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.

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.

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.

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.

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.

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.

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.

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.

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.

Percutaneous left atrial appendage closure using the LAmbre device in patients with atrial fibrillation and left atrial appendage thrombus.

Background: Left atrial appendage closure (LAAC) is considered a valid alternative for the prevention of thromboembolic stroke in patients with persistent left atrial appendage thrombus (LAAT) despite adequate anticoagulation. However, the data on LAAC using the LAmbre device for patients with LAAT is limited. This study was performed to explore efficacy and safety as well as to share the experience of the modified LAAC procedure with the LAmbre device. Materials and methods: A total of 7 patients with persistent LAAT despite adequate anticoagulation underwent modified LAAC with the LAmbre device between November 2019 and April 2022. Transesophageal echocardiography was performed 3 months postoperatively to detect device-related thrombosis and peridevice leak. The patients' clinical events were evaluated during the perioperative and follow-up periods. Results: The median age, CHA2DS2-VASc score, and HAS-BLED score of all patients were 71 [53-73], 3 [2-4], and 2 [2-3], respectively. In the procedure, a cerebral protection system was used in two patients. LAAC with the LAmbre device was successfully performed in all patients without perioperative events. During the median follow-up of 383 [325-865] days, postoperative transesophageal echocardiography was performed in six (85.7%) patients. Device-related thrombosis was detected in one (16.7%) patient, and no significant peridevice leak was observed. No thromboembolic event or bleeding event occurred in any patients. Conclusion: LAAC with the LAmbre device is effective and safe when performed by experienced operators in highly selected patients with LAAT after adequate anticoagulation.

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.

Combined atrial fibrillation ablation and left atrial appendage closure: Watchman vs. LAmbre devices.

Background: Left atrial appendage closure (LAAC) combined with radiofrequency catheter ablation is an emerging one-stop hybrid procedure for non-valvular atrial fibrillation (AF). This study was performed to compare the efficacy and safety of the Watchman device vs. the LAmbre device for this combined procedure. Methods: Two hundred and thirty two patients with AF who underwent the combined procedure were enrolled and divided into two subgroups depending on the device choice: the Watchman-combined group (n = 118) and the LAmbre-combined group (n = 114). The periprocedural and follow-up adverse events in both groups were documented. Results: The mean CHA2DS2-VASc score and HAS-BLED score in the Watchman-combined group and LAmbre-combined group were 3.7 ± 1.5 vs. 3.8 ± 1.5 and 2.5 ± 1.1 vs. 2.3 ± 1.1, respectively (all P > 0.05). Successful LAAC was achieved in all patients. The rate of major periprocedural complications and AF recurrence at 6 months post-procedure were similar between the Watchman-combined group and LAmbre-combined group (0.8 vs. 0.9%, P = 1.00; 22.0 vs. 15.8%, P = 0.23). During 2.6 ±0 .7 vs.1.6 ± 1.6 years follow-up, the rate of major clinical adverse events, including stroke and major bleeding, were comparable between the Watchman-combined group and the LAmbre-combined group (2.6 vs. 1.1% per 100 patient-years, P = 0.33). The intraprocedural peri-device leakage (PDL) rate was similar between the Watchman-combined group and the LAmbre-combined group (5.1 vs. 6.1%, P = 0.73), but the PDL rate was significantly higher at 3-6 months transesophageal echocardiography (TEE) follow-up than the intraprocedural PDL rate in both groups (21.6 vs. 5.1%; 36.6 vs. 6.1%, respectively), with a more obvious increase in minimal PDL rate in the LAmbre-combined group than the Watchman-combined group (36.6 vs. 21.6%, P < 0.05). Conclusion: The Watchman and LAmbre devices were comparable in efficacy and safety for the combined procedure. The minimal PDL rate at short-term TEE follow-up was higher in the LAmbre-combined group than the Watchman-combined group.

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.

Enhancing Acsl4 in absence of mTORC2/Rictor drove ß-cell dedifferentiation via inhibiting FoxO1 and promoting ROS production.

Rapamycin insensitive companion of mechanistic target of Rapamycin (Rictor), the key component of mTOR complex 2 (mTORC2), controls both ß-cell proliferation and function. We sought to study whether long chain acyl-CoA synthetase 4 (Acsl4) worked downstream of Rictor/mTORC2 to maintain ß-cell functional mass. We found Acsl4 was positively regulated by Rictor at transcriptional and posttranslational levels in mouse ß-cell. Infecting adenovirus expressing Acsl4 in ß-cell-specific-Rictor-knockout (ßRicKO) islets and Min6 cells knocking down Rictor with lentivirus-expressing siRNA-oligos targeting Rictor(siRic), recovered the ß-cell dysplasia but not dysfunction. Cell bioenergetic experiment performed with Seahorse XF showed that Acsl4 could not rescue the dampened glucose oxidation in Rictor-lacking ß-cell, but further promoted lipid oxidation. Transposase-Accessible Chromatin (ATAC) and H3K27Ac chromatin immunoprecipitation (ChIP) sequencing studies reflected the epigenetic elevated molecular signature for ß-cell dedifferentiation and mitigated oxidative defense/response. These results were confirmed by the observations of elevated acetylation and ubiquitination of FoxO1, increased protein levels of Gpx1 and Hif1an, excessive reactive oxygen species (ROS) production and diminished MafA in Acsl4 overexpressed Rictor-lacking ß-cells. In these cells, antioxidant treatment significantly recovered MafA level and insulin content. Inducing lipid oxidation alone could not mimic the effect of Acsl4 in Rictor lacking ß-cell. Our study suggested that Acsl4 function in ß-cell was context dependent and might facilitate ß-cell dedifferentiation with attenuated Rictor/mTORC2 activity or insulin signaling via posttranslational inhibiting FoxO1 and epigenetically enhancing ROS induced MafA degradation.

Secretory Galectin-3 promotes hepatic steatosis via regulation of the PPARγ/CD36 signaling pathway.

Galectin-3 (Gal3) is an essential regulator of a number of metabolic disorders. Previous studies have established that Gal3 is a positive regulator of inflammation, fibrosis, and insulin resistance. However, its function in the early pathogenesis of hepatic lipid accumulation in non-alcoholic fatty liver disease (NAFLD) remains unresolved. Here, we demonstrate the presence of significantly upregulated extracellular concentrations of Gal3 in the fatty livers of high-fat diet (HFD)-induced mice. Systemic inhibition of Gal3 by injection of TD139 reduced the accumulation of lipid in the livers of HFD-fed mice, accompanied by the decreased expression of CD36 and peroxisome proliferator-activated receptor-gamma (PPARγ). Treatment with Gal3 protein elicited the opposite response in palmitic acid (PA)-induced HepG2 hepatocytes. It was additionally discovered that Gal3 positively regulates CD36 transcription by increased activation of PPARγ, thereby increasing fatty acid uptake, resulting in hepatic steatosis. In conclusion, the present study confirmed the roles of Gal3 in hepatic lipid metabolism in both in vitro and in vivo studies and revealed that Gal3 is a secretory protein that promotes hepatic steatosis through the PPARγ-CD36-dependent pathway, suggesting that targeting Gal3 may represent a potential therapeutic approach for the treatment of NAFLD and related metabolic disorders.

Pyrotinib Combined With Vinorelbine in HER2-Positive Metastatic Breast Cancer: A Multicenter Retrospective Study.

INTRODUCTION: Pyrotinib plus capecitabine has been approved in China for human epidermal growth factor receptor 2 (HER2)-positive metastatic breast cancer (MBC). Meanwhile, vinorelbine is another important chemotherapy option for MBC available in oral and intravenous forms. Thus, pyrotinib plus vinorelbine may represent a new treatment option, particularly for patients with failed capecitabine treatment. This study reported the first real-world data for pyrotinib plus vinorelbine therapy in HER2+ MBC. METHODS: HER2+ MBC patients (n = 97) treated with pyrotinib plus vinorelbine in six institutions across China from May 2018 to June 2020 were enrolled. Progression-free survival (PFS), objective response rate (ORR), overall survival (OS), and toxicity profiles were determined. RESULTS: Sixty-seven percent of patients received more than two lines of systematic therapy. Nearly all patients (97.9%) had received trastuzumab and 50.5% were administered lapatinib. When combined with pyrotinib, 74.2% received oral and 25.8% received intravenous vinorelbine. Median PFS (mPFS) was 7.8 (range, 4.7-10.8) months for all patients. The mPFS in patients administered pyrotinib as second-line therapy and third-or-higher-line therapy were 12.0 and 6.4 months, respectively. Patients who received pyrotinib plus oral or intravenous vinorelbine had similar mPFS (7.8 vs. 6.4 months, p = 0.871). The 23 patients with brain metastases had mPFS of 6.3 (range, 3.4-9.2) months. Lapatinib-naïve patients had significantly longer PFS than lapatinib-treated patients (10.8 months vs. 5.6 months, p = 0.020). Median OS was not achieved. The ORR for 96 patients was 34.3%. Common grade 3 and 4 adverse events were diarrhea (22.7%), neutropenia (7.2%), and leukopenia (4.1%). CONCLUSIONS: Pyrotinib plus vinorelbine therapy demonstrated promising effects in HER2+ MBC with tolerable toxicity, particularly in patients with second-line treatment and without prior lapatinib treatment, as well as in patients with brain metastases. Oral vinorelbine is a useful alternative to the intravenous form when combined with pyrotinib. CLINICAL TRIAL REGISTRATION: [ClinicalTrials.gov], identifier [NCT04517305].

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.

Depletion of gut microbiota induces skeletal muscle atrophy by FXR-FGF15/19 signalling.

Background: Recent evidence indicates that host-gut microbiota crosstalk has nonnegligible effects on host skeletal muscle, yet gut microbiota-regulating mechanisms remain obscure.Methods: C57BL/6 mice were treated with a cocktail of antibiotics (Abx) to depress gut microbiota for 4 weeks. The profiles of gut microbiota and microbial bile acids were measured by 16S rRNA sequencing and ultra-performance liquid chromatography (UPLC), respectively. We performed qPCR, western blot and ELISA assays in different tissue samples to evaluate FXR-FGF15/19 signaling.Results: Abx treatment induced skeletal muscle atrophy in mice. These effects were associated with microbial dysbiosis and aberrant bile acid (BA) metabolism in intestine. Ileal farnesoid X receptor (FXR)-fibroblast growth factor 15 (FGF15) signaling was inhibited in response to microbial BA disturbance. Mechanistically, circulating FGF15 was decreased, which downregulated skeletal muscle protein synthesis through the extracellular-signal-regulated protein kinase 1/2 (ERK1/2) signaling pathway. Treating Abx mice with FGF19 (human FGF15 ortholog) partly reversed skeletal muscle loss.Conclusions: These findings indicate that the BA-FXR-FGF15/19 axis acts as a regulator of gut microbiota to mediate host skeletal muscle.

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.