Epitranscriptomic Mass Spectrometry.

Every chemical group that is added to any one of the canonical ribonucleotides in a transcript would create a specific RNA modification. Currently, 170+ RNA modifications have been identified. A specific epitranscriptome refers to all the RNA modifications in a given biological system and is considered to play an important role in the regulations of cellular activities. Mass spectrometry-based methods have proven to be the most accurate way to identify RNA modifications and determine the amount of each detectable modification. Relating to the recent development of mapping specific RNA modifications within a transcriptome, the profiling of all RNA modifications can serve as a prescreening tool for mapping and provides support for analyzing the data obtained from mapping. In this chapter, the details for setting up a commonly used mass spectrometry-based method to profile all the RNA modifications in specific epitranscriptomes are described, and the possible options if available are discussed.

Theory of Mind and Empathy in Adults With Epilepsy: A Meta-Analysis.

Mounting evidence suggests that social cognitive abilities [including theory of mind (ToM) and empathy] are impaired in adult patients with epilepsy. Although the deficits in overall ToM in epilepsy have been documented well, the effects of epilepsy on empathic ability and specific subcomponents of ToM remain unclear. The primary aim of this study was to provide the first meta-analytic integration of ToM and empathy in adult patients with epilepsy, and to decompose these constructs to clearly differentiate their distinct (cognitive ToM and affective empathy) and overlapping (affective ToM/cognitive empathy) components. This meta-analysis included 28 studies. Adult patients with temporal lobe epilepsy (TLE) and frontal lobe epilepsy (FLE) showed impairments in cognitive ToM and affective ToM/cognitive empathy compared to the healthy controls (HCs); no group differences were identified for affective empathy. Besides, cognitive ToM was impaired in adult patients with idiopathic generalized epilepsy (IGE) and focal seizures (caused by epileptogenic foci) outside the temporal and frontal lobes (extra-TLE/FLE) and no group differences were evident for affective ToM/cognitive empathy compared to the HCs. Moreover, relative to the HCs, no group differences were identified for affective empathy in adult patients with IGE. Additionally, no (statistically) significant difference was observed between the magnitude of ToM/empathy impairment in adult patients who underwent and those who did not undergo epilepsy surgery. These quantitative findings suggest differential impairment of the core aspects of social cognitive processing in adult patients with epilepsy, which may contribute to the development of structured cognitive interventions (i.e., social cognitive training) for adult patients with epilepsy.

Epitranscriptomic profile of Lactobacillus agilis and its adaptation to growth on inulin.

OBJECTIVE: Ribonucleic acids (RNA) are involved in many cellular functions. In general, RNA is made up by only four different ribonucleotides. The modifications of RNA (epitranscriptome) can greatly enhance the structural diversity of RNA, which in turn support some of the RNA functions. To determine whether the epitranscriptome of a specific probiotic is associated with its adaptation to the source of energy, Lactobacillus agilis (YZ050) was selected as a model and its epitranscriptome was profiled and compared by using mass spectrometry. RESULTS: The L. agilis epitranscriptome (minus rRNA modifications) consists of 17 different RNA modifications. By capturing the L. agilis cells during exponential growth, reproducible profiling was achieved. In a comparative study, the standard source of energy (glucose) in the medium was substituted by a prebiotic inulin, and a downward trend in the L. agilis epitranscriptome was detected. This marks the first report on a system-wide variation of a bacterial epitranscriptome that resulted from adapting to an alternative energy source. No correlation was found between the down-regulated RNA modifications and the expression level of corresponding writer genes. Whereas, the expression level of a specific exonuclease gene, RNase J1, was detected to be higher in cells grown on inulin.

A theoretical perspective of the physical properties of different RNA modifications with respect to RNA duplexes.

Epitranscriptomic variations include >140 different RNA modifications, many of which can serve as disease biomarkers. Owing to the challenges on synthesizing modified RNA oligos, majority of earlier studies on the effects of RNA modifications to RNA duplexes focused on selected individual epitranscriptomic variation. There are also limited development on the computational modeling of RNA duplexes containing a specific epitranscriptomic variation. This study aims to theoretically estimate the physical properties of different modified ribonucleosides and compare their variations with respect to altering the molecular structure of an RNA duplex.

Blood neurofilament light chain in Parkinson disease and atypical parkinsonisms: A protocol for systematic review and meta-analysis.

BACKGROUND: Neurofilament light chain (NfL), an index of neuroaxonal injury, is a promising diagnostic and prognostic fluid biomarker with high translational value in many neurodegenerative disorders. Blood NfL measurement has been an exciting and active field of research in idiopathic Parkinson disease (PD) and atypical parkinsonisms. However, blood NfL levels in these parkinsonisms from existing literature were inconsistent. No comprehensive meta-analysis has ever been conducted. METHODS: Three major biomedical electronic databases PubMed, Embase, and Web of Science were comprehensively searched from inception to July 10, 2020. This protocol will be prepared based on the guidelines recommended by the statement of Preferred Reporting Items for Systematic Review and Meta-Analysis Protocols (PRISMA-P). Original observational studies that measured blood (serum/plasma) NfL concentrations in patients with parkinsonisms (multiple system atrophy [MSA], progressive supranuclear palsy [PSP], corticobasal syndrome [CBS], and dementia with Lewy bodies [DLB]), and healthy controls (HCs) will be included. Quality assessment of the included studies will be performed using the Newcastle Ottawa Scale (NOS). Meta-analyses will be conducted using the STATA software version 13.0. The standardized mean differences as the measure of effect size and 95% confidence intervals were calculated for each comparison of blood NfL levels. Heterogeneity analysis, sensitivity analysis, publication bias, subgroup analysis, and meta-regression analysis will be carried out to test the robustness of the results. RESULTS: The meta-analysis will obtain the effect sizes of blood NfL levels in the following comparisons: PD versus HC, MSA versus HC, PSP versus HC, CBS versus HC, DLB versus HC, MSA versus PD, PSP versus PD, CBS versus PD, and DLB versus PD. CONCLUSIONS: The present meta-analysis will provide the quantitative evidence of NfL levels in idiopathic PD and atypical parkinsonisms, hoping to facilitate differential diagnoses in clinical practice. REGISTRATION NUMBER: INPLASY202070091.

Cerebrospinal fluid and blood levels of neurofilament light chain in Parkinson disease: A protocol for systematic review and meta-analysis.

BACKGROUND: Parkinson disease (PD) is a common neurodegenerative disorder. Elevations of neurofilament light chain (NfL) concentrations in the cerebrospinal fluid (CSF) and blood are a marker of neuronal/axonal injury and degeneration. However, CSF and blood NfL alterations in patients with PD from existing studies remain inconclusive. To better understand these conflicting data, we will conduct a meta-analysis. METHODS: We will comprehensively search PubMed, Embase, and Web of Science databases from each database's inception to 7th June, 2020. This protocol will conform to the Preferred Reporting Items for Systematic review and Meta-Analysis Protocols. We will only include original studies published in English that evaluated differences of NfL concentrations in the CSF or blood between idiopathic PD patients and healthy controls. The Newcastle-Ottawa Scale will be used to evaluate the quality of the included studies. Meta-analyses will be carried out using the STATA software version 13.0. Between-group difference of NfL concentrations in the CSF and blood will be expressed as the weighted standardized mean difference. A random-effects model will be used. Supplementary analyses, such as heterogeneity analysis, sensitivity analysis, publication bias, subgroup analysis, and meta-regression analysis will be performed. RESULTS: The meta-analysis will provide the differences of NfL concentrations in the CSF and blood between patients with PD and healthy controls and will show the magnitudes of their effect sizes. CONCLUSIONS: This meta-analysis will provide the evidence of NfL concentrations in the CSF and blood in PD and we hope that our study has an important impact on clinical practice. REGISTRATION NUMBER: INPLASY202060025.

Inflammatory cytokine levels in multiple system atrophy: A protocol for systematic review and meta-analysis.

BACKGROUND: Multiple system atrophy (MSA) is a fatal neurodegenerative disease that progresses very rapidly and has a poor prognosis. Some studies indicate that the level of inflammatory cytokines may be related to MSA. However, no consistent conclusion has been drawn yet. The purpose of our research is to perform a meta-analysis to investigate whether the level of inflammatory cytokines is altered in MSA. METHODS: Case-control studies on inflammatory cytokine levels in MSA will be searched in the following 3 databases: PubMed, Embase, and Web of Science from the database start time to March 17, 2020. Two independent authors will conduct research selection, data extraction, and quality evaluation. Data synthesis, subgroup analysis, sensitivity analysis, and the meta-analysis will be performed using Stata15.0 software. RESULTS: This study will provide a comprehensive review of all studies on inflammatory cytokine levels in MSA. CONCLUSION: To the best of our knowledge, this study will be the first meta-analysis that provides the quantitative evidence of inflammatory cytokine levels in MSA. REGISTRATION NUMBER: INPLASY202060034.

Carbon Monoxide Inhibits the Expression of Proteins Associated with Intestinal Mucosal Pyroptosis in a Rat Model of Sepsis Induced by Cecal Ligation and Puncture.

BACKGROUND Carbon monoxide (CO) has anti-inflammatory effects and protects the intestinal mucosal barrier in sepsis. Pyroptosis, or cell death associated with sepsis, is mediated by caspase-1 activation. This study aimed to investigate the role of CO on the expression of proteins associated with intestinal mucosal pyroptosis in a rat model of sepsis induced by cecal ligation and puncture (CLP). MATERIAL AND METHODS The rat model of sepsis was developed using CLP. Male Sprague-Dawley rats (n=120) were divided into six study groups: the sham group (n=20); the CLP group (n=20); the hemin group (treated with ferric chloride and heme) (n=20); the zinc protoporphyrin IX (ZnPPIX) group (n=20); the CO-releasing molecule 2 (CORM-2) group (n=20); and the inactive CORM-2 (iCORM-2) group (n=20). Hemin and CORM-2 were CO donors, and ZnPPIX was a CO inhibitor. In the six groups, the seven-day survival curves, the fluorescein isothiocyanate (FITC)-labeled dextran 4000 Da (FD-4) permeability assay, levels of intestinal pyroptosis proteins caspase-1, caspase-11, and gasdermin D (GSDMD) were measured by confocal fluorescence microscopy. Proinflammatory cytokines interleukin (IL)-18, IL-1ß, and high mobility group box protein 1 (HMGB1) were measured by Western blot and enzyme-linked immunosorbent assay (ELISA). RESULTS CO reduced the mortality rate in rats with sepsis and reduced intestinal mucosal permeability and mucosal damage. CO also reduced the expression levels of IL-18, IL-1ß, and HMGB1, and reduced pyroptosis by preventing the cleavage of caspase-1 and caspase-11. CONCLUSIONS In a rat model of sepsis induced by CLP, CO had a protective role by inhibiting intestinal mucosal pyroptosis.

Long non-coding RNA GAS5 regulates human B lymphocytic leukaemia tumourigenesis and metastasis by sponging miR-222.

Accumulating evidence has shown that lncRNA GAS5 is a novel tumour-promoting RNA that contributes to tumour progression by sponging miRNAs. However, the detailed role of lncRNA GAS5 in B lymphocytic leukaemia is still unclear. A qRT-PCR assay was used to examine the levels of lncRNA GAS5 and miR-222 in leukomonocytes of patients with B lymphocytic leukaemia and in healthy donors. Raji cells were transfected with GAS5 overexpression or shRNA-GAS5 plasmids for 48⁢h, and cell proliferation was assessed by the CCK-8 assay, while apoptosis and cell cycle progression were assessed using flow cytometry. The Transwell assay was applied to detect the invasion of Raji cells with GAS5 overexpression or knockdown. The dual luciferase reporter assay and regression curve were conducted to evaluate the binding interaction between lncRNA GAS5 and miR-222. The results showed that the expression of lncRNA GAS5 was decreased in B lymphocytic leukaemia patients compared with the healthy group, and the levels of lncRNA GAS5 in B lymphocytic leukaemia cell lines were significantly higher than those in the normal B cell line, whereas the levels of miR-222 were increased in B lymphocytic leukaemia patients compared with the healthy group. Moreover, cell culture experiments indicated that lncRNA GAS5 overexpression decreased B lymphocytic leukaemia cell proliferation, promoted B lymphocytic leukaemia cell apoptosis, arrested B lymphocytic leukaemia cells in the G1 phase of the cell cycle, and inhibited B lymphocytic leukaemia cell invasion. Finally, the luciferase reporter assay showed a direct target interaction between lncRNA GAS5 and miR-222. The regression analysis showed a negative correlation between the levels of lncRNA GAS5 and miR-222. Thus, our data suggested that lncRNA GAS5 could effectively sponge miR-222 to modulate human B lymphocytic leukaemia cell tumourigenesis and metastasis. This work advances our understanding of the clinical significance of lncRNA GAS5 from the perspective of lncRNA-miRNA regulation.

Identification of key genes and pathways using bioinformatics analysis in septic shock children.

BACKGROUND AND HYPOTHESIS: Sepsis is still one of the reasons for serious infectious diseases in pediatric intensive care unit patients despite the use of anti-infective therapy and organ support therapy. As it is well-known, the effect of single gene or pathway does not play a role in sepsis. We want to explore the interaction of two more genes or pathways in sepsis patients for future works. We hypothesize that the discovery from the available gene expression data of pediatric sepsis patients could know the process or improve the situation. METHODS AND RESULTS: The gene expression profile dataset GSE26440 of 98 septic shock samples and 32 normal samples using whole blood-derived RNA samples were generated. A total of 1,108 upregulated and 142 downregulated differentially expressed genes (DEGs) were identified in septic shock children using R software packages. The Gene Ontology (GO) enrichment and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway were analyzed using DAVID software; Gene Set Enrichment Analysis method was also used for enrichment analysis of the DEGs. The protein-protein interaction (PPI) network and the top 10 hub genes construction of the DEGs were constructed via plug-in Molecular Complex Detection and cytoHubba of Cytoscape software. From the PPI network, the top 10 hub genes, which are all upregulated DEGs in the septic shock children, were identified as GAPDH, TNF, EGF, MAPK3, IL-10, TLR4, MAPK14, IL-1ß, PIK3CB, and TLR2. Some of them were involved in one or more significant inflammatory pathways, such as the enrichment of tumor necrosis factor (TNF) pathway in the activation of mitogen-activated protein kinase activity, toll-like receptor signaling pathway, nuclear factor-κB signaling pathway, PI3K-Akt signaling pathway, and TNF signaling pathway. These findings support future studies on pediatric septic shock.

Elevated IL-7Rα is linked to recurrence and poorer survival of gastric adenocarcinoma.

IL-7Rα expression has been suggested to be involved in the development of cancer and has been reported to be linked to poor overall survival in patients with lung cancer. However, no evidence has been reportedregarding the significance of IL-7Rα expression in gastric adenocarcinoma (GA) untilnow. In the present investigation, to understand the clinicopathological significance of IL-7Rα expression in GA, expression of IL-7Rα was evaluated using immunohistochemistry in 121 cases of paired GA and its corresponding normal controls. As further confirmation, detection of IL-7Rα expression was extended from the protein level to the mRNA level using qRT-PCR. Clinicopathological association was statistically analyzed between IL-7Rα expression and clinicopathological variables, including demographic, T classification, clinical stage, lymph nodes metastases, differentiation, recurrence or not, and overall prognosis. IL-7Rα expression was markedly up-regulated in GA tissues relative to paired normal controls at both the protein or mRNA level. Elevation of IL-7Rα was markedly associated with lymph nodes metastases (P=0.006), differentiation (P=0.005), recurrence (P=0.043), and poor overall prognosis (P=0.039). There were trends toward statistical significance forboth T classification (P=0.063) and clinical stage (P=0.065) despite no significant associations found. Together, our study is the first toanalyze the significance of IL-7Rα expression in GA, suggesting its potential predictive value for recurrence and overall prognosis.