Search bioRxiv⌕ Search

bioRxiv · 10.1101/2021.01.18.424378

Human Tear Metabolomics Using Liquid Chromatography-Q Exactive-HF Mass Spectrometry

Abstract

AimTo putatively identify and characterise human tear metabolites in a normal subject on an untargeted platform of liquid chromatography-Q exactive-HF mass spectrometry. MethodsFour samples of unstimulated tears were collected from both eyes on four consecutive days between 1 - 2 pm using a microcapillary tube and pooled from both eyes each day. Untargeted analysis of the tears was performed by chromatographic separation of constituent metabolites in both CSH-C18RP (Charged Surface Hybrid-C18 Reversed Phase) and SeQuant ZIC-pHILIC (Zwitterionic-polymeric Hydrophilic Interaction Liquid Chromatography) columns, followed by heated electrospray ionization (HESI) and the acquisition of mass spectra using QExactive-HF mass spectrometer. Compound Discoverer software (v2.0) was used for data analysis. ResultEighty-two metabolites were tentatively identified. Seventy compounds (85.4 %) were observed in all four samples with a coefficient of variation (CV) less than 25 %. Fifty-nine metabolites (71.9 %) were novel in the healthy tears. Amino acids were the most frequently detected metabolites in the tears (28 %), followed by carbohydrates (12.2 %), carboxylic acids (8.5 %), carnitines (6.1 %) and glycerophospholipids (4.9 %), respectively. ConclusionThe current untargeted platform is capable of detecting a range of tear metabolites across several biological categories. This study provides a baseline for further ocular surface studies.

Explore related subjects

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Shrestha, G. S., Vijay, A. K., Stapleton, F., Pickford, R., Carnt, N.. 2021-01-18. Human Tear Metabolomics Using Liquid Chromatography-Q Exactive-HF Mass Spectrometry. https://doi.org/10.1101/2021.01.18.424378

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

Genomic features and instability of linezolid resistance in vancomycin-resistant Enterococcus faecalis ST525

This study investigated the mechanisms of oxazolidinone resistance and genomic background in clinical ST525 Enterococcus faecalis isolates, a poorly characterized lineage reported in Brazilian hospitals as either vancomycin-resistant (VRE) or linezolid- and vancomycin-resistant (LVRE). Five LVREfs from intensive care unit patients (linezolid MICs, 8-32 mg/L; vancomycin MICs, >256 mg/L) carried only G2576T and G2505A (in three of four rrl copies) as known linezolid resistance determinants, despite variable linezolid MICs. During serial in vitro passages without antibiotic pressure, isolates with initial MICs of 8-16 mg/L exhibited progressive MIC reductions accompanied by reversion of mutant to wild-type rrl copies, whereas the isolate with an initial MIC of 32 mg/L maintained high-level resistance without reversion. Additional domain V substitutions emerged during MIC decline, while growth kinetics remained broadly similar. Whole-genome sequencing of a representative isolate (LVREfs L7) revealed a ~2.8-Mb chromosome enriched in mobile genetic elements (~8.6%), lacking a functional CRISPR-Cas system. A plasmid-borne prototype Tn1546 carrying vanA, devoid of internal insertion sequences, was found inserted into a Tn3-family transposase gene, a platform not typically associated with vanA mobilization. Together, these findings indicate that ST525 LVREfs, whose genomic features are consistent with long-term persistence in hospitals, may pose a challenge to routine susceptibility testing. A single mutational mechanism can yield variable linezolid MICs, and the ratio of mutated vs wild-type rrl copies can become heterogeneous in the absence of antibiotic pressure, without correlating directly with these values, contrary to the well-documented copy number-MIC correlation.

molecular biology↗

Global repression of mesenchymal genes in epithelial cells by the histone demethylase LSD1

Epithelial-mesenchymal transition (EMT) is an essential process in development, tissue repair, and tumour metastasis, and is triggered by SNAI, ZEB and TWIST transcription factors, that recruit lysine-specific demethylase 1 (LSD1) to repress epithelial genes such as E-cadherin. In mesenchymal cells, LSD1 inhibition restores E-cadherin expression and reduces migration and invasion, consistent with LSD1 inhibition reverting EMT, and offering a therapeutic modality for EMT-associated disease. Recent data, however, suggest context-dependent roles for LSD1, as its inhibition in epithelial cells increases mesenchymal marker expression, potentially promoting EMT. To investigate this discrepancy, we mapped genome-wide binding of LSD1 in HCT116 epithelial cells and used rapid degron-mediated ablation of endogenous LSD1 to measure changes in nascent and steady-state transcription and chromatin accessibility. In epithelial cells, LSD1 binds constitutively-accessible, primed mesenchymal promoters. These are rapidly derepressed after LSD1 ablation, with activation of SNAI2 and ZEB1, which repress epithelial hallmarks such as E-cadherin. Re-introduction of LSD1 downregulates SNAI2 and ZEB1 but, surprisingly, further represses E-cadherin, indicating sustained loss of epithelial characteristics. Collectively, our results show that LSD1 maintains epithelial identity by repressing mesenchymal genes, questioning the therapeutic utility of LSD1 inhibition for EMT control.

molecular biology↗

The long noncoding RNA FOSIL shapes the dynamics of FOS induction

Immediate-early genes require rapid, transient, and precisely tuned transcriptional activation in response to extracellular signals, yet how this kinetic precision is achieved remains poorly understood. We characterize FOSIL (LINC01220), an inducible lncRNA locus downstream of FOS. Depleting FOSIL RNA delays heregulin (HRG)-induced FOS mRNA and protein accumulation and prolongs the response, indicating that FOSIL sharpens both the onset and the shutoff of the induction wave. Capture Micro-C maps show that FOSIL depletion weakens the chromatin boundary between FOS and FOSIL and increases local compaction across the pre-assembled FOS-FOSIL neighborhood during serum starvation, demonstrating that basal FOSIL production maintains a locally insulated, poised conformation prior to signal arrival. Upon HRG stimulation, FOSIL depletion blunts the rapid movement of the locus toward nuclear speckles, diminishes early speckle-proximal FOS transcription, and extends late firing at speckle-distant alleles. At single transcription active sites, nascent FOSIL activity correlates with closer speckle proximity and higher FOS output, and activating the endogenous FOSIL promoter by CRISPRa, but not supplying FOSIL RNA in trans, enhances both speckle association and FOS induction. Together, these findings support a mechanism where endogenous FOSIL activity coordinates pre-stimulus chromatin folding with dynamic nuclear speckle positioning to fine-tune the onset, amplitude, and resolution of immediate-early gene expression.

molecular biology↗