Super-enhancer omics in stem cell.

The hallmarks of stem cells, such as proliferation, self-renewal, development, differentiation, and regeneration, are critical to maintain stem cell identity which is sustained by genetic and epigenetic factors. Super-enhancers (SEs), which consist of clusters of active enhancers, play a central role in maintaining stemness hallmarks by specifically transcriptional model. The SE-navigated transcriptional complex, including SEs, non-coding RNAs, master transcriptional factors, Mediators and other co-activators, forms phase-separated condensates, which offers a toggle for directing diverse stem cell fate. With the burgeoning technologies of multiple-omics applied to examine different aspects of SE, we firstly raise the concept of "super-enhancer omics", inextricably linking to Pan-omics. In the review, we discuss the spatiotemporal organization and concepts of SEs, and describe links between SE-navigated transcriptional complex and stem cell features, such as stem cell identity, self-renewal, pluripotency, differentiation and development. We also elucidate the mechanism of stemness and oncogenic SEs modulating cancer stem cells via genomic and epigenetic alterations hijack in cancer stem cell. Additionally, we discuss the potential of targeting components of the SE complex using small molecule compounds, genome editing, and antisense oligonucleotides to treat SE-associated organ dysfunction and diseases, including cancer. This review also provides insights into the future of stem cell research through the paradigm of SEs.

The Burgeoning Significance of Liquid-Liquid Phase Separation in the Pathogenesis and Therapeutics of Cancers.

Liquid-liquid phase separation (LLPS) is a physiological phenomenon that parallels the mixing of oil and water, giving rise to compartments with diverse physical properties. Biomolecular condensates, arising from LLPS, serve as critical regulators of gene expression and control, with a particular significance in the context of malignant tumors. Recent investigations have unveiled the intimate connection between LLPS and cancer, a nexus that profoundly impacts various facets of cancer progression, including DNA repair, transcriptional regulation, oncogene expression, and the formation of critical membraneless organelles within the cancer microenvironment. This review provides a comprehensive account of the evolution of LLPS from the molecular to the pathological level. We explore the mechanisms by through which biomolecular condensates govern diverse cellular physiological processes, encompassing gene expression, transcriptional control, signal transduction, and responses to environmental stressors. Furthermore, we concentrate on potential therapeutic targets and the development of small-molecule inhibitors associated with LLPS in prevalent clinical malignancies. Understanding the role of LLPS and its interplay within the tumor milieu holds promise for enhancing cancer treatment strategies, particularly in overcoming drug resistance challenges. These insights offer innovative perspectives and support for advancing cancer therapy.

Equilibrative nucleotide transporter ENT3 (SLC29A3): A unique transporter for inherited disorders and cancers.

As a crucial gene associated with diseases, the SLC29A3 gene encodes the equilibrative nucleoside transporter 3 (ENT3). ENT3 plays an essential regulatory role in transporting intracellular hydrophilic nucleosides, nucleotides, hydrophilic anticancer and antiviral nucleoside drugs, energy metabolism, subcellular localization, protein stability, and signal transduction. The mutation and inactivation of SLC29A3 are intimately linked to the occurrence, development, and prognosis of various human tumors. Moreover, many hereditary human diseases, such as H syndrome, pigmentary hypertrichosis and non-autoimmune insulin-dependent diabetes mellitus (PHID) syndrome, Faisalabad histiocytosis (FHC), are related to SLC29A3 mutations. This review explores the mechanisms of SLC29A3 mutations and expression alterations in inherited disorders and cancers. Additionally, we compile studies on the inhibition of ENT3, which may serve as an effective strategy to potentiate the anticancer activity of chemotherapy. Thus, the synopsis of genetics, permeant function and drug therapy of ENT3 provides a new theoretical and empirical foundation for the diagnosis, prognosis of evaluation and treatment of various related diseases.

Pueraria thomsonii Radix Water Extract Alleviate Type 2 Diabetes Mellitus in db/db Mice through Comprehensive Regulation of Metabolism and Gut Microbiota.

Type 2 diabetes mellitus (T2DM) is an increasingly prevalent and serious health problem. Its onset is typically associated with metabolic disorders and disturbances in the gut microbiota. Previous studies have reported the anti-T2DM effects of Pueraria thomsonii Radix as a functional food. However, the mechanism of action is still unknown. In this study, rich polyphenols and polysaccharides from Pueraria Thomsonii Radix water extract (PTR) were quantitatively determined, and then the effects of PTR on db/db mice were evaluated by pharmacology, metabolomics, and 16S rRNA gene sequencing. The results showed that PTR could alleviate pancreatic tissue damage, significantly decrease fasting blood glucose (FBG), fasting serum insulin (FINS), homeostasis model assessment insulin resistance (HOMA-IR), urinary glucose (UGLU), and urinary albumin/creatinine ratio (UACR). Metabolomics showed that the Diabetes Control (DM) group produced 109 differential metabolites, of which 74 could be regulated by PTR. In addition, 16S rRNA sequencing was performed in fecal samples and results showed that PTR could reduce the Firmicutes/Bacteroidetes(F/B) ratio and regulate three beneficial bacteria and one harmful bacterium. In conclusion, the results showed that PTR could ameliorate the T2DM symptoms, metabolic disorder, and gut microbiota imbalance of db/db mice, and it was superior to metformin in some aspects. We suggested for the first time that γ-aminobutyric acid (GABA) may be involved in the regulation of the microbiota-gut-brain axis (MGB) and thus affects the metabolic disorders associated with T2DM. This study will provide a scientific basis for the development of functional food with PTR.

Corrigendum: Bibliometric analysis of evolutionary trends and hotspots of super-enhancers in cancer.

[This corrects the article DOI: 10.3389/fphar.2023.1192855.].

Bibliometric analysis of evolutionary trends and hotspots of super-enhancers in cancer.

Introduction: In the past decade, super-enhancer (SE) has become a research hotspot with increasing attention on cancer occurrence, development, and prognosis. To illustrate the hotspots of SE in cancer research and its evolutionary tendency, bibliometric analysis was carried out for this topic. Methods: Literature published before Dec 31, 2022, in WOSCC, was systematically classified, and Citespace, bibliometric.com/app, and GraphPad Prism analyzed the data. Results: After screening out inappropriate documents and duplicate data, 911 publications were selected for further bibliometric analysis. The top five research areas were Oncology (257, 28.211%), Cell Biology (210, 23.052%), Biochemistry Molecular Biology (209, 22.942%), Science Technology Other Topics (138, 15.148%), and Genetics Heredity (132, 14.490%). The United States of America (United States) has the highest number of documents (462, 50.71%), followed by China (303, 33.26%). Among the most productive institutions, four of which are from the United States and one from Singapore, the National University of Singapore. Harvard Medical School (7.68%) has the highest percentage of articles. Young, Richard A, with 32 publications, ranks first in the number of articles. The top three authors came from Whitehead Institute for Biomedical Research as a research team. More than two-thirds of the research are supported by the National Institutes of Health of the United States (337, 37.654%) and the United States Department of Health Human Services (337, 37.654%). And "super enhancer" (525), "cell identity" (258), "expression" (223), "cancer" (205), and "transcription factor" (193) account for the top 5 occurrence keywords. Discussion: Since 2013, SE and cancer related publications have shown a rapid growth trend. The United States continues to play a leading role in this field, as the top literature numbers, affiliations, funding agencies, and authors were all from the United States, followed by China and European countries. A high degree of active cooperation is evident among a multitude of countries. The role of SEs in cell identity, gene transcription, expression, and inhibition, as well as the relationship between SEs and TFs, and the selective inhibition of SEs, have received much attention, suggesting that they are hot issues for research.

Adherence to a healthy lifestyle and its association with cognitive impairment in community-dwelling older adults in Shanghai.

Introduction: There is a growing body of recent literature linking the association of specific or multiple lifestyles with cognitive impairment, but most of these studies have been conducted in Western populations, and it is necessary to study multiple lifestyles and cognitive abilities in different populations, with the primary population of this study being a select group of community-dwelling older adults in Shanghai, China. Methods: The sample included 2,390 community-dwelling Chinese participants. Their cognitive function was assessed using the Mini-Mental State Examination (MMSE). We defined a healthy lifestyle score on the basis of being non-smoking, performing ≥210 min/wk moderate/vigorous-intensity physical activity, having light to moderate alcohol consumption, eating vegetables and fruits daily, having a body mass index (BMI) of 18.5-23.9 kg/m2, and having a waist-to-hip ratio (WHR) <0.90 for men and <0.85 for women, for an overall score ranging from 0 to 6. Results: Compared with participants with ≤2 healthy lifestyle factors, the adjusted odds ratio (OR) and 95% confidence interval (CI) for participants with 4, 5, and 6 healthy lifestyle factors were 0.53 (95% CI, 0.29-0.98), 0.40 (95% CI, 0.21-0.75), and 0.36 (95% CI, 0.16-0.79), respectively. Only WHR (OR = 0.54, 95% CI = 0.37-0.78) and physical activity (OR = 0.69, 95% CI = 0.51-0.92) were associated with cognitive impairment. A healthy lifestyle correlated with overall cognition (ß = 0.066, orientation (ß = 0.049), language ability (ß = 0.060), delayed recall (ß = 0.045) and executive function (ß = 0.044) (P all < 0.05). Conclusion: The study provides evidence on an inverse association between healthy lifestyles and cognitive impairment. We investigated whether healthy lifestyle was related to specific cognitive functions to provide a theoretical basis for accurate clinical prescription.

Prognostic Value of Pretreatment Prognostic Nutritional Index in Patients With Renal Cell Carcinoma: A Meta-Analysis.

BACKGROUND: The pretreatment prognostic nutritional index (PNI) is correlated with poor prognosis in several malignancies. However, the prognostic role of PNI in patients with renal cell carcinoma (RCC) remains unclear. Therefore, we performed a meta-analysis to investigate the prognostic significance of PNI in patients with RCC. METHODS: We searched the PubMed, Web of Science, Embase, Scopus, and Cochrane Library databases up to February 2021. Pooled hazard ratios (HRs) and 95% confidence intervals (CIs) were used to estimate correlation between PNI and survival endpoints in RCC. RESULTS: Ten studies with 4,908 patients were included in the meta-analysis. The pooled results indicated that a low PNI associated with poor overall survival (HR = 2.10, 95% CI = 1.67-2.64, p<0.001), shorter progression-free survival, disease-free survival, recurrence-free survival (HR = 1.99, 95% CI = 1.67-2.36, p<0.001), and poor cancer-specific survival (HR = 2.95, 95% CI = 1.61-5.39, p<0.001). Additionally, the prognostic ability of PNI was not affected by subgroup analysis factors. CONCLUSION: The meta-analysis indicated that low PNI associated with shorter survival outcomes in patients with RCC. Therefore, PNI could be used as an effective prognostic indicator in RCC.

Exendin-4 Reversed the PC12 Cell Damage Induced by circRNA CDR1as/miR-671/GSK3ß Signaling Pathway.

The purpose of this paper is to study the effect of circRNA cerebellar degeneration-related protein 1 antisense RNA(CDR1as)/miR-671/GSK3ß signaling pathway on PC12 cell injury and the mechanism of Exendin-4 (Ex-4) in PC12 cell injury protection. Quantitative reverse-transcription polymerase chain reaction (qRT-PCR) was used to detect the expression levels of circular RNA CDR1as and miR-671 in PC12 cells. By overexpressing or knocking out CDR1as, miR-671, and GSK3ß, the role of CDR1as, miR-671, and GSK3ß in PC12 cell injury was analyzed. The binding of CDR1as to miR-671 and GSK3ß to miR-671 was verified by dual luciferase reporter assay. PC12 cells were treated with 1-methyl-4 phenyl-pyridine ion (MPP+) to construct a PC12 cell damage model. PC12 cell transfection experiments were used to confirm the role of CDR1as/miR-671/GSK3ß signal axis in PC12 cell damage, and the role of Ex-4 in the association of circRNA CDR1as/miR-671/GSK3ß signaling axis and PC12 cell damage. PC12 cell damage was detected by 3-(4,5-dimethyl thiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT) and cellular lactate dehydrogenase (LDH) release. Ex-4 reversed the phosphorylation levels of PI3K, AKT, and GSK-3ß in MPP+-treated PC12 cells, and reduced MPP+-induced PC12 cell damage. CircRNA CDR1as upregulated the expression of GSK3ß by sponge miR-671. Ex-4 downregulated CDR1as expression and upregulated miR-671 expression in MPP+-induced PC12 cell. Silencing of CDR1as reduced MPP+-induced PC12 cell damage. CDR1as transfection downregulated the expression of miR-671 in PC12 cells, promoted the expression and phosphorylated of GSK3ß, and induced PC12 cell damage. GSK3ß silencing reversed CDR1as-induced PC12 cell damage. CDR1as promoted the phosphorylation level of GSK3ß in PC12 cells to cause cell damage; Ex-4 reversed the phosphorylation of GSK3ß caused by CDR1as in PC12 cells and reduced the PC12 cell damage caused by CDR1as. Ex-4 reverses the damage of PC12 cells induced by CDR1as/miR-671/GSK3ß signaling pathway.

[Research and progress on diagnosis and treatment of intervertebral space infection].

As the disc surgery were extensively developed, the incidence of intervertebral space infection was significantly increased. Due to a lack of specificity, early diagnosis is difficult and it is prone to misdiagnose. Intervertebral disc puncture sampling microorganism culture is a gold standard of antibiotic selection, but the positive detection rate needs to be improved. At present, different medical institutions have different opinious in epidemiology, treatment experiences, the choice of antibiotic treatment, the course of treatment and the way of operation. In recent years, magnetic resonance imaging, fluorine deoxidization glucose positron emission computed tomography scanning, the imaging application mediated percutaneous intervertebral disc, spinal puncture percutaneous endoscopic debridement and lavage drainage and percutaneous internal fixation combined with anterior posterior incision provide more choices for early diagnosis and treatment. Intervertebral infection should attract more attention to the prevention, early diagnosis, early specific pathogens. Doctors' experience and patients' actual situation should be considered when choosing a appropriate treatment. During the treatment, we should be closely monitored laboratory indexes and timely adjust plan of the treatment, and shorten the treatment time and prevent other complications through the auxiliary treatment.

Acidic pH retards the fibrillization of human Islet Amyloid Polypeptide due to electrostatic repulsion of histidines.

The human Islet Amyloid Polypeptide (hIAPP) is the major constituent of amyloid deposits in pancreatic islets of type-II diabetes. IAPP is secreted together with insulin from the acidic secretory granules at a low pH of approximately 5.5 to the extracellular environment at a neutral pH. The increased accumulation of extracellular hIAPP in diabetes indicates that changes in pH may promote amyloid formation. To gain insights and underlying mechanisms of the pH effect on hIAPP fibrillogenesis, all-atom molecular dynamics simulations in explicit solvent model were performed to study the structural properties of five hIAPP protofibrillar oligomers, under acidic and neutral pH, respectively. In consistent with experimental findings, simulation results show that acidic pH is not conducive to the structural stability of these oligomers. This provides a direct evidence for a recent experiment [L. Khemtemourian, E. Domenech, J. P. F. Doux, M. C. Koorengevel, and J. A. Killian, J. Am. Chem. Soc. 133, 15598 (2011)], which suggests that acidic pH inhibits the fibril formation of hIAPP. In addition, a complementary coarse-grained simulation shows the repulsive electrostatic interactions among charged His18 residues slow down the dimerization process of hIAPP by twofold. Besides, our all-atom simulations reveal acidic pH mainly affects the local structure around residue His18 by destroying the surrounding hydrogen-bonding network, due to the repulsive interactions between protonated interchain His18 residues at acidic pH. It is also disclosed that the local interactions nearby His18 operating between adjacent ß-strands trigger the structural transition, which gives hints to the experimental findings that the rate of hIAPP fibril formation and the morphologies of the fibrillar structures are strongly pH-dependent.

Molecular dynamics simulation study on the molecular structures of the amylin fibril models.

The structural characterization of amyloid fibers is one of the most investigated areas in structural biology. Recently, protofibril models for amylin, i.e., the 37-residue human islet amyloid polypeptide or hIAPP were suggested by two groups based on NMR (Biochemistry 2007, 46, 13505-13522) and X-ray (Protein Sci. 2008, 17, 1467-1474) techniques. However, there are significant differences in the two models which maybe originate from the polymorphic nature of amylin fibrils. To obtain further insights into the packing and stability features of the different models, we performed a series of molecular dynamics simulations on them. Our analysis showed that even pairs of ß-sheets composed of a limited number of ß-strands are stable in the 100-ns simulations, which suggests that steric zipper interactions at a ß-sheet-ß-sheet interface strongly contribute to the stability of these amyloid aggregates. For both models, outer strands are more flexible, which might coincide with the dynamical requirement that outer strands act as growing sites facilitating conformational changes of new incoming chains. Moreover, simulation results showed that the X-ray models are structurally more compact than the NMR models and have more intimate patterns, which lead to more rigid amyloid models. As a result, the X-ray models are energetically more stable than the NMR models. Further modeling analyses verify the most likely amylin fibril model among both NMR and X-ray models. Upon further study of the force-induced dissociation of a single chain from the protofibrils, the binding energy and the mechanical stability of the fibril models are revealed. On these bases, it is possible to reconcile the crystallographic and the NMR data on the basic amylin fiber unit.

Dynamical stability and assembly cooperativity of ß-sheet amyloid oligomers--effect of polarization.

The soluble intermediate oligomers of amyloidogenic proteins are suspected to be more cytotoxic than the mature fibrils in neurodegenerative disorders. Here, the dynamic stability and assembly cooperativity of a model oligomer of human islet amyloid polypeptide (hIAPP) segments were explored by means of all-atom molecular dynamics (MD) simulations under different force fields including AMBER99SB, OPLS, and polarized protein-specific charge (PPC) model. Simulation results show that the dynamic stability of ß-sheet oligomers is seriously impacted by electrostatic polarization. Without inclusion of polarization (simulation under standard AMBER and OPLS force field), the ß-sheet oligomers are dynamically unstable during MD simulation. For comparison, simulation results under PPC give significantly more stable dynamical structures of the oligomers. Furthermore, calculation of electrostatic interaction energy between the neighboring ß strands with an approximate polarizable method produces energetic evidence for cooperative assembly of ß-strand oligomers. This result supports a picture of downhill-like cooperative assembly of ß strands during fibrillation process. The present study demonstrates the critical role of polarization in dynamic stability and assembly cooperativity of ß-sheet-rich amyloid oligomers.

Effects of cholesterol on pore formation in lipid bilayers induced by human islet amyloid polypeptide fragments: a coarse-grained molecular dynamics study.

Disruption of the cellular membrane by the amyloidogenic peptide, islet amyloid polypeptide (IAPP), has been considered as one of the mechanisms of ß-cell death during type 2 diabetes. The N-terminal region (residues 1-19) of the human version of IAPP is suggested to be primarily responsible for the membrane-disrupting effect of the full-length hIAPP peptide. However, the detailed assembly mode of hIAPP1-19 with membrane remains unclear. To gain insight into the interactions of hIAPP1-19 oligomer with the model membrane, we have employed coarse-grained molecular dynamics self-assembly simulations to study the aggregation of hIAPP1-19 fragments in the binary lipid made of zwitterionic dipalmitoylphosphatidylcholine (DPPC) and anionic dipalmitoylphosphatidylserine (DPPS) in the presence and absence of different levels of cholesterol content. The membrane-destabilizing effect of hIAPP1-19 is found to be modulated by the presence of cholesterol. In the absence of cholesterol, hIAPP1-19 aggregates prefer to locate inside the bilayer, forming pore-like assemblies. While in the presence of cholesterol molecules, the lipid bilayer becomes more ordered and stiff, and the hIAPP1-19 aggregates are dominantly positioned at the bilayer-water interface. The action of cholesterol may suggest a possible way to maintain the membrane integrity by small molecule interference.

The molecular basis of distinct aggregation pathways of islet amyloid polypeptide.

Abnormal aggregation of islet amyloid polypeptide (IAPP) into amyloid fibrils is a hallmark of type 2 diabetes. In this study, we investigated the initial oligomerization and subsequent addition of monomers to growing aggregates of human IAPP at the residue-specific level using NMR, atomic force microscopy, mass spectroscopy, and computational simulations. We found that in solution IAPPs rapidly associate into transient low-order oligomers such as dimers and trimers via interactions between histidine 18 and tyrosine 37. This initial event is proceeded by slow aggregation into higher-order spherical oligomers and elongated fibrils. In these two morphologically distinct types of aggregates IAPPs adopt structures with markedly different residual flexibility. Here we show that the anti-amyloidogenic compound resveratrol inhibits oligomerization and amyloid formation via binding to histidine 18, supporting the finding that this residue is crucial for on-pathway oligomer formation.

Non-hinge-binding pyrazolo[1,5-a]pyrimidines as potent B-Raf kinase inhibitors.

As part of our research effort to discover B-Raf kinase inhibitors, we prepared a series of C-3 substituted N-(3-(pyrazolo[1,5-a]pyrimidin-7-yl)phenyl)-3-(trifluoromethyl)benzamides. X-ray crystallography studies revealed that one of the more potent inhibitors (10n) bound to B-Raf kinase without forming a hinge-binding hydrogen bond. With basic amine residues appended to C-3 aryl residues, cellular activity and solubility were enhanced over previously described compounds of this class.

3,4-Dihydropyrimido(1,2-a)indol-10(2H)-ones as potent non-peptidic inhibitors of caspase-3.

Cysteine-dependant aspartyl protease (caspase) activation has been implicated as a part of the signal transduction pathway leading to apoptosis. It has been postulated that caspase-3 inhibition could attenuate cell damage after an ischemic event and thereby providing for a novel neuroprotective treatment for stroke. As part of a program to develop a small molecule inhibitor of caspase-3, a novel series of 3,4-dihydropyrimido(1,2-a)indol-10(2H)-ones (pyrimidoindolones) was identified. The synthesis, biological evaluation and structure-activity relationships of the pyrimidoindolones are described.

Synthesis and activity of tryptophan sulfonamide derivatives as novel non-hydroxamate TNF-alpha converting enzyme (TACE) inhibitors.

A novel series of non-hydroxamate tryptophan sulfonamide derivatives containing a butynyloxy P1' moiety was identified as inhibitors of TNF-alpha converting enzyme (TACE). The structure-activity relationship of the series was examined via substitution on the tryptophan indole ring. Of the compounds investigated, 2-(4-(but-2-ynyloxy)phenylsulfonamido)-3-(1-(4-methoxybenzyl)-1H-indol-3-yl)propanoic acid (12p) has the best in vitro potency against isolated TACE enzyme with an IC(50) of 80 nM. Compound 12p also shows good selectivity over MMP-1, -13, -14.

Assembly dynamics of two-beta sheets revealed by molecular dynamics simulations.

The assembly dynamics of two beta sheets with different initial separation distances are explored by multiple all-atom molecular dynamics simulations with the presence of explicit water solvent. The beta sheet is composed of seven identical peptides in an antiparallel fashion. The peptide sequence is the 20-29 segment of human Islet amyloid polypeptide. Our simulations show that the assembly occurs not only in the lateral direction but also along the longitudinal direction, which provides a new insight into the assembly pathway at the early stage of fibril elongation. Based on Poisson-Boltzmann free energy analysis and quasiharmonic configuration entropy estimation, the entropic contribution is found to play an important role in the longitudinal assembly. Moreover, a possible oligomeric state with cyclic form is suggested based on one assembly model found in the simulations, illustrating the polymorphic nature of aggregation of the amyloidogenic peptide.

Conformation preorganization: effects of S20G mutation on the structure of human islet amyloid polypeptide segment.

The missense mutation S20G in the human islet amyloid polypeptide (hIAPP) is supposed to be associated with the early onset of type II diabetes (T2DM) in Asian population. How such a single-point mutation induces variation of the conformation distribution and the amyloidogenic properties of hIAPP is still unknown. We studied the conformational ensembles of hIAPP segment 15-27 in both wild type and the S20G mutant type by performing extensive replica exchange molecular dynamics simulations in explicit solvent model. Our results reveal that the residue G20 initiates a turnlike structure in the neighborhood, facilitating the formation of long-ranged contacts. Moreover, we find that the point mutation favors protofibril model of full length hIAPP suggested recently based on experimental measurements. Such a conformational preorganization will decrease the entropy cost during the process of peptide self-assembly, which is a possible explanation of the faster fibrillation of hIAPP S20G mutant than that of the wild type found by experiments.