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PLOS One logoLink to PLOS One
. 2024 Oct 3;19(10):e0311357. doi: 10.1371/journal.pone.0311357

Panel of serum biomarkers for differential diagnosis of idiopathic interstitial lung disease and interstitial lung disease-secondary to systemic autoimmune rheumatic disease

Miriana d’Alessandro 1,*, Paolo Cameli 1, Caroline V Cotton 2, Janine A Lamb 3, Laura Bergantini 1, Sara Gangi 1, Sarah Sugden 3, Lisa G Spencer 4, Bruno Frediani 5, Robert P New 6, Hector Chinoy 6,7, Elena Bargagli 1, Edoardo Conticini 5
Editor: Masataka Kuwana8
PMCID: PMC11449321  PMID: 39361584

Abstract

Background

Interstitial lung disease (ILD) may complicate the course of systemic autoimmune rheumatic disease (SARD) and diagnostic biomarkers are needed. Krebs von den Lungen-6 (KL-6), ferritin (FER) and interleukin 6 (IL-6) have been involved in the ILD development. Our study aimed to compare KL-6, FER, IL-6 and soluble mesothelin-related peptide (SMRP) concentrations in a cohort of idiopathic and SARD-ILD.

Methods

3169 patients were enrolled in the “UK Biomarkers in Interstitial Lung Disease (UK-BILD) Study”. We selected patients affected by SARD-ILD and idiopathic ILD (usual interstitial pneumonia-idiopathic pulmonary fibrosis and fibrotic non-specific interstitial pneumonia). Serum marker concentrations were measured through chemiluminescent assays (Fujirebio Europe, Ghent, Belgium).

Results

1013 patients were selected for the study: 520 (51.3%) had idiopathic ILD and 493 (48.7%) SARD-ILD. Idiopathic ILD patients displayed higher KL-6 values than SARD-ILD (p = 0.0002). FER and SMRP, though within normal ranges, were significantly higher in idiopathic ILD (p<0.0001). Logistic regression showed good sensitivity (69.4%) and specificity (80.4%) selecting the variables FER and KL-6 concentrations, age and gender-male correlated with a diagnosis of idiopathic ILD.

Conclusion

Our study showed the excellent diagnostic value of KL-6 for detecting ILD, which irrespective of the final diagnosis and extent of disease, is always elevated and is a reliable biomarker of lung fibrosis in various diseases, ranging from idiopathic to autoimmune forms. Our study proposed an ILD differentiation model including clinical background. In this context, combination of serum markers and clinical data, as seen in our cohort, may lead to a further improvement in diagnostic accuracy for ILD.

Introduction

Interstitial lung disease (ILD) may complicate the course of systemic autoimmune rheumatic disease (SARD) [1,2], and is one of the leading causes of morbidity and mortality [3,4]. No definite diagnostic work-up has yet been validated for these patients, nor does robust evidence exist for optimal management, as SARD-ILD not always responds to conventional immunosuppressants, which are the mainstay of therapy for SARD. Diagnosis and management of SARD-ILD requires a comprehensive, multidisciplinary, individualized approach that relies mainly on pulmonary function tests (PFT), high-resolution computed tomography (HRCT) of the chest and sometimes also lung biopsy [5]. A multidisciplinary assessment is highly recommended by international guidelines for the diagnostic pathway of ILD, including at least pulmonologists, radiologists, rheumatologists, in order to optimise the diagnostic accuracy and guarantee the earliest and more proper therapeutic proposal. Despite this recommendation, a significant percentage of ILD patients still receives a “working diagnosis”, since clinical symptoms and immunological assessment may not always be sufficient for a confident diagnosis and potentially invasive samplings (such as cryobiopsy or lung surgical biopsy) may not be suitable due to the frailty of clinical conditions [6]. Non-invasive biomarkers for early detection of lung involvement and its severity are badly needed.

Krebs von den Lungen-6 (KL-6) is a high-molecular-weight glycoprotein mainly expressed on proliferating, regenerating and injured type II alveolar epithelial cells (AECs) [7]. It has been suggested as a mainly prognostic serum marker of fibrosis in ILD patients, including those with idiopathic pulmonary fibrosis (IPF) [8,9] and hypersensitivity pneumonitis (HP) [10,11], as well as in SARD-ILD patients, including those with anti-synthetase syndrome (ASS) [12], dermatomyositis (DM) [13,14], systemic sclerosis (SSc) [1518], primary Sjögren’s syndrome (pSS) [19,20], rheumatoid arthritis (RA) [21,22] and ANCA-associated vasculitis [23]. KL-6 concentrations seem to have a positive correlation with the degree of lung impairment detectable by HRCT and a negative correlation with forced vital capacity (FVC) and diffusing capacity of the lungs for carbon monoxide (DLCO) [24]. Since this correlation reflects the severity of SARD-ILD, it can be useful to select patients who could benefit from HRCT and PFT and spare others excessive exposure to radiation and unnecessary procedures, while reducing healthcare costs. Interestingly, in patients with confirmed ILD, KL-6 may decrease during remission of inflammatory activity, but usually remains above normal values.

As far as other serum biomarkers are concerned, ferritin (FER) is a key protein of iron metabolism capable of sequestering large amounts of iron, and thus serves the dual function of iron detoxification and iron storage; it seems to be an important regulator of the immune system, playing a central role in autoimmune diseases [25]. A growing body of data shows that serum FER is correlated with disease activity and poor prognosis in anti-MDA5-positive DM-ILD patients [26,27], with reported cut-off values that vary from 500 to 1500 ng/ml [28]. Conversely, no data exists on serum FER in other forms of SARD. Interleukin 6 (IL-6) is a pleiotropic cytokine involved in the physiology of virtually every organ system. Controlling IL-6 activity is potentially an effective approach in the treatment of various autoimmune and inflammatory diseases. On the other hand, like calretinin, a well-known marker correlated with IPF severity, soluble mesothelin-related peptide (SMRP) is a surface marker of mesothelial cells, such as pleural mesothelial cells (PMC). No data is available on the role of SMRP in SARD-ILD patients. Nevertheless, recent evidence highlights the role of mesothelin (MSLN which binds cancer antigen CA-125 also known as MUC16) in pulmonary fibrosis, suggesting that MSLN is involved in cell adhesion [29]. The literature reports a role of MUC16 in the development and progression of IPF through the TGF-β1 canonical pathway. The above evidence suggests that FER, KL-6, SMRP and IL-6 may provide a serum biomarker profile that can distinguish the progression of fibrotic damage due to inflammatory activity in SARD-ILD, making it possible to optimize therapeutic management with immunosuppressants and/or antifibrotics.

Here we explore the landscape of serum biomarkers in idiopathic and SARD-ILD in a large cohort of patients from the UK Biomarkers in Interstitial Lung Disease (UK-BILD) Study. The primary endpoint of our study was to assess serum concentrations of IL-6, SMRP, KL-6 and FER in a large cohort of idiopathic or non-idiopathic ILD patients. Secondary endpoints were: to assess whether these biomarkers may be considered specific for SARD-ILD as distinct from idiopathic ILD; to evaluate the association with clinical and imaging findings; and to construct a panel for differential diagnosis.

Methods

Patients included in the “UK Biomarkers in Interstitial Lung Disease (UK-BILD) Study” were retrospectively enrolled from 39 UK recruitment centres between 07th January 2015 and 07th December 2018. The UK-BILD cohort recruited 3169 in which patients must have HRCT-proven ILD, and their investigations must have included “routine” serology. All recruiting clinicians completed a two-page clinical proforma documenting the following data: age, gender, ethnicity, smoking history, diagnosis of SARD-ILD and idiopathic ILD, SARD signs (including Raynaud, arthralgia/arthritis, sclerodactyly, calcinosis, elevated CK, mechanic’s hands, myalgia, periungual erythema, telangiectasia), ILD signs (including digital clubbing, inspiratory crackles, pulmonary hypertension features) and recruiting centre information.

The SARD-ILD group included patients with a diagnosis of pSS, RA, systemic lupus erythematous (SLE), mixed connective tissue disease (MCTD), polymyositis (PM), dermatomyositis (DM), undifferentiated connective tissue disease (UCTD), limited and diffuse SSc and unknown CTD, according to international classification criteria [3037]. The idiopathic ILD group included patients with a diagnosis of usual interstitial pneumonia-(UIP-)IPF and fibrotic non-specific interstitial pneumonia (NSIP), diagnosed according to American Thoracic Society/European Respiratory Society (ATS/ERS) guidelines [38]. In all Centres, multidisciplinary discussion for diagnostic assessment included respiratory physicians, radiologists, rheumatologists and, in case of tissue sampling for diagnostic purposes, histopathologists, all with a specific expertise in ILD setting. The study was conducted according to the guidelines of the Declaration of Helsinki and approved for “UK Biomarkers in Interstitial Lung Disease (UK-BILD) Study”. All patients gave their written informed consent to participation in the study.

For biomarker analysis, inclusion criteria were a diagnosis of IPF, idiopathic NSIP and SARD-ILD; exclusion criteria were a diagnosis of hypersensitivity pneumonitis, sarcoidosis, asbestosis, idiopathic cryptogenic organizing pneumonia, respiratory bronchiolitis, Langerhans cell’s histiocytosis, lymphangioleiomyomatosis, desquamative interstitial pneumonia, acute interstitial pneumonia, lack of serum sample, insufficient or no clinical data, a previous diagnosis (last 5 years) of malignancy and too few patients for statistical analysis.

Serum samples were obtained from recruited patients, anonymized in an electronic database and marker concentrations were measured singly by KL-6, IL-6, FER and SMRP reagent assays (Fujirebio Europe, Ghent, Belgium). The reagents were designed for fully automated chemiluminescent enzyme immunoassay with the LUMIPULSE G System (Fujirebio Europe, Ghent, Belgium). The principle of the assay is agglutination of sialylated carbohydrate antigen with KL-6, IL-6, FER and SMRP mAbs by antigen-antibody reaction. The change in absorbance was measured to determine serum concentrations of KL-6 expressed in U/mL, IL-6 in pg/mL, FER in ng/mL and SMRP in nmol/L. Reference calibrator values were 0 and 1000 ng/mL for FER, 0, 2 and 100 nmol/L for SMRP, 0, 500 and 10000 U/mL for KL-6 and 0, 20, 400 and 1000 pg/mL for IL-6. The reference intervals for FER concentrations in the low range were 31.5–75.0 ng/mL, and in the high range 280–520 ng/mL. The reference ranges for SMRP were 1.11–1.84 nmol/L (low) and 9.39–15.65 nmol/L (high), and for KL-6 258–387 U/mL (low) and 659–988 U/mL (high). For IL-6 we used the standardized reference ranges 32.2–49.4 pg/mL (low) and 195–299 pg/mL (high) [39].

Statistical analysis

All data is reported as mean ± standard deviation or median and interquartile range (IQR), as appropriate. The Shapiro-Wilk test was used to determine normal distribution. Multiple comparisons were assessed by non-parametric one-way ANOVA (Kruskal-Wallis test) and the Dunn test. The validity of serum marker concentrations used to distinguish SARD-ILD and idiopathic ILD patients was assessed by areas under the receiver operating characteristic (AUROC) curve. Sensitivity and specificity were calculated for cut-offs of the different variables. The Youden index (J = max [sensitivity + specificity − 1]) was used to establish the best cut-offs.

Patients were further stratified according to HRCT findings and comparative analysis of serum marker concentrations were performed within and between the following groups: the idiopathic ILD group included probable fibrotic NSIP on HRCT (IPF confirmed at multidisciplinary discussion, >65 years old, without UIP confirmation at lung biopsy), definite UIP and definite fibrotic NSIP (UIP confirmed at lung biopsy). For SARD patients, those with RA and SSc displaying a UIP pattern (SARD-UIP) were considered separately from those with NSIP (SARD-NSIP).

Machine learning analysis with variable-importance plot was performed to construct a model selecting variables to make accurate predictions. The more a model relies on a variable to make predictions, the more important it is for the model. Binomial logistic regression and ROC curve analysis were used to predict the diagnostic value of each serum marker/clinical parameter for SARD-ILD against clinical diagnosis. Supervised Principal Component Analysis using Kaiser-Guttman rule was performed in an exploratory approach to identify trends in immunological (KL-6, IL-6, SMRP, FER) and demographic (age) features by 2D representation of the multi-dimensional data set.A p-value less than 0.05 was considered statistically significant. Statistical analysis was performed with GraphPad Prism 9.3 and Jamovi software 2.3.

Results

The total number of patients selected for the study from UK-BILD cohort was 1239. We excluded 108 (8.7%) from the study due to insufficient or unavailable demographic and clinical data, 103 (8.3%) due to malignancies, 3 (0.2%) due to inclusion body myositis, 1 due to anti-synthetase syndrome (0.08%) and 11 (0.9%) due to an unknown disease subtype. The remaining 1013 patients (median and interquartile range, 70 (61–77) years) were enrolled in the study: 520 (51.3%) had idiopathic ILD and 493 (48.7%) had been diagnosed with SARD-ILD. Their demographic, clinical and immunological data is reported in Table 1.

Table 1. Demographic data, including age, gender, smoking and ethnicity in idiopathic ILD and SARD-ILD groups.

  Idiopathic ILD (N = 520) SARD-ILD (N = 493) p value
age  
    Median (IQR) 73.5 (68–79) 64 (54–72) <0.0001
Gender, n (%) <0.0001
    Female 132.0 (25.4%) 326.0 (66.1%)  
    Male 388.0 (74.6%) 167.0 (33.9%)  
smoking history, n (%) <0.0001
    Never smoker 167.0 (32.1%) 246.0 (49.9%)  
    Former or current smoker 353.0 (67.9%) 247.0 (50.1%)  
ARD subgroup, n (%)
    SSc Limited 48.0 (9.7%)  
    SSc Diffuse 24.0 (4.9%)  
    UCTD 42.0 (8.5%)  
    CTD (Unknown) 6.0 (1.2%)  
    MCTD 29.0 (5.9%)  
    PM 27.0 (5.5%)  
    DM 26.0 (5.3%)  
    Sjogren syndrome 21.0 (4.3%)  
    RA 198.0 (40.2%)  
    SLE 19.0 (3.9%)  
    Other 53.0 (10.8%)  
Ethnicity, n (%) <0.0001
    Caucasian 512.0 (98.5%) 382.0 (77.5%)  
    Asian 6.0 (1.2%) 44.0 (8.9%)  
    African 0.0 (0.0%) 15.0 (3.0%)  
    Afro-Caribbean 1.0 (0.2%) 38.0 (7.7%)  
    Others–specify 0.0 (0.0%) 7.0 (1.4%)  
    Mixed–specify 1.0 (0.2%) 7.0 (0.0%)  
IPF diagnosis, n (%)
    Not-UIP 47.0 (9.0%)  
    Definite UIP by HRCT 332.0 (63.8%)
    Definite Fib NSIP on HRCT and LBx with UIP 35.0 (6.7%)
    Probable Fib NSIP on HRCT no LBx, >65 yrs old and MDT diagnosis IPF 106.0 (20.4%)  
PULMONARY SIGNS/SYMPTOMS
Clubbing, n (%) <0.0001
    No 377.0 (72.5%) 450.0 (91.3%)  
    Yes 143.0 (27.5%) 43.0 (8.7%)  
End inspiratory crackle, n (%) <0.0001
    No 150.0 (28.8%) 197.0 (40.0%)  
    Yes 370.0 (71.2%) 296.0 (60.0%)  
Pulmonary hypertension*, n (%) 0.1510
    No 508.0 (97.7%) 475.0 (96.3%)  
    Yes 12.0 (2.3%) 18.0 (3.7%)  
ARD SIGNS/SYMPTOMS:
Sclerodactyly, n (%) <0.0001
    No 519.0 (99.8%) 437.0 (88.6%)  
    Yes 1.0 (0.2%) 56.0 (11.4%)  
Calcinosis, n (%) <0.0001
    No 519.0 (99.8%) 473.0 (95.9%)  
    Yes 1.0 (0.2%) 20.0 (4.1%)  
Raised ck, n (%) <0.0001
    No 517.0 (99.4%) 443.0 (89.9%)  
    Yes 3.0 (0.6%) 50.0 (10.1%)  
Mechanic’s hand, n (%) <0.0001
    No 519.0 (99.8%) 458.0 (92.9%)  
    Yes 1.0 (0.2%) 35.0 (7.1%)  
Myalgia, n (%) <0.0001
    None 518.0 (99.6%) 429.0 (87.0%)  
    Yes 2.0 (0.4%) 64.0 (13.0%)  
Periungual erythema, n (%) 0.0043
    No 492.0 (94.6%) 440.0 (89.2%)  
    Yes 28.0 (5.4%) 53.0 (10.8%)  
Telangiectasia, n (%) <0.0001
    No 518.0 (99.6%) 447.0 (90.7%)  
    Yes 2.0 (0.4%) 46.0 (9.3%)  
Arthralgia/arthritis, n (%) <0.0001
    No 508.0 (97.7%) 213.0 (43.2%)  
    Yes 12.0 (2.3%) 280.0 (56.8%)  
Raynaud, n (%) <0.0001
    No 510.0 (98.1%) 311.0 (63.1%)  
    Yes 10.0 (1.9%) 182.0 (36.9%)  
Laboratory parameters:
KL-6 U/mL  
    Mean (SD) 1604.4 (1235.2) 1522.9 (1430.8) 0.0002
FER ng/mL  
    Mean (SD) 134.3 (138.4) 87.3 (105.4) <0.0001
IL-6 pg/mL  
    Mean (SD) 87.8 (222.4) 99.6 (241.4) 0.4673
SMRP nmol/L  
    Mean (SD) 1.2 (0.7) 1.1 (0.7) <0.0001

Clinical findings including ATD subgroups, HRCT patterns and rheumatological signs. Immunological data including serum concentrations of KL-6, FER, IL-6 and SMRP in the ILD and SARD-ILD groups. Abbreviations: ILD, interstitial lung disease; SARD, autoimmune rheumatic disease; RA, rheumatoid arthritis; SLE, systemic lupus erythematous; MCTD, mixed connective tissue disease; UCTD, undifferentiated connective tissue disease; PM, polymyositis; DM, dermatomyositis; SSc, systemic sclerosis; CTD, connective tissue disease; IPF, idiopathic pulmonary fibrosis; UIP, usual interstitial pneumonia; HRCT, high resolution computed tomography; NSIP, non-specific interstitial pneumonia; MDT, multidisciplinary discussion team; LBx, lung biopsy; KL-6, krebs von den lungen-6; FER, ferritin; IL-6, interleukin-6; SMRP, soluble mesothelin-related peptide.

*: Defined as mean pulmonary arterial pressure > 20 mmHg, measured through right heart catheterization.

Idiopathic ILD versus SARD-ILD

A higher percentage of older males and former smokers (p<0.0001) was found in the idiopathic ILD group (Table 1). As expected, the two groups showed a clear discrepancy in terms of clinical features. Comparative analysis of serum biomarkers showed higher KL-6 concentrations (Fig 1A) in idiopathic ILD than in SARD-ILD patients (p = 0.0002). Although SMRP and FER concentrations were higher in idiopathic ILD than in SARD-ILD patients (p<0.0001), they remained within normal ranges. IL-6 concentrations were similar in the two groups and were in the normal range. Fig 1B shows the ROC curve to distinguish the two groups on the basis of a SMRP cut-off value of 0.88 nmol/L (sensitivity 52%, specificity 64%), a FER cut-off value of 59.15 ng/mL (sensitivity 54%, specificity 67%) and a KL-6 cut-off value of 1281 U/mL (sensitivity 59%, specificity 54%).

Fig 1. KL-6, FER, IL-6 and SMRP concentrations in SARD-ILD and idiopathic ILD groups.

Fig 1

Comparative analysis of median concentrations of four markers in the two subgroups (1a) and ROC curve (1b) of serum biomarkers of patients with idiopathic ILD and SARD-ILD reporting specificity, sensitivity, area under the curve and diagnostic accuracy. Abbreviations: KL-6, Krebs von den Lungen-6; FER, ferritin; IL-6, interleukin-6; SMRP, soluble mesothelin-related peptide; ILD, interstitial lung diseases; SARD-ILD, systemic autoimmune rheumatic diseases associated with interstitial lung diseases.

Machine learning analysis with variable-importance plot (Fig 2) was used to select variables to include in the model to obtain accurate predictions. The more a model relies on a variable to make predictions, the more important it is for the model. The variables selected were age, gender-male, FER, SMRP, smoking history, ethnicity-Asian, IL-6, ethnicity-Afro-Caribbean and KL-6: the resulting model showed an accuracy of 0.755 (kappa 0.5087) and AUROC 0.81.

Fig 2.

Fig 2

Variable-importance plot (a) selecting variables to include in the model to obtain accurate predictions: Age, gender-male, FER, SMRP, smoking history, ethnicity-Asian, IL-6, ethnicity-Afro-Caribbean and KL-6. The area under the receiver operating characteristics (AUC-ROC) curve (b) of the model was 0.81.Abbreviations: KL-6, Krebs von den Lungen-6; FER, ferritin; IL-6, interleukin-6; SMRP, soluble mesothelin-related peptide; ILD, interstitial lung diseases; SARD-ILD, systemic autoimmune rheumatic diseases associated with interstitial lung diseases.

Binomial logistic regression analysis (S1 Table) was performed to understand the effect of demographic (gender, age, ethnicity and smoking history) and immunological (SMRP, FER, KL-6 and IL-6) features on the diagnosis of idiopathic and SARD ILD. The variables most associated with idiopathic ILD were higher concentrations of FER (p = 0.0028) and KL-6 (p = 0.0340), age (p<0.0001) and gender-male (p<0.0001). Higher serum concentrations of FER, KL-6 and IL-6 were recorded in males than females (p<0.0001, p = 0.0014 and p = 0.0209, respectively). The variable ethnicity (Asian and Afro-Caribbean vs Caucasian) was associated with SARD-ILD (p<0.0001). The logistic regression model (Fig 3A) showed an AUROC of 0.832 with best sensitivity (69.4%) and specificity (80.4%).

Fig 3.

Fig 3

Logistic regression model (a) showed an area under the curve (AUC) of 0.832 and an accuracy of 0.75. Principal Component Analysis (b) plot showed that the idiopathic ILD and SARD-ILD groups separated on the basis of the selected variables with a total variance of 47.4%. Abbreviations: PC, principal component; ILD, interstitial lung diseases; SARD-ILD, systemic autoimmune rheumatic diseases associated with interstitial lung diseases.

The supervised Principal Component Analysis plot (Fig 3B) shows how the two groups (idiopathic ILD and SARD-ILD) separated on the basis of selected variables. The first and second components explained 47.4% of the total variance based on immunological and clinical findings showing good clustering for idiopathic ILD and SARD-ILD. The scree plot of Eigenvalues for each principal component was reported in S1 Fig.

According to HRCT stratification, serum markers were compared within and between groups and significant differences were reported in Table 2.

Table 2. Serum markers concentrations in groups of patients stratified according to HRCT findings: The idiopathic ILD group included probable fibrotic NSIP on HRCT (IPF confirmed at multidisciplinary discussion, >65 years old, without UIP confirmation at lung biopsy), definite UIP and definite fibrotic NSIP (UIP confirmed at lung biopsy).

Pairwise comparisons—SMRP nmol/L Weight P values
SARD-NSIP idiopathic probable fibrotic NSIP 47.904 0.0092
SARD-NSIP Definite UIP 52.858 0.0026
SARD-UIP idiopathic definite UIP -41.369 0.0403
Pairwise comparisons—FER ng/mL  
SARD-NSIP idiopathic probable fibrotic NSIP 63.024 0.0001
SARD-NSIP DefiniteUIP 67.027 < .0001
Probable fibrotic NSIP SARD-UIP -70.562 < .0001
Definite UIP SARD-UIP -81.872 < .0001
Definite fibrotic NSIP SARD-UIP -40.380 0.0493
Pairwise comparisons—IL6 pg/mL  
SARD-NSIP idiopathic fibrotic NSIP 5.233 0.0030
SARD-NSIP Definite UIP 5.750 0.0007
SARD-NSIP SARD-UIP 6.528 < .0001
idiopathic fibroticNSIP Probable fibrotic NSIP -4.114 0.0422
Pairwise comparisons—KL6 U/mL  
SARD-NSIP SARD-UIP -42.924 0.0291
Probable fibrotic NSIP SARD-UIP -48.549 0.0079
Definite UIP SARD-UIP -60.183 0.0003

For SARD patients, those with RA and SSc displaying a UIP pattern (SARD-UIP) were considered separately from those with NSIP (SARD-NSIP). Abbreviations: SARD, autoimmune rheumatic disease; NSIP, non-specific interstitial pneumonia; UIP, usual interstitial pneumonia; KL-6, krebs von den lungen-6; FER, ferritin; IL-6, interleukin-6; SMRP, soluble mesothelin-related peptide.

SARD-ILD subgroup analysis

Patients with SARD were further subdivided according to the specific diagnosis and serum markers, and were compared within and between groups, as well as with idiopathic ILD group (Fig 4).

Fig 4. Box plots reported serum marker concentrations in idiopathic interstitial lung disease (ILD) versus SARD-ILD subgroups: Rheumatoid arthritis (RA), systemic lupus erythematous (SLE), mixed connective tissue disease (MCTD), polymyositis (PM), dermatomyositis (DM), systemic sclerosis (SSc), undifferentiated connective tissue disease (UCTD), connective tissue disease (CTD).

Fig 4

The statistically significant differences of each serum marker concentration between the disease groups were reported in the tables below the box plots.

Finally, patients with SARD were further subdivided according to their signs and symptoms. Those who complained of Raynaud symptoms had lower serum concentrations of SMRP and FER (p<0.0001); arthralgia/arthritis was associated with lower KL-6, SMRP and FER (p = 0.0048, p = 0.0002 and p<0.0001, respectively); sclerodactyly and mechanic’s hands with lower FER (p = 0.0192 and p = 0.0364, respectively); elevated CK with lower SMRP, FER and IL-6 concentrations (p<0.0001, p = 0.0096 and p = 0.0004, respectively); myalgia with lower SMRP and FER concentrations (p = 0.0032 and p = 0.0191) and periungual erythema with lower SMRP values (p = 0.0110).

Concerning pulmonary signs, patients who showed clubbing showed higher serum concentrations of FER and KL-6 (p = 0.0347 and p = 0.0004, respectively) as well as end inspiratory crackle (p = 0.0279 and p = 0.0002, respectively).

Discussion

Our multicentre, retrospective study is the first and largest to evaluate an extended panel of serum biomarkers in patients with different types of ILD, including SARD-ILD. We observed normal serum concentrations of IL-6, FER and SMRP in both groups, whereas KL-6 appeared above normal cut-off in most patients but was significantly higher in the idiopathic ILD group.

These findings, underlining the greater sensitivity and accuracy of KL-6 in the diagnosis of ILD, are not surprising. As early as 2000, Nakajima et al. evaluated serum KL-6 in SARD patients with and without ILD, demonstrating the potential of KL-6 as predictor of lung interstitial involvement and proposing it as a marker of disease activity [40]. Since then, other studies, mainly focusing on SSc, have shown the reliable diagnostic and prognostic value of KL-6 in SARD-ILD: KL-6 seems able to distinguish patients with and without lung involvement at an early stage and shows moderate to high correlations with lung function parameters and quantitative HRCT scores of lung interstitial involvement [41]. The specificity of KL-6 is shown by its capacity to distinguish fibrotic ILD from other types of lung involvement, such as nodular or haemorrhagic pattern in ANCA-associated vasculitis [23].

Ours is the first study to attempt a direct comparison of KL-6 in two groups of ILD. A statistically significant difference was detected: patients suffering from idiopathic ILD displayed higher levels of KL-6 than SARD-ILD patients, suggesting that this biomarker has very high specificity for idiopathic ILD and that different cut-off values are needed for other types of ILD. Likewise FER and SMRP, though within normal ranges, were significantly higher in idiopathic ILD, whereas no statistically significant difference was found for IL-6, which remained within its normal range.

These findings enabled us to build a model with an accuracy of 0.755 for differential diagnosis of idiopathic ILD and SARD-ILD based on the following variables: age, gender-male, FER, SMRP, smoking history, Asian and Afro-Caribbean ethnicity, IL-6 and KL-6. FER and KL-6 concentrations, age and gender-male predicted the diagnosis of idiopathic ILD.

Identification of biomarkers by machine learning classifiers to assist diagnose RA-ILD has been proposed by Qin et al [22]. KL-6 concentration, D-dimer, and tumor markers greatly aided RA-ILD identification. Machine learning algorithms combined with traditional biostatistical analysis could be helpful to diagnose RA-ILD patients and identify biomarkers potentially associated with the disease. Recently, Huang et al [42] proposed multiple machine learning models trained with a large number of proteins involved in the immune pathway consistently distinguished CTD-ILD from IPF in challenging cases and improved clinical decision making.

This is of paramount importance in practice, first because it may help refine and accelerate diagnostic work-up, secondly and more importantly because unnecessary treatment can be avoided and therapy can be targeted.

In order to reduce the risk of bias and to bring our analysis into line with clinical practice, where HRCT has already been performed upon referral, patients were stratified according to radiological pattern. Notably, serum concentrations of FER and SMRP were significantly higher in patients with idiopathic NSIP and UIP than in those with SARD-NSIP and UIP, respectively. At the same time, not only were serum concentrations of KL-6 higher in idiopathic NSIP and UIP patients than in those with SARD-UIP, but also in patients with SARD-NSIP than in those with SARD-UIP.

In a nutshell, elevated levels of KL-6 in a patient with suspected or even radiologically confirmed lung fibrosis are associated with a high probability of ILD. Although FER and SMRP may be in the normal ranges, their increase suggests a diagnosis of idiopathic ILD, and does not support a diagnosis of SARD-ILD. New cut-off values for FER and SMRP, specific for lung fibrosis, could make these biomarkers even more useful in clinical practice.

When we analysed patients with any form of SARD in order to refine panel sensitivity and specificity, we failed to find any statistically significant differences between subgroups, except in the case of IL-6, which was higher in rheumatoid arthritis patients. This is unsurprising given the pivotal role of this cytokine in the pathogenesis of RA.

On the other hand, interesting insights emerged from clinical findings: patients presenting with signs and symptoms of advanced lung fibrosis (end inspiratory crackles and digital clubbing) had higher serum levels of FER and KL-6, while lower levels of FER, KL-6 and SMRP were recorded in those with extra-pulmonary signs (i.e. arthralgia/arthritis, sclerodactyly, elevated CK, myalgia, periungual erythema, mechanic’s hands).

Our study has several limitations: 1) lack of any information about disease activity of the concomitant rheumatic disorders at the time of serum collection; 2) since no lung function data was recorded in UK-BILD, we were unable to compare functional data with serological and imaging findings; 3) autoimmune profile was not included in the proforma: these aspects may have been relevant for stratifying DM subtypes (namely dermatomyositis with anti-MDA5, in which FER is increased) and to refine the diagnosis of many idiopathic NSIP potentially hiding antisynthetase syndrome [43]; such an aspect is worthwhile to be further indagated in upcoming studies; 4) since we lacked a control group of SARD without ILD, we were unable to assess the specificity of FER, SMRP and IL-6.

In conclusion, our study showed the good diagnostic value of KL-6 for detecting ILD, which irrespective of the final diagnosis and extent of disease, seems to be a reliable biomarker of lung fibrosis in various diseases, ranging from idiopathic to autoimmune forms. We confirmed that KL-6 values above 500 U/mL seem to support a diagnosis of ILD in SARD patients (i.e. SSc or IIM-ILD) prior or complementary to HCRT. We also found that assay of serum concentrations of KL-6, combined with FER and SMRP, is useful for differential diagnosis: serum cut-off values of KL-6, FER and SMRP, the latter two within normal values, were validated for differential diagnosis of idiopathic ILD and SARD-ILD. To the best of our knowledge, this is the first time that FER has been thoroughly investigated in patients with lung fibrosis, other than dermatomyositis with anti-MDA5. At the same time, there was no previous data on the role of SMRP in ILD patients and ours is the first study to report higher serum concentrations of SMRP in idiopathic ILD than in SARD-ILD patients, suggesting its potential for differential diagnosis. In this context, combination of serum markers and clinical data, as seen in our cohort, may lead to a further improvement in diagnostic accuracy for ILD.

Supporting information

S1 Table. Binomial logistic regression was performed to understand the effect of demographic (gender, age, ethnicity and smoking history) and immunological (SMRP, FER, KL-6 and IL-6) features on the diagnosis of idiopathic ILD and SARD-ILD.

The statistically significant variables was marked in bold (p values columns).

(DOCX)

pone.0311357.s001.docx (2.5MB, docx)
S1 Fig. The scree plot method for Kaiser-Guttman’s rule to conduct supervised Principal Component Analysis in an exploratory approach for identifying trends in immunological (KL-6, IL-6, SMRP, FER) and demographic (age) features by 2D representation of the multi-dimensional data set.

(DOCX)

pone.0311357.s002.docx (2.5MB, docx)

Acknowledgments

The authors acknowledged FUJIREBIO for the laboratory reagents, and our patients’ associations Profondi Respiri and Un Soffio di speranza “Il sogno di Emanuela” ONLUS for their constant help.

Abbreviations

ILD

interstitial lung disease

SARD-ILD

ILD associated with systemic autoimmune rheumatic diseases

KL-6

Krebs von den Lungen-6

IL-6

interleukin-6

FER

ferritin

SMRP

soluble mesothelin-related peptide

PFT

pulmonary function tests

HRCT

high-resolution computed tomography

IPF

idiopathic pulmonary fibrosis

DM

dermatomyositis

SSc

systemic sclerosis

RA

rheumatoid arthritis

UK-BILD

UK Biomarkers in Interstitial Lung Disease; pSS primary Sjogren syndrome

SLE

systemic lupus erythematous SLE

MCTD

mixed connective tissue disease

PM

polymyositis

UCTD

undifferentiated connective tissue disease

UIP

usual interstitial pneumonia

NSIP

non-specific interstitial pneumonia

AUROC

areas under the receiver operating characteristic

Data Availability

All relevant data are within the manuscript and its Supporting Information files.

Funding Statement

The author(s) received no specific funding for this work.

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Decision Letter 0

Masataka Kuwana

13 Aug 2024

PONE-D-24-29428Panel of serum biomarkers for differential diagnosis of idiopathic interstitial lung disease and interstitial lung disease-secondary to autoimmune rheumatic diseasePLOS ONE

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Reviewer #1: The is the biomarker study using the large scale of ILD cases. In addition to well-known KL-6, IL-6, and ferritin, a novel marker, SMRP, is investigated as well. Although this is the hot topics of ILD field, I have following concerns.

Major points

[1] The rationale of the study does not seem clear.

Why should the authors use biomarkers to further distinguish between primary and secondary conditions that are already clinically and clearly distinct? It is not clear what is unresolved and why this study is needed.

[2] Abstract and Results

1) “Primary and secondary-ILD”

Define what is “primary ILD” and “secondary ILD”.

2) “ARD”

Systemic autoimmune rheumatic diseases (SARDs) may be better to use.

3) “idiopathic ILD”, “idiopathic UIP”, “idiopathic NSIP”, “ARD-NSIP”, “ARD-UIP”

What kind of guidelines have used these terms? Proper terminology and definitions are needed.

[3] Introduction

Many of the references on the role of KL-6 are published around 2022, but the authors should cite the original paper on the topics. In researching the field, the authors do not appear to have a good grasp of previous research. Reviewing the references once again. Here are the samples.

1) Instead of reference #3, the following paper may help the authors in literature search.

Ishikawa N, Hattori N, Yokoyama A, Kohno N. Respir. Investig. 2012, 50, 3-13.

2) KL-6 was most studied in SSc-ILD. KL-6 was shown to have a prognostic role on the following paper.

Kuwana M, Shirai Y, Takeuchi T. J Rheumatol. 2016 Oct;43(10):1825-1831.

[4] Discussion

The conclusion part is too long and not coherent.

Minor points

[5] Introduction

Ferritin, IL-6, and KL-6 are familiar in the field of ILD. However, SMRP is not.

Explain the reason the authors picked up and investigate it among so many biomarker candidates.

[6] Methods

1) The authors have not mentioned the definition of SSc, MCTD, and UCTD.

2) Mention the definition of “pulmonary hypertension” listed in the Table 1.

3) The results of logistic regression analysis and multivariate analysis were described in the discussion part. Explain them in the methods part.

4) Who examined the HRCT findings?

[7] Figure 1a

We can see 0 and 1 groups. Labeling is required.

[8] Figure 2a

Why did the authors bring IL-6 into the analysis? IL-6 was not shown to distinguish the two groups significantly in Figure 1?

[9] Figure 2a and 4

The letter size of the labeling is too small to see.

Reviewer #2: This paper investigates the utility of KL-6, ferritin, IL-6, and SMRP (soluble mesothelin-related peptide) as biomarkers in distinguishing idiopathic interstitial lung disease (ILD) from ILD associated with autoimmune rheumatic diseases. It proposes a diagnostic model that incorporates clinical background information. Although the study is insightful, the choice of biomarkers, particularly IL-6 and SMRP, appears abrupt and lacks sufficient rationale. The introduction provides a rich explanation of KL-6, but the discussion of ferritin, IL-6, and SMRP in relation to ILD, supported by previous studies, is insufficient. A more robust and logical explanation for selecting these biomarkers is needed. Additionally, the quality of the figures, including resolution and text size, needs improvement to meet the standards of a scholarly article. While the discussion highlights the strengths of the study, it falls short of comparing the findings with previous research, especially concerning the use of machine learning in ILD differentiation and modeling.

Overall, the study's design, the results presented (including the quality of figures), the logical structure of the discussion, and the alignment between the content of the paper and the conclusions emphasized in the abstract are lacking in maturity and refinement. Below are the identified issues:

Major Comments:

1. As mentioned in the overall assessment, the selection of IL-6 and SMRP from the myriad of inflammatory cytokines appears abrupt. The introduction provides a detailed explanation of KL-6, but the discussion of ferritin (FER), IL-6, and SMRP, supported by previous studies, in relation to ILD is insufficient. A clear rationale for selecting IL-6 and SMRP from the numerous ILD-related biomarkers is required.

2. From a clinical application perspective, while specialized tests like IL-6 and SMRP are valuable, the study should also consider practical biomarkers like SP-D and SP-A, which are used in clinical settings alongside KL-6.

3. In the Methods section, if there is a classification criterion for ARD, it should be included. Is there a specific reason for using ARD instead of connective tissue disease (CTD)? The basis for selecting various symptoms and examination findings, such as elevated CK, as ARD signs should be explained with reference to literature.

4. The Methods section lacks citations related to the classification of MCTD and SSc. Anti-synthetase syndrome and UCTD are mentioned in the Results, but their classification criteria should be referenced in the Methods section.

5. The definitions and classifications of chest HRCT findings in ILD should be organized and included in the Methods section, not the Results.

6. The resolution of all figures is poor, and the text is faint and small, making them difficult to read.

7. In Figure 1a, it is unclear whether the vertical axis values (0 or 1) correspond to idiopathic ILD or ARD-ILD.

8. Detailed descriptions of the statistical methods used in Principal Component Analysis are necessary. Was the analysis conducted according to Kaiser-Guttman’s rule using the scree plot method? A scree plot should be added as a supplementary figure. How were the absolute variables selected?

9. In Table 2, why does the number of diseases compared vary for each serum biomarker? What does "W" stand for?

10. In Figure 4, the diseases compared are unclear. It seems that only statistically significant differences are presented, but the rationale is not provided, making it difficult to understand. The figure legends are also insufficient.

11. The discussion focuses on emphasizing the strengths of the study's findings, but lacks a comparison with previous research, especially regarding ILD differentiation using machine learning and related models.

12. In the Abstract’s discussion, the focus should be on proposing an "ILD differentiation model including clinical background," but instead, the emphasis seems to be on the utility of serum SMRP levels.

Minor Comments:

13. In Table 1, the ARD subgroup should be arranged in the order of SSc Limited, SSc Diffuse, UCTD, and CTD (Unknown).

14. In the Binomial logistic regression analysis (Table S1), it would be less confusing for readers if the comparison targets were labeled as idiopathic ILD and ARD-ILD rather than primary and secondary ILD.

**********

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Reviewer #2: No

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PLoS One. 2024 Oct 3;19(10):e0311357. doi: 10.1371/journal.pone.0311357.r002

Author response to Decision Letter 0


3 Sep 2024

Dear Editor,

The authors would like to thank you and appreciate the Reviewer for the constructive comments. We also thank the Reviewer for the effort and time put into the review of the manuscript. The comments are encouraging, and the Reviewer appears to share our judgement that this study and its results are important and worth publication. Each comment has been carefully considered point by point and responded to. Please see below our detailed response to the comments raised, which you can find in italic. Changes provided in the revised manuscript are in red. The manuscript has been revised according to the Reviewer’s suggestions and has been significantly improved. We are hoping that its final version deserves publication in “Plos One”.

Reviewer #1: The is the biomarker study using the large scale of ILD cases. In addition to well-known KL-6, IL-6, and ferritin, a novel marker, SMRP, is investigated as well. Although this is the hot topics of ILD field, I have following concerns.

Major points

[1] The rationale of the study does not seem clear.

Why should the authors use biomarkers to further distinguish between primary and secondary conditions that are already clinically and clearly distinct? It is not clear what is unresolved and why this study is needed.

Thanks for giving us the chance to clarify such a crucial aspect of our study. In the common clinical practice, clearly distinguishing between primary and secondary ILD is not always easy. For instance, it is not so uncommon to have patients who were previously diagnosed with idiopathic NSIP and then display a positivity of any MSA. This is, according to us, a major point, because while idiopathic ILD may benefit from antifibrotic agents, secondary ones may require a prompt immunosuppressive treatment. Indeed, a multidisciplinary assessment is highly recommended by international guidelines for the diagnostic pathway of ILD, including at least pulmonologists, radiologists, rheumatologists, in order to optimise the diagnostic accuracy and guarantee the earliest and more proper therapeutic proposal. It is worthy to consider that, despite this recommendation, a significant percentage of ILD patients still receives a “working diagnosis”, since clinical symptoms and immunological assessment may not always be sufficient for a confident diagnosis and potentially invasive samplings (such as cryobiopsy or lung surgical biopsy) may not be suitable due to the frailty of clinical conditions (Am J Respir Crit Care Med. 2019 Nov 1;200(9):1146-1153. doi: 10.1164/rccm.201903-0493OC.). For this reason, the validation and discovery of non-invasive and reproducible biomarkers that may help to improve our diagnostic accuracy is highly needed.

In this setting, in order to validate our findings and our proposed biomarkers, we needed a cohort of patients in whom a definite diagnosis was already performed.

We added such finding in the introduction section of revised manuscript as follows:

“A multidisciplinary assessment is highly recommended by international guidelines for the diagnostic pathway of ILD, including at least pulmonologists, radiologists, rheumatologists, in order to optimise the diagnostic accuracy and guarantee the earliest and more proper therapeutic proposal. Despite this recommendation, a significant percentage of ILD patients still receives a “working diagnosis”, since clinical symptoms and immunological assessment may not always be sufficient for a confident diagnosis and potentially invasive samplings (such as cryobiopsy or lung surgical biopsy) may not be suitable due to the frailty of clinical conditions (Am J Respir Crit Care Med. 2019 Nov 1;200(9):1146-1153. doi: 10.1164/rccm.201903-0493OC.)”

[2] Abstract and Results

1) “Primary and secondary-ILD”

Define what is “primary ILD” and “secondary ILD”.

Thanks for evidencing this mistake. “Primary” and “secondary” ILD were changed into “idiopathic” and “SARD”: we hope that the manuscript could look now more homogeneous in terminology

2) “ARD”

Systemic autoimmune rheumatic diseases (SARDs) may be better to use.

The definition has been modified accordingly

3) “idiopathic ILD”, “idiopathic UIP”, “idiopathic NSIP”, “ARD-NSIP”, “ARD-UIP”

What kind of guidelines have used these terms? Proper terminology and definitions are needed.

Thanks for raising this point. pSS, RA, SLE, MCTD, SSc and IIM were diagnosed according to currently available classification criteria (see ref. 24-27), while idiopathic ILD according to American Thoracic Society/European Respiratory Society (ATS/ERS) guidelines (ref. 28).

[3] Introduction

Many of the references on the role of KL-6 are published around 2022, but the authors should cite the original paper on the topics. In researching the field, the authors do not appear to have a good grasp of previous research. Reviewing the references once again. Here are the samples.

1) Instead of reference #3, the following paper may help the authors in literature search.

Ishikawa N, Hattori N, Yokoyama A, Kohno N. Respir. Investig. 2012, 50, 3-13.

2) KL-6 was most studied in SSc-ILD. KL-6 was shown to have a prognostic role on the following paper.

Kuwana M, Shirai Y, Takeuchi T. J Rheumatol. 2016 Oct;43(10):1825-1831.

Thank you for the suggestion, we modified it accordingly.

[4] Discussion

The conclusion part is too long and not coherent.

Thanks for the suggestion: the conclusion has been shortened to a few bullet points which are more useful for the comprehension of the manuscript.

Minor points

[5] Introduction

Ferritin, IL-6, and KL-6 are familiar in the field of ILD. However, SMRP is not.

Explain the reason the authors picked up and investigate it among so many biomarker candidates.

Thanks for raising this important point: as correctly stated, no study has to date evaluated the role of SMRP in ILD. Nevertheless, recent evidence highlights the role of mesothelin (MSLN which binds cancer antigen CA-125 also known as MUC16) in pulmonary fibrosis, suggesting that MSLN is involved in cell adhesion [Rump et al., 2004]. The literature also reports a role of MUC16 in the development and progression of IPF through the TGF-β1 canonical pathway. In this regard, taking action from these preliminary findings, we decided to assess whether SMRP, aside from “classical” biomarkers, could give interesting insights in this field. Such a statement has been added in “Introduction” section.

[6] Methods

1) The authors have not mentioned the definition of SSc, MCTD, and UCTD.

Thank you. The classification criteria of the abovementioned criteria has been added, accordingly.

New references were added in the revised manuscript:

SSC: 24122180

MCTD: R. Kasukawa, T. Too, S. Miyawaki, H. Yoshida, K. Tanimoto, M. Nobunaga, et al. Preliminary diagnostic criteria for classification of mixed connective tissue disease

UCTD: “Due to the lack of validated diagnostic or classification criteria, we employed the preliminary ones relased in 1999 (10544849)

ASS: 21138882

2) Mention the definition of “pulmonary hypertension” listed in the Table 1.

Thanks for your comment. According to your advice, we have added the definition of pulmonary hypertension as defined by international guidelines, that we apply for our patients in the multidisciplinary evaluation according to our Centre protocol.

3) The results of logistic regression analysis and multivariate analysis were described in the discussion part. Explain them in the methods part.

Thank you for the comment. We moved the results of logistic regression analysis and multivariate analysis in the results section.

4) Who examined the HRCT findings?

Thanks for your comment that helped us to further clarify this aspect for the readers. In the Centres included in the study, all patients with a clinical suspect or diagnosis of ILD undergo a specific diagnostic pathway, including a multidisciplinary discussion to optimise the diagnostic accuracy, according to international guidelines. Therefore, HRCT images are performed and reviewed by radiologists with a specific expertise on this field, that are part of the multidisciplinary group.

To better clarify this point, we have added a specific sentence in the Methods’ section.

[7] Figure 1a

We can see 0 and 1 groups. Labeling is required.

Thanks for the comment. We modified it accordingly. Moreover, we replaced “SARD-ILD” instead of “ARD-ILD” as suggested above.

[8] Figure 2a

Why did the authors bring IL-6 into the analysis? IL-6 was not shown to distinguish the two groups significantly in Figure 1?

Thank you for the comment. We performed the unsupervised machine learning analysis with variable importance plot to construct a model selecting variables to make accurate predictions. In figure 2a we reported all variables, though not statistically significant in the comparative analysis, to demonstrate that IL-6 did not affect the diagnosis SARD-ILD vs Idiopathic ILD. Here is reported the variable importance plot without IL-6 concentrations.

[9] Figure 2a and 4

The letter size of the labeling is too small to see.

Thank you for the comment. We modified the figures accordingly.

Reviewer #2: This paper investigates the utility of KL-6, ferritin, IL-6, and SMRP (soluble mesothelin-related peptide) as biomarkers in distinguishing idiopathic interstitial lung disease (ILD) from ILD associated with autoimmune rheumatic diseases. It proposes a diagnostic model that incorporates clinical background information. Although the study is insightful, the choice of biomarkers, particularly IL-6 and SMRP, appears abrupt and lacks sufficient rationale. The introduction provides a rich explanation of KL-6, but the discussion of ferritin, IL-6, and SMRP in relation to ILD, supported by previous studies, is insufficient. A more robust and logical explanation for selecting these biomarkers is needed. Additionally, the quality of the figures, including resolution and text size, needs improvement to meet the standards of a scholarly article. While the discussion highlights the strengths of the study, it falls short of comparing the findings with previous research, especially concerning the use of machine learning in ILD differentiation and modeling.

Overall, the study's design, the results presented (including the quality of figures), the logical structure of the discussion, and the alignment between the content of the paper and the conclusions emphasized in the abstract are lacking in maturity and refinement. Below are the identified issues:

Major Comments:

1. As mentioned in the overall assessment, the selection of IL-6 and SMRP from the myriad of inflammatory cytokines appears abrupt. The introduction provides a detailed explanation of KL-6, but the discussion of ferritin (FER), IL-6, and SMRP, supported by previous studies, in relation to ILD is insufficient. A clear rationale for selecting IL-6 and SMRP from the numerous ILD-related biomarkers is required.

Thanks for raising this important point: as correctly stated, no study has to date evaluated the role of SMRP in ILD. Nevertheless, recent evidence highlights the role of mesothelin (MSLN which binds cancer antigen CA-125 also known as MUC16) in pulmonary fibrosis, suggesting that MSLN is involved in cell adhesion [Rump et al., 2004]. The literature also reports a role of MUC16 in the development and progression of IPF through the TGF-β1 canonical pathway. In this regard, taking action from these preliminary findings, we decided to assess whether SMRP, aside from “classical” biomarkers, could give interesting insights in this field. Such a statement has been added in “Introduction” section.

Interleukin-6 (IL-6) is a pleiotropic cytokine involved in the physiology of virtually every organ system. Controlling IL-6 activity is potentially an effective approach in the treatment of various autoimmune and inflammatory diseases. The recent introduction of tocilizumab, a humanised monoclonal antibody targeting IL-6R, is further evidence of the role of IL-6 in the pathogenesis of RA. Baricitinib is a JAK inhibitor that blocks intracellular signalling pathways of inflammatory cytokines recommended for Rheumatoid arthritis (RA) patients not responding to initial treatment. Baricitinib was demonstrated to be a safe immune modulator that reduces the concentrations of biomarkers of lung fibrosis and inflammation in RA patients, including a subgroup with interstitial lung involvement.

As a result, we included IL-6 and SMRP concentrations in different SARD-ILD compared with idiopathic ILD.

2. From a clinical application perspective, while specialized tests like IL-6 and SMRP are valuable, the study should also consider practical biomarkers like SP-D and SP-A, which are used in clinical settings alongside KL-6.

Thank you for the suggestion. We selected four markers detectable at the same time using a few microliters (about 150uL) of serum through the chemiluminescence method using Fujirebio reagents. We included KL-6, ferritin and IL-6 as valuable markers in the contest of idiopathic interstitial lung diseases and in a few types of SARD-ILD (e.g. RA).

To date no study has evaluated the role of SMRP in ILD. Nevertheless, recent evidence highlights the role of mesothelin (MSLN which binds cancer antigen CA-125 also known as MUC16) in pulmonary fibrosis, suggesting that MSLN is involved in cell adhesion. An epithelial cell's apical surface is covered with transmembrane mucins, which are large glycoproteins. Cell surface mucins are characterized by non-covalent sodium dodecyl sulfate-labile bonds holding dimerizations of two dissimilar subunits together (α and β chains). It is highly glycosylated and entirely extracellular. High glycosylation levels in this extracellular domain contribute to barrier formation in addition to protecting the protein backbone from proteolytic attacks by hosts. In addition to the putative phosphorylation sites present in all transmembrane mucins intracellular tails, these tails differ in sequence and length and do not contain conserved domains. It is nevertheless believed that transmembrane mucins contribute significantly to cellular proliferation, apoptosis, and epithelial to mesenchymal transition processes, in accordance with IPF observations. According to the above information, the lung is predominantly composed of MUC1, MUC4, and MUC16 TM mucins.

3. In the Methods section, if there is a classification criterion for ARD, it should be included. Is there a specific reason for using ARD instead of connective tissue disease (CTD)? The basis for selecting various symptoms and examination findings, such as elevated CK, as ARD signs should be explained with reference to literature.

Thanks for raising this important point. All classification criteria were added (unfortunately, some of them were not mentioned in the first version of the manuscript) and can now be found among the references. In terms of inclusion criteria, we reckon that the choice of including not only CTD but ARD “in general” can not easily understandable and deserves some clarifications: first, the occurrence of ILD is not limited to CTD, but has been reported in up to 10% of patients with RA and its precocious diagnosis and management remain an authentic dilemma. Secondly, the most common pattern of ILD in RA is UIP, which, in turn, is usually present only in SSc among CTDs, which generally have a NSIP pattern. At the same time, the pathological mechanisms of RA, driven also by IL-6 (which is less prominent in SSc, as proved by the uncertain efficacy of TCZ in this condition), could potentially aid in evaluating differences and similarities of ILD development in such diseases. Same when comparing RA with IIM and other CTDs, in which the role of IL-6 is classically considered less important, while other agents (e.g. B cells, IFN) carry a crucial pathogenetic role. Therefore, if excluding such an important and prevalent condition like RA would have been a strong limitation of our study, its inclusion may hopefully strongly corroborate our findings.

4. The Methods section lacks citations related to the classification of MCTD and SSc. Anti-synthetase syndrome and UCTD are mentioned in the Results, but their classification criteria should be referenced in the Methods section.

Thank you: all missing cr

Attachment

Submitted filename: point by point reply UKBILD-Plos One.docx

pone.0311357.s003.docx (269.3KB, docx)

Decision Letter 1

Masataka Kuwana

15 Sep 2024

PONE-D-24-29428R1Panel of serum biomarkers for differential diagnosis of idiopathic interstitial lung disease and interstitial lung disease-secondary to systemic autoimmune rheumatic diseasePLOS ONE

Dear Dr. Dalessandro,

Thank you for submitting your manuscript to PLOS ONE. After careful consideration, we feel that it has merit but does not fully meet PLOS ONE’s publication criteria as it currently stands. Therefore, we invite you to submit a revised version of the manuscript that addresses the points raised during the review process.

The manuscript was much improved by revisions, but one of the reviewers still has suggestions for improved quality of the contents. 

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Kind regards,

Masataka Kuwana, MD, PhD

Academic Editor

PLOS ONE

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Comments to the Author

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Reviewer #1: All comments have been addressed

Reviewer #2: (No Response)

**********

2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #1: Yes

Reviewer #2: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #1: Yes

Reviewer #2: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #1: Yes

Reviewer #2: Yes

**********

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PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #1: Yes

Reviewer #2: Yes

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6. Review Comments to the Author

Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #1: (No Response)

Reviewer #2: Comments for Authors

Regarding Major Comment 3, the response provided is insufficient.

The question raised was whether there exists a previously established definition for the term or disease concept of ARD (systemic ARD). For instance, the concept of UCTD has been in use since its proposal by LeRoy et al. (LeRoy EC, Maricq HR, Kahaleh MB. Undifferentiated connective tissue syndromes. Arthritis Rheum. 1980 Jan;23(1):1-9.). Is there an established concept for SARD? If so, a reference should be cited, and the concept should be briefly described. If it is not an established term (i.e., coined by the authors), a brief explanation of the rationale behind using the term "SARD" should be provided.

Regarding Major Comment 9, the response is again insufficient.

If Table 2 presents only statistically significant results, this should be clearly stated in the figure legend. Additionally, “W” should be described as “weight” in the legend.

Regarding Minor Comment 13, Table 1 has not been revised as requested.

The authors' response is also unclear. Please arrange the order of the ARD subgroup diseases in Table 1 as follows: SSc Limited, SSc Diffuse, UCTD, etc.

**********

7. PLOS authors have the option to publish the peer review history of their article (what does this mean?). If published, this will include your full peer review and any attached files.

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Reviewer #1: No

Reviewer #2: No

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PLoS One. 2024 Oct 3;19(10):e0311357. doi: 10.1371/journal.pone.0311357.r004

Author response to Decision Letter 1


16 Sep 2024

Dear Editor,

The authors would like to thank you and appreciate the Reviewer for the constructive comments. We also thank the Reviewer for the effort and time put into the review of the manuscript. The comments are encouraging, and the Reviewer appears to share our judgement that this study and its results are important and worth publication. Each comment has been carefully considered point by point and responded to. Please see below our detailed response to the comments raised, which you can find in italic. Changes provided in the revised manuscript are in red. The manuscript has been revised according to the Reviewer’s suggestions and has been significantly improved. We are hoping that its final version deserves publication in “Plos One”.

Reviewer #2: Comments for Authors

Regarding Major Comment 3, the response provided is insufficient.

The question raised was whether there exists a previously established definition for the term or disease concept of ARD (systemic ARD). For instance, the concept of UCTD has been in use since its proposal by LeRoy et al. (LeRoy EC, Maricq HR, Kahaleh MB. Undifferentiated connective tissue syndromes. Arthritis Rheum. 1980 Jan;23(1):1-9.). Is there an established concept for SARD? If so, a reference should be cited, and the concept should be briefly described. If it is not an established term (i.e., coined by the authors), a brief explanation of the rationale behind using the term "SARD" should be provided.

We are sorry for the unclear answer to your question. Systemic autoimmune rheumatic diseases (SARD) is a term that covers a broad spectrum of clinical conditions of autoimmune aetiology and, in particular, ILD has been reported in association with several SARD, particularly RA, SSc, IIM, CTD and AAV. The term was first proposed in 1995 (Sénecal et al., J Rheumatol) in a cohort of patients displaying anti-SSA/SSB positivity and the most recent, comprehensive, definition was given in a recently published review (Guthridge et al., Nat Med, 2022, PMID 35788174), whose reference has been therefore added to the bibliography of our manuscript. Finally, specifically focusing on lung involvement in rheumatic diseases, the recently published recommendations of the British Society of Rheumatology employ the term SARD for ILD associated with CTD, AAV, IIM, RA etc. (Hannah et al., Rheumatol Adv Pract, 2024)

Regarding Major Comment 9, the response is again insufficient.

If Table 2 presents only statistically significant results, this should be clearly stated in the figure legend. Additionally, “W” should be described as “weight” in the legend.

Thank you for the comment. We included the description of “W” at the top of the column and we improved the caption of table 2 as follows:

“Table 2. Serum markers concentrations in groups of patients stratified according to HRCT findings: the idiopathic ILD group included probable fibrotic NSIP on HRCT (IPF confirmed at multidisciplinary discussion, >65 years old, without UIP confirmation at lung biopsy), definite UIP and definite fibrotic NSIP (UIP confirmed at lung biopsy). For SARD patients, those with RA and SSc displaying a UIP pattern (SARD-UIP) were considered separately from those with NSIP (SARD-NSIP). Abbreviations: SARD, autoimmune rheumatic disease; NSIP, non-specific interstitial pneumonia; UIP, usual interstitial pneumonia; KL-6, krebs von den lungen-6; FER, ferritin; IL-6, interleukin-6; SMRP, soluble mesothelin-related peptide.”

Regarding Minor Comment 13, Table 1 has not been revised as requested.

The authors' response is also unclear. Please arrange the order of the ARD subgroup diseases in Table 1 as follows: SSc Limited, SSc Diffuse, UCTD, etc.

Thank you for the suggestions. We modified the table 1 accordingly.

Attachment

Submitted filename: point-by-point reply_rev2.docx

pone.0311357.s004.docx (16KB, docx)

Decision Letter 2

Masataka Kuwana

18 Sep 2024

Panel of serum biomarkers for differential diagnosis of idiopathic interstitial lung disease and interstitial lung disease-secondary to systemic autoimmune rheumatic disease

PONE-D-24-29428R2

Dear Dr. Dalessandro,

We’re pleased to inform you that your manuscript has been judged scientifically suitable for publication and will be formally accepted for publication once it meets all outstanding technical requirements.

Within one week, you’ll receive an e-mail detailing the required amendments. When these have been addressed, you’ll receive a formal acceptance letter and your manuscript will be scheduled for publication.

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Kind regards,

Masataka Kuwana, MD, PhD

Academic Editor

PLOS ONE

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Comments to the Author

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Reviewer #2: All comments have been addressed

**********

2. Is the manuscript technically sound, and do the data support the conclusions?

The manuscript must describe a technically sound piece of scientific research with data that supports the conclusions. Experiments must have been conducted rigorously, with appropriate controls, replication, and sample sizes. The conclusions must be drawn appropriately based on the data presented.

Reviewer #2: Yes

**********

3. Has the statistical analysis been performed appropriately and rigorously?

Reviewer #2: Yes

**********

4. Have the authors made all data underlying the findings in their manuscript fully available?

The PLOS Data policy requires authors to make all data underlying the findings described in their manuscript fully available without restriction, with rare exception (please refer to the Data Availability Statement in the manuscript PDF file). The data should be provided as part of the manuscript or its supporting information, or deposited to a public repository. For example, in addition to summary statistics, the data points behind means, medians and variance measures should be available. If there are restrictions on publicly sharing data—e.g. participant privacy or use of data from a third party—those must be specified.

Reviewer #2: Yes

**********

5. Is the manuscript presented in an intelligible fashion and written in standard English?

PLOS ONE does not copyedit accepted manuscripts, so the language in submitted articles must be clear, correct, and unambiguous. Any typographical or grammatical errors should be corrected at revision, so please note any specific errors here.

Reviewer #2: Yes

**********

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Please use the space provided to explain your answers to the questions above. You may also include additional comments for the author, including concerns about dual publication, research ethics, or publication ethics. (Please upload your review as an attachment if it exceeds 20,000 characters)

Reviewer #2: "The revised manuscript has been sufficiently improved. I hope this study proposes novel biomarker candidates for SARD-ILD and contributes to the advancement of research in understanding the pathogenesis of SARD-ILD.

**********

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Reviewer #2: No

**********

Acceptance letter

Masataka Kuwana

24 Sep 2024

PONE-D-24-29428R2

PLOS ONE

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Associated Data

    This section collects any data citations, data availability statements, or supplementary materials included in this article.

    Supplementary Materials

    S1 Table. Binomial logistic regression was performed to understand the effect of demographic (gender, age, ethnicity and smoking history) and immunological (SMRP, FER, KL-6 and IL-6) features on the diagnosis of idiopathic ILD and SARD-ILD.

    The statistically significant variables was marked in bold (p values columns).

    (DOCX)

    pone.0311357.s001.docx (2.5MB, docx)
    S1 Fig. The scree plot method for Kaiser-Guttman’s rule to conduct supervised Principal Component Analysis in an exploratory approach for identifying trends in immunological (KL-6, IL-6, SMRP, FER) and demographic (age) features by 2D representation of the multi-dimensional data set.

    (DOCX)

    pone.0311357.s002.docx (2.5MB, docx)
    Attachment

    Submitted filename: point by point reply UKBILD-Plos One.docx

    pone.0311357.s003.docx (269.3KB, docx)
    Attachment

    Submitted filename: point-by-point reply_rev2.docx

    pone.0311357.s004.docx (16KB, docx)

    Data Availability Statement

    All relevant data are within the manuscript and its Supporting Information files.


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