Search

Your search keyword '"Heesch, Sebastiaan Van"' showing total 12 results
Start Over Author "Heesch, Sebastiaan Van"
12 results on '"Heesch, Sebastiaan Van"'

1. Figure S10 from The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy

Author

Martin, Michael V., primary, Aguilar-Rosas, Salvador, primary, Franke, Katka, primary, Pieterse, Mark, primary, Langelaar, Jamie van, primary, Schreurs, Renée, primary, Bijlsma, Maarten F., primary, Besselink, Marc G., primary, Koster, Jan, primary, Timens, Wim, primary, Khasraw, Mustafa, primary, Ashley, David M., primary, Keir, Stephen T., primary, Ottensmeier, Christian H., primary, King, Emma V., primary, Verheij, Joanne, primary, Waasdorp, Cynthia, primary, Valk, Peter J.M., primary, Engels, Sem A.G., primary, Oostenbach, Ellen, primary, van Dinter, Jip T., primary, Hofman, Damon A., primary, Mok, Juk Yee, primary, van Esch, Wim J.E., primary, Wilmink, Hanneke, primary, Monkhorst, Kim, primary, Verheul, Henk M.W., primary, Poel, Dennis, primary, Hiltermann, T. Jeroen N., primary, Kempen, Léon C.L.T. van, primary, Groen, Harry J.M., primary, Aerts, Joachim G.J.V., primary, Heesch, Sebastiaan van, primary, Löwenberg, Bob, primary, Plasterk, Ronald, primary, and Kloosterman, Wigard P., primary

Published
2024
Full Text
View/download PDF

2. Data from The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy

Author

Martin, Michael V., primary, Aguilar-Rosas, Salvador, primary, Franke, Katka, primary, Pieterse, Mark, primary, Langelaar, Jamie van, primary, Schreurs, Renée, primary, Bijlsma, Maarten F., primary, Besselink, Marc G., primary, Koster, Jan, primary, Timens, Wim, primary, Khasraw, Mustafa, primary, Ashley, David M., primary, Keir, Stephen T., primary, Ottensmeier, Christian H., primary, King, Emma V., primary, Verheij, Joanne, primary, Waasdorp, Cynthia, primary, Valk, Peter J.M., primary, Engels, Sem A.G., primary, Oostenbach, Ellen, primary, van Dinter, Jip T., primary, Hofman, Damon A., primary, Mok, Juk Yee, primary, van Esch, Wim J.E., primary, Wilmink, Hanneke, primary, Monkhorst, Kim, primary, Verheul, Henk M.W., primary, Poel, Dennis, primary, Hiltermann, T. Jeroen N., primary, Kempen, Léon C.L.T. van, primary, Groen, Harry J.M., primary, Aerts, Joachim G.J.V., primary, Heesch, Sebastiaan van, primary, Löwenberg, Bob, primary, Plasterk, Ronald, primary, and Kloosterman, Wigard P., primary

Published
2024
Full Text
View/download PDF

3. Supplementary Tables S1-S12 from The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy

Author

Martin, Michael V., primary, Aguilar-Rosas, Salvador, primary, Franke, Katka, primary, Pieterse, Mark, primary, Langelaar, Jamie van, primary, Schreurs, Renée, primary, Bijlsma, Maarten F., primary, Besselink, Marc G., primary, Koster, Jan, primary, Timens, Wim, primary, Khasraw, Mustafa, primary, Ashley, David M., primary, Keir, Stephen T., primary, Ottensmeier, Christian H., primary, King, Emma V., primary, Verheij, Joanne, primary, Waasdorp, Cynthia, primary, Valk, Peter J.M., primary, Engels, Sem A.G., primary, Oostenbach, Ellen, primary, van Dinter, Jip T., primary, Hofman, Damon A., primary, Mok, Juk Yee, primary, van Esch, Wim J.E., primary, Wilmink, Hanneke, primary, Monkhorst, Kim, primary, Verheul, Henk M.W., primary, Poel, Dennis, primary, Hiltermann, T. Jeroen N., primary, Kempen, Léon C.L.T. van, primary, Groen, Harry J.M., primary, Aerts, Joachim G.J.V., primary, Heesch, Sebastiaan van, primary, Löwenberg, Bob, primary, Plasterk, Ronald, primary, and Kloosterman, Wigard P., primary

Published
2024
Full Text
View/download PDF

5. Small Nucleolar RNAs: Players in Human Development and Disease

Author

Verstappen, Noud, Heesch, Sebastiaan van (Thesis Advisor), Verstappen, Noud, and Heesch, Sebastiaan van (Thesis Advisor)

Abstract

Throughout the late 20th century, small nucleolar RNAs (snoRNAs) were identified as a novel class of non-coding RNA. SnoRNAs comprise three main classes based on conserved sequence motifs: C/D box, H/ACA box and Cajal body-associated snoRNAs. Their canonical function is to provide specificity to discrete ribonucleoprotein complexes, which post-transcriptionally modify ribosomal RNAs and spliceosomal small nuclear RNAs. It has become increasingly clear that snoRNAs can adopt unexpected cellular functions, ranging from the regulation of chromatin states to cell-cell communication. In addition, snoRNAs are intimately involved in cellular programs critical to development, as revealed by studies from model organisms. In this writing assignment, the ever expanding repertoire of snoRNA biology will be reviewed with an ultimate focus on developmental disease.

Published
2023

6. Standardized annotation of translated open reading frames

Author

Wellcome Trust, National Human Genome Research Institute (US), European Molecular Biology Laboratory, National Institutes of Health (US), State Secretariat for Education, Research and Innovation (Switzerland), Stowers Institute for Medical Research, Cancer Prevention and Research Institute of Texas, Howard Hughes Medical Institute, Russian Science Foundation, European Research Council, European Commission, Fondation Leducq, Canadian Institutes of Health Research, Canada Research Chairs, National Science Foundation (US), Medical Research Council (UK), Fonds de Recherche du Québec, Mudge, Jonathan M., Ruiz-Orera, Jorge, Prensner, John R., Brunet, Marie A., Calvet, Ferriol, Jungreis, Irwin, González, José Manuel, Magrane, Michele, Martinez, Thomas F., Felicitas Schulz, Jana, Yang, Yucheng T., Albà, M. Mar, Aspden, Julie Louise, Baranov, Pavel V., Bazzini, Ariel A., Bruford, Elspeth, Martín, María Jesús, Calviello, Lorenzo, Chen, Jin, Couso, Juan Pablo, Deutsch, Eric W., Flicek, Paul, Frankish, Adam, Gerstein, Mark, Hubner, Norbert, Ingolia, Nicholas T., Kellis, Manolis, Menschaert, Gerben, Moritz, Robert L., Ohler, Uwe, Roucou, Xavier, Saghatelian, Alan, Weissman, Jonathan S., Heesch, Sebastiaan van, Wellcome Trust, National Human Genome Research Institute (US), European Molecular Biology Laboratory, National Institutes of Health (US), State Secretariat for Education, Research and Innovation (Switzerland), Stowers Institute for Medical Research, Cancer Prevention and Research Institute of Texas, Howard Hughes Medical Institute, Russian Science Foundation, European Research Council, European Commission, Fondation Leducq, Canadian Institutes of Health Research, Canada Research Chairs, National Science Foundation (US), Medical Research Council (UK), Fonds de Recherche du Québec, Mudge, Jonathan M., Ruiz-Orera, Jorge, Prensner, John R., Brunet, Marie A., Calvet, Ferriol, Jungreis, Irwin, González, José Manuel, Magrane, Michele, Martinez, Thomas F., Felicitas Schulz, Jana, Yang, Yucheng T., Albà, M. Mar, Aspden, Julie Louise, Baranov, Pavel V., Bazzini, Ariel A., Bruford, Elspeth, Martín, María Jesús, Calviello, Lorenzo, Chen, Jin, Couso, Juan Pablo, Deutsch, Eric W., Flicek, Paul, Frankish, Adam, Gerstein, Mark, Hubner, Norbert, Ingolia, Nicholas T., Kellis, Manolis, Menschaert, Gerben, Moritz, Robert L., Ohler, Uwe, Roucou, Xavier, Saghatelian, Alan, Weissman, Jonathan S., and Heesch, Sebastiaan van

Abstract

Ribosome profiling (Ribo-seq) has extended our understanding of the translational ‘vocabulary’ of the human genome, uncovering thousands of open reading frames (ORFs) within long noncoding RNAs (lncRNAs) and presumed untranslated regions (UTRs) of protein-coding genes. However, reference gene annotation projects have been circumspect in their incorporation of these ORFs because of uncertainties about their experimental reproducibility and physiological roles. Yet, it is clear that certain ‘Ribo-seq ORFs’ make stable proteins, others mediate gene regulation, and many have medical implications. Ultimately, the absence of standardized ORF annotation has created a circular problem: while Ribo-seq ORFs remain unrecognized by reference annotation databases, this lack of recognition will thwart studies examining their roles. Here, we outline a community-led effort involving Ensembl/GENCODE, the HUGO Gene Nomenclature Committee (HGNC), UniProtKB, HUPO/HPP and PeptideAtlas to produce a standardized catalog of 7,264 human Ribo-seq ORFs; a path to bring protein-level evidence for Ribo-seq ORFs into reference annotation databases; and a roadmap to facilitate research in the global community.

Published
2022

7. Quantitative and qualitative liver proteome characteriztics of two inbred rat strains from integrative transcriptomics and proteomics analysis

Author

Teck Yew Low, Heesch, Sebastiaan Van, Toorn, Henk Van Den, Giansanti, Piero, Cristobal, Alba, Breukelen, Bas Van, Shabaz Mohammed, Cuppen, Edwin, Albert JR Heck, and Guryev, Victor

Abstract

presented in: ASMS in Minneapolis, Minnesota 2013 With whole genome sequence data and de novo transcriptome assembly from 2 inbred rat strains, we extended the publicly available rat proteindatabase with novel protein predictions, transcript isoforms and RNAediting events. By performing ultra-deep proteomics, we identi ed 27,038 protein entries from this database with 0% FDR. Our data encompasses evidence, in the form of unique peptides, for 792 GENSCAN predictions, 112 non-synonymous SNVs and 118 novel RNA-editing and RNA splicing events. .

Published
2014
Full Text
View/download PDF

8. Quantitative and qualitative liver proteome characteriztics of two inbred rat strains from integrative transcriptomics and proteomics

Author

Teck Yew Low, Heesch, Sebastiaan Van, Toorn, Henk Van Den, Breukelen, Bas Van, Shabaz Mohammed, Cuppen, Edwin, Albert JR Heck, and Guryev, Victor

Abstract

presented in:Keystone Symposia: Omics Meets Cell Biology: Applications to Human Health and Disease in Taos, New Mexico, 2014 Quantitative and qualitative protein characteristics differ between individuals and are regulated at genomic, transcriptomic and post-transcriptional levels. Here, we integrated in-depth transcriptome and proteome analyses of liver tissues from two rat strains to unravel the interactions within and between these layers. We obtained peptide evidence for 12,989 rat liver proteins, including 792 novel gene predictions, 337 novel splice events, 112 non-synonymous variants, and 54 RNA editing sites. Respectively, quantitative RNA-Seq and proteomics data correlate highly between strains, but poorly when two data types are compared within a strain, indicating extensive non-genetic regulation. Our multi-level analysis identified a genomic variant in the promoter of the most differentially expressed gene Cyp17a1, a previously reported top hit in GWAS for human hypertension, as a potential contributor to the hypertension phenotype in SHR rats. These results demonstrate the power of and need for integrative analysis for understanding genetic control of molecular dynamics and phenotypic diversity in a system-wide manner.

Published
2014
Full Text
View/download PDF

9. PLETHORA Gene Regulatory Network Guides Growth and Cell Differentiation in Arabidopsis Roots.

Author

Santuari, Luca, Sanchez-Perez, Gabino F., Luijten, Marijn, Rutjens, Bas, Terpstra, Inez, Berke, Lidija, Gorte, Maartje, Prasad, Kalika, Bao, Dongping, Timmermans-Hereijgers, Johanna L.P.M., Maeo, Kenichiro, Nakamura, Kenzo, Shimotohno, Akie, Pencik, Ales, Novak, Ondrej, Ljung, Karin, Heesch, Sebastiaan van, Bruijn, Ewart de, Cuppen, Edwin, and Willemsen, Viola

Published
2016
Full Text
View/download PDF

10. Additional file 1: of Molecular dissection of germline chromothripsis in a developmental context using patient-derived iPS cells

Author

Middelkamp, Sjors, Heesch, Sebastiaan Van, A. Braat, Ligt, Joep De, Iterson, Maarten Van, Simonis, Marieke, Roosmalen, Markus Van, Kelder, Martijn, Kruisselbrink, Evelien, Hochstenbach, Ron, Verbeek, Nienke, Ippel, Elly, Adolfs, Youri, R. Pasterkamp, Wigard Kloosterman, Ewart Kuijk, and Cuppen, Edwin

Subjects
3. Good health
Abstract

Document containing all supplemental figures and legends. (PDF 30908Â kb)

11. Additional file 1: of Molecular dissection of germline chromothripsis in a developmental context using patient-derived iPS cells

Author

Middelkamp, Sjors, Heesch, Sebastiaan Van, A. Braat, Ligt, Joep De, Iterson, Maarten Van, Simonis, Marieke, Roosmalen, Markus Van, Kelder, Martijn, Kruisselbrink, Evelien, Hochstenbach, Ron, Verbeek, Nienke, Ippel, Elly, Adolfs, Youri, R. Pasterkamp, Wigard Kloosterman, Ewart Kuijk, and Cuppen, Edwin

Subjects
3. Good health
Abstract

Document containing all supplemental figures and legends. (PDF 30908Â kb)

12. The Neo-Open Reading Frame Peptides That Comprise the Tumor Framome Are a Rich Source of Neoantigens for Cancer Immunotherapy.

Author

Martin MV, Aguilar-Rosas S, Franke K, Pieterse M, Langelaar JV, Schreurs R, Bijlsma MF, Besselink MG, Koster J, Timens W, Khasraw M, Ashley DM, Keir ST, Ottensmeier CH, King EV, Verheij J, Waasdorp C, Valk PJM, Engels SAG, Oostenbach E, van Dinter JT, Hofman DA, Mok JY, van Esch WJE, Wilmink H, Monkhorst K, Verheul HMW, Poel D, Hiltermann TJN, Kempen LCLTV, Groen HJM, Aerts JGJV, Heesch SV, Löwenberg B, Plasterk R, and Kloosterman WP

Subjects
Humans, Peptides immunology, Antigens, Neoplasm immunology, Antigens, Neoplasm genetics, Immunotherapy methods, Open Reading Frames, Neoplasms immunology, Neoplasms therapy
Abstract

Identification of immunogenic cancer neoantigens as targets for therapy is challenging. Here, we integrate the whole-genome and long-read transcript sequencing of cancers to identify the collection of neo-open reading frame peptides (NOP) expressed in tumors. We termed this collection of NOPs the tumor framome. NOPs represent tumor-specific peptides that are different from wild-type proteins and may be strongly immunogenic. We describe a class of hidden NOPs that derive from structural genomic variants involving an upstream protein coding gene driving expression and translation of noncoding regions of the genome downstream of a rearrangement breakpoint, i.e., where no gene annotation or evidence for transcription exists. The entire collection of NOPs represents a vast number of possible neoantigens particularly in tumors with many structural genomic variants and a low number of missense mutations. We show that NOPs are immunogenic and epitopes derived from NOPs can bind to MHC class I molecules. Finally, we provide evidence for the presence of memory T cells specific for hidden NOPs in peripheral blood from a patient with lung cancer. This work highlights NOPs as a major source of possible neoantigens for personalized cancer immunotherapy and provides a rationale for analyzing the complete cancer genome and transcriptome as a basis for the detection of NOPs., (©2024 American Association for Cancer Research.)

Published
2024
Full Text
View/download PDF

Catalog

Books, media, physical & digital resources
See catalog results