Frontiers in mass spectrometry-based clinical proteomics for cancer diagnosis and treatment

Abstract

Numerous omics studies, primarily genomics analyses, have been conducted to fully understand the molecular biological characteristics of cancer. In recent years, the depth of proteomic analysis, which comprehensively analyzes proteins and molecules that function directly in vivo, has increased dramatically. Proteomics using mass spectrometry (MS) is a promising technology to directly examine proteoforms, including post-translational modifications and variants originating from genomic aberrations. Recent advances in MS-based proteomics have enabled direct, in depth, and quantitative analysis of the expression levels of various cancer-related proteins, as well as their cancer-specific proteoforms, and proteins that fluctuate with cancer initiation and progression in cell lines and tissue samples. Additionally, the integration of proteomic data with genomic, epigenomic, and transcriptomic data has formed the growing field of proteogenomics, which is already yielding new biological and diagnostic knowledge. Deep proteomic profiling provides clinically useful information in various aspects, including understanding the mechanisms of cancer development and progression and discovering targets for diagnosis and drug development. Furthermore, it is expected to make a significant contribution to the promotion of personalized medicine. In this review, recent advances and impacts in MS-based clinical proteomics are highlighted with a focus on oncology.

Keywords: biomarker; cancer; glycoproteomics; mass spectrometry; proteogenomics.

FIGURE 1

Liquid chromatography tandem mass spectrometry (LC‐MS/MS) workflow for proteomics. Proteins are extracted and digested into peptides by enzymes such as trypsin. Prior to digestion, enrichment steps, such as immunoprecipitation, can be performed. Peptides are separated by LC and then introduced and detected at the mass analyzer. In the global method, a full spectrum of peptide ions is obtained, followed by fragmentation to identify the peptide sequence. In targeted proteomics, peptides with a known mass‐to‐charge ratio (m/z) are selected at the first quadrupole (Q1) and then fragmented and monitored

FIGURE 2

Prostate cancer–specific glycoforms on serum prostate‐specific antigen (PSA). Characteristic N‐glycan structures of PSA whose blood level increases with the progression of prostate cancer. Human PSA has a single N‐glycan at Asn69. Glycan nomenclature follows the Symbol Nomenclature for Glycans guidelines

FIGURE 3

Lectin histochemical staining of prostate tissue specimens and proposed model for the production of prostate cancer–specific glycoforms on prostate‐specific antigen (PSA). LacdiNAc structures are rarely expressed in normal prostate tissue, while prostate cancer cells showed a characteristic tendency to express glycoproteins containing LacdiNAc and α2,3‐sialylated structures, resulting in increased multisialylated LacdiNAc structures on PSA of prostate cancer patients. These findings were consistent with the results of glycoform analysis of PSA by mass spectrometry

FIGURE 4

Schematic workflow for immunopeptidomics by a proteogenomics approach. General sample preparation of immunopeptides (left panel) and neoantigen identification by proteogenomics approach (right panel) are shown. The central mediators of cancer immunotherapy are immunopeptides that are specifically presented only by cancer cells. The tumor‐specific immunopeptides are called neoantigens. The immunopeptide is presented extracellularly by forming a human leukocyte antigen (HLA) complex. After isolating the HLA complex by immunoprecipitation, an enriched immunopeptide sample can be obtained through the dissociation of the HLA complex and the immunopeptide purification process (left panel). In the discovery phase, the general proteomics approach, which refers to the canonical sequence of the human proteome, can only identify antigens that can be presented by both nontumor and normal cells (upper right panel). Therefore, careful verification of the cancer specificity of the antigen (e.g., whether the source protein of the antigen is highly expressed in cancer cells) is critical for practical application. The proteogenomics approach identifies neoantigens by reference to the amino acid sequence of cancer‐specific mutations constructed from genomic and transcriptomic information (lower right panel). Identification of neoantigens by mass spectrometry (MS) generally ensures natural and actual presentation and cancer specificity of the antigen of interest, contributing to more effective antigen selection

FIGURE 5

Transcending single omics to integrated multiomics. A few decades ago, genomics, transcriptomics, and proteomics were established independently as academic disciplines. Following the massive advances in deep sequencing technology, new frontiers in the proteome landscape are emerging with the development of mass spectrometry (MS). MS‐based proteomics now bridges an individual's genomic blueprint with clinically relevant physiology as proteogenomics and, beyond that, as multiomics