Scratching the Surface with Cell Surface Proteomics

Proteomics, or the comprehensive evaluation of the set of proteins present in a specific biological context, is a critical field that has become increasingly central to biological and pharmaceutical research, especially as technological advances enable these large-scale studies to be performed with increasing ease. One area of particular interest is cell surface proteomics or “surfaceomics,” which seeks to characterize and evaluate the suite of proteins present on the surfaces of various cell types under given conditions. Cell surface proteins carry out a range of critical cellular functions and include transporters that regulate passage across the plasma membrane, receptors that receive and transmit key biochemical signals, antigens critical to immune system function, and factors involved in cell adhesion and migration. Their vital cellular functions, as well as their relative accessibility, make cell surface proteins attractive as both pharmaceutical targets and clinical biomarkers. In fact, 60-70% of FDA-approved drugs target surface proteins, highlighting their relevance in the treatment of human disease.

However, the study of surface proteins can be challenging for several reasons. Surface proteins are typically characterized by limited solubility, making extraction difficult. They are often poorly digestible due to limited cleavage sites, and their aggregability can restrict protease access. Despite accounting for as much as one-third of all proteins, cell surface proteins make up only 2% of the proteome by abundance, posing further analytical difficulties. The post-translational modifications (PTMs) of cell surface proteins are also distinctive, dominated by glycosylation rather than the myriad of reversible PTMs characteristic of cytosolic proteins. To address these and other challenges, a range of specialized techniques have been developed to support the identification, evaluation, and analysis of proteins on the cell surface. As a result of these advances, cell surface proteins can be effectively targeted for drug discovery and development, supporting the creation of novel therapeutics.

Cell surface proteins are particularly appealing as pharmaceutical targets thanks to their biological functions. Cell surface proteins play crucial roles in a wide range of cellular processes, especially in the context of signaling networks. By disrupting a signaling pathway at the membrane receptor, scientists can ablate downstream intracellular signaling to effectively modulate gene expression and cellular activity. This logic has led to the therapeutic targeting of several families of cell surface proteins, perhaps most notably G protein coupled receptors (GPCRs). While large-scale screening of compounds against membrane protein targets poses particular challenges, GPCR ligands have been effectively identified in high throughput using affinity selection mass spectrometry (ASMS), a powerful biophysical assay that enables label-free screening of a wide range of protein and oligo targets. ASMS has been successfully used to identify compounds that bind the chemokine receptor CXCR4, the muscarinic acetylcholine receptor M2, and the A2A adenosine receptor.  By coupling this approach with technologies designed to effectively solubilize membrane-bound proteins (such as Cube Biotech’s NativeMP™ platform), scientists can screen for small-molecule binders more readily than ever before.

Beyond their potential as therapeutic targets, cell surface proteins offer significant value as biomarkers. In addition to providing relevant information about a cell’s identity or disease state, cell surface proteins are readily accessible to imaging agents and other tool compounds, facilitating analysis by flow cytometry and similar techniques. Cell surface profiling has been used to define signatures associated with cellular subtypes, such as for the discrimination of classical, intermediate, and non-classical monocytes, as well as to identify and isolate relevant cellular subpopulations from heterogeneous samples. Cell surface biomarkers have been particularly well studied in cancer, and researchers have developed comprehensive surfaceome profiles for dozens of cancer types. This knowledge supports the ongoing development of diagnostic techniques for early cancer detection, probes for the sensitive and selective imaging of tumor cells, and personalized therapeutics tailored to individual patients. By characterizing the surfaceome compositions of cells affected by cancer and other diseases – as well as understanding how those surfaceomes change in response to cellular perturbations – scientists can effectively develop novel pharmaceuticals against a broad spectrum of disease-relevant targets.

Whether directly targeted by small-molecule drugs, probed to determine cell type or diagnose disease, or interrogated to better understand fundamental molecular processes, cell surface proteins offer promise to a broad range of biological endeavors. While their effective study has been historically hindered by associated technical barriers, the development of processing methods and analysis techniques optimized for cell surface proteins has made their analysis increasingly tractable. By partnering with experienced service providers to overcome these challenges, researchers can improve their chances of efficiently identifying, characterizing, and targeting relevant cell surface proteins, ultimately leading to the discovery and development of novel compounds for the diagnosis and treatment of human disease.

Our scientists have significant expertise in the high-throughput screening of cell surface proteins, as well as in leveraging proteomic and chemoproteomic assays towards the analysis of cell surface targets. To learn more about how our capabilities could accelerate your drug discovery and development research, send us a message.

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