Online now: our bulk and single-cell transcriptome profiling of #SARSCoV2 infected cell lines (Calu-3, Caco-2, H1299)
biorxiv.org/content/10.110…
– summary follows in the thread below
biorxiv.org/content/10.110…
– summary follows in the thread below
Comparison of amount of viral RNA in the different cell lines, and subgenomic RNAs.
In contrast to Calu-3 cells, Caco-2 cells do not sense foreign RNA. ISG induction was only seen in Calu-3. An interesting gene, ARRDC3, not previously associated with virus infections, was induced in both cell lines.
Small RNA profiling showed induction of miR-155 for both SARS-CoV and SARS-CoV-2, and induction of miRNAs originating from the vault RNAs.
Single-cell sequencing showed again stronger induction of ISGs for SARS-CoV-2 compared to SARS-CoV, with an "on-off-switch" for e.g. IFIT2. Interferon genes IFNB/L are expressed in only a subset of cells.
RNA velocity/intron count analysis showed sequential induction of IRF and NF-kappaB signaling. Only in a short time window the two overlap; in there, interferon genes are transcribed.
The Hsp90 gene HSP90AA1 was induced in cells bearing viral transcripts in the "slow motion" infection in H1299 cell lines.
An inhibitor of Hsp90 activity, 17-AAG (a geldanamycin derivate) could inhibit viral replication by 50% at around 500-800 nM.
All data immediately available:
shiny.mdc-berlin.de/COV/ for interactively browsing the Calu-3 scRNA-seq data
ncbi.nlm.nih.gov/geo/query/acc.… for raw data and some processed data
mdc-berlin.de/singlecell-SAR… for more supplementary material
shiny.mdc-berlin.de/COV/ for interactively browsing the Calu-3 scRNA-seq data
ncbi.nlm.nih.gov/geo/query/acc.… for raw data and some processed data
mdc-berlin.de/singlecell-SAR… for more supplementary material
Great team effort! By @mo_kirstin @vedranfranke Asija Diag @Lina93783344 @RobertArsie Filippos Klironomos @dkoppstein Salah Ayoub, Christopher Buccitelli Anja Richter @ILegnini Andranik Ivanov, Tommaso Mari, Jan Papies @MarcelAMller @NiemeyerDaniela …
… @SelbachLab @AltunaAkalin @N_Rajewsky @c_drosten @landthaler_m – thanks to @BrinkmannLab @Sander_Lab @marcoyannic @Friedemann1 and many others for comments and discussions!
This work wouldn't have been possible without our previous work on another coronavirus and the Herpes simplex virus 1 single-cell RNA-seq study (nature.com/articles/s4146…) – so a particular shout out to all Corona and Herpes researchers out there!
Please post your comments here or on in the comment section on biorxiv.org/content/10.110… – also, point me to recent studies that should be cited which we might have missed!
Ok now pics with white background…
Comparison viral load and viral subgenomic RNAs
Comparison viral load and viral subgenomic RNAs
In contrast to Calu-3 cells, Caco-2 cells do not sense foreign RNA. ISG induction was only seen in Calu-3. An interesting gene, ARRDC3, not previously associated with virus infections, was induced in both cell lines.
Small RNA profiling showed induction of miR-155 for both SARS-CoV and SARS-CoV-2, and induction of miRNAs originating from the vault RNAs.
Single-cell sequencing showed again stronger induction of ISGs for SARS-CoV-2 compared to SARS-CoV, with an "on-off-switch" for e.g. IFIT2. Interferon genes IFNB/L are expressed in only a subset of cells.
RNA velocity/intron count analysis showed sequential induction of IRF and NF-kappaB signaling. Only in a short time window the two overlap; in there, interferon genes are transcribed.
The Hsp90 gene HSP90AA1 was induced in cells bearing viral transcripts in the "slow motion" infection in H1299 cell lines. An inhibitor of Hsp90 activity, 17-AAG (a geldanamycin derivate) could inhibit viral replication by 50% at around 500-800 nM.
