eSVD-DE: cohort-wide differential expression in single-cell RNA-seq data using exponential-family embeddings.

BACKGROUND: Single-cell RNA-sequencing (scRNA) datasets are becoming increasingly popular in clinical and cohort studies, but there is a lack of methods to investigate differentially expressed (DE) genes among such datasets with numerous individuals. While numerous methods exist to find DE genes for scRNA data from limited individuals, differential-expression testing for large cohorts of case and control individuals using scRNA data poses unique challenges due to substantial effects of human variation, i.e., individual-level confounding covariates that are difficult to account for in the presence of sparsely-observed genes. RESULTS: We develop the eSVD-DE, a matrix factorization that pools information across genes and removes confounding covariate effects, followed by a novel two-sample test in mean expression between case and control individuals. In general, differential testing after dimension reduction yields an inflation of Type-1 errors. However, we overcome this by testing for differences between the case and control individuals' posterior mean distributions via a hierarchical model. In previously published datasets of various biological systems, eSVD-DE has more accuracy and power compared to other DE methods typically repurposed for analyzing cohort-wide differential expression. CONCLUSIONS: eSVD-DE proposes a novel and powerful way to test for DE genes among cohorts after performing a dimension reduction. Accurate identification of differential expression on the individual level, instead of the cell level, is important for linking scRNA-seq studies to our understanding of the human population.

Development of a high-throughput dual-stream liquid chromatography-tandem mass spectrometry method to screen for inhibitors of glutamate carboxypeptidase II.

RATIONALE: Glutamate carboxypeptidase II (GCPII) catalyzes the hydrolysis of N-acetylaspartylglutamate (NAAG) to yield glutamate (Glu) and N-acetylaspartate (NAA). Inhibition of GCPII has been shown to remediate the neurotoxicity of excess Glu in a variety of cell and animal disease models. A robust high-throughput liquid chromatography-tandem mass spectrometry (LC/MS/MS) method was needed to quantify GCPII enzymatic activity in a biochemical high-throughput screening assay. METHODS: A dual-stream LC/MS/MS method was developed. Two parallel eluent streams ran identical HILIC gradient methods on BEH-Amide (2 × 30 mm) columns. Each LC channel was run independently, and the cycle time was 2 min per channel. Overall throughput was 1 min per sample for the dual-channel integrated system. Multiply injected acquisition files were split during data review, and batch metadata were automatically paired with raw data during the review process. RESULTS: Two LC sorbents, BEH-Amide and Penta-HILIC, were tested to separate the NAAG cleavage product Glu from isobaric interference and ion suppressants in the bioassay matrix. Early elution of NAAG and NAA on BEH-Amide allowed interfering species to be diverted to waste. The limit of quantification was 0.1 pmol for Glu. The Z-factor of this assay averaged 0.85. Over 36 000 compounds were screened using this method. CONCLUSIONS: A fast gradient dual-stream LC/MS/MS method for Glu quantification in GCPII biochemical screening assay samples was developed and validated. HILIC separation chemistry offers robust performance and unique selectivity for targeted positive mode quantification of Glu, NAA, and NAAG.

Identification of cell-type-specific marker genes from co-expression patterns in tissue samples.

MOTIVATION: Marker genes, defined as genes that are expressed primarily in a single-cell type, can be identified from the single-cell transcriptome; however, such data are not always available for the many uses of marker genes, such as deconvolution of bulk tissue. Marker genes for a cell type, however, are highly correlated in bulk data, because their expression levels depend primarily on the proportion of that cell type in the samples. Therefore, when many tissue samples are analyzed, it is possible to identify these marker genes from the correlation pattern. RESULTS: To capitalize on this pattern, we develop a new algorithm to detect marker genes by combining published information about likely marker genes with bulk transcriptome data in the form of a semi-supervised algorithm. The algorithm then exploits the correlation structure of the bulk data to refine the published marker genes by adding or removing genes from the list. AVAILABILITY AND IMPLEMENTATION: We implement this method as an R package markerpen, hosted on CRAN (https://CRAN.R-project.org/package=markerpen). SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Lipid-injured hepatocytes release sOPN to improve macrophage migration via CD44 engagement and pFak-NFκB signaling.

BACKGROUND: The key characteristics in the pathogenesis of nonalcoholic steatohepatitis (NASH) are hepatic lipotoxicity, inflammatory cell infiltration (activated macrophages, in part), and varying degrees of fibrosis. The fatty acid palmitate (PA) can cause hepatocyte cellular dysfunction, but whether and how this process contributes to macrophage-associated inflammation is not well understood. This study aimed to explore whether lipid-injured hepatocytes result in the secretion of osteopontin (sOPN), and how sOPN induces macrophage migration to steatosis hepatocytes. METHODS: Human hepatocellular carcinoma HepG2 cells were incubated with PA to establish the lipotoxicity in hepatocytes model in vitro. The released sOPN was isolated, characterized, and applied to macrophage-like cells differentiated from the human monocytic cell line THP-1 cells. C57BL/6 mice were fed either chow or a diet high in fructose-fat-glucose (FFG) to induce NASH in vivo. Some NASH model mice were also given siSPP1 for two weeks to inhibit the expression of OPN. Related tissues were collected and analyzed by histology, immunofluorescence, ELISA, qRT-PCR, and western blotting. RESULTS: PA upregulated OPN expression and release in human hepatocytes, which drove the migration of macrophages. Incubation of HepG2 cells with palmitate increased mRNA expression and secretion of OPN in cell culture supernatants. Compared with the BSA and siSPP1 groups, treatment with the supernatant derived from PA-treated hepatocytes promoted macrophage migration and activation. The sOPN induction of macrophage migration occurred via CD44 engagement and activation of the pFak-NFκB signaling pathway. Likewise, administration of siSPP1 to NASH mice inhibited the expression and release of OPN, which was associated with decreased liver dysfunction, inflammatory cell infiltration, and even fibrosis. CONCLUSIONS: sOPN, which is released from lipid-injured hepatocytes, emerges as a cytokine driving the migration of macrophages, contributing to an inflammatory response in NASH.

Identifying SLC27A5 as a potential prognostic marker of hepatocellular carcinoma by weighted gene co-expression network analysis and in vitro assays.

BACKGROUND: The incidence and mortality rates of hepatocellular carcinoma are among the highest of all cancers all over the world. However the survival rates are relatively low due to lack of effective treatments. Efforts to elucidate the mechanisms of HCC and to find novel prognostic markers and therapeutic targets are ongoing. Here we tried to identify prognostic genes of HCC through co-expression network analysis. METHODS: We conducted weighted gene co-expression network analysis with a microarray dataset GSE14520 of HCC from Gene Expression Omnibus database and identified a hub module associated with HCC prognosis. Function enrichment analysis of the hub module was performed. Clinical information was analyzed to select candidate hub genes. The expression profiles and survival analysis of the selected genes were performed using additional datasets (GSE45267 and TCGA-LIHC) and the hub gene was identified. GSEA and in vitro experiments were conducted to further verify the function of the hub gene. RESULTS: Genes in the hub module were mostly involved in the metabolism pathway. Four genes (SLC27A5, SLC10A1, PCK2 and FMO4) from the module were identified as candidate hub genes according to correlation analysis with prognostic indicators. All these genes were significantly down-regulated in tumor tissues compared with non-tumor tissues in additional datasets. After survival analysis and network construction, SLC27A5 was selected as a prognostic marker. GSEA analysis and in vitro assays suggested that SLC27A5 downregulation promoted tumor cell migration via enhancing epithelial-mesenchymal transition. CONCLUSION: SLC27A5 is a potential biomarker of HCC and SLC27A5 downregulation promoted HCC progression by enhancing EMT.

The glucose-lowering effects of α-glucosidase inhibitor require a bile acid signal in mice.

AIMS/HYPOTHESIS: Bile-acid (BA) signalling is crucial in metabolism homeostasis and has recently been found to mediate the therapeutic effects of glucose-lowering treatments, including α-glucosidase inhibitor (AGI). However, the underlying mechanisms are yet to be clarified. We hypothesised that BA signalling may be required for the glucose-lowering effects and metabolic benefits of AGI. METHODS: Leptin receptor (Lepr)-knockout (KO) db/db mice and high-fat high-sucrose (HFHS)-fed Fxr (also known as Nr1h4)-KO mice were treated with AGI. Metabolic phenotypes and BA signalling in different compartments, including the liver, gut and endocrine pancreas, were evaluated. BA pool profiles were analysed by mass spectrometry. The islet transcription profile was assayed by RNA sequencing. The gut microbiome were assayed by 16S ribosomal RNA gene sequencing. RESULTS: AGI lowered microbial BA levels in BA pools of different compartments in the body, and increased gut BA reabsorption in both db/db and HFHS-fed mouse models via altering the gut microbiome. The AGI-induced changes in BA signalling (including increased activation of farnesoid X receptor [FXR] in the liver and inhibition of FXR in the ileum) echoed the alterations in BA pool size and composition in different organs. In Fxr-KO mice, the glucose- and lipid-lowering effects of AGI were partially abrogated, possibly due to the Fxr-dependent effects of AGI on decelerating beta cell replication, alleviating insulin hypersecretion and improving hepatic lipid and glucose metabolism. CONCLUSIONS/INTERPRETATION: By regulating microbial BA metabolism, AGI elicited diverse changes in BA pool composition in different host compartments to orchestrate BA signalling in the whole body. The AGI-induced changes in BA signalling may be partly required for its glucose-lowering effects. Our study, hence, sheds light on the promising potential of regulating microbial BA and host FXR signalling for the treatment of type 2 diabetes. DATA AVAILABILITY: Sequencing data are available from the BioProject Database (accession no. PRJNA600345; www.ncbi.nlm.nih.gov/bioproject/600345).

FlashPCA2: principal component analysis of Biobank-scale genotype datasets.

MOTIVATION: Principal component analysis (PCA) is a crucial step in quality control of genomic data and a common approach for understanding population genetic structure. With the advent of large genotyping studies involving hundreds of thousands of individuals, standard approaches are no longer feasible. However, when the full decomposition is not required, substantial computational savings can be made. RESULTS: We present FlashPCA2, a tool that can perform partial PCA on 1 million individuals faster than competing approaches, while requiring substantially less memory. AVAILABILITY AND IMPLEMENTATION: https://github.com/gabraham/flashpca . CONTACT: gad.abraham@unimelb.edu.au. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Phosphorylation of Dgk1 Diacylglycerol Kinase by Casein Kinase II Regulates Phosphatidic Acid Production in Saccharomyces cerevisiae.

In the yeast Saccharomyces cerevisiae, Dgk1 diacylglycerol (DAG) kinase catalyzes the CTP-dependent phosphorylation of DAG to form phosphatidic acid (PA). The enzyme in conjunction with Pah1 PA phosphatase controls the levels of PA and DAG for the synthesis of triacylglycerol and membrane phospholipids, the growth of the nuclear/endoplasmic reticulum membrane, and the formation of lipid droplets. Little is known about how DAG kinase activity is regulated by posttranslational modification. In this work, we examined the phosphorylation of Dgk1 DAG kinase by casein kinase II (CKII). When phosphate groups were globally reduced using nonspecific alkaline phosphatase, Triton X-100-solubilized membranes from DGK1-overexpressing cells showed a 7.7-fold reduction in DAG kinase activity; the reduced enzyme activity could be increased 5.5-fold by treatment with CKII. Dgk1(1-77) expressed heterologously in Escherichia coli was phosphorylated by CKII on a serine residue, and its phosphorylation was dependent on time as well as on the concentrations of CKII, ATP, and Dgk1(1-77). We used site-specific mutagenesis, coupled with phosphorylation analysis and phosphopeptide mapping, to identify Ser-45 and Ser-46 of Dgk1 as the CKII target sites, with Ser-46 being the major phosphorylation site. In vivo, the S46A and S45A/S46A mutations of Dgk1 abolished the stationary phase-dependent stimulation of DAG kinase activity. In addition, the phosphorylation-deficient mutations decreased Dgk1 function in PA production and in eliciting pah1Δ phenotypes, such as the expansion of the nuclear/endoplasmic reticulum membrane, reduced lipid droplet formation, and temperature sensitivity. This work demonstrates that the CKII-mediated phosphorylation of Dgk1 regulates its function in the production of PA.

Transcription factor Reb1p regulates DGK1-encoded diacylglycerol kinase and lipid metabolism in Saccharomyces cerevisiae.

In the yeast Saccharomyces cerevisiae, the DGK1-encoded diacylglycerol kinase catalyzes the CTP-dependent phosphorylation of diacylglycerol to form phosphatidate. This enzyme, in conjunction with PAH1-encoded phosphatidate phosphatase, controls the levels of phosphatidate and diacylglycerol for phospholipid synthesis, membrane growth, and lipid droplet formation. In this work, we showed that a functional level of diacylglycerol kinase is regulated by the Reb1p transcription factor. In the electrophoretic mobility shift assay, purified recombinant Reb1p was shown to specifically bind its consensus recognition sequence (CGGGTAA, -166 to -160) in the DGK1 promoter. Analysis of cells expressing the PDGK1-lacZ reporter gene showed that mutations (GT→TG) in the Reb1p-binding sequence caused an 8.6-fold reduction in ß-galactosidase activity. The expression of DGK1(reb1), a DGK1 allele containing the Reb1p-binding site mutation, was greatly lower than that of the wild type allele, as indicated by analyses of DGK1 mRNA, Dgk1p, and diacylglycerol kinase activity. In the presence of cerulenin, an inhibitor of de novo fatty acid synthesis, the dgk1Δ mutant expressing DGK1(reb1) exhibited a significant defect in growth as well as in the synthesis of phospholipids from triacylglycerol mobilization. Unlike DGK1, the DGK1(reb1) expressed in the dgk1Δ pah1Δ mutant did not result in the nuclear/endoplasmic reticulum membrane expansion, which occurs in cells lacking phosphatidate phosphatase activity. Taken together, these results indicate that the Reb1p-mediated regulation of diacylglycerol kinase plays a major role in its in vivo functions in lipid metabolism.

eSVD-DE: Cohort-wide differential expression in single-cell RNA-seq data using exponential-family embeddings.

Background: Single-cell RNA-sequencing (scRNA) datasets are becoming increasingly popular in clinical and cohort studies, but there is a lack of methods to investigate differentially expressed (DE) genes among such datasets with numerous individuals. While numerous methods exist to find DE genes for scRNA data from limited individuals, differential-expression testing for large cohorts of case and control individuals using scRNA data poses unique challenges due to substantial effects of human variation, i.e., individual-level confounding covariates that are difficult to account for in the presence of sparsely-observed genes. Results: We develop the eSVD-DE, a matrix factorization that pools information across genes and removes confounding covariate effects, followed by a novel two-sample test in mean expression between case and control individuals. In general, differential testing after dimension reduction yields an inflation of Type-1 errors. However, we overcome this by testing for differences between the case and control individuals' posterior mean distributions via a hierarchical model. In previously published datasets of various biological systems, eSVD-DE has more accuracy and power compared to other DE methods typically repurposed for analyzing cohort-wide differential expression. Conclusions: eSVD-DE proposes a novel and powerful way to test for DE genes among cohorts after performing a dimension reduction. Accurate identification of differential expression on the individual level, instead of the cell level, is important for linking scRNA-seq studies to our understanding of the human population.

Images, Words, and Imagination: Accessible Descriptions to Support Blind and Low Vision Art Exploration and Engagement.

The lack of accessible information conveyed by descriptions of art images presents significant barriers for people with blindness and low vision (BLV) to engage with visual artwork. Most museums are not able to easily provide accessible image descriptions for BLV visitors to build a mental representation of artwork due to vastness of collections, limitations of curator training, and current measures for what constitutes effective automated captions. This paper reports on the results of two studies investigating the types of information that should be included to provide high-quality accessible artwork descriptions based on input from BLV description evaluators. We report on: (1) a qualitative study asking BLV participants for their preferences for layered description characteristics; and (2) an evaluation of several current models for image captioning as applied to an artwork image dataset. We then provide recommendations for researchers working on accessible image captioning and museum engagement applications through a focus on spatial information access strategies.

Twice-daily rivaroxaban after percutaneous left atrial appendage closure for atrial fibrillation.

Background and aim: Rivaroxaban is an emerging oral anticoagulant for postoperative anticoagulation after percutaneous left atrial appendage closure (LAAC). Because a once-daily dosing regimen of rivaroxaban causes fluctuations in the drug plasma concentration, we studied the feasibility and safety of twice-daily rivaroxaban as a postoperative anticoagulation regimen for patients with atrial fibrillation (AF) undergoing LAAC. Methods: This study involved patients with AF who underwent LAAC and took rivaroxaban postoperatively. A total of 326 patients who received a standard total dose (15 or 20 mg) of rivaroxaban based on their creatinine clearance rate were divided into the twice-daily (BID) rivaroxaban group (n = 208) and once-daily (QD) rivaroxaban group (n = 118) according to their anticoagulation strategy. Transesophageal echocardiography was recommended at 3-6 months postoperatively to check for device-related thrombosis (DRT). Clinical outcomes were evaluated during postoperative anticoagulation. Results: The median CHA2DS2-VASc score (4 [3, 5] vs. 4 [3, 5], p = 0.28) and HAS-BLED score (2 [2, 3] vs. 2 [2, 3], p = 0.48) were not significantly different between the groups. During the anticoagulation period (4.1 ± 0.7 vs. 4.1 ± 0.9 months, p = 0.58), 148 (71.2%) patients in the BID group and 75 (63.6%) in the QD group underwent follow-up transesophageal echocardiography. There were no statistically significant differences between the two groups in terms of DRT (1.4% vs. 2.7%, p = 0.60), minor bleeding (8.2% vs. 11.0%, p = 0.39), thromboembolic events (1.0% vs. 0.8%, p = 1.00), major bleeding (0.5% vs. 0.8%, p = 1.00), or death. Conclusion: A short course of twice-daily rivaroxaban following LAAC is a feasible alternative regimen with a low rate of major bleeding events, DRT, and thromboembolic events for patients with AF.

Gradient-based sparse principal component analysis with extensions to online learning.

Sparse principal component analysis is an important technique for simultaneous dimensionality reduction and variable selection with high-dimensional data. In this work we combine the unique geometric structure of the sparse principal component analysis problem with recent advances in convex optimization to develop novel gradient-based sparse principal component analysis algorithms. These algorithms enjoy the same global convergence guarantee as the original alternating direction method of multipliers, and can be more efficiently implemented with the rich toolbox developed for gradient methods from the deep learning literature. Most notably, these gradient-based algorithms can be combined with stochastic gradient descent methods to produce efficient online sparse principal component analysis algorithms with provable numerical and statistical performance guarantees. The practical performance and usefulness of the new algorithms are demonstrated in various simulation studies. As an application, we show how the scalability and statistical accuracy of our method enable us to find interesting functional gene groups in high-dimensional RNA sequencing data.

A novel epithelial-mesenchymal transition-related lncRNA signature predicts prognosis and immune status in endometrioid endometrial cancer.

The pathogenesis and progression of endometrial cancer (EC) are associated with epithelial-mesenchymal transition (EMT) and long noncoding RNAs (lncRNAs). In the present study, we aimed to identify an EMT-related lncRNA signature and evaluate its prognostic value in EC. We obtained the expression profile of lncRNAs and clinical information of patients with endometrioid EC from The Cancer Genome Atlas database (N = 401). We identified a signature of 5 EMT-related lncRNAs and calculated the risk score of each patient. Next, we validated the independence of the prognostic value of the EMT-related lncRNA signature. Furthermore, we performed Gene Set Enrichment Analysis to identify potential molecular function and Kyoto Encyclopedia of Genes and Genomes pathways related to the EMT-related lncRNA signature. Tumor microenvironment analysis and immune checkpoint blockade (ICB) response prediction were also assessed. Survival analysis revealed that the high-risk group, based on the EMT-related lncRNA signature, had a poorer prognosis than the low-risk group in the training, testing, and entire sets. The predictive value of the EMT-related lncRNA signature was independent of age, The International Federation of Gynecology and Obstetrics stage, tumor grade, and body mass index. Time-dependent receiver operating characteristic curves also demonstrate the prognostic accuracy of this risk model. Gene Set Enrichment Analysis showed that cytokine-cytokine receptor interaction, glycolysis/gluconeogenesis, and IL-17 signaling pathway were significantly enriched. Furthermore, tumor microenvironment analysis indicated a significant negative correlation between the immune score and EMT-related lncRNA signature risks core, while the low-risk group was more likely to respond to ICB therapy than the high-risk group. A reliable EMT-related lncRNA signature of endometrioid EC was identified that could be utilized as an independent prognostic biomarker to predict patient survival outcomes and provide references for the option of ICB therapy.

Pituitrin Injection before Hysteroscopic Curettage for Treating Type I Cesarean Scar Pregnancy in Comparison with Uterine Artery Embolization: A Retrospective Study.

Background: The effectiveness and safety of pituitrin injection coupled with hysteroscopy and suction curettage as treatment for type I cesarean scar pregnancy (CSP) have not been studied enough in the literature, by comparing it to uterine artery embolization (UAE) followed by suction curettage we aim to determine its efficacy. Materials and Methods: Data of 53 patients (the PIT group) with type I CSP treated with pituitrin injection combined with hysteroscopic suction curettage and 137 patients (the UAE group) with type I CSP treated with UAE followed by suction curettage were collected in retrospect. The clinical data were analyzed statistically to compare the efficacy and safety between the two groups. Results: The PIT group had a shorter duration of postoperative vaginal bleeding, postoperative hospitalization, and overall hospitalization length (P < 0.05). The PIT group had lower overall hospitalization costs and a lower rate of adverse events than the UAE group (P < 0.05). There was no significant difference between the two groups in terms of treatment success rate, the average length of operation, blood loss during the procedure, time when serum ß-hCG returned to normal range, and menstrual recovery time after hospital release (P > 0.05). Conclusion: UAE and pituitrin injection followed by hysteroscopic suction curettage are good choices for type I CSP treatment. However, pituitrin injection with hysteroscopic suction curettage outperforms UAE followed by suction curettage. Thus, pituitrin injection may be an option of high priority for type I CSP.

Testosterone elevation in ovarian adult granulosa cell tumor: A case report and review of the literature.

RATIONALE: Adult granulosa cell tumors (AGCT) mainly secret estrogen, but few androgens. It is rarer to have amenorrhea and hyperandrogenemia as clinical features. Here, we report a rare case of right side AGCTs with amenorrhea and hyperandrogenemia in a 19-year-old female. PATIENT CONCERNS: The 19-year-old patient was admitted to our hospital due to amenorrhea for more than 1 year, and discovery of pelvic mass for 4 months. The gynecological ultrasound and computed tomography (CT) cannot define the nature of the mass. Surprisingly, an elevation in testosterone levels was also measured. DIAGNOSIS AND INTERVENTIONS: The present patient underwent laparoscopic right salpingo-oophorectomy and partial omentectomy and biopsy of the peritoneum. OUTCOMES: After the surgery, the testosterone value was down to normal. The patient menstrual cramps on August 13, 2021. Her clitoris is smaller than the front. Up to August 1, 2022, there was no obvious sign of recurrence. LESSONS: Androgen-secreting AGCT is rare. We hope that this case can strengthen gynecologists' early diagnosis and treatment of this disease and improve the prognosis.

High blood galectin-3 level associated with risk of frailty in aging.

Background: Frailty is one of the most problematic expressions of population aging, but its underlying mechanism has not been fully elucidated. Circulating galectin-3 (Gal-3) is involved in the pathogenesis of many age-related diseases. This study aims to explore the influence of circulating Gal-3 on the regulation of frailty and aging and to identify the potential mechanism further. Methods: In this cross-sectional analysis, the Fried frailty phenotype (FP) was assessed among 149 community elderly residents in Shanghai. Peripheral blood mononuclear cells (PBMCs) were isolated by the Ficoll-Paque density gradient method, and differentially expressed genes (DEGs) encoding transcription factors in frailty were detected by Illumina and bioinformatics analyzed with R software. Gene Ontology (GO) enrichment analyses and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed to explore the functional roles of these DEGs and the target genes related to frailty phenotypes. The serum Gal-3 concentration was tested by enzyme-linked immunosorbent assay (ELISA). Mouse frailty phenotype was used to construct an in vivo model of frailty, after which the serum levels of circulating Gal-3 and its gene expression levels in mouse tissues were determined. Results: Participants' mean age was 72.04 ± 7.05 years. In total, 21.48% were frail and 36.91% were pre-frail. The mean serum Gal-3 concentration was 46.34 ± 17.99 ng/mL in frail participants, 32.30 ± 8.14 ng/mL in pre-frail participants, and 26.00 ± 5.87 ng/mL in non-frail individuals (p < 0.001). Significant positive correlations between serum Gal-3 level and FP score, SARC-F score, C-reactive protein (CRP), interleukin-6, etc., were observed. In addition, the KEGG pathway and GO enrichment analyses showed that 265 DEGs in PBMCs of frail participants were mainly related to inflammatory response, translation, RNA binding, protein binding, ribosome, and primary immunodeficiency. LGALS3 was identified as the overlapping gene between frailty-related DEGs and aging-related DEGs. The elevated serum Gal-3 concentration in the in vivo model of frailty was consistent with the results in participants. Conclusion: In both community-dwelling older adults and aged mice, serum Gal-3 concentration was positively correlated with frailty. This circulating mediator may be a promising indicator of frailty. Clinical trial registration: Chinese Clinical Trial Registry identifier, ChiCTR2000036399.

Phosphatidate phosphatase activity plays key role in protection against fatty acid-induced toxicity in yeast.

The PAH1-encoded phosphatidate (PA) phosphatase in Saccharomyces cerevisiae is a pivotal enzyme that produces diacylglycerol for the synthesis of triacylglycerol (TAG) and simultaneously controls the level of PA used for phospholipid synthesis. Quantitative lipid analysis showed that the pah1Δ mutation caused a reduction in TAG mass and an elevation in the mass of phospholipids and free fatty acids, changes that were more pronounced in the stationary phase. The levels of unsaturated fatty acids in the pah1Δ mutant were unaltered, although the ratio of palmitoleic acid to oleic acid was increased with a similar change in the fatty acid composition of phospholipids. The pah1Δ mutant exhibited classic hallmarks of apoptosis in stationary phase and a marked reduction in the quantity of cytoplasmic lipid droplets. Cells lacking PA phosphatase were sensitive to exogenous fatty acids in the order of toxicity palmitoleic acid > oleic acid > palmitic acid. In contrast, the growth of wild type cells was not inhibited by fatty acid supplementation. In addition, wild type cells supplemented with palmitoleic acid exhibited an induction in PA phosphatase activity and an increase in TAG synthesis. Deletion of the DGK1-encoded diacylglycerol kinase, which counteracts PA phosphatase in controlling PA content, suppressed the defect in lipid droplet formation in the pah1Δ mutant. However, the sensitivity of the pah1Δ mutant to palmitoleic acid was not rescued by the dgk1Δ mutation. Overall, these findings indicate a key role of PA phosphatase in TAG synthesis for protection against fatty acid-induced toxicity.

Ileal FXR-FGF15/19 signaling activation improves skeletal muscle loss in aged mice.

Sarcopenia is the age-related decrease in skeletal muscle mass, and current therapies for this disease are ineffective. We previously showed that ileal farnesoid X receptor (FXR)-fibroblast growth factor 15/19 (FGF15/19) signaling acts as a regulator of gut microbiota to mediate host skeletal muscle. However, the therapeutic potential of this pathway for sarcopenia is unknown. This study showed that ileal FXR-FGF15/19 signaling was downregulated in older men and aged male mice due to changes in the gut microbiota and microbial bile acid metabolism during aging. In addition, the intestine-specific FXR agonist fexaramine increased skeletal muscle mass and improve muscle performance in aged mice. Ileal FXR activation increased skeletal muscle protein synthesis in a FGF15/19-dependent way, indicating that ileal FXR-FGF15/19 signaling is a potential therapeutic target for sarcopenia.

First-Principles Study on the Structural, Electronic, and Lithium Storage Properties of Ti3C2T2 (T = O, F, H, OH) MXene.

The structures of bare Ti3C2 and functionalized Ti3C2T2 (T = O, F, H, OH) MXenes were constructed, and the effect of surface functional groups T2 (T = O, F, H, OH) on the structural, electronic, and lithium storage properties were investigated by first-principles calculations. The results show that the proximity of surface functional groups will induce some lattice distortion of Ti3C2T2 MXene. The degree of lattice distortion depends mainly on the adsorption position of functional groups and the types of surface functional groups. From the point of view of forming energy, the surface functional groups tend to be located at the CCP site. From the energy band and DOS results, the presence of surface functional groups has a significant effect on the valence band, while it has a slight impact on the conduction band. In terms of lithium storage, lithium atom adsorption starts from the HCP position for bare Ti3C2, while functionalized Ti3C2T2 starts from the CCP position. The double-layer lithium storage capacity of bare Ti3C2 and Ti3C2O2 were 639.78 mAh/g and 537.22 mAh/g, respectively. And the single-layer lithium storage capacity of Ti3C2F2 was 130.77 mAh/g.