Project description:The present study describes a novel xenograft-based biomarker discovery platform and proves its usefulness in the discovery of novel serum markers for prostate cancer (PCa). By immunizing immuno-competent mice with serum from nude mice bearing PCa xenografts, an antibody response against xenograft-derived antigens was elicited. By probing protein microarrays with serum from immunized mice, several PCa-derived antigens were identified, of which a subset was successfully retrieved in serum from mice bearing PCa xenografts and validated in human serum samples of PCa patients. In conclusion, this novel method allows for the identification of low abundant cancer-derived serum proteins, circumventing dynamic range and host-response issues in standard patient cohort proteomics comparisons.
Project description:The present study describes a novel xenograft-based biomarker discovery platform and proves its usefulness in the discovery of novel serum markers for prostate cancer (PCa). By immunizing immuno-competent mice with serum from nude mice bearing PCa xenografts, an antibody response against xenograft-derived antigens was elicited. By probing protein microarrays with serum from immunized mice, several PCa-derived antigens were identified, of which a subset was successfully retrieved in serum from mice bearing PCa xenografts and validated in human serum samples of PCa patients. In conclusion, this novel method allows for the identification of low abundant cancer-derived serum proteins, circumventing dynamic range and host-response issues in standard patient cohort proteomics comparisons. To perform a large-scale identification of antibodies generated against human PCa-derived proteins in the serum of immunized mice, sera from mice immunized with either depleted serum, full serum or both from PC346 and PC339-bearing mice as well as preimmune serum and serum from mice immunized with normal mouse serum were incubated onto ProtoArrays. These ProtoArrays contain approximately 8,000 partial and full-length human proteins, expressed as N-terminal glutathione S-transferase (GST) fusion proteins. To detect antibodies bound to spotted proteins, ProtoArrays were developed using a fluorescent labeled secondary antibody. Before being used for immunization, serum from xenografted mice was not treated (full) or depleted for most abundant proteins (depleted). Two arrays were hybridized with pre-immune serum and one array with serum from an immune competent mouse that was immunized with serum from a nude mouse. Six arrays were performed using serum from immune competent mice that were immunized with serum from xenograft-bearing nude mice.
Project description:Background and Aims: The diagnosis of Inflammatory Bowel Diseases (IBD), ulcerative colitis (UC), and Crohn's disease (CD), relies on clinical and pathologic criteria. Non-invasive precision medicine tools to diagnose IBD and discriminate between UC and CD are needed to personalize management. Serum proteomics identified protein biomarkers capable of diagnosing IBD and differentiating Crohn’s disease from ulcerative colitis subtypes. Methods: We obtained serum samples from 47 IBD and non-IBD patients seen in a tertiary care pediatric gastroenterology clinic and applied SomaScan proteomics to measure 1,305 proteins to discriminate between IBD and non-IBD and UC and CD. Four proteins were further validated by immunoassays in two cohorts of 295 and 105 individuals and multi-protein predictors were developed using Support Vector Machines (SVM). Findings: The SomaScan discovery phase identified 95 serum protein biomarkers (BH p<0.01) that differentiated IBD from non-IBD and 70 proteins (p<0.01) that distinguished UC from CD. Pathway analysis linked specific inflammatory processes and vascular functions to IBD and UC versus CD. An 8-protein classifier achieved an AUC of 0.95 for identifying IBD. Significant elevation of four key predictor proteins (MMP1, MMP3, Resistin, Haptoglobin) in IBD was validated by ELISA in the expanded cohort (N=295). The 4-protein SVM predictor achieved an AUC of 0.86 and 0.90 for IBD discrimination in two independent cohorts. A separate 4-protein SVM predictor for differentiating UC from CD achieved an AUC of 0.93 in independent validation. Interpretation: Patients with pediatric-onset IBD have a unique serum protein signature associated with pro-inflammatory and vascular pathways. Additional studies are needed to determine whether these dysregulated proteins can be used in conjunction with traditional risk factors to support non-invasive biomarkers that identify IBD and discriminate between its subtypes. The diagnosis of Inflammatory Bowel Diseases (IBD), ulcerative colitis (UC), and Crohn's disease (CD), relies on clinical and pathologic criteria. Non-invasive precision medicine tools to diagnose IBD and discriminate between UC and CD are needed to personalize management. Serum proteomics identified protein biomarkers capable of diagnosing IBD and differentiating Crohn’s disease from ulcerative colitis subtypes. Methods We obtained serum samples from 47 IBD and non-IBD patients seen in a tertiary care pediatric gastroenterology clinic and applied SomaScan proteomics to measure 1,305 proteins to discriminate between IBD and non-IBD and UC and CD. Four proteins were further validated by immunoassays in two cohorts of 295 and 105 individuals and multi-protein predictors were developed using Support Vector Machines (SVM). Findings Som The SomaScan discovery phase identified 95 serum protein biomarkers (BH p<0.01) that differentiated IBD from non-IBD and 70 proteins (p<0.01) that distinguished UC from CD. Pathway analysis linked specific inflammatory processes and vascular functions to IBD and UC versus CD. An 8-protein classifier achieved an AUC of 0.95 for identifying IBD. Significant elevation of four key predictor proteins (MMP1, MMP3, Resistin, Haptoglobin) in IBD was validated by ELISA in the expanded cohort (N=295). The 4-protein SVM predictor achieved an AUC of 0.86 and 0.90 for IBD discrimination in two independent cohorts. A separate 4-protein SVM predictor for differentiating UC from CD achieved an AUC of 0.93 in independent validation. Interpretation Patients with pediatric-onset IBD have a unique serum protein signature associated with pro-inflammatory and vascular pathways. Additional studies are needed to determine whether these dysregulated proteins can be used in conjunction with traditional risk factors to support non-invasive biomarkers that identify IBD and discriminate between its subtypes.
Project description:S100A8 and S100A9 (aliases MRP8 and MRP14) are highly expressed in neutrophils and monocytes and are classified as damage-associated molecular pattern (DAMP) molecules or alarm molecules. However, the role of S100A8/A9 in aortic dissection has not been reported. In the present study, by employing an unbiased proteomics approach and RNA sequencing analysis , we found that the protein expression of calcium binding proteins S100A8/A9 were upregulated in the aorta and serum of TAAAD patients and also in a mouse model.
Project description:Reliable non-invasive tools to diagnose at risk metabolic dysfunction-associated steatohepatitis (MASH) are urgently needed to improve management. We developed a risk stratification score incorporating proteomics-derived serum markers with clinical variables to identify high risk MASH patients (NAFLD Activity Score (NAS) >4 and fibrosis score >2). In this three-phase proteomic study of biopsy-proven metabolic dysfunction-associated steatotic fatty liver disease (MASLD), we first developed a multi-protein predictor for discriminating NAS>4 based on SOMAscan proteomics quantifying 1,305 serum proteins from 57 US patients. Four key predictor proteins were verified by ELISA in the expanded US cohort (N=168), and enhanced by adding clinical variables to create the 9-feature MASH Dx Score which predicted MASH and also high risk MASH (F2+). The MASH Dx Score was validated in two independent, external cohorts from Germany (N=139) and Brazil (N=177). The discovery phase identified a 6-protein classifier that achieved an AUC of 0.93 for identifying MASH. Significant elevation of four proteins (THBS2, GDF15, SELE, IGFBP7) was verified by ELISA in the expanded discovery and independently in the two external cohorts. MASH Dx Score incorporated these proteins with established MASH risk factors (age, BMI, ALT, diabetes, hypertension) to achieve good discrimination between MASH and MASLD without MASH (AUC:0.87- discovery; 0.83- pooled external validation cohorts), with similar performance when evaluating high risk MASH F2-4 (vs. MASH F0-1 and MASLD without MASH). The MASH Dx Score offers the first reliable non-invasive approach combining novel, biologically plausible ELISA-based fibrosis markers and clinical parameters to detect high risk MASH in patient cohorts from the US, Brasil and Europe.
Project description:To elucidate the molecular mechanism behind the anti-NAFLD effect of HDCA, we screened for potential HDCA binding proteins using biotin-labeled HDCA and HuProt human proteome microarray.