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.

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.

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.

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.

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.

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.

The rectal mucosal immune environment and HIV susceptibility among young men who have sex with men.

Young men who have sex with men (YMSM) represent a particularly high-risk group for HIV acquisition in the US, despite similarly reported rates of sexual activity as older, adult MSM (AMSM). Increased rates of HIV infection among YMSM compared to AMSM could be partially attributable to differences within the rectal mucosal (RM) immune environment associated with earlier sexual debut and less lifetime exposure to receptive anal intercourse. Using an ex vivo explant HIV challenge model, we found that rectal tissues from YMSM supported higher levels of p24 at peak viral replication timepoints compared to AMSM. Among YMSM, the RM was characterized by increased CD4+ T cell proliferation, as well as lower frequencies of tissue resident CD8+ T cells and pro-inflammatory cytokine producing CD4+ and CD8+ T cells. In addition, the microbiome composition of YMSM was enriched for anaerobic taxa that have previously been associated with HIV acquisition risk, including Prevotella, Peptostreptococcus, and Peptoniphilus. These distinct immunologic and microbiome characteristics were found to be associated with higher HIV replication following ex vivo challenge of rectal explants, suggesting the RM microenvironment of YMSM may be uniquely conducive to HIV infection.

Effects of fertilizer application on phthalate ester pollution and the soil microbial community in plastic-shed soil on long-term fertilizer experiment.

Due to the use of agricultural film, the pollution of phthalate esters (PAEs) in plastic-shed soils has attracted increasing attention. In this study, we used watermelon as a planting system and investigated the effects of organic fertilizer and chemical fertilizer application on the degradation of PAEs by evaluating soil nutrients and soil bacterial communities in plastic-shed soil. The dibutyl phthalate (DBP) concentration in the organic fertilizer soil was only 58.2% in the zero-fertilization control (CK) soil, but the concentrations of monohexyl phthalate (MEHP) and mono-n-butyl ester (MBP), the metabolites of PAEs, were found to be higher. The concentration of MBP is ten times that of DBP. The results showed that fertilization, especially the application of organic fertilizers, had a significant effect on the degradation of PAEs. There were specific biomarkers in different fertilization treatments. Among the microbiome community, Planifilum had the highest relative abundance in the organic fertilizer (OF) soil, and the highest proportion of Thermodesulfovibrionia was detected in the chemical fertilizer (CF) soil. These biomarkers were significantly correlated with PAEs and their metabolites. The relative abundance of Thermomonosporaceae was significantly positively correlated with DBP. Planifilum and Thermaerobacter, which significantly increased in organic fertilizer soil, showed a significant negative correlation with DBP and a significant positive correlation with MBP. The relative abundances of Planifilum and Geobacillus were elevated in the OF soil and may be able to co-metabolize soil nitrogen and PAEs. PAEs and their metabolites in soils had significant effects on soil microbes, as did the soil nutrients including available phosphorus (AP), alkali-hydrolysable nitrogen (Alkali-N), and organic matter (OM). Our research provides scientific support for the use of fertilizers to reduce PAE contamination but also warns of the potential risks of PAE metabolites.

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.

Expert consensus statement on therapeutic drug monitoring and individualization of linezolid.

Linezolid is an oxazolidinone antibacterial drug, and its therapeutic drug monitoring and individualized treatment have been challenged since its approval. With the in-depth clinical research of linezolid, we have changed our attitude toward its therapeutic drug monitoring and our view of individualized treatment. On the basis of summarizing the existing clinical studies, and based on the practical experience of each expert in their respective professional fields, we have formed this expert consensus. Our team of specialists is a multidisciplinary team that includes pharmacotherapists, clinical pharmacology specialists, critical care medicine specialists, respiratory specialists, infectious disease specialists, emergency medicine specialists and more. We are committed to the safe and effective use of linezolid in patients in need, and the promotion of its therapeutic drug monitoring.

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.

Condomless receptive anal intercourse is associated with markers of mucosal inflammation in a cohort of men who have sex with men in Atlanta, Georgia.

INTRODUCTION: We previously showed that the rectal mucosal immune environment among men who have sex with men (MSM) engaging in condomless receptive anal intercourse (CRAI) is immunologically distinct from that of men who do not engage in anal intercourse (AI). Here, we further examined these differences with quantitative immunohistochemistry to better understand the geographic distribution of immune markers of interest. METHODS: We enrolled a cohort of MSM engaging in CRAI (n = 41) and men who do not engage in AI (n = 21) between October 2013 and April 2015. Participants were healthy, HIV-negative men aged 18-45 from the metro Atlanta area. We performed rectal mucosal sampling via rigid sigmoidoscopy during two study visits separated by a median of nine weeks and timed with sexual activity for MSM engaging in CRAI. We used standardized, automated immunohistochemistry and quantitative image analysis to investigate the rectal mucosal distribution of neutrophils (MPO), IL-17-producing cells (IL-17) and Tregs (FOXP3) in the lamina propria, and cellular proliferation (Ki67) and adherens junction protein (E-cadherin) in the epithelium. We examined associations between biomarker expression and the rectal mucosal microbiota composition by 16s rRNA sequencing. RESULTS: Relative to the colonic crypt base, IL-17, FOXP3, and MPO expression increased towards the rectal lumen, while Ki67 decreased and E-cadherin was more uniformly distributed. Throughout the rectal mucosa distribution examined, MSM engaging in CRAI had higher mean lamina propria MPO expression (p = 0.04) and epithelial Ki67 (p = 0.04) compared to controls. There were no significant differences in IL-17, FOXP3 or E-cadherin expression. We found no significant associations of the five biomarkers with the global rectal microbiota composition or the individual taxa examined. CONCLUSIONS: Understanding the mucosal distribution of inflammatory mediators can enhance our knowledge of the earliest events in HIV transmission. Neutrophil enrichment and crypt epithelial cell proliferation likely represent sub-clinical inflammation in response to CRAI in the rectal mucosa of MSM, which could increase the risk for HIV acquisition. However, the contributory role of the microbiota in mucosal inflammation among MSM remains unclear. HIV prevention may be enhanced by interventions that reduce inflammation or capitalize on the presence of specific inflammatory mechanisms during HIV exposure.

An E2F5-TFDP1-BRG1 Complex Mediates Transcriptional Activation of MYCN in Hepatocytes.

Liver regeneration is characterized by cell cycle reentrance of hepatocytes. N-Myc, encoded by MYCN, is a member of the Myc family of transcription factors. Elevation of MYCN expression has been noted in the course of liver regeneration whereas the underlying mechanism remains unclear. Here we describe that up-regulation of MYCN expression, as measured by quantitative PCR, Western blotting, and immunohistochemical staining, paralleled liver regeneration in animal and cell models. MYCN expression was up-regulated as a result of transcriptional activation. Ingenuity pathway analysis (IPA) revealed several up-stream transcriptional regulators for MYCN and RNA interference validated E2F5 and TFDP1 as essential for hepatocyte growth factor (HGF)-induced MYCN trans-activation. Further examination showed that deficiency of BRG1, a chromatin remodeling protein, attenuated MYCN induction during liver regeneration. BRG1 interacted with and was recruited by E2F5/TFDP1 to the MYCN promoter. Mechanistically, BRG1 might play a role regulating histone H3 acetylation and H3K4 trimethylation and facilitating/stabilizing the binding of RNA polymerase II surrounding the MYCN promoter. Over-expression of ectopic MYCN in BRG1-null hepatocytes overcame deficiency of proliferation. Importantly, a positive correlation between MYCN expression and BRG1/E2F5/TFDP1 expression was observed in human liver specimens. In conclusion, our data identify a novel epigenetic pathway where an E2F5-TFDP1-BRG1 complex regulates MYCN transcription to promote liver regeneration.

Down-Regulation of CXXC5 De-Represses MYCL1 to Promote Hepatic Stellate Cell Activation.

Liver fibrosis is mediated by myofibroblasts, a specialized cell type involved in wound healing and extracellular matrix production. Hepatic stellate cells (HSC) are the major source of myofibroblasts in the fibrotic livers. In the present study we investigated the involvement of CXXC-type zinc-finger protein 5 (CXXC5) in HSC activation and the underlying mechanism. Down-regulation of CXXC5 was observed in activated HSCs compared to quiescent HSCs both in vivo and in vitro. In accordance, over-expression of CXXC5 suppressed HSC activation. RNA-seq analysis revealed that CXXC5 influenced multiple signaling pathways to regulate HSC activation. The proto-oncogene MYCL1 was identified as a novel target for CXXC5. CXXC5 bound to the proximal MYCL1 promoter to repress MYCL1 transcription in quiescent HSCs. Loss of CXXC5 expression during HSC activation led to the removal of CpG methylation and acquisition of acetylated histone H3K9/H3K27 on the MYCL1 promoter resulting in MYCL1 trans-activation. Finally, MYCL1 knockdown attenuated HSC activation whereas MYCL1 over-expression partially relieved the blockade of HSC activation by CXXC5. In conclusion, our data unveil a novel transcriptional mechanism contributing to HSC activation and liver fibrosis.

Enhancing the thermoelectric properties of SnTe via introducing PbTe@C core-shell nanostructures.

SnTe is an emerging IV-VI metal chalcogenide, but its low Seebeck coefficient and high thermal conductivity mainly originating from the high hole concentration limit its thermoelectric performance. In this work, an amorphous carbon core-shell-coated PbTe nanostructure prepared by a "bottom-up" method is first incorporated into the Sn1-ySbyTe matrix to enhance the thermoelectric performance of SnTe. The square-like PbTe nanoparticles maintain their original cubic morphology and do not grow up obviously after the SPS process due to the coating of the C layer, bringing about the formation of nanopores locally, while Sb alloying induces Sb point defects and Sb-rich precipitates. All these unique hierarchical microstructures finally lead to an ultralow lattice thermal conductivity (∼0.48 W-1 m-1 K-1) approaching amorphous limits (∼0.40 W-1 m-1 K-1). In addition, the incorporation of PbTe@C core-shell nanostructures decreases the carrier mobility obviously with a slight loss in carrier concentration, resulting in the deterioration of electrical properties to a certain extent. As a result, a peak thermoelectric figure of merit (ZT) of 1.07 is achieved for Sn0.89Sb0.11Te-5%PbTe@C at 873 K, which is approximately 154.76% higher than that of pristine SnTe. This work provides a new strategy to enhance the thermoelectric performance of SnTe and also offers a new insight into other related thermoelectric systems.

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.

Constraining PERMANOVA and LDM to within-set comparisons by projection improves the efficiency of analyses of matched sets of microbiome data.

BACKGROUND: Matched-set data arise frequently in microbiome studies. For example, we may collect pre- and post-treatment samples from a set of individuals, or use important confounding variables to match data from case participants to one or more control participants. Thus, there is a need for statistical methods for data comprised of matched sets, to test hypotheses against traits of interest (e.g., clinical outcomes or environmental factors) at the community level and/or the operational taxonomic unit (OTU) level. Optimally, these methods should accommodate complex data such as those with unequal sample sizes across sets, confounders varying within sets, and continuous traits of interest. METHODS: PERMANOVA is a commonly used distance-based method for testing hypotheses at the community level. We have also developed the linear decomposition model (LDM) that unifies the community-level and OTU-level tests into one framework. Here we present a new strategy that can be used with both PERMANOVA and the LDM for analyzing matched-set data. We propose to include an indicator variable for each set as covariates, so as to constrain comparisons between samples within a set, and also permute traits within each set, which can account for exchangeable sample correlations. The flexible nature of PERMANOVA and the LDM allows discrete or continuous traits or interactions to be tested, within-set confounders to be adjusted, and unbalanced data to be fully exploited. RESULTS: Our simulations indicate that our proposed strategy outperformed alternative strategies, including the commonly used one that utilizes restricted permutation only, in a wide range of scenarios. Using simulation, we also explored optimal designs for matched-set studies. The flexibility of PERMANOVA and the LDM for a variety of matched-set microbiome data is illustrated by the analysis of data from two real studies. CONCLUSIONS: Including set indicator variables and permuting within sets when analyzing matched-set data with PERMANOVA or the LDM is a strategy that performs well and is capable of handling the complex data structures that frequently occur in microbiome studies. Video Abstract.

Inhibition of HMGB1 Suppresses Hepatocellular Carcinoma Progression via HIPK2-Mediated Autophagic Degradation of ZEB1.

Autophagy is a conserved catabolic process maintaining cellular homeostasis and reportedly plays a critical role in tumor progression. Accumulating data show that autophagic activity is inhibited in hepatocellular carcinoma. However, the underlying molecular basis of impaired autophagy in HCC remains unclear. In this study, we revealed that autophagic activity was suppressed by HMGB1 in a HIPK2-dependent way. Targeting HMGB1 could inhibit the degradation of HIPK2, as a result of which, autophagic degradation of ZEB1 was enhanced by reprogramming glucose metabolism/AMPK/mTOR axis. Moreover, we demonstrated that selectively degradation of ZEB1 was responsible for HCC growth inhibition in HMGB1 deficient cells. Lastly, we found the combination therapy of HMGB1 inhibitor and rapamycin achieved a better anti-HCC effect. These results demonstrate that impaired autophagy is controlled by HMGB1 and targeting HMGB1 could suppress HCC progression via HIPK2-mediated autophagic degradation of ZEB1.

Elevated HMGB1 expression induced by hepatitis B virus X protein promotes epithelial-mesenchymal transition and angiogenesis through STAT3/miR-34a/NF-κB in primary liver cancer.

HBV infection plays a crucial role in primary liver cancer development. Also, HBV related liver cancer has higher invasiveness and earlier discovered distant metastasis. HBV-encoded X protein (HBx) exerts various biological functions on liver cancer progression, including proliferation, invasion, and venous metastasis. There is evidence that High-mobility group box 1 (HMGB1) promotes epithelial-mesenchymal transition (EMT) and angiogenesis of tumors, including liver cancer. Therefore, this study investigates whether HMGB1 mediates HBx-induced EMT and angiogenesis in HBV related liver cancer. We collected 76 tumor samples of primary liver cancer patients to analyze the relationship between HMGB1 and portal vein tumor thrombus (PVTT) in HBV related liver cancer. To test the influence of HMGB1 on EMT and angiogenesis, we constructed HBx lentivirus transfected HepG2/Huh7 cell lines and performed invasion assays, tube formation and in vivo metastatic experiments. We evaluated HMGB1 and STAT3/miR-34a/NF-κB pathway in vivo and in vitro by immunoblot, quantitative real-time polymerase chain reaction (qRT-PCR), immunofluorescence and immunohistochemistry analysis. Subsequent RNA interference (RNAi) and luciferase reporter assay were conducted to detect the functional correlation between HMGB1 and STAT3/miR-34a/NF-κB pathway. Our results showed enhanced expression of HMGB1 in HBV related liver cancer, especially with PVTT, while HMGB1 expression was associated with tumor invasion and metastasis. Further experiments indicated that the activation of STAT3 mediated HBx-induced HMGB1, which is involved in EMT and tumor angiogenesis. Besides, HMGB1 expression stimulated by HBx was dependent on the activation of the NF-κB signaling pathway, which was inhibited by miR-34a, while STAT3 suppressed the expression of miR-34a. Moreover, extracellular HMGB1 induced the IL-6/STAT3/miR-34a axis activation, which indicated a reciprocal relationship between HMGB1 and miR-34a. Collectively, our study provided evidence to reveal that HBx-mediated high expression of HMGB1 accounted for EMT and tumor angiogenesis in HBV related liver cancer, and HMGB1 may be a potential target for predicting venous metastasis.