2,390
Views
6
CrossRef citations to date
0
Altmetric
Research Paper

Predicting candidate therapeutic drugs for sepsis-induced acute respiratory distress syndrome based on transcriptome profiling

, , , ORCID Icon &
Pages 1369-1380 | Received 24 Feb 2021, Accepted 12 Apr 2021, Published online: 27 Apr 2021

References

  • Peck TJ, Hibbert KA Recent advances in the understanding and management of ARDS. F1000Res 2019; 8.
  • Nick JA, Caceres SM, Kret JE, et al. Extremes of interferon-stimulated gene expression associate with worse outcomes in the acute respiratory distress syndrome. PLoS One. 2016;11(9):e0162490.
  • Zimmerman JJ, Akhtar SR, Caldwell E, et al. Incidence and Outcomes of Pediatric Acute Lung Injury. Pediatrics. 2009;124(1):87–95.
  • Wang M, Yan JJ, He XX, et al. Candidate genes and pathogenesis investigation for sepsis-related acute respiratory distress syndrome based on gene expression profile. Biol Res. 2016;49:25-33.
  • Hussain M, Xu C, Ahmad M, et al. Acute respiratory distress syndrome: bench-to-bedside approaches to improve drug development. Clin Pharmacol Ther. 2018;104(3):484–494.
  • Hurford WE. Neuromuscular Blockade Applicability in Early Acute Respiratory Distress Syndrome. Anesthesiology. 2020;132(6):1577–1584.
  • Pont MJ, Honders MW, Kremer AN, et al. Microarray gene expression analysis to evaluate cell type specific expression of targets relevant for immunotherapy of hematological malignancies. PLoS One. 2016;11(5):e0155165.
  • Kangelaris KN, Prakash A, Liu KD, et al. Increased expression of neutrophil-related genes in patients with early sepsis-induced ARDS. Am J Physiol Lung Cell Mol Physiol. 2015;308(11):L1102–13.
  • Jiang Y, Rosborough BR, Chen J, et al. Single cell RNA sequencing identifies an early monocyte gene signature in acute respiratory distress syndrome. JCI Insight. 2020;5:13.
  • Dolinay T, Kim YS, Howrylak J, et al. Inflammasome-regulated cytokines are critical mediators of acute lung injury. Am J Respir Crit Care Med. 2012;185(11):1225–1234. .
  • Robinson MD, McCarthy DJ, Smyth GK. edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics. 2010;26(1):139–140.
  • Sherman BT, Huang Da W, Tan Q, et al. DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis. BMC Bioinformatics. 2007;8(1):426. .
  • Subramanian A, Tamayo P, Mootha VK, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005;102(43):15545–15550. .
  • Von Mering C. STRING: a database of predicted functional associations between proteins. Nucleic Acids Res. 2003;31(1):258–261.
  • Xu L, He X, Zhou Y, et al. Connectivity map analysis identifies fisetin as a treatment compound for osteoporosis through activating the PI3K-AKT signaling pathway in mouse pre-osteoblastic MC3T3-E1 cells. Curr Pharm Biotechnol. 2021;22. DOI:10.2174/1389201022666210301141238.
  • Cao J, Duan Y, Liu Y, et al. Metabolomics coupled with SystemsDock reveal the protective effect and the potential active components of Naozhenning granule against traumatic brain injury. J Ethnopharmacol. 2021;22:112247.
  • Stables MJ, Newson J, Ayoub SS, et al. Priming innate immune responses to infection by cyclooxygenase inhibition kills antibiotic-susceptible and -resistant bacteria. Blood. 2010;116(16):2950–2959.
  • Westman EL, Canova MJ, Radhi IJ, et al. Bacterial inactivation of the anticancer drug doxorubicin. Chem Biol. 2012;19(10):1255–1264. .
  • Fischer N, Sechet E, Friedman R, et al. Histone deacetylase inhibition enhances antimicrobial peptide but not inflammatory cytokine expression upon bacterial challenge. Proc Natl Acad Sci U S A. 2016;113(21):E2993–3001. .
  • Ashbaugh DG, Bigelow DB, Petty TL, et al. Acute respiratory distress in adults. Lancet. 1967;2(7511):319–323.
  • Brun-Buisson C, Minelli C, Bertolini G. et al. Epidemiology and outcome of acute lung injury in European intensive care units. Results from the ALIVE study. Intensive Care Med. 2004;30(1):51–61.
  • Maybauer MO, Maybauer DM, Herndon DN. Incidence and outcomes of acute lung injury. N Engl J Med. 2006;354(4): 416–417. author reply −7.
  • Wang R, Sun B, Li X, et al. Mechanical ventilation strategy guided by transpulmonary pressure in severe acute respiratory distress syndrome treated with venovenous extracorporeal membrane oxygenation. Crit Care Med. 2020;48(9):1280–1288.
  • Villar J, Blanco J, Anon JM, et al. The ALIEN study: incidence and outcome of acute respiratory distress syndrome in the era of lung protective ventilation. Intens Care Med. 2011;37(12):1932–1941.
  • Batah SS, Fabro AT. Pulmonary pathology of ARDS in COVID-19: a pathological review for clinicians. Respir Med. 2021;176:106239.
  • Rosborough BR, Chen J, Jiang YL, et al. Single cell RNA sequencing reveals novel inflammatory mechanisms of human acute respiratory distress syndrome. J Immunol. 2020;204:1.
  • Englert JA, Cho MH, Lamb AE, et al. Whole blood RNA sequencing reveals a unique transcriptomic profile in patients with ARDS following hematopoietic stem cell transplantation. Respir Res. 2019;20(1):15.
  • Yu XA, Davenport JW, Urtishak KA, et al. Genome-wide TOP2A DNA cleavage is biased toward translocated and highly transcribed loci. Genome Res. 2017;27(7):1238–1249.
  • Morimoto S, Tsuda M, Bunch H, et al. II DNA topoisomerases cause spontaneous double-strand breaks in Genomic DNA. Genes Basel. 2019;10:11.
  • Heintzman DR, Campos LV, Byl JAW, et al. Topoisomerase II Is Crucial for Fork Convergence during Vertebrate Replication Termination. Cell Rep. 2019;29(2):422.
  • Sharma S, Aldred MA, Damage DNA. Repair in pulmonary arterial hypertension. Genes-Basel. 2020;11(10): 1224-1241.
  • Da Silva Sergio LP, Mencalha AL, De Souza Da Fonseca A, et al. DNA repair and genomic stability in lungs affected by acute injury. Biomed Pharmacother. 2019;119:109412.
  • Yang X, Kui L, Tang M, et al. High-throughput transcriptome profiling in drug and biomarker discovery. Front Genet. 2020;11:19.
  • Huang CT, Hsieh CH, Chung YH, et al. Perturbational gene-expression signatures for combinatorial drug discovery. iScience. 2019;15:291–306.
  • Lamb J. The connectivity map: a new tool for biomedical research. Nat Rev Cancer. 2007;7(1):54–60.
  • Qu XA, Rajpal DK. Applications of connectivity map in drug discovery and development. Drug Discov Today. 2012;17(23–24):1289–1298.
  • Skok Z, Zidar N, Kikelj D, et al. Dual inhibitors of human DNA topoisomerase II and other cancer-related targets. J Med Chem. 2020;63(3):884–904.