OncoVar: an integrated database and analysis platform for oncogenic driver variants in cancers.

The prevalence of neutral mutations in cancer cell population impedes the distinguishing of cancer-causing driver mutations from passenger mutations. To systematically prioritize the oncogenic ability of somatic mutations and cancer genes, we constructed a useful platform, OncoVar (https://oncovar.org/), which employed published bioinformatics algorithms and incorporated known driver events to identify driver mutations and driver genes. We identified 20 162 cancer driver mutations, 814 driver genes and 2360 pathogenic pathways with high-confidence by reanalyzing 10 769 exomes from 33 cancer types in The Cancer Genome Atlas (TCGA) and 1942 genomes from 18 cancer types in International Cancer Genome Consortium (ICGC). OncoVar provides four points of view, 'Mutation', 'Gene', 'Pathway' and 'Cancer', to help researchers to visualize the relationships between cancers and driver variants. Importantly, identification of actionable driver alterations provides promising druggable targets and repurposing opportunities of combinational therapies. OncoVar provides a user-friendly interface for browsing, searching and downloading somatic driver mutations, driver genes and pathogenic pathways in various cancer types. This platform will facilitate the identification of cancer drivers across individual cancer cohorts and helps to rank mutations or genes for better decision-making among clinical oncologists, cancer researchers and the broad scientific community interested in cancer precision medicine.

Metformin exerts anti-tumor effects via Sonic hedgehog signaling pathway by targeting AMPK in HepG2 cells.

Metformin, a traditional first-line pharmacological treatment for type 2 diabetes, has recently been shown to have anti-cancer effects on hepatocellular carcinoma (HCC). However, the molecular mechanism underlying the anti-tumor activity of metformin remains unclear. The Sonic hedgehog (Shh) signaling pathway is closely associated with the initiation and progression of HCC. Therefore, the aim of the current study was to investigate the effects of metformin on the biological behavior of HCC and the underlying functional mechanism of metformin in the Shh pathway. HCC was induced in HepG2 cells using recombinant human Shh (rhShh). The effects of metformin on proliferation and metastasis were evaluated using in vitro proliferation, wound healing, and invasion assays. The mRNA and protein expression levels of proteins related to the Shh pathway were measured using western blotting, quantitative PCR, and immunofluorescence staining. Metformin inhibited rhShh-induced proliferation and metastasis. Furthermore, metformin decreased the mRNA and protein expression of Shh pathway components, including Shh, Ptch, Smo, and Gli-1. Silencing of AMPK in the presence of metformin revealed that metformin exerted its inhibitory effects via AMPK. Our findings demonstrate that metformin suppresses the migration and invasion of HepG2 cells via AMPK-mediated inhibition of the Shh pathway.

Posttranslational modifications in diabetes: Mechanisms and functions.

As one of the most widespread chronic diseases, diabetes and its accompanying complications affect approximately one tenth of individuals worldwide and represent a growing cause of morbidity and mortality. Accumulating evidence has proven that the process of diabetes is complex and interactive, involving various cellular responses and signaling cascades by posttranslational modifications (PTMs). Therefore, understanding the mechanisms and functions of PTMs in regulatory networks has fundamental importance for understanding the prediction, onset, diagnosis, progression, and treatment of diabetes. In this review, we offer a holistic summary and illustration of the crosstalk between PTMs and diabetes, including both types 1 and 2. Meanwhile, we discuss the potential use of PTMs in diabetes treatment and provide a prospective direction for deeply understanding the metabolic diseases.

DNA methylation plays important roles in retinal development and diseases.

DNA methylation is important in developing and post-mitotic cells in various tissues. Recent studies have shown that DNA methylation is highly dynamic, and plays important roles during retinal development and aging. In addition, the dynamic regulation of DNA methylation is involved in the occurrence and development of age-related macular degeneration and diabetic retinopathy and shows potential in disease diagnoses and prognoses. This review introduces the epigenetic concepts of DNA methylation and demethylation with an emphasis on their regulatory roles in retinal development and related diseases. Moreover, we propose exciting ideas such as its crosstalk with other epigenetic modifications and retinal regeneration, to provide a potential direction for understanding retinal diseases from the epigenetic perspective.

OncoBase: a platform for decoding regulatory somatic mutations in human cancers.

Whole-exome and whole-genome sequencing have revealed millions of somatic mutations associated with different human cancers, and the vast majority of them are located outside of coding sequences, making it challenging to directly interpret their functional effects. With the rapid advances in high-throughput sequencing technologies, genome-scale long-range chromatin interactions were detected, and distal target genes of regulatory elements were determined using three-dimensional (3D) chromatin looping. Herein, we present OncoBase (http://www.oncobase.biols.ac.cn/), an integrated database for annotating 81 385 242 somatic mutations in 68 cancer types from more than 120 cancer projects by exploring their roles in distal interactions between target genes and regulatory elements. OncoBase integrates local chromatin signatures, 3D chromatin interactions in different cell types and reconstruction of enhancer-target networks using state-of-the-art algorithms. It employs informative visualization tools to display the integrated local and 3D chromatin signatures and effects of somatic mutations on regulatory elements. Enhancer-promoter interactions estimated from chromatin interactions are integrated into a network diffusion system that quantitatively prioritizes somatic mutations and target genes from a large pool. Thus, OncoBase is a useful resource for the functional annotation of regulatory noncoding regions and systematically benchmarking the regulatory effects of embedded noncoding somatic mutations in human carcinogenesis.

Gdf11 gene transfer prevents high fat diet-induced obesity and improves metabolic homeostasis in obese and STZ-induced diabetic mice.

BACKGROUND: The growth differentiation factor 11 (GDF11) was shown to reverse age-related hypertrophy on cardiomyocytes and considered as anti-aging rejuvenation factor. The role of GDF11 in regulating metabolic homeostasis is unclear. In this study, we investigated the functions of GDF11 in regulating metabolic homeostasis and energy balance. METHODS: Using a hydrodynamic injection approach, plasmids carrying a mouse Gdf11 gene were delivered into mice and generated the sustained Gdf11 expression in the liver and its protein level in the blood. High fat diet (HFD)-induced obesity was employed to examine the impacts of Gdf11 gene transfer on HFD-induced adiposity, hyperglycemia, insulin resistance, and hepatic lipid accumulation. The impacts of GDF11 on metabolic homeostasis of obese and diabetic mice were examined using HFD-induced obese and STZ-induced diabetic models. RESULTS: Gdf11 gene transfer alleviates HFD-induced obesity, hyperglycemia, insulin resistance, and fatty liver development. In obese and STZ-induced diabetic mice, Gdf11 gene transfer restores glucose metabolism and improves insulin resistance. Mechanism study reveals that Gdf11 gene transfer increases the energy expenditure of mice, upregulates the expression of genes responsible for thermoregulation in brown adipose tissue, downregulates the expression of inflammatory genes in white adipose tissue and those involved in hepatic lipid and glucose metabolism. Overexpression of GDF11 also activates TGF-ß/Smad2, PI3K/AKT/FoxO1, and AMPK signaling pathways in white adipose tissue. CONCLUSIONS: These results demonstrate that GDF11 plays an important role in regulating metabolic homeostasis and energy balance and could be a target for pharmacological intervention to treat metabolic disease.

The Relationship of Neutrophil-to-Lymphocyte Ratio or Platelet-to-Lymphocyte Ratio and Pancreatic Cancer in Patients with Type 2 Diabetes.

BACKGROUND: The objective of the current study is to determine the importance of neutrophil-to-lymphocyte ratio (NLR) and platelet-to-lymphocyte ratio (PLR) in combination with cancer antigen 199 (CA199) in the diagnosis of pancreatic cancer (PC) in patients with type 2 diabetes. METHODS: The study population comprised 45 PC patients with type 2 diabetes, 50 patients with type 2 diabetes alone, and 60 control subjects. All data was mined from the electronic records of the First Affiliated Hospital of Guangxi Medical University in Nanning, Guangxi, China. RESULTS: We found that the NLRs and PLR of PC patients with type 2 diabetes were higher compared to patients with type 2 diabetes alone and healthy subjects. A receiver operating characteristic (ROC) curve analysis for the diagnosis of PC in type 2 diabetic patients revealed that the combination of NLR and CA199 had higher specificity than either NLR or CA199 alone, while the combination of PLR and CA199 had higher sensitivity than either PLR or CA199 alone. The area under the ROC curve (AUROC) for PLR combined with CA199 was significantly larger than CA199 alone, and the AUROC for NLR combined with CA199 was also larger than CA199 alone, al-though this difference was not significant. CONCLUSIONS: Combining PLR and CA199 values could allow earlier diagnosis of PC in type 2 diabetic patients.

TET1 modulates H4K16 acetylation by controlling auto-acetylation of hMOF to affect gene regulation and DNA repair function.

The Ten Eleven Translocation 1 (TET1) protein is a DNA demethylase that regulates gene expression through altering statue of DNA methylation. However, recent studies have demonstrated that TET1 could modulate transcriptional expression independent of its DNA demethylation activity; yet, the detailed mechanisms underlying TET1's role in such transcriptional regulation remain not well understood. Here, we uncovered that Tet1 formed a chromatin complex with histone acetyltransferase Mof and scaffold protein Sin3a in mouse embryonic stem cells by integrative genomic analysis using publicly available ChIP-seq data sets and a series of in vitro biochemical studies in human cell lines. Mechanistically, the TET1 facilitated chromatin affinity and enzymatic activity of hMOF against acetylation of histone H4 at lysine 16 via preventing auto-acetylation of hMOF, to regulate expression of the downstream genes, including DNA repair genes. We found that Tet1 knockout MEF cells exhibited an accumulation of DNA damage and genomic instability and Tet1 deficient mice were more sensitive to x-ray exposure. Taken together, our findings reveal that TET1 forms a complex with hMOF to modulate its function and the level of H4K16Ac ultimately affect gene expression and DNA repair.

Correlation between hematological parameters and ancylostomiasis: A retrospective study.

OBJECTIVE: Our aim intended to determine the relationship between hematological parameters (neutrophil-to-lymphocyte ratio [NLR], platelet-to-lymphocyte ratio [PLR], and eosinophil-to-lymphocyte ratio [ELR]) and ancylostomiasis. METHODS: There were 140 patients with ancylostomiasis and 159 healthy controls enrolled in this study. All data were collected from electronic medical records of the First Affiliated Hospital of Guangxi Medical University. RESULTS: The levels of NLR, PLR, and ELR in ancylostomiasis patients were significantly higher than those in the healthy controls (all P = 0.000). A receiver operating characteristic curve was generated to assess the diagnostic efficacy of these three hematological parameters. ELR (AUC = 0.850; sensitivity = 75.00%; specificity = 86.80%) showed the superior AUC than those of NLR (AUC = 0.718; sensitivity = 53.57%; specificity = 88.68%) and PLR (AUC = 0.806; sensitivity = 68.57%; specificity = 86.79%), respectively. A multivariate regression model using the two selected indices (RBC and ELR) was established with the model's sensitivity and specificity reached 82.86% and 96.23%, respectively. In the ancylostomiasis patient group, NLR (r = -0.452, P = 0.000) and PLR (r = -0.357, P = 0.000) were reversely associated with eosinophils. CONCLUSION: The pretreatment levels of the three hematological parameters (NLR, PLR, and ELR) may serve as valuable indicators for distinguishing patients with ancylostomiasis from healthy controls. NLR and PLR are negatively associated with the previous indicator, eosinophils.

A PP4-phosphatase complex dephosphorylates gamma-H2AX generated during DNA replication.

The histone H2A variant H2AX is rapidly phosphorylated in response to DNA double-stranded breaks to produce gamma-H2AX. gamma-H2AX stabilizes cell-cycle checkpoint proteins and DNA repair factors at the break site. We previously found that the protein phosphatase PP2A is required to resolve gamma-H2AX foci and complete DNA repair after exogenous DNA damage. Here we describe a three-protein PP4 phosphatase complex in mammalian cells, containing PP4C, PP4R2, and PP4R3beta, that specifically dephosphorylates ATR-mediated gamma-H2AX generated during DNA replication. PP4 efficiently dephosphorylates gamma-H2AX within mononucleosomes in vitro and does not directly alter ATR or checkpoint kinase activity, suggesting that PP4 acts directly on gamma-H2AX in cells. When the PP4 complex is silenced, repair of DNA replication-mediated breaks is inefficient, and cells are hypersensitive to DNA replication inhibitors, but not radiomimetic drugs. Therefore, gamma-H2AX elimination at DNA damage foci is required for DNA damage repair, but accomplishing this task involves distinct phosphatases with potentially overlapping roles.

GATA transcription factors in vertebrates: evolutionary, structural and functional interplay.

GATA transcription factors perform conserved and essential roles during animal development, including germ-layer specification, hematopoiesis, and cardiogenesis. The evolutionary history and the changes in selection pressures following duplication of the six GATA family members in vertebrates have not been completely understood. Recently, we explored multiple databases to find GATAs in different vertebrate species. Using these sequences, we have performed molecular phylogenetic analyses using Maximum Likelihood and Bayesian methods, and statistical tests of tree topologies, to ascertain the phylogenetic relationship and selection pressures among GATA proteins. Seventy-one full-length cDNA sequences from 24 vertebrate species were extracted from multiple databases. By phylogenetic analyses, we investigated the origin, conservation, and evolution of the GATAs. Six GATA genes in vertebrates might be formed by gene duplication. The inferred evolutionary transitions that separate members which belong to different gene clusters correlated with changes in functional properties. Selection analysis and protein structure analysis were combined to explain Darwinian selection in GATA sequences and these changes brought putative biological significance. 26 positive selection sites were detected in this process. This study reveals the evolutionary history of vertebrate GATA paralogous and positively selected sites likely relevant for the distinct functional properties of the paralogs. It provides a new perspective for understanding the origin and evolution and biological functions of GATAs, which will help to uncover the GATAs' biological roles, evolution and their relationship with associated diseases; in addition, other complex multidomain families and also larger superfamilies can be investigated in a similar way.

The development of using function word "zài" to learn novel verbs in young Mandarin speakers.

The present research examined whether Mandarin-speaking children could use function words to learn novel verbs and recognize verbs in a new sentential context. In Experiment 1, 3- to 6-year-old children were taught two novel verbs supported by the verb marker "zài." The 5- and 6-year-old children successfully used the function word "zài" to learn novel verbs, but the 3- and 4-year-olds failed to interpret the novel words as verbs. In Experiment 2 and 3, the children had to recognize the newly learned verbs in new sentences containing a different function word (a different verb-biased marker "le" or a non-verb-biased marker "shì"). Results showed that the 5-year-old children could recognize the newly learned verbs with another verb-biased marker "le," but only the 6-year-old children could recognize the newly learned verbs with the non-verb-biased marker "shì." The study verified that Mandarin-speaking children could use the function word "zài" to determine a novel word as a verb and revealed that such an ability appeared between the ages of 4 and 5 years. In addition, the ability to extend a newly learned verb across different morphosyntactic markers is developed in 5- to 6-year-olds.

3D Spheroids Facilitate Differentiation of Human Adipose-Derived Mesenchymal Stem Cells into Hepatocyte-Like Cells via p300-Mediated H3K56 Acetylation.

Hepatocyte-like cells (HLCs) that are differentiated from mesenchymal stem cells (MSCs) provide a valuable resource for drug screening and cell-based regeneration therapy. Differentiating HLCs into 3D spheroids enhances their phenotypes and functions. However, the molecular mechanisms underlying MSCs hepatogenic differentiation are not fully understood. In this study, we generated HLCs from human adipose-derived mesenchymal stem cells (hADMSCs) in both 2D and 3D cultures. We performed an acetyl-proteomics assay on the HLCs derived from both 2D and 3D differentiation and identified a differential change in H3K56 acetylation between the 2 differentiated cells. Our findings revealed that 3D differentiation activated ALB gene transcription by increasing the acetylation level of H3K56, thereby enhancing the phenotypes and functions of HLCs and further promoting their maturation. Notably, inhibiting p300 reduced the acetylation level of H3K56 during hepatogenic differentiation, leading to decreased phenotypes and functions of HLCs, whereas activation of p300 promoted hepatogenic differentiation, suggesting that p300 plays a critical role in this process. In summary, our study demonstrates a potential mechanism through which 3D spheroids differentiation facilitates hADMSCs differentiation into HLCs by promoting p300-mediated H3K56 acetylation, which could have significant clinical applications in liver regeneration and disease modeling.

Comparative Study of Two Common In Vitro Models for the Pancreatic Islet with MIN6.

BACKGROUND: Islet transplantation is currently considered the most promising method for treating insulin-dependent diabetes. The two most-studied artificial islets are alginate-encapsulated ß cells or ß cell spheroids. As three-dimensional (3D) models, both artificial islets have better insulin secretory functions and transplantation efficiencies than cells in two-dimensional (2D) monolayer culture. However, the effects of these two methods have not been compared yet. Therefore, in this study, cells from the mouse islet ß cell line Min6 were constructed as scaffold-free spheroids or alginate-encapsulated dispersed cells. METHODS: MIN6 cell spheroids were prepared by using Agarose-base microwell arrays. The insulin secretion level was determined by mouse insulin ELISA kit, and the gene and protein expression status of the MIN6 were performed by Quantitative polymerase chain reaction and immunoblot, respectively. RESULTS: Both 3D cultures effectively promoted the proliferation and glucose-stimulated insulin release (GSIS) of MIN6 cells compared to 2D adherent cells. Furthermore, 1% alginate-encapsulated MIN6 cells demonstrated more significant effects than the spheroids. In general, three pancreatic genes were expressed at higher levels in response to the 3D culture than to the 2D culture, and pancreatic/duodenal homeobox-1 (PDX1) expression was higher in the cells encapsulated in 1% alginate than that in the spheroids. A western blot analysis showed that 1% alginate-encapsulated MIN6 cells activated the phosphoinositide 3-kinase (PI3K)/serine/threonine protein kinase (AKT)/forkhead transcription factor FKHR (FoxO1) pathway more than the spheroids, 0.5% alginate-, or 2% alginate-encapsulated cells did. The 3D MIN6 culture, therefore, showed improved effects compared to the 2D culture, and the 1% alginate-encapsulated MIN6 cells exhibited better effects than the spheroids. The upregulation of PDX1 expression through the activation of the PI3K/AKT/FoxO1 pathway may mediate the improved cell proliferation and GSIS in 1% alginate-encapsulated MIN6 cells. CONCLUSION: This study may contribute to the construction of in vitro culture systems for pancreatic islets to meet clinical requirements.

CARD9 in host immunity to fungal, bacterial, viral, and parasitic infections: An update.

Microbial infection, caused by fungi, bacteria, viruses, and parasites, significantly contributes to the global death burden and health costs. The innate and adaptive immune systems orchestrate a multifaceted signaling response to invading pathogens as the human antimicrobial system. In this process, caspase recruitment domain-containing protein 9 (CARD9) emerges as a critical intermediary adaptor molecule to participate in regulating a series of antimicrobial immune reactions. Previous publications have confirmed that CARD9 plays a crucial role in fungal, bacterial, viral, and parasitic infections. In this study, we aim to provide an update on the recent clinical and basic studies where the mechanism and function of CARD9 have been further studied and understood. In addition, we summarize the latest treatment and prevention strategies based on CARD9 and discuss the current perspectives and future direction of CARD9.

Lactate: The Mediator of Metabolism and Immunosuppression.

The Warburg effect, one of the hallmarks of tumors, produces large amounts of lactate and generates an acidic tumor microenvironment via using glucose for glycolysis. As a metabolite, lactate not only serves as a substrate to provide energy for supporting cell growth and development but also acts as an important signal molecule to affect the biochemical functions of intracellular proteins and regulate the biological functions of different kinds of cells. Notably, histone lysine lactylation (Kla) is identified as a novel post-modification and carcinogenic signal, which provides the promising and potential therapeutic targets for tumors. Therefore, the metabolism and functional mechanism of lactate are becoming one of the hot fields in tumor research. Here, we review the production of lactate and its regulation on immunosuppressive cells, as well as the important role of Kla in hepatocellular carcinoma. Lactate and Kla supplement the knowledge gap in oncology and pave the way for exploring the mechanism of oncogenesis and therapeutic targets. Research is still needed in this field.

Metformin: A Potential Candidate for Targeting Aging Mechanisms.

Aging is a universal phenomenon in all biological organisms, defined by the loss of reproductive capacity and a progressive decline in fitness. In humans, aging is further associated with an increased incidence of disease conditions. The current aging population has become a primary public burden of the 21st century. Therefore, to delay the aging process and maintain fitness in the aging population, the discovery of novel anti-aging drugs remains an urgent need. In recent years, metformin, a widely used hypoglycemic drug, has attracted growing attention in the field of anti-aging research. Reportedly, numerous studies have indicated that metformin regulates aging-related pathways, possibly delaying the aging process by modulating these pathways. The elucidation of these anti-aging effects may provide insights into the age-retarding potential of metformin. The present review focuses on the predominant molecular mechanisms associated with aging, as well as the anti-aging effects of metformin.

Advances in Biological Function and Clinical Application of Small Extracellular Vesicle Membrane Proteins.

Small extracellular vesicles are membrane-bound vesicles secreted into extracellular spaces by virtually all types of cells. These carry a large number of membrane proteins on their surface that are incorporated during their biogenesis in cells. The composition of the membrane proteins hence bears the signature of the cells from which they originate. Recent studies have suggested that the proteins on these small extracellular vesicles can serve as biomarkers and target proteins for the diagnosis and treatment of diseases. This article classifies small extracellular vesicle membrane proteins and summarizes their pathophysiological functions in the diagnosis and treatment of diseases.

FoxP3-miR-150-5p/3p suppresses ovarian tumorigenesis via an IGF1R/IRS1 pathway feedback loop.

Ovarian cancer (OC) causes more deaths than any other gynecological cancer. Many cellular pathways have been elucidated to be associated with OC development and progression. Specifically, the insulin-like growth factor 1 receptor/insulin receptor substrate 1 (IGF1R/IRS1) pathway participates in OC development. Moreover, accumulating evidence has shown that microRNA deregulation contributes to tumor initiation and progression. Here, our study aimed to investigate the molecular functions and regulatory mechanisms of miR-150, specifically, in OC. We found that the expression of miR-150-5p/3p and their precursor, mir-150, was downregulated in OC tissues; lower mir-150 levels were associated with poor OC patient outcomes. Ectopic mir-150 expression inhibited OC cell growth and metastasis in vitro and in vivo. Furthermore, both IRS1 and IGF1R were confirmed as direct targets of miR-150-5p/3p, and the miR-150-IGF1R/IRS1 axis exerted antitumor effects via the PI3K/AKT/mTOR pathway. Forkhead box protein 3 (FoxP3) positively regulated the expression of miR-150-5p/3p by binding to the mir-150 promoter. In turn, the PI3K/AKT/mTOR pathway downregulated FoxP3 and miR-150-5p/3p. Taken together, these findings indicate that a complex FoxP3-miR-150-IGF1R/IRS1-PI3K/AKT/mTOR feedback loop regulates OC pathogenesis, providing a novel mechanism for miR-150 as a tumor suppressor miRNA in OC.

The hepatic AMPK-TET1-SIRT1 axis regulates glucose homeostasis.

Ten-eleven translocation methylcytosine dioxygenase 1 (TET1) is involved in multiple biological functions in cell development, differentiation, and transcriptional regulation. Tet1 deficient mice display the defects of murine glucose metabolism. However, the role of TET1 in metabolic homeostasis keeps unknown. Here, our finding demonstrates that hepatic TET1 physically interacts with silent information regulator T1 (SIRT1) via its C-terminal and activates its deacetylase activity, further regulating the acetylation-dependent cellular translocalization of transcriptional factors PGC-1α and FOXO1, resulting in the activation of hepatic gluconeogenic gene expression that includes PPARGC1A, G6PC, and SLC2A4. Importantly, the hepatic gluconeogenic gene activation program induced by fasting is inhibited in Tet1 heterozygous mice livers. The adenosine 5'-monophosphate-activated protein kinase (AMPK) activators metformin or AICAR-two compounds that mimic fasting-elevate hepatic gluconeogenic gene expression dependent on in turn activation of the AMPK-TET1-SIRT1 axis. Collectively, our study identifies TET1 as a SIRT1 coactivator and demonstrates that the AMPK-TET1-SIRT1 axis represents a potential mechanism or therapeutic target for glucose metabolism or metabolic diseases.