Affinity proteomics discovers decreased levels of AMFR in plasma from Osteoporosis patients

Abstract

PurposeAffinity proteomic approaches by antibody bead arrays enable multiplexed analysis of proteins in body fluids. In the presented study, we investigated blood plasma within osteoporosis to discovery differential protein profiles and to propose novel biomarkers candidates for subsequent studies.Experimental designStarting with 4608 antibodies and plasma samples from 22 women for an untargeted screening, a set of 72 proteins were suggested for further analysis. Complementing these with targets from literature and other studies, a targeted bead array of 180 antibodies was built to profile for 92 proteins in plasma samples of 180 women from two independent population‐based studies.ResultsDifferential profiles between osteoporosis patients and matched controls were discovered for 12 proteins in at least one of the two study sets. Among these targets, the levels of autocrine motility factor receptor (AMFR) were concordantly lower in plasma of female osteoporosis patients. Subsequently, verification of anti‐AMFR antibody selectivity was conducted using high‐density peptide and protein arrays, and Western blotting.Conclusions and clinical relevanceFurther validation in additional study sets will be needed to determine the clinical value of the observed decrease in AMFR plasma levels in osteoporosis patients, but AMFR may aid our understanding of disease mechanisms and could support existing tools for diagnosis and monitoring of patient mobility within osteoporosis.

Immunocapture strategies in translational proteomics

“…[ 71 ] This approach, which is the most common in epidemiological studies of proteomics compares protein levels between multiple groups divided by disease status and aims to discover proteins with differential “expression”. At the stage of sample recruitment, there are several important considerations to make: to establish a large enough sample size to achieve a sufficient statistical power that allows us to detect small difference between groups,[ 72 ] to minimize preanalytical variables (e.g., differential handling of the samples) [ 73 ] in order to enable conclusive interpretations related to the phenotype rather than the sample type and sample handling [ 73 , 74 ] and to properly match samples in order to measure disease-related difference rather than individual heterogeneity. [ 72 ] For the recruited samples, analysis should be performed after randomization, preventing possible association of experimental factors (e.g., sample collection order, reading order) with protein profiles [ 72 ] and should be accomplished during sample collection to avoid confounding by admission order.…”

Affinity Proteomics Exploration of Melanoma Identifies Proteins in Serum with Associations to T-Stage and Recurrence

“…At the time of study, 4595 antibodies were available and included due to a concentration suitable for immobilization onto beads (>0.05 mg/ml). This study was performed in parallel to previously presented investigations for multiple sclerosis [21] and osteoporosis [26] , [27] . The melanoma-associated profiles have not been highlighted as main candidates in any of the other studies.…”

Epitopes of anti-RIFIN antibodies and characterization of rif-expressing Plasmodium falciparum parasites by RNA sequencing

“…Custom ultra-dense peptide microarrays obtained in collaboration with Roche-Nimblegen were applied for epitope region mapping as described before 41 42 . An array containing 175,000 peptides of 12 amino acids in length and with an 11-residue overlap was designed to cover the PfMC2TM family (3D7 and IT background), PHISTs (3D7), RIFINs (3D7 and IT, without pseudogenes), STEVORs (3D7 and IT, without pseudogenes or STEVOR-like proteins), SURFINs (3D7 and IT) and several PfEMP1s (3D7var2csa, ITvar60, ITvar09, PAvar0, TM284var1, HB3var6, 3D7var4, FCR3S1.6) ( Supplementary Data S3 ).…”