Genetics and Genomics of Pulmonary Fibrosis: Charting the Molecular Landscape and Shaping Precision Medicine

Updates in Diagnostic Tools for ILD

Interstitial lung disease (ILD) is a group of diffuse parenchymal disorders, which are diagnosed in many cases by multidisciplinary discussion (MDD). In some cases, diagnosis can be challenging, and the addition of histopathology can increase diagnostic confidence. The tools to obtain a histopathological sample to diagnose ILD are expanding. In this review, we will discuss the various modalities, their sensitivities and specificities, and procedural complication rates. In this review, we conducted a comprehensive review of literature focusing on emerging and established diagnostic tools for ILD. A systematic search of peer-reviewed publications was performed using PubMed with a focus on clinical trials, retrospective and prospective cohort studies, and systematic reviews. The key diagnostic modalities in focus were genomic classifier (GC), transbronchial cryobiopsy (TBLC), surgical lung biopsy (SLB), endobronchial ultrasound cryobiopsy (EBUS-C), genetic testing, and speckled transthoracic echocardiography (STE). Data extracted from these studies focused on diagnostic yield, specificity, sensitivity, and procedural complication rate. Genomic classifier, a gene-based molecular diagnostic tool, has a high specificity for histological usual interstitial pneumonia (UIP). However, in cases of a negative result, it often results in a need for further invasive sampling by TBLC or SLB. TBLC results in a larger histological sample, which can increase diagnostic yield and increase diagnostic confidence at MDD. Recent prospective trials have compared this modality with SLB and found 63-77% interobserver agreement between pathologists. SLB remains the gold standard with diagnostic yields reported to be more than 90%. EBUS-C has shown promising results increasing diagnostic yield in patients with suspected sarcoidosis or lymphoma. All diagnostic modalities have procedural complications with most common being pneumothorax, bleeding and, rarely, death. Advancements in diagnostic tools for interstitial lung disease (ILD) have significantly improved accuracy. Even though surgical lung biopsy remains the gold standard, the alternative modalities are promising and provide a promising yield with a lower procedural risk.

[Research Progress of Anti-lung Cancer Drug-related Interstitial Lung Disease]

Lung cancer is the cancer with the highest incidence and mortality rate worldwide. In addition to the diversified treatment and prolonged lifespan in view of the development of medical technology, the side effect of medicine should not be ignored. Drug-induced interstitial lung disease (DI-ILD) is also commonly encountered during this process, and ILD triggered by the treatment of lung cancer characterized by the inflammation and scarring of lung tissue after the antitumor treatment in lung cancer leads to a poor prognosis and high mortality. The diagnosis and treatment of ILD caused by anti-lung cancer agents remains challenging in clinical settings and requires joint efforts from multidisciplinary team (MDT). This review systematically updates the epidemiology, molecular pathogenesis, genomics/genetics study, diagnosis and treatment of ILD related to anti-lung cancer agents. By the integration of the latest evidences, the paper offers clinical work references for early diagnosis of ILD related to anti-lung cancer agents to enhance the survival and quality of life of the lung cancer patients.
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Genetic Testing Utilization in the U.S. Registry for Childhood Interstitial and Diffuse Lung Diseases

INTRODUCTION

Childhood interstitial and diffuse lung diseases (chILD) comprise a diverse group of rare disorders. Identifying the underlying cause is crucial for treatment, prognosis, and estimating recurrence risk. The objective of this study was to assess the utilization of genetic testing for subjects enrolled in the United States National Registry for ChILD, a multicenter observational study.

METHODS

Genetic data from participating sites were reviewed and analyzed in relationship to clinical characteristics.

RESULTS

Of 609 children enrolled from 22 centers, genetic testing was performed for 55.5% (n = 338). Genetic testing results were positive (diagnostic) for 22.8% (n = 77), negative for 60.7% (n = 205), and uncertain for 16.6% (n = 56). Most testing was performed through gene panels (55.9%), followed by exome sequencing (ES) or whole genome sequencing (WGS) (26.9%), single gene testing (24.6%), and/or chromosomal microarray (11.8%). For participants with positive (diagnostic) genetic testing results, the majority were diagnosed through gene panel (33.8%; n = 26) or single gene testing (32.5%; n = 25). The most common diagnosis confirmed by genetic testing was SFTPC-associated surfactant metabolism dysfunction. Of the 59 subjects with unclassified ILD, only 22% (n = 13) had undergone ES or WGS, 61% (n = 36) had received panel testing, and 27% (n = 16) did not have any genetic testing reported.

CONCLUSION

The utilization of genetic testing has been variable in infants and children enrolled in the ChILD Registry. Additional efforts are needed to develop genetic testing recommendations for children with suspected ILD. Furthermore, there is opportunity for broader utilization of ES/WGS and genetic discovery for children with lung disease of unclear etiology.

The Dawn of Precision Medicine in Fibrotic Interstitial Lung Disease

TOPIC IMPORTANCE

Interstitial lung diseases (ILDs) represent a broad group of heterogeneous parenchymal lung diseases. Some ILDs progress, causing architectural distortion and pulmonary fibrosis, and thus are called fibrotic ILDs. Recent studies have shown a beneficial effect of antifibrotic therapy in fibrotic ILDs other than idiopathic pulmonary fibrosis (IPF) that manifest progressive pulmonary fibrosis (PPF). However, it remains challenging to predict which patients with fibrotic ILDs will demonstrate PPF. Precision medicine approaches could identify patients at risk for progression and guide treatment in patients with IPF or PPF.

REVIEW FINDINGS

Multiple biomarkers able to highlight disease susceptibility risk, to provide an accurate diagnosis, and to prognosticate or assess treatment response have been identified. Advances in precision medicine led to the identification of endotypes that could discriminate patients with different fibrotic ILDs or patients with different disease courses. Importantly, recent studies have shown that particular compounds were efficacious only in particular endotypes. The aforementioned findings are promising. However, implementation in clinical practice remains an unmet need.

SUMMARY

Substantial progress has been observed in the context of precision medicine approaches in fibrotic ILDs in recent years. Nonetheless, infrastructure, financial, regulatory, and ethical challenges remain before precision medicine can be implemented in clinical practice. Overcoming such barriers and moving from a one-size-fits-all approach to patient-centered care could improve patient quality of life and survival substantially.

Modification of the course of disease progression in idiopathic pulmonary fibrosis by pirfenidone: evidence of the potential for disease reversal

Idiopathic pulmonary fibrosis (IPF) is a fibrosing pneumonia of unknown causation with a chronic, progressive course that may be modified by treatment with the antifibrotic agents, pirfenidone and nintedanib. Both drugs have been shown to slow disease progression, but, in rare cases, pirfenidone has been shown to stabilise and even improve lung function. We present a case of a patient whose lung function and pathognomonic features on CT imaging improved significantly on commencement of treatment with pirfenidone. Withholding pirfenidone was associated with a functional and morphological deterioration on imaging that subsequently reversed and stabilised following recommencement of this treatment. We discuss potential mechanisms that might explain this treatment response, compare our case to others described previously and the potential consequences that restricted prescribing within a specified range of vital capacity may have on the opportunity to influence the natural history of IPF early before irreversible fibrosis develops.

Spatial transcriptomics identifies molecular niche dysregulation associated with distal lung remodeling in pulmonary fibrosis

Large-scale changes in the structure and cellular makeup of the distal lung are a hallmark of pulmonary fibrosis (PF), but the spatial contexts that contribute to disease pathogenesis have remained uncertain. Using image-based spatial transcriptomics, we analyzed the gene expression of 1.6 million cells from 35 unique lungs. Through complementary cell-based and innovative cell-agnostic analyses, we characterized the localization of PF-emergent cell types, established the cellular and molecular basis of classical PF histopathologic features and identified a diversity of distinct molecularly defined spatial niches in control and PF lungs. Using machine learning and trajectory analysis to segment and rank airspaces on a gradient of remodeling severity, we identified compositional and molecular changes associated with progressive distal lung pathology, beginning with alveolar epithelial dysregulation and culminating with changes in macrophage polarization. Together, these results provide a unique, spatially resolved view of PF and establish methods that could be applied to other spatial transcriptomic studies.

Human respiratory airway progenitors derived from pluripotent cells generate alveolar epithelial cells and model pulmonary fibrosis

Human lungs contain unique cell populations in distal respiratory airways or terminal and respiratory bronchioles (RA/TRBs) that accumulate in persons with lung injury and idiopathic pulmonary fibrosis (IPF), a lethal lung disease. As these populations are absent in rodents, deeper understanding requires a human in vitro model. Here we convert human pluripotent stem cells (hPS cells) into expandable spheres, called induced respiratory airway progenitors (iRAPs), consisting of ~98% RA/TRB-associated cell types. One hPS cell can give rise to 1010 iRAP cells. We differentiate iRAPs through a stage consistent with transitional type 2 alveolar epithelial (AT2) cells into a population corresponding to mature AT1 cells with 95% purity. iRAPs with deletion of Heřmanský-Pudlák Syndrome 1 (HPS1), which causes pulmonary fibrosis in humans, replicate the aberrant differentiation and recruitment of profibrotic fibroblasts observed in IPF, indicating that intrinsic dysfunction of RA/TRB-associated alveolar progenitors contributes to HPS1-related IPF. iRAPs may provide a system suitable for IPF drug discovery and validation.

Gender Differences Are a Leading Factor in 5-Year Survival of Patients with Idiopathic Pulmonary Fibrosis over Antifibrotic Therapy Reduction

BACKGROUND

Idiopathic pulmonary fibrosis (IPF) is a chronic, progressive lung disease with a median survival of 3-5 years. Antifibrotic therapies like pirfenidone and nintedanib slow progression, but the outcomes vary. Gender may influence disease presentation, progression, and response to treatment. This study evaluates the impact of gender on the 5-year survival, pharmacological management, and clinical outcomes of patients with IPF.

METHODS

A retrospective cohort study of 254 IPF patients was conducted, with 164 (131 males:33 females) having complete data. Patients underwent spirometry, DLCO, and 6 min walk tests. Data on comorbidities, smoking, antifibrotic therapy type, dosage adjustments, and adverse events were collected. We used Kaplan-Meier survival curves and logistic regression to assess gender-related differences in outcomes.

RESULTS

Men had worse lung function at diagnosis (FVC 74.9 ± 18.5 vs. 87.2 ± 20.1% of pred.; p < 0.001) and a higher smoking prevalence (74% vs. 30%; p < 0.001). Women had better survival (51.2 vs. 40.8 ± 19.2 months; p = 0.005) despite more frequent biopsy use (36% vs. 17%; p = 0.013). Women tolerated longer therapy better (p = 0.001). No differences were found between patients receiving reduced antifibrotic dosing and those receiving full dosing.

CONCLUSIONS

Gender has a significant impact on IPF outcomes, with women demonstrating better survival and tolerance to long-term therapy. In contrast, reducing antifibrotic treatment does not appear to significantly affect survival outcomes. These findings underscore the need for future research on gender-specific management approaches.

Progressive lung fibrosis: reprogramming a genetically vulnerable bronchoalveolar epithelium

Idiopathic pulmonary fibrosis (IPF) is etiologically complex, with well-documented genetic and nongenetic origins. In this Review, we speculate that the development of IPF requires two hits: the first establishes a vulnerable bronchoalveolar epithelium, and the second triggers mechanisms that reprogram distal epithelia to initiate and perpetuate a profibrotic phenotype. While vulnerability of the bronchoalveolar epithelia is most often driven by common or rare genetic variants, subsequent injury of the bronchoalveolar epithelia results in persistent changes in cell biology that disrupt tissue homeostasis and activate fibroblasts. The dynamic biology of IPF can best be contextualized etiologically and temporally, including stages of vulnerability, early disease, and persistent and progressive lung fibrosis. These dimensions of IPF highlight critical mechanisms that adversely disrupt epithelial function, activate fibroblasts, and lead to lung remodeling. Together with better recognition of early disease, this conceptual approach should lead to the development of novel therapeutics directed at the etiologic and temporal drivers of lung fibrosis that will ultimately transform the care of patients with IPF from palliative to curative.

Interstitial Lung Disease Epidemiology in the Past Three Decades: A Narrative Review

Current epidemiological data on interstitial lung disease (ILD) are still poor. The principal cause of the discordant data is associated with a heterogeneous group of respiratory diseases that includes a large number, about 200 families, with low frequency, distinct and sometimes unknown etiology, and different progression. In fact, some conditions spontaneously resolve, whereas others, such as IPF and most non-IPF ILDs, progress to respiratory failure and death despite treatment. Furthermore, epidemiological data are limited. The scope of the narrative review is to report ILD incidence and prevalence in registries from different countries in the last three decades. We identified 20 ILD registries (17 prospective and 3 retrospective) from major countries in Europe (n = 10), Asia (n = 7), North America (n = 2), and Oceania (n = 1). Significant discrepancies in ILD and ILD subtype prevalence and incidence among countries are reported in registries. These discrepancies could be determined by different ethnicities and socioeconomic conditions as well as by updates in disease diagnosis and classification. ILD epidemiological registries are progressively ameliorating through better adherence to updated guidelines and classification codes. An accurate and definite diagnosis and compilation of ILD epidemiological registries will be useful for a more precise monitoring of disease progression and treatment. Future research to identify the populations with the highest risk factors, including genetic and molecular studies, and implementation of disease progression scores are needed to improve ILD clinical assessment.

Genetic evidence reveals a causal relationship between rheumatoid arthritis and interstitial lung disease

Background/purpose: Previous epidemiological studies have associated interstitial lung disease (ILD) with rheumatoid arthritis (RA), yet the causality of this relationship remains uncertain. This study aimed to investigate the genetic causal link between ILD and RA. Methods: Genome-wide association study (GWAS) statistics for ILD and RA were collected from public datasets. Relevant single-nucleotide polymorphisms (SNPs) were selected by executing quality control steps from the GWAS summary results. A two-sample bidirectional Mendelian randomization (MR) analysis was performed to assess the causal relationship between the two conditions. The MR analysis primarily used the inverse variance weighting (IVW), weighted median (WM), and MR-Egger regression methods. Sensitivity analyses, including MR-Egger, leave-one-out, and MR Pleiotropy RESidual Sum and Outlier (MR-PRESSO), were conducted to evaluate the heterogeneity and pleiotropy. Replication analyses using Asian datasets were also conducted to enhance the robustness of our findings. Results: In the European population, RA was found to increase the risk of ILD by 9.6% (OR: 1.096, 95% CI: 1.023-1.174, p = 0.009). Conversely, ILD was associated with a 12.8% increased risk of RA (OR: 1.128, 95% CI: 1.013-1.256, p = 0.029). Replication analyses from Asian GWAS further supported these findings, particularly the increased risk of ILD attributable to RA (OR: 1.33, 95% CI: 1.18-1.49, p-value <0.001). Conclusion: Our findings underscore the clinical importance of screening for ILD in RA patients and suggest that effective management of RA could significantly benefit ILD patients. The potential applicability of novel RA treatments to ILD warrants further exploration. Additionally, racial disparities in the manifestation of these diseases should not be overlooked, as they may offer new perspectives for targeted therapies in diverse populations.