ESR projects

Research project

Discerning the role of the NFkB pathway in inflammation, immunodeficiency and atopy through rare IEI

Rationale and Objectives

MALT1 serves as a scaffold protein for the CBM complex which is a key activator of the canonical NFkB pathway in the immune system. Additionally, it has a para-caspase function cleaving several proteins, including regulatory components of the NFkB pathway itself.  Rare autosomal recessive defects in this gene cause type 2 inflammation, severe lymphoproliferation and combined immunodeficiency. CARMIL-2 deficiency is another AR defect with similar presentation to MALT1, including severe dermatitis and colitis as well as chronic and recurrent viral and bacterial infections. CARMIL2 mediates CARD11 activation downstream of CD28 co-signaling in lymphocytes. In this project, we aim to dissect the effect of MALT1 and CARMIL2 mutations in different immune cells and better understand the mechanism underlying inflammation, atopy and lymphoproliferation in these defects.

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1) To compare samples from patients with MALT1 and CARMIL2 patients to healthy controls, as well as to samples of patients with NEMO and IKBKB deficiencies, which are associated primarily with immunodeficiency.

2) To stimulate patient PBMC’s with various canonical and non-canonical NFkB stimulators and use sc-RNA-seq and ATAC-seq to dissect the transcriptional and epigenetic regulation of the NFkB pathway in different cell types.

3) To induce different defects of CARMIL2 and MALT1 in primary B- and T-cell lines, including null- and paracaspase-specific defects in the case of MALT1, and dissect the effect of these defects in the transcriptional and epigenetic levels post stimulation.

4) To generate induce pluripotent stem cells from patient cells and investigate the role of MALT1 and CARMIL2 in T- and B-cell differentiation.

5) In collaboration of Dr. Schwartz in RFHMO (GI), to induce organoids from gastrointestinal biopsies of CARMIL2 patients and dissect the role of CARMIL2 defects in inducing gut inflammation.

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Expected results

This project will provide a deep understanding on the regulatory pathways of CARMIL2 and MALT1 and their role in T- and B-cell differentiation and function as well as inflammation.

Planned secondments

GRL (Vento-Tormo) to utilize sc-RNAseq to identify the transcriptional profile of primary cells and cell lines upon stimulations, m15-m17 (2 months); qGenomics to identify epigenomic regulation of NFkB pathway through methylome analysis, m18-20 (2 months); EMBL (Zaugg) to create gene regulatory networks for patients with mutations in CARMIL2 and MALT1, m22-24 (2 months);  IJC  to determine impact of MALT1 and CARMIL2 defects on the epigenomic regulation of immune cells, m25-27 (2 months); and UKLFR (Warnatz) to analyse B-cell differentiation and function in CARMIL2 and MALT1 mutated cells, m28-30 (2 months).

PhD programme

PhD in Biomedicine, Hebrew University in Jerusalem, Israel.