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Biology subjects

Sun, Z.

Publications and source records attributed to Sun, Z..

At least 109 records · Page 6Linked to original sources

ARIH1 deficiency impairs spatial learning and memory via GIRK2 upregulation in hippocampal CaMKII-expressing neurons in mice

Alterations of Ariadne RBR E3 Ubiquitin Protein Ligase 1 (ARIH1), a human homologue of Drosophila Ari, have been associated with a number of human diseases. Given the importance of ubiquitin-proteasome system in learning and memory, whether ARIH1 involves in the process has not been explored. Here we report that ARIH1-deficent mice exhibited a defect in learning and memory evidenced in Morris water maze and in novel object recognition tests without changes in basal motor activity, anxiety, and depressive behaviors. We found that ARIH1 deficiency resulted in an upregulation of G protein-gated inwardly rectifying potassium channel 2 (GIRK2) in dorsal hippocampus that was attributed to the impaired ubiquitination and degradation. Locally injection of ARIH1-expressing lentivirus to restore the ARIH1 expression of dorsal hippocampus in ARIH1+/- mice restored the impaired learning and memory. Moreover, selective knockdown ARIH1 in dorsal hippocampal calcium-calmodulin-dependent protein kinase II (CaMKII)-expressing neurons, but not for parvalbumin+ (PV) or somatostatin+ (SST) neurons, in naive mice was sufficient to mimic the damage in learning and memory of ARIH1+/- mice. Lastly, we demonstrated that systemically or locally inhibition of GIRK activity was able to improve ARIH1 deficiency-induced decline of learning and memory in ARIH1+/- mice. The present study discovered the clear role of ARIH1 in mediating learning and memory, defect of ARIH1 resulted in upregulation of GIRK2 in hippocampal CaMKII-expressing neurons via modulating the ubiquitination and degradation GIRK2.

neuroscience↗

A pan-gene catalogue of Asian cultivated rice

The rice genome underpins fundamental research and breeding, but the Nipponbare (japonica) reference does not fully encompass the genetic diversity of Asian rice. To address this gap, the Rice Population Reference Panel (RPRP) was developed, comprising high-quality assemblies of 16 rice cultivars to represent japonica, indica, aus, and aromatic varietal groups. The RPRP has been consistently annotated, supported by extensive experimental data and here we report the computational assignment, characterization and dissemination of stably identified pan-genes. We identified 25,178 core pan-genes shared across all cultivars, alongside cultivar-specific and family-enriched genes. Core genes exhibit higher gene expression and proteomic evidence, higher confidence protein domains and AlphaFold structures, while cultivar-specific genes were enriched for domains under selective breeding pressure, such as for disease resistance. This resource, integrated into public databases, enables researchers to explore genetic and functional diversity via a population-aware "reference guide" across rice genomes, advancing both basic and applied research.

genomics↗

Machine Learning-Enhanced Extraction of Protein Signatures of Renal Cell Carcinoma from Proteomics Data

In this study, we generated label-free data-independent acquisition (DIA)-based liquid chromatography (LC)-mass spectrometry (MS) proteomics data from 261 renal cell carcinomas (RCC) and 195 normal adjacent tissues (NAT). The RCC tumors included 48 non-clear cell renal cell carcinomas (non-ccRCC) and 213 ccRCC. A total of 219,740 peptides and 11,943 protein groups were identified with 9,787 protein groups per sample on average. We adopted a comprehensive approach to select representative samples with different mutation sites, considering histopathological, immune, methylation, and non-negative matrix factorization (NMF)-based subtypes, along with clinical characteristics (gender, grade, and stage) to capture the complexity and diversity of ccRCC tumors. We used machine learning identified 55 protein signatures that distinguish RCC tumors from NATs. Furthermore, 39 protein signatures that differentiate different RCC tumor subtypes were also identified. Our findings offer an extensive perspective of the proteomic landscape in RCC, illuminating specific proteins that serve to distinguish RCC tumors from NATs and among various RCC tumor subtypes.

cancer biology↗

GPR182 is a lipoprotein receptor for dietary fat absorption

The lymphatic system plays a central role in lipid absorption, which transports chylomicrons from the small intestine to the circulation. However, the molecular mechanism by which chylomicrons get into the intestinal lymphatics is unknown. Here we demonstrated that GPR182, a receptor in lymphatic endothelial cells (LECs), mediates dietary fat absorption. GPR182 knockout mice are resistant to dietary-induced obesity. GPR182 ablation in mice leads to poor lipid absorption and thereby a delay in growth during development. GPR182 binds and endocytoses lipoproteins broadly. Mechanistically, loss of GPR182 prevents chylomicrons from entering the lacteal lumen of the small intestine. GPR182 blockage with a monoclonal antibody (mAb) protects mice from dietary induced obesity. Together, our study identifies GPR182 as a lipoprotein receptor that mediates dietary fat absorption.

physiology↗

Leopard Cats Occupied Human Settlements in China for 3,500 years before the Arrival of Domestic cats in 600-900 CE around the Tang Dynasty

The earliest cats in human settlements in China were not domestic cats (Felis catus), but native leopard cats (Prionailurus bengalensis). To trace when and how domestic cats arrived in East Asia, we analyzed 22 feline bones from 14 sites across China spanning 5,000 years. Nuclear and mitochondrial genomes revealed that leopard cats began occupying anthropogenic scenes around 5,400 years ago and last appeared in 150 CE. Following several centuries gap of archeological feline remains, the first known domestic cat (706-883 CE) in China was identified in Shaanxi during the Tang Dynasty. Genomic analysis suggested a white or partially white coat and a link to a contemporaneous domestic cat from Kazakhstan, indicating a likely dispersal route via the Silk Road. The two felids once independently occupied ancient anthropogenic environments in China but followed divergent paths and reached different destinations in human-animal interactions.

evolutionary biology↗

Genetic basis of partner choice

Previous genetic studies of human assortative mating have primarily focused on searching for its genomic footprint but have revealed limited insights into its biological and social mechanisms. Combining insights from the economics of the marriage market with advanced tools in statistical genetics, we perform the first genome-wide association study (GWAS) on a latent index for partner choice. Using 206,617 individuals from four global cohorts, we uncover phenotypic characteristics and social processes underlying assortative mating. We identify a broadly robust genetic component of the partner choice index between sexes and several countries and identify its genetic correlates. We also provide solutions to reduce assortative mating-driven biases in genetic studies of complex traits by conditioning GWAS summary statistics on the genetic associations with the latent partner choice index.

genetics↗

Microglial plasticity governed by state-specific enhancer landscapes

Single-cell transcriptomic studies have identified distinct microglial subpopulations with shared and divergent gene signatures across development, aging and disease. Whether these microglial subsets represent ontogenically separate lineages of cells, or they are manifestations of plastic changes of microglial states downstream of some converging signals is unknown. Furthermore, despite the well-established role of enhancer landscapes underlying the identity of microglia, to what extent histone modifications and DNA methylation regulate microglial state switches at enhancers have not been defined. Here, using genetic fate mapping, we demonstrate the common embryonic origin of proliferative-region-associated microglia (PAM) enriched in developing white matter, and track their dynamic transitions into disease-associated microglia (DAM) and white matter-associated microglia (WAM) states in disease and aging contexts, respectively. This study links spatiotemporally discrete microglial states through their transcriptomic and epigenomic plasticity, while revealing state-specific histone modification profiles that govern state switches in health and disease.

neuroscience↗

Infection and herbicide exposure implicate c-Abl kinase in α-Synuclein Ser129 phosphorylation

BackgroundParkinsons disease is a complex multifactorial neurodegenerative disorder characterized by -Synuclein aggregation in Lewy bodies, with phosphorylation at serine 129 (pSer129) being a critical pathological hallmark. However, the exact mechanisms by which environmental triggers lead to this disease phenotype remain poorly understood. In this study we compare the effects of an exemplary infection and a certain pesticide exposure on the generation of pSer129 -Synuclein, with a focus on the involvement of cellular kinases in this process. MethodsTwo distinct environmental stressors were applied to neuronal cells: the pesticide rotenone and the well-studied gastric bacterium Helicobacter pylori (H. pylori). Phosphorylation of Ser129 -Synuclein was assessed by immunofluorescent staining and Western blotting. Cells were treated with mechanistically distinct c-Abl inhibitors, and pSer129 -Synuclein was detected using Western blotting and activities of the upstream serine-threonine kinase were predicted by kinase profiling and Western blotting, analyzed by one-way ANOVA followed by Tukeys multiple comparisons test. Moreover, transcriptome analyses of treated cells were performed and ingenuity pathway analysis and Deseq2 were applied to unravel the affected neurodegenerative pathways. ResultsThe functional analysis of our RNA sequence data demonstrated that both H. pylori and rotenone induced oxidative stress and neuroinflammation by stimulating neurodegenerative pathways. Rotenone and H. pylori activated c-Abl, likely through the induced oxidative stress and promoted -Synuclein phosphorylation. The kinase inhibitors Ponatinib and Asciminib effectively prevented pSer129 -Synuclein accumulation and reversed associated gene expression changes induced by rotenone or H. pylori. Moreover, GSK3{beta} appeared to be involved in the induction of Ser129 phosphorylation via activated c-Abl. Furthermore, H. pyloris vacuolating cytotoxin appeared to play a crucial role in the phosphorylation of pSer129 -Synuclein by c-Abl. ConclusionsThese findings highlight the pivotal role of c-Abl in -Synucleopathies and provide insights into shared mechanisms between infection and pesticide exposure, offering potential therapeutic targets for Parkinsons disease and related pathologies involving -Synuclein modification.

neuroscience↗

Super-omics and PCAS reveal rheumatoid arthritis as a tumor-like disease

Rheumatoid arthritis (RA) is a debilitating systemic autoimmune disorder that significantly impairs quality of life. To elucidate the molecular alterations in RA progression, we performed comprehensive super-omics analyses on synovial tissues from patients with joint trauma, arthritis, and RA. These analyses included transcriptomics, proteomics, metabolomics, microbiomics, and fourteen PTMs (phosphorylation, acetylation, lactylation, O-GlcNAc glycosylation, arginine monomethylation, lysine monomethylation, lysine dimethylation, lysine trimethylation, succinylation, malonylation, glutarylation, tyrosine nitration, N-glycosylation, and O-glycosylation). Additionally, we developed a protein-centered association study (PCAS) method to integrate these complex datasets. Using this approach, we identified key proteins, such as STK17B, and its interactors, which may be crucial in RA pathogenesis. Tumor-like features, including aberrant angiogenesis and epithelial-mesenchymal transition, were observed in RA, alongside the potential involvement of oncogenes and tumor suppressor genes. Finally, we constructed a molecular interaction blueprint of RA, providing a comprehensive framework for advancing RA pathogenesis, diagnosis, and therapy.

immunology↗

Novel Carbohydrate-substituted Indazole Derivatives Targeting SGLT1 Enhance the Efficacy of Receptor Tyrosine Kinase Inhibitors in Cancer Therapy

Withdrawal StatementThe authors have withdrawn this manuscript because [Because we need to conduct a completely different re-examination of the mechanism behind the article]. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

cancer biology↗

Stress-activated neuronal ensemble in the supramammillary nucleus stores anxiety but not memory

Anxiety is a prevalent negative emotional state induced by stress; however, the neural mechanism underlying anxiety is still largely unknown. We used acute and chronic stress to induce anxiety and test anxiety-like behavior; immunostaining, multichannel extracellular electrophysiological recording and Ca2+ imaging to evaluate neuronal activity; and virus-based neuronal tracing to label circuits and manipulate circuitry activity. Here, we identified a hypothalamic region, the supramammillary nucleus (SuM), plays important role in anxiety-like behavior. We then characterized a small ensemble of stress-activated neurons (SANs) that are recruited by stress. These SANs respond specifically to stress, and their activation robustly increases anxiety-like behavior in male mice. We also found that ventral subiculum (vSub)-SuM projection but not dorsal subiculum (dSub)-SuM projections encode anxiety-like behavior and that inhibition of these vSub-SuM projections has an antianxiety effect. These results indicate that the reactivation of stress-activated supramammillary cells and relevant neural circuits are important neural processes underlying anxiety-like behavior.

neuroscience↗

Preclinical Evaluation of P4B-2412 as Phosphodiesterase 4B Radioligand for Positron Emission Tomography Imaging

Phosphodiesterase 4B (PDE4B) plays a critical role in cAMP hydrolysis and is highly expressed in brain regions associated with neuroinflammation and neurodegenerative disorders. Selective PDE4B radioligands hold significant potential for elucidating disease mechanisms and enabling target occupancy measurements. In this study, we developed [18F]P4B-2412, a novel PDE4B-selective radioligand, and evaluated its utility for PET imaging. [18F]P4B-2412 was synthesized with high radiochemical yield (27.2%), excellent radiochemical purity (99%), and favorable molar activity (66.2 {+/-} 2.5 GBq/mol). In vitro autoradiography revealed high PDE4B binding, while dynamic PET imaging demonstrated high in vivo specificity for PDE4B in rodent brain regions. Notably, [18F]P4B-2412 exhibited excellent metabolic stability in vitro and in vivo. These findings establish [18F]P4B-2412 as a promising PET probe for imaging PDE4B in vivo, offering a valuable tool for investigating neuroinflammation and advancing CNS drug development.

neuroscience↗

Enzyme-independent functions of HDAC3 in the adult heart

The cardioprotective effects of histone deacetylase (HDAC) inhibitors (HDIs) are at odds with the deleterious effects of HDAC depletion. Here, we use HDAC3 as a prototype HDAC to address this contradiction. We show that adult-onset cardiac-specific depletion of HDAC3 in mice causes cardiac hypertrophy and contractile dysfunction on a high-fat diet (HFD), excluding developmental disruption as a major reason for the contradiction. Genetically abolishing HDAC3 enzymatic activity without affecting its protein level does not cause cardiac dysfunction on HFD. HDAC3 depletion causes robust downregulation of lipid oxidation/bioenergetic genes and upregulation of antioxidant/anti-apoptotic genes. In contrast, HDAC3 enzyme activity abolishment causes much milder changes in far fewer genes. The abnormal gene expression is cardiomyocyte-autonomous and can be rescued by an enzyme-dead HDAC3 mutant but not by an HDAC3 mutant ({Delta}33-70) that lacks interaction with the nuclear-envelope protein lamina-associated polypeptide 2{beta} (LAP2{beta}). Tethering LAP2{beta} to the HDAC3 {Delta}33-70 mutant restored its ability to rescue gene expression. Finally, HDAC3 depletion, not loss of HDAC3 enzymatic activity, exacerbates cardiac contractile functions upon aortic constriction. These results suggest that the cardiac function of HDAC3 in adults is not attributable to its enzyme activity, which has implications for understanding the cardioprotective effects of HDIs.

physiology↗

Nascent RNA profiling reveals regulation of gene transcription through productive reiterative initiation in bacteria

Productive reiterative initiation, an alternative transcription process accompanying RNA slippage relative to the template DNA and RNA polymerase, results in the incorporation of additional nucleotides into transcripts. However, a comprehensive understanding of the mechanisms underlying productive reiterative initiation and its functional implications has been hindered due to the complexity of heterogenous slippage transcripts. Here, we develop and employ 5 Terminal Native Elongating Transcript Sequencing (5TNET-seq) to identify and quantify productive reiterative initiation events in Escherichia coli. 5TNET-seq reveals that over 51% of promoters exhibit productive reiterative initiation. The conserved promoter - 10 region, an appropriate spacer between the -10 region and the TSS, and the transcription initiation region associated with weak RNA-DNA hybrid stability, particularly "AAA" and "TTT" trinucleotide tracts, contribute to high productive reiterative initiation. In addition, up to four nucleotides can be added in a single cycle of productive reiterative initiation. A smaller transcription bubble is observed during productive reiterative initiation, which may stabilize the transcription initiation complex to regulate gene transcription. Our results suggest that productive reiterative initiation emerges as an inherent transcription process regulating biological processes, including cell wall synthesis, independent of protein regulators.

microbiology↗

Candida albicans a comprehensive view of the proteome

We describe a new release of the Candida albicans PeptideAtlas proteomics spectral resource (build 2024-03), providing a sequence coverage of 79.5% at the canonical protein level, matched mass spectrometry spectra, and experimental evidence identifying 3382 and 536 phosphorylated serine and threonine sites with false localization rates of 1% and 5.3%, respectively. We provide a tutorial on how to use the PeptideAtlas and associated tools to access this information. The C. albicans PeptideAtlas summary web page provides "Build overview", "PTM coverage", "Experiment contribution", and "Dataset contribution" information. The protein and peptide information can also be accessed via the Candida Genome Database via hyperlinks on each protein page. This allows users to peruse identified peptides, protein coverage, post-translational modifications (PTMs), and experiments identifying each protein. Given the value of understanding the PTM landscape in the sequence of each protein, a more detailed explanation of how to interpret and analyse PTM results is provided in the PeptideAtlas of this important pathogen. Candida albicans PeptideAtlas web page: https://db.systemsbiology.net/sbeams/cgi/PeptideAtlas/buildDetails?atlas_build_id=578

microbiology↗

Assessment of DNA methylation from a single genomic region of ELOV2 is sufficient to predict chronological age

Estimation of chronological age is particularly informative in forensic contexts. Assessment of DNA methylation status allows for the prediction of age, though the accuracy and ease of manipulation may vary across different models. In this study, we started with a carefully designed discovery cohort recruiting more elderly subjects than other age categories, to diminish the effect of epigenetic drifting. We analyzed DNA methylation from a single genomic region of ELOV2, which was sufficient to construct an age-prediction model comprising 15 CpG sites. This model is further validated by an independent cohort as well as a multi-center test using trace dried bloodstains. The nature of our analytical pipeline, when combined the assessment of a single genomic locus with high-throughput sequencing, can easily be scaled up with low cost. Taken together, we propose a new age-prediction model featuring accuracy, ease of manipulation, high-throughput, and low cost. This model can be readily applied in both classic and newly emergent forensic contexts that require age estimation.

genetics↗

Relaxation selective Intravoxel Incoherent Motion Imaging of Microvascular Perfusion and Fluid Compartments in the Human Choroid Plexus

The choroid plexus (ChP) plays an important role in the glymphatic system of the human brain as the primary source of the cerebrospinal fluid (CSF) production. Development of a non-invasive imaging technique is crucial for studying its function and age-related neurofluid dynamics. This study developed a relaxation-selective intravoxel incoherent motion (IVIM) technique to assess tissue and fluid compartments in the ChP in a prospective cross-sectional study involving 83 middle-aged to elderly participants (age: 61.5 {+/-} 17.1 years old) and 15 young controls (age: 30.7 {+/-} 2.9 years old). Using a 3T MRI scanner, IVIM, FLAIR-IVIM, LongTE-IVIM, and VASO-LongTE-IVIM were employed to measure diffusivity and volume fractions of fluid compartments and evaluate aging effects on microvascular perfusion and interstitial fluid (ISF). FLAIR-IVIM identified an additional ISF compartment with free-water-like diffusivity (2.4 {+/-} 0.9 x10-3 mm2/s). Older adults exhibited increased ChP volume (2320 {+/-} 812 mm3 vs 1470 {+/-} 403 mm3, p=0.0017), reduced perfusion (6.5 {+/-} 4.7 vs 3.6 {+/-} 2.9 x10-3 mm{superscript 2}/s, p=0.0088), decreased ISF volume fraction (0.58 {+/-} 0.09 vs 0.67 {+/-} 0.06, p=0.0042), and lower tissue diffusivity (1.16 {+/-} 0.14 vs 1.29 {+/-} 0.17 x10-3 mm{superscript 2}/s, p=0.031) compared to younger adults. Relaxation-selective IVIM may offers enhanced specificity for characterizing age-related changes in ChP structure and fluid dynamics.

neuroscience↗

Dysregulated RNA splicing induces regeneration failure in alcohol-associated liver disease

Individuals with progressive liver failure are at a high risk of mortality without liver transplantation. However, our understanding of derailed regenerative responses in failing livers is limited. Here, we performed comprehensive multi-omic profiling of healthy and diseased human livers using bulk and single-nucleus RNA-plus ATAC-seq. We report that hepatic immune milieu alterations in alcohol-associated liver disease (ALD) prevent hepatocytes from transitioning to a proliferative progenitor-like state, trapping them into an unproductive intermediate state. We discovered striking changes in RNA binding protein (RBP) expression, particularly ESRP, PTBP, and SR families, that cause misregulation of developmentally controlled RNA splicing in ALD. Our data pinpoint ESRP2 as a pivotal disease-sensitive RBP and support a causal role of its deficiency in ALD pathogenesis. Notably, splicing defects in ESRP2-targets Tcf4 and Slk, amongst others, directly alter their nuclear localization and activities, disrupting WNT and Hippo signaling pathways, which are critical for normal liver regeneration. We demonstrate that changes in stromal cell populations enrich failing ALD livers with TGF-{beta}, which suppresses ESRP2-driven epithelial splicing program and replaces functional parenchyma with quasi-progenitor-like cells lacking liver-specific functions. This unprecedented account of transcriptional and post-transcriptional dysregulation in ALD suggests that targeting misspliced RNAs could improve recovery and serve as biomarkers for poor ALD outcomes.

molecular biology↗