Deep Visual Proteomics defines single-cell identity and heterogeneity

• Despite the availabilty of imaging-based and mass-spectrometry-based methods for spatial proteomics, a key challenge remains connecting images with single-cell-resolution protein abundance measurements. Here, we introduce Deep Visual Proteomics (DVP), which combines artificial-intelligence-driven image analysis of cellular phenotypes with automated single-cell or single-nucleus laser microdissection and ultra-high-sensitivity mass spectrometry. DVP links protein abundance to complex cellular or subcellular phenotypes while preserving spatial context. By individually excising nuclei from cell culture, we classified distinct cell states with proteomic profiles defined by known and uncharacterized proteins. In an archived primary melanoma tissue, DVP identified spatially resolved proteome changes as normal melanocytes transition to fully invasive melanoma, revealing pathways that change in a spatial manner as cancer progresses, such as mRNA splicing dysregulation in metastatic vertical growth that coincides with reduced interferon signaling and antigen presentation. The ability of DVP to retain precise spatial proteomic information in the tissue context has implications for the molecular profiling of clinical samples. 

Subject headings

MEDICIN OCH HÄLSOVETENSKAP  -- Medicinska och farmaceutiska grundvetenskaper -- Cell- och molekylärbiologi (hsv//swe)

MEDICAL AND HEALTH SCIENCES  -- Basic Medicine -- Cell and Molecular Biology (hsv//eng)

Keyword

Cell culture

Cells

Dermatology

Mass spectrometry

Molecular biology

Oncology

Tissue

Cell identity

Cellular phenotypes

Cellulars

Image-analysis

Laser microdissections

Link protein

Proteomics

Single cell resolution

Single cells

Ultra-high-sensitivity

Proteins

interferon

messenger RNA

proteome

acinar cell carcinoma

adult

antigen presentation

Article

cell heterogeneity

cell nucleus

controlled study

female

human

human cell

human tissue

interferon signaling

laser microdissection

melanocyte

melanoma

middle aged

molecular fingerprinting

phenotype

protein fingerprinting

RNA splicing

salivary gland carcinoma

single cell analysis

U2OS cell line

chemistry

genetics

laser capture microdissection

procedures

Humans

Publication and Content Type

ref (subject category)

art (subject category)