Biology subjects

Huan, Y.

Publications and source records attributed to Huan, Y..

10 recordsLinked to original sources

bioRxiv2026

Highly Sensitive Chemigenetic FRET-Based Kinase Biosensors

Fluorescent protein-based biosensors have transformed the study of cell physiology and pathology by enabling direct, live-cell measurements of biochemical activities with spatiotemporal precision. FRET-based biosensors offer a quantitative and well-defined readout mechanism popular among researchers, but have struggled to break free of characteristically low dynamic ranges and overall dependence on the cyan-yellow spectral region. Chemigenetic approaches that combine synthetic fluorophores with self-labeling protein tags represent an attractive solution to these longstanding constraints. Here, we pair different fluorescent protein donors with a HaloTag acceptor conjugated to a far-red fluorophore to obtain a suite of highly sensitive, chemigenetic FRET-based kinase activity biosensors with red-shifted emission and unprecedented dynamic range. We demonstrate the generalizability of this chemigenetic platform by developing biosensors for multiple kinases, as well as small GTPases and second messengers, all while maintaining high sensitivity. The high sensitivity and spectral tunability of these chemigenetic tools enabled us to perform robust multiplexed activity imaging of receptor-mediated signaling networks to quantitatively map isoform-specific coupling by GPCRs, as well as clear visualization of kinase activity in acute brain slices via two-photon fluorescence lifetime imaging. Our chemigenetic sensor toolkit thus provides the sensitivity and dimensionality needed to illuminate the spatiotemporal regulation of signaling networks in cells and tissues.

cell biology↗

bioRxiv2025

PQBP1-dependent alternative RNA splicing underlies high calorie diet-induced cognitive impairment

High calorie-high fat diet (HFD) has been implicated as a pathological modifier of brain diseases including neurodegenerative dementias, but the detailed molecular mechanisms remain largely unknown. Here we report that HFD suppresses PPAR{gamma}-mediated transcriptional expression of PQBP1, a RNA splicing factor implicated in human intellectual disability and Alzheimers disease. RNAseq-based comprehensive analyses of alternative RNA splicing (AS) in HFD-fed mice for 1 or 6 weeks and in PQBP1-cKO mice reveal their common changes, which weigh on synapse-related genes. Betweenness-based extraction of core molecules from the common changes reveals CASK, Cacnb1 and Cyfip2 as key molecules of the network. Both CASK and Cacnb1 regulate STXBP1, a causative gene for infantile epilepsy syndrome and an essential factor for synapse vesicle release, via their direct interaction. In addition, our analysis suggests that Syt1 plays a role specifically in HFD for 1 week. HFD-induced AS isoforms of CASK, Cacnb1, Cyfip2 and Syt1 impair pre-synapse vesicle release in primary neurons. AAV-PQBP1, AAV-CASK, AAV-Cacnb1, AAV-Cyfip2 or AAV-Syt1 rescues synapse and/or cognitive dysfunctions in HFD mice, genetically supporting the pathological PQBP1-presynase axis in HFD. Moreover, immunohistochemistry experiments suggest that the pathological axis plays roles not only in excitatory neurons, but also in inhibitory neurons of the brain. Collectively, our results unravel a novel molecular mechanism for brain dysfunction when mice are exposed to a HFD.

neuroscience↗

bioRxiv2025

Single-cell Characterization of DNA Hydroxymethylation of the Mouse Brain During Aging

DNA methylation dynamics, including 5-hydroxymethylcytosine (5hmC) and 5-methylcytosine (5mC), critically regulate brain function, yet conventional methods cannot distinguish these modifications, obscuring their distinct roles in gene regulation and aging. We present Joint- Cabernet, a bisulfite-free single-cell platform enabling simultaneous profiling of 5hmC, 5mC, and transcriptomes. Applying Joint-Cabernet to 84,071 nuclei from adult and aged mouse brains, we resolved cell-type-specific DNA hydroxymethylation landscapes, revealing elevated 5hmCG and 5hmCH levels in transcriptionally active genes across neuronal subtypes and spatial gradients in cortical layers. During aging, 5hmCG accumulates globally but is selectively enriched at open chromatin loci, aligning with the upregulation of cell-type-specific genes in distinct brain cell types. This single-cell DNA methylation brain cell atlas provides a framework for studying methylation- driven mechanisms in brain aging and neurodegenerative diseases.

genetics↗

bioRxiv2024

BrainUnit: Integrating Physical Units into High-Performance AI-Driven Scientific Computing

Artificial intelligence (AI) is revolutionizing scientific research across various disciplines. The foundation of scientific research lies in rigorous scientific computing based on standardized physical units. However, current mainstream high-performance numerical computing libraries for AI generally lack native support for physical units, significantly impeding the integration of AI methodologies into scientific research. To fill this gap, we introduce BrainUnit, a unit system designed to seamlessly integrate physical units into AI libraries, with a focus on compatibility with JAX. BrainUnit offers a comprehensive library of over 2000 physical units and more than 300 unit-aware mathematical functions. It is fully compatible with JAX transformations, allowing for automatic differentiation, just-in-time compilation, vectorization, and parallelization while maintaining unit consistency. We demonstrate BrainUnits efficacy through several use cases in brain dynamics modeling, including detailed biophysical neuron simulations, multiscale brain network modeling, neuronal activity fitting, and cognitive task training. Our results show that BrainUnit enhances the accuracy, reliability, and interpretability of scientific computations across scales, from ion channels to whole-brain networks, without impacting performance. By bridging the gap between abstract computational frameworks and physical units, BrainUnit represents a crucial step towards more robust and physically grounded AI-driven scientific computing.

neuroscience↗

bioRxiv2023

Urine proteomic analysis of patients with schizophrenia

We tried to explore the difference of urinary proteome between unmedicated schizophrenia patients and normal people through a small number of cases. The results showed that a total of 35 differential proteins were screened in the schizophrenia group compared with the healthy control group. Through random grouping evaluation, it has 91.4 % credibility. Fifteen of the differentially expressed proteins were reported to be related to schizophrenia mechanism, drug target or nervous system regulation. Among them, the aromatic amino acid decarboxylase related to the pathogenesis of schizophrenia can distinguish all 10 patients and 9 normal people with 100 % accuracy in this study, and the AUC value of 17 proteins is greater than or equal to 0.9. The biological pathways enriched by differentially expressed proteins include ephrin receptor signaling pathway, positive regulation of long-term potentiation (LTP), etc. This study shows that urine proteomics can reflect the difference between schizophrenia and healthy controls, and has the potential as a diagnostic marker.

biochemistry↗

bioRxiv2021

Carbon Fiber Electrodes for Intracellular Recording and Stimulation

To understand neural circuit dynamics, it is critical to manipulate and record from many neurons, ideally at the single neuron level. Traditional recording methods, such as glass microelectrodes, can only control a small number of neurons. More recently, devices with high electrode density have been developed, but few of them can be used for intracellular recording or stimulation in intact nervous systems, rather than on neuronal cultures. Carbon fiber electrodes (CFEs) are 8 micron-diameter electrodes that can be organized into arrays with pitches as low as 80 {micro}m. They have been shown to have good signal-to-noise ratios (SNRs) and are capable of stable extracellular recording during both acute and chronic implantation in vivo in neural tissue such as rat motor cortex. Given the small fiber size, it is possible that they could be used in arrays for intracellular stimulation. We tested this using the large identified and electrically compact neurons of the marine mollusk Aplysia californica. The cell bodies of neurons in Aplysia range in size from 30 to over 250 {micro}m. We compared the efficacy of CFEs to glass microelectrodes by impaling the same neurons cell body with both electrodes and connecting them to a DC coupled amplifier. We observed that intracellular waveforms were essentially identical, but the amplitude and SNR in the CFE were lower than in the glass microelectrode. CFE arrays could record from 3 to 8 neurons simultaneously for many hours, and many of these recordings were intracellular as shown by recording from the same neuron using a glass microelectrode. Stimulating through CFEs coated with platinum-iridium had stable impedances over many hours. CFEs not within neurons could record local extracellular activity. Despite the lower SNR, the CFEs could record synaptic potentials. Thus, the stability for multi-channel recording and the ability to stimulate and record intracellularly make CFEs a powerful new technology for studying neural circuit dynamics.

neuroscience↗

bioRxiv2021

Dynamic urine proteome changes in a rat model of simvastatin-induced skeletal muscle injury.

BackgroundStatin-associated muscle symptoms (SAMS) are the main side effects of statins. Currently, there are no effective biomarkers for accurate clinical diagnosis. Urine is not subject to homeostatic control and therefore accumulates early changes, making it an ideal biomarker source. We therefore examined urine proteome changes associated with SAMS in an animal model. MethodsHere, we established a SAMS rat model by intragastric intubation with simvastatin (80 mg/kg). Biochemical analyses and hematoxylin and eosin (H&E) staining were used to evaluate the degree of muscle injury. The urine proteome on days 3, 6, 9 and 14 was profiled using liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) with the data-independent acquisition (DIA) method. ResultsDifferential proteins on day 14 of SAMS were mainly associated with glycolysis/gluconeogenesis, pyruvate metabolism, metabolism of reactive oxygen species and apoptosis, all of which were reported to be associated with the pathological mechanism of SAMS. Among the 14 differentially expressed proteins on day 3, FIBG, OSTP and CRP were associated with muscle damage, while EHD1, CUBN and FINC were associated with the pathogenic mechanisms of SAMS. MYG and PRVA increased dramatically compared with CK elevation in serum on day 14 of SAMS. ConclusionsOur preliminary results indicated that the urine proteome can reflect early changes in the SAMS rat model, providing the potential for monitoring drug side effects in future clinical research.

biochemistry↗

bioRxiv2020

Urine proteome changes in a chronic unpredictable mild stress (CUMS) mouse model of major depressive disorder

BackgroundMajor depressive disorder (MDD) is a prevalent complex psychiatric disorder with a high prevalence rate. Because MDD is a systemic multifactorial disorder involving complex interactions and disturbances of various molecular pathways, there are no effective biomarkers for clinical diagnosis. Urine is not subjected to homeostatic control, allowing it to reflect the sensitive and comprehensive changes that occur in various diseases. In this study, we examined the urine proteome changes in a CUMS mouse model of MDD. MethodsMale C57BL/6 mice were subjected to chronic unpredictable mild stress for 5 weeks. The tail suspension test (TST) and sucrose consumption test (SCT) were then applied to evaluate depression-like behaviors. The urine proteomes on day 0 and day 36 in the CUMS group were profiled by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS). ResultsA total of 45 differential proteins were identified, 24 of which have been associated with the pathogenic mechanisms of MDD, while 10 proteins have been previously suggested as MDD biomarkers. There was an average of two differential proteins that were identified through 1048574 random combination statistical analyses, indicating that at least 95% of the differential proteins were reliable and not the result of random combination. The differential proteins were mainly associated with blood coagulation, inflammatory responses and central nervous system development. ConclusionsOur preliminary results indicated that the urine proteome can reflect changes associated with MDD in the CUMS model, which provides potential clues for the diagnosis of clinical MDD patients.

neuroscience↗

bioRxiv2019

Early urine proteome changes in an implanted bone cancer rat model

In this study, Walker 256 cells were implanted into rat tibiae. Urine samples were then collected on days 3, 5, 7, and 13 and were analyzed by liquid chromatography-tandem mass spectrometry (LC-MS/MS). With label-free quantification, 25 proteins were found to change significantly in the urine of the tumor group mice compared with the proteins in the urine of the control group mice; this was even the case when there were no significant lesions identified in the Computed Tomography(CT) examination. Among these differentially proteins, 7 were reported to be associated with tumor bone metastasis. GO analysis shows that the differential proteins on day 3 were involved in several responses, including the acute phase response, the adaptive immune response and the innate immune response. The differentially proteins on day 7 were involved in the mineral absorption pathway. The differentially proteins on day 13 were involved in vitamin D binding and calcium ion binding. These processes may be associated with bone metastasis. Our results demonstrate that urine could sensitively reflect the changes in the early stage of implanted bone cancer; this provides valuable clues for future studies of urine biomarkers for tumor bone metastasis.

cancer biology↗

bioRxiv2019

Early urinary protein changes in the tumor-forming process of the NuTu-19 lung metastasis

The early detection of cancer is essential for effective intervention. Urine, which lacks homeostatic control, has been used to reflect early systemic changes in subcutaneous cancer models. However, urine has not been used to predict whether tumors will be formed in animal models. In this study, a cancer model was established by the tail-vein injection of 2 million NuTu-19 tumor cells. Approximately half of the rats formed lung metastatic carcinoma tumors. Urine samples were randomly selected from 4 tumor-forming rats and 4 non-tumor-forming rats on day 0/12/27/39/52 and analyzed by label-free proteomic quantitative analysis. Compared to day 0, a total of 180 and 118 urinary proteins in tumor-forming and non-tumor-forming rats, respectively, showed significant changes. Functional enrichment analysis of the differential proteins in tumor-forming rats revealed similar events during cancer metastasis cascades and tumor progression, such as the migration of tumor cell lines, coagulation system, TGF-{beta} signaling, the STAT3 pathway and the adhesion of myeloid cells and alveolar macrophages. The differential proteins in non-tumor-forming rats were associated with agranulocyte/granulocyte adhesion and diapedesis, glutathione biosynthesis, IL-12 signaling and vitamin metabolism. After validation by parallel reaction monitoring (PRM) targeted proteomics quantitative analysis, a total of 22 urinary proteins showed significant changes in the early phase of the lung tumor formation process, 5 of which have been associated with the mechanisms of lung cancer, while 3 have been suggested as lung cancer biomarkers. Another 14 urinary proteins showed significant changes in the early phase in non-tumor-forming rats. Our results indicate that urine proteins could differentiate early tumor-forming and non-tumor-forming status.

cancer biology↗