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Article ; Online: Proteomics and peritoneal dialysis: early days but clear potential.

Brewis, Ian A / Topley, Nicholas

Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association

2010 Volume 25, Issue 6, Page(s) 1749–1753

MeSH term(s)	Ascitic Fluid/chemistry ; Biomarkers/analysis ; Electrophoresis, Gel, Two-Dimensional ; Humans ; Peritoneal Dialysis/trends ; Protein Array Analysis ; Protein Interaction Mapping ; Proteome/isolation & purification ; Proteomics/trends ; Tandem Mass Spectrometry
Chemical Substances	Biomarkers ; Proteome
Language	English
Publishing date	2010-03-26
Publishing country	England
Document type	Comment ; Editorial
ZDB-ID	90594-x
ISSN	1460-2385 ; 0931-0509
ISSN (online)	1460-2385
ISSN	0931-0509
DOI	10.1093/ndt/gfq145
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Article ; Online: Sperm surface proteomics: from protein lists to biological function.

Brewis, Ian A / Gadella, Barend M

Molecular human reproduction

2010 Volume 16, Issue 2, Page(s) 68–79

Abstract: Proteomics technologies have matured significantly in recent years and proteomics driven research articles in reproductive biology and medicine are increasingly common. The key challenge is to move from lists of identified proteins to informed ... ...

Abstract	Proteomics technologies have matured significantly in recent years and proteomics driven research articles in reproductive biology and medicine are increasingly common. The key challenge is to move from lists of identified proteins to informed understanding of biological function. This review introduces the range of proteomics workflows most commonly used for protein identification before focusing on the mammalian sperm cell at fertilization as an exemplar for proteomic studies. We review the work of others on entire cells but then argue that proper subcellular fractionation and proper solubilization strategies offers critical advantages to achieving increased biological understanding. In relation to understanding initial gamete recognition events at fertilization (capacitation, zona binding and acrosomal exocytosis) it is imperative to study the sperm surface proteome by using purified plasma membrane fractions. Although this task is challenging there are now strategies at our disposal to achieve comprehensive coverage of the proteins at the sperm surface. Within this context it is also important to understand the milieu of the sperm cell during transit from the testis to the oviduct as proteins (or other entities) from the genital tract epithelia and fluids may also affect the composition and organization of proteins on the sperm surface. Finally the arguments presented for studying the cell plasma membrane proteome to understand the role of the cell surface equally apply to all cell types with important roles in reproductive function.
MeSH term(s)	Animals ; Cell Membrane/metabolism ; Humans ; Male ; Models, Biological ; Proteins/metabolism ; Proteomics ; Spermatozoa/metabolism
Chemical Substances	Proteins
Language	English
Publishing date	2010-02
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	1324348-2
ISSN	1460-2407 ; 1360-9947
ISSN (online)	1460-2407
ISSN	1360-9947
DOI	10.1093/molehr/gap077
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Article ; Online: Proteomics technologies for the global identification and quantification of proteins.

Brewis, Ian A / Brennan, P

Advances in protein chemistry and structural biology

2010 Volume 80, Page(s) 1–44

Abstract: This review provides an introduction for the nonspecialist to proteomics and in particular the major approaches available for global protein identification and quantification. Proteomics technologies offer considerable opportunities for improved ... ...

Abstract	This review provides an introduction for the nonspecialist to proteomics and in particular the major approaches available for global protein identification and quantification. Proteomics technologies offer considerable opportunities for improved biological understanding and biomarker discovery. The central platform for proteomics is tandem mass spectrometry (MS) but a number of other technologies, resources, and expertise are absolutely required to perform meaningful experiments. These include protein separation science (and protein biochemistry in general), genomics, and bioinformatics. There are a range of workflows available for protein (or peptide) separation prior to tandem MS and subsequent bioinformatics analysis to achieve protein identifications. The predominant approaches are 2D electrophoresis (2DE) and subsequent MS, liquid chromatography-MS (LC-MS), and GeLC-MS. Beyond protein identification, there are a number of well-established options available for protein quantification. Difference gel electrophoresis (DIGE) following 2DE is one option but MS-based methods (most commonly iTRAQ-Isobaric Tags for Relative and Absolute Quantification or SILAC-Stable Isotope Labeling by Amino Acids) are now the preferred options. Sample preparation is critical to performing good experiments and subcellular fractionation can additionally provide protein localization information compared with whole cell lysates. Differential detergent solubilization is another valid option. With biological fluids, it is possible to remove the most abundant proteins by immunodepletion. Sample enrichment is also used extensively in certain analyses and most commonly in phosphoproteomics with the initial purification of phosphopeptides. Proteomics produces considerable datasets and resources to facilitate the necessary extended analysis of this data are improving all the time. Beyond the opportunities afforded by proteomics there are definite challenges to achieving full proteomic coverage. Proteomes are highly complex and identifying and quantifying low abundance proteins is a significant issue. Additionally, the analysis of poorly soluble proteins, such as membrane proteins and multiprotein complexes, is difficult. However, it is without doubt that proteomics has already provided significant insights into biological function and this will continue as the technology continues to improve. We also anticipate that the promise of proteomics in terms of biomarker discovery will increasingly be realized.
MeSH term(s)	Chromatography, Liquid ; Humans ; Peptides/analysis ; Proteins/analysis ; Proteome/analysis ; Proteomics/methods ; Proteomics/trends ; Tandem Mass Spectrometry
Chemical Substances	Peptides ; Proteins ; Proteome
Language	English
Publishing date	2010
Publishing country	Netherlands
Document type	Journal Article ; Review
ISSN	1876-1631 ; 1876-1623
ISSN (online)	1876-1631
ISSN	1876-1623
DOI	10.1016/B978-0-12-381264-3.00001-1
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Article ; Online: Prostate stromal cell proteomics analysis discriminates normal from tumour reactive stromal phenotypes.

Webber, Jason P / Spary, Lisa K / Mason, Malcolm D / Tabi, Zsuzsanna / Brewis, Ian A / Clayton, Aled

Oncotarget

2016 Volume 7, Issue 15, Page(s) 20124–20139

Abstract: Changes within interstitial stromal compartments often accompany carcinogenesis, and this is true of prostate cancer. Typically, the tissue becomes populated by myofibroblasts that can promote progression. Not all myofibroblasts exhibit the same negative ...

Abstract	Changes within interstitial stromal compartments often accompany carcinogenesis, and this is true of prostate cancer. Typically, the tissue becomes populated by myofibroblasts that can promote progression. Not all myofibroblasts exhibit the same negative influence, however, and identifying the aggressive form of myofibroblast may provide useful information at diagnosis. A means of molecularly defining such myofibroblasts is unknown. We compared protein profiles of normal and diseased stroma isolated from prostate cancer patients to identify discriminating hallmarks of disease-associated stroma. We included the stimulation of normal stromal cells with known myofibroblast inducers namely soluble TGFβ and exosome-associated-TGFβ and compared the function and protein profiles arising. In all 6-patients examined, diseased stroma exhibited a pro-angiogenic influence on endothelial cells, generating large multicellular vessel-like structures. Identical structures were apparent following stimulation of normal stroma with exosomes (5/6 patients), but TGFβ-stimulation generated a non-angiogenic stroma. Proteomics highlighted disease-related cytoskeleton alterations such as elevated Transgelin (TAGLN). Many of these were also changed following TGFβ or exosome stimulation and did not well discriminate the nature of the stimulus. Soluble TGFβ, however triggered differential expression of proteins related to mitochondrial function including voltage dependent ion channels VDAC1 and 2, and this was not found in the other stromal types studied. Surprisingly, Aldehyde Dehydrogenase (ALDH1A1), a stem-cell associated protein was detected in normal stromal cells and found to decrease in disease. In summary, we have discovered a set of proteins that contribute to defining disease-associated myofibroblasts, and emphasise the similarity between exosome-generated myofibroblasts and those naturally arising in situ.
Language	English
Publishing date	2016-04-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	2560162-3
ISSN	1949-2553 ; 1949-2553
ISSN (online)	1949-2553
ISSN	1949-2553
DOI	10.18632/oncotarget.7716
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Article ; Online: Proteomics-based identification of cancer-associated proteins in chronic lymphocytic leukaemia

Suliman A. Alsagaby / Ian A. Brewis / Rajendran Vijayakumar / Fahad A. Alhumaydhi / Ameen S. Alwashmi / Naif K. Alharbi / Waleed Al Abdulmonem / Mariappan Premanathan / Guy Pratt / Christopher Fegan / Christopher Pepper / Paul Brennan

Electronic Journal of Biotechnology, Vol 52, Iss , Pp 1-

2021 Volume 12

Abstract: ... cancer-associated proteins in this disease.How to cite: Alsagaby SA, Brennan P, Brewis IA, et al ...

Abstract	Background: Chronic lymphocytic leukaemia (CLL) is a neoplasm of B-cells characterized by variable prognosis. Exploring the proteome of CLL cells may provide insights into the disease. Therefore, eleven proteomics experiments were conducted on eleven primary CLL samples. Results: We reported a CLL proteome consisting of 919 proteins (false discovery rate (FDR) ≤ 1%) whose identification was based on the sequencing of two or more distinct peptides (FDR of peptide sequencing ≤ 1%). Mass spectrometry-based protein identification was validated for four different proteins using Western blotting and specific antibodies in different CLL samples. Small sizes of nucleolin (~57 kDa and ~68 kDa) showed a potential association with good prognosis CLL cells (n = 8, p < 0.01). Compared with normal B-cells, CLL cells over-expressed thyroid hormone receptor-associated protein 3 (THRAP3; n = 9; p = 0.00007), which is implicated in cell proliferation; and heterochromatin protein 1-binding protein 3 (HP1BP3; n = 10; p = 0.0002), which promotes cell survival and tumourogenesis. A smaller form of HP1BP3, which may correspond to HP1BP3 isoform-2, was specifically identified in normal B-cells (n = 10; p = 0.0001). HP1BP3 and THRAP3 predicted poor prognosis of CLL (p ≤ 0.05). Consistently, THRAP3 and HP1BP3 were found to be associated with cancer-related pathways (p ≤ 0.05). Conclusions: Our findings add to the known proteome of CLL and confirm the prognostic importance of two novel cancer-associated proteins in this disease.How to cite: Alsagaby SA, Brennan P, Brewis IA, et al. Proteomics-based identification of cancer-associated proteins in chronic lymphocytic leukaemia. Electron J Biotechnol 2021;51. https://doi.org/10.1016/j.ejbt.2021.04.006
Keywords	Biomarkers ; Cancer-associated proteins ; Chronic lymphocytic leukaemia ; HP1BP3 ; Nucleolin ; Proteomics ; Biotechnology ; TP248.13-248.65 ; Biology (General) ; QH301-705.5
Subject code	610
Language	English
Publishing date	2021-07-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Bicarbonate-dependent serine/threonine protein dephosphorylation in capacitating boar spermatozoa.

Alnagar, Fahima A / Brennan, Paul / Brewis, Ian A

Journal of andrology

2010 Volume 31, Issue 4, Page(s) 393–405

Abstract: This study investigates the dynamics of serine/threonine (S/T) protein phosphorylation in sperm incubated under capacitating (C) conditions using the boar as a model system. For the first time, this approach has identified multiple dephosphorylation ... ...

Abstract	This study investigates the dynamics of serine/threonine (S/T) protein phosphorylation in sperm incubated under capacitating (C) conditions using the boar as a model system. For the first time, this approach has identified multiple dephosphorylation events that occur in a bicarbonate-dependent fashion. Different phospho-(S/T) kinase substrate antibodies were used, and dephosphorylation of 5 S/T phosphoproteins was observed in C sperm compared with noncapacitated (N) cells. Specifically, dephosphorylation of 96-, 90-, 64-, and 55-kd proteins was detected by immunoblotting using 2 phospho-Akt substrate antibodies and a phosphoprotein kinase A substrate antibody. In addition, dephosphorylation of a 105-kd protein was detected using a phospho-ATM/ATR substrate antibody. In contrast, no dephosphorylation was observed using a phosphoprotein kinase C substrate antibody, and increased tyrosine phosphorylation of 32- and 20-kd proteins was detected in C compared with N sperm. Immunolocalization experiments revealed subtle changes in the pattern expression as well as a reduction of phosphorylation in C sperm. Whereas sperm incubated in N medium containing dibutyryl cAMP (dbcAMP) and 3-isobutyl-1-methylxanthine (IBMX) did not show protein dephosphorylation, incubation in C medium with dbcAMP/IBMX showed dephosphorylation as well as increased phosphorylation of other proteins (p68, p51, and p29). Finally, calyculin A, a phosphatase inhibitor, prevented dephosphorylation of p96, p90, p64, and p55 but not p105. Based on these data, we propose 2 pathways of protein dephosphorylation that are active during capacitation and independent of cAMP. Together, this provides direct evidence for more complex S/T phosphorylation dynamics than has been previously described for sperm undergoing capacitation.
MeSH term(s)	1-Methyl-3-isobutylxanthine ; Animals ; Bicarbonates/metabolism ; Bucladesine ; Fluorescent Antibody Technique ; Immunoblotting ; Male ; Oxazoles ; Phosphorylation ; Protein Phosphatase 1/antagonists & inhibitors ; Protein Phosphatase 2/antagonists & inhibitors ; Protein-Serine-Threonine Kinases/metabolism ; Protein-Tyrosine Kinases/metabolism ; Sperm Capacitation ; Spermatozoa/enzymology ; Swine
Chemical Substances	Bicarbonates ; Oxazoles ; Bucladesine (63X7MBT2LQ) ; calyculin A (7D07U14TK3) ; Protein-Tyrosine Kinases (EC 2.7.10.1) ; Protein-Serine-Threonine Kinases (EC 2.7.11.1) ; Protein Phosphatase 1 (EC 3.1.3.16) ; Protein Phosphatase 2 (EC 3.1.3.16) ; 1-Methyl-3-isobutylxanthine (TBT296U68M)
Language	English
Publishing date	2010-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	604624-1
ISSN	1939-4640 ; 0196-3635
ISSN (online)	1939-4640
ISSN	0196-3635
DOI	10.2164/jandrol.109.008383
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Article: Proteomics-based identification of cancer-associated proteins in chronic lymphocytic leukaemia

Alsagaby, Suliman A / Brewis, Ian A / Vijayakumar, Rajendran / Alhumaydhi, Fahad A / Alwashmi, Ameen S / Alharbi, Naif K / Al Abdulmonem, Waleed / Premanathan, Mariappan / Pratt, Guy / Fegan, Christopher / Pepper, Christopher / Brennan, Paul

Electronic Journal of Biotechnology. 2021 July, v. 52

2021

Abstract: ... associated proteins in this disease.How to cite: Alsagaby SA, Brennan P, Brewis IA, et al. Proteomics-based ...

Abstract	Chronic lymphocytic leukaemia (CLL) is a neoplasm of B-cells characterized by variable prognosis. Exploring the proteome of CLL cells may provide insights into the disease. Therefore, eleven proteomics experiments were conducted on eleven primary CLL samples.We reported a CLL proteome consisting of 919 proteins (false discovery rate (FDR) ≤ 1%) whose identification was based on the sequencing of two or more distinct peptides (FDR of peptide sequencing ≤ 1%). Mass spectrometry-based protein identification was validated for four different proteins using Western blotting and specific antibodies in different CLL samples. Small sizes of nucleolin (~57 kDa and ~68 kDa) showed a potential association with good prognosis CLL cells (n = 8, p < 0.01). Compared with normal B-cells, CLL cells over-expressed thyroid hormone receptor-associated protein 3 (THRAP3; n = 9; p = 0.00007), which is implicated in cell proliferation; and heterochromatin protein 1-binding protein 3 (HP1BP3; n = 10; p = 0.0002), which promotes cell survival and tumourogenesis. A smaller form of HP1BP3, which may correspond to HP1BP3 isoform-2, was specifically identified in normal B-cells (n = 10; p = 0.0001). HP1BP3 and THRAP3 predicted poor prognosis of CLL (p ≤ 0.05). Consistently, THRAP3 and HP1BP3 were found to be associated with cancer-related pathways (p ≤ 0.05).Our findings add to the known proteome of CLL and confirm the prognostic importance of two novel cancer-associated proteins in this disease.How to cite: Alsagaby SA, Brennan P, Brewis IA, et al. Proteomics-based identification of cancer-associated proteins in chronic lymphocytic leukaemia. Electron J Biotechnol 2021;51. https://doi.org/10.1016/j.ejbt.2021.04.006
Keywords	biotechnology ; cell proliferation ; cell viability ; heterochromatin ; leukemia ; mass spectrometry ; peptides ; prognosis ; proteome ; proteomics ; thyroid hormones
Language	English
Dates of publication	2021-07
Size	p. 1-12.
Publishing place	Elsevier B.V.
Document type	Article
Note	NAL-AP-2-clean
ISSN	0717-3458
DOI	10.1016/j.ejbt.2021.04.006
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Involvement of complexin 2 in docking, locking and unlocking of different SNARE complexes during sperm capacitation and induced acrosomal exocytosis.

Tsai, Pei-Shiue J / Brewis, Ian A / van Maaren, Jillis / Gadella, Bart M

PloS one

2012 Volume 7, Issue 3, Page(s) e32603

Abstract: Acrosomal exocytosis (AE) is an intracellular multipoint fusion reaction of the sperm plasma membrane (PM) with the outer acrosomal membrane (OAM). This unique exocytotic event enables the penetration of the sperm through the zona pellucida of the oocyte. ...

Abstract	Acrosomal exocytosis (AE) is an intracellular multipoint fusion reaction of the sperm plasma membrane (PM) with the outer acrosomal membrane (OAM). This unique exocytotic event enables the penetration of the sperm through the zona pellucida of the oocyte. We previously observed a stable docking of OAM to the PM brought about by the formation of the trans-SNARE complex (syntaxin 1B, SNAP 23 and VAMP 3). By using electron microscopy, immunochemistry and immunofluorescence techniques in combination with functional studies and proteomic approaches, we here demonstrate that calcium ionophore-induced AE results in the formation of unilamellar hybrid membrane vesicles containing a mixture of components originating from the two fused membranes. These mixed vesicles (MV) do not contain the earlier reported trimeric SNARE complex but instead possess a novel trimeric SNARE complex that contained syntaxin 3, SNAP 23 and VAMP 2, with an additional SNARE interacting protein, complexin 2. Our data indicate that the earlier reported raft and capacitation-dependent docking phenomenon between the PM and OAM allows a specific rearrangement of molecules between the two docked membranes and is involved in (1) recruiting SNAREs and complexin 2 in the newly formed lipid-ordered microdomains, (2) the assembly of a fusion-driving SNARE complex which executes Ca(2+)-dependent AE, (3) the disassembly of the earlier reported docking SNARE complex, (4) the recruitment of secondary zona binding proteins at the zona interacting sperm surface. The possibility to study separate and dynamic interactions between SNARE proteins, complexin and Ca(2+) which are all involved in AE make sperm an ideal model for studying exocytosis.
MeSH term(s)	Acrosome/metabolism ; Acrosome/ultrastructure ; Acrosome Reaction ; Adaptor Proteins, Vesicular Transport/metabolism ; Animals ; Bicarbonates/pharmacology ; Calcium/metabolism ; Cell Membrane/metabolism ; Exocytosis/physiology ; Male ; Membrane Fusion ; Nerve Tissue Proteins/metabolism ; Protein Binding/drug effects ; Protein Transport/drug effects ; Proteomics ; SNARE Proteins/metabolism ; Secretory Vesicles/drug effects ; Secretory Vesicles/metabolism ; Sperm Capacitation/physiology ; Sus scrofa
Chemical Substances	Adaptor Proteins, Vesicular Transport ; Bicarbonates ; Nerve Tissue Proteins ; SNARE Proteins ; complexin II ; Calcium (SY7Q814VUP)
Language	English
Publishing date	2012-03-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ISSN	1932-6203
ISSN (online)	1932-6203
DOI	10.1371/journal.pone.0032603
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: Proteomics analysis of cancer exosomes using a novel modified aptamer-based array (SOMAscan™) platform.

Webber, Jason / Stone, Timothy C / Katilius, Evaldas / Smith, Breanna C / Gordon, Bridget / Mason, Malcolm D / Tabi, Zsuzsanna / Brewis, Ian A / Clayton, Aled

Molecular & cellular proteomics : MCP

2014 Volume 13, Issue 4, Page(s) 1050–1064

Abstract: We have used a novel affinity-based proteomics technology to examine the protein signature of small secreted extracellular vesicles called exosomes. The technology uses a new class of protein binding reagents called SOMAmers® (slow off-rate modified ... ...

Abstract	We have used a novel affinity-based proteomics technology to examine the protein signature of small secreted extracellular vesicles called exosomes. The technology uses a new class of protein binding reagents called SOMAmers® (slow off-rate modified aptamers) and allows the simultaneous precise measurement of over 1000 proteins. Exosomes were highly purified from the Du145 prostate cancer cell line, by pooling selected fractions from a continuous sucrose gradient (within the density range of 1.1 to 1.2 g/ml), and examined under standard conditions or with additional detergent treatment by the SOMAscan™ array (version 3.0). Lysates of Du145 cells were also prepared, and the profiles were compared. Housekeeping proteins such as cyclophilin-A, LDH, and Hsp70 were present in exosomes, and we identified almost 100 proteins that were enriched in exosomes relative to cells. These included proteins of known association with cancer exosomes such as MFG-E8, integrins, and MET, and also those less widely reported as exosomally associated, such as ROR1 and ITIH4. Several proteins with no previously known exosomal association were confirmed as exosomally expressed in experiments using individual SOMAmer® reagents or antibodies in micro-plate assays. Western blotting confirmed the SOMAscan™-identified enrichment of exosomal NOTCH-3, L1CAM, RAC1, and ADAM9. In conclusion, we describe here over 300 proteins of hitherto unknown association with prostate cancer exosomes and suggest that the SOMAmer®-based assay technology is an effective proteomics platform for exosome-associated biomarker discovery in diverse clinical settings.
MeSH term(s)	Biomarkers, Tumor/metabolism ; Cell Line, Tumor ; Exosomes/genetics ; Exosomes/metabolism ; Genes, Essential ; Humans ; Male ; Microarray Analysis/methods ; Nanotechnology ; Prostatic Neoplasms/metabolism ; Proteomics/methods
Chemical Substances	Biomarkers, Tumor
Language	English
Publishing date	2014-02-06
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2075924-1
ISSN	1535-9484 ; 1535-9476
ISSN (online)	1535-9484
ISSN	1535-9476
DOI	10.1074/mcp.M113.032136
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Article ; Online: Proteomics-based strategies to identify proteins relevant to chronic lymphocytic leukemia.

Alsagaby, Suliman A / Khanna, Sanjay / Hart, Keith W / Pratt, Guy / Fegan, Christopher / Pepper, Christopher / Brewis, Ian A / Brennan, Paul

Journal of proteome research

2014 Volume 13, Issue 11, Page(s) 5051–5062

Abstract: Chronic lymphocytic leukemia (CLL), a malignant B-cell disorder, is characterized by a heterogeneous clinical course. Two-dimensional nano liquid chromatography (2D-nano-LC) coupled with matrix-assisted laser desorption/ionization time-of-flight tandem ... ...

Abstract	Chronic lymphocytic leukemia (CLL), a malignant B-cell disorder, is characterized by a heterogeneous clinical course. Two-dimensional nano liquid chromatography (2D-nano-LC) coupled with matrix-assisted laser desorption/ionization time-of-flight tandem mass spectrometry (MALDI-TOF/TOF MS) (LC-MALDI) was used to perform qualitative and quantitative analysis on cellular extracts from 12 primary CLL samples. We identified 728 proteins and quantified 655 proteins using isobaric tag-labeled extracts. Four strategies were used to identify disease-related proteins. First, we integrated our CLL proteome with published gene expression data of normal B-cells and CLL cells to highlight proteins with preferential expression in the transcriptome of CLL. Second, as CLL's outcome is heterogeneous, our quantitative proteomic data were used to indicate heterogeneously expressed proteins. Third, we used the quantitative data to identify proteins with differential abundance in poor prognosis CLL samples. Fourth, hierarchical cluster analysis was applied to identify hidden patterns of protein expression. These strategies identified 63 proteins, and 4 were investigated in a CLL cohort (39 patients). Thyroid hormone receptor-associated protein 3, T-cell leukemia/lymphoma protein 1A, and S100A8 were associated with high-risk CLL. Myosin-9 exhibited reduced expression in CLL samples from high-risk patients. This study shows the usefulness of proteomic approaches, combined with transcriptomics, to identify disease-related proteins.
MeSH term(s)	Aged ; Aged, 80 and over ; Biomarkers, Tumor/analysis ; Biomarkers, Tumor/blood ; Calgranulin A/metabolism ; Cluster Analysis ; Follow-Up Studies ; Humans ; Kaplan-Meier Estimate ; Leukemia, Lymphocytic, Chronic, B-Cell/blood ; Leukemia, Lymphocytic, Chronic, B-Cell/mortality ; Leukemia, Lymphocytic, Chronic, B-Cell/pathology ; Leukemia, Lymphocytic, Chronic, B-Cell/therapy ; Leukemia, T-Cell/metabolism ; Microarray Analysis ; Middle Aged ; Molecular Motor Proteins/metabolism ; Myosin Heavy Chains/metabolism ; Prognosis ; Proteins/analysis ; Proteins/metabolism ; Proteomics/methods ; Reproducibility of Results ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; Tandem Mass Spectrometry/methods
Chemical Substances	Biomarkers, Tumor ; Calgranulin A ; MYH9 protein, human ; Molecular Motor Proteins ; Proteins ; Myosin Heavy Chains (EC 3.6.4.1)
Language	English
Publishing date	2014-11-07
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2078618-9
ISSN	1535-3907 ; 1535-3893
ISSN (online)	1535-3907
ISSN	1535-3893
DOI	10.1021/pr5002803
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