1. YKL-40 In a search of new bone proteins, the glycoprotein YKL-40 was identified in 1989 to be secreted in vitro in large amount by the human osteosarcoma cell line MG63. The protein was named YKL-40 based on its three N-terminal aminoacids Tyrosine (Y), Lysine (K) and Leucine (L) and its molecular mass of 40 kDa (Johansen et al. 1992). This protein was later found to be similar to a protein secreted by differentiated smooth muscle cells from swine explants of the thoracic aorta (Millis et al. 1985), to a protein isolated from the whey protein secretions of bovine mammary secretions during the nonlactating period (Rejman et al. 1988), and to a heparin binding protein secreted by human synovial cells (Nyirkos et al. 1990). In the last few years there has been a growing number of publications concerning YKL-40 and the “Story about YKL-40” has probably just started. The protein has several names: “YKL-40” (Johansen et al. 1992), “Human Cartilage glycoprotein-39 (HC gp39)” (Hakala et al. 1993), “Breast regressing protein 39 Kd (brp-39)” (Morrison et al. 1994), “38-kDa heparin-binding glycoprotein (gp38k)” (Shackelton et al. 1995), “Chitinase-3-like-1 (CHI3L1)” (Rehli et al. 1997), “Chondrex” (Harvey et al. 1998), and “40 kDa mammary gland protein (MGP-40)” (Mohanty et al. 2003). Hopefully, there will in the future be consensus of its name. In this thesis the protein is named YKL-40.

Studies on serum YKL-40 as a biomarker in diseases with inflammation, tissue remodelling, fibroses and cancer

Recent studies have demonstrated the need for complementing cellular genomic information with specific information on expressed proteins, or proteomics, since the correlation between the two is poor. Typically, proteomic information is gathered by analyzing samples on two-dimensional gels with the subsequent identification of specific proteins of interest by using trypsin digestion and mass spectrometry in a process termed peptide mass fingerprinting. These procedures have, as a rule, been labor-intensive and manual, and therefore of low throughput. The development of automated proteomic technology for processing large numbers of samples simultaneously has made the concept of profiling entire proteomes feasible at last. In this study, we report the initiation of the (eventual) complete profile of the rat mitochondrial proteome by using high-throughput automated equipment in combination with a novel fractionation technique using minispin affinity columns. Using these technologies, approximately one hundred proteins could be identified in several days. In addition, separate profiles of calcium binding proteins, glycoproteins, and hydrophobic or membrane proteins could be generated. Because mitochondrial dysfunction has been implicated in numerous diseases, such as cancer, Alzheimer's disease and diabetes, it is probable that the identification of the majority of mitochondrial proteins will be a beneficial tool for developing drug and diagnostic targets for associated diseases.

High-throughput profiling of the mitochondrial proteome using affinity fractionation and automation.

Methods for samples preparation in proteomic research

Efficient and Specific Removal of Albumin from Human Serum Samples

The use of proteomics for efficient, accurate, and complete analysis of clinical samples poses a variety of technical challenges. The presence of higher abundance proteins in the plasma, such as albumin, may mask the detection of lower abundance proteins such as the cytokines. Methods have been proposed to deplete the sample of these higher abundance proteins to facilitate detection of those with lower abundance. In this study, a commercially available albumin depletion kit was used to determine if removal of albumin would measurably reduce detection of lower abundance cytokine proteins in human plasma. The Montage Albumin Deplete Kit (Millipore) was used to deplete albumin from LPS-stimulated whole blood from 15 normal human donors. Albumin depletion was measured using the BCG reagent and SDS-PAGE, and cytokine recovery was determined by a microassay immunoassay that measures both pro- and anti-inflammatory cytokines. Average albumin depletion from the samples was 72%. However, several cytokines were also significantly reduced when the albumin was removed from the plasma. Additionally, there was a variable reduction in cytokine recovery from a known mixture of cytokines in a minimal amount of plasma that were loaded onto the columns. These data demonstrate that there may be a non-specific loss of cytokines following albumin depletion, which may confound subsequent proteomic analysis.

Albumin depletion of human plasma also removes low abundance proteins including the cytokines.

ProtoClear is a proprietary technique for clearing albumin and immunoglobulin G (IgG) from human serum samples. Albumin constitutes 57-71% of total serum protein and IgG ranges from 8-26%. Removal of these two proteins alone clears approximately 75% of the total protein present in serum and allows the detection of the remaining proteins that are present in far lower concentrations. ProtoClear effectively removed >95% of human serum albumin (HSA) and >97% of human IgG as measured by an anti-HSA competitive immunoassay and a radial immunodiffusion assay, respectively. ProtoClear was far more specific at removing albumin and IgG than Cibracon Blue Dye chromatography (Cibracon Blue), the typically utilized alternative. Comparing two-dimensional (2-D) gels of serum cleared by either Cibracon Blue or by ProtoClear, it was apparent that Cibracon Blue removed a number of proteins in addition to albumin. Following removal of albumin and IgG from serum, we found a significant improvement in the resolution of polypeptide spots detected on two-dimensional gels.

Improved two-dimensional gel electrophoresis representation of serum proteins by using ProtoClear.

YKL-40 concentrations in serum were determined by an ELISA at 3 occasions during 19 months for 57 early RA patients. The results were related to biochemical and radiographic measures at each time point. YKL-40 correlated significantly to ESR and CRP throughout the study. Correlations between YKL-40 and radiographic findings scored by the Larsen method were fairly weak both for absolute values at each time point (Rs 0.212-0.319) and for progression over time (Rs 0.152-0.301). Baseline YKL-40 could predict radiographic progression with a specificity and sensitivity of only slightly over 50%. ESR and CRP correlated stronger than YKL-40 to joint damage progression and in a multiple regression model ESR was the only significant variable explaining the variance of this radiographic measure. We conclude that serial measurements of serum YKL-40 did not provide information that could not be obtained by conventional biochemical measures of disease activity.

Justine Whaley

Papers

Improved two-dimensional gel electrophoresis representation of serum proteins by using ProtoClear.

The relationship between serum levels of YKL-40 and disease progression in patients with early rheumatoid arthritis