PI: Prof.dr. Frank Holstege
Single-cell genomics:
“Solving pediatric cancer one cell at a time.” The step from single gene to genomics approaches transformed the Life Sciences in the early part of this millennium. Single cell genomics is likely to be equally transformative. This is especially true for cancer research where it has been extremely difficult to study tumor heterogeneity - until the advent of single cell genomics that is. In collaboration with the Van Oudenaarden group, we have set up relatively cheap and robust single cell mRNA sequencing technology, along with an appropriate data processing pipeline. Often in collaboration with other groups, this is being applied across a spectrum of different research questions derived from a variety of pediatric cancers. These questions deal with developmental biology, determining the cell type of origin for example, to the composition of tumor stroma, identifying tumor-invasive immune cells, investigating tumor clonality and predicting individual treatment response.
Soft tissue sarcomas:
In children, soft tissue sarcomas have been relatively poorly studied because they consist of many different types of cancer that individually do not occur frequently. As with many other cancers, a major bottle-neck is the availability of appropriate cellular models to investigate tumor development and new treatment options. We have focused on setting up so-called tumor organoid technology in order to culture genetically stable “tumoroids”: tumor cells directly derived from primary tumors and grown under specific laboratory conditions. This is successfully working for rhabdomyosarcomas as well as for a few other soft tissue sarcoma types. Development of protocols for other soft tissue sarcomas is underway. The tumoroids that we already have in culture are now being used for drug screens, for genetic (CRISPR-Cas9) screens to find synthetic lethal pathways and the causes of treatment resistance, as well as for analysis of transcription regulation mechanisms to determine the prime tumor-driving targets of oncogenic transcription-, chromatin- and epigenetic-factors.
Pediatric cancer genomics:
An ever-growing array of genomics technologies is changing the molecular diagnosis of cancer, as well as contributing to research into cancer etiology. In collaboration with molecular pathology (Tops) and the computation group (Kemmeren), we are establishing a number of standard genomics technologies that we aim to apply to all new patients. Some of these are part of routine diagnosis. Others are more experimental, for which informed consent will be first asked. The technologies encompass whole genome sequencing (WGS), whole exome sequencing (WES), panel WES, RNA sequencing and DNA methylation analysis. These technologies will be tested side-by-side for a fixed period, after which an assessment will be made to decide which to continue and for which purpose.
Research in the Holstege group is funded by KiKa, NWO, KWF and the ERC Advanced grant project DynaMech 671174.
Kemmeren P, Sameith K, van de Pasch LA, Benschop JJ, Lenstra TL, Margaritis T, O'Duibhir E, Apweiler E, van Wageningen S, Ko CW, van Heesch S, Kashani MM, Ampatziadis-Michailidis G, Brok MO, Brabers NA, Miles AJ, Bouwmeester D, van Hooff SR, van Bakel H, Sluiters E, Bakker LV, Snel B, Lijnzaad P, van Leenen D, Groot Koerkamp MJ, Holstege FC. Large-scale genetic perturbations reveal regulatory networks and an abundance of gene-specific repressors. (2014) Cell, 157(3):740-752. PubMed PMID: 24766815
van Hooff SR, Leusink FK, Roepman P, Baatenburg de Jong RJ, Speel EJ, van den Brekel MW, van Velthuysen ML, van Diest PJ, van Es RJ, Merkx MA, Kummer JA, Leemans CR, Schuuring E, Langendijk JA, Lacko M, de Herdt MJ, Jansen JC, Brakenhoff RH, Slootweg PJ, Takes RP, Holstege FC. Validation of a gene expression signature for assessment of lymph node metastasis in oral squamous cell carcinoma. (2012) Journal of Clinical Oncology, 30(33):4104-4110. PubMed PMID: 23045589
Lenstra TL, Benschop JJ, Kim T, Schulze JM, Brabers NA, Margaritis T, van de Pasch LA, van Heesch SA, Brok MO, Groot Koerkamp MJ, Ko CW, van Leenen D, Sameith K, van Hooff SR, Lijnzaad P, Kemmeren P, Hentrich T, Kobor MS, Buratowski S, Holstege FC. The specificity and topology of chromatin interaction pathways in yeast. (2011) Molecular Cell, 42(4):536-549. PubMed PMID: 21596317
van Wageningen S, Kemmeren P, Lijnzaad P, Margaritis T, Benschop JJ, de Castro IJ, van Leenen D, Groot Koerkamp MJ, Ko CW, Miles AJ, Brabers N, Brok MO, Lenstra TL, Fiedler D, Fokkens L, Aldecoa R, Apweiler E, Taliadouros V, Sameith K, van de Pasch LA, van Hooff SR, Bakker LV, Krogan NJ, Snel B, Holstege FC Functional overlap and regulatory links shape genetic interactions between signaling pathways. (2010) Cell, 143(6):991-1004. PubMed PMID: 21145464
Roepman P, Wessels LF, Kettelarij N, Kemmeren P, Miles AJ, Lijnzaad P, Tilanus MG, Koole R, Hordijk GJ, van der Vliet PC, Reinders MJ, Slootweg PJ, Holstege FC. An expression profile for diagnosis of lymph node metastases from primary head and neck squamous cell carcinomas. (2005) Nature Genetics, 37(2):182-186. PubMed PMID: 15640797
