Biology subjects

Tang, X.

Publications and source records attributed to Tang, X..

At least 73 records · Page 4Linked to original sources

bioRxiv2024

Astrocytic modulation of population encoding in mouse visual cortex via GABA transporter 3 revealed by multiplexed CRISPR/Cas9 gene editing

Astrocytes, which are increasingly recognized as pivotal constituents of brain circuits governing a wide range of functions, express GABA transporter 3 (Gat3), an astrocyte-specific GABA transporter responsible for maintenance of extra-synaptic GABA levels. Here, we examined the functional role of Gat3 in astrocyte-mediated modulation of neuronal activity and information encoding. First, we developed a multiplexed CRISPR construct applicable for effective genetic ablation of Gat3 in the visual cortex of adult mice. Using in vivo two-photon calcium imaging of visual cortex neurons in Gat3 knockout mice, we observed changes in spontaneous and visually driven single neuronal response properties such as response magnitudes and trial-to-trial variability. Gat3 knockout exerted a pronounced influence on population-level neuronal activity, altering the response dynamics of neuronal populations and impairing their ability to accurately represent stimulus information. These findings demonstrate that Gat3 in astrocytes profoundly shapes the sensory information encoding capacity of neurons and networks within the visual cortex.

neuroscience↗

bioRxiv2024

BC-Design: A Biochemistry-Aware Framework for High-Precision Inverse Protein Folding

Inverse protein design (IPD) extends the classical problem of inverse protein folding (IPF) by not only recovering a sequence compatible with a given backbone geometry but also generating a range of new sequences that satisfy the physicochemical constraints required for a stable fold with a specified (often designed) function. Recent progress has incorporated biochemical properties as discrete per-residue features, but such localized signals cannot represent the continuous hydrophobic and electrostatic environments that span protein surfaces and interior volumes. Here we introduce BC-DO_SCPLOWESIGNC_SCPLOW, a biochemistry-aware inverse design framework that integrates geometric structure with smoothly varying hydrophobicity and charge properties. The later are represented independent of residue coordinates, on compact point clouds sampled throughout protein surfaces and interiors. This formulation provides a natural spatial description of physicochemical environments and enriches structural cues without specifying amino-acid identities. On the CATH 4.2 benchmark, BC-DO_SCPLOWESIGNC_SCPLOW achieves 90% sequence recovery and generalizes robustly across protein lengths, contact-order regimes, and major fold classes. Masking experiments further demonstrate an interpretable fidelity-diversity control: full biochemical context yields high-fidelity reconstructions, whereas withholding information enables exploratory variant generation. Beyond diagnostic benchmarks, BC-DO_SCPLOWESIGNC_SCPLOW demonstrably improves functional design outcomes across diverse settings. It increases enzyme-substrate affinity, enhances peptide-receptor design accuracy, and achieves state-of-the-art recovery and structural fidelity in antibody loop (CDRH3) modeling. In these applications, the model not only reconstructs native-like sequences but also proposes plausible functional variants that preserve catalytic or binding geometry--such as generating CDRH3 loops that maintain antigen-contact configurations while offering new sequence solutions. These results show that integrating continuous physicochemical properties with structural geometry enables practical, function-oriented protein design, going beyond backbone-conditioned recovery.

bioinformatics↗

bioRxiv2024

Motor compensations, not sensory errors, regulate serial dependence in naturalistic speech production

Motor control is essential for organisms to efficiently interact with the environment by maintaining accurate action and adjusting to future changes. Speech production, one of the most complex motor behaviors, relies on a feedback control process to detect sensory errors and trigger updates in a feedforward control process that implements compensations. However, the specific contributions of these critical processes in sensorimotor learning during continuous vocal production remain debated. Here, we used two experimental designs in five experiments to dissociate these mechanisms. First, we employed a serial-dependence design with randomized pitch perturbations, dissociating the influences of sensory errors and motor compensation on subsequent vocalizations on a trial-by-trial basis. We found that motor compensation, rather than sensory errors, predicted the compensatory responses in the subsequent trials, suggesting instantaneous serial learning mediated by updates in the feedforward process. This compensation-driven serial learning was generalized across productions of different vowel categories. Second, we further implemented a serial-dependence adaptation design in a sentential context, where auditory perturbation occurred only on a preceding syllable. Any learning effects in its subsequent syllable without pitch perturbation would reflect changes in the speech motor representation. Our results consistently revealed that compensation in the preceding syllable predicted pitch changes in the subsequent syllable, but only when the two adjacent syllables were embedded within a word boundary. Collectively, the study provides ecological-valid evidence supporting that error-based motor compensation, incorporating cognitive and linguistic constraints, directly regulates the speech motor representation and mediates the instantaneous serial learning in successive actions.

neuroscience↗

bioRxiv2024

Pharmacological inhibition of Fms-like kinase 3 (FLT3) promotes neuronal maturation and suppresses seizure in a mouse model

Fms-like tyrosine kinase 3 (FLT3) is a receptor tyrosine kinase predominantly expressed in blood and brain cells. While the FLT3 signaling pathway has been extensively studied in blood cell development and leukemia, its role in the brain remains largely unexplored. Through our groups previous high-throughput drug screening work unexpectedly found that several small molecule FLT3 inhibitors (FLT3i), including KW-2449 and Sunitinib, enhance expression of the gene encoding chloride transporter KCC2 in neurons. KCC2 is crucial for brain development and function, and its dysregulation is linked to many brain diseases. These findings suggest previously unrecognized roles of FLT3 signaling in brain health and disease that have yet to be systematically studied. In this study, we utilized a functional genomics approach to investigate the transcriptomic changes induced by pharmacological inhibition of the FLT3 pathway in brain cells, including cultured primary mouse neurons, a human stem cell-derived neuronal model of Rett syndrome (RTT), and human stem cell-derived microglia cultures. Our results show that treating human or mouse neurons with FLT3i drugs significantly upregulates genes crucial for brain development while downregulating genes linked to neuroinflammation. In contrast, FLT3i treatment of human microglia, which do not express FLT3, has no effect on their gene expression, highlighting the cell type-specific roles of FLT3 signaling in the brain. To further understand how FLT3 signaling regulates the expression of neuronal maturation genes such as KCC2, we conducted a curated CRISPR screen that identified a number of transcription factors involved in FLT3i-mediated KCC2 activation in neurons. The mRNA and protein levels of several neurodevelopmental disorder (NDD) risk genes are significantly upregulated in FLT3i-treated neurons, indicating potential therapeutic applications of FLT3i in rescuing underexpression and/or haploinsufficiency of disease-associated genes. In our in vivo studies, we evaluated the efficacy of the FLT3i drug KW-2449 in mice, demonstrating that it can effectively cross the blood-brain barrier, induce KCC2 protein expression for up to 24 hours after a single injection, and reduces seizure activity in a chemoconvulsant-induced mouse model of temporal lobe epilepsy. Collectively, our findings uncover previously unrecognized roles of neuron-specific FLT3 signaling in promoting neuronal maturation and reducing neuroinflammation. These results suggest that FLT3 kinase signaling regulates a transcriptional program vital for brain development and function, position it as a promising therapeutic target for NDD treatment.

neuroscience↗

bioRxiv2024

Characterization of the cellular and subcellular distribution of fms-like tyrosine kinase 3 (FLT3) and other neuronal proteins using an alkaline phosphatase (AP) immunolabeling method

Precisely localizing the spatial distribution of proteins within various cell types in the brain, and in sub-cellular compartments such as the synapses, is critical for generating and testing hypothesis to elucidating the function of target proteins in the brain. The fms-like tyrosine kinase-3 (FLT3) has been studied extensively in the context of blood cell development and leukemia pathogenesis, but little is known about its role in the brain. Previous work characterizing FLT3 protein expression in the brain have not yielded convincing results, mainly limited by the low expression level of FLT3 and poor sensitivity of standard immunolabeling method using fluorescent secondary antibody. In this study, we report the systematic characterization of FLT3 protein localization during brain development using a highly sensitive immunolabeling methodology based on alkaline phosphatase (AP) polymer biochemistry. Our results reveal a previously unknown neuron-selective FLT3 expression pattern in both mouse and human cerebellum tissue samples, and demonstrate a gradual increase in the total FLT3 protein level and a cytosolic-to-dendritic change in subcellular FLT3 distribution during mouse cerebellum development. Through combining the AP immunolabeling of FLT3 with standard immunostaining of various cell type markers to achieve hybrid co-labeling of multiple antigens in tissue sections, we demonstrate that the main cell type that express FLT3 in the cerebellum is PV+, Calbindin+ Purkinje cells. To expand the use case of AP immunolabeling method in labeling neuronal proteins, we show robust labeling of Kir2.1, a potassium channel protein that is expressed at low level in neurons, in brain tissue sections collected from mouse, pig, and human brains. We further established that the AP immunolabeling method can be used in human stem cell-derived neurons to detect postsynaptic density scaffold protein PSD95 within fine subcellular structures such as dendritic spines and synapses, in cultured primary mouse cortical neurons and human stem cell-derived neurons. To our knowledge, our work represents the first report of applying AP immunolabeling to detect neuronal protein expression in brain tissue and cell samples. Moreover, our work reveals a previously unknown neuron-specific pattern of FLT3 expression in the brain, providing the foundation for further mechanistic studies to uncover its role in brain development and functioning.

neuroscience↗

bioRxiv2024

Test-retest reliability of resting-state EEG intrinsic neural timescales

Intrinsic neural timescales (INTs), which reflect the duration of neural information storage within local brain regions and capacity for information integration, are typically measured using autocorrelation windows (ACWs). Extraction of INTs from resting-state brain activity has been extensively applied in psychiatric disease research. Given the potential of INTs as a neural marker for psychiatric disorders, investigating their reliability is crucial. This study, using an open-source database, aimed to evaluate the test-retest reliability of ACW-0 and ACW-50 under both eyes-open and eyes-closed conditions across three sessions. The intraclass correlation coefficients (ICCs) were employed to quantify the reliability of the INTs. Our results showed that INTs exhibited good reliability (ICC > 0.6) at the whole-brain level across different index types and eye states. Spatially, except for the right temporal region in the eyes-open condition, all other regions showed moderate-to-high ICCs. Over 60% of the electrodes demonstrated moderate-to-high INT ICCs under both eyes-open and eyes-closed conditions, with ACW-0 being more stable than ACW-50. This present study comprehensively assessed the reliability of INT under various conditions, providing robust evidence for their stability in neuroscience and psychiatry.

neuroscience↗

bioRxiv2024

Association study of Plasmodium falciparum Acetyl-CoA Synthetase Mutations S868G and V949I with antimalarial drugs

Plasmodium falciparum acetyl-CoA synthetase (PfACAS) protein is an important source of acetyl-CoA. We detected the mutations S868G and V949I in PfACAS by whole-genome sequencing analysis in some recrudescent parasites after antimalarial treatment with artesunate and dihydroartemisinin-piperaquine, suggesting that they may confer drug resistance. Using CRISPR/Cas9 technology, we engineered parasite lines carrying the PfACAS S868G and V949I mutations in two genetic backgrounds and evaluated their susceptibility to antimalarial drugs in vitro. The results demonstrated that PfACAS S868G and V949I mutations alone or in combination were not enough to provide resistance to antimalarial drugs.

microbiology↗

bioRxiv2024

PlasGO: enhancing GO-based function prediction for plasmid-encoded proteins based on genetic structure

Plasmid, as a mobile genetic element, plays a pivotal role in facilitating the transfer of traits, such as antimicrobial resistance, among the bacterial community. Annotating plasmid-encoded proteins with the widely used Gene Ontology (GO) vocabulary is a fundamental step in various tasks, including plasmid mobility classification. However, GO prediction for plasmid-encoded proteins faces two major challenges: the high diversity of functions and the limited availability of high-quality GO annotations. Thus, we introduce PlasGO, a tool that leverages a hierarchical architecture to predict GO terms for plasmid proteins. PlasGO utilizes a powerful protein language model to learn the local context within protein sentences and a BERT model to capture the global context within plasmid sentences. Additionally, PlasGO allows users to control the precision by incorporating a self-attention confidence weighting mechanism. We rigorously evaluated PlasGO and benchmarked it against six state-of-the-art tools in a series of experiments. The experimental results collectively demonstrate that PlasGO has achieved commendable performance. PlasGO significantly expanded the annotations of the plasmid-encoded protein database by assigning high-confidence GO terms to over 95% of previously unannotated proteins, showcasing impressive precision of 0.8229, 0.7941, and 0.8870 for the three GO categories, respectively, as measured on the novel protein test set.

bioinformatics↗

bioRxiv2024

H2A.Z deposition at meiotic prophase I underlies homologous recombination and pachytene genome activation during male meiosis

Accurate meiotic progression is important for gamete formation and the generation of genetic diversity. However, little is known about the identity of chromatin regulators that underlie mammalian meiosis in vivo. Here, we identify the multifaceted functions of the chromatin remodeler ZNHIT1 in governing meiosis. The expression of Znhit1 gradually increases during the meiotic prophase, and Znhit1 knockout in spermatocytes results in arrested pachytene development, impaired DNA double-strand break repair, and defective homologous recombination. Single-cell RNA sequencing and transcriptome analysis reveal that Znhit1 loss dysregulates meiotic transcriptional programs at the pachytene stage. Chromatin immunoprecipitation data show that ZNHIT1 is needed for the incorporation of the histone variant H2A.Z into pachytene chromatin. Moreover, we found that H2A.Z cooperates with the transcription factor A-MYB to co-bind DNA elements and control gene activity. Our findings provide insights into the regulatory mechanisms governing meiotic progression and highlight ZNHIT1 as a critical regulator of meiotic progression.

developmental biology↗

bioRxiv2024

Acetyl-CoA Synthetase Mutations S868G and V949I Do Not Confer Resistance to Antimalarial Drugs in vitro in Plasmodium falciparum.

microbiology↗

bioRxiv2024

Brain implantation of tissue-level-soft bioelectronics 1 via embryonic development

The design of bioelectronics capable of stably tracking brain-wide, single-cell, and millisecond-resolved neural activities in the developing brain is critical to the study of neuroscience and neurodevelopmental disorders. During development, the three-dimensional (3D) structure of the vertebrate brain arises from a 2D neural plate1,2. These large morphological changes previously posed a challenge for implantable bioelectronics to track neural activity throughout brain development3-9. Here, we present a tissue-level-soft, sub-micrometer-thick, stretchable mesh microelectrode array capable of integrating into the embryonic neural plate of vertebrates by leveraging the 2D-to-3D reconfiguration process of the tissue itself. Driven by the expansion and folding processes of organogenesis, the stretchable mesh electrode array deforms, stretches, and distributes throughout the entire brain, fully integrating into the 3D tissue structure. Immunostaining, gene expression analysis, and behavioral testing show no discernible impact on brain development or function. The embedded electrode array enables long-term, stable, brain-wide, single-unit-single-spike-resolved electrical mapping throughout brain development, illustrating how neural electrical activities and population dynamics emerge and evolve during brain development.

bioengineering↗

bioRxiv2024

Realigning representational drift in mouse visual cortex by flexible brain-machine interfaces

The ability to stably decode brain activity is crucial for brain-machine interfaces (BMIs), which are often compromised by recording instability due to immune responses and probe drifting. In addition, many brain regions undergo intrinsic dynamics such as "representational drift", in which neural activities associated with stable sensation and action continually change over time. In this study, we employed tissue-like flexible electrode arrays for recording visual stimulus-dependent single-unit action potentials in the mouse visual cortex. The flexible electrode array enabled us to record action potentials from the same neurons over extended periods under visual stimuli, allowing us to characterize the representational drift during these stimuli. With this approach, we tested hypotheses about the origins and mechanisms of representational drift, tracked latent dynamics transformation, and modeled these dynamics with affine transformation. Our findings enabled the construction of a single, long-term stable, high-performance visual information decoder that accounts for representational drift, potentiating chronically stable flexible BMIs in brain regions experiencing representational drifts.

bioengineering↗

bioRxiv2024

Mapping Endothelial-Macrophage Interactions in Diabetic Vasculature: Role of TREM2 in Vascular Inflammation and Ischemic Response

Diabetes mellitus (DM) significantly accelerates vascular diseases like peripheral arterial disease (PAD). Endothelial cells (ECs) and macrophages (M{Phi}s) singularly and synergistically are important contributors to DM-associated vascular dysfunction. Single-cell (sc) profiling technologies are revealing the true heterogeneity of ECs and M{Phi}s, but how this cellular diversity translates to cell-cell interactions, and consequentially vascular function, remains unknown. We leveraged scRNA sequencing and spatial transcriptome (ST) profiling to analyze human mesenteric arteries from non-diabetic (ND) and type 2 diabetic (T2D) donors. We generated a transcriptome and interactome map encompassing the major arterial cells and highlighted Triggering Receptor Expressed on Myeloid Cells 2 (TREM2) as a top T2D-induced gene in mononuclear phagocytes (MPs), with concomitant increases of TREM2 ligands in ECs. We verified DM-associated TREM2 induction in cell and mouse models, and found that TREM2 inhibition decreases pro-inflammatory responses in MPs and ECs, as well as increases EC migration in vitro. Furthermore, TREM2 inhibition using a neutralizing antibody enhanced ischemic recovery and flow reperfusion in DM mice subjected to hindlimb ischemia, suggesting that TREM2 promotes ischemic injury in DM. Finally, in human PAD, co-existing DM was associated with greater expression of TREM2 and its interaction with ECs, with a further increase in ischemic tissue compared to patient-matched non-ischemic tissue. Collectively, our study presents the first atlas of human diabetic vessels with single cell and spatial resolution, and identifies TREM2-EC interaction as a key driver of diabetic vasculopathies, the targeting of which may offer an opportunity to ameliorate vascular dysfunction associated with DM-PAD.

cell biology↗

bioRxiv2024

Glial state changes and neuroinflammatory RIPK1 signaling are a key feature of ALS pathogenesis

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease that causes motor neuron loss in the brain and spinal cord. Neuroinflammation driven by activated microglia and astrocytes is prominent in ALS, but an understanding of cell state dynamics and which pathways contribute to the disease remains unclear. Single nucleus RNA sequencing of ALS spinal cords demonstrated striking changes in glial cell states, including increased expression of inflammatory and glial activation markers. Many of these signals converged on RIPK1 and the necroptotic cell death pathway. Activation of the necroptosis pathway in ALS spinal cords was confirmed in a large bulk RNA sequencing dataset and at the protein level. Blocking RIPK1 kinase activity delayed symptom onset and motor impairment and modulated glial responses in SOD1G93A mice. We used a human iPSC-derived motor neuron, astrocyte, and microglia tri-culture system to identify potential biomarkers secreted upon RIPK1 activation, inhibited pharmacologically in vitro, and modulated in the CSF of people with ALS treated with a RIPK1 inhibitor. These data reveal ALS-enriched glial populations associated with inflammation and suggest a deleterious role for neuroinflammatory signaling in ALS pathogenesis.

neuroscience↗

bioRxiv2024

Mechanical forces pattern endocardial Notch activation via mTORC2-PKC pathway

Notch signaling has been identified as a key regulatory pathway in patterning the endocardium through activation of endothelial-to-mesenchymal transition (EMT) in the atrioventricular canal (AVC) and proximal outflow tract (OFT) region. However, the precise mechanism underlying Notch activation remains elusive. By transiently blocking the heartbeat of E9.5 mouse embryos, we found that Notch activation in the arterial endothelium was dependent on its ligand Dll4, whereas the reduced expression of Dll4 in the endocardium led to a ligand-depleted field, enabling Notch to be specifically activated in AVC and OFT by regional increased shear stress. The strong shear stress altered the membrane lipid microdomain structure of endocardial cells, which activated mTORC2 and PKC and promoted Notch1 cleavage even in the absence of strong ligand stimulation. These findings highlight the role of mechanical forces as a primary cue for endocardial patterning and provide insights into the mechanisms underlying congenital heart diseases of endocardial origin.

developmental biology↗

bioRxiv2024

OmicsFootPrint: a framework to integrate and interpret multi-omics data using circular images and deep neural networks

The OmicsFootPrint framework addresses the need for advanced multi-omics data analysis methodologies by transforming data into intuitive two-dimensional circular images and facilitating the interpretation of complex diseases. Utilizing Deep Neural Networks and incorporating the SHapley Additive exPlanations (SHAP) algorithm, the framework enhances model interpretability. Tested with The Cancer Genome Atlas (TCGA) data, OmicsFootPrint effectively classified lung and breast cancer subtypes, achieving high Area Under Curve (AUC) scores-- 0.98{+/-}0.02 for lung cancer subtype differentiation, 0.83{+/-}0.07 for breast cancer PAM50 subtypes, and successfully distinguished between invasive lobular and ductal carcinomas in breast cancer, showcasing its robustness. It also demonstrated notable performance in predicting drug responses in cancer cell lines, with a median AUC of 0.74, surpassing nine existing methods. Furthermore, its effectiveness persists even with reduced training sample sizes. OmicsFootPrint marks an enhancement in multi-omics research, offering a novel, efficient, and interpretable approach that contributes to a deeper understanding of disease mechanisms.

bioinformatics↗

bioRxiv2024

The Dsc ubiquitin ligase complex identifies transmembrane degrons to degrade orphaned proteins at the Golgi

The Golgi apparatus is essential for protein sorting, yet its quality control mechanisms are poorly understood. Here we show that the Dsc ubiquitin ligase complex, particularly the rhomboid pseudo-protease subunit, Dsc2, assesses the hydrophobic length of -helical transmembrane domains (TMDs) at the Golgi. Thereby the Dsc complex interacts with orphaned ER and Golgi proteins that have shorter TMDs and ubiquitinates them for targeted degradation. Some Dsc substrates will be K63 polyubiquitinated for ESCRT dependent vacuolar degradation or K48 polyubiquitinated for endosome and Golgi associated proteasomal degradation (EGAD). Other Dsc substrates are exclusively extracted by Cdc48 for EGAD. The accumulation of Dsc substrates entails a specific increase in glycerophospholipids with shorter and asymmetric fatty acyl chains. Hence, the Dsc complex mediates the selective degradation of orphaned proteins at the sorting center of cells, which prevents their spreading across other organelles and thus preserves cellular membrane protein and lipid composition.

cell biology↗

bioRxiv2024

High performance TadA-8e derived cytosine and dual base editors with undetectable off-target effects in plants

Cytosine base editors (CBEs) and adenine base editors (ABEs) are powerful tools to install precise C-to-T and A-to-G base edits in living organisms. In recently years, a highly efficient ABE based on engineered TadA-8e, known as ABE8e, has been developed to confer highly efficient A-to-G editing in mammalian cells and plants. Interestingly, TadA-8e can be further evolved and engineered to confer cytosine base editing. In this study, we compare in rice and tomato cells a serial of engineered CBEs derived from TadA-8e and identify TadCBEa, TadCBEd, and TadCBEd_V106W as efficient CBEs with high editing purity, while maintaining the relatively narrow editing window of ABE8e. Excitingly, we show TadDE is a new class of dual base editor where a single deaminase domain promotes simultaneous C-to-T and A-to-G base editing in plant cells. Multiplexed base editing is demonstrated in transgenic rice plants with TadCBEa and TadDE. Furthermore, no off-target effects of TadCBEa and TadDE can be detected by whole genome and transcriptome sequencing of the transgenic lines, suggesting high editing specificity. Finally, we demonstrate two gain-of-function crop engineering applications in rice by using the efficient dual base editor, TadDE. In the first case, herbicide resistance alleles of OsALS are introduced by TadDE. In the second case, synonymous mutations are generated in OsSPL14, making its transcript resistant to OsMIR156-mediated degradation. Together, this study reports TadA-8e derived CBEs and a dual base editor with high editing activity, purity, and specificity. They are valuable additions to the expanding plant base editing toolbox.

molecular biology↗