Peptideins are a newly proposed category of microproteins encoded by non-canonical open reading frames (ncORFs) in genomic regions previously considered non-coding, such as lncRNAs and 5' UTRs. They are typically shorter than 100 amino acids and were identified through large-scale proteogenomic analyses. Unlike conventional microproteins, many peptideins do not resemble known protein folds, and their functions are only beginning to be characterised.

Systematic CRISPR/Cas9 loss-of-function screens targeting non-canonical ORFs revealed that approximately 10% to 17% of translated microproteins are required for cancer cell fitness, a rate comparable to canonical protein-coding genes. In a screen of 553 small ORFs, 57 were identified as essential for cancer cell survival (PMID: 33510483).

SF3B1 and SRSF2 are splicing factors frequently mutated in cancers, particularly myeloid malignancies. Mutations in these factors can alter transcript isoform production, bypassing upstream canonical start codons that normally repress the translation of internal microprotein-encoding ORFs. This creates a splicing-dependent mechanism for selective microprotein expression in cancer cells.

The BAG6 pathway is a protein quality control system that triages and degrades non-canonical translation products bearing hydrophobic C-terminal domains. It normally prevents the accumulation of aberrant peptides. The hypothesis proposes that oncogenic recoding via alternative transcript isoforms may override this filter, allowing essential scaffolding microproteins to accumulate selectively in cancer cells.

Several candidates have been identified. GREP1, a secreted microprotein in breast cancer, is accessible to neutralizing antibodies. APPLE binds the ERK-PP1/PP2A interface, offering a target for small-molecule PPI disruptors. EMBOW occupies the WDR5 WIN-site, which is already targeted by existing inhibitors. Non-canonical ORF-derived peptides also serve as tumour-specific antigens for immunotherapy in tumours with low mutational burden (PMID: 38985879).

The standard control is a start-codon mutation (ATG to ATT or AGG) in the microprotein ORF while preserving the host transcript RNA structure. If the phenotype is lost upon abolishing translation but the RNA remains intact, the effect is protein-dependent. Rescue with a synonymous-codon-recoded microprotein cDNA provides additional confirmation.

Partially. Many peptideins lack sequence conservation beyond primates, limiting the utility of conventional mouse models for some candidates. Patient-derived xenograft (PDX) models and humanised systems offer alternatives. For conserved candidates like ASDURF, genetic mouse models remain viable.