The bromodomain (BrD) is a conserved structural module found in chromatin- and transcription-associated proteins that acts as the primary reader for acetylated lysine residues. This basic activity ...endows BrD proteins with versatile functions in the regulation of protein-protein interactions mediating chromatin-templated gene transcription, DNA recombination, replication and repair. Consequently, BrD proteins are involved in the pathogenesis of numerous human diseases. In this Review, we highlight our current understanding of BrD biology, and discuss the latest development of small-molecule inhibitors targeting BrDs as emerging epigenetic therapies for cancer and inflammatory disorders.
Many prostate lesions have 'large gland' morphology with gland size similar to or larger than benign glands, complex glandular architecture including papillary, cribriform, and solid, and significant ...cytological atypia in glandular epithelium with nucleomegaly, prominent nucleoli, or anisonucleosis. The most common and clinically important lesions with 'large gland' morphology include high-grade prostatic intraepithelial neoplasia (HGPIN), PIN-like carcinoma, ductal adenocarcinoma, and intraductal carcinoma. These lesions have diverse clinical significance and management implications. HGPIN refers to proliferation of glandular epithelium that displays severe cytological atypia within the confines of prostatic ducts and acini. A HGPIN diagnosis in biopsies connotes ~25% risk of detection of cancer in repeat biopsies. It has been accepted as the main precursor lesion to invasive carcinoma. PIN-like carcinoma is a variant of acinar carcinoma that is morphologically reminiscent of HGPIN and is composed of large cancer glands lined with pseudostratified epithelium. Its clinical outcome is similar to that of usual acinar carcinomas and is graded as Gleason score 3+3=6. Ductal adenocarcinoma comprises large glands lined with tall columnar and pseudostratified epithelium. It is more aggressive than acinar carcinomas and is associated with higher stage disease and greater risk of PSA recurrence and mortality. Intraductal carcinoma is an intraglandular/ductal neoplastic proliferation of glandular epithelial cells that results in marked expansion of glandular architecture and nuclear atypia that often exceeds that in invasive carcinomas. In majority of cases, it is thought to represent retrograde extension of invasive carcinoma into pre-existing ducts and acini. Rarely it may represent a peculiar form of carcinoma with predilection for intraductal location. It is considered an adverse pathological feature and is seen almost always in high-grade and volume carcinoma and harbingers worse clinical outcomes. This article reviews 'new' information on the clinical and pathological features of HGPIN, PIN-like carcinoma, ductal carcinoma, and intraductal carcinoma, and focuses morphological features that aid the differential diagnosis.
Biofuel cells (BFCs) based on enzymes and microorganisms have been recently received considerable attention because they are recognized as an attractive type of energy conversion technology. In ...addition to the research activities related to the application of BFCs as power source, we have witnessed recently a growing interest in using BFCs for self‐powered electrochemical biosensing and electrochemical logic biosensing applications. Compared with traditional biosensors, one of the most significant advantages of the BFCs‐based self‐powered electrochemical biosensors and logic biosensors is their ability to detect targets integrated with chemical‐to‐electrochemical energy transformation, thus obviating the requirement of external power sources. Following my previous review (Electroanalysis 2012, 24, 197–209), the present review summarizes, discusses and updates the most recent progress and latest advances on the design and construction of BFCs‐based self‐powered electrochemical biosensors and logic biosensors. In addition to the traditional approaches based on substrate effect, inhibition effect, blocking effect and gene regulation effect for BFCs‐based self‐powered electrochemical biosensors and logic biosensors design, some new principles including enzyme effect, co‐stabilization effect, competition effect and hybrid effect are summarized and discussed by me in details. The outlook and recommendation of future directions of BFCs‐based self‐powered electrochemical biosensors and logic biosensors are discussed in the end.
Neurological disorders significantly outnumber diseases in other therapeutic areas. However, developing drugs for central nervous system (CNS) disorders remains the most challenging area in drug ...discovery, accompanied with the long timelines and high attrition rates. With the rapid growth of biomedical data enabled by advanced experimental technologies, artificial intelligence (AI) and machine learning (ML) have emerged as an indispensable tool to draw meaningful insights and improve decision making in drug discovery. Thanks to the advancements in AI and ML algorithms, now the AI/ML‐driven solutions have an unprecedented potential to accelerate the process of CNS drug discovery with better success rate. In this review, we comprehensively summarize AI/ML‐powered pharmaceutical discovery efforts and their implementations in the CNS area. After introducing the AI/ML models as well as the conceptualization and data preparation, we outline the applications of AI/ML technologies to several key procedures in drug discovery, including target identification, compound screening, hit/lead generation and optimization, drug response and synergy prediction, de novo drug design, and drug repurposing. We review the current state‐of‐the‐art of AI/ML‐guided CNS drug discovery, focusing on blood–brain barrier permeability prediction and implementation into therapeutic discovery for neurological diseases. Finally, we discuss the major challenges and limitations of current approaches and possible future directions that may provide resolutions to these difficulties.
To identify the molecular mechanisms and novel therapeutic targets of late-onset Alzheimer’s Disease (LOAD), we performed an integrative network analysis of multi-omics profiling of four cortical ...areas across 364 donors with varying cognitive and neuropathological phenotypes. Our analyses revealed thousands of molecular changes and uncovered neuronal gene subnetworks as the most dysregulated in LOAD. ATP6V1A was identified as a key regulator of a top-ranked neuronal subnetwork, and its role in disease-related processes was evaluated through CRISPR-based manipulation in human induced pluripotent stem cell-derived neurons and RNAi-based knockdown in Drosophila models. Neuronal impairment and neurodegeneration caused by ATP6V1A deficit were improved by a repositioned compound, NCH-51. This study provides not only a global landscape but also detailed signaling circuits of complex molecular interactions in key brain regions affected by LOAD, and the resulting network models will serve as a blueprint for developing next-generation therapeutic agents against LOAD.
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•Development of gene network models of four cortical areas affected by LOAD•Identification of region-specific molecular changes and gene subnetworks in LOAD•ATP6V1A is a top key regulator of a neuronal subnetwork most disrupted in LOAD•NCH-51 normalizes neuronal impairment and neurodegeneration caused by ATP6V1A deficit
Employing an integrative network biology approach, Wang et al. identify critical gene subnetworks associated with late-onset Alzheimer’s disease (LOAD) and predict ATP6V1A as a key regulator of a neuron-specific subnetwork most affected by LOAD. ATP6V1A deficit causes neuronal impairment and neurodegeneration, which are normalized by a predicted compound, NCH-51.
BRD4, a major tandem-bromodomain-containing transcription regulator, has two isoforms. The long isoform (BRD4L) has an extended C terminus that binds transcription cofactors, while the short isoform ...(BRD4S) lacks this C-terminal extension. Unlike BRD4L, the role of BRD4S in gene transcription remains unclear. Here, we report that, in human cancer cells, BRD4S forms nuclear puncta that possess liquid-like properties and that colocalize with BRD4L, MED1 and sites of histone H3 lysine 27 acetylation. BRD4 puncta are correlated with BRD4S but not BRD4L expression levels. BRD4S knockdown reduces BRD4S condensation, and ectopic expression promotes puncta formation and target gene transcription. BRD4S nuclear condensation is mediated by its intrinsically disordered regions and binding of its bromodomains to DNA and acetylated chromatin, respectively, and BRD4S phosphorylation diminishes BRD4 condensation. Our study illuminates a previously unappreciated role of BRD4S in organizing chromatin and transcription factors through phase separation to sustain gene transcription in chromatin for cancer cell proliferation.
BRD4 assembles transcriptional machinery at gene super-enhancer regions and governs the expression of genes that are critical for cancer progression. However, it remains unclear whether BRD4-mediated ...gene transcription is required for tumor cells to develop drug resistance. Our data show that prolonged treatment of luminal breast cancer cells with AKT inhibitors induces FOXO3a dephosphorylation, nuclear translocation, and disrupts its association with SirT6, eventually leading to FOXO3a acetylation as well as BRD4 recognition. Acetylated FOXO3a recognizes the BD2 domain of BRD4, recruits the BRD4/RNAPII complex to the CDK6 gene promoter, and induces its transcription. Pharmacological inhibition of either BRD4/FOXO3a association or CDK6 significantly overcomes the resistance of luminal breast cancer cells to AKT inhibitors in vitro and in vivo. Our study reports the involvement of BRD4/FOXO3a/CDK6 axis in AKTi resistance and provides potential therapeutic strategies for treating resistant breast cancer.
Precise control over the size, shape, composition, structure, and crystal phase of random alloy and intermetallic nanocrystals has been intensively explored in technologically important applications ...in recent years. Different from the monometallic nanocrystals and other types of structural nanocrystals such as core–shell and heterostructured nanocrystals, well-defined multimetallic random alloy and intermetallic nanocrystals exhibit unique and intriguing physicochemical properties, serving as ideal models for benefiting the structure-to-property studies. As such, random alloy and intermetallic nanocrystals have attracted extensive attention and interest in scientific research and shown huge potential in various fields. In this review, we focus specifically on summarizing the synthetic principles and strategies developed to form random alloy and intermetallic nanocrystals with enhanced performance. Some representative examples are purposely selected for emphasizing basic concepts and mechanistic understanding. We then highlight the fascinating properties and widespread applications of random alloy and intermetallic nanocrystals in electrocatalysis, heterogeneous catalysis, optical and photocatalysis, as well as magnetism and conclude the review by addressing the prospects and current challenges for the controlled synthesis of random alloy and intermetallic nanocrystals.
Nitryl cyanide, O
NCN, as a new high-energy molecule, has not yet been successfully synthesized. It has prompted us to conduct a theoretical study of its possible space structures and properties. The ...RESP charges and the most stable spatial structures demonstrate that crystal morphology is affected by both the main nonbonded interactions and the molecular arrangement. The crystal structure prediction indicated that there are seven structures, namely P1, P2
, P2
2
2
, P2
/c, Pna2
, Pbca, and C2/c. The most stable space structure is likely to be Pna2
and the corresponding cell parameters are Z = 4, a = 8.69 Å, b = 9.07 Å, c = 9.65 Å, and α = β = γ = 90.0°. To further study the intermolecular interactions of TNTA, a series of theoretical analyses were employed, including Hirshfeld surface analysis and fingerprint plots. The pyrolysis mechanism and properties show that high temperatures can promote decomposition. The systematic search approach can be a new strategy to identify structures effectively and has the potential to provide systematic theoretical guidance for the synthesis of TNTA.
Lysine acetylation is a fundamental post-translational modification that plays an important role in the control of gene transcription in chromatin in an ordered fashion. The bromodomain, the ...conserved structural module present in transcription-associated proteins, functions exclusively to recognize acetyl-lysine on histones and non-histone proteins. The structural analyses of bromodomains' recognition of lysine-acetylated peptides derived from histones and cellular proteins provide detailed insights into the differences and unifying features of biological ligand binding selectivity by the bromodomains. Newly developed small-molecule inhibitors targeting bromodomain proteins further highlight the functional importance of bromodomain/acetyl-lysine binding as a key mechanism in orchestrating molecular interactions and regulation in chromatin biology and gene transcription. These new studies argue that modulating bromodomain/acetyl-lysine interactions with small-molecule chemicals offer new opportunities to control gene expression in a wide array of human diseases including cancer and inflammation. This article is part of a Special Issue entitled: Molecular mechanisms of histone modification function.
•Structure and function of bromodomains as the acetyl-lysine binding domains.•Small molecule inhibitors of bromodomains.•Bromodomain inhibitors as epigenetic chemical modulators to control gene transcriptional activation.
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