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252 results on '"Vermeulen, P B"'

1. The Effect of Histopathological Growth Patterns of Colorectal Liver Metastases on the Survival Benefit of Adjuvant Hepatic Arterial Infusion Pump Chemotherapy

Author

Filipe, W. F., Meyer, Y. M., Buisman, F. E., van den Braak, R. R. J. Coebergh, Galjart, B., Höppener, D. J., Jarnagin, W. R., Kemeny, N. E., Kingham, T. P., Nierop, P. M. H., van der Stok, E. P., Grünhagen, D. J., Vermeulen, P. B., Groot Koerkamp, B., Verhoef, C., and D’Angelica, M. I.

Published
2023
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2. An idiosyncratic zonated stroma encapsulates desmoplastic liver metastases and originates from injured liver

Author

Fernández Moro, Carlos, Geyer, Natalie, Harrizi, Sara, Hamidi, Yousra, Söderqvist, Sara, Kuznyecov, Danyil, Tidholm Qvist, Evelina, Salmonson Schaad, Media, Hermann, Laura, Lindberg, Amanda, Heuchel, Rainer L., Martín-Bernabé, Alfonso, Dhanjal, Soniya, Navis, Anna C., Villard, Christina, del Valle, Andrea C., Bozóky, Lorand, Sparrelid, Ernesto, Dirix, Luc, Strell, Carina, Östman, Arne, Schmierer, Bernhard, Vermeulen, Peter B., Engstrand, Jennie, Bozóky, Béla, and Gerling, Marco

Published
2023
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3. Reproducible radiomics through automated machine learning validated on twelve clinical applications

Author

Starmans, Martijn P. A., van der Voort, Sebastian R., Phil, Thomas, Timbergen, Milea J. M., Vos, Melissa, Padmos, Guillaume A., Kessels, Wouter, Hanff, David, Grunhagen, Dirk J., Verhoef, Cornelis, Sleijfer, Stefan, Bent, Martin J. van den, Smits, Marion, Dwarkasing, Roy S., Els, Christopher J., Fiduzi, Federico, van Leenders, Geert J. L. H., Blazevic, Anela, Hofland, Johannes, Brabander, Tessa, van Gils, Renza A. H., Franssen, Gaston J. H., Feelders, Richard A., de Herder, Wouter W., Buisman, Florian E., Willemssen, Francois E. J. A., Koerkamp, Bas Groot, Angus, Lindsay, van der Veldt, Astrid A. M., Rajicic, Ana, Odink, Arlette E., Deen, Mitchell, T., Jose M. Castillo, Veenland, Jifke, Schoots, Ivo, Renckens, Michel, Doukas, Michail, de Man, Rob A., IJzermans, Jan N. M., Miclea, Razvan L., Vermeulen, Peter B., Bron, Esther E., Thomeer, Maarten G., Visser, Jacob J., Niessen, Wiro J., and Klein, Stefan

Subjects
Electrical Engineering and Systems Science - Image and Video Processing, Computer Science - Computer Vision and Pattern Recognition
Abstract

Radiomics uses quantitative medical imaging features to predict clinical outcomes. Currently, in a new clinical application, finding the optimal radiomics method out of the wide range of available options has to be done manually through a heuristic trial-and-error process. In this study we propose a framework for automatically optimizing the construction of radiomics workflows per application. To this end, we formulate radiomics as a modular workflow and include a large collection of common algorithms for each component. To optimize the workflow per application, we employ automated machine learning using a random search and ensembling. We evaluate our method in twelve different clinical applications, resulting in the following area under the curves: 1) liposarcoma (0.83); 2) desmoid-type fibromatosis (0.82); 3) primary liver tumors (0.80); 4) gastrointestinal stromal tumors (0.77); 5) colorectal liver metastases (0.61); 6) melanoma metastases (0.45); 7) hepatocellular carcinoma (0.75); 8) mesenteric fibrosis (0.80); 9) prostate cancer (0.72); 10) glioma (0.71); 11) Alzheimer's disease (0.87); and 12) head and neck cancer (0.84). We show that our framework has a competitive performance compared human experts, outperforms a radiomics baseline, and performs similar or superior to Bayesian optimization and more advanced ensemble approaches. Concluding, our method fully automatically optimizes the construction of radiomics workflows, thereby streamlining the search for radiomics biomarkers in new applications. To facilitate reproducibility and future research, we publicly release six datasets, the software implementation of our framework, and the code to reproduce this study., Comment: 33 pages, 4 figures, 4 tables, 2 supplementary figures, 3 supplementary table, submitted to Medical Image Analysis; revision

Published
2021

4. Histopathological growth patterns of liver metastasis: updated consensus guidelines for pattern scoring, perspectives and recent mechanistic insights

Author

Latacz, Emily, Höppener, Diederik, Bohlok, Ali, Leduc, Sophia, Tabariès, Sébastien, Fernández Moro, Carlos, Lugassy, Claire, Nyström, Hanna, Bozóky, Béla, Floris, Giuseppe, Geyer, Natalie, Brodt, Pnina, Llado, Laura, Van Mileghem, Laura, De Schepper, Maxim, Majeed, Ali W., Lazaris, Anthoula, Dirix, Piet, Zhang, Qianni, Petrillo, Stéphanie K., Vankerckhove, Sophie, Joye, Ines, Meyer, Yannick, Gregorieff, Alexander, Roig, Nuria Ruiz, Vidal-Vanaclocha, Fernando, Denis, Larsimont, Oliveira, Rui Caetano, Metrakos, Peter, Grünhagen, Dirk J., Nagtegaal, Iris D., Mollevi, David G., Jarnagin, William R., D’Angelica, Michael I, Reynolds, Andrew R., Doukas, Michail, Desmedt, Christine, Dirix, Luc, Donckier, Vincent, Siegel, Peter M., Barnhill, Raymond, Gerling, Marco, Verhoef, Cornelis, and Vermeulen, Peter B.

Published
2022
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9. Consensus guidelines for the use and interpretation of angiogenesis assays

Author

Nowak-Sliwinska, Patrycja, Alitalo, Kari, Allen, Elizabeth, Anisimov, Andrey, Aplin, Alfred C, Auerbach, Robert, Augustin, Hellmut G, Bates, David O, van Beijnum, Judy R, Bender, R Hugh F, Bergers, Gabriele, Bikfalvi, Andreas, Bischoff, Joyce, Böck, Barbara C, Brooks, Peter C, Bussolino, Federico, Cakir, Bertan, Carmeliet, Peter, Castranova, Daniel, Cimpean, Anca M, Cleaver, Ondine, Coukos, George, Davis, George E, De Palma, Michele, Dimberg, Anna, Dings, Ruud PM, Djonov, Valentin, Dudley, Andrew C, Dufton, Neil P, Fendt, Sarah-Maria, Ferrara, Napoleone, Fruttiger, Marcus, Fukumura, Dai, Ghesquière, Bart, Gong, Yan, Griffin, Robert J, Harris, Adrian L, Hughes, Christopher CW, Hultgren, Nan W, Iruela-Arispe, M Luisa, Irving, Melita, Jain, Rakesh K, Kalluri, Raghu, Kalucka, Joanna, Kerbel, Robert S, Kitajewski, Jan, Klaassen, Ingeborg, Kleinmann, Hynda K, Koolwijk, Pieter, Kuczynski, Elisabeth, Kwak, Brenda R, Marien, Koen, Melero-Martin, Juan M, Munn, Lance L, Nicosia, Roberto F, Noel, Agnes, Nurro, Jussi, Olsson, Anna-Karin, Petrova, Tatiana V, Pietras, Kristian, Pili, Roberto, Pollard, Jeffrey W, Post, Mark J, Quax, Paul HA, Rabinovich, Gabriel A, Raica, Marius, Randi, Anna M, Ribatti, Domenico, Ruegg, Curzio, Schlingemann, Reinier O, Schulte-Merker, Stefan, Smith, Lois EH, Song, Jonathan W, Stacker, Steven A, Stalin, Jimmy, Stratman, Amber N, Van de Velde, Maureen, van Hinsbergh, Victor WM, Vermeulen, Peter B, Waltenberger, Johannes, Weinstein, Brant M, Xin, Hong, Yetkin-Arik, Bahar, Yla-Herttuala, Seppo, Yoder, Mervin C, and Griffioen, Arjan W

Subjects
Biochemistry and Cell Biology, Biological Sciences, Regenerative Medicine, Animals, Biological Assay, Guidelines as Topic, Humans, Mice, Neoplasms, Neovascularization, Pathologic, Angiogenesis, Aortic ring, Endothelial cell migration, Proliferation, Microfluidic, Zebrafish, Chorioallantoic membrane, Vascular network, Intussusceptive angiogenesis, Retinal vasculature, Corneal angiogenesis, Hindlimb ischemia, Myocardial angiogenesis, Recombinant proteins, Tip cells, Plug assay, Vessel co-option, Clinical Sciences, Pharmacology and Pharmaceutical Sciences, Oncology & Carcinogenesis, Biochemistry and cell biology
Abstract

The formation of new blood vessels, or angiogenesis, is a complex process that plays important roles in growth and development, tissue and organ regeneration, as well as numerous pathological conditions. Angiogenesis undergoes multiple discrete steps that can be individually evaluated and quantified by a large number of bioassays. These independent assessments hold advantages but also have limitations. This article describes in vivo, ex vivo, and in vitro bioassays that are available for the evaluation of angiogenesis and highlights critical aspects that are relevant for their execution and proper interpretation. As such, this collaborative work is the first edition of consensus guidelines on angiogenesis bioassays to serve for current and future reference.

Published
2018

12. Histopathological growth patterns as biomarker for adjuvant systemic chemotherapy in patients with resected colorectal liver metastases

Author

Buisman, Florian E., van der Stok, Eric P., Galjart, Boris, Vermeulen, Peter B., Balachandran, Vinod P., Coebergh van den Braak, Robert R. J., Creasy, John M., Höppener, Diederik J., Jarnagin, William R., Kingham, T. Peter, Nierop, Pieter M. H., Sadot, Eran, Shia, Jinru, Groot Koerkamp, Bas, Grünhagen, Dirk J., D’Angelica, Michael, and Verhoef, Cornelis

Published
2020
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20. Vessel co-option mediates resistance to anti-angiogenic therapy in liver metastases

Author

Frentzas, Sophia, Simoneau, Eve, Bridgeman, Victoria L, Vermeulen, Peter B, Foo, Shane, Kostaras, Eleftherios, Nathan, Mark R, Wotherspoon, Andrew, Gao, Zu-hua, Shi, Yu, Van den Eynden, Gert, Daley, Frances, Peckitt, Clare, Tan, Xianming, Salman, Ayat, Lazaris, Anthoula, Gazinska, Patrycja, Berg, Tracy J, Eltahir, Zak, Ritsma, Laila, van Rheenen, Jacco, Khashper, Alla, Brown, Gina, Nyström, Hanna, Sund, Malin, Van Laere, Steven, Loyer, Evelyne, Dirix, Luc, Cunningham, David, Metrakos, Peter, and Reynolds, Andrew R

Published
2016
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39. Histopathological growth patterns of colorectal liver metastasis exhibit little heterogeneity and can be determined with a high diagnostic accuracy

Author

Höppener, D J, Nierop, P M H, Herpel, E, Rahbari, N N, Doukas, M, Vermeulen, P B, Grünhagen, D J, Verhoef, C, Höppener, D J, Nierop, P M H, Herpel, E, Rahbari, N N, Doukas, M, Vermeulen, P B, Grünhagen, D J, and Verhoef, C

Abstract

Colorectal liver metastases (CRLM) exhibit distinct histopathological growth patterns (HGPs) that are indicative of prognosis following surgical treatment. This study aims to assess the reliability and replicability of this histological biomarker. Within and between metastasis HGP concordance was analysed in patients who underwent surgery for CRLM. An independent cohort was used for external validation. Within metastasis concordance was assessed in CRLM with ≥ 2 tissue blocks. Similarly, concordance amongst multiple metastases was determined in patients with ≥ 2 resected CRLM. Diagnostic accuracy [expressed in area under the curve (AUC)] was compared by number of blocks and number of metastases scored. Interobserver agreement (Cohen's k) compared to the gold standard was determined for a pathologist and a PhD candidate without experience in HGP assessment after one and two training sessions. Both the within (95%, n = 825) and the between metastasis (90%, n = 363) HGP concordance was high. These results could be replicated in the external validation cohort with a within and between metastasis concordance of 97% and 94%, respectively. Diagnostic accuracy improved when scoring 2 versus 1 blocks(s) or CRLM (AUC = 95.9 vs. 97.7 [p = 0.039] and AUC = 96.5 vs. 93.3 [p = 0.026], respectively), but not when scoring 3 versus 2 blocks or CRLM (both p > 0.2). After two training sessions the interobserver agreement for both the pathologist and the PhD candidate were excellent (k = 0.953 and k = 0.951, respectively). The histopathological growth patterns of colorectal liver metastasis exhibit little heterogeneity and can be determined with a high diagnostic accuracy, making them a reliable and replicable histological biomarker.

Published
2019

44. Quantitative methylation profiling in tumor and matched morphologically normal tissues from breast cancer patients

Author

van Marck Eric A, van Laere Steven J, van Dam Peter, Limame Ridha, Trinh Xuan B, Svensson Cecilia, Bovie Catherine, Van der Auwera Ilse, Dirix Luc Y, and Vermeulen Peter B

Subjects
Neoplasms. Tumors. Oncology. Including cancer and carcinogens, RC254-282
Abstract

Abstract Background In the present study, we determined the gene hypermethylation profiles of normal tissues adjacent to invasive breast carcinomas and investigated whether these are associated with the gene hypermethylation profiles of the corresponding primary breast tumors. Methods A quantitative methylation-specific PCR assay was used to analyze the DNA methylation status of 6 genes (DAPK, TWIST, HIN-1, RASSF1A, RARβ2 and APC) in 9 normal breast tissue samples from unaffected women and in 56 paired cancerous and normal tissue samples from breast cancer patients. Results Normal tissue adjacent to breast cancer displayed statistically significant differences to unrelated normal breast tissues regarding the aberrant methylation of the RASSF1A (P = 0.03), RARβ2 (P = 0.04) and APC (P = 0.04) genes. Although methylation ratios for all genes in normal tissues from cancer patients were significantly lower than in the cancerous tissue from the same patient (P ≤ 0.01), in general, a clear correlation was observed between methylation ratios measured in both tissue types for all genes tested (P < 0.01). When analyzed as a categorical variable, there was a significant concordance between methylation changes in normal tissues and in the corresponding tumor for all genes tested but RASSF1A. Notably, in 73% of patients, at least one gene with an identical methylation change in cancerous and normal breast tissues was observed. Conclusions Histologically normal breast tissues adjacent to breast tumors frequently exhibit methylation changes in multiple genes. These methylation changes may play a role in the earliest stages of the development of breast neoplasia.

Published
2010
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45. mRNA expression profiles of colorectal liver metastases as a novel biomarker for early recurrence after partial hepatectomy

Author

van der Stok, E P, Smid, M, Sieuwerts, A M, Vermeulen, P B, Sleijfer, S, Ayez, N, Grünhagen, D J, Martens, J W M, Verhoef, C, van der Stok, E P, Smid, M, Sieuwerts, A M, Vermeulen, P B, Sleijfer, S, Ayez, N, Grünhagen, D J, Martens, J W M, and Verhoef, C

Abstract

BACKGROUND: Identification of specific risk groups for recurrence after surgery for isolated colorectal liver metastases (CRLM) remains challenging due to the heterogeneity of the disease. Classical clinicopathologic parameters have limited prognostic value. The aim of this study was to identify a gene expression signature measured in CRLM discriminating early from late recurrence after partial hepatectomy.METHODS: CRLM from two patient groups were collected: I) with recurrent disease ≤12 months after surgery (N = 33), and II) without recurrences and disease free for ≥36 months (N = 30). The patients were clinically homogeneous; all had a low clinical risk score (0-2) and did not receive (neo-) adjuvant chemotherapy. Total RNA was hybridised to Illumina arrays, and processed for analysis. A leave-one-out cross validation (LOOCV) analysis was performed to identify a prognostic gene expression signature.RESULTS: LOOCV yielded an 11-gene profile with prognostic value in relation to recurrent disease ≤12 months after partial hepatectomy. This signature had a sensitivity of 81.8%, with a specificity of 66.7% for predicting recurrences (≤12 months) versus no recurrences for at least 36 months after surgery (X2 P < 0.0001).CONCLUSION: The current study yielded an 11-gene signature at mRNA level in CRLM discriminating early from late or no relapse after partial hepatectomy.

Published
2016

46. Growth pattern of colorectal liver metastasis as a marker of recurrence risk

Author

Eefsen, R L, Vermeulen, P B, Christensen, I J, Laerum, O D, Mogensen, M B, Rolff, H C, Van den Eynden, G G, Høyer-Hansen, G, Osterlind, K, Vainer, B, Illemann, M, Eefsen, R L, Vermeulen, P B, Christensen, I J, Laerum, O D, Mogensen, M B, Rolff, H C, Van den Eynden, G G, Høyer-Hansen, G, Osterlind, K, Vainer, B, and Illemann, M

Abstract

Despite improved therapy of advanced colorectal cancer, the median overall survival (OS) is still low. A surgical removal has significantly improved survival, if lesions are entirely removed. The purpose of this retrospective explorative study was to evaluate the prognostic value of histological growth patterns (GP) in chemonaive and patients receiving neo-adjuvant therapy. Two-hundred-fifty-four patients who underwent liver resection of colorectal liver metastases between 2007 and 2011 were included in the study. Clinicopathological data and information on neo-adjuvant treatment were retrieved from patient and pathology records. Histological GP were evaluated and related to recurrence free and OS. Kaplan-Meier curves, log-rank test and Cox regression analysis were used. The 5-year OS was 41.8% (95% CI 33.8-49.8%). Growth pattern evaluation of the largest liver metastasis was possible in 224 cases, with the following distribution: desmoplastic 63 patients (28.1%); pushing 77 patients (34.4%); replacement 28 patients (12.5%); mixed 56 patients (25.0%). The Kaplan-Meier analyses demonstrated that patients resected for liver metastases with desmoplastic growth pattern had a longer recurrence free survival (RFS) than patients resected for non-desmoplastic liver metastases (p=0.05). When patients were stratified according to neo-adjuvant treatment in the multivariate Cox regression model, hazard ratios for RFS compared to desmoplastic were: pushing (HR=1.37, 95% CI 0.93-2.02, p=0.116), replacement (HR=2.16, 95% CI 1.29-3.62, p=0.003) and mixed (HR=1.70, 95% CI 1.12-2.59, p=0.013). This was true for chemonaive patients as well as for patients who received neo-adjuvant treatment.

Published
2015

47. Inflammation and uPAR-Expression in Colorectal Liver Metastases in Relation to Growth Pattern and Neo-adjuvant Therapy

Author

Eefsen, R L, Engelholm, L, Alpizar-Alpizar, W, Van den Eynden, G G E, Vermeulen, P B, Christensen, I J, Laerum, O D, Rolff, Hans Christian, Høyer-Hansen, G, Vainer, B, Osterlind, K, Illemann, M, Eefsen, R L, Engelholm, L, Alpizar-Alpizar, W, Van den Eynden, G G E, Vermeulen, P B, Christensen, I J, Laerum, O D, Rolff, Hans Christian, Høyer-Hansen, G, Vainer, B, Osterlind, K, and Illemann, M

Abstract

Proteolytic activity and inflammation in the tumour microenvironment affects cancer progression. In colorectal cancer (CRC) liver metastases it has been observed that three different immune profiles are present, as well as proteolytic activity, determined by the expression of urokinase-type plasminogen activator (uPAR).The main objectives of this study were to investigate uPAR expression and the density of macrophages (CD68) and T cells (CD3) as markers of inflammation in resected CRC liver metastases, where patients were neo-adjuvantly treated with chemotherapy with or without the angiogenesis inhibitor bevacizumab. Chemonaive patients served as a control group. The markers were correlated to growth patterns (GP) of liver metastases, i.e. desmoplastic, pushing and replacement GP. It was hypothesised that differences in proteolysis and inflammation could reflect tumour specific growth and therapy related changes in the tumour microenvironment. In chemonaive patients, a significantly higher level of uPAR was observed in desmoplastic liver metastases in comparison to pushing GP (p = 0.01) or replacement GP (p = 0.03). A significantly higher density of CD68 was observed in liver metastases with replacement GP in comparison to those with pushing GP (p = 0.01). In liver metastases from chemo treated patients, CD68 density was significantly higher in desmoplastic GP in comparison to pushing GP (p = 0.03). In chemo and bevacizumab treated patients only a significant lower CD3 expression was observed in liver metastases with a mixed GP than in those with desmoplastic (p = 0.01) or pushing GP (p = 0.05). Expression of uPAR and the density of macrophages at the tumour margin of liver metastasis differ between GP in the untreated patients. A higher density of T cells was observed in the bevacizumab treated patients, when desmoplastic and pushing metastases were compared to liver metastases with a mix of the GP respectively, however no specific correlations between the immun

Published
2015

48. Non-angiogenic tumours and their influence on cancer biology

Author

Donnem, Tom, Reynolds, Andrew R., Kuczynski, Elizabeth A., Gatter, Kevin, Vermeulen, Peter B., Kerbel, Robert S., Harris, Adrian L., and Pezzella, Francesco

Abstract

Solid tumours need a blood supply, and a large body of evidence has previously suggested that they can grow only if they induce the development of new blood vessels, a process known as tumour angiogenesis. On the basis of this hypothesis, it was proposed that anti-angiogenic drugs should be able to suppress the growth of all solid tumours. However, clinical experience with anti-angiogenic agents has shown that this is not always the case. Reports of tumours growing without the formation of new vessels can be found in the literature dating back to the 1800s, yet no formal recognition, description and demonstration of their special biological status was made until recently. In 1996, we formally recognized and described non-angiogenic tumours in lungs where the only blood vessels present were those originating from normal lung tissue. This is far from an isolated scenario, as non-angiogenic tumour growth has now been observed in tumours of many different organs in both humans and preclinical animal models. In this Opinion article, we summarize how these tumours were discovered and discuss what we know so far about their biology and the potential implications of this knowledge for cancer treatment.

Published
2018
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49. Detection and prognostic significance of circulating tumour cells in patients with metastatic breast cancer according to immunohistochemical subtypes

Author

Peeters, D J E, primary, van Dam, P-J, additional, Van den Eynden, G G M, additional, Rutten, A, additional, Wuyts, H, additional, Pouillon, L, additional, Peeters, M, additional, Pauwels, P, additional, Van Laere, S J, additional, van Dam, P A, additional, Vermeulen, P B, additional, and Dirix, L Y, additional

Published
2013
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50. Semiautomated isolation and molecular characterisation of single or highly purified tumour cells from CellSearch enriched blood samples using dielectrophoretic cell sorting

Author

Peeters, D J E, primary, De Laere, B, additional, Van den Eynden, G G, additional, Van Laere, S J, additional, Rothé, F, additional, Ignatiadis, M, additional, Sieuwerts, A M, additional, Lambrechts, D, additional, Rutten, A, additional, van Dam, P A, additional, Pauwels, P, additional, Peeters, M, additional, Vermeulen, P B, additional, and Dirix, L Y, additional

Published
2013
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