DC projects

Research project

Exploring TET-mediated epigenetic control in NF-kB mutated patients

Rationale and Objectives

Mutations NF-κB subunits encoding-genes result in a common variable immunodeficiency (CVID) phenotype with recurrent infections and autoimmunity. However, CVID penetrance in NF-κB mutated patients is incomplete, thus suggesting the involvement of yet unknown mechanisms including epigenetics, as recently shown by the Ballestar’s and the Vento-Tormo’s groups. TET enzymes are needed for balanced blood cell differentiation towards lymphoid and myeloid lineages. Recent work by the Ballestar’s and Sardina’s groups has uncovered mechanism linking TET2-mediated active DNA demethylation with NF-κB activity indicating cooperativity between both mechanisms in mounting immune responses. Our hypothesis is the CVID phenotype onset in NFKB-mutated patients might be triggered by TET-mediated epigenomic rewiring caused by physiological aging of the immune system. Such hidden phenotype has been observed in TET2-mutated HSPCs developing myeloid malignancies only when exposed to inflammatory cues.

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1) To perform genome-wide profiling of TET-mediated 5hmC mark in B and T cell populations harboring different NFKB genetic variants.

2) To assess TET2 chromatin binding on B and T cell populations isolated harboring different NFKB genetic variants.

3) If genetic variants of interest are unavailable within the consortium cohort, to introduce them by CRISPR/Cas9 in HSPCs and T cell progenitors (from donors) and differentiate them into the B and T cells subsets of interest.

4) To utilize the NFKB-mutated cellular models to perturb TET activity and study chromatin changes and cellular differentiation capacity towards the lymphoid lineage.

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Expected results

1) To uncover aberrant 5hmC deposition and TET2 recruitment to the chromatin in NFKB mutated CVID patients according to their disease penetrance.

2) To elucidate the role of TET enzymes in the phenotypic onset of CVID.

3) To potentially identify environmental cues leading to altered TET activity and favouring CVID manifestation.

Planned secondments

SRF (Di Micco) to receive training on standards for gene correction, m10-m13 (2 months). IRB (Geiger) to learn CRISPR screens, m13-m16 (2 months); EMBL (Zaugg), to receive training on standards for genome-wide data analysis, m16-m17 (1 month). Finally, DC2 will learn how to convert the output from his/her gene editing experiments by doing secondments at Alia m22-m24 (2 months) and at OneChain m27-m28 (1month).

PhD programme

PhD in Biomedicine, University of Barcelona (UB), Spain