235
Views
0
CrossRef citations to date
0
Altmetric
ORIGINAL RESEARCH

Single-Cell RNA Sequencing and Transcriptome Analysis Revealed the Immune Microenvironment and Gene Markers of Acute Respiratory Distress Syndrome

, ORCID Icon, , , , , , , , & show all
Pages 3205-3217 | Received 18 May 2023, Accepted 27 Jul 2023, Published online: 01 Aug 2023

References

  • Sinha P, Bos LD. Pathophysiology of the acute respiratory distress syndrome: insights from clinical studies. Crit Care Clin. 2021;37(4):795–815. doi:10.1016/j.ccc.2021.05.005
  • Zhang J, Luo Y, Wang X, et al. Global transcriptional regulation of STAT3- and MYC-mediated sepsis-induced ARDS. Ther Adv Respir Dis. 2019;13:1753466619879840.
  • Zheng X, Luo Y, Li Q, et al. Two gene set variation index as biomarker of bacterial and fungal sepsis. Biomed Res Int. 2020;2020:8182358. doi:10.1155/2020/8182358
  • Zhang Q, Wang Y, Qu D, Yu J, Yang J. Role of HDAC6 inhibition in sepsis-induced acute respiratory distress syndrome (Review). Exp Ther Med. 2021;21(5):422. doi:10.3892/etm.2021.9866
  • Bellani G, Laffey JG, Pham T, et al. Epidemiology, patterns of care, and mortality for patients with acute respiratory distress syndrome in intensive care units in 50 countries. JAMA. 2016;315(8):788–800. doi:10.1001/jama.2016.0291
  • Ming T, Dong M, Song X, et al. Integrated analysis of gene co-expression network and prediction model indicates immune-related roles of the identified biomarkers in sepsis and sepsis-induced acute respiratory distress syndrome. Front Immunol. 2022;13:897390. doi:10.3389/fimmu.2022.897390
  • Lu J, Li Q, Wu Z, et al. Two gene set variation indexes as potential diagnostic tool for sepsis. Am J Transl Res. 2020;12(6):2749–2759.
  • Feng J, Pang J, He D, et al. Identification of genes with altered methylation and its role in early diagnosis of sepsis-induced acute respiratory distress syndrome. Int J Gen Med. 2021;14:243–253. doi:10.2147/IJGM.S287960
  • Gragossian A, Siuba MT. Acute respiratory distress syndrome. Emerg Med Clin North Am. 2022;40(3):459–472. doi:10.1016/j.emc.2022.05.002
  • Hu Q, Hao C, Tang S. From sepsis to acute respiratory distress syndrome (ARDS): emerging preventive strategies based on molecular and genetic researches. Biosci Rep. 2020;40(5). doi:10.1042/BSR20200830
  • Meyer NJ, Gattinoni L, Calfee CS. Acute respiratory distress syndrome. Lancet. 2021;398(10300):622–637. doi:10.1016/S0140-6736(21)00439-6
  • Feng K, Huang W, Shang J, et al. Knockdown of lncRNA-ASLNC12002 alleviates epithelial-mesenchymal transition of type II alveolar epithelial cells in sepsis-induced acute respiratory distress syndrome. Hum Cell. 2023;36(2):568–582. doi:10.1007/s13577-022-00837-8
  • Quinton LJ, Walkey AJ, Mizgerd JP. Integrative physiology of pneumonia. Physiol Rev. 2018;98(3):1417–1464. doi:10.1152/physrev.00032.2017
  • Swenson KE, Swenson ER. Pathophysiology of acute respiratory distress syndrome and COVID-19 lung injury. Crit Care Clin. 2021;37(4):749–776. doi:10.1016/j.ccc.2021.05.003
  • Lu J, Zeng X, Lu W, et al. Documenting the immune response in patients with COVID-19-induced acute respiratory distress syndrome. Front Cell Dev Biol. 2023;11:633. doi:10.3389/fcell.2023.1207960
  • Huang J, Wang B, Tao S, et al. D-tagatose protects against oleic acid-induced acute respiratory distress syndrome in rats by activating PTEN/PI3K/AKT pathway. Front Immunol. 2022;13:928312. doi:10.3389/fimmu.2022.928312
  • Lu J, Lv S, Pang J, et al. M2c macrophages protect mice from adriamycin-induced nephropathy by upregulating CD62L in tregs. Mediators Inflamm. 2022;2022:1153300. doi:10.1155/2022/1153300
  • Liu Z, Liu D, Wang Z, et al. Association between inflammatory biomarkers and acute respiratory distress syndrome or acute lung injury risk: a systematic review and meta-analysis. Wien Klin Wochenschr. 2022;134(1–2):24–38. doi:10.1007/s00508-021-01971-3
  • Battaglini D, Al-Husinat L, Normando AG, et al. Personalized medicine using omics approaches in acute respiratory distress syndrome to identify biological phenotypes. Respir Res. 2022;23(1):318. doi:10.1186/s12931-022-02233-0
  • 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). doi:10.1172/jci.insight.135678
  • Panda R, Castanheira FV, Schlechte JM, et al. A functionally distinct neutrophil landscape in severe COVID-19 reveals opportunities for adjunctive therapies. JCI Insight. 2022;7(2). doi:10.1172/jci.insight.152291
  • Mo J, Yang Y, Feng J, et al. Single-cell analysis reveals dysregulated inflammatory response in peripheral blood immunity in patients with acute respiratory distress syndrome. Front Cell Dev Biol. 2023;11:1199122. doi:10.3389/fcell.2023.1199122
  • Pont F, Tosolini M, Fournie JJ. Single-Cell Signature Explorer for comprehensive visualization of single cell signatures across scRNA-seq datasets. Nucleic Acids Res. 2019;47(21):e133.
  • Trapnell C, Cacchiarelli D, Grimsby J, et al. The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells. Nat Biotechnol. 2014;32(4):381–386. doi:10.1038/nbt.2859
  • Ritchie ME, Phipson B, Wu D, et al. limma powers differential expression analyses for RNA-sequencing and microarray studies. Nucleic Acids Res. 2015;43(7):e47. doi:10.1093/nar/gkv007
  • Wu T, Hu E, Xu S, et al. clusterProfiler 4.0: a universal enrichment tool for interpreting omics data. Innovation. 2021;2(3):100141. doi:10.1016/j.xinn.2021.100141
  • Williams JG, Joshi R, Haslam D, et al. Multi-omic characterization of pediatric ARDS via nasal brushings. Respir Res. 2022;23(1):181. doi:10.1186/s12931-022-02098-3
  • Robin X, Turck N, Hainard A, Tiberti N, Lisacek F, Sanchez JC, Muller M. pROC: an open-source package for R and S+ to analyze and compare ROC curves. BMC Bioinform. 2011;12(1):77. doi:10.1186/1471-2105-12-77
  • Hanzelmann S, Castelo R, Guinney J. GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinform. 2013;14:7. doi:10.1186/1471-2105-14-7
  • Zeng X, Feng J, Yang Y, et al. Screening of key genes of sepsis and septic shock using bioinformatics analysis. J Inflamm Res. 2021;14:829–841. doi:10.2147/JIR.S301663
  • Zhao C, Mo J, Zheng X, et al. Identification of an alveolar macrophage-related core gene set in acute respiratory distress syndrome. J Inflamm Res. 2021;14:2353–2361. doi:10.2147/JIR.S306136
  • Sinha S, Rosin NL, Arora R, et al. Dexamethasone modulates immature neutrophils and interferon programming in severe COVID-19. Nat Med. 2022;28(1):201–211. doi:10.1038/s41591-021-01576-3
  • Zingaropoli MA, Nijhawan P, Carraro A, et al. Increased sCD163 and sCD14 plasmatic levels and depletion of peripheral blood pro-inflammatory monocytes, myeloid and plasmacytoid dendritic cells in patients with severe COVID-19 pneumonia. Front Immunol. 2021;12:627548. doi:10.3389/fimmu.2021.627548
  • Jimenez-Duran G, Luque-Martin R, Patel M, et al. Pharmacological validation of targets regulating CD14 during macrophage differentiation. EBioMedicine. 2020;61:103039. doi:10.1016/j.ebiom.2020.103039
  • Roussel M, Ferrant J, Reizine F, et al. Comparative immune profiling of acute respiratory distress syndrome patients with or without SARS-CoV-2 infection. Cell Rep Med. 2021;2(6):100291. doi:10.1016/j.xcrm.2021.100291
  • Mahida RY, Price J, Lugg ST, et al. CD14-positive extracellular vesicles in bronchoalveolar lavage fluid as a new biomarker of acute respiratory distress syndrome. Am J Physiol Lung Cell Mol Physiol. 2022;322(4):L617–L624. doi:10.1152/ajplung.00052.2022
  • Zhu G, Liu Y, Zhang W, Huang Y, Li K. CD27(+)TIM-1(+) memory B cells promoted the development of Foxp3(+) Tregs and were associated with better survival in acute respiratory distress syndrome. Immunol Res. 2018;66(2):281–287. doi:10.1007/s12026-017-8983-2
  • Ramaswamy A, Brodsky NN, Sumida TS, et al. Immune dysregulation and autoreactivity correlate with disease severity in SARS-CoV-2-associated multisystem inflammatory syndrome in children. Immunity. 2021;54(5):1083–1095 e1087. doi:10.1016/j.immuni.2021.04.003
  • Torres M, Casado G, Vigon L, et al. Changes in the immune response against SARS-CoV-2 in individuals with severe COVID-19 treated with high dose of vitamin D. Biomed Pharmacother. 2022;150:112965. doi:10.1016/j.biopha.2022.112965
  • Mallis P, Michalopoulos E, Chatzistamatiou T, Stavropoulos-Giokas C. Mesenchymal stromal cells as potential immunomodulatory players in severe acute respiratory distress syndrome induced by SARS-CoV-2 infection. World J Stem Cells. 2020;12(8):731–751. doi:10.4252/wjsc.v12.i8.731
  • Yao C, Bora SA, Parimon T, et al. Cell-type-specific immune dysregulation in severely ill COVID-19 patients. Cell Rep. 2021;34(1):108590. doi:10.1016/j.celrep.2020.108590
  • Lu Q, Yu S, Meng X, et al. MicroRNAs: important regulatory molecules in acute lung injury/acute respiratory distress syndrome. Int J Mol Sci. 2022;23(10):5545.
  • Pryzdial ELG, Leatherdale A, Conway EM. Coagulation and complement: key innate defense participants in a seamless web. Front Immunol. 2022;13:918775. doi:10.3389/fimmu.2022.918775
  • Noureen N, Ye Z, Chen Y, Wang X, Zheng S. Signature-scoring methods developed for bulk samples are not adequate for cancer single-cell RNA sequencing data. Elife. 2022;11:e71994.
  • 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–L1113. doi:10.1152/ajplung.00380.2014
  • Qu M, Zhang H, Chen Z, et al. The role of ferroptosis in acute respiratory distress syndrome. Front Med. 2021;8:651552. doi:10.3389/fmed.2021.651552