Biology subjects

Kverneland, A.

Publications and source records attributed to Kverneland, A..

2 recordsLinked to original sources

bioRxiv2025

Benchmarking enrichment and depletion methods for quantitative plasma proteomics in different plasma types and the correlation to clinical routine assays.

Plasma proteomics based on mass spectrometry has great potential for biomarker discovery. Plasma is challenging for mass spectrometry due to high dynamic range in protein abundance. Several workflows have been developed to overcome this, and in this study, we compare prominent workflows using platelet-poor-(PPP), platelet-rich plasma (PRP) and serum (SER). Our results show that depletion workflows including Top14 depletion and acid precipitation allow quantification of very different proteomes than methods based on enrichments of extracellular vesicles such as bead-based enrichment or ultracentrifugation. Enrichment methods are superior in terms of proteome depth and quantitative performance but may be less robust in large cohorts. There is a very high correlation between PPP and PRP samples with all methods and less to SER samples - especially with enrichment workflows. The correlation of 10 protein measurements, performed by clinical routine processes on a Cobas system, showed heterogeneous results. Low abundant proteins with biological dynamics within a healthy cohort, including c-reactive protein and lipoprotein(a), correlated very well to proteomic workflows while others, including albumin and transferrin, correlated poorly. In conclusion, the workflow for plasma proteomics should be aligned with the aim of the analysis and the setup of the sample collection. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=85 SRC="FIGDIR/small/686186v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@10b62a7org.highwire.dtl.DTLVardef@79d4f1org.highwire.dtl.DTLVardef@8b21a3org.highwire.dtl.DTLVardef@4d85d9_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG

biochemistry↗

bioRxiv2025

Checkpoint receptors in circulating γδ T cells can discern the outcome of cancer immunotherapy

Gamma delta ({gamma}{delta}) T cells are innate-like lymphocytes that in humans can be broadly classified into two main subtypes based on their unique TCR{delta} chain, V{delta}1 and V{delta}2. Both subsets have potent anti-tumor properties and the presence of V{delta}1 cells in the tumor is often associated with positive prognosis. Herein, we investigated the molecular interplay between immune checkpoint receptors (ICRs), IC blockade (ICB) therapy and {gamma}{delta} T cells. We show that ICRs display differential expression and regulation by the JAK-STAT pathway in circulating V{delta}1 and V{delta}2 cells and identify constitutive (e.g. TIGIT, PD-1) and inducible (e.g. TIM-3, LAG-3, CTLA-4) ICRs. In melanoma, V{delta}1 cells, especially in patients who did not respond to ICB or required combination therapy, expressed high levels of ICR, TOX and inhibitory killer Ig-like receptors (KIR) transcripts, reminiscent of an exhaustion transcriptional signature. At the same time all {gamma}{delta} T cells had a prominent downregulation in AP-1 transcription factors. Patient derived cells were functionally competent, although induction of LAG-3 and CTLA-4 was impaired. In the context of anti-PD-1 monotherapy, V{delta}1 cells specifically bound high levels of therapeutic antibody but only in patients who responded to treatment, revealing a potential new prognostic marker for evaluating the efficacy of ICB therapy. Finally, expression of KIR genes in V{delta}1 cells was downregulated in response to successful ICB therapy. Collectively, our data indicate an intricate relationship between ICRs, putatively also KIRs, and {gamma}{delta} T cells and reveal novel approaches by which these cells can be harnessed in order to discern or improve cancer immunotherapy.

immunology↗