Plasma proteomics, the Human Proteome Project, and cancer-associated alternative splice variant proteins

Abstract

This article addresses three inter-related subjects: the development of the Human Plasma Proteome Peptide Atlas, the launch of the Human Proteome Project, and the emergence of alternative splice variant transcripts and proteins as important features of evolution and pathogenesis. The current Plasma Peptide Atlas provides evidence on which peptides have been detected for every protein confidently identified in plasma; there are links to their spectra and their estimated abundance, facilitating the planning of targeted proteomics for biomarker studies. The Human Proteome Project (HPP) combines a chromosome-centric C-HPP with a biology and disease-driven B/D-HPP, upon a foundation of mass spectrometry, antibody, and knowledgebase resource pillars. The HPP aims to identify the approximately 7000 "missing proteins" and to characterize all proteins and their many isoforms. Success will enable the larger research community to utilize newly-available peptides, spectra, informative MS transitions, and databases for targeted analyses of priority proteins for each organ and disease. Among the isoforms of proteins, splice variants have the special feature of greatly enlarging protein diversity without enlarging the genome; evidence is accumulating of striking differential expression of splice variants in cancers. In this era of RNA-sequencing and advanced mass spectrometry, it is no longer sufficient to speak simply of increased or decreased expression of genes or proteins without carefully examining the splice variants in the protein mixture produced from each multi-exon gene. This article is part of a Special Issue entitled: Biomarkers: A Proteomic Challenge.

Keywords: Biomarker; Human Plasma Peptide Atlas; Human Proteome Peptide Atlas; Human Proteome Project; Splice variant protein; Splice variant transcript.

Fig. 1

The scheme of Farrah et al. [8], for six levels of stringency or redundancy in generating the Human Plasma Peptide Atlas, with six shaded bars (two of which overlap). Beginning at the bottom: Exhaustive set: contains any protein sequence in the atlas' combined protein sequence database (Swiss-Prot 2010–04 + IPI v3.71 + Ensembl v57.37) that includes at least one identified peptide. Sequence-unique set: exhaustive set with exact duplicates removed. Peptide-set-unique set: a subset of the sequence-unique set within which no two protein sequences include the exact same set of identified peptides. Not subsumed set: peptide-set-unique set with subsumed protein sequences removed (those for which the identified peptides form a proper subset of the identified peptides for another protein sequence). Canonical set: a subset of the not subsumed set within which no protein sequence includes more than 80% of the peptides of any other member of the set. Protein sequences that are not subsumed, but are not canonical are called possibly distinguished, because each has a peptide set that is close, but not identical, to that of a canonical protein sequence. Covering set: a minimal set of protein sequences that can explain all of the identified peptides.

Fig. 2

Scheme for the organization of the Human Proteome Project (HPP), showing the mass spectrometry (MS), antibody-based protein capture (AB), and knowledgebase (KB) resource pillars, the chromosome-centric “adopt-a-chromosome” approach, and the complementary biology and disease-driven approach. From Legrain et al. [4] with permission.

Fig. 3

The Chromosome-centric Human Proteome Project teams by chromosome and national leadership (a) and the Biology and the Disease-driven Human Proteome Project teams (b) by organ, biofluid, biological processes, or disease. Details about all the teams can be found at www.thehpp.org, as well as www.c-hpp.org.

Fig. 4

Scheme of a multi-exon gene with pre-mRNA to be spliced to produce mRNA. [See text for details.]

Fig. 5

Variation in splice transcript expression across six ERBB2+ cell lines, two each from colon, stomach and breast (see text). (a) Septin 9 (SEPT9) transcript expression for seven different transcripts from this gene. (b) Relative abundance (in fragments per kilobase of transcript per million fragments, FPKM) of the shorter variant of ERBB2 (ENSP00000385185). (c) Relative expression levels of splice transcripts of three genes around ERBB2 on chromosome 17. (d) Relative expression levels of the shorter transcript variant of Ppp1r1b. From [34].