The Role of RNAi in Mammalian Cells in Response to Sindbis virus infection

Abstract Viruses are obligate intracellular parasites that need to interact with their host in order to replicate successfully. The understanding of this complex interaction between host and virus is essential for developing new therapeutic strategies as viral infections pose a serious challenge in healthcare, and also because viruses impose enormous costs on the economy. This study focused on the role of RNA interference in the interaction between an RNA virus (Sindbis virus) and its mammalian host cell. A sensitive image–based viral replication assay was developed to follow Sindbis virus replication in HEK293C cells and the main anti-viral innate responses to virus infection described. Virus replication increased in Dicer and RNA helicase A (RHA) knockout cells, but not when the central regulator of interferon synthesis IRF3 was knocked out. High-throughput Solexa Illumina sequencing was used to detect small viral RNA (svRNA) in Sindbis virus (SINV) infected human cells, and to detect changes in the cellular microRNA (miRNA) expression profile. Very few vsRNA sequences were detected by sequencing during virus infection, and I argue that they are random degradation products, not Dicer-generated svRNAs. Due to the very low level of svRNAs, these were undetectable using northern blotting. We have also found that the expression profile for cellular miRNAs did not change in the early stages of virus infection according to the sequencing data, a finding which was verified by northern blotting. A functional RNAi assay was developed to assess the activity and function of the RNAi system in cells subjected to cellular stress, type I interferon, infection and dsRNA, and northern blotting was used to verify the sequencing data. I have found that certain stress signals -double stranded RNA and SINV infection- decrease the efficiency of siRNA knockdowns in a siRNA-based knockdown assay system. I have identified two host factors important in Sindbis replication (Dicer, RHA). The lack of vsRNA fragments led to the conclusion that during virus infection the siRNA pathway is suppressed by either the cell or the virus itself, although SINV has been shown not to have any RNAi suppressors in previous studies conducted on its insect vector. This can be explained by the fact that both RNAi and the innate immunity detect the same molecule, dsRNA, placing these two systems into direct competition for the same substrate. My hypothesis is that the siRNA pathway of RNAi is suppressed so that Dicer does not process the long dsRNA into small, 21nt fragments, which are invisible to the innate immune system

Small RNA analysis in Sindbis virus infected human HEK293 cells

In contrast to the defence mechanism of RNA interference (RNAi) in plants and invertebrates, its role in the innate response to virus infection of mammals is a matter of debate. Since RNAi has a well-established role in controlling infection of the alphavirus Sindbis virus (SINV) in insects, we have used this virus to investigate the role of RNAi in SINV infection of human cells

Human miRNA expression profiles remain unchanged during early SINV infection (0, 4 and 6phi).

<p>(A) Scatter plots of miRNA expression levels indicate no significant change in expression in HEK293 cells between 0 and 4 hpi (top panel) and 4 and 6 hpi (bottom panel). x and y axes show the normalised expression levels of the miRNAs (log2 scale). (B) Northern blot validation of candidate miRNAs in SINV AR339 and infectious clone TR339 indicate no change in expression. The Northern blots are biological triplicates. The equal loading is shown by U6.</p

Size class and complexity distributions of sequencing reads.

<p>Size distribution and complexity are shown for (A) all reads, (B) reads mapping to the Human genome, (C) reads mapping to the SINV genome. Subplots A1, B1 and C1 show the read number for 21–24 mers at 0, 4 and 6hpi. Subplots A2, B2 and C2 show the complexity for each size class from 17–27 mers, where the complexity is the ratio of non-redundant reads to redundant reads.</p

Analysis of SINV matching reads indicate degradation.

<p>(A) Nucleotide variation across the genome (x axis) at 0, 4 and 6 hpi on both positive and negative strands is indicated by the number of unique sRNAs (0 to 300 and 0 to −300, respectively) which vary at a given position (y axis). This analysis indicates a high similarity of the Sindbis variants present in the cell to the reference sequence. The open reading frames are indicated by black boxes at the top. (B) Variation of expression level (log2 scale) for SINV matching reads. The figure shows the distribution of viral reads along the SINV genome (x axis). Positive values on y axis indicate the abundance of reads mapping to the positive strand of the virus, negative values indicate the abundance of reads mapping to the negative strand. Black represents the 4hpi reads, grey represents the 6hpi reads. (C) Variation of p Value presented on the y axis for a <i>x</i>² significance test on the size class distribution compared to a random uniform distribution for windows of length 100 nt along the SINV genome (x axis). Black represents 4hpi and grey represents 6hpi sRNA samples.</p

Infection and replication of SINV in HEK293 cells.

<p>(A). Northern blot showing SINV full length genome (49 S) and subgenomic (26 S) positive strand RNA rapidly accumulates in HEK293 cells from 2hpi and increasing through 8 hpi. The probe consisted of P32 end-labelled primers at positions 7568–7631 in the genome. The 28 S and 18 S RNA bands stained with ethidium bromide are displayed to demonstrate equal loading. (B) Immunostaining of SINV in HEK293 cells using rabbit anti E2 glycoprotein antibody detected SINV E2 translation increasing over 4, 6 and 8 hpi with over 95% of cells infected with well-defined replication centres (visualised with an anti-rabbit secondary antibody labelled with Alexa488 and nuclei are shown with DAPI).</p