Biology subjects

Zhang, F.

Publications and source records attributed to Zhang, F..

At least 145 records · Page 8Linked to original sources

bioRxiv2025

Modification of Non-photochemical Quenching Pathways in the C4 Model Plant Setaria viridis Revealed Shared and Unique Photoprotection Mechanisms as Compared to C3 Plants

Light is essential for photosynthesis; however, excess light can increase the accumulation of photoinhibitory reactive oxygen species that reduce photosynthetic efficiency. Plants have evolved photoprotective non-photochemical quenching (NPQ) pathways to dissipate excess light energy. In tobacco and soybean (C3 plants), overexpression of three NPQ genes, violaxanthin de-epoxidase (VDE), Photosystem II Subunit S (PsbS), and zeaxanthin epoxidase (ZEP), hereafter VPZ, resulted in faster NPQ induction and relaxation kinetics, and increased crop yields in field conditions. NPQ is well-studied in C3 plants; however, NPQ and the translatability of the VPZ approach in C4 plants is poorly understood. The green foxtail Setaria viridis is an excellent model to study photosynthesis and photoprotection in C4 plants. To understand the regulation of NPQ and photosynthesis in C4 plants, we performed transient overexpression in Setaria protoplasts and generated (and employed) stable transgenic Setaria plants overexpressing one of the three Arabidopsis NPQ genes or all three NPQ genes (AtVPZ lines). Overexpressing (OE) AtVDE and AtZEP in Setaria produced similar results as in C3 plants, with increased or reduced zeaxanthin (thus NPQ), respectively. However, overexpressing AtPsbS appeared to be challenging in Setaria, with largely reduced NPQ in protoplasts and under-represented homozygous AtPsbS-OE lines, potentially due to competitive and tight heterodimerization of AtPsbS and SvPsbS proteins. Furthermore, Setaria AtVPZ lines had increased zeaxanthin, faster NPQ induction, higher NPQ level, but slower NPQ relaxation. Despite this, AtVPZ lines had improved growth as compared to wildtype under several conditions, especially high temperatures, which is not related to the faster relaxation of NPQ but may be attributable to increased zeaxanthin and NPQ in C4 plants. Our results identified shared and unique characteristics of the NPQ pathway in C4 model Setaria as compared to C3 plants and provide insights to improve C4 crop yields under fluctuating environmental conditions.

plant biology↗

bioRxiv2025

Rational Design and Optimization of a Potent IDO1 Proteolysis Targeting Chimera (PROTAC)

Indoleamine 2,3-dioxygenase 1 (IDO1) is a potently immunosuppressive protein that inhibits antitumor immunity through both tryptophan metabolism and non-enzymatic functions. Pharmacological therapies targeting IDO1 enzyme activity have generally failed to improve the overall survival of patients with cancer. Developing new therapeutic agents that are capable of neutralizing both enzyme-and non-enzyme-derived immunosuppressive IDO1 effects is therefore of high interest. We previously described the development of a novel Proteolysis Targeting Chimera (PROTAC), NU223612, that degrades IDO1 in cultured human glioblastoma (GBM) cells, as well as in well-established brain tumors, in vivo. In this study, we rationally optimized the composition, rigidity, and linker orientation of the PROTAC structure to create NU227326, which degrades IDO1 with a DC50 of 5 nM in human GBM cells. Mechanistic studies showed that IDO1 degradation occurred through the ubiquitin-proteasome system and was sustained for at least 2 days, supporting NU227326 as a highly potent IDO1 PROTAC suitable for further studies in GBM and other human cancers.

biochemistry↗

bioRxiv2024

TCPGdb: A comprehensive T cell perturbation genomics database for identification of critical T cell regulators

CAR-T therapies utilizing T cells engineered with chimeric antigen receptors (CARs) have revolutionized the treatment of hematologic and immune-related malignancies. However, the anti-tumor capability of engineered CAR-T cells are often not persistent, which greatly dampen its clinical efficacy. To address this limitation, massive parallel genetic screens were widely used to identified novel targets and regulators that enhance T cell anti-tumor capability and persistence in tumor microenvironment. We hypothesized that by combining the pooled screen data from multiple independent genetic screens we could provide a systematic, comprehensive, and robust analysis of the effect of gene perturbation on T-cell based immunotherapies. After collecting data from previously published T cell screens, including CRISPR-based and ORF-based screens, through Gene Expression Omnibus (GEO), we reprocessed the gene hits summary and conducting a pathway enrichment analysis. A T cell screen perturbation score (TPS) was employed to quantifies the impact of the gene on T cell function. Additionally, gene expression data (both bulk RNA level and single-cell RNA level) from autoimmune disease and T cell-derived cancers were analyzed to pick up gene perturbations that potentially augment T cell proliferation. We integrated all data and analysis on 27 T-cells screens into our state-of-the-art T cell perturbation genomics database (TCPGdb), which is made easily accessible through our webserver and allows users to interactively explore the impact of query genes on T cell function based on prior screen data and our TPS scoring module. TCPGdb is publicly accessible at http://tcpgdb.sidichenlab.org/.

bioinformatics↗

bioRxiv2024

Non-invasive diagnosis of early chronic colitis cancerization via amplified sensing of miRNA-21 in NIR-IIb window

Early diagnosis of the colitis-associated colorectal cancer (CRC) is of great significance for improving prognosis and survival rates. However, the clinical used colonoscopy and biopsy methods are invasive and lack of sensitivity at early stage of cancerization. Herein, we present an amplified sensing strategy in the second near-infrared b (NIR-IIb, 1500-1700 nm) window for non-invasive in situ visualization of early cancerization biomarker miRNA-21. A CRC nanosensor composed of Er3+ doped lanthanide nanoparticles, DNAzyme, and IR820 dye is designed as a NIR-IIb ratiometric luminescence reporter, providing rapid feedback and high sensitive miRNA-21 detection with limit of detection (LOD) of 1.26 pM. This strategy enables a non-invasive detection of colitis-associated cancerization up to [~]4 weeks ahead of the clinically used biopsy analysis, providing a promising alternative for early diagnosis of chronic colitis cancerization and guidance for therapeutic management.

bioengineering↗

bioRxiv2024

Noninvasively real-time monitoring in-vivo immune cell and tumor cell interaction by NIR-II nanosensor

Immunocytotherapy holds significant promise as a novel cancer treatment, but its effectiveness is often hindered by delayed responses, requiring evaluations every two to three weeks based on current diagnostic methods. Early assessment of immune cell-tumor cell interactions could provide more timely insights into therapeutic efficacy, enabling adjustments to treatment plans. In this study, we report a noninvasive nanosensor (C8R-DSNP) for real-time monitoring of in vivo immune cell activities in the second near-infrared long-wavelength (NIR-II-L) window (1500-1900 nm), which offers deep tissue transparency. The C8R-DSNP responds rapidly to caspase-8, a key apoptotic signaling molecule generated during interactions between natural killer (NK-92) immune cells and tumor cells. Using ratiometric NIR-II-L fluorescence imaging, we captured dynamic in vivo observations of NK-92 cell engagement with tumor cells in a mouse model. These results demonstrated cancer cell apoptosis that happens as early as 4.5 hours after NK-92 cell infusion. Additionally, in vitro urine imaging confirmed the initiation of apoptosis via cleaved fluorescent small molecules, while single-cell tracking within blood vessels and tumors further elucidated immune cell dynamics. This real-time NIR-II-L monitoring approach offers valuable insights for optimizing immunocytotherapy strategies.

bioengineering↗

bioRxiv2024

A molecularly defined brain circuit module for regulating the panic-like defensive state

Panic is an episode of strong defensive state, characterized by intense fear and severe physical symptoms such as elevated cardiorespiratory activities. How the brain generates panic state remains poorly understood. Here, we developed a robot-based experimental paradigm to evoke panic-like defensive state in mice. When stimulated by the robot, the mice exhibited jumping escapes and elevated cardiorespiratory activities. With this paradigm, we identified Cbln2-expressing (Cbln2+) neurons in the posterior hypothalamic nucleus (PHN) as a key neuronal population essential for the induction of panic-like defensive state. Activation of Cbln2+ PHN neurons induced behavioral and physical symptoms of panic-like defensive state. These neurons were strongly activated by noxious mechanical stimuli and encode jumping escape vigor. They were synaptically innervated by anxiety-associated brain areas and provoked panic-like defensive state via their projection to the periaqueductal gray. Together, our results reveal a molecularly defined circuit module that regulates the panic-like defensive state in mice.

neuroscience↗

bioRxiv2024

Arginyltransferase1 drives a mitochondria-dependent program to induce cell death

Cell death regulation is essential for stress adaptation and/or signal response. Past studies have shown that eukaryotic cell death is mediated by an evolutionarily conserved enzyme, arginyltransferase1 (Ate1). The downregulation of Ate1, as seen in many types of cancer, prominently increases cellular tolerance to a variety of stressing conditions. Conversely, in yeast and mammalian cells, Ate1 is elevated under acute oxidative stress conditions and this change appears to be essential for triggering cell death. However, studies of Ate1 were conventionally focused on its function in inducing protein degradation via the N-end rule pathway in the cytosol, leading to an incomplete understanding of the role of Ate1 in cell death. Our recent investigation shows that Ate1 dually exists in the cytosol and mitochondria, the latter of which has an established role in cell death initiation. Here, by using budding yeast as a model organism, we found that mitochondrial translocation of Ate1 is promoted by the presence of oxidative stressors and is essential for inducing cell death with characteristics of apoptosis. Also, we found that Ate1-induced cell death is dependent on the formation of the mitochondrial permeability pore and at least partly dependent on the action of mitochondria-contained factors including the apoptosis-inducing factor, but is not directly dependent on mitochondrial electron transport chain activity or its derived reactive oxygen species (ROS). Furthermore, our evidence suggests that, contrary to widespread assumptions, the cytosolic protein degradation pathways including ubiquitin-proteasome, autophagy, or endoplasmic reticulum (ER) stress response has little or negligible impacts on Ate1-induced cell death. We conclude that Ate1 controls the mitochondria-dependent cell death pathway.

biochemistry↗

bioRxiv2024

Spatially Resolved in vivo CRISPR Screen Sequencing via Perturb-DBiT

Perturb-seq enabled the profiling of transcriptional effects of genetic perturbations in single cells but lacks the ability to examine the impact on tissue environments. We present Perturb-DBiT for simultaneous co- sequencing of spatial transcriptome and guide RNAs (gRNAs) on the same tissue section for in vivo CRISPR screen with genome-scale gRNA libraries, offering a comprehensive understanding of how genetic modifications affect cellular behavior and tissue architecture. This platform supports a variety of delivery vectors, gRNA library sizes, and tissue preparations, along with two distinct gRNA capture methods, making it adaptable to a wide range of experimental setups. In applying Perturb-DBiT, we conducted un-biased knockouts of tens of genes or at genome-wide scale across three cancer models. We mapped all gRNAs in individual colonies and corresponding transcriptomes in a human cancer metastatic colonization model, revealing clonal dynamics and cooperation. We also examined the effect of genetic perturbation on the tumor immune microenvironment in an immune-competent syngeneic model, uncovering differential and synergistic perturbations in promoting immune infiltration or suppression in tumors. Perturb-DBiT allows for simultaneously evaluating the impact of each knockout on tumor initiation, development, metastasis, histopathology, and immune landscape. Ultimately, it not only broadens the scope of genetic inquiry, but also lays the groundwork for developing targeted therapeutic strategies.

genomics↗

bioRxiv2024

Restoration of PKM1 improves functional maturation of human stem-cell derived-β cell by regulating PEP metabolism

Human stem cell-derived {beta} (SC-{beta}) cells still exhibit limited glucose response required for insulin secretion due to glycolytic bottlenecks, yet how these metabolic abnormalities impact glucose response and functional maturation of SC-{beta} cells remains unclear. In this study, we identified a metabolic checkpoint located at PEP accumulation that impeded the functional maturation, which was rescued by restoration of pyruvate kinase 1 (PKM1). Glucose-tracing metabolomics in human stem cell-derived islets revealed abnormal glycolytic PEP accumulation at resting condition, resulting in impaired calcium response and insulin secretion upon high glucose or glycolytic metabolite stimulation. Mechanistically, elevated PEP significantly raised intracellular basal calcium levels, leading to downregulated expression of genes involved in TCA cycle elucidated by single cell transcriptomics. Furthermore, the activity of pyruvate kinase, which metabolizes PEP, was notably reduced due to low PKM1 expression. By overexpressing PKM1, the impairment of TCA-related genes caused by PEP accumulation was reversed via modulating PEP metabolism, resulting in enhanced calcium responses and insulin secretion upon high glucose stimulation. Together, we discovered a novel role of PKM1-regulated PEP metabolism in mediating the functional maturation of human SC-{beta} cells. This study highlights the importance of metabolic reprogramming in human SC-{beta} cell maturation, advancing cell therapy approaches for diabetes treatment.

cell biology↗

bioRxiv2024

Neratinib, a clinical drug against breast cancer, protects against atherosclerosis via ASK1 inhibition

Atherosclerosis commences with endothelial dysfunction and the retention of cholesterol within the vessel wall, followed by a chronic inflammatory response. Cholesterol-lowering strategies (such as statins and PCSK9 inhibitors) are primarily used for treating patients with atherosclerotic cardiovascular diseases, but leaving the therapeutic dilemma of residual inflammatory risk. To address this challenge, we employed Connectivity Map (CMap) screening for inflammation mechanism-based anti-atherosclerotic compounds using perturbational datasets obtained from TNF and IL-1{beta}-stimulated human endothelial cells. This screening process allow us to identify Neratinib, a clinical drug against breast cancer, as the hit compound with potential anti-inflammatory actions in endothelial cells. Further studies reveal that Neratinib inhibited endothelial cell inflammation elicited by three different pro-inflammatory stimuli (TNF, IL-1{beta} and LPS). Intriguingly, the anti-inflammatory effect of Neratinib was independent of its classical target HER2/ERBB2 inhibition. Mechanistically, Neratinib directly binds ASK1 and suppresses ASK1 activation. In both male and female Ldlr-/- mice, treatment with Neratinib decreased the plaque area, reduced the necrotic core size and mitigated macrophage infiltration to stabilize plaques. Lastly, we observed that Neratinib, in conjunction with the use of Rosuvastatin (a standard lipid-lowering drug), led to a reduction in serum lipids, and produced synergistic anti-atherosclerotic effects. Olink proteomics study suggested that combination treatment alleviated inflammation-related cytokines/chemokines in the serum from Ldlr-/- mice. Taken together, these findings support the concept that Neratinib could be tested for its potential as a "repurposed" drug for vascular inflammation and atherosclerosis, thereby streamlining efforts to translate preclinical discoveries to clinical testing in humans. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=108 SRC="FIGDIR/small/622073v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@78ef07org.highwire.dtl.DTLVardef@194f56forg.highwire.dtl.DTLVardef@7d65e4org.highwire.dtl.DTLVardef@ac7fe3_HPS_FORMAT_FIGEXP M_FIG C_FIG One Sentence SummaryNeratinib protects against atherosclerosis by reducing endothelial inflammation via ASK1 inhibition

pharmacology and toxicology↗

bioRxiv2024

Bioinformatics of combined nuclear and mitochondrial phylogenomics to define key nodes for the classification of Coleoptera

Nuclear genome sequencing is resource-intensive and not practical for building densely sampled phylogenetic trees of the most species rich lineages of animals, while mitochondrial genomes can be sequenced and analysed with relative ease. Here, we develop a conceptual approach and bioinformatics workflow for combining nuclear single-copy orthologs with less informative but densely sampled mitochondrial genomes, for a detailed tree of Coleoptera (beetles). Basal relationships of Coleoptera were first inferred from >2,000 BUSCO loci mined from GenBanks Short Read Archive for 119 exemplars of all major lineages under various substitution models and levels of matrix completion, to reveal universally supported nodes. Second, the corresponding mitogenomes were extracted and combined with an additional 373 species selected for broad taxonomic and biogeographic coverage, roughly in proportion to the known global species diversity of Coleoptera. Bioinformatic processing of mitogenomes was conducted with a novel pipeline for rapid, accurate annotation of protein-coding genes. Finally, phylogenetic trees from all 492 mitogenomes were generated under a backbone constraint from the universal basal nodes, which produced a well-supported tree of the major lineages at family and superfamily level. Being genetically unlinked and showing unique character variation, mitogenomes provide a unique perspective of the phylogeny. Comparison with three recent nuclear phylogenomic studies resulted in the recognition of >80 nodes universally present across all analyses. These may now support the higher classification of Coleoptera and serve as backbone of further studies, as numerous full mitogenomes and mitochondrial DNA barcodes are added to an increasingly complete phylogenetic tree of this super-diverse insect order.

evolutionary biology↗

bioRxiv2024

Fiber Microstructure Quantile (FMQ) Regression: A Novel Statistical Approach for Analyzing White Matter Bundles from Periphery to Core

The structural connections of the brains white matter are critical for brain function. Diffusion MRI tractography enables the in-vivo reconstruction of white matter fiber bundles and the study of their relationship to covariates of interest, such as neurobehavioral or clinical factors. In this work, we introduce Fiber Microstructure Quantile (FMQ) Regression, a new statistical approach for studying the association between white matter fiber bundles and scalar factors (e.g., cognitive scores). Our approach analyzes tissue microstructure measures based on quantile-specific bundle regions. These regions are defined in a data-driven fashion according to the quantiles of fractional anisotropy (FA) of a population fiber bundle, which pools all individuals bundles. The FA quantiles induce a natural subdivision of a fiber bundle, defining regions from the periphery (low FA) to the core (high FA) of the population fiber bundle. To investigate how fiber bundle tissue microstructure relates to covariates of interest, we employ the statistical technique of quantile regression. Unlike ordinary regression, which only models a conditional mean, quantile regression models the conditional quantiles of a response variable. This enables the proposed analysis, where a quantile regression is fitted for each quantile-specific bundle region. To demonstrate FMQ Regression, we perform an illustrative study in a large healthy young adult tractography dataset derived from the Human Connectome Project-Young Adult (HCP-YA), focusing on particular bundles expected to relate to particular aspects of cognition and motor function. In comparison with traditional regression analyses based on FA Mean and Automated Fiber Quantification (AFQ), we find that FMQ Regression provides a superior model fit with the lowest mean squared error. This demonstrates that FMQ Regression captures the relationship between scalar factors and white matter microstructure more effectively than the compared approaches. Our results suggest that FMQ Regression, which enables FA analysis in data-driven regions defined by FA quantiles, is more powerful for detecting brain-behavior associations than AFQ, which enables FA analysis in regions defined along the trajectory of a bundle. FMQ Regression finds significant brain-behavior associations in multiple bundles, including findings unique to males or to females. In both males and females, language performance is significantly associated with FA in the left arcuate fasciculus, with stronger associations in the bundles periphery. In males only, memory performance is significantly associated with FA in the left uncinate fasciculus, particularly in intermediate regions of the bundle. In females only, motor performance is significantly associated with FA in the left and right corticospinal tracts, with a slightly lower relationship at the bundle periphery and a slightly higher relationship toward the bundle core. No significant relationships are found between executive function and cingulum bundle FA. Our study demonstrates that FMQ Regression is a powerful statistical approach that can provide insight into associations from bundle periphery to bundle core. Our results also identify several brain-behavior relationships unique to males or to females, highlighting the importance of considering sex differences in future research.

neuroscience↗

bioRxiv2024

Investigating Brain and Biological Development in Children and Their Relationship with Physical, Mental, and Academic Outcomes

Brain age and biological age, estimated using machine learning models with brain imaging and biological features, have emerged as promising biomarkers for predicting a broad range of health outcomes in adults. However, very few studies have examined the counterpart of brain age and biological age in children, that is Brain Development Index (BRDI) and Biological Development Index (BIDI). Existing studies on BRDI and BIDI are largely cross-sectional and do not provide adequate information on their temporal trajectory and predictive power for future health outcomes in children. Additionally, the interconnectedness of BRDI and BIDI across multiple health domains, especially child-specific developmental outcomes, remains underexplored. Our study utilized brain imaging features and blood-based biomarkers from the Adolescent Brain and Child Development (ABCD) study to assess the trajectory of BRDI and BIDI over multiple time points. We examined their relationships with physical, mental, and academic health outcomes. Lastly, we utilize Bayesian network analysis to examine the relationship between the two indexes and their subcomponents. We found that delayed BRDI and BIDI were significantly associated with adverse future health outcomes across several domains. In addition, Bayesian network analysis revealed BRDI and BIDI subcomponents influence one another across different organ systems. Additionally, males exhibited more advanced BRDI, while females showed more advanced BIDI, revealing important sex differences in adolescent development. This research provides the first comprehensive analysis of BRDI and BIDI trajectories, revealing their predictive power for future health outcomes and offering new insights into the interconnected development of brain and biological systems in children.

developmental biology↗

bioRxiv2024

SIRT4 enhances the cytotoxicity of NK cells toward hepatic stellate cells and reverses liver fibrosis via AMPKα/P-p53/NKG2DL pathway

Natural killer (NK) cells exhibit antifibrotic properties in liver fibrosis (LF) by suppressing activated hepatic stellate cells (HSCs). SIRT4, a mitochondrial regulatory protein, plays a crucial role as a link between energy metabolism and cell viability. However, the role of SIRT4 in the cytotoxicity of NK cells toward HSCs remains unexplored. In this study, we found that SIRT4 was markedly downregulated in both mouse models and patients with LF. The loss of SIRT4 reduced the cytotoxicity of NK cells against activated HSCs, while its overexpression enhanced this cytotoxicity. Mechanistically, SIRT4 activates AMPK to promote p53 phosphorylation and facilitates its nuclear translocation, which induces the transcription of ULBP1 and ULBP2, members of the NK group 2D Legend (NKG2DL) family of molecules. Finally, overexpression of SIRT4 activated mouse hepatic NK cells and reversed LF by constructing adeno-associated viruses (AAV) that specifically target HSCs. Thus, SIRT4 is essential for the cytotoxicity of NK cells toward HSCs, and AAV8-pGAFP-SIRT4 may serve as a therapeutic approach for managing LF. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=199 SRC="FIGDIR/small/615768v1_ufig1.gif" ALT="Figure 1"> View larger version (55K): org.highwire.dtl.DTLVardef@1e6e987org.highwire.dtl.DTLVardef@edcc2dorg.highwire.dtl.DTLVardef@1f7c2bcorg.highwire.dtl.DTLVardef@111d81d_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2024

SC-MAMBA2: Leveraging State-Space Models for Efficient Single-Cell Ultra-Long Transcriptome Modeling

AO_SCPLOWBSTRACTC_SCPLOWThe rapid advancement of single-cell sequencing technology has significantly deepened our understanding of cellular heterogeneity, yet it concurrently presents substantial challenges for the unified modeling of single-cell data. Simultaneously, pre-trained foundation models have achieved notable success in domains such as natural language processing and image analysis. However, extending these models to accommodate ultra-long single-cell transcriptome sequences, characterized by an extensive number of genes, remains a formidable task. In this study, we introduce SC-MAMBA2, based on the MAMBA2 architecture, meticulously designed with a bidirectional modeling approach tailored for single-cell transcriptomics data. As the first single-cell foundation model to integrate state-space models (SSMs) underlying MAMBA2 architecture, SC-MAMBA2 features over 625 million parameters, covers more than 60,000 genes, and was pre-trained on a dataset of over 57 million cells, making it the most comprehensive solution for processing ultra-long transcriptome sequences. Extensive bench-marking across a diverse array of downstream tasks consistently demonstrates that SC-MAMBA2 surpasses state-of-the-art models, delivering superior accuracy and enhanced computational efficiency.

cell biology↗

bioRxiv2024

Change in brain molecular landscapes following electrical stimulation of the nucleus accumbens

Deep brain stimulation (DBS) targeting the nucleus accumbens (NAc) is a promising therapeutic intervention for treatment-resistant neuropsychiatric disorders such as depression, anxiety, and addiction. However, the molecular mechanisms underlying the clinical efficacy of NAc DBS remain largely unknown. One approach to address this question is by performing spatial gene expression analysis on cells located in different regions of the same circuit following NAc DBS. In this study, we utilized high-resolution spatial transcriptomics (Stereo-seq) to investigate gene expression changes induced by NAc DBS in the mouse brain. Mice were randomly allocated to received continuous electrical stimulation (0.1 mA, 130 Hz) or sham treatment (electrode implanted, no electrical stimulation given) for one week, and subsequent Stereo-seq analysis identified differentially expressed genes (DEGs) across various brain regions. Our findings reveal widespread alterations in synaptic function and neuronal connectivity, particularly in glutamate receptor-expressing neurons in the NAc, which play a key role in the reward circuitry. Functional enrichment analysis highlighted changes in transporter activity and glutamate receptor binding in brain regions such as the anterior cingulate cortex and lateral septal nucleus. Single-cell resolution mapping further identified key molecular players, including Nlgn1, Snca, PDE10a, and Syt1, which are critical for synaptic plasticity and neurotransmitter release, and have been implicated in various psychiatric disorders. These findings shed light on the molecular underpinnings of NAc DBS and provide insights into its therapeutic potential in modulating neural circuits associated with neuropsychiatric disorders.

molecular biology↗

bioRxiv2024

Generation of a PARPi-sensitive homozygous BRCA1-methylated OVCAR8 cell line using targeted CRISPR gene editing

Up to 17% of high grade serous ovarian carcinomas (HGSOC) harbour BRCA1 promoter methylation (meBRCA1), making them susceptible to treatment with targeted PARP inhibitor (PARPi) therapy. Unfortunately, meBRCA1 loss can be acquired following PARPi or platinum chemotherapy, resulting in BRCA1 re-expression and PARPi resistance. Our understanding of meBRCA1 stability in HGSOC is currently limited, in part due to a paucity of pre-clinical models with homozygous meBRCA1. Herein, we describe the generation of a several OVCAR8 cell line derivatives containing landing pad constructs, for future functional studies, and representing various BRCA1 states, including a homozygous meBRCA1 variant. Our PARPi resistant OVCAR8 has two methylated BRCA1 copies and one unmethylated copy, enabling BRCA1 expression. CRISPR-Cas9 gene editing was used to delete copies of the BRCA1 gene in landing pad-containing clones of this cell line (A6 and H4). We produced one variant with deletion of all BRCA1 copies (H4-53), and another with two copies deleted and only a single methylated gene copy remaining (A6-30 - validated further using nanopore long-read sequencing). These both lacked BRCA1 gene expression and were sensitive to PARPi treatment. The A6-30 line was transplanted into immunocompromised mice to generate a xenograft model that retained homozygous meBRCA1 and demonstrated some response to PARPi in vivo. Thus, using CRISPR gene editing we have created several novel isogenic HGSOC cell line models, including one with homozygous meBRCA1, that will support future studies of meBRCA1 stability and PARPi resistance.

cancer biology↗

bioRxiv2024

Haplotype-resolved assemblies provide insights into genomic makeup of the oldest grapevine cultivar (Munage) in Xingjiang

AbstractsMunage, an ancient grape variety that has been cultivated for thousands of years in Xinjiang, China, is recognized for its exceptional fruit traits. There are two main types of Munage: white fruit (WM) and red fruit (RM). However, the lack of a high-quality genomic resources has impeded effective breeding and restricted the potential for expanding these varieties to other growing regions. In this study, we assembled haplotype-resolved genome assemblies for WM and RM, alongside integrated whole genome resequencing (WGS) data and transcriptome data to illuminate specific mutations and associated genes in Munake and the genes associated with fruit color traits. Selective analysis between Munage clones and Eurasian grapes suggested that adaptive selection exists in Munage grapes, with genes enriched in processes including cell maturation, plant epidermal cell differentiation, and root epidermal cell differentiation. The study examined the mutations within Munage grapes and found that the genes PMAT2 on chromosome 12 and MYB123 on chromosome 13 are likely responsible for color variation in RM. These findings provide crucial genetic resources for investigating the genetics of the ancient Chinese grape variety, Munage, and will facilitate the genetic improvement in grapevine.

genomics↗