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Showing 1 to 12 of 29 entries
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Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer.

Nature biotechnology

Ouspenskaia T, Law T, Clauser KR, Klaeger S, Sarkizova S, Aguet F, Li B, Christian E, Knisbacher BA, Le PM, Hartigan CR, Keshishian H, Apffel A, Oliveira G, Zhang W, Chen S, Chow YT, Ji Z, Jungreis I, Shukla SA, Justesen S, Bachireddy P, Kellis M, Getz G, Hacohen N, Keskin DB, Carr SA, Wu CJ, Regev A.
PMID: 34663921
Nat Biotechnol. 2021 Oct 18; doi: 10.1038/s41587-021-01021-3. Epub 2021 Oct 18.

Tumor-associated epitopes presented on MHC-I that can activate the immune system against cancer cells are typically identified from annotated protein-coding regions of the genome, but whether peptides originating from novel or unannotated open reading frames (nuORFs) can contribute to...

SARS-CoV-2 infected cells present HLA-I peptides from canonical and out-of-frame ORFs.

bioRxiv : the preprint server for biology

Weingarten-Gabbay S, Klaeger S, Sarkizova S, Pearlman LR, Chen DY, Bauer MR, Taylor HB, Conway HL, Tomkins-Tinch CH, Finkel Y, Nachshon A, Gentili M, Rivera KD, Keskin DB, Rice CM, Clauser KR, Hacohen N, Carr SA, Abelin JG, Saeed M, Sabeti PC.
PMID: 33024965
bioRxiv. 2020 Oct 26; doi: 10.1101/2020.10.02.324145.

T cell-mediated immunity may play a critical role in controlling and establishing protective immunity against SARS-CoV-2 infection; yet the repertoire of viral epitopes responsible for T cell response activation remains mostly unknown. Identification of viral peptides presented on class...

Author Correction: Blockade of IL-22 signaling reverses erythroid dysfunction in stress-induced anemias.

Nature immunology

Raundhal M, Ghosh S, Myers SA, Cuoco MS, Singer M, Carr SA, Waikar SS, Bonventre JV, Ritz J, Stone RM, Steensma DP, Regev A, Glimcher LH.
PMID: 34522041
Nat Immunol. 2021 Nov;22(11):1465. doi: 10.1038/s41590-021-01031-y.

No abstract available.

Optimized Liquid and Gas Phase Fractionation Increases HLA-Peptidome Coverage for Primary Cell and Tissue Samples.

Molecular & cellular proteomics : MCP

Klaeger S, Apffel A, Clauser KR, Sarkizova S, Oliveira G, Rachimi S, Le PM, Tarren A, Chea V, Abelin JG, Braun DA, Ott PA, Keshishian H, Hacohen N, Keskin DB, Wu CJ, Carr SA.
PMID: 34391888
Mol Cell Proteomics. 2021;20:100133. doi: 10.1016/j.mcpro.2021.100133. Epub 2021 Aug 12.

MS is the most effective method to directly identify peptides presented on human leukocyte antigen (HLA) molecules. However, current standard approaches often use 500 million or more cells as input to achieve high coverage of the immunopeptidome, and therefore,...

Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer.

Nature biotechnology

Ouspenskaia T, Law T, Clauser KR, Klaeger S, Sarkizova S, Aguet F, Li B, Christian E, Knisbacher BA, Le PM, Hartigan CR, Keshishian H, Apffel A, Oliveira G, Zhang W, Chen S, Chow YT, Ji Z, Jungreis I, Shukla SA, Justesen S, Bachireddy P, Kellis M, Getz G, Hacohen N, Keskin DB, Carr SA, Wu CJ, Regev A.
PMID: 34663921
Nat Biotechnol. 2021 Oct 18; doi: 10.1038/s41587-021-01021-3. Epub 2021 Oct 18.

Tumor-associated epitopes presented on MHC-I that can activate the immune system against cancer cells are typically identified from annotated protein-coding regions of the genome, but whether peptides originating from novel or unannotated open reading frames (nuORFs) can contribute to...

Author Correction: Blockade of IL-22 signaling reverses erythroid dysfunction in stress-induced anemias.

Nature immunology

Raundhal M, Ghosh S, Myers SA, Cuoco MS, Singer M, Carr SA, Waikar SS, Bonventre JV, Ritz J, Stone RM, Steensma DP, Regev A, Glimcher LH.
PMID: 34522041
Nat Immunol. 2021 Nov;22(11):1465. doi: 10.1038/s41590-021-01031-y.

No abstract available.

Novel Antibodies for the Simple and Efficient Enrichment of Native O-GlcNAc Modified Peptides.

Molecular & cellular proteomics : MCP

Burt RA, Dejanovic B, Peckham HJ, Lee KA, Li X, Ounadjela JR, Rao A, Malaker SA, Carr SA, Myers SA.
PMID: 34678516
Mol Cell Proteomics. 2021 Oct 20;20:100167. doi: 10.1016/j.mcpro.2021.100167. Epub 2021 Oct 20.

Antibodies against posttranslational modifications (PTMs) such as lysine acetylation, ubiquitin remnants, or phosphotyrosine have resulted in significant advances in our understanding of the fundamental roles of these PTMs in biology. However, the roles of a number of PTMs remain...

Multiomic characterization of oncogenic signaling mediated by wild-type and mutant RIT1.

Science signaling

Lo A, Holmes K, Kamlapurkar S, Mundt F, Moorthi S, Fung I, Fereshetian S, Watson J, Carr SA, Mertins P, Berger AH.
PMID: 34846918
Sci Signal. 2021 Nov 30;14(711):eabc4520. doi: 10.1126/scisignal.abc4520. Epub 2021 Nov 30.

[Figure: see text].

Proteogenomic characterization of pancreatic ductal adenocarcinoma.

Cell

Cao L, Huang C, Cui Zhou D, Hu Y, Lih TM, Savage SR, Krug K, Clark DJ, Schnaubelt M, Chen L, da Veiga Leprevost F, Eguez RV, Yang W, Pan J, Wen B, Dou Y, Jiang W, Liao Y, Shi Z, Terekhanova NV, Cao S, Lu RJ, Li Y, Liu R, Zhu H, Ronning P, Wu Y, Wyczalkowski MA, Easwaran H, Danilova L, Mer AS, Yoo S, Wang JM, Liu W, Haibe-Kains B, Thiagarajan M, Jewell SD, Hostetter G, Newton CJ, Li QK, Roehrl MH, Fenyö D, Wang P, Nesvizhskii AI, Mani DR, Omenn GS, Boja ES, Mesri M, Robles AI, Rodriguez H, Bathe OF, Chan DW, Hruban RH, Ding L, Zhang B, Zhang H.
PMID: 34534465
Cell. 2021 Sep 16;184(19):5031-5052.e26. doi: 10.1016/j.cell.2021.08.023.

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer with poor patient survival. Toward understanding the underlying molecular alterations that drive PDAC oncogenesis, we conducted comprehensive proteogenomic analysis of 140 pancreatic cancers, 67 normal adjacent tissues, and 9 normal...

Automating UbiFast for High-throughput and Multiplexed Ubiquitin Enrichment.

Molecular & cellular proteomics : MCP

Rivera KD, Olive ME, Bergstrom EJ, Nelson AJ, Lee KA, Satpathy S, Carr SA, Udeshi ND.
PMID: 34592423
Mol Cell Proteomics. 2021 Sep 27;20:100154. doi: 10.1016/j.mcpro.2021.100154. Epub 2021 Sep 27.

Robust methods for deep-scale enrichment and site-specific identification of ubiquitylation sites are necessary for characterizing the myriad roles of protein ubiquitylation. To this end we previously developed UbiFast, a sensitive method for highly multiplexed ubiquitylation profiling where K-ϵ-GG peptides...

Author Correction: Blockade of IL-22 signaling reverses erythroid dysfunction in stress-induced anemias.

Nature immunology

Raundhal M, Ghosh S, Myers SA, Cuoco MS, Singer M, Carr SA, Waikar SS, Bonventre JV, Ritz J, Stone RM, Steensma DP, Regev A, Glimcher LH.
PMID: 34522041
Nat Immunol. 2021 Nov;22(11):1465. doi: 10.1038/s41590-021-01031-y.

No abstract available.

Multiomic characterization of oncogenic signaling mediated by wild-type and mutant RIT1.

Science signaling

Lo A, Holmes K, Kamlapurkar S, Mundt F, Moorthi S, Fung I, Fereshetian S, Watson J, Carr SA, Mertins P, Berger AH.
PMID: 34846918
Sci Signal. 2021 Nov 30;14(711):eabc4520. doi: 10.1126/scisignal.abc4520. Epub 2021 Nov 30.

[Figure: see text].

Showing 1 to 12 of 29 entries