Idiopathic pulmonary fibrosis (IPF) is a devastating pulmonary disease with no curative treatment other than lung transplantation that results from maladaptive responses to lung epithelial injury; however, the underlying mechanisms remain unclear, and treatment options are limited. Here, we showed that deficiency in the innate immune receptor toll-like receptor 5 (TLR5) is associated with IPF in humans and with increased susceptibility to bleomycin-induced pulmonary fibrosis in mice and that activation of lung epithelial TLR5 through a synthetic flagellin analog protected mice from experimental fibrosis. Mechanistically, epithelial TLR5 activation induced antimicrobial gene expression and ameliorated lung dysbiosis after injury. In contrast, TLR5 deficiency in mice and patients with IPF was associated with lung dysbiosis. Elimination of the microbiome in mice through administration of antibiotics abolished the protective effect of TLR5, and reconstitution of the microbiome by fecal microbiota transplantation rescued the observed phenotype. In conclusion, these studies revealed that TLR5 protects against pulmonary fibrosis through effects on the lung microbiota, providing insight into therapeutic approaches that may ultimately benefit patients with IPF.

The MUC5B promoter variant rs35705950 is the dominant risk factor for the development of idiopathic pulmonary fibrosis (IPF), yet its low penetrance remains unexplained. All eight founder strains of the Diversity Outbred (DO) mouse population carry the risk allele at the orthologous site, yet exhibited variable bleomycin-induced MUC5B expression and fibrosis severity. Herein, using the DO bleomycin model, we find that the Muc5b locus regulates MUC5B expression at 3 weeks, and at 10 weeks, several quantitative trait loci (QTLs) are associated with radiologic features of lung fibrosis, such as parenchymal consolidations. Cross-species integrations with human IPF studies reveal heterogeneous epithelial patterns and variable correlation with MUC5B among orthologous QTL genes, and expression of novel proteins in pathognomonic lesions of IPF. This study establishes a radiomics-genetics resource generated from DO mice subjected to bleomycin-induced lung injury, enabling systematic dissection of genetically driven heterogeneity in addition to MUC5B in lung imaging traits.

Rationale:Idiopathic pulmonary fibrosis (IPF) is a rare, chronic, progressive lung disease with high mortality and few treatment options. Using an additive genetic model, genome-wide association studies (GWAS) have identified multiple risk loci highlighting new genes and pathways of interest. Since IPF risk could also be influenced by non-additive effects, we hypothesised that association analyses using alternative genetic models may provide additional mechanistic insight. Objectives:To perform GWAS of IPF susceptibility to detect associations where the underlying effects are consistent with recessive or dominant genetic models. Methods:We performed GWAS of IPF susceptibility, with logistic regression assuming dominant or recessive genetic models, including 5,159 IPF cases, from clinically-curated sources, and 27,459 controls. We functionally annotated independent signals and performed variant-to-gene mapping, applying fine-mapping to define potentially causal variants and genes. We assessed differential expression levels of genes of interest in publicly available single cell RNAseq data and in primary cells derived from IPF donors and controls. Main Results:We identified five genome-wide significant signals, under a recessive model, that had not been reported previously. These included exonic variants in the cell-cycle gene Polyamine-Modulated Factor 1 (PMF1) and in Epsin 3 (EPN3) genes. We also observed evidence of increased PMF1 expression in airway basal cells of IPF patients compared to controls. Conclusions:Using alternative genetic models in IPF susceptibility GWAS identified new signals and genes, providing new insights into IPF pathogenesis and potential future therapies.

Rationale:Preclinical familial pulmonary fibrosis (FPF) represents an early stage of fibrotic lung disease, yet the compartment- and cell-specific molecular programs preceding fibrosis remain poorly understood. Objective:To define spatially organized molecular signatures associated with preclinical FPF and identify tissue-informed circulating biomarkers linked to early fibrotic remodeling. Methods:We performed integrated multi-omic profiling of histologically preserved and remodeled lung regions from subjects with preclinical FPF, Idiopathic Pulmonary Fibrosis (IPF), and controls using spatial transcriptomics, single-nucleus RNA sequencing (snRNAseq), and blood proteomics. Differential expression and pathway enrichment analyses were performed across spatial compartments and epithelial cell states. Results:Histologically preserved lung regions in preclinical FPF demonstrated transcriptional abnormalities including stress-response, ciliary, and extracellular matrix-associated programs despite minimal architectural distortion. Spatial analyses identified alterations in alveolar niche molecular programs accompanied by increasing profibrotic signaling across preserved and tissue remodeled lung compartments. Compared with advanced IPF, preclinical FPF retained epithelial repair and surfactant-associated signatures. Integration with snRNAseq demonstrated enrichment of alveolar and airway epithelial cell dysregulated states associated with transitional phenotypes previously implicated in IPF. Compartment- and epithelial-associated transcriptional signatures identified in lung tissue were partially represented in the peripheral blood. Conclusion:Preclinical FPF is characterized by compartment- and cell-specific molecular programs that precede established fibrosis. We identified distinct alveolar, airway, and vascular molecular signatures and epithelial remodeling states represented in the peripheral blood. These findings provide an initial framework for molecular classification of early stages of pulmonary fibrosis and support future studies evaluating minimally invasive approaches for disease stratification and precision therapeutics. At a Glance Commentary:Scientific Knowledge on the Subject: The molecular events preceding a diagnosis of pulmonary fibrosis remain poorly understood. Most mechanistic studies in Idiopathic Pulmonary Fibrosis (IPF) have relied on end-stage explanted lungs, limiting insight into the compartment- and cell-specific molecular programs associated with early stages of pulmonary fibrosis.What this study adds to the field: Using integrated spatial transcriptomics, single-cell sequencing, and peripheral blood proteomic profiling, we demonstrate that preclinical familial pulmonary fibrosis (FPF) is characterized by compartment- and cell-specific molecular programs that precede clinically detectable fibrosis. Spatial analyses identified distinct alveolar, airway, and vascular molecular signatures, while single cell analysis confirmed the presence of epithelial dysregulated states. These signatures are partially represented in the peripheral blood. Our findings provide an initial framework for biologically informed classification of early stages of pulmonary fibrosis and future minimally invasive approaches for disease stratification.

RATIONALE:Common and rare variants that are associated with the risk of developing idiopathic pulmonary fibrosis (IPF) have been identified predominantly in European ancestry populations. OBJECTIVES:To better understand the genetic variants that contribute to IPF in individuals with Asian ancestry, we conducted a genome-wide association study of IPF in East Asian populations. METHODS:We included 1026 patients with IPF and compared them to 1723 unaffected controls of Japanese and Korean ancestry. Genome-wide association analysis was conducted in the Japanese and Korean ancestry cohorts separately and combined using meta-analysis. Restricted maximum likelihood was used to estimate the SNP-based heritability and local ancestry of chromosome 11 was inferred for each subject. MEASUREMENTS AND MAIN RESULTS:We identified loci on chromosomes 4 (FAM13A; rs7690839), 5 (TERT; rs7734992), 6 (DSP; rs2076295), and 11 (MUC5B; rs35705950) that were significantly associated with risk of IPF. Importantly, the sentinel variants in each of these loci are the same as, or in strong linkage disequilibrium with, the risk variants that have been observed in studies of European ancestry populations. In aggregate, common variants (not including the MUC5B promoter variant) account for approximately 25% of the risk of developing IPF in these East Asian ancestry cohorts. Moreover, local ancestry analysis indicates that the presence of MUC5B promoter variant in the East Asian population is not a result of admixture with European ancestry populations. CONCLUSIONS:We conclude that the IPF risk loci in East Asian populations are shared with those of European ancestry populations, although their risk allele frequencies and effect sizes differ. These findings indicate shared genetic risk factors of IPF across ancestries.

Background:Idiopathic pulmonary fibrosis (IPF) is a rare, incurable lung disease with a median survival of 3-5 years after diagnosis. Treatment options are limited. Genetic association studies can identify new genes involved in disease that might represent potential new drug targets, and it has been shown that drug targets with support from genetic studies are more likely to be successful in clinical development. Previous genome-wide association studies (GWAS) of IPF susceptibility have identified more than 20 signals implicating genes involved in multiple mechanisms, including telomere dysfunction, cell-cell adhesion, host defence immunity, various signalling pathways and, more recently, mitotic spindle assembly complex. Aim:To leverage new datasets and genotype imputation to discover further genes involved in development of IPF that could yield new pathobiological avenues for exploration and to guide future drug target discovery. Methods:We conducted a GWAS of IPF susceptibility including seven IPF case-control studies comprising 5,159 IPF cases and 27,459 controls of European ancestry, where IPF diagnosis was made by a respiratory clinician according to international guidelines. Genotypes were obtained from Whole Genome Sequencing (WGS) or from array-based imputation to the TOPMed WGS reference panel. New signals were replicated in independent biobanks with IPF defined using Electronic Healthcare Records. Bayesian fine-mapping was performed to identify the most likely causal variant(s) and bioinformatic investigation undertaken to map associated variants to putative causal genes. Results:We identified three novel genetic signals of association with IPF susceptibility. Genes prioritised by functional evidence at these signals included MUC1, which encodes a large transmembrane glycoprotein and known biomarker of lung fibrosis, and NTN4 encoding Netrin-4 whose known roles include angiogenesis. The third signal may map to SLC6A6, a taurine and beta-alanine transporter gene, previously implicated in retinal, cardiac and kidney dysfunction. Conclusion:Our study has identified new associations not previously identified by previous large biobank-based studies thereby highlighting the value of utilising clinically-curated IPF case-control studies, and new genotype imputation. We present new evidence for disease-driving roles of MUC1 and of endothelial cell and vascular changes in IPF.

BACKGROUND & AIMS:The ADMIRE CD trial demonstrated the efficacy and safety of darvadstrocel in patients with complex perianal fistulas from Europe and Israel. The efficacy and safety of darvadstrocel in an expanded patient population was investigated. METHODS:ADMIRE CD II (ClinicalTrials.gov, Number: NCT03279081) was a phase 3, double-blind, randomized, placebo-controlled trial conducted in Europe, Israel, and North America. Adults with Crohn's disease and complex perianal fistulas with ≤2 internal openings and ≤3 external openings and inadequate response to immunosuppressive agents or biologics were randomized 1:1 to receive darvadstrocel (a dispersion of 120 × 106 stem cells in 24 mL sterile buffered solution) or placebo. Both groups underwent curettage and closure of the internal opening. The primary endpoint was combined remission (closure of all treated external openings and absence of collections >2 cm) at week 24. RESULTS:Overall, 568 patients were randomized to receive darvadstrocel (n = 283) or placebo (n = 285); 249 and 246, respectively, completed the trial. At week 24, combined remission was achieved in 138 of 283 (48.8%) patients in the darvadstrocel group and 132 of 285 (46.3%) in the placebo group (estimated treatment difference: 2.4%; 95% CI, -5.8 to 10.6; P = .571). There were no significant differences in key secondary endpoints for darvadstrocel vs placebo (clinical remission at week 24 [P = .515] and time to clinical remission [P = .374]). Treatment-emergent adverse events were infrequent and experienced by similar proportions of patients receiving darvadstrocel (203/278 [73.0%]) and placebo (201/274 [73.4%]). CONCLUSIONS:ADMIRE CD II did not meet its primary endpoint of combined remission at week 24, with no statistically significant difference between darvadstrocel and placebo. No new safety signals were identified for darvadstrocel. CLINICALTRIALS:gov, Number: NCT002209456.

Introduction Interstitial lung abnormalities (ILAs) are early imaging markers of interstitial lung disease and pulmonary fibrosis. Occupational exposures to fumes and dusts are widespread and may especially impact individuals with familial susceptibility. We aimed to investigate the associations between occupational inhaled exposures and the risk of ILAs in individuals with potential familial susceptibility to pulmonary fibrosis.Methods We analysed data from 266 relatives of patients with familial or sporadic pulmonary fibrosis, enrolled in two cohorts: the Clinical Genetics and Screening for Pulmonary Fibrosis (n=184) and the Genetics of Pulmonary Fibrosis Study (n=82). Occupational exposures were determined through standardised questionnaires and categorised as vehicle fumes, non-vehicle fumes, mineral dusts, organic dusts, any fumes, any dusts or any dusts or fumes. Risk of ILAs was evaluated using modified Poisson models adjusted for age, sex and smoking status.Results The mean age of participants was 59.7 years and 23.7% had ILAs. Any occupational inhalational exposure was more common among participants with ILAs (27.0% for any fume) than among those without ILAs (16.7% for any fume). Exposure to any fumes, encompassing both vehicle and non-vehicle fumes, was associated with increased risk of ILAs (risk ratio (RR): 1.59, 95% CI 1.02 to 2.49). Similar positive but non-significant associations were observed for other exposures, including organic dusts, vehicle fumes, non-vehicle fumes and composite exposure.Discussion Occupational inhaled fume exposure is associated with higher risk of ILAs in individuals with potential familial susceptibility to pulmonary fibrosis. This highlights the potential value of considering occupational exposures in screening at-risk populations.

Summary We report that biallelic LRRK2 loss-of-function (LoF) causes a Mendelian form of interstitial lung disease characterized by alveolar epithelial cell dysfunction and lung fibrosis in two brothers with a homozygous nonsense variant. Integrated clinical, imaging, histopathological, and biomarker analyses showed absent LRRK2 protein, reduced Rab10 phosphorylation, impaired alveolar type 2 cell function, and disrupted surfactant homeostasis. Consistent with a recessive genetic disorder, heterozygous LoF carriers have not been reported to have a lung phenotype. Additional biallelic LRRK2 LoF cases were identified in ILD cohorts, linking LRRK2 LoF to lung disease, in contrast to heterozygous activating missense variants that cause Parkinson’s disease (PD).

RATIONALE:Idiopathic Pulmonary Fibrosis (IPF) is characterized by chronic progressive pulmonary fibrosis and high mortality. Genetic markers, summarized into a polygenic risk score (PRS), associate with IPF in well-phenotyped research cohorts. OBJECTIVES:To evaluate the performance of the PRS using real-world data from routinely captured electronic healthcare records. METHODS:We conducted an observational study evaluating the association of a PRS for IPF with electronic healthcare record diagnosis of IPF as well as lung transplant-free survival in four independent cohorts; the Mass General Brigham Biobank (MGBB), Mayo Clinic Biobank (MCBB), Mayo Clinic Tapestry Cohort (Tapestry), and U.K. Biobank (UKBB). We used multivariable logistic regression and multivariable Cox proportional hazards models adjusting for age, gender, and principal components of ancestry. The cohorts then underwent fixed and random effects meta-analysis. MEASUREMENTS AND MAIN RESULTS:Of 37,709; 44,195; 43,202; and 447,422 participants from MGBB, MCBB, Tapestry and UKBB respectively, 1,015 (2.7%) 2,879 (6.5%), 1,310 (3.0%), and 2,742 (0.6%) participants had an IPF diagnosis. Meta-analysis demonstrated a high-risk PRS associated with IPF diagnosis, OR 2.88 (95%CI 2.41-3.44) compared to all other individuals. A high-risk PRS also associated with the composite endpoint of mortality or lung transplant among those with an IPF diagnosis, HR 1.23(95%CI 1.11-1.35) compared to all other individuals. CONCLUSIONS:A PRS can identify those at risk for an IPF diagnosis and mortality in biobank-scale data, which may have implications for clinical decisions. Further work is necessary to evaluate the utility of adding genetics in clinical settings.

INTRODUCTION:Advanced therapies infrequently achieve complete fistula closure in patients with Crohn's disease (CD). The primary objective of the STOMP2 clinical trial was to determine whether the implantable autologous cell therapy AVB-114 is effective in inducing remission of persistent Crohn's perianal fistulas versus standard of care. METHODS:Eligible patients had a single perianal fistula tract and had failed previous treatment or had documented medication intolerance to biologic or conventional CD therapy. All enrolled subjects underwent surgical fistula optimization and adipose tissue biopsy collection (to manufacture AVB-114) followed by 1:1 randomization to either standard of care (repeat fistula optimization including seton replacement) or AVB-114 implantation. The primary end point was combined fistula remission at 36 weeks, defined as closure of the external opening, no drainage of fluid despite gentle finger compression, and no collections >2 cm in at least 2 of the 3 dimensions on MRI. RESULTS:Subjects at 14 US sites were equally randomized to SoC (N = 24) or AVB-114 (N = 24). Week 36 combined remission was 8.3% and 45.8% for subjects randomized to SoC and AVB-114, respectively (38% difference, 95% CI 11%-60%; P = 0.0078). At week 36, MRI revealed no subjects with collections >2 cm, radiological improvement (≥50% decrease in the Magnetic Resonance Novel Index for Fistula Imaging in Crohn's Disease (MAGNIFI-CD) score from baseline) in 1 SoC subject and 3 AVB-114 subjects, and radiological healing (complete resolution of T2-weighted hyperintensity in fistula tract) in 2 SoC subjects and 5 AVB-114 subjects. Through week 36, there were 40 and 56 treatment emergent adverse events for SoC and AVB-114, respectively. There were no serious treatment emergent adverse events in the AVB-114 group through week 36. DISCUSSION:A significantly higher proportion of patients treated with AVB-114 achieved combined remission vs SoC, and the treatment was well tolerated. These data support the safety and efficacy of AVB-114 in persistent Crohn's perianal fistulas.

Biological sex has systemic effects on gene expression, cell behavior, and disease etiology. Despite these widespread effects, sex as a biological variable is understudied, particularly in chronic lung diseases. In idiopathic pulmonary fibrosis (IPF), 70% of patients are male, and male patients have overall worse survival post-diagnosis. While behavioral differences between sexes might account for some of the epidemiological differences, the contribution of underlying biology is not known. In this study, we performed regional proteomic analysis via laser-captured microdissection-coupled mass spectrometry and analyzed the data for sex-biased protein expression. We discovered that even in control lung, sex differences existed in both airway and alveolar regions. Sex differences became more pronounced in diseased regions, with sex-biased expression of diverse proteins including those involved in extracellular vesicle secretion, cellular metabolism, and extracellular matrix remodeling. These data suggest that baseline sex differences in lung proteome may contribute to sex-specific susceptibility, progression, and clinical outcomes in IPF, underscoring the need for future mechanistic and clinical studies to account for sex as a biological variable.

Idiopathic pulmonary fibrosis (IPF) is a progressive, fatal lung disease that develops in response to chronic epithelial injury. Unlike injury-induced homeostatic lung repair during which fibroblasts undergo apoptosis and clearance, the lungs of IPF patients continue to accumulate apoptosis-resistant, pro-fibrotic, extracellular matrix-producing fibroblasts. Here, we show that prevention of PDGFRα+ fibroblast apoptosis by conditional BCL-2 expression leads to the emergence and persistence of senescent, pro-fibrotic fibroblasts along with enduring, pathologic fibrotic lung remodeling. Additionally, spatial transcriptomic studies of human IPF lungs confirmed the presence of senescent, BCL-2 expressing α-smooth muscle actin+ myofibroblasts in fibrotic regions. Of translational significance, selective BCL-2 inhibition with ABT-199 in fibrotic mice re-engaged the apoptotic pathway in fibroblasts, reduced senescence, and promoted fibrosis resolution and lung regeneration. Our findings suggest that sustained BCL-2 expression in fibroblasts prevents homeostatic lung repair, drives persistent fibrosis and is a therapeutically relevant target to reverse persistent pulmonary fibrosis.

RATIONALE:IPF is an irreversible and progressive type of lung fibrosis that is pathologically characterized as spatially heterogeneous. Despite the identified dominant risk factor for IPF as the gain-of-function MUC5B promoter variant, little is understood for how MUC5B drives lung fibrosis. OBJECTIVES:We used spatial transcriptomics from idiopathic pulmonary fibrosis (IPF) and unaffected control lung tissue to further understand the pathogenesis of MUC5B-driven lung fibrosis. METHODS:We captured 43 fields of view in 15 IPF and 13 controls with and without the MUC5B promoter variant using the CosMx® platform and identified 19 cell types via semi-supervised clustering. MEASUREMENTS AND MAIN RESULTS:MUC5B was ectopically expressed in AT2 cells in controls with the risk variant. We observed a decreased proportion of AT2 cells in controls and an increased proportion of aberrant basaloid cells in IPF associated with the MUC5B risk variant. We identified co-localized expression of MUC5B in respiratory bronchioles with 13 genes including the endoplasmic reticulum (ER) stress marker XBP1 and distal secretory markers SCGB3A1 and SCGB1A1. Experimentally, we demonstrated a direct relationship between MUC5B expression and ER stress in bronchiolar epithelia in vitro and validated the co-expression of MUC5B and XBP1 in the IPF lung. CONCLUSIONS:Based on our results, we conclude that MUC5B injures alveolar and bronchiolar epithelia that results in loss of AT2 cells and an increase in aberrant basaloid cells which initiates ER stress and a secretory phenotype in the terminal respiratory bronchiole, establishing a persistently injured distal airspace.