Dynamic thresholding and tissue dissociation optimization for CITE-seq identifies differential surface protein abundance in metastatic melanoma.

Autor: Lischetti U; Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland.; Department of Biomedicine, University Hospital Basel, University of Basel, 4031, Basel, Switzerland., Tastanova A; Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland. Aizhan.Tastanova@usz.ch., Singer F; ETH Zurich, NEXUS Personalized Health Technologies, Wagistrasse 18, 8952, Schlieren, Switzerland.; SIB Swiss Institute of Bioinformatics, Zurich, Switzerland., Grob L; ETH Zurich, NEXUS Personalized Health Technologies, Wagistrasse 18, 8952, Schlieren, Switzerland.; SIB Swiss Institute of Bioinformatics, Zurich, Switzerland., Carrara M; ETH Zurich, NEXUS Personalized Health Technologies, Wagistrasse 18, 8952, Schlieren, Switzerland.; SIB Swiss Institute of Bioinformatics, Zurich, Switzerland., Cheng PF; Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland., Martínez Gómez JM; Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland., Sella F; Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland., Haunerdinger V; Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland., Beisel C; Department of Biosystems Science and Engineering, ETH Zurich, Mattenstrasse 26, 4058, Basel, Switzerland., Levesque MP; Department of Dermatology, University Hospital Zurich, University of Zurich, Zurich, Switzerland. Mitchell.Levesque@usz.ch.
Jazyk: angličtina
Zdroj: Communications biology [Commun Biol] 2023 Aug 10; Vol. 6 (1), pp. 830. Date of Electronic Publication: 2023 Aug 10.
DOI: 10.1038/s42003-023-05182-6
Abstrakt: Multi-omics profiling by CITE-seq bridges the RNA-protein gap in single-cell analysis but has been largely applied to liquid biopsies. Applying CITE-seq to clinically relevant solid biopsies to characterize healthy tissue and the tumor microenvironment is an essential next step in single-cell translational studies. In this study, gating of cell populations based on their transcriptome signatures for use in cell type-specific ridge plots allowed identification of positive antibody signals and setting of manual thresholds. Next, we compare five skin dissociation protocols by taking into account dissociation efficiency, captured cell type heterogeneity and recovered surface proteome. To assess the effect of enzymatic digestion on transcriptome and epitope expression in immune cell populations, we analyze peripheral blood mononuclear cells (PBMCs) with and without dissociation. To further assess the RNA-protein gap, RNA-protein we perform codetection and correlation analyses on thresholded protein values. Finally, in a proof-of-concept study, using protein abundance analysis on selected surface markers in a cohort of healthy skin, primary, and metastatic melanoma we identify CD56 surface marker expression on metastatic melanoma cells, which was further confirmed by multiplex immunohistochemistry. This work provides practical guidelines for processing and analysis of clinically relevant solid tissue biopsies for biomarker discovery.
(© 2023. Springer Nature Limited.)
Databáze: MEDLINE
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