Dataset Information

Melanoma spliced and linear HLA-I peptides

ABSTRACT: In this project we have identifed and linear and spliced HLA-I bound peptides to LM-MEl-44, 53 and 33 cell lines in two different condition, treated and not treated with interferone gamma.

INSTRUMENT(S): Orbitrap Fusion

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Melanocyte, Cell Culture

DISEASE(S): Skin Melanoma

SUBMITTER: Pouya Faridi

LAB HEAD: Anthony Purcell

PROVIDER: PXD014397 | Pride | 2020-09-25

REPOSITORIES: Pride

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Publications

Spliced Peptides and Cytokine-Driven Changes in the Immunopeptidome of Melanoma.

Faridi Pouya P Woods Katherine K Ostrouska Simone S Deceneux Cyril C Aranha Ritchlynn R Duscharla Divya D Wong Stephen Q SQ Chen Weisan W Ramarathinam Sri H SH Lim Kam Sian Terry C C TCC Croft Nathan P NP Li Chen C Ayala Rochelle R Cebon Jonathan S JS Purcell Anthony W AW Schittenhelm Ralf B RB Behren Andreas A

Cancer immunology research 20200916 10

Antigen recognition by CD8<sup>+</sup> T cells is governed by the pool of peptide antigens presented on the cell surface in the context of HLA class I complexes. Studies have shown not only a high degree of plasticity in the immunopeptidome, but also that a considerable fraction of all presented peptides is generated through proteasome-mediated splicing of noncontiguous regions of proteins to form novel peptide antigens. Here, we used high-resolution mass spectrometry combined with new bioinform ...[more]

PMID: 32938616

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Project description:T cell activation leads to dramatic changes in cellular phenotype. We used CD3/CD28-activated human CD4 T cells to study how RNA binding proteins define the post-transcriptional landscape. Using RIPseq, we identified the RNA interactome of U2AF2 and show at the global level that U2AF2 binds the majority of transcripts that are differentially expressed and/or alternatively spliced during CD4 T cell activation. A unique protein interactome centered on U2AF2 is assembled in response to activation. Knocking down specific U2AF2 interacting partners (U2AF1, SYNCRIP, SRRM2, ILF2) selectively affects cytokine secretion and expression of activation markers. Furthermore, the expression and/or alternative splicing of transcripts important for immune cell function are also affected by knocking down these U2AF2 interacting proteins. U2AF1 and SYNCRIP knockdowns affect the proteins and transcripts bound to U2AF2, altering the transcriptome. Our work highlights the importance of RNA binding protein complexes in regulating the differential expression and alternative splicing that defines T cell activation. HTA 2.0 microarray results of total from a primary CD4 T cell culture after treatment with siRNAs (Control, U2AF1, SRRM2, SYNCRIP, and ILF2) and 24 hours after anti-CD3/CD28 bead activation Please note that the Series supplementary 'TotalRNA_HTA2_all_siRNA_100414.xslx' file has multiple worksheets containing: 1) Differentially expressed genes in ctrl siRNA vs. U2AF1 siRNA; 2) Differntially spliced genes in ctrl siRNA vs. U2AF1 siRNA; 3) Differentially spliced exons in ctrl siRNA vs. U2AF1 siRNA; 4) Differentially expressed genes in ctrl siRNA vs. SRRM2 siRNA; 5) Differntially spliced genes in ctrl siRNA vs. SRRM2 siRNA; 6) Differentially spliced exons in ctrl siRNA vs. SRRM2 siRNA; 7) Differentially expressed genes in ctrl siRNA vs. SYNCRIP siRNA; 8) Differntially spliced genes in ctrl siRNA vs. SYNCRIP siRNA; 9) Differentially spliced exons in ctrl siRNA vs. SYNCRIP siRNA; 10) Differentially expressed genes in ctrl siRNA vs. ILF2 siRNA; 11) Differntially spliced genes in ctrl siRNA vs. ILF2 siRNA; 12) Differentially spliced exons in ctrl siRNA vs. ILF2 siRNA

Dataset Information

Melanoma spliced and linear HLA-I peptides

Publications

Spliced Peptides and Cytokine-Driven Changes in the Immunopeptidome of Melanoma.

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