Integrative analysis of relative abundance data and presence-absence data of the microbiome using the LDM.

SUMMARY: We previously developed the LDM for testing hypotheses about the microbiome that performs the test at both the community level and the individual taxon level. The LDM can be applied to relative abundance data and presence-absence data separately, which work well when associated taxa are abundant and rare, respectively. Here, we propose LDM-omni3 that combines LDM analyses at the relative abundance and presence-absence data scales, thereby offering optimal power across scenarios with different association mechanisms. The new LDM-omni3 test is available for the wide range of data types and analyses that are supported by the LDM. AVAILABILITY AND IMPLEMENTATION: The LDM-omni3 test has been added to the R package LDM, which is available on GitHub at https://github.com/yijuanhu/LDM. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

The impact of ibuprofen on valproic acid plasma concentration in pediatric patients.

The combination of valproic acid (VPA) and ibuprofen are common in children with epilepsy. Three case reports investigated that ibuprofen might decrease the plasma concentration of VPA, however, no cohort study was published to evaluate the interaction of ibuprofen on VPA plasma concentration in pediatric patients.Data from patients with measured VPA trough concentrations (C0) were retrospectively collected in a Chinese teaching and tertiary Children's Hospital from January 2017 to June 2019. The samples measured within 6 weeks of the last ibuprofen administration were considered ibuprofen combination samples. Patients with paired samples before and after ibuprofen administration were additionally analysed. The effects of ibuprofen on the VPA through concentration to dose (C0/D) ratio were investigated. The proportion of samples with achieved target concentrations of VPA (50-100 mg/L) and the corresponding required dosage were compared. Moreover, subgroup analysis according to the interval between the last ibuprofen dosage and C0 measurement was performed.A total of 616 samples from 434 patients, of whom 16 had paired samples, were included. VPA C0/D decreased when ibuprofen was administered by 7.5% and 30.6% of the total samples and paired samples, respectively. The interaction was significant within 1 week of the last ibuprofen dose. No significant differences were observed in the proportion of target concentration achieved and VPA dose requirement when ibuprofen was combined.A moderate effect of ibuprofen on VPA C0/D was observed within 1 week of ibuprofen administration; the target concentration and required doses of VPA were comparable.

Tigecycline-Induced Tooth Discoloration in Children Younger than Eight Years.

Tetracycline may cause tooth discoloration when used in young children during tooth development. Whether tigecycline, a tetracycline derivative, has either a similar adverse event or not remains unclear. We assessed the discoloration of the permanent teeth of patients <8 years old after tigecycline exposure. These patients were identified through a retrospective chart review in a Chinese children's hospital. Those who had at least one erupted permanent tooth after tigecycline exposure were interviewed, examined, and photographed by an experienced pediatric dentist and independently assessed by another senior dentist to detect tetracycline-like tooth discoloration. We identified 101 patients who were exposed to tigecycline, 12 of whom were included. The mean daily dose of tigecycline was 2.3 mg/kg of body weight (standard deviation, 0.6), and the median duration was 12.5 days (interquartile range [IQR], 8.0 to 19.3). The median age of exposure was 5.2 years (IQR, 4.5 to 7.4), and the median age of dental examination was 9.1 years (IQR, 9.0 to 10.3). Two patients (16.7%) developed yellow discoloration: a girl having yellow discoloration with white-to-yellow opacities in the upper lateral incisors and lower incisors and a boy with a suspicious buccal yellow discoloration and enamel dysplasia in the second molars. The incidence and extent of tigecycline-associated dental adverse events remain unclear due to the small sample size and inadequate follow-up period.

Diltiazem on tacrolimus exposure and dose sparing in Chinese pediatric primary nephrotic syndrome: impact of CYP3A4, CYP3A5, ABCB1, and SLCO1B3 polymorphisms.

PURPOSE: To evaluate the role of diltiazem on tacrolimus sparing in pediatric primary nephrotic syndrome (PNS) and its relation to CYP3A4, CYP3A5, ABCB1, and SLCO1B3 polymorphisms. METHODS: The PNS children treated with tacrolimus and with steady-state trough concentration (C0) were retrospectively collected. The impacts of diltiazem on tacrolimus dose-adjusted C0 (C0/D), target concentration achievement, and required dose were evaluated. Meanwhile, the relationship between the polymorphisms (including CYP3A4*1G, CYP3A5*3, ABCB1-C3435T, and SCLO1B3) and dose-sparing effect were investigated. RESULTS: A total of 71 children with 535 concentrations, including 16 children with concomitant diltiazem, were involved. Significantly increased C0/D (94.0 vs 83.8 ng/mL per mg/kg, p = 0.038) and lower required daily dose of tacrolimus (0.056 vs 0.064 mg/kg, p = 0.003) were observed in patients co-administered with diltiazem. Subpopulation carrying CYP3A4*1G, CYP3A5*1, ABCB1-3435TT, or SLCO1B3-699AA was presented with enhanced increment in tacrolimus C0/D by 38.8-102.9%. CONCLUSION: Moderate effect of diltiazem on tacrolimus sparing, which might relate to the polymorphisms of CYP3A4, CYP3A5, ABCB1, and SLCO1B3, was documented.

SHP2 protects endothelial cell barrier through suppressing VE-cadherin internalization regulated by MET-ARF1.

Vascular endothelial (VE)-cadherin junctional localization is known to play a central role in vascular development, endothelial barrier integrity, and homeostasis. The sarcoma homology domain containing protein tyrosine phosphatase (SHP)2 has been shown to be involved in regulating endothelial barrier function; however, the mechanisms remain largely unknown. In this work SHP2 knockdown in an HUVEC monolayer increased VE-cadherin internalization and endothelial barrier permeability. Loss of SHP2 specifically augmented the GTPase activity of ADP-ribosylation factor (ARF)-1. ARF1 knockdown or inhibition of its guanine nucleotide exchange factors (GEFs) markedly attenuated VE-cadherin internalization and barrier hyperpermeability induced by SHP2 deficiency. SHP2 knockdown increased the total and phosphorylated levels of MET, whose activity was necessary for ARF1 activation and VE-cadherin internalization. Furthermore, constitutive endothelium-specific deletion of Shp2 in mice led to disrupted endothelial cell junctions, massive hemorrhage, and lethality in embryos. Induced and endothelium-specific deletion of Shp2 in adult mice resulted in lung hyperpermeability. Inhibitors for ARF1-GEF or MET used in pregnant mice prevented the vascular leakage in endothelial Shp2-deleted embryos. Together, our findings define a novel role of SHP2 in stabilizing junctional VE-cadherin in the resting endothelial barrier through suppressing MET and ARF1 activation.-Zhang, J., Huang, J., Qi, T., Huang, Y., Lu, Y., Zhan, T., Gong, H., Zhu, Z., Shi, Y., Zhou, J., Yu, L., Zhang, X., Cheng, H., Ke, Y. SHP2 protects endothelial cell barrier through suppressing VE-cadherin internalization regulated by MET-ARF1.

Evaluation of Concentration Errors and Inappropriate Dose Tailoring of Tacrolimus Caused by Sampling-Time Deviations in Pediatric Patients With Primary Nephrotic Syndrome.

BACKGROUND: Tacrolimus dosing is routinely tailored based on its trough level (C0) drawn by therapeutic drug monitoring in pediatric patients with primary nephrotic syndrome. However, this concentration is often inaccurate owing to inappropriate practice, such as deviation of sampling time (DST). The quantitative relationship between DST and C0 remains unclear. METHODS: Tacrolimus concentration at nominal sampling times (12 hours after last dose) and 32 deviation scenarios (12 ± 4 hours every 15 minutes) was predicted using a previously validated population pharmacokinetic model based on 162 scenarios of 100 primary nephrotic syndrome patients involved in the population pharmacokinetic model and derived virtual patients. Concentration error (CE) and relative CE (RCE) were evaluated, and the correlation between DST and RCE was evaluated by subgroup analysis using linear regression. Ultimately, the inappropriate dosing possibly misled by incorrect C0 was simulated in a real-patient cohort according to the target range (5-10 ng/mL). RESULTS: Approximately 7% of RCE was caused at every 1-hour of DST. DST was the most major contributor of RCE (r = 0.773-0.804). Patients with early sampling, older age, high body weight, high dose, low aspartate transaminase level, high corticosteroid dose, and without combination of azole antifungal agents were revealed to have high RCE. Approximately 7%-36% and 9%-25% of inappropriate dose tailoring may be caused by early and delayed sampling, respectively. In addition, patients with early sampling or high-dose tacrolimus had a higher risk of inappropriate dosing than patients with delayed sampling [hazard ratio = 1.53, 95% confidence interval (CI): 1.03-2.27, P = 0.048], and low-dose tacrolimus (P < 0.0001). CONCLUSIONS: A moderate bias of concentration and dose tailoring was revealed within 4 hours of DST. In addition, a high risk of bias was found in patients with early sampling and high-dose tacrolimus.

Underlying Mechanism of Insulin Resistance: A Bioinformatics Analysis Based on Validated Related-Genes from Public Disease Databases.

BACKGROUND The underlying mechanism of insulin resistance is complex; bioinformatics analysis is used to explore the mechanism based differential expression genes (DEGs) obtained from omics analysis. However, the expression and role of most DEGs involved in bioinformatics analysis are invalidated. This study aimed to disclose the mechanism of insulin resistance via bioinformatics analysis based on validated insulin resistance-related genes (IRRGs) collected from public disease-gene databases. MATERIAL AND METHODS IRRGs were collected from 4 disease databases including NCBI-Gene, CTD, RGD, and Phenopedia. GO and KEGG analysis of IRRGs were performed by DAVID. Then, the STRING database was employed to construct a protein-protein interaction (PPI) network of IRRGs. The module analysis and hub genes identification were carried out by MCODE and cytoHubba plugin of Cytoscape based on the primary PPI network, respectively. RESULTS A total of 1195 IRRGs were identified. Response to drug, hypoxia, insulin, positive regulation of transcription from RNA polymerase II promoter, cell proliferation, inflammatory response, negative regulation of apoptotic process, glucose homeostasis, cellular response to insulin stimulus, and aging were proposed as the crucial functions related to insulin resistance. Ten insulin resistance-related pathways included the pathways of insulin resistance, pathways in cancer, adipocytokine, prostate cancer, PI3K-Akt, insulin, AMPK, HIF-1, prolactin, and pancreatic cancer signaling pathway were revealed. INS, AKT1, IL-6, TP53, TNF, VEGFA, MAPK3, EGFR, EGF, and SRC were identified as the top 10 hub genes. CONCLUSIONS The current study presented a landscape view of possible underlying mechanism of insulin resistance by bioinformatics analysis based on validated IRRGs.

PEGylated versus non-PEGylated drugs: A cross-sectional analysis of adverse events in the FDA Adverse Event Reporting System (FAERS) Database
.

OBJECTIVE: PEGylation is commonly used to optimize pharmacological properties and improve the clinical response of drugs. Due to the inherent toxicity of polyethylene glycol (PEG) and pharmacological changes induced by PEGylation, the safety may be altered and required to be explored. This study explored the adverse events (AEs) associated with PEGylation by comparing pharmacovigilance data of PEGylated and parent drugs. MATERIALS AND METHODS: We conducted a disproportionality analysis of spontaneous reports associated with PEGylated and corresponding parent medications from the FDA Adverse Event Reporting System database recorded between the 1st quarter of 2004 and the 4th quarter of 2018 at the level of preferred terms (PTs) and standard MedDRA queries (SMQs), respectively. The AEs probably different in risk due to changed pharmacological effects and inherent toxicity of PEG were analyzed. RESULTS: A total of 259,428 cases associated to six drug pairs (filgrastim, asparaginase, interferon α-2a, interferon α-2b,interferon ß-1a, and liposomal doxorubicin) were collected. Although 95% of PTs were comparable between the two groups, PTs of deep vein thrombosis, pancreatitis acute, diabetes mellitus, liver disorder, disorientation, aphasia and infection, and SMQ of embolic and thrombotic events were significantly alleviated by PEGylation. No PT was significantly enhanced by PEGylation. CONCLUSION: The pharmacovigilance profiles of PEGylated and non-PEGylated agents were similar. Further clinical assessment is required to validate the pharmacovigilance data.

Increased levels of Gab1 and Gab2 adaptor proteins skew interleukin-4 (IL-4) signaling toward M2 macrophage-driven pulmonary fibrosis in mice.

M2-polarized macrophages, also known as alternatively activated macrophages, have long been associated with pulmonary fibrosis; however, the mechanism has not been fully defined. Gab1 and Gab2 proteins belong to the Gab family of adaptors and are integral components of the signal specificity in response to various extracellular stimuli. In this report, we found that levels of both Gab1 and Gab2 were elevated in M2-polarized macrophages isolated from bleomycin-induced fibrotic lungs. In vitro Gab1/2 deficiency in bone marrow-derived macrophages abrogated IL-4-mediated M2 polarization. Furthermore, in vivo conditional removal of Gab1 (Gab1MyKO) and germ line knock-out of Gab2 (Gab2-/-) in macrophages prevented a bias toward the M2 phenotype and attenuated bleomycin-induced fibrotic lung remodeling. In support of these observations, Gab1/2 were involved in responses predominated by IL-4 signaling, an essential determinant for macrophage M2 polarization. Further investigation revealed that both Gab1 and -2 are recruited to the IL-4 receptor, synergistically enhancing downstream signal amplification but conferring IL-4 signal preference. Mechanistically, the loss of Gab1 attenuated AKT activation, whereas the absence of Gab2 suppressed STAT6 activation in response to IL-4 stimulation, both of which are commonly attributed to M2-driven pulmonary fibrosis in mice. Taken together, these observations define a non-redundant role of Gab docking proteins in M2 polarization, adding critical insights into the pathogenesis of idiopathic pulmonary fibrosis.

Retrospective analysis of tigecycline shows that it may be an option for children with severe infections.

AIM: This study assessed the efficacy and safety of tigecycline in children with life-threatening infections. METHODS: We retrospectively reviewed the clinical records of patients treated with tigecycline from June 2012 to May 2014 in a Chinese tertiary centre. RESULTS: The study comprised 24 patients (14 male) with a median age of four years (range, 50 days-12 years). The most frequently isolated microorganism, most common isolation site and type of infection were Acinetobacter baumannii, tracheal aspirate fluid and ventilator-associated pneumonia, respectively. Tigecycline was administered at a loading dose of 1.5 or 2.0 mg/kg and 1.0 mg/kg every 12 hours after that. The average duration of treatment was 11.6 ± 5.8 days. The clinical response and microbiological eradication rate were 37.5% and 29.2%, respectively. Six of the patients we studied (25.0%) died, and three of these deaths were considered to be infection related. Adverse drug reactions were identified in four patients (16.7%) during the treatment, including abnormal liver function, prolonged prothrombin time and diarrhoea. CONCLUSION: Our findings suggest that tigecycline may be an option for children with severe infections. However, more prospective, controlled trials are required to objectively evaluate the efficacy and safety of tigecycline in children.

CHEK2 knockout is a therapeutic target for TP53-mutated hepatocellular carcinoma.

Currently, there is still a lack of novel and effective drug targets to improve the prognosis of hepatocellular carcinoma (HCC). Additionally, the role of CHEK2 in HCC has not been reported yet. The eQTLgen database and two HCC Genome-Wide Association Study (GWAS) datasets (ieu-b-4953, ICD10 C22.0) were used to find the drug target: CHEK2. Next, Colony, Edu, ß-gal, and cell cycle analysis were facilitated to evaluate the role of CHEK2 knockout in HCC. In addition, Nultin-3 was added to evaluate the apoptosis of TP53-mutated HCC cells with CHEK2 knockout. Furthermore, MitoSox, electron microscopy, mitochondrial ATP, and NADH+/NADH levels were assessed in the CHEK2 knockout HCC cells with or without Metformin. Finally, cell-derived tumor xenograft was used to evaluate the role of CHEK2 knockout in vivo. We initially identified a potential drug target, CHEK2, through GWAS data analysis. Furthermore, we observed a significant upregulation of CHEK2 expression in HCC, which was found to be correlated with a poor prognosis. Subsequently, the results indicated that knocking out CHEK2 selectively affects the proliferation, cell cycle, senescence, and apoptosis of TP53-mutant HCC cells. Additionally, the introduction of Nultin-3 further intensified the functional impact on TP53-mutant cells. Then ClusterProfiler results showed high CHEK2 and TP53 mutation group was positively enriched in the mitochondrial ATP pathway. Then we used MitoSox, electron microscopy, mitochondrial ATP, and NADH + /NADH assay and found knockout of CHECK could induce the ATP pathway to inhibit the growth of HCC. Our research introduces a novel drug target for TP53-mutant HCC cells via mitochondrial ATP, addressing the limitation of Nultin-3 as a standalone treatment that does not induce tumor cell death.

Impact of pharmacist antimicrobial dosing adjustments in septic patients on continuous renal replacement therapy in an intensive care unit.

BACKGROUND: Correct dosing of antimicrobial drugs in septic patients receiving continuous renal replacement therapy (CRRT) is complex. This study aimed to evaluate the effects of dosing adjustments performed by pharmacists on the length of intensive care unit (ICU) stay, ICU cost, and antimicrobial adverse drug events (ADEs). METHODS: A single-center, 2-phase (pre-/post-intervention) study was performed in an ICU of a university-affiliated hospital. Septic patients receiving CRRT in the post-intervention phase received a specialized antimicrobial dosing service from critical care pharmacists, whereas patients in the pre-intervention phase received routine medical care without involving pharmacists. The 2 phases were compared to evaluate the outcomes of pharmacist interventions. RESULTS: Pharmacists made 183 antimicrobial dosing adjustment recommendations for septic patients receiving CRRT. Changes in CRRT-related variables (116, 63.4%) were the most common risk factors for dosing errors, and ß-lactams (101, 55.2%) were the antimicrobials most commonly associated with dosing errors. Dosing adjustments were related to a reduced length of ICU stay from 10.7 ± 11.1 days to 7.7 ± 8.3 days (p = 0.037) in the intervention group, and to cost savings of $3525 (13,463 ± 12,045 vs. 9938 ± 8811, p = 0.038) per septic patient receiving CRRT in the ICU. Suspected antimicrobial adverse drug events in the intervention group were significantly fewer than in the pre-intervention group (19 events vs. 8 events, p = 0.048). CONCLUSIONS: The involvement of pharmacists in antimicrobial dosing adjustments in septic patients receiving CRRT is associated with a reduced length of ICU stay, lower ICU costs, and fewer ADEs. Hospitals may consider employing clinical pharmacists in ICUs.

Multidimensional landscape of non-alcoholic fatty liver disease-related disease spectrum uncovered by big omics data: Profiling evidence and new perspectives.

Characterized by hepatic lipid accumulation, non-alcoholic fatty liver disease (NAFLD) is a multifactorial metabolic disorder that could promote the progression of non-alcoholic steatohepatitis (NASH), cirrhosis, and hepatocellular carcinoma (HCC). Benefiting from recent advances in omics technologies, such as high-throughput sequencing, voluminous profiling data in HCC-integrated molecular science into clinical medicine helped clinicians with rational guidance for treatments. In this review, we conclude the majority of publicly available omics data on the NAFLD-related disease spectrum and bring up new insights to inspire next-generation therapeutics against this increasingly prevalent disease spectrum in the post-genomic era.

Roles of N6-methyladenosine epitranscriptome in non-alcoholic fatty liver disease and hepatocellular carcinoma.

Non-alcoholic fatty liver disease (NAFLD) is a typical chronic liver disease connected to a high risk of developing hepatocellular carcinoma (HCC). The development of NAFLD and HCC has been associated with changes in epigenetics, such as histone modifications and micro RNA (miRNA)-mediated processes. Recently, in the realm of epitranscriptomics, RNA alterations have become important regulators. N6-methyladenosine (m6A) is the most common and crucial alteration for controlling mRNA stability, splicing, and translation. It is particularly important for controlling liver disease progression and hepatic function. This review aims to conclude recent research on the functions of m6A epitranscriptome in the molecular mechanisms behind NAFLD and HCC development, with special attention to the effects of m6A alteration on how HCC develops and its possible roles in the progression of NAFLD to HCC. Additionally, the review discusses the possible effects of m6A alteration on the treatment and diagnostic of NAFLD and HCC. It is crucial to remember that m6A modification is a reversible action controlled via the coordinated functions of the proteins that write and delete, enabling quick adaptability to environmental changes. The review also discusses m6A-binding proteins' function in mRNA alternative splicing, translation, and degradation and their ability to modulate mRNA stability and processing. Understanding RNA modification regulation and its part in the emergence of HCC and NAFLD may provide new avenues for diagnosing and treating these diseases.

Towards an integrated health risk assessment framework of soil heavy metals pollution: Theoretical basis, conceptual model, and perspectives.

The health risk of soil heavy metals pollution has been gaining increasing public concern. However, many countries have not set their own health risk assessment (HRA) framework and most of the existing studies directly referred to the USEPA risk assessment model and parameters. For those countries that do not propose an original HRA framework, the experience of developed countries is crucial for advancing their own HRA system. This study systematically reviewed the development of HRA framework in some representative developed countries. The theoretical basis, conceptual model, progress, and challenges of HRA researches concerning soil heavy metals pollution were summarized. By recalling and comparing the health risk-related laws and guidance in the USA, UK, and Japan, results showed that the construction of HRA framework varied between these countries, but HRA has become the main method for deriving their soil environmental criteria. We further summarized the evaluation scales, land use types, exposure pathways, and sensitive receptors of HRA studies, and highlighted the key parameters affecting health risk outputs. There has been a shift toward the incorporation of probabilistic modeling, metals bioavailability, and sources emission characteristics into recent HRA studies. Nonetheless, challenges remained on how to minimize the uncertainty of generating probability distribution and detecting metal bioavailability. To facilitate the development of HRA framework, it was advised that developing countries should strengthen the theoretical researches of health risk and localization researches of exposure factors. Future directions are suggested to tend to: 1) promote sensitive analysis to quantify the impact of distribution assumptions on health risk outputs, 2) derive reasonable risk threshold and consistent evaluation protocol for bioavailability-based health risk assessment method, and 3) strive to explore the combined health effect of exposure to heavy metals in soil through source-media-receptor integrated studies.

Aberrant acetylated modification of FGF21­KLB signaling contributes to hepatocellular carcinoma metastasis through the ß­catenin pathway.

ß­Klotho (KLB) is a vital element of the fibroblast growth factor (FGF) receptor complex and acts as a co­receptor to facilitate the binding of FGF19 and FGF21 to the FGFRs on the target cells. The present study aimed to determine the contribution of FGF21­KLB signaling to hepatocellular carcinoma (HCC) metastasis. KLB expression was measured in HCC tissues and cell lines using western blot and reverse transcription­quantitative PCR. Furthermore, the proliferation, apoptosis and metastasis capacity of KLB­knockdown Huh7 cells (human HCC cell line) were assessed by Cell Counting Kit­8 assay, 5­ethynyl­2'­deoxyuridine assay, flow cytometry, wound­healing assay and Transwell assay. Enrichment analysis was used to explore the underlying regulatory mechanisms of KLB. The metastasis potential of human HCC cells in the context of FGF21 with or without KLB inhibition was determined in vitro and in vivo. Acetylated modification of KLB was determined using a co­immunoprecipitation assay. The results indicated a significant upregulation of KLB in HCC tissues compared with the corresponding normal tissues. In addition, KLB expression was closely associated with HCC metastasis. Migration and invasion assays revealed that KLB knockdown promoted the metastatic capability of HCC cells. Gene set variation analysis and subsequent mechanistic investigations revealed that KLB is the upstream regulatory factor of ß­catenin signaling. Furthermore, FGF21 was indicated to suppress HCC metastasis by inhibiting ß­catenin signaling­driven epithelial­mesenchymal transition (EMT), while KLB knockdown and simultaneous FGF21 overexpression promoted HCC cell motility. Histone deacetylase 3 (HDAC3) was further characterized as the potential deacetylase for KLB. Furthermore, the results revealed that HDAC3 inhibitor­mediated acetylated modification led to KLB inactivation, resulting in the blockade of FGF21­KLB signaling, which further triggered the expression of EMT induction­related genes in Huh7 cells. In conclusion, the present study demonstrated that aberrant acetylated modification of KLB inhibited FGF21­KLB signaling, thereby promoting ß­catenin signaling­driven EMT and HCC metastasis.

Mitochondria-Associated Endoplasmic Reticulum Membrane (MAM) Is a Promising Signature to Predict Prognosis and Therapies for Hepatocellular Carcinoma (HCC).

BACKGROUND: The roles of mitochondria and the endoplasmic reticulum (ER) in the progression of hepatocellular carcinoma (HCC) are well established. However, a special domain that regulates the close contact between the ER and mitochondria, known as the mitochondria-associated endoplasmic reticulum membrane (MAM), has not yet been investigated in detail in HCC. METHODS: The TCGA-LIHC dataset was only used as a training set. In addition, the ICGC and several GEO datasets were used for validation. Consensus clustering was applied to test the prognostic value of the MAM-associated genes. Then, the MAM score was constructed using the lasso algorithm. In addition, uncertainty of clustering in single-cell RNA-seq data using a gene co-expression network (AUCell) was used for the detection of the MAM scores in various cell types. Then, CellChat analysis was applied for comparing the interaction strength between the different MAM score groups. Further, the tumor microenvironment score (TME score) was calculated to compare the prognostic values, the correlation with the other HCC subtypes, tumor immune infiltration landscape, genomic mutations, and copy number variations (CNV) of different subgroups. Finally, the response to immune therapy and sensitivity to chemotherapy were also determined. RESULTS: First, it was observed that the MAM-associated genes could differentiate the survival rates of HCC. Then, the MAM score was constructed and validated using the TCGA and ICGC datasets, respectively. The AUCell analysis indicated that the MAM score was higher in the malignant cells. In addition, enrichment analysis demonstrated that malignant cells with a high MAM score were positively correlated with energy metabolism pathways. Furthermore, the CellChat analysis indicated that the interaction strength was reinforced between the high-MAM-score malignant cells and T cells. Finally, the TME score was constructed, which demonstrated that the HCC patients with high MAM scores/low TME scores tend to have a worse prognosis and high frequency of genomic mutations, while those with low MAM scores/high TME scores were more likely to have a better response to immune therapy. CONCLUSIONS: MAM score is a promising index for determining the need for chemotherapy, which reflects the energy metabolic pathways. A combination of the MAM score and TME score could be a better indicator to predict prognosis and response to immune therapy.

A prospective health risks analysis of regulatory limits for heavy metals in rice from representative organizations and countries worldwide: Are they protective?

Heavy metals contamination in rice has been one of the most public concerns globally; thus, many countries and organizations issued the maximum acceptable limits (MALs) of their concentrations in rice to regulate food safety and health risks. However, the applicability of these MALs has rarely been thoroughly evaluated. This study collected the MALs of heavy metals for rice from representative countries and organizations around the world. We assessed the critical health risks in the case of metal concentrations that reached the MALs for the first time. Results showed great variability of rice regulation limits owing to different processing methods (paddy, polished, and brown rice) and metal types (mainly focusing on inorganic As, Cd, and Pb). Risk analysis revealed that the inorganic As limits and part of Cd limits for polished rice generated relatively high health risks, indicating that their risks may be underestimated. Monte Carlo simulation further showed that the daily intake rate of rice (IRrice) is the largest contributor to total variances for the derivation of MALs, and regulation limits decreased with the augment of IRrice. Overall, we suggest a cautious reduction in the allowable limits of certain metals (such as inorganic As and part of Cd) in rice as their health risks and toxicity may be underestimated.

FOXO1 regulates Th17 cell-mediated hepatocellular carcinoma recurrence after hepatic ischemia-reperfusion injury.

BACKGROUND: Hepatic ischemia-reperfusion injury (IRI) is considered as an effecting factor for hepatocellular carcinoma (HCC) recurrence. Th17/Treg cells are a pair of essential components in adaptive immune response in liver IRI, and forkhead box O1 (FOXO1) has the properties of maintaining the function and phenotype of immune cells. Herein, we illuminated the correlation and function between Th17/Treg cell balance and FOXO1 in IRI-induced HCC recurrence. METHODS: RNA sequencing was performed on naive CD4+ T cells from normal and IRI model mice to identify relevant transcription factors. Western blotting, qRT-PCR, immunohistochemical staining, and flow cytometry were performed in IRI models to indicate the effect of FOXO1 on the polarization of Th17/Treg cells. Then, transwell assay of HCC cell migration and invasion, clone formation, wound healing assay, and Th17 cells adoptively transfer was utilized to assess the function of Th17 cells in IRI-induced HCC recurrence in vitro and in vivo. RESULTS: Owning to the application of RNA sequencing, FOXO1 was screened and assumed to perform a significant function in hepatic IRI. The IRI model demonstrated that up-regulation of FOXO1 alleviated IR stress by attenuating inflammatory stress, maintaining microenvironment homeostasis, and reducing the polarization of Th17 cells. Mechanistically, Th17 cells accelerated IRI-induced HCC recurrence by shaping the hepatic pre-metastasis microenvironment, activating the EMT program, promoting cancer stemness and angiogenesis, while the upregulation of FOXO1 can stabilize the liver microenvironment homeostasis and alleviate the negative effects of Th17 cells. Moreover, the adoptive transfer of Th17 cells in vivo revealed its inducing function in IRI-induced HCC recurrence. CONCLUSIONS: These results indicated that FOXO1-Th17/Treg axis exerts a crucial role in IRI-mediated immunologic derangement and HCC recurrence, which could be a promising target for reducing the HCC recurrence after hepatectomy. Liver IRI affects the balance of Th17/Treg cells by inhibiting the expression of FOXO1, and the increase of Th17 cells has the ability to induce HCC recurrence through EMT program, cancer stemness pathway, the formation of premetastatic microenvironment and angiogenesis.

TP53 mutation-related senescence is an indicator of hepatocellular carcinoma patient outcomes from multiomics profiles.

TP53 mutation frequently occurs in hepatocellular carcinoma (HCC). Senescence also plays a vital role in the ongoing process of HCC. P53 is believed to regulate the advancement of senescence in HCC. However, the exact mechanism of TP53 mutation-related senescence remains unclear. In this study, we found the TP53 mutation was positively correlated with senescence in HCC, and the differential expressed genes were primarily located in macrophages. Our results proved that the risk score could have an independent and vital role in predicting the prognosis of HCC patients. In addition, HCC patients with a high risk score may most probably benefit from immune checkpoint block therapy. We also found the risk score is elevated in chemotherapy-treated HCC samples, with a high level of senescence-associated secretory phenotype. Finally, we validated the risk-score genes in the protein level and noticed the risk score is positively related with M2 polarization. Of note, we considered that the risk score under the TP53 mutation and senescence is a promising biomarker with the potential to aid in predicting prognosis, defining tumor environment characteristics, and assessing the benefits of immunotherapy for HCC patients.