ESR6

Epigenomics of macrophage phenotypes and the contribution of transcription processes contributing to phenotype switch.

University of Debrecen

University of Debrecen

Hungary

Partner Profile
László Nagy
László NagySupervisor at University of Debrecen, NLab

Description

The progressive failure of muscle repair and an altered inflammatory response can lead to fibrosis that in turn can also negatively influence stem cells functionality (Nelson et al., 2012; Serrano and Munoz-Canoves, 2017).

Macrophages (MPs) subsets show mixed phenotypes that exhibit different functions mixing subsets that are beneficial for myogenesis and other subsets that are detrimental promoting fibrosis (Juban et al., 2018).

However, surface markers allowing to target precisely those subsets, as well as the major signaling pathways controling their behavior, are lacking.

ESR6 will study the epigenetic changes underlying the transition from inflammatory to repair MPs in both acute (CTX) and chronic (mdx) muscle injury on FACS-isolated Ly6Chi and Ly6Clow (and specific subsets identified according to the markers identified above) MP populations using single cell and bulk approaches at various time points at various time points. ATAC-seq experiments will be carried out to determine the open chromatin regions along with ChIP-seq of active (H4Ac and H3K27Ac) and repressive (H3K27Met3) histone marks.

ESR6 will built an epigenomic landscape dataset. Transcriptomic analyses will be also carried out from the same populations and changing gene sets and their genomic regulators will be determined using the bioinformatics pipelines developed at UNIDEB. The candidate transcription factors will be prioritized and their suitability as targets evaluated.

In a separate set of studies, candidate transcription factors will be analysed for their contribution of MPs gene expression and immunophenotype, including the heme-regulated transcription factor, BACH-1 (Patsalos et al., 2019; Sun et al., 2004). Using BACH-1 KO mice ESR6 will carry on transcriptomic analyses on MPs and the involvement of the BACH-1 mediated pathways in disease progression will be identified by intersecting the datasets derived from wild type animals and DMD models.

Objectives
  • To isolate and characterize the chromatin structure of inflammatory Ly6Chi and repair Ly6Clow MPs from models of acute injury and DMD using ATAC-seq and ChIP-seq

  • To identify transcriptional regulatory molecules and pathways controlling the transition from inflammatory to repair MPs using RNA-Seq

  • To mechanistically dissect the role and contribution of select transcription pathways (BACH-1) using LOF studies in vivo to MPs assisted muscle repair in acute injury and in models of DMD

Duration

36 months

Enrolment in Doctoral degree

PhD program in Molecular Cell and Immune Biology at the Faculty of Medicine at University of Debrecen

References

Juban, G., Saclier, M., Yacoub-Youssef, H., Kernou, A., Arnold, L., Boisson, C., Ben Larbi, S., Magnan, M., Cuvellier, S., Theret, M., et al. (2018). AMPK Activation Regulates LTBP4-Dependent TGF-beta1 Secretion by Pro-inflammatory Macrophages and Controls Fibrosis in Duchenne Muscular Dystrophy. Cell Rep 25, 2163-2176 e2166.
Nelson, G., Wordsworth, J., Wang, C., Jurk, D., Lawless, C., Martin-Ruiz, C., and von Zglinicki, T. (2012). A senescent cell bystander effect: senescence-induced senescence. Aging cell 11, 345-349.
Patsalos, A., Tzerpos, P., Halasz, L., Nagy, G., Pap, A., Giannakis, N., Lyroni, K., Koliaraki, V., Pintye, E., Dezso, B., et al. (2019). The BACH1-HMOX1 Regulatory Axis Is Indispensable for Proper Macrophage Subtype Specification and Skeletal Muscle Regeneration. J Immunol 203, 1532-1547.
Serrano, A.L., and Munoz-Canoves, P. (2017). Fibrosis development in early-onset muscular dystrophies: Mechanisms and translational implications. Semin Cell Dev Biol 64, 181-190.
Sun, J., Brand, M., Zenke, Y., Tashiro, S., Groudine, M., and Igarashi, K. (2004). Heme regulates the dynamic exchange of Bach1 and NF-E2-related factors in the Maf transcription factor network. Proc Natl Acad Sci U S A 101, 1461-1466.

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