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PXD028936 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleProteogenomic subtyping of chronic lymphocytic leukemia identifies subgroups with contrasting clinical outcome and distinct ex-vivo drug response profile
DescriptionWe have performed a comprehensive proteomic analysis of clinical patient samples of chronic lymphocytic leukemia (CLL) alongside genome-, transcriptome- and ex-vivo drug response profiling. Trisomy 12 and IGHV mutation status had the strongest impact on the proteome and transcriptome; and SF3B1 mutations preferentially affected the proteome. Unsupervised clustering of the proteome data partitioned CLL patients into six protein based subgroups (PG) with contrasting clinical behavior. PG1-4 could be explained by the impact of trisomy 12 and IGHV mutation status on protein abundances and another subgroup (PG6), was enriched for TP53 mutations. In addition we uncovered a new subgroup (PG5) only detectable from the proteome, characterized by low expression of central B-cell receptor proteins, altered splicing, metabolic reprogramming and increased sensitivity to proteasomal inhibition. https://www.ebi.ac.uk/pride/archive/projects/PXD024544
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterMattias Vesterlund
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListTMT6plex-126 reporter+balance reagent acylated residue; phosphorylated residue; iodoacetamide derivatized residue
InstrumentQ Exactive
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-10-04 10:03:06ID requested
12022-10-17 05:54:08announced
22023-11-14 07:36:36announced2023-11-14: Updated project metadata.
Publication List
Herbst SA, Vesterlund M, Helmboldt AJ, Jafari R, Siavelis I, Stahl M, Schitter EC, Liebers N, Brinkmann BJ, Czernilofsky F, Roider T, Bruch PM, Iskar M, Kittai A, Huang Y, Lu J, Richter S, Mermelekas G, Umer HM, Knoll M, Kolb C, Lenze A, Cao X, Ö, sterholm C, Wahnschaffe L, Herling C, Scheinost S, Ganzinger M, Mansouri L, Kriegsmann K, Kriegsmann M, Anders S, Zapatka M, Del Poeta G, Zucchetto A, Bomben R, Gattei V, Dreger P, Woyach J, Herling M, M, ü, ller-Tidow C, Rosenquist R, Stilgenbauer S, Zenz T, Huber W, Tausch E, Lehti, ö J, Dietrich S, Proteogenomics refines the molecular classification of chronic lymphocytic leukemia. Nat Commun, 13(1):6226(2022) [pubmed]
Keyword List
submitter keyword: Lymphoblast, B-cell, Chronic Lymphoblastic Leukemia,Proteogenomics, Human, LC-MS,Leukemia, Cancer, Clinical samples., HiRIEF, Proteomics
Contact List
Janne Lehtiö
contact affiliationDepartment of Oncology-Pathology, Karolinska Institutet and Science for Life Laboratory
contact emailjanne.lehtio@ki.se
lab head
Mattias Vesterlund
contact affiliationKarolinska Institutet
contact emailmattias.vesterlund@ki.se
dataset submitter
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Dataset FTP location
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