Biology subjects

Yang, Y.

Publications and source records attributed to Yang, Y..

At least 523 records · Page 29Linked to original sources

bioRxiv2024

Systematic screen of RNA binding proteins that enhance circular RNA translation

Translatable circular RNAs (circRNAs) have emerged as a promising alternative to linear mRNA as new therapeutics due to its improved stability. The translation of circRNAs is mainly driving by internal ribosome entry site (IRES) or IRES-like elements, which is under regulation by various trans-acting RNA binding proteins (RBPs). Here we designed a cell-based system to systematically screen RBPs that enhance translation of circRNAs, and identified a total of 68 proteins as putative activators of noncanonical translation. These translation activators mainly involved in the functions of RNA processing, ribosomal biogenesis and translation initiation. Furthermore, we developed a machine learning algorithm to extract common sequence features of these activators, which predicted more potential RBPs with translation activator activities. The newly identified and predicted activators were subsequently demonstrated to promote the IRES-mediated circRNA translation in a context-dependent fashion. This investigation provides new insights to discover functions for IRES trans-acting factors and to expand the toolbox for engineered RBPs in RNA synthetic biology.

molecular biology↗

bioRxiv2024

CILP from Cartilage Intermediate Zone Inhibits Hyaline Cartilage Fibrosis and Chondrocyte Ferroptosis via Keap1-Nrf2 Axis in Early Osteoarthritis Exercise Therapy

By analyzing the single-cell RNA-Seq libraries, the roles of cartilage intermediate layer protein (CILP) and the cartilage intermediate zone in early osteoarthritis (OA) exercise therapy were explored. An early OA rat model was established via a 4-week anterior cruciate ligament transection. The effect of moderate exercise was confirmed using histology, the open-field test, and gait analysis. The response of the cartilage intermediate zone to mechanical stimulation was explored using multiplex fluorescent immunohistochemical staining. Radiomics was used to evaluate the relatively damaged and undamaged areas in the cartilage of patients with OA. CILP was OE and KD in early OA chondrocytes, and quantitative proteomics, yeast one-hybrid, co-immunoprecipitation, Nrf2 and ubiquitination assays were used to investigate its mechanism. We found that moderate exercise upregulates CILP in the cartilage intermediate zone. CILP recovers the type II/I collagen, Sox9, and -SMA expression ratios, and reduces Keap1-Nrf2 dimer stability, inhibiting Nrf2 ubiquitination and promoting Nrf2 nuclear translocation. Nrf2 nuclear translocation activates SLC7A11, HO-1, GPX4, and SOD-1 expression, decreases MDA content, and increases GSH content, inhibiting chondrocyte ferroptosis and promoting fibrocartilage hyalinization. In conclusion, the exercise-induced cartilage intermediate zone and CILP-Keap1-Nrf2 axis inhibit hyaline cartilage fibrosis and chondrocyte ferroptosis to alleviate early OA.

cell biology↗

bioRxiv2024

In vivo genome editing of human hematopoietic stem cells for treatment of blood disorders by mRNA delivery

Ex vivo autologous hematopoietic stem cells (HSCs) gene therapy provides promising new treatments for hematological disorders. However, current methods involve complex processes and chemotherapeutic conditioning, leading to limited accessibility for treatment and significant side effects. Here, we developed an antibody-free targeted lipid nanoparticles (LNPs) for mRNA delivery to HSCs in vivo, enabling efficient base editing of the HBG target in human HSCs to reactivate fetal hemoglobin in derived erythroid cells. Delivery of ABE8e/sgRNA mRNA with optimized structure LNPs achieves efficient in vivo base editing of HBG in transfusion-dependent {beta}-thalassemia (TDT) patients derived HSCs engrafted in immunodeficient NCG-X mice, showing restored globin chain balance in erythroid cells. Our research indicated that utilizing LNPs for delivery of genome editor achieves efficient editing of endogenous genes of human HSCs. Notably, this non-viral delivery system eliminates the need for harvesting or mobilizing HSCs, providing a potent and one-time treatment potential for blood disorders like sickle cell disease (SCD) and TDT. HighlightsO_LIAntibody-free targeted LNPs system achieves efficient mRNA delivery and base editing in human bone marrow cells including HSCs via one-time intravenous injection. C_LIO_LIDelivery of ABE8e/sgRNA mRNA with optimized LNPs achieves efficient in vivo base editing of HBG in TDT patients derived HSCs engrafted in immunodeficient NCG-X mice, showing restored globin chain balance in erythroid cells. C_LIO_LILNPs efficiently deliver gene editing system to the BM for in vivo editing of human HSCs, providing preclinical evidence for the next generation non-viral gene therapy for blood disorders. C_LI

bioengineering↗

bioRxiv2024

Alzheimer's Disease Patient Brain Extracts Induce Multiple Pathologies in Vascularized Neuroimmune Organoids for Disease Modeling and Drug Discovery

Alzheimers Disease (AD) is the most common cause of dementia afflicting 55 million individuals worldwide, with limited treatment available. Current AD models mainly focus on familial AD (fAD), which is due to genetic mutations. However, models for studying sporadic AD (sAD), which represents over 95% of AD cases without specific genetic mutations, are severely limited. Moreover, the fundamental species differences between humans and animals might significantly contribute to clinical failures for AD therapeutics that have shown success in animal models, highlighting the urgency to develop more translational human models for studying AD, particularly sAD. In this study, we developed a complex human pluripotent stem cell (hPSC)-based vascularized neuroimmune organoid model, which contains multiple cell types affected in human AD brains, including human neurons, microglia, astrocytes, and blood vessels. Importantly, we demonstrated that brain extracts from individuals with sAD can effectively induce multiple AD pathologies in organoids four weeks post-exposure, including amyloid beta (A{beta}) plaques-like aggregates, tau tangles-like aggregates, neuroinflammation, elevated microglial synaptic pruning, synapse/neuronal loss, and impaired neural network. Furthermore, after treatment with Lecanemab, an FDA-approved drug targeting A{beta}, AD brain extract exposed organoids showed a significant reduction of amyloid burden. Thus, the neuroimmune organoid model provides a unique opportunity to study AD, particularly sAD under a pathophysiological relevant three-dimensional (3D) human cell environment. It also holds great promise to facilitate AD drug development, particularly for immunotherapies.

neuroscience↗

bioRxiv2024

Posterior parietal cortex mediates rarity-induced decision bias and learning under uncertainty

Optimal decision-making under uncertainty is critical for survival, yet real-world decisions often deviate from optimality. Here, we report a rarity-induced bias in humans and mice, where rare events exert a stronger and more persistent impact on future decisions than common events. Optogenetic manipulations demonstrate two opposing roles of the posterior parietal cortex (PPC): generating rarity-induced bias throughout learning, and driving optimal choices in the expert stage. In vivo recordings support both roles: preceding rare rewards enhance the activity of PPC neurons encoding the biased choice while suppressing neurons encoding the opposite choice, causing bias; learning enhances the stimulus-encoding capacity of PPC neurons, promoting optimal choices. A data-driven metacognitive model recapitulated the bias and learning process, and predicted PPCs causal role in learning, as validated by optogenetics. Our study uncovers an evolutionarily conserved rarity impact in decision-making, and elucidates essential roles of PPC in mediating rarity-induced bias and learning under uncertainty.

neuroscience↗

bioRxiv2024

Omega-3 fatty acid normalizes postsynaptic density proteins via miRNAs regulation in hippocampus and prevents DEHP-induced impairment of learning and memory in mice

AbstractsDEHP is the most widely used plasticizer in many products. However, growing evidence has indicated that DEHP may induce neurotoxicity. DEHP exposure affects mircoRNAs (miRNAs) expression in brain. A growing body of evidence suggests that nutrients and other bioactive food components prevent neurotoxicity through regulation of miRNA expression. Due to the increasing concern about the risks of DEHP to human health, we explored the neuroprotective effect of Omega-3 fatty acid (Omega-3FA) on subchronic DEHP-induced neurotoxicity in mice, and the potential involved miRNAs and their targets in the protective action of Omega-3FA against DEHP-induced neurotoxicity. Omega-3FA protected against the DEHP-induced impairment of learning and memory and alleviated the thinning of postsynaptic density (PSD) thickness in hippocampal synapses. We observed that there are fourteen up or down regulated miRNAs associated PSD in DEHP exposure which were normalized by Omega-3FA treatment. Protein targets in PSD of these differentially expressed miRNAs were predicted. Furthermore, the expression levels of protein mGluR5, Homer1, and NMDAR2B were carried out via Western blot, for further verifying PSD associated miRNAs targets are involved in neuroprotection of Omega-3FA against DEHP. These findings suggested that Omega-3FA protected DEHP-induced impairment of learning and memory as well as synaptic structure alteration in the hippocampus by regulating the expression of PSD associated miRNAs and their targets. Thus, Omega-3FA should be included in diet to prevent or suppress neurotoxicity caused by continuous exposure to DEHP.

neuroscience↗

bioRxiv2024

S100a4+ alveolar macrophages accelerate the progression of precancerous atypical adenomatous hyperplasia by promoting fatty acid metabolism

Lung cancer is preceded by premalignant lesions, and what factors drive this transformation and the potential regulatory mode in the context of tumor initiation remain to be elucidated. In the course of precancerous lesions, we found a phasic shift in metabolic patterns. Macrophages are a heterogeneous cell population with high plasticity in the tumor microenvironment. Single-cell interaction and metabolic analyses highlighted a cellular state, S100a4+ alveolar macrophages, which exhibited distinct fatty acid metabolic activity, such as palmitic acid metabolism, at the atypical adenomatous hyperplasia stage, accompanied by an angiogenic-promoting function in a pre-neoplastic setting. These findings were reproducible in human single-cell transcriptomes and had been confirmed by histopathological staining and in vitro cell coculture assays. Taken together, the results from this study demonstrated that the S100a4+ alveolar macrophage subset contributes to tumorigenesis by altering its metabolic state, suggesting that metabolic interventions targeting this cell state in the early stage of disease may delay neoplastic transformation of the lung epithelium.

cancer biology↗

bioRxiv2024

Human TRPV4 engineering yields an ultrasound-sensitive actuator for sonogenetics

AbstractSonogenetics offers non-invasive and cell-type specific modulation of cells genetically engineered to express ultrasound-sensitive actuators. Finding an ion channel to serve as sonogenetic actuator it critical for advancing this promising technique. Here, we show that ultrasound can activate human TRP channel hTRPV4. By screening different hTRPV4 variants, we identify a mutation F617L that increases mechano-sensitivity of this channel to ultrasound, while reduces its sensitivity to hypo-osmolarity, elevated temperature, and agonist. This altered sensitivity profile correlates with structural differences in hTRPV4-F617L compared to wild-type channels revealed by our cryo-electron microscopy analysis. We also show that hTRPV4-F617L can serve as a sonogenetic actuator for neuromodulation in freely moving mice. Our findings demonstrate the use of structure-guided mutagenesis to engineer ion channels with tailored properties of ideal sonogenetic actuators.

biophysics↗

bioRxiv2024

Illumination mediates a switch in both active sensing and control in weakly electric fish

To execute sensory-guided behavior, the nervous system must manage uncertainty within multiple streams of information. There are two highly nonlinear mechanisms for achieving this: 1) sensory reweighting, an internal neural computation which places more emphasis on sensory information that exhibits the least uncertainty, e.g. in a Bayesian framework, and 2) active sensing, an overt behavior that seeks to improve the quality of sensory information before it enters the nervous system. Here we show that animals solve both of these nonlinear problems concurrently. We studied how the weakly electric glass knifefish Eigenmannia virescens alters its movement dynamics under parametric manipulations of illumination. We hypothesized a concomitant switch in both overt active sensing and internal multisensory reweighting. To test this, we varied illumination levels from 0.1 to 210 lx as fish tracked a moving refuge. We discovered that in a neighborhood of a critical threshold (on the order of 1 to 10 lx), small increases in illumination led to dramatic changes in both active sensing and multisensory control, specifically in 1) steep reductions in fish head and tail movements and 2) decreased refuge tracking phase lag. Outside of this threshold, large changes in illumination only caused small changes in active sensing and control. A control-theoretic model that dynamically modulates the weights of vision and electrosense due to illumination changes corroborates our findings. These findings underscore the complex, multipartite, nonlinear nature of locomotor control and the remarkable ability of the nervous system to execute multiple parallel strategies for managing sensory uncertainty.

animal behavior and cognition↗

bioRxiv2024

HEXIM1 homodimer binds two sites on 7SK RNA to release autoinhibition for P-TEFb inactivation

Hexim proteins are key RNA-dependent regulators of eukaryotic transcription through 7SK-dependent sequestration and inactivation of the kinase P-TEFb (Cdk9-CyclinT1/2) in the 7SK RNP. P-TEFb activity drives release of RNA polymerase II from promoter-proximal pausing for eukaryotic and HIV-1 transcription. The molecular mechanism by which 7SK binding overcomes an intrinsic Hexim autoinhibition for subsequent P-TEFb inactivation has remained unresolved. Here, using NMR and biophysical methods we demonstrate that Hexim1 homodimer engages two high-affinity sites on 7SK RNA. This dual-site binding triggers a conformational rearrangement in Hexim1s disordered central region that unmasks the Cdk9-binding site, which is otherwise sequestered within an intermonomer dimer interface. These findings reveal how Hexim autoinhibition dictates its specificity for 7SK RNA and prevents premature P-TEFb inhibition in the absence of 7SK, thereby providing a mechanistic understanding of Hexim/P-TEFb assembly into the 7SK RNP and further considerations for understanding Hexim-Tat competition during viral transcription.

biophysics↗

bioRxiv2024

An all-in-one AAV vector for cardiac-specific gene silencing by an adenine base editor

ABE editing outcomes are highly variable and unpredictable, depending on various factors. Therefore, the success rate of creating targeted A*T-to-G*C conversions using ABE is not high. But utilizing ABE to target RNA splicing sites for gene silencing has a higher success rate. Another challenge for base editing in the heart is that traditional ABE is too large in size, necessitating dual AAV delivery. Whether single AAV delivery can be achieved remains to be explored. In this study, we demonstrated how the diversity of Cas9 homologs and screening of sgRNAs can facilitate cardiac base editing. Single-AAV base editing outperformed dual-AAV systems in the heart, potentially benefiting from chromatin accessibility-guided sgRNA selection. These findings have important implications for the development of more effective and predictable base editing tools for cardiac gene therapy.

molecular biology↗

bioRxiv2024

Knockout of the SfVipR1 gene confers high-level resistance to Bacillus thuringiensis Vip3Aa toxin in Spodoptera frugiperda

BackgroundBacillus thuringiensis (Bt) insecticidal proteins, including Cry proteins and vegetative insecticidal proteins (Vips), are extensively utilized in transgenic crops due to their efficacy and safety. The fall armyworm, Spodoptera frugiperda, has evolved practical resistance to Cry1Fa, yet no practical resistance to Vip3Aa has been documented. However, both laboratory selection and field screen studies indicate a high potential for this pest to evolve resistance to Vip3Aa, making it crucial to evaluate potential resistance genes. HaVipR1 has recently been identified as a key determinant of Vip3Aa resistance in the cotton bollworm, Helicoverpa armigera. This study investigated whether the HaVipR1-homologous gene in S. frugiperda (SfVipR1) is similarly involved in Vip3Aa resistance. ResultsWe employed CRISPR/Cas9 technology to generate a homozygous knockout strain of SfVipR1. In comparison with the parent susceptible YJ-19 strain, the knockout strain (Sfru-KO) exhibited high-level resistance to Vip3Aa (>1875-fold) but showed no resistance to Cry1Fa. This acquired resistance to Vip3Aa is autosomal, recessive, and genetically linked to the deletion mutation in SfVipR1 within the Sfru-KO strain of S. frugiperda. ConclusionDisruption of SfVipR1 results in high-level resistance to Vip3Aa, highlighting SfVipR1 has a critical role in Vip3Aa toxicity in S. frugiperda, despite the exact mechanism remaining unclear. Early detection of SfVipR1 mutant alleles in the field is essential for developing adaptive resistance management strategies against S. frugiperda.

genetics↗

bioRxiv2024

GPR30 in spinal cholecystokinin-positive neurons modulates neuropathic pain via mediating descending facilitation

Neuropathic pain, a major health problem affecting 7-10% of the global population, lacks effective treatment due to its elusive mechanisms. Cholecystokinin-positive (CCK+) neurons in the spinal dorsal horn (SDH) are critical for neuropathic pain, yet the underlying molecular mechanisms remain unclear. Here, we show that the membrane estrogen receptor G-protein coupled estrogen receptor (GPER/GPR30) in spinal neurons was significantly upregulated in chronic constriction injury (CCI) mice and that inhibition of GPR30 in CCK+ neurons reversed CCI-induced neuropathic pain. Furthermore, GPR30 in spinal CCK+ neurons was essential for the enhancement of AMPA-mediated excitatory synaptic transmission in CCI mice. Moreover, GPR30 was expressed in spinal CCK+ neurons that received direct projection from the primary sensory cortex (S1-SDH). Chemogenetic inhibition of S1-SDH post-synaptic neurons alleviated CCI-induced neuropathic pain. Conversely, chemogenetic activation of these neurons mimicked neuropathic pain symptoms, which were attenuated by spinal inhibition of GPR30. Finally, we confirmed that GPR30 in S1-SDH post-synaptic neurons was required for CCI-induced neuropathic pain. Taken together, our findings suggest that GPR30 in spinal CCK+ neurons and S1-SDH postsynaptic neurons is pivotal for neuropathic pain, thereby representing a promising therapeutic target for neuropathic pain.

neuroscience↗

bioRxiv2024

Distinct duration and diet dependent lipid profiles and renal complicationsin GCK-MODY

Heterozygous inactivating mutations in the glucokinase (GCK) gene cause one of the most common types of maturity-onset diabetes of the young type 2 (MODY2), also named GCK-MODY. Studies suggest that, unlike other types of diabetes, patients with GCK-MODY do not have increased risk of diabetic complications and therefore do not typically require antihyperglycemic therapy. However, long-term outcomes of GCK-MODY on lipid profiles and chronic complications under different dietary scenarios remain unclear. Herein, using a knock-in mouse model expressing a novel MODY causing mutation GCK-Q26L (GCKMut), we examined age- and diet-related lipid profiles and diabetic complications. We found that, although GCKMut mice exhibited mild elevated blood glucose, the lipid profiles, body fat composition, and diabetic kidney disease (DKD) were initially improved in high-fat-diet (HFD) fed mice at the age of 28 weeks, supporting potential beneficial effects of GCKMut on lipid metabolism and kidney health. Unexpectedly however, those protective effects diminished by 40 weeks, and became more severe dyslipidemia and kidney injury associated with renal fibrosis and inflammation at 60-week-old mice fed with normal diet (ND) or HFD. Those findings revealed distinct duration- and diet-dependent effects of inactivating GCK mutation on lipid profiles and DKD, highlighting previously unrealized long-term chronic complications in GCK-MODY.

physiology↗

bioRxiv2024

Patterned wireless transcranial optogenetics generates artificial perception

Synthesizing perceivable artificial neural inputs independent of typical sensory channels remains a fundamental challenge in the development of next-generation brain-machine interfaces. Establishing a minimally invasive, wirelessly effective, and miniaturized platform with long-term stability is crucial for creating a clinically meaningful interface capable of mediating artificial perceptual feedback. In this study, we demonstrate a miniaturized fully implantable wireless transcranial optogenetic encoder designed to generate artificial perceptions through digitized optogenetic manipulation of large cortical ensembles. This platform enables the spatiotemporal orchestration of large-scale cortical activity for remote perception genesis via real-time wireless communication and control, with optimized device performance achieved by simulation-guided methods addressing light and heat propagation during operation. Cue discrimination during operant learning demonstrates the wireless genesis of artificial percepts sensed by mice, where spatial distance across large cortical networks and sequential order-based analyses of discrimination performance reveal principles that adhere to general perceptual rules. These conceptual and technical advancements expand our understanding of artificial neural syntax and its perception by the brain, guiding the evolution of next-generation brain-machine communication.

neuroscience↗

bioRxiv2024

Glutamatergic regulation of miRNA-containing exosome precursor trafficking and secretion from cortical neurons

Neuronal exosomes are emerging secreted signals that play important roles in the CNS. Currently little is known about how glutamatergic signaling affects the subcellular localization of exosome precursor intraluminal vesicles (ILVs), microRNA (miR) packaging into ILVs, and in vivo neuronal exosome spreading. By selectively labeling ILVs and exosomes with GFP-tagged human CD63 (hCD63-GFP) in cortical neurons, we found that glutamate stimulation significantly redistributes subcellular localization of hCD63-GFP+ ILVs especially decreases its co-localization with multi-vesicular body (MVB) marker Rab7 while substantially promoting exosome secretion. Interestingly, glutamate stimulation only modestly alters exosomal miR profiles based on small RNA sequencing. Subsequent in vivo cortical neuronal DREADD activation leads to significantly more widespread hCD63-GFP+ area in hCD63-GFPf/+ mice, consistently supporting the stimulatory effect of glutamatergic activation on neuronal exosome secretion and spreading. Moreover, in situ localization of hCD63-GFP+ ILVs and secreted exosomes from specialized Hb9+ and DAT+ neurons were also illustrated in the CNS.

neuroscience↗

bioRxiv2024

Functional MRI reveals regional changes of brain activity after five days of focal high-density theta burst stimulation (hdTBS) of the rat brain

BackgroundThe therapeutic effects of transcranial magnetic stimulation (TMS) likely stem from neuroplasticity induced by repeated sessions over time. While animal models offer insights into TMS-induced plasticity, a rodent model that faithfully replicates prolonged TMS conditions in humans is still lacking. Objective/HypothesisDevelop a rat model that mimics the spatial and temporal patterns of TMS in humans. MethodsExperiments were conducted on two cohorts of healthy adult rats (N=33). In cohort 1, rats underwent surgical implantation of microelectrodes for motor evoked potential (MEP) recording. With a rodent-specific coil and the high-density theta burst stimulation (hdTBS) paradigm, under awake condition, rats received daily TMS at 100% motor threshold for five days (days 1-5) to the hindlimb motor cortex. Cortical excitability was measured by input-output (I-O) curves on Day 0 (pre-hdTBS baseline) and Day 6 (post-hdTBS). The second cohort received identical TMS and underwent fMRI to map cerebral blood volume (CBV) on Days 0 and 6. ResultsDaily hdTBS session for 5 days significantly up-shifted I-O curves only in the TMS group (N=9), not in the sham group (N=7), indicating enhanced cortical excitability. fMRI data showed that, compared to sham group (N=9), rats receiving hdTBS (N=8) had increased basal CBV in several brain regions proximal and distal to the stimulation site, suggesting enhanced basal metabolism. Conclusion(s)Daily hdTBS session for 5 days focally delivered to the motor cortex of naive rats significantly altered basal brain activity in a network of brain regions, opening a novel platform for further investigating TMS-induced plasticity.

neuroscience↗

bioRxiv2024

The Plastisphere: Marine fungi communities in the plastics age

Fungi play important roles in biofilms, are very versatile in their ecological role, and are considered as plastic degraders. Here we aim to increase the resolution of the fungal members of the Plastisphere, to understand fungal substrate specificities and related potential ecological impacts. Fifteen-month-old fungal Plastisphere communities were investigated on 9 different plastic types and glass in seawater from the North Sea. By integrating scanning electron microscopy (SEM) imaging, ITS-based fingerprinting, and re-evaluated 18S rRNA gene sequence data through a fungal-specific phylogeny-based pipeline, we observed fungal Plastispheres and identified specific characteristics based on morphotypes, phylogeny, and biodiversity across different substrate types. Plastic types selected for specific fungal communities with polyolefine communities indicating significantly higher diversity compared to all other plastic types. Furthermore, specific plastic types may select for specific fungal taxa and their potential hosts, highlighting the complexity of marine biofilm food webs, and related ecological implications.

microbiology↗