key: cord-0846714-cywa6iim authors: Sharma, Arun; Garcia, Gustavo; Wang, Yizhou; Plummer, Jasmine T.; Morizono, Kouki; Arumugaswami, Vaithilingaraja; Svendsen, Clive N. title: Human iPSC-Derived Cardiomyocytes , are Susceptible to SARS-CoV-2 Infection date: 2020-06-29 journal: Cell Rep Med DOI: 10.1016/j.xcrm.2020.100052 sha: 21c6ebdf73db2458c3053573a5233748b50d015f doc_id: 846714 cord_uid: cywa6iim Summary Coronavirus disease 2019 (COVID-19) is a pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 is defined by respiratory symptoms, but cardiac complications including viral myocarditis are also prevalent. Although ischemic and inflammatory responses caused by COVID-19 can detrimentally affect cardiac function, the direct impact of SARS-CoV-2 infection on human cardiomyocytes is not well-understood. Here, we utilize human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) as a model to examine the mechanisms of cardiomyocyte-specific infection by SARS-CoV-2. Microscopy and RNA-sequencing demonstrate that SARS-CoV-2 can enter hiPSC-CMs via ACE2. Viral replication and cytopathic effect induce hiPSC-CM apoptosis and cessation of beating after 72 hours of infection. SARS-CoV-2 infection activates innate immune response and antiviral clearance gene pathways, while inhibiting metabolic pathways and suppressing ACE2 expression. These studies show that SARS-CoV-2 can infect hiPSC-CMs in vitro, establishing a model for elucidating infection mechanisms and potentially a cardiac-specific antiviral drug screening platform. Coronavirus disease 2019 (COVID-19) is a pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). COVID-19 is defined by respiratory symptoms, but Coronavirus disease 2019 (COVID- 19) , which is caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has been declared an international pandemic, causing the hospitalization and deaths of hundreds of thousands of people worldwide 1 . SARS-CoV-2, a single-stranded enveloped RNA virus, is known to use the ACE2 receptor to enter host lung tissue, followed by rapid viral replication 2 . Clinical presentation demonstrates predominantly pulmonary symptoms, including cough, shortness of breath, pneumonia, and acute respiratory distress syndrome 3 . However, there is mounting evidence that SARS-CoV-2 infection may cause cardiac complications including elevated cardiac stress biomarkers, arrhythmias, and heart failure 4 . A recent study demonstrated significantly elevated troponin levels among some COVID-19 patients, indicating cardiac injury, and notably, cardiac injury was associated with increased risk of mortality 5 . The etiology of cardiac injury in COVID-19, however, remains unclear. Cardiac injury may be ischemia-mediated, and the profound inflammatory and hemodynamic impacts seen in COVID- 19 have been hypothesized to cause atherosclerotic plaque rupture or oxygen supply-demand mismatch resulting in ischemia 3 . Alternatively, cardiac tissue expresses the ACE2 receptor, further suggesting the feasibility of direct SARS-CoV-2 internalization in cardiomyocytes 6 . ACE2 is also upregulated specifically in cardiomyocytes during dilated and hypertrophic cardiomyopathy 7 . Importantly, the related SARS-CoV virus has been noted to localize within the myocardium 8 , and recent studies 9 have shown 79% sequence conservation in the viral genomes of SARS-CoV and SARS-CoV-2. Structurally, both viruses use the ACE2 receptor to enter cells and bind with similar affinities to ACE2 10 . Given these similarities to SARS-CoV, it is plausible that SARS-CoV-2 could also use ACE2 to enter adult cardiomyocytes. Preliminary COVID-19 clinical case reports have raised suspicion for cardiac injury mediated by direct myocardial SARS-CoV-2 infection and resulting fulminant myocarditis [11] [12] [13] . A recent multi-organ autopsy study of COVID-19 patients detected SARS-CoV-2 viral RNA in the heart via PCR 14 . However, the gold standard for confirming SARS-CoV-2 localization in cardiomyocytes is endomyocardial biopsy (EMB), an invasive procedure, and additional safety precautions also must be taken to conduct EMB in the setting of COVID-19. Thus, there are currently limited clinical data demonstrating localization of SARS-CoV-2 to adult human cardiomyocytes. In order to gain further insights into the cardiac pathophysiology of COVID-19, it will be critical to determine whether SARS-CoV-2 can directly infect isolated human cardiomyocytes. Elucidating the pathogenic mechanism of cardiac injury in COVID-19 in vitro could ultimately guide therapeutic strategies. Antiviral agents could potentially mitigate cardiac complications if the underlying mechanism of cardiac injury is direct myocardial viral infection. Primary human cardiomyocytes are difficult to obtain and maintain for research use. Improved methods to convert human induced pluripotent stem cells (hiPSCs) to multiple somatic lineages have enabled in vitro mass production of patient-specific cells, including hiPSC-derived cardiomyocytes (hiPSC-CMs) 15 . The hiPSC-CMs express relevant proteins found in adult human CMs, can spontaneously contract, can be made in weeks using defined differentiation protocols, and can be genetically customized using genome editing 16 . HiPSC-CMs express ACE2, which increases in expression over 90 days of differentiation 17 . The hiPSC-CMs are also responsive to inotropic drugs such as norepinephrine, and beating rates can be controlled via electrical stimulation 18 . Because hiPSC-CMs can be purified and replated for downstream applications, research groups in academia and industry now utilize these cells for cardiovascular disease modeling and high-throughput drug screening assays. HiPSC-CMs can recapitulate cellular phenotypes for cardiovascular diseases including various forms of cardiomyopathy 19, 20 and druginduced cardiotoxicity 21, 22 . Notably, hiPSC-CMs have also shown promise as an in vitro model for studying the mechanisms of direct cardiomyocyte viral infection in the context of viral myocarditis. A previous study demonstrated that coxsackievirus B3 (CVB3), one of the major causative agents for viral myocarditis, can rapidly infect and proliferate within hiPSC-CMs 23 . CVB3, like SARS-CoV-2, is a positive-sense, single-stranded RNA virus, although unlike SARS-CoV-2, it does not have a viral envelope. The hiPSC-CMs produce the coxsackie and adenovirus receptor protein, which is needed for infection by CVB3. Detrimental virus-induced cytopathic effect was observed in hiPSC-CMs within hours of CVB3 infection, manifesting in cell death and contractility irregularities. Importantly, this study also established hiPSC-CMs as a cardiac-specific antiviral drug screening platform, and demonstrated that drugs such as interferon beta and ribavirin can stymie CVB3 proliferation in vitro 23 . Interferon beta was able to transcriptionally activate viral clearance gene networks in CVB3-infected hiPSC-CMs. Here, the aforementioned foundational viral myocarditis study is extended to assess the effect of SARS-CoV-2 on hiPSC-CMs. We show that hiPSC-CMs are susceptible to SARS-CoV-2 infection, resulting in functional alterations, transcriptional changes, and cytopathic effects. These cellular phenotypes occurred in the absence of systemic inflammatory and hemodynamic impacts, establishing an in vitro cardiac platform to study SARS-CoV-2 infection. An hiPSC control line (02iCTR) was generated by the Cedars-Sinai Medical Center iPSC Core from peripheral blood mononuclear cells and shown to be fully pluripotent 24 . The hiPSCs were differentiated into hiPSC-CMs using an established monolayer differentiation protocol utilizing small molecule modulators of Wnt signaling 25 . Differentiated hiPSC-CMs were metabolically purified by depriving cells of glucose, as previously demonstrated 25 . Purified hiPSC-CMs expressed standard cardiac sarcomeric markers cardiac troponin T (cTnT) and α-actinin ( Figure 1A ). Purified hiPSC-CMs were replated into 96-well plates at 100,000 cells per well and allowed to regain contractility (Supplemental Movie 1) before being subjected to SARS-CoV-2 infection. Figure 1D) . Cells from both infected and mock conditions were stained for cardiac marker cardiac troponin T (cTnT) and SARS-CoV-2 viral capsid "spike" protein ( Figure 1B) . The infected hiPSC-CMs stained positively for spike protein, suggesting that SARS-CoV-2 can establish active infection in hiPSC-CMs. As demonstrated previously 2 , pre-treatment of infected hiPSC-CMs with an ACE2 antibody significantly diminished viral protein expression and plaque forming unit production, suggesting that ACE2 is critical for SARS-CoV-2 internalization in hiPSC-CMs (Supplemental Figure 1 ). infection, whereas mock wells continued to contract ( Figure 1G ). Taken together, these results indicate that hiPSC-CMs are susceptible to ACE2-mediated SARS-CoV-2 infection and downstream detrimental cytopathic effects, that the SARS-CoV-2 may be able to replicate in distinct perinuclear locations within hiPSC-CMs by co-opting cellular organelles for viral protein translation, and that SARS-CoV-2 infection significantly reduces functional contractility in hiPSC-CMs. The hiPSC-CMs infected with 0.1 MOI SARS-CoV-2 for 72 hours were also harvested for We predict that future studies will be able to use hiPSC-CMs as a cardiac-specific antiviral drug screening platform, in similar fashion to previous studies with coxsackievirus B3 on hiPSC-CMs 23 . A variety of antiviral approaches ranging from repurposed small molecules, such as nucleoside analogues or viral polymerase inhibitors, to novel antibodies and antisense oligonucleotides have been proposed for COVID-19 and are currently being tested in vitro and in clinical trials 29 . HiPSC-CMs could serve as a cardiac-specific auxiliary cell type for in vitro preclinical efficacy studies for any drug aiming to stymie SARS-CoV-2 proliferation. In parallel, drug-induced arrhythmias and QT-interval prolongation can also be examined for antiviral compounds in pre-clinical development, given that some existing COVID-19 drug treatments exhibit these off-target cardiotoxicities 30 . Due to the enormity of the current COVID-19 pandemic, and the increasing evidence for associated cardiac symptoms, innovative approaches using technologies such as the hiPSC-CMs presented here will critical to further understand and counteract SARS-CoV-2 infection. The cellular immaturity of hiPSC-derivative cell types must be considered in this model. It is known that hiPSC-CMs are electrophysiologically, structurally, and genetically immature in comparison to their adult counterparts 31 , although biomechanical efforts to mature these cells towards an adult phenotype have recently gained traction 32 . However, even in these immature cells, the current study showed overt virus-induced cardiotoxicity and physiological effects at SARS-CoV-2 MOIs ranging from 0.001 to 0.1. Since expression of ACE2 increases as hiPSC-CMs mature in in vitro culture 17 , one could hypothesize that after maturation, older hiPSC-CMs would be even more susceptible to SARS-CoV-2 infection. Significant additional data are needed to test these possibilities. The results presented here are in an isolated in vitro system, devoid of any immune system cellular components that are thought to be critical to the many aspects of the COVID-19 viral response in vivo 33 virus localizing in the heart of a COVID-19 patient, albeit not specifically in the cardiomyocytes 13 . A recent multi-organ autopsy study also showed SARS-CoV-2 viral RNA in the heart 14 . Additional clinical data are needed, but this raises the question of whether the SARS-CoV-2 enters the heart via a viremic phase or through macrophages clearing the virus from the lungs. It remains to be seen whether direct cardiomyocyte infection may contribute to the variety of in vivo cardiac clinical sequelae presented by patients with COVID-19, such as arrhythmias, elevated cardiac troponin biomarkers, or heart failure. Nonetheless, we establish that hiPSC-CMs in vitro are susceptible to SARS-CoV-2 infection. We acknowledge that this work represents an area of study that is rapidly growing in relevance, and thus we apologize to any authors whose work we were not able to include here. We thank Dr. Soshana Svendsen for editing the manuscript. We thank the Cedars-Sinai Center for Bioinformatics and Functional Genomics core facility for their assistance with RNA-sequencing. Research from the Svendsen laboratory has been supported by the National Institutes of Health (5UG3NS105703) and the Cedars-Sinai Board of Governor's Regenerative Medicine Institute. Arun Sharma is supported by an institutional training grant (T32 HL116273). A.S., V.A., and C.N.S. designed analyses, analyzed data, and drafted the manuscript. A.S. and G.G. conducted experiments and acquired data. Y.W. and J.T.P assisted with genomics and bioinformatics analysis. K.M. assisted with the ACE2 antibody experiment. A.S., V.A., and C.N.S. analyzed data. All authors contributed to the final manuscript. The authors declare no competing interests. Human iPSC-CMs exhibit standard sarcomeric markers including cardiac troponin T (cTnT) and α-actinin with DAPI as nuclear counterstain. B) Immunofluorescence for cTnT and SARS-CoV-2 "spike" protein demonstrates that hiPSC-CMs can be infected by SARS-CoV-2. SARS-CoV-2 spike protein is not present in mock infected cultures. C) HiPSC-CMs after SARS-CoV-2 infection, but not mock infection, exhibit signs of cellular apoptosis, indicated by morphological changes seen in bright field (BF) and cleaved caspase-3 production. TNNT2 and TNNC1 represent cardiac markers, whereas CKMT2 represents mitochondrial enzymes. CXCL2, IL1B, IL11, and OAS3 represent innate immune response and viral clearance genes. * p<0.05. F) Top: Downregulated transcriptional pathways based on gene ontology (GO) analysis, visualized using REViGO. Significantly downregulated pathways include mitochondrial transport, oxidative phosphorylation, oxidation-reduction processes, and muscle contraction. Bottom: Top 10 most significant GO terms associated with downregulated pathways are related to mitochondrial function. G) Top: Upregulated transcriptional pathways based on gene ontology (GO) analysis, visualized using REViGO. Significantly upregulated pathways include response to organic substance, immune system process, and apoptotic process. Bottom: Top 10 most significant GO terms associated with upregulated pathways are related to response to organic stimulus. Further information and requests for resources and reagents should be directed to and will be fulfilled by the Lead Contact, Clive Svendsen (Clive.Svendsen@cshs.org). This study did not generate new unique reagents. The gene expression data from this study are found at Gene Expression Omnibus with accession no. GSE150392. Additional Supplemental Items are available from Mendeley Data at http://dx.doi.org/10.17632/5xcdrpb22v.2 The appropriate institutional review board (IRB) and stem cell research oversight committee (SCRO) were consulted at UCLA and Cedars-Sinai Medical Center. The 02iCTR hiPSC line (male, clinically normal, no known associated disease) was derived from human peripheral blood mononuclear cells and has been published previously 24 The iPSC differentiation work in the Svendsen Lab is carried out under "Pro00021505: Svendsen Stem Cell Program", authorized by the Cedars-Sinai Medical Center IRB. Initially, hiPSCs were grown on Matrigel and maintained in mTeSR1 (STEMCELL Technologies). The hiPSC-CMs were generated from hiPSCs using a small-molecule mediated differentiation approach that modulates Wnt signaling 25 . Briefly, this approach uses the CHIR99021 GSK3β inhibitor from days 0-2 to initiate mesoderm specification, followed by Wnt-C59 Wnt inhibitor at days 3-5 to initiate cardiac specification. From days 0-7 of differentiation, cells are maintained in RPMI 1640 + B27 supplement without insulin. Cells began beating at approximately day 7 postdifferentiation, at which point medium was changed to RPMI 1640 + B27 supplement with insulin. Cardiomyocytes were metabolically selected from other differentiated cells by conducting glucose deprivation in RPMI 1640 without glucose + B27 supplement with insulin as previously described 25 . After selection, hiPSC-CMs were replated as a monolayer into 96-well plate format at 100,000 cells per well in hiPSC-CM culture medium, RPMI 1640 + B27 supplement with insulin. SARS-CoV-2 was passaged once in Vero-E6 cells (ATCC) and viral stocks were aliquoted and stored at -80 o C. Virus titer was measured in Vero-E6 cells by TCID 50 assay. Vero-E6 cells were cultured in DMEM growth media containing 10% fetal bovine serum, 2 mM L-glutamine, penicillin (100 units/ml), streptomycin (100 units/ml), and 10 mM HEPES. Cells were incubated at 37°C with 5% CO 2 . For hiPSC-CM infection, viral inoculum (MOI of 0.1, or 1 plaque forming unit per 10 cells) was prepared using serum-free media, unless otherwise specified. Culture media from each well containing hiPSC-CMs was removed and replaced with 250 µL of prepared inoculum. For mock infection, serum-free media (250 µL/well) alone was added. The inoculated plates were incubated for 1 hour at 37°C with 5% CO 2 . The inoculum was spread by gently tilting the plate sideways every 15 minutes. At the end of incubation, the inoculum was replaced with fresh hiPSC-CM culture medium. Cells remained at 37°C with 5% CO 2 for 72 hours before analysis. After 72 hours of SARS-CoV-2 infection (or mock), live cell images and videos were obtained by bright field microscope (Leica DMIL LED). For immunofluorescence, separate wells of hiPSC-CMs were fixed with 4% paraformaldehyde in phosphate-buffered saline (PBS) for 20 minutes. The fixed samples were then permeabilized and blocked for 1 hour in a "blocking solution" containing PBS with 2% bovine serum albumin, 5% donkey serum, 5% goat serum, AB_2556543). Samples were then rinsed 5 times for 2 minutes each with PBS containing 0.3% Triton X-100, followed by DAPI diluted in PBS at 1:5000 for 10 minutes. Immunofluorescence images were quantified using ImageJ software. DAPI was used to count total cell numbers in order to obtain a percentage of cells positive for dsRNA, spike protein, or cleaved caspase-3. The human iPSC-CMs were infected with SARS-CoV-2 at varying MOIs of 0.1, 0.01 and 0.001 in 96-well plate (Supplemental Figure 1C) . Mock infected cells received only the media used for preparing the SARS-CoV-2 inoculum. After 1-hour incubation at 37°C with 5% CO 2 , the inocula were replaced with fresh media followed by PBS (phosphate buffered saline) wash. At each timepoint (days 1, 2 and 3), cell culture supernatant samples from mock and SARS-CoV-2 infected wells were collected and stored at -80°C. Viral production by infected iPSC-CMs at each timepoint was measured by quantifying TCID 50 (Median Tissue Culture Infectious Dose). In brief, Vero-E6 cells were plated in 96-well plate at a density of 5 x10 3 cells/well. The next day, culture supernatants collected from hiPSC-CMs at various timepoints were subjected to 10fold serial dilutions (10 -1 to 10 -6 ) and inoculated onto Vero-E6 cells. The cells were incubated at 37°C with 5% CO 2 . After 72 hours, each inoculated well was examined for presence or absence of viral cytopathic effect and percent infected dilutions immediately above and immediately below 50% were determined. TCID 50 was calculated as described previously 34 . TCID 50 values of each viral MOIs at different timepoints were subjected to statistical analysis and plotted in a line graph. To quantify virus titer after 72 hour SARS-CoV-2 infection dose response on hiPSC-CMs (Supplemental Figure 1) , culture supernatants from each MOI condition were subjected to 10fold serial dilutions and added to Vero-E6 cells in a 96-well plate. At 48 hours post infection on Vero-E6, the cells were fixed in methanol and subjected to immunostaining using dsRNA antibody. Immunostained viral plaques were counted in the highest viral dilution-containing wells. Plaque forming unit per milliliter (PFU/mL) of culture supernatant was calculated for each condition. The hiPSC-CMs were pretreated with anti-ACE2 antibody (R&D Systems Cat# AF933, RRID: AB_355722; 20 µg/well in 100 µL media) for 1 hour. Untreated hiPSC-CMs and non-specific antibody (anti-TIM4 antibody, R&D Systems Cat# AF2929, RRID: AB_2240431; 20 µg/well in 100 µL media) treated cells were included as controls. After 1 hour of antibody pretreatment at 37°C, SARS-CoV-2 viral inoculum (MOI of 0.01) was added to each well. Subsequently at 1hour post-infection (hpi), virus inoculum was replaced with fresh media. 72 hours later, the cells were fixed with 4% paraformaldehyde for immunofluorescence analysis. After 72-hour viral treatment, cells designated for transcriptomic analysis were harvested in Trizol and total RNA extracted using a Qiagen RNEasy Mini Kit. Total RNA was then used for library preparation and sequencing. The SMART-Seq V4 Ultra Low RNA Input Kit for Sequencing (Takara Bio USA, Inc., Mountain View, CA) was used for reverse transcription and generation of double stranded cDNA for library preparation using the Nextera XT Library Preparation kit (Illumina, San Diego, CA). Total RNA quality was analyzed via the 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) and RNA quantified using QubitTM (ThermoFisher Scientific, Waltham, MA) fluorometric quantitation. An input of 10 ng total RNA was used for oligo(dT)-primed reverse transcription, cDNA amplification, and cDNA cleanup. The cDNA was analyzed on the 4200 TapeStation (Agilent Technologies). Quantification of cDNA was performed using Qubit. cDNA normalized to 30 pg/mL was fragmented and sequencing primers added simultaneously. A limiting-cycle PCR added Index 1 (i7) adapters, Index 2 (i5) adapters, and sequences required for cluster formation on the sequencing flow cell. Indexed libraries were cleaned up, library size verification performed on the 4200 TapeStation, and library quantified via Qubit. Libraries were sequenced on a NextSeq 500 using with a 1x75 bp read length and coverage of ~60M reads/cell. Raw reads obtained from RNA-Seq were aligned to the transcriptome using STAR (version was performed with DESeq2 Bioconductor package version 1.10.1 in R version 3.6.3. Each gene was fitted into a negative binomial generalized linear model, and the Wald test was applied to assess the differential expressions between two sample groups by DESeq2. Benjamini and Hochberg procedure was applied to adjust for multiple hypothesis testing, and differential expression gene candidates were selected with a false discovery rate less than 0.05. For visualization of coordinated gene expression in samples, a two-way hierarchical clustering with Pearson correlation distance matrix was performed with samples and differentially-expressed candidates using the Bioconductor g-plots package (version 3.0.3) in R. Gene ontology analysis and visualization conducted using REViGO online software 37 . Thirty-second video clips were taken of mock and infected hiPSC-CMs at 72 hours after viral infection. A beats-per-minute measurement was obtained by manually counting individual beats in a 30-second video and multiplying by 2 to extrapolate to 1 minute. For statistical analyses, the Student's t test was used for comparison between two datasets. Excel or Prism software was used for statistical analysis. Data are presented as mean ± standard deviation as indicated in figure legends. A p value of <0.05 is considered statistically significant and is denoted by *. Images used for statistical analysis were randomly chosen within a well of interest. Other statistical details can be found in figure legends. No data were excluded. Figure 1G ). Thirty-second video clips (in triplicate) were taken of mock and infected hiPSC-CMs at 72 hours after viral infection. Cells were infected at MOI 0.1. 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Cell death and differentiation Improvements in methods for calculating virus titer estimates from TCID50 and plaque assays STAR: ultrafast universal RNA-seq aligner RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome ):e21800. eTOC: Sharma et al demonstrate that human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) are susceptible to SARS-CoV-2 infection. This establishes a platform for understanding the mechanisms of cardiac-specific infection by SARS-CoV-2 in vitro, and could potentially be employed to develop antiviral compounds. Highlights: • Human iPSC-derived cardiomyocytes are susceptible to SARS-CoV-2 infection • ACE2 antibody blunts SARS-CoV-2 infection in cardiomyocytes •