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Histone proteomic associated with epigenetic studies revealed a Ghost proteome in PC1/3 KD macrophages involved in anti - tumoral resistance under IL - 10 stimulation

ABSTRACT: In our previous work, our investigation on macrophages has allowed us to show that the inhibition of the enzyme proprotein convertase (PC1/3) controls the activation of macrophages. We demonstrated that PC1/3 knockdown (KD) in macrophages would exhibit an increased secretion of pro-inflammatory and anti-tumoral factors. In this biological context, we assessed for histone modifications and for the presence and contribution of a “Ghost proteome” in these macrophages. In addition, we have identified a set of alternative proteins (AltProts) that have a key role in regulating various signaling pathways. In this study, to further investigate the underlying mechanisms involved in resistance of PC1/3 KD macrophages to anti-inflammatory stimuli, we have conducted a proteomics-systems biology study to assess the epigenome variation focusing on histone modifications and to investigate for the potential contribution of AltProts in regulating PC1/3 KD macrophages resistance. Results from our study have indicated the presence of significant variations in histone modifications along with the identification of 28 AltProts with in part involved in anti-tumoral resistance under IL-10 stimulation. These findings highlight that key role of altered epigenome histone modifications in driving resistance and indicates that, like the reference proteins, AltProts have major impact in the field of epigenetics and regulation of gene expression as shown in our results

INSTRUMENT(S): Q Exactive

ORGANISM(S): Rattus Norvegicus (rat)

TISSUE(S): Cell Culture

SUBMITTER: Soulaimane Aboulouard

LAB HEAD: Michel Salzet

PROVIDER: PXD020610 | Pride | 2021-02-12

REPOSITORIES: Pride

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Project description:Epigenetic modification of the mammalian genome by DNA methylation (5-methylcytosine) has a profound impact on chromatin structure, gene expression and maintenance of cellular identity. Recent demonstration that members of the Ten-eleven translocation (Tet) family proteins can convert 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC) raised the possibility that Tet proteins are capable of establishing a distinct epigenetic state. We have recently demonstrated that Tet1 is specifically expressed in murine embryonic stem (ES) cells and is required for ES cell self-renewal and maintenance. Using chromatin immunoprecipitation coupled with high-throughput DNA sequencing (ChIP-seq), here we show that Tet1 is preferentially bound to CpG-rich sequences at promoters of both transcriptionally active and Polycomb-repressed genes. Despite a general increase in levels of DNA methylation at Tet1 binding-sites, Tet1 depletion does not lead to down-regulation of all the Tet1 targets. Interestingly, while Tet1-mediated promoter hypomethylation is required for maintaining the expression of a group of transcriptionally active genes, it is also required for repression of Polycomb-targeted developmental regulators. Tet1 contributes to silencing of this group of genes by facilitating recruitment of PRC2 to CpG-rich gene promoters. Thus, our study not only establishes a role for Tet1 in modulating DNA methylation levels at CpG-rich promoters, but also reveals a dual function of Tet1 in promoting transcription of pluripotency factors as well as participating in the repression of Polycomb-targeted developmental regulators. Chromatin or genomic DNA extracted from control (Con) or Tet1 knockdown (KD) mouse ES cells was immunoprecipitated with indicated antibodies and analyzed by NimbleGen 2.1M mouse whole genome tiling microarrays (a 4-array set covering the entired non-repetitive portion of mouse genome). Whole cell extract (WCE) was used as input controls in IP/input experiments. In IP/IP experiments, immunoprecipitated DNA from Con KD and Tet1 KD ES cells was directly compared on the same microarrays.

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Histone proteomic associated with epigenetic studies revealed a Ghost proteome in PC1/3 KD macrophages involved in anti - tumoral resistance under IL - 10 stimulation

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