Metabolic targeting of NRF2 potentiates the efficacy of the TRAP1 inhibitor G-TPP through reduction of ROS detoxification in colorectal cancer

Tumor necrosis factor receptor-associated protein 1 (TRAP1) is a mitochondrial homolog of HSP90 chaperones. It plays an important role in protection against oxidative stress and apoptosis by regulating reactive oxidative species (ROS). To further elucidate the mechanistic role of TRAP1 in regulating tumor cell survival, we used gamitrinib-triphenylphosphonium (G-TPP) to inhibit TRAP1 signaling pathways in colon cancer. Inhibition of TRAP1 by G-TPP disrupted redox homeostasis and induced cell death. However, colon cancers show a wide range of responses to G-TPP treatment through the induction of variable ER stress responses and ROS accumulation. Interestingly, a strong inverse correlation was observed between the expression of TRAP1 and antioxidant genes in colon tumor tissues using the GSE106582 database. Using a luciferase reporter assay, we detected increased transcriptional activation of antioxidant response elements (AREs) in G-TPP-treated DLD1 and RKO cells but not in SW48 cells. We found that G-TPP induced upregulation of GRP78, CHOP and PARP cleavage in G-TPP-sensitive cells (SW48). In contrast, G-TPP treatment of G-TPP-resistant cells (DLD1 and RKO) resulted in excessive activation of the antioxidant gene NRF2, leading to ROS detoxification and improved cell survival. The NRF2 target genes HO1 and NQO1 were upregulated in G-TPP-treated DLD1 cells, making the cells more resistant to G-TPP treatment. Furthermore, treatment with both a NRF2 inhibitor and a TRAP1 inhibitor led to excessive ROS production and exacerbated G-TPP-induced cell death in G-TPP-resistant cells. Taken together, dual targeting of TRAP1 and NRF2 may potentially overcome colon cancer resistance by raising cellular ROS levels above the cytotoxic threshold.

Abstract 5077: Proteomics analysis of extracellular vesicles from pancreatic cancer cells and cancer associated fibroblasts

Extracellular vesicles (EVs) are comprised of lipid bound vesicles secreted by cells into the extracellular environment with various roles in cell-to-cell communication. Recent studies have implicated EVs in cell proliferation, epithelial-mesenchymal transition (EMT), metastasis, angiogenesis, and mediating the interaction of tumor cells and tumor microenvironment. To systematically characterize the EVs associated with pancreatic cancer, we performed proteomic and functional analyses on the protein contents of EVs released from pancreatic cancer lines, CAF cell lines and a normal pancreatic epithelial cell line. More than 1400 non-redundant proteins were identified in each EV proteome derived from these cell lines. The common EV proteins identified in these cell lines were enriched in biological processes such as vesicle-mediated transport and exocytosis. Protein networks relevant to pancreatic tumorigenesis, such as of EMT, complement and coagulation components, were significantly enriched in the EVs from cancer cells or CAFs in comparison to normal pancreatic epithelial cells. These findings support the roles of EVs as a potential mediator in transmitting EMT signals and complement response in the tumor microenvironment and possibly contributing to coagulation defects related to cancer development.

Citation Format: Sharon Pan, Lisa A. Lai, Diane M. Simeone, David W. Dawson, Yuanqing Yan, Tatjana Crnogorac-Jurcevic, Ru Chen, Teresa A. Brentnall. Proteomics analysis of extracellular vesicles from pancreatic cancer cells and cancer associated fibroblasts [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5077.

X-aptamers targeting Thy-1 membrane glycoprotein in pancreatic ductal adenocarcinoma

Modified DNA aptamers incorporated with amino-acid like side chains or drug-like ligands can offer unique advantages and enhance specificity as affinity ligands. Thy-1 membrane glycoprotein (THY1 or CD90) was previously identified as a biomarker candidate of neovasculature in pancreatic ductal adenocarcinoma (PDAC). The current study developed and evaluated modified DNA X-aptamers targeting THY1 in PDAC. The expression and glycosylation of THY1 in PDAC tumor tissues were assessed using immunohistochemistry and quantitative proteomics. Bead-based X-aptamer library that contains 108 different sequences was used to screen for high affinity THY1 X-aptamers. The sequences of the X-aptamers were analyzed with the next-generation sequencing. The affinities of the selected X-aptamers to THY1 were quantitatively evaluated with flow cytometry. Three high affinity THY1 X-aptamers, including XA-B217, XA-B216 and XA-A9, were selected after library screening and affinity binding evaluation. These three X-aptamers demonstrated a high binding affinity and specificity to THY1 protein and the THY1 expressing cell lines, using THY1 antibody as a comparison. The development of these X-aptamers provides highly specific and non-immunogenic affinity ligands for THY1 binding in the context of biomarker development and clinical applications. They could be further exploited to assist molecular imaging of PDAC targeting THY1.

Systemic Proteome Alterations Linked to Early Stage Pancreatic Cancer in Diabetic Patients

BACKGROUND

Diabetes is a risk factor associated with pancreatic ductal adenocarcinoma (PDAC), and new adult-onset diabetes can be an early sign of pancreatic malignancy. Development of blood-based biomarkers to identify diabetic patients who warrant imaging tests for cancer detection may represent a realistic approach to facilitate earlier diagnosis of PDAC in a risk population.

METHODS

A spectral library-based proteomic platform was applied to interrogate biomarker candidates in plasma samples from clinically well-defined diabetic cohorts with and without PDAC. Random forest algorithm was used for prediction model building and receiver operating characteristic (ROC) curve analysis was applied to evaluate the prediction probability of potential biomarker panels.

RESULTS

Several biomarker panels were cross-validated in the context of detection of PDAC within a diabetic background. In combination with carbohydrate antigen 19-9 (CA19-9), the panel, which consisted of apolipoprotein A-IV (APOA4), monocyte differentiation antigen CD14 (CD14), tetranectin (CLEC3B), gelsolin (GSN), histidine-rich glycoprotein (HRG), inter-alpha-trypsin inhibitor heavy chain H3 (ITIH3), plasma kallikrein (KLKB1), leucine-rich alpha-2-glycoprotein (LRG1), pigment epithelium-derived factor (SERPINF1), plasma protease C1 inhibitor (SERPING1), and metalloproteinase inhibitor 1 (TIMP1), demonstrated an area under curve (AUC) of 0.85 and a two-fold increase in detection accuracy compared to CA19-9 alone. The study further evaluated the correlations of protein candidates and their influences on the performance of biomarker panels.

CONCLUSIONS

Proteomics-based multiplex biomarker panels improved the detection accuracy for diagnosis of early stage PDAC in diabetic patients.

Gut Microbial Protein Expression in Response to Dietary Patterns in a Controlled Feeding Study: A Metaproteomic Approach

Although the gut microbiome has been associated with dietary patterns linked to health, microbial metabolism is not well characterized. This ancillary study was a proof of principle analysis for a novel application of metaproteomics to study microbial protein expression in a controlled dietary intervention. We measured the response of the microbiome to diet in a randomized crossover dietary intervention of a whole-grain, low glycemic load diet (WG) and a refined-grain, high glycemic load diet (RG). Total proteins in stools from 9 participants at the end of each diet period (n = 18) were analyzed by LC MS/MS and proteins were identified using the Human Microbiome Project (HMP) human gut microbiome database and UniProt human protein databases. T-tests, controlling for false discovery rate (FDR) <10%, were used to compare the Gene Ontology (GO) biological processes and bacterial enzymes between the two interventions. Using shotgun proteomics, more than 53,000 unique peptides were identified including microbial (89%) and human peptides (11%). Forty-eight bacterial enzymes were statistically different between the diets, including those implicated in SCFA production and degradation of fatty acids. Enzymes associated with degradation of human mucin were significantly enriched in the RG diet. These results illustrate that the metaproteomic approach is a valuable tool to study the microbial metabolism of diets that may influence host health.

Metaproteomics Study of the Gut Microbiome

Proteomics is a widely used method for defining the protein composition of a complex sample. As this approach allows for identification and quantification of proteins across a broad dynamic range as well as detection of post-translational modifications, proteomics is an ideal platform to investigate the gut microbiome at a functional level. The gut microbiome is a dynamic environment which is crucial for overall health and fitness. Imbalances in the gut microbiome can influence nutrient absorption, pathogen resistance, inflammation, and various human diseases. Metaproteomic analysis of the gut microbiome is currently being performed on bacteria isolated from (1) fecal samples (2) colonic lavage, or (3) colon biopsies. Investigation of the gut microbiome has demonstrated that within the colon, there are distinct communities based on spatial location, and separable from the gut microbiomes isolated from stool. In addition to expanding our understanding of host-bacterial interactions for human health and disease, gut microbiome analysis is being utilized for biomarker development to discriminate normal individuals and diseased (i.e., inflammatory bowel disease or colon cancer) patients as well as to monitor disease activity and prognosis.

Disrupting glutamine metabolic pathways to sensitize gemcitabine-resistant pancreatic cancer

Pancreatic cancer is a lethal disease with poor prognosis. Gemcitabine has been the first line systemic treatment for pancreatic cancer. However, the rapid development of drug resistance has been a major hurdle in gemcitabine therapy leading to unsatisfactory patient outcomes. With the recent renewed understanding of glutamine metabolism involvement in drug resistance and immuno-response, we investigated the anti-tumor effect of a glutamine analog (6-diazo-5-oxo-L-norleucine) as an adjuvant treatment to sensitize chemoresistant pancreatic cancer cells. We demonstrate that disruption of glutamine metabolic pathways improves the efficacy of gemcitabine treatment. Such a disruption induces a cascade of events which impacts glycan biosynthesis through Hexosamine Biosynthesis Pathway (HBP), as well as cellular redox homeostasis, resulting in global changes in protein glycosylation, expression and functional effects. The proteome alterations induced in the resistant cancer cells and the secreted exosomes are intricately associated with the reduction in cell proliferation and the enhancement of cancer cell chemosensitivity. Proteins associated with EGFR signaling, including downstream AKT-mTOR pathways, MAPK pathway, as well as redox enzymes were downregulated in response to disruption of glutamine metabolic pathways.

Biomarkers for colitis-associated colorectal cancer

Patients with extensive ulcerative colitis (UC) of more than eight years duration have an increased risk of colorectal cancer. Molecular biomarkers for dysplasia and cancer could have a great clinical value in managing cancer risk in these UC patients. Using a wide range of molecular techniques - including cutting-edge OMICS technologies - recent studies have identified clinically relevant biomarker candidates from a variety of biosamples, including colonic biopsies, blood, stool, and urine. While the challenge remains to validate these candidate biomarkers in multi-center studies and with larger patient cohorts, it is certain that accurate biomarkers of colitis-associated neoplasia would improve clinical management of neoplastic risk in UC patients. This review highlights the ongoing avenues of research in biomarker development for colitis-associated colorectal cancer.

Proteins associated with pancreatic cancer survival in patients with resectable pancreatic ductal adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal disease with a dismal prognosis. However, while most patients die within the first year of diagnosis, very rarely, a few patients can survive for >10 years. Better understanding the molecular characteristics of the pancreatic adenocarcinomas from these very-long-term survivors (VLTS) may provide clues for personalized medicine and improve current pancreatic cancer treatment. To extend our previous investigation, we examined the proteomes of individual pancreas tumor tissues from a group of VLTS patients (survival ≥10 years) and short-term survival patients (STS, survival <14 months). With a given analytical sensitivity, the protein profile of each pancreatic tumor tissue was compared to reveal the proteome alterations that may be associated with pancreatic cancer survival. Pathway analysis of the differential proteins identified suggested that MYC, IGF1R and p53 were the top three upstream regulators for the STS-associated proteins, and VEGFA, APOE and TGFβ-1 were the top three upstream regulators for the VLTS-associated proteins. Immunohistochemistry analysis using an independent cohort of 145 PDAC confirmed that the higher abundance of ribosomal protein S8 (RPS8) and prolargin (PRELP) were correlated with STS and VLTS, respectively. Multivariate Cox analysis indicated that 'High-RPS8 and Low-PRELP' was significantly associated with shorter survival time (HR=2.69, 95% CI 1.46-4.92, P=0.001). In addition, galectin-1, a previously identified protein with its abundance aversely associated with pancreatic cancer survival, was further evaluated for its significance in cancer-associated fibroblasts. Knockdown of galectin-1 in pancreatic cancer-associated fibroblasts dramatically reduced cell migration and invasion. The results from our study suggested that PRELP, LGALS1 and RPS8 might be significant prognostic factors, and RPS8 and LGALS1 could be potential therapeutic targets to improve pancreatic cancer survival if further validated.

Up-regulation of mitochondrial chaperone TRAP1 in ulcerative colitis associated colorectal cancer

AIM: To characterize tumor necrosis factor receptor-associated protein 1 (TRAP1) expression in the progression of ulcerative colitis (UC)-associated colorectal cancer.

METHODS: Chronic UC is an inflammatory bowel disease that predisposes to colorectal cancer. Immunohistochemical analysis was used to evaluate TRAP1 expression on tissue microarrays containing colonic tissues from 42 UC progressors (patients with cancer or dysplasia) and 38 non-progressors (dysplasia/cancer free patients). Statistical analyses of the TRAP1 immunohistochemistry staining were performed using GraphPad Prism. Differences in the TRAP1 level between non-progressors and progressors were tested for statistical significance using the Mann-Whitney test. Receiver operating characteristic curve method was used to quantify marker performance in distinguishing diseased cases from controls.

RESULTS: TRAP1 was up-regulated in the colon tissues from UC progressors, but not in the colon tissues from UC non-progressors. Moreover, up-regulation of TRAP1 preceded the neoplastic changes: it was present in both the dysplastic and non-dysplastic tissues of UC progressors. When TRAP1 staining in rectal tissue was used as a diagnostic marker, it could distinguish progressors from non-progressors with 59% sensitivity and 80% specificity. Our study further showed that the increase of TRAP1 expression positively correlated with the degree of inflammation in the colorectal cancer tissues, which could be related to the increased oxidation present in the colonic mucosa from UC progressors. We then investigated the cellular proteome changes underlying oxidative stress, and found that oxidative stress could induce up-regulation of TRAP1 along with several other negative modulators of apoptosis.

CONCLUSION: These results suggest that oxidative stress in long standing UC could lead to the increase of cytoprotective protein TRAP1, which in turn could promote cancer progression by preventing or protecting the oxidative damaged epithelial cells from undergoing apoptosis. TRAP1 could be a potential diagnostic marker for UC associated colorectal cancer.

Quantitative glycoproteomics analysis reveals changes in N-glycosylation level associated with pancreatic ductal adenocarcinoma

Glycosylation plays an important role in epithelial cancers, including pancreatic ductal adenocarcinoma. However, little is known about the glycoproteome of the human pancreas or its alterations associated with pancreatic tumorigenesis. Using quantitative glycoproteomics approach, we investigated protein N-glycosylation in pancreatic tumor tissue in comparison with normal pancreas and chronic pancreatitis tissue. The study lead to the discovery of a roster of glycoproteins with aberrant N-glycosylation level associated with pancreatic cancer, including mucin-5AC (MUC5AC), carcinoembryonic antigen-related cell adhesion molecule 5 (CEACAM5), insulin-like growth factor binding protein (IGFBP3), and galectin-3-binding protein (LGALS3BP). Pathway analysis of cancer-associated aberrant glycoproteins revealed an emerging phenomenon that increased activity of N-glycosylation was implicated in several pancreatic cancer pathways, including TGF-β, TNF, NF-kappa-B, and TFEB-related lysosomal changes. In addition, the study provided evidence that specific N-glycosylation sites within certain individual proteins can have significantly altered glycosylation occupancy in pancreatic cancer, reflecting the complexity of the molecular mechanisms underlying cancer-associated glycosylation events.

Pan-colonic field defects are detected by CGH in the colons of UC patients with dysplasia/cancer

BAC arrays were used to evaluate genomic instability along the colon of patients with ulcerative colitis (UC). Genomic instability increases with disease progression and biopsies more proximal to dysplasia showed increased instability. Pan-colonic field copy number gain or loss involving small (<1Mb) regions were detected in most patients and were particularly apparent in the UC progressor patients who had dysplasia or cancer. Chromosomal copy gains or losses affecting large regions were mainly restricted to dysplastic biopsies. Areas of significant chromosomal losses were detected in the UC progressors on chromosomes 2q36, 3q25, 3p21, 4q34, 4p16.2, 15q22, and 16p13 (p-value⩽0.04). These results extend our understanding of the dynamic nature of pan-colonic genomic instability in this disease.

Abstract 5742: Up-regulation of mitochondrial chaperone TRAP1 in cancer precursors associated with chronic inflammation

Chronic ulcerative colitis (UC) is an inflammatory bowel disease that predisposes to colorectal cancer. In chronic UC patients, the colon epithelium undergoes repeated cycles of inflammation and tissue repair, resulting in oxidative stress and accumulation of reactive oxidative species (ROS). Excessive ROS can cause oxidative stress, which may subsequently lead to damage in DNA, proteins and lipids. Using proteomics analysis of colonic mucosa from UC patients with neoplasia, we identified TNF receptor-associated protein 1(TRAP1) in the UC cancer precursors. TRAP1 is a mitochondrial chaperone which protects against oxidative stress and apoptosis. We further investigated TRAP1 in the progression of UC-associated colorectal cancer using immunohistochemistry and tissue microarray. Quantification of protein oxidation in the colonic epithelia revealed that oxidative stress was present in the colonic mucosa in both UC patients with dysplasia/cancer (progressors) and UC patients without dysplasia/cancer (non-progressors). However, TRAP1 was only up-regulated in UC progressors, but not in the non-progressors. Moreover, up-regulation of TRAP1 preceded the histological changes: it was present in both the dysplastic and non-dysplastic tissue of the UC progressors. We then investigated the cellular proteome changes underlying oxidative stress, and found that up-regulation of TRAP1 could be induced by oxidative stress. These results suggest that UC cancer arises in the setting of oxidative stress. Such oxidative stress subsequently induces the cytoprotective protein TRAP1. TRAP1 in turn appears to promote cancer progression by preventing the oxidative-damaged epithelial cells from undergoing apoptosis.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5742. doi:1538-7445.AM2012-5742

Ulcerative colitis-associated colorectal cancer arises in a field of short telomeres, senescence, and inflammation

Inflammation plays a role in the progression to cancer and it is linked to the presence of senescent cells. Ulcerative colitis (UC) is a chronic inflammatory disease that predisposes to colorectal cancer. Tumorigenesis in this setting is associated with telomere shortening that can be observed in the nondysplastic epithelium of UC patients with high-grade dysplasia (HGD) or cancer (UC progressors). We hypothesized that a preneoplastic field of inflammation, telomere shortening, and senescence underlies tumor progression in UC progressors. Multiple biopsies of varying histologic grade were collected along the colon of nine UC progressors and analyzed for telomere length, DNA damage, senescence, p53, p16, and chronic and acute inflammation. Twenty biopsies from four UC nonprogressors and twenty-one biopsies from control individuals without UC were also analyzed. Short telomeres and increased DNA damage, senescence, and infiltrating leukocytes were observed in biopsies located less than 10 cm from HGD or cancer. Low-grade dysplasia (LGD) had the shortest telomeres along with the highest levels of senescence and infiltrating leukocytes, whereas HGD biopsies showed the opposite pattern. The expression of p16 and p53 was low in nondysplastic biopsies but progressively increased in LGD and HGD. In addition, high levels of infiltrating leukocytes were associated with telomere shortening, senescence, and reduced p53 expression. These results suggest that dysplasia arises in a preneoplastic field of chronic inflammation, which leads to telomere shortening, DNA damage, and senescence. Our findings argue that senescence acts as a tumor suppressor mechanism that is abrogated during the transition from LGD to HGD in UC.

Abstract 5072: Protein signatures associated with dysplasia of ulcerative colitis

Ulcerative colitis (UC) is an inflammatory bowel disease affecting approximately half a million patients in the United States. Patients with extensive UC of more than eight years duration have an increased risk of colorectal cancer, approximating 0.5-1% per year of colitis. There are major challenges with UC cancer surveillance. Unlike sporadic colon cancer, dysplasia or cancer in UC frequently occurs in benign-appearing colonic mucosa of UC patients without evidence of a polyp. Therefore, an objective molecular biomarker of dysplasia would aid the clinical management of cancer risk in UC patients. We apply a novel, highly sensitive quantitative proteomics approach combining with cutting-edge bioinformatics to develop protein signatures for detecting the neoplastic dysplasia presented in the normal-appearing (i.e., non-dysplastic) colon and rectum for prediction of cancer risk of UC patients. A list of dysregulated proteins potentially associated with colon cancer was identified using large-scale quantitative global protein profiling. Functional analysis was performed to explore the mechanisms that may underlie UC neoplastic progression. Mitochondrial proteins, cytoskeletal proteins, RAS superfamily, proteins relating to apoptosis and metabolism are the important protein groups or pathways differentially expressed in the non-dysplastic and dysplastic tissues of UC progressors, suggesting their importance in UC neoplastic progression. The resultant protein candidates have been ranked and are being rigorously validated using complementary methods, including immunohistochemistry and emerging technology of targeted quantitative proteomics. A molecular signature combining multiple proteins has displayed a statistically significant difference in distinguishing patients with dysplasia/cancer from patients without dysplasia/cancer. Protein biomarker candidates identified in this study may potentially be useful in predictive risk assessment and/or early diagnosis of inflammatory bowel disease associated colorectal cancer.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 5072. doi:10.1158/1538-7445.AM2011-5072

Array-based comparative genomic hybridization in ulcerative colitis neoplasia: single non-dysplastic biopsies distinguish progressors from non-progressors

Approximately 10% of ulcerative colitis patients develop colorectal neoplasia. At present, identification of this subset is markedly limited and necessitates lifelong colonoscopic surveillance for the entire ulcerative colitis population. Better risk markers are needed to focus surveillance onto the patients who are most likely to benefit. Using array-based comparative genomic hybridization, we analyzed single, non-dysplastic biopsies from three patient groups: ulcerative colitis progressors (n=9) with cancer or high-grade dysplasia at a mean distance of 18 cm from the analyzed site; ulcerative colitis non-progressors (n=8) without dysplasia during long-term surveillance; and non-ulcerative colitis normal controls (n=2). Genomic DNA from fresh colonic epithelium purified from stroma was hybridized to 287 (low-density) and 4342 (higher-density) feature bacterial artificial chromosome arrays. Sample-to-reference fluorescence ratios were calculated for individual chromosomal targets and globally across the genome. The low-density arrays yielded pronounced genomic gains and losses in 3 of 9 (33%) ulcerative colitis progressors but in none of the 10 control patients. Identical DNA samples analyzed on the higher-density arrays, using a combination of global and individual high variance assessments, distinguished all nine progressors from all 10 controls. These data confirm that genomic alterations in ulcerative colitis progressors are widespread, even involving single non-dysplastic biopsies that are far distant from neoplasia. They therefore show promise toward eliminating full colonoscopic surveillance with extensive biopsy sampling in the majority of ulcerative colitis patients.

Deletion at fragile sites is a common and early event in Barrett's esophagus

Barrett's esophagus (BE) is a premalignant intermediate to esophageal adenocarcinoma, which develops in the context of chronic inflammation and exposure to bile and acid. We asked whether there might be common genomic alterations that could be identified as potential clinical biomarker(s) for BE by whole genome profiling. We detected copy number alterations and/or loss of heterozygosity at 56 fragile sites in 20 patients with premalignant BE. Chromosomal fragile sites are particularly sensitive to DNA breaks and are frequent sites of rearrangement or loss in many human cancers. Seventy-eight percent of all genomic alterations detected by array-CGH were associated with fragile sites. Copy number losses in early BE were observed at particularly high frequency at FRA3B (81%), FRA9A/C (71.4%), FRA5E (52.4%), and FRA 4D (52.4%), and at lower frequencies in other fragile sites, including FRA1K (42.9%), FRAXC (42.9%), FRA 12B (33.3%), and FRA16D (33.3%). Due to the consistency of the region of copy number loss, we were able to verify these results by quantitative PCR, which detected the loss of FRA3B and FRA16D, in 83% and 40% of early molecular stage BE patients, respectively. Loss of heterozygosity in these cases was confirmed through pyrosequencing at FRA3B and FRA16D (75% and 70%, respectively). Deletion and genomic instability at FRA3B and other fragile sites could thus be a biomarker of genetic damage in BE patients and a potential biomarker of cancer risk.

Abstract 4562: Alteration of mitochondrial proteome in neoplastic progression of ulcerative colitis

Patients with extensive ulcerative colitis (UC) have an increased risk of colon cancer. Current colonoscopic surveillance of these patients is expensive, time consuming, and invasive. An objective biomarker of dysplasia would aid the clinical management of cancer risk in UC patients. The purpose of this study is to investigate alterations in mitochondrial proteome during UC neoplastic progression to: 1) better understand the underlying mechanisms of neoplastic progression in UC; and 2) employ this knowledge for improved, more cost effective surveillance for UC cancer. Stable isotope labeling and tandem mass spectrometry were used to identify differential mitochondrial proteins associated with UC neoplastic progression. We identified 23, 31 and 32 mitochondrial proteins dysregulated in the colonic epithelium of UC non-progressors (UC patients who do not progress to dysplasia), and the non-dysplastic and dysplastic epithelium of UC progressors (UC patients who have dysplasia/cancer), respectively by at least 1.5-fold change. Nine of the mitochondrial proteins displayed gradually increasing dysregulation from UC non-progressor mucosa to UC progressor non-dysplastic mucosa and finally the worst changes were present in the dysplasia itself. One of the dysregulated mitochondrial proteins, carbamoyl-phosphate synthase 1 (CPS1) was further studied by immunohistochemistry (IHC) analysis. The expression level of CPS1 was significantly higher in UC progressors (in both dysplastic N=9 and non-dysplastic biopsies N=10) than non-progressors (N=29, P&lt;0.003). If the IHC score of 1+ or higher was used as a cutoff, CPS1 could achieve 90% sensitivity and 59% specificity in distinguishing a rectal UC progressor non-dysplastic biopsy from a rectal UC non-progressor biopsy. To further evaluate the mechanism for mitochondrial protein changes in UC, a disease of chronic inflammation, we investigated protein oxidation and carbonylation of the mitochondria during UC neoplastic progression. Carbonyl-modified proteins in UC dysplastic biopsies were enriched using hydrazide-based chemistry and identified by proteomics analysis. We identified 19 carbonylated mitochondrial proteins in UC dysplasia. Several heat shock proteins were among these oxidized mitochondrial proteins. Oxidation of mitochondrial proteins can cause dysfunction of mitochondria, which may in turn contribute to neoplastic progression. In summary, we discovered that mitochondrial proteins are dysregulated in UC neoplastic progression and this is likely caused by chronic oxidation. The mitochondrial proteins become dysregulated early in tumorigenesis, with the changes present in non-dysplastic mucosa of patients with dysplasia. One of these proteins, CPS1, is significantly overexpressed in the normal appearing mucosa of UC progressors and may serve as a biomarker of dysplasia elsewhere in the colon.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4562.

Abstract 3203: Ulcerative colitis-associated colorectal cancer arises in a field of short telomeres, increased senescence, and inflammation

Introduction: Around 10% of patients with ulcerative colitis (UC) will develop colorectal cancer in their lifetime. The tumorigenic process involves progression from non-dysplastic colonic epithelium to dysplasia (indefinite, low grade (LGD) or high grade (HGD)), and cancer. We have previously demonstrated that the non-dysplastic epithelium from UC patients with HGD or cancer (UC progressors) harbors molecular abnormalities, but the extent of this field effect is unknown. Our goal is to characterize the field effect of telomere shortening, senescence, and inflammation in the colon of UC progressors in order to determine the role of these alterations in UC tumorigenesis and their potential as biomarkers of cancer risk.

Material and Methods: For 9 UC progressors an average of 7 biopsies (min 5, max 10) including HGD, LGD, and non-dysplastic normal appearing mucosa, were collected along the colon and analyzed for the following parameters: (1) telomere length: measured by Quantitative-PCR; (2) DNA damage: measured by immunofluorescence of γ-H2AX; (3) senescence: measured by immunofluorescence of Dec1; and (4) inflammation: measured by the classical pathological index of acute inflammation, the levels of lymphocytes in lamina propria, and the amount of lymphoid aggregates. In addition, we analyzed 5 biopsies collected along the colon from 4 UC non-progressors (patients without HGD or cancer) and 10 control biopsies from individuals without UC.

Results: Telomeres were significantly shorter in non-dysplastic biopsies of UC progressors compared to non-progressors and the shortening had a widespread field effect, as it was observed throughout the colon of UC progressors. However, telomere shortening was more pronounced in non-dysplastic biopsies located less than 10 cm from HGD or cancer. These biopsies also showed significantly higher levels of DNA damage, senescence, and lamina propria lymphocytes. Interestingly, LGD biopsies had the shortest telomeres and the highest levels of senescence and lamina propria lymphocytes, while HGD biopsies showed telomere lengthening and a significant decrease in senescence and lamina propria lymphocytes. In addition, high levels of lamina propria lymphocytes were associated with telomere shortening and senescence.

Conclusions: Our results indicate that there is a field effect of telomere shortening, DNA damage, senescence, and inflammation that is at least 10 cm in length, in the region where dysplasia and cancer arise. Telomeres lengthen and senescence is abrogated in the transition from LGD to HGD. The presence of telomere shortening in non-dysplastic epithelium along the colon of UC progressors suggests that it might have a potential value as a cancer risk biomarker.

Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 3203.

Ulcerative colitis is a disease of accelerated colon aging: evidence from telomere attrition and DNA damage

BACKGROUND & AIMS

Telomere shortening is implicated in cancer and aging and might link these 2 biologic events. We explored this hypothesis in ulcerative colitis (UC), a chronic inflammatory disease that predisposes to colorectal cancer and in which shorter telomeres have been associated with chromosomal instability and tumor progression.

METHODS

Telomere length was measured by quantitative polymerase chain reaction in colonocytes and leukocytes of 2 different sets of UC patients and compared with normal controls across a wide range of ages. For a subset of patients, telomere length was measured in epithelium and stroma of right and left colon biopsy specimens. A third set of biopsy specimens was analyzed for phosphorylation of histone H2AX (gammaH2AX), a DNA damage signal, by immunofluorescence and for telomere length by quantitative fluorescence in situ hybridization. Relationships between telomere length, gammaH2AX intensity, age, disease duration, and age of disease onset were explored.

RESULTS

Colonocyte telomeres shorten with age almost twice as rapidly in UC patients as in normal controls. This extensive shortening occurs within approximately 8 years of disease duration. Leukocyte telomeres are slightly shorter in UC patients than in controls, but telomeres of colon stromal cells are unaffected. gammaH2AX intensity is higher in colonocytes of UC patients than in controls and is not dependent on age or telomere length.

CONCLUSIONS

Colonocytes of UC patients show premature shortening of telomeres, which might explain the increased and earlier risk of cancer in this disease. Shorter leukocyte telomeres and increased gammaH2AX in colonocytes might reflect oxidative damage secondary to inflammation.

Increasing genomic instability during premalignant neoplastic progression revealed through high resolution array-CGH

Chromosomal instability is regarded as an underlying mechanism of neoplastic progression, integral to the clonal selection and evolution that leads to cancer. We evaluated chromosomal instability in premalignant Barrett's esophagus tissue using high resolution Affymetrix mapping 100K SNP arrays as patients progressed through three molecular stages of disease-CDKN2A(LOH) only, CDKN2A(LOH)/TP53(LOH), and CDKN2A(LOH)/TP53(LOH) with aneuploidy. Within individuals over time, we observed increases in both numbers and sizes of regions of LOH or copy number change. In the earliest CDKN2A(LOH) only samples, we detected few regions with both copy change and LOH, whereas copy loss and LOH were highly correlated in more advanced samples. These data indicate that genomic instability increases in severity and changes character during neoplastic progression. In addition, distinct patterns of clonal evolution could be discerned within a segment of Barrett's esophagus. Overall, this study illustrates that pre-malignant disease can be associated with extensive instability and clonal dynamics that evolve from an initial stage characterized by small recombination-based alterations to one with larger copy change events likely associated with mitotic instability.

A novel yeast mutant that is defective in regulation of the Anaphase-Promoting Complex by the spindle damage checkpoint

The accurate segregation of sister chromatids at the metaphase to anaphase transition in Saccharomyces cerevisiae is regulated by the activity of the anaphase-promoting complex or cyclosome (APC/C). In the event of spindle damage or monopolar spindle attachment, the spindle checkpoint is activated and inhibits APC/C activity towards the anaphase inhibitor Pds1p, resulting in a cell cycle arrest at metaphase. We have identified a novel allele of a gene for an APC/C subunit, cdc16-183, in S. cerevisiae. cdc16-183 mutants arrest at metaphase at 37 degrees C, and are supersensitive to the spindle-damaging agent nocodazole, which activates the spindle checkpoint, at lower temperatures. This supersensitivity to nocodazole cannot be explained by impairment of the spindle checkpoint pathway, as cells respond normally to spindle damage with a stable metaphase arrest and high levels of Pds1p. Despite showing metaphase arrest at G2/M at 37 degrees C, cdc16-183 mutants are able to perform tested G1 functions normally at this temperature. This is the first demonstration that a mutation in a core APC/C subunit can result in a MAD2-dependent arrest at the restrictive temperature. Our results suggest that the cdc16-183 mutant may have a novel APC/C defect(s) that mimics or activates the spindle checkpoint pathway.