Proteomic Analysis Identifies GSN as a Noninvasive Circulating Serum Biomarker for Predicting Early Recurrence of Hepatocellular Carcinoma

High-Throughput Proteomics Reveals a Novel Small Open Reading Frame-Encoded Peptide That Promotes Hepatocellular Carcinoma Invasion and Migration

Long noncoding RNAs (lncRNAs) are closely associated with tumor development, and increasing evidence suggests that small open reading frame (smORF) within lncRNAs also have the capability to encode smORF-encoded peptides (SEPs). Here, we thoroughly uncovered the SEP expression profile of hepatocellular carcinoma (HCC) from tumor and adjacent nontumor tissues of 154 HCC patients using high-throughput mass spectrometry (MS). A total of 208 SEPs were identified, with no significant difference in abundance and stability compared with coding region proteins. Notably, the peptide encoded by LINC01007 (LINC01007-33AA) was significantly upregulated in HCC tissues (p < 0.05) and could serve as an independent risk factor affecting prognosis (HR [95% CI]: 1.31[1.01-1.7]). This endogenous peptide was further confirmed at both the mRNA and protein levels, and its overexpression significantly enhances the invasion and migration of HCC cells. These findings highlight the potential of MS-based methods to identify novel noncoding sequence encoded functional peptides associated with tumor progression.

The 2024 Report on the Human Proteome from the HUPO Human Proteome Project

The Human Proteome Project (HPP), the flagship initiative of the Human Proteome Organization (HUPO), has pursued two goals: (1) to credibly identify at least one isoform of every protein-coding gene and (2) to make proteomics an integral part of multiomics studies of human health and disease. The past year has seen major transitions for the HPP. neXtProt was retired as the official HPP knowledge base, UniProtKB became the reference proteome knowledge base, and Ensembl-GENCODE provides the reference protein target list. A function evidence FE1-5 scoring system has been developed for functional annotation of proteins, parallel to the PE1-5 UniProtKB/neXtProt scheme for evidence of protein expression. This report includes updates from neXtProt (version 2023-09) and UniProtKB release 2024_04, with protein expression detected (PE1) for 18138 of the 19411 GENCODE protein-coding genes (93%). The number of non-PE1 proteins ("missing proteins") is now 1273. The transition to GENCODE is a net reduction of 367 proteins (19,411 PE1-5 instead of 19,778 PE1-4 last year in neXtProt). We include reports from the Biology and Disease-driven HPP, the Human Protein Atlas, and the HPP Grand Challenge Project. We expect the new Functional Evidence FE1-5 scheme to energize the Grand Challenge Project for functional annotation of human proteins throughout the global proteomics community, including π-HuB in China.