Pulmonology
Abstract
Relatively little is known about interactions between the airway microbiome and airway host transcriptome in asthma. Since asthma affects and is affected by the entire airway, studying the upper (e.g., nasal) and lower (e.g., bronchial) airways together represents a powerful approach to understanding asthma. Here, we performed a systematic, integrative study of the nasal and bronchial microbiomes and nasal and bronchial host transcriptomes of children with severe persistent asthma and healthy controls. We found that (a) the microbiomes and host transcriptomes of asthmatic children are each distinct by site (nasal versus bronchial); (b) among asthmatic children, Moraxella and Alloiococcus are hub genera in the nasal microbiome, while there are no hubs among bronchial genera; (c) bronchial Actinomyces is negatively associated with bronchial genes for inflammation, suggesting Actinomyces may be protective; (d) compared with healthy children, asthmatic children express more nasal genes for ciliary function and harbor more nasal Streptococcus; and (e) nasal genera such as Corynebacterium are negatively associated with significantly more nasal genes for inflammation in healthy versus asthmatic children, suggesting a potentially stronger protective role for such nasal genera in healthy versus asthmatic children. Our systematic, integrative study provides a window into host-microbiome associations in asthma.
Authors
Yoojin Chun, Anh Do, Galina Grishina, Alexander Grishin, Gang Fang, Samantha Rose, Chantal Spencer, Alfin Vicencio, Eric Schadt, Supinda Bunyavanich
Abstract
Recent studies have presented compelling evidence that it is not tissue-resident, but rather monocyte-derived alveolar macrophages (TR-AMs vs. Mo-AMs) are essential to development of experimental lung fibrosis. However, whether Apolipoprotein E (ApoE), which is produced abundantly by Mo-AMs in the lung, plays a role in the pathogenesis is unclear. In this study, we found that pulmonary ApoE was almost exclusively produced by Mo-AMs in mice with bleomycin induced lung fibrosis. We showed although ApoE was not necessary for developing maximal fibrosis in bleomycin injured lung, it was required for the resolution of this pathology. We found that ApoE directly bound to Collagen I and mediated Collagen I phagocytosis in vitro and in vivo, and this process was dependent on low density lipoprotein receptor-related protein 1 (LPR1). Furthermore, interference of ApoE/LRP1 interaction impaired the resolution of lung fibrosis in bleomycin treated wild-type mice. In contrast, supplementation of ApoE promoted this process in ApoE–/– animals. In conclusion, Mo-AM derived ApoE is beneficial to the resolution of lung fibrosis, supporting the notion that Mo-AMs may have distinct functions in different phases of lung fibrogenesis. The findings also suggest a novel therapeutic target for treating lung fibrosis, to which effective remedies remain scarce.
Authors
Huachun Cui, Dingyuan Jiang, Sami Banerjee, Na Xie, Tejaswini Kulkarni, Rui-Ming Liu, Steven R. Duncan, Gang Liu
Abstract
Our integrative genomic and functional analysis identified transforming acidic coiled-coil–containing protein 2 (TACC2) as a chronic obstructive pulmonary disease (COPD) candidate gene. Here, we found that smokers with COPD exhibit a marked decrease in lung TACC2 protein levels relative to smokers without COPD. Single cell RNA sequencing reveals that TACC2 is expressed primarily in lung epithelial cells in normal human lungs. Furthermore, suppression of TACC2 expression impairs the efficiency of homologous recombination repair and augments spontaneous and cigarette smoke extract–induced (CSE-induced) DNA damage and cytotoxicity in immortalized human bronchial epithelial cells. By contrast, enforced expression of TACC2 attenuates the CSE effects. We also found that CSE enhances TACC2 degradation via the ubiquitin-proteasome system mediated by the ubiquitin E3 ligase subunit, F box L7. Furthermore, cellularly expressed TACC2 proteins harboring naturally occurring mutations exhibited altered protein lifespan coupled with modified DNA damage repair and cytotoxic responses. CS triggers emphysematous changes accompanied by accumulated DNA damage, apoptosis of alveolar epithelia, and lung inflammation in Tacc2–/– compared with Tacc2+/+ mice. Our results suggest that CS destabilizes TACC2 protein in lung epithelia by the ubiquitin proteasome system, leading to subsequent DNA damage, cytotoxicity, and emphysema.
Authors
Rama K. Mallampalli, Xiuying Li, Jun-Ho Jang, Tomasz Kaminski, Aki Hoji, Tiffany Coon, Divay Chandra, Starr Welty, Yaqun Teng, John Sembrat, Mauricio Rojas, Yutong Zhao, Robert Lafyatis, Chunbin Zou, Frank Sciurba, Prithu Sundd, Li Lan, Toru Nyunoya
Abstract
Interleukin-3 (IL3) receptor α (IL3Rα) is the alpha subunit of the ligand-specific IL3 receptor and initiates intracellular signaling in response to IL3. IL3 amplifies pro-inflammatory signaling and cytokine storm in murine sepsis models. Here we found that RNFT2 (RING finger transmembrane-domain containing protein 2, also TMEM118), a previously uncharacterized RING finger ubiquitin E3 ligase, negatively regulated IL3-dependent cellular responses through IL3Rα ubiquitination and degradation in the proteasome. In vitro, IL3 stimulation promoted IL3Rα proteasomal degradation dependent on RNFT2, and we identified IL3Rα Lysine 357 as a ubiquitin acceptor site. We determined that LPS-priming reduces RNFT2 abundance, extends IL3Rα half-life, and sensitizes cells to the effects of IL3, acting synergistically to increase pro-inflammatory signaling. In vivo, IL3 synergized with LPS to exacerbate lung inflammation in LPS and Pseudomonas aeruginosa-challenged mice; conversely, IL3 neutralization reduced LPS-induce lung injury. Further, RNFT2 over-expression reduced lung inflammation and injury, whereas Rnft2 knockdown exacerbated inflammatory responses in LPS-induced murine lung injury. Lastly, we examined RNFT2 and IL3Rα in human lung explants from patients with Cystic Fibrosis, and also showed that IL3 is elevated in mechanically-ventilated critically ill humans at risk for Acute Respiratory Distress Syndrome (ARDS). These results identify RNFT2 as a negative regulator of IL3Rα, and show a potential role for the RNFT2/IL3Rα/IL3 axis in regulating innate immune responses in the lung.
Authors
Yao Tong, Travis B. Lear, John Evankovich, Yanwen Chen, James D. Londino, Michael M. Myerburg, Yingze Zhang, Iulia D. Popescu, John F. McDyer, Bryan J. McVerry, Karina C. Lockwood, Michael J. Jurczak, Yuan Liu, Bill B. Chen
Abstract
Community-acquired pneumonia is a widespread disease with significant morbidity and mortality. Alveolar macrophages are tissue-resident lung cells that play a crucial role in innate immunity against bacteria that cause pneumonia. We hypothesized that alveolar macrophages display adaptive characteristics after resolution of bacterial pneumonia. We studied mice one to six months after self-limiting lung infections with Streptococcus pneumoniae, the most common cause of bacterial pneumonia. Alveolar macrophages, but not other myeloid cells recovered from the lung, showed long-term modifications of their surface marker phenotype. The remodeling of alveolar macrophages was: (i) long-lasting (still observed 6 months post infection), (ii) regionally localized (only observed in the affected lobe after lobar pneumonia), and (iii) associated with macrophage-dependent enhanced protection against another pneumococcal serotype. Metabolomic and transcriptomic profiling revealed that alveolar macrophages of mice that recovered from pneumonia had new baseline activities and altered responses to infection that better resembled those of adult humans. The enhanced lung protection after mild and self-limiting bacterial respiratory infections includes a profound remodeling of the alveolar macrophage pool that is long-lasting, compartmentalized, and manifest across surface receptors, metabolites, and both resting and stimulated transcriptomes.
Authors
Antoine Guillon, Emad I. Arafa, Kimberly A. Barker, Anna C. Belkina, Ian M.C. Martin, Anukul T. Shenoy, Alicia K. Wooten, Carolina Lyon De Ana, Anqi Dai, Adam Labadorf, Jaileene Hernandez-Escalante, Hans Dooms, Helene Blasco, Katrina E. Traber, Matthew R. Jones, Lee J. Quinton, Joseph P. Mizgerd
Abstract
Pulmonary Langerhans cell histiocytosis (PLCH) is a rare, smoking-related, lung disease characterized by dendritic cell (DC) accumulation, bronchiolocentric nodule formation, and cystic lung remodeling. Approximately 50% of PLCH patients harbor somatic BRAF-V600E mutations in cells of the myeloid/monocyte lineage. However, the rarity of the disease and lack of animal models has impeded the study of PLCH pathogenesis. Here, we established a cigarette smoke (CS)-exposed, BRAF-V600E mutant mouse model that recapitulates many hallmark characteristics of PLCH. We show that CD11c-targeted expression of BRAF-V600E increases DC responsiveness to stimuli, including the chemokine CCL20, and that mutant DC accumulation in the lungs of CS-exposed mice is due to both increased cellular viability and enhanced recruitment. Moreover, we report that the chemokine CCL7 is secreted from DCs and human peripheral blood monocytes in a BRAF-V600E-dependent manner, suggesting a possible mechanism for recruitment of cells known to dominate PLCH lesions. Inflammatory lesions and airspace dilation in BRAF-V600E mice in response to CS are attenuated by transitioning animals to filtered air and treatment with a BRAF-V600E inhibitor, PLX4720. Collectively, this model provides mechanistic insights into the role of DCs, the BRAF-V600E mutation and CS exposure in PLCH pathogenesis, and provides a platform to develop therapeutic targets.
Authors
Huan Liu, Andrew R. Osterburg, Jennifer Flury, Zulma Swank, Dennis W. McGraw, Nishant Gupta, Kathryn A. Wikenheiser-Brokamp, Ashish Kumar, Abdellatif Tazi, Yoshikazu Inoue, Masaki Hirose, Francis X. McCormack, Michael Borchers
Abstract
The T helper 2 (Th2) inflammatory cytokine interleukin-13 (IL-13) has been associated with both obstructive and fibrotic lung diseases; however, its specific effect on the epithelial stem cells in the gas exchange compartment of the lung (alveolar space) has not been explored. Here, we used in vivo lung models of homeostasis and repair, ex vivo organoid platforms, and potentially novel quantitative proteomic techniques to show that IL-13 disrupts the self-renewal and differentiation of both murine and human type 2 alveolar epithelial cells (AEC2s). Significantly, we find that IL-13 promotes ectopic expression of markers typically associated with bronchiolar airway cells and commonly seen in the alveolar region of lung tissue from patients with idiopathic pulmonary fibrosis. Furthermore, we identify a number of proteins that are differentially secreted by AEC2s in response to IL-13 and may provide biomarkers to identify subsets of patients with pulmonary disease driven by “Th2-high” biology.
Authors
Kristen M. Glisinski, Adam J. Schlobohm, Sarah V. Paramore, Anastasiya Birukova, M. Arthur Moseley, Matthew W. Foster, Christina E. Barkauskas
Abstract
Alternative polyadenylation (APA) is a widespread and important mechanism in regulation of gene expression. Dysregulation of the 3’ UTR cleavage and polyadenylation represents a common characteristic among many disease states including lung fibrosis. In this study, we investigated the role of mammalian cleavage factor I (CFIm)-mediated APA in regulating the extracellular matrix production in response to mechanical stimuli from stiffened matrix simulating the fibrotic lungs. We found that stiff matrix downregulates expression of CFIm68, CFIm59 and CFIm25 subunits, and promotes APA in favor of the proximal poly(A) site usage in the 3’ UTRs of type I collagen (COL1A1) and fibronectin (FN1) in primary human lung fibroblasts. Knockdown and overexpression of each individual CFIm subunit demonstrated that CFIm68 and CFIm25 are indispensable attributes of stiff matrix-induced APA and overproduction of COL1A1, whereas CFIm does not appear to mediate stiffness-regulated FN1 APA. Furthermore, expression of the CFIm subunits is associated with matrix stiffness in vivo in a bleomycin-induced mouse model of pulmonary fibrosis. These data suggest that stiff matrix instigates type I collagen biogenesis by selectively targeting mRNA transcripts for 3’ UTR shortening. The current study uncovered a potential mechanism for regulation of the CFIm complex by mechanical cues under fibrotic conditions.
Authors
Zijing Zhou, Jing Qu, Li He, Yi Zhu, Shanzhong Yang, Feng Zhang, Ting Guo, Hong Peng, Ping Chen, Yong Zhou
Abstract
BACKGROUND. Mitochondrial dysfunction, a proposed mechanism of COPD pathogenesis, is associated with the leakage of mitochondrial DNA (mtDNA), which may be detected extracellularly in various bodily fluids. Despite evidence for the increased prevalence of chronic kidney disease in COPD subjects and for mitochondrial dysfunction in the kidneys of murine COPD models, whether urine mtDNA (u-mtDNA) associates with measures of disease severity in COPD is unknown. METHODS. Cell-free u-mtDNA, defined as copy number of mitochondrially-encoded NADH dehydrogenase-1 (MTND1) gene, was measured by real-time quantitative PCR and normalized to urine creatinine in cell-free urine samples from participants in the Subpopulations and Intermediate Outcome Measures in COPD Study (SPIROMICS) cohort. Urine albumin/creatinine ratios (UACR) were measured in the same samples. Associations between u-mtDNA and UACR and clinical disease parameters, including FEV1 % predicted, clinical measures of exercise tolerance, respiratory symptom burden, and chest CT measures of lung structure were examined. RESULTS. U-mtDNA and UACR levels were measured in never smokers (n = 64), smokers without airflow obstruction (n = 109), participants with mild/moderate COPD (n = 142), and participants with severe COPD (n = 168). U-mtDNA was associated with increased respiratory symptom burden, especially among smokers without COPD. Significant sex differences in u-mtDNA levels were observed with females having higher u-mtDNA levels across all study subgroups. U-mtDNA associated with worse spirometry and CT emphysema in males only, and worse respiratory symptoms in females only. Similar associations were not found with UACR. CONCLUSION. U-mtDNA levels may help to identify distinct clinical phenotypes and underlying pathobiological differences in males versus females with COPD.
Authors
William Z. Zhang, Michelle C. Rice, Katherine L. Hoffman, Clara Oromendia, Igor Barjaktarevic, J. Michael Wells, Annette T. Hastie, Wassim W. Labaki, Christopher B. Cooper, Alejandro P. Comellas, Gerard J. Criner, Jerry A. Krishnan, Robert Paine III, Nadia N. Hansel, Russell P. Bowler, R. Graham Barr, Stephen P. Peters, Prescott G. Woodruff, Jeffrey L. Curtis, Meilan K. Han, Karla V. Ballman, Fernando J. Martinez, Augustine M.K. Choi, Kiichi Nakahira, Suzanne M. Cloonan, Mary E. Choi
Abstract
Integrins, the extracellular matrix receptors that facilitate cell adhesion and migration, are necessary for organ morphogenesis; however, their role in maintaining adult tissue homeostasis is poorly understood. To define the functional importance of β1 integrin in adult mouse lung, we deleted it post-development in type 2 alveolar epithelial cells (AECs). Aged β1 integrin-deficient mice exhibited chronic obstructive pulmonary disease (COPD)-like pathology characterized by emphysema, lymphoid aggregates, and increased macrophage infiltration. These histopathological abnormalities were preceded by β1 integrin-deficient AEC dysfunction such as excessive reactive oxygen species production and up-regulation of NF-κB-dependent chemokines, including CCL2. Genetic deletion of the CCL2 receptor, Ccr2, in mice with β1 integrin-deficient type 2 AECs impaired recruitment of monocyte-derived macrophages and resulted in accelerated inflammation and severe premature emphysematous destruction. These lungs exhibited reduced AEC efferocytosis and excessive numbers of inflamed type 2 AECs, demonstrating the requirement for recruited monocyte-macrophages in limiting lung injury and remodeling in the setting of a chronically inflamed epithelium. These studies support a critical role for β1 integrin in alveolar homeostasis in the adult lung.
Authors
Erin J. Plosa, John T. Benjamin, Jennifer M. Sucre, Peter M. Gulleman, Linda A. Gleaves, Wei Han, Seunghyi Kook, Vasiliy V. Polosukhin, Scott M. Haake, Susan H. Guttentag, Lisa R. Young, Ambra Pozzi, Timothy S. Blackwell, Roy Zent
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