Thyroid cancer prognostic biomarker ARL4A and its relationship with immune infiltration.

BACKGROUND: Thyroid cancer (THCA) is a prevalent form of cancer with high rates of morbidity and mortality. The small GTPase ADP-ribosylation factor-like 4A (ARL4A) is integral to various cellular processes, including cytoskeletal restructuring, vesicular transport, cell migration, and neuronal development. However, the role of ARL4A as a clinical predictor, particularly its relation to immune cell infiltration in THCA, remains unclear. METHODS: A combination of experimental studies and analysis of online databases was employed to investigate ARL4A expression in THCA. Clinical and pathological data from THCA patients were compiled for a comprehensive subgroup analysis. The Kaplan-Meier and Cox regression methods were utilized to evaluate the prognostic significance of ARL4A in THCA patients. Finally, the "Cancer Genome Atlas" was analyzed to explore the correlation between immune cell infiltration, ARL4A expression, and their joint impact on prognosis. RESULTS: ARL4A exhibited low expression in THCA. An elevated ARL4A was associated with poor prognosis. Moreover, the expression of ARL4A was correlated with the age, gender, and pathological stage of THCA patients. Finally, ARL4A expression was found to be negatively correlated with immune cell infiltration and influenced the prognosis of patients through changes in the immune environment. CONCLUSION: ARL4A may serve as a potential biomarker for the diagnosis and treatment of THCA, impacting the prognosis of patients through the modulation of the immune microenvironment.

GPNMB+ Gal-3+ hepatic parenchymal cells promote immunosuppression and hepatocellular carcinogenesis.

Hepatocellular carcinoma (HCC) formation is a multi-step pathological process that involves evolution of a heterogeneous immunosuppressive tumor microenvironment. However, the specific cell populations involved and their origins and contribution to HCC development remain largely unknown. Here, comprehensive single-cell transcriptome sequencing was applied to profile rat models of toxin-induced liver tumorigenesis and HCC patients. Specifically, we identified three populations of hepatic parenchymal cells emerging during HCC progression, termed metabolic hepatocytes (HCMeta ), Epcam+ population with differentiation potential (EP+Diff ) and immunosuppressive malignant transformation subset (MTImmu ). These distinct subpopulations form an oncogenic trajectory depicting a dynamic landscape of hepatocarcinogenesis, with signature genes reflecting the transition from EP+Diff to MTImmu . Importantly, GPNMB+ Gal-3+ MTImmu cells exhibit both malignant and immunosuppressive properties. Moreover, SOX18 is required for the generation and malignant transformation of GPNMB+ Gal-3+ MTImmu cells. Enrichment of the GPNMB+ Gal-3+ MTImmu subset was found to be associated with poor prognosis and a higher rate of recurrence in patients. Collectively, we unraveled the single-cell HCC progression atlas and uncovered GPNMB+ Gal-3+ parenchymal cells as a major subset contributing to the immunosuppressive microenvironment thus malignance in HCC.

In Situ Hydrogel Polymerization to Form a Flexible Polysaccharide Synergetic Binder Network for Stabilizing SiOx/C Anodes.

Today, the commercial application of silicon oxides (SiOx, 1 < x < 2) in lithium-ion batteries (LIBs) still faces the challenge of rapid performance degradation. In this work, by integrating hydrothermal and physicomechanical processes, water-soluble locust bean gum (LBG) and xanthan gum (XG) are utilized to in situ form an LBG@XG binder network to improve the performance of SiOx/C anodes. As a synergy of LBG and XG polysaccharides in hydrogel polymerization, LBG@XG can tightly wrap around SiOx/C particles to prevent plate damage. The flexible SiOx/C anode with the LBG@XG binder exhibits capacity retentions of 74.1% and 76.4% after 1000 cycles at 0.5 A g-1 and 1 A g-1, respectively. The full battery capacity remains stable for 100 cycles at 1 C and the rate performance is excellent (103 mAh g-1 at 3 C). This LBG@XG is demonstrated to be highly electronegative and has a strong attraction to SiOx/C particles, thereby reducing the expansion and increasing the stability of the SiOx/C anodes when coupled with the flexible binder network. In addition to the promising LBG@XG binder, this work also provides a research idea for developing green water-based binders suitable for application in the SiOx/C anodes of LIBs.

LAPTM4B-YAP loop feedback amplification enhances the stemness of hepatocellular carcinoma.

Hepatocellular carcinoma (HCC) is highly heterogeneous, and stemness signatures are frequently elevated in HCC tumor cells to generate heterogeneous subtypes via multidirectional differentiation. However, the mechanisms affecting the regulation of stemness in HCC remain unclear. In this study, we identified that lysosome-associated protein transmembrane-4ß (LAPTM4B) was significantly overexpressed in stem-like tumor cell populations with multidirectional differentiation potential at the single cell level, and verified that LAPTM4B was closely related to stemness of HCC using in vitro and in vivo experiments. Mechanistically, elevated LAPTM4B suppresses Yes-associated protein (YAP) phosphorylation and ubiquitination degradation. In turn, stabilized YAP localizes to the nucleus and binds to cAMP responsive element binding protein-1 (CREB1), which promotes transcription of LAPTM4B. Overall, our findings suggest that LAPTM4B forms a positive feedback loop with YAP, which maintains the stemness of HCC tumor cells and leads to an unfavorable prognosis for HCC patients.

Sulfur metabolism in subtropical marine mangrove sediments fundamentally differs from other habitats as revealed by SMDB.

Shotgun metagenome sequencing provides the opportunity to recover underexplored rare populations and identify difficult-to-elucidate biochemical pathways. However, information on sulfur genes, including their sequences, is scattered in public databases. Here, we introduce SMDB ( https://smdb.gxu.edu.cn/ )-a manually curated database of sulfur genes based on an in-depth review of the scientific literature and orthology database. The SMDB contained a total of 175 genes and covered 11 sulfur metabolism processes with 395,737 representative sequences affiliated with 110 phyla and 2340 genera of bacteria/archaea. The SMDB was applied to characterize the sulfur cycle from five habitats and compared the microbial diversity of mangrove sediments with that of other habitats. The structure and composition of microorganism communities and sulfur genes were significantly different among the five habitats. Our results show that microorganism alpha diversity in mangrove sediments was significantly higher than in other habitats. Genes involved in dissimilatory sulfate reduction were abundant in subtropical marine mangroves and deep-sea sediments. The neutral community model results showed that microbial dispersal was higher in the marine mangrove ecosystem than in others habitats. The Flavilitoribacter of sulfur-metabolizing microorganism becomes a reliable biomarker in the five habitats. SMDB will assist researchers to analyze genes of sulfur cycle from the metagenomic efficiently.

The advanced lung cancer inflammation index predicts chemotherapy response and infection risk in multiple myeloma patients receiving induction chemotherapy.

Objective: This study aims to determine the clinical significance of the advanced lung cancer inflammation index (ALI) in predicting prognosis, chemotherapy response, and infection risk in newly diagnosed multiple myeloma (MM) patients receiving induction therapy. Methods: A retrospective analysis of the clinical characteristics and laboratory data of 111 newly diagnosed MM patients from the Haematology Department of the Third Xiangya Hospital of Central South University from January 2014 to March 2020 was performed. We first determined the relationship between ALI and overall survival (OS), as well as clinical and laboratory parameters. Second, predictive factors for chemotherapy response were analysed by univariate and multivariate regression analyses. Third, univariate regression analysis of risk factors was performed using infection as the evaluable outcome. Results: Of the 111 evaluable patients, the low ALI group (<32.7) exhibited significantly poorer survival than the high ALI group (51 months versus 77 months). Multivariable analysis showed that advanced age, chemotherapy response and serum calcium level were independent prognostic factors for OS. Better chemotherapy efficacy in the high ALI group (89.3%) than in the low ALI group (42.2%) (p < 0.001) was noted. Multivariate analysis suggested that only ALI [HR: 0.110, 95% CI (0.035-0.350), p = 0.000] is an independent predictive factor in evaluating the efficiency of induction chemotherapy. Forty patients (36.04%) presented with infection after induction chemotherapy. Univariate analysis suggested that low ALI and abnormal renal function increase risk of infection in newly diagnosed MM patients. Conclusion: Our study confirmed that ALI is not only a prognostic biomarker for newly diagnosed patients, but also predicts chemotherapy efficacy in newly diagnosed MM patients receiving induction therapy.

MicrobioSee: A Web-Based Visualization Toolkit for Multi-Omics of Microbiology.

With the upgrade and development of the high-throughput sequencing technology, multi-omics data can be obtained at a low cost. However, mapping tools that existed for microbial multi-omics data analysis cannot satisfy the needs of data description and result in high learning costs, complex dependencies, and high fees for researchers in experimental biology fields. Therefore, developing a toolkit for multi-omics data is essential for microbiologists to save effort. In this work, we developed MicrobioSee, a real-time interactive visualization tool based on web technologies, which could visualize microbial multi-omics data. It includes 17 modules surrounding the major omics data of microorganisms such as the transcriptome, metagenome, and proteome. With MicrobioSee, methods for plotting are simplified in multi-omics studies, such as visualization of diversity, ROC, and enrichment pathways for DEGs. Subsequently, three case studies were chosen to represent the functional application of MicrobioSee. Overall, we provided a concise toolkit along with user-friendly, time-saving, cross-platform, and source-opening for researchers, especially microbiologists without coding experience. MicrobioSee is freely available at https://microbiosee.gxu.edu.cn.

Single cell transcriptional diversity and intercellular crosstalk of human liver cancer.

Liver cancer arises from the evolutionary selection of the dynamic tumor microenvironment (TME), in which the tumor cell generally becomes more heterogeneous; however, the mechanisms of TME-mediated transcriptional diversity of liver cancer remain unclear. Here, we assess transcriptional diversity in 15 liver cancer patients by single-cell transcriptome analysis and observe transcriptional diversity of tumor cells is associated with stemness in liver cancer patients. Tumor-associated fibroblast (TAF), as a potential driving force behind the heterogeneity in tumor cells within and between tumors, was predicted to interact with high heterogeneous tumor cells via COL1A1-ITGA2. Moreover, COL1A1-mediated YAP-signaling activation might be the mechanistic link between TAF and tumor cells with increased transcriptional diversity. Strikingly, the levels of COL1A1, ITGA2, and YAP are associated with morphological heterogeneity and poor overall survival of liver cancer patients. Beyond providing a potential mechanistic link between the TME and heterogeneous tumor cells, this study establishes that collagen-stimulated YAP activation is associates with transcriptional diversity in tumor cells by upregulating stemness, providing a theoretical basis for individualized treatment targets.

GEP-EpiSeeker: a gene expression programming-based method for epistatic interaction detection in genome-wide association studies.

BACKGROUND: Identification of epistatic interactions provides a systematic way for exploring associations among different single nucleotide polymorphism (SNP) and complex diseases. Although considerable progress has been made in epistasis detection, efficiently and accurately identifying epistatic interactions remains a challenge due to the intensive growth of measuring SNP combinations. RESULTS: In this work, we formulate the detection of epistatic interactions by a combinational optimization problem, and propose a novel evolutionary-based framework, called GEP-EpiSeeker, to detect epistatic interactions using Gene Expression Programming. In GEP-EpiSeeker, we propose several tailor-made chromosome rules to describe SNP combinations, and incorporate Bayesian network-based fitness evaluation into the evolution of tailor-made chromosomes to find suspected SNP combinations, and adopt the Chi-square test to identify optimal solutions from suspected SNP combinations. Moreover, to improve the convergence and accuracy of the algorithm, we design two genetic operators with multiple and adjacent mutations and an adaptive genetic manipulation method with fuzzy control to efficiently manipulate the evolution of tailor-made chromosomes. We compared GEP-EpiSeeker with state-of-the-art methods including BEAM, BOOST, AntEpiSeeker, MACOED, and EACO in terms of power, recall, precision and F1-score on the GWAS datasets of 12 DME disease models and 10 DNME disease models. Our experimental results show that GEP-EpiSeeker outperforms comparative methods. CONCLUSIONS: Here we presented a novel method named GEP-EpiSeeker, based on the Gene Expression Programming algorithm, to identify epistatic interactions in Genome-wide Association Studies. The results indicate that GEP-EpiSeeker could be a promising alternative to the existing methods in epistasis detection and will provide a new way for accurately identifying epistasis.

Remote ischemic post­conditioning alleviates ischemia/reperfusion­induced intestinal injury via the ERK signaling pathway­mediated RAGE/HMGB axis.

Intestinal ischemia reperfusion (I/R) injury is a tissue and organ injury that frequently occurs during surgery and significantly contributes to the pathological processes of severe infection, injury, shock, cardiopulmonary insufficiency and other diseases. However, the mechanism of intestinal I/R injury remains to be elucidated. A mouse model of intestinal I/R injury was successfully established and the model mice were treated with remote ischemic post­conditioning (RIPOC) and/or an ERK inhibitor (CC­90003), respectively. Histopathological changes of the intestinal mucosa were determined by hematoxylin and eosin staining. In addition, the levels of high­mobility group box 1 (HMGB1) and receptor for advanced glycation end products (RAGE) expression were confirmed by reverse transcription­quantitative polymerase chain reaction, western blotting and immunohistochemistry assays. The levels of antioxidants, oxidative stress markers (8­OHdG) and interleukin 1 family members were evaluated by ELISA assays and the levels of NF­κB pathway proteins were analyzed by western blotting. The data demonstrated that RIPOC could attenuate the histopathological features of intestinal mucosa in the intestinal I/R­injury mouse models via the ERK pathway. It was also revealed that HMGB1 and RAGE expression in the mouse models could be markedly reduced by RIPOC (P<0.05) and that these reductions were associated with inhibition of the ERK pathway. Furthermore, it was demonstrated that RIPOC produced significant antioxidant and anti­inflammatory effects following an intestinal I/R injury and that these effects were mediated via the ERK pathway (P<0.05). In addition, RIPOC was demonstrated to suppress the NF­κB (p65)/NLR family pyrin domain containing 3 (NLRP3) inflammatory pathways in the intestinal I/R injury mouse models via the ERK pathway. The findings of the present study demonstrated that RIPOC helped to protect mice with an intestinal I/R injury by downregulating the ERK pathway.

The hepatic senescence-associated secretory phenotype promotes hepatocarcinogenesis through Bcl3-dependent activation of macrophages.

BACKGROUND: Liver cancer is one of the most common malignancies in the world with a poor prognosis. Hepatocellular carcinoma (HCC) is the most prevalent primary liver cancer, accounting for 80-90% of cases. The initiation and progression of HCC are closely associated with chronic liver inflammation. In addition, HCC is often accompanied by cell senescence. Senescent hepatocytes can secrete various inflammatory factors, collectively called the senescence-associated secretory phenotype (SASP). The SASP has been confirmed to promote the occurrence of liver cancer by affecting the inflammatory microenvironment. However, its role and the underlying mechanism of hepatic SASP in hepatocarcinogenesis are not clearly understood. Therefore, a better understanding of the pathogenic mechanisms of the effect of the hepatic SASP on the occurrence of HCC is still needed. METHODS: The study aims to explore the role of SASP factors and the underlying mechanism in tumorigenesis and the progression of HCC in vivo. We used diethylnitrosamine (DEN) combined with carbon tetrachloride (CCl4) (DEN-CCl4) to establish liver cancer model in wild-type (WT) mice and Bcl3 knockout (Bcl3-/-) mice. ß-galactosidase (ß-gal) staining was performed to evaluate the degree of cellular senescence. Immunohistochemistry (IHC) were used to detect the degree of cellular senescence and the activation of macrophage. PCR chip and clinical tissue chip assays were used to estimate the RNA levels of SASP factors and NF-κB related genes, and their protein levels were examined by Western blot assays. RESULTS: DEN-CCl4 induced cellular senescence in mouse hepatocytes. In addition, senescent hepatocytes might release a variety of inflammatory factors that further activate macrophages, thereby changing the microenvironmental state and promoting the occurrence of HCC. Mechanistically, the NF-κB pathway is important because it regulates the SASP. Therefore, we used a PCR chip to detect the expression of NF-κB-related genes in senescent liver tissue. Our results showed that the expression of Bcl3 was increased in senescent hepatocytes, and knocking out Bcl3 significantly inhibited the secretion of hepatocyte SASP factors and the activation of macrophages, thereby inhibiting hepatocarcinogenesis. Finally, in clinical tissues adjacent to HCC tissues in patients, the expression of Bcl3 and IL-8 correlated with poor prognosis in HCC patients. CONCLUSION: The hepatic SASP can further induce the activation of macrophages during hepatocarcinogenesis, thereby promoting the occurrence of HCC, and that this process is closely related to the expression of Bcl3 in hepatocytes.

A TNFR2-hnRNPK Axis Promotes Primary Liver Cancer Development via Activation of YAP Signaling in Hepatic Progenitor Cells.

Most primary liver cancer (PLC) cases progress mainly due to underlying chronic liver inflammation, yet the underlying mechanisms of inflammation-mediated PLC remain unclear. Here we uncover a TNF receptor II (TNFR2)-hnRNPK-YAP signaling axis in hepatic progenitor cells (HPC) essential for PLC development. TNFR2, but not TNF receptor I (TNFR1), was required for TNFα-induced activation of YAP during malignant transformation of HPCs and liver tumorigenesis. Mechanistically, heterogeneous nuclear ribonuclear protein K (hnRNPK) acted downstream of TNFα-TNFR2 signaling to directly interact with and stabilize YAP on target gene promoters genome-wide, therefore coregulating the expression of YAP target genes. Single-cell RNA sequencing confirmed the association of TNFR2-hnRNPK with YAP expression and the pathologic importance of HPC. Accordingly, expressions of TNFR2, hnRNPK, and YAP were all upregulated in PLC tissues and were strongly associated with poor prognosis of PLC including patient survival. Collectively, this study clarifies the differential roles of TNFRs in HPC-mediated tumorigenesis, uncovering a TNFR2-hnRNPK-centered mechanistic link between the TNFα-mediated inflammatory milieu and YAP activation in HPCs during PLC development. SIGNIFICANCE: This work defines how hnRNPK links TNFα signaling and Hippo pathway transcription coactivator YAP in hepatic progenitor cells during primary liver tumorigenesis.

Poly(vinylene carbonate)-Based Composite Polymer Electrolyte with Enhanced Interfacial Stability To Realize High-Performance Room-Temperature Solid-State Sodium Batteries.

Solid-state rechargeable batteries using polymer electrolytes have been considered, which can avoid safety issues and enhance energy density. However, commercial application of the polymer electrolyte solid-state battery is still significantly limited by the low room-temperature ionic conductivity, poor mechanical properties, and weak interfacial compatibility between the electrolyte and electrode, especially for the room-temperature solid-state rechargeable battery. In this work, a poly(vinylene carbonate)-based composite polymer electrolyte (PVC-CPE) is reported for the first time to realize room-temperature solid-state sodium batteries with high performances. This in situ solidified PVC-CPE possesses superior ionic conductivity (0.12 mS cm-1 at 25 °C), high Na+ transference number (tNa+ = 0.60), as well as enhanced electrode/electrolyte interfacial stability. Notably, the composite cathode NaNi1/3Fe1/3Mn1/3O2 (c-NFM) is designed through the in situ growth of the polymer electrolyte inside the electrode to decrease interfacial resistance and facilitate effective ion transport in electrode/electrolyte interfaces. It is demonstrated that the solid-state c-NFM/PVC-CPE/Na battery assembled by a one-step in situ solidification method exhibits remarkably enhanced cell performances at room temperature compared with a reference NFM/PVC-CPE/Na assembled through a conventional ex situ method. The battery presents a high initial specific capacity of 104.2 mA h g-1 at 0.2 C with a capacity retention of 86.8% over 250 cycles and ∼80.2 mA h g-1 at 1 C. This study suggests that PVC-CPE is a very promising electrolyte for solid-state sodium batteries. This study also suggests a new method to design high-performance polymer electrolytes for other solid-state rechargeable batteries to realize high safety and considerable electrochemical performance at room temperature.