Early Detection of Cystic Fibrosis Acute Pulmonary Exacerbations by Exhaled Breath Condensate Metabolomics

Molecular monitoring of lung allograft health: is it ready for routine clinical use?

Maintenance of long-term lung allograft health in lung transplant recipients (LTRs) requires a fine balancing act between providing sufficient immunosuppression to reduce the risk of rejection whilst at the same time not over-immunosuppressing individuals and exposing them to the myriad of immunosuppressant drug side-effects that can cause morbidity and mortality. At present, lung transplant physicians only have limited and rather blunt tools available to assist them with this task. Although therapeutic drug monitoring provides clinically useful information about single time point and longitudinal exposure of LTRs to immunosuppressants, it lacks precision in determining the functional level of immunosuppression that an individual is experiencing. There is a significant gap in our ability to monitor lung allograft health and therefore tailor optimal personalised immunosuppression regimens. Molecular diagnostics performed on blood, bronchoalveolar lavage or lung tissue that can detect early signs of subclinical allograft injury, differentiate rejection from infection or distinguish cellular from humoral rejection could offer clinicians powerful tools in protecting lung allograft health. In this review, we look at the current evidence behind molecular monitoring in lung transplantation and ask if it is ready for routine clinical use. Although donor-derived cell-free DNA and tissue transcriptomics appear to be the techniques with the most immediate clinical potential, more robust data are required on their performance and additional clinical value beyond standard of care.

Breath of fresh insight: unraveling the evolution of our understanding of cystic fibrosis pulmonary exacerbations

PURPOSE OF REVIEW

Pulmonary exacerbations are critical events with significant negative impacts in persons with cystic fibrosis, but their diagnosis and management are highly variable. Highly effective modulator therapies have greatly improved health and reduced exacerbation events, but have also reshaped how they present. This review discusses the complexities of the diagnosis and management of pulmonary exacerbations as well as the emerging work and evidence in this area.

RECENT FINDINGS

The shifting epidemiology and our understanding of risk factors for pulmonary exacerbations are discussed. As symptoms may be more subtle in the modulator context, novel technologies including studies of remote monitoring are presented. The continued relevance of pulmonary exacerbations, the heterogeneity in their management, as well as current and forthcoming clinical trials to optimize treatment approaches are detailed.

SUMMARY

In spite of the dramatic reductions in pulmonary exacerbations, airway infections persist, a proportion of persons with cystic fibrosis either on or off modulator therapies continue to experience exacerbation events, and long-term data is lacking. Innovative approaches and studies will be crucial to enable standardized and generalizable strategies to improve outcomes in persons with cystic fibrosis.

Biomarkers of nitrosative stress in exhaled breath condensate and serum among patients with cystic fibrosis

PURPOSE

The measurement of biomarkers in exhaled breath condensate (EBC) offers a non-invasive way to assess airway disease and can be easily done in a clinical setting among patients with cystic fibrosis (CF). The role of oxidative and nitrosative stress in the complex pathophysiology of CF is widely accepted and biomarkers of oxidative and nitrosative stress can be measured in the serum and EBC. To our knowledge, this is the first study to assess markers of nitrosative stress in EBC and serum, collected simultaneously from the CF patients.

PATIENTS AND METHODS

Paired EBC and serum samples were collected from 36 stable patients with CF and 14 healthy controls. Markers of nitrosative stress ‒ 3-nitrotyrosine and nitrate/nitrite were measured in the EBC and serum using an enzyme-linked immunosorbent assay.

RESULTS

We found no differences in 3-nitrotyrosine and nitrate/nitrite in the EBC of patients with CF as compared to healthy controls (125.37 ​± ​3.29 vs. 126.24 ​± ​2.21 ​nmol/L, p ​= ​0.218; 12.66 ​± ​7.23 vs. 8.79 ​± ​4.83 ​μmol/L, p ​= ​0.133, respectively). Furthermore, 3-nitrotyrosine and nitrate/nitrite were significantly higher in the serum of patients with CF as compared to the healthy controls (0.13 ​± ​0.02 vs. 0.11 ​± ​0.01 ​nmol/mg protein, p ​= ​0.003; 70.78 ​± ​22.55 vs. 53.08 ​± ​8.5 ​μmol/L, p ​= ​0.009, respectively). No correlations were found between the markers determined in the EBC and serum.

CONCLUSIONS

The results of the EBC nitrosative stress biomarkers should be interpreted with caution, especially in patients with stable disease, as the EBC values may be independent on levels of circulating markers that are elevated in the serum of patients with stable CF.

Metabolomics of airways disease in cystic fibrosis

While discovery metabolomic studies have identified many potential biomarkers of cystic fibrosis (CF) airways disease, relatively few have been validated. We review the recent literature to identify the most promising metabolomic findings as those repeatedly observed over multiple studies. Reproducible metabolomic findings include increased airway amino acids and small peptides in CF airways, as well as changes in phospholipids and sphingolipids. Other commonly altered pathways include adenosine metabolism, polyamine synthesis, and oxidative stress. These pathways represent potential biomarkers and therapeutic targets, though findings require reevaluation in the era of highly effective modulator therapies. Analysis of airway biomarkers in exhaled breath holds promise for non-invasive detection, though technical challenges will need to be overcome.

Non-Small Cell Lung Cancer Detection and Subtyping by UPLC-HRMS-Based Tissue Metabolomics

Non-small cell lung cancer (NSCLC) is the prevalent histological subtype of lung cancer. In this study, we performed ultraperformance liquid chromatography-high-resolution mass spectrometry (UPLC-HRMS)-based metabolic profiling of 227 tissue samples from 79 lung cancer patients with adenocarcinoma (AC) or squamous cell carcinoma (SCC). Orthogonal partial least squares-discriminant analysis (oPLS-DA) analyses showed that AC, SCC, and NSCLC tumors were discriminated from adjacent noncancerous tissue (ANT) and distant noncancerous tissue (DNT) samples with good accuracies (91.3, 100, and 88.3%), sensitivities (85.7, 100, and 83.9%), and specificities (94.3, 100, and 90.7%), using 12, 4, and 7 discriminant metabolites, respectively. The discriminant panel for AC detection included valine, sphingosine, glutamic acid γ-methyl ester, and lysophosphatidylcholine (LPC) (16:0), levels of which in tumor tissues were significantly altered. Valine, sphingosine, LPC (18:1), and leucine derivatives were used for SCC detection. The discrimination between AC and SCC had 96.8% accuracy, 98.2% sensitivity, and 85.7% specificity using a five-metabolite panel, of which valine and creatine had significant differences. The classification models were further verified with external validation sets, showing a promising prospect for NSCLC tissue detection and subtyping.

Ganoderic acids-rich ethanol extract from Ganoderma lucidum protects against alcoholic liver injury and modulates intestinal microbiota in mice with excessive alcohol intake

Alcoholic liver injury is mainly caused by excessive alcohol consumption and has become a global public health problem threatening human health. It is well known that Ganoderma lucidum possesses various excellent beneficial effects on liver function and lipid metabolism. The purpose of this study was to evaluate the underlying protective effect and action mechanism of ganoderic acids-rich G. lucidum ethanol extract (GLE) on alcohol-induced liver injury in mice with excessive alcohol intake. Results showed that oral administration of GLE could obviously inhibit the abnormal increases of serum triglyceride (TG), total cholesterol (TC), low density lipoprotein cholesterol (LDL-C), aspartate aminotransferase (AST) and alanine aminotransferase (ALT), and also significantly protect the liver against alcohol-induced excessive hepatic lipid accumulation and pathological changes. In addition, alcohol-induced oxidative stress in liver was significantly ameliorated by the dietary intervention of GLE through reducing the hepatic levels of maleic dialdehyde (MDA) and lactate dehydrogenase (LDH), and increasing the hepatic levels of glutathione (GSH), catalase (CAT), superoxide dismutase (SOD) and alcohol dehydrogenase (ADH). Compared with the model group, GLE intervention significantly ameliorated the intestinal microbial disorder by elevating the relative abundance of Ruminiclostridium_9, Prevotellaceae_UCG-001, Oscillibacter, [Eubacterium]_xylanophilum_group, norank_f_Clostridiates_vadinBB60_group, GCA-900066225, Bilophila, Ruminococcaceae_UCG-009, norank_f_Desulfovibrionaceae and Hydrogenoanaerobacterium, but decreasing the proportion of Clostridium_sensu_stricto_1. Furthermore, liver metabolomic profiling suggested that GLE intervention had a significant regulatory effect on the composition of liver metabolites in mice with excessive alcohol intake, especially the levels of some biomarkers involved in primary bile acid biosynthesis, riboflavin metabolism, tryptophan metabolism, biosynthesis of unsaturated fatty acids, fructose and mannose metabolism, glycolysis/gluconeogenesis. Additionally, dietary supplementation with GLE significantly regulated the mRNA levels of key genes related to fatty acids metabolism, ethanol catabolism and inflammatory response in liver. Conclusively, these findings indicate that GLE has a potentially beneficial effect on alleviating alcohol-induced liver injury and may be developed as a promising functional food ingredient.

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Phytochemical analysis revealed that ethanol extract of Gaoderma lucidum (GLE) is rich in ganoderic acids.

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GLE ameliorated lipid metabolism, antioxidant function and inflammatory response in mice with excessive alcohol intake.

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Liver metabolomics based on UPLC-QTOF/MS was performed to reveal the underlying hepatoprotective effect of GLE.

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GLE intervention alleviated alcoholic liver injury partly through regulating the “gut-liver-metabolite”axis.

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Hepatic gene transcriptions related to lipid metabolism and inflammation were remarkablyinfluenced by GLE intervention.

Metabolomic Biomarkers to Predict and Diagnose Cystic Fibrosis Pulmonary Exacerbations: A Systematic Review

INTRODUCTION

Metabolomics is an emerging area of research and has the potential to identify clinical biomarkers for predicting or diagnosing cystic fibrosis (CF) pulmonary exacerbations (PEx).

OBJECTIVE

To identify clinically promising metabolites across different sample sources that can be used to predict or diagnose PEx in CF.

EVIDENCE REVIEW

Searches for original literature were completed through EMBASE, MEDLINE, and all databases on the Web of Science with no restrictions on language or publication date. Gray literature was collected through Google Scholar. Additional studies were obtained by contacting authors and searching reference lists of candidate papers. The patient population included individuals with CF. Studies involving patients who underwent lung transplantation were excluded. The outcome was the prediction or diagnosis of pulmonary exacerbations from metabolites directly measured from biological samples. Search results were downloaded and imported into Covidence and duplicates were removed automatically. Any remaining duplicates were manually tagged and excluded. Two independent reviewers screened each abstract for eligibility and repeated this process for full texts. Risk of bias was conducted using QUADAS-2 by two independent reviewers. A third author resolved any remaining conflicts.

RESULTS

A combined 3974 relevant abstracts were identified and 115 full texts were assessed for eligibility. The final 25 studies underwent data extraction for study design, patient demographics, studied metabolites, concentration values, and diagnostic accuracy values. Included studies differed considerably in methodologies, sample specimen types (exhaled breath condensate [EBC], sputum, saliva, plasma, urine), and disease states. We identified 19 unique metabolites that were measured by two or more studies of which 2 have the potential to predict PEx (EBC 4-hydroxycyclohexylcarboxylic acid [4-HCHC] and lactic acid) and 6 to diagnose PEx (EBC 4-HCHC and lactic acid, sputum lactic acid and nitrate, and plasma arginine and methionine).

CONCLUSION AND RELEVANCE

This systematic review has identified promising metabolites for further study in CF. Certain metabolites may provide clinical potential in predicting or diagnosing PEx, but further validation studies are required. With better tools to aid in the earlier identification of PEx, clinicians can implement preventative measures to mitigate airway damage.Systematic Review Registration: https://www.crd.york.ac.uk/prospero/.

Sweat metabolomics before and after intravenous antibiotics for pulmonary exacerbation in people with cystic fibrosis

BACKGROUND

People with cystic fibrosis (PWCF) suffer from acute unpredictable reductions in pulmonary function associated with a pulmonary exacerbation (PEx) that may require hospitalization. PEx symptoms vary between PWCF without universal diagnostic criteria for diagnosis and response to treatment.

RESEARCH QUESTION

We characterized sweat metabolomes before and after intravenous (IV) antibiotics in PWCF hospitalized for PEx to determine feasibility and define biological alterations by IV antibiotics for PEx.

STUDY DESIGN AND METHODS

PWCF with PEx requiring hospitalization for IV antibiotics were recruited from clinic. Sweat samples were collected using the Macroduct® Sweat Collection System at admission prior to initiation of IV antibiotics and after completion prior to discharge. Samples were analyzed for metabolite changes using ultra-high-performance liquid chromatography/tandem accurate mass spectrometry.

RESULTS

Twenty-six of 29 hospitalized PWCF completed the entire study. A total of 326 compounds of known identity were detected in sweat samples. Of detected metabolites, 147 were significantly different between pre-initiation and post-completion of IV antibiotics for PEx (average treatment 14 days). Global sweat metabolomes changed from before and after IV antibiotic treatment. We discovered specific metabolite profiles predictive of PEx status as well as enriched biologic pathways associated with PEx. However, metabolomic changes were similar in PWCF who failed to return to baseline pulmonary function and those who did not.

INTERPRETATION

Our findings demonstrate the feasibility of non-invasive sweat metabolomic profiling in PWCF and the potential for sweat metabolomics as a prospective diagnostic and research tool to further advance our understanding of PEx in PWCF.

Breathomics: Review of Sample Collection and Analysis, Data Modeling and Clinical Applications

Metabolomics research is rapidly gaining momentum in disease diagnosis, on top of other Omics technologies. Breathomics, as a branch of metabolomics is developing in various frontiers, for early and noninvasive monitoring of disease. This review starts with a brief introduction to metabolomics and breathomics. A number of important technical issues in exhaled breath collection and factors affecting the sampling procedures are presented. We review the recent progress in metabolomics approaches and a summary of their applications on the respiratory and non-respiratory diseases investigated by breath analysis. Recent reports on breathomics studies retrieved from Scopus and Pubmed were reviewed in this work. We conclude that analyzing breath metabolites (both volatile and nonvolatile) is valuable in disease diagnoses, and therefore believe that breathomics will turn into a promising noninvasive discipline in biomarker discovery and early disease detection in personalized medicine. The problem of wide variations in the reported metabolite concentrations from breathomics studies should be tackled by developing more accurate analytical methods and sophisticated numerical analytical alogorithms.

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.

Proteomics and Metabolomics for Cystic Fibrosis Research

The aim of this review article is to introduce the reader to the state-of-the-art of the contribution that proteomics and metabolomics sciences are currently providing for cystic fibrosis (CF) research: from the understanding of cystic fibrosis transmembrane conductance regulator (CFTR) biology to biomarker discovery for CF diagnosis. Our work particularly focuses on CFTR post-translational modifications and their role in cellular trafficking as well as on studies that allowed the identification of CFTR molecular interactors. We also show how metabolomics is currently helping biomarker discovery in CF. The most recent advances in these fields are covered by this review, as well as some considerations on possible future scenarios for new applications.