained 75 BAs and normal gastric and esophageal mucosae samples. BA tissue samples demonstrated overexpression of ErbB3 (42%), Dr5 (90%) and Znf146 (30%) when compared with normal tissues. In conclusion, we have identified and validated several novel proteins that are involved in Barrett's carcinogenesis.
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Affiliation(s)
- DunFa Peng
- Department of Surgery, Vanderbilt University Medical Center, Nashville, TN 37232, USA
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19
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Abstract
OBJECTIVES The objective of this study was to determine simple prognostic criteria for differentiation of canine solitary lung tumour cases into those that will and will not benefit from thoracic surgery. METHODS This was a retrospective study using the records of cases presented to Davies Veterinary Specialists, Hitchin, UK, from December 1998 to December 2005. Survival analyses were performed using the Kaplan-Meier and logrank methods. Potentially significant variables were evaluated by multivariate Cox analysis. RESULTS Forty-two patients met the inclusion criteria. Primary tumour stage T1, absence of neoplastic lymph nodes and metastases, and papillary tumour type were statistically significant favourable prognostic indicators on univariate analysis. Multivariate analysis attributed significance to primary tumour stage T1 and papillary type only. Median survival times were 555 days for T1N0M0 tumours of papillary type and 72 days for the remainder. CLINICAL SIGNIFICANCE Survival time following surgery in dogs with primary lung tumours was poor except in clinical stage T1N0M0 cases. These data support use of clinical techniques to dichotomise cases as T1N0M0 or other, improving decision making in thoracic surgery. These data validate initiation of prospective studies examining the role of chemotherapy in the management of advanced cases.
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Affiliation(s)
- G A Polton
- Davies Veterinary Specialists, Manor Farm, Business Park, Higham Gobion, Hitchin, Hertfordshire SG5 3HR, UK
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20
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Razvi MH, Peng D, Dar AA, Powell SM, Frierson HF, Moskaluk CA, Washington K, El‐Rifai W. Transcriptional oncogenomic hot spots in Barrett's adenocarcinomas: serial analysis of gene expression. Genes Chromosomes Cancer 2007; 46:914-28. [PMID: 17636545 PMCID: PMC7165894 DOI: 10.1002/gcc.20479] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Serial analysis of gene expression (SAGE) provides quantitative and comprehensive expression profiling in a given cell population. In our efforts to define gene expression alterations in Barrett's-related adenocarcinomas (BA), we produced eight SAGE libraries and obtained a total of 457,894 expressed tags with 32,035 (6.9%) accounting for singleton tags. The tumor samples produced an average of 71,804 tags per library, whereas normal samples produced an average of 42,669 tags per library. Our libraries contained 67,200 unique tags representing 16,040 known gene symbols. Five hundred and sixty-eight unique tags were differentially expressed between BAs and normal tissue samples (at least twofold; P<or=0.05), 395 of these matched to known genes. Interestingly, the distribution of altered genes was not uniform across the human genome. Overexpressed genes tended to cluster in well-defined hot spots located in certain chromosomes. For example, chromosome 19 had 26 overexpressed genes, of which 18 mapped to 19q13. Using the gene ontology approach for functional classification of genes, we identified several groups that are relevant to carcinogenesis. We validated the SAGE results of five representative genes (ANPEP, ECGF1, PP1201, EIF5A1, and GKN1) using quantitative real-time reverse-transcription PCR on 31 BA samples and 26 normal samples. In addition, we performed an immunohistochemistry analysis for ANPEP, which demonstrated overexpression of ANPEP in 6/7 (86%) Barrett's dysplasias and 35/65 (54%) BAs. ANPEP is a secreted protein that may have diagnostic and/or prognostic significance for Barrett's progression. The use of genomic approaches in this study provided useful information about the molecular pathobiology of BAs.
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Affiliation(s)
- Mohammad H. Razvi
- Department of Surgery, Vanderbilt University Medical Center, Nashville, TN
| | - Dunfa Peng
- Department of Surgery, Vanderbilt University Medical Center, Nashville, TN
| | - Altaf A. Dar
- Department of Surgery, Vanderbilt University Medical Center, Nashville, TN
| | - Steven M. Powell
- Division of Gastroenterology, Vanderbilt University Medical Center, Nashville, TN
| | - Henry F. Frierson
- Department of Pathology, University of Virginia, Charlottesville, VA
| | | | - Kay Washington
- Department of Pathology, Vanderbilt University Medical Center, Nashville, TN
| | - Wael El‐Rifai
- Department of Surgery, Vanderbilt University Medical Center, Nashville, TN
- Department of Cancer Biology, Vanderbilt University Medical Center, Nashville, TN
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21
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Powell SM, O'Donnell S, Ruckley R. Scar excision in revision neck surgery. Clin Otolaryngol 2007; 32:312-3. [PMID: 17651295 DOI: 10.1111/j.1365-2273.2007.01431.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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22
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Powell SM, Brooke GN, Whitaker HC, Reebye V, Gamble SC, Chotai D, Dart DA, Belandia B, Bevan CL. Mechanisms of androgen receptor repression in prostate cancer. Biochem Soc Trans 2007; 34:1124-7. [PMID: 17073766 DOI: 10.1042/bst0341124] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Anti-androgens used in prostate cancer therapy inhibit AR (androgen receptor) activity via largely unknown mechanisms. Although initially successful in most cases, they eventually fail and the disease progresses. We need to elucidate how anti-androgens work to understand why they fail, and prolong their effects or design further therapies. Using a cellular model, we found different anti-androgens have diverse effects on subcellular localization of AR, revealing that they work via different mechanisms and suggesting that an informed sequential treatment regime may benefit patients. In the presence of the anti-androgens bicalutamide and hydroxyflutamide, a significant proportion of the AR is translocated to the nucleus but remains inactive. Receptor inhibition under these conditions is likely to involve recruitment of co-repressor proteins, which interact with antagonist-occupied receptor but inhibit receptor-dependent transcription. Which co-repressors are required in vivo for AR repression by anti-androgens is not clear, but one candidate is the Notch effector Hey1. This inhibits ligand-dependent activity of the AR but not other steroid receptors. Further, it is excluded from the nucleus in most human prostate cancers, suggesting that abnormal subcellular distribution of co-repressors may contribute to the aberrant hormonal responses observed in prostate cancer. A decrease in co-repressor function is one possible explanation for the development of anti-androgen-resistant prostate cancer, and this suggests that it may not occur at the gross level of protein expression.
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Affiliation(s)
- S M Powell
- Androgen Signalling Laboratory, Department of Oncology, Imperial College London, Hammersmith Hospital, London W12 0NN, UK
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23
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Lee OJ, Hong SM, Razvi MH, Peng D, Powell SM, Smoklin M, Moskaluk CA, El-Rifai W. Expression of calcium-binding proteins S100A2 and S100A4 in Barrett's adenocarcinomas. Neoplasia 2006; 8:843-50. [PMID: 17032501 PMCID: PMC1715926 DOI: 10.1593/neo.06481] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this study, we investigated the mRNA and protein expression of S100A2 and S100A4 in adenocarcinomas of the stomach and esophagus. Real-time reverse transcription-polymerase reaction analysis on 72 tumors revealed frequent overexpression of S100A2 and S100A4 in Barrett's adenocarcinomas (BAs) (P < .01). Immunohistochemical analysis on tumor tissue microarrays that contained 187 tumors showed absent to weak staining for S100A2 in all normal gastric mucosa samples, whereas normal esophageal mucosa samples demonstrated moderate to strong nuclear staining. Contrary to the nuclear expression of S100A2 in normal esophageal mucosa, two thirds of Barrett's dysplasia and BAs that overexpressed S100A2 demonstrated stronger cytosolic staining than nuclear staining (P < .001). Overexpression of S100A2 protein was more frequently seen in well-differentiated tumors than in others (P = .02). Moderate to strong staining of S100A4 was detected in two thirds of tumors and was frequently observed in the presence of Barrett's esophagus (P = .02). Similar to S100A2, the expression of S100A4 was predominantly cytosolic in two thirds of the tumors (P = .001). There was a significant correlation between S100A4 overexpression and lymph node metastasis (N(2)-N(4)) (P = .027). These results demonstrate frequent cytosolic overexpression of S100A2 and S100A4 in BAs. Further studies are ongoing to understand the biological significance of these S100A proteins in Barrett's tumorigenesis.
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Affiliation(s)
- Ok-Jae Lee
- Department of Surgery and Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
- Department of Internal Medicine and Institute of Health Science, College of Medicine, Gyeongsang National University, Jinju, Republic of Korea
| | - Seung-Mo Hong
- Department of Pathology, University of Virginia Health System, Charlottesville, VA, USA
| | - Mohammad H Razvi
- Department of Surgery and Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dunfa Peng
- Department of Surgery and Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Steven M Powell
- Division of Gastroenterology, University of Virginia Health System, Charlottesville, VA, USA
| | - Mark Smoklin
- Department of Biostatistics, University of Virginia Health System, Charlottesville, VA, USA
| | | | - Wael El-Rifai
- Department of Surgery and Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN, USA
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Gamble SC, Chotai D, Odontiadis M, Dart DA, Brooke GN, Powell SM, Reebye V, Varela-Carver A, Kawano Y, Waxman J, Bevan CL. Prohibitin, a protein downregulated by androgens, represses androgen receptor activity. Oncogene 2006; 26:1757-68. [PMID: 16964284 DOI: 10.1038/sj.onc.1209967] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Prohibitin (PHB) is a cell cycle regulatory protein, known to repress E2F1-mediated gene activation via recruitment of transcriptional regulatory factors such as retinoblastoma and histone deacetylase 1 (HDAC1). We previously identified PHB as a target protein of androgen signaling in prostate cancer cells and showed that downregulation of PHB is required for androgen-induced cell cycle entry in these cells. We now present evidence that PHB, which has 54% homology at the protein level to the oestrogen receptor corepressor REA (repressor of oestrogen receptor activity), can repress androgen receptor (AR)-mediated transcription and androgen-dependent cell growth. Depletion of endogenous PHB resulted in an increase in expression of the androgen-regulated prostate-specific antigen gene. The repression appears to be specific to androgen and closely related receptors, as it is also evident for the glucocorticoid and progesterone, but not oestrogen, receptors. In spite of interaction of PHB with HDAC1, HDAC activity is not required for this repression. Although AR and PHB could be co-immunoprecipitated, no direct interaction was detectable, suggesting that PHB forms part of a repressive complex with the AR. Competition with the co-activator SRC1 further suggests that formation of a complex with AR, PHB and other cofactors is the mechanism by which repression is achieved. It appears then that repression of AR activity is one mechanism by which PHB inhibits androgen-dependent growth of prostate cells. Further, this study implies that the AR itself could, by mediating downregulation of a corepressor, be involved in the progression of prostate tumours to the hormone refractory stage.
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Affiliation(s)
- S C Gamble
- Department of Oncology, Imperial College London, Hammersmith Hospital Campus, London, UK
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25
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Abstract
CCAAT element binding protein beta (C/EBPbeta) is an important regulator of cell growth, differentiation and in promoting tumor invasiveness. C/EBPbeta is located on chromosome 20q, which is amplified in many solid tumors including gastric cancers (GC). We sought to characterize the status of C/EBPbeta expression in GCs, which was recently found to repres TFF1 gene. Microarray analysis revealed overexpression of C/EBPbeta in 25 of 27 (93%) GC when compared to 12 normal gastric tissue samples. RT-PCR analysis confirmed the overexpression of C/EBPbeta transcripts in 54 of 59 (91%) GC. In total, 15 of 18 gastric tumors exhibited at least fivefold higher C/EBPbeta transcript levels compared to their corresponding adjacent normal gastric tissue samples. Moreover, immunohistochemistry analysis demonstrated increased nuclear staining of C/EBPbeta in 10 of 13 GC and at least fourfold overexpression of C/EBPbeta in three primary GC compared to adjacent normal gastric tissue. Furthermore, a striking correlation of decreased TFF1 expression with increased C/EBPbeta was observed in the gastric tumors studied. Microarray analysis demonstrated a loss of TFF1 expression in all 27 GC cases examined, of which 25 exhibited high C/EBPbeta expression compared to normal gastric tissue. RT-PCR analysis revealed loss of TFF1 expression in 56 of 59 gastric tumors in which 54 of these tumors exhibited overexpression of C/EBPbeta. Immunohistochemical analysis revealed overexpression of C/EBPbeta in 10 of 13 gastric tumors that exhibited low expression of TFF1 at the protein level. Thus, overexpression of the transcription factor C/EBPbeta in the majority of GCs is a novel finding.
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Affiliation(s)
- N V Sankpal
- Department of Internal Medicine, University of Virginia Health System, Charlottesville, 22908, USA
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26
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Abstract
OBJECTIVE To identify the frequency of Internet use by colorectal cancer patients. MATERIALS AND METHODS Fifty patients interviews. RESULTS Only four patients (8%) had used the internet to access information about colorectal cancer though 36% would have used it if a site had been recommended. CONCLUSION The Internet is a resource rarely used by patients but there is potential for its use as an adjunct to written and verbal information.
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Affiliation(s)
- S M Powell
- Colorectal Surgical Unit, Royal Victoria Infirmary, Newcastle upon Tyne, UK
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27
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Johnson AH, Frierson HF, Zaika A, Powell SM, Roche J, Crowe S, Moskaluk CA, El-Rifai W. Expression of tight-junction protein claudin-7 is an early event in gastric tumorigenesis. Am J Pathol 2005; 167:577-84. [PMID: 16049341 PMCID: PMC1603560 DOI: 10.1016/s0002-9440(10)62999-9] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Trefoil factor-1 (Tff1) expression is remarkably down-regulated in nearly all human gastric cancers. Therefore, we used the Tff1 knockout mouse model to detect molecular changes in preneoplastic gastric dysplasia. Oligonucleotide microarray gene expression analysis of gastric dysplasia of Tff1-/- mice was compared to that of normal gastric mucosa of wild-type mice. The genes most overexpressed in Tff1-/- mice included claudin-7 (CLDN7), early growth response-1 (EGR1), and epithelial membrane protein-1 (EMP1). Quantitative real-time reverse transcriptase-polymerase chain reaction and immunohistochemistry showed that Cldn7 was overexpressed in all 10 Tff1-/- gastric dysplasia samples. Comparison with our serial analysis of gene expression database of human gastric cancer revealed similar deregulation in human gastric cancers. Quantitative real-time reverse transcriptase-polymerase chain reaction of human gastric adenocarcinoma samples indicated that, of these three genes, CLDN7 was the most frequently up-regulated gene. Using immunohistochemistry, both mouse and human gastric glands overexpressed Cldn7 in dysplastic but not surrounding normal glands. Cldn7 expression was observed in 30% of metaplasia, 80% of dysplasia, and 70% of gastric adenocarcinomas. Interestingly, 82% of human intestinal-type gastric adenocarcinomas expressed Cldn7 whereas diffuse-type gastric adenocarcinomas did not (P < 0.001). These results suggest that Cldn7 expression is an early event in gastric tumorigenesis that is maintained throughout tumor progression.
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Affiliation(s)
- Adam H Johnson
- Digestive Health Center of Excellence, University of Virginia Health System, P.O. Box 800708, Charlottesville, VA 22908-0708, USA
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28
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Fox CA, Sapinoso LM, Zhang H, Zhang W, McLeod HL, Petroni GR, Mullick T, Moskaluk CA, Frierson HF, Hampton GM, Powell SM. Altered expression of TFF-1 and CES-2 in Barrett's Esophagus and associated adenocarcinomas. Neoplasia 2005; 7:407-16. [PMID: 15967118 PMCID: PMC1501154 DOI: 10.1593/neo.04715] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2004] [Revised: 11/05/2004] [Accepted: 11/08/2004] [Indexed: 11/18/2022] Open
Abstract
Identification of biomarkers to recognize individuals with Barrett's esophagus (BE) predisposed to develop malignancy is currently a pressing issue. We utilized gene expression profiling to compare molecular signatures of normal esophagus and stomach, BE, and adenocarcinoma (AC) to identify such potential biomarkers. Over 22,000 genes were analyzed by oligonucleotide microarrays on 38 unique RNA Unsupervised and supervised clusterings were performed on a subset of 2849 genes that varied most significantly across the specimens. Immunohistochemistry (IHC) for two of the significantly differentially expressed gene products was performed on tissue microarrays. Unsupervised clustering identified two discernable molecular BE profiles, one of which was similar to normal gastric tissue ("BE1"), and another that was shared by several of the AC specimens ("BE2"). The BE1 profile included expression of several genes that have been described as tumor-suppressor genes, most notably trefoil factor 1 (TFF-1). The BE2 profile included expression of genes previously found overexpressed in cancers, such as carboxylesterase-2 (CES-2). IHC demonstrated the loss of TFF-1 late in the progression of BE to AC. It also revealed CES-2 as being upregulated in AC documented to have arisen in the presence of BE. These potential biomarkers, as well as the relative expression of genes from BE1 versus those from BE2, may be validated in the future to aid in risk stratification and guide treatment protocols in patients with BE and associated AC.
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Affiliation(s)
- Charles A Fox
- Digestive Health Center of Excellence, Division of Gastroenterology and Hepatology, University of Virginia, Charlottesville, VA 22908, USA
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29
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Sankpal NV, Mayo MW, Powell SM. Transcriptional repression of TFF1 in gastric epithelial cells by CCAAT/enhancer binding protein-beta. ACTA ACUST UNITED AC 2005; 1728:1-10. [PMID: 15777639 DOI: 10.1016/j.bbaexp.2004.12.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2004] [Revised: 12/13/2004] [Accepted: 12/16/2004] [Indexed: 01/08/2023]
Abstract
TFF1 is a member of a unique family of gastrointestinal peptides. Loss of TFF1 expression has been observed in the majority of human gastric cancers and the biological significance of this loss has been demonstrated in a Tff1 knockout mouse model. However, few TFF1 gene mutations or allelic loss have also been documented. To understand the molecular mechanism repressing the TFF1 gene expression, the 5'-flanking region of the human TFF1 gene was characterized. We found a repressor region (-241 to -84), which is active in MKN45 and IMGE5 cells expressing endogenous TFF1 gene. A consensus binding site for C/EBPbeta was identified and EMSA analysis demonstrated specific binding of CEBPbeta. Mutation of this C/EBPbeta element potentiated the transactivation of TFF1 by 50% and 145% for MKN45 and IMGE5 cells respectively. Furthermore, co-transfection of C/EBPbeta isoforms specifically decreased TFF1 promoter activity. These findings suggest that C/EBPbeta is involved in the down-regulating of TFF1 gene expression and this mode of repression may account at least in part for the loss of TFF1 gene expression in transformed human and mice gastric epithelial cells.
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Affiliation(s)
- Narendra V Sankpal
- Division of Gastroenterology and Hepatology, University of Virginia Health System, Charlottesville, VA 22908-0708, USA
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30
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French AJ, Petroni G, Thibideau SN, Smolkin M, Bissonette E, Roviello F, Harper JC, Koch BR, Anderson SA, Hebbring SJ, Powell SM. Allelic imbalance of 8p indicates poor survival in gastric cancer. J Mol Diagn 2005; 6:243-52. [PMID: 15269302 PMCID: PMC1867637 DOI: 10.1016/s1525-1578(10)60517-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Gastric cancer is a common tumor worldwide and a tremendous health burden. However, the underlying mechanisms of tumorigenesis in this cancer's development are primarily undefined. Allelic imbalance (AI) of 8p has been reported in many cancers, yet, the target(s) of alteration and the importance of allelic imbalance on this chromosomal arm in gastric carcinoma development remained to be characterized. Our findings confirmed a high rate of AI on 8p in gastric cancers. Moreover, we demonstrated that AI on 8p, either overall or at marker D8S560, was associated with poorer survival in patients with gastric cancer. Finally, gastric cancers with a high rate of microsatellite instability were significantly associated with noncardia tumors and with female gender.
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Affiliation(s)
- Amy J French
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
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31
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Abstract
IQGAP1 is recognized as a negative regulator of cell-cell adhesion at adherens junctions in several cell types, including gastric mucosal cells. The histopathologic appearance of diffuse gastric carcinoma is defined by non- or poorly cohesive tumor cells, indicating abnormal intercellular adhesion. Hence, we screened 38 gastric cancers for activating point mutations in IQGAP1. In 2 of the 33 diffuse gastric cancers, there was a missense nucleotide change predicted to alter the amino acid sequence in the GAP-related domain, which includes part of the binding site for the activated small G proteins Cdc42 and Rac1. Many intronic IQGAP1 gene changes were observed, and several occurred more frequently in diffuse-type gastric cancers than in intestinal-type gastric cancers. A highly variable pentanucleotide repeat was identified in the final intron of IQGAP1. The most expanded six-repeat sequence was present exclusively in diffuse-type gastric cancers. Additionally, 19 diffuse cases and two intestinal cases exhibited silent coding region nucleotide alterations. Taken together, our results suggest that IQGAP1 coding sequence mutations are not a frequent event in gastric cancer, but do occur in a subset of diffuse-type gastric carcinomas. Additional studies analyzing other proteins involved in cell adhesion may lead to a better molecular understanding of the histopathologic appearance of diffuse gastric cancers.
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Affiliation(s)
- Leah E Morris
- Department of Biology, University of Virginia, Charlottesville, Virginia 22908-0708, USA
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32
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Koon N, Zaika A, Moskaluk CA, Frierson HF, Knuutila S, Powell SM, El-Rifai W. Clustering of molecular alterations in gastroesophageal carcinomas. Neoplasia 2004; 6:143-9. [PMID: 15140403 PMCID: PMC1502088 DOI: 10.1593/neo.03385] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Gene expression levels are regulated at many levels. Integration of genome-wide analyses for the study of DNA and RNA provides a unique tool to detect genetic alterations in the cancer genome. In this study, we generated and integrated DNA amplification data from comparative genomic hybridization (CGH) and serial analyses of gene expression (SAGE) in order to obtain a molecular profile of gastroesophageal junction (GEJ) carcinomas. DNA amplifications mapped to specific chromosomal regions and were frequently seen at 1q, 4q, 5q, 6p, 7p, 8q, 17q, and 20q. Using SAGE, we obtained over 156,432 tags from GEJ adenocarcinomas and normal gastric mucosa. These tags were assigned to UniGene clusters. Chromosomal positions for overexpressed genes were obtained to produce a GEJ carcinoma transcriptome map. A total of 123 genes was significantly overexpressed (more than fivefold; P <.01) in one or more SAGE libraries. This gene overexpression map was integrated and compared to the chromosomal CGH ideogram. Several chromosomal arms that had frequent DNA amplifications showed frequent gene expression alterations such as chromosomes 1 (15 genes), 2 (9 genes), 6 (6 genes), 11 (6 genes), 12 (8 genes), and 17 (13 genes). Despite the relatively large DNA amplification regions, overexpressed genes frequently mapped and clustered to small chromosomal regions at early-replicating (Giemsa light) bands such as 1q21.3 (nine genes), 6p21.3 (five genes), and 17q21 (eight genes). These results provide a comprehensive tool to search for DNA amplifications and overexpressed genes in GEJ carcinoma. The observed phenomenon of the presence of large amplification areas, yet clustering of overexpressed genes to relatively small loci, may suggest a high organization of chromatin and cancer-related genes in the nucleus.
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Affiliation(s)
- Natalie Koon
- Digestive Health Center of Excellence University of Virginia Health System, Charlottesville, VA 22908-0708, USA
| | - Alexander Zaika
- Digestive Health Center of Excellence University of Virginia Health System, Charlottesville, VA 22908-0708, USA
| | - Christopher A Moskaluk
- Department of Pathology, University of Virginia Health System, Charlottesville, VA 22908-0708, USA
| | - Henry F Frierson
- Department of Pathology, University of Virginia Health System, Charlottesville, VA 22908-0708, USA
| | - Sakari Knuutila
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland
| | - Steven M Powell
- Digestive Health Center of Excellence University of Virginia Health System, Charlottesville, VA 22908-0708, USA
| | - Wa'el El-Rifai
- Digestive Health Center of Excellence University of Virginia Health System, Charlottesville, VA 22908-0708, USA
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33
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Wang Z, Shen D, Parsons DW, Bardelli A, Sager J, Szabo S, Ptak J, Silliman N, Peters BA, van der Heijden MS, Parmigiani G, Yan H, Wang TL, Riggins G, Powell SM, Willson JKV, Markowitz S, Kinzler KW, Vogelstein B, Velculescu VE. Mutational analysis of the tyrosine phosphatome in colorectal cancers. Science 2004; 304:1164-6. [PMID: 15155950 DOI: 10.1126/science.1096096] [Citation(s) in RCA: 385] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Tyrosine phosphorylation, regulated by protein tyrosine phosphatases (PTPs) and kinases (PTKs), is important in signaling pathways underlying tumorigenesis. A mutational analysis of the tyrosine phosphatase gene superfamily in human cancers identified 83 somatic mutations in six PTPs (PTPRF, PTPRG, PTPRT, PTPN3, PTPN13, PTPN14), affecting 26% of colorectal cancers and a smaller fraction of lung, breast, and gastric cancers. Fifteen mutations were nonsense, frameshift, or splice-site alterations predicted to result in truncated proteins lacking phosphatase activity. Five missense mutations in the most commonly altered PTP (PTPRT) were biochemically examined and found to reduce phosphatase activity. Expression of wild-type but not a mutant PTPRT in human cancer cells inhibited cell growth. These observations suggest that the mutated tyrosine phosphatases are tumor suppressor genes, regulating cellular pathways that may be amenable to therapeutic intervention.
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Affiliation(s)
- Zhenghe Wang
- Sidney Kimmel Comprehensive Cancer Center, Howard Hughes Medical Institute, Johns Hopkins University Medical Institutions, Baltimore, MD 21231, USA
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Moskaluk CA, Zhang H, Powell SM, Cerilli LA, Hampton GM, Frierson HF. Cdx2 protein expression in normal and malignant human tissues: an immunohistochemical survey using tissue microarrays. Mod Pathol 2004; 16:913-9. [PMID: 13679455 DOI: 10.1097/01.mp.0000086073.92773.55] [Citation(s) in RCA: 208] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Cdx2 has been identified as a marker of colon cancer in RNA-profiling experiments. We show here that the detection of Cdx2 protein by immunohistochemistry correlates well with RNA transcript levels as detected by oligonucleotide microarrays. Using tissue microarrays containing most normal tissue types and an antibody to the Cdx2 protein, strong diffuse Cdx2 staining was only seen in the nuclei of small and large intestinal epithelium and portions of the pancreatic duct system. In tissue microarrays containing 745 cancers from many anatomic sites, colonic adenocarcinomas showed strong extensive staining in 90% of cases, with adenocarcinomas of the stomach, esophagus, and ovary (endometrioid and mucinous types) showing extensive staining in only 20-30% of cases. Other types of carcinomas showed extensive staining in only </=1% of cases. Of 30 neuroendocrine tumors examined, carcinoids of the midgut and hindgut had the most cases with extensive staining (73% and 44%, respectively), thus paralleling the distribution of Cdx2 expression in adenocarcinomas. Cdx2 shows a limited range of expression in the spectrum of human tissues and neoplasia and thus may have utility in determining the site of origin of tumors in certain clinical situations.
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Affiliation(s)
- Christopher A Moskaluk
- Department of Pathology, University of Virginia Health System, Charlottesville, Virginia 22908, USA.
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35
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Samuels Y, Wang Z, Bardelli A, Silliman N, Ptak J, Szabo S, Yan H, Gazdar A, Powell SM, Riggins GJ, Willson JKV, Markowitz S, Kinzler KW, Vogelstein B, Velculescu VE. High frequency of mutations of the PIK3CA gene in human cancers. Science 2004; 304:554. [PMID: 15016963 DOI: 10.1126/science.1096502] [Citation(s) in RCA: 2657] [Impact Index Per Article: 132.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Affiliation(s)
- Yardena Samuels
- Sidney Kimmel Comprehensive Cancer Center, Howard Hughes Medical Institute, The Johns Hopkins University Medical Institutions, Baltimore, MD 21231, USA
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36
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Powell SM, Christiaens V, Voulgaraki D, Waxman J, Claessens F, Bevan CL. Mechanisms of androgen receptor signalling via steroid receptor coactivator-1 in prostate. Endocr Relat Cancer 2004; 11:117-30. [PMID: 15027889 DOI: 10.1677/erc.0.0110117] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The androgen receptor (AR) is a member of the nuclear receptor superfamily. These ligand-activated transcription factors usually contain two activation functions, a ligand-independent activation function 1(AF1) in the divergent N-terminal domain and a ligand-dependent AF2 in the more conserved C-terminal ligand-binding domain. To promote transcription from target promoters, DNA-bound nuclear receptors recruit coactivator proteins that promote transcription by modifying histones within nucleosomes, resulting in altered topology of chromatin to allow access of the basal transcriptional machinery, or stabilising the pre-initiation complex. It is well known that most coactivators interact with AF2 of many nuclear receptors via conserved, helical LxxLL motifs (where L is leucine and x is any amino acid). The AF2 of the AR is very weak, but we were able to demonstrate that its intrinsic ligand-dependent activity is potentiated by steroid receptor coactivator-1 (SRC1) and that this region interacts with coactivators via LxxLL motifs. However, a mutant SRC1 coactivator with no functional LxxLL motifs was still able to potentiate AR activity. We found that SRC1 can also be recruited to (and increase activity of) AF1 of the AR via a conserved, glutamine-rich region. Point mutations within this region abolish SRC1 interaction with AF1 and also abolish or severely impair its ability to potentiate AR activity on all promoters tested. Thus the AR interacts with SRC1 via two different regions and the AF1 interaction is functionally the more important, although the contribution of the two interactions varies in a promoter-dependent fashion. SRC1 then potentiates receptor activity via recruitment of CBP/p300, a histone acetyltranferase. This is important in the context of prostate cancer as SRC1 and other coactivators including CBP are coexpressed with AR in the luminal epithelial cells of the prostate, where over 90% of prostate tumours arise. There is a need for effective second-line prostate cancer therapy aimed at blocking the AR pathway when anti-androgen therapy has failed. Since there is growing evidence that nuclear receptor cofactors may be implicated in the progression of hormone-dependent tumours to hormone-independent states, novel targets could include the interaction of AR with coactivator proteins. We suggest that the N-terminal interaction would be a more specific and effective target in the case of prostate cancer than the LxxLL/AF2 interaction.
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Affiliation(s)
- S M Powell
- Prostate Cancer Research Group, Department of Cancer Medicine, Imperial College London, Hammersmith Hospital, London W12 0NN, UK
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37
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Affiliation(s)
- Y W Wong
- Department of Dermatology, Old Road, Churchill Hospital, Oxford, Oxfordshire, OX3 7LJ, UK.
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38
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Beckler AD, Roche JK, Harper JC, Petroni G, Frierson HF, Moskaluk CA, El-Rifai W, Powell SM. Decreased abundance of trefoil factor 1 transcript in the majority of gastric carcinomas. Cancer 2003; 98:2184-91. [PMID: 14601088 DOI: 10.1002/cncr.11789] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
BACKGROUND Gastric carcinoma is one of the leading causes of cancer-related death worldwide, but the mechanisms underlying its development and progression still remain largely uncharacterized. As loss of trefoil factor 1 (TFF1) expression leads to neoplastic growth in the antropyloric mucosa of mice, the authors sought to comprehensively study the human TFF1 gene in primary gastric carcinomas. METHODS The authors studied the human TFF1 gene in primary gastric carcinomas and normal gastric mucosa at the DNA, RNA, and protein levels through DNA sequencing, quantitative real-time reverse transcriptase-polymerase chain reaction, and immunohistochemistry. RESULTS Strikingly, TFF1 mRNA expression was significantly decreased in all 37 gastric carcinomas studied compared with normal gastric mucosa. Furthermore, six tumor/normal pairs with available histologic samples demonstrated a marked decrease in protein expression in tumor samples. Screening of the entire TFF1 coding region in a panel of 42 human gastric tumors did not reveal any somatic mutations, although a few rare germline sequence variants were identified. CONCLUSIONS These findings demonstrated a significant decrease in the TFF1 transcript in the majority of human gastric carcinomas along with a corresponding reduction in protein expression, both of which occurred in the absence of gene mutation. Dysregulation of TFF1 expression at the transcript level was a critical event in the development of most gastric carcinomas.
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Affiliation(s)
- Andrew D Beckler
- Department of Medicine, University of Virginia Health System, Charlottesville, Virginia 22908, USA
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Harper JC, Adams RB, Powell SM. Xenografting Human Colon Cancers. Colorectal Cancer 2003; 50:21-4. [DOI: 10.1385/1-59259-084-5:21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Beckler A, Moskaluk CA, Zaika A, Hampton GM, Powell SM, Frierson HF, El-Rifai W. Overexpression of the 32-kilodalton dopamine and cyclic adenosine 3?,5?-monophosphate-regulated phosphoprotein in common adenocarcinomas. Cancer 2003; 98:1547-51. [PMID: 14508844 DOI: 10.1002/cncr.11654] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND The 32-kilodalton dopamine and cyclic adenosine 3',5'-monophosphate-regulated phosphoprotein (DARPP-32) is the only known protein that can act as a protein phosphatase-1 inhibitor or a protein kinase inhibitor. It is known as a neurogenic protein that plays a major role in dopamine regulation in the central nervous system. Recently, DARPP-32 and a truncated isoform, t-DARPP, have been cloned in gastric carcinoma. The extent of DARPP-32 and t-DARPP expression in human epithelial tissues and carcinomas remained unknown. METHODS Using tissue microarrays and an antibody to DARPP-32, the authors evaluated the immunohistochemical findings in 43 different normal epithelium human tissue samples and in 187 samples of common carcinomas of breast, prostate, colon, and stomach. RESULTS DARPP-32 proteins were expressed at varying levels in several types of normal epithelial tissues outside of the central nervous system. Using quantitative real-time reverse transcriptase-polymerase chain reaction analysis, the authors demonstrated that both DARPP-32 and t-DARPP mRNAs frequently were overexpressed in carcinomas of the breast, prostate, colon, and stomach compared with normal tissue samples. Immunohistochemical analysis of tissue microarrays that contained 187 carcinoma samples confirmed the strong expression of DARPP-32 proteins in these tumor types. CONCLUSIONS The current study provides the first evidence that DARPP-32 expression is not limited to dopamine signaling in normal cells of the central nervous system. The pattern of expression of DARPP-32 proteins in normal epithelial tissues suggests that these proteins play an important role in epithelial signaling that may be tissue specific. Moreover, the observation that DARPP-32 and t-DARPP frequently are overexpressed in common subtypes of human adenocarcinomas suggest that these proteins may be important in tumorigenesis.
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Affiliation(s)
- Andy Beckler
- Department of Medicine, Division of Gastroenterology, University of Virginia Health System, Charlottesville, Virginia 22908-0708, USA
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Ascaño JJ, Powell SM. Determination of cancer allelotype. Methods Mol Biol 2003; 222:295-307. [PMID: 12710694 DOI: 10.1385/1-59259-328-3:295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jennifer J Ascaño
- Division of Gastroenterology, University of Virginia Health System, Charlottesville, USA
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Frierson HF, Moskaluk CA, Powell SM, Zhang H, Cerilli LA, Stoler MH, Cathro H, Hampton GM. Large-scale molecular and tissue microarray analysis of mesothelin expression in common human carcinomas. Hum Pathol 2003; 34:605-9. [PMID: 12827615 DOI: 10.1016/s0046-8177(03)00177-1] [Citation(s) in RCA: 129] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The 40-kilodalton processed glycoprotein, mesothelin, is highly expressed in epithelial mesotheliomas and adenocarcinomas of the ovary (serous papillary) and pancreas, but its expression in a large series of other common carcinomas has not been completely explored. In the present study, we used oligonucleotide and tissue microarrays to profile the expression of the mesothelin gene (MSLN) and encoded protein, respectively. Among 150 carcinomas of multiple anatomic sites, we found the highest average expression of MSLN in serous carcinomas of the ovary and adenocarcinomas of the pancreas, consistent with previous reports, as well as measurable but less-striking expression in pulmonary, gastric/esophageal, and colorectal adenocarcinomas. On tissue microarrays containing 621 carcinomas derived from the same and additional sites as those profiled by gene expression, mesothelin immunoreactivity was highest in cancers of the ovary (serous papillary, endometrioid, and undifferentiated) and pancreas, with less frequent staining seen in adenocarcinomas of the endometrium, lung, and stomach/esophagus. Some immunopositivity was observed in 42% of pulmonary adenocarcinomas, including 18% that had >50% of tumor cells that were immunoreactive. Some 14% of breast and 30% of colorectal adenocarcinomas showed immunopositivity, but no case contained >50% tumor cells that were immunoreactive. Mesothelin was either entirely absent or present in <5% of carcinomas of the prostate, bladder/ureter, liver, kidney, and thyroid. Overall, we observed good concordance between the results obtained by oligonucleotide and tissue microarrays. This large study of the MSLN gene and protein expression in common carcinomas provides data for future investigations that evaluate the utility of mesothelin/megakaryocyte potentiating factor as a potential serum tumor marker or target of immunotoxin-based therapy in human cancers.
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Affiliation(s)
- Henry F Frierson
- Department of Pathology, University of Virginia Health System, Charlottesville 22908, USA
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Abstract
In this work, the use of MRI to stage gastric neoplasia in a mouse model of spontaneous gastric cancer is demonstrated. The methodology involves 1) the use of deuterated water ((2)H(2)O) to distend the stomach, and to provide negative contrast between the stomach and the lumen without inducing susceptibility-based field shifts; 2) GlucaGen to minimize motion artifacts that arise from peristalsis; and 3) Gd-DTPA to enhance contrast between the dysplasia/tumor and the normal wall. Initial images are presented from a Tff1 -/- homozygous knock-out model of gastric cancer and a heterozygous C57BL6/J control mouse. There are clear differences between the two types of animals in the MR appearance of the stomach. The distended stomach of the control mouse has a smooth perimeter and a thin wall, and an absence of nodules. The stomach of the Tff1 -/- mouse demonstrates a thickened wall; a jagged, irregular surface; and protruding nodules that are bright after injection of Gd-DTPA.
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Affiliation(s)
- Stuart S Berr
- Department of Radiology, University of Virginia, Charlottesville 22908, USA.
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Abstract
AIM: To investigate CpG methylation and single nucleotide polymorphism (SNP) of a specific promoter region of hMLH1 in primary gastric carcinoma.
METHODS: Primary gastric carcinomas (n = 80), their corresponding normal mucosal samples, and gastric mucosal biopsies from normal/gastritis control patients (n = 54) were used. Hypermethylation at -253 nt and -251 nt in relation with the translational start site and SNP of a silencing specific region (-339 nt-46 nt) in the hMLH1 promoter were analyzed by Bst UI-combined bisulfite assay (COBRA), denaturing high performance liquid chromatogram (DHPLC), and sequencing.
RESULTS: (A) The specific methylation at -253 nt and -251 nt was observed in 2 of 60 primary gastric carcinomas, but neither in all of the corresponding mucosa nor in normal/gastritis samples, by Bst UI-COBRA and DHPLC. (B) The hMLH1 promoter was methylated homogeneously in the xenograft of the primary gastric carcinoma with the methylated and unmethylated hMLH1. (C) The pattern of SNP at -93 nt of the hMLH1 promoter in 54 Chinese patients with gastric carcinoma was the same as that in the control patients: 51% was A/G heteroalleles, 34% and 15% were A/A and G/G homoalleles, respectively.
CONCLUSION: Biallelic inactivation of hMLH1 by epigenetic silencing existed in human primary gastric carcinoma homogeneously. Hypermethylation of hMLH1 may play a role in the early stage of development of a few gastric carcinomas. The SNP at -93 nt is not related to the susceptibility of gastric carcinomas.
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Affiliation(s)
- Da-Jun Deng
- Peking University Health Science Center and Beijing Institute for Cancer Research, Beijing, 100034, China.
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El-Rifai W, Moskaluk CA, Abdrabbo MK, Harper J, Yoshida C, Riggins GJ, Frierson HF, Powell SM. Gastric cancers overexpress S100A calcium-binding proteins. Cancer Res 2002; 62:6823-6. [PMID: 12460893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2023]
Abstract
Serial analysis of gene expression provides quantitative and comprehensive expression profiling in a given cell population. In our efforts to define the genes overexpressed in carcinoma of the stomach, we performed serial analysis of gene expression analyses on dissected neoplastic and normal gastric epithelia. We identified 91,334 expressed tags, including 26,633 that were unique. The 20 most up-regulated genes (P < 0.01) in gastric cancer (GC) compared with normal gastric epithelia included several keratins that are specific for epithelial cells such as keratin 6A, 13, and 17. Interestingly, five calcium-binding proteins (S100A2, S100A7, S100A8, S100A9, and S100A10) were overexpressed. Quantitative real-time PCR on primary GC samples demonstrated overexpression of S100A2 in 18 of 20 tumors (90%). The other calcium-binding proteins were overexpressed in 25-45% of the GC samples that we studied. Our results indicate that S100A proteins may be important for gastric tumorigenesis. Additional investigations are required to elucidate the biological role of calcium-binding proteins in cancer.
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Affiliation(s)
- Wa'el El-Rifai
- Department of Medicine, University of Virginia Health System, Charlottesville, Virginia 22908-0708, USA.
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El-Rifai W, Smith MF, Li G, Beckler A, Carl VS, Montgomery E, Knuutila S, Moskaluk CA, Frierson HF, Powell SM. Gastric cancers overexpress DARPP-32 and a novel isoform, t-DARPP. Cancer Res 2002; 62:4061-4. [PMID: 12124342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Gastric carcinoma is the second most common cause of cancer-related death worldwide. Recently, we have demonstrated that expressed sequence tag AA552509 was frequently amplified and the most consistently overexpressed target at 17q in gastric cancers. Herein, we report that DARPP-32 (dopamine and cAMP-regulated phosphoprotein of M(r) 32,000) is the target gene for overexpression of expressed sequence tag AA552509. In addition, we have identified full-length cDNA of DARPP-32 (GenBank accession number AF464196) with 467 bp of additional untranslated mRNA nucleotides upstream of the previously known translation start site in exon 1. Additionally, we have discovered a novel truncated isoform of DARPP-32 that we named t-DARPP (GenBank accession number AY070271), which is also overexpressed in gastric cancers. Using quantitative real-time reverse transcription-PCR, Western blots, and staining of tumor tissue arrays, the two DARPP mRNA transcripts and proteins were overexpressed in gastric cancer cells and exhibited abundant protein overexpression in neoplastic but not normal gastric epithelial cells. DARPP-32 is the only known protein that acts as a protein phosphatase 1 inhibitor or a protein kinase A inhibitor. The novel truncated isoform, t-DARPP, lacks the phosphorylation site related to protein phosphatase 1 inhibition but maintains the phosphorylation site with the protein kinase A inhibitory effect. Our results reveal for the first time the presence of these signaling molecules in human cancer and suggest that they may be important for gastric tumorigenesis.
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Affiliation(s)
- Wa'el El-Rifai
- Department of Medicine, University of Virginia Health System, Charlottesville, Virginia 22908-0708, USA.
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Varis A, Wolf M, Monni O, Vakkari ML, Kokkola A, Moskaluk C, Frierson H, Powell SM, Knuutila S, Kallioniemi A, El-Rifai W. Targets of gene amplification and overexpression at 17q in gastric cancer. Cancer Res 2002; 62:2625-9. [PMID: 11980659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
DNA copy number gains and amplifications at 17q are frequent in gastriccancer, yet systematic analyses of the 17q amplicon have not been performed. In this study, we carried out a comprehensive analysis of copy number and expression levels of 636 chromosome 17-specific genes in gastric cancer by using a custom-made chromosome 17-specific cDNA microarray. Analysis of DNA copy number changes by comparative genomic hybridization on cDNA microarray revealed increased copy numbers of 11 known genes (ERBB2, TOP2A, GRB7, ACLY, PIP5K2B, MPRL45, MKP-L, LHX1, MLN51, MLN64, and RPL27) and seven expressed sequence tags (ESTs) that mapped to 17q12-q21 region. To investigate the genes transcribed at the 17q, we performed gene expression analyses on an identical cDNA microarray. Our expression analysis showed overexpression of 8 genes (ERBB2, TOP2A, GRB2, AOC3, AP2B1, KRT14, JUP, and ITGA3) and two ESTs. Of the commonly amplified transcripts, an uncharacterized EST AA552509 and the TOP2A gene were most frequently overexpressed in 82% of the samples. Additional studies will be initiated to understand the possible biological and clinical significance of these genes in gastric cancer development and progression.
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Affiliation(s)
- Asta Varis
- Department of Medical Genetics, University of Helsinki and Helsinki University Central Hospital, Helsinki 00290, Finland
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Abstract
Gastric cancer is one of the world's most common cancers and is a leading cause of cancer death worldwide. Neoplasia of the stomach is mainly composed of adenocarcinomas, which for more than 95% of cases. Although mesenchymal tumors (i.e., stromal tumors, leiomyomas and leiomyosarcomas, and schwannomas), primary lymphomas, and carcinoid tumors can also arise in the stomach, malignant tumors of these types occur much less often.
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Affiliation(s)
- Wa'el el-Rifai
- Department of Medicine, Division of Gastroenterology and Hepatology, University of Virginia, Box 800798, Charlottesville, VA 22908-0708, USA
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Abstract
Gastric cancer is one of the leading causes of cancer mortality in the world. Gastric adenocarcinomas account for more than 95% of gastric tumors, whereas gastrointestinal stromal tumors (GISTs) are the most common neoplasms of the rare gastric mesenchymal tumors. Although the incidence of mid-distal gastric adenocarcinomas is decreasing, the incidence of gastroesophageal junctional tumors and Barrett's adenocarcinomas is increasing for unknown reasons. The majority of gastric tumors are sporadic in nature. However, there are rare, inherited gastric cancer predisposition traits, such as germline p53 (Li-Fraumeni syndrome) as well as E-cadherin (CDH1) alterations in familial diffuse gastric cancers. Gastric cancer has been observed to be part of the spectrum of neoplasms associated with germline mismatch repair gene (MMR) alterations that give rise to the hereditary nonpolyposis colorectal cancer (HNPCC) entity. Comparative genomic hybridization analyses have identified several amplifications and losses of DNA copy numbers in gastric cancers. Loss of heterozygosity (LOH) studies have shown several chromosomal loci with significant allelic loss, thus indicating the possibility of harboring a tumor suppressor gene important in gastric tumorigenesis. Microsatellite instability (MIS) and associated alteration of the TGF-bIIR, IGFRII, BAX, E2F-4, hMSH3, and hMSH6 genes are found in a subset of gastric carcinomas. Cell adhesion molecule abnormalities such as those involving CDH1 may play an important role in diffuse-type gastric cancer development. Although, multiple somatic alterations have been described in gastric carcinomas at the molecular level, the significance of these changes in gastric tumorigenesis remains to be established in most instances. The critical molecular alterations in gastric cancers that may lead to advances in our armamentarium to combat this lethal disease remain to be fully characterized.
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Affiliation(s)
- Wa'el El-Rifai
- Department of Medicine, Division of Gastroenterology/Hepatology, University of Virginia, Charlottesville, VA 22908, USA
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