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Systematic identification of minor histocompatibility antigens predicts outcomes of allogeneic hematopoietic cell transplantation

The success of hematopoietic cell transplants is predicted by profiling minor histocompatibility antigens.

Nicoletta Cieri
Nidhi Hookeri
Catherine J. Wu
Research21 Aug 2024
Nature Biotechnology

Volume: 43, P: 971-982
Correction: Corrigendum: Proteogenomic integration reveals therapeutic targets in breast cancer xenografts

Kuan-lin Huang
Shunqiang Li
Li Ding
Amendments and CorrectionsOpen Access25 Apr 2017
Nature Communications

Volume: 8, P: 1
Unannotated proteins expand the MHC-I-restricted immunopeptidome in cancer

New tumor epitopes are discovered by ribosome profiling and immunopeptidome mass spectrometry.

Tamara Ouspenskaia
Travis Law
Aviv Regev
Research18 Oct 2021
Nature Biotechnology

Volume: 40, P: 209-217
Addendum: A breast cancer stem cell niche supported by juxtacrine signalling from monocytes and macrophages

Haihui Lu
Karl R. Clauser
Robert A. Weinberg
Amendments and Corrections27 Nov 2015
Nature Cell Biology

Volume: 17, P: 1607
Suppression of pancreatic ductal adenocarcinoma growth and metastasis by fibrillar collagens produced selectively by tumor cells

Pancreatic ductal adenocarcinoma has a collagen-rich dense extracellular matrix that promotes malignancy of cancer cells. Here, the authors show that fibrillar collagen that is cancer-cell-derived, but not stroma-derived, selectively restrains tumor growth under control of their pC-proteinase, BMP1.

Chenxi Tian
Ying Huang
Richard O. Hynes
ResearchOpen Access20 Apr 2021
Nature Communications

Volume: 12, P: 1-16
Workflow enabling deepscale immunopeptidome, proteome, ubiquitylome, phosphoproteome, and acetylome analyses of sample-limited tissues

Patient samples are often available in limited amounts, restricting the number of possible omics analyses. Here the authors present MONTE, a workflow that enables serial HLA-I and HLA-II immunopeptidome, ubiquitylome, proteome, phosphoproteome, and acetylome data collection from patient samples.

Jennifer G. Abelin
Erik J. Bergstrom
Steven A. Carr
ResearchOpen Access03 Apr 2023
Nature Communications

Volume: 14, P: 1-22
Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics

The identification of HLA peptides by mass spectrometry is non-trivial. Here, the authors extended and used the wealth of data from the ProteomeTools project to improve the prediction of non-tryptic peptides using deep learning, and show their approach enables a variety of immunological discoveries.

Mathias Wilhelm
Daniel P. Zolg
Bernhard Kuster
ResearchOpen Access07 Jun 2021
Nature Communications

Volume: 12, P: 1-12
Microscaled proteogenomic methods for precision oncology

Connecting genomics and proteomics allows the development of more efficient and specific treatments for cancer. Here, the authors develop proteogenomic methods to defining cancer signaling in-vivo starting from core needle biopsies and with application to a HER2 breast cancer focused clinical trial.

Shankha Satpathy
Eric J. Jaehnig
Matthew J. Ellis
ResearchOpen Access27 Jan 2020
Nature Communications

Volume: 11, P: 1-16
Proteogenomic integration reveals therapeutic targets in breast cancer xenografts

Patient-derived xenografts recapitulate major genomic signatures and transcriptome profiles of their original tumours. Here, the authors, performing proteomic and phosphoproteomic analyses of 24 breast cancer PDX models, demonstrate that druggable candidates can be identified based on a comprehensive proteogenomic profiling.

Kuan-lin Huang
Shunqiang Li
Li Ding
ResearchOpen Access28 Mar 2017
Nature Communications

Volume: 8, P: 1-17
A large peptidome dataset improves HLA class I epitope prediction across most of the human population

Prediction of HLA class I epitopes is improved in accuracy and breath with peptidomes from 95 mono-allelic cell lines.

Siranush Sarkizova
Susan Klaeger
Derin B. Keskin
Research16 Dec 2019
Nature Biotechnology

Volume: 38, P: 199-209
Proteogenomics connects somatic mutations to signalling in breast cancer

Quantitative mass-spectrometry-based proteomic and phosphoproteomic analyses of genomically annotated human breast cancer samples elucidates functional consequences of somatic mutations, narrows candidate nominations for driver genes within large deletions and amplified regions, and identifies potential therapeutic targets.

Philipp Mertins
D. R. Mani
Steven A. Carr
Research25 May 2016
Nature

Volume: 534, P: 55-62
Phenotype, specificity and avidity of antitumour CD8⁺ T cells in melanoma

The authors use single-cell profiling and T cell receptor specificity screening to show how tumour antigen recognition shapes the phenotypes of CD8⁺ T cells and antitumour immune responses.

Giacomo Oliveira
Kari Stromhaug
Catherine J. Wu
Research21 Jul 2021
Nature

Volume: 596, P: 119-125
A pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease

Rational strategies to prioritize candidate biomarkers should save resources and accelerate progress in diagnostics development. Addona et al. integrate proteomics into a pipeline for biomarker validation and use it to identify markers of cardiovascular injury in a scenario where patients serve as their own biological controls.

Terri A Addona
Xu Shi
Steven A Carr
Research19 Jun 2011
Nature Biotechnology

Volume: 29, P: 635-643
A breast cancer stem cell niche supported by juxtacrine signalling from monocytes and macrophages

Weinberg and colleagues report that monocytes and macrophages interact with stem-like human mammary epithelial cells to create a breast cancer stem cell niche.

Haihui Lu
Karl R. Clauser
Robert A. Weinberg
Research28 Sept 2014
Nature Cell Biology

Volume: 16, P: 1105-1117
Site-specific identification and quantitation of endogenous SUMO modifications under native conditions

SUMOylation is post-translational modification implicated in several biological pathways. Here the authors describe an approach for the global profiling of SUMO attachment sites under native conditions that also allows the parallel determination of SUMO and Ub attachments.

Ryan J. Lumpkin
Hongbo Gu
Elizabeth A. Komives
ResearchOpen Access27 Oct 2017
Nature Communications

Volume: 8, P: 1-11
Author Correction: Deep learning boosts sensitivity of mass spectrometry-based immunopeptidomics

Mathias Wilhelm
Daniel P. Zolg
Bernhard Kuster
Amendments and CorrectionsOpen Access23 Jun 2021
Nature Communications

Volume: 12, P: 1
PANOPLY: a cloud-based platform for automated and reproducible proteogenomic data analysis

D. R. Mani
Myranda Maynard
Steven A. Carr
Correspondence26 May 2021
Nature Methods

Volume: 18, P: 580-582
Noncanonical open reading frames encode functional proteins essential for cancer cell survival

Noncanonical open reading frames are shown to be essential for cancer cell function.

John R. Prensner
Oana M. Enache
Todd R. Golub
Research28 Jan 2021
Nature Biotechnology

Volume: 39, P: 697-704
Bead-based profiling of tyrosine kinase phosphorylation identifies SRC as a potential target for glioblastoma therapy

Du et al. describe a bead-based method for high-throughput detection of phosphorylated tyrosine kinases and use it to profile 130 human cancer lines. They show that the tyrosine kinase SRC is frequently activated in glioblastoma cells and that a SRC inhibitor blocks the growth of glioblastoma tumors.

Jinyan Du
Paula Bernasconi
Todd R Golub
Research21 Dec 2008
Nature Biotechnology

Volume: 27, P: 77-83
Integrated proteomic analysis of post-translational modifications by serial enrichment

A mass spectrometry–based method using serial enrichments of different post-translational modifications (SEPTM) enables high-coverage proteomic analysis of multiple PTMs from a single biological sample.

Philipp Mertins
Jana W Qiao
Steven A Carr
Research09 Jun 2013
Nature Methods

Volume: 10, P: 634-637
Cancer proteogenomics: current impact and future prospects

This Review examines recent developments in proteogenomics, key findings from the proteogenomic analyses of a wide range of cancers and emerging applications of proteogenomics to translational studies and immuno-oncology, as well as discussing future prospects regarding integration into clinical trials and patient care.

D. R. Mani
Karsten Krug
Steven A. Carr
Reviews02 Mar 2022
Nature Reviews Cancer

Volume: 22, P: 298-313
Antibodies to biotin enable large-scale detection of biotinylation sites on proteins

Enrichment of biotinylated peptides using an anti-biotin antibody results in substantially improved biotinylation site identifications by mass spectrometry compared to traditional streptavidin-based biotinylated protein enrichment.

Namrata D Udeshi
Kayvon Pedram
Steven A Carr
Research16 Oct 2017
Nature Methods

Volume: 14, P: 1167-1170
Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography–mass spectrometry

This protocol describes a workflow for multiplexed deep-scale, quantitative proteome and phosphoproteome analysis of tumor tissue samples. The procedure includes step-by-step instructions for all stages, from sample preparation to data analysis.

Philipp Mertins
Lauren C. Tang
Steven A. Carr
Protocols09 Jul 2018
Nature Protocols

Volume: 13, P: 1632-1661
Quantitative proteomic profiling of the extracellular matrix of pancreatic islets during the angiogenic switch and insulinoma progression

Alexandra Naba
Karl R. Clauser
Richard O. Hynes
ResearchOpen Access10 Jan 2017
Scientific Reports

Volume: 7, P: 1-12
Quantitative, multiplexed workflow for deep analysis of human blood plasma and biomarker discovery by mass spectrometry

This protocol describes the deep-scale analysis of the blood plasma proteome. By combining abundant protein depletion, sample multiplexing with isobaric labeling and fractionation, this enables rapid quantification of >4,500 plasma proteins.

Hasmik Keshishian
Michael W Burgess
Steven A Carr
Protocols27 Jul 2017
Nature Protocols

Volume: 12, P: 1683-1701

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