Project description:To identify the dynamic changes of cytokines in the ApoE-/- mice atherosclerotic plaque, heart, and serum upon β-adrenergic stimulation (isoproterenol, 5 mg/kg body weight) at 0.5hrs, 1hrs, 3hrs and 24hrs using mouse cytokine antibody arrays.
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:β-cell specific Mettl14 knock-out mice display reduced N6-methyladenosine (m6A) levels and recapitulate human Type II diabetes (T2D) islet phenotype with early diabetes onset and mortality secondary to decreased β-cell proliferation and insulin degranulation. To gain insights into the role of m6A in regulating the IGF1/insulin -> AKT - > PDX1 pathway and to dissect the signaling networks modulating AKT phosphorylation, we subjected freshly isolated islets from control and Mettl14 knock-out mice to phospho-antibody microarrays.
Project description:Protein and phosphorylation (Phospho Explorer Antibody Array, FullMoonBioscience, #PEX100) profiling of peritoneal monocytes (pooled lavages from 3-4 mice / condition) was carried out according to the manufacturer’s instructions.
Project description:The aim of the study was to determine the epitope targeted by four different HumAbs and the cross-reactivity to linear peptide epitopes of 10 different Neisserial Heparin Binding Antigen (NHBA) variants. the HumAbs were diluted at 1:60 and incubated on a custom PepStar Peptide Microarray platform printed with 561 different peptides.
Project description:The aim of the study was to determine the epitope targeted by four different HumAbs and the cross-reactivity to linear peptide epitopes of 5 different Neisserial adesin A (NadA) variants. the HumAbs were diluted at 1:200 and incubated on a custom PepStar Peptide Microarray platform printed with 348 different peptides.
Project description:The aim of the study was to determine the epitope targeted by 5 different HumAbs and the cross-reactivity to linear peptide epitopes of 12 different factor H binding protein (fHbp) variants. The HumAbs were diluted at 1:200 and incubated on a custom PepStar Peptide Microarray platform printed with 363 different peptides.
Project description:Introduction: Serous ovarian cancer is the leading cause of gynecological cancers, with a 5-year survival rate below 45% due in part to the nonspecific symptoms and lack of accurate screening for early detection. In comparison, patients diagnosed at an early stage have a five-year survival rate of 92%, demonstrating the urgent need for biomarkers for the early detection of disease. Serum from patients with serous ovarian cancer contain antibodies to tumor antigens that are potential biomarkers for early detection. The purpose of this study is to identify a panel of novel serum autoantibody (AAb) biomarkers for the early diagnosis of serous ovarian cancer. Methods: To detect AAb we probed high-density programmable protein microarrays (NAPPA) containing 10,247 antigens with sera from patients with serous ovarian cancer (n = 30 cases/ 30 healthy controls) and measured bound IgG. We identified 735 promising tumor antigens using cutoff values of 10% sensitivity at 95% specificity and K-value>0.8, as well as visual analysis and evaluated these with an independent set of serous ovarian cancer sera (n = 30 cases/ 30 benign disease controls/ 30 heathy controls). Thirty-nine potential tumor autoantigens were identified with sensitivities ranging from 3 to 39.7% sensitivity at 95% specificity and were retested using an orthogonal programmable ELISA assay. A total of 13 potential tumor antigens were identified for further validation using an independent ovarian cancer sera set (n = 44 cases/ 34 healthy controls). Sensitivities at 95% specificity were calculated and a serous ovarian cancer classifier was constructed. In addition, we evaluated a longitudinal study using blinded serous pre-diagnostic ovarian cancer sera (n = 9 cases/ 90 controls) to examine the value of three (CTAG1, CTAG2, and p53) of these AAb in comparison to CA 125. Results: We identified 11-AAbs (ICAM3, CTAG2, p53, STYXL1, PVR, POMC, NUDT11, TRIM39, UHMK1, KSR1, and NXF3) that distinguished serous ovarian cancer cases from healthy controls with a combined 45% sensitivity at 100% specificity. In our longitudinal analysis, p53- and CTAG-AAb were detected up to 9 months prior to ovarian cancer diagnosis and increased with CA 125 levels. Conclusion: These are potential circulating biomarkers for the early detection of serous ovarian cancer, and warrant confirmation in larger clinical cohorts. In addition, p53- and CTAG1/2-AAb are detected in a subset of women with ovarian cancer up to 9 months prior to clinical diagnosis. Their utility as a biomarker for early detection, beyond CA 125, warrant further investigation.
Project description:Our objective was to identify the potential autoantibody markers in meningiomas using high-density human proteome arrays (~17,000 full-length recombinant human proteins). This study revealed the dysregulation of 489 and 104 proteins in grades I and II of meningioma, respectively, along with the enrichment of signalling pathways which play a major role in the manifestation of the disease. This study revealed the dysregulation of 489 and 104 proteins in grades I and II of meningioma, respectively, along with the enrichment of signalling pathways which play a major role in the manifestation of the disease. Autoantibody targets like IGHG4, CRYM, EFCAB2, STAT6, HDAC7A and CCNB1 were dysregulated across both grades.
Project description:The study objective was to find new biomarkers of treatment response and adverse events in patients receiving neoadjuvant therapy for locally advanced rectal cancer. Patients received neoadjuvant chemotherapy (NACT) followed by chemoradiotherapy (CRT) and underwent treatment evaluation four weeks after CRT completion. Radical pelvic surgery was planned 2-4 weeks later. Patients were scored for treatment adverse events, according to Common Terminology Criteria for Adverse Events (CTCAE) version 3.0, throughout the neoadjuvant treatment course, including at NACT and CRT completion. Treatment response was assessed by histologic ypTN staging and tumor regression grade (TRG) scoring, as well as progression-free survival (time from Inclusion date to Date of local relapse or Date of metastatic disease, whichever came first) recorded for five years after surgery.