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Meijerink group

The focus of our group is to identify physiologic and pathogenic dependencies that drive disease development, therapy resistance and relapse in children with T-cell leukemia or lymphomas. This will elucidate disease-specific targets for new therapeutic compounds, which will improve the development of patient-tailored treatment protocols and reduce long-term morbidity in these children.

PI: Dr. Jules Meijerink
Description of our Research and molecular toolbox

The Meijerink group is one of the pioneering research groups in molecular-genetic characterization and profiling of T-cell malignancies, with T-ALL as prime target disease since the year 2001. This has led to a profound insight in the acquisition of specific mutations in pivotal pathways that result in the pathologic transformation of normal early T-cells during developmental processes in the thymus. T-ALL is characterized by chromosomal rearrangements activating specific oncogenic transcription factors as disease initiating and driving genetic events. These events facilitate developmental arrest of pre-leukemic, immature T-cells associated with unique expression signatures that distinguishes four major disease subtypes denoted as ETP-ALL, TLX, proliferative and TALLMO. It promotes acquisition of additional mutations that deregulate important cellular processes including NOTCH1, IL7R-JAK-STAT, RAS-MEK-ERK or PTEN-PI3K-AKT signaling.

The research program is focused on the identification of chromosomal markers/mutations in T-cell malignancies in children by using high-resolution screening techniques such as next-generation sequencing, and to investigate their prognostic relevance in relation to therapy resistance mechanisms and relapse. This improved understanding of leukemogenic pathways has already pointed and will point to potential therapeutic targets for this disease using targeted, high-precision medicines. The clinical usefulness and the application of such targeted compounds is investigated using genetically modified cell line-based and patient-derived xenograft leukemia models that have been developed. Identified disease-driving mechanisms are studied for conservation in children with other types of malignancies.

Research performed in my research group is focused on the following topics:

  • Identifying molecular-cytogenetic pathogenic mechanisms and their prognostic relevance in T-cell acute lymphoblastic leukemia (T-ALL) and T-cell lymphomas at disease presentation and relapse. For this, we use high-resolution and state-of-art molecular technologies including next-generate sequencing, ChIP-seq, 4C-seq, Hi-C, lentiviral transduction, CRISPR-Cas9 mutagenesis, Luciferase reporter assays on primary patient cells, cell line disease models, T-cell stromal support cultures, xenograft transplantation models of primary/relapsed patient samples and/or conditional knock-in/-out transgenic mouse models.
  • Improved understanding of leukemia cell dependencies towards essential signaling pathways for early T-cell development. For this, we perform signaling profiling by gene expression analysis (micro-arrays, RNA-sequencing) and mass spectrometry-based analysis of the (phospho)proteome, also in relation to normal T-cell development.
  • Improved understanding of disease presentation, maintenance and selection of therapy-resistant subclones in the context of stromal and epithelial niche interactions. For this, we are developing thymus and bone marrow niche models (including cell identification by single cell RNA sequencing).
  • Based on this knowledge, to pinpoint potential drugable targets in (relapsed) pediatric T-ALL and providing proof-of-principle pre-clinical drug-testing based on compound toxicity screens. For this, we make use of xenograft transplantation models of primary patient leukemic cells to facilitate in vitro and in vivo drug testing.
"Oncogene and niche dependencies provide chances for future treatment strategies for T-cell leukemia and lymphoma" Dr. Jules Meijerink - PI
Identification of drugs that restore steroid response in acute T-cell leukemia with over-activated IL7R signaling (Stichting Kinderen Kankervrij, KIKA-219, 2015, 4yr).

Synthetic steroids are one of the most important drugs in pediatric ALL treatment, and poor response to steroid-treatment has been associated with therapy failure and disease relapse. Endogenous steroids are pivotal during normal immature T-cell selection processes whereby TCR-associated signals can override steroid-induced apoptotic signals. Therefore, we hypothesize that aberrant crosstalk between signaling pathways and steroid-induced signaling result in diminished responses of malignant T-cell leukemia cells towards synthetic steroids.

Whole-genome sequencing revealed that IL7R signaling mutations occur in nearly 40 percent of T-ALL patients and especially in early thymic progenitor-ALL (ETP-ALL) and TLX subtypes. Furthermore, several deletions in the steroid receptor NR3C1 were found in ETP-ALL patients with chromosomal 5q deletions. In this study, we found strong indications that mutant IL7R signaling is associated with a diminished steroid response and reduced survival and therefore points to a mechanism that enhances steroid resistance. We therefore aim to reveal the molecules downstream of over-activated IL7R-signaling that cause steroid resistance, and test which inhibitors sensitize the steroid response in a preclinical setting. Some promising inhibitors of the IL7R pathway are part of clinical trials for other diseases and will be tested immediately for their ability to restore steroid responsiveness of T-ALL cells. Sensitization to steroid treatment will possibly enable dose reduction of high-intense chemotherapeutic treatment protocols without compromising cure-rates and is crucial in reducing long-term detrimental treatment effects


 

Oncogenic cooperation between the chromosomal architecture protein CTCF and the T-cell factor BCL11B in normal and malignant T-cell development (Stichting Kinderen Kankervrij, KiKa-244, 2015, 3yr)

BCL11B is an essential transcription factor that regulates pre- to post-commitment transitions that are essential during normal alpha/beta T-cell development. We found that established T-ALL subtypes either express pre-commitment (including ETP-ALL and TLX-subtypes) or post-commitment gene signatures (including proliferative and TALLMO subtypes). This indicates that the developmental context is crucial for the pathogenicity of driving oncogenic events in this disease.

Most TLX T-ALL cases harbor a translocation of the TLX3 oncogene into the BCL11B locus, inactivating one functional BCL11B allele. These patients that belong to the TLX-subtype are strongly associated with gamma/delta T-cell development, that had not been connected with pre-commitment T-cell development before. Approximately half of all TLX3-BCL11B rearranged T-ALL patients carry heterozygous deletions of the chromatin architectural CCCTC-binding factor (CTCF), a chromosomal architectural protein that insulates transcriptionally active from inactive chromosomal regions. Importantly, Ctcf- or Bcl11b-deficient mice have seemingly identical phenotypes of increased numbers of gamma/delta T-cells but reduced numbers of alpha/beta T-cells. From both these observations we hypothesize that (1) BCL11B is the transcriptional regulator that functionally collaborates with CTCF at T-cell commitment. (2) CTCF loss may be accompanied by TLX3 driven transcriptional deregulation of expanded chromosomal regions of in T-ALL.


Functional antagonism between the ETP-ALL oncogene MEF2C and NOTCH signaling in early thymocyte precursor cells. (Stichting Kinderen Kankervrij, KiKa-295, 2017, 4yr)

We identified the MEF2C transcription factor as oncogene for early T-cell progenitor ALL (ETP-ALL) patients, a most immature form of T-ALL that traditionally was linked with poor outcome. In our research towards the pathogenic mechanism of MEF2C, we observed functional antagonism between MEF2C- and NOTCH-signaling pathways using cell line models derived from the ETP-ALL cell line LOUCY.

Using these models, knockdown of MEF2C provokes cellular differentiation, which can be highly potentiated through activation of the NOTCH1 pathway. In contrast, cells retain an immature phenotype upon (over)expression of MEF2C despite a NOTCH1-activating environment. We hypothesize that MEF2C and NOTCH1 represent antagonistic or competitive signaling pathways in ETP cells whereby ectopic expression of MEF2C blocks NOTCH1-promoted T-cell maturation, resulting in ETP-ALL. This hypothesis is strongly supported by functional and genetic data in T-ALL and ETP-ALL patients frequently lack NOTCH1 signaling mutations in contrast to other T-ALL subgroups. In this study, we aim to

  1. Identify MEF2C-regulated ETP-ALL signature genes by MEF2C ChIP-seq analysis in primary ETP-ALL patient samples followed by integration of ChIP-seq data with gene expression profiles from normal ETP subsets and ETP-ALL patients.
  2. Study the transcriptional changes in our LOUCY-based MEF2C- and NOTCH1-modulation models in relation to MEF2C and NOTCH1 signaling.
  3. Determine whether MEF2C and NOTCH expression signatures represent mutually exclusive pathways at the single cell level in normal early T-cell progenitor (ETP) cells.
  4. Explore underlying mechanisms that explain functional antagonism between MEF2C and NOTCH1 signaling pathways.
  5. Identification of compounds that specifically inhibit MEF2C and target ETP-ALL.



Identification of biomarkers by whole-genome sequencing and phospho-proteomics to predict responses to high-precision medicines in T-cell acute lymphoblastic leukemia. (Dutch Cancer Foundation, KWF-10355, 2016, 4yr)

In the last decade, intensive multi-agent combination treatment has boosted survival and cure to approximately 80 percent of pediatric T-cell acute lymphoblastic leukemia (T-ALL) patients. The outcome for relapsed patients remains poor, and acquired therapy resistance characterizes relapsed T-ALL in particular. A major disadvantage of high-intensive treatment protocols is the frequent appearance of detrimental late toxic effects. New cancer therapies by the introduction of high precision medicines are therefore urgently needed in clinical practice as part of patient-tailored treatment that prevents disease relapse and improves cure-rates while diminishing late treatment effects. Next-generation sequencing and phospho-proteomic analysis techniques have proven useful to identify mutations in signaling molecules or aberrantly activated pathways in cancer patients that will form the rational for targeted treatment by small molecule, precision medicines in future treatment strategies. 

Using whole genome next-generation sequencing and phospho-proteomics in primary leukemia cells of 50 pediatric T-cell acute lymphoblastic leukemia patients, we will pinpoint chromosomal rearrangements, mutations or aberrantly (in)activated molecules that represent important regulators of leukemia maintenance and growth. These data will be investigated in relation to leukemia response levels to clinically relevant precision inhibitors as tested in high throughput cytotoxicity assays. Four most promising inhibitors will be tested as proof-of-principle for their therapeutic potential to eradicate T-cell leukemia cells in a preclinical, in vivo model system based on transplantation of patient-derived xenografted cells in mice. A systematic screen for potential targets in combination with in vitro response levels of leukemia cells towards high-precision medicines has not been performed for pediatric T-ALL patients. This study will clarify whether leukemia sensitivity towards such small molecule inhibitors can be explained by mutations or activation of important cellular processes and signal transduction pathways. It will therefore pinpoint activated or mutant molecules that can be used as molecular biomarkers to predict sensitivity of T-ALL patients to particular new precision inhibitors. Translational data as obtained in this project will help to design new clinical trials for T-ALL patients.


 

Members of the Meijerink group