Study generates a picture of the myocardial transcriptional landscape of COVID-19

In a recent study posted to the medRxiv* preprint server, researchers profiled cardiac tissue transcriptomes of coronavirus disease 2019 (COVID-19) patients.

Background

Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), the virus causing COVID-19, has been implicated in pulmonary and extra-pulmonary disease, including cardiac complications. Acute myocardial injury has been observed in the initial stages of COVID-19. Besides, growing evidence indicates the persistence of cardiac dysfunction even after recovery from acute illness. COVID-19-recovered individuals might be at an increased risk of arrhythmias, heart failure, chest pain, and vascular complications than SARS-CoV-2-naïve individuals.

Autopsies of COVID-19 patients revealed the presence of negative-sense ribonucleic acid (RNA) of SARS-CoV-2, indicating acute viral replication in the myocardium. Cardiac complications are not unique to COVID-19; influenza A virus (IAV) is also associated with myocardial infarction, atrial fibrillation, endocarditis, and tachycardia. However, it is uncertain whether the cardiomyocyte damage is linked to the virus’s presence or the secondary effect of immune responses in IAV infection.

Hence, the contribution to cardiac-related complications induced by IAV or SARS-CoV-2 infection remains unclear and contentious. Analysis of transcriptomes from myocardial tissues of patients might serve as unique tools to characterize host responses against extra-respiratory viral infections.

About the study

In the present study, researchers profiled the myocardial transcriptomes of COVID-19, pandemic H1N1 (pH1N1) influenza, and control patients using targeted spatial transcriptomics. Myocardial tissues were obtained from patients upon approval for post-mortem biopsies by families. The infection status of patients was confirmed by quantitative reverse transcription-polymerase chain reaction (RT-qPCR). Tissue microarray (TMA) was performed on cores of SARS-CoV-2, pH1N1, and control patients. Immunohistochemical analysis was performed with antibodies targeting the spike protein of SARS-CoV-2. RNA profiling was performed using Nanostring GeoMX digital spatial profiler (DSP) on a freshly prepared TMA slide.

GeoMX DSP measured RNA abundance of more than 1800 genes, including four SARS-CoV-2-specific genes, 22 add-in COVID-19-related genes, two negative control genes, and 32 internal reference genes. Transcriptomes of regions of interest (ROIs) were quantified, and, overall, 48 ROIs were analyzed, including 16 COVID-19, four pH1N1, and 28 controls. Gene set enrichment analysis (GSEA) was performed using gene sets obtained from the molecular signatures database, C2 and C5 categories, and Kyoto encyclopedia of genes and genomes (KEGG) pathways.

Results

Cardiac tissue samples were obtained at autopsy from seven SARS-CoV-2, two pH1N1, and six control patients. Immunohistochemistry analysis revealed edema in all COVID-19 patients and myocarditis in one patient. All COVID-19 samples lacked viral RNA, as inferred from RNAscope analysis. Increased interferon (IFN) response genes expression was observed in pH1N1 patients compared to COVID-19 patients. Contrastingly, the expression of chemokine ligands like C-C motif chemokine ligand 15 (CCL15) was elevated in COVID-19 patients. A significant differential expression (DE) of synovial sarcoma X family member 1 (SSX1) and CCL15 was observed in COVID-19 sets compared to controls.

Moreover, heat shock protein family A member 1A (HSPA1A) was significantly upregulated in COVID-19 samples compared to controls. Anti-viral IFN responses were more robust in pH1N1 samples than in control samples. Overlapping DE genes were compared among the three cohorts, revealing COVID-19-exclusive upregulation of 16 genes and downregulation of 24 genes. Among those upregulated were the inflammatory response-associated NFAT Activating Protein with ITAM Motif 1(NFAM1) gene and tumor necrosis factor receptor gene, TNFRSF10A. Notably, the cardioprotective gene, interleukin 1 like receptor 1 (IL1RL1), encoding suppressor of tumorigenicity 2 (ST2), was downregulated.

GSEA revealed downregulation of complement activation pathway- and IFN-related gene sets in COVID-19 samples compared to pH1N1 samples. Furthermore, gene sets upregulated in COVID-19 samples relative to pH1N1 samples were associated with deoxyribonucleic acid (DNA) damage and repair, cell cycle, and cellular abnormality. Compared to control samples, COVID-19 samples exhibited upregulation of cell death and senescence-related gene sets. COVID-19 samples also had significantly enriched myeloid and leucocyte gene sets. Lastly, Gamma-H2A histone family member X (γ-H2AX) staining, a characteristic biomarker of DNA damage, was performed. Two COVID-19 samples produced significant γ-H2AX signals, indicating DNA damage in cardiac tissues.

Conclusions

The gene clusters altered by COVID-19 were distinct from pH1N1 influenza and mainly involved DNA damage, repair pathways, and cell cycle arrest pathways. LIG4, a DNA ligase involved in DNA repair, was significantly upregulated in COVID-19 samples, indicating that SARS-CoV-2-induced DNA damage in cardiac cells might have triggered its expression. Specific mitochondrial function- and metabolic regulation-associated gene clusters were downregulated in COVID-19 specimens. SARS-CoV-2-induced changes in mitochondrial activity might enable evasion of innate immunity mediated by mitochondria.

Overall, the study provided critical insights into the transcriptomic profiles of cardiac tissues in deceased COVID-19 subjects. However, a few limitations exist, including the restricted analysis of autopsied subjects which is unlikely to reflect the comprehensive spectrum of COVID-19, and the small sample size, particularly of the pH1N1 cohort.

*Important notice

medRxiv publishes preliminary scientific reports that are not peer-reviewed and, therefore, should not be regarded as conclusive, guide clinical practice/health-related behavior, or treated as established information.

Written by

Tarun Sai Lomte

Tarun is a writer based in Hyderabad, India. He has a Master’s degree in Biotechnology from the University of Hyderabad and is enthusiastic about scientific research. He enjoys reading research papers and literature reviews and is passionate about writing.