Characterization of ALTO-encoding circular RNAs expressed by Merkel cell polyomavirus and trichodysplasia spinulosa polyomavirus

Abstract

Circular RNAs (circRNAs) are a conserved class of RNAs with diverse functions, including serving as messenger RNAs that are translated into peptides. Here we describe circular RNAs generated by human polyomaviruses (HPyVs), some of which encode variants of the previously described alternative large T antigen open reading frame (ALTO) protein. Circular ALTO RNAs (circALTOs) can be detected in virus positive Merkel cell carcinoma (VP-MCC) cell lines and tumor samples. CircALTOs are stable, predominantly located in the cytoplasm, and N6-methyladenosine (m6A) modified. The translation of MCPyV circALTOs into ALTO protein is negatively regulated by MCPyV-generated miRNAs in cultured cells. MCPyV ALTO expression increases transcription from some recombinant promoters in vitro and upregulates the expression of multiple genes previously implicated in MCPyV pathogenesis. MCPyV circALTOs are enriched in exosomes derived from VP-MCC lines and circALTO-transfected 293T cells, and purified exosomes can mediate ALTO expression and transcriptional activation in MCPyV-negative cells. The related trichodysplasia spinulosa polyomavirus (TSPyV) also expresses a circALTO that can be detected in infected tissues and produces ALTO protein in cultured cells. Thus, human polyomavirus circRNAs are expressed in human tumors and infected tissues and express proteins that have the potential to modulate the infectious and tumorigenic properties of these viruses.

Role of Virus-Induced Host Cell Epigenetic Changes in Cancer

“…The LT and sT encoding region of MCPyV contains an alternative reading frame which encodes the ALTO protein with unknown function [ 359 ]. A recent study identified two viral circRNAs derived from ALTO mRNA, circALTO1 (762 nucleotides in length) and circALTO2 (940 nucleotides long) in MCPyV-positive MCC cell lines, whereas only circALTO2 was detected in virus-positive tumors, suggesting that the abundance of the circALTO isoforms might differ in vivo [ 346 ]. The circALTOs were stable, predominantly located in the cytoplasm, and enriched in exosomes.…”

“…Proteins encoded by these genes included components of NFκB signaling pathway, transcription factors, and inflammatory and anti-viral cytokines, suggesting the circALTO can modulate genes and pathways implicated in MCPyV pathogenesis. As circALTOs are enriched in exosomes, it is tempting to the speculate that circALTOs could prepare recipient cells for MCPyV infection and promote tumor development [ 346 ]. MCPyV may encode additional circRNAs because potential circRNAs were predicted upstream of genes encoding the capsid protein VP2 [ 346 ].…”

“…As circALTOs are enriched in exosomes, it is tempting to the speculate that circALTOs could prepare recipient cells for MCPyV infection and promote tumor development [ 346 ]. MCPyV may encode additional circRNAs because potential circRNAs were predicted upstream of genes encoding the capsid protein VP2 [ 346 ]. Another study identified a 762 nucleotide long circRNA, which the authors designated circMCV-T, in MCPyV-positive MCC cell lines and tumor samples [ 347 ].…”

From Merkel Cell Polyomavirus Infection to Merkel Cell Carcinoma Oncogenesis

“…The authors hypothesize that overprinting genes such as these evolve in viruses as a strategy to maximize the coding potential of relatively small genomes (Carter et al, 2013 ). Recently, several ALTO-encoding circular RNAs have been identified in MCPyV-positive MCC cell lines and tumor tissues (Yang et al, 2021 ). MCPyV ALTO translated from these circular RNAs has the ability to transactivate recombinant promoters, as well as, a number of key cellular genes involved in MCPyV pathogenesis.…”

“…MCPyV ALTO translated from these circular RNAs has the ability to transactivate recombinant promoters, as well as, a number of key cellular genes involved in MCPyV pathogenesis. Therefore, MCPyV ALTO protein may be able to modulate MCPyV infectious and tumorigenic potential through transcription regulation (Yang et al, 2021 ).…”