The application of tumor antigen-based immunotherapy is hindered by the rarity of validated immunogenic peptides.In this study,we aimed to investigate the potential of circular RNAs(circRNAs)as a novel source of tumor...The application of tumor antigen-based immunotherapy is hindered by the rarity of validated immunogenic peptides.In this study,we aimed to investigate the potential of circular RNAs(circRNAs)as a novel source of tumor antigen peptides in hepatobiliary tumor organoids.Using RNA-sequencing(RNA-seq)with an algorithm-based score tool,3950 translated tumor-specific circRNAs were predicted to generate 18971 antigen peptides in 27 organoids.In view of the antigen landscape,11 amino acid length(mer)peptides and human leukocyte antigen(HLA)-A binding peptides harbored the highest immunogenicity-related scores.In three out of five analyzed organoids,13 predicted antigen peptides were directly confirmed as HLA-A,-B,and-C(HLA-ABC)binding peptides with mass spectrometry(MS)-based immunopeptidomics.CircRNA-derived tumor-specific peptides presented by the HLA-ABC molecules stimulated cluster of differentiation 8(CD8)T cells to exhibit increased CD107a interferonγ(IFNγ)co-expressions and IFNγsecretion in flow cytometry and enzyme-linked immunosorbent assay(ELISA).Cytotoxic T cell activity targeting the organoids,induced by the immunogenic circRNA-derived peptides,was verified in a killing assay.Notably,the antigen peptide YGFNEILKK from circTBC1D15 was not only recognized as an HLA-ABC-presented peptide of the organoids but also drastically reduced the tumor organoid survival rate.Our findings highlight a crucial subset for generating tumor antigens,which has implications for targeting tumor-specific circRNAs in cancers.展开更多
Classical human leukocyte antigen(HLA)molecules of the major histocompatibility classⅡ(MHCⅡ)complex present peptides for the development,surveillance and activation of CD4^(+) T cells.The nonclassical MHCⅡ-like pro...Classical human leukocyte antigen(HLA)molecules of the major histocompatibility classⅡ(MHCⅡ)complex present peptides for the development,surveillance and activation of CD4^(+) T cells.The nonclassical MHCⅡ-like protein HLA-DM(DM)catalyzes the exchange and loading of peptides onto MHCⅡmolecules,thereby shaping MHCⅡimmunopeptidomes.Natural variations of DM in both chains of the protein(DMA and DMB)have been hypothesized to impact peptide presentation,but no evidence for altered function has been reported.Here we define the presence of DM allotypes in human populations covered by the 1000 Genomes Project and probe their activity.The functional properties of several allotypes are investigated and show strong enhancement of peptide-induced T cell activation for a particular combination of DMA and DMB.Biochemical evidence suggests a broader pH activity profile for the new variant relative to that of the most commonly expressed DM allotype.Immunopeptidome analysis indicates that the compartmental activity of the new DM heterodimer extends beyond the late endosome and suggests that the natural variation of DM has profound effects on adaptive immunity when antigens bypass the canonical processing pathway.展开更多
Autoreactive CD8^(+)T cells play a key role in type 1 diabetes(T1D),but the antigen spectrum that activates autoreactive CD8^(+)T cells remains unclear.Endoplasmic reticulum stress(ERS)has been implicated inβ-cell au...Autoreactive CD8^(+)T cells play a key role in type 1 diabetes(T1D),but the antigen spectrum that activates autoreactive CD8^(+)T cells remains unclear.Endoplasmic reticulum stress(ERS)has been implicated inβ-cell autoantigen generation.Here,we analyzed the major histocompatibility complex class I(MHC-I)-associated immunopeptidome(MIP)of isletβ-cells under steady and ERS conditions and found that ERS reshaped the MIP ofβ-cells and promoted the MHC-I presentation of a panel of conventional self-peptides.Among them,OTUB2_(58-66 ) showed immunodominance,and the corresponding autoreactive CD8^(+)T cells were diabetogenic in nonobese diabetic(NOD)mice.High glucose intake upregulated pancreatic OTUB2 expression and amplified the OTUB2_(58-66 )-specific CD8^(+)T-cell response in NOD mice.Repeated OTUB2_(58-66 )administration significantly reduced the incidence of T1D in NOD mice.Interestingly,peripheral blood mononuclear cells(PBMCs)from patients with T1D,but not from healthy controls,showed a positive IFN-γresponse to human OTUB2 peptides.This study provides not only a new explanation for the role of ERS in promotingβ-cell-targeted autoimmunity but also a potential target for the prevention and treatment of T1D.The data are available via ProteomeXchange with the identifier PXD041227.展开更多
基金the National Natural Science Foundation of China(U21A20376,82102871,81988101,81903184,81790633,and 81830054)the Innovation Program of Shanghai Municipal Education Commission(2019-01-07-00-07E00065)+1 种基金the National Science Foundation of Shanghai(21XD1404600,21JC1406600,and 22140901000)the China Postdoctoral Science Foundation(2020M671007).
文摘The application of tumor antigen-based immunotherapy is hindered by the rarity of validated immunogenic peptides.In this study,we aimed to investigate the potential of circular RNAs(circRNAs)as a novel source of tumor antigen peptides in hepatobiliary tumor organoids.Using RNA-sequencing(RNA-seq)with an algorithm-based score tool,3950 translated tumor-specific circRNAs were predicted to generate 18971 antigen peptides in 27 organoids.In view of the antigen landscape,11 amino acid length(mer)peptides and human leukocyte antigen(HLA)-A binding peptides harbored the highest immunogenicity-related scores.In three out of five analyzed organoids,13 predicted antigen peptides were directly confirmed as HLA-A,-B,and-C(HLA-ABC)binding peptides with mass spectrometry(MS)-based immunopeptidomics.CircRNA-derived tumor-specific peptides presented by the HLA-ABC molecules stimulated cluster of differentiation 8(CD8)T cells to exhibit increased CD107a interferonγ(IFNγ)co-expressions and IFNγsecretion in flow cytometry and enzyme-linked immunosorbent assay(ELISA).Cytotoxic T cell activity targeting the organoids,induced by the immunogenic circRNA-derived peptides,was verified in a killing assay.Notably,the antigen peptide YGFNEILKK from circTBC1D15 was not only recognized as an HLA-ABC-presented peptide of the organoids but also drastically reduced the tumor organoid survival rate.Our findings highlight a crucial subset for generating tumor antigens,which has implications for targeting tumor-specific circRNAs in cancers.
基金supported by the Deutsche Forschungsgemeinschaft(DFG)C.F.is thankful for funding by the DFG(FR-1325/17–1,SFB958(project Z03)+1 种基金TRR186(projects A05,A11))M.A.-B.is thankful for funding from the Freie Universität Berlin Forschungskommision.
文摘Classical human leukocyte antigen(HLA)molecules of the major histocompatibility classⅡ(MHCⅡ)complex present peptides for the development,surveillance and activation of CD4^(+) T cells.The nonclassical MHCⅡ-like protein HLA-DM(DM)catalyzes the exchange and loading of peptides onto MHCⅡmolecules,thereby shaping MHCⅡimmunopeptidomes.Natural variations of DM in both chains of the protein(DMA and DMB)have been hypothesized to impact peptide presentation,but no evidence for altered function has been reported.Here we define the presence of DM allotypes in human populations covered by the 1000 Genomes Project and probe their activity.The functional properties of several allotypes are investigated and show strong enhancement of peptide-induced T cell activation for a particular combination of DMA and DMB.Biochemical evidence suggests a broader pH activity profile for the new variant relative to that of the most commonly expressed DM allotype.Immunopeptidome analysis indicates that the compartmental activity of the new DM heterodimer extends beyond the late endosome and suggests that the natural variation of DM has profound effects on adaptive immunity when antigens bypass the canonical processing pathway.
基金National Natural Science Foundation of China(No.82071825 and No.81871301)National Key Research and Development Program(No.2016YFA0502204)Shandong Provincial Natural Science Fund(ZR2023MH201).
文摘Autoreactive CD8^(+)T cells play a key role in type 1 diabetes(T1D),but the antigen spectrum that activates autoreactive CD8^(+)T cells remains unclear.Endoplasmic reticulum stress(ERS)has been implicated inβ-cell autoantigen generation.Here,we analyzed the major histocompatibility complex class I(MHC-I)-associated immunopeptidome(MIP)of isletβ-cells under steady and ERS conditions and found that ERS reshaped the MIP ofβ-cells and promoted the MHC-I presentation of a panel of conventional self-peptides.Among them,OTUB2_(58-66 ) showed immunodominance,and the corresponding autoreactive CD8^(+)T cells were diabetogenic in nonobese diabetic(NOD)mice.High glucose intake upregulated pancreatic OTUB2 expression and amplified the OTUB2_(58-66 )-specific CD8^(+)T-cell response in NOD mice.Repeated OTUB2_(58-66 )administration significantly reduced the incidence of T1D in NOD mice.Interestingly,peripheral blood mononuclear cells(PBMCs)from patients with T1D,but not from healthy controls,showed a positive IFN-γresponse to human OTUB2 peptides.This study provides not only a new explanation for the role of ERS in promotingβ-cell-targeted autoimmunity but also a potential target for the prevention and treatment of T1D.The data are available via ProteomeXchange with the identifier PXD041227.
