Distinctive metabolic profiles between Cystic Fibrosis mutational subclasses and lung function

Burkholderia cepacia complex in cystic fibrosis: critical gaps in diagnosis and therapy

Burkholderia cepacia complex (Bcc) is a bacterial group with 'natural' multi-antimicrobial resistance. This complex has generated epidemic outbreaks across the world. In people with cystic fibrosis (CF), Bcc can cause severe lung infections that lead to accelerated lung damage, which can be complicated by necrotizing pneumonia accompanied by high fevers, leucocytosis, and bacteraemia, which commonly causes fatal outcomes. Specifically, infection by Burkholderia cenocepacia is considered an exclusion criterion for lung transplantation. The species of Bcc exhibit both genetic and phenotypic hypervariability that complicate their accurate microbiological identification. Automated methods such as MALDI-TOF can err in the determination of species. Their slow growth even in selective agars and the absence of international consensuses on the optimal conditions for their isolation make early diagnosis a difficult challenge to overcome. The absence of correlations between antibiograms and clinical results has resulted in the absence of standardized cut-off values of antimicrobial susceptibility, a fact that brings a latent risk since incorrect antibiotic therapy can induce the selection of more aggressive variants that worsen the clinical picture of the host, added to the absence of a clear therapeutic guide for the eradication of pulmonary infections by Bcc in patients with CF, resulting in frequently ineffective treatments. There is an urgent need to standardize methods and diagnostic tools that would allow an early and accurate diagnosis, as well as to perform clinical studies of the effectiveness of available antibiotics to eradicate Bcc infections, which would allow us to establish standardized therapeutic schemes for Bcc-infected patients.

Ophthalmic acid is a glutathione regulating tripeptide

Since its discovery in 1958 in the lens of cows, ophthalmic acid (OPH) has stood in the shadow of its anti-oxidant analog: glutathione (GSH). Lacking the thiol group that gives GSH many of its important properties, ophthalmic acid's function has remained elusive, and it has been widely presumed to be an accidental product of the same enzymes. In this review, we compile evidence demonstrating that OPH is a ubiquitous metabolite found in bacteria, plants, fungi, and animals, produced through several layers of metabolic regulation. We discuss the limitations of the oft-repeated suggestions that aberrations in OPH levels should solely indicate GSH deficiency or oxidative stress. Finally, we discuss the available literature and suggest OPH's role in metabolism as a GSH-regulating tripeptide; controlling both cellular and organelle influx and efflux of GSH, as well as modulating GSH-dependent reactions and signaling. Ultimately, we hope that this review reinvigorates and directs more research into this versatile metabolite.

Diagnosis and Therapeutic Strategies Based on Nucleic Acid Aptamers Selected against Pseudomonas aeruginosa: The Challenge of Cystic Fibrosis

Antimicrobial resistance (AMR) is a rapidly spreading global health problem, and approximately five million deaths associated with AMR pathogens were identified prior to the COVID-19 pandemic. Pseudomonas aeruginosa has developed increasing AMR, and in patients with cystic fibrosis (CF) colonized by this bacterium, rare phenotypes have emerged that complicate the diagnosis and treatment of the hosts, in addition to multiple associated "epidemic strains" with high morbidities and mortalities. The conjugation of aptamers with fluorochromes or nanostructures has allowed the design of new identification strategies for Pseudomonas aeruginosa with detection limits of up to 1 cell ⋅ mL-1 , and the synergy of aptamers with antibiotics, antimicrobial peptides and nanostructures has exhibited promising therapeutic qualities. Some selected aptamers against this bacterium have shown intrinsic antimicrobial activity. However, these aptamers have been poorly evaluated in clinical isolates and have shown decreased interactions for CF isolates, demonstrating, in these cases, uncommon phenotypes resulting from the selective qualities of this disease as well as the great adaptive capacity of the pathogen. Therefore, finding an aptamer or set of aptamers that have the ability to recognize strange phenotypes of this bacillus is crucial in the battle against AMR.

Bridging of host-microbiota tryptophan partitioning by the serotonin pathway in fungal pneumonia

The aromatic amino acid L-tryptophan (Trp) is essentially metabolized along the host and microbial pathways. While much is known about the role played by downstream metabolites of each pathways in intestinal homeostasis, their role in lung immune homeostasis is underappreciated. Here we have examined the role played by the Trp hydroxylase/5-hydroxytryptamine (5-HT) pathway in calibrating host and microbial Trp metabolism during Aspergillus fumigatus pneumonia. We found that 5-HT produced by mast cells essentially contributed to pathogen clearance and immune homeostasis in infection by promoting the host protective indoleamine-2,3-dioxygenase 1/kynurenine pathway and limiting the microbial activation of the indole/aryl hydrocarbon receptor pathway. This occurred via regulation of lung and intestinal microbiota and signaling pathways. 5-HT was deficient in the sputa of patients with Cystic fibrosis, while 5-HT supplementation restored the dysregulated Trp partitioning in murine disease. These findings suggest that 5-HT, by bridging host-microbiota Trp partitioning, may have clinical effects beyond its mood regulatory function in respiratory pathologies with an inflammatory component.

Recent advances in proteomic-based diagnostics of cystic fibrosis

INTRODUCTION

Cystic fibrosis (CF) is a genetic disease characterized by thick and sticky mucus accumulation, which may harm numerous internal organs. Various variables such as gene modifiers, environmental factors, age of diagnosis, and CF transmembrane conductance regulator (CFTR) gene mutations influence phenotypic disease diversity. Biomarkers that are based on genomic information may not accurately represent the underlying mechanism of the disease as well as its lethal complications. Therefore, recent advancements in mass spectrometry (MS)-based proteomics may provide deep insights into CF mechanisms and cellular functions by examining alterations in the protein expression patterns from various samples of individuals with CF.

AREAS COVERED

We present current developments in MS-based proteomics, its application, and findings in CF. In addition, the future roles of proteomics in finding diagnostic and prognostic novel biomarkers.

EXPERT OPINION

Despite significant advances in MS-based proteomics, extensive research in a large cohort for identifying and validating diagnostic, prognostic, predictive, and therapeutic biomarkers for CF disease is highly needed.

Metabolomics profiling distinctively identified end-stage renal disease patients from chronic kidney disease patients

Chronic kidney disease (CKD) is a serious public health problem characterized by progressive kidney function loss leading to end-stage renal disease (ESRD) that demands dialysis or kidney transplantation. Early detection can prevent or delay progression to ESRD. The study aimed to gain new insights into the perturbed biochemical reactions and to identify novel distinct biomarkers between ESRD and CKD. Serum samples of 32 patients with ESRD (n = 13) and CKD (n = 19) were analyzed using chemical isotope labeling liquid chromatography-mass spectrometry metabolomics approach. A total of 193 metabolites were significantly altered in ESRD compared to CKD and were mainly involved in aminoacyl-tRNA biosynthesis, branched-chain amino acid (BCAA) biosynthesis, taurine metabolism, and tryptophan metabolism. Three kynurenine derivatives, namely, 2-aminobenzoic acid, xanthurenic acid, and hydroxypicolinic acid were upregulated in ESRD compared to CKD due to the significant decrease in glomerular filtration rate with the progression of CKD to ESRD. N-Hydroxy-isoleucine, 2-aminobenzoic acid, and picolinic acid yielded AUC > 0.99 when analyzed using Receiver Operating Characteristic (ROC) analysis. Our findings suggest that inhibiting the kynurenine pathway might be a promising target to delay CKD progression and that metabolites with high discriminative ability might serve as potential prognostic biomarkers to monitor the progression of CKD to ESRD or used in combination with current markers to indicate the status of kidney damage better.

Biomarker discovery in galactosemia: Metabolomics with UPLC/HRMS in dried blood spots

Introduction:Galactosemia (GAL) is a genetic disorder that results in disturbances in galactose metabolism and can lead to life-threatening complications. However, the underlying pathophysiology of long-term complications in GAL remains poorly understood. Methods: In this study, a metabolomics approach using ultra-performance liquid chromatography coupled with high-resolution mass spectrometry was used to investigate metabolomic changes in dried blood spots of 15 patients with GAL and 39 healthy individuals. Results: The study found that 2,819 metabolites underwent significant changes in patients with GAL compared to the control group. 480 human endogenous metabolites were identified, of which 209 and 271 were upregulated and downregulated, respectively. PA (8:0/LTE4) and ganglioside GT1c (d18:0/20:0) metabolites showed the most significant difference between GAL and the healthy group, with an area under the curve of 1 and 0.995, respectively. Additionally, the study identified potential biomarkers for GAL, such as 17-alpha-estradiol-3-glucuronide and 16-alpha-hydroxy DHEA 3-sulfatediphosphate. Conclusion: This metabolomics study deepened the understanding of the pathophysiology of GAL and presented potential biomarkers that might serve as prognostic biomarkers to monitor the progression or support the clinical diagnosis of GAL.

Network Analysis to Identify Multi-Omic Correlations in the Lower Airways of Children With Cystic Fibrosis

The leading cause of morbidity and mortality in cystic fibrosis (CF) is progressive lung disease secondary to chronic airway infection and inflammation; however, what drives CF airway infection and inflammation is not well understood. By providing a physiological snapshot of the airway, metabolomics can provide insight into these processes. Linking metabolomic data with microbiome data and phenotypic measures can reveal complex relationships between metabolites, lower airway bacterial communities, and disease outcomes. In this study, we characterize the airway metabolome in bronchoalveolar lavage fluid (BALF) samples from persons with CF (PWCF) and disease control (DC) subjects and use multi-omic network analysis to identify correlations with the airway microbiome. The Biocrates targeted liquid chromatography mass spectrometry (LC-MS) platform was used to measure 409 metabolomic features in BALF obtained during clinically indicated bronchoscopy. Total bacterial load (TBL) was measured using quantitative polymerase chain reaction (qPCR). The Qiagen EZ1 Advanced automated extraction platform was used to extract DNA, and bacterial profiling was performed using 16S sequencing. Differences in metabolomic features across disease groups were assessed univariately using Wilcoxon rank sum tests, and Random forest (RF) was used to identify features that discriminated across the groups. Features were compared to TBL and markers of inflammation, including white blood cell count (WBC) and percent neutrophils. Sparse supervised canonical correlation network analysis (SsCCNet) was used to assess multi-omic correlations. The CF metabolome was characterized by increased amino acids and decreased acylcarnitines. Amino acids and acylcarnitines were also among the features most strongly correlated with inflammation and bacterial burden. RF identified strong metabolomic predictors of CF status, including L-methionine-S-oxide. SsCCNet identified correlations between the metabolome and the microbiome, including correlations between a traditional CF pathogen, Staphylococcus, a group of nontraditional taxa, including Prevotella, and a subnetwork of specific metabolomic markers. In conclusion, our work identified metabolomic characteristics unique to the CF airway and uncovered multi-omic correlations that merit additional study.

Transcriptome analysis of tumor-derived mesenchymal progenitor cells shows that CHST15 is a fibrosis regulator of retroperitoneal liposarcoma

Background

Retroperitoneal liposarcoma (RPLS) is a rare, biologically heterogeneous tumor with distinct clinical characteristics, such as frequent local recurrence, repeated relapse, and rare distant metastasis. No effective targeted therapy is available for RPLS. Here, we aim to determine the pathological functions and therapeutic potential of carbohydrate sulfotransferase 15 (CHST15) in RPLS.

Methods

Tumor-derived mesenchymal progenitor cells (MPCs) and normal adipose derived mesenchymal stem cells (MSCs) were obtained from patients with RPLS. MPCs and MSCs were isolated and characterized based on surface markers, proliferation, and differentiation using flow cytometry and molecular staining. Transcriptome analysis was performed to decipher expression profile of differentiation-related genes in 3 paired MSCs and MPCs. Further confirmation of genes were performed using quantitative real-time polymerase chain reaction (qRT-PCR). Plasmids overexpressing CHST15 were transfected into adipose MSCs to examine fibrosis-related gene expression at mRNA level by real-time PCR.

Results

The tumor stromal-derived MPCs expressed CD105, CD73, and CD90, and exhibited osteogenic and adipogenic differentiation potential in vitro. The proliferation of tumor-derived MPCs was significantly lower than that of normal adipose-derived MSCs (P<0.001). Transcriptome analysis revealed upregulation of IL-7R, ALPL, PKNOX2, and CHST15 in tumor-derived MPCs. CHST15 was highly expressed in tumor-derived MPCs (P<0.001). CHST15 mediated fibrosis-related FGF2 gene expression in MSCs (P<0.05) and MPCs (P<0.001).

Conclusions

CHST15 is upregulated in tumor-derived MPCs and regulates fibrosis in RPLS. This provides clues for development of novel therapeutic strategies by targeting CHST15-induced MPC activation in RPLS.