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.
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.
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.
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
- 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.
- Study the transcriptional changes in our LOUCY-based MEF2C- and NOTCH1-modulation models in relation to MEF2C and NOTCH1 signaling.
- Determine whether MEF2C and NOTCH expression signatures represent mutually exclusive pathways at the single cell level in normal early T-cell progenitor (ETP) cells.
- Explore underlying mechanisms that explain functional antagonism between MEF2C and NOTCH1 signaling pathways.
- 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.
Canté-Barrett, K., Mendes, R.D., Li, Y., Vroegindeweij, E. Pike-Overzet, K., Wabeke, T., Langerak, A.W., Pieters, R., Staal, F.J.T., Meijerink, J.P.P. Loss of CD44dim expression from early progenitor cells marks T-cell lineage commitment in the human thymus. Frontiers in Immunology. 2017. Jan 20;8:32. doi: 10.3389/fimmu.2017.00032. eCollection 2017. PubMed PMID: 28163708
Li, Y., Buijs-Gladdines, J.G., Canté-Barrett, K., Stubbs, A.P., Vroegindeweij, E.M., Smits, W.K., van Marion, R., Dinjens, W.N., Horstmann, M., Kuiper, R.P., Buijsman, R.C., Zaman, G.J., van der Spek, P.J., Pieters, R., Meijerink, J.P. IL-7 Receptor Mutations and Steroid Resistance in Pediatric T cell Acute Lymphoblastic Leukemia: A Genome Sequencing Study. PLoS Med. 2016 Dec 20;13(12). PubMed PMID: 27997540
Canté-Barrett, K., Spijkers-Hagelstein, J., Buijs-Gladdines, J., Uitdehaag, J., Smits, W., Van der Zwet, J., Buijsman, R., Zaman, G., Pieters, R., Meijerink, J.P.P. MEK and PI3K-AKT inhibitors synergistically block activated IL7-receptor signaling in T-cell acute lymphoblastic leukemia. Leukemia 2016, May 13. Sep;30(9):1832-43. PubMed PMID: 27174491
Mendes, R.D., Sarmento, L.M., Canté-Barrett, K., Zuurbier, L., Buijs-Gladdines J.G.C.A.M., Póvoa, V., Smits, W.K., Abecasis, M., J. Yunes, A., Sonneveld, E., Horstmann, M.A., Pieters, R., Barata, J.T. and Meijerink, J.P.P. PTEN micro-deletions in T-cell acute lymphoblastic leukemia are caused by illegitimate RAG-mediated recombination events. Blood. 2014, Jul 24;124(4):567-78. PubMed PMID: 24904117
Homminga, I., Pieters, R., Langerak, A., de Rooi, J.J., Stubbs, A., Buijs-Gladdines, J., Kooi, C., Klous, P., Van Vlierberghe, P., Ferrando, A.A., Cayuela, J.M., Blanchet, O., Verhaaf, B., Beverloo, B., Horstmann, M., De Haas, V., De Laat, W., Soulier, J., Sigaux, F., Meijerink, J.P.P. NKX2-1 and MEF2C define novel oncogenic pathways in T-cell acute lymphoblastic leukemia. Cancer Cell, 2011, 19:484-97. PubMed PMID: 21481790
Van der Zwet, J.C.G., Smits, K., Buijs-Gladdines, J.G.C.A.M., Pieters, R. and Meijerink, J.P.P. Recurrent NR3C1 aberrations at first diagnosis provoke steroid resistance in pediatric T-cell acute lymphoblastic leukemia patients. Hemasphere. 2020. In press.
Cordo’, V., Van der Zwet, J.C.G., Canté-Barrett, K., Pieters, R. and Meijerink, J.P.P. T-cell acute lymphoblastic leukemia: a roadmap to targeted therapies. Blood Cancer Discovery, 2020. November 24 2020 DOI:10.1158/2643-3230.BCD-20-0093.
Canté-Barrett, K., Holtzer, L., Van Ooijen, H., Hagelaar, R., Cordo’, R., Verhaegh, W., Van de Stolpe, A. and Meijerink, J.P.P. A Molecular Test for Quantifying Functional Notch Signaling Pathway Activity in Human Cancer. Cancers 2020, 12(11), 3142. doi: 10.3390/cancers12113142. Pubmed ID: 33120947
Kroeze, E., Loeffen, J.L.C., Poort, V.M., Meijerink, J.P.P. T-cell lymphoblastic lymphoma and leukemia: different diseases from a common pre-malignant progenitor? Blood Advances, 2020, Jul 28;4(14):3466-3473. doi: 10.1182/bloodadvances.2020001822. Pubmed ID: 32722786
Van Der Zwet, J.C.G., Cordo', V., Cante-Barrett, K., Meijerink, J.P.P. Multi-omic approaches to improve outcome for T-cell acute lymphoblastic leukemia patients. Adv Biol Regul. 2019 Aug 26:100647. doi:10.1016/j.jbior.2019.100647. Pubmed ID: 31523030
Canté-Barrett, K., Mendes, R.D., Li, Y., Vroegindeweij, E. Pike-Overzet, K., Wabeke, T., Langerak, A.W., Pieters, R., Staal, F.J.T., Meijerink, J.P.P. Loss of CD44dim expression from early progenitor cells marks T-cell lineage commitment in the human thymus. Frontiers in Immunology. 2017. Jan 20;8:32. doi: 10.3389/fimmu.2017.00032. eCollection 2017. Pubmed ID: 28163708
Li, Y., Buijs-Gladdines, J.G., Cante-Barrett, K., Stubbs, A.P., Vroegindeweij, E.M., Smits, W.K., van Marion, R., Dinjens, W.N., Horstmann, M., Kuiper, R.P., Buijsman, R.C., Zaman, G.J., van der Spek, P.J., Pieters, R., Meijerink, J.P. IL-7 Receptor Mutations and Steroid Resistance in Pediatric T cell Acute Lymphoblastic Leukemia: A Genome Sequencing Study. PLoS Med. 2016 Dec 20;13(12). Pubmed ID: 27997540