The employment of liquid chromatography-mass spectrometry (LC-MS) untargeted and targeted metabolomics has led to the discovery of novel biomarkers and improved the understanding of various disease ...mechanisms. Numerous strategies have been reported to expand the metabolite coverage in LC-MS-untargeted and targeted metabolomics. To improve the sensitivity of low-abundance or poor-ionized metabolites for reducing the amount of clinical sample, chemical derivatization methods are used to target different functional groups. Proper sample preparation is beneficial for reducing the matrix effect, maintaining the stability of the LC-MS system, and increasing the metabolite coverage. Machine learning has recently been integrated into the workflow of LC-MS metabolomics to accelerate metabolite identification and data-processing automation, and increase the accuracy of disease classification and clinical outcome prediction. Due to the rapidly growing utility of LC-MS metabolomics in discovering disease markers, this review will address the recent advances in the field and offer perspectives on various strategies for expanding metabolite coverage, chemical derivatization, sample preparation, clinical disease markers, and machining learning for disease modeling.
Mammalian innate immune sensor STING (STimulator of INterferon Gene) was recently found to originate from bacteria. During phage infection, bacterial STING sense c-di-GMP generated by the CD-NTase ...(cGAS/DncV-like nucleotidyltransferase) encoded in the same operon and signal suicide commitment as a defense strategy that restricts phage propagation. However, the precise binding mode of c-di-GMP to bacterial STING and the specific recognition mechanism are still elusive. Here, we determine two complex crystal structures of bacterial STING/c-di-GMP, which provide a clear picture of how c-di-GMP is distinguished from other cyclic dinucleotides. The protein-protein interactions further reveal the driving force behind filament formation of bacterial STING. Finally, we group the bacterial STING into two classes based on the conserved motif in β-strand lid, which dictate their ligand specificity and oligomerization mechanism, and propose an evolution-based model that describes the transition from c-di-GMP-dependent signaling in bacteria to 2'3'-cGAMP-dependent signaling in eukaryotes.
Blood–brain barrier (BBB) disruption contributes to neurodegenerative diseases. Loss of tight junction (TJ) proteins in cerebral endothelial cells (ECs) is a leading cause of BBB breakdown. We ...recently reported that miR‐195 provides vasoprotection, which urges us to explore the role of miR‐195 in BBB integrity. Here, we found cerebral miR‐195 levels decreased with age, and BBB leakage was significantly increased in miR‐195 knockout mice. Furthermore, exosomes from miR‐195‐enriched astrocytes increased endothelial TJ proteins and improved BBB integrity. To decipher how miR‐195 promoted BBB integrity, we first demonstrated that TJ proteins were metabolized via autophagic–lysosomal pathway and the autophagic adaptor p62 was necessary to promote TJ protein degradation in cerebral ECs. Next, proteomic analysis of exosomes revealed miR‐195‐suppressed thrombospondin‐1 (TSP1) as a major contributor to BBB disruption. Moreover, TSP1 was demonstrated to activate selective autophagy of TJ proteins by increasing the formation of claudin‐5‐p62 and ZO1‐p62 complexes in cerebral ECs while TSP1 impaired general autophagy. Delivering TSP1 antibody into the circulation showed dose‐dependent reduction of BBB leakage by 20%–40% in 25‐month‐old mice. Intravenous or intracerebroventricular injection of miR‐195 rescued TSP1‐induced BBB leakage. Dementia patients with BBB damage had higher levels of serum TSP1 compared to those without BBB damage (p = 0.0015), while the normal subjects had the lowest TSP1 (p < 0.0001). Taken together, the study implies that TSP1‐regulated selective autophagy facilitates the degradation of TJ proteins and weakens BBB integrity. An adequate level of miR‐195 can suppress the autophagy–lysosome pathway via a reduction of TSP1, which may be important for maintaining BBB function.
The present study revealed that thrombospondin‐1 (TSP1) is a key factor for BBB leakage and miR‐195 protects BBB integrity. We showed that cerebral miR‐195 reduces with age and blood‐brain barrier (BBB) leakage is increased in miR‐195 knockout mice. miR‐195‐regulated thrombospondin‐1 impairs BBB via selective autophagy of tight junctions. Furthermore, circulating TSP1 was higher in BBB‐damaged patients, which implied TSP1 as a new biomarker of BBB damage.
The oxidized 1‐palmitoyl‐2‐arachidonoyl‐sn‐glycero‐3‐phosphocholine (ox‐PAPC) products in human high‐density lipoproteins (HDLs) were investigated by low‐flow capillary electrophoresis‐mass ...spectrometry (low‐flow CE‐MS). To accelerate the optimization, native PAPC (n‐PAPC) standard was first analyzed by a commercial CE instrument with a photodiode array detector. The optimal separation buffer contained 60% (v/v) acetonitrile, 40% (v/v) methanol, 20 mM ammonium acetate, 0.5% (v/v) formic acid, and 0.1% (v/v) water. The selected separation voltage and capillary temperature were 20 kV and 23°C. The optimal CE separation buffer was then used for the low‐flow CE‐MS analysis. The selected MS conditions contained heated capillary temperature (250°C), capillary voltage (10 V), and injection time (1 s). No sheath gas was used for MS. The linear range for n‐PAPC was 2.5–100.0 µg/mL. The coefficient of determination (R2) was 0.9918. The concentration limit of detection was 1.52 µg/mL, and the concentration limit of quantitation was 4.60 µg/mL. The optimal low‐flow CE‐MS method showed good repeatability and sensitivity. The ox‐PAPC products in human HDLs were determined based on the in vitro ox‐PAPC products of n‐PAPC standard. Twenty‐one ox‐PAPC products have been analyzed in human HDLs. Uremic patients showed significantly higher levels of 15 ox‐PAPC products than healthy subjects.
The complexity of the proteome often limits the number of identified proteins in the nanoflow LC-MS (nanoLC-MS) analysis of samples. Therefore, peptide fractionation is essential for reducing the ...sample complexity and improving the proteome coverage. In this study, to achieve high-pH reversed-phase (RP)-well plate fractionation for high-throughput proteomics analysis, C18 particles were coated on a 96-well plate, and the sample-loading processes were optimized for high-pH fractionation. The sample capacity of the high-pH RP-well plate was estimated to be ~6 μg of protein. There were 1.85- and 1.71-fold increases in the number of protein groups and peptides identified, respectively, with high-pH RP-well plate fractionation, compared to those without fractionation. In addition, with alkaline C18 well plate fractionation, exosome markers could be detected using ~1 μg of a protein digest of exosomes by microflow LC-MS (microLC-MS). These results illustrate that high-pH RP-well plate fractionation has superior sensitivity and effectiveness in preparing trace amounts of proteins for deep proteome analysis.
Graphical abstract
The adrenal gland responds to heat stress by epinephrine and glucocorticoid release to alleviate the adverse effects. This study investigated the effect of acute heat stress on the protein profile ...and histone modification in the adrenal gland of layer-type country chickens. A total of 192 roosters were subject to acute heat stress and thereafter classified into a resistant or susceptible group according to body temperature change. The iTRAQ analysis identified 80 differentially expressed proteins, in which the resistant group had a higher level of somatostatin and hydroxy-δ-5-steroid dehydrogenase but a lower parathymosin expression in accordance with the change of serum glucocorticoid levels. Histone modification analysis identified 115 histone markers. The susceptible group had a higher level of tri-methylation of histone H3 lysine 27 (H3K27me3) and showed a positive crosstalk with K36me and K37me in the H3 tails. The differential changes of body temperature projected in physiological regulation at the hypothalamus-pituitary-adrenal axis suggest the genetic heterogeneity in basic metabolic rate and efficiency for heat dissipation to acclimate to thermal stress and maintain body temperature homeostasis. The alteration of adrenal H3K27me3 level was associated with the endocrine function of adrenal gland and may contribute to the thermotolerance of chickens.
Rationale
Chronic pancreatitis (CP) is a pancreatic disease with poor prognosis and pancreatic cancer (PC) is one of the most lethal types of cancer that is symptomless in the early stage. Because ...the clinical and image findings of CP can overlap that of pancreatic cancer (PC) which leads to confusion in the diagnosis and treatment of PC, discovery/verification/validation of more accurate protein biomarkers to diagnose CP and PC is in urgent need.
Methods
The PubMed, Web of Science, and Google Scholar were searched using the keywords: ‘biomarker’, ‘marker’, ‘chronic pancreatitis’, “pancreatic cancer” or “proteomics” for highly related researches. We focused on the articles published after the year 2005 in this review.
Results
We introduce the background to CP and PC and summarize the diagnosis of CP and PC, analytically validated protein biomarkers, and proteomic approaches for discovery/verification/validation. The potential use of mass spectrometry (MS) in clinical diagnosis is also discussed.
Conclusions
Continuously improving sensitivity of MS can provide deeper proteome for new marker discovery and high reliability for protein marker verification, validation, and clinical diagnosis. The analytically validated protein markers could be considered as targeted protein biomarkers for developing a MS platform in the clinical validation process or clinical diagnosis of CP and PC.
We examine whether initiations of bank loans with financial covenants motivate banks to monitor borrowers’ accounting practice and result in a higher quality of reported accruals and a better ...information environment for firms. We document that, relative to loans without financial covenants, loans with financial covenants lead to an improvement in accrual quality measured by the extent to which accruals can be mapped into cash flows. The effect of loan covenants on accrual quality is stronger when external monitoring by non‐bank stakeholders (i.e., institutional investors and financial analysts) is weaker. Furthermore, initiations of bank loans with financial covenants are related to subsequent improvements in analysts’ information environment. The evidence supports the view that bank monitoring improves accounting quality.
This study examines whether the availability of traded credit default swaps (CDS) influences the referenced firms' incentive to smooth their performance. We show that with the introduction of CDS ...trading on their debt, CDS-referenced firms (CDS firms) lower both their earnings and cash flow volatility. Specifically, earnings volatility declines faster than cash flow volatility, which is consistent with income smoothing behavior. The effect of CDS trading on performance smoothing is qualitatively similar under different market and economic conditions. These results support the notion that CDS firms smooth their performance to avoid renegotiation with CDS-protected creditors. We also find that CDS firms smooth their cash flows via hedging with derivatives and smooth their earnings using discretionary accruals after the inception of CDS trading.
Parkinson's disease (PD) is a common neurodegenerative disease. The pathological hallmark of PD is a progressive loss of dopaminergic neurons in the substantia nigra (SN) pars compacta in the brain, ...ultimately resulting in severe striatal dopamine deficiency and the development of primary motor symptoms (e.g., resting tremor, bradykinesia) in PD. Acupuncture has long been used in traditional Chinese medicine to treat PD for the control of tremor and pain. Accumulating evidence has shown that using electroacupuncture (EA) as a complementary therapy ameliorates motor symptoms of PD. However, the most appropriate timing for EA intervention and its effect on dopamine neuronal protection remain unclear. Thus, this study used the 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-lesioned mouse model (systemic-lesioned by intraperitoneal injection) and the 1-methyl-4-phenylpyridinium (MPP⁺)-lesioned rat model (unilateral-lesioned by intra-SN infusion) of PD, to explore the therapeutic effects and mechanisms of EA at the GB34 (Yanglingquan) and LR3 (Taichong) acupoints. We found that EA increased the latency to fall from the accelerating rotarod and improved striatal dopamine levels in the MPTP studies. In the MPP⁺ studies, EA inhibited apomorphine induced rotational behavior and locomotor activity, and demonstrated neuroprotective effects via the activation of survival pathways of Akt and brain-derived neurotrophic factor (BDNF) in the SN region. In conclusion, we observed that EA treatment reduces motor symptoms of PD and dopaminergic neurodegeneration in rodent models, whether EA is given as a pretreatment or after the initiation of disease symptoms. The results indicate that EA treatment may be an effective therapy for patients with PD.
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