Dataset Information

Quantitative Proteomic Profiles of Chronic Lymphocytic Leukaemia

ABSTRACT: Chronic lymphocytic leukaemia (CLL) is a common, adult B-cell leukaemia that has challenges in prognosis and treatment. It is characterised by a heterogeneous clinical course with multiple distinct phenotypes currently defined genetically or with target-specific monoclonal antibodies. While many studies have examined specific protein targets or global mRNA expression in CLL, few have attempted to characterise expression across the whole proteome. To achieve a non-biased, global proteomics characterisation, 14 CLL samples representing the genetic mutant subgroups NOTCH1, SF3B1 and WT, were subjected to quantitative mass spectrometry and compared with normal B cells using two isobaric tag experiments (TMT 10-plex). 6150 proteins were fully quantitated revealing a strong correlation between the regulated proteins across the CLL samples, independent of subtype. >800 proteins demonstrated significant upregulation (p<0.05) across the CLL samples. In addition to several novel cell surface markers, overexpressed proteins were strongly indicative of dysregulation to mRNA processing, spliceosome activity, transcriptional control by RNA pol II and epigenetic mechanisms (all p<10-10). A strong enrichment was observed for proteins coded by chromosome 12, often observed with trisomy in CLL (p<0.001). Downregulated proteins included cell adhesion molecules such as integrins and suggested a reduced capacity for endothelial transmigration (both p<10-10). These findings confirm many previous observations of CLL-specific protein overexpression (eg. CD5, ROR1, matriptase) and identify several novel surface targets for investigation. They also suggest that strong patterns of protein expression exist across CLL subtypes. Together, these results demonstrate the potential of proteomics and advocate the characterisation of further cancer samples by such methods.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): B Cell, B-lymphocyte, Chronic Lymphocytic Leukemia Cell

DISEASE(S): Chronic Lymphocytic Leukemia

SUBMITTER: Harvey Johnston

LAB HEAD: Spiro Garbis

PROVIDER: PXD002004 | Pride | 2018-01-26

REPOSITORIES: Pride

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Publications

Proteomics Profiling of CLL Versus Healthy B-cells Identifies Putative Therapeutic Targets and a Subtype-independent Signature of Spliceosome Dysregulation.

Johnston Harvey E HE Carter Matthew J MJ Larrayoz Marta M Clarke James J Garbis Spiro D SD Oscier David D Strefford Jonathan C JC Steele Andrew J AJ Walewska Renata R Cragg Mark S MS

Molecular & cellular proteomics : MCP 20180124 4

Chronic lymphocytic leukemia (CLL) is a heterogeneous B-cell cancer exhibiting a wide spectrum of disease courses and treatment responses. Molecular characterization of RNA and DNA from CLL cases has led to the identification of important driver mutations and disease subtypes, but the precise mechanisms of disease progression remain elusive. To further our understanding of CLL biology we performed isobaric labeling and mass spectrometry proteomics on 14 CLL samples, comparing them with B-cells f ...[more]

PMID: 29367434

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Project description:Chronic lymphocytic leukaemia (CLL) is renowned for its variable clinical course and response to therapy, suggesting a role for precision medicine. However, the molecular basis of CLL variability remains incompletely understood. Recent developments in data independent acquisition (DIA) -MS technologies, such as SWATH (Sequential Windowed Acquisition of all THeoretical fragments), provide an opportunity to study the pathophysiology of CLL at the proteome level. This report describes the sample replication and data handling requirements for SWATH-MS analysis of clinical samples. A CLL-specific spectral library compromising over 1,500,000 spectra with digital information for over 150,000 peptides has been generated to enable the quantification of up to 7736 proteins. To assess the reproducibility of the assay, SWATH-MS analysis was performed on 6 cryopreserved CLL patient samples, incorporating biological (IGHV mutational status), sample preparation and MS technical replicates. Quantitative information was obtained for 5169 proteins (<1% FDR) across 54 SWATH-MS acquisitions. These analyses showed that SWATH-MS is a highly reproducible technique. However, replicate sample preparations on different days was identified as the main source of variation. To overcome the effect of variation between sample preparation batches, different computational approaches for batch correction were tested. All approaches successfully removed technical variability whilst retaining proteomic differences between clinical subgroups. Functional enrichment analysis of proteins associated to IGHV mutational status highlighted the importance of metabolic remodelling in the biology of CLL and overlapped significantly with previous studies based on gene expression profiling. Finally, an approach to perform statistical power analysis in proteomics studies was developed. This approach could be used to drive the design of future CLL SWATH-MS studies. These fundamental requirements for DIA approaches should be widely applicable to other clinical proteomics studies.

			Action	DRS
	11JAN15_CLL_A.msf	Msf
	12JAN14_CLL_B.msf	Msf
	17Dec14_CLL_A_1.raw	Raw
	17Dec14_CLL_A_10.raw	Raw
	17Dec14_CLL_A_19.raw	Raw