Impaired activation of transposable elements in SARS-CoV-2 infection

Abstract

Emerging evidence shows that transposable elements (TEs) are induced in response to viral infections. This TE induction is suggested to trigger a robust and durable interferon response, providing a host defense mechanism. Here, we analyze TE expression changes in response to SARS-CoV-2 infection in different human cellular models. Unlike other viruses, SARS-CoV-2 infection does not lead to global upregulation of TEs in primary cells. We report a correlation between TEs activation and induction of interferon-related genes, suggesting that failure to activate TEs may account for the weak interferon response. Moreover, we identify two variables that explain most of the observed diverseness in immune responses: basal expression levels of TEs in the pre-infected cells and the viral load. Finally, analyzing the SARS-CoV-2 interactome and the epigenetic landscape around the TEs activated following infection, we identify SARS-CoV-2 interacting proteins, which may regulate chromatin structure and TE transcription. This work provides a possible functional explanation for SARS-CoV-2 success in its fight against the host immune system and suggests that TEs could serve as potential drug targets for COVID-19.

Keywords: COVID-19; SARS-CoV-2; epigenetics; interferon response; transposable elements.

Figure 1. TEs expression changes in response to SARS‐CoV‐2 and IAV infections

1. A

   Log2 fold‐change in expression level of TE subfamilies (DNA, SINE, LINE, and LTR) in NHBE cells in response to IFNB treatment and in response to SARS‐CoV‐2 and IAV infections. SARS‐CoV‐2 viral levels (green) are depicted in the bottom panel.

2. B

   Same as (A) for SARS‐CoV‐2 infection in different cellular systems and IAV infection in A549 cell line.

3. C, D

   TE induction levels are correlated with SARS‐CoV‐2 viral levels (C) and also with TE basal levels preinfection (D). Linear regression coefficients are 0.17 and −0.39 for viral load and basal TE level, respectively (R ² = 0.78). PBMC were removed from the regression because they had essentially zero viral load. IAV* marks an independent dataset from Schmidt et al. The number of replicates for each sample is n = 3, except for IFNB treatment for which n = 2.

Figure EV1. Impaired TE activation in response to SARS‐CoV‐2 infection

1. A

   The 95‐percentile of TE subfamilies log2 fold‐changes in response to IFNB treatment, and to SARS‐CoV‐2 and IAV infection in different cellular systems by class.

2. B

   The distribution of log2 fold‐changes of TE subfamilies in response to SARS‐CoV‐2 infection and IFNB treatment at different times in NHBE cells.

3. C

   The percentage of upregulated IFN‐related genes located near TEs that are upregulated following SARS‐CoV‐2 and IAV infections among all IFN‐related genes located near upregulated TEs.

Figure 2. TE induction precedes and predicts IFN response

1. A

   The IFN transcriptional response for SARS‐CoV‐2 infection in different cellular systems.

2. B

   Same as (A) for NHBE and iAT2 cells. For A549 IAV there is one experiment from Blanco‐Melo et al and one from Schmidt et al (marked by an asterisk).

3. C

   The IFN transcriptional response of A549 cells overexpressing the ACE2 receptor dramatically decreases upon Ruxolitinib treatment.

4. D

   TE upregulation persists even with Ruxolitinib treatment.

5. E

   IFN transcriptional changes correlate with the TE induction levels among SARS‐CoV‐2‐infected cells (red) and among NHBE cells (black). TE response is calculated as the 95‐percentile of log2 fold‐change of all TE subfamilies.

6. F

   The percentages of upregulated genes out of all genes and the percentages of upregulated genes that are near upregulated TEs in response to SARS‐CoV‐2 infection in different cellular systems.

7. G

   The fraction of upregulated IFN‐related genes that are located near upregulated TEs.

Figure 3. TE classes that are induced by SARS‐CoV‐2 in A549 cells have a unique epigenetic profile

1. A

   Hierarchical clustering of histone modifications signal in noninfected A549 cells around all upregulated TEs in response to SARS‐CoV‐2 infection in A549 cells.

2. B–F

   Percentage of TEs with peaks of H3K36me3 (B), H3K79me2 (C), H3K27ac (D), H3K27me3 (E) and H3K9me3 (F) on SARS‐CoV‐2‐induced TEs, IAV induced TEs, IAV induced TEs that reside in the proximity of upregulated IFN response genes and on all expressed TEs outside genes. Asterisks mark significance level of the difference compared with all expressed TE outside genes: one asterisk marks FDR‐adjusted P‐value < 0.05 and two asterisks mark P < 0.001, requiring at least a twofold difference in Fisher's exact test. n = 39,528 DNA elements, n = 94,474 LTR elements, n = 151,223 LINE elements, and n = 214,879 SINE elements. For full statistics see Dataset EV3.

Figure EV2. Upregulation of TEs with bivalent epigenetic signature contributes to gene expression response to SARS‐CoV‐2 infection

1. A

   Percentage of TEs with the bivalent signature of H3K9me3 and H3K36me3 marks.

2. B

   Shown are UCSC tracks for the H3K9me3‐H3K36me3 bivalently marked LINE copy L1PA13, which is upregulated following SARS‐CoV‐2 infection in A549 cells, but not in response to IAV infection. The TE is located near the IFN‐related gene IFNE which is also upregulated in these cells in response to SARS‐CoV‐2 infection.

3. C

   Same as (B) for the LINE copy L1M3 and the TFPI2 gene.

Figure EV3. TE families that are induced by SARS‐CoV‐2 in A549 cells have a unique epigenetic profile

1. A–D

   Percentage of TEs with peaks of H3K36me3 (A), H3K79me2 (B), H3K27ac (C), and H3K27me3 (D) on SARS‐CoV‐2‐induced TEs, IAV induced TEs and on all expressed TEs outside genes. Shown are DNA families (first column), LTR families (second column) and LINE and SINE families (third column). Asterisks mark significance level of the difference compared with all expressed TE outside genes: one asterisk marks FDR‐adjusted P‐value < 0.05 and two asterisks mark P < 0.001, requiring at least a twofold difference in Fisher's exact test.

Figure 4. TE response is correlated with epigenetic and mitochondrial gene expression changes

1. A

   Gene ontology analysis of genes correlated (green) and inversely correlated (red) with TE response to SARS‐CoV‐2 infection.

2. B

   Distribution of TE response‐gene correlations for genes that increase with TE expression in iAT2 cells. Black represents correlation distribution of all genes. Correlation distribution of epifactors are in green.

3. C

   The LFC of gene expression following SARS‐CoV‐2 infection vs the TE response in different systems for SETD2, BRD2 and BRD4, three SARS‐CoV‐2 interactome‐related epigenetic factors. n = 3 replicates for each of mock and infected cells.

4. D

   A model for SARS‐CoV‐2 impaired TE activation. (1) SARS‐CoV‐2 infection of normal lung epithelial cells results in low viral load, weak IFN response, and modest TE upregulation, predominantly of TEs not located in the proximity of IFN response genes, and which are enriched with H3K9me3 and H3K36me3. A specific SARS‐CoV‐2 interacting protein may sequester SETD2 away from the otherwise H3K36m3‐enriched TEs, enabling their transcription. (2) IAV infection induces TEs activation and IFN response. H3K27m3 marked TEs are prone to be upregulated, inducing near IFN gene activation. The illustration was created with BioRender.com.