Biology subjects

LIU, C.

Publications and source records attributed to LIU, C..

10 recordsLinked to original sources

bioRxiv2026

Distinct cellular DNA methylation mechanisms underlie common and rare genetic risk for brain disorders

Noncoding genetic variation contributes to brain disorder risk, but the mechanisms through which it acts in specific brain cell types remain unclear. DNA methylation (DNAm), a highly cell type-specific regulatory layer in the brain, may mediate noncoding genetic risk, yet whether methylation at CG (mCG) and neuron-enriched non-CG (mCH) dinucleotides contribute differently to that risk remains unknown. Here we develop a deep learning framework that predicts DNAm from DNA sequence and estimates variant effects across 186 brain cell subtypes in both mCG and mCH, leveraging single-nucleus DNAm profiles from 46 brain regions. The models reveal distinct transcription factor (TF) programs underlying the two methylation contexts, with mCH-associated TFs showing stronger evolutionary constraint. Predicted variant effects agree closely with cell type-matched mQTLs in both direction and magnitude. Common variants predicted to affect mCG, particularly in excitatory neurons, show substantially greater heritability enrichment for brain-related traits than variants affecting mCH. By contrast, noncoding de novo mutations in autism preferentially perturb mCH, but not mCG, at conserved neuronal regulatory regions. This pattern is replicated across two independent cohorts totaling 5,782 probands and 4,053 unaffected siblings. Together, these findings indicate that common and rare noncoding variants contribute to brain disorders through distinct DNA methylation mechanisms.

genetics↗

bioRxiv2025

GSK-3 regulates CD4-CD8 cooperation needed to generate super-armed CD8+ cytolytic T cells against tumors

While immune checkpoint blockade (ICB) has revolutionized cancer treatment, the key T-cell signaling pathways responsible for its potency remain unclear. GSK-3 is an inhibitory kinase that is most active in resting T-cells. In this study, we demonstrate that GSK-3 facilitates PD-1 blockade, an effect seen by modulating CD4 T-cell help for CD8+ CTL responses against ICB resistant tumors. We show that GSK-3 controls metabolic reprogramming towards glycolysis and synergizes with PD-1 to induce a transcriptional program that reduces suppressive CD4+ Treg numbers while generating super-armed effector-memory CD8+ CTLs that express an unprecedented 7/9 granzymes from the genome. Crucially, we found that GSK-3 cooperates with PD-1 blockade to determine the dependency of CD8+ CTLs on help from CD4+ T-cells. Our study unravels a novel cooperative PD-1 blockade-dependent signaling pathway that potentiates CTL responses against tumors, offering a new strategy to overcome immunotherapy resistance by modulating CD4+ helper and CD8+ cytotoxic functions. SignificanceThis study demonstrates for the first time that GSK-3 controls the crosstalk between CD4+ and CD8+ T cells, synergizing with anti-PD-1 therapy to overcome resistance to checkpoint blockade and to generate super-armed CD8+ effector cells in cancer immunotherapy. This newly uncovered GSK-3-dependent CD4-CD8 T-cell crosstalk mechanism presents a new approach to enhance anti-PD-1 immunotherapy.

immunology↗

bioRxiv2024

Dimorphic Neural Network Architecture Prioritizes Sexual-related Behaviors in Male C.elegans

Neural network architecture determines its functional output. However, the detailed mechanisms are not well characterized. In this study, we focused on the neural network architectures of male and hermaphrodite C. elegans and the association with sexually dimorphic behaviors. We applied graph theory and computational neuroscience methods to systematically discern the features of these two neural networks. Our findings revealed that a small percentage of sexual-specific neurons exerted dominance throughout the entire male neural net-work, suggesting males prioritized sexual-related behavior outputs. Based on the structural and dynamical characteristics of two complete neural networks, sub-networks containing sex-specific neurons and their immediate neighbors, or sub-networks exclusively comprising sex-shared neurons, we predicted dimorphic behavioral outcomes for males and hermaphrodites. To verify the prediction, we performed behavioral and calcium imaging experiments and dissected a circuit that is specific for the increased spontaneous local search in males for mate-searching. Our research sheds light on the neural circuits that underlie sexually dimorphic behaviors in C. elegans, and provides significant insights into the inter-connected relationship between network architecture and functional outcomes at the whole-brain level.

neuroscience↗

bioRxiv2024

Chemically Induced Nuclear Pore Complex Protein Degradation via E3 Ligase TRIM21

Despite the exciting progress of the bifunctional degrader molecules, also known as proteolysis-targeting chimeras (PROTACs), the rapidly expanding field is still significantly hampered by the lacking of available E3 ligase ligands. Our research bridges this gap by uncovering a series of small-molecule ligands to the E3 ligase TRIM21 through DNA-Encoded Library (DEL) technology. We confirmed their interaction with TRIM21 using crystallography and demonstrated their anti-proliferative effects across various cancer cell types. Furthermore, proteomic studies identified that the mRNA Export Factor GLE1, and the Nuclear Pore Complex Protein NUP155, were significantly down-regulated upon TRIM21 ligand treatment. This degradation required TRIM21 and was ubiquitin-proteasome-dependent. More specifically, NUP155 was the primary target for the TRIM21 ligands, while GLE1 was considered a passenger target upon the initial degradation of NUP155. Using immunofluorescence techniques, we further demonstrated that the degradation of GLE1 and NUP155 proteins impaired the integrity of the nuclear envelope, leading to cell death. Highlighted by this research, a novel mode of action has been discovered for the TRIM21 E3 ligase ligand, acting as a monovalent degrader that triggers de novo interaction with functional complex proteins and induces their degradation.

cell biology↗

bioRxiv2024

Discovery and Engineering of a New BvCas12a Nuclease for Mammalian Genome Editing and Nucleic Acid Detection

Cas12a is an RNA-guided endonuclease that has emerged as a powerful gene-editing tool. We have identified a novel Cas protein, BvCas12a, from Butyricimonas virosa with a 5-TYTN protospacer adjacent motif (PAM). BvCas12a exhibits double-stranded DNA cleavage activity in vitro and genome editing activity in eukaryotic cells. Though the editing efficiency of BvCas12a is marginally lower than that of AsCas12a, the editing specificity of BvCas12a in eukaryotic cells is comparable or superior to that of AsCas12a. Moreover, BvCas12a exhibits substantial collateral activity and can detect HPV DNA effectively and accurately in conjunction with isothermal amplification, highlighting its potential in nucleic acid diagnostics. Furthermore, we have engineered BvCas12a to create two variants, BvCas12a-R (N549R, T606P) and BvCas12a-RVR (N549R, K555V, C559R, T606P). These variants recognize expanded 5-YYN and 5-YN PAM in vitro, respectively. Additionally, they exhibit higher editing activity than wild-type BvCas12a and recognize 5-YYN PAM in vivo at all sites detected. In conclusion, we have identified a novel BvCas12a protein with high specificity and engineered two variants with broader PAM compatibility and improved genome editing efficiency. These findings offer a potent gene editing tool for application in scientific research, gene therapy, and nucleic acid diagnostics.

genomics↗

bioRxiv2023

Structural determinants of the direct inhibition of GIRK channels by Sigma-1 receptor antagonist

G-protein-gated inward rectifier K+ (GIRK) channels play critical roles in the regulation of the excitability of cardiomyocytes and neurons and include GIRK1, GIRK2, GIRK3 and GIRK4 subfamily members. BD1047 dihydrobromide (BD1047) is one of the representative antagonists of multi-functional Sigma-1 receptor (S1R). In the analysis of the effect of BD1047 on the inhibition of Gi-coupled receptors by S1R using GIRK channel as an effector, we observed that BD1047 directly inhibits GIRK current even in the absence of S1R. Thus, we aimed to clarify the effect of BD1047 on GIRK channels and its structural determinants. By electrophysiological recordings in Xenopus oocytes, we observed that BD1047 directly inhibited the current of GIRK channels, producing a much stronger inhibition of GIRK4 channels compared to GIRK2. It also inhibited the ACh-induced native GIRK current in isolated rat atrial myocytes. Chimeric and mutagenesis studies of GIRK2 and GIRK4 combining with molecular docking analysis, demonstrate the importance of the Leu77 on the proximal N-terminal cytoplasmic region of GIRK4 for the inhibition by BD1047. The activator of GIRK channel, ivermectin, competed with BD1047 at Leu77 on GIRK4. This study provides us with a novel inhibitor of GIRK channels and information for developing pharmacological treatments for GIRK4 associated diseases. Key pointsO_LISigma-1 receptor antagonist, BD1047, directly inhibits the current of GIRK channels. It strongly inhibits GIRK4 channels but only weakly inhibits GIRK2. C_LIO_LIBD1047 inhibits the ACh-induced GIRK current in isolated rat atrial myocyte. C_LIO_LILeu77 on the proximal N-terminal of GIRK4 is essential for the inhibition by BD1047. C_LIO_LIBinding of BD1047 adjacent to Leu77, but not to Leu77Ile, was confirmed by molecular docking analysis. C_LIO_LIThe activator of GIRK channel, ivermectin, competes with BD1047 at Leu77 on GIRK4. C_LI

biophysics↗

bioRxiv2023

Evaluating performance and applications of sample-wise cell deconvolution methods on human brain transcriptomic data

Sample-wise deconvolution methods have been developed to estimate cell-type proportions and gene expressions in bulk-tissue samples. However, the performance of these methods and their biological applications has not been evaluated, particularly on human brain transcriptomic data. Here, nine deconvolution methods were evaluated with sample-matched data from bulk-tissue RNAseq, single-cell/nuclei (sc/sn) RNAseq, and immunohistochemistry. A total of 1,130,767 nuclei/cells from 149 adult postmortem brains and 72 organoid samples were used. The results showed the best performance of dtangle for estimating cell proportions and bMIND for estimating sample-wise cell-type gene expression. For eight brain cell types, 25,273 cell-type eQTLs were identified with deconvoluted expressions (decon-eQTLs). The results showed that decon-eQTLs explained more schizophrenia GWAS heritability than bulk-tissue or single-cell eQTLs alone. Differential gene expression associated with multiple phenotypes were also examined using the deconvoluted data. Our findings, which were replicated in bulk-tissue RNAseq and sc/snRNAseq data, provided new insights into the biological applications of deconvoluted data.

genomics↗

bioRxiv2022

Controlling the bioelectrical properties of neurons with ferritin-based Magnetogenetics

Magnetogenetics promises remote control of neurons, but its validity is questioned due to controversies surrounding the underlying mechanisms and deficits in reproducibility. Recent studies discovered that ferritin, used in Magnetogenetics, transduces radiofrequency (RF) magnetic fields into biochemical signals (reactive oxygen species and oxidized lipids). Magnetic stimulation of ferritin-tethered TRPV channels induces Ca2+ responses and modulates behavior but electrophysiological studies indicate that a particular channel, Magneto2.0, is ineffective in affecting the neuronal bioelectrical properties. We investigated this problem using the Magnetogenetic technique FeRIC. We resolved the electromagnetic interference caused by RF in patch-clamp recordings and supported the data with voltage imaging experiments. In neurons expressing TRPV4FeRIC, RF depolarizes the membrane potential and increases the spiking frequency. In neurons expressing the chloride-permeable TMEM16AFeRIC, RF hyperpolarizes the membrane potential and decreases the spiking frequency. Our study reveals the control of neuronal bioelectrical properties with Magnetogenetics that is non-instantaneous, long-lasting, and moderate, but effective and comparable to that induced by endogenous signaling molecules.

neuroscience↗

bioRxiv2021

Analyses of the Autism-associated Neuroligin-3 R451C Mutation in Human Neurons Reveals a Gain-of-Function Synaptic Mechanism

Mutations in many synaptic genes are associated with autism spectrum disorders (ASDs), suggesting that synaptic dysfunction is a key driver of ASD pathogenesis. Among these mutations, the R451C-substitution in the NLGN3 gene that encodes the postsynaptic adhesion molecule Neuroligin-3 is noteworthy because it was the first specific mutation linked to ASDs. In mice, the corresponding Nlgn3 R451C-knockin mutation recapitulates social interaction deficits of ASD patients and produces synaptic abnormalities, but the impact of the NLGN3 R451C-mutation on human neurons has not been investigated. Here, we generated human knock-in neurons with the NLGN3 R451C-mutation. Strikingly, analyses of NLGN3 R451C-mutant neurons revealed that the R451C-mutation decreased NLGN3 protein levels but enhanced the strength of excitatory synapses without affecting inhibitory synapses. No significant cell death and endoplasmic reticulum stress were detected. Importantly, the augmentation of excitatory transmission was confirmed in vivo with human neurons transplanted into mouse forebrain. Using single-cell RNA-seq experiments with co-cultured excitatory and inhibitory NLGN3 R451C-mutant neurons, we identified differentially expressed genes in relatively mature human neurons that corresponded to synaptic gene expression networks. Moreover, gene ontology and enrichment analyses revealed convergent gene networks associated with ASDs and other mental disorders. Our findings suggest that the NLGN3 R451C-mutation induces a gain-of-function enhancement in excitatory synaptic transmission that may contribute to the pathophysiology of ASDs.

neuroscience↗

bioRxiv2021

Spatiotemporal specificity of correlated DNA methylation and gene expression pairs across different human tissues and stages of brain development

DNA methylation (DNAm) that occurs on promoter regions is primarily considered to repress gene expression. Previous studies indicated that DNAm could also show positive correlations with gene expression. Both DNAm and gene expression profiles are known to be tissue- and development-specific. This study aims to investigate how DNAm and gene expression are coordinated across different human tissues and developmental stages, as well as the biological significance of such correlations. By analyzing 2,239 samples with both DNAm and gene expression data in the same human subjects obtained from six published datasets, we evaluated the correlations between gene and CpG pairs (GCPs) at cis-regions and compared significantly correlated GCPs (cGCPs) across different tissues and brains at different age groups. A total of 37,363 cGCPs were identified in the six datasets; approximately 38% of the cGCPs were positively correlated. The majority (>90%) of cGCPs were tissue- or development-specific. We also observed that the correlation direction can be opposite in different tissues and ages. Further analysis highlighted the importance of cGCPs for their cellular functions and potential roles in complex traits and human diseases. For instance, early developmental brain possessed a highly unique set of cGCPs that were associated with neurogenesis and psychiatric disorders. By assessing the epigenetic factors involved in cGCPs, we discovered novel regulatory mechanisms of positive cGCPs distinct from negative cGCPs, which were related to multiple factors, such as H3K27me3, CTCF, and JARD2. The catalog of cGCPs compiled can be used to guide functional interpretation of genetic and epigenetic studies.

genetics↗