Away with you Holmes, begone Poirot, and bye-bye Nancy Drew, because a terrific team of epigenetic detectives has solved an epitranscriptomic cold case to reveal the “Y” of aggressive colon tumors by linking CpG island promoter DNA hypermethylation of a key epitranscriptomic modifier and a transfer RNA (tRNA) modification to tumorigenesis.
Epitranscriptomics includes the modification of tRNA, which regulates the translation of RNA into protein. For example, the modification of phenylalanine-tRNA at guanosine 37 to form wybutosine (yW, originally named “Y”) increases translation complex stability to ensure translation. Research published 45 years ago described the tumor-specific loss of yW, although what caused this loss and “Y” it promoted tumorigenesis remained a mystery.
Intercellular investigators from the Manel Esteller lab at the Josep Carreras Leukaemia Research Institute (Barcelona, Spain) recently studied the why of “Y,” and they now report a link between epigenetic gene silencing, the loss of the Y epitranscriptomic modification, and altered mRNA homeostasis to colon tumorigenesis.
So what did the investigative team headed by Rosselló-Tortella and colleagues discover when they put this epitranscriptomic modification under the magnifying glass?
- Data mining of The Cancer Genome Atlas and Sanger Cell Lines Project databases highlights the link between DNA hypermethylation of a promoter CpG island and transcriptional silencing of the tRNA-yW Synthesizing Protein 2 (TYW2), which codes a critical enzyme for yW synthesis
- Bisulfite genomic sequencing and TYW2 RNA/protein analysis in colorectal cancer cell lines confirms this link
- The epigenetic silencing of TYW2 in colorectal cancer cells inhibits the yW modification of phenylalanine-tRNA, which alters the ribosomal reading frame to form premature stop codons and induce the nonsense-mediated decay of mRNAs such as ROBO1, a proposed colorectal tumor suppressor
- Analysis of early-stage colorectal cancer patients reveals the epigenetic inactivation of TYW2 in colon cancer patients with poorer survival, suggesting that early-stage tumors contain transformed cells likely to metastasize
- Interestingly, CRISPR/Cas9-mediated deletion of TYW2 in TYW2-expressing colorectal cancer cells fosters an enhanced tumorigenic profile, with elevated cell migration and an epithelial-to-mesenchymal transition
Overall, this curious team of researchers established that epigenetic gene silencing impacts epitranscriptomics and has provided further support for the link between tRNA modifications and tumorigenesis.
Senior author Manel Esteller concludes, “Since the original discovery in 1975, there has been much biochemical work to characterize the enzymes involved in the different steps that lead to the desired nucleotide “Y”, a hypermodified guanine, but without connecting this characterization with its defect in tumor biology. We have built the bridge between these two worlds by demonstrating that the epigenetic silencing of the TYW2 gene is the cause of the loss of the elusive nucleotide “Y”.”
For more details on the critical clues and evidence that solved this epitranscriptomic cold case, see PNAS, August 2020.