Clusters of comorbidities in idiopathic pulmonary fibrosis

Exploring TβRI inhibitors from Arenaria kansuensis based on 3D-QSAR, molecular docking and molecular dynamics simulation methods and its anti-pulmonary fibrosis molecular mechanism validation

ETHNOPHARMACOLOGICAL RELEVANCE

Pulmonary fibrosis (PF) is a kind of interstitial lung disease that seriously threatens human life and health. Up to now, there is no specifically therapeutic drug. Arenaria kansuensis, a typical Tibetan medicine, has been previously proved to have anti-PF pharmacological activity by our group. However, the specific target and molecular mechanism of pharmacological active ingredients from it are still unknown.

AIM OF THE STUDY

This study aimed to explore the molecular mechanism and specific target of pharmacological active ingredients from A. kansuensis for treating PF.

MATERIALS AND METHODS

Virtual screening including 3D-QSAR, molecular docking and molecular dynamics simulation were used to screen TβRI inhibitor. CETSA experiment was used to verify the interaction between GAK (a β-carboline alkaloid isolated from A. kansuensis) and TβRI. Cell and molecular experiments including observation of cell morphology and Western blot were applied to investigate the molecular mechanism of action of GAK for treating PF. Animal experiments including physiological index, immunohistochemistry and ELISA were used to comprehensively evaluate the anti-PF effect of GAK and explore the corresponding mechanism of action.

RESULTS

Results of 3D-QSAR experiment indicated that GAK is a much stronger potential TβRI inhibitor, molecular mechanism study showed that 30 μM GAK could significantly keep TβRI more stable which indicated that the direct binding interaction between GAK and TβRI, it targetedly inhibited TβRI through forming hydrogen bonds with LYS232, SER280 and ASP351 and the binding energies is -56.05 kcal/mol. In vitro experiment showed GAK could suppress downstream signal pathways of TβRI including MAPK, PI3K/AKT and NF-κB pathways during EMT process. In vivo experiment showed that GAK could improve the survival rate and body weight of PF mice, alleviate the symptoms of histopathological severity, inflammatory cell infiltration and collagen deposition in lung tissue of PF mice through inhibiting EMT process of PF.

CONCLUSIONS

This work not only provided evidence to support GAK as a novel TβRI inhibitor for treating PF through multiple pathways, but also reveal the specific target and molecular mechanism of β-carboline alkaloids from A. kansuensis for treating PF.

Fibroblast activation protein and disease severity, progression, and survival in idiopathic pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is characterized by progressive fibrosis in the lungs. Activated fibroblasts play a central role in fibrogenesis and express fibroblast activation protein α. A truncated, soluble form (sFAP) can be measured in blood and is a potential novel biomarker of disease activity. The aim was to study the association between sFAP and clinical, radiological, and histopathological measures of disease severity, progression, and survival in a prospective, multicentre, real-world cohort of patients with IPF. Patients with IPF were recruited from the tertiary interstitial lung disease centres in Denmark and followed for up to 3 years. Baseline serum levels of sFAP were measured by ELISA in patients with IPF and compared to healthy controls. Pulmonary function tests, 6-minute walk test and quality of life measures were performed at baseline and during follow-up. The study included 149 patients with IPF. Median sFAP in IPF was 49.6 ng/mL (IQR: 43.1-61.6 ng/mL) and in healthy controls 73.8 ng/mL (IQR: 62.1-92.0 ng/mL). Continuous sFAP was not associated with disease severity, progression or survival (p > 0.05). After dichotomization of sFAP below or above mean sFAP + 2 SD for healthy controls, higher levels of sFAP were associated with lower FVC % predicted during follow-up (p < 0.01). Higher than normal serum levels of sFAP were associated with longitudinal changes in FVC % predicted, but sFAP did not show clear associations with other baseline or longitudinal parameters. As such, sFAP has limited use as a biomarker of disease progression or survival in patients with IPF.

Clinical, radiological and histopathological features of patients with familial pulmonary fibrosis

BACKGROUND

In familial pulmonary fibrosis (FPF) at least two biological relatives are affected. Patients with FPF have diverse clinical features.

RESEARCH QUESTION

We aimed to characterize demographic and clinical features, re-evaluate high-resolution computed tomography (HRCT) scans and histopathology of surgical lung biopsies, assess survival and investigate the suitability of risk prediction models for FPF patients.

STUDY DESIGN

A retrospective cohort study.

METHODS

FPF data (n = 68) were collected from the medical records of Oulu University Hospital (OUH) and Oulaskangas District Hospital between 1 Jan 2000 and 11 Jan 2023. The inclusion criterion was pulmonary fibrosis (PF) (ICD 10-code J84.X) and at least one self-reported relative with PF. Clinical information was gathered from hospital medical records. HRCT scans and histology were re-evaluated.

RESULTS

Thirty-seven (54.4%) of the patients were men, and 31 (45.6%) were women. The mean ages of the women and men were 68.6 and 61.7 years, respectively (p = 0.003). Thirty-seven (54.4%) patients were nonsmokers. The most common radiological patterns were usual interstitial pneumonia (UIP) (51/75.0%), unclassifiable (8/11.8%) and nonspecific interstitial pneumonia (NSIP) (3/4.4%). Pleuroparenchymal fibroelastosis (PPFE) was observed as a single or combined pattern in 13.2% of the patients. According to the 2022 guidelines for idiopathic pulmonary fibrosis (IPF), the patients were categorized as UIP (31/45.6%), probable UIP (20/29.4%), indeterminate for UIP (7/10.3%) or alternative diagnosis (10/14.7%). The histopathological patterns were UIP (7/41.2%), probable UIP (1/5.9%), indeterminate for UIP (8/47.2%) and alternative diagnosis (1/5.9%). Rare genetic variants were found in 9 patients; these included telomerase reverse transcriptase (TERT, n = 6), telomerase RNA component (TERC, n = 2) and regulator of telomere elongation helicase 1 (RTEL1, n = 1). Half of the patients died (n = 29) or underwent lung transplantation (n = 5), with a median survival of 39.9 months. The risk prediction models composite physiology index (CPI), hazard ratio (HR) 1.07 (95.0% CI 1.04-1.10), and gender-age-physiology index (GAP) stage I predicted survival statistically significantly (p<0.001) compared to combined stages II and III.

CONCLUSIONS

This study confirmed the results of earlier studies showing that FPF patients' radiological and histopathological patterns are diverse. Moreover, radiological and histological features revealed unusual patterns and their combinations.

Symptom-based drug prediction of lifestyle-related chronic diseases using unsupervised machine learning techniques

BACKGROUND AND OBJECTIVES

Lifestyle-related diseases (LSDs) impose a substantial economic burden on patients and health care services. LSDs are chronic in nature and can directly affect the heart and lungs. Therapeutic interventions only based on symptoms can be crucial for prompt treatment initiation in LSDs, as symptoms are the first information available to clinicians. So, this work aims to apply unsupervised machine learning (ML) techniques for developing models to predict drugs from symptoms for LSDs, with a specific focus on pulmonary and heart diseases.

METHODS

The drug-disease and disease-symptom associations of 143 LSDs, 1271 drugs, and 305 symptoms were used to compute direct associations between drugs and symptoms. ML models with four different algorithms - K-Means, Bisecting K-Means, Mean Shift, and Balanced Iterative Reducing and Clustering using Hierarchies (BIRCH) - were developed to cluster the drugs using symptoms as features. The optimal model was saved in a server for the development of a web application. A web application was developed to perform the prediction based on the optimal model.

RESULTS

The Bisecting K-means model showed the best performance with a silhouette coefficient of 0.647 and generated 138 drug clusters. The drugs within the optimal clusters showed good similarity based on i) gene ontology annotations of the gene targets, ii) chemical ontology annotations, and iii) maximum common substructure of the drugs. In the web application, the model also provides a confidence score for each predicted drug while predicting from a new set of input symptoms.

CONCLUSION

In summary, direct associations between drugs and symptoms were computed, and those were used to develop a symptom-based drug prediction tool for LSDs with unsupervised ML models. The ML-based prediction can provide a second opinion to clinicians to aid their decision-making for early treatment of LSD patients. The web application (URL - http://bicresources.jcbose.ac.in/ssaha4/sdldpred) can provide a simple interface for all end-users to perform the ML-based prediction.

Real-world practice of idiopathic pulmonary fibrosis: Results from a 2000-2016 cohort

The study aimed to investigate comorbidities, major adverse respiratory events, and mortality in patients with idiopathic pulmonary fibrosis (IPF). We established an IPF cohort and a comparative cohort matched for sex, age, and the date of IPF diagnosis. We recorded the most frequent comorbidities, the proportions, and time durations to the episode of major adverse respiratory events and death. Both cohorts were followed up to the end of 2016. We included 921 patients in the IPF cohort and 3,677 individuals in the comparative cohort. Comorbidities associated with IPF included pulmonary hypertension, chronic obstructive pulmonary disease, heart failure, asthma, and gastroesophageal reflux disease. The IPF cohort was more likely to have pneumonia (47.6 vs 12.0%), acute respiratory failure (17.8 vs 4.30%), chronic respiratory failure (4.23 vs 0.63%), and death (36.3 vs 15.0%) than the comparative cohort. The time durations to the first episode of pneumonia, acute respiratory failure, chronic respiratory failure, and death were 2.09 ± 2.98, 3.12 ± 3.62, 3.20 ± 4.03, and 3.27 ± 3.03 years in the IPF cohort. In conclusion, patients with IPF had significant comorbidities, particularly pulmonary and cardiovascular comorbidities. The duration from diagnosis to the major adverse respiratory events or death was short.

Effects of comorbid chronic kidney disease on mortality in idiopathic pulmonary fibrosis patients and influence of pirfenidone

Chronic kidney disease (CKD) is a comorbidity in idiopathic pulmonary fibrosis (IPF), and managing IPF with CKD is challenging due to limited options for antifibrotic therapy. The aim of this study was to examine the prevalence of CKD and prescription status of pirfenidone in IPF patients and to analyze its impact on mortality. Data from the Korean National Health Insurance Service (NHIS) database between October 2015 and September 2021 were used. IPF and CKD were defined based on both International Classification of Diseases 10th Revision (ICD-10) codes and Rare Intractable Disease (RID) codes. The risk of mortality was assessed based on accompanying CKD with or without antifibrotic therapy. Among 5038 patients with IPF, 8.4% had comorbid CKD and 83.3% with CKD did not receive renal replacement therapy (RRT). Patients with IPF and CKD were older, predominantly male, and had more frequent comorbidities such as cardiovascular disease and diabetes mellitus than subjects without CKD. Pirfenidone was prescribed to 105 (24.6%) of 426 CKD patients, and 89.5% of them did not receive RRT. Pirfenidone was also prescribed to 775 (16.8%) of 4612 IPF patients without CKD. Significant difference was not found in all-cause mortality between the IPF patients with or without CKD regardless of pirfenidone treatment. The use of antifibrotics in IPF patients with CKD is limited due to CKD severity; however, evidence is lacking. Mortality did not increase with accompanying CKD regardless of antifibrotic use. Further research on IPF and CKD is needed.

A serologically assessed neo-epitope biomarker of cellular fibronectin degradation is related to pulmonary fibrosis

BACKGROUND

Idiopathic pulmonary fibrosis (IPF) is characterized by excessive extracellular matrix (ECM) remodeling, herein ECM degradation. Fibronectin (FN) is an important component of the ECM that is produced by multiple cell types, including fibroblasts. Extra domain B (EDB) is specific for a cellular FN isoform which is found in the ECM. We sought to develop a non-invasive test to investigate whether matrix metalloproteinase 8 (MMP-8) degradation of EDB in cellular FN results in a specific protein fragment that can be assessed serologically and if levels relate to pulmonary fibrosis.

METHOD

Cellular FN was cleaved in vitro by MMP-8 and a protein fragment was identified by mass spectrometry. A monoclonal antibody (mAb) was generated, targeting a neo-epitope originating from EDB in cellular FN. Utilizing this mAb, a neo-epitope specific enzyme-linked immunosorbent assay (FN-EDB) was developed and technically validated. Serum FN-EDB was assessed in an IPF cohort (n=98), registered at clinicaltrials.gov (NCT02818712), and in healthy controls (n=35).

RESULTS

The FN-EDB assay had high specificity for the MMP-8 degraded neo-epitope and was technically robust. FN-EDB serum levels were not influenced by age, sex, ethnicity, or BMI. Moreover, FN-EDB serum levels were significantly higher in IPF patients (median 31.38 [IQR 25.79-46.84] ng/mL) as compared to healthy controls (median 28.05 [IQR 21.58-33.88] ng/mL, p=0.023).

CONCLUSION

We developed the neo-epitope specific FN-EDB assay, a competitive ELISA, as a tool for serological assessment of MMP-8 mediated degradation of EDB in cellular FN. This study indicates that degradation of EDB in cellular FN is elevated in IPF and warrants further investigation.

Telomere length associates with chronological age and mortality across racially diverse pulmonary fibrosis cohorts

Pulmonary fibrosis (PF) is characterized by profound scarring and poor survival. We investigated the association of leukocyte telomere length (LTL) with chronological age and mortality across racially diverse PF cohorts. LTL measurements among participants with PF stratified by race/ethnicity were assessed in relation to age and all-cause mortality, and compared to controls. Generalized linear models were used to evaluate the age-LTL relationship, Cox proportional hazards models were used for hazard ratio estimation, and the Cochran-Armitage test was used to assess quartiles of LTL. Standardized LTL shortened with increasing chronological age; this association in controls was strengthened in PF (R = -0.28; P < 0.0001). In PF, age- and sex-adjusted LTL below the median consistently predicted worse mortality across all racial groups (White, HR = 2.21, 95% CI = 1.79-2.72; Black, HR = 2.22, 95% CI = 1.05-4.66; Hispanic, HR = 3.40, 95% CI = 1.88-6.14; and Asian, HR = 2.11, 95% CI = 0.55-8.23). LTL associates uniformly with chronological age and is a biomarker predictive of mortality in PF across racial groups.

Current best clinical practices for monitoring of interstitial lung disease

INTRODUCTION

Interstitial lung diseases (ILDs) are a heterogeneous group of inflammatory and/or fibrotic conditions with variable outcome and often a dismal prognosis. Since many ILDs are progressive in nature, monitoring of signs and symptoms of progression is essential to inform treatment decisions and patient counseling. Monitoring of ILDs is a multimodality process and includes all aspects of the disease, e.g. measurement of pulmonary function and exercise capacity, symptom registration and quality of life (QoL), imaging, comorbidities and/or involvement of other organs to assess disease activity, symptom burden, treatment effects, adverse events, the need for supportive and palliative care, and lung transplantation.

AREAS COVERED

For this narrative review, we searched the PUBMED database to identify articles relevant for monitoring ILDs, including pulmonary function tests, exercise capacity, imaging, telemedicine, symptoms, and QoL.

EXPERT OPINION

Due to the high heterogeneity of the ILDs and their disease course, an individualized multimodality approach must be applied. Future strategies include use of telemedicine for home monitoring of lung function and symptoms, use of artificial intelligence to support automatized guidance of patients, computerized evaluation of ILD changes on imaging, and new imaging tools with less radiation dosage.

Colchicine Is a Weapon for Managing the Heart Disease Among Interstitial Lung Disease With Viral Infection: Have We Found the Holy Grail?

Background

This study investigated the effect of colchicine use on the risks of heart disease (HD), pericarditis, endocarditis, myocarditis, cardiomyopathy, cardiac arrhythmia, and cardiac failure in patients having interstitial lung disease (ILD) with virus infection (ILD cohort).

Methods

We retrospectively enrolled ILD cohort between 2000 and 2013 from the Longitudinal Health Insurance Database and divided them into colchicine users (n = 12,253) and colchicine non-users (n = 12,253) through propensity score matching. The event of interest was the diagnosis of HD. The incidence of HD was analyzed using multivariate Cox proportional hazards models between colchicine users and the comparison cohort after adjustment for age, sex, medication, comorbidities, and index date based on the time-dependent analysis.

Results

Colchicine users had a significantly lower risk of HD (aHR = 0.87, 95% confidence interval (CI]) = 0.82–0.92) than did the colchicine non-user. For colchicine non-users as the reference, the aHR (95% CI) of the patients who received colchicine of 2–7, 8–30, 31–150, and &gt; 150 days were 0.89 (0.81–0.98), 0.84 (0.76–0.94), 090 (0.80–0.99), and 0.83 (0.74–0.93), respectively; regardless of duration use, the lower risk of HD persisted in colchicine users. The cumulative incidence of HD in colchicine users was significantly lower than that in the colchicine non-users (log-rank p &lt; 0.001).

Conclusion

The addition of short-term or long-term colchicine to standard medical therapy may have benefits to prevent the HD among the ILD patients concurrent with a virus infection or comorbidities even in elderly patients.

Predicting checkpoint inhibitors pneumonitis in non-small cell lung cancer using a dynamic online hypertension nomogram

OBJECTIVES

Checkpoint inhibitors pneumonitis (CIP) is one of the most lethal adverse events in non-small cell lung cancer (NSCLC) patients treated with immune checkpoint inhibitors (ICIs). Currently, there is no recognized and effective predictive model to predict CIP in NSCLC.

MATERIALS AND METHODS

This study retrospectively analyzed 460 NSCLC patients who were first treated with ICIs. Patients were divided into three cohorts based on the occurrence of CIP: any grade CIP cohort, grade ≥ 2 CIP cohort and grade ≥ 3 CIP cohort.

RESULTS

A dynamic hypertension nomogram was constructed with elements including hypertension, interstitial lung disease (ILD), emphysema at baseline, and higher baseline platelet/lymphocyte ratio (PLR). The C indices of the training cohort and the internal and external validation cohort in any grade CIP cohort were 0.872, 0.833 and 0.840, respectively. The constructed hypertension nomogram was applied to grade ≥ 2 cohort and grade ≥ 3 cohort, and their C indices were 0.844 and 0.866, respectively. Compared with the non-hypertension nomogram, the hypertension nomogram presented better predictive power.

CONCLUSIONS

After validated by internal and external validation cohorts, the dynamic online hypertension has the potential to become a convenient, intuitive, and personalized clinical tool for assessing the risk of CIP in NSCLC patients.

Comorbidities in unclassifiable interstitial lung disease

BACKGROUND

Comorbidities are common in interstitial lung diseases (ILD) and have an important association with survival, but the frequency and prognostic impact of comorbidities in unclassifiable interstitial lung disease (uILD) remains elusive. We aimed to describe the prevalence of comorbidities and assess the impact on survival in patients with uILD. Furthermore, we aimed to identify and characterize potential phenotypes based on clusters of comorbidities and examine their association with disease progression and survival.

METHODS

Incident patients diagnosed with uILD were identified at two ILD referral centers in Denmark and Germany from 2003 to 2018. The diagnosis uILD was based on multidisciplinary team meetings. Clinical characteristics and comorbidities were extracted from ILD registries and patient case files. Survival analyses were performed using Cox regression analyses, disease progression was analyzed by linear mixed effects models, and clusters of comorbidities were analyzed using self-organizing maps.

RESULTS

A total of 249 patients with uILD were identified. The cohort was dominated by males (60%), former (49%) or current (15%) smokers, median age was 70 years, mean FVC was 75.9% predicted, and mean DLCO was 49.9% predicted. One-year survival was 89% and three-year survival was 73%. Eighty-five percent of the patients had ≥ 1 comorbidities, 33% had ≥ 3 comorbidities and 9% had ≥ 5 comorbidities. The only comorbidity associated with excess mortality was dyslipidemia. No association between survival and number of comorbidities or the Charlson comorbidity index was observed. Three clusters with different comorbidities profiles and clinical characteristics were identified. A significant annual decline in FVC and DLCO % predicted was observed in cluster 1 and 2, but not in cluster 3. No difference in mortality was observed between the clusters.

CONCLUSIONS

The comorbidity burden in uILD is lower than reported in other types of ILD and the impact of comorbidities on mortality needs further clarification. Three clusters with distinct comorbidity profiles were identified and could represent specific phenotypes. No difference in mortality was observed between clusters, but slower disease progression was observed in cluster 3. Better understanding of disease behavior and mortality will require further studies of subgroups of uILD with longer observation time.

Clusters of comorbidities in fibrotic hypersensitivity pneumonitis

BACKGROUND

Hypersensitivity pneumonitis (HP) is a type of interstitial lung disease (ILD) with a variable disease course and prognosis ranging from inflammatory and self-limiting to irreversible and progressive pulmonary fibrosis. Comorbidities are common in HP and may have an impact on prognosis. Due to the heterogeneity of HP presentation and progression, the identification of specific phenotypes in relationship to disease course and outcome is essential. The aim of this study was to identify clusters of comorbidities which could represent phenotypes in fibrotic HP and examine their impact on prognosis.

METHODS

Patients diagnosed with fibrotic HP at a tertiary referral center for ILD were included. Comorbidities were systematically registered and clusters of comorbidities were identified using cluster analyses. Disease progression and survival was estimated for each cluster.

RESULTS

The cohort comprised 211 patients with 53.6% males, mean age 63.0, baseline FVC 72.7%, DLCO 44.1%. Median follow-up time was 1.8 years (IQR 0.7-3.9). Three clusters with distinct comorbidity profiles and clinical characteristics were identified. One cluster dominated by elder male patients with predominantly cardiovascular diseases was associated with more respiratory hospitalizations and a worse prognosis. Differences in pulmonary function or exercise capacity trajectories between clusters were not observed.

CONCLUSIONS

Three clusters with distinct comorbidities were identified and could represent phenotypes in fibrotic HP not previously recognized. The worst prognosis was observed in a cluster dominated by elder males with cardiovascular diseases. Increased focus on prevention and treatment of comorbidities could potentially improve the prognosis of patients with fibrotic HP.

Validation of a derived version of the IPF-specific Saint George's Respiratory Questionnaire

Background

Health-related quality of life (HRQL) is impaired in patients with idiopathic pulmonary fibrosis (IPF). HRQL is often measured using the St. George’s Respiratory Questionnaire (SGRQ) despite the development of an IPF-specific version (SGRQ-I). Using data from a real-world cohort of patients with IPF, we aimed to transform SGRQ into a derived version of SGRQ-I, SGRQ-I_der, to examine the cross-sectional and longitudinal validity of SGRQ-I_der and to compare SGRQ-I_der to SGRQ-I.

Methods

Based on results from SGRQ, SGRQ-I_der was derived applying the algorithm used to develop SGRQ-I. Of the 50 items in SGRQ, 34 items were retained in SGRQ-I_der. Response options for seven items were collapsed and minor adjustments were made to the weights of two items after correspondence with the developers of SGRQ-I. Cross-sectional validation, responsiveness and minimal clinically important difference (MCID) were assessed by comparison to other HRQL instruments, pulmonary function tests and 6-min walk test performed at baseline, 6 and 12 months. Furthermore, the association between SGRQ-I_der scores and mortality was examined.

Results

A total of 150 IPF patients participated and 124 completed follow-up at 12 months. SGRQ-I_der performed comparably to SGRQ-I with a high concurrent validity, good test–retest reliability and high known-groups validity. SGRQ-I_der was responsive to change in HRQL and physiological anchors. MCID of SGRQ-I_der for improvement and deterioration was 3.5 and 5.7, respectively. SGRQ-I_der scores were associated with mortality in both univariate (HR 1.82, 95% CI 1.42–2.34 per 20-point increase) and multivariate analyses (HR 1.57, 95% CI 1.20–2.05 per 20-point increase).

Conclusions

The SGRQ-I_der is a valid, reliable and responsive HRQL instrument in patients with IPF and has psychometric properties comparable to SGRQ-I. Thus, SGRQ results can reliably be transformed into the SGRQ-I_der. The MCID estimates were calculated for improvement and deterioration separately. Increasing SGRQ-I_der score was associated with increased mortality.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12931-021-01853-2.