UBQLN1 links proteostasis and mitochondria function to telomere maintenance in human embryonic stem cells.

BACKGROUND: Telomeres consist of repetitive DNA sequences at the chromosome ends to protect chromosomal stability, and primarily maintained by telomerase or occasionally by alternative telomere lengthening of telomeres (ALT) through recombination-based mechanisms. Additional mechanisms that may regulate telomere maintenance remain to be explored. Simultaneous measurement of telomere length and transcriptome in the same human embryonic stem cell (hESC) revealed that mRNA expression levels of UBQLN1 exhibit linear relationship with telomere length. METHODS: In this study, we first generated UBQLN1-deficient hESCs and compared with the wild-type (WT) hESCs the telomere length and molecular change at RNA and protein level by RNA-seq and proteomics. Then we identified the potential interacting proteins with UBQLN1 using immunoprecipitation-mass spectrometry (IP-MS). Furthermore, the potential mechanisms underlying the shortened telomeres in UBQLN1-deficient hESCs were analyzed. RESULTS: We show that Ubiquilin1 (UBQLN1) is critical for telomere maintenance in human embryonic stem cells (hESCs) via promoting mitochondrial function. UBQLN1 deficiency leads to oxidative stress, loss of proteostasis, mitochondria dysfunction, DNA damage, and telomere attrition. Reducing oxidative damage and promoting mitochondria function by culture under hypoxia condition or supplementation with N-acetylcysteine partly attenuate the telomere attrition induced by UBQLN1 deficiency. Moreover, UBQLN1 deficiency/telomere shortening downregulates genes for neuro-ectoderm lineage differentiation. CONCLUSIONS: Altogether, UBQLN1 functions to scavenge ubiquitinated proteins, preventing their overloading mitochondria and elevated mitophagy. UBQLN1 maintains mitochondria and telomeres by regulating proteostasis and plays critical role in neuro-ectoderm differentiation.

Machine Learning Identification of Nutrient Intake Variations across Age Groups in Metabolic Syndrome and Healthy Populations.

This study undertakes a comprehensive examination of the intricate link between diet nutrition, age, and metabolic syndrome (MetS), utilizing advanced artificial intelligence methodologies. Data from the National Health and Nutrition Examination Survey (NHANES) spanning from 1999 to 2018 were meticulously analyzed using machine learning (ML) techniques, specifically extreme gradient boosting (XGBoost) and the proportional hazards model (COX). Using these analytic methods, we elucidated a significant correlation between age and MetS incidence and revealed the impact of age-specific dietary patterns on MetS. The study delineated how the consumption of certain dietary components, namely retinol, beta-cryptoxanthin, vitamin C, theobromine, caffeine, lycopene, and alcohol, variably affects MetS across different age demographics. Furthermore, it was revealed that identical nutritional intakes pose diverse pathogenic risks for MetS across varying age brackets, with substances such as cholesterol, caffeine, and theobromine exhibiting differential risks contingent on age. Importantly, this investigation succeeded in developing a predictive model of high accuracy, distinguishing individuals with MetS from healthy controls, thereby highlighting the potential for precision in dietary interventions and MetS management strategies tailored to specific age groups. These findings underscore the importance of age-specific nutritional guidance and lay the foundation for future research in this area.

The tumor-intrinsic role of the m6A reader YTHDF2 in regulating immune evasion.

Tumors evade attacks from the immune system through various mechanisms. Here, we identify a component of tumor immune evasion mediated by YTH domain-containing family protein 2 (YTHDF2), a reader protein that usually destabilizes m6A-modified mRNA. Loss of tumoral YTHDF2 inhibits tumor growth and prolongs survival in immunocompetent tumor models. Mechanistically, tumoral YTHDF2 deficiency promotes the recruitment of macrophages via CX3CL1 and enhances mitochondrial respiration of CD8+ T cells by impairing tumor glycolysis metabolism. Tumoral YTHDF2 deficiency promotes inflammatory macrophage polarization and antigen presentation in the presence of IFN-γ. In addition, IFN-γ induces autophagic degradation of tumoral YTHDF2, thereby sensitizing tumor cells to CD8+ T cell-mediated cytotoxicity. Last, we identified a small molecule compound that preferentially induces YTHDF2 degradation, which shows a potent antitumor effect alone but a better effect when combined with anti-PD-L1 or anti-PD-1 antibodies. Collectively, YTHDF2 appears to be a tumor-intrinsic regulator that orchestrates immune evasion, representing a promising target for enhancing cancer immunotherapy.

Tibetan tea consumption prevents obesity by modulating the cellular composition and metabolic reprogramming of white adipose tissue.

Obesity, a global health concern, is linked with numerous metabolic and inflammatory disorders. Tibetan tea, a traditional Chinese beverage rich in theabrownin, is investigated in this study for its potential anti-obesity effects. Our work demonstrates that Tibetan tea consumption in C57BL/6J mice significantly mitigates obesity-related phenotypic changes without altering energy intake. Computational prediction revealed that Tibetan tea consumption reconstructs gene expression in white adipose tissue (WAT), promoting lipid catabolism and thereby increasing energy expenditure. We also note that Tibetan tea suppresses inflammation in WAT, reducing adipocyte hyperplasia and immune cell infiltration. Furthermore, Tibetan tea induces profound metabolic reprogramming, influencing amino acid metabolic pathways, specifically enhancing glutamine synthesis, which in turn suppresses pro-inflammatory chemokine production. These findings highlight Tibetan tea as a potential candidate in obesity prevention, providing a nuanced understanding of its capacity to modulate the cellular composition and metabolic landscape of WAT.

High CTCF expression mediated by FGD5-AS1/miR-19a-3p axis is associated with immunosuppression and pancreatic cancer progression.

The most common reason for cancer-related death globally is predicted to be pancreatic cancer (PC), one of the deadliest cancers. The CCCTC-binding factor (CTCF) regulates the three-dimensional structure of chromatin, was reported to be highly regulated in various malignancies. However, the underlying biological functions and possible pathways via which CTCF promotes PC progression remain unclear. Herein, we examined the CTCF function in PC and discovered that CTCF expression in PC tissues was significantly raised compared to neighboring healthy tissues. Additionally, Kaplan-Meier survival analysis demonstrated a strong connection between elevated CTCF expression and poor patient prognosis. A study of the ROC curve (receiver operating characteristic) revealed an AUC value for CTCF of 0.968. Subsequent correlation analysis exhibited a strong relationship between immunosuppression and CTCF expression in PC. CTCF knockdown significantly inhibited the malignant biological process of PC in vitro and in vivo, suggesting that CTCF may be a potential PC treatment target. We also identified the FGD5 antisense RNA 1 (FGD5-AS1)/miR-19a-3p axis as a possible upstream mechanism for CTCF overexpression. In conclusion, our data suggest that ceRNA-mediated CTCF overexpression contributes to the suppression of anti-tumor immune responses in PC and could be a predictive biomarker and potential PC treatment target.

BHLHE40, a potential immune therapy target, regulated by FGD5-AS1/miR-15a-5p in pancreatic cancer.

Pancreatic cancer, as one of the neoplasms with the highest degree of malignancy, has become a main disease of concerns in recent years. BHLHE40, a critical transcription factor for remodeling of the tumor immune microenvironment, has been described to be substantially increased in a variety of tumor-associated immune cells. Nevertheless, the pro-cancer biological functions and underlying molecular mechanisms of BHLHE40 for pancreatic cancer and its unique microenvironment are unclear. Hereby, we investigated the pro-oncogenic role of BHLHE40 in the pancreatic cancer microenvironment by bioinformatics analysis and cell biology experiments and determined that the expression of BHLHE40 was obviously elevated in pancreatic cancer tissues than in adjacent normal tissues. In parallel, Kaplan-Meier survival analysis unveiled that lower expression of BHLHE40 was strongly associated with better prognosis of patients. Receiver operating characteristic (ROC) curve analysis confirmed the accuracy of the BHLHE40-related prediction model. Subsequent, spearman correlation analysis observed that higher expression of BHLHE40 might be involved in immunosuppression of pancreatic cancer. Silencing of BHLHE40 could inhibit proliferation, invasion, and apoptosis of pancreatic cancer in vitro and in vivo, implying that BHLHE40 is expected to be a potential therapeutic target for pancreatic cancer. In addition, we explored and validated the FGD5-AS1/miR-15a-5p axis as a potential upstream regulatory mode for high expression of BHLHE40 in pancreatic cancer. In summary, our data showed that ceRNA involved in the regulation of BHLHE40 contributes to the promotion of immunosuppressive response in pancreatic and is expected to be a diagnostic marker and potential immunotherapeutic target for pancreatic cancer.

YTHDF2 orchestrates tumor-associated macrophage reprogramming and controls antitumor immunity through CD8+ T cells.

Despite tumor-associated macrophages (TAMs) playing a key role in shaping the tumor microenvironment (TME), the mechanisms by which TAMs influence the TME and contribute to cancer progression remain unclear. Here, we show that the N6-methyladenosine reader YTHDF2 regulates the antitumor functions of TAMs. YTHDF2 deficiency in TAMs suppressed tumor growth by reprogramming TAMs toward an antitumoral phenotype and increasing their antigen cross-presentation ability, which in turn enhanced CD8+ T cell-mediated antitumor immunity. YTHDF2 deficiency facilitated the reprogramming of TAMs by targeting interferon-γ-STAT1 signaling. The expression of YTHDF2 in TAMs was regulated by interleukin-10-STAT3 signaling. Selectively targeting YTHDF2 in TAMs using a Toll-like receptor 9 agonist-conjugated small interfering RNA reprogrammed TAMs toward an antitumoral phenotype, restrained tumor growth and enhanced the efficacy of PD-L1 antibody therapy. Collectively, our findings describe the role of YTHDF2 in orchestrating TAMs and suggest that YTHDF2 inhibition is an effective approach to enhance cancer immunotherapy.

Hiplot: a comprehensive and easy-to-use web service for boosting publication-ready biomedical data visualization.

Complex biomedical data generated during clinical, omics and mechanism-based experiments have increasingly been exploited through cloud- and visualization-based data mining techniques. However, the scientific community still lacks an easy-to-use web service for the comprehensive visualization of biomedical data, particularly high-quality and publication-ready graphics that allow easy scaling and updatability according to user demands. Therefore, we propose a community-driven modern web service, Hiplot (https://hiplot.org), with concise and top-quality data visualization applications for the life sciences and biomedical fields. This web service permits users to conveniently and interactively complete a few specialized visualization tasks that previously could only be conducted by senior bioinformatics or biostatistics researchers. It covers most of the daily demands of biomedical researchers with its equipped 240+ biomedical data visualization functions, involving basic statistics, multi-omics, regression, clustering, dimensional reduction, meta-analysis, survival analysis, risk modelling, etc. Moreover, to improve the efficiency in use and development of plugins, we introduced some core advantages on the client-/server-side of the website, such as spreadsheet-based data importing, cross-platform command-line controller (Hctl), multi-user plumber workers, JavaScript Object Notation-based plugin system, easy data/parameters, results and errors reproduction and real-time updates mode. Meanwhile, using demo/real data sets and benchmark tests, we explored statistical parameters, cancer genomic landscapes, disease risk factors and the performance of website based on selected native plugins. The statistics of visits and user numbers could further reflect the potential impact of this web service on relevant fields. Thus, researchers devoted to life and data sciences would benefit from this emerging and free web service.

Effects of in vitro digestion and fecal fermentation on the stability and metabolic behavior of polysaccharides from Craterellus cornucopioides.

The present study aimed to investigate the digestion and fermentation behavior of a novel polysaccharide named CCP from Craterellus cornucopioides. Results revealed that in vitro digestion could significantly decrease the molecular weight of CCPs. However, only a small amount of free glucose monosaccharide was released, and there was no noticeable change in the antioxidant activity throughout this digestion period, demonstrating that the main structure of CCPs was relatively stable under the simulated digestive conditions. The content of reducing sugar (1.11 mg mL-1) was significantly increased by fermentation in vitro of gut microbiota. The pH value in the fecal culture significantly decreased to 6.68, suggesting that CCPs could be broken down and utilized by gut microbiota. The concentrations of total short-chain fatty acids, acetic, propionic and n-butyric acids significantly increased compared to the blank. Simultaneously, CCPs could remarkably modulate the composition and abundance of beneficial microbiota, especially Bacteroidetes. Therefore, CCPs could potentially be a functional food to prevent disease by promoting gut health.

Preparation and characterization of Konjac glucomannan and pullulan composite films for strawberry preservation.

The present study aims to develop the new composite films by blending Konjac glucomannan (KGM) and pullulan with different ratios and concentrations. The structural, physical, barrier properties and morphology of the films were investigated and the practical use on strawberry preservation at 4 ± 1 °C, 85 %±5% relative humidity (RH) and 25 ± 1 °C, 55 %±5% RH was evaluated. Fourier transform infrared and scanning electron microscopy indicated the well-dispersion of film matrix was due to the good compatibility of the components. The mechanical and barrier properties of blend films were markedly enhanced although the light transmittance of which were decreased slightly. It was a further proof that 1% (w/v) KGM/pullulan (with the mass ratio of 2:1) blend film could decrease the weight loss significantly and maintain the titratable acidity, soluble solids and skin color on the strawberry preservation, thus improving the qualities of strawberries during storage time and offering a potential alternative to synthetic materials.

Preparation and characterization of chitosan films with three kinds of molecular weight for food packaging.

Recently, chitosan film has been widely used to extend the shelf life of food. In this study, high, medium and low molecular weight of chitosan were used as raw materials to prepare a series of films (C1-C27) by controlling the content of chitosan and glycerol, and their mechanical properties, water vapor permeability (WVP), oxygen transmittance (OP), morphology and antibacterial properties were characterized as well. The results indicated that all films had film-forming properties. Among them, the film C16 with high molecular weight, high chitosan content and 50% glycerol/chitosan (w/w) exhibited the excellent transparency (91.2%), elongation at break (28.948%), tensile strength (77.963 MPa), WVP (1.46 × 10-12gcm/cm2·sPa), smooth morphology, denser structure and antibacterial property (Staphylococcus aureus and Escherichia coli). Meanwhile, the preservation properties of chitosan films were evaluated by strawberry preservation. Almost all the studied films had better preservation effect than the commercially available PE films, especially of which the film C16 was the best compared with others. It maintained the physical and chemical parameters (weight loss ratio, total soluble solids, titratable acidity, total ascorbic acid and color change) of strawberry most obviously. Hence, chitosan films had great potential for the industrial application of fruit preservation.

The purification, structural characterization and antidiabetic activity of a polysaccharide from Anoectochilus roxburghii.

Anoectochilus roxburghii, a traditional Chinese medicinal herb, has been widely used for treating numerous chronic diseases. In this study, a polysaccharide from A. roxburghii (ARPs-p) was purified by anion exchange and size exclusion chromatography. The structural characteristics of ARPs-p were systematically investigated for the first time via numerous chromatographic techniques, periodic acid oxidation, Smith degradation, methylation analysis, FTIR spectroscopy and 1D/2D NMR spectroscopy. The results showed that ARPs-p is a heteropolysaccharide with a molecular weight of 97 kDa; it consists of 97.75% glucose, 1.2% galactose and trace amounts of galacturonic acid, and its backbone structure is composed of →3)-ß-d-Glcp-(1→ with some branching points at O-6 linked to non-reducing end units or 6-O-linked Glcp units. Furthermore, streptozotocin (STZ)-induced diabetic mouse experiments suggested that ARPs-p has excellent antihyperglycemic, antioxidant and antihyperlipidemic activities, in which 1,3-ß-d-glucan, the main component of ARPs-p, plays a vital role.