Biology subjects

Kong, E.

Publications and source records attributed to Kong, E..

10 recordsLinked to original sources

bioRxiv2026

Photon-Resolved Excitation-Denoised (PRED) Three-Photon Imaging Improves Detection of Neuronal Activity in Awake and Behaving Mice

Three-photon microscopy (3PM) has enabled the optical access of neurons [~]500-1500 {micro}m below the brain surface but has been limited to slow imaging frame rates or small total imaged areas by competing constraints: a high peak power requirement for nonlinear excitation, and the need to limit total average power. Additionally, the high sensitivity to laser power fluctuations and the inherently dim signals introduce additional challenges and add error. When combined with other effects, like brain motion in behaving animals, 3P imaging of neuronal activity during animal behavior has remained inadequate. Herein, we systematically address these limitations by 1) carefully balancing scanning speed with power requirements, 2) using a deeply cooled silicon photomultiplier detector and Bayesian statistics-based processing (PRED-correction) to reduce excess noise, and 3) by spatiotemporal shaping of excitation pulses. Our improvements enable rapid (20-30Hz) imaging of calcium activity in the dorsal hippocampal dentate gyrus of behaving mice, allowing the identification of spatially tuned neurons and the recapitulation of established functional properties across different cell types in this brain region. PRED-3P imaging provides a new approach to functional characterization of cells deep in the brain that were previously inaccessible to two-photon imaging.

neuroscience↗

bioRxiv2026

Stress-induced vtRNA1-1 modulates redox homeostasis and ferroptosis susceptibility in hepatocellular carcinoma cells

Ferroptosis is a unique form of regulated cell death characterized by iron-dependent lipid peroxidation. Although the molecular details of ferroptosis regulation have been widely explored, the contributions of short non-coding RNAs (ncRNAs) to ferroptosis regulation, other than miRNAs remain poorly understood. Here, we identified vault RNA1-1 (vtRNA1-1) as a previously unrecognized short ncRNA regulator of ferroptosis in hepatocellular carcinoma (HCC) cells. vtRNA1-1 expression was upregulated by ferroptosis inducers and exhibited strong negative correlation with ferroptosis sensitivity, thus protecting cells from ferroptosis. vtRNA1-1 levels were elevated in selected ferroptosis-resistant cells, while its depletion reversed the phenotype thus resensitizing these cells to ferroptosis. These findings suggested a contribution of vtRNA1-1 to both intrinsic and acquired ferroptosis resistance. Mechanistically, we uncovered that increased oxidative stress, which potentiates lipid peroxidation, specifically induced expression of the vtRNA1-1 paralog in an NF-{kappa}B dependent manner. Elevated vtRNA1-1 levels suppressed NF-{kappa}B-mediated pro-oxidant gene expression, thereby limiting reactive oxygen species (ROS) accumulation and alleviating oxidative stress. Taken together, oxidative stress-inducible vtRNA1-1 governs redox balance by forming a reciprocal regulatory loop with NF-{kappa}B and this loop determines ferroptosis susceptibility by adjusting basal ROS levels. Our findings provide unprecedented insights into the regulation of redox homeostasis in HCC cells mediated by a short ncRNA and uncovered vtRNA1-1 as a potential therapeutic target for overcoming ferroptosis resistance in liver cancer.

molecular biology↗

bioRxiv2025

Immune transcriptomic differences in paediatric patients with SARS-CoV-2 compared to other lower respiratory tract infections

The clinical severity of SARS-CoV-2 infection in children varies, with asymptomatic or mild illness predominating and a minority developing severe disease. Understanding the immunological responses that underlie severity of disease may guide future development of preventive or therapeutic interventions. This study compared whole blood transcriptomes of healthy children (N=127), children with mild/asymptomatic SARS-CoV-2 infection (N=71) and children hospitalised with severe SARS-COV-2 (N=41), lower respiratory tract illness (LRTI) or LRTI due to Respiratory Syncytial Virus (RSV-LRTI) (N=47) or Pulmonary Tuberculosis (PTB) (N=47). We identified >5000 differentially expressed genes including: OLFM4, IFI27, CBX7, IGF2BP3, OTOF for severe SARS-CoV-2; IFI27, OTOF, SIGLEC1, IFI44L and USP18 for RSV-LRTI, and MMP8, LTF, IGF2BP3, GPR84, CD177, C1QC and DEFA4 for PTB, at false discovery rate (FDR) <0.05. Pathway analysis identified enrichment for neutrophil degranulation, interferon gamma signalling, overexpression of ribosomal proteins and depletion of immune response in severe SARS-CoV-2 compared to healthy (SAR-COV-2 uninfected) children. Weighted Gene Co-expression Network Analysis (WGCNA) identified 10 correlated gene modules shared between LRTI showing similar underlying response mechanisms. Cellular decomposition analysis identified the depletion of 22 cell types in severe SARS-CoV-2, 16 for RSV-LRTI and 21 for PTB compared to healthy SARS-CoV-2 uninfected control children. We identified 82 genes important for discriminating asymptomatic/mild from severe SARS-CoV-2 including CBX7, TRAF1, ZNF324 and CASS4; 93 healthy from severe SARS-CoV-2 including RORC, CBX7, NR3C2, MID2 and ADAMTS2; 110 genes for RSV-LRTI and 95 for PTB children which can be used for future therapeutic targets. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=99 SRC="FIGDIR/small/687132v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@13db618org.highwire.dtl.DTLVardef@7df9e2org.highwire.dtl.DTLVardef@a0a448org.highwire.dtl.DTLVardef@818cef_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Somatic copy number mutations contribute to fitness in transplantation models of spontaneous human breast cancer metastasis

The contribution of somatic gene dosage mutations (CNA) to breast cancer metastasis remains poorly defined. Using 9 transplantable human neoadjuvant-naive triple-negative breast cancer xenografts, we studied the fitness of copy number clones in spontaneous metastasis from orthotopic transplant sites. Metastatic site preference was strongly patient-dependent, and the emergence of metastases exhibited a general trend toward slower growth at the orthotopic site. In our models, single-cell whole-genome sequencing of primary and metastatic sites showed that distant metastases were most often the result of minor prevalence clones at the orthotopic site, suggesting that some metastatic phenotypes may be weakly negatively fit at the primary site. We validated the existence of a fitness hierarchy of copy number clones using a previously established paradigm of remixing and retransplanting clones. Single-cell clone analysis of competitive repopulation and re-emergence of metastases showed that CNAs arising in cancer evolution can mediate metastatic fitness. Moreover, some clones displaying strong metastatic tendency exhibited weaker survival at the primary site, consistent with the notion that metastatic phenotypes could have a fitness cost at the primary site. Finally, we conducted RNA-seq analysis combined with DriverNet analysis to dissect the contribution of CNA-mediated versus genome-independent transcriptional states. CNA mutations appeared to contribute strongly to transcriptional differences between clones. Among clones of high metastatic potential, we observed CNA-mediated and CNA-independent convergence on pathways such as epithelial-mesenchymal transition (EMT), established as mediators of metastatic cell survival at distant sites. Taken together, our data point to a contribution of CNA-mediated cancer evolution to metastatic states and identify distant-site context as a key determinant of CNA-mediated fitness.

cancer biology↗

bioRxiv2025

A Physically-Realistic Simulator and Cosine-Based Decoder for MERFISH Spatial Transcriptomics

Imaging-based spatial transcriptomics technologies have opened new avenues for studying cellular organization and gene expression within intact tissues. However, the accuracy of downstream analyses depends critically on the decoding step that reconstructs barcodes from fluorescence patterns and maps them to gene identities. Despite a growing number of decoding methods, systematic benchmarking has been limited. Here, we introduce Serval, a modular framework for developing and benchmarking decoding methods across diverse spatial transcriptomics platforms. Serval separates key decoding stages into independently configurable modules, enabling flexible integration of alternative algorithms. Using this framework, we develop the Cosine decoder, a novel method that improves transcript recovery by optimizing cosine similarity to known barcodes. We evaluate Cosine and baseline methods on synthetic and real MERFISH datasets, showing that Cosine achieves higher transcript recovery and superior correlation with expression references compared to existing methods. Furthermore, we demonstrate that the Serval framework generalizes beyond MERFISH. By extending to the DART-FISH platform, we show that Cosine improves transcript recovery, clustering stability and supports more direct annotation of complex biological structures such as the human primary motor cortex. These results establish that modular decoding frameworks facilitate robust, platformagnostic benchmarking, ultimately supporting more accurate spatial transcriptomics analysis across diverse biological samples.

bioinformatics↗

bioRxiv2025

The GLP-1R Agonist Semaglutide Reduces Motivated Running and Alters Dopamine Dynamics in the Nucleus Accumbens

Glucagon-like peptide-1 receptor (GLP-1R) agonists have recently emerged as powerful tools for the treatment of obesity through their ability to suppress food intake. However, their effects on non-ingestive motivated behaviors remain incompletely understood. Here, we show that the long-acting GLP-1R agonist semaglutide (SG) suppresses voluntary wheel running in both lean and diet-induced obese mice. Importantly, this suppression of activity was not caused by hypophagia and was accompanied by decreased motivation, with SG-treated mice displaying reduced effort for wheel access in a progressive ratio task. Real-time measurements of dopamine via fiber photometry revealed specific dopamine changes in the nucleus accumbens at both the beginning and end of running bouts, with SG-treated animals showing amplified dopamine dynamics at these key behavioral timepoints. Collectively, these data reveal important non-ingestive behavioral effects of GLP-1R agonism and suggest a role for dopamine circuits in mediating reductions of volitional activity following SG treatment.

neuroscience↗

bioRxiv2024

Recurrent Connectivity Shapes Spatial Coding in Hippocampal CA3 Subregions

Stable and flexible neural representations of space in the hippocampus are crucial for navigating complex environments. However, how these distinct representations emerge from the underlying local circuit architecture remains unknown. Using two-photon imaging of CA3 subareas during active behavior, we reveal opposing coding strategies within specific CA3 subregions, with proximal neurons demonstrating stable and generalized representations and distal neurons showing dynamic and context-specific activity. To test the causal role of excitatory connectivity in neural computation, we employed a genetic manipulation approach in which local disruption of glutamatergic synaptic transmission impaired context-specific spatial coding in distal CA3. Aligned with these experimental results, we show in artificial neural network models that varying the recurrence level causes these differences in coding properties to emerge. We confirmed the contribution of recurrent connectivity to functional heterogeneity by characterizing the representational geometry of neural recordings and comparing it with theoretical predictions of neural manifold dimensionality. Our results indicate that local circuit organization, particularly recurrent connectivity among excitatory neurons, plays a key role in shaping complementary spatial representations within the hippocampus. HighlightsO_LIProximodistal CA3 subregions implement complementary coding strategies in relation to time and context C_LIO_LIDisrupting excitatory recurrence in distal CA3 impairs context-discriminative neural coding C_LIO_LISparse and dense neural networks capture the functional heterogeneity of CA3 subcircuits C_LIO_LIRecurrence level tunes the geometry of neural manifolds both in vivo and in silico C_LI

neuroscience↗

bioRxiv2022

DHHC3 mediated Cadm4 palmitoylation regulates myelination in CNS

Cell adhesion molecule 4 (Cadm4) plays important roles on plasma membrane (PM) to regulate myelin formation and the downregulation of Cadm4 is a prominent feature in many demyelination diseases. However, how Cadm4 maintains its level on PM has been elusive. Here, we identify that Cadm4 is palmitoylated at cysteine-347 (C347) and palmitoylation regulates the stable localization of Cadm4 on PM, as blocking palmitoylation by mutating C347 into alanine (C347A) results in the dissociation of Cadm4 from PM and targeting for degradation. Intriguingly, blocking Cadm4 palmitoylation by introducing C347A (Cadm4-KI) causes myelin abnormalities in CNS, characterized by loss of myelination, myelin infoldings and hypermyelination. Moreover, it is uncovered that Cadm4 palmitoylation is catalyzed by DHHC3, reducing Cadm4 palmitoylation by the deletion of DHHC3 renders the redistribution of Cadm4 for degrading. Consistently, the genetic deletion of DHHC3 leads to downregulated Cadm4 palmitoylation and defects in CNS myelination, virtually phenocopies that of the Cadm4-KI mice. Our findings suggest a mechanism that the stable localization of Cadm4 on PM regulated by protein palmitoylation is vital for myelination in CNS.

neuroscience↗

bioRxiv2019

Dissociation of solid tumour tissues with cold active protease for single-cell RNA-seq minimizes conserved collagenase associated stress responses

BackgroundSingle-cell RNA sequencing (scRNAseq) is a powerful tool for studying complex biological systems, such as tumour heterogeneity and tissue microenvironments. However, the sources of technical and biological variation in primary solid tumour tissues and patient-derived mouse xenografts for scRNAseq, are not well understood. Here, we used low temperature (6{degrees}C) protease and collagenase (37{degrees}C) to identify the transcriptional signatures associated with tissue dissociation across a diverse scRNAseq dataset comprising 128,481 cells from patient cancer tissues, patient-derived breast cancer xenografts and cancer cell lines.\n\nResultsWe observe substantial variation in standard quality control (QC) metrics of cell viability across conditions and tissues. From FACS sorted populations gated for cell viability, we identify a sub-population of dead cells that would pass standard data filtering practices, and quantify the extent to which their transcriptomes differ from live cells. We identify a further subpopulation of transcriptomically \"dying\" cells that exhibit up-regulation of MHC class I transcripts, in contrast with live and fully dead cells. From the contrast between tissue protease dissociation at 37{degrees}C or 6{degrees}C, we observe that collagenase digestion results in a stress response. We derive a core gene set of 512 heat shock and stress response genes, including FOS and JUN, induced by collagenase (37{degrees}C), which are minimized by dissociation with a cold active protease (6{degrees}C). While induction of these genes was highly conserved across all cell types, cell type-specific responses to collagenase digestion were observed in patient tissues. We observe that the yield of cancer and non-cancer cell types varies between tissues and dissociation methods.\n\nConclusionsThe method and conditions of tumour dissociation influence cell yield and transcriptome state and are both tissue and cell type dependent. Interpretation of stress pathway expression differences in cancer single cell studies, including components of surface immune recognition such as MHC class I, may be especially confounded. We define a core set of 512 genes that can assist with identification of such effects in dissociated scRNA-seq experiments.

genomics↗

bioRxiv2018

Genome-wide study identifies 611 loci associated with risk tolerance and risky behaviors

Humans vary substantially in their willingness to take risks. In a combined sample of over one million individuals, we conducted genome-wide association studies (GWAS) of general risk tolerance, adventurousness, and risky behaviors in the driving, drinking, smoking, and sexual domains. We identified 611 approximately independent genetic loci associated with at least one of our phenotypes, including 124 with general risk tolerance. We report evidence of substantial shared genetic influences across general risk tolerance and risky behaviors: 72 of the 124 general risk tolerance loci contain a lead SNP for at least one of our other GWAS, and general risk tolerance is moderately to strongly genetically correlated ([Formula] to 0.50) with a range of risky behaviors. Bioinformatics analyses imply that genes near general-risk-tolerance-associated SNPs are highly expressed in brain tissues and point to a role for glutamatergic and GABAergic neurotransmission. We find no evidence of enrichment for genes previously hypothesized to relate to risk tolerance.

genetics↗