Table 1. List of selected proteins differentially expressed between healthy donors and CLL patients identified by LC-HR-MS/MS.
| Protein (UniProt accession) | Fold change/P value | Proposed function (cell localization) | Relation to cancer | |
|---|---|---|---|---|
| LC-HR-MS/MS analysis: | 1st | 2nd | Group A—CLL associated proteins | |
| BCL-2- B-cell lymphoma 2 (P10415) | 24.5 1.1x10-7 | 6.4 3.4x10-3 | Suppresses apoptosis (mitochondria) | Over-expressed in CLL [41] |
| IGHD- immunoglobulin heavy constant delta (P01880) | 44.2 2.3x10-6 | >1000 2.1x10-13 | Major antigen receptor on the surface of B-cells (secreted, plasma membrane) | Mutation in IGHD used in prognosis of CLL [42] |
| KSYK- spleen tyrosine kinase (P43405) | 6.8 7.5x10-6 | 4.0 2.4x10-4 | Mediates signal transduction (plasma membrane, cytoplasm) | Enhanced expression in CLL [43] |
| NFKB2- NF-kappa-B p100 (Q00653) | 21.6 3.1x10-6 | 93.3 9.9x10-3 | Transcription factor, involves in inflammation, immunity, differentiation, tumorigenesis and apoptosis (nucleus, cytoplasm) | NF-kappa B2/p100 induces Bcl-2 expression in CLL [44] |
| CD74- HLA class II histocompatibility antigen gamma chain (P04233) | 5.1 1.7x10-4 | 5.1 4.5x10-5 | MHC class II antigen processing (plasma membrane) | CD74 expression correlates with ZAP70 in CLL [45] |
| LC-HR-MS/MS analysis: | 1st | 2nd | Group B–Cancer associated proteins | |
| VDAC1- voltage dependent anion channel 1 (P21796) | 5.3 2.8x10-5 | 4.8 4.8x10-4 | Ions and metabolites transport. Involves in apoptosis (OMM, plasma membrane) | Over expressed in different tumor tissues [46] |
| VDAC2- voltage dependent anion channel 2 (P45880) | 3.1 1.4x10-3 | 4.5 7.4x10-4 | Transport of ions and metabolites (OMM) | High levels in liver cancer [47] |
| AIF- apoptosis inducing factor | 10.6 3.6x10-9 | ___ | Initiator of apoptosis (mitochondria, in apoptosis translocates to nucleus) | Overexpressed in cancer [48,49,50] |
| IDH3A- isocitrate dehydrogenase 3 (P50213) | 2.6 7.1x10-3 | 6.8 9.6x10-5 | TCA cycle (mitochondria) | IDH1, IDH2 mutated in leukemia and brain tumors [51,52] |
| BRI3B- BRI3-binding protein (HCCRBP-1) (Q8WY22) | 5.8 2.9x10-5 | 389.4 2.7x10-3 | Outer mitochondrial membrane | Induce tumorigenesis through p53 stabilization [53] |
| PPWD1- peptidylprolyl isomerase domain and WD repeat containing 1 (Q96BP3) | 35.7 9.7x10-5 | 105.4 7.7x10-3 | Accelerates the folding of proteins, possibly involved in pre-mRNA splicing (nucleus) | Marker for pancreatic cancer [54] |
| GELS- gelsolin (P06396) | -3.3 4.3x10-3 | -5.0 4.0x10-3 | Actin modulating protein (secreted, cytoplasm) | Down regulated in leukemia, cervical and breast cancer [55,56] |
| LTBP1-latent TGFβ binding protein 1 (Q14766) | -4.7 1.6x10-5 | -6.2 7.9x10-3 | Associates with pro-TGFβ complex. Modulates TGFβ activity (secreted) | Increased expression in human glioma cells [57] |
| LC-HR-MS/MS analysis: | 1st | 2nd | Group C—Newly identified CLL associated proteins | |
| ADH5- alcohol dehydrogenase 5 (P11766) | 2.8 8.1x10-4 | 3.5 7.8x10-4 | Metabolism of alcohols and aldehydes (cytoplasm) | No direct association reported |
| AK3- adenylate kinase 3 (Q9UIJ7) | 29.9 3.0x10-5 | 4.1 1.9x10-3 | Maintaining the homeostasis of cellular nucleotides (mitochondria) | No direct association reported |
| DDX46- DEAD box protein 46 (Q7L014) | 9.1 1.9x10-5 | 201.4 1.2x10-3 | Pre-mRNA processing (nucleus) | No direct association reported |
| AP3B1- AP-3 complex subunit beta-1 (O00203) | 9.6 1.7x10-4 | 698.8 8.5x10-5 | Biogenesis of late endosomal/ lysosomal structures (Golgi membrane) | No direct association reported |
Two independent LC-HR-MS/MS experiments were performed as described in the Materials and Methods section. From each experiment, differentially expressed proteins (p-value <0.01, FC ≥|2|) were filtered and proteins differentially expressed in both experiments were selected. Proteins of relevance to CLL or with potential as biomarkers are listed. For each protein, the name, fold change and p-value in each experiment, as well as its function, subcellular localization and relevance to cancer are indicated. Proteins were divided into three groups based on their known association to CLL, relation to metabolism or potential as metabolism-unrelated biomarkers for CLL.