Project description:In search for peptides with higher or special binding affinity and for further understanding of the mode of action, a full substitutional analysis of peptide PeB using microarrays was performed. Thus, 152 PeB mutant variants were generated. In each of them, the full-length sequence was preserved except for only one amino acid from the eight loop-forming amino acids of the original PeB peptide (ARDFYDYDVFYYAMD) which was substituted with the 19 remaining natural amino acids. To assess binding, influenza material was labeled with a protein reacting fluorophore.
Project description:This dataset contains peptide array information from 1516 patients from 12 different cancer types, 2 infectious diseases, and healthy controls using leave one out cross validation. This array is library 2 (GPL14921).
Project description:This dataset contains peptide array information from 120 patients from 5 different cancer types using classic blinded test/train method. This array is library 1 (GPL17600).
Project description:Lyme borreliosis (LB) is a common infection of domestic dogs in areas where there is enzootic transmission of the agent Borrelia burgdorferi. Immunodiagnostic assays for canine antibodies to B. burgdorferi are usually based on whole-cell preparations as substrate and, consequently, interpretation of results is confounded by antibody cross-reactivity between borrelial antigens and those of other bacterial species. To more broadly characterize the antibody responses to B. burgdorferi infection and to assess the diversity in those responses between individual dogs, we examined sera from 32 adult, colony-bred beagle dogs that were experimentally infected with B. burgdorferi through tick bites and compared those on a protein microarray with sera from uninfected dogs in their antibody reactivities to various recombinant chromosome- and plasmid-encoded B. burgdorferi proteins, including 24 of the serotype-defining OspC proteins of North America. The profiles of immunogenic proteins for the dogs were largely similar to those for humans and natural reservoir rodents. These included the decorin-binding protein DbpB, BBA36, BBA57, BBA64, fibronectin-binding protein BBK32, VlsE, FlaB and other flagellar structural proteins, Erp proteins, Bdr proteins, and all of the OspC proteins. In addition, the canine sera bound to the presumptive lipoproteins BBB14 and BB0844, which infrequently elicited antibodies in humans or rodents. Although the beagle, like most other domestic dog breeds, has a small effective population size and features extensive linkage disequilibrium, the group of animals here demonstrated diversity in antibody responses by measures of antibody levels and specificities for conserved proteins, like DbpB, and polymorphic ones, like OspC.
Project description:12 wild-type C57BL/6 (B6) mice were divided into 4 groups: control group, IFN-α group, LPS group, and IFN-α+ LPS group, every group contained 3 mice (n=3). IFN-α was administrated i.p. to IFN-α group and IFN-α+ LPS group once daily (QD) for 7 days at a medium dose of 105units/kg weight, PBS was administrated i.p. to control group and LPS group QD for 7 days at the same volume. LPS group and IFN-α+ LPS group were injected i.v. with 10 μg LPS for one mouse on the 8th day. Control group and IFN-α group were injected i.v. with PBS at the same volume. 6 h later, mice were sacrificed to harvest spleens for protein microarray experiment. Mouse Cytokine Antibody Array 3(62) was purchased from Ray Biotech, Norcross GA, US.
Project description:Rheumatoid arthritis is a prototypical autoimmune arthritis affecting nearly 1% of the world population and is a significant cause of worldwide disability. Though prior studies have demonstrated the appearance of RA-related autoantibodies years before the onset of clinical RA, the pattern of immunologic events preceding the development of RA remains unclear. To characterize the evolution of the autoantibody response in the preclinical phase of RA, we used a novel multiplex autoantigen array to evaluate development of the anti-citrullinated protein antibodies (ACPA) and to determine if epitope spread correlates with rise in serum cytokines and imminent onset of clinical RA. To do so, we utilized a cohort of 81 patients with clinical RA for whom stored serum was available from 1-12 years prior to disease onset. We evaluated the accumulation of ACPA subtypes over time and correlated this accumulation with elevations in serum cytokines. We then used logistic regression to identify a profile of biomarkers which predicts the imminent onset of clinical RA (defined as within 2 years of testing). We observed a time-dependent expansion of ACPA specificity with the number of ACPA subtypes. At the earliest timepoints, we found autoantibodies targeting several innate immune ligands including citrullinated histones, fibrinogen, and biglycan, thus providing insights into the earliest autoantigen targets and potential mechanisms underlying the onset and development of autoimmunity in RA. Additionally, expansion of the ACPA response strongly predicted elevations in many inflammatory cytokines including TNF-α, IL-6, IL-12p70, and IFN-γ. Thus, we observe that the preclinical phase of RA is characterized by an accumulation of multiple autoantibody specificities reflecting the process of epitope spread. Epitope expansion is closely correlated with the appearance of preclinical inflammation, and we identify a biomarker profile including autoantibodies and cytokines which predicts the imminent onset of clinical arthritis.
Project description:Triple-negative breast cancer (TNBC) is a heterogeneous and aggressive disease where limited therapeutic options are available. A significant correlation exists between presence of intratumoral macrophages, tumor progression, and poor outcomes in TNBC. Preclinical in vivo studies revealed that inhibition of myelomonocytic colony stimulating factor 1 (CSF1) or its receptor (CSF1R), plus cytotoxic therapy decreases primary tumor growth kinetics and pulmonary metastases by CD8+ T cell-dependent mechanisms. To evaluate safety and tolerability of this immune-based therapeutic strategy, we conducted a phase Ib/II clinical trial evaluating Pexidartinib (PLX3397), a small molecule CSF1R inhibitor plus Eribulin chemotherapy in patients with heavily pretreated metastatic TNBC. Correlate analyses from baseline revealed increased leukocyte activation biomarkers, increased presence of CD8+ and CD4+ T central memory cells, and increased PD-1 expression on CD4+ T cells in patients experiencing a partial response or stable disease, together providing evidence of enhanced anti-tumor immunity. We hypothesized that addition of either PD-1 and PD-L1-blockade following CSF1R inhibition and chemotherapy would lead to a further enhanced anti-tumor T cell response. To test this, we evaluated tumor-bearing MMTV-PyMT transgenic mice comparing addition of PD-1- or PD-L1-blockade to Pexidartinib/Paclitaxel therapy. This revealed tumor regression in ~60% of transgenic mice with combined PD-1, but not PD-L1-blockade. Analysis of mammary tumors from mice treated with the PD-1 combination revealed activation and expansion of short-lived effector and memory T cells, and unique clonally-expanded T cells not observed with the PD-L1-blockade combination. These clinical and preclinical findings together provide rationale for addition of CSF1/CSF1R inhibitors to chemotherapy and PD-1-blocakde to further improve outcomes for patients with BC.
Project description:To comprehensively analyze the effects of mTORC1 inhibition on GSK3, we employed the use of a PI3K/mTOR-specific phospho-antibody microarray that analyzed the site-specific phosphorylation of over 130 kinases within the PI3K/mTOR pathway. The phosphorylation levels of different kinases in monocytes were measured when stimulated with LPS in the presence or absence of a kind of mTORC1 inhibitor, rapamycin