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Wang, G.

Publications and source records attributed to Wang, G..

At least 145 records · Page 8Linked to original sources

C9orf50 is a Targetable Spliceosome Regulator for Cancer Immunotherapy

Cancer cells harbor cell-intrinsic programs capable of sculpting immunogenic landscapes, yet molecular brakes that enforce immune evasion remain poorly defined. Here, we identify C9ORF50, a previously uncharacterized intrinsically disordered protein, as a liquid-liquid phase separation-driven regulator of RNA processing and actionable immunotherapy target. Genetic ablation of C9ORF50 induces selective intron retention in spliceosome component transcripts, leading to cytoplasmic accumulation of immunogenic double-stranded RNA (dsRNA). This dsRNA activates type I interferon pathway that in turn orchestrates a chemokine secretory program critical for T cell recruitment. The resultant enhancement of tumor immunogenicity and reprogramming of tumor immune microenvironment drives robust antitumor immunity, effectively converting immunologically "cold" tumors to "hot" phenotypes. Therapeutic targeting of C9ORF50 via RNA interference achieved robust tumor suppression in syngeneic models, suggesting its translational relevance. Notably, C9ORF50 exhibits tumor-predominant expression, with minimal baseline levels detected in healthy tissues or immune cell populations, underscoring its potential safety as a therapeutic target. Our study not only identifies C9ORF50 as a novel LLPS-dependent regulator of RNA splicing but also establishes it as a promising and potentially safe therapeutic target for cancer immunotherapy.

cancer biology↗

The entorhinal spatial map integrates visual identity information of landmarks

The location and identity of landmarks provide spatial and nonspatial information of an environment, respectively, to guide spatial navigation. While the medial entorhinal cortex (MEC) is essential for representing spatial information, it is unclear whether it also encodes landmark identity. Here, we conducted two-photon calcium imaging of the MEC when mice navigated in multiple virtual environments, and discovered a general ability of the MEC to encode landmark identity through cue cells, which responded to individual landmarks during virtual navigation. Cue cells represented landmark identity by exhibiting more distinct activity patterns between visually disparate landmarks than identical ones. The representation was modulated by the spatial shift of cue cell activity relative to landmark location. Moreover, the identity encoding by the same cue cell population changed between different environments but was maintained within the same environment despite increased experience. In contrast, landmark location encoding by cue cells was regulated by experience, suggesting different mechanisms underlying the encodings of landmark identity and location. Finally, compared to cue cells, grid cells weakly encoded landmark identity but more robustly encoded landmark location. Thus, the MEC integrates both spatial and nonspatial information during navigation, but potentially through different circuit mechanisms.

neuroscience↗

Optimized upstream analytical workflow for single-nucleus transcriptomics in main metabolic tissues

Single-nucleus RNA sequencing (snRNA-seq) has emerged as a powerful approach for studying cellular heterogeneity in metabolic tissues. However, snRNA-seq analysis remains challenging due to low gene expression and data complexity. Here, we introduce an optimized analytical workflow for snRNA-seq data from 67 samples across white adipose tissue, muscle, liver and the hypothalamus. We emphasized the importance of key steps including ambient RNA removal, doublet identification and data integration to ensure accurate downstream analysis. This workflow offers a valuable resource for researchers in metabolism, facilitating deeper insights into cellular diversity and metabolic function through rigorous snRNA-seq analysis.

bioinformatics↗

Virus-host interactome reveals host cellular pathways perturbed by tick-borne encephalitis virus infection

Tick-borne encephalitis virus (TBEV) poses an increasingly significant threat to public health. Here, we delved into the virus-host interactome and discovered that TBEV has a profound impact on multiple host cellular pathways. Viral pre-membrane protein (prM), non-structural proteins NS1, NS2B3, NS4A, and NS5 remodel the hosts innate immune responses. PrM and NS2B3 are involved in autophagy, NS4A is associated with neurodegenerative diseases, and NS5 participates in spliceosome dynamics, ribosomal biogenesis, cell cycle regulation, and DNA damage response. Notably, TBEV infection causes G0/G1 cell cycle arrest in host cells. NS5 interacts with histone acetyltransferase P300 to upregulate P16 expression, suppressing CDK4 and resulting in cell cycle arrest. Elevated P16 and reduced CDK4 levels were observed in TBEV-infected brain organoids. The P300 inhibitors and CDK4 agonist can reverse virus-induced cell cycle arrest and inhibit viral replication. Further analysis uncovered potential antiviral targets like KAT6A, XIAP, and RIOK1/BRD9. These findings provide valuable insights into TBEV pathogenicity and hold promise for antiviral drug development.

microbiology↗

Single-cell multiome and spatial profiling reveals pancreas cell type-specific gene regulatory programs driving type 1 diabetes progression

Cell type-specific regulatory programs that drive type 1 diabetes (T1D) in the pancreas are poorly understood. Here we performed single nucleus multiomics and spatial transcriptomics in up to 32 non-diabetic (ND), autoantibody-positive (AAB+), and T1D pancreas donors. Genomic profiles from 853,005 cells mapped to 12 pancreatic cell types, including multiple exocrine sub- types. Beta, acinar, and other cell types, and related cellular niches, had altered abundance and gene activity in T1D progression, including distinct pathways altered in AAB+ compared to T1D. We identified epigenomic drivers of gene activity in T1D and AAB+ which, combined with genetic association, revealed causal pathways of T1D risk including antigen presentation in beta cells. Finally, single cell and spatial profiles together revealed widespread changes in cell-cell signaling in T1D including signals affecting beta cell regulation. Overall, these results revealed drivers of T1D progression in the pancreas, which form the basis for therapeutic targets for disease prevention.

genomics↗

Amyloid-β precursor protein promotes tumor growth by establishing an immune-exclusive tumor microenvironment

During initiation and progression, cancerous tissue hijacks a series of elaborate tissue homeostatic mechanisms to avoid immune surveillance, including neuro-immune interactions. Here, we show that amyloid-{beta} precursor protein (APP) and its {beta}-cleavage product amyloid-{beta}1-42 (A{beta}1-42), well-known in the pathogenesis of Alzheimers disease (AD), are expressed in multiple cancer tissues. However, the oncogenic activity of APP is due to its E1 domain, instead of A{beta}1-42. Mechanistically, APP restricts immune cells influx into tumor microenvironment (TME) and impairs CD8+ T cell and NK cell-based immunity, by dampening type I interferon (IFN) response in TME. We also provide proof-of-concept that vaccination targeting APP is effective for cancer prevention. Our current study reveals a previously unrecognized role of APP in cancer immune surveillance, and provides a new strategy for cancer prevention and treatment by targeting APP.

cancer biology↗

ZSeeker: An optimized algorithm for Z-DNA detection in genomic sequences

Z-DNA is an alternative left-handed helical form of DNA with a zigzag-shaped backbone that differs from the right-handed canonical B-DNA helix. Z-DNA has been implicated in various biological processes, including transcription, replication, and DNA repair, and can induce genetic instability. Repetitive sequences of alternating purines and pyrimidines have the potential to adopt Z-DNA structures. ZSeeker is a novel computational tool developed for the accurate detection of potential Z-DNA-forming sequences in genomes, addressing limitations of prior methods. By introducing a novel methodology informed and validated by experimental data, ZSeeker enables the refined detection of potential Z-DNA-forming sequences. Built both as a standalone Python package and as an accessible web interface, ZSeeker allows users to input genomic sequences, adjust detection parameters, and view potential Z-DNA sequence distributions and Z-scores via downloadable visualizations. Our Web Platform provides a no-code solution for Z-DNA identification, with a focus on accessibility, user-friendliness, speed and customizability. By providing efficient, high-throughput analysis and enhanced detection accuracy, ZSeeker has the potential to support significant advancements in understanding the roles of Z-DNA in normal cellular functions, genetic instability, and its implications in human diseases. AvailabilityZSeeker is released as a Python package under the GPL license as a multi-platform application and is available at: https://github.com/Georgakopoulos-Soares-lab/ZSeeker. A web-interface of ZSeeker is publicly available at https://zseeker.netlify.app/.

bioinformatics↗

Molecular basis of vitamin K-dependent protein γ-glutamyl carboxylation

Gamma-glutamyl carboxylase (GGCX) in human is the sole enzyme responsible for catalyzing the carboxylation of glutamate (Glu) to {gamma}-carboxyglutamate (Gla), a process that relies on the deprotonation of reduced vitamin K. This post-translational modification of vitamin K-dependent proteins (VKDPs) plays a pivotal role in numerous biological processes. Mutations in GGCX are responsible for multiple clinical phenotypes; however, the molecular mechanisms of GGCX activity and its pathology remain poorly understood. In this study, we reported the cryo-electron microscopy (cryo-EM) structures of GGCX bound with the either FIX or FX, two VKDPs and vitamin K, and employed the biochemical and cellular assays as well as molecular dynamics simulations to elucidate its dual-catalytic properties. The enzyme comprises a transmembrane domain that anchors the vitamin K-binding site, along with an ER luminal domain that facilitates binding of coagulation factor IX (FIX) at the exosite. The catalytic center orchestrates the oxidation of vitamin K and the carboxylation of Glu residues through a Cap-H2 coupling mechanism, along where disease-associated mutations in GGCX are predominantly clustered. These findings offer a comprehensive molecular framework for understanding the allosteric regulation of GGCXs dual enzymatic activities and provide valuable insights for developing strategies to monitor and therapeutically target vitamin K metabolism in related diseases.

biochemistry↗

Dysregulation of cell migration by matrix metalloproteinases in geleophysic dysplasia

Geleophysic dysplasia (GD) is characterized by short stature, brachydactyly, joint limitations, a distinctive facial appearance, as well as cardiac and respiratory dysfunction that can be life-threatening. GD is caused by pathogenic variants in the ADAMTSL2, FBN1, or LTBP3 genes. While dermal fibroblasts derived from affected individuals have shown poor organization of the extracellular matrix (ECM), it remains elusive how the disorganized ECM contributes to GD pathogenesis. To understand the molecular mechanisms in GD, we isolated and characterized primary human dermal fibroblasts from affected individuals with ADAMTSL2 and FBN1 variants. We found that the secretion of ECM proteins including ADAMTSL2, FBN1, and Fibronectin were impaired in GD fibroblasts. Increased cell migration was observed in GD fibroblasts carrying ADAMTSL2 or FBN1 variants, which was associated with up-regulation of MMP-1 and MMP-14, two proteases related to cell mobility. The enhanced cell migration and up-regulation of MMP-1 and MMP-14 were corroborated in mouse primary dermal fibroblasts carrying pathogenic variants in Adamtsl2 and in lung and heart tissues from Adamtsl2-knockout mice. A pan MMP inhibitor, GM6001, inhibited the migration of GD fibroblasts. Overall, our results suggest that MMP-1/-14 up-regulation play a role in the development of GD and may be utilized as a treatment target.

cell biology↗

Intense oocyte competition builds the female reproductive reserve in mice

During the process of ovariogenesis, more than two-thirds of germ cells are sacrificed to enhance the quality of the remaining oocytes. But the detail process of selection is not completely understood in mammals. Here, by creating a high resolution 4- dimensional ovariogenesis imaging system, we recorded the progress of oocyte fate determination in live mouse ovaries, and discovered an oocyte competition mechanism that determines the survival of oocytes. We found that dominant oocytes catch and absorb the cell debris from sacrificed oocytes to enrich their cytoplasm for survival. Single-cell sequencing demonstrated that this competition follows a classic autophagy- driven model. Blocking competition by suppressing autophagy resulted in an enlarged pool of survived oocytes. However, these oocytes lacking competition were unable to fully develop and contribute to fertility. Our study suggests that mammals have evolved a unique intensive competition system to enhance oocyte quality, necessary to support their long reproductive lifespan.

developmental biology↗

Acquisition of ampliconic sequences marks a selfish mouse t-haplotype

Mendelian genetics posits equal transmission of alleles, but selfish alleles can bias the transmission of large genomic regions or entire chromosomes1-4. One long-standing question is how transmission bias evolves to encompass large genomic regions. Mus musculus (house mouse) t-haplotypes exhibit up to 99% transmission bias from heterozygous males5-14 and harbor selfish alleles9-14 genetically linked to large inversions spanning the proximal half of chromosome 1715-20. Here, by generating a high-quality, single-haplotype assembly of a t- haplotype, we reveal the evolution of eight large amplicons with known11,13,21 and candidate selfish alleles as a distinct genetic feature. Three amplicons are conserved in closely related Mus species, and two have known selfish alleles in the oldest inversion, implicating amplicons and an inversion drove the origins of a selfish chromosome 17 [~]3MYA. The remaining t- haplotype amplicons harbor gene families expressed predominantly in haploid spermatids, newly acquired retrogenes, and the most differentially expressed genes in wild-type/t-haplotype spermatids. Targeted deletion of a [~]1.8Mb amplicon with candidate selfish alleles on the t- haplotype reduces selfish transmission in heterozygous males by 3%. Notably, the evolution of selfish allele-containing amplicons and inversions on the t-haplotype parallels mammalian sex chromosome evolution as signatures of selfish transmission. We propose amplicon acquisition and large inversions initiate evolutionary arms races between selfish haplotypes and serve as genome-wide signatures of selfish transmission.

genetics↗

Transcriptome responses of two Halophila stipulacea seagrass populations from pristine and impacted habitats, to single and combined thermal and excess nutrient stressors, reveal local adaptive features and core stress-response genes

In their natural habitats, seagrasses face multiple abiotic stressors, which can often occur simultaneously. However, most studies investigating the effects of environmental stressors on seagrasses have focused on growth and physiological responses to single stressors. Here, we examined the transcriptome responses of the tropical seagrass Halophila stipulacea collected from a northern Gulf of Aqaba pristine site (South Beach - SB) and an anthropogenically-impacted site (Tur Yam - TY), grown in a mesocosm, and exposed to ecologically-relevant, single and combined, thermal and excess nutrient stressors. The combined thermal and nutrient stressor elicited greater transcriptome reprogramming than the single stressors in both populations and induced the expression of a combination-specific set of genes involved in abiotic and biotic stress responses. Furthermore, thermal stress exerted a more dominant influence than excess nutrient stress upon the transcriptome response to the combined stress. Transcriptomes of plants from the impacted TY site displayed reduced plasticity, the presence of genes exhibiting a "stress-ready" mode of expression under all stresses, and increased resilience (recovery to control transcriptomes). We also identified core stress-response genes that could be leveraged as early indicators of stress in the field. Overall, our data suggest that environmental conditions in seagrass habitats can drive local molecular adaptation, and that the response of seagrasses to combined stressors associated with climate change and coastal anthropogenic stressors cannot be predicted from the response to single stressors.

plant biology↗

Sequencing-based Spatial Transcriptomics with scRNA-seq Sensitivity

The advent of spatial transcriptomics has dramatically expanded our ability to study the vast network of cell-cell interactions at the molecular level in tissue. Among current methods, sequencing-based approaches have great potential in discovering because of its unbiased capture. In the last couple of years, the spatial resolution for the capture addresses has been significantly improved from 100 m to <1 m, well below the size of a mammalian cell. However, the capture efficiency has always been a pain point, [~]one order of magnitude lower than that of single cell RNA sequencing (scRNA-seq). The low capture efficiency limits the depth and breadth of its applications in the study of complex biological systems and diseases. Here, we introduce Salus Spatial transcriptomic system (Salus-STS), which provides [~]1 m capture resolution and a capture efficiency [~]1 order of magnitude higher than other current methods. Analysis with sub-cellular resolution becomes practical for sequencing-based spatial transcriptomics.

molecular biology↗

Melatonin attenuates kidney injury by alleviating lysosomal damage in diabetic kidney disease

Proteinuria-induced damage to renal tubular epithelial cells is one of the main causes of diabetic kidney disease (DKD), and the clearance of overloaded albumin by lysosomes is crucial for maintaining the homeostasis of renal tubular epithelial cells. Therefore, lysosomal damage is closely related to the pathogenesis of DKD, but effective prevention and treatment measures are still lacking. Melatonin (MLT) is secreted by the pineal gland and can not only regulate circadian rhythms but also maintain lysosomal homeostasis. In this study, we demonstrate the presence of significant lysosomal damage in renal tubules of DKD patients, which causes autophagy impairment and a concomitant oxidative stress imbalance; however, MLT can upregulate transcription factor EB (TFEB) to improve lysosomal damage and restore the biosynthesis in this organelle. Mechanistically, MLT may protect lysosomes via the upregulation of TFEB and the miR-205-5p-LRP-1 pathway in renal tubules, thus improving autophagy dysfunction and oxidative imbalance in DKD.

pathology↗

Highly efficient organ-targeting transport through the ventral midline interstitial channels injection: a new development of interstitium

How to improve the drugs bioavailability has always been a hot and difficult topic. Conventional drug delivery methods, such as oral administration and the blood circulation system, suffer from issues such as low targeting efficiency, low bioavailability, and high side effects. Recently, interstitium has gradually been recognized as an important new organ. Interstitial injection allows small molecules to move through interstitial channels with interstitial fluid flow and be transported to organs, providing new possibilities for drug delivery. In this study, using fluorescein sodium as a drug model, we systematically investigated the distribution of the fluorescein sodium in organs and body surface of the rats after ventral midline interstitial channels injection. In addition, we observed the microstructure of the ventral midline interstitial channels of abdominal wall and the effects of channels ligation on fluorescein sodium delivery and target organs, to explore the mechanism of interstitial injection. We found that fluorescein sodium can be efficiently transported to the uterus and ovaries along the ventral midline interstitial channels, and the parallel fibers and interconnected interstitial spaces of the channels facilitate long-distance transport of solutes. Additionally, the blockage of the transmission through those channels had results in a significant decrease in targeted transport efficiency over long distances, a decrease in oestrogen levels, organ coefficients, and body weights in female rats. Therefore, the ventral midline interstitial channels with free fluid flow may be a potential communication pathway between body surface and organs. These findings have significant value in the development of drug delivery.

physiology↗

A General Strategy to Endow Dyes with Genic Fluorescence for Wash-Free Imaging of Proteins in Living Cells

Fluorescent dyes are the main fluorophore for protein labeling and fluorescent imaging in living cells. However, due to the inevitable nonspecific binding of the dye to non-targets within the cell, background signals are generated, which severely affect the imaging quality. Here, we endow the dye with genic fluorescence by introducing a fluorescent proteins FRET pair, such that only the dye bound to the target protein emits fluorescence ({lambda}ex = FPs, {lambda}em = Dyes), while nonspecifically bound dye remains non-fluorescent. This significantly improves the signal-to-noise ratio (SNR) in wash-free imaging. This strategy is achieved by fusing the Halo-tag to fluorescent proteins (sfGFP, mCherry) that can generate FRET with Halo dyes O-Rho and Si-Rho. The FPs serve as the donor, and the FRET mechanism imparts genic fluorescence property to O-Rho and Si-Rho. Since the excitation wavelength of the donor ({lambda}ex = FPs) cannot excite the unspecifically dye fluorescence, background fluorescence interference is reduced. We further improved the SNR by increasing the FRET efficiency between the FPs and dyes. The system was used for four-color super-resolution imaging of target proteins and dynamic SIM tracking of mitochondria. In addition, the genic FRET fluorophore constructed with the ultra-stable mStayGold showed significant photobleaching resistance and can be used for long-term dynamic super-resolution imaging. Theoretically, by selecting appropriate FRET pairs, this method can improve the SNR of any fluorophore, providing a new labeling strategy for live-cell wash-free imaging.

biochemistry↗

KAT8 facilitates the proliferation of cancer cells through enhancing E7 function in HPV-associated cervical cancer

Persistent human papillomavirus (HPV) infection serves as the principal etiological factor in cervical cancer, with the oncoprotein E7, encoded by the virus, playing a key role in tumorigenesis. Despite this, targeted therapeutic strategies against E7 remain underexplored. KAT8, a lysine acetyltransferase, significantly contributes to oncogenesis through the regulation of transcription. However, its involvement in cervical cancer remains inadequately characterized. This study employs HPV18-positive HeLa and HPV16-positive SiHa cell lines to investigate how KAT8 modulates E7 expression and function in cervical cancer cells. Upon KAT8 knockdown, a marked reduction in cell viability is observed, alongside a downregulation of E7 expression. This is associated with elevated levels of retinoblastoma protein (pRb) and decreased E2F1 expression, indicating that KAT8 depletion inhibits E7 expression, resulting in E2F1 inactivation and cell cycle arrest. Furthermore, KAT8 is found to directly bind to the promoter regions of the HPV18 LCR, enhancing transcription of the HPV18 E7 gene. This study also demonstrates that KAT8 is essential for the acetylation of E7, and plays a critical role in facilitating the interaction between pRb/E2F1 and E7 in cervical cancer cells. In conclusion, these results highlight KAT8 as a key driver of cervical cancer progression, promoting HPV E7 expression and its associated oncogenic signaling pathways.

cancer biology↗

Synergistic activation of the human phosphate exporter XPR1 by KIDINS220 and inositol pyrophosphate

Inorganic phosphate (Pi) is fundamental to life, and its intracellular concentration must be tightly regulated to prevent toxicity. XPR1, the only known phosphate exporter, plays a crucial role in maintaining this delicate balance. However, the mechanisms underlying the function and regulation of XPR1 remain elusive until now. Here we present cryo-electron microscopy structures of the human XPR1-KIDINS220 complex in both substrate-free closed states and substrate-bound outward-open states, as well as the structure of an XPR1 mutant alone in a substrate-bound inward-facing state. In the presence of inositol hexaphosphate (InsP6) and phosphate, the XPR1-KIDINS220 complex adopts an outward-open conformation. InsP6 binds both the SPX domain and the peripheral juxtamembrane regions of XPR1, indicative of an active phosphate-export state. Conversely, in the absence of either phosphate or InsP6, the complex assumes a closed state, where the extracellular half of transmembrane 9 occupies the outward cavity, and a C-terminal plug-in loop blocks the intracellular cavity. Notably, XPR1 without KIDINS220 adopts a closed state despite the presence of phosphate and InsP6. The functional mutagenesis experiments further demonstrate that InsP6, whose concentrations fluctuate in response to Pi availability, functions synergistically with KIDINS220 to regulate the phosphate export activity of XPR1. These findings not only elucidate the intricate mechanisms of cellular phosphate regulation but also hold promise for the development of targeted therapies for ovarian cancer, where XPR1 plays a significant role.

biophysics↗