UFOPLAN- Pediatric acute lymphocytic leukemia ALL (German Federal Office for Radiation Protection)
Integrated genomic and functional analyses of TCF3-HLF-positive ALL
Pediatric ALL is characterized by chromosomal translocations that cause gene fusions involving master regulators of hematopoietic development.
In a collaborative project, we aimed at comparing the molecular pathology between two different leukemia types both disrupting one allele of TCF3, which drives the B-cell differentiation program upstream of PAX5.:the t(1;19) fusing TCF3 to the DNA-binding domain of PBX1 associated with a good prognosis.and the dismal t(17;19)(q22;p13), resulting in the fusion TCF3-HLF.
The two leukemia subtypes shared a gene expression signature of B-lymphoid cells, but also showed striking differences..We found that expression of TCF3-HLF leads to transcriptional reprogramming in B lymphoid progenitors in the context of PAX5 haploinsufficiency, towards an immature, hybrid hematopoietic state. TCF3 breakpoints occurred in hotspots indicative of terminal deoxynucleotide transferase (TdT) activity characteristic of an early B cell stage. Using In silico analysis, we predicted 39 potential HLF targets in TCF3-HLF samples, including SNAI2,, GPC4 and BMP3 involved in stem cell proliferation A profound cellular reprogramming occurred in TCF3-HLF towards a drug-resistant state reflected by stem cell, mesenchyme-derived and myeloid signatures. Drug response profiling in patient-derived xenografts, which had maintained the tumor’s genomic and transcriptome landscapes, identified resistance to most of the 98 tested drugs, but extreme sensitivity towards the BCL2-specific inhibitor ABT-199, indicating new therapeutic options for this fatal ALL subtype (Fisher et al. Nature genetics, 2015).
International Cancer Genome Consortium
Pediatric brain tumors (ICGC Pedbrain, www.pedbraintumor.org)
Transcriptome analysis of large pediatric brain tumor cohorts
As part of the International Cancer Genome Consortium (ICGC), in ICGC Pedbrain,we generated RNAseq data and analysed the transcriptomes of 164 medulloblastomas (MB), 90 pilocytic astrocytomas (PA) and 50 glioblastomas (GBM).
MB is the most common malignant brain tumour in children arising in the cerebellum or medulla/brain stem and shows biological and clinical heterogeneity. Previous studies idnetified four main groups of MBs with distinct clinical, biological and genetic profiles. WNT tumours, associated to a favourable prognosis, characterized by activated wingless pathway signalling, tumours showing hedgehog pathway activation with intermediate prognosis, and group 3 and 4 tumours, that are less well characterized and clinically challenging.
Our group identified the first medulloblastoma-associated gene fusion, involving the SHH gene (Jones et al. 2012). We identified gene expression signatures specifying nine different MB sub-groups either reflecting their cells of origin or re-programming of the tumor cells and identifying novel pathways . In group 3, we found one cluster enriched for rhodopsin and markers associated to visual perception, one myc-driven cluster, and one that is expressing a set of early develomental genes. We are particulary interested in the sub-group specific transcriptional networks.
Fig: Top: Nodes and edges of the different transcriptional networks specific to MB sub-groups represented by the different colors. Bot: in situ hybridisation of the mouse ortholog of LMX1 and BARH1.
Pilocytic astrocytoma (PA) accounting for ~20% of all pediatric brain tumors, is typically associated with mitogen-activated protein kinase (MAPK) pathway alterations. By integrating genome and transcriptome information surveying a cohort of 96 tumors, we demonstrated that PA is indeed a single pathway disease, featuring novel gene genes fusions involving the RAS pathway, such as BRAF or the kinase domain of the NTRK2 oncogene (Jones et al. 2013).
Colorectal carcinoma (CRC) is the third most common cancer worldwide and the second most common cancer in Europe, representing a major healthcare burden. KRAS mutations are used as predictive marker of therapeutical response to antibodies targeting EGFR, however, the resistance to therapeutics remains poorly understood. The IMI Oncotrack international project (www.oncotrack.com) aims at analysing a prospective CRC cohort with „multi-omics“ technologies for identifying novel biomarkers of disease and drug response.
The Yaspo group is coordinating the genomic and transcriptomic analysis of the CRC cohort and matching patient-derived models. Together with the spin-off Alacris Theranostics, we have analysed, whole genome, exome, microRNA and RNAseq data of more than 100 tumors, 60 xenografts and 40 spheroid cell models. Based on these data, our main research directions focus on:
1 - Identifying specific signaling pathways in CRC sub-groups
2 - Dissecting tumor heterogeneity and clonal evolution in tumor models
3 - Correlating drug sensitivity of the models with molecular biomarkers
Besides hallmarks mutations in APC, Wnt signaling and RAF/RAS pathway, we identified novel somatic changes in chromatin remodelling complex and epigenetic factors, which we are currently investigating,. We observed significant intra-tumoral heterogeneity, reflected in pre-clinical models of the tumors often displaying a different molecular setup than their donors. Further, expression of stem cell markers was significantly different in the models, either due to epigenetic reprogramming and/or to clonal evolution. We are investigating this in cooperation with Mats Nielson, (Uppsala, Sweden) who is using a combination of multi fluorescent labelling and in situ hybridisation.