The cancer-associated microprotein CASIMO1 controls cell proliferation and interacts with squalene epoxidase modulating lipid droplet formation

Abstract

Breast cancer is a leading cause of cancer-related death in women. Small open reading frame (sORF)-encoded proteins or microproteins constitute a new class of molecules often transcribed from presumed long non-coding RNA transcripts (lncRNAs). The translation of some of these sORFs has been confirmed, but their cellular function and importance remains largely unknown. Here, we report the identification and characterization of a novel microprotein of 10 kDa, which we named Cancer-Associated Small Integral Membrane Open reading frame 1 (CASIMO1). CASIMO1 RNA is overexpressed predominantly in hormone receptor-positive breast tumors. Its knockdown leads to decreased proliferation in multiple breast cancer cell lines. Its loss disturbs the organization of the actin cytoskeleton, leads to inhibition of cell motility, and causes a G/G cell cycle arrest. The proliferation phenotype upon overexpression is observed only with CASIMO1 protein expression, but not with a non-translatable mutant attributing the effects to the sORF-derived protein rather than a lncRNA function. CASIMO1 microprotein interacts with squalene epoxidase (SQLE), a key enzyme in cholesterol synthesis and a known oncogene in breast cancer. Overexpression of CASIMO1 leads to SQLE protein accumulation without affecting its RNA levels and increased lipid droplet clustering, while knockdown of CASIMO1 decreased SQLE protein abundance and ERK phosphorylation downstream of SQLE. Importantly, SQLE knockdown mimicked the CASIMO1 knockdown phenotype and in turn SQLE overexpression fully rescued the effect of CASIMO1 knockdown. These findings establish CASIMO1 as the first functional microprotein that plays a role in carcinogenesis and is implicated in the cell lipid homeostasis.

The Long Noncoding RNA Cancer Susceptibility 9 and RNA Binding Protein Heterogeneous Nuclear Ribonucleoprotein L Form a Complex and Coregulate Genes Linked to AKT Signaling

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Non-coding transcript variants of protein-coding genes – what are they good for?

“…It is increasingly being accepted that a large proportion of transcripts annotated as lncRNAs harbor smORFs and express micropeptides which may be stable enough to be functional [63][64][65]. Majority of the lncRNA products from the bifunctional or hybrid genes could be of this category and may express micropeptides which are functionally related to their canonical mRNA encoded proteins.…”

An oncopeptide regulates m6A recognition by the m6A reader IGF2BP1 and tumorigenesis

“…In our present study, our findings reveal that the lncRNA LINC00266-1 participates in the m 6 A recognition by m 6 A readers and the lncRNA LINC00266-1 exerts its m 6 A recognition regulation by encoding an oncopeptide instead of an RNA molecule. Our and previous studies showed that a limited number of lncRNAs and circRNAs could encode proteins/peptides to regulate tumorigenesis [37][38][39][40] . Our findings further confirmed that some peptides are hidden in some previously annotated lncRNAs.…”