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Proteomics profiling of CLL versus healthy B-cells identifies putative therapeutic targets and a subtype-independent signature of spliceosome dysregulation

Proteomics profiling of CLL versus healthy B-cells identifies putative therapeutic targets and a subtype-independent signature of spliceosome dysregulation
Proteomics profiling of CLL versus healthy B-cells identifies putative therapeutic targets and a subtype-independent signature of spliceosome dysregulation
Chronic lymphocytic leukaemia (CLL) is a heterogeneous B-cell cancer exhibiting a wide spectrum of disease courses and treatment responses. Molecular characterisation of RNA and DNA from CLL cases has led to the identification of important driver mutations and disease sub-types, but the precise mechanisms of disease progression remain elusive. To further our understanding of CLL biology we performed isobaric labelling and mass spectrometry proteomics on 14 CLL samples, comparing them with B-cells from healthy donors (HDB). Of 8694 identified proteins, ~6000 were relatively quantitated between all samples (q<0.01). A clear CLL signature, independent of subtype, of 544 significantly overexpressed proteins relative to HDB was identified, highlighting establishedhallmarks of CLL (eg. CD5, BCL2, ROR1 and CD23 overexpression). Previously unrecognised surface markers demonstrated overexpression (eg. CKAP4, PIGR, TMCC3 and CD75) and three of these (LAX1, CLEC17A and ATP2B4) were implicated in B-cell receptor signalling, which plays an important role in CLL pathogenesis. Several other proteins (eg. Wee1, HMOX1/2, HDAC7 and INPP5F) were identified with significant overexpression that also represent potential targets. Western blotting confirmed overexpression of a selection of these proteins in an independent cohort. mRNA processing machinery were broadly upregulated across the CLL samples. Spliceosome components demonstrated consistent overexpression (p=1.3x10-21) suggesting dysregulation in CLL, independent of SF3B1 mutations. This study highlights the potential of proteomics in the identification of putative CLL therapeutic targets and reveals a subtype-independent protein expression signature in CLL.
1535-9476
Johnston, Harvey
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Carter, Matthew
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Larrayoz, Marta
952a54b7-c539-4f37-8818-0129e634e999
Clarke, James, Ian
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Garbis, Spiros
7067fd19-50c9-4d42-9611-f370289470bd
Oscier, David G
c2620a1d-25bb-48f7-9651-f5d023636381
Strefford, Jonathan
3782b392-f080-42bf-bdca-8aa5d6ca532f
Steele, Andrew
4349f6aa-2e3a-49a8-be73-7716056ae089
Walewska, Renata
326c1001-fcdb-452a-aa53-2c82a1ca39a5
Cragg, Mark
ec97f80e-f3c8-49b7-a960-20dff648b78c
Johnston, Harvey
dbd189e4-c79b-4a6e-8447-925d5c409eab
Carter, Matthew
3baac102-d80c-42ba-ab4d-ad339a48169e
Larrayoz, Marta
952a54b7-c539-4f37-8818-0129e634e999
Clarke, James, Ian
867dce7c-1a12-42f2-acc3-63c440ff0024
Garbis, Spiros
7067fd19-50c9-4d42-9611-f370289470bd
Oscier, David G
c2620a1d-25bb-48f7-9651-f5d023636381
Strefford, Jonathan
3782b392-f080-42bf-bdca-8aa5d6ca532f
Steele, Andrew
4349f6aa-2e3a-49a8-be73-7716056ae089
Walewska, Renata
326c1001-fcdb-452a-aa53-2c82a1ca39a5
Cragg, Mark
ec97f80e-f3c8-49b7-a960-20dff648b78c

Johnston, Harvey, Carter, Matthew, Larrayoz, Marta, Clarke, James, Ian, Garbis, Spiros, Oscier, David G, Strefford, Jonathan, Steele, Andrew, Walewska, Renata and Cragg, Mark (2018) Proteomics profiling of CLL versus healthy B-cells identifies putative therapeutic targets and a subtype-independent signature of spliceosome dysregulation. Molecular & Cellular Proteomics. (doi:10.1074/mcp.RA117.000539).

Record type: Article

Abstract

Chronic lymphocytic leukaemia (CLL) is a heterogeneous B-cell cancer exhibiting a wide spectrum of disease courses and treatment responses. Molecular characterisation of RNA and DNA from CLL cases has led to the identification of important driver mutations and disease sub-types, but the precise mechanisms of disease progression remain elusive. To further our understanding of CLL biology we performed isobaric labelling and mass spectrometry proteomics on 14 CLL samples, comparing them with B-cells from healthy donors (HDB). Of 8694 identified proteins, ~6000 were relatively quantitated between all samples (q<0.01). A clear CLL signature, independent of subtype, of 544 significantly overexpressed proteins relative to HDB was identified, highlighting establishedhallmarks of CLL (eg. CD5, BCL2, ROR1 and CD23 overexpression). Previously unrecognised surface markers demonstrated overexpression (eg. CKAP4, PIGR, TMCC3 and CD75) and three of these (LAX1, CLEC17A and ATP2B4) were implicated in B-cell receptor signalling, which plays an important role in CLL pathogenesis. Several other proteins (eg. Wee1, HMOX1/2, HDAC7 and INPP5F) were identified with significant overexpression that also represent potential targets. Western blotting confirmed overexpression of a selection of these proteins in an independent cohort. mRNA processing machinery were broadly upregulated across the CLL samples. Spliceosome components demonstrated consistent overexpression (p=1.3x10-21) suggesting dysregulation in CLL, independent of SF3B1 mutations. This study highlights the potential of proteomics in the identification of putative CLL therapeutic targets and reveals a subtype-independent protein expression signature in CLL.

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Accepted/In Press date: 23 January 2018
e-pub ahead of print date: 24 January 2018

Identifiers

Local EPrints ID: 417670
URI: https://eprints.soton.ac.uk/id/eprint/417670
ISSN: 1535-9476
PURE UUID: b36fb6d3-6c65-46bb-a906-79c2262869be
ORCID for Jonathan Strefford: ORCID iD orcid.org/0000-0002-0972-2881
ORCID for Andrew Steele: ORCID iD orcid.org/0000-0003-0667-1596
ORCID for Mark Cragg: ORCID iD orcid.org/0000-0003-2077-089X

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Date deposited: 09 Feb 2018 17:30
Last modified: 14 Mar 2019 05:16

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Contributors

Author: Harvey Johnston
Author: Matthew Carter
Author: Marta Larrayoz
Author: James, Ian Clarke
Author: Spiros Garbis
Author: David G Oscier
Author: Andrew Steele ORCID iD
Author: Renata Walewska
Author: Mark Cragg ORCID iD

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