ArticleCommunications biology2023
Dynamic thresholding and tissue dissociation optimization for CITE-seq identifies differential surface protein abundance in metastatic melanoma.
Article in Communications biology, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed, 14 citations in OpenAlex.
- CAPTAIN: a multimodal foundation model pretrained on co-assayed single-cell RNA and protein.Nature communications · 2026Article
- Molecular characterization of directly reprogrammed neurons from human fibroblasts using single cell RNA sequencing.Scientific reports · 2026Article
- Key Considerations on CITE-Seq for Single-Cell Multiomics.Proteomics · 2025Review
- Uncovering the regulatory landscape of early human B cell lymphopoiesis and its implications in the pathogenesis of B-ALL.Science advances · 2025Article
- Role of intratumoral heterogeneity in metastatic progression and drug resistance.Discover oncology · 2025Review
- Spatially resolved subcellular protein-protein interactomics in drug-perturbed lung-cancer cultures and tissues.Nature biomedical engineering · 2025Article
- Single-Cell Multi-Omics: Insights into Therapeutic Innovations to Advance Treatment in Cancer.International journal of molecular sciences · 2025Review
- Individualization of Testicular Cells for Single-Cell Subcellular Immunocytochemistry and Cell Culture Applications.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Stromal Cell Isolation from Hematopoietic Organs.Journal of visualized experiments : JoVE · 2024Article
- Advancing immunotherapy for melanoma: the critical role of single-cell analysis in identifying predictive biomarkers.Frontiers in immunology · 2024Review
- Detection of isoforms and genomic alterations by high-throughput full-length single-cell RNA sequencing in ovarian cancer.Nature communications · 2023Article
- Dynamic thresholding and tissue dissociation optimization for CITE-seq identifies differential surface protein abundance in metastatic melanoma.Communications biology · 2023Article
Corrections and comments
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Authors and funding
11 authors at 4 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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.
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