Metabolomics analysis identifies novel plasma biomarkers of cystic fibrosis pulmonary exacerbation

The Cytidine N-Acetyltransferase NAT10 Promotes Thalamus Hemorrhage-Induced Central Poststroke Pain by Stabilizing Fn14 Expression in Thalamic Neurons

The recognition of RNA N4-acetylcytidine (ac4C) modification as a significant type of gene regulation is growing; nevertheless, whether ac4C modification or the N-acetyltransferase 10 protein (NAT10, the only ac4C "writer" that is presently known) participates in thalamus hemorrhage (TH)-induced central poststroke pain (CPSP) is unknown. Here, we observed NAT10 was primarily located in the neuronal nuclei of the thalamus of mice, with Fn14 and p65. An increase of NAT10 mRNA and protein expression levels in the ipsilateral thalamus was observed from days 1 to 14 after TH. Inhibition of NAT10 by several different approaches attenuated Fn14 and p65 upregulation of TH mice, as well as tissue injury in the thalamus on the ipsilateral side, and the development and maintenance of contralateral nociceptive hypersensitivities. NAT10 overexpression increased Fn14 and p65 expression and elicited nociceptive hypersensitivities in naïve mice. Our findings suggest that ac4C modification and NAT10 participate in TH-induced CPSP by activating the NF-κB pathway through upregulating Fn14 in thalamic neurons. NAT10 could serve as a promising new target for CPSP treatment.

What diagnostic tests are available for respiratory infections or pulmonary exacerbations in cystic fibrosis: A scoping literature review

A scoping review methodological framework formed the basis of this review. A search of two electronic databases captured relevant literature published from 2013. 1184 articles were screened, 200 of which met inclusion criteria. Included studies were categorised as tests for either respiratory infections OR pulmonary exacerbations. Data were extracted to ascertain test type, sample type, and indication of use for each test type. For infection, culture is the most common testing method, particularly for bacterial infections, whereas PCR is utilised more for the diagnosis of viral infections. Spirometry tests, indicating lung function, facilitate respiratory infection diagnoses. There is no clear definition of what an exacerbation is in persons with CF. A clinical checklist with risk criteria can determine if a patient is experiencing an exacerbation event, however the diagnosis is clinician-led and will vary between individuals. Fuchs criteria are one of the most frequently used tests to assess signs and symptoms of exacerbation in persons with CF. This scoping review highlights the development of home monitoring tests to facilitate earlier and easier diagnoses, and the identification of novel biomarkers for indication of infections/exacerbations as areas of current research and development. Research is particularly prevalent regarding exhaled breath condensate and volatile organic compounds as an alternative sampling/biomarker respectively for infection diagnosis. Whilst there are a wide range of tests available for diagnosing respiratory infections and/or exacerbations, these are typically used clinically in combination to ensure a rapid, accurate diagnosis which will ultimately benefit both the patient and clinician.

Circulating Metabolite Biomarkers of Glycemic Control in Youth-Onset Type 2 Diabetes

OBJECTIVE

We aimed to identify metabolites associated with loss of glycemic control in youth-onset type 2 diabetes.

RESEARCH DESIGN AND METHODS

We measured 480 metabolites in fasting plasma samples from the TODAY (Treatment Options for Type 2 Diabetes in Adolescents and Youth) study. Participants (N = 393; age 10-17 years) were randomly assigned to metformin, metformin plus rosiglitazone, or metformin plus lifestyle intervention. Additional metabolomic measurements after 36 months were obtained in 304 participants. Cox models were used to assess baseline metabolites, interaction of metabolites and treatment group, and change in metabolites (0-36 months), with loss of glycemic control adjusted for age, sex, race, treatment group, and BMI. Metabolite prediction models of glycemic failure were generated using elastic net regression and compared with clinical risk factors.

RESULTS

Loss of glycemic control (HbA1c ≥8% or insulin therapy) occurred in 179 of 393 participants (mean 12.4 months). Baseline levels of 33 metabolites were associated with loss of glycemic control (q < 0.05). Associations of hexose and xanthurenic acid with treatment failure differed by treatment randomization; youths with higher baseline levels of these two compounds had a lower risk of treatment failure with metformin alone. For three metabolites, changes from 0 to 36 months were associated with loss of glycemic control (q < 0.05). Changes in d-gluconic acid and 1,5-AG/1-deoxyglucose, but not baseline levels of measured metabolites, predicted treatment failure better than changes in HbA1c or measures of β-cell function.

CONCLUSIONS

Metabolomics provides insight into circulating small molecules associated with loss of glycemic control and may highlight metabolic pathways contributing to treatment failure in youth-onset diabetes.

Arteriovenous metabolomics in pigs reveals CFTR regulation of metabolism in multiple organs

Mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene cause cystic fibrosis (CF), a multiorgan disease that is characterized by diverse metabolic defects. However, other than specific CFTR mutations, the factors that influence disease progression and severity remain poorly understood. Aberrant metabolite levels have been reported, but whether CFTR loss itself or secondary abnormalities (infection, inflammation, malnutrition, and various treatments) drive metabolic defects is uncertain. Here, we implemented comprehensive arteriovenous metabolomics in newborn CF pigs, and the results revealed CFTR as a bona fide regulator of metabolism. CFTR loss impaired metabolite exchange across organs, including disruption of lung uptake of fatty acids, yet enhancement of uptake of arachidonic acid, a precursor of proinflammatory cytokines. CFTR loss also impaired kidney reabsorption of amino acids and lactate and abolished renal glucose homeostasis. These and additional unexpected metabolic defects prior to disease manifestations reveal a fundamental role for CFTR in controlling multiorgan metabolism. Such discovery informs a basic understanding of CF, provides a foundation for future investigation, and has implications for developing therapies targeting only a single tissue.

Changes in fecal lipidome after treatment with ivacaftor without changes in microbiome or bile acids

BACKGROUND

Alterations in gastrointestinal health are prominent manifestations of cystic fibrosis (CF) and can independently impact pulmonary function. Ivacaftor has been associated with robust improvements in pulmonary function and weight gain, but less is known about the impact of ivacaftor on the fecal microbiome, lipidome, and bile acids.

METHODS

Stool samples from 18 patients with CF and gating mutations (ages 6-61 years, 13 pancreatic insufficient) were analyzed for fecal microbiome and lipidome composition as well as bile acid concentrations at baseline and after 3 months of treatment with ivacaftor. Microbiome composition was also assessed in a healthy reference cohort.

RESULTS

Alpha and beta diversity of the microbiome were different between CF and reference cohort at baseline, but no treatment effect was seen in the CF cohort between baseline and 3 months. Seven lipids increased with treatment. No differences were seen in bile acid concentrations after treatment in CF. At baseline, 403 lipids and unconjugated bile acids were different between pancreatic insufficient (PI-CF) and sufficient (PS-CF) groups and 107 lipids were different between PI-CF and PS-CF after 3 months of treatment.

CONCLUSIONS

The composition and diversity of the fecal microbiome were different in CF as compared to a healthy reference, and did not change after 3 months of ivacaftor. We detected modest differences in the fecal lipidome with treatment. Differences in lipid and bile acid profiles between PS-CF and PI-CF were attenuated after 3 months of treatment.

N4-acetylcytidine modifies primary microRNAs for processing in cancer cells

N4 acetylcytidine (ac4C) modification mainly occurs on tRNA, rRNA, and mRNA, playing an important role in the expression of genetic information. However, it is still unclear whether microRNAs have undergone ac4C modification and their potential physiological and pathological functions. In this study, we identified that NAT10/THUMPD1 acetylates primary microRNAs (pri-miRNAs) with ac4C modification. Knockdown of NAT10 suppresses and augments the expression levels of mature miRNAs and pri-miRNAs, respectively. Molecular mechanism studies found that pri-miRNA ac4C promotes the processing of pri-miRNA into precursor miRNA (pre-miRNA) by enhancing the interaction of pri-miRNA and DGCR8, thereby increasing the biogenesis of mature miRNA. Knockdown of NAT10 attenuates the oncogenic characters of lung cancer cells by regulating miRNA production in cancers. Moreover, NAT10 is highly expressed in various clinical cancers and negatively correlated with poor prognosis. Thus, our results reveal that NAT10 plays a crucial role in cancer initiation and progression by modulating pri-miRNA ac4C to affect miRNA production, which would provide an attractive therapeutic strategy for cancers.

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.

NAT10-mediated RNA acetylation enhances HNRNPUL1 mRNA stability to contribute cervical cancer progression

N4-acetylcytidine (ac4C) is a lately discovered nucleotide modification that has been shown to be closely implicated in cancer. N-acetyltransferase10(NAT10) acts as an enzyme that regulates mRNA acetylation modifications. Currently, the role of NAT10-mediated RNA acetylation modification in cervical cancer remains to be elucidated. On the basis of transcriptome analysis of TCGA and GEO open datasets (GSE52904, GSE29570, GSE122697), NAT10 is upregulated in cervical cancer tissues and correlated with poor prognosis. Knockdown of NAT10 suppressed the cell proliferation, invasion, and migration of cervical cancer cells. The in vivo oncogenic function of NAT10 was also confirmed in xenograft models. Combined RNA-seq and acRIP-seq analysis revealed HNRNPUL1 as the target of NAT10 in cervical cancer. NAT10 positively regulate HNRNPUL1 expression by promoting ac4C modification and stability of HNRNPUL1 mRNA. Furthermore, depletion of HNRNPUL1 suppressed the cell division, invasion, and migration of cervical cancer. HNRNPUL1 overexpression partially restored cellular function in cervical cancer cells with NAT10 knockdown. Thus, this study demonstrates that NAT10 contributes to cervical cancer progression by enhancing HNRNPUL1 mRNA stability via ac4C modification, and NAT10-ac4C-HNRNPUL1 axis might be a potential target for cervical cancer therapy.

Association of Metabolites, Nutrients, and Toxins in Maternal and Cord Serum with Asthma, IgE, SPT, FeNO, and Lung Function in Offspring

The role of metabolites, nutrients, and toxins (MNTs) in sera at the end of pregnancy and of their association with offspring respiratory and allergic disorders is underexplored. Untargeted approaches detecting a variety of compounds, known and unknown, are limited. In this cohort study, we first aimed at discovering associations of MNTs in grandmaternal (F0) serum with asthma, immunoglobulin E, skin prick tests, exhaled nitric oxide, and lung function parameters in their parental (F1) offspring. Second, for replication, we tested the identified associations of MNTs with disorders in their grandchildren (F2-offspring) based on F2 cord serum. The statistical analyses were sex-stratified. Using liquid chromatography/high-resolution mass spectrometry in F0, we detected signals for 2286 negative-ion lipids, 59 positive-ion lipids, and 6331 polar MNTs. Nine MNTs (one unknown MNT) discovered in F0-F1 and replicated in F2 showed higher risks of respiratory/allergic outcomes. Twelve MNTs (four unknowns) constituted a potential protection in F1 and F2. We recognized MNTs not yet considered candidates for respiratory/allergic outcomes: a phthalate plasticizer, an antihistamine, a bile acid metabolite, tryptophan metabolites, a hemiterpenoid glycoside, triacylglycerols, hypoxanthine, and polyphenol syringic acid. The findings suggest that MNTs are aspirants for clinical trials to prevent adverse respiratory/allergic outcomes.

The Cytidine N-Acetyltransferase NAT10 Participates in Peripheral Nerve Injury-Induced Neuropathic Pain by Stabilizing SYT9 Expression in Primary Sensory Neurons

RNA N4-acetylcytidine (ac4C) modification is increasingly recognized as an important layer of gene regulation; however, the involvement of ac4C in pain regulation has not been studied. Here, we report that N-acetyltransferase 10 protein (NAT10; the only known ac4C "writer") contributes to the induction and development of neuropathic pain in an ac4C-dependent manner. Peripheral nerve injury increases the levels of NAT10 expression and overall ac4C in injured dorsal root ganglia (DRGs). This upregulation is triggered by the activation of upstream transcription factor 1 (USF1), a transcription factor that binds to the Nat10 promoter. Knock-down or genetic deletion of NAT10 in the DRG abolishes the gain of ac4C sites in Syt9 mRNA and the augmentation of SYT9 protein, resulting in a marked antinociceptive effect in nerve-injured male mice. Conversely, mimicking NAT10 upregulation in the absence of injury evokes the elevation of Syt9 ac4C and SYT9 protein and induces the genesis of neuropathic-pain-like behaviors. These findings demonstrate that USF1-governed NAT10 regulates neuropathic pain by targeting Syt9 ac4C in peripheral nociceptive sensory neurons. Our findings establish NAT10 as a critical endogenous initiator of nociceptive behavior and a promising new target for treating neuropathic pain.SIGNIFICANCE STATEMENT The cytidine N4-acetylcytidine (ac4C), a new epigenetic RNA modification, is crucial for the translation and stability of mRNA, but its role for chronic pain remains unclear. Here, we demonstrate that N-acetyltransferase 10 (NAT10) acts as ac4C N-acetyltransferase and plays an important role in the development and maintenance of neuropathic pain. NAT10 was upregulated via the activation of the transcription factor upstream transcription factor 1 (USF1) in the injured dorsal root ganglion (DRG) after peripheral nerve injury. Since pharmacological or genetic deleting NAT10 in the DRG attenuated the nerve injury-induced nociceptive hypersensitivities partially through suppressing Syt9 mRNA ac4C and stabilizing SYT9 protein level, NAT10 may serve as an effective and novel therapeutic target for neuropathic pain.

Proteomics and metabolomics profiling reveal panels of circulating diagnostic biomarkers and molecular subtypes in stable COPD

BACKGROUND

Chronic obstructive pulmonary disease (COPD) is a complex and heterogeneous disease with high morbidity and mortality, especially in advanced patients. We aimed to develop multi-omics panels of biomarkers for the diagnosis and explore its molecular subtypes.

METHODS

A total of 40 stable patients with advanced COPD and 40 controls were enrolled in the study. Proteomics and metabolomics techniques were applied to identify potential biomarkers. An additional 29 COPD and 31 controls were enrolled for validation of the obtained proteomic signatures. Information on demographic, clinical manifestation, and blood test were collected. The ROC analyses were carried out to evaluate the diagnostic performance, and experimentally validated the final biomarkers on mild-to-moderate COPD. Next, molecular subtyping was performed using proteomics data.

RESULTS

Theophylline, palmitoylethanolamide, hypoxanthine, and cadherin 5 (CDH5) could effectively diagnose advanced COPD with high accuracy (auROC = 0.98, sensitivity of 0.94, and specificity of 0.95). The performance of the diagnostic panel was superior to that of other single/combined results and blood tests. Proteome based stratification of COPD revealed three subtypes (I-III) related to different clinical outcomes and molecular feature: simplex COPD, COPD co-existing with bronchiectasis, and COPD largely co-existing with metabolic syndrome, respectively. Two discriminant models were established using the auROC of 0.96 (Principal Component Analysis, PCA) and 0.95 (the combination of RRM1 + SUPV3L1 + KRT78) in differentiating COPD and COPD with co-morbidities. Theophylline and CDH5 were exclusively elevated in advanced COPD but not in its mild form.

CONCLUSIONS

This integrative multi-omics analysis provides a more comprehensive understanding of the molecular landscape of advanced COPD, which may suggest molecular targets for specialized therapy.

Integrated proteomics and metabolomics reveal variations in pulmonary fibrosis development and the potential therapeutic effect of Shuangshen Pingfei formula

ETHNOPHARMACOLOGICAL RELEVANCE

Shuangshen Pingfei formula (SSPF), a Chinese medicine prescription, has been prescribed to alleviate PF. However, little is known about the molecular mechanism underlying PF progression and the regulatory mechanism in SSPF.

AIMS OF THE STUDY

To discriminate the molecular alterations underlying the development of pulmonary fibrosis (PF) and reveal the regulatory mechanism of Shuangshen Pingfei formula (SSPF).

MATERIALS AND METHODS

An integrated analysis of a time-course pathology combined with proteomics and metabolomics was performed to investigate changes in body weight, survival rate, lung coefficient, histopathology, proteins, and metabolites of lung tissues at different time points upon bleomycin (BLM) exposure and SSPF treatment.

RESULTS

The results showed that PF progression was characterized by gradually aggravated fibrosis accompanied by inflammation with extended exposure (7, 14, and 21 days). SSPF significantly attenuated lung fibrosis, as evidenced by increased weight, and reduced lung coefficients and fibrosis scores. Moreover, 368 common differentially expressed proteins (DEPs) were identified, and 102 DEPs were continuously and monotonically upregulated via proteomics among the three BLM treatments. The DEPs were principally involved in extracellular matrix (ECM) remodeling and arginine and proline (AP) metabolic reprogramming. Additionally, metabolomics analyses revealed that BLM exposure mainly affected six metabolism pathways, including 34 differentially regulated metabolites (DRMs). Furthermore, correlation analysis found that several DEPs and DRMs, including L-ornithine, S-adenosyl-L-methionine, ARG, and AOC1, were associated with arginine and proline metabolism, and 8,9-EET, 8,9-DHET, CYP2B, etc., were involved in arachidonic acid (AA) metabolism, suggesting that these two pathways play a critical role in the development of fibrosis. After SSPF treatment, the related protein expression and metabolic disorders were regulated, implying that SSPF provides potential solutions to target these pathways for benefit in the treatment of PF.

CONCLUSION

Our data suggest that ECM remodeling, and metabolic reprogramming of AP and AA are distinctive features of PF development. Simultaneously, we confirmed that SSPF could effectively regulate metabolic disorders, indicating its potential clinical application for PF therapy. Our findings using multiple approaches provide a molecular-scale perspective on the mechanisms of PF progression and the amelioration of SSPF.

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.

Mechanisms exploration of Terrestrosin D on pulmonary fibrosis based on plasma metabolomics and network pharmacology

Terrestrosin D (TED) is the active ingredient of Tribulus terrestris L., which is used in traditional Chinese medicine (TCM) formulations and has a wide range of pharmacological activities. A previous study showed that TED alleviated bleomycin (BLM)-induced pulmonary fibrosis (PF) in mice. However, the mechanisms underlying the therapeutic effect of TED are still unclear and need further investigation. In this study, we evaluated the effect of TED in a mice of BLM-induced PF in terms of histopathological and biochemical indices. UHPLC-MS-based plasma metabolomics combined with network pharmacology was used to explore the pathological basis of PF and the mechanism of action of TED. Histological and biochemical analyses showed that TED mitigated inflammatory injury in the lungs, especially at the dosage of 20 mg/kg. Furthermore, BLM changed the plasma metabolite profile in the mice, which was reversed by TED via regulation of amino acid and lipid metabolism. Subsequently, a biomarkers-targets-disease network was constructed, tumor necrosis factor (TNF)-α and transforming growth factor (TGF)-β1 were identified as the putative therapeutic targets of TED. Both factors were quantitatively analyzed by enzyme-linked immunosorbent assay (ELISA). Taken together, the combination of UHPLC-MS-based metabolomics and network pharmacology can unveil the mechanisms of diseases and drug action.

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.

Mechanistic Investigation of Xuebijing for Treatment of Paraquat-Induced Pulmonary Fibrosis by Metabolomics and Network Pharmacology

After paraquat (PQ) poisoning, it is difficult to accurately diagnose patients' condition by only measuring their blood PQ concentration. Therefore, it is important to establish an accurate method to assist in the diagnosis of PQ poisoning, especially in the early stages. In this study, a gas chromatography-mass spectrometry (GC-MS) metabonomics strategy was established to obtain metabolite information. A random forest algorithm was used to search for potential biomarkers of PQ poisoning, and data mining and network pharmacological analysis were used to evaluate the active components, drug-disease targets, and key pathways of Xuebijing (XBJ) injection in the treatment of PQ-induced pulmonary fibrosis. Targets from the network pharmacology analysis and metabolites from plasma metabolomics were jointly analyzed to select crucial metabolic pathways. Finally, molecular docking technology and in vitro experiments were used to verify the pathway targets to further reveal the potential mechanisms underlying the antipulmonary fibrosis effect of XBJ. Metabonomics studies showed that l-valine, glycine, citric acid, d-mannose, d-galactose, maltose, l-tryptophan, and arachidonic acid contributed more to the differentiation of different groups than other metabolites. Compared with the control group, the PQ poisoning group had higher levels of l-valine, glycine, citric acid, l-tryptophan, and arachidonic acid, and lower levels of d-mannose, d-galactose, and maltose. After treatment with XBJ injection, the relative levels of these metabolites were reversed. The network pharmacological analysis screened a total of 180 targets, mainly involving multiple signaling pathways and metabolic pathways, which jointly played an antipulmonary fibrosis effect. Based on the combined analysis of 180 targets and 8 different metabolites, arachidonic acid metabolism was selected as the key metabolic pathway. Molecular docking analysis showed that the XBJ compound had strong binding activity with the target protein. Western blot results showed that XBJ injection could reduce the inflammatory response by downregulating the expressions of p-p65, p-IKBα, and p-IKKβ, thus inhibiting the development of PQ-induced pulmonary fibrosis. In summary, the combined results from metabolomics and network pharmacology studies showed that Xuebijing has the characteristics of multitarget, multichannel, and multicomponent action in the treatment of pulmonary fibrosis caused by PQ.

Pharmaceutical targeting of succinate dehydrogenase in fibroblasts controls bleomycin-induced lung fibrosis

Idiopathic pulmonary fibrosis (IPF) is characterized by excessive deposition of extracellular matrix in the lung with fibroblast-to-myofibroblast transition, leading to chronically compromising lung function and death. However, very little is known about the metabolic alterations of fibroblasts in IPF, and there is still a lack of pharmaceutical agents to target the metabolic dysregulation. Here we show a glycolysis upregulation and fatty acid oxidation (FAO) downregulation in fibroblasts from fibrotic lung, and perturbation of glycolysis and FAO affects fibroblasts transdifferentiation. In addition, there is a significant accumulation of succinate both in fibrotic lung tissues and myofibroblasts, where succinate dehydrogenase (SDH) operates in reverse by reducing fumarate to succinate. Then succinate contributes to glycolysis upregulation and FAO downregulation by stabilizing HIF-1α, which promotes the development of lung fibrosis. In addition, we identify a near-infrared small molecule dye, IR-780, as a targeting agent which stimulates mild inhibition of succinate dehydrogenase subunit A (SDHA) in fibroblasts, and which inhibits TGF-β1 induced SDH and succinate elevation, then to prevent fibrosis formation and respiratory dysfunction. Further, enhanced cell retention of IR-780 is shown to promote severe inhibition of SDHA in myofibroblasts, which may contribute to excessive ROS generation and selectively induces myofibroblasts to apoptosis, and then therapeutically improves established lung fibrosis in vivo. These findings indicate that targeting metabolic dysregulation has significant implications for therapies aimed at lung fibrosis and succinate dehydrogenase is an exciting new therapeutic target to treat IPF.

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Glycolysis upregulation and fatty acid oxidation (FAO) downregulation in fibroblasts lead to lung fibrosis.

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Succinate contributes to metabolic dysregulation of fibroblasts by stabilizing HIF-1α.

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Succinate dehydrogenase is an exciting new therapeutic target to treat IPF.

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IR-780 can be a promising agent to control lung fibrosis by targeting succinate dehydrogenase.

Metabolic reprogramming: A driver of cigarette smoke-induced inflammatory lung diseases

Cigarette smoking is a well-known risk factor for pulmonary diseases, including chronic obstructive pulmonary disease (COPD), asthma and pulmonary fibrosis. Despite major progress in dissecting the mechanisms associated with disease development and progression, findings only represent one aspect of multifaceted disease. A crucial consequence of this approach is that many therapeutic treatments often fail to improve or reverse the disease state as other conditions and variables are insufficiently considered. To expand our understanding of pulmonary diseases, omics approaches, particularly metabolomics, has been emerging in the field. This strategy has been applied to identify putative biomarkers and novel mechanistic insights. In this review, we discuss metabolic profiles of patients with COPD, asthma, and idiopathic pulmonary fibrosis (IPF) with a focus on the direct effects of cigarette smoking in altering metabolic regulation. We next present cell- and animal-based experiments and point out the therapeutic potential of targeting metabolic reprogramming in inflammatory lung diseases. In addition, the obstacles in translating these findings into clinical practice, including potential adverse effects and limited pharmacological efficacy, are also addressed.

Distinctive metabolic profiles between Cystic Fibrosis mutational subclasses and lung function

INTRODUCTION

Cystic fibrosis (CF) is a lethal multisystemic disease of a monogenic origin with numerous mutations. Functional defects in the cystic fibrosis transmembrane conductance receptor (CFTR) protein based on these mutations are categorised into distinct classes having different clinical presentations and disease severity.

OBJECTIVES

The present study aimed to create a comprehensive metabolomic profile of altered metabolites in patients with CF, among different classes and in relation to lung function.

METHODS

A chemical isotope labeling liquid chromatography-mass spectrometry metabolomics was used to study the serum metabolic profiles of young and adult CF (n = 39) patients and healthy controls (n = 30). Comparisons were made at three levels, CF vs. controls, among mutational classes of CF, between CF class III and IV, and correlated the lung function findings.

RESULTS

A distinctive metabolic profile was observed in the three analyses. 78, 20, and 13 significantly differentially dysregulated metabolites were identified in the patients with CF, among the different classes and between class III and IV, respectively. The significantly identified metabolites included amino acids, di-, and tri-peptides, glutathione, glutamine, glutamate, and arginine metabolism. The top significant metabolites include 1-Aminopropan-2-ol, ophthalmate, serotonin, cystathionine, and gamma-glutamylglutamic acid. Lung function represented by an above-average FEV1% level was associated with decreased glutamic acid and increased guanosine levels.

CONCLUSION

Metabolomic profiling identified alterations in different amino acids and dipeptides, involved in regulating glutathione metabolism. Two metabolites, 3,4-dihydroxymandelate-3-O-sulfate and 5-Aminopentanoic acid, were identified in common between the three anlayses and may represent as highly sensitive biomarkers for CF.

Emerging role of N4-acetylcytidine modification of RNA in gene regulation and cellular functions

Post-transcriptional chemical modification of RNA is rapidly emerging as a key player in regulating gene expression and has propelled the development of 'epitranscriptomics' or 'RNA epigenetics' as a frontier area of research. Several RNA modifications are known to decorate RNAs and impact its structure and function. One such recently discovered modification is acetylation of RNA i.e. N4-acetylcytidine (ac4C) chemical modification. N4-acetylcytidine is an ancient and evolutionarily conserved modification, which maps to a wide spectrum of RNAs from archaea bacteria to humans. This modification results in a variety of functional outcomes which impact normal development and disease. In this review, we summarize the recent progress, emerging methods, biological implications and the future challenges for ac4C modification.

Utilizing centralized biorepository samples for biomarkers of cystic fibrosis lung disease severity

BACKGROUND

Circulating biomarkers reflective of lung disease activity and severity have the potential to improve patient care and accelerate drug development in CF. The objective of this study was to leverage banked specimens to test the hypothesis that blood-based biomarkers discriminate CF children segregated by lung disease severity.

METHODS

Banked serum samples were selected from children who were categorized into two extremes of phenotype associated with lung function ('mild' or 'severe') based on CF-specific data and were matched on age, gender, CFTR genotype, and P. aeruginosa infection status. Targeted inflammatory proteins, lipids, and discovery metabolite profiles were measured in these serum samples.

RESULTS

The severe cohort, characterized by a lower CF-specific FEV1 percentile, had significantly higher circulating concentrations of high sensitivity C-reactive protein, serum amyloid A, granulocyte colony stimulating factor, and calprotectin compared to the mild cohort. The mild cohort tended to have higher serum linoleic acid concentrations. The metabolite arabitol was lower in the severe cohort while other CF relevant metabolic pathways showed non-significant differences after adjusting for multiple comparisons. A sensitivity analysis to correct for biased estimates that may result from selecting subjects using an extremes of phenotype approach confirmed the protein biomarker findings.

CONCLUSIONS

Circulating inflammatory proteins differ in CF children segregated by lung function. These findings serve to demonstrate the value of maintaining centralized, high quality patient derived samples for future research, with linkage to clinical information to answer testable hypotheses in biomarker development.

Dried Blood Spot-Based Metabolomic Profiling in Adults with Cystic Fibrosis

Mucoviscidosis of the respiratory, gastrointestinal, and genitourinary tracts is the major pathology in patients with cystic fibrosis (CF), a lethal monogenic panethnic and multisystemic disease most commonly identified in Caucasians. Currently, the measurement of immuno reactive trypsinogen in dry blood spots (DBSs) is the gold-standard method for initial newborn screening for CF, followed by targeted CF transmembrane regulator (CFTR) mutation analysis, and ultimate confirmation with abnormally elevated sweat chloride. Previous metabolomics studies in patients with CF reported on different biomarkers such as breath 2-aminoacetophenone produced during acute and chronic infection in human tissues, including the lungs of CF patients. Herein, we used liquid and gas chromatography-mass spectrometry-based targeted metabolomics profiling to identify potentially reliable, sensitive, and specific biomarkers in DBSs collected from 69 young and adult people including CF patients (n = 39) and healthy control (n = 30). A distinctive metabolic profile including 26 significantly differentially expressed metabolites involving amino acids, glycolysis, mitochondrial and peroxisomal metabolism, and sorbitol pathways was identified. Specifically, the osmolyte (sorbitol) was remarkably downregulated in CF patients compared to healthy controls indicating perturbation in the sorbitol pathway, which may be responsible for the mucoviscidosis seen in patients with CF. The significance of our findings is supported by the clinical utility of inhaled mannitol and hypertonic saline in patients with CF. The systemic administration of sorbitol in such patients may confer additional benefits beyond the respiratory system, especially in those with misfolded CFTR proteins.

A comprehensive analysis of metabolomics and transcriptomics in non-small cell lung cancer

Non-small cell lung cancer (NSCLC) remains a leading cause of cancer death globally. More accurate and reliable diagnostic methods/biomarkers are urgently needed. Joint application of metabolomics and transcriptomics technologies possesses the high efficiency of identifying key metabolic pathways and functional genes in lung cancer patients. In this study, we performed an untargeted metabolomics analysis of 142 NSCLC patients and 159 healthy controls; 35 identified metabolites were significantly different between NSCLC patients and healthy controls, of which 6 metabolites (hypoxanthine, inosine, L-tryptophan, indoleacrylic acid, acyl-carnitine C10:1, and lysoPC(18:2)) were chosen as combinational potential biomarkers for NSCLC. The area under the curve (AUC) value, sensitivity (SE), and specificity (SP) of these six biomarkers were 0.99, 0.98, and 0.99, respectively. Potential diagnostic implications of the metabolic characteristics in NSCLC was studied. The metabolomics results were further verified by transcriptomics analysis of 1027 NSCLC patients and 108 adjacent peritumoral tissues from TCGA database. This analysis identified 2202 genes with significantly different expressions in cancer cells compared to normal controls, which in turn defined pathways implicated in the metabolism of the compounds revealed by metabolomics analysis. We built a fully connected network of metabolites and genes, which shows a good correspondence between the transcriptome analysis and the metabolites selected for diagnosis. In conclusion, this work provides evidence that the metabolic biomarkers identified may be used for NSCLC diagnosis and screening. Comprehensive analysis of metabolomics and transcriptomics data offered a validated and comprehensive understanding of metabolism in NSCLC.

Untargeted Metabolomics Analysis of Esophageal Squamous Cell Carcinoma Discovers Dysregulated Metabolic Pathways and Potential Diagnostic Biomarkers

Background: Esophageal squamous cell carcinoma (ESCC) is one of the most fatal diseases worldwide. Because early diagnosis is difficult, ESCC is mostly diagnosed at an advanced stage, leading to a poor overall prognosis. The purpose of this study was to explore the differences between plasma metabolic profiles in ESCC patients and healthy controls and to establish a diagnostic model of ESCC.

Methods: In this study, a cohort of 310 subjects, containing 140 ESCC patients and 170 healthy controls (HC), was recruited. Participants were randomly separated into a training set (80 ESCCs, 80 HCs) and a validation set (60 ESCCs, 90 HCs) and their plasma metabolomics profiles were analyzed by ultra-performance liquid chromatography-tandem quadruple time-of-flight mass spectrometry (UPLC-QTOF/MS) technique. Univariate statistical analysis and multivariate analysis (MVA) methods were used to identify differential metabolites. Finally, the dysregulated pathways associated with ESCC were further explored and the diagnostic performance of the biomarker panel was evaluated.

Results: Metabolic analyses identified 34 significant metabolites involved in the metabolism of amino acids, phospholipids, fatty acids, purine, and choline. Farthermore, an effective diagnostic model for ESCC was constructed based on eight metabolites. This panel of biomarkers consisted of hypoxanthine, proline betaine, indoleacrylic acid, inosine, 9-decenoylcarnitine, tetracosahexaenoic acid, LPE (20:4), and LPC (20:5). The model was verified and evaluated in the validation set. The AUC value of the ROC curve was 0.991(95% CI: 0.981-1.000, CI, Confidence interval), with a sensitivity (SE) of 98.8% and a specificity (SP) of 94.9% for the training set and 0.965(95% CI: 0.936-0.993), with a SE of 88.3% and a SP of 88.9% for the validation set. Among them, three biomarkers, indoleacrylic acid, LPC (20:5), and LPE (20:4), exhibited a trend associated with the ESCC progression.

Conclusions: Our study identified a novel plasma biomarker panel, which clearly distinguishes ESCC patients and provides insight into the mechanisms of ESCC. This finding may form the basis for the development of a minimally invasive method for ESCC detection.

The Processing, Gene Regulation, Biological Functions, and Clinical Relevance of N4-Acetylcytidine on RNA: A Systematic Review

N4-acetylcytidine (ac4C) is often considered to be a conservative, chemically modified nucleoside present on tRNA and rRNA. Recent studies have shown extensive ac4C modifications in human and yeast mRNAs. ac4C helps to correctly read codons during translation and improves translation efficiency and the stability of mRNA. At present, the research of ac4C involves a variety of detection methods. The formation of ac4C is closely related to N-acetyltransferase 10 (NAT10) and its helpers, such as putative tRNA acetyltransferase (TAN1) for tRNA ac4C and small nucleolar RNA (snoRNA) for rRNA ac4C. Also, ac4C is associated with the development, progression, and prognosis of a variety of human diseases. Here, we summarize the history of ac4C research and the detection technologies of ac4C. We then summarized the role and mechanism of ac4C in gene-expression regulation and demonstrated the relevance of ac4C to a variety of human diseases, especially cancer. Finally, we list the future challenges of the ac4C research and demonstrate a research strategy for the interactions among several abundant modified nucleosides on mRNA.

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

The most common cause of death in cystic fibrosis (CF) patients is progressive lung function decline, which is punctuated by acute pulmonary exacerbations (APEs). A major challenge is to discover biomarkers for detecting an oncoming APE and allow for pre-emptive clinical interventions. Metabolic profiling of exhaled breath condensate (EBC) samples collected from CF patients before, during, and after APEs and under stable conditions (n = 210) was performed using ultraperformance liquid chromatography (UPLC) coupled to Orbitrap mass spectrometry (MS). Negative ion mode MS data showed that classification between metabolic profiles from "pre-APE" (pending APE before the CF patient had any signs of illness) and stable CF samples was possible with good sensitivities (85.7 and 89.5%), specificities (88.4 and 84.1%), and accuracies (87.7 and 85.7%) for pediatric and adult patients, respectively. Improved classification performance was achieved by combining positive with negative ion mode data. Discriminant metabolites included two potential biomarkers identified in a previous pilot study: lactic acid and 4-hydroxycyclohexylcarboxylic acid. Some of the discriminant metabolites had microbial origins, indicating a possible role of bacterial metabolism in APE progression. The results show promise for detecting an oncoming APE using EBC metabolites, thus permitting early intervention to abort such an event.

Metabolomics in genetic testing

Metabolomics is an intriguing field of study providing a new readout of the biochemical activities taking place at the moment of sampling within a subject's biofluid or tissue. Metabolite concentrations are influenced by several factors including disease, environment, drugs, diet and, importantly, genetics. Metabolomics signatures, which describe a subject's phenotype, are useful for disease diagnosis and prognosis, as well as for predicting and monitoring the effectiveness of treatments. Metabolomics is conventionally divided into targeted (i.e., the quantitative analysis of a predetermined group of metabolites) and untargeted studies (i.e., analysis of the complete set of small-molecule metabolites contained in a biofluid without a pre-imposed metabolites-selection). Both approaches have demonstrated high value in the investigation and understanding of several monogenic and multigenic conditions. Due to low costs per sample and relatively short analysis times, metabolomics can be a useful and robust complement to genetic sequencing.

Metabonomics reveals altered metabolites related to inflammation and energy utilization at recovery of cystic fibrosis lung exacerbation

Background

Cystic fibrosis lung disease is characterized by chronic bacterial infections in the setting of mucus abnormalities. Patients experience periodic exacerbations that manifest with increased respiratory symptoms that require intensification of therapy with enhanced airway clearance and intravenous (IV) antibiotics.

Objectives

In an observational study we tested if the profile of metabolites in serum distinguished the pre-from post-exacerbation state and which systemically measurable pathways were affected during the process to recovery.

Methods

Serum collected within 48 h of start and completion, respectively of IV antibiotics was collected from people with CF ages 6–30 years. Three day food records were collected prior to each sample. To reduce variation between subjects only subjects who had pancreatic insufficiency, had similar CF mutations, and did not have CF liver disease or diabetes were included. Metabolomic profiling was conducted by Ultrahigh Performance Liquid Chromatography-Tandem Mass Spectroscopy with metabolites being identified based on retention time/index, mass to charge ratio and comparison to known compounds. Biostatistical analyses used paired t-test with correction for multiple comparisons and orthogonal partial least square discriminant analysis.

Results

Thirty subjects (20 male) with a mean ± SEM age of 15.3 ± 1.2 years participated, 17 of whom had matched food-records. Lung function was significantly improved post-therapy compared to pre-therapy, (mean ± SEM) 75 ± 4% vs. 68 ± 4% predicted (n = 26). Serum metabonomics showed distinction of the pre-vs. post-therapy groups with 123 compounds contributing to the differentiation pre-versus post-antibiotics by multiple biostatistical analyses. Compounds and pathways affected included bile acids and microbial derived amino acid metabolites, increases in lipid classes of the glycerophospholipid, glycerolipids, cholesterol, phopsholipids, and most pronounced, the class of sphingolipids. Changes in n6/n3 fatty acids, decreased polyamines but increased metabolites in the nitric oxide pathway, and changes in the tryptophan-kynurenine pathway indicated decreased inflammation at resolution of exacerbation.

Conclusions

Changes in serum metabolites that distinguished CF pulmonary exacerbation vs. resolution of symptoms showed evidence of decreased inflammation and improvement from a catabolic state.

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Serum metabonomics distinguishes cystic fibrosis exacerbation to resolution state.

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Distinguishing pathways indicate alterations in (gut) microbiome and bile acids.

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Serum metabolites at resolution show decreased inflammation and oxidative stress.

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Lipid markers indicate improvement from a catabolic state at exacerbation.

Metabolomics toward personalized medicine

Metabolomics, which is the metabolites profiling in biological matrices, is a key tool for biomarker discovery and personalized medicine and has great potential to elucidate the ultimate product of the genomic processes. Over the last decade, metabolomics studies have identified several relevant biomarkers involved in complex clinical phenotypes using diverse biological systems. Most diseases result in signature metabolic profiles that reflect the sums of external and internal cellular activities. Metabolomics has a major role in clinical practice as it represents >95% of the workload in clinical laboratories worldwide. Many of these metabolites require different analytical platforms, such as Nuclear Magnetic Resonance (NMR), Mass Spectrometry (MS), and Ultra Performance Liquid Chromatography (UPLC), while many clinically relevant metabolites are still not routinely amenable to detection using currently available assays. Combining metabolomics with genomics, transcriptomics, and proteomics studies will result in a significantly improved understanding of the disease mechanisms and the pathophysiology of the target clinical phenotype. This comprehensive approach will represent a major step forward toward providing precision medical care, in which individual is accounted for variability in genes, environment, and personal lifestyle. In this review, we compare and evaluate the metabolomics strategies and studies that focus on the discovery of biomarkers that have "personalized" diagnostic, prognostic, and therapeutic value, validated for monitoring disease progression and responses to various management regimens.

Urinary metabolomics reveals unique metabolic signatures in infants with cystic fibrosis

BACKGROUND

Biologic pathways and metabolic mechanisms underpinning early systemic disease in cystic fibrosis (CF) are poorly understood. The Baby Observational and Nutrition Study (BONUS) was a prospective multi-center study of infants with CF with a primary aim to examine the current state of nutrition in the first year of life. Its secondary aim was to prospectively explore concurrent nutritional, metabolic, respiratory, infectious, and inflammatory characteristics associated with early CF anthropometric measurements. We report here metabolomics differences within the urine of these infants as compared to infants without CF.

METHODS

Urine metabolomics was performed for 85 infants with predefined clinical phenotypes at approximately one year of age enrolled in BONUS via Ultrahigh Performance Liquid Chromatography-Tandem Mass Spectroscopy (UPLC-MS/MS). Samples were stratified by disease status (non-CF controls (n = 22); CF (n = 63, All-CF)) and CF clinical phenotype: respiratory hospitalization (CF Resp, n = 22), low length (CF LL, n = 23), and low weight (CF LW, n = 15).

RESULTS

Global urine metabolomics profiles in CF were heterogeneous, however there were distinct metabolic differences between the CF and non-CF groups. Top pathways altered in CF included tRNA charging and methionine degradation. ADCYAP1 and huntingtin were identified as predicted unique regulators of altered metabolic pathways in CF compared to non-CF. Infants with CF displayed alterations in metabolites associated with bile acid homeostasis, pentose sugars, and vitamins.

CONCLUSIONS

Predicted metabolic pathways and regulators were identified in CF infants compared to non-CF, but metabolic profiles were unable to discriminate between CF phenotypes. Targeted metabolomics provides an opportunity for further understanding of early CF disease.

TRIAL REGISTRATION

United States ClinicalTrials.Gov registry NCT01424696 (clinicaltrials.gov).

Metabolomic responses to lumacaftor/ivacaftor in cystic fibrosis

BACKGROUND

Cystic fibrosis (CF) is a life-limiting disease caused by a defect in the cystic fibrosis transmembrane conductance regulator (CFTR) gene. Lumacaftor/Ivacaftor is a novel CFTR modulator approved for patients that are homozygous for Phe508del CFTR, but its clinical effectiveness varies amongst patients, making it difficult to determine clinical responders. Therefore, identifying biochemical biomarkers associated with drug response are clinically important for follow-up studies.

METHODS

Serum metabolomics was performed on twenty patients with CF pre- and 6-month post-Lumacaftor/Ivacaftor response via Ultrahigh Performance Liquid Chromatography-Tandem Mass Spectroscopy (UPLC-MS/MS). Correlation with clinical variables was performed.

RESULTS

Metabolomics analysis demonstrated 188 differentially regulated metabolites between patients pre- and post-Lumacaftor/Ivacaftor initiation, with a predominance of lipid and amino acid alterations. The top 30 metabolites were able to differentiate pre- and post-Lumacaftor/Ivacaftor status in greater than 90% of patients via a random-forest confusion matrix. Alterations in bile acids, phospholipids, and bacteria-associated metabolites were the predominant changes associated with drug response. Importantly, changes in metabolic patterns were associated with clinical responders.

CONCLUSIONS

Selected key lipid and amino acid metabolic pathways were significantly affected by Lumacaftor/Ivacaftor initiation and similar pathways were affected in clinical responders. Targeted metabolomics may provide useful and relevant biomarkers of CFTR modulator responses.

Development of the respiratory tract microbiota in cystic fibrosis

PURPOSE OF REVIEW

Progression of lung disease in cystic fibrosis (CF) is punctuated by Pseudomonas aeruginosa infection and recurrent pulmonary exacerbations, and is the major determinant of a patient's life expectancy. With the advent of novel deep-sequencing techniques, polymicrobial bacterial assemblages rather than single pathogens seem to be responsible for the deterioration of pulmonary function. This review summarizes recent insights into the development of the CF respiratory tract microbiome, with its determinants and its relations to clinical parameters.

RECENT FINDINGS

Research has moved from microbiota snapshots to intensive sampling over time, in an attempt to identify biomarkers of progression of CF lung disease. The developing respiratory tract microbiota in CF is perturbed by various endogenous and exogenous factors from the first months of life on. This work has revealed that both major pathogens such as P. aeruginosa and newly discovered players such as anaerobic species seem to contribute to CF lung disease. However, their interrelations remain to be unraveled.

SUMMARY

Long-term follow-up of microbiome development and alterations in relation to progression of lung disease and treatment is recommended. Moreover, integrating this information with other systems such as the metabolome, genome, mycome and virome is likely to contribute significantly to insights into host-microbiome interactions and thereby CF lung disease pathogenesis.

Making It Last: Storage Time and Temperature Have Differential Impacts on Metabolite Profiles of Airway Samples from Cystic Fibrosis Patients

Metabolomics has great potential for uncovering biomarkers of the disease state in CF and many other contexts. However, sample storage timing and temperature may alter the abundance of clinically relevant metabolites. To assess whether existing samples are stable and to direct future study design, we conducted untargeted GC-MS metabolomic analysis of CF sputum samples after one or two freeze-thaw cycles and storage at 4°C and −20°C for 4 to 8 weeks. Overall, storage at −20°C and freeze-thaw cycles had little impact on metabolite profiles; however, storage at 4°C shifted metabolite abundances significantly. GC-MS profiling will aid in our understanding of the CF lung, but care should be taken in studies using sputum samples to ensure that samples are properly stored.

Metabolites of human or microbial origin have the potential to be important biomarkers of the disease state in cystic fibrosis (CF). Clinical sample collection and storage conditions may impact metabolite abundances with clinical relevance. We measured the change in metabolite composition based on untargeted gas chromatography-mass spectrometry (GC-MS) when CF sputum samples were stored at 4°C, −20°C, or −80°C with one or two freeze-thaw cycles. Daily measurements were taken for 1 week and then weekly for 4 weeks (4°C) and 8 weeks (−20°C). The metabolites in samples stored at −20°C maintained abundances similar to those found at−80°C over the course of 8 weeks (average change in Bray-Curtis distance, 0.06 ± 0.04) and were also stable after one or two freeze-thaw cycles. However, the metabolite profiles of samples stored at 4°C shifted after 1 day and continued to change over the course of 4 weeks (average change in Bray-Curtis distance, 0.31 ± 0.12). The abundances of several amino acids and other metabolites increased with time of storage at 4°C but remained constant at −20°C. Storage temperature was a significant factor driving the metabolite composition (permutational multivariate analysis of variance: r² = 0.32 to 0.49, P < 0.001). CF sputum samples stored at −20°C at the time of sampling maintain a relatively stable untargeted GC-MS profile. Samples should be frozen on the day of collection, as more than 1 day at 4°C impacts the global composition of the metabolites in the sample.

IMPORTANCE Metabolomics has great potential for uncovering biomarkers of the disease state in CF and many other contexts. However, sample storage timing and temperature may alter the abundance of clinically relevant metabolites. To assess whether existing samples are stable and to direct future study design, we conducted untargeted GC-MS metabolomic analysis of CF sputum samples after one or two freeze-thaw cycles and storage at 4°C and −20°C for 4 to 8 weeks. Overall, storage at −20°C and freeze-thaw cycles had little impact on metabolite profiles; however, storage at 4°C shifted metabolite abundances significantly. GC-MS profiling will aid in our understanding of the CF lung, but care should be taken in studies using sputum samples to ensure that samples are properly stored.

Mapping targetable inflammation and outcomes with cystic fibrosis biomarkers

Cystic fibrosis is characterized by an overly exuberant neutrophilic inflammatory response to pathogens and other stimuli that starts very early in disease. The overwhelming nature of this response is a primary cause of remodeling and destruction of the airways, suggesting that anti-inflammatory therapies could be beneficial in CF. However, finding therapies that can effectively reduce the inflammatory response without compromising host defenses remains elusive. New approaches towards mapping inflammatory targets promise to aid in developing novel therapeutic strategies and improve outcomes in individuals with CF.

Antibiotic Treatment Preventing Necrotising Enterocolitis Alters Urinary and Plasma Metabolomes in Preterm Pigs

Necrotising enterocolitis (NEC) is a serious gut inflammatory condition in premature neonates, onset and development of which depend on the gut microbiome. Attenuation of the gut microbiome by antibiotics can reduce NEC incidence and severity. However, how the antibiotics-suppressed gut microbiome affects the whole-body metabolism in NEC-sensitive premature neonates is unknown. In formula-fed preterm pigs, used as a model for preterm infants, plasma and urinary metabolomes were investigated by LC-MS and ¹H NMR, with and without antibiotic treatment immediately after birth. While it reduced the gut microbiome density and NEC lesions as previously reported, the antibiotic treatment employed in the current study affected the abundance of 44 metabolites in different metabolic pathways. In antibiotics-treated pigs, tryptophan metabolism favored the kynurenine pathway, relative to the serotonin pathway, as shown by specific metabolites. Metabolites associated with the gut microbiome, including 3-phenyllactic acid, 4-hydroxyphenylacetic acid, and phenylacetylglycine, all from phenylalanine, and three bile acids showed lower levels in the antibiotics-treated pigs where the gut microbiome was extensively attenuated. Findings in the current study warrant further investigation of metabolic and developmental consequences of antibiotic treatment in preterm neonates.

Special considerations for the treatment of pulmonary exacerbations in children with cystic fibrosis

INTRODUCTION

Cystic fibrosis (CF) is a disease characterized by recurrent flares of respiratory symptoms, known as pulmonary exacerbations (PExs), which have a cumulative, detrimental effect on lung function decline and overall mortality. Although much research has been done on the effects of PExs in adults with CF, considerably less is known about these events in young children with CF. Areas covered: This review describes the typical presentation of PExs in children and their impact on long-term clinical outcomes. Traditional and new monitoring techniques, such as pulmonary function testing using multiple breath washout, radiographic modalities and microbiological screening methods are reviewed. Finally, the choice, administration and duration of antimicrobial treatment as well as the potential use of antiviral therapy is discussed. Expert commentary: Although it is now well recognized that a significant proportion of patients do not recover their lung function following PExs, to date, little progress has been made to improve outcomes in this group. Additional therapies, to complement antimicrobials, may be required to treat infection and inflammation during PExs. Trials of anti-inflammatories such as corticosteroids or other novel drugs need to be done in the setting of PExs with the goal of complete lung function recovery for all individuals with CF.

Pediatric Pulmonology year in review 2015: Part 4

In this article, we highlight cystic fibrosis (CF) research published in Pediatric Pulmonology during 2015. Articles from other journals that reflect similar themes, and those of special importance, are also included. Pediatr Pulmonol. 2016;51:754-765. © 2016 Wiley Periodicals, Inc.

Metabolic Profiling Regarding Pathogenesis of Idiopathic Pulmonary Fibrosis

Idiopathic pulmonary fibrosis (IPF) is a progressive, eventually fatal disease characterized by fibrosis of the lung parenchyma and loss of lung function. IPF is believed to be caused by repetitive alveolar epithelial cell injury and dysregulated repair process including uncontrolled proliferation of lung (myo) fibroblasts and excessive deposition of extracellular matrix proteins in the interstitial space; however, the pathogenic pathways involved in IPF have not been fully elucidated. In this study, we attempted to characterize metabolic changes of lung tissues involved in the pathogenesis of IPF using gas chromatography-mass spectrometry-based metabolic profiling. Partial least-squares discriminant analysis (PLS-DA) model generated from metabolite data was able to discriminate between the control subjects and IPF patients (R(2)X = 0.37, R(2)Y = 0.613 and Q(2) (cumulative) = 0.54, receiver operator characteristic AUC > 0.9). We discovered 25 metabolite signatures of IPF using both univariate and multivariate statistical analyses (FDR < 0.05 and VIP score of PLS-DA > 1). These metabolite signatures indicated alteration in metabolic pathways: adenosine triphosphate degradation pathway, glycolysis pathway, glutathione biosynthesis pathway, and ornithine aminotransferase pathway. The results could provide additional insight into understanding the disease and potential for developing biomarkers.

Lessons learned from metabolomics in cystic fibrosis

Cystic fibrosis is a mono-genetic multi-system disease; however, respiratory manifestations cause the main morbidity and mortality where chronic bacterial infections lead to bronchiectasis and ultimately respiratory failure. Metabolomics allows a relatively complete snapshot of metabolic processes in a sample using different mass spectrometry methods. Sample types used for discovery of biomarkers or pathomechanisms in cystic fibrosis (CF) have included blood, respiratory secretions, and exhaled breath to date. Metabolomics has shown distinction of CF vs. non-CF for matrices of blood, exhaled breath, and respiratory epithelial cultures, each showing different pathways. Severity of lung disease has been addressed by studies in bronchoalveolar lavage and exhaled breath condensate showing separation by metabolites that the authors of each study related to inflammation; e.g., ethanol, acetone, purines. Lipidomics has been applied to blood and sputum samples showing associations with lung function and Pseudomonas aeruginosa infection status. Finally, studies of bacteria grown in vitro showed differences of bacterial metabolites to be associated with clinical parameters. Metabolomics, in the sense of global metabolomic profiling, is a powerful technique that has allowed discovery of pathways that had not previously been implicated in CF. These may include purines, mitochondrial pathways, and different aspects of glucose metabolism besides the known differences in lipid metabolism in CF. However, targeted studies to validate such potential metabolites and pathways of interest are necessary. Studies evaluating metabolites of bacterial origin are in their early stages. Thus further well-designed studies could be envisioned.