Biology subjects

Bendes, A.

Publications and source records attributed to Bendes, A..

5 recordsLinked to original sources

bioRxiv2024

Longitudinal blood microsampling and proteome monitoring facilitate timely intervention in experimental type 1 diabetes

Symptoms of immune-mediated diseases (IMIDs) typically appear after irreversible tissue damage, making early interventions based on pre-symptomatic indicators crucial. Current efforts to identify molecular markers of early disease lack the resolution, convenience and cost efficiency required to prevent irreversible tissue damage. Analyzing frequently self-collected samples, such as dried blood spots (DBS), could enable the earlier detection of diseases, identify disease-predictive markers and facilitate tailored interventions. To test this, we regularly microsampled a mouse model infected with a type 1-diabetes (T1D)-associated virus. This longitudinal DBS sample collection was analyzed for 92 circulating proteins, revealing transient molecular changes in virus-infected animals that would have been missed with less frequent sampling. Machine learning predicted infection status after day 2 post-infection with >90% accuracy, enabling well-timed treatment of virus-infected animals and diabetes prevention. Our study demonstrates the utility of frequent blood microsampling to monitor disease during the pre-symptomatic phase, allowing for timely interventions. TeaserFrequent blood microsampling detects early biomarkers, enabling timely intervention in immune-mediated diseases

systems biology↗

bioRxiv2023

Expanding the GPCR-RAMP interactome

Receptor activity-modifying proteins (RAMPs) can form complexes with G protein-coupled receptors (GPCRs) and regulate their cellular trafficking and pharmacology. RAMP interactions have been identified for about 50 GPCRs, but only a few GPCR-RAMP complexes have been studied in detail. To elucidate a complete interactome between GPCRs and the three RAMPs, we developed a customized library of 215 Dual Epitope-Tagged (DuET) GPCRs representing all GPCR subfamilies. Using a multiplexed suspension bead array (SBA) assay, we identified 122 GPCRs that showed strong evidence for interaction with at least one RAMP. We screened for native interactions in three cell lines and found 23 GPCRs that formed complexes with RAMPs. Mapping the GPCR-RAMP interactome expands the current system-wide functional characterization of RAMP-interacting GPCRs to inform the design of selective GPCR-targeted therapeutics. One-Sentence SummaryNovel complexes between G protein-coupled receptors and interacting proteins point to a system-wide regulation of GPCR function.

biochemistry↗

bioRxiv2022

Multiplexed selectivity screening of anti-GPCR antibodies

G protein-coupled receptors (GPCRs) control critical cellular signaling pathways. Therapeutic agents, such as antibodies (Abs), are being developed to modulate GPCR signaling pathways. However, validating the selectivity of anti-GPCR Abs is challenging due to sequence similarities of individual receptors within GPCR subfamilies. To address this, we developed a multiplexed immunoassay to test >400 anti-GPCR Abs from the Human Protein Atlas targeting a customized library of 215 expressed and solubilized GPCRs representing all GPCR subfamilies. We found that ~61% of Abs were selective for their intended target, ~11% to bind off-target, and ~28% not to bind any GPCR. Antigens of on-target Abs were, on average, significantly longer, more disordered, and less likely to be buried in the interior of the GPCR protein than the other Abs. These results provide important insights into the immunogenicity of GPCR epitopes and form a basis for the design of therapeutic Abs and the detection of pathological auto-antibodies. TEASERA multiplexed library-to-library selectivity analysis of 400 anti-GPCR antibodies within subfamilies of 200 solubilized receptors.

biochemistry↗

bioRxiv2020

Facets of individual-specific health signatures determined from longitudinal plasma proteome profiling

BackgroundPrecision medicine approaches aim to tackle diseases on an individual level through molecular profiling. Despite the growing knowledge about diseases and the reported diversity of molecular phenotypes, the descriptions of human health on an individual level have been far less elaborate. MethodsTo provide insights into the longitudinal protein signatures of well-being, we profiled blood plasma collected over one year from 101 clinically healthy individuals using multiplexed antibody assays. After applying an antibody validation scheme, we utilized > 700 protein profiles for in-depth analyses of the individuals short-term health trajectories. FindingsWe found signatures of circulating proteomes to be highly individual-specific. Considering technical and longitudinal variability, we observed both stable and fluctuating proteins in the circulation, as well as networks of proteins that covaried over time. For each participant, there were unique protein profiles and some of these could be explained by associations to genetic variants. InterpretationThis study demonstrates that there was noticeable diversity among clinically healthy subjects, and facets of individual-specific signatures emerged by monitoring the variability of the circulating proteomes over time. Longitudinal profiling of circulating proteomes has the potential to enable a more personal hence precise assessment of health states, and thereby provide a valuable component of precision medicine approaches. FundingThis work was supported by the Erling Persson Foundation for the KTH Centre for Precision Medicine and the Swedish Heart and Lung Foundation for the SCAPIS project. We also acknowledge the Knut and Alice Wallenberg Foundation for funding the Human Protein Atlas project, Science for Life Laboratory for Plasma Profiling Facility, and the Swedish Research Council (Grant no 2017-00641).

biochemistry↗

bioRxiv2019

Systematic Development Of Sandwich Immunoassays For The Plasma Secretome

The plasma proteome offers a clinically useful window into human health and disease. With recent progress made on the development of highly multiplexed immunoassays with high sample throughput, a remaining need is to establish a pipeline for validating the individual proteins that build such bio-signatures by using targeted assays. In order to streamline such efforts, we developed a workflow to build dual binder sandwich immunoassays (SIA) and chose to evaluate this on proteins predicted to be secreted form cells and tissues. Utilizing the multiplexing capacities of the bead array technology, we first screened ~ 1,800 unique antibody pairs against 209 protein targets and collected data from dilution series of recombinant proteins as well as EDTA plasma. Employing 624 unique antibodies from the Human Protein Atlas, we obtained dilution-dependent curves in plasma and concentration-dependent curves of full-length proteins for 102 (49%) of the targets. For 22 protein assays, the longitudinal, inter-individual and technical performance was determined in a set of plasma samples collected from 18 healthy subjects every third month over one year. Lastly, we compared 14 of these assays with SIAs composed of other binders, proximity extension assays and affinity-free targeted mass spectrometry. Our workflow provides a multiplexed approach to screen for SIA pairs that suggests using at least three antibodies per target. This design is applicable for a wider range of targets of the plasma proteome, while the assays can be applied for discovery but also to validate emerging candidates derived from other platforms.

biochemistry↗