Normal Airway Epithelial Cells Research Articles

Abstract 7544: Bromodomain and extra-terminal protein inhibitors deplete nuclear factor 1C and reduce stemness and growth of human small cell lung cancer cells in vitro and in vivo

Abstract Objectives: Recent insights regarding mechanisms mediating stemness, heterogeneity, and metastatic potential of lung cancers have yet to be fully translated to effective regimens for the treatment of these malignancies. This study sought to examine complex epigenetic mechanisms underpinning the aggressiveness of SCLC, with a focus on understanding those mediating stemness in these highly lethal cancers. Methods: Normal small airway epithelial cells (SAECs) were reprogrammed into iPSCs, validated by various assays, such as spectral karyotyping and teratoma formation. Genome-wide chromatin landscapes of lung iPSCs (Lu-iPSC) and SAECs, as well as NSCLC and SCLC lines were characterized using RNA-seq, DNA methylome, and DNase-hypersensitivity sequencing (DHS). Gene knock-downs were established using siRNA/shRNA techniques, along with qRT-PCR, immunoblotting, proliferation, and tumorigenicity assays. Glycolysis was analyzed using Seahorse assays. In-silico analysis of the NFIC promoter was performed using TFmapper. NFIC and related gene expression in human SCLC cells following NFIC or Bromodomain-containing protein (BRD) knockdown or exposure to BET inhibitors (BETi) were evaluated. Stemness scores were calculated using established RNA-seq criteria, and gene set enrichment analyses were conducted. Proliferation assays and xenograft models were used for in-vitro and in-vivo SCLC growth assessment. Results: RNA-seq,DNA methylome and DHS analyses revealed shared characteristics among SAEC, Lu-iPSC, SCLC, and NSCLC, whereas SOXs and POUs showed strong activity in Lu-iPSC but not SCLC. NFIC, with elevated chromatin occupancy in SCLC, exhibited increased expression compared to SAEC. NFIC KD in SCLC significantly curtailed cell growth in-vitro and in-vivo, affecting multiple pathways, including glycolysis and stem cell signaling etc, confirmed by Seahorse assays. Furthermore, we identified occupancy sites for BRD4 in the NFIC promoter, and knockdown of BRD4, but not BRD2 or BRD3, reduced NFIC expression in SCLC cells. BET inhibitor (BETi) treatment dose-dependently decreased NFIC expression in SCLC lines and human SCLC PDXs, irrespective of subtype. BETi treatment also reduced SCLC stemness and showed a significant overlap in gene regulation with NFIC knockdown, affecting pathways related to gluconeogenesis, neuronal differentiation, and embryonic organ morphogenesis. Importantly, BETi treatment effectively reduced SCLC cell growth in-vitro and in-vivo, suggesting the potential therapeutic value of targeting NFIC via BET inhibition in SCLC. Conclusions: NFIC, a unique transcription factor in SCLC, emerges as a key downstream target of BRD4. These findings underscore the potential druggability of NFIC in clinical settings, provide compelling rationale for evaluating BETi for SCLC therapy. Citation Format: Haitao Wang, Ruihong Wang, Frank Villa-Hernandez, Vivek Shukla, Lyuba Varticovski, Songjoon Baek, Frank Echtenkamp, Sudheer Kumar Gara, Mary R. Zhang, Stephanie Shiffka, Razi Raziuddin, Leonard M. Neckers, W. Marston Linehan, Gordon L. Hager, Shamus R. Carr, Chuong D. Hoang, Haobin Chen, David S. Schrump. Bromodomain and extra-terminal protein inhibitors deplete nuclear factor 1C and reduce stemness and growth of human small cell lung cancer cells in vitro and in vivo [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7544.

Autologous Airway Basal Cell Transplantation Alleviates Airway Epithelium Defect in Recurrent Benign Tracheal Stenosis.

Airway epithelium defects are a hallmark of recurrent benign tracheal stenosis (RBTS). Reconstructing an intact airway epithelium is of great importance in airway homeostasis and epithelial wound healing and has great potential for treating tracheal stenosis. An experimental study was conducted in canines to explore the therapeutic effect of autologous basal cell transplantation in restoring airway homeostasis. First, airway mucosae from human patients with recurrent tracheal stenosis were analyzed by single-cell RNA sequencing. Canines were then randomly divided into tracheal stenosis, Stent, Stent + Cells, and Stent + Cells + Biogel groups. Autologous airway basal cells of canines in the Stent + Cells and Stent + Cells + Biogel groups were transplanted onto the stenotic airway after modeling. A biogel was coated on the airway prior to basal cell transplantation in the Stent + Cells + Biogel group. After bronchoscopic treatments, canines were followed up for 16 weeks. Single-cell RNA sequencing demonstrated packed airway basal cells and an absence of normal airway epithelial cells in patients with RBTS. Autologous airway basal cell transplantation, together with biogel coating, was successfully performed in the canine model. Follow-up observation indicated that survival time in the Stent + Cells + Biogel group was significantly prolonged, with a higher (100%) survival rate compared with the other groups. In terms of pathological and bronchoscopic findings, canines that received autologous basal cell transplantation showed a reduction in granulation hyperplasia as well as airway re-epithelialization with functionally mature epithelial cells. Autologous airway basal cell transplantation might serve as a novel regenerative therapy for airway re-epithelialization and inhibit recurrent granulation hyperplasia in benign tracheal stenosis.

Increased expression of miR146a dysregulates TLR2-induced HBD2 in airway epithelial cells from patients with COPD.

Airway epithelial cells from patients with COPD show suboptimal innate immune responses to nontypeable Haemophilus influenzae (NTHi) and Toll-like receptor (TLR)2 ligands despite expressing TLR2 similar to normal airway epithelial cells, but the underlying mechanisms are poorly understood. Normal or COPD mucociliary-differentiated airway epithelial cells were treated with TLR2 agonists or infected with NTHi and expression of β-defensin (HBD)2 was examined. Interleukin-1 receptor-associated kinase (IRAK)-1 and microRNA (miR)146a were genetically inhibited in normal and COPD airway epithelial cell cultures, respectively, and HBD2 responses to TLR2 ligands were determined. IRAK-1 expression in lung sections was determined by immunofluorescence microscopy. Compared to normal, COPD airway epithelial cell cultures showed impaired expression of HBD2 in response to TLR2 agonists or NTHi infection. Apical secretions from TLR2 agonist-treated normal, but not COPD, airway epithelial cells efficiently killed NTHi. Knockdown of HBD2 significantly reduced NTHi killing by apical secretions of normal airway epithelial cells. Compared to normal, COPD cells showed significantly reduced expression of IRAK-1 and this was associated with increased expression of miR146a. Inhibition of miR146a increased the expression of IRAK-1, improved the expression of HBD2 in response to TLR2 agonists in COPD cells and enhanced the killing of bacteria by apical secretions obtained from TLR2 agonist-treated COPD cells. Bronchial epithelium of COPD patients showed reduced expression of IRAK-1. These results suggest that reduced levels of IRAK-1 due to increased expression of miR146a may contribute to impaired expression of TLR2-induced HBD2 in COPD airway epithelial cells.

Transcriptomic atlas of GNAT family members in pulmonary epithelia under pathological conditions using single‐cell and bulk cell sequencing

Transcriptomic atlas of GNAT family members in pulmonary epithelia under pathological conditions using single‐cell and bulk cell sequencing

Epidermal growth factor receptors siRNA-conjugated collagen modified gold nanoparticles for targeted imaging and therapy of lung cancer

Epidermal growth factor receptor (EGFR), a critical factor promotes lung cancer cell proliferation and survival. Knockdown of EGFR expression thus promise beating lung cancer clinically. Functionalized gold nanoparticles may serve an effective vehicle carrying theranostic bio-active materials. Herein, physically gold nanoparticles were fabricated with biocompatible collagen to improve siRNA loading capacity carrying EGFR siRNA to treat lung cancer. Physic-chemical properties were comprehensively characterized for the collagen gold nanoparticle (C–Au), and with EGFR siRNA conjugation, C–Au-EGFRsi namely. Issues of biocompatibility were addressed. Interestingly, C–Au appeared more biocompatible to normal airway epithelial cells (BEAS-2B) than to cancer cells (A549) in terms of ROS production, cell cycle behavior, and cell growth influence. The C–Au demonstrated comparable or even more efficient, compared with lipofetamine, in carrying siRNA to knockdown EGFR of A549 cells. Endocytosis mediated cell entry for the collagen gold nanoparticles, and endosome-lysosomal pathway involved transporting and metabolizing these nanoparticles. In xenograft mice model, substantial tumor suppression effects were observed treating with C–Au-EGFRsi, in which tumor weight reduced 30% for lipofetamine carrier, and down to 70% for C–Au carrier. Particularly, overall survival rate was improved for both treatment groups with lipofetamine and C–Au carrier, respectively.

CC16-TNF-α negative feedback loop formed between Clara cells and normal airway epithelial cells protects against diesel exhaust particles exposure-induced inflammation.

CC16 is almost exclusively expressed in non-ciliated epithelial Clara cells, and widely used as a Clara cell marker. Diesel exhaust particles (DEPs), the fine particulate matters produced by diesel engines, cause or exacerbate airway-related diseases. Our previous study documented that DEP inhibits the CC16 expression in the immortalized mouse Clara cell line through methylation of C/EBPα promoter. However, the molecular mechanism by which DEP regulates CC16 secretion is unclear. Here, we isolated CC16 containing Clara cells (CC16+) from human distal lung, and found that DEP inhibited CC16 secretion from CC16+ cells via methylation of C/EBPα and inhibition of Munc18b transcription. CC16+ cell conditioned media containing different concentrations of CC16 was prepared and used for culture of airway epithelial cells BEAS-2B with no expression of CC16. A positive correlation was observed between CC16 level and DEP-induced autophagy activity, and a negative correlation between CC16 level and DEP-induced pro-inflammatory cytokine TNF-α, IL-6, and IL-8 level, suggesting that CC16 might mitigate DEP-induced inflammation via promoting autophagy in BEAS-2B cells. This result was further confirmed by adding recombinant CC16 to BEAS-2B cells exposed to DEP. Moreover, CC16 level was significantly increased when CC16+ cells were cultured in BEAS-2B cell conditioned medium containing TNF-α or the normal medium supplemented with recombinant TNF-α, suggesting that TNF-α induced CC16 production and secretion from CC16+ cells. Collectively, these data point that CC16 and TNF-α form a negative feedback loop, and this negative feedback loop between Clara cells and normal airway epithelial cells protects against DEP exposure-induced inflammation.

RETRACTED: Two new luminescent Cd(II) coordination polymers and their application values on children bronchopneumonia

Two Cd(II) coordination polymers namely, [Cd(L)(phen)(H 2 O)] n ( 1 ) and [Cd(L)(bpe) 0.5 ] n ( 2 ) (H 2 L is 4,4′-{[1,2-phenylenebis-(methylene)]}bis(oxy)dibenzoic acid, bpe is 1,2-bis(-4-pyridyl)ethane and phen is 1,10-phenanthroline), have been created by the mixed-ligand self-assembly strategy. Moreover, the two compounds’ luminescent and photocatalytic performances were also studied. The treatment activity and nursing application values on children bronchopneumonia was explored and specific mechanism was investigated simultaneously. First of all, the ELISA detection kit was implemented to detect the TNF-α and IL-6 levels released into the respiratory secretions after treatment of compound. Furthermore, the real time RT-PCR was conducted to determine the activation levels of NF-κb signaling pathway in the airway epithelial cells. Finally, the cytotoxicity of the coordination polymers on normal airway epithelial cells was assessed through the CCK-8 assay.

Abstract 2350: xCT overexpression induces metabolic reprogramming, epigenetic alterations, and DNA damage in precancerous airway epithelial cells

Abstract Metabolic reprogramming and genomic instability are two hallmarks of cancer known to drive tumorigenesis. While each has been investigated individually, there is a growing interest in their interplay during early cancer development. High expression of the cystine/glutamate antiporter SLC7A11 (xCT) is frequently observed in lung cancer. Our laboratory previously demonstrated that overexpressing xCT in normal bronchial airway epithelial cells induced metabolic reprogramming and caused cells to display precancerous properties, such as increased proliferation and colony formation in soft agar. In this study, we further investigated the effects of xCT overexpression in the airway epithelium with the goal of elucidating the role of xCT in influencing cancer-driving hallmarks and the interplay of these hallmarks during early tumorigenesis. We hypothesized that xCT overexpression-induced metabolic reprogramming leads to epigenetic changes through the perturbation of epigenetic-related metabolite levels. Furthermore, we posited that this altered epigenome changes the expression levels of key genes involved in genome stability maintenance, ultimately inducing genomic instability. Utilizing a LC-MS/MS-based metabolomic analysis, we observed significantly altered levels of 224 different metabolites in our xCT overexpressing cells, including metabolites involved in epigenetic processes such as S-adenosylhomocysteine and acetyl-CoA. We found that xCT overexpression alters several global histone modifications, increasing H3K9me3 and H3K9ac by 3.2 (P = 0.02) and 3.9-fold (P = 0.02) respectively. We also showed that xCT overexpression increased global DNA methylation by 56% (P = 0.04). Additionally, RNA-seq revealed significant alterations (logFC>2 or <0.5, pAdj<0.05) in the expression of over 100 genes, including a significant decrease in the expression of certain tumor suppressor genes such as TRIM29, and a significant increase in the expression of certain proto-oncogenes, such as CCND1. Finally, we discovered that xCT overexpression induces DNA damage, increasing the percentage of damaged DNA in comet tails in a comet assay by 15.1% (P = 0.002). Taken together, xCT overexpression in normal bronchial airway epithelial cells induces metabolic reprogramming, alters the epigenetic landscape and gene expression, and causes higher levels of DNA damage. Future experiments elucidating causal links between these processes, including ChIP-seq and WGBS are underway. This study provides a promising foundation for the connections between xCT-induced metabolic reprogramming, epigenetic alterations, and genomic instability, an imperative step in elucidating an effective, potentially multifaceted approach to preventing lung cancer development. Citation Format: Dalton Hill, Jamshedur Rahman, Christien Kluwe, Jamey Young, Emily Hodges, Pierre P. Massion. xCT overexpression induces metabolic reprogramming, epigenetic alterations, and DNA damage in precancerous airway epithelial cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2350.

Abstract 2525: Low frequency TP53 mutations in airway epithelial cells serve as lung cancer risk biomarker

Abstract Background: Lung cancer is the leading cause of cancer-related death in men and women in the United States. Based on evidence from controlled trials in the United States and Europe that low dose CT (LDCT) screening significantly reduces lung cancer mortality, the United States Preventative Services Tasks Force (USPSTF) recommends LDCT screening for individuals with high demographic risk based on age and smoking history. However, a large fraction of lung cancers occur in individuals who do not meet LDCT screening threshold criteria. Thus, there is a need for biomarkers that supplement demographic factors to more accurately detect those at highest lung cancer risk and include additional individuals who will benefit from LDCT screening. An initial study from this lab demonstrated that TP53 mutations with 0.05-1.0% variant allele fraction (VAF) were significantly more prevalent (p<0.005) in grossly normal airway epithelial cell (AEC) specimens from lung cancer cases compared to non-cancer controls matched for smoking and age. Here, we present an expanded follow-up study aimed at testing this biomarker according to PRospective-specimen-collection, retrospective-Blinded-Evaluation (PRoBE) design. Methods: AEC specimens were prospectively collected through the National Cancer Institute Early Detection Research Network (EDRN) program from 60 subjects at high demographic risk for lung cancer by bronchoscopic brush biopsy at Vanderbilt University Medical Center. Genomic (g)DNA was extracted from each AEC specimen and stored at -80 degrees Celsius. Subjects matched for age and smoking history who subsequently did or did not develop lung cancer were identified and gDNA specimens, blinded with respect to cancer status, were shipped to the University of Toledo. gDNA specimens were quantified and 50,000 gDNA copies were included in each NGS library preparation. Synthetic DNA internal standards (IS) were prepared for multiple lung cancer driver mutations within the TP53 gene and mixed with each AEC gDNA specimen prior to competitive multiplex PCR NGS library preparation. By controlling for technical error, this approach enables reliable detection of mutations with VAF as low as 5 x 10-4 (0.05%) (Craig et al, BMC Cancer, 2019). Results: Following library preparation and sequencing on Illumina Novaseq, there was sufficient library complexity to detect TP53 VAF <0.05% in >90% of AEC specimens. The data are currently in pipeline analysis. After analysis is complete, VCF files will be sent to Vanderbilt for unblinding and validation of the biomarker. Conclusions: Based on preliminary data, we expect that sufficient AEC gDNA is available from most subjects enrolled in the EDRN program for TP53 low VAF biomarker analysis, and the previously reported method (Craig et al, BMC Cancer, 2019) is reliable and feasible. The current study should provide additional information regarding validity of the biomarker. Citation Format: Daniel J. Craig, Erin L. Crawford, Pierre P. Massion, Thomas Morrison, James C. Willey. Low frequency TP53 mutations in airway epithelial cells serve as lung cancer risk biomarker [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2525.

Differential Modulation of β2AR Mediated cAMP/PKA/CREB Signaling Cascade in Normal versus Asthmatic Airway Epithelial Cells

Nearly 25 million people in the U.S. suffer from asthma. While there is no panacea for asthma, symptomatic relief is achieved by the current therapeutic interventions, including β2-adrenergic receptor (β2AR) agonists. Chronic usage of β2AR agonists can have serious implications like airway hyper-responsiveness and receptor desensitization, and along with unknown mechanisms, can ultimately culminate into tachyphylaxis to the response. Previously, our laboratory has extensively explored the critical role of reactive oxygen species (ROS) in modulating β2AR function. To begin to assess the physiological role of the β2AR-ROS linkage in asthma, here, we assessed Isoproterenol (ISO)-induced β2AR mediated Gαs/cAMP/CREB pathway in small airway epithelial cells from asthma patients (SAEC-A) compared to those from non-diseased control patients (SAEC-N). Given the importance of β2AR mediated cAMP production and its role in airway bronchodilation, as well as tachyphylaxis that occurs upon chronic use of β2AR agonists, our results may shed light on the role of oxidants in altering β2AR responses in asthma. To assess cAMP levels, cells were analyzed using highly sensitive luciferase-based biosensor. Briefly, SAEC were transfected with GloSensorTM -22F cAMP plasmid (8μg) using Lipofectamine3000. Luminescence was measured following treated with the ISO. To assess the effects of downstream cAMP-mediated transcription, cells were stimulated with H2O, Forskolin (FSK) (10 μM) & ISO (100μM) for 20 min and lysed. Lysates were resolved using SDS-PAGE and immunoprobed for phospho-cAMP response element-binding protein (pCREB), total CREB and β-actin. Similarly, SAEC-N/A lysates were assessed for Adenylyl Cyclase (AC-5/6) and Phosphodiesterase (PDE4) by immunoblot. β2AR agonism with ISO significantly increased cAMP production in SAEC from asthma patients compared to non-diseased control. In spite of elevated cAMP production in asthmatic SAEC, both ISO and FSK were able to induce significant increase in CREB phosphorylation, leading to heightened pCREB/CREB response in SAEC-N as compared to SAEC-A. ISO-mediated increased cAMP response in asthmatic SAEC compared to non-diseased control, were linked with physiologically altered expression of key cAMP mediators, specifically, heightened basal expression of AC-5/6 and PDE4, in asthmatic SAEC compared to SAEC-N. ISO mediated increased cAMP production in asthmatic SAEC indicated altered agonist modulated β2AR downstream signaling in diseased versus non-diseased SAEC. Further, heightened basal expression of AC-5/6 in asthmatic SAEC supports the above mentioned consequence. In addition, elevated CREB phosphorylation in non-diseased SAEC suggests alterations of β2AR-mediated PKA/CREB signaling in asthma. Future results will probe the effects of elevated ROS in these signal cascades.

Eosinophil Responses at the Airway Epithelial Barrier during the Early Phase of Influenza A Virus Infection in C57BL/6 Mice.

Eosinophils, previously considered terminally differentiated effector cells, have multifaceted functions in tissues. We previously found that allergic mice with eosinophil-rich inflammation were protected from severe influenza and discovered specialized antiviral effector functions for eosinophils including promoting cellular immunity during influenza. In this study, we hypothesized that eosinophil responses during the early phase of influenza contribute to host protection. Using in vitro and in vivo models, we found that eosinophils were rapidly and dynamically regulated upon influenza A virus (IAV) exposure to gain migratory capabilities to traffic to lymphoid organs after pulmonary infection. Eosinophils were capable of neutralizing virus upon contact and combinations of eosinophil granule proteins reduced virus infectivity through hemagglutinin inactivation. Bi-directional crosstalk between IAV-exposed epithelial cells and eosinophils occurred after IAV infection and cross-regulation promoted barrier responses to improve antiviral defenses in airway epithelial cells. Direct interactions between eosinophils and airway epithelial cells after IAV infection prevented virus-induced cytopathology in airway epithelial cells in vitro, and eosinophil recipient IAV-infected mice also maintained normal airway epithelial cell morphology. Our data suggest that eosinophils are important in the early phase of IAV infection providing immediate protection to the epithelial barrier until adaptive immune responses are deployed during influenza.

Abstract PO-001: xCT expression alters the epigenome and induces genomic instability

Abstract Metabolic reprogramming, remodeling of the epigenetic landscape, and genomic instability are three processes that drive tumorigenesis. While each has been investigated individually, there is a growing interest in the interplay between each process during early cancer development. High expression of the cystine/glutamate antiporter SLC7A11 (xCT) is frequently seen in lung cancer. Our lab previously demonstrated overexpression of xCT in normal bronchial airway epithelial cells is sufficient to induce metabolic reprogramming. In this study, we investigated the effects of xCT overexpression in normal bronchial airway epithelial cells. We hypothesize that xCT overexpression both induces genomic instability and alters the epigenome in normal bronchial airway epithelial cells through the perturbation of intracellular metabolite levels. Through utilizing an alkaline comet assay, we discovered that xCT overexpression induces DNA damage, increasing the percentage of DNA in the comet tail by 15.1% (P=0.002). Furthermore, we found that xCT overexpression induces alterations to the histone modification landscape, most notably increasing H3K9me3 and H3K9ac by 3.2 and 3.9-fold (P=0.08) respectively. Finally, xCT overexpression shows higher tumorigenic potential through increased colony formation in a soft agar assay. Taken together, xCT overexpression in normal bronchial airway epithelial cells increases tumorigenic potential, induces metabolic reprogramming, causes higher levels of DNA damage, and alters the epigenetic landscape. Future experiments elucidating the links between these processes, including ChIP-seq and whole-genome bisulfite sequencing are currently underway. Establishing causal links between metabolic reprogramming, epigenetic alterations, and genomic instability are imperative in elucidating an effective, potentially multifaceted approach to treating early-stage lung cancer. Citation Format: Dalton Hill, Jamshedur Rahman, Christien Kluwe, Pierre P. Massion. xCT expression alters the epigenome and induces genomic instability [abstract]. In: Abstracts: AACR Special Virtual Conference on Epigenetics and Metabolism; October 15-16, 2020; 2020 Oct 15-16. Philadelphia (PA): AACR; Cancer Res 2020;80(23 Suppl):Abstract nr PO-001.

Abstract 4609: TP53, PIK3CA, and BRAF somatic mutations in airway epithelial field of injury associated with lung cancer risk

Abstract Background: Lung cancer is the leading cause of cancer-related death in men and women, and cigarette smoking is the most significant preventable risk factor. Early detection through annual low dose CT screening reduces mortality but has low positive predictive value and specificity, in part due to low lung cancer incidence (<10%) among those who currently meet screening criteria. Thus, there is a need for biomarkers that reliably detect those at highest lung cancer risk, thereby enabling more effectivescreening. The purpose of this study was to test the hypothesis that high risk for lung cancer is characterized by high prevalence of low variant allele frequency (VAF) somatic mutations among known lung cancer driver genes in normal airway epithelial cells (AEC). Methods: Synthetic DNA internal standards (IS) were prepared for each of 11 lung cancer driver genes and mixed with each AEC genomic (g)DNA specimen prior to competitive multiplex PCR amplicon NGS library preparation. A custom Perl script was developed to separate IS reads and respective specimen gDNA reads from each target into separate files for parallel variant frequency analysis. This approach enabled reliable detection of mutations with VAF as low as 5 x 10-4 (0.05%). This method was then applied in a retrospective case-control study. Specifically, AEC specimens were collected by bronchoscopic brush biopsy from the normal airways of 19 subjects, including eleven lung cancer cases and eight non-cancer controls, and the association of lung cancer risk with AEC driver gene mutations was tested. Results: TP53 mutations with 0.05-1.0% VAF were more prevalent (p<0.005) and significantly more enriched for tobacco smoke and age-associated mutation signatures in AEC from lung cancer cases compared to non-cancer controls matched for smoking and age. Further, PIK3CA and BRAF mutations in this VAF range were identified in AEC from cases but not controls. Conclusions: Measurement of very low frequency mutations in the 0.05-1.0% VAF range enabled identification of an AEC somatic mutation field of injury associated with lung cancer risk. A biomarker comprising TP53, PIK3CA, and BRAF somatic mutations may better stratify individuals for optimal lung cancer screening and prevention outcomes. Citation Format: Daniel J. Craig, Thomas Morrison, Sadik Khuder, Erin L. Crawford, Leihong Wu, Joshua Xu, Thomas M. Blomquist, James C. Willey. TP53, PIK3CA, and BRAF somatic mutations in airway epithelial field of injury associated with lung cancer risk [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4609.

Abstract 3377: NSCLC subtype-associated molecular and cellular alterations in the normal-appearing bronchial epithelium

Abstract Rationale: We have previously identified lung cancer-associated gene expression alterations in normal bronchial airway epithelial cells of ever smokers with and without lung cancer. It is unclear, however, whether or not gene expression in the bronchial airway also reflects non-small cell lung cancer (NSCLC) subtypes. In this study, we sought to identify airway gene expression differences between patients with squamous (LUSC) and adenocarcinoma (LUAD) NSCLC and determine if these reflect changes in cell type composition or cell type-specific expression. Methods: Bronchial brushings from ever smokers with NSCLC from the AEGIS I (153 LUSC; 148 LUAD; 154 benign) & II (82 LUSC; 102 LUAD; 74benign) trials were profiled by whole-genome microarrays. The NSCLC-associated gene expression alterations were identified using a linear model adjusting for smoking status in AEGIS I and confirmed in AEGIS II via GSEA. Enriched biological pathways were identified using EnrichR. In parallel, bronchial airway brushings collected from ever smokers undergoing bronchoscopy for suspect lung cancer (17 subjects) were profiled via scRNA-seq using the CEL-Seq2 protocol (3264 cells). Seurat was used to correct for batch effects and identify distinct cell populations. Genes differentially expressed between cell populations using a negative binomial model were clustered into gene sets using WGCNA. Per patient metagene scores were computed across the datasets for each gene set, and differences in these scores between NSCLC subtypes were evaluated using a linear model adjusting for smoking status. Results: 451 differentially expressed genes were found between LUSC v LUAD patients (FDR < 0.05). Genes involved in ciliary function were enriched among genes up-regulated in LUAD whereas keratinization and cancer-associated pathway genes were enriched among LUSC up-regulated genes (FDR < 0.05). In the scRNA-seq data, 15 populations of cells were identified that expressed known epithelial or immune cell type markers. Using WGCNA to cluster genes that distinguish the cell populations (5148 genes, FDR < 0.05) identified 12 gene sets (GS). In AEGIS I, LUSC patients had higher expression of a mitochondrial GS expressed highly in basal cells, a secretory-cell GS, and lower expression of a ionocyte-specific GS than LUAD patients (p = 0.041, 0.0043 and 2.06e-06 respectively). Both LUAD and LUSC patients have lower expression levels of the immune GSs than the benign patients (p = 0.00034 and 0.0008). Concordant results were found in the AEGIS II samples with the same methods. Conclusion: We leveraged bulk and single cell gene expression data and identified molecular differences in the airway field of injury among ever smokers with LUSC versus LUAD that are highly expressed specific cell populations. Our results suggest that there are different responses to injury in the normal-appearing airway that are associated with NSCLC subtype. Citation Format: Xingyi Shi, Jiarui Zhang, Steven Callori, Joshua Campbell, Denise Fine, Yaron Gesthalter, Gang Liu, Xiaohui Xiao, Avrum Spira, Marc Lenburg, Jennifer Beane. NSCLC subtype-associated molecular and cellular alterations in the normal-appearing bronchial epithelium [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 3377.

Abstract 1137: Deep targeted and whole exome sequencing identifies driver mutations in the airway epithelium of individuals at high risk for lung cancer

Abstract Insights into tumor mutational burden of the airway epithelium may play important role in stratifying individuals at different levels of risk for lung cancer. Comparison of the genetic profiles of normal airway epithelial cells to tumor mutations can yield valuable information regarding shared mutations as well as presence of neoantigens. We hypothesized that cytologically normal bronchial epithelium of patients with lung cancer and those at high risk for lung cancer harbor driver mutations that can be identified by deep targeted sequencing of selected genes implicated in cancer and whole exome sequencing. We performed next generation sequence-based CAPP-Seq (CAncer Personalized Profiling by deep Sequencing) and whole exome sequencing (WES) of DNA from the bronchial epithelial cells from the bronchial brushings of individuals at-risk (low and high) for lung cancer and patients with lung cancer. Bronchial brushings were collected from consented individuals at the time of bronchoscopy at Vanderbilt University Medical Center and the Nashville Veterans Affairs Medical Center. We used Tammemagi risk model to calculate the risk of developing lung cancer. Lung tumor tissues from matched individuals were also sequenced. Using CAPPSeq, a total of 129 mutations were identified in bronchial brushings. Among individuals without cancer, driver mutations included TP53, PIK3CA, NOTCH1, KRAS, MET, CUL3, NF1, KEAP1 and EGFR mutations in 5 out of 13 high risk and 2 out of 7 low risk individuals. Among individuals with cancer, 13 out of 22 brushings harbored driver mutations in TP53, PIK3CA, ARID1A, PTEN, NOTCH1, KRAS, MET, NFE2L2, CUL3, NF1, and KEAP1 of which mutations in TP53 and PTEN were identified in both tumor and bronchial brushings. At least one mutation was called in 18 brushings of individuals with lung cancer. Mutations detected in both individuals with and without cancer were TP53, PIK3CA, NOTCH1, KRAS, MET, CUL3, and NF1. Using WES on the DNA from the same bronchial brushings (low risk-9; high risk-8 and lung cancer-17), we identified 90 mutations that were also identified by CAPPSeq. Most of the mutations identified by CAPPSeq with >5% variant allelic frequencies (VAF) were also identified by WES. However, WES was not sensitive enough to identify mutations with less than 0.5% VAF. Out of 9 mutations in TP53 identified in the brushings by CAPPSeq, 4 were identified by WES. Mutation in KMTD2, a histone methylation enzyme and believed to be a tumor suppressor, was identified by WES in the brushings and the tumor tissues of patients with lung cancer as well as in one high risk brushings. We identified mutations in cancer driver genes in the bronchial brushings of individuals with and without lung cancer. This field of cancerization effect may provide a tool for risk assessment for lung cancer. This research was funded by U01CA196405 to PPM. Citation Format: SM Jamshedur Rahman, Shih-kai Chu, Shilin Zhao, Yong Zou, Angela Hui, Thomas Stricker, Maximilian Diehn, Pierre P. Massion. Deep targeted and whole exome sequencing identifies driver mutations in the airway epithelium of individuals at high risk for lung cancer [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1137.

Coupled CRC 2D and ALI 3D Cultures Express Receptors of Emerging Viruses and Are More Suitable for the Study of Viral Infections Compared to Conventional Cell Lines.

Infections of emerging and reemerging viruses (SARS-CoVs, influenza H1N1, etc.) largely and globally affect human health. Animal models often fail to reflect a physiological status because of species tropism of virus infection. Conventional cell lines are usually genetically and phenotypically different from primary cells. Developing an in vitro physiological model to study the infection of emerging viruses will facilitate our understanding of virus-host cell interactions, thereby benefiting antiviral drug discovery. In the current work, we first established normal airway epithelial cells (upper and lower airway track) in 2D and 3D culture systems using conditional reprogramming (CR) and air-liquid interface (ALI) techniques. These long-term cultures maintained differentiation potential. More importantly, these cells express two types of influenza virus receptors, α2-6-Gal- and α2-3-Gal-linked sialic acids, and angiotensin-converting enzyme 2 (ACE2), a receptor for SARS-CoVs as well. These cells were permissive to the infection of pandemic influenza H1N1 (H1N1pdm). In contrast, the lung cancer cell line A549 and immortalized airway epithelial cells (16HBE) were not susceptible to H1N1 infection. A virus-induced cytopathic effect (CPE) on 2D CRC cultures developed in a time-dependent manner. The pathological effects were also readily observed spreading from the apical layer to the basal layer of the 3D ALI culture. This integrated 2D CRC and 3D ALI cultures provide a physiological and personalized in vitro model to study the infection of emerging viruses. This novel model can be used for studying virus biology and host response to viral infection and for antiviral drug discovery.

Conditionally Reprogrammed Human Normal Airway Epithelial Cells at ALI: A Physiological Model for Emerging Viruses.

Cancer cell lines have been used widely in cancer biology, and as biological or functional cell systems in many biomedical research fields. These cells are usually defective for many normal activities or functions due to significant genetic and epigenetic changes. Normal primary cell yields and viability from any original tissue specimens are usually relatively low or highly variable. These normal cells cease after a few passages or population doublings due to very limited proliferative capacity. Animal models (ferret, mouse, etc.) are often used to study virus-host interaction. However, viruses usually need to be adapted to the animals by several passages due to tropism restrictions including viral receptors and intracellular restrictions. Here we summarize applications of conditionally reprogrammed cells (CRCs), long-term cultures of normal airway epithelial cells from human nose to lung generated by conditional cell reprogramming (CR) technology, as an ex vivo model in studies of emerging viruses. CR allows to robustly propagate cells from non-invasive or minimally invasive specimens, for example, nasal or endobronchial brushing. This process is rapid (2 days) and conditional. The CRCs maintain their differentiation potential and lineage functions, and have been used for studies of adenovirus, rhinovirus, respiratory syncytial virus, influenza viruses, parvovirus, and SARS-CoV. The CRCs can be easily used for air-liquid interface (ALI) polarized 3D cultures, and these coupled CRC/ALI cultures mimic physiological conditions and are suitable for studies of viral entry including receptor binding and internalization, innate immune responses, viral replications, and drug discovery as an ex vivo model for emerging viruses.

Rhinovirus-infected COPD airway cells modulates innate immune function of alveolar macrophages via TGF-β1

Abstract Airway epithelium, a primary target for rhinovirus (RV), modulates innate immune responses of other cell types including, pulmonary macrophages. The majority of RV-infected patients with chronic obstructive pulmonary disease (COPD) also acquire secondary bacterial infections. We hypothesized that COPD airway epithelial cells (AEC) affect pulmonary macrophage innate immune functions through secreted products, thus promoting secondary bacterial infections. Pulmonary macrophages were pretreated with spent medium of RV- or sham-infected normal and COPD AEC and examined for innate immune responses to non-typeable H. influenzae (NTHI). Macrophages pretreated with spent medium from RV-infected COPD, but not normal AEC showed a defect in bacterial phagocytosis, and in the expression of cathelicidin, an antimicrobial peptide, and enhanced expression of CCL-20, TNF-α and CXCL-10 in response to NTHi. Proteomic analysis identified the presence of TGF-β1, tenascin C, fibronectin-1 in the secretome of RV-infected COPD, but not normal AEC. Neutralization of TGF-β1 abolished the inhibitory effects of spent medium from RV-infected COPD AEC on NTHi-induced cathelicidin and restored phagocytosis without significantly affecting NTHi-stimulated CCL-20, TNF-α and CXCL-10 in macrophages. These results indicate that RV-induced TGF-β1 secretion in COPD AEC attenuates the innate immune responses required for optimal clearing of bacteria by pulmonary macrophages and, this may increase the risk for acquiring secondary bacterial infections. At the same time, secretome from RV-infected COPD AEC may also increase inflammation via enhancing the bacteria-induced pro-inflammatory cytokines.

Intratracheal GLP-1 receptor agonist treatment up-regulates mucin via p38 and exacerbates emphysematous phenotype in mucus hypersecretory obstructive lung diseases

Glucagon-like peptide-1 (GLP-1) is a gastrointestinal hormone that stimulates glucose-mediated insulin production by pancreatic beta cells. It is also associated with protective effects in multiple tissues. GLP-1 receptor is highly expressed in pulmonary tissue, hinting possible pulmonary delivery of GLP-1 drugs. However, little is known about the role of GLP-1 signaling in the lung, especially in mucus hypersecretory obstructive lung diseases. Here, we showed that treatment with exendin-4, a clinically available GLP-1 receptor agonist, up-regulates mucin expression in normal airway epithelial cells and in the lung of normal mice, indicating mucus stimulatory effect of GLP-1 under physiological condition. Exendin-4 also increased mucin expression in in vitro cellular and in vivo murine models of obstructive lung diseases via the activation of p38 MAP kinase. Notably, mucin induction in vivo exacerbated key pulmonary abnormalities including emphysematous phenotypes, implying that GLP-1 signaling in the lung is detrimental under pulmonary obstructive condition. Another GLP-1 receptor agonist liraglutide had similar induction of mucin. Together, our studies not only demonstrate novel physiological and pathological roles of GLP-1 in the lung but may also caution against the clinical use of inhaled GLP-1 receptor agonists in the patients with obstructive lung diseases.

Rhinovirus-Induced SIRT-1 via TLR2 Regulates Subsequent Type I and Type III IFN Responses in Airway Epithelial Cells.

IFN responses to viral infection are necessary to establish intrinsic antiviral state, but if unchecked can lead to heightened inflammation. Recently, we showed that TLR2 activation contributes to limitation of rhinovirus (RV)-induced IFN response in the airway epithelial cells. We also demonstrated that compared with normal airway epithelial cells, those from patients with chronic obstructive pulmonary disease (COPD) show higher IFN responses to RV, but the underlying mechanisms are not known. Initially, RV-induced IFN responses depend on dsRNA receptor activation and then are amplified via IFN-stimulated activation of JAK/STAT signaling. In this study, we show that in normal cells, TLR2 limits RV-induced IFN responses by attenuating STAT1 and STAT2 phosphorylation and this was associated with TLR2-dependent SIRT-1 expression. Further, inhibition of SIRT-1 enhanced RV-induced IFN responses, and this was accompanied by increased STAT1/STAT2 phosphorylation, indicating that TLR2 may limit RV-induced IFN responses via SIRT-1. COPD airway epithelial cells showed attenuated IL-8 responses to TLR2 agonist despite expressing TLR2 similar to normal, indicating dysregulation in TLR2 signaling pathway. Unlike normal, COPD cells failed to show RV-induced TLR2-dependent SIRT-1 expression. Pretreatment with quercetin, which increases SIRT-1 expression, normalized RV-induced IFN levels in COPD airway epithelial cells. Inhibition of SIRT-1 in quercetin-pretreated COPD cells abolished the normalizing effects of quercetin on RV-induced IFN expression in these cells, confirming that quercetin exerts its effect via SIRT-1. In summary, we show that TLR2 is required for limiting RV-induced IFNs, and this pathway is dysregulated in COPD airway epithelial cells, leading to exaggerated IFN production.