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de Klaver W, de Wit M, Bolijn A, Tijssen M, Delis-van Diemen P, Lemmens M, Spaander MC, Dekker E, van Leerdam ME, Coupé VM, van Boxtel R, Clevers H, Carvalho B, Meijer GA. Polyketide synthase positive Escherichia coli one-time measurement in stool is not informative of colorectal cancer risk in a screening setting. J Pathol 2024; 263:217-225. [PMID: 38551073 DOI: 10.1002/path.6276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 12/21/2023] [Accepted: 02/22/2024] [Indexed: 05/12/2024]
Abstract
Environmental factors like the pathogenicity island polyketide synthase positive (pks+) Escherichia coli (E. coli) could have potential for risk stratification in colorectal cancer (CRC) screening. The association between pks+ E. coli measured in fecal immunochemical test (FIT) samples and the detection of advanced neoplasia (AN) at colonoscopy was investigated. Biobanked FIT samples were analyzed for both presence of E. coli and pks+ E. coli and correlated with colonoscopy findings; 5020 CRC screening participants were included. Controls were participants in which no relevant lesion was detected because of FIT-negative results (cut-off ≥15 μg Hb/g feces), a negative colonoscopy, or a colonoscopy during which only a nonadvanced polyp was detected. Cases were participants with AN [CRC, advanced adenoma (AA), or advanced serrated polyp (ASP)]. Existing DNA isolation and quantitative polymerase chain reaction (qPCR) procedures were used for the detection of E. coli and pks+ E. coli in stool. A total of 4542 (90.2%) individuals were E. coli positive, and 1322 (26.2%) were pks+ E. coli positive. The prevalence of E. coli in FIT samples from individuals with AN was 92.9% compared to 89.7% in FIT samples of controls (p = 0.010). The prevalence of pks+ E. coli in FIT samples from individuals with AN (28.6%) and controls (25.9%) was not significantly different (p = 0.13). The prevalences of pks+ E. coli in FIT samples from individuals with CRC, AA, or ASP were 29.6%, 28.3%, and 32.1%, respectively. In conclusion, the prevalence of pks+ E. coli in a screening population was 26.2% and did not differ significantly between individuals with AN and controls. These findings disqualify the straightforward option of using a snapshot measurement of pks+ E. coli in FIT samples as a stratification biomarker for CRC risk. © 2024 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Willemijn de Klaver
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, Location University of Amsterdam, Amsterdam, The Netherlands
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Meike de Wit
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Anne Bolijn
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marianne Tijssen
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Margriet Lemmens
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Manon Cw Spaander
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Evelien Dekker
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, Location University of Amsterdam, Amsterdam, The Netherlands
| | - Monique E van Leerdam
- Department of Gastrointestinal Oncology, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Veerle Mh Coupé
- Department of Epidemiology and Data Science, Amsterdam University Medical Centers, Location VU Medical Center, Amsterdam, The Netherlands
| | - Ruben van Boxtel
- Princess Máxima Center for pediatric oncology, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
| | - Hans Clevers
- Princess Máxima Center for pediatric oncology, Utrecht, The Netherlands
- Oncode Institute, Utrecht, The Netherlands
- University Medical Center Utrecht, Utrecht, The Netherlands
- Hubrecht Institute, Utrecht, the Netherlands
- Pharma, Research and Early Development (pRED) of F. Hoffmann-La Roche Ltd, Basel, Switzerland
| | - Beatriz Carvalho
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Gerrit A Meijer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
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2
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Wisse PHA, de Klaver W, van Wifferen F, van Maaren-Meijer FG, van Ingen HE, Meiqari L, Huitink I, Bierkens M, Lemmens M, Greuter MJE, van Leerdam ME, Spaander MCW, Dekker E, Coupé VMH, Carvalho B, de Wit M, Meijer GA. The multitarget faecal immunochemical test for improving stool-based colorectal cancer screening programmes: a Dutch population-based, paired-design, intervention study. Lancet Oncol 2024; 25:326-337. [PMID: 38346438 DOI: 10.1016/s1470-2045(23)00651-4] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2023] [Revised: 12/08/2023] [Accepted: 12/15/2023] [Indexed: 03/02/2024]
Abstract
BACKGROUND The faecal immunochemical test (FIT) is widely employed for colorectal cancer screening. However, its sensitivity for advanced precursor lesions remains suboptimal. The multitarget FIT (mtFIT), measuring haemoglobin, calprotectin, and serpin family F member 2, has demonstrated enhanced sensitivity for advanced neoplasia, especially advanced adenomas, at equal specificity to FIT. This study aimed to prospectively validate and investigate the clinical utlitity of mtFIT versus FIT in a setting of population-based colorectal cancer screening. METHODS Individuals aged 55-75 years and who were eligible for the Dutch national FIT-based colorectal cancer screening programme were invited to submit both a FIT and mtFIT sample collected from the same bowel movement. Positive FIT (47 μg/g haemoglobin cutoff) or mtFIT (based on decision-tree algorithm) led to a colonoscopy referral. The primary outcome was the relative detection rate of mtFIT versus FIT for all advanced neoplasia. Secondary outcomes were the relative detection rates of colorectal cancer, advanced adenoma, and advanced serrated polyps individually and the long-term effect of mtFIT-based versus FIT-based programmatic screening on colorectal cancer incidence, mortality, and cost, determined with microsimulation modelling. The study has been registered in ClinicalTrials.gov, NCT05314309, and is complete. FINDINGS Between March 25 and Dec 7, 2022, 35 786 individuals were invited to participate in the study, of whom 15 283 (42·7%) consented, and 13 187 (86·3%) of 15 283 provided both mtFIT and FIT samples with valid results. Of the 13 187 participants, 6637 (50·3%) were male and 6550 (49·7%) were female. mtFIT showed a 9·11% (95% CI 8·62-9·61) positivity rate and 2·27% (95% CI 2·02-2·54) detection rate for advanced neoplasia, compared with a positivity rate of 4·08% (3·75-4·43) and a detection rate of 1·21% (1·03-1·41) for FIT. Detection rates of mtFIT versus FIT were 0·20% (95% CI 0·13-0·29) versus 0·17% (0·11-0·27) for colorectal cancer; 1·64% (1·43-1·87) versus 0·86% (0·72-1·04) for advanced adenoma, and 0·43% (0·33-0·56) versus 0·17% (0·11-0·26) for advanced serrated polyps. Modelling demonstrated that mtFIT-based screening could reduce colorectal cancer incidence by 21% and associated mortality by 18% compared with the current Dutch colorectal cancer screening programme, at feasible costs. Furthermore, at equal positivity rates, mtFIT outperformed FIT in terms of diagnostic yield. At an equally low positivity rate, mtFIT-based screening was predicted to further decrease colorectal cancer incidence by 5% and associated mortality by 4% compared with FIT-based screening. INTERPRETATION The higher detection rate of mtFIT for advanced adenoma compared with FIT holds the potential to translate into additional and clinically meaningful long-term colorectal cancer incidence and associated mortality reductions in programmatic colorectal cancer screening. FUNDING Stand Up to Cancer, Dutch Cancer Society, Dutch Digestive Foundation, and Health~Holland.
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Affiliation(s)
- Pieter H A Wisse
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands; Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Willemijn de Klaver
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands; Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, Location University of Amsterdam, Amsterdam, Netherlands
| | - Francine van Wifferen
- Department of Epidemiology and Data Science, Amsterdam University Medical Centers, Location Vrije Universiteit, Amsterdam, Netherlands
| | | | - Huub E van Ingen
- Department of Clinical Chemistry, Star-shl, Rotterdam, Netherlands
| | - Lana Meiqari
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Iris Huitink
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Mariska Bierkens
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Margriet Lemmens
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Marjolein J E Greuter
- Department of Epidemiology and Data Science, Amsterdam University Medical Centers, Location Vrije Universiteit, Amsterdam, Netherlands
| | - Monique E van Leerdam
- Department of Gastro-intestinal Oncology, Netherlands Cancer Institute, Amsterdam, Netherlands; Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, Netherlands
| | - Manon C W Spaander
- Department of Gastroenterology and Hepatology, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Evelien Dekker
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, Location University of Amsterdam, Amsterdam, Netherlands
| | - Veerle M H Coupé
- Department of Epidemiology and Data Science, Amsterdam University Medical Centers, Location Vrije Universiteit, Amsterdam, Netherlands
| | - Beatriz Carvalho
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Meike de Wit
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands
| | - Gerrit A Meijer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, Netherlands.
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Jodal HC, Akwiwu EU, Lemmens M, Delis-van Diemen PM, Klotz D, Leon LG, Lakbir S, de Wit M, Fijneman RJ, van Leerdam ME, Dekker E, Spaander MC, Meijer GA, Løberg M, Coupé VM, Kalager M, Carvalho B. Risk Prediction of Metachronous Colorectal Cancer from Molecular Features of Adenomas: A Nested Case-Control Study. Cancer Res Commun 2023; 3:2292-2301. [PMID: 37921412 PMCID: PMC10642372 DOI: 10.1158/2767-9764.crc-23-0186] [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] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 09/22/2023] [Accepted: 10/31/2023] [Indexed: 11/04/2023]
Abstract
Current morphologic features defining advanced adenomas (size ≥10 mm, high-grade dysplasia or ≥25% villous component) cannot optimally distinguish individuals at high risk or low risk of metachronous colorectal cancer (me-CRC), which may result in suboptimal surveillance. Certain DNA copy-number alterations (CNAs) are associated with adenoma-to-carcinoma progression. We aimed to evaluate whether these molecular features can better predict an individual's risk of me-CRC than the morphologic advanced adenoma features.In this nested case-control study, 529 individuals with a single adenoma at first colonoscopy were selected from a Norwegian adenoma cohort. DNA copy-number profiles were determined, by low-coverage whole-genome sequencing. Prevalence of CNAs in advanced and non-advanced adenomas and its association (OR) with me-CRC was assessed. For the latter, cases (with me-CRC) were matched to controls (without me-CRC) on follow-up, age and sex.CNAs associated with adenoma-to-carcinoma progression were observed in 85/267 (32%) of advanced adenomas and in 27/262 (10%) of non-advanced adenomas. me-CRC was statistically significantly associated, also after adjustment for other variables, with age at baseline [OR, 1.14; 95% confidence interval CI), 1.03-1.26; P = 0.012], advanced adenomas (OR, 2.46; 95% CI, 1.50-4.01; P < 0.001) and with the presence of ≥3 DNA copy-number losses (OR, 1.90; 95% CI. 1.02-3.54; P = 0.043).Molecularly-defined high-risk adenomas were associated with me-CRC, but the association of advanced adenoma with me-CRC was stronger. SIGNIFICANCE Identifying new biomarkers may improve prediction of me-CRC for individuals with adenomas and optimize surveillance intervals to reduce risk of colorectal cancer and reduce oversurveillance of patients with low risk of colorectal cancer. Use of DNA CNAs alone does not improve prediction of me-CRC. Further research to improve risk classification is required.
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Affiliation(s)
- Henriette C. Jodal
- Clinical Effectiveness Research Group, University of Oslo, Oslo, Norway
- Clinical Effectiveness Research Group, Oslo University Hospital, Oslo, Norway
- Section of Oncology, Drammen Hospital, Vestre Viken Hospital Trust, Drammen, Norway
| | - Eddymurphy U. Akwiwu
- Department of Epidemiology and Data Science, Amsterdam Public Health Research Group, Amsterdam University Medical Centers, Location VU Medical Center, Amsterdam, the Netherlands
| | - Margriet Lemmens
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | | | - Dagmar Klotz
- Clinical Effectiveness Research Group, University of Oslo, Oslo, Norway
- Department of Pathology, Oslo University Hospital, Oslo, Norway
| | - Leticia G. Leon
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Soufyan Lakbir
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
- Bioinformatics Group, Department of Computer Science, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Meike de Wit
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Remond J.A. Fijneman
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Monique E. van Leerdam
- Department of Gastrointestinal Oncology, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, the Netherlands
| | - Evelien Dekker
- Department of Gastroenterology and Hepatology, Amsterdam University Medical Centers, Location Academic Medical Center, Amsterdam, the Netherlands
| | - Manon C.W. Spaander
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Gerrit A. Meijer
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Magnus Løberg
- Clinical Effectiveness Research Group, University of Oslo, Oslo, Norway
- Clinical Effectiveness Research Group, Oslo University Hospital, Oslo, Norway
| | - Veerle M.H. Coupé
- Department of Epidemiology and Data Science, Amsterdam Public Health Research Group, Amsterdam University Medical Centers, Location VU Medical Center, Amsterdam, the Netherlands
| | - Mette Kalager
- Clinical Effectiveness Research Group, University of Oslo, Oslo, Norway
- Clinical Effectiveness Research Group, Oslo University Hospital, Oslo, Norway
| | - Beatriz Carvalho
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands
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Jodal HC, Akwiwu EU, Leon LG, Lemmens M, Delis-van Diemen P, Klotz D, de Wit M, Fijneman R, van Leerdam M, Dekker E, Spaander MCW, Meijer GA, Bretthauer M, Løberg M, Coupé VMH, Kalager M, Carvalho B. Abstract A004: Molecular adenoma features to predict metachronous colorectal cancer risk: A nested-case control study. Cancer Res 2022. [DOI: 10.1158/1538-7445.crc22-a004] [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: 12/03/2022]
Abstract
Abstract
Introduction: In colorectal cancer (CRC) surveillance, adenoma characteristics such as size, number of adenomas, dysplasia, and villous components, are used as indicators for risk of developing metachronous cancer and guide the surveillance interval. The current risk groups (e.g., advanced adenomas) cannot optimally distinguish high risk from low risk, which may result in suboptimal surveillance strategies. Specific DNA copy number aberrations are associated with risk of colorectal adenoma-to-carcinoma progression, but these aberrations are present in only a subset of advanced adenomas. Therefore, we hypothesize that specific DNA copy number aberrations may better predict the risk of CRC than advanced adenoma. Aim: To evaluate whether a molecularly-defined high-risk adenoma is a better risk factor for CRC than the presently used advanced adenoma. Materials and methods: DNA copy number profiles were determined, by means of low-coverage whole genome sequencing, on a series of 529 adenomas, selected from a Norwegian adenoma cohort. We retrieved detailed information on adenoma characteristics and whether adenoma patients were subsequently diagnosed with CRC or not. By univariate and multivariate regression analysis we estimated the odds ratio for association between the development of CRC and baseline presence of advanced adenoma versus presence of a molecularly-defined high-risk adenoma, respectively. Results: Molecular high-risk features were observed in 85/267 (32%) of advanced adenomas and in 27/262 (10%) of non-advanced adenomas. The odds ratio for developing metachronous CRC was 3.58 (p=2.84E-8) and 1.90 (p=0.012), when an advanced adenoma or molecular high-risk adenoma was detected at the baseline colonoscopy, respectively. In the multivariate regression analysis only advanced adenoma was as a significant risk factor for CRC. Conclusion: Molecularly-defined high-risk adenomas are associated with an increased risk of CRC. However, the advanced adenoma is a stronger predictor for risk of CRC.
Citation Format: Henriette C. Jodal, Eddymurphy U. Akwiwu, Leticia G. Leon, Margriet Lemmens, Pien Delis-van Diemen, Dagmar Klotz, Meike de Wit, Remond Fijneman, Monique van Leerdam, Evelien Dekker, Manon C. W. Spaander, Gerrit A. Meijer, Michael Bretthauer, Magnus Løberg, Veerle M. H. Coupé, Mette Kalager, Beatriz Carvalho. Molecular adenoma features to predict metachronous colorectal cancer risk: A nested-case control study [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer; 2022 Oct 1-4; Portland, OR. Philadelphia (PA): AACR; Cancer Res 2022;82(23 Suppl_1):Abstract nr A004.
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Affiliation(s)
- Henriette C. Jodal
- 1Clinical Effectiveness Research Group, University of Oslo and Oslo University Hospital, Oslo, Norway,
| | | | | | | | | | - Dagmar Klotz
- 1Clinical Effectiveness Research Group, University of Oslo and Oslo University Hospital, Oslo, Norway,
| | - Meike de Wit
- 3Netherlands Cancer Institute, Amsterdam, Netherlands,
| | | | | | - Evelien Dekker
- 2Amsterdam University Medical Centers, Amsterdam, Netherlands,
| | | | | | - Michael Bretthauer
- 1Clinical Effectiveness Research Group, University of Oslo and Oslo University Hospital, Oslo, Norway,
| | - Magnus Løberg
- 1Clinical Effectiveness Research Group, University of Oslo and Oslo University Hospital, Oslo, Norway,
| | | | - Mette Kalager
- 1Clinical Effectiveness Research Group, University of Oslo and Oslo University Hospital, Oslo, Norway,
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Monteiro MN, Almeida-Marques C, de Wit M, Dusseldorp V, Bishop-Currey L, Piersma SR, Pham TV, Knol JC, Sadeghi H, Meijer G, Fijneman RJA, Hausser A, Bijnsdorp IV, Jimenez CR. Abstract CC03-01: Exosome pathway inhibition as therapeutic strategy in colorectal cancer. Mol Cancer Ther 2021. [DOI: 10.1158/1535-7163.targ-21-cc03-01] [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
Exosomes are small extracellular vesicles (~100 nm) that are secreted by all cells and participate in cellular communication. Tumor-derived exosomes play a role in cancer progression by affecting the tumor microenvironment and establishing the pro-metastatic niche. Cancer cells are reported to have an increased release of exosomes, in addition to modulating their cargo. Therefore, blocking exosome secretion by cancer cells could halt cancer progression and be a promising novel drug-target for therapy. Global insight into the functional protein players of this process is key for development of a successful therapeutic strategy. To identify novel drug targets, Mass Spectrometry (MS)-based proteomics was performed on a unique sample set collected from 22 patients, comprising multiple fractions (tissue lysate, soluble secretome and extracellular vesicles) of matched normal and colorectal cancer (CRC) tissues (n=18) and adenomas (n=4). Available CPTAC phospho-proteomic CRC dataset was used to identify phospho-proteins that regulate the potential drug targets. Network clustering was performed using ClusterOne and gene ontology using BinGO (cytoscape). CD63 was measured using confocal microscopy. Exosome release using Coomassie stained gels and TSG101 expression using Western blot. Gene Ontology revealed deregulated pathways in normal versus cancer comparison that were linked to vesicle trafficking. Mainly, the ESCRT-pathway of the exosome biogenesis machinery was down-regulated in cancer while alternative proteins related to endocytosis and exosome release were up-regulated. Targeted data mining to the exosome biogenesis pathway revealed 12 up-regulated proteins (FC<1.5, p<0.05) and 14 proteins with increased cellular phosphorylation levels (p<0.05). Three upstream kinases with increased overall activity in CRC context, assessed by the INKA algorithm, were selected for further functional analysis using drugs in clinical trials or FDA-approved. To this end, two CRC cell lines were treated at IC50-correspondent dose for 16h. All three drugs caused a decrease in released exosomes after kinase inhibition, as evaluated by Coomassie staining and TSG101 levels. Intracellular immunofluorescent staining of multivesicular bodies (MVBs) by CD63, revealed increased intensity after treatment. This increase in CD63 intensity suggests an intracellular accumulation of MVBs which indicates an inability of the cell to release the exosomes. We aim to further validate the mechanisms of action underlying the inhibition of kinase-mediated exosome production and release after treatment using (phospho-)proteomics. Furthermore, we will assess its effect on exosome-mediated migration/invasion and angiogenesis. In conclusion, we describe a unique clinical dataset to identify drug targets in the exosome-release pathway, which presents a novel therapeutic strategy against CRC.
Citation Format: Madalena N. Monteiro, Catarina Almeida-Marques, Meike de Wit, Valerie Dusseldorp, Logan Bishop-Currey, Sander R. Piersma, Thang V. Pham, Jaco C. Knol, Hanieh Sadeghi, Gerrit Meijer, Remond J. A. Fijneman, Angelika Hausser, Irene V. Bijnsdorp, Connie R. Jimenez. Exosome pathway inhibition as therapeutic strategy in colorectal cancer [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2021 Oct 7-10. Philadelphia (PA): AACR; Mol Cancer Ther 2021;20(12 Suppl):Abstract nr CC03-01.
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Affiliation(s)
| | | | - Meike de Wit
- 2The Netherlands Cancer Institute, Amsterdam, Netherlands,
| | | | | | | | - Thang V. Pham
- 1VU University Medical Center, Amsterdam, Netherlands,
| | - Jaco C. Knol
- 1VU University Medical Center, Amsterdam, Netherlands,
| | | | - Gerrit Meijer
- 2The Netherlands Cancer Institute, Amsterdam, Netherlands,
| | | | - Angelika Hausser
- 3Institute of Cell Biology and Immunology, University of Stuttgart, Stuttgart, Germany
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6
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de Klaver W, Wisse PHA, van Wifferen F, Bosch LJW, Jimenez CR, van der Hulst RWM, Fijneman RJA, Kuipers EJ, Greuter MJE, Carvalho B, Spaander MCW, Dekker E, Coupé VMH, de Wit M, Meijer GA. Clinical Validation of a Multitarget Fecal Immunochemical Test for Colorectal Cancer Screening : A Diagnostic Test Accuracy Study. Ann Intern Med 2021; 174:1224-1231. [PMID: 34280333 DOI: 10.7326/m20-8270] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/09/2022] Open
Abstract
BACKGROUND The fecal immunochemical test (FIT) is used in colorectal cancer (CRC) screening, yet it leaves room for improvement. OBJECTIVE To develop a multitarget FIT (mtFIT) with better diagnostic performance than FIT. DESIGN Diagnostic test accuracy study. SETTING Colonoscopy-controlled series. PARTICIPANTS Persons (n = 1284) from a screening (n = 1038) and referral (n = 246) population were classified by their most advanced lesion (CRC [n = 47], advanced adenoma [n = 135], advanced serrated polyp [n = 30], nonadvanced adenoma [n = 250], and nonadvanced serrated polyp [n = 53]), along with control participants (n = 769). MEASUREMENTS Antibody-based assays were developed and applied to leftover FIT material. Classification and regression tree (CART) analysis was applied to biomarker concentrations to identify the optimal combination for detecting advanced neoplasia. Performance of this combination, the mtFIT, was cross-validated using a leave-one-out approach and compared with FIT at equal specificity. RESULTS The CART analysis showed a combination of hemoglobin, calprotectin, and serpin family F member 2-the mtFIT-to have a cross-validated sensitivity for advanced neoplasia of 42.9% (95% CI, 36.2% to 49.9%) versus 37.3% (CI, 30.7% to 44.2%) for FIT (P = 0.025), with equal specificity of 96.6%. In particular, cross-validated sensitivity for advanced adenomas increased from 28.1% (CI, 20.8% to 36.5%) to 37.8% (CI, 29.6% to 46.5%) (P = 0.006). On the basis of these results, early health technology assessment indicated that mtFIT-based screening could be cost-effective compared with FIT. LIMITATION Study population is enriched with persons from a referral population. CONCLUSION Compared with FIT, the mtFIT showed better diagnostic accuracy in detecting advanced neoplasia because of an increased detection of advanced adenomas. Moreover, early health technology assessment indicated that these results provide a sound basis to pursue further development of mtFIT as a future test for population-based CRC screening. A prospective screening trial is in preparation. PRIMARY FUNDING SOURCE Stand Up to Cancer/Dutch Cancer Society, Dutch Digestive Foundation, and HealthHolland.
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Affiliation(s)
- Willemijn de Klaver
- Netherlands Cancer Institute and Amsterdam University Medical Centers, location Academic Medical Center, Amsterdam, the Netherlands (W.d.K.)
| | - Pieter H A Wisse
- Netherlands Cancer Institute, Amsterdam, and Erasmus MC University Medical Center, Rotterdam, the Netherlands (P.H.W.)
| | - Francine van Wifferen
- Amsterdam University Medical Centers, location VU University Medical Center, Amsterdam, the Netherlands (F.V., C.R.J., M.J.G., V.M.H.C.)
| | - Linda J W Bosch
- Netherlands Cancer Institute, Amsterdam, the Netherlands (L.J.B., R.J.F., B.C., M.d.W., G.A.M.)
| | - Connie R Jimenez
- Amsterdam University Medical Centers, location VU University Medical Center, Amsterdam, the Netherlands (F.V., C.R.J., M.J.G., V.M.H.C.)
| | | | - Remond J A Fijneman
- Netherlands Cancer Institute, Amsterdam, the Netherlands (L.J.B., R.J.F., B.C., M.d.W., G.A.M.)
| | - Ernst J Kuipers
- Erasmus MC University Medical Center, Rotterdam, the Netherlands (E.J.K., M.C.S.)
| | - Marjolein J E Greuter
- Amsterdam University Medical Centers, location VU University Medical Center, Amsterdam, the Netherlands (F.V., C.R.J., M.J.G., V.M.H.C.)
| | - Beatriz Carvalho
- Netherlands Cancer Institute, Amsterdam, the Netherlands (L.J.B., R.J.F., B.C., M.d.W., G.A.M.)
| | - Manon C W Spaander
- Erasmus MC University Medical Center, Rotterdam, the Netherlands (E.J.K., M.C.S.)
| | - Evelien Dekker
- Amsterdam University Medical Centers, location Academic Medical Center, Amsterdam, the Netherlands (E.D.)
| | - Veerle M H Coupé
- Amsterdam University Medical Centers, location VU University Medical Center, Amsterdam, the Netherlands (F.V., C.R.J., M.J.G., V.M.H.C.)
| | - Meike de Wit
- Netherlands Cancer Institute, Amsterdam, the Netherlands (L.J.B., R.J.F., B.C., M.d.W., G.A.M.)
| | - Gerrit A Meijer
- Netherlands Cancer Institute, Amsterdam, the Netherlands (L.J.B., R.J.F., B.C., M.d.W., G.A.M.)
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7
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Mathios D, Johansen JS, Cristiano S, Medina JE, Phallen J, Larsen KR, Bruhm DC, Niknafs N, Ferreira L, Adleff V, Chiao JY, Leal A, Noe M, White JR, Arun AS, Hruban C, Annapragada AV, Jensen SØ, Ørntoft MBW, Madsen AH, Carvalho B, de Wit M, Carey J, Dracopoli NC, Maddala T, Fang KC, Hartman AR, Forde PM, Anagnostou V, Brahmer JR, Fijneman RJA, Nielsen HJ, Meijer GA, Andersen CL, Mellemgaard A, Bojesen SE, Scharpf RB, Velculescu VE. Detection and characterization of lung cancer using cell-free DNA fragmentomes. Nat Commun 2021; 12:5060. [PMID: 34417454 PMCID: PMC8379179 DOI: 10.1038/s41467-021-24994-w] [Citation(s) in RCA: 141] [Impact Index Per Article: 47.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/12/2021] [Indexed: 12/12/2022] Open
Abstract
Non-invasive approaches for cell-free DNA (cfDNA) assessment provide an opportunity for cancer detection and intervention. Here, we use a machine learning model for detecting tumor-derived cfDNA through genome-wide analyses of cfDNA fragmentation in a prospective study of 365 individuals at risk for lung cancer. We validate the cancer detection model using an independent cohort of 385 non-cancer individuals and 46 lung cancer patients. Combining fragmentation features, clinical risk factors, and CEA levels, followed by CT imaging, detected 94% of patients with cancer across stages and subtypes, including 91% of stage I/II and 96% of stage III/IV, at 80% specificity. Genome-wide fragmentation profiles across ~13,000 ASCL1 transcription factor binding sites distinguished individuals with small cell lung cancer from those with non-small cell lung cancer with high accuracy (AUC = 0.98). A higher fragmentation score represented an independent prognostic indicator of survival. This approach provides a facile avenue for non-invasive detection of lung cancer. DNA from tumour cells can be detected in the blood of cancer patients. Here, the authors show that cell free DNA fragmentation patterns can identify lung cancer patients and when this information is further interrogated it can be used to predict lung cancer histological subtype.
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Affiliation(s)
- Dimitrios Mathios
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Stephen Cristiano
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jamie E Medina
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jillian Phallen
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Klaus R Larsen
- Department of Respiratory Medicine, Infiltrate Unit, Bispebjerg Hospital, Copenhagen, Denmark
| | - Daniel C Bruhm
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Noushin Niknafs
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Leonardo Ferreira
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Vilmos Adleff
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Jia Yuee Chiao
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alessandro Leal
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michael Noe
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - James R White
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Adith S Arun
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Carolyn Hruban
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Akshaya V Annapragada
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Sarah Østrup Jensen
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | | | | | - Beatriz Carvalho
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Meike de Wit
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | | | | | | | | | - Patrick M Forde
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Valsamo Anagnostou
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Julie R Brahmer
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Remond J A Fijneman
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Hans Jørgen Nielsen
- Department of Surgical Gastroenterology 360, Hvidovre Hospital, Hvidovre, Denmark
| | - Gerrit A Meijer
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | | | - Anders Mellemgaard
- Department of Oncology, Herlev and Gentofte Hospital, Copenhagen, Denmark
| | - Stig E Bojesen
- Department of Clinical Biochemistry, Herlev and Gentofte Hospital, Copenhagen, Denmark
| | - Robert B Scharpf
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA. .,Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Victor E Velculescu
- The Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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8
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Vaes N, Schonkeren SL, Rademakers G, Holland AM, Koch A, Gijbels MJ, Keulers TG, de Wit M, Moonen L, Van der Meer JRM, van den Boezem E, Wolfs TGAM, Threadgill DW, Demmers J, Fijneman RJA, Jimenez CR, Vanden Berghe P, Smits KM, Rouschop KMA, Boesmans W, Hofstra RMW, Melotte V. Loss of enteric neuronal Ndrg4 promotes colorectal cancer via increased release of Nid1 and Fbln2. EMBO Rep 2021; 22:e51913. [PMID: 33890711 PMCID: PMC8183412 DOI: 10.15252/embr.202051913] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 03/09/2021] [Accepted: 03/11/2021] [Indexed: 12/28/2022] Open
Abstract
The N-Myc Downstream-Regulated Gene 4 (NDRG4), a prominent biomarker for colorectal cancer (CRC), is specifically expressed by enteric neurons. Considering that nerves are important members of the tumor microenvironment, we here establish different Ndrg4 knockout (Ndrg4-/- ) CRC models and an indirect co-culture of primary enteric nervous system (ENS) cells and intestinal organoids to identify whether the ENS, via NDRG4, affects intestinal tumorigenesis. Linking immunostainings and gastrointestinal motility (GI) assays, we show that the absence of Ndrg4 does not trigger any functional or morphological GI abnormalities. However, combining in vivo, in vitro, and quantitative proteomics data, we uncover that Ndrg4 knockdown is associated with enlarged intestinal adenoma development and that organoid growth is boosted by the Ndrg4-/- ENS cell secretome, which is enriched for Nidogen-1 (Nid1) and Fibulin-2 (Fbln2). Moreover, NID1 and FBLN2 are expressed in enteric neurons, enhance migration capacities of CRC cells, and are enriched in human CRC secretomes. Hence, we provide evidence that the ENS, via loss of Ndrg4, is involved in colorectal pathogenesis and that ENS-derived Nidogen-1 and Fibulin-2 enhance colorectal carcinogenesis.
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Affiliation(s)
- Nathalie Vaes
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Simone L Schonkeren
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Glenn Rademakers
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Amy M Holland
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Alexander Koch
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Marion J Gijbels
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
- Department of Molecular GeneticsCardiovascular Research Institute Maastricht (CARIM)MaastrichtThe Netherlands
- Department of Medical BiochemistryAcademic Medical CenterAmsterdamThe Netherlands
| | - Tom G Keulers
- Department of RadiotherapyGROW‐School for Oncology and Developmental Biology and Comprehensive Cancer Center Maastricht MUMC+Maastricht UniversityMaastrichtThe Netherlands
| | - Meike de Wit
- Department of Medical Oncology and Oncoproteomics LaboratoryCancer Center AmsterdamVrije Universiteit AmsterdamAmsterdam UMCAmsterdamThe Netherlands
- Department of PathologyNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Laura Moonen
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Jaleesa R M Van der Meer
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Edith van den Boezem
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Tim G A M Wolfs
- Department of PediatricsGROW‐School for Oncology and Developmental BiologyMaastricht UniversityMaastrichtThe Netherlands
| | - David W Threadgill
- Department of Molecular and Cellular MedicineTexas A&M University Health Science CenterCollege StationTXUSA
- Department of Biochemistry and BiophysicsTexas A&M UniversityCollege StationTXUSA
| | - Jeroen Demmers
- Proteomics CenterErasmus University Medical CenterRotterdamThe Netherlands
| | | | - Connie R Jimenez
- Department of Medical Oncology and Oncoproteomics LaboratoryCancer Center AmsterdamVrije Universiteit AmsterdamAmsterdam UMCAmsterdamThe Netherlands
| | - Pieter Vanden Berghe
- Laboratory for Enteric Neuroscience (LENS) and Translational Research Center for Gastrointestinal Disorders (TARGID)Department of Chronic Diseases, Metabolism and AgeingKU LeuvenLeuvenBelgium
| | - Kim M Smits
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
| | - Kasper M A Rouschop
- Department of RadiotherapyGROW‐School for Oncology and Developmental Biology and Comprehensive Cancer Center Maastricht MUMC+Maastricht UniversityMaastrichtThe Netherlands
| | - Werend Boesmans
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
- Biomedical Research Institute (BIOMED)Hasselt UniversityHasseltBelgium
| | - Robert M W Hofstra
- Department of Clinical GeneticsErasmus University Medical CenterRotterdamThe Netherlands
| | - Veerle Melotte
- Department of PathologyGROW–School for Oncology and Developmental BiologyMaastricht University Medical CenterMaastrichtThe Netherlands
- Department of Clinical GeneticsErasmus University Medical CenterRotterdamThe Netherlands
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9
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Greuter MJ, Carvalho B, Wit MD, Dekker E, Spaander MC, Meijer GA, Engeland MV, Coupé VM. Can a biomarker triage test reduce colonoscopy burden in fecal immunochemical test screening? J Comp Eff Res 2020; 9:563-571. [PMID: 32462913 DOI: 10.2217/cer-2019-0130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Aim: To assess the potential of biomarker triage testing (BM-TT) in the Dutch colorectal cancer (CRC) screening program. Materials & methods: Using the Adenoma and Serrated pathway to Colorectal CAncer model, we simulated fecal immunochemical test (FIT)47-screening and various FIT plus BM-TT screening scenarios in which only individuals with both a positive FIT and BM-TT are referred to colonoscopy. Results: Adding a low polyp sensitivity BM-TT to FIT-screening reduced colonoscopy burden (89-100%) while increasing CRC mortality (27-41%) compared with FIT47-screening only. The FIT plus high polyp sensitivity BM-TT scenarios also decreased colonoscopy burden (71-89%) while hardly affecting CRC mortality (FIT47 0-4% increase, FIT15 2-7% decrease). Conclusion: Adding a BM-TT to FIT-screening considerably reduces colonoscopy burden, but could also decrease screening effectiveness. Combining FIT15 with a high polyp sensitivity BM-TT seems most promising.
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Affiliation(s)
- Marjolein Je Greuter
- Department of Epidemiology & Biostatistics, Decision Modeling Center, Amsterdam UMC - Vrije Universiteit Amsterdam, The Netherlands
| | - Beatriz Carvalho
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Meike de Wit
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Evelien Dekker
- Department of Gastroenterology, Amsterdam UMC - Academic Medical Center, Amsterdam, The Netherlands
| | - Manon Cw Spaander
- Department of Gastroenterology & Hepatology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Gerrit A Meijer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Manon van Engeland
- Department of Pathology, GROW - School for Oncology & Developmental Biology, Maastricht, The Netherlands
| | - Veerle Mh Coupé
- Department of Epidemiology & Biostatistics, Decision Modeling Center, Amsterdam UMC - Vrije Universiteit Amsterdam, The Netherlands
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10
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Komor MA, Bosch LJ, Coupé VM, Rausch C, Pham TV, Piersma SR, Mongera S, Mulder CJ, Dekker E, Kuipers EJ, van de Wiel MA, Carvalho B, Fijneman RJ, Jimenez CR, Meijer GA, de Wit M. Proteins in stool as biomarkers for non-invasive detection of colorectal adenomas with high risk of progression. J Pathol 2020; 250:288-298. [PMID: 31784980 PMCID: PMC7065084 DOI: 10.1002/path.5369] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 10/07/2019] [Accepted: 11/28/2019] [Indexed: 12/15/2022]
Abstract
Screening to detect colorectal cancer (CRC) in an early or premalignant state is an effective method to reduce CRC mortality rates. Current stool-based screening tests, e.g. fecal immunochemical test (FIT), have a suboptimal sensitivity for colorectal adenomas and difficulty distinguishing adenomas at high risk of progressing to cancer from those at lower risk. We aimed to identify stool protein biomarker panels that can be used for the early detection of high-risk adenomas and CRC. Proteomics data (LC-MS/MS) were collected on stool samples from adenoma (n = 71) and CRC patients (n = 81) as well as controls (n = 129). Colorectal adenoma tissue samples were characterized by low-coverage whole-genome sequencing to determine their risk of progression based on specific DNA copy number changes. Proteomics data were used for logistic regression modeling to establish protein biomarker panels. In total, 15 of the adenomas (15.8%) were defined as high risk of progressing to cancer. A protein panel, consisting of haptoglobin (Hp), LAMP1, SYNE2, and ANXA6, was identified for the detection of high-risk adenomas (sensitivity of 53% at specificity of 95%). Two panels, one consisting of Hp and LRG1 and one of Hp, LRG1, RBP4, and FN1, were identified for high-risk adenomas and CRCs detection (sensitivity of 66% and 62%, respectively, at specificity of 95%). Validation of Hp as a biomarker for high-risk adenomas and CRCs was performed using an antibody-based assay in FIT samples from a subset of individuals from the discovery series (n = 158) and an independent validation series (n = 795). Hp protein was significantly more abundant in high-risk adenoma FIT samples compared to controls in the discovery (p = 0.036) and the validation series (p = 9e-5). We conclude that Hp, LAMP1, SYNE2, LRG1, RBP4, FN1, and ANXA6 may be of value as stool biomarkers for early detection of high-risk adenomas and CRCs. © 2019 Authors. Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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Affiliation(s)
- Malgorzata A Komor
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.,Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands
| | - Linda Jw Bosch
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Veerle Mh Coupé
- Department of Epidemiology and Biostatistics, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands
| | - Christian Rausch
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Thang V Pham
- Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands
| | - Sander R Piersma
- Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands
| | - Sandra Mongera
- Department of Pathology, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands
| | - Chris Jj Mulder
- Department of Gastroenterology and Hepatology, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands
| | - Evelien Dekker
- Department of Gastroenterology and Hepatology, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Ernst J Kuipers
- Department of Gastroenterology and Hepatology, Erasmus MC University Medical Center, Rotterdam, The Netherlands
| | - Mark A van de Wiel
- Department of Epidemiology and Biostatistics, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands
| | - Beatriz Carvalho
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Remond Ja Fijneman
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Connie R Jimenez
- Department of Medical Oncology, Amsterdam UMC, VU University Medical Center, Amsterdam, The Netherlands
| | - Gerrit A Meijer
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Meike de Wit
- Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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11
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Komor MA, de Wit M, van den Berg J, Martens de Kemp SR, Delis-van Diemen PM, Bolijn AS, Tijssen M, Schelfhorst T, Piersma SR, Chiasserini D, Sanders J, Rausch C, Hoogstrate Y, Stubbs AP, de Jong M, Jenster G, Carvalho B, Meijer GA, Jimenez CR, Fijneman RJA. Molecular characterization of colorectal adenomas reveals POFUT1 as a candidate driver of tumor progression. Int J Cancer 2019; 146:1979-1992. [PMID: 31411736 PMCID: PMC7027554 DOI: 10.1002/ijc.32627] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 07/11/2019] [Indexed: 12/11/2022]
Abstract
Removal of colorectal adenomas is an effective strategy to reduce colorectal cancer (CRC) mortality rates. However, as only a minority of adenomas progress to cancer, such strategies may lead to overtreatment. The present study aimed to characterize adenomas by in‐depth molecular profiling, to obtain insights into altered biology associated with the colorectal adenoma‐to‐carcinoma progression. We obtained low‐coverage whole genome sequencing, RNA sequencing and tandem mass spectrometry data for 30 CRCs, 30 adenomas and 18 normal adjacent colon samples. These data were used for DNA copy number aberrations profiling, differential expression, gene set enrichment and gene‐dosage effect analysis. Protein expression was independently validated by immunohistochemistry on tissue microarrays and in patient‐derived colorectal adenoma organoids. Stroma percentage was determined by digital image analysis of tissue sections. Twenty‐four out of 30 adenomas could be unambiguously classified as high risk (n = 9) or low risk (n = 15) of progressing to cancer, based on DNA copy number profiles. Biological processes more prevalent in high‐risk than low‐risk adenomas were related to proliferation, tumor microenvironment and Notch, Wnt, PI3K/AKT/mTOR and Hedgehog signaling, while metabolic processes and protein secretion were enriched in low‐risk adenomas. DNA copy number driven gene‐dosage effect in high‐risk adenomas and cancers was observed for POFUT1, RPRD1B and EIF6. Increased POFUT1 expression in high‐risk adenomas was validated in tissue samples and organoids. High POFUT1 expression was also associated with Notch signaling enrichment and with decreased goblet cells differentiation. In‐depth molecular characterization of colorectal adenomas revealed POFUT1 and Notch signaling as potential drivers of tumor progression. What's new? Removal of colorectal adenomas is an effective strategy to reduce colorectal cancer (CRC) mortality rates. However, as only a minority of adenomas progress to cancer, such strategies may lead to overtreatment. While high‐risk adenomas, defined by specific DNA copy number aberrations, have an increased risk of progression, the mechanisms underlying colorectal adenoma‐to‐carcinoma progression remain unclear. This molecular characterization of colorectal adenomas, CRCs, and normal adjacent colon samples demonstrates that biological processes inherent to CRC are already more active in high‐risk adenomas compared to low‐risk adenomas. Moreover, the findings highlight POFUT1 and Notch signaling as potential drivers of colorectal tumor development.
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Affiliation(s)
- Malgorzata A Komor
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncoproteomics Laboratory, Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Amsterdam, The Netherlands
| | - Meike de Wit
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Jose van den Berg
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Sanne R Martens de Kemp
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands.,Oncoproteomics Laboratory, Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Amsterdam, The Netherlands
| | | | - Anne S Bolijn
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Marianne Tijssen
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Tim Schelfhorst
- Oncoproteomics Laboratory, Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Amsterdam, The Netherlands
| | - Sander R Piersma
- Oncoproteomics Laboratory, Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Amsterdam, The Netherlands
| | - Davide Chiasserini
- Oncoproteomics Laboratory, Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Amsterdam, The Netherlands
| | - Joyce Sanders
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Christian Rausch
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Youri Hoogstrate
- Department of Urology, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Andrew P Stubbs
- Department of Bioinformatics, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Guido Jenster
- Department of Urology, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Beatriz Carvalho
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Gerrit A Meijer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Connie R Jimenez
- Oncoproteomics Laboratory, Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Amsterdam, The Netherlands
| | - Remond J A Fijneman
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | -
- See Appendix for consortium members
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12
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Bosch LJW, de Wit M, Pham TV, Coupé VMH, Hiemstra AC, Piersma SR, Oudgenoeg G, Scheffer GL, Mongera S, Sive Droste JT, Oort FA, van Turenhout ST, Larbi IB, Louwagie J, van Criekinge W, van der Hulst RWM, Mulder CJJ, Carvalho B, Fijneman RJA, Jimenez CR, Meijer GA. Novel Stool-Based Protein Biomarkers for Improved Colorectal Cancer Screening: A Case-Control Study. Ann Intern Med 2017; 167:855-866. [PMID: 29159365 DOI: 10.7326/m17-1068] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The fecal immunochemical test (FIT) for detecting hemoglobin is used widely for noninvasive colorectal cancer (CRC) screening, but its sensitivity leaves room for improvement. OBJECTIVE To identify novel protein biomarkers in stool that outperform or complement hemoglobin in detecting CRC and advanced adenomas. DESIGN Case-control study. SETTING Colonoscopy-controlled referral population from several centers. PARTICIPANTS 315 stool samples from one series of 12 patients with CRC and 10 persons without colorectal neoplasia (control samples) and a second series of 81 patients with CRC, 40 with advanced adenomas, and 43 with nonadvanced adenomas, as well as 129 persons without colorectal neoplasia (control samples); 72 FIT samples from a third independent series of 14 patients with CRC, 16 with advanced adenomas, and 18 with nonadvanced adenomas, as well as 24 persons without colorectal neoplasia (control samples). MEASUREMENTS Stool samples were analyzed by mass spectrometry. Classification and regression tree (CART) analysis and logistic regression analyses were performed to identify protein combinations that differentiated CRC or advanced adenoma from control samples. Antibody-based assays for 4 selected proteins were done on FIT samples. RESULTS In total, 834 human proteins were identified, 29 of which were statistically significantly enriched in CRC versus control stool samples in both series. Combinations of 4 proteins reached sensitivities of 80% and 45% for detecting CRC and advanced adenomas, respectively, at 95% specificity, which was higher than that of hemoglobin alone (P < 0.001 and P = 0.003, respectively). Selected proteins could be measured in small sample volumes used in FIT-based screening programs and discriminated between CRC and control samples (P < 0.001). LIMITATION Lack of availability of antibodies prohibited validation of the top protein combinations in FIT samples. CONCLUSION Mass spectrometry of stool samples identified novel candidate protein biomarkers for CRC screening. Several protein combinations outperformed hemoglobin in discriminating CRC or advanced adenoma from control samples. Proof of concept that such proteins can be detected with antibody-based assays in small sample volumes indicates the potential of these biomarkers to be applied in population screening. PRIMARY FUNDING SOURCE Center for Translational Molecular Medicine, International Translational Cancer Research Dream Team, Stand Up to Cancer (American Association for Cancer Research and the Dutch Cancer Society), Dutch Digestive Foundation, and VU University Medical Center.
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Affiliation(s)
- Linda J W Bosch
- From Netherlands Cancer Institute, Amsterdam; VU University Medical Center, Amsterdam; MDxHealth, Herstal, and Ghent University, Ghent, Belgium; and Kennemer Gasthuis, Haarlem, the Netherlands
| | - Meike de Wit
- From Netherlands Cancer Institute, Amsterdam; VU University Medical Center, Amsterdam; MDxHealth, Herstal, and Ghent University, Ghent, Belgium; and Kennemer Gasthuis, Haarlem, the Netherlands
| | - Thang V Pham
- From Netherlands Cancer Institute, Amsterdam; VU University Medical Center, Amsterdam; MDxHealth, Herstal, and Ghent University, Ghent, Belgium; and Kennemer Gasthuis, Haarlem, the Netherlands
| | - Veerle M H Coupé
- From Netherlands Cancer Institute, Amsterdam; VU University Medical Center, Amsterdam; MDxHealth, Herstal, and Ghent University, Ghent, Belgium; and Kennemer Gasthuis, Haarlem, the Netherlands
| | - Annemieke C Hiemstra
- From Netherlands Cancer Institute, Amsterdam; VU University Medical Center, Amsterdam; MDxHealth, Herstal, and Ghent University, Ghent, Belgium; and Kennemer Gasthuis, Haarlem, the Netherlands
| | - Sander R Piersma
- From Netherlands Cancer Institute, Amsterdam; VU University Medical Center, Amsterdam; MDxHealth, Herstal, and Ghent University, Ghent, Belgium; and Kennemer Gasthuis, Haarlem, the Netherlands
| | - Gideon Oudgenoeg
- From Netherlands Cancer Institute, Amsterdam; VU University Medical Center, Amsterdam; MDxHealth, Herstal, and Ghent University, Ghent, Belgium; and Kennemer Gasthuis, Haarlem, the Netherlands
| | - George L Scheffer
- From Netherlands Cancer Institute, Amsterdam; VU University Medical Center, Amsterdam; MDxHealth, Herstal, and Ghent University, Ghent, Belgium; and Kennemer Gasthuis, Haarlem, the Netherlands
| | - Sandra Mongera
- From Netherlands Cancer Institute, Amsterdam; VU University Medical Center, Amsterdam; MDxHealth, Herstal, and Ghent University, Ghent, Belgium; and Kennemer Gasthuis, Haarlem, the Netherlands
| | - Jochim Terhaar Sive Droste
- From Netherlands Cancer Institute, Amsterdam; VU University Medical Center, Amsterdam; MDxHealth, Herstal, and Ghent University, Ghent, Belgium; and Kennemer Gasthuis, Haarlem, the Netherlands
| | - Frank A Oort
- From Netherlands Cancer Institute, Amsterdam; VU University Medical Center, Amsterdam; MDxHealth, Herstal, and Ghent University, Ghent, Belgium; and Kennemer Gasthuis, Haarlem, the Netherlands
| | - Sietze T van Turenhout
- From Netherlands Cancer Institute, Amsterdam; VU University Medical Center, Amsterdam; MDxHealth, Herstal, and Ghent University, Ghent, Belgium; and Kennemer Gasthuis, Haarlem, the Netherlands
| | - Ilhame Ben Larbi
- From Netherlands Cancer Institute, Amsterdam; VU University Medical Center, Amsterdam; MDxHealth, Herstal, and Ghent University, Ghent, Belgium; and Kennemer Gasthuis, Haarlem, the Netherlands
| | - Joost Louwagie
- From Netherlands Cancer Institute, Amsterdam; VU University Medical Center, Amsterdam; MDxHealth, Herstal, and Ghent University, Ghent, Belgium; and Kennemer Gasthuis, Haarlem, the Netherlands
| | - Wim van Criekinge
- From Netherlands Cancer Institute, Amsterdam; VU University Medical Center, Amsterdam; MDxHealth, Herstal, and Ghent University, Ghent, Belgium; and Kennemer Gasthuis, Haarlem, the Netherlands
| | - Rene W M van der Hulst
- From Netherlands Cancer Institute, Amsterdam; VU University Medical Center, Amsterdam; MDxHealth, Herstal, and Ghent University, Ghent, Belgium; and Kennemer Gasthuis, Haarlem, the Netherlands
| | - Chris J J Mulder
- From Netherlands Cancer Institute, Amsterdam; VU University Medical Center, Amsterdam; MDxHealth, Herstal, and Ghent University, Ghent, Belgium; and Kennemer Gasthuis, Haarlem, the Netherlands
| | - Beatriz Carvalho
- From Netherlands Cancer Institute, Amsterdam; VU University Medical Center, Amsterdam; MDxHealth, Herstal, and Ghent University, Ghent, Belgium; and Kennemer Gasthuis, Haarlem, the Netherlands
| | - Remond J A Fijneman
- From Netherlands Cancer Institute, Amsterdam; VU University Medical Center, Amsterdam; MDxHealth, Herstal, and Ghent University, Ghent, Belgium; and Kennemer Gasthuis, Haarlem, the Netherlands
| | - Connie R Jimenez
- From Netherlands Cancer Institute, Amsterdam; VU University Medical Center, Amsterdam; MDxHealth, Herstal, and Ghent University, Ghent, Belgium; and Kennemer Gasthuis, Haarlem, the Netherlands
| | - Gerrit A Meijer
- From Netherlands Cancer Institute, Amsterdam; VU University Medical Center, Amsterdam; MDxHealth, Herstal, and Ghent University, Ghent, Belgium; and Kennemer Gasthuis, Haarlem, the Netherlands
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13
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Komor MA, Pham TV, Piersma SR, Bolijn AS, Schelfhorst T, Diemen PMDV, Tijssen M, Hiemstra AC, Wit MD, Carvalho B, Meijer GA, Jimenez CR, Fijneman RJ. Abstract 1559: Proteogenomic analysis of alternative splicing in colorectal adenoma-to-carcinoma progression. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-1559] [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
Early diagnosis of colorectal cancer (CRC) and identification of its precursor lesions (adenomas) is crucial in reducing CRC mortality rates. The fecal immunochemical test (FIT) is a non-invasive CRC screening test that detects human protein hemoglobin. Although FIT is beneficial in its current form with a sensitivity of ~65% for detection of CRC and ~27% for adenomas, its performance is still suboptimal and needs to be further improved. Adenoma-to-carcinoma progression is accompanied by alternative splicing, which results in expression of tumor-specific protein variants. These may yield novel biomarkers suitable for improving detection of progressive adenomas and CRCs.
Aim
We aim to identify novel biomarkers to improve early detection of CRC.
Materials and methods
RNA was isolated from 3D organoid cultures derived from 5 adenomas and 4 CRC tissues. RNA and proteins were isolated from 18 healthy human colon tissues, 30 adenomas and 30 CRCs. Samples were analyzed by RNA sequencing (Illumina) and in-depth tandem mass spectrometry proteomics (QExactive). For both organoid- and tissue-datasets differential splicing analysis was performed on RNA level to enrich the sequence database, against which mass spectra were searched, with predicted protein isoforms.
Results
Comparative splicing analysis between CRC and adenoma organoids revealed ~90 differentially spliced genes, yielding candidate biomarkers from epithelial origin. In the tissues, differential splicing analysis between CRCs and controls and between CRCs and adenomas identified over 1000 of splice variants. These include known alternatively spliced genes involved in cancer such as CD44 and VEGFA and a number of candidates overlapping with the isoforms derived from the organoids. Proteomics analysis revealed that approximately 150 of the splice variants were expressed on protein level.
Conclusion and Discussion
We have confirmed that adenoma-to-carcinoma progression is accompanied by aberrant splicing. Analysis of the organoid cultures allowed us to identify gene isoforms from (neoplastic) epithelial origin. Tissue analysis yielded tumor-specific splice variants that represent novel protein candidate biomarkers for early detection of CRC. The diagnostic performance of these splice variant proteins will be validated in series of stool and FIT samples.
Citation Format: Malgorzata A. Komor, Thang V. Pham, Sander R. Piersma, Anne S. Bolijn, Tim Schelfhorst, Pien M. Delis-van Diemen, Marianne Tijssen, Annemieke C. Hiemstra, Meike de Wit, Beatriz Carvalho, Gerrit A. Meijer, Connie R. Jimenez, Remond J. Fijneman. Proteogenomic analysis of alternative splicing in colorectal adenoma-to-carcinoma progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1559. doi:10.1158/1538-7445.AM2017-1559
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Affiliation(s)
| | - Thang V. Pham
- 2VU University Medical Center, Amsterdam, Netherlands
| | | | | | | | | | | | | | - Meike de Wit
- 1Netherlands Cancer Insitute, Amsterdam, Netherlands
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14
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de Wit M, Carvalho B, Delis-van Diemen PM, van Alphen C, Beliën JAM, Meijer GA, Fijneman RJA. Lumican and versican protein expression are associated with colorectal adenoma-to-carcinoma progression. PLoS One 2017; 12:e0174768. [PMID: 28481899 PMCID: PMC5421768 DOI: 10.1371/journal.pone.0174768] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 03/15/2017] [Indexed: 11/22/2022] Open
Abstract
Background One prominent event associated with colorectal adenoma-to-carcinoma progression is genomic instability. Approximately 85% of colorectal cancer cases exhibit chromosomal instability characterized by accumulation of chromosome copy number aberrations (CNAs). Adenomas with gain of chromosome 8q, 13q, and/or 20q are at high risk of progression to cancer. Tumor progression is also associated with expansion of the extracellular matrix (ECM) and the activation of non-malignant cells within the tumor stroma. The glycoproteins versican and lumican are overexpressed at the mRNA level in colon carcinomas compared to adenomas, and are associated with the formation of tumor stroma. Purpose The aim of this study was to characterize versican and lumican protein expression in tumor progression and investigate their association with CNAs commonly associated with adenoma-to-carcinoma progression. Methods Tissue microarrays were constructed with colon adenomas and carcinomas that were characterized for MSI-status and DNA copy number gains of chromosomes 8q, 13q and 20q. Sections were immunohistochemically stained for lumican and versican. Protein expression levels were evaluated using digitized slides, and scores were finally dichotomized into a positive or negative score per sample. Results Lumican and versican expression were both observed in neoplastic cells and in the tumor stroma of colon adenomas and carcinomas. Lumican expression was more frequently present in epithelial cells of carcinomas than adenomas (49% versus 18%; P = 0.0001) and in high-risk adenomas and carcinomas combined compared to low-risk adenomas (43% versus 16%; P = 0.005). Versican staining in the tumor stroma was more often present in high-risk adenomas combined with carcinomas compared to low-risk adenomas (57% versus 36%; P = 0.03) and was associated with the presence of gain of 13q (71% versus 44%; P = 0.04). Conclusion Epithelial lumican and stromal versican protein expression are increased during colorectal adenoma-to-carcinoma progression.
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Affiliation(s)
- Meike de Wit
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands
| | - Beatriz Carvalho
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands
| | - Pien M. Delis-van Diemen
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands
| | - Carolien van Alphen
- Department of Medical Oncology, VU University Medical Center, Amsterdam, the Netherlands
| | - Jeroen A. M. Beliën
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands
| | - Gerrit A. Meijer
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands
| | - Remond J. A. Fijneman
- Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands
- Department of Pathology, VU University Medical Center, Amsterdam, the Netherlands
- * E-mail:
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15
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Carvalho B, Diosdado B, Droste JSTS, Bolijn AS, Wit MD, Burink MV, Fijneman RJA, Grieken NCTV, Meijer GA. Abstract A04: Chromosomal aberrations implicated in colorectal adenoma to carcinoma progression as markers of high-risk colorectal adenomas. Cancer Res 2017. [DOI: 10.1158/1538-7445.crc16-a04] [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: Colorectal adenomas are precursor lesions of colorectal cancer. About 5% of colorectal adenomas are estimated to progress to colorectal cancer (CRC). The currently used histo-pathological characteristics to identify adenomas at risk of malignant progression, i.e. scoring of size ≥ 10mm, villous component or high grade dysplasia, are not sufficiently sensitive and specific and prone to inter-observer variability. Integrating molecular markers reflecting the underlying biology of CRC into the current classification system is expected to better characterize adenomas at high-risk of progression.
Aim: Here we compared the prevalence of genetic changes, in particular DNA copy number changes, between advanced and non-advanced adenomas.
Methods: Formalin-fixed paraffin-embedded tissue samples from 121 patients (mean age 65.4±11.6, 52.9% male) with colorectal adenomas (63 non-advanced adenomas and 58 advanced adenomas) were retrospectively collected from the archives of the department of pathology of the VU - University medical center (VUmc), Amsterdam, the Netherlands. DNA was extracted and DNA copy number analysis was performed using Multiplex Ligation-dependent Probe Amplification (MLPA), focusing on 7 chromosomal regions previously associated with adenoma-to-carcinoma progression, namely 8p, 15q, 17p and 18q loss and 8q,13q and 20q gain (1). Comparison of DNA copy number aberrations between sub-groups was done using a Chi-square test, or Fisher's exact test when appropriate. For multivariate analysis logistic regression was used. Data analysis was performed using SPSS version 22 (IBM SPSS Statistics) and p-values below 0.05 were considered to be statistically significant (using two-sided tests).
Results: Of the adenomas analyzed 23.1% (28/121) showed at least one gain or loss of the investigated chromosomal regions. Two or more chromosomal aberrations were present in 22.4 % (13/58) of the advanced adenomas and 1.6% (1/63) of the non-advanced adenomas (p=0,001). Since advanced colorectal adenomas are defined based on their histological characteristics ((tubulo)villous component and/or high degree dysplasia and/or ≥ 10mm), we searched for associations of these histological features with the analyzed chromosomal aberrations (CAE's). Multivariate analysis showed that only gains of 13q and 20q were significantly associated with adenomas ≥ 10mm (p=0.01 and p=0.003, respectively) and losses of 18q were significantly associated with high-grade dysplasia (p=0.04).
Conclusion: Our data indicate that DNA copy number alterations are not as frequent as expected in advanced adenomas and are also found in non-advanced and diminutive lesions. Combining histological and molecular features in adenoma follow-up studies could increase the knowledge on malignant potential of adenomas.
(1) Hermsen et al, Gastroenterology, 2002; 123:1109-1119
Citation Format: Beatriz Carvalho, Begoña Diosdado, Jochim S. Terhaar Sive Droste, Anne S. Bolijn, Meike de Wit, Myrthe van Burink, Remond JA Fijneman, Nicole CT van Grieken, Gerrit A. Meijer. Chromosomal aberrations implicated in colorectal adenoma to carcinoma progression as markers of high-risk colorectal adenomas. [abstract]. In: Proceedings of the AACR Special Conference on Colorectal Cancer: From Initiation to Outcomes; 2016 Sep 17-20; Tampa, FL. Philadelphia (PA): AACR; Cancer Res 2017;77(3 Suppl):Abstract nr A04.
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Affiliation(s)
| | - Begoña Diosdado
- 1The Netherlands Cancer Institute, Amsterdam, The Netherlands,
| | | | - Anne S. Bolijn
- 1The Netherlands Cancer Institute, Amsterdam, The Netherlands,
| | - Meike de Wit
- 1The Netherlands Cancer Institute, Amsterdam, The Netherlands,
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16
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Lenos K, Goos JACM, Vuist IM, den Uil SH, Delis-van Diemen PM, Belt EJT, Stockmann HBAC, Bril H, de Wit M, Carvalho B, Giblett S, Pritchard CA, Meijer GA, van Kooyk Y, Fijneman RJA, van Vliet SJ. MGL ligand expression is correlated to BRAF mutation and associated with poor survival of stage III colon cancer patients. Oncotarget 2016; 6:26278-90. [PMID: 26172302 PMCID: PMC4694901 DOI: 10.18632/oncotarget.4495] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 06/18/2015] [Indexed: 12/26/2022] Open
Abstract
Colorectal cancer (CRC) is the third most prevalent cancer type worldwide with a mortality rate of approximately 50%. Elevated cell-surface expression of truncated carbohydrate structures such as Tn antigen (GalNAcα-Ser/Thr) is frequently observed during tumor progression. We have previously demonstrated that the C-type lectin macrophage galactose-type lectin (MGL), expressed by human antigen presenting cells, can distinguish healthy tissue from CRC through its specific recognition of Tn antigen. Both MGL binding and oncogenic BRAF mutations have been implicated in establishing an immunosuppressive microenvironment. Here we aimed to evaluate whether MGL ligand expression has prognostic value and whether this was correlated to BRAF(V600E) mutation status. Using a cohort of 386 colon cancer patients we demonstrate that high MGL binding to stage III tumors is associated with poor disease-free survival, independent of microsatellite instability or adjuvant chemotherapy. In vitro studies using CRC cell lines showed an association between MGL ligand expression and the presence of BRAF(V600E). Administration of specific BRAF(V600E) inhibitors resulted in decreased expression of MGL-binding glycans. Moreover, a positive correlation between induction of BRAF(V600E) and MGL binding to epithelial cells of the gastrointestinal tract was found in vivo using an inducible BRAF(V600E) mouse model. We conclude that the BRAF(V600E) mutation induces MGL ligand expression, thereby providing a direct link between oncogenic transformation and aberrant expression of immunosuppressive glycans. The strong prognostic value of MGL ligands in stage III colon cancer patients, i.e. when tumor cells disseminate to lymph nodes, further supports the putative immune evasive role of MGL ligands in metastatic disease.
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Affiliation(s)
- Kristiaan Lenos
- Department of Molecular Cell Biology and Immunology, VU University Medical Center, Amsterdam, The Netherlands.,Current address: Laboratory of Experimental Oncology and Radiobiology, Center for Experimental Molecular Medicine, Academic Medical Center, Amsterdam, The Netherlands
| | - Jeroen A C M Goos
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
| | - Ilona M Vuist
- Department of Molecular Cell Biology and Immunology, VU University Medical Center, Amsterdam, The Netherlands.,Current address: Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Sjoerd H den Uil
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands.,Department of Surgery, Spaarne Gasthuis, Haarlem, The Netherlands
| | - Pien M Delis-van Diemen
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands.,Current address: Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Eric J Th Belt
- Department of Surgery, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Herman Bril
- Department of Pathology, Spaarne Gasthuis, Haarlem, The Netherlands
| | - Meike de Wit
- Department of Medical Oncology, VU University Medical Center Amsterdam, The Netherlands.,Current address: Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Beatriz Carvalho
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands.,Current address: Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Susan Giblett
- Department of Biochemistry, University of Leicester, Leicester, UK
| | | | - Gerrit A Meijer
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands.,Current address: Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Yvette van Kooyk
- Department of Molecular Cell Biology and Immunology, VU University Medical Center, Amsterdam, The Netherlands
| | - Remond J A Fijneman
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands.,Current address: Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Sandra J van Vliet
- Department of Molecular Cell Biology and Immunology, VU University Medical Center, Amsterdam, The Netherlands
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17
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Jimenez CR, de Wit M, Knol JC, de Reus I, Schelfhorst T, Bishop-Currey L, Dusseldorp V, van Grieken N, Beekhof R, Piersma SR, Pham TV, Smit EF, Fijneman RJA, Meijer G, Verheul HMW. Abstract 3885: Peptide-mediated ‘miniprep’ isolation of extracellular vesicles for high-throughput proteomics; method evaluation and application in colon cancer. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-3885] [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: Extracellular vesicles (EVs) are cell-secreted membrane vesicles enclosed by a lipid bilayer derived from endosomes or from the plasma membrane. Since they are released into body fluids, and their cargo includes tissue-specific and disease-related molecules, EVs represent a rich source for disease biomarkers. However, standard ultracentrifugation methods for EV isolation (UC-EV) are laborious, time-consuming, and require high inputs. Recently a novel isolation method was described, which can be performed at small ‘miniprep’ scale, utilizes specific Heat Shock Protein (HSP)-binding peptides to aggregate HSP-decorated EVs (Ghosh et al. (2014), PLoS ONE 9:e110443). Using cancer secretome and biofluid samples, the authors showed enrichment of exosome markers for their method (abbreviated HSP-EV here) but a detailed description of the captured EV proteomes in comparison to the gold-standard ultracentrifugation (UC) method and application to small tumor proximal fluid samples is lacking.
Approach: Here we used label-free proteomics of replicate EV isolations from HT-29 cancer cell-conditioned medium to compare EV fractions captured using the new HSP peptide method and UC. Subsequently we applied this novel method to profile EVs released from fresh human colorectal tumors (CRC) (n = 17) and colon adenoma (n = 4) tissue as well as patient-matched normal colon tissue.
Results: Despite a 30-fold different input scale (UC-EV: 60 ml versus HSP-EV: 2 ml), both methods yielded comparable numbers of identified proteins (3115 versus 3085), with reproducible identifications (72.5% versus 75.5%) and spectral count-based quantification (average CV 31% versus 27%). EVs obtained by either method contained established EV markers and proteins linked to vesicle-related gene ontologies. In the EV fraction of the tissue secretomes 6390 proteins were identified, of which 471 proteins were significantly 5-fold more present in CRC samples than in normal tissue EVs. Gene ontology analysis revealed enrichment of nuclear proteins involved in DNA damage response, chromosome organization and RNA processing in the CRC EVs.
Conclusion: The HSP-EV method provides an advantageous, simple and rapid approach for EV isolation from small amounts of biological samples, enabling high-throughput analysis in a biomarker discovery setting.
Citation Format: Connie R. Jimenez, Meike de Wit, Jaco C. Knol, Inge de Reus, Tim Schelfhorst, Logan Bishop-Currey, Valerie Dusseldorp, Nicole van Grieken, Robin Beekhof, Sander R. Piersma, Thang V. Pham, Egbert F. Smit, Remond JA Fijneman, Gerrit Meijer, Henk MW Verheul. Peptide-mediated ‘miniprep’ isolation of extracellular vesicles for high-throughput proteomics; method evaluation and application in colon cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3885.
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Affiliation(s)
- Connie R. Jimenez
- 1OncoProteomics Laboratory, Department of Medical Oncology VU University Medical Center, Amsterdam, Netherlands
| | - Meike de Wit
- 1OncoProteomics Laboratory, Department of Medical Oncology VU University Medical Center, Amsterdam, Netherlands
| | - Jaco C. Knol
- 1OncoProteomics Laboratory, Department of Medical Oncology VU University Medical Center, Amsterdam, Netherlands
| | - Inge de Reus
- 1OncoProteomics Laboratory, Department of Medical Oncology VU University Medical Center, Amsterdam, Netherlands
| | - Tim Schelfhorst
- 1OncoProteomics Laboratory, Department of Medical Oncology VU University Medical Center, Amsterdam, Netherlands
| | - Logan Bishop-Currey
- 1OncoProteomics Laboratory, Department of Medical Oncology VU University Medical Center, Amsterdam, Netherlands
| | - Valerie Dusseldorp
- 1OncoProteomics Laboratory, Department of Medical Oncology VU University Medical Center, Amsterdam, Netherlands
| | - Nicole van Grieken
- 2Department of Pathology, VU University Medical Center, Amsterdam, Netherlands
| | - Robin Beekhof
- 1OncoProteomics Laboratory, Department of Medical Oncology VU University Medical Center, Amsterdam, Netherlands
| | - Sander R. Piersma
- 1OncoProteomics Laboratory, Department of Medical Oncology VU University Medical Center, Amsterdam, Netherlands
| | - Thang V. Pham
- 1OncoProteomics Laboratory, Department of Medical Oncology VU University Medical Center, Amsterdam, Netherlands
| | - Egbert F. Smit
- 3Department of Pulmonary Diseases, VU University Medical Center, Amsterdam, Netherlands
| | - Remond JA Fijneman
- 4Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands., Amsterdam, Netherlands
| | - Gerrit Meijer
- 4Department of Pathology, The Netherlands Cancer Institute, Amsterdam, the Netherlands., Amsterdam, Netherlands
| | - Henk MW Verheul
- 1OncoProteomics Laboratory, Department of Medical Oncology VU University Medical Center, Amsterdam, Netherlands
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18
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Knol JC, de Reus I, Schelfhorst T, Beekhof R, de Wit M, Piersma SR, Pham TV, Smit EF, Verheul HM, Jiménez CR. Peptide-mediated 'miniprep' isolation of extracellular vesicles is suitable for high-throughput proteomics. EuPA Open Proteom 2016; 11:11-15. [PMID: 29900106 PMCID: PMC5988555 DOI: 10.1016/j.euprot.2016.02.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 01/12/2016] [Accepted: 02/16/2016] [Indexed: 01/14/2023]
Abstract
Extracellular vesicles (EVs) are cell-secreted membrane vesicles enclosed by a lipid bilayer derived from endosomes or from the plasma membrane. Since EVs are released into body fluids, and their cargo includes tissue-specific and disease-related molecules, they represent a rich source for disease biomarkers. However, standard ultracentrifugation methods for EV isolation are laborious, time-consuming, and require high inputs. Ghosh and co-workers recently described an isolation method utilizing Heat Shock Protein (HSP)-binding peptide Vn96 to aggregate HSP-decorated EVs, which can be performed at small 'miniprep' scale. Based on microscopic, immunoblot, and RNA sequencing analyses this method compared well with ultracentrifugation-mediated EV isolation, but a detailed proteomic comparison was lacking. Therefore, we compared both methods using label-free proteomics of replicate EV isolations from HT-29 cell-conditioned medium. Despite a 30-fold different scale (ultracentrifugation: 60 ml/Vn96-mediated aggregation: 2 ml) both methods yielded comparable numbers of identified proteins (3115/3085), with similar reproducibility of identification (72.5%/75.5%) and spectral count-based quantification (average CV: 31%/27%). EV fractions obtained with either method contained established EV markers and proteins linked to vesicle-related gene ontologies. Thus, Vn96 peptide-mediated aggregation is an advantageous, simple and rapid approach for EV isolation from small biological samples, enabling high-throughput analysis in a biomarker discovery setting.
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Affiliation(s)
- Jaco C. Knol
- OncoProteomics Laboratory, Dept. Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, The Netherlands
| | - Inge de Reus
- OncoProteomics Laboratory, Dept. Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, The Netherlands
| | - Tim Schelfhorst
- OncoProteomics Laboratory, Dept. Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, The Netherlands
| | - Robin Beekhof
- OncoProteomics Laboratory, Dept. Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, The Netherlands
| | - Meike de Wit
- OncoProteomics Laboratory, Dept. Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, The Netherlands
| | - Sander R. Piersma
- OncoProteomics Laboratory, Dept. Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, The Netherlands
| | - Thang V. Pham
- OncoProteomics Laboratory, Dept. Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, The Netherlands
| | - Egbert F. Smit
- Department of Pulmonary Diseases, VU University Medical Center, The Netherlands
| | - Henk M.W. Verheul
- OncoProteomics Laboratory, Dept. Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, The Netherlands
| | - Connie R. Jiménez
- OncoProteomics Laboratory, Dept. Medical Oncology, VUmc-Cancer Center Amsterdam, VU University Medical Center, The Netherlands
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19
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Bosch LJW, de Wit M, Hiemstra AC, Piersma S, Pham T, Oudgenoeg G, Scheffer G, Mongera S, Komor M, Terhaar Sive Droste J, Oort FA, van Turenhout S, Ben Larbi I, Mulder CJJ, Carvalho B, Fijneman RJA, Jimenez C, Meijer GA. Abstract 1563: Stool proteomics reveals novel candidate biomarkers for colorectal cancer screening. Cancer Res 2015. [DOI: 10.1158/1538-7445.am2015-1563] [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
Introduction and objectives: Early detection of colorectal cancer (CRC) and its precursor lesions is an effective approach to reduce CRC mortality rates. The fecal immunochemical test (FIT) is a non-invasive CRC screening test that detects small traces of the blood protein hemoglobin. Although beneficial in its current form, the FIT test characteristics leave room for improvement. The aim of the present study was to identify and validate novel protein biomarkers in stool that complement or outperform the current hemoglobin-based test, to improve its diagnostic accuracy.
Methods: Proteins isolated from stool from 10 subjects without any signs of colorectal neoplasia (controls) at colonoscopy and from 12 CRC patients were analyzed by GeLC-MS/MS (discovery set). Data were analyzed by comparing protein abundancies, measured as spectral counts. Analysis of differential proteins was performed using the beta-binomial test. Findings were validated by mass spectrometry (Q-Exactive) in an independent series of 292 stool samples obtained from control subjects (n = 109) and subjects with adenomas (n = 55), advanced adenomas (n = 53), or CRCs (n = 75).
Results and Discussion: In total 830 human proteins were identified in the discovery set, of which 134 were significantly enriched in CRC. These included 78 proteins that were significantly more enriched in FIT-negative CRC stool samples compared to controls. Preliminary analysis of the validation set indicates that more than half of these markers are significantly more abundant in CRC samples compared to controls.
Conclusion: Proteome profiling of stool samples revealed novel candidate biomarkers to improve current CRC screening tests. More data analysis is currently ongoing to select most promising protein biomarkers for clinical assay development.
Citation Format: Linda JW Bosch, Meike de Wit, Annemieke C. Hiemstra, Sander Piersma, Thang Pham, Gideon Oudgenoeg, George Scheffer, Sandra Mongera, Malgorzata Komor, Jochim Terhaar Sive Droste, Frank A. Oort, Sietze van Turenhout, Ilhame Ben Larbi, Chris JJ Mulder, Beatriz Carvalho, Remond JA Fijneman, Connie Jimenez, Gerrit A. Meijer. Stool proteomics reveals novel candidate biomarkers for colorectal cancer screening. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 1563. doi:10.1158/1538-7445.AM2015-1563
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Affiliation(s)
| | | | | | | | - Thang Pham
- VU Univ. Medical Ctr., Amsterdam, Netherlands
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20
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Dragomir A, de Wit M, Johansson C, Uhlen M, Pontén F. The role of SATB2 as a diagnostic marker for tumors of colorectal origin: Results of a pathology-based clinical prospective study. Am J Clin Pathol 2014; 141:630-8. [PMID: 24713733 DOI: 10.1309/ajcpww2urz9jkqju] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
OBJECTIVES Immunohistochemistry is an important extension to clinical information and morphology, and prevails as an invaluable tool for establishing a correct cancer diagnosis in clinical diagnostic pathology. The applicability of immunohistochemistry is limited by the availability of validated cell- and cancer-type specific antibodies, rendering an unmet need to discover, test, and validate novel markers. The SATB2 protein is selectively expressed in glandular cells from the lower gastrointestinal tract and expression is retained in a large majority of primary and metastatic colorectal cancers. METHODS We analyzed the expression of SATB2 in all clinical cases (n = 840), in which immunohistochemistry for detection of CK20 was deemed necessary for a final diagnosis. RESULTS SATB2 showed a high sensitivity (93%) and specificity (77%) to determine a cancer of colorectal origin and in combination with CK7 and CK20, the specificity increased to 100%. CONCLUSIONS We conclude that SATB2 provides a new and advantageous supplement for clinical differential diagnostics.
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Affiliation(s)
- Anca Dragomir
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Meike de Wit
- Department of Medical Oncology, VU Medical Center, Amsterdam, The Netherlands
| | | | - Mathias Uhlen
- Science for Life Laboratory, KTH-Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Pontén
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
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de Wit M, Kant H, Piersma SR, Pham TV, Mongera S, van Berkel MPA, Boven E, Pontén F, Meijer GA, Jimenez CR, Fijneman RJA. Colorectal cancer candidate biomarkers identified by tissue secretome proteome profiling. J Proteomics 2014; 99:26-39. [PMID: 24418523 DOI: 10.1016/j.jprot.2014.01.001] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2013] [Revised: 12/01/2013] [Accepted: 01/01/2014] [Indexed: 12/18/2022]
Abstract
UNLABELLED Colorectal cancer (CRC) is a major health problem. Biomarkers associated with molecular changes in cancer cells can aid early detection, diagnosis, prognosis, therapy selection, and disease monitoring. Tumor tissue secretomes are a rich source of candidate biomarkers. To identify CRC protein biomarkers, secretomes of four pairs of human CRC tissue and patient-matched normal colon tissue samples, and secretomes of five CRC cell lines were analyzed by GeLC-MS/MS. Subsequent data analysis was based on label-free spectral counting, Ingenuity Pathway Analysis, Secretome/SignalP, STRING and Cytoscape, resulting in 2703 protein identifications in the tissue secretomes, of which 409 proteins were significantly more present in CRC samples than in controls. Biomarker selection of 76 candidates was based on consistent and abundant over-representation in cancer- compared to control-secretomes, and presumed neoplastic origin. Overlap analysis with previously obtained datasets revealed 21 biomarkers suited for early detection of CRC. Immunohistochemistry confirmed overexpression in CRC of one candidate marker (MCM5). In conclusion, a human reference dataset of 76 candidate biomarkers was identified for which we illustrate that combination with existing pre-clinical datasets allows pre-selection of biomarkers for blood- or stool-based assays to support clinical management of CRC. Further dedicated validation studies are required to demonstrate their clinical applicability. BIOLOGICAL SIGNIFICANCE Tissue secretome proteomes are a rich source of candidate biomarkers. Several secretome proteome datasets have been obtained from pre-clinical in vitro and in vivo colorectal cancer (CRC) model systems, yielding promising CRC biomarkers obtained under well-defined experimentally controlled conditions. However, which of these biomarker proteins are actually secreted by human CRC samples was not known. To our knowledge, this is the first study that directly compares secretome proteomes from clinically relevant human CRC tissues to patient-matched normal colon tissues. We identified 76 human CRC protein biomarkers that may facilitate blood-based or stool-based assay development to support clinical management of CRC. Overlap analysis with datasets from well-defined pre-clinical studies helps to determine what clinical application suits these human CRC biomarkers best, i.e. early detection, diagnosis, prognosis, therapy selection, and/or disease monitoring of CRC. This is demonstrated for a CRC mouse model dataset, revealing 21 human CRC biomarkers suited for early detection of CRC.
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Affiliation(s)
- Meike de Wit
- Department of Pathology (Tumor Profiling Unit), VU University Medical Center, Amsterdam, The Netherlands; Department of Medical Oncology (OncoProteomics Laboratory), VU University Medical Center, Amsterdam, The Netherlands
| | - Huub Kant
- Department of Medical Oncology (OncoProteomics Laboratory), VU University Medical Center, Amsterdam, The Netherlands
| | - Sander R Piersma
- Department of Medical Oncology (OncoProteomics Laboratory), VU University Medical Center, Amsterdam, The Netherlands
| | - Thang V Pham
- Department of Medical Oncology (OncoProteomics Laboratory), VU University Medical Center, Amsterdam, The Netherlands
| | - Sandra Mongera
- Department of Pathology (Tumor Profiling Unit), VU University Medical Center, Amsterdam, The Netherlands
| | - Maaike P A van Berkel
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Epie Boven
- Department of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Fredrik Pontén
- Department of Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Gerrit A Meijer
- Department of Pathology (Tumor Profiling Unit), VU University Medical Center, Amsterdam, The Netherlands
| | - Connie R Jimenez
- Department of Medical Oncology (OncoProteomics Laboratory), VU University Medical Center, Amsterdam, The Netherlands.
| | - Remond J A Fijneman
- Department of Pathology (Tumor Profiling Unit), VU University Medical Center, Amsterdam, The Netherlands.
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Knol JC, de Wit M, Albrethsen J, Piersma SR, Pham TV, Mongera S, Carvalho B, Fijneman RJA, Meijer GA, Jiménez CR. Proteomics of differential extraction fractions enriched for chromatin-binding proteins from colon adenoma and carcinoma tissues. Biochim Biophys Acta 2013; 1844:1034-43. [PMID: 24361553 DOI: 10.1016/j.bbapap.2013.12.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2013] [Revised: 10/28/2013] [Accepted: 12/10/2013] [Indexed: 12/11/2022]
Abstract
BACKGROUND Altered nuclear and genomic structure and function are hallmarks of cancer cells. Research into nuclear proteins in human tissues could uncover novel molecular processes in cancer. Here, we examine biochemical tissue fractions containing chromatin-binding (CB) proteins in the context of colorectal cancer (CRC) progression. METHODS CB protein-containing fractions were biochemically extracted from human colorectal tissues, including carcinomas with chromosomal instability (CIN), carcinomas with microsatellite instability (MIN), and adenomas. The CB proteins were subjected to label-free LC-MS/MS and the data were analyzed by bioinformatics. RESULTS Over 1700 proteins were identified in the CB fraction from colonic tissues, including 938 proteins associated with nuclear annotation. Of the latter, 169 proteins were differential between adenomas and carcinomas. In this adenoma-versus-carcinoma comparison, apart from specific changes in components of the splicing and protein translational machineries, we also identified significant changes in several proteins associated with chromatin-directed functions. Furthermore, several key cell cycle proteins as well as those involved in cellular stress were increased, whereas specific components of chromosome segregation and DNA recombination/repair systems were decreased. CONCLUSIONS Our study identifies proteomic changes at the subnuclear level that are associated with CRC and may be further investigated. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge.
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Affiliation(s)
- Jaco C Knol
- OncoProteomics Laboratory, Dept. of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Meike de Wit
- OncoProteomics Laboratory, Dept. of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Jakob Albrethsen
- OncoProteomics Laboratory, Dept. of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands; Rigshospitalet, Blegdamsvej 9, Copenhagen, Denmark
| | - Sander R Piersma
- OncoProteomics Laboratory, Dept. of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Thang V Pham
- OncoProteomics Laboratory, Dept. of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Sandra Mongera
- Department of Pathology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Beatriz Carvalho
- Department of Pathology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Remond J A Fijneman
- Department of Pathology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Gerrit A Meijer
- Department of Pathology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Connie R Jiménez
- OncoProteomics Laboratory, Dept. of Medical Oncology, VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands.
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Piersma SR, Warmoes MO, de Wit M, de Reus I, Knol JC, Jiménez CR. Whole gel processing procedure for GeLC-MS/MS based proteomics. Proteome Sci 2013; 11:17. [PMID: 23617947 PMCID: PMC3656797 DOI: 10.1186/1477-5956-11-17] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Accepted: 04/11/2013] [Indexed: 12/24/2022] Open
Abstract
Background SDS-PAGE followed by in-gel digestion (IGD) is a popular workflow in mass spectrometry-based proteomics. In GeLC-MS/MS, a protein lysate of a biological sample is separated by SDS-PAGE and each gel lane is sliced in 5–20 slices which, after IGD, are analyzed by LC-MS/MS. The database search results for all slices of a biological sample are combined yielding global protein identification and quantification for each sample. In large scale GeLC-MS/MS experiments the manual processing steps including washing, reduction and alkylation become a bottleneck. Here we introduce the whole gel (WG) procedure where, prior to gel slice cutting, the processing steps are carried out on the whole gel. Results In two independent experiments human HCT116 cell lysate and mouse tumor tissue lysate were separated by 1D SDS PAGE. In a back to back comparison of the IGD procedure and the WG procedure, both protein identification (>80% overlap) and label-free protein quantitation (R2=0.94) are highly similar between procedures. Triplicate analysis of the WG procedure of both HCT116 cell lysate and formalin-fixed paraffin embedded (FFPE) tumor tissue showed identification reproducibility of >88% with a CV<20% on protein quantitation. Conclusions The whole gel procedure allows for reproducible large-scale differential GeLC-MS/MS experiments, without a prohibitive amount of manual processing and with similar performance as conventional in-gel digestion. This procedure will especially enable clinical proteomics for which GeLC-MS/MS is a popular workflow and sample numbers are relatively high.
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Affiliation(s)
- Sander R Piersma
- Department of Medical Oncology, OncoProteomics Laboratory, VU University Medical Center, Amsterdam, The Netherlands.
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24
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de Wit M, Fijneman RJ, Verheul HM, Meijer GA, Jimenez CR. Proteomics in colorectal cancer translational research: Biomarker discovery for clinical applications. Clin Biochem 2013; 46:466-79. [DOI: 10.1016/j.clinbiochem.2012.10.039] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 10/30/2012] [Accepted: 10/31/2012] [Indexed: 12/22/2022]
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Schaaij-Visser TBM, de Wit M, Lam SW, Jiménez CR. The cancer secretome, current status and opportunities in the lung, breast and colorectal cancer context. Biochim Biophys Acta 2013; 1834:2242-58. [PMID: 23376433 DOI: 10.1016/j.bbapap.2013.01.029] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 01/18/2013] [Accepted: 01/23/2013] [Indexed: 12/20/2022]
Abstract
Despite major improvements on the knowledge and clinical management, cancer is still a deadly disease. Novel biomarkers for better cancer detection, diagnosis and treatment prediction are urgently needed. Proteins secreted, shed or leaking from the cancer cell, collectively termed the cancer secretome, are promising biomarkers since they might be detectable in blood or other biofluids. Furthermore, the cancer secretome in part represents the tumor microenvironment that plays a key role in tumor promoting processes such as angiogenesis and invasion. The cancer secretome, sampled as conditioned medium from cell lines, tumor/tissue interstitial fluid or tumor proximal body fluids, can be studied comprehensively by nanoLC-MS/MS-based approaches. Here, we outline the importance of current cancer secretome research and describe the mass spectrometry-based analysis of the secretome. Further, we provide an overview of cancer secretome research with a focus on the three most common cancer types: lung, breast and colorectal cancer. We conclude that the cancer secretome research field is a young, but rapidly evolving research field. Up to now, the focus has mainly been on the discovery of novel promising secreted cancer biomarker proteins. An interesting finding that merits attention is that in cancer unconventional secretion, e.g. via vesicles, seems increased. Refinement of current approaches and methods and progress in clinical validation of the current findings are vital in order to move towards applications in cancer management. This article is part of a Special Issue entitled: An Updated Secretome.
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Affiliation(s)
- Tieneke B M Schaaij-Visser
- OncoProteomics Laboratory, Dept. of Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands; Division of Molecular Genetics and Centre for Biomedical Genetics, The Netherlands Cancer Institute, Amsterdam, The Netherlands
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Sillars-Hardebol AH, Carvalho B, Tijssen M, Beliën JAM, de Wit M, Delis-van Diemen PM, Pontén F, van de Wiel MA, Fijneman RJA, Meijer GA. TPX2 and AURKA promote 20q amplicon-driven colorectal adenoma to carcinoma progression. Gut 2012; 61:1568-75. [PMID: 22207630 DOI: 10.1136/gutjnl-2011-301153] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
BACKGROUND AND OBJECTIVE Progression of a colorectal adenoma to invasive cancer occurs in a minority of adenomas and is the most crucial step in colorectal cancer pathogenesis. In the majority of cases, this is associated with gain of a substantial part of chromosome 20q, indicating that multiple genes on the 20q amplicon may drive carcinogenesis. The aim of this study was to identify genes located on the 20q amplicon that promote progression of colorectal adenoma to carcinoma. DESIGN Functional assays were performed for 32 candidate driver genes for which a positive correlation between 20q DNA copy number and mRNA expression had been demonstrated. Effects of gene knockdown on cell viability, anchorage-independent growth, and invasion were analysed in colorectal cancer cell lines with 20q gain. Colorectal tumour protein expression was examined by immunohistochemical staining of tissue microarrays. RESULTS TPX2, AURKA, CSE1L, DIDO1, HM13, TCFL5, SLC17A9, RBM39 and PRPF6 affected cell viability and/or anchorage-independent growth. Chromosome 20q DNA copy number status correlated significantly with TPX2 and AURKA protein levels in a series of colorectal adenomas and carcinomas. Moreover, downmodulation of TPX2 and AURKA was shown to inhibit invasion. CONCLUSION These data identify TPX2 (20q11) and AURKA (20q13.2) as two genes located on distinct regions of chromosome 20q that promote 20q amplicon-driven progression of colorectal adenoma to carcinoma. Therefore the selection advantage imposed by 20q gain in tumour progression is achieved by gain-of-function of multiple cancer-related genes-knowledge that can be translated into novel tests for early diagnosis of progressive adenomas.
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Affiliation(s)
- Anke H Sillars-Hardebol
- VU University Medical Center, Department of Pathology, De Boelelaan 1117, Amsterdam, The Netherlands.
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Sillars-Hardebol AH, Carvalho B, Beliën JA, de Wit M, Delis-van Diemen PM, Tijssen M, van de Wiel MA, Pontén F, Meijer GA, Fijneman RJA. CSE1L, DIDO1 and RBM39 in colorectal adenoma to carcinoma progression. Cell Oncol (Dordr) 2012; 35:293-300. [DOI: 10.1007/s13402-012-0088-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/24/2012] [Indexed: 01/22/2023] Open
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de Wit M, Belt EJT, Delis-van Diemen PM, Carvalho B, Coupé VMH, Stockmann HBAC, Bril H, Beliën JAM, Fijneman RJA, Meijer GA. Lumican and versican are associated with good outcome in stage II and III colon cancer. Ann Surg Oncol 2012; 20 Suppl 3:S348-59. [PMID: 22711178 PMCID: PMC3857876 DOI: 10.1245/s10434-012-2441-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [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: 10/07/2011] [Indexed: 12/29/2022]
Abstract
BACKGROUND Tumor stroma plays an important role in the progression and metastasis of colon cancer. The glycoproteins versican and lumican are overexpressed in colon carcinomas and are associated with the formation of tumor stroma. The aim of the present study was to investigate the potential prognostic value of versican and lumican expression in the epithelial and stromal compartment of Union for International Cancer Control (UICC) stage II and III colon cancer. METHODS Clinicopathological data and tissue samples were collected from stage II (n = 226) and stage III (n = 160) colon cancer patients. Tissue microarrays were constructed with cores taken from both the center and the periphery of the tumor. These were immunohistochemically stained for lumican and versican. Expression levels were scored on digitized slides. Statistical evaluation was performed. RESULTS Versican expression by epithelial cells in the periphery of the tumor, i.e., near the invasive front, was correlated to a longer disease-free survival for the whole cohort (P = 0.01), stage III patients only (P = 0.01), stage III patients with microsatellite-instable tumors (P = 0.04), and stage III patients with microsatellite-stable tumors who did not receive adjuvant chemotherapy (P = 0.006). Lumican expression in epithelial cells overall in the tumor was correlated to a longer disease-specific survival in stage II patients (P = 0.05) and to a longer disease-free survival and disease-specific survival in microsatellite-stable stage II patients (P = 0.02 and P = 0.004). CONCLUSIONS Protein expression of versican and lumican predicted good clinical outcome for stage III and II colon cancer patients, respectively.
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Affiliation(s)
- Meike de Wit
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands
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de Wit M, Jimenez CR, Carvalho B, Belien JAM, Delis-van Diemen PM, Mongera S, Piersma SR, Vikas M, Navani S, Pontén F, Meijer GA, Fijneman RJA. Cell surface proteomics identifies glucose transporter type 1 and prion protein as candidate biomarkers for colorectal adenoma-to-carcinoma progression. Gut 2012; 61:855-64. [PMID: 21890811 DOI: 10.1136/gutjnl-2011-300511] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
BACKGROUND AND OBJECTIVE Early detection of colon adenomas at high risk of progression and early-stage colorectal cancer (CRC) is an effective approach to reduce CRC death rates. Current screening methods lack specificity as they detect many adenomas that will never progress to CRC. The authors aimed to identify cell surface protein biomarkers with extracellular domains that could be targeted for molecular imaging and discriminate low-risk adenomas and normal colon from high-risk adenomas and CRC. DESIGN Cell surface proteins of five CRC cell lines were biotinylated, isolated and analysed by in-depth proteomics using gel electrophoresis and nanoliquid chromatography coupled to tandem mass spectrometry. Differential expression in adenomas and CRCs was based on mRNA expression and verified by immunohistochemical staining of tissue microarrays. RESULTS In total, 2609 proteins were identified in the cell surface fractions. Of these, 44 proteins were selected as promising cell surface candidate biomarkers for adenoma-to-carcinoma progression based on the following criteria: protein identification in at least four out of five cell lines, a predicted (trans)membrane location and increased mRNA expression in CRCs compared to adenomas. Increased protein expression in high-risk adenomas and CRCs compared to low-risk adenomas was confirmed by immunohistochemistry for glucose transporter type 1 (gene symbol SLC2A1; p<0.00001) and prion protein (gene symbol PRNP; p<0.005). CONCLUSION This study revealed glucose transporter type 1, prion protein and 42 other cell surface candidate biomarkers for adenoma-to-carcinoma progression that could potentially serve as targets for emerging molecular imaging modalities like optical imaging, ¹⁹F-MRI and positron emission tomography.
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Affiliation(s)
- Meike de Wit
- Department of Pathology-Tumor Profiling Unit, VU University Medical Center, Amsterdam, The Netherlands
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de Wit M, Belt EJ, van Diemen PMD, Carvalho B, Coupé VM, Stockmann HB, Bril H, Belien JA, Fijneman RJ, Meijer GA. Abstract 4526: Lumican and Versican predict good outcome in stage II and III colon cancer. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-4526] [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 and Purpose: Tumor stroma plays an important role in the progression and metastasis of colon cancer. The glycoproteins versican and lumican are overexpressed in colon carcinomas and are associated with the formation of tumor stroma. The aim of the present study was to investigate the potential prognostic value of versican and lumican expression in the epithelial and stromal compartment of stage II and III colon cancer. Methods: Clinicopathological data and tissue samples were collected from stage II (n=226) and stage III (n=160) colon cancer patients. Tissue microarrays (TMAs) were constructed with cores taken both from the center and the periphery of the tumor. These were immunohistochemically stained for lumican and versican. Expression levels were scored on digitized slides. Statistical evaluation was performed using SPSS. Results: Versican expression by epithelial cells in the periphery of the tumor, i.e., near the invasive front, was correlated to a longer disease free survival (DFS) for the whole cohort (P=0.01), stage III patients only (P=0.01), stage III patients with microsatellite instable (MSI) tumors (P=0.04) and stage III patients with microsatellite stable (MSS) tumors who did not receive adjuvant chemotherapy (P=0.006). Lumican expression in epithelial cells overall in the tumor was correlated to a longer disease specific survival (DSS) in stage II patients (P=0.05) and to a longer DFS and DSS in MSS stage II patients (P=0.02 and P=0.004). Conclusion: In the present series, protein expression of versican and lumican predicted good clinical outcome for stage III and stage II colon cancer patients, respectively.
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 4526. doi:1538-7445.AM2012-4526
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Affiliation(s)
- Meike de Wit
- 1VU University Medical Center, Amsterdam, Netherlands
| | - Eric J. Belt
- 1VU University Medical Center, Amsterdam, Netherlands
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Sillars-Hardebol AH, Carvalho B, Belien JA, de Wit M, Delis-van Diemen PM, Tijssen M, van de Wiel MA, Ponten F, Meijer GA, Fijneman RJA. Abstract 109: CSE1L, a 20q gain passenger that drives colorectal adenoma to carcinoma progression. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-109] [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 ‘Driver genes’ are defined as genes that promote the tumorigenic process upon acquirement of somatic alterations. Gain of chromosome 20q is an important factor in the progression of colorectal adenomas to carcinomas. Previously we identified TPX2 and AURKA as two genes that drive 20q amplification in colorectal adenoma to carcinoma progression, based on correlation of mRNA and protein expression levels with 20q DNA copy number status while functionally influencing cancer processes. These findings are consistent with the hypothesis that the selection advantage imposed by 20q gain in colorectal adenoma to carcinoma progression is achieved by gain-of-function of multiple cancer-related genes at chromosome 20q, rather than affecting a single driver gene. In addition to TPX2 and AURKA, other 20q genes such as CSE1L may further contribute to tumor progression. Aim We here investigated whether CSE1L is another 20q located gene that drives colorectal adenoma to carcinoma progression, in a 20q gain-dependent manner. Methods Functional effects of CSE1L on cell viability, anchorage-independent growth and invasion were investigated upon gene knockdown using the SW480 colorectal cancer cell line. CSE1L protein expression levels were examined by immunohistochemical evaluation of tissue microarrays containing a series of colorectal adenoma and carcinoma samples, which were characterized by genome-wide (microarray-based) DNA and mRNA profiling. Results CSE1L knockdown affected cell viability and anchorage-independent growth. CSE1L mRNA expression levels correlated with chromosome 20q DNA copy number status. However, CSE1L protein expression was not associated with 20q gain, although its expression was increased in carcinomas compared to adenomas. Conclusion CSE1L appears to be a driver of colorectal tumor progression based on its functional effects combined with increased protein expression levels in carcinomas compared to adenomas. However, the lack of correlation between CSE1L protein expression levels and 20q DNA copy number status in colorectal adenoma to carcinoma progression implies that CSE1L is merely a passenger rather than a driver of chromosome 20q amplification, suggesting that CSE1L protein levels are subject to post-transcriptional regulation in a 20q gain-independent manner.
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 109. doi:1538-7445.AM2012-109
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Affiliation(s)
| | | | | | - Meike de Wit
- 1VU University Medical Center, Amsterdam, Netherlands
| | | | | | | | - Fredrik Ponten
- 2The Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
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Fijneman RJA, de Wit M, Pourghiasian M, Piersma SR, Pham TV, Warmoes MO, Lavaei M, Piso C, Smit F, Delis-van Diemen PM, van Turenhout ST, Terhaar sive Droste JS, Mulder CJJ, Blankenstein MA, Robanus-Maandag EC, Smits R, Fodde R, van Hinsbergh VWM, Meijer GA, Jimenez CR. Proximal fluid proteome profiling of mouse colon tumors reveals biomarkers for early diagnosis of human colorectal cancer. Clin Cancer Res 2012; 18:2613-24. [PMID: 22351690 DOI: 10.1158/1078-0432.ccr-11-1937] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [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
PURPOSE Early detection of colorectal cancer (CRC) and its precursor lesions is an effective approach to reduce CRC mortality rates. This study aimed to identify novel protein biomarkers for the early diagnosis of CRC. EXPERIMENTAL DESIGN Proximal fluids are a rich source of candidate biomarkers as they contain high concentrations of tissue-derived proteins. The FabplCre;Apc(15lox/+) mouse model represents early-stage development of human sporadic CRC. Proximal fluids were collected from normal colon and colon tumors and subjected to in-depth proteome profiling by tandem mass spectrometry. Carcinoembryonic antigen (CEA) and CHI3L1 human serum protein levels were determined by ELISA. RESULTS Of the 2,172 proteins identified, quantitative comparison revealed 192 proteins that were significantly (P < 0.05) and abundantly (>5-fold) more excreted by tumors than by controls. Further selection for biomarkers with highest specificity and sensitivity yielded 52 candidates, including S100A9, MCM4, and four other proteins that have been proposed as candidate biomarkers for human CRC screening or surveillance, supporting the validity of our approach. For CHI3L1, we verified that protein levels were significantly increased in sera from patients with adenomas and advanced adenomas compared with control individuals, in contrast to the CRC biomarker CEA. CONCLUSION These data show that proximal fluid proteome profiling with a mouse tumor model is a powerful approach to identify candidate biomarkers for early diagnosis of human cancer, exemplified by increased CHI3L1 protein levels in sera from patients with CRC precursor lesions.
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Affiliation(s)
- Remond J A Fijneman
- Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands.
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Sillars-Hardebol AH, Carvalho B, Beliën JAM, de Wit M, Delis-van Diemen PM, Tijssen M, van de Wiel MA, Pontén F, Fijneman RJA, Meijer GA. BCL2L1has a functional role in colorectal cancer and its protein expression is associated with chromosome 20q gain. J Pathol 2012; 226:442-450. [DOI: 10.1002/path.2983] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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Sillars-Hardebol AH, Carvalho B, Tijssen M, Beliën JA, de Wit M, Delis-van Diemen PM, Pontén F, van de Wiel MA, Fijneman RJ, Meijer GA. Abstract 3042: TPX2 and AURKA promote 20q amplicon driven colorectal adenoma-to-carcinoma progression. Cancer Res 2011. [DOI: 10.1158/1538-7445.am2011-3042] [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: Gain of a large segment of chromosome 20q is associated with progression of colorectal adenomas into carcinomas, implying that multiple genes on the 20q amplicon drive carcinogenesis. Candidate driver genes are expected to be expressed at mRNA and protein levels that correlate with the 20q amplicon DNA copy number status, while functionally affecting one or several cancer-related processes. Integration of CGH profiles with mRNA profiles of a series of colorectal tumors revealed thirty-two candidate genes whose DNA copy number status correlated with mRNA expression levels.
Aim: To functionally analyse the effects of the candidate oncogenes on cancer-related processes by downregulation using siRNA strategies.
Results: Downmodulation of TPX2 (20q11.2) and AURKA (20q13.2) mRNA expression in CRC cell lines with 20q gain affected cell viability, anchorage-independent growth, and invasion. Moreover, immunohistochemical evaluation demonstrated a significant correlation between their protein levels and 20q DNA copy number status in a series of colorectal adenomas and carcinomas.
Conclusion: These data demonstrate that at least two genes located on distinct regions of chromosome 20q promote colorectal adenoma-to-carcinoma progression and indicate that TPX2, like AURKA, is a promising target for anti-cancer drug development.
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 3042. doi:10.1158/1538-7445.AM2011-3042
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Affiliation(s)
| | - Beatriz Carvalho
- 1Department of Pathology, VU University Medical Center, Amsterdam, Netherlands
| | - Marianne Tijssen
- 1Department of Pathology, VU University Medical Center, Amsterdam, Netherlands
| | - Jeroen A.M. Beliën
- 1Department of Pathology, VU University Medical Center, Amsterdam, Netherlands
| | - Meike de Wit
- 1Department of Pathology, VU University Medical Center, Amsterdam, Netherlands
| | | | - Fredrik Pontén
- 2Department of Genetics and Pathology, The Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Mark A. van de Wiel
- 3Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, Netherlands
| | | | - Gerrit A. Meijer
- 1Department of Pathology, VU University Medical Center, Amsterdam, Netherlands
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Fijneman RJ, Kant H, de Wit M, Piersma SR, Pham TV, Warmoes M, Mongera S, Verheul HM, Meijer GA, Jimenez CR. Abstract 4627: Proximal fluid proteome profiling of human colorectal cancer tissue reveals candidate biomarkers for CRC screening. Cancer Res 2010. [DOI: 10.1158/1538-7445.am10-4627] [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: Colorectal cancer (CRC) is the second leading cause of cancer death in the Western world. Detection of CRC at an early stage of disease is associated with a much better prognosis for the patient, and is a realistic approach to reduce CRC mortality rates. Several randomised trials have shown that FOBT screening, ie detection of blood-derived haem in feces, reduces CRC mortality by ∼16%. However, it is commonly recognized that sensitivity and specificity of non-invasive CRC screening tests need to be improved, for which novel biomarkers are urgently needed.
Aim: The aim of this study is to identify novel protein biomarkers that can be used for development of a blood-based or stool-based screening test for early diagnosis of CRC.
Approach: Tumor “proximal fluids” are a rich source of tumor-derived proteins, comprising proteins that are either secreted, shed by membrane vesicles (exosomes), or externalized due to cell death. Fresh human colon carcinoma tissue and matched normal colon tissue samples were obtained from four patients directly following surgery. Histological evaluation indicated large variation among tumor samples in staging (I, III, and 2x IV) and type (3 adenocarcinomas, 1 mucinous tumor). Tissues were briefly rinsed and incubated in PBS at 37°C for one hour. Proximal fluids of normal and CRC tissues were collected and subjected to in-depth proteome profiling by a GeLC-MS/MS workflow. Quantitative comparisons were based on label-free spectral counting, p-values were calculated using the Mantel Haenszel test, and the single-test threshold for significance was set to p<1e-5 to withstand correction for multiple testing. Ingenuity Pathway Analysis (IPA) was used to support data interpretation.
Results: A total of 2817 proteins were identified from proximal fluids of human colon carcinoma and patient-matched normal colon control tissues. Of these, 55 proteins were consistently and significantly (single test p<0.00001) more secreted by CRC samples than by controls. Data integration with a previously obtained mouse colon tumor proximal fluid proteome indicated 26 overlapping candidates, including several minichromosome maintenance MCM proteins that have been proposed in literature as markers for (stool-based) CRC screening.
Conclusion & Discussion: We conclude that proximal fluid proteome profiling of human CRC tissue is a powerful strategy to discover novel candidate biomarkers for CRC screening. Despite large variation in tumor stage and type between the four samples analyzed more than 50 candidate CRC biomarkers were identified. Further validation studies are required to investigate whether these candidates are robust biomarkers for CRC screening.
Acknowledgments: This research is supported by the Cancer Center Amsterdam.
Note: This abstract was not presented at the AACR 101st Annual Meeting 2010 because the presenter was unable to attend.
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 4627.
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Affiliation(s)
| | - Huub Kant
- 1VU University Medical Center, Amsterdam, Netherlands
| | - Meike de Wit
- 1VU University Medical Center, Amsterdam, Netherlands
| | | | - Thang V. Pham
- 1VU University Medical Center, Amsterdam, Netherlands
| | - Marc Warmoes
- 1VU University Medical Center, Amsterdam, Netherlands
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Sillars-Hardebol AH, Carvalho B, de Wit M, Postma C, Delis-van Diemen PM, Mongera S, Ylstra B, van de Wiel MA, Meijer GA, Fijneman RJA. Identification of key genes for carcinogenic pathways associated with colorectal adenoma-to-carcinoma progression. Tumour Biol 2010; 31:89-96. [PMID: 20358421 PMCID: PMC2848338 DOI: 10.1007/s13277-009-0012-1] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Accepted: 12/21/2009] [Indexed: 12/04/2022] Open
Abstract
Colorectal adenomas form a biologically and clinically distinct intermediate stage in development of colorectal cancer (CRC) from normal colon epithelium. Only 5% of adenomas progress into adenocarcinomas, indicating that malignant transformation requires other biological alterations than those involved in adenoma formation. The present study aimed to explore which cancer-related biological processes are affected during colorectal adenoma-to-carcinoma progression and to identify key genes within these pathways that can serve as tumor markers for malignant transformation. The activity of 12 cancer-related biological processes was compared between 37 colorectal adenomas and 31 adenocarcinomas, using the pathway analysis tool Gene Set Enrichment Analysis. Expression of six gene sets was significantly increased in CRCs compared to adenomas, representing chromosomal instability, proliferation, differentiation, invasion, stroma activation, and angiogenesis. In addition, 18 key genes were identified for these processes based on their significantly increased expression levels. For AURKA and PDGFRB, increased mRNA expression levels were verified at the protein level by immunohistochemical analysis of a series of adenomas and CRCs. This study revealed cancer-related biological processes whose activities are increased during malignant transformation and identified key genes which may be used as tumor markers to improve molecular characterization of colorectal tumors.
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Affiliation(s)
- Anke H. Sillars-Hardebol
- Department of Pathology (Tumor Profiling Unit), VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Beatriz Carvalho
- Department of Pathology (Tumor Profiling Unit), VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Meike de Wit
- Department of Pathology (Tumor Profiling Unit), VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Cindy Postma
- Department of Pathology (Tumor Profiling Unit), VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Pien M. Delis-van Diemen
- Department of Pathology (Tumor Profiling Unit), VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Sandra Mongera
- Department of Pathology (Tumor Profiling Unit), VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Bauke Ylstra
- Department of Pathology (Tumor Profiling Unit), VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Mark A. van de Wiel
- Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands
- Department of Mathematics, VU University, Amsterdam, The Netherlands
| | - Gerrit A. Meijer
- Department of Pathology (Tumor Profiling Unit), VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
| | - Remond J. A. Fijneman
- Department of Pathology (Tumor Profiling Unit), VU University Medical Center, De Boelelaan 1117, 1081HV Amsterdam, The Netherlands
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Albrethsen J, Knol JC, Piersma SR, Pham TV, de Wit M, Mongera S, Carvalho B, Verheul HMW, Fijneman RJA, Meijer GA, Jimenez CR. Subnuclear proteomics in colorectal cancer: identification of proteins enriched in the nuclear matrix fraction and regulation in adenoma to carcinoma progression. Mol Cell Proteomics 2010; 9:988-1005. [PMID: 20089989 DOI: 10.1074/mcp.m900546-mcp200] [Citation(s) in RCA: 57] [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] [Indexed: 12/25/2022] Open
Abstract
Abnormalities in nuclear phenotype and chromosome structure are key features of cancer cells. Investigation of the protein determinants of nuclear subfractions in cancer may yield molecular insights into aberrant chromosome function and chromatin organization and in addition may yield biomarkers for early cancer detection. Here we evaluate a proteomics work flow for profiling protein constituents in subnuclear domains in colorectal cancer tissues and apply this work flow to a comparative analysis of the nuclear matrix fraction in colorectal adenoma and carcinoma tissue samples. First, we established the reproducibility of the entire work flow. In a reproducibility analysis of three nuclear matrix fractions independently isolated from the same colon tumor homogenate, 889 of 1,047 proteins (85%) were reproducibly identified at high confidence (minimally two peptides per protein at 99% confidence interval at the protein level) with an average coefficient of variance for the number of normalized spectral counts per protein of 30%. This indicates a good reproducibility of the entire work flow from biochemical isolation to nano-LC-MS/MS analysis. Second, using spectral counting combined with statistics, we identified proteins that are significantly enriched in the nuclear matrix fraction relative to two earlier fractions (the chromatin-binding and intermediate filament fractions) isolated from six colorectal tissue samples. The total data set contained 2,059 non-redundant proteins. Gene ontology mining and protein network analysis of nuclear matrix-enriched proteins revealed enrichment for proteins implicated in "RNA processing" and "mRNA metabolic process." Finally, an explorative comparison of the nuclear matrix proteome in colorectal adenoma and carcinoma tissues revealed many proteins previously implicated in oncogenesis as well as new candidates. A subset of these differentially expressed proteins also exhibited a corresponding change at the mRNA level. Together, the results show that subnuclear proteomics of tumor tissue is feasible and a promising avenue for exploring oncogenesis.
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Affiliation(s)
- Jakob Albrethsen
- OncoProteomics Laboratory, Department of Medical Oncology, VU University Medical Center (VUmc)-Cancer Center Amsterdam, The Netherlands
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