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Transcriptome profiling of expanding pancreas progenitors derived from the H1 human pluripotent stem cells using a combination of mitogenic signals, RA signalling suppression and selective inhibition of the TGFb and Wnt signalling pathways

ABSTRACT: Transcriptome profiling of expanding pancreas progenitors derived from the H1 human pluripotent stem cells using a combination of mitogenic signals, RA signalling suppression and selective inhibition of the TGFb and Wnt signalling pathways

PROVIDER: PRJNA892896 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR21999114_1.fastq.gz	Fastqsanger.gz
	SRR21999114_2.fastq.gz	Fastqsanger.gz
	SRR21999115_1.fastq.gz	Fastqsanger.gz
	SRR21999115_2.fastq.gz	Fastqsanger.gz
	SRR21999116_1.fastq.gz	Fastqsanger.gz

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Project description:Background: Rheumatoid arthritis (RA) is a complex heterogenous autoimmune disease and achieving long term disease remission is an elusive goal for patients, thus implying improvement in drug targeting is necessary. Kinases are intracellular signalling mediators and key to sustaining the inflammatory process in RA. Therefore, oral inhibitors of specific kinases, such as Cyclin Dependent Kinases (CDKs) and Janus Kinase (JAKs), are under development or have been approved. However, the cell signalling mechanisms in treatment naïve RA patients is yet to be explored, which may facilitate targeted therapy stratification. Methods: We undertook phosphoproteome and total proteome analysis of 8 pre-treatment synovial biopsies of RA patients using label-free mass spectrometry. Results: The analysis revealed a clear separation of the phosphoproteome and proteome profile between the lymphoid and myeloid RA pathotypes. Differential expression analysis and function enrichment showed that the degree of inflammatory state and specific signalling activities are associated with different RA pathotypes. The lymphoid pathotype was enriched with immunological pathways and associated with Mammalian Target Of Rapamycin (MTOR) signalling, whereas the myeloid pathotype was associated with Mitogen-Activated Protein Kinase (MAPK) and CDK mediated signalling. This analysis also highlighted kinases not previously linked to RA, such as Serine/Threonine Protein Kinase N1 (PKN1) in the lymphoid pathotype and Protein Kinase, DNA-Activated, Catalytic Subunit (PRKDC) in the myeloid pathotypes. Certain phosphosites were also highly correlated with clinical features, such as Disabled Homolog 2 (DAB2)-Ser723 with Disease Activity Score (DAS)-28, and so these may be potential biomarkers of disease progression and response. Conclusions: These data provide evidence that specific phosphoproteome and proteome signatures are associated with different RA pathotypes and may have clinical utility for stratifying patients as part of a personalised medicine approach.

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Transcriptome profiling of expanding pancreas progenitors derived from the H1 human pluripotent stem cells using a combination of mitogenic signals, RA signalling suppression and selective inhibition of the TGFb and Wnt signalling pathways

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