Abstract
Background
Lung cancer (LC) causes more deaths worldwide than any other cancer type. Despite advances in therapeutic strategies, the fatality rate of LC cases remains high (95%) since the majority of patients are diagnosed at late stages when patient prognosis is poor. Analysis of the International Association for the Study of Lung Cancer (IASLC) database indicates that early diagnosis is significantly associated with favorable outcome. However, since symptoms of LC at early stages are unspecific and resemble those of benign pathologies, current diagnostic approaches are mostly initiated at advanced LC stages.
Methods
We developed a LC diagnosis test based on the analysis of distinct RNA isoforms expressed from the GATA6 and NKX2-1 gene loci, which are detected in exhaled breath condensates (EBCs). Levels of these transcript isoforms in EBCs were combined to calculate a diagnostic score (the LC score). In the present study, we aimed to confirm the applicability of the LC score for the diagnosis of early stage LC under clinical settings. Thus, we evaluated EBCs from patients with early stage, resectable non-small cell lung cancer (NSCLC), who were prospectively enrolled in the EMoLung study at three sites in Germany.
Results
LC score-based classification of EBCs confirmed its performance under clinical conditions, achieving a sensitivity of 95.7%, 91.3% and 84.6% for LC detection at stages I, II and III, respectively.
Conclusions
The LC score is an accurate and non-invasive option for early LC diagnosis and a valuable complement to LC screening procedures based on computed tomography.
1 Introduction
Current LC diagnostic strategies include chest X-ray (CXR), low-dose helical computed tomography (CT), positron emission tomography CT (PET CT) and morphological invasive sampling. However, diagnostic approaches are often initiated at advanced stages since the majority of patients is asymptomatic at early stages of the disease. Studies implementing CT demonstrated that early diagnosis is crucial to reduce the extremely high case fatality rate of LC (95%) [1,2,3,4]. Unfortunately, CT-based LC screening approaches in high risk populations is a procedure with very high percentage of false-positive observations (> 90%) and hence low specificity (73.4%) [5], resulting in unnecessary follow-up CT scans, bronchoscopy, or even surgery [6,7,8]. Accordingly, there is an increasing need of employing less invasive diagnostic methods and biomarkers to complement the success of CT for LC diagnosis.
Collection of exhaled breath through cooling devices provides options for the development of non-invasive LC diagnostic methods [9,10,11,12,13,14,15]. Following this idea, we previously established reproducible standard operating procedures (SOPs) for a complete LC diagnosis method, consisting of EBC collection, storage, and processing for isoform-specific expression analysis [16]. We showed that RNA purified from EBCs can be used for qRT–PCR-based isoform-specific expression analysis of GATA6 and NKX2-1, two genes important for embryonic lung development [17, 18] and with implications in LC [19,20,21,22,23,24,25]. The levels of adult and embryonic transcript isoforms from GATA6 and NKX2-1 were measured in EBCs and combined into one diagnostic score (LC score). The high performance of the LC score-based diagnosis was confirmed in an independent validation cohort [16]. However, the results of our previous study did not prove its usefulness under clinical conditions, for which the clinical study EMoLung was designed. Furthermore, we increased the number of early stage LC samples (I-II) in EMoLung, which was relatively low in our previous study, to determine the performance of the LC score for early LC diagnosis.
2 Methods
2.1 Study design and study population
The study was performed according to the principles set out in the WMA Declaration of Helsinki and to the protocols approved by the institutional review board and ethics committee of the University of Lübeck (AZ: 17-065). A flowchart depicting different steps of the clinical study EMoLung is represented in Fig. S1a (Supplementary Material). Patients were prospectively enrolled into EMoLung as they were undergoing diagnostic evaluation for LC, prior to surgery, at the LungenClinic Grosshansdorf GmbH (LCG), the Asklepios Klinik Gauting GmbH (ASK), and the Thoraxklinik at Heidelberg University Hospital (TKUH). After surgical intervention, cases were reviewed by an expert panel of pathologists, radiologists, pulmonologists and oncologists in the different cohorts according to the current diagnostic criteria for morphological features and immunophenotypes recommended by the International Union Against Cancer [26]. Additional inclusion criteria were (i) a non-small cell lung cancer (NSCLC) diagnosis, (ii) clinical stage I-III according to TNM classification 8th edition, (iii) patient following the recommendation of a curative tumor resection, (iv) index of the Eastern Cooperative Oncology Group (ECOG) being ≤ 2, (v) patient age ≥ 18 years, and (vi) patient having signed an informed written consent. Patients diagnosed with small cell lung cancer (SCLC) and patients receiving neoadjuvant chemotherapy or chemoradiotherapy were excluded. Patients enrolled into the EMoLung will be followed up for up to 2 years after surgical resection, in which EBCs will be collected before surgical resection, 3, 12, 18 and 24 months after surgical resection and/or at the time of recurrence. For the current study, only the base line EBCs were included. The study population is described in Fig. S1b (Supplementary Material), Table 1 and Table S1 (Supplementary Material). Briefly, the LC group consisted of 121 EBCs from 103 LC patients (99 NSCLC and 4 carcinoid), including 5 EBCs from 3 stage IV NSCLC patients to confirm previous results [16]. The control group comprised 46 EBCs from 23 donors, who either had no diagnosis of LC (36 EBCs from 13 donors), or were originally suspected to be LC patients but subsequently, pathologically diagnosed as non-malignant (10 EBCs from 10 donors).
2.2 EBC collection, gene expression analysis and LC score
EBC collection, gene expression analysis by qRT–PCR and LC score calculation were performed as previously described [16]. Briefly, EBC collection was performed using the RTube (Respiratory Research) as described online (http://www.res piratoryresearch.com/products-rtube-how.htm) and following the guidelines for EBC sampling by the ERS/ATS Task Force [27, 28]. Total RNA isolation from EBC was performed using 500 µl of sample and the RNeasy Micro Kit (Qiagen). Complementary DNA (cDNA) was synthetized using the High Capacity cDNA Reverse Transcription kit (Applied Biosystem) with 0.5–0.7 µg total RNA. RT reaction without adding enzyme was used as negative control. qRT–PCRs were performed using SYBR® Green on the Step One plus Real-time PCR system (Applied Biosystems) using the primers previously described [16]. Briefly, 1 × concentration of the SYBR Green master mix, 250 nM each forward and reverse primer, and 3.5 µl (EBC) from a sixfold diluted RT reaction were used for the gene-specific qPCR. Isoform expression values were determined by calculating 2^(-Ct-value) for each of the three technical replicate measurements and, subsequently, taking the mean of these values. Then, the Em/Ad isoform ratios of GATA6 and NKX2-1 were used to calculate the LC score as previously described [16]:
A sample with LC score > 0 will be classified as a lung cancer sample; otherwise, the samples are classified as control samples (see Table S8 in Supplementary Material).
2.3 Statistical analysis
The levels of adult and embryonic isoforms of GATA6 and NKX2-1 in each EBC were measured in triplicates and implemented for calculation of the LC score as previously described [16]. All EBCs were measured in one of three laboratories. In addition, a sample of 10 EBCs was analyzed in triplicates by different operators in the three laboratories. Statistical analysis was performed using R (4.0.2), Excel Solver and Graph Prism (v.5). Distribution of data was visualized as box plots and the corresponding five-number summaries are given in Table S1 (Supplementary Material). Two-sided Mann–Whitney U tests were calculated with one randomly picked measurement per sample to determine the statistical significance in two-group comparisons of LC scores. To provide evidence that there is no difference with respect to the LC scores between LC stages (Fig. 2d) or between LC subtypes (Fig. S3a in Supplementary Material), we applied the Mann–Whitney U test in an anticonservative way, treating replicated measurements for the same patient as independent observations. This is uncritical, because even such an anticonservative procedure did not detect any significant effect. To evaluate the differences between laboratories in Fig. 2a, b Two-sided Mann–Whitney U test was performed considering one value per donor that was randomly selected from the replicate measurements. The test values and assay IDs are provided in Tables S1, S2, S6 and S7 (see Supplementary Material). P-values < 0.05 were considered statistically significant. The inter-lab variability of LC scores was assessed by a ternary Bland–Altman plot and by Bland–Altman plots [29]. The performances of different LC predictors were assessed with receiver operator characteristics (ROC) analysis (R package ROCR [30]) by randomly picking exactly one replicate per donor from Lab1 in case of Fig. 1b, and one replicate per donor from all Labs in case of Fig. 1c. Sensitivities, specificities, and the respective 95% confidence intervals were calculated from [https://www2.ccrb.cuhk.edu.hk/stat/confidence%20interval/Diagnostic%20Statistic.htm] using cross tables, in which each observation was weighted by the inverse number of replicates for the selected patient.
3 Results
3.1 LC score-based classification of EBCs under clinical settings
We performed isoform-specific expression analysis by qRT–PCR after total RNA isolation from EBCs and calculated the LC scores from each patient as previously described [16] (Fig. 1a). In control EBCs (46 EBC measurements from 23 donors, Table 1 and Table S1 in Supplementary Material) the LC score was generally below 0 (the threshold above which samples are classified as LC), with a median of − 2.605 and an interquartile range of 2.770. In agreement with our previous work [16], the LC score in EBCs of LC patients was significantly higher and generally above 0 (121 EBC measurements from 103 patients; P = 7.3E-9), with a median of 3.717 and an interquartile range of 3.982 (Fig. 1a, Table 1 and Table S1 in Supplementary Material). These results confirm that samples with a LC score greater than zero can be classified as LC (Table S8 in Supplementary Material). To compare the performance of the LC score-based classification of the EBCs collected in EMoLung under clinical settings to the previous study under pre-clinical settings [16], we calculated ROC curves [30] (Fig. 1b and Table S3 in Supplementary Material). The area under the curve (AUC) value of the clinical study EMoLung was 0.89, whereas the AUC value of the previous pre-clinical study [16] was 0.99. Further, ROC curves for each transcript isoform, the isoform expression ratios, and for the LC score (Fig. 1c, d and Table S4 in Supplementary Material) confirmed that EBC classification achieved by the LC score was substantially better than any threshold-based classification using the expression or expression ratios of transcript isoforms from GATA6 and NKX2-1 alone.
3.2 Reliable detection of stage I and II LC using the LC score
To further characterize the usefulness of the LC score under clinical conditions, EBCs for this study were prospectively collected in three different clinical centers and analyzed by different operators in three different laboratories. Sample grouping by clinical centers (Fig. 2a and Table S1 in Supplementary Material) revealed that the median LC score increased from -0.520 in control EBCs (15 measurements from 14 donors) to 4.125 (P = 2.4E-5) in EBCs of LC patients (80 measurements from 62 patients) in the clinical center 1 (LCG), from -5.837 in control EBCs (4 measurements from 4 donors) to 3.867 (P = 7.3E-5) in LC EBCs (26 measurements from 26 patients) in the clinical center 2 (ASK) and from -3.982 in control EBCs (4 measurements from 2 donors) to 0.640 (P = 0.015) in LC EBCs (15 measurements from 15 patients) in the clinical center 3 (TKUH).
Similarly, sample grouping by laboratories (Fig. 2b and Table S1 in Supplementary Material) revealed that the median LC score increased from -3.793 in control EBCs (3 measurements for 1 donor) to 3.173 in EBCs of LC patients (9 measurements for 9 patients) in the laboratory 1; from -0.175 in control EBCs (2 measurements for 1 donor) to 6.183 in LC EBCs (9 measurements for 9 patients) in the laboratory 2; and from -1.468 in control EBCs (3 measurements for 1 donor) to 4.689 in LC EBCs (9 measurements for 9 patients) in the laboratory 3. Interestingly, comparisons among different laboratories showed non-significant differences (Table S7 in Supplementary Material). Moreover, the reliability of the LC score-based EBC classification was monitored by a ternary Bland–Altman plot (Fig. 2c) and Bland–Altman plots [29] (Fig. S2 in Supplementary Material). In summary, the LC score proved to be highly reliable when used in different clinics and labs, corroborating its usefulness under clinical conditions.
To demonstrate that the LC score can be used for early detection of LC, samples were grouped based on TNM classification [26] (Fig. 2d, Table 1 and Table S1 in Supplementary Material). Remarkably, the median LC score increased from -2.605 in the control EBCs (46 measurements from 23 donors) to 3.604 (P = 9.7E-9) and 4.080 (P = 1.6E-6) in EBCs from patients with LC at stages I (54 measurements from 46 patients) and II (25 measurements from 23 patients), respectively. In addition, performance assessment of the LC score showed a sensitivity of 95.7% and 91.3% for stages I and II LC (Fig. 2d and Table S2 in Supplementary Material), thereby demonstrating the potential of the method for early detection of LC.
4 Discussion
Performance assessment of the LC score based on the complete EBC set used in the current study revealed a sensitivity of 92.2% and specificity of 82.6% (Table S5 in Supplementary Material), compared to the sensitivity of 98.3% and specificity of 89.7% in the previous study [16]. The reduced performance of the LC score in EMoLung might be explained by increasing variance in the data due to the implementation of clinical conditions, including the participation of different centers and laboratories. Nevertheless, the statistical performance achieved by the LC score in EMoLung was still high, demonstrating the robustness of the LC score under clinical conditions. To the best of our knowledge, our LC score is the first attempt to establish a mathematical score based on the expression of embryonic- or adult-specific transcript variants. The use of isoform ratios as building blocks of the LC score make it resilient to variations that may occur at different steps of the procedure, including RNA isolation, cDNA synthesis or PCR amplification. In addition, the utility of EBCs for expression analysis has been underlined by recent studies comparing non-coding transcripts in NSCLC patients versus control donors [10, 31, 32]. Among the limitations of the present study, the LC score does not allow the distinction of LC stages (Table S2 in Supplementary Material) or NSCLC subtypes (Fig. S3 in Supplementary Material). This has already been observed in our previous study [13]. A plausible explanation for these limitations may be the sparsity of covariates included to our present LC score limiting the level of detail of its predictions. Thus, while our results are promising, we propose a larger prospective study under clinical conditions with repetitive measurements from various patients at different stages of a therapeutic approach, as this is currently ongoing within the clinical study EMoLung (Fig. S1a), and it will the scope of future reports.
Despite the limitations of EMoLung, the correct classification of Stage I-II LC samples using the LC score is encouraging. Thus, we propose that the incorporation of our method into the current protocols for patients undergoing diagnostic evaluation for pulmonary diseases characterized by hyperproliferation will be beneficial. Furthermore, complementing CT-based LC screening with our technology in high-risk populations would strengthen the screening protocols. We hypothesize that implementation of the LC score together with CT may reduce the false-positive rate of CT imaging, for example, in cases with suspicious image findings, thereby preventing individuals from unnecessary exposure to high dose of radiation or surgery.
5 Conclusions
In this study, we validated in clinical settings a LC diagnostic test based on the analysis of distinct RNA isoforms expressed by the GATA6 and NKX2-1 gene loci detected in EBCs. LC score-based classification of EBCs achieved a sensitivity of 95.7%, 91.3% and 84.6% for LC detection at stages I-III, respectively. The LC score is an accurate and non-invasive option for early LC diagnosis and a valuable complement to LC screening procedures based on computed tomography.
Data availability
The datasets supporting the conclusions of this article are included within the article and its online Supplementary Material nformation. The data that support this study are available from the corresponding authors upon reasonable request.
Abbreviations
- AC:
-
Adenocarcinoma
- ACC:
-
Adenoid cystic carcinoma
- ASK:
-
Asklepios Klinik Gauting GmbH
- CT:
-
Computed tomography
- Ctrl:
-
Control
- CXR:
-
Chest X-ray
- EBCs:
-
Exhaled breath condensates
- IASLC:
-
International Association for the Study of Lung Cancer
- LC:
-
Lung cancer
- LCC:
-
Large-cell carcinoma
- LCG:
-
LungenClinic Grosshansdorf GmbH
- NSCLC:
-
Non-small cell lung cancer
- PET:
-
Positron emission tomography
- SCC:
-
Squamous cell carcinoma
- SOPs:
-
Standard operating procedures
- SVM:
-
Linear support vector machine
- TKUH:
-
Thoraxklinik at Heidelberg University Hospital
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Acknowledgements
We thank Roswitha Bender, Marlen Szewczyk and Milena Schmidt for administrative and technical support.
Funding
Ole Ammerpohl, Guillermo Barreto, Martin Reck, Sabine Wessels and Marc Schneider are funded by the German Center for Lung Research (Deutsches Zentrum für Lungenforschung, DZL) (82DZL00402) through the clinical study EMoLung. The work in the labs of Guillermo Barreto was funded by the Max-Planck-Society (MPG, Munich, Germany), the “Deutsche Forschungsgemeinschaft” (DFG, Bonn, Germany) (BA 4036/4-1), the “Centre National de la Recherche Scientifique” (CNRS, France), “Délégation Centre-Est” (CNRS-DR6) and the “Lorraine Université” (LU, France) through the initiative “Lorraine Université d'Excellence” (LUE) and the dispositive “Future Leader”. Karla Rubio was funded by the “Consejo de Ciencia y Tecnología del Estado de Puebla” (CONCYTEP, Puebla, Mexico) through the initiative International Laboratory EPIGEN. Jason M. Müller is member of the Cologne Graduate School of Ageing Research. Aditi Mehta and Olivia Merkel were funded by ERC-2014-StG – 637830. The work in the lab of Indrabahadur Singh was funded by the DFG (Bonn, Germany) through Emmy Noether program (SI 2620/1-1). The work in the lab of Thomas Braun is supported by the Deutsche Forschungsgemeinschaft (DFG), Excellence Cluster Cardio-Pulmonary Institute (CPI), Transregional Collaborative Research Center TRR 81 TP A02, SFB 1213 TP B02, TRR 267 TP A05 and the German Center for Cardiovascular Research.
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KR, AM, TAR, IS, CK, MGS, MK and GB designed and performed the experiments. GB, KR, MR, OA and IW designed the study. KR, JMM, AT and GB analyzed the data. TO, IK, SW, MAS, ME, TM, OM and TB were involved in study design and data analysis. GB, KR, AT, JMM, TB, AM, MR, ME and TM wrote the manuscript. All authors discussed the results and commented on the manuscript.
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The study was performed according to the principles set out in the WMA Declaration of Helsinki and to the protocols approved by the institutional review board and ethics committee of the University of Lübeck (AZ: 17-065). A flowchart depicting different steps of the non-interventional clinical study EMoLung is represented in Fig. S1a (Supplementary Material). All participants provided informed written consent.
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Competing interests
Sabine Wessels reports grants and personal fees from German Center for Lung Research (DZL) during the conduct of the study. Thomas Muley reports grants and non-financial support, outside the submitted work, from Roche Diagnostics GmbH, Penzberg, Germany. Martin Reck reports personal fees, outside the submitted work, from Amgen, AstraZeneca, BMS, Boehringer-Ingelheim, Lilly, Merck, MSD, Mirati, Novartis, Pfizer, Roche and Samsung Bioepis. Guillermo Barreto reports personal fees as scientific advisor, outside the submitted work, from a company in USA. There are two patents related to this work, European Patent with the number EP2999797A1 and USA Patent with the number US20200181717A1. The remaining authors declare that they have no competing interests with this study.
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Rubio, K., Müller, J.M., Mehta, A. et al. Preliminary results from the EMoLung clinical study showing early lung cancer detection by the LC score. Discov Onc 14, 181 (2023). https://doi.org/10.1007/s12672-023-00799-9
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DOI: https://doi.org/10.1007/s12672-023-00799-9