Evolution of multiple omics approaches to define pathophysiology of pediatric acute respiratory distress syndrome

Abstract

Pediatric acute respiratory distress syndrome (PARDS), though both common and deadly in critically ill children, lacks targeted therapies. The development of effective pharmacotherapies has been limited, in part, by lack of clarity about the pathobiology of pediatric ARDS. Epithelial lung injury, vascular endothelial activation, and systemic immune activation are putative drivers of this complex disease process. Prior studies have used either hypothesis-driven (e.g., candidate genes and proteins, in vitro investigations) or unbiased (e.g., genome-wide association, transcriptomic, metabolomic) approaches to predict clinical outcomes and to define subphenotypes. Advances in multiple omics technologies, including genomics, transcriptomics, proteomics, and metabolomics, have permitted more comprehensive investigation of PARDS pathobiology. However, omics studies have been limited in children compared to adults, and analyses across multiple tissue types are lacking. Here, we synthesized existing literature on the molecular mechanism of PARDS, summarized our interrogation of publicly available genomic databases to determine the association of candidate genes with PARDS phenotypes across multiple tissues and cell types, and integrated recent studies that used single-cell RNA sequencing (scRNA-seq). We conclude that novel profiling methods such as scRNA-seq, which permits more comprehensive, unbiased evaluation of pathophysiological mechanisms across tissue and cell types, should be employed to investigate the molecular mechanisms of PRDS toward the goal of identifying targeted therapies.

Keywords: acute respiratory distress syndrome; biomarker; genetics; genomics; medicine; pediatrics; single-cell profiling.

Figure 1.. The relationships between ARDS candidate genes and phenotypes reported by genome-wide association studies.

The nodes (circles) represent genes (light gray, gene symbols not italicized) or phenotypes (dark gray), and the associated genotype–phenotype pairs are connected by curved lines. For clear visualization, the original phenotypes reported by individual studies were simplified (Supplementary file 2). Node size is proportional to reported number of genotype–phenotype associations. The biological characteristics of ARDS, including pulmonary inflammation, systemic inflammation, and vascular endothelial activation, are associated with multiple candidate genes for ARDS. Abbreviations: ACE = angiotensin I-converting enzyme; AGER = advanced glycosylation end product-specific receptor; AGT = angiotensin; ANGPT = angiopoietin; ARDS = acute respiratory distress syndrome; CARMIL1 = capping protein regulator and myosin 1 linker 1; CFTR = cystic fibrosis transmembrane conductance regulator; CXCL8 = C-X-C motif chemokine ligand; EPAS1 = endothelial PAS domain protein 1; FER = feline encephalitis virus-related tyrosine kinase; FLT1 = fms-related receptor tyrosine kinase 1; HSPG = heparan sulfate proteoglycan; IL = interleukin; KLK2 = kallikrein-related peptidase 2; SFTP = surfactant protein; LTA = lymphotoxin alpha; MAP3K1 = mitogen-activated protein kinase 1; MBL = mannose binding lectin; NFE2L2 = nuclear factor, erythroid-like, BZIP transcription factor 2; PPFIA = protein tyrosine phosphatase receptor type F interacting protein alpha; SELP = selectin P; THBD = thrombomodulin; TNF = tumor necrosis factor; VCAM1 = vascular cell adhesion molecule 1; VEGFA = vascular endothelial growth factor A; vWF = von Willebrand Factor.

Figure 2.. Phases of ARDS pathogenesis.

Panel A shows alveolar–capillary interface in a state of good health. Panels B, C, and D, respectively, show the three phases of ARDS development with candidate biomarkers indicated by cell type. Candidate biomarkers indicate dysregulation following a physiologic insult with transition from (A) health to (B) exudative, (C) proliferative, and (D) fibrotic phases of illness. Patients may present to care in different phases of ARDS development, may progress through phases at different rates, and biology differ depending on cause of ARDS and patient age. Figure was created using Biorender.com. Abbreviations: ACE = angiotensin-converting enzyme; ANG1/ANGPT1 = angiopoietin 1; ANG2/ANGPT2 = angiopoietin 2; ARDS = acute respiratory distress syndrome; AT1 = type I alveolar cell; AT2 = type II alveolar cell; EGF = epidermal growth factor; GM-CSF = granulocyte-macrophage colony-stimulating factor; HGF = hepatocyte growth factor; IGF = insulin like growth factor; IL-1β = interleukin 1 beta; IL-6 = interleukin 6; IL-8 = interleukin 8; IRF4 = interferon regulatory factor 4; KGF = keratinocyte growth factor; M1 = type I macrophage; M2 = type II macrophage; NAMPT = nicotinamide phosphoribosyltransferase; NET = neutrophil extracellular trap; PAI1 = plasminogen activator inhibitor type 1; PBEF = pre-B-cell colony-enhancing factor; PDGF = platelet-derived growth factor; PROC = protein C, inactivator of coagulation factors Va and VIIIa; RAGE = receptor for advanced glycation end-products; SERPINE1 = serpin family E member 1; SFTPB = surfactant protein B; sICAM/ICAM1 = intercellular adhesion molecule 1; SPB = surfactant-associated protein B; SPD = surfactant-associated protein D; STAT6 = signal transducer and activator of transcription 6; sTM = soluble thrombomodulin; TGF-β = transforming growth factor beta; THBD = thrombomodulin; TIE2 (TEK) = tyrosine kinase with immunoglobulin- and EGF-like domains 1; TNF = tumor necrosis factor; VEGF/VEGFA = vascular endothelial growth factor A; vWF = von Willebrand Factor.

Figure 3.. Cell type-specific expression pattern of ARDS candidate genes.

Relative expression levels of ARDS candidate genes are shown across cell types from lung autopsy sample from ARDS caused by COVID-19 (A) and peripheral blood mononuclear cells a generally heathy individual (B). Expression levels are scaled to show relative levels across all cell types from 0 (blue) to 1 (red). The size of circle is proportional to the cells expressing a gene for each cell type (from 0% to 75%). AT1 and AT2: alveolar type I and II cells; FB: fibroblasts; ECM-high: high expression of extracellular matrix components (i.e., COL6A3, COL1A2, and COL3A1); MDM: monocyte-derived macrophages. Source data for this figure are provided in a table, Figure 3—source data 1.

Figure 4.. Multi-omics approaches to define endotypes of pediatric acute respiratory distress syndrome (PARDS).

Investigational methods, including hypothesis-driven and unbiased investigations, have led to discovery of multiple contributions to ARDS pathobiology, including systemic inflammation, endothelial activation, and alveolar injury. These processes affect diverse cell and tissue types, including lymphocytes, macrophages, neutrophils, vascular endothelial cells, and two types of alveolar cells. The degree of systemic inflammation, endothelial activation, and alveolar injury across cell and tissue types has helped to define ARDS endotypes, which have been differentially associated with relevant clinical outcomes, including the development of ARDS in patients who have experienced clinical risk factors for the disease, mortality, and long-term morbidity from ARDS. Names of proteins implicated in PARDS as opposed to adult ARDS are depicted in red. Figure was created using Biorender.com. Abbreviations: ACE = angiotensin-converting enzyme; ANGPT1, -2 = angiopoietin 1, 2; CCL3 = C-C motif chemokine ligand 3; ESM1 = endothelial cell-specific molecule 1; FLT1 = fms-related receptor tyrosine kinase 1; GM-CSF = granulocyte-macrophage colony-stimulating factor; HGF = hepatocyte growth factor; HSPA1b = heat shock protein family A (Hsp70) member 1B; IL- = interleukin-; IRF4 = interferon regulatory factor 4; KGF = keratinocyte growth factor; LTA = lymphotoxin alpha; M0, M1, M2 = type 0, I, II macrophage; NAMPT = nicotinamide phosphoribosyltransferase; NET = neutrophil extracellular trap; SERPINE1 = serpin family E member 1; STAT1, -6 = signal transducer and activator of transcription-1,6; TGF-β = transforming growth factor beta; THBD = thrombomodulin; TIE2 = tyrosine kinase with immunoglobulin like and EGF like domains 1; VCAM1 = vascular cell adhesion molecule 1; VEGF = vascular endothelial growth factor A; vWF = von Willebrand Factor.