During SARS-CoV-2 infection, the virus transforms the infected host cell into factories that produce new viral particles. As infection progresses, the infected cells undergo numerous changes in various pathways. One of these changes is the occurrence of a cytokine storm, which leads to severe symptoms. In this study, we examined the transcriptomic changes caused by COVID-19 by analyzing RNA-seq data obtained from COVID-19-positive patients as well as COVID-19-negative donors. RNA-seq data were collected for the purpose of identification of potential biomarkers associated with a different course of the disease. We analyzed the first datasets, consisting of 96 samples to validate our methods. The objective of this publication is to report the pilot results. To explore potential biomarkers related to disease severity, we conducted a differential expression analysis of human transcriptome, focusing on COVID-19 positivity and symptom severity. Given the large number of potential biomarkers we identified, we further performed pathway enrichment analysis with terms from Kyoto Encyclopedia of Genes and Genomics (KEGG) to obtain a more profound understanding of altered pathways. Our results indicate that pathways related to immune processes, response to infection, and multiple signaling pathways were affected. These findings align with several previous studies that also reported the influence of SARS-CoV-2 infection on these pathways.

Comenius University in Bratislava Medical Faculty Institute of Medical Biology Genetics and Clinical Genetics Špitálska 24 Bratislava Slovakia

Department of Infectology and Geographical Medicine Faculty of Medicine Comenius University in Brati Slava Bratislava Slovakia

Medirex Group Academy Nitra Slovakia

Zobrazit více v PubMed

Aggarwal BB. Signalling pathways of the TNF superfamily: a double-edged sword. Nat Rev Immunol. 2003;3:745–756. doi: 10.1038/nri1184. PubMed DOI

Akimoto C, Kitagawa H, Matsumoto T, Kato S. Spermatogenesis-specific association of SMCY and MSH5. Genes Cells. 2008;13:623–633. doi: 10.1111/j.1365-2443.2008.01193.x. PubMed DOI

Al-Qahtani AA, Pantazi I, Alhamlan FS, Alothaid H, Matou-Nasri S, Sourvinos G, Vergadi E, Tsatsanis C (2022) SARS-CoV-2 modulates inflammatory responses of alveolar epithelial type II cells via PI3K/AKT pathway. Front Immunol 13. 10.3389/fimmu.2022.1020624 PubMed PMC

Andrews S (2010) FastQC: a quality control tool for high throughput sequence data. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc. Accessed 23 May 2023

Baggiolini M, Clark-Lewis I. Interleukin-8, a chemotactic and inflammatory cytokine. FEBS Lett. 1992;307:97–101. doi: 10.1016/0014-5793(92)80909-Z. PubMed DOI

Bass A, Liu Y, Dakshanamurthy S. Single-cell and bulk RNASeq profiling of COVID-19 patients reveal immune and inflammatory mechanisms of infection-induced organ damage. Viruses. 2021;13:2418. doi: 10.3390/v13122418. PubMed DOI PMC

Bolger AM, Lohse M, Usadel B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–2120. doi: 10.1093/bioinformatics/btu170. PubMed DOI PMC

Cucinotta D, Vanelli M. WHO Declares COVID-19 a Pandemic. Acta Biomed. 2020;91:157–160. PubMed PMC

Daamen AR, Bachali P, Bonham CA, Somerville L, Sturek JM, Grammer AC, Kadl A, Lipsky PE (2022) COVID-19 patients exhibit unique transcriptional signatures indicative of disease severity. Front Immunol 13. 10.3389/fimmu.2022.989556 PubMed PMC

DESeq2 manual (Accessed 23.05. 2023) (n.d.) Available Online: https://bioconductor.org/packages/devel/bioc/manuals/DESeq2/man/DESeq2.pdf

Fricke-Galindo I, Falfán-Valencia R. Genetics insight for COVID-19 susceptibility and severity: a review. Front Immunol. 2021;12:622176. doi: 10.3389/fimmu.2021.622176. PubMed DOI PMC

Hata K, Andoh A, Shimada M, Fujino S, Bamba S, Araki Y, Okuno T, Fujiyama Y, Bamba T. IL-17 stimulates inflammatory responses via NF-kappaB and MAP kinase pathways in human colonic myofibroblasts. Am J Physiol Gastrointest Liver Physiol. 2002;282(6):G1035–G1044. doi: 10.1152/ajpgi.00494.2001. PubMed DOI

Henderson LA, Canna SW, Schulert GS, Volpi S, Lee PY, Kernan KF, Caricchio R, Mahmud S, Hazen MM, Halyabar O, Hoyt KJ, Han J, Grom AA, Gattorno M, Ravelli A, Benedetti F, Behrens EM, Cron RQ, Nigrovic PA. On the alert for cytokine storm: immunopathology in COVID-19. Arthritis Rheumatol. 2020;72:1059–1063. doi: 10.1002/art.41285. PubMed DOI PMC

Hernández Borrero LJ, El-Deiry WS (2021) Tumor suppressor p53: biology, signaling pathways, and therapeutic targeting. Biochim Biophys Acta Rev Cancer 1876:188556. 10.1016/j.bbcan.2021.188556. https://github.com/bahlolab/bioinfotools/blob/master/SAMtools/flagstat.md (Accessed 23.05. 2023). (n.d.) PubMed PMC

Huang J, Hume AJ, Abo KM, Werder RB, Villacorta-Martin C, Alysandratos KD, Beermann ML, Simone-Roach C, Lindstrom-Vautrin J, Olejnik J, Suder EL, Bullitt E, Hinds A, Sharma A, Bosmann M, Wang R, Hawkins F, Burks EJ, Saeed M, Wilson AA, Mühlberger E, Kotton DN. SARS-CoV-2 infection of pluripotent stem cell-derived human lung alveolar type 2 cells elicits a rapid epithelial-intrinsic inflammatory response. Cell Stem Cell. 2020;27:962–973.e7. doi: 10.1016/j.stem.2020.09.013. PubMed DOI PMC

Jackson H, Rivero CI, Broderick C, Habgood-Coote D, D’Souza G, Nichols S, Vito O, Gómez-Rial J, Rivero-Velasco C, Rodríguez-Núñez N, Barbeito-Castiñeiras G, Pérez-Freixo H, Barreiro-de Acosta M, Cunnington AJ, Herberg JA, Wright VJ, Gómez-Carballa A, Salas A, Levin M, Martinon-Torres F, Cristina CS. Characterisation of the blood RNA host response underpinning severity in COVID-19 patients. Sci Rep. 2022;12:12216. doi: 10.1038/s41598-022-15547-2. PubMed DOI PMC

Jamison DA, Anand Narayanan S, Trovão NS, Guarnieri JW, Topper MJ, Moraes-Vieira PM, Zaksas V, Singh KK, Wurtele ES, Beheshti A. A comprehensive SARS-CoV-2 and COVID-19 review, Part 1: Intracellular overdrive for SARS-CoV-2 infection. Eur J Hum Genet. 2022;30:889–898. doi: 10.1038/s41431-022-01108-8. PubMed DOI PMC

Kawasaki T, Kawai T. Toll-like Receptor Signaling Pathways Front Immunol. 2014;5:461. doi: 10.3389/fimmu.2014.00461. PubMed DOI PMC

Kolberg L, Raudvere U, Kuzmin I, Vilo J, Peterson H (2020) gprofiler2 -- an R package for gene list functional enrichment analysis and namespace conversion toolset g:Profiler. F1000Res 9:709. 10.12688/f1000research.24956.2 PubMed PMC

Li H (2013) Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. arXiv:1303.3997v2 [q-bio.GN]

Li F, Li J, Wang PH, Yang N, Huang J, Ou J, Xu T, Zhao X, Liu T, Huang X, Wang Q, Li M, Yang L, Lin Y, Cai Y, Chen H, Zhang Q. SARS-CoV-2 spike promotes inflammation and apoptosis through autophagy by ROS-suppressed PI3K/AKT/mTOR signaling. Biochim Biophys Acta Mol Basis Dis. 2021;1867:166260. doi: 10.1016/j.bbadis.2021.166260. PubMed DOI PMC

Liao Y, Smyth GK, Shi W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. 2014;30:923–930. doi: 10.1093/bioinformatics/btt656. PubMed DOI

Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15:550. doi: 10.1186/s13059-014-0550-8. PubMed DOI PMC

Maier W, Batut B (2023) Mutation calling, viral genome reconstruction and lineage/clade assignment from SARS-CoV-2 sequencing data. Galaxy Training at training.galaxyproject.org. https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/sars-cov-2-variant-discovery/tutorial.html

Mehta P, McAuley DF, Brown M, Sanchez E, Tattersall RS, Manson JJ. COVID-19: consider cytokine storm syndromes and immunosuppression. Lancet. 2020;395:1033–1034. doi: 10.1016/S0140-6736(20)30628-0. PubMed DOI PMC

Navarro-Costa P, Plancha CE, Gonçalves J. Genetic dissection of the AZF regions of the human Y chromosome: thriller or filler for male (in)fertility? J Biomed Biotechnol. 2010;2010:1–18. doi: 10.1155/2010/936569. PubMed DOI PMC

Ng DL, Granados AC, Santos YA, Servellita V, Goldgof GM, Meydan C, Sotomayor-Gonzalez A, Levine AG, Balcerek J, Han LM, Akagi N, Truong K, Neumann NM, Nguyen DN, Bapat SP, Cheng J, Martin CS, Federman S, Foox J, Gliwa AS, Reyes K, Chao-Yang P, Guevara H, Wadford D, Miller S, Mason C, Chiu CY (2021) A diagnostic host response biosignature for COVID-19 from RNA profiling of nasal swabs and blood. Sci Adv 7:eabe5984. 10.1126/sciadv.abe5984 PubMed PMC

Oude Munnink BB, Worp N, Nieuwenhuijse DF, Sikkema RS, Haagmans B, Fouchier RAM, Koopmans M. The next phase of SARS-CoV-2 surveillance: real-time molecular epidemiology. Nat Med. 2021;27:1518–1524. doi: 10.1038/s41591-021-01472-w. PubMed DOI

Rawlings JS, Rosler KM, Harrison DA. The JAK/STAT signaling pathway. J Cell Sci. 2004;117:1281–1283. doi: 10.1242/jcs.00963. PubMed DOI

Rhoades NS, Pinski AN, Monsibais AN, Jankeel A, Doratt BM, Cinco IR, Ibraim I, Messaoudi I. Acute SARS-CoV-2 infection is associated with an increased abundance of bacterial pathogens, including Pseudomonas aeruginosa in the nose. Cell Rep. 2021;36:109637. doi: 10.1016/j.celrep.2021.109637. PubMed DOI PMC

Tan L, Wang Q, Zhang D, Ding J, Huang Q, Tang YQ, Wang Q, Miao H. Correction: Lymphopenia predicts disease severity of COVID-19: a descriptive and predictive study. Signal Transduct Target Ther. 2020;5:61. doi: 10.1038/s41392-020-0159-1. PubMed DOI PMC

Thompson RC, Simons NW, Wilkins L, Cheng E, Del Valle DM, Hoffman GE, Cervia C, Fennessy B, Mouskas K, Francoeur NJ, Johnson JS, Lepow L, Le Berichel J, Chang C, Beckmann AG, Wang Y, Nie K, Zaki N, Tuballes K, Sebra R, Merad M, Gnjatic S, Tuballes K, Barcessat V, Cedillo MA, Yuan D, Huckins L, Roussos P, Marron T, Glicksberg BS, Nadkarni G, Heath JR, Boyman O, Kim-Schulze S, Schadt EE, Charney AW, Beckmann ND. Molecular states during acute COVID-19 reveal distinct etiologies of long-term sequelae. Nat Med. 2023;29:236–246. doi: 10.1038/s41591-022-02107-4. PubMed DOI PMC

Tobon-Velasco J, Cuevas E, Torres-Ramos M. Receptor for AGEs (RAGE) as MEDIATOR of NF-kB pathway activation in neuroinflammation and oxidative stress. CNS Neurol Disord Drug Targets. 2014;13:1615–1626. doi: 10.2174/1871527313666140806144831. PubMed DOI

Wang D, Hu B, Hu C, Zhu F, Liu X, Zhang J, Wang B, Xiang H, Cheng Z, Xiong Y, Zhao Y, Li Y, Wang X, Peng Z. Clinical characteristics of 138 hospitalized patients with 2019 novel coronavirus–infected pneumonia in Wuhan, China. JAMA. 2020;323:1061–1069. doi: 10.1001/jama.2020.1585. PubMed DOI PMC

Wu F, Zhao S, Yu B, Chen YM, Wang W, Song ZG, Hu Y, Tao ZW, Tian JH, Pei YY, Yuan ML, Zhang YL, Dai FH, Liu Y, Wang QM, Zheng JJ, Xu L, Holmes EC, Zhang YZ. A new coronavirus associated with human respiratory disease in China. Nature. 2020;579:265–269. doi: 10.1038/s41586-020-2008-3. PubMed DOI PMC

York RD, Yao H, Dillon T, Ellig CL, Eckert SP, McCleskey EW, Stork PJS. Rap1 mediates sustained MAP kinase activation induced by nerve growth factor. Nature. 1998;392:622–626. doi: 10.1038/33451. PubMed DOI

Zhang YL, Wang RC, Cheng K, Ring BZ, Su L (2017) Roles of Rap1 signaling in tumor cell migration and invasion. Cancer Biol Med 14:90–99. 10.20892/j.issn.2095-3941.2016.0086 PubMed PMC

Zhu M, Liu Y, Koonpaew S, Granillo O, Zhang W. Positive and negative regulation of FcεRI-mediated signaling by the adaptor protein LAB/NTAL. J Exp Med. 2004;200:991–1000. doi: 10.1084/jem.20041223. PubMed DOI PMC