Sebastiaan van Heesch Group

Microprotein biology and immunotherapy target discovery in childhood cancer

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Our Focus

At the Princess Máxima Center, Europe’s largest research hospital fully dedicated to childhood cancer, our lab specializes in advancing microprotein biology and immunotherapy target discovery. We develop and apply cutting-edge sequencing, proteomics, and computational methods to uncover and study the “dark genome” and proteome, with a focus on identifying novel human microproteins. These small proteins hold vast potential for understanding the mechanisms driving cancer and for developing innovative therapeutic targets.  

  

Central to our research is ribosome profiling (Ribo-seq), a powerful tool to investigate the translational landscape of cancer cells, revealing new insights into RNA usage and microprotein production. By integrating Ribo-seq with advanced genomic, transcriptomic, and proteomic approaches, we aim to uncover actionable targets for precision immunotherapies and cancer vaccines, benefiting both paediatric and adult patients.  

  

Additionally, we co-lead an international consortium to establish standards for identifying, annotating, and interpreting non-canonical open reading frames (ORFs) and newly discovered proteins. Our interdisciplinary approach bridges fundamental research and translational applications, paving the way for personalized treatments that align with the unique molecular profiles of individual patients.  

Main research questions:  

  

What are the roles of novel human microproteins in paediatric and adult cancers?  

How can these microproteins be harnessed as targets for cancer immunotherapies and vaccines?  

About Sebastiaan van Heesch

My Research

Sebastiaan van Heesch is a group leader at Princess Máxima Center for Pediatric Oncology, a junior Oncode Investigator at Oncode Institute, and vice chair of the Therapeutic Vaccines workstream at Oncode Accelerator - a Dutch nation-wide program that aims to accelerate the preclinical development of cancer vaccines. Trained at the Hubrecht Institute (PhD) and the MDC Berlin (postdoc), Sebastiaan has developed a passion for RNA systems biology, proteogenomics, and cancer immunotherapy. Within the Princess Máxima Center - Europe’s largest research hospital fully dedicated to battling childhood cancer, the van Heesch lab develops and applies advanced sequencing and computational methods to find and characterize new microproteins, find new cancer mechanisms, and select those microproteins that may serve as targets for immunotherapy.

Awards
  • 2023: NWO VIDI Award

  • 2019: DZHK Postdoc Excellence Award

  • 2015: NWO Rubicon Award

  • 2015: EMBO Long-Term Fellowship

Key Publications
  1. Hofman DA, Ruiz-Orera J, Yannuzzi I, Murugesan R, Brown A, Clauser KR, Condurat AL, van Dinter JT, Engels SAG, Goodale A, van der Lugt J, Abid T, Wang L, Zhou KN, Vogelzang J, Ligon KL, Phoenix TN, Roth JA, Root DE, Hubner N, Golub TR, Bandopadhayay P, van Heesch S, Prensner JR. Translation of non-canonical open reading frames as a cancer cell survival mechanism in childhood medulloblastoma. Molecular Cell (2024) Jan 261-276. e18. doi: https://doi.org/10.1016/j.molcel.2023.12.003

  2. Prensner JR, Abelin JG, Kok LW, Clauser KR, Mudge JM, Ruiz-Orera J, Bassani-Sternberg M, Deutsch EW, van Heesch S. What can Ribo-seq, immunopeptidomics, and proteomics tell us about the non-canonical proteome? Molecular Cellular Proteomics. (2023) Aug 10:100631. doi: https://doi.org/10.1016/j.mcpro.2023.100631

  3. Sandmann CL, Schulz JF, Ruiz-Orera J, Kirchner M, Ziehm M, Adami E, Marczenke M, Christ A, Liebe N, Greiner J, Schoenenberger A, Muecke MB, Liang N, Moritz RL, Sun Z, Deutsch EW, Gotthardt M, Mudge JM, Prensner JR, Willnow TE, Mertins P, van Heesch S, Hubner N. Evolutionary origins and interactomes of human, young microproteins and small peptides translated from short open reading frames. Molecular Cell (2023) Mar 16;83(6):994-1011.e18. doi: https://doi.org/10.1016/j.molcel.2023.01.023

  4. Mudge JM, Ruiz-Orera J, Prensner JR, Brunet MA, Calvet F, Jungreis I, Gonzalez JM, Magrane M, Martinez TF, Schulz JF, Yang YT, Albà MM, Aspden JL, Baranov PV, Bazzini AA, Bruford E, Martin MJ, Calviello L, Carvunis AR, Chen J, Couso JP, Deutsch EW, Flicek P, Frankish A, Gerstein M, Hubner N, Ingolia NT, Kellis M, Menschaert G, Moritz RL, Ohler U, Roucou X, Saghatelian A, Weissman JS, van Heesch S. Standardized annotation of translated open reading frames. Nature Biotechnology (2022) Jul;40(7):994-999. https://doi.org/10.1038/s41587-022-01369-0

  5. van Heesch S, Witte F, Schneider-Lunitz V, Schulz JF, Adami E, Faber AB, Kirchner M, Maatz H, Blachut S, Sandmann CL, Kanda M, Worth CL, Schafer S, Calviello L, Merriott R, Patone G, Hummel O, Wyler E, Obermayer B, Mücke MB, Lindberg EL, Trnka F, Memczak S, Schilling M, Felkin LE, Barton PJR, Quaife NM, Vanezis K, Diecke S, Mukai M, Mah N, Oh SJ, Kurtz A, Schramm C, Schwinge D, Sebode M, Harakalova M, Asselbergs FW, Vink A, de Weger RA, Viswanathan S, Widjaja AA, Gärtner-Rommel A, Milting H, Dos Remedios C, Knosalla C, Mertins P, Landthaler M, Vingron M, Linke WA, Seidman JG, Seidman CE, Rajewsky N, Ohler U, Cook SA, Hubner N. The Translational Landscape of the Human Heart. Cell (2019) 178(1):242-260.e29. https://doi.org/10.1016/j.cell.2019.05.010

Members

Sebastiaan van Heesch
Group leader
Alisa Potter    
Phd student
Ana Pinheiro Lopes    
Postdoc
Damon Hofman    
Phd student
Edwin Werf    
Technician
Emma Westerink    
Research analist
Ferhat Alkan    
Technician
Kazuma Nakatani    
Postdoc
Komal Yadav    
Research analist
Leron Kok    
Phd student
Luuk Broeils    
Phd student
Marina Reixachs Sole    
Phd student
Martina Jovancheva    
Phd student
Sanne Luijcx    
Technician
Simon Venneman    
Project manager
Ting Luo    
Reseach Analist
Wouter Makkinje    
Technician