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1.
Annu Rev Biochem ; 90: 375-401, 2021 06 20.
Article in English | MEDLINE | ID: mdl-33441035

ABSTRACT

Codon usage bias, the preference for certain synonymous codons, is found in all genomes. Although synonymous mutations were previously thought to be silent, a large body of evidence has demonstrated that codon usage can play major roles in determining gene expression levels and protein structures. Codon usage influences translation elongation speed and regulates translation efficiency and accuracy. Adaptation of codon usage to tRNA expression determines the proteome landscape. In addition, codon usage biases result in nonuniform ribosome decoding rates on mRNAs, which in turn influence the cotranslational protein folding process that is critical for protein function in diverse biological processes. Conserved genome-wide correlations have also been found between codon usage and protein structures. Furthermore, codon usage is a major determinant of mRNA levels through translation-dependent effects on mRNA decay and translation-independent effects on transcriptional and posttranscriptional processes. Here, we discuss the multifaceted roles and mechanisms of codon usage in different gene regulatory processes.


Subject(s)
Codon Usage , Gene Expression , Protein Biosynthesis , Protein Folding , Animals , Eukaryota/genetics , Humans , RNA, Messenger/genetics , RNA, Messenger/metabolism , RNA, Transfer/genetics , RNA, Transfer/metabolism , Ribosomes/genetics , Ribosomes/metabolism
2.
Nature ; 620(7975): 756-761, 2023 Aug.
Article in English | MEDLINE | ID: mdl-37468634

ABSTRACT

Van der Waals assembly enables the design of electronic states in two-dimensional (2D) materials, often by superimposing a long-wavelength periodic potential on a crystal lattice using moiré superlattices1-9. This twistronics approach has resulted in numerous previously undescribed physics, including strong correlations and superconductivity in twisted bilayer graphene10-12, resonant excitons, charge ordering and Wigner crystallization in transition-metal chalcogenide moiré structures13-18 and Hofstadter's butterfly spectra and Brown-Zak quantum oscillations in graphene superlattices19-22. Moreover, twistronics has been used to modify near-surface states at the interface between van der Waals crystals23,24. Here we show that electronic states in three-dimensional (3D) crystals such as graphite can be tuned by a superlattice potential occurring at the interface with another crystal-namely, crystallographically aligned hexagonal boron nitride. This alignment results in several Lifshitz transitions and Brown-Zak oscillations arising from near-surface states, whereas, in high magnetic fields, fractal states of Hofstadter's butterfly draw deep into the bulk of graphite. Our work shows a way in which 3D spectra can be controlled using the approach of 2D twistronics.

3.
Nature ; 624(7991): 378-389, 2023 Dec.
Article in English | MEDLINE | ID: mdl-38092917

ABSTRACT

Recent advances in single-cell technologies have led to the discovery of thousands of brain cell types; however, our understanding of the gene regulatory programs in these cell types is far from complete1-4. Here we report a comprehensive atlas of candidate cis-regulatory DNA elements (cCREs) in the adult mouse brain, generated by analysing chromatin accessibility in 2.3 million individual brain cells from 117 anatomical dissections. The atlas includes approximately 1 million cCREs and their chromatin accessibility across 1,482 distinct brain cell populations, adding over 446,000 cCREs to the most recent such annotation in the mouse genome. The mouse brain cCREs are moderately conserved in the human brain. The mouse-specific cCREs-specifically, those identified from a subset of cortical excitatory neurons-are strongly enriched for transposable elements, suggesting a potential role for transposable elements in the emergence of new regulatory programs and neuronal diversity. Finally, we infer the gene regulatory networks in over 260 subclasses of mouse brain cells and develop deep-learning models to predict the activities of gene regulatory elements in different brain cell types from the DNA sequence alone. Our results provide a resource for the analysis of cell-type-specific gene regulation programs in both mouse and human brains.


Subject(s)
Brain , Chromatin , Single-Cell Analysis , Animals , Humans , Mice , Brain/cytology , Brain/metabolism , Cerebral Cortex/cytology , Chromatin/chemistry , Chromatin/genetics , Chromatin/metabolism , Deep Learning , DNA Transposable Elements/genetics , Gene Regulatory Networks/genetics , Neurons/metabolism
4.
EMBO J ; 42(20): e113743, 2023 10 16.
Article in English | MEDLINE | ID: mdl-37661833

ABSTRACT

Mitochondria play essential roles in cancer cell adaptation to hypoxia, but the underlying mechanisms remain elusive. Through mitochondrial proteomic profiling, we here find that the prolyl hydroxylase EglN1 (PHD2) accumulates on mitochondria under hypoxia. EglN1 substrate-binding region in the ß2ß3 loop is responsible for its mitochondrial translocation and contributes to breast tumor growth. Furthermore, we identify AMP-activated protein kinase alpha (AMPKα) as an EglN1 substrate on mitochondria. The EglN1-AMPKα interaction is essential for their mutual mitochondrial translocation. After EglN1 prolyl-hydroxylates AMPKα under normoxia, they rapidly dissociate following prolyl-hydroxylation, leading to their immediate release from mitochondria. In contrast, hypoxia results in constant EglN1-AMPKα interaction and their accumulation on mitochondria, leading to the formation of a Ca2+ /calmodulin-dependent protein kinase 2 (CaMKK2)-EglN1-AMPKα complex to activate AMPKα phosphorylation, ensuring metabolic homeostasis and breast tumor growth. Our findings identify EglN1 as an oxygen-sensitive metabolic checkpoint signaling hypoxic stress to mitochondria through its ß2ß3 loop region, suggesting a potential therapeutic target for breast cancer.


Subject(s)
AMP-Activated Protein Kinases , Breast Neoplasms , Female , Humans , AMP-Activated Protein Kinases/metabolism , Breast Neoplasms/genetics , Breast Neoplasms/metabolism , Hypoxia , Hypoxia-Inducible Factor-Proline Dioxygenases/genetics , Hypoxia-Inducible Factor-Proline Dioxygenases/metabolism , Mitochondria/metabolism , Proteomics
5.
Proc Natl Acad Sci U S A ; 121(26): e2320835121, 2024 Jun 25.
Article in English | MEDLINE | ID: mdl-38900797

ABSTRACT

Upper aerodigestive squamous cell carcinoma (UASCC) is a common and aggressive malignancy with few effective therapeutic options. Here, we investigate amino acid metabolism in this cancer, surprisingly noting that UASCC exhibits the highest methionine level across all human cancers, driven by its transporter LAT1. We show that LAT1 is also expressed at the highest level in UASCC, transcriptionally activated by UASCC-specific promoter and enhancers, which are directly coregulated by SCC master regulators TP63/KLF5/SREBF1. Unexpectedly, unbiased bioinformatic screen identifies EZH2 as the most significant target downstream of the LAT1-methionine pathway, directly linking methionine metabolism to epigenomic reprogramming. Importantly, this cascade is indispensable for the survival and proliferation of UASCC patient-derived tumor organoids. In addition, LAT1 expression is closely associated with cellular sensitivity to inhibition of the LAT1-methionine-EZH2 axis. Notably, this unique LAT1-methionine-EZH2 cascade can be targeted effectively by either pharmacological approaches or dietary intervention in vivo. In summary, this work maps a unique mechanistic cross talk between epigenomic reprogramming with methionine metabolism, establishes its biological significance in the biology of UASCC, and identifies a unique tumor-specific vulnerability which can be exploited both pharmacologically and dietarily.


Subject(s)
Carcinoma, Squamous Cell , Gene Expression Regulation, Neoplastic , Large Neutral Amino Acid-Transporter 1 , Methionine , Methionine/metabolism , Humans , Large Neutral Amino Acid-Transporter 1/metabolism , Large Neutral Amino Acid-Transporter 1/genetics , Carcinoma, Squamous Cell/genetics , Carcinoma, Squamous Cell/metabolism , Carcinoma, Squamous Cell/pathology , Enhancer of Zeste Homolog 2 Protein/metabolism , Enhancer of Zeste Homolog 2 Protein/genetics , Cell Line, Tumor , Epigenesis, Genetic , Epigenomics/methods , Head and Neck Neoplasms/genetics , Head and Neck Neoplasms/metabolism , Head and Neck Neoplasms/pathology , Mice , Squamous Cell Carcinoma of Head and Neck/genetics , Squamous Cell Carcinoma of Head and Neck/metabolism , Squamous Cell Carcinoma of Head and Neck/pathology , Animals , Cell Proliferation , Kruppel-Like Transcription Factors/metabolism , Kruppel-Like Transcription Factors/genetics , Cellular Reprogramming/genetics
6.
Circ Res ; 134(8): e72-e91, 2024 Apr 12.
Article in English | MEDLINE | ID: mdl-38456298

ABSTRACT

BACKGROUND: CNP (C-type natriuretic peptide), an endogenous short peptide in the natriuretic peptide family, has emerged as an important regulator to govern vascular homeostasis. However, its role in the development of atherosclerosis remains unclear. This study aimed to investigate the impact of CNP on the progression of atherosclerotic plaques and elucidate its underlying mechanisms. METHODS: Plasma CNP levels were measured in patients with acute coronary syndrome. The potential atheroprotective role of CNP was evaluated in apolipoprotein E-deficient (ApoE-/-) mice through CNP supplementation via osmotic pumps, genetic overexpression, or LCZ696 administration. Various functional experiments involving CNP treatment were performed on primary macrophages derived from wild-type and CD36 (cluster of differentiation 36) knockout mice. Proteomics and multiple biochemical analyses were conducted to unravel the underlying mechanism. RESULTS: We observed a negative correlation between plasma CNP concentration and the burden of coronary atherosclerosis in patients. In early atherosclerotic plaques, CNP predominantly accumulated in macrophages but significantly decreased in advanced plaques. Supplementing CNP via osmotic pumps or genetic overexpression ameliorated atherosclerotic plaque formation and enhanced plaque stability in ApoE-/- mice. CNP promoted an anti-inflammatory macrophage phenotype and efferocytosis and reduced foam cell formation and necroptosis. Mechanistically, we found that CNP could accelerate HIF-1α (hypoxia-inducible factor 1-alpha) degradation in macrophages by enhancing the interaction between PHD (prolyl hydroxylase domain-containing protein) 2 and HIF-1α. Furthermore, we observed that CD36 bound to CNP and mediated its endocytosis in macrophages. Moreover, we demonstrated that the administration of LCZ696, an orally bioavailable drug recently approved for treating chronic heart failure with reduced ejection fraction, could amplify the bioactivity of CNP and ameliorate atherosclerotic plaque formation. CONCLUSIONS: Our study reveals that CNP enhanced plaque stability and alleviated macrophage inflammatory responses by promoting HIF-1α degradation, suggesting a novel atheroprotective role of CNP. Enhancing CNP bioactivity may offer a novel pharmacological strategy for treating related diseases.


Subject(s)
Atherosclerosis , Plaque, Atherosclerotic , Humans , Mice , Animals , Plaque, Atherosclerotic/metabolism , Atherosclerosis/drug therapy , Atherosclerosis/genetics , Atherosclerosis/prevention & control , Macrophages/metabolism , Foam Cells/metabolism , Mice, Knockout , Apolipoproteins E , Mice, Inbred C57BL
7.
Nature ; 588(7837): 250-253, 2020 12.
Article in English | MEDLINE | ID: mdl-33299189

ABSTRACT

Capillary condensation of water is ubiquitous in nature and technology. It routinely occurs in granular and porous media, can strongly alter such properties as adhesion, lubrication, friction and corrosion, and is important in many processes used by microelectronics, pharmaceutical, food and other industries1-4. The century-old Kelvin equation5 is frequently used to describe condensation phenomena and has been shown to hold well for liquid menisci with diameters as small as several nanometres1-4,6-14. For even smaller capillaries that are involved in condensation under ambient humidity and so of particular practical interest, the Kelvin equation is expected to break down because the required confinement becomes comparable to the size of water molecules1-22. Here we use van der Waals assembly of two-dimensional crystals to create atomic-scale capillaries and study condensation within them. Our smallest capillaries are less than four ångströms in height and can accommodate just a monolayer of water. Surprisingly, even at this scale, we find that the macroscopic Kelvin equation using the characteristics of bulk water describes the condensation transition accurately in strongly hydrophilic (mica) capillaries and remains qualitatively valid for weakly hydrophilic (graphite) ones. We show that this agreement is fortuitous and can be attributed to elastic deformation of capillary walls23-25, which suppresses the giant oscillatory behaviour expected from the commensurability between the atomic-scale capillaries and water molecules20,21. Our work provides a basis for an improved understanding of capillary effects at the smallest scale possible, which is important in many realistic situations.

8.
Nucleic Acids Res ; 52(4): 1878-1895, 2024 Feb 28.
Article in English | MEDLINE | ID: mdl-38153123

ABSTRACT

The exonuclease ISG20L2 has been initially characterized for its role in the mammalian 5.8S rRNA 3' end maturation, specifically in the cleavage of ITS2 of 12S precursor ribosomal RNA (pre-rRNA). Here, we show that human ISG20L2 is also involved in 18S pre-rRNA maturation through removing the ITS1 region, and contributes to ribosomal biogenesis and cell proliferation. Furthermore, we determined the crystal structure of the ISG20L2 nuclease domain at 2.9 Å resolution. It exhibits the typical αßα fold of the DEDD 3'-5' exonuclease with a catalytic pocket located in the hollow near the center. The catalytic residues Asp183, Glu185, Asp267, His322 and Asp327 constitute the DEDDh motif in ISG20L2. The active pocket represents conformational flexibility in the absence of an RNA substrate. Using structural superposition and mutagenesis assay, we mapped RNA substrate binding residues in ISG20L2. Finally, cellular assays revealed that ISG20L2 is aberrantly up-regulated in colon adenocarcinoma and promotes colon cancer cell proliferation through regulating ribosome biogenesis. Together, these results reveal that ISG20L2 is a new enzymatic member for 18S pre-rRNA maturation, provide insights into the mechanism of ISG20L2 underlying pre-rRNA processing, and suggest that ISG20L2 is a potential therapeutic target for colon adenocarcinoma.


Subject(s)
Adenocarcinoma , Colonic Neoplasms , Animals , Humans , RNA, Ribosomal, 18S/metabolism , RNA Precursors/genetics , RNA Precursors/metabolism , Adenocarcinoma/genetics , Colonic Neoplasms/genetics , RNA, Ribosomal/genetics , RNA, Ribosomal/metabolism , Ribosomes/genetics , Ribosomes/metabolism , RNA Processing, Post-Transcriptional , Exonucleases/genetics , Exonucleases/metabolism , RNA, Ribosomal, 5.8S/genetics , Mammals/genetics
9.
Nucleic Acids Res ; 52(13): 7740-7760, 2024 Jul 22.
Article in English | MEDLINE | ID: mdl-38932701

ABSTRACT

Androgen receptor- (AR-) indifference is a mechanism of resistance to hormonal therapy in prostate cancer (PC). Here we demonstrate that ONECUT2 (OC2) activates resistance through multiple drivers associated with adenocarcinoma, stem-like and neuroendocrine (NE) variants. Direct OC2 gene targets include the glucocorticoid receptor (GR; NR3C1) and the NE splicing factor SRRM4, which are key drivers of lineage plasticity. Thus, OC2, despite its previously described NEPC driver function, can indirectly activate a portion of the AR cistrome through epigenetic activation of GR. Mechanisms by which OC2 regulates gene expression include promoter binding, enhancement of genome-wide chromatin accessibility, and super-enhancer reprogramming. Pharmacologic inhibition of OC2 suppresses lineage plasticity reprogramming induced by the AR signaling inhibitor enzalutamide. These results demonstrate that OC2 activation promotes a range of drug resistance mechanisms associated with treatment-emergent lineage variation in PC and support enhanced efforts to therapeutically target OC2 as a means of suppressing treatment-resistant disease.


Subject(s)
Adenocarcinoma , Benzamides , Drug Resistance, Neoplasm , Gene Expression Regulation, Neoplastic , Nitriles , Prostatic Neoplasms , Receptors, Androgen , Receptors, Glucocorticoid , Male , Humans , Receptors, Androgen/metabolism , Receptors, Androgen/genetics , Adenocarcinoma/genetics , Adenocarcinoma/pathology , Adenocarcinoma/metabolism , Adenocarcinoma/drug therapy , Receptors, Glucocorticoid/metabolism , Receptors, Glucocorticoid/genetics , Prostatic Neoplasms/genetics , Prostatic Neoplasms/pathology , Prostatic Neoplasms/metabolism , Prostatic Neoplasms/drug therapy , Drug Resistance, Neoplasm/genetics , Benzamides/pharmacology , Cell Line, Tumor , Nitriles/pharmacology , Phenylthiohydantoin/pharmacology , Phenylthiohydantoin/analogs & derivatives , Nerve Tissue Proteins/genetics , Nerve Tissue Proteins/metabolism , Epigenesis, Genetic , RNA-Binding Proteins/metabolism , RNA-Binding Proteins/genetics , Neuroendocrine Tumors/genetics , Neuroendocrine Tumors/pathology , Neuroendocrine Tumors/metabolism , Neuroendocrine Tumors/drug therapy , Animals , Cell Lineage/genetics , Mice
10.
Proc Natl Acad Sci U S A ; 120(29): e2213824120, 2023 07 18.
Article in English | MEDLINE | ID: mdl-37428923

ABSTRACT

Cohn et al. (2019) conducted a wallet drop experiment in 40 countries to measure "civic honesty around the globe," which has received worldwide attention but also sparked controversies over using the email response rate as the sole metric of civic honesty. Relying on the lone measurement may overlook cultural differences in behaviors that demonstrate civic honesty. To investigate this issue, we conducted an extended replication study in China, utilizing email response and wallet recovery to assess civic honesty. We found a significantly higher level of civic honesty in China, as measured by the wallet recovery rate, than reported in the original study, while email response rates remained similar. To resolve the divergent results, we introduce a cultural dimension, individualism versus collectivism, to study civic honesty across diverse cultures. We hypothesize that cultural differences in individualism and collectivism could influence how individuals prioritize actions when handling a lost wallet, such as contacting the wallet owner or safeguarding the wallet. In reanalyzing Cohn et al.'s data, we found that email response rates were inversely related to collectivism indices at the country level. However, our replication study in China demonstrated that the likelihood of wallet recovery was positively correlated with collectivism indicators at the provincial level. Consequently, relying solely on email response rates to gauge civic honesty in cross-country comparisons may neglect the vital individualism versus collectivism dimension. Our study not only helps reconcile the controversy surrounding Cohn et al.'s influential field experiment but also furnishes a fresh cultural perspective to evaluate civic honesty.


Subject(s)
Individuality , Humans , China
11.
Bioinformatics ; 40(4)2024 Mar 29.
Article in English | MEDLINE | ID: mdl-38426310

ABSTRACT

MOTIVATION: Predicting molecular properties is a pivotal task in various scientific domains, including drug discovery, material science, and computational chemistry. This problem is often hindered by the lack of annotated data and imbalanced class distributions, which pose significant challenges in developing accurate and robust predictive models. RESULTS: This study tackles these issues by employing pretrained molecular models within a few-shot learning framework. A novel dynamic contrastive loss function is utilized to further improve model performance in the situation of class imbalance. The proposed MolFeSCue framework not only facilitates rapid generalization from minimal samples, but also employs a contrastive loss function to extract meaningful molecular representations from imbalanced datasets. Extensive evaluations and comparisons of MolFeSCue and state-of-the-art algorithms have been conducted on multiple benchmark datasets, and the experimental data demonstrate our algorithm's effectiveness in molecular representations and its broad applicability across various pretrained models. Our findings underscore MolFeSCues potential to accelerate advancements in drug discovery. AVAILABILITY AND IMPLEMENTATION: We have made all the source code utilized in this study publicly accessible via GitHub at http://www.healthinformaticslab.org/supp/ or https://github.com/zhangruochi/MolFeSCue. The code (MolFeSCue-v1-00) is also available as the supplementary file of this paper.


Subject(s)
Algorithms , Benchmarking , Drug Discovery , Models, Molecular , Software
12.
Brain ; 2024 Jul 04.
Article in English | MEDLINE | ID: mdl-38963812

ABSTRACT

The medial prefrontal cortex (mPFC) has been implicated in the pathophysiology of social impairments including social fear. However, the precise subcortical partners that mediate mPFC dysfunction on social fear behaviour have not been identified. Employing a social fear conditioning paradigm, we induced robust social fear in mice and found that the lateral habenula (LHb) neurons and LHb-projecting mPFC neurons are synchronously activated during social fear expression. Moreover, optogenetic inhibition of the mPFC-LHb projection significantly reduced social fear responses. Importantly, consistent with animal studies, we observed an elevated prefrontal-habenular functional connectivity in subclinical individuals with higher social anxiety characterized by heightened social fear. These results unravel a crucial role of the prefrontal-habenular circuitry in social fear regulation and suggest that this pathway could serve as a potential target for the treatment of social fear symptom often observed in many psychiatric disorders.

13.
Proc Natl Acad Sci U S A ; 119(4)2022 01 25.
Article in English | MEDLINE | ID: mdl-35046043

ABSTRACT

Receptor usage defines cell tropism and contributes to cell entry and infection. Coxsackievirus B (CVB) engages coxsackievirus and adenovirus receptor (CAR), and selectively utilizes the decay-accelerating factor (DAF; CD55) to infect cells. However, the differential receptor usage mechanism for CVB remains elusive. This study identified VP3-234 residues (234Q/N/V/D/E) as critical population selection determinants during CVB3 virus evolution, contributing to diverse binding affinities to CD55. Cryoelectron microscopy (cryo-EM) structures of CD55-binding/nonbinding isolates and their complexes with CD55 or CAR were obtained under both neutral and acidic conditions, and the molecular mechanism of VP3-234 residues determining CD55 affinity/specificity for naturally occurring CVB3 strains was elucidated. Structural and biochemical studies in vitro revealed the dynamic entry process of CVB3 and the function of the uncoating receptor CAR with different pH preferences. This work provides detailed insight into the molecular mechanism of CVB infection and contributes to an in-depth understanding of enterovirus attachment receptor usage.


Subject(s)
CD55 Antigens/metabolism , Coxsackievirus Infections/metabolism , Coxsackievirus Infections/virology , Enterovirus B, Human/physiology , Host-Pathogen Interactions , Receptors, Virus/metabolism , Amino Acid Sequence , Amino Acid Substitution , Binding Sites , Enterovirus B, Human/ultrastructure , Humans , Models, Molecular , Protein Binding , Protein Conformation , Protein Interaction Domains and Motifs , Receptors, Virus/chemistry , Structure-Activity Relationship , Virus Attachment
14.
Genomics ; 116(1): 110763, 2024 01.
Article in English | MEDLINE | ID: mdl-38110129

ABSTRACT

Since smallpox was eradicated in 1980, the monkeypox virus (MPXV) has emerged as the most threatening orthopoxvirus in the world. In this study, we conducted a comprehensive analysis of the currently published complete genome sequences of the monkeypox virus. The core/variable regions were identified through core-pan analysis of MPXV. Besides single-nucleotide polymorphisms, our study also revealed that specific genes, multi-copy genes, repeat sequences, and recombination fragments are primarily distributed in the variable region. This result suggests that variable regions are not only more susceptible to single-base mutations, but also to events such as gene loss or gain, as well as recombination. Taken together, our results demonstrate the genomic characteristics of the core/variable regions of MPXV, and contribute to our understanding of the evolution of MPXV.


Subject(s)
Monkeypox virus , Mpox (monkeypox) , Humans , Monkeypox virus/genetics , Genomics , Mutation , Polymorphism, Single Nucleotide
15.
Nano Lett ; 24(15): 4546-4553, 2024 Apr 17.
Article in English | MEDLINE | ID: mdl-38588452

ABSTRACT

Organic materials have attracted extensive attention for potassium-ion batteries due to their flexible structure designability and environmental friendliness. However, organic materials generally suffer from unavoidable dissolution in aprotic electrolytes, causing an unsatisfactory electrochemical performance. Herein, we designed a weakly solvating electrolyte to boost the potassium storage performance of perylene-3,4,9,10-tetracarboxylic dianhydride (PTCDA). The electrolyte induces an in situ morphology evolution and achieves a nanowire structure. The weakly dissolving capability of ethylene glycol diethyl ether-based electrolyte and unique nanowire structure effectively avoid the dissolution of PTCDA. As a result, PTCDA shows excellent cycling stability (a capacity retention of 89.1% after 2000 cycles) and good rate performance (70.3 mAh g-1 at 50C). In addition, experimental detail discloses that the sulfonyl group plays a key role in inducing morphology evolution during the charge/discharge process. This work opens up new opportunities in electrolyte design for organic electrodes and illuminates further developments of potassium-ion batteries.

16.
Med Res Rev ; 44(5): 1971-2014, 2024 09.
Article in English | MEDLINE | ID: mdl-38515232

ABSTRACT

Atropisomerism, an expression of axial chirality caused by limited bond rotation, is a prominent aspect within the field of medicinal chemistry. It has been shown that atropisomers of a wide range of compounds, including established FDA-approved drugs and experimental molecules, display markedly different biological activities. The time-dependent reversal of chirality in atropisomers poses complexity and obstacles in the process of drug discovery and development. Nonetheless, recent progress in understanding atropisomerism and enhanced characterization methods have greatly assisted medicinal chemists in the effective development of atropisomeric drug molecules. This article provides a comprehensive review of their special design thoughts, synthetic routes, and biological activities, serving as a reference for the synthesis and biological evaluation of bioactive atropisomers in the future.


Subject(s)
Drug Design , Drug Discovery , Stereoisomerism , Humans , Animals
17.
J Cell Mol Med ; 28(11): e18366, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38856956

ABSTRACT

Ischemic stroke is one of the main causes of disability and death. However, recanalization of occluded cerebral arteries is effective only within a very narrow time window. Therefore, it is particularly important to find neuroprotective biological targets for cerebral artery recanalization. Here, gene expression profiles of datasets GSE160500 and GSE97537 were downloaded from the GEO database, which were related to ischemic stroke in rats. Olfactory receptor 78 (Olfr78) was screened, and which highly associated with Calcium signalling pathway and MAPK pathway. Interacting protein of Olfr78, Prkaca, was predicted by STRING, and their interaction was validated by Co-IP analysis. Then, a rat model of middle cerebral artery occlusion/reperfusion (MCAO/R) and a neuronal cell model stimulated by oxygen-glucose deprivation/reoxygenation (OGD/R) were constructed, and the results showed that expression of Olfr78 and Prkaca was downregulated in MCAO rats and OGD/R-stimulated neurons. Overexpression of Olfr78 or Prkaca inhibited the secretion of inflammatory factors, Ca2+ overload, and OGD/R-induced neuronal apoptosis. Moreover, Overexpression of Prkaca increased protein levels of cAMP, PKA and phosphorylated p38 in OGD/R-stimulated neurons, while SB203580, a p38 inhibitor, treatment inhibited activation of the cAMP/PKA-MAPK pathway and counteracted the effect of Olfr78 overexpression on improvement of neuronal functions. Meanwhile, overexpression of Olfr78 or Prkaca markedly inhibited neuronal apoptosis and improved brain injury in MCAO/R rats. In conclusion, overexpression of Olfr78 inhibited Ca2+ overload and reduced neuronal apoptosis in MCAO/R rats by promoting Prkaca-mediated activation of the cAMP/PKA-MAPK pathway, thereby improving brain injury in cerebral ischaemia-reperfusion.


Subject(s)
Apoptosis , Cyclic AMP , Rats, Sprague-Dawley , Receptors, Odorant , Reperfusion Injury , Animals , Reperfusion Injury/metabolism , Reperfusion Injury/genetics , Rats , Male , Cyclic AMP/metabolism , Receptors, Odorant/metabolism , Receptors, Odorant/genetics , Brain Ischemia/metabolism , Brain Ischemia/genetics , Brain Ischemia/pathology , MAP Kinase Signaling System/drug effects , Cyclic AMP-Dependent Protein Kinases/metabolism , Brain Injuries/metabolism , Brain Injuries/etiology , Brain Injuries/pathology , Neurons/metabolism , Disease Models, Animal , Infarction, Middle Cerebral Artery/metabolism , Signal Transduction
18.
PLoS Med ; 21(3): e1004363, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38547436

ABSTRACT

BACKGROUND: Premenstrual disorders (PMDs) and perinatal depression (PND) share symptomology and the timing of symptoms of both conditions coincide with natural hormonal fluctuations, which may indicate a shared etiology. Yet, there is a notable absence of prospective data on the potential bidirectional association between these conditions, which is crucial for guiding clinical management. Using the Swedish nationwide registers with prospectively collected data, we aimed to investigate the bidirectional association between PMDs and PND. METHODS AND FINDINGS: With 1,803,309 singleton pregnancies of 1,041,419 women recorded in the Swedish Medical Birth Register during 2001 to 2018, we conducted a nested case-control study to examine the risk of PND following PMDs, which is equivalent to a cohort study, and transitioned that design into a matched cohort study with onward follow-up to simulate a prospective study design and examine the risk of PMDs after PND (within the same study population). Incident PND and PMDs were identified through clinical diagnoses or prescribed medications. We randomly selected 10 pregnant women without PND, individually matched to each PND case on maternal age and calendar year using incidence density sampling (N: 84,949: 849,482). We (1) calculated odds ratio (OR) and 95% confidence intervals (CIs) of PMDs using conditional logistic regression in the nested case-control study. Demographic factors (country of birth, educational level, region of residency, and cohabitation status) were adjusted for. We (2) calculated the hazard ratio (HR) and 95% CIs of PMDs subsequent to PND using stratified Cox regression in the matched cohort study. Smoking, BMI, parity, and history of psychiatric disorders were further controlled for, in addition to demographic factors. Pregnancies from full sisters of PND cases were identified for sibling comparison, which contrasts the risk within each set of full sisters discordant on PND. In the nested case-control study, we identified 2,488 PMDs (2.9%) before pregnancy among women with PND and 5,199 (0.6%) among controls. PMDs were associated with a higher risk of subsequent PND (OR 4.76, 95% CI [4.52,5.01]; p < 0.001). In the matched cohort with a mean follow-up of 7.40 years, we identified 4,227 newly diagnosed PMDs among women with PND (incidence rate (IR) 7.6/1,000 person-years) and 21,326 among controls (IR 3.8). Compared to their matched controls, women with PND were at higher risk of subsequent PMDs (HR 1.81, 95% CI [1.74,1.88]; p < 0.001). The bidirectional association was noted for both prenatal and postnatal depression and was stronger among women without history of psychiatric disorders (p for interaction < 0.001). Sibling comparison showed somewhat attenuated, yet statistically significant, bidirectional associations. The main limitation of this study was that our findings, based on clinical diagnoses recorded in registers, may not generalize well to women with mild PMDs or PND. CONCLUSIONS: In this study, we observed a bidirectional association between PMDs and PND. These findings suggest that a history of PMDs can inform PND susceptibility and vice versa and lend support to the shared etiology between both disorders.


Subject(s)
Depression , Humans , Female , Pregnancy , Cohort Studies , Sweden/epidemiology , Prospective Studies , Case-Control Studies , Risk Factors
19.
Eur J Neurosci ; 59(3): 446-456, 2024 Feb.
Article in English | MEDLINE | ID: mdl-38123158

ABSTRACT

The anterior cingulate cortex (ACC) and visual cortex are integral components of the neurophysiological mechanisms underlying migraine, yet the impact of altered connectivity patterns between these regions on migraine treatment remains unknown. To elucidate this issue, we investigated the abnormal causal connectivity between the ACC and visual cortex in patients with migraine without aura (MwoA), based on the resting-state functional magnetic resonance imaging data, and its predictive ability for the efficacy of nonsteroidal anti-inflammatory drugs (NSAIDs). The results revealed increased causal connectivity from the bilateral ACC to the lingual gyrus (LG) and decreased connectivity in the opposite direction in nonresponders compared with the responders. Moreover, compared with the healthy controls, nonresponders exhibited heightened causal connectivity from the ACC to the LG, right inferior occipital gyrus (IOG) and left superior occipital gyrus, while connectivity patterns from the LG and right IOG to the ACC were diminished. Based on the observed abnormal connectivity patterns, the support vector machine (SVM) models showed that the area under the receiver operator characteristic curves for the ACC to LG, LG to ACC and bidirectional models were 0.857, 0.898, and 0.939, respectively. These findings indicate that neuroimaging markers of abnormal causal connectivity in the ACC-visual cortex circuit may facilitate clinical decision-making regarding NSAIDs administration for migraine management.


Subject(s)
Migraine without Aura , Visual Cortex , Humans , Gyrus Cinguli/diagnostic imaging , Magnetic Resonance Imaging/methods , Migraine without Aura/pathology , Visual Cortex/diagnostic imaging , Anti-Inflammatory Agents, Non-Steroidal/pharmacology , Anti-Inflammatory Agents, Non-Steroidal/therapeutic use , Anti-Inflammatory Agents , Brain
20.
Biochem Cell Biol ; 102(3): 252-261, 2024 Jun 01.
Article in English | MEDLINE | ID: mdl-38417127

ABSTRACT

Diabetic kidney disease (DKD) is a major contributor to chronic kidney disease. Hydrogen sulfide (H2S) serves as an endogenous gaseous signaling molecule capable of safeguarding renal function within the context of DKD. However, the underlying mechanisms need to be elucidated. This study was undertaken to unveil the mechanisms by which H2S counteracts against DKD. Utilizing mice and human renal tubular epithelial (HK-2) cells, we demonstrated a reduction in cystathionine-γ-lyase/H2S levels within renal tissues of db/db mice and in HK-2 cells subjected to hyperglycemic and hyperlipidemic environments. Notably, we observed that sodium hydrosulfide (NaHS) supplementation could serve as an exogenous source of H2S. Exogenous H2S exhibited the capacity to mitigate the accumulation of reactive oxygen species and attenuate the degradation of superoxide dismutase 2 (SOD2) by Lon protease homolog 1 induced by hyperglycemia and hyperlipidemia, thus affording cellular protection against mitochondrial apoptosis. Consequently, NaHS treatment led to decreased serum levels of blood urea nitrogen and serum creatinine, reflecting alleviated renal damage and thereby preserving renal function in db/db mice. Based on these findings, we propose that exogenous H2S exerts a protective role against DKD by inhibiting SOD2 degradation.


Subject(s)
Diabetic Nephropathies , Hydrogen Sulfide , Superoxide Dismutase , Animals , Hydrogen Sulfide/metabolism , Hydrogen Sulfide/pharmacology , Diabetic Nephropathies/metabolism , Diabetic Nephropathies/drug therapy , Mice , Humans , Superoxide Dismutase/metabolism , Male , Kidney/metabolism , Kidney/drug effects , Mice, Inbred C57BL , Reactive Oxygen Species/metabolism , Diabetes Mellitus, Experimental/metabolism , Diabetes Mellitus, Experimental/drug therapy
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