Pulmonology
Abstract
The acute respiratory distress syndrome (ARDS) results from overwhelming pulmonary inflammation. Prior bulk RNA sequencing provided limited insights into ARDS pathogenesis. We used single cell RNA sequencing to probe ARDS at a higher resolution. Peripheral blood mononuclear cells of patients with pneumonia and sepsis with early ARDS were compared to that of sepsis patients who did not develop ARDS. Monocyte clusters from ARDS patients revealed multiple distinguishing characteristics in comparison to monocytes from patients without ARDS including down-regulation of SOCS3 expression accompanied by a pro-inflammatory signature with up-regulation of multiple type I IFN-induced genes, especially in CD16+ cells. To generate an ARDS risk score, we identified up-regulation of 29 genes in the monocytes of these patients, and 17 showed a similar profile in cells of patients in independent cohorts. Monocytes had increased expression of RAB11A, known to inhibit neutrophil efferocytosis, ATP2B1, a calcium pump that exports Ca2+ implicated in endothelial barrier disruption, and SPARC, associated with processing of pro-collagen to collagen. These data show that monocytes of ARDS patients up-regulate expression of genes not just restricted to those associated with inflammation. Together, our findings identify molecules that are likely involved in ARDS pathogenesis that may inform biomarker and therapeutic development.
Authors
Yale Jiang, Brian R. Rosborough, Jie Chen, Sudipta Das, Georgios D. Kitsios, Bryan J. McVerry, Rama K. Mallampalli, Janet S. Lee, Anuradha Ray, Wei Chen, Prabir Ray
Abstract
Background Currently recommended traditional spirometry outputs do not reflect their relative contributions to airflow, and we hypothesized that machine learning algorithms can be trained on spirometry data to identify these structural phenotypes. Methods Participants enrolled in a large multicenter study (COPDGene) were included. The data points from expiratory flow-volume curves were trained using a deep learning model to predict structural phenotypes of COPD on computed tomography (CT), and results were compared with traditional spirometry metrics and an optimized random forest classifier. Area under the receiver operating characteristic curve (AUC) and weighted F-score were used to measure the discriminative accuracy of a fully convolutional neural network, Random Forest, and traditional spirometry metrics to phenotype CT as normal, emphysema-predominant (>5% emphysema), airway-predominant (Pi10>median), and mixed phenotypes. Similar comparisons were made for the detection of functional small airway disease phenotype (fSAD>20% on parametric response mapping). Results Among 8,980 individuals, neural network was more accurate in discriminating predominant emphysema/airway phenotypes (AUC 0.80, 95%CI 0.79-0.81) than traditional measures of spirometry, FEV1/FVC (AUC 0.71, 95%CI 0.69-0.71) and FEV1 %predicted (AUC 0.70, 95%CI 0.68-0.71) ), and random forest classifier (AUC 0.78, 95%CI 0.77-0.79). The neural network was also more accurate in discriminating predominant emphysema/small airway phenotypes (AUC 0.91, 95%CI 0.90-0.92) than FEV1/FVC (AUC 0.80, 95%CI 0.78-0.82), FEV1 %predicted (AUC 0.83, 95%CI 0.80-0.84), and with comparable accuracy with random forest classifier (AUC 0.90, 95%CI 0.88-0.91). Conclusions Structural phenotypes of COPD can be identified from spirometry using deep learning and machine learning approaches, demonstrating their potential to identify individuals for targeted therapies.
Authors
Sandeep Bodduluri, Arie Nakhmani, Joseph M. Reinhardt, Carla G. Wilson, Merry-Lynn N. McDonald, Ramaraju Rudraraju, Byron C Jaeger, Nirav R. Bhakta, Peter J. Castaldi, Frank C. Sciurba, Chengcui Zhang, Purushotham V. Bangalore, Surya P. Bhatt
Abstract
BACKGROUND. The numbers of fatal cases of Coronavirus Disease 2019 (COVID-19) continue to increase rapidly around the world. We aim to retrospectively investigate potential roles of factors, mainly immunologic parameters, in early predicting outcomes of patients with COVID-19. METHODS. A total of 1,018 patients confirmed COVID-19 were enrolled in our retrospective study from two centers. The data of clinical features, laboratory tests, immunological tests, radiological findings, and outcomes were collected. Univariate and multivariable logistic regression analysis were performed to evaluate factors associated with in-hospital mortality. Receiver operator characteristic (ROC) curves and survival curves were plotted to evaluate the clinical usefulness. RESULTS. Compared to the survival patients, the counts of all T lymphocytes subsets were markedly lower in non-survivors(P < 0.001), especially in CD8+ T cells (96.89 vs 203.98 cells/μl, P < 0.001) . Among all tested cytokines, IL-6 elevated most significantly with an upward trend of more than ten times (56.16 vs 5.36 pg/mL, P < 0.001). By a multivariable logistic regression analysis, two immunological indicators were found to be associated with in-hospital mortality, including IL-6 > 20 pg/mL (OR = 9.781; 95%CI, 6.304–15.174; P < 0.001) and CD8+ T cell count < 165 cells/μl (OR = 5.930; 95%CI, 3.677–9.562; P < 0.001), after adjusting confounding factors (age, gender, and underlying diseases). All the patients were divided into four groups according to levels of IL-6 and CD8+ T cells. The group with IL-6 > 20 pg/mL and CD8+ T cell count < 165 cells/μl had more old and male patients, as well as more proportion of patients with comorbidities, ventilation, ICU admission, shock, and death than those of any other group (P < 0.001). Furthermore, the ROC curve of the model combining IL-6 (>20 pg/mL) and CD8+ T cell count(<165 cells/μl) displayed more favorable discrimination than that of CURB-65 score (area under curve (AUC) = 0.907 vs 0.843, P < 0.001). Hosmer-Lemeshow test showed a good fitting of the model with no statistical significance (P = 0.581). CONCLUSIONS. We firstly identify two reliable prognostic indicators, IL-6 (>20 pg/mL) and CD8+ T cell count (<165 cells/μl), which can accurately stratify patients into risk categories and predict mortality of patients with COVID-19. Those two indicators combined may guide clinicians to evaluate patient prognosis and make appropriate decisions.
Authors
Miao Luo, Jing Liu, Weiling Jiang, Shuang Yue, Huiguo Liu, Shuang Wei
Abstract
Patients with hereditary or acquired hemolytic anemias have a high risk of developing in-situ thrombosis of the pulmonary vasculature. While pulmonary thrombosis is a major morbidity associated with hemolytic disorders, the etiological mechanism underlying hemolysis-induced pulmonary thrombosis remains largely unknown. Here, we use intravital lung microscopy in mice for the first time to assess the pathogenesis of pulmonary thrombosis following deionized-water induced acute intravascular hemolysis. Acute hemolysis triggered the development of αIIbβ3-dependent platelet-rich thrombi in precapillary pulmonary arterioles, which led to the transient impairment of pulmonary blood flow. The hemolysis-induced pulmonary thrombosis was phenocopied with intravenous ADP- but not thrombin-triggered pulmonary thrombosis. Consistent with a mechanism involving ADP release from hemolyzing erythrocytes, the inhibition of platelet-P2Y12 purinergic-receptor signaling attenuated pulmonary thrombosis and rescued blood flow in the pulmonary arterioles of mice following intravascular hemolysis. These findings are the first in vivo studies to suggest that acute intravascular hemolysis promotes ADP-dependent platelet activation leading to thrombosis in the pre-capillary pulmonary arterioles and that thrombin generation most likely does not play a significant role in the pathogenesis of acute hemolysis-triggered pulmonary thrombosis.
Authors
Tomasz Brzoska, Ravi Vats, Margaret F. Bennewitz, Egemen Tutuncuoglu, Simon C. Watkins, Margaret V. Ragni, Matthew D. Neal, Mark T. Gladwin, Prithu Sundd
Abstract
BACKGROUND. Dysregulation of L-arginine metabolism has been proposed to occur in severe asthma patients. The effects of L-arginine supplementation on L-arginine metabolite profiles in these patients is unknown. We hypothesized that severe asthmatics with low fractional exhaled nitric oxide (FeNO) would have fewer asthma exacerbations with the addition of L-arginine to their standard asthma medications compared to placebo and would demonstrate the greatest changes in metabolite profiles. METHODS. Participants were enrolled in a single-center, cross-over, double-blinded, L-arginine intervention trial at the University of California-Davis (NCT01841281). Subjects received placebo or L-arginine, dosed orally at 0.05mg/kg (ideal body weight) twice daily. The primary endpoint was moderate asthma exacerbations. Longitudinal plasma metabolite levels were measured using mass spectrometry. A linear mixed-effect model with subject-specific intercepts was used for testing treatment effects. RESULTS. A cohort of 50 subjects was included in the final analysis. L-arginine did not significantly decrease asthma exacerbations in the overall cohort. Higher citrulline levels and a lower arginine availability index (AAI) were associated with higher FeNO (P-value = 0.005 and 2.51 x 10–9 respectively). Higher AAI was associated with lower exacerbation events. The eicosanoid prostaglandin H2 (PGH2) and Nα-Acetyl-L-arginine were found to be good predictors for differentiating clinical responders and non-responders. CONCLUSIONS. There was no statistically significant decrease in asthma exacerbations in the overall cohort with L-arginine intervention. PGH2, Nα-Acetyl-L-arginine and the AAI could serve as predictive biomarkers in future clinical trials that intervene in the arginine metabolome.
Authors
Shu-Yi Liao, Megan R. Showalter, Angela L. Linderholm, Lisa M. Franzi, Celeste Kivler, Yao Li, Michael R. Sa, Zachary A. Kons, Oliver Fiehn, Lihong Qi, Amir A. Zeki, Nicholas J. Kenyon
Abstract
BACKGROUND. Severe acute respiratory coronavirus 2 (SARS-CoV-2) caused coronavirus disease 2019 (COVID-19) has become a pandemic. This study addressed the clinical and immunopathological characteristics of severe COVID-19. METHODS. Sixty-nine COVID-19 patients were classified into as severe and non-severe groups to analyze their clinical and laboratory characteristics. A panel of blood cytokines was quantified over time. Biopsy specimens from two deceased cases were obtained for immunopathological, ultrastructural, and in situ hybridization examinations. RESULTS. Circulating cytokines, including IL8, IL6, TNFα, IP10, MCP1, and RANTES, were significantly elevated in severe COVID-19 patients. Dynamic IL6 and IL8 were associated with disease progression. SARS-CoV-2 was demonstrated to infect type II, type I pneumocytes and endothelial cells, leading to severe lung damage through cell pyroptosis and apoptosis. In severe cases, lymphopenia, neutrophilia, depletion of CD4+ and CD8+ T lymphocytes, and massive macrophage and neutrophil infiltrates were observed in both blood and lung tissues. CONCLUSIONS. A panel of circulating cytokines could be used to predict disease deterioration and inform clinical interventions. Severe pulmonary damage was predominantly attributed to both SARS-CoV-2 caused cytopathy and immunopathologic damage. Strategies that encourage pulmonary recruitment and overactivation of inflammatory cells by suppressing cytokine storm might improve the outcomes of severe COVID-19 patients.
Authors
Shaohua Li, Lina Jiang, Xi Li, Fang Lin, Yijin Wang, Boan Li, Tianjun Jiang, Weimin An, Shuhong Liu, Hongyang Liu, Pengfei Xu, Lihua Zhao, Lixin Zhang, Jinsong Mu, Hongwei Wang, Jiarui Kang, Yan Li, Lei Huang, Caizhong Zhu, Shousong Zhao, Jiangyang Lu, Junsheng Ji, Jingmin Zhao
Abstract
Alveolar macrophages (AM) play a central role in initiation and resolution of lung inflammation, but the integration of these opposing core functions is poorly understood. AM expression of cholesterol-25-hydroxylase (CH25H), the primary biosynthetic enzyme for 25-hydroxycholesterol (25HC), far exceeds that of macrophages in other tissues, but no role for CH25H has been defined in lung biology. As 25HC is an agonist for the anti-inflammatory nuclear receptor, Liver X Receptor (LXR), we speculated that CH25H might regulate inflammatory homeostasis in the lung. Here, we show that, of natural (oxy)sterols, 25HC is uniquely induced in the inflamed lung of mice and humans. Ch25h-/- mice fail to induce 25HC and LXR target genes in the lung after LPS inhalation and exhibit delayed resolution of airway neutrophilia which can be rescued by systemic treatment with either 25HC or synthetic LXR agonists. LXR-null mice also display delayed resolution, suggesting that native oxysterols promote resolution. During resolution, Ch25h is induced in macrophages upon their encounter with apoptotic cells and is required for LXR-dependent prevention of AM lipid overload, induction of Mertk, efferocytic resolution of airway neutrophilia, and induction of TGFb. CH25H/25HC/LXR is thus an inducible metabolic axis that programs AMs for efferocytic resolution of inflammation.
Authors
Jennifer H. Madenspacher, Eric D. Morrell, Kymberly M. Gowdy, Jeffrey G. McDonald, Bonne M. Thompson, Ginger W. Muse, Jennifer Martinez, Seddon Y. Thomas, Carmen Mikacenic, Jerry A. Nick, Edward Abraham, Stavros Garantziotis, Renee D. Stapleton, Julie M. Meacham, Mary Jane Thomassen, William J. Janssen, Donald N. Cook, Mark M. Wurfel, Michael B. Fessler
Abstract
Although aging represents the most important epidemiologic risk factor for fibrotic disease, the reasons for this are incompletely understood. Excess collagen deposition in tissues is the sine qua non of tissue fibrosis and can be viewed as an imbalance between collagen production and collagen degradation. Yet we still lack a detailed understanding of the changes that take place during development, maturation and aging in extracellular-matrix (ECM) dynamics. Resolution of fibrosis is impaired in aging and this impairment may explain why age is the most important risk factor for fibrotic diseases such as Idiopathic Pulmonary Fibrosis. However, ECM dynamics and impaired resolution of fibrosis in aging remain understudied. Here we show that cell-mediated collagen uptake and degradation are diminished in aged animals and this finding correlates with downregulation of the collagen endocytic receptor Mrc2. We identify Myeloid Zinc Finger-1 as a novel transcriptional regulator of Mrc2 and both this transcription factor and Mrc2 are downregulated in multiple tissues and organisms in an age-dependent manner. Thus, cell-mediated degradation of collagen is an essential process that promotes resolution of fibrosis and impairment in this process contributes to age-related fibrosis.
Authors
Michael J. Podolsky, Christopher D. Yang, Carlos Lizama, Ritwik Datta, Steven K. Huang, Stephen L. Nishimura, Sarah L. Dallas, Paul Wolters, Claude Jourdan Le Saux, Kamran Atabai
Abstract
Infections due to carbapenem-resistant Klebsiella pneumoniae have emerged as a global threat due to its wide-spread antimicrobial resistance. Transplant recipients and patients with hematologic malignancies have high mortality rate suggesting host factors in susceptibility. We developed a model of pulmonary infection using ST258 C4, KPC-2 clone, which are predominant Klebsiella pneumoniae carbapenemase (KPC)-producing bacteria, and demonstrated that Rag2-/-Il2rg-/- mice, but not wildtype C57BL/6 or Rag2-/- mice, were susceptible to this opportunistic infection. Using single-cell RNA-seq in infected Rag2-/- mice, we identified distinct clusters of Ifng+ NK cells and Il17a+, Il22+, and inducible T-cell costimulatory molecule (ICOS)+ group 3 innate lymphoid cells (ILCs) that were critical for host resistance. As solid organ transplantation is a risk factor, we generated a more clinically relevant model using FK506 in wildtype C57BL/6 mice. We further demonstrated that immunotherapy with recombinant IL-22 treatment ameliorated the ST258 pulmonary infection in both FK506 treated WT mice and Rag2-/-Il2rg-/- mice via hepatic IL-22ra1 signaling. These data support the development of host directed immunotherapy as an adjunct treatment to new antibiotics.
Authors
Naoki Iwanaga, Ivy Sandquist, Alanna Wanek, Janet E. McCombs, Kejing Song, Jay Kolls
Abstract
Abnormal wound repair has been observed in the airway epithelium of patients with chronic respiratory diseases including asthma. Therapies focusing on repairing vulnerable airways, particularly in early life, present an extremely novel treatment strategy. We report defective lower airway epithelial cell repair to strongly associate with common pre-school and school-aged wheezing phenotypes, characterised by aberrant migration patterns and reduced α5β1 integrin expression. Next generation sequencing identified the PI3K/Akt pathway as the top upstream transcriptional regulator of α5β1 integrin, where Akt activation enhanced repair and α5β1 integrin expression in primary cultures from children with wheeze. Conversely, inhibition of PI3K/Akt signaling in primary cultures from children without wheeze reduced α5β1 expression and attenuated repair. Importantly, the FDA-approved drug celecoxib, and its non-COX2-inhibiting analogue dimethyl-celecoxib, stimulated the PI3K/Akt-integrin α5β1 axis and restored airway epithelial repair in cells from children with wheeze. When compared with published clinical datasets the identified transcriptomic signature was also associated with viral-induced wheeze exacerbations highlighting the clinical potential of such therapy. Collectively, these results identify airway epithelial restitution via targeting the PI3K/Akt-integrin axis as a novel therapeutic avenue for childhood wheeze and asthma. We propose that the next step in the therapeutic development process should be a proof-of-concept clinical trial since relevant animal models to test the crucial underlying premise are unavailable.
Authors
Thomas Iosifidis, Erika N. Sutanto, Alysia Buckley, Laura A. Coleman, Erin E. Gill, Amy H. Lee, Kak-Ming Ling, Jessica Hillas, Kevin Looi, Luke W. Garratt, Kelly M. Martinovich, Nicole C. Shaw, Samuel T. Montgomery, Elizabeth Kicic-Starcevich, Yuliya V. Karpievitch, Peter Le Souef, Ingrid A. Laing, Shyan Vijayasekaran, Francis J. Lannigan, Paul J. Rigby, Robert E.W. Hancock, Darryl Knight, Stephen M. Stick, Anthony Kicic, on behalf of WAERP, on behalf of AusREC
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