Deciphering transcriptional regulation of NF-kB target genes using integrative omics approaches

Description du projet

Disséquer le mécanisme d’activation transcriptionnelle de NF‑kB

Les facteurs de transcription appartenant à la famille du facteur nucléaire kB (NF‑kB) orchestrent l’expression de gènes clés impliqués dans les réponses immunitaires, la prolifération et l’apoptose. Parallèlement, de nouvelles preuves suggèrent que NF‑kB joue un rôle dans l’apparition et la progression du cancer. Par conséquent, pour développer un traitement anti‑NF‑kB contre le cancer, il faudrait cibler sélectivement les gènes NF‑kB associés à la transformation maligne. Dans cette optique, le projet RegulatioNFkB, financé par l’UE, propose d’étudier le mécanisme d’activation transcriptionnelle médiée par NF‑kB en se concentrant sur les régions promotrices de gènes sensibles à NF‑kB. Les chercheurs emploieront l’édition du génome ainsi que la spectrométrie de masse pour identifier les facteurs de transcription et les autres protéines qui interagissent au niveau des promoteurs de ces gènes.

Objectif

NF-kB is a family of transcription factors that regulate expression of genes that are involved in various cellular processes such as apoptosis, proliferation and differentiation. The NF-kB pathway is implicated in the initiation and progression of cancer and cancer cell drug resistance. Unfortunately, global NF-kB inhibition is harmful to the immune system; therefore, inhibition of a subset of NF-kB target genes that are linked to malignant transformation would be more appropriate. Different NF-kB target genes display distinct transcription activation kinetics, indicating that the molecular mechanisms driving expression of NF-kB target genes are strikingly diverse. Thus, it is highly interesting to study the factors that are involved in transcriptional activation of individual NF-kB responsive genes, both from a fundamental and clinical perspective. Here, we will develop two innovative strategies based on CRISPR/Cas9 based genome targeting combined with mass spectrometry-based technology to isolate single NF-kB target gene promoters upon NF-kB pathway activation and identify their constituents. We will also apply a complementary approach, ATAC-sequencing, to identify transcription factors that are involved in activation of NF-kB responsive genes. Moreover, we will study the underlying mechanisms and characterize the function of proteins that interact with NF-kB responsive promoters. Finally, the described mechanisms discovered in cancer cell lines will be verified and validated in small intestinal organoids, a non-transformed cell model for homeostasis in the intestinal epithelium. This ambitious and multidisciplinary project will greatly benefit from my expert knowledge regarding the NF-kB pathway combined with the expertise of the host laboratory in mass spectrometry and genomics. The project is expected to have a major impact in the research area of gene expression regulation in general and molecular cancer research focusing on the NF-kB pathway in particular.