One for all – Human kidney Caki-1 cells are highly susceptible to infection with corona- and other respiratory viruses

Abstract

Despite the vast increase in research activity in the coronavirus field over the past two years, researchers are still heavily reliant on non-human cells, for example Vero E6, highly heterogeneous or not fully differentiated cells, such as Calu-3, or not naturally susceptible cell lines overexpressing receptor ACE2 and other accessory factors, such as TMPRSS2. Complex cell models, such as primary cell-derived air-liquid interface epithelial models are highly representative of human tissues but are expensive and time-consuming to develop and maintain and have limited suitability for high-throughput analysis. In vitro investigations of host-pathogen interactions of viruses is highly reliant on suitable cell and tissue culture models and results are only as good as the model they have been validated in. Here, we show the use of a highly characterized human kidney cell line, Caki-1, for infection with three human coronaviruses: Betacoronaviruses severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and Middle Eastern respiratory syndrome coronavirus (MERS-CoV) and Alphacoronavirus human coronavirus 229E (hCoV-229E). Caki-1 cells show equal or superior susceptibility to all three coronaviruses when compared to other commonly used cells lines for the cultivation of the respective virus. Furthermore, we used a panel of antibodies generated against 21 SARS-CoV-2-encoded proteins to identify their location in the infected Caki-1 cells using immunocytochemistry. Most importantly, Caki-1 cells are also susceptible to two other respiratory viruses, Influenza A virus and RSV, making them an ideal model for cross-comparison of not only a broad range of coronaviruses but respiratory viruses in general.

Differential RNA editing landscapes in host cell versus the SARS-CoV-2 genome

“…In our study, we applied a pipeline for variant detection and RNA editing analysis based on the REDItools package to detect changes in host as well as the SARS-CoV-2 viral genome using a permissive in vitro cell line, Caki-1. 26 Our data indicate that the number of mutations within the viral genome in EDB-α-1 is higher than in EDB-2, which remains relatively stable throughout passaging. The most frequent substitution type observed in EDB-α-1 strain was C-U, while in EDB-2 no obvious pattern was observed.…”

“… 41 Alternatively, early levels of EDB-α-1 production are lagging behind EDB-2 at 24 hpi and response induction may be delayed. 26 However, EDB-α-1 48 hpi stimulation levels are still below ISG expression levels observed in EDB-2 at 24 hpi.…”

“…The Caki-1 cell line, a human kidney-derived cancer cell line, was chosen for being highly susceptible to SARS-CoV-2, other corona- and respiratory viruses, as well as being interferon competent. 26 Cells were inoculated at MOI = 0.1 with either variant. Following infection, cellular RNAs were harvested at 24 or 48 hpi and subjected to 150 bp paired-end RNA Illumina sequencing analysis (150PE RNAseq; Figure 1 A).…”

“…Caki-1 (purchased from AMSBio, ATCC reference HTB-46) are a kidney cell line with epithelial morphology isolated from a 49-year old Caucasian male. They have been reported to have a deletion in CDKN2 ( https://www.cbioportal.org/ , Accessed 30/10/2022, 65 , 66 also 26 ). Cells were authenticated by AMSBio, and were routinely tested for mycoplasma during culturing.…”

“…SARS-CoV-2 variants utilized in this study are EDB-2 (B1.5 at the time, now B.1), EDB-α-1 (B.1.1.7), EDB-δ-1 (B.1.617.2), and EDB-ο-BA.1-1 (B.1.1.529, BA.1) at passage 2 unless otherwise stated. 26 Infectivity was quantified by endpoint titration on Vero E6 cells (ATCC CRL-1586) with the exception of EDB-ο-BA.1-1 which was isolated and quantified on Caki-1 cells. Briefly, cells were plated to confluence 1-day prior to infection on 96-well plates.…”