Laboratory of Translational Genetics
Our laboratory is interested in the discovery of genetic or epigenetic markers, either as susceptibility factors for cancer development, as prognostic markers to improve the molecular genetic annotation of cancer or as predictive markers for targeted cancer therapies. In particular, our main interest lies in understanding which (epi)-genetic factors modulate hypoxia-driven tumorigenesis or predict response to therapies targeting hypoxia-driven oncogenesis, such as anti-angiogenic therapies .
One of our main research topics is to investigate how hypoxia influences the cancer epigenome, possibly by regulating TET hydroxylase activity and affecting DNA demethylation. Notably, TET hydroxylases belong to the same family of dioxygenases as the PHDs, which target hypoxia-inducible factors for degradation and are considered key mediators of the hypoxic response.
Legend: Since TET hydroxylases belong to the same family of hydroxylases as the PHDs, we hypothesize that TETs might also be O2 and 2OG-dependent. This would suggest that TET-mediated demethylation acts as a regulator of gene expression under numerous pathological conditions involving hypoxia, including carcinogenesis, tumor metastasis and cancer stemness.
First, we postulate that gene promoters can be hypermethylated, because DNA demethylation - as initiated by the TET hydroxylases - is impaired at low O2. To this aim, we are studying the direct dependence of these hydroxylases on O2, as well as the overall and locus-specific changes of their product, 5-hydroxymethylation (5hmC), under hypoxic and low 2OG conditions. Secondly, because much of the hypoxic response is executed through HIFs, we will investigate how epigenetic modulators, such as TET hydroxylases, modulate the hypoxia response program, and to what extent the genome-wide binding profiles of the former and the latter overlap under hypoxic conditions, possibly to maintain HIF binding sites in an unmethylated and transcriptionally active state. Thirdly, we are assessing whether 5hmC methylation profiles are tissue- or tumor-specific and to what extent differences are imposed by differential tissue-specific TET hydroxylase activities. Tumor-specific 5hmC profiles will be used to construct a comprehensive panel of 5hmC sites and screen for the prognostic or predictive relevance of 5hmC in various cancers. Finally, we also assess the relevance of DNA demethylation events imposed by tumor hypoxia in the context of metastasis and the cancer stem cell niche. Relevant demethylation sites will be functionally validated, and their potential as therapeutic targets assessed by interfering with their epigenetic regulation.
DNA methylation is essential for vertebrate development and physiology, and stably represses ectopic and heterochronic transcription of genes. However, despite decades of research, it remains unclear whether DNA methylation can directly repel the binding of transcription factors (TFs). We are investigating whether hypoxia-inducible factors (HIFs) represent such an example, i.e. that their binding is sensitive to methylation of the CpG dinucleotide in its binding site. under this model, the set of hypoxia response elements (HREs) that are activatable in a cell are predetermined by that cells DNA methylation pattern, as established under normoxic conditions. Differential methylation of HREs could thus underlie cell-type-specific binding of HIFs and the associated gene activation and hypoxic response. Likewise, cancer-assocated changes in DNA methylation patterns could drive differential responses of tumor cells to exposure to hypoxia
Although improved compared to placebo, only a minority of colorectal, lung and breast cancer patients treated with the angiogenic inhibitor, bevacizumab, seem to benefit at the level of progression-free and overall survival. The underlying mechanisms of this non-responsiveness are not yet known, and biomarkers that identify responders to anti-angiogenic therapies are urgently needed. We are currently conducting studies that aim to identify genetic markers predictive for anti-angiogenic therapies. We have set-up a number of joint initiatives with pharmaceutical companies to get access to large patients cohorts (>6000 patients are currently being studied) and are participating in an FP7-funder project (Angiopredict) to identify such markers.
Legend: Pancreatic cancer patients with a rs9582036-A allele have improved overall survival when treated with bevacizumab.
Data integration methods such as Bayesian modeling, are used to develop genomic signatures of response. Potential biomarkers are validated using primary endothelial cultures (HUVECs) and a variety of functional angiogenesis-related in vitro and in vivo assays (proliferation, migration, vessel assembly, tip cell formation, etc.). So far, we already identified and validated a genetic variant in VEGFR1 as a response marker for bevacizumab treatment outcome (Lambrechts et al. Lancet Oncology 2012).
We are putting significant efforts into methods aimed at the identification of somatic alterations in DNA derived from FFPE tumor blocks and collected in the context of phase 2 or 3 clinical trials with targeted cancer therapies. For instance, we are routinely genotyping hotspot mutations in various oncogene pathways using Sequenom Massarray, determining copy number alterations of cancer genes using Illumina SNP arrays, or applying whole-genome and exome sequencing on specific series of solid tumors and matched germline DNAs using a HiSEQ2000 Illumina sequencer. In particular, we are studying a unique series of tumors with mismatch repair deficiency and have already discovered mutation patterns of therapeutic and diagnostic relevance in these tumors. We are also involved in a large-scale project that uses exome-sequencing and SNP array profiling of primary and relapsed tumors from patients with sensitive or relapsed ovarian cancer to identify markers of platinum response. Finally, we are also performing exome-sequencing in several collaborative projects, such as with C. Sotiriou and C Desmedt (Bordet Institute) to reveal heterogeneity of primary and metastatic breast cancer, or with C. Blanpain to identify novel driver mutations in mouse skin tumors arising due to mutagen exposure to the skin.
Legend: Copy Number Alterations in a uterine leiomyosarcoma as revealed by whole-genome sequencing.
Finally, we are also taking part in several large-scale international initiatives that aim to unravel the complex genetic basis of breast, ovarium and endometrial cancer (BCAC, OCAC and ECAC). Up to 6,000 of our DNA samples from patients with these gynaecologic cancers have been genotyped on Illumina SNP chips together with >100,000 samples from at least 50 other studies. The scale of these multi-centered efforts is unprecedented and will lead to the identification of numerous novel cancer susceptibility loci. Additional correlations with disease characteristics, disease severity and outcome will also identify novel prognostic markers of these cancers. We are actively contributing to this large-scale initiative and are also leading a number of projects within these initiatives.