DNA mismatch repair-deficient
colorectal cancers (
CRCs) accumulate numerous frameshift mutations at repetitive sequences recognized as
microsatellite instability (MSI). When coding mononucleotide repeats (cMNRs) are affected,
tumors accumulate frameshift mutations and
premature termination codons (PTC) potentially leading to truncated
proteins. Nonsense-mediated RNA decay (NMD) can degrade PTC-containing transcripts and protect from such faulty
proteins. As it also regulates normal transcripts and cellular physiology, we tested whether NMD genes themselves are targets of MSI frameshift mutations. A high frequency of cMNR frameshift mutations in the UPF3A gene was found in MSI CRC cell lines (67.7%), MSI colorectal
adenomas (55%) and
carcinomas (63%). In normal colonic crypts, UPF3A expression was restricted to single
chromogranin A-positive cells. SILAC-based proteomic analysis of KM12 CRC cells revealed UPF3A-dependent down-regulation of several
enzymes involved in
cholesterol biosynthesis. Furthermore, reconstituted UPF3A expression caused alterations of 85 phosphosites in 52
phosphoproteins. Most of them (38/52, 73%) reside in nuclear
phosphoproteins involved in regulation of gene expression and RNA splicing. Since UPF3A mutations can modulate the (phospho)proteomic signature and expression of
enzymes involved in
cholesterol metabolism in CRC cells, UPF3A may influence other processes than NMD and loss of UPF3A expression might provide a growth advantage to MSI CRC cells.