Presence of cancer-associated mutations in exhaled breath condensates of healthy individuals by next generation sequencing

Exhaled breath condensate contains extracellular vesicles (EVs) that carry miRNA cargos of lung tissue origin that can be selectively purified and analyzed

Lung diseases, including lung cancer, are rising causes of global mortality. Despite novel imaging technologies and the development of biomarker assays, the detection of lung cancer remains a significant challenge. However, the lung communicates directly with the external environment and releases aerosolized droplets during normal tidal respiration, which can be collected, stored and analzsed as exhaled breath condensate (EBC). A few studies have suggested that EBC contains extracellular vesicles (EVs) whose microRNA (miRNA) cargos may be useful for evaluating different lung conditions, but the cellular origin of these EVs remains unknown. In this study, we used nanoparticle tracking, transmission electron microscopy, Western blot analyses and super resolution nanoimaging (ONi) to detect and validate the identity of exhaled EVs (exh-EVs). Using our customizable antibody-purification assay, EV-CATCHER, we initially determined that exh-EVs can be selectively enriched from EBC using antibodies against three tetraspanins (CD9, CD63 and CD81). Using ONi we also revealed that some exh-EVs harbour lung-specific proteins expressed in bronchiolar Clara cells (Clara Cell Secretory Protein [CCSP]) and Alveolar Type II cells (Surfactant protein C [SFTPC]). When conducting miRNA next generation sequencing (NGS) of airway samples collected at five different anatomic levels (i.e., mouth rinse, mouth wash, bronchial brush, bronchoalveolar lavage [BAL] and EBC) from 18 subjects, we determined that miRNA profiles of exh-EVs clustered closely to those of BAL EVs but not to those of other airway samples. When comparing the miRNA profiles of EVs purified from matched BAL and EBC samples with our three tetraspanins EV-CATCHER assay, we captured significant miRNA expression differences associated with smoking, asthma and lung tumor status of our subjects, which were also reproducibly detected in EVs selectively purified with our anti-CCSP/SFTPC EV-CATCHER assay from the same samples, but that confirmed their lung tissue origin. Our findings underscore that enriching exh-EV subpopulations from EBC allows non-invasive sampling of EVs produced by lung tissues.

Next Generation Sequencing for miRNA Detection on the Exhaled Breath Condensate: A Pilot Study

Introduction:

Exhaled breath condensate (EBC) sampling has been suggested as a less-invasive and cost-effective method to detect biological macromolecules, including miRNA. To explore the feasibility of its use as a biomarker of early effects of asbestos exposure, we conducted a preliminary test on male volunteers by comparing the miRNA profile in the EBC and the plasma using 2 different sequencing platforms.

Methods:

Six male volunteers, all retired and unexposed to dust or fumes, participated in the test. RNA was extracted from 200 μL EBC samples and same-size plasma samples. Sample aliquots were processed in 2 laboratories using 2 different sequencing platforms: a MiSeq Illumina^® platform and a more performing HiSeq Illumina^® platform.

Results:

The HiSeq3000^® sequencing platform identified twice as many unique molecular indexes (UMI)-validated miRNA as the MiSeq^® platform. The Spearman’s correlation coefficient between EBC counts and plasma counts was significant in 5/6 subjects with either platform (MiSeq^® = 0.128-0.508, P = .026-<.001; HiSeq^® = 0.156-0.412, P = .001-<.001). The intraclass correlation coefficient confirmed the consistency of the miRNA profile over the 6 participants with both biospecimens. Exploring the agreement between the EBC and plasma samples with Bland-Altman plots showed that using the HiSeq3000^® platform substantially improved the EBC miRNA detection rate.

Conclusion:

Our preliminary study confirms that, when using the HiSeq^® sequencing platform, EBC sampling is a suitable, non-invasive method to detect the miRNA profile in healthy subjects.

[Advances on Collection and Analysis of Volatile Organic Compounds in the Diagnosis of Lung Cancer]

Lung cancer is a leading cause of cancer-related morbidity and mortality globally, which is the biggest menace to the health and life of the population. Screening and early detection of lung cancer are effective in reducing its mortality, and the measurement of volatile organic compounds (VOCs) has become a promising clinical means for early detection, course detection and prognosis management of lung cancer, with advantages of rapid speed, non-invasiveness and convenience. Now, a variety of VOCs collection ways and analysis methods have emerged at home and abroad. This report summarized three aspects, including VOCs collection, multiple methods of analysis and progress in the diagnosis and treatment of lung cancer. At last, we discussed the limitations and prospects of VOCs analysis.
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An Update on the Use of Exhaled Breath Analysis for the Early Detection of Lung Cancer

Lung cancer has historically been the main responsible for cancer associated deaths. Owing to this is our current inability to screen for and diagnose early pathological findings, preventing us from a timely intervention when cure is still achievable. Over the last decade, together with the extraordinary progress in therapeutical alternatives in the field, there has been an ongoing search for a biomarker that would allow for this. Numerous technologies have been developed but their clinical application is yet to come. In this review, we provide an update on volatile organic compounds, a non-invasive method that can hold the key for detecting early metabolic pathway changes in carcinogenesis. For its compilation, web-based search engines of scientific literature such as PubMed were explored and reviewed, using articles, research, and papers deemed meaningful by authors discretion. After a brief description, we depict how this technique can complement current methods and present the value of electronic noses in the identification of the “breathprint”. Lastly, we bring some of the latest updates in the field together with the current limitations and final remarks.

Exhaled breath analysis in disease detection

Investigating the use of exhaled breath analysis to diagnose and monitor different diseases has attracted much interest in recent years. This review introduces conventionally used methods and some emerging technologies aimed at breath analysis and their relevance to lung disease, airway inflammation, gastrointestinal disorders, metabolic disorders and kidney diseases. One section correlates breath components and specific diseases, whereas the other discusses some unique ideas, strategies, and devices to analyze exhaled breath for the diagnosis of some common diseases. This review aims to briefly introduce the potential application of exhaled breath analysis for the diagnosis and screening of various diseases, thereby providing a new avenue for the detection of non-invasive diseases.

Macromolecular biomarkers of chronic obstructive pulmonary disease in exhaled breath condensate

Biomarkers provide important diagnostic and prognostic information on heterogeneous diseases such as chronic obstructive pulmonary disease (COPD). However, finding a suitable specimen for clinical analysis of biomarkers for COPD is challenging. Exhaled breath condensate (EBC) sampling is noninvasive, rapid, cost-effective and easily repeatable. EBC sampling has also provided recent progress in the identification of biological macromolecules, such as lipids, proteins and DNA in EBC samples, which has increased its utility for clinical scientists. In this article, we review applications involving EBC sampling for the analysis of COPD biomarkers and discuss its future potential.

Exhaled Breath Condensate: A Non-Invasive Source for Tracking of Genetic and Epigenetic Alterations in Lung Diseases

Lung diseases have been recognized as an extensive cause of morbidity and mortality in the worldwide. The high degree of clinical heterogeneity and nonspecific initial symptoms of lung diseases contribute to a delayed diagnosis. So, the molecular and genomic profiling play a pivotal role in promoting the pulmonary diseases. Exhaled breath condensate (EBC) as a novel and potential method for sampling the respiratory epithelial lining fluid is to assess the inflammatory and oxidative stress biomarkers, drugs and genetic alterations in the pathophysiologic processes of lung diseases. The recent studies on the analysis of EBC from both a genetic and epigenetic point of view were searched from database and reviewed. This review provides an overview of the current findings in the tracking of genomic and epigenetic alterations which are potentially effective in better management of cancer detection. In addition, respiratory microbiota DNA using EBC samples in association with pulmonary disease especially lung cancer were investigated. Various studies have concluded that EBC has a great potential for analysis of nuclear and mitochondrial DNA alterations as well as epigenetic modifications and identification of respiratory microbiome. Next-generation sequencing (NGS) based genomic profiling of EBC samples is recommended as a promising approach to establish personalized based prevention, diagnosis, treatment and post-treatment follow-ups for patients with lung diseases especially lung cancer.

Epidermal Growth Factor in Exhaled Breath Condensate as Diagnostic Method for Non-Small Cell Lung Cancer

OBJECTIVE

Lung cancer is one of the most common malignant tumors in humans. Finding a highly sensitive and specific marker is very important. This study investigated the clinical significance of epidermal growth factor in exhaled breath condensate and serum of patients with non-small cell lung cancer.

METHODS

From October 17, 2013, to June 5, 2017, exhaled breath condensate and blood samples from 155 patients with non-small cell lung cancer, 63 patients with benign pulmonary nodules, and 115 healthy controls were collected using a breath condenser. Each sample was analyzed by enzyme-linked immunosorbent assay.

RESULTS

Epidermal growth factor level in the exhaled breath condensate from the non-small cell lung cancer group (197.86 ± 60.67 pg/mL) was higher than that in the healthy group (124.75 ± 36.09 pg/mL), P < .05. Epidermal growth factor level in the exhaled breath condensate of the smoking group (208.85 ± 40.94 pg/mL) was higher than that of the nonsmoking group (185.52 ± 36.88 pg/mL), P < .05. Epidermal growth factor level in the exhaled breath condensate in phases III and IV of non-small cell lung cancer group (212.17 ± 35.41 pg/mL) was higher than that in phases I and II (173.91 ± 38.08 pg/mL), P < .05. Epidermal growth factor level in the exhaled breath condensate of the death group (241.05 ± 27.19 pg/mL) was higher than that of the survival group (188.75 ± 37.07 pg/mL), P < .05. The epidermal growth factor exhaled breath condensate levels were positively correlated with the serum epidermal growth factor levels with a correlation coefficient of 0.495 (P < .05). The sensitivity and specificity of epidermal growth factor exhaled breath condensate test were 80.0% and 89.6%, respectively.

CONCLUSION

The detection of epidermal growth factor level in exhaled breath condensate exhibits is important in the diagnosis, disease monitoring, and prognosis of non-small cell lung cancer.

Exhaled breath analysis in the diagnosis of head and neck cancer

Head and neck cancer (HNC) comprises a heterogeneous group of upper aerodigestive tract malignant neoplasms, the most frequent of which is squamous cell carcinoma. HNC forms the eighth most common cancer type and the incidence is increasing. However, survival has improved only moderately during the past decades. Currently, early diagnosis remains the mainstay for improving treatment outcomes in this patient population. Unfortunately, screening methods to allow early detection of HNC are not yet established. Therefore, many cases are still diagnosed at advanced stage, compromising outcomes. Exhaled breath analysis (EBA) is a diagnostic tool that has been recently introduced for many cancers. Breath analysis is non-invasive, cost-effective, time-saving, and can potentially be applied for cancer screening. Here, we provide a summary of the accumulated evidence on the feasibility of EBA in the diagnosis of HNC.

Tips for improving the quality and quantity of the extracted DNA from exhaled breath condensate samples

There is a growing interest in the tracking of genetic and epigenetic alterations in exhaled breath condensate (EBC) samples. The effects of different procedures on the quality and quantity of DNA in EBC were studied. The results demonstrated that sodium acetate precipitation and oligo (dT) improved the quality of the extracted DNA significantly (p < 0.01). Also, sodium acetate precipitation, using oligo (dT), incubation at 70 °C and SDS treatment increased the quantity of DNA significantly (p < 0.01). These results showed the advantages of the chemical and physical manipulations for improving the quality and quantity of the extracted DNA from EBC samples.

Exhaled breath condensate biomarkers for lung cancer

Lung cancer is the main cause of cancer incidence and mortality worldwide and the identification of clinically useful biomarkers for lung cancer detection at both early and metastatic stage is a pressing medical need. Although many improvements have been made in the treatment and in the early screening of this cancer, most diagnosis are made at a late stage, when a lot of genetic and epigenetic changes have occurred. A promising source of biomarkers reflective of the pathogenesis of lung cancer is exhaled breath condensate (EBC), a biological fluid and a natural matrix of the respiratory tract. Molecules such as DNAs, RNAs, proteins, metabolites and volatile compounds are present in EBC, and their presence/absence or their variation in concentrations can be used as biomarkers. The aims of this review are to briefly describe exhaled breath composition, firstly, and then to document some of the EBC candidate biomarkers for lung cancer by dividing them according to their origin (genome, transcriptome, epigenome, metabolome, proteome and microbiota) in order to demonstrate the potential use of EBC as a helpful tool in cancer diagnostics, molecular profiling, therapy monitoring and screening of high risk individuals.

Atypical Histiocytic Lesion Preceding a Peripheral T-Cell Lymphoma Involving the Skin Exhibiting the Same Molecular Alterations

Peripheral T-cell lymphoma (PTCL), not otherwise specified (NOS) is a diagnosis of exclusion, showing extreme cytological and phenotypic heterogeneity. Skin involvement of PTCL may be primary or secondary. Diagnosis of histiocytosis may be difficult, requiring clinical-pathological correlation. We describe a laryngeal atypical histiocytic lesion (AHL) and a nasal PTCL, NOS with cutaneous involvement in the same patient presenting with peculiar histopathologic and immunophenotypic features. The laryngeal neoplasm showed morphological and immunophenotypic evidence of histiocytic differentiation and does not fit any other category of the WHO classification nor the revised classification of histiocytosis. The nasal and cutaneous lesions presented features close to natural killer/T-cell lymphoma and gamma-delta T-cell lymphoma but did not meet accurately the WHO criteria. A somatic activating Q61K mutation was found on exon 3 of the NRAS gene in both AHL and PTCL, NOS. The mutation on NRAS gene in both AHL and PTCL, NOS may suggest a common origin from a precursor cell.

cfDNA in exhaled breath condensate (EBC) and contamination by ambient air: toward volatile biopsies

Exhaled breath is a source of volatile and nonvolatile biomarkers in the body that can be accessed non-invasively and used for monitoring. The collection of lung secretions by conventional methods such as bronchoalveolar lavage, induced sputum collection, and core biopsies is limited by the invasive nature of these methods. Non-invasive collection of exhaled breath condensate (EBC) provides fluid samples that are representative of airway lining fluids. Various volatile and nonvolatile biomarkers can be detected in volatile condensates, such as H₂O₂, nitric oxide, lipid mediators, cytokines, chemokines, DNA, and microRNAs. Studies have examined cell-free DNA (cfDNA) in plasma samples from non-small-cell lung cancer patients, offering to new insights and fostering development of the liquid biopsy. However, few studies have examined cfDNA in EBC samples. This study examined whether EBC is an appropriate source of cfDNA using housekeeping-gene-specific primer probes and quantitative real-time polymerase chain reaction in healthy subjects. Ambient (room) air is contaminated with DNA, so caution is needed. Preliminary studies indicated that volatile biopsies are becoming an important diagnostic tool in lung cancer.

Intratumor heterogeneity and tissue distribution of KRAS mutation in non-small cell lung cancer: implications for detection of mutated KRAS oncogene in exhaled breath condensate

Purpose

Mutated KRAS oncogene in exhaled breath condensate (EBC) can be a genetic marker of non-small cell lung cancer (NSCLC). However, a possibility of inhomogeneous distribution in cancer tissue and intratumor heterogeneity of KRAS mutation may decrease its significance. We investigated a status of KRAS point mutation and its sequence at codon 12 in 51 NSCLC patients after tumor resection. The comparison of KRAS mutation status between EBC–DNA and cancer tissue was performed in 19 cases.

Methods

Five cancer tissue samples from disparate tumor regions and one from normal lung were harvested at surgery. EBC was collected for DNA analysis the previous day. KRAS point mutations at codon 12 were detected using mutant-enriched PCR technique and pyrosequenced.

Results

Forty-six cancers revealed concordance of KRAS mutation status: 27 contained mutated KRAS and 19 had only wild KRAS. Five NSCLCs revealed inhomogeneous distribution of KRAS mutation. Two different mutations were found in 14 NSCLCs and the most frequent one was G12D and G12V (n = 8). No mutated KRAS was found in normal lung. The concordance ratios of KRAS sequence in codon 12 between EBC–DNA and cancer were 18/19 for NSCLC patients and 11/12 for KRAS mutation positive NSCLC.

Conclusions

Intratumor heterogeneity and inhomogeneous distribution of KRAS point mutation in codon 12 in cancer tissue can occur in NSCLCs. There was a high accordance between KRAS mutation status in EBC–DNA and cancer tissue in NSCLC patients what suggests usefulness of monitoring KRAS mutation in EBC–DNA as a biomarker of NSCLC.

Real life adjuvant chemotherapy uptake and survival in patients with non-small cell lung cancer after complete resection

OBJECTIVES

Adjuvant chemotherapy (AC) in non-small cell lung cancer (NSCLC) has become a standard of care in patients with stages IIA, IIB, and IIIA after complete tumor resection. Utilization and outcome of AC in routine practice is described in a few studies, with non-conclusive results.

MATERIALS AND METHODS

This retrospective study included consecutive patients with NSCLC who underwent curative-intent surgery. Data of AC uptake in stages IB (tumor of ≥4 cm in diameter), II, and IIIA, and reasons of AC omission were evaluated according to medical records. Mortality risk among patients treated with surgery (only) and different types of AC in routine practice was compared.

RESULTS

AC was applied to 79% of patients with stages IB (tumor of ≥4 cm in diameter), II, and IIIA, and was associated with an improved median of overall survival (HR = 0.69; 95% CI = 0.44-1.06). Significantly longer survival was achieved in the sub-group treated with platinum and oral vinorelbine (HR = 0.575, 95% CI = 0.339-0.974), and the longest survival was among patients treated with oral vinorelbine and cisplatin (HR = 0.371, 95% CI = 0.168-0.820).

CONCLUSIONS

AC utilization should be based on co-operation between surgeons, pneumo-oncologists, and patients. Rational use of AC offers better survival in routine practice.

Clinical framework for next generation sequencing based analysis of treatment predictive mutations and multiplexed gene fusion detection in non-small cell lung cancer

Precision medicine requires accurate multi-gene clinical diagnostics. We describe the implementation of an Illumina TruSight Tumor (TST) clinical NGS diagnostic framework and parallel validation of a NanoString RNA-based ALK, RET, and ROS1 gene fusion assay for combined analysis of treatment predictive alterations in non-small cell lung cancer (NSCLC) in a regional healthcare region of Sweden (Scandinavia). The TST panel was clinically validated in 81 tumors (99% hotspot mutation concordance), after which 533 consecutive NSCLCs were collected during one-year of routine clinical analysis in the healthcare region (~90% advanced stage patients). The NanoString assay was evaluated in 169 of 533 cases. In the 533-sample cohort 79% had 1-2 variants, 12% >2 variants and 9% no detected variants. Ten gene fusions (five ALK, three RET, two ROS1) were detected in 135 successfully analyzed cases (80% analysis success rate). No ALK or ROS1 FISH fusion positive case was missed by the NanoString assay. Stratification of the 533-sample cohort based on actionable alterations in 11 oncogenes revealed that 66% of adenocarcinomas, 13% of squamous carcinoma (SqCC) and 56% of NSCLC not otherwise specified harbored ≥1 alteration. In adenocarcinoma, 10.6% of patients (50.3% if including KRAS) could potentially be eligible for emerging therapeutics, in addition to the 15.3% of patients eligible for standard EGFR or ALK inhibitors. For squamous carcinoma corresponding proportions were 4.4% (11.1% with KRAS) vs 2.2%. In conclusion, multiplexed NGS and gene fusion analyses are feasible in NSCLC for clinical diagnostics, identifying notable proportions of patients potentially eligible for emerging molecular therapeutics.