Biology subjects

Hsu, C.-L.

Publications and source records attributed to Hsu, C.-L..

At least 19 recordsLinked to original sources

bioRxiv2026

Mild and Reversible Proprioception Perturbation Suggests Causal Biomechanics for Memory-Dependent Spatial Behavior in Mice

The neural system at the periphery is a frontline for embodied cognition, yet an acute, mild perturbation to dissect functional causality is hard to achieve. Peripheral neural processes and the central nervous system may work in concert to generate sophisticated representations regarding self and environments in the brain. This hypothesis, together with the underlying mechanisms, is particularly difficult to test for certain sensory inputs due to the lack of reversible manipulation techniques. Long postulated as a component for path integration, proprioception is one of such modalities. In this study, we developed a murine experimental system to manipulate proprioceptive inputs during memory-dependent localization task (which required precise operant-conditioned licks) in spatial virtual reality (VR). Through bioluminescent optogenetics (luminopsin) selectively expressed in the parvalbumin-positive neurons of the dorsal root ganglia in mice, proprioceptive processing was compromised directly from the periphery to bypass the bottleneck of specific central targeting, which results from the lack of anatomically or genetically dedicated proprioceptive circuits in the brain. In-vivo IVIS imaging and behavior suggested the effects of luminopsin last for roughly 20 minutes. While mice exhibited normal performance in tasks relying on gross motor skills, they showed subtle deficits in challenging spatial tasks that required integration of past movements. These observations support a task-specific role for proprioception, and demonstrate a potential of chemogenetics-like, rapidly reversible strategies for characterizing peripherally defined sensory contribution to spatial cognition. Future work will optimize this approach; for instance, to activate opsins by light with millisecond precision. To our knowledge, this is a first causal demonstration for acute participation of proprioception in path-integration biomechanics, enabling the first temporally defined method for mild perturbation of path-integration mechanisms.

neuroscience↗

bioRxiv2026

Rpd3L Coordinates Chromatin State and Transcription-Replication Conflict Resolution through H3K4 Methylation-Dependent and Independent Mechanisms

Faithful genome duplication requires coordination between transcription and replication. Disruption of this coordination causes transcription-replication conflicts (TRCs), leading to replication stress and genome instability. How chromatin regulators modulate these processes remains unclear. Here, we show that the Rpd3L histone deacetylase complex dynamically modulates chromatin state to control replication fork progression and buffer TRCs in Saccharomyces cerevisiae. Rpd3L is targeted through both histone H3 lysine 4 methylation-dependent recruitment and methylation-independent mechanisms engaged under replication stress. Loss of H3K4 methylation or Rpd3L function promotes histone acetylation, accelerates fork progression through transcribed regions, and increases transcription-associated genome instability. Balanced acetylation at multiple histone lysines is required to stabilize replication forks under stress. While histone deacetylase complexes have been implicated in repairing damaged forks, our findings reveal that Rpd3L acts preemptively to modulate chromatin state and replication dynamics during TRCs, defining a chromatin-based mechanism that safeguards genome stability.

molecular biology↗

bioRxiv2026

Engineering a performance-improved, axon-targeted kalium channelrhodopsin for optogenetic neuropathway inhibition

Optogenetic neuropathway inhibition is a powerful approach for dissecting circuit functions. This strategy, however, frequently encounters practical challenges due to insufficient expression or performance of the optogenetic silencer on axonal projections/terminals. HcKCR1, a light-gated potassium-selective channel from Hyphochytrium catenoides, has shown great promise for optogenetic inhibition. Unfortunately, the application of HcKCR1 in neuropathway manipulations is hindered by its unsatisfactory gating properties and poor axonal trafficking. To overcome these hurdles, we first engineered a performance-improved HcKCR1 (piKCR) that allowed more reliable neuronal inhibition at low intensities of green or red light. We next engineered an axon-targeted piKCR (piKCR.AT) that demonstrated long-range axonal trafficking and optical presynaptic inhibition in the mouse hippocampus. When piKCR.AT was expressed in the cerebellar Purkinje Cells (PCs), optical manipulation of PC outputs to the deep cerebellar nuclei robustly disrupted mouse movement on the balance beam. With enhanced performance and axonal distribution, piKCR.AT may provide new opportunities for elucidating neuropathway functions in health and diseases.

bioengineering↗

bioRxiv2025

A topologically conserved unstructured region helps positioning the evolutionarily conserved Prp40 WW domains to promote non-canonical intron splicing

Newly transcribed introns are immediately identified by early splicing factors that recognize the intron 5 splice site (5SS) and branch site (BS). In the budding yeast, these critical splice-site sequences are generally constrained, whereas degeneracy is the rule in higher eukaryotes. Yet, [~]40% of the yeast introns do diverge, to a certain degree, from the canonical sequences. Exactly how these non-canonical introns are recognized and spliced remains unknown. Here we show that the conserved Prp40 WW domains promote non-canonical intron splicing by enhancing stable U1 snRNP and BBP recruitments. AlphaFold predicts a topologically conserved unstructured region between Prp40 WW and FF domains. Alignment of the AlphaFold Prp40 structure with published U1 snRNP structure positions WW domains adjacent to 5SS and Luc7, which is known to be critical for 5SS recognition. Indeed, deletion of this unstructured region negatively impacts on splicing of the non-canonical 5SS introns. Taken together, our results suggest that the conserved WW domains may have evolved to deal with the highly degenerate 5SS and BS sequences in higher eukaryotes, so as to accommodate increased splicing complexity. HighlightsO_LIThe evolutionarily conserved Prp40 WW domains promote splicing of introns harboring non-canonical 5 splice site or branch site. C_LIO_LIPrp40 WW domains enhance stable U1 snRNP and BBP recruitments to nascent transcripts containing non-canonical splice sites. C_LIO_LIA topologically conserved unstructured region between WW and FF domains helps to position Prp40 WW domains close to the 5 splice site. C_LIO_LIThe N-terminal WW domain sterically hinders conformational rearrangements required for efficient release of a BBP variant during spliceosome assembly. C_LIO_LIA reporter assay identified 13 non-canonical introns whose splicing, under various environmental conditions, depend on Prp40 WW domains. C_LI

biochemistry↗

bioRxiv2025

deCYPher: Star Allele-Resolution Computational Framework of Pharmacogenes for Haplotype-Resolved Long-Read Assemblies

Although existing next-generation sequencing (NGS) tools, such as Aldy and Cyrius, have been applied for allele typing, they cannot achieve complete accuracy due to various genomic challenges including pseudogenes, structural variations, hybrid genes, copy number variations, and gene deletions. These complexities make accurate pharmacogene interpretation more challenging, despite the crucial role pharmacogenomics plays in precision medicine. We developed deCYPher, a tool that generates personalized pharmacogenomic reports from haplotype-resolved assemblies. The tool enables analysis of all PharmVar 1A level genes, such as CYP2B6, CYP2C9, CYP2C19, CYP2D6, CYP3A5, CYP4F2, DPYD, NUDT15, and SLCO1B1. Applied to all HPRC haplotypes (including both release 1 and release 2 data), deCYPher demonstrated high accuracy in resolving complex gene structures. In the case of CYP2D6, release 1 identified 6% gene multiplications, 6% full gene deletions, and 4% CYP2D6/CYP2D7 hybrids. By contrast, release 2 demonstrated an increased prevalence of multiplications (14%) and hybrids (11%), while the frequency of full gene deletions remained comparable at 5%. Comparison with pb-StarPhase revealed discrepancies in 12 of 94 assemblies in the release 1 dataset. For instance, in sample HG02257, Aldy, Cyrius, and deCYPher consistently identified the genotype as *2/*35, whereas pb-StarPhase reported *2/*2. Notably, the *35-defining variants were present in the BAM and VCF files in the pb-StarPhase pipeline, but the local read depth over the *35-specific region was only 5x in HG02257-p, suggesting that the misclassification likely resulted from insufficient coverage - a known limitation of pb-StarPhase under low-depth conditions.

bioinformatics↗

bioRxiv2025

gAIRR-wgs: An Algorithm to Genotype T Cell Receptor Alleles Using Whole Genome Sequencing Data

T cell receptor (TR) genes, including variable (TR_V), diversity (TR_D), and joining (TR_J) segments, exhibit allelic diversity that is critical to adaptive immunity. Growing evidence has identified associations between TR genes and immune-related diseases. Germline variants may influence TR gene function and subsequent usage, highlighting the importance of accurate TR allele profiling. However, accurately identifying germline TR from standard WGS data remains challenging due to short read lengths, limited depth, and high sequence similarity. To address these challenges, we developed gAIRR-wgs, for WGS-based TR allele typing. By incorporating novel alleles from HPRC individuals, gAIRR-wgs exhibited excellent performance in allele calling, with F1 scores of 100.0% for TR_D, 99.8% for TR_J, and 98.3% for TR_V. Applying this pipeline to 1,492 individuals from the Taiwan Biobank (TWB), we identified 449 novel TR alleles, 277 of which overlapped with HPRC release 1 data of mixed ethnicity and are absent in the IMGT database. Further population comparison analysis revealed significant TR allele distribution differences across global populations, showing population-specific patterns and diversity variations between ethnic groups. We also discovered TWB-specific deletion polymorphisms affecting contiguous TRGV and TRBV genes, which are not recorded in the gnomAD database and undetected by standard structural variant callers, highlighting the need for tailored approaches to resolve complex immune gene regions. In conclusion, gAIRR-wgs enables accurate TR allele calling from standard WGS data using feasible computational resources and reveals substantial immunogenetic diversity in population cohorts.

bioinformatics↗

bioRxiv2025

Ca2+ Plateau Potentials Reflect Cross-Theta Cortico-Hippocampal Input Dynamics and Acetylcholine for Rapid Formation of Efficient Place-Cell Code

A central tenet of Systems Neuroscience lies in an understanding of memory and behavior through learning rules, but synaptic plasticity has rarely been shown to create functional single-neuron code in a causal and biophysically rooted manner. Behavioral Time-Scale Synaptic Plasticity (BTSP), identified in vivo, holds a great potential for explaining instantaneous hippocampal selectivity emergence by long-term potentiation (LTP), yet the cellular and endogenous mechanisms are unknown, impeding broader conceptualization of this novel rule for its algorithmic, systems-level and theoretical implications. Here, we addressed this gap by in-vivo, ex-vivo, in-silico and computational approaches to seek neurophysiologically inspired protocols for synaptically evoking Ca2+ plateau potentials and inducing potentiation in the CA1. We found induction of BTSP-LTP is best explained by a theta-oscillation-paced, gradually developed cellular state being supported with precisely timed weak ramping inputs. Remarkably, the previously presumed one-shot LTP for in-vivo place-field formation is possible under the influence of muscarinic activation. Through modeling, the notion of acetylcholine-gated BTSP gave rise to a computational advantage for low-interference continual learning. We further demonstrated that biophysics of Transient Receptor Potential (TRPM) and NMDA receptor (NMDAR) channels powerfully shapes the cross-theta dynamics underlying BTSP. These results which cover pre-, post-synaptic and neuromodulatory factors and their timing suggest fundamental principles for graded plateau potentials and hippocampal LTP induction. Overall, our work dissects cellular mechanisms potentially important for a prominent in-vivo hippocampal plasticity phenomenon, and offers a biological basis for framing BTSP as an input-dynamics-aware, neuromodulation-tuned synaptic algorithm.

neuroscience↗

bioRxiv2025

TypeAssembly: Copy number estimation and allele typing for haplotype assemblies

Accurately annotating complex genes in the human genome, particularly from haplotype assemblies, remains a significant challenge. To overcome this, we developed TypeAssembly, a local alignment-based framework for copy number estimation and allele typing. Operating in two modes, mode-FASTA and mode-VCF, TypeAssembly can define alleles by either sequence or variant information. We successfully applied it to annotate 41 genes in the MHC locus, 17 KIR genes, and, for the first time, 15 pharmacogenes across 466 haplotype assemblies. This study establishes TypeAssembly as a robust method for accurately annotating complex genomic regions and provides an evaluation of existing gene annotations and callers.

bioinformatics↗

bioRxiv2025

CASTLE: a training-free foundation-model pipeline for cross-species behavioral classification

Accurately and efficiently quantifying animal behavior at scale without intensive manual labeling is a long-standing challenge for neuroscience and ethology. Keypoint-based tracking emphasizes simplicity and efficiency but loses the richness of posture and context, while emerging foundation models capture pixel-level details, yet often require nontrivial efforts of retraining and can be more sensitive to backgrounds or lighting. Here, we present CASTLE, a training-free pipeline that addresses all these issues by synergistically combining foundation models for segmentation, tracking, and feature extraction. By isolating regions-of-interest (ROI), CASTLE first generates "focused (ROI-masked)" and orientation-invariant latent features, capturing rich postural details in zero-shot, fine-tuning-free manners. Following ROI isolation, CASTLE, through an interactive "Behavior Microscope" module, supports hierarchical clustering, for progressive, human-in-the-loop embedding and clustering. This enables raw-image-assisted discovery of behavioral classes without predefined categories. Across mice, Drosophila and C. elegans, CASTLE matches expert class annotations (>90%), reveals disease-relevant phenotypes in Parkinsonian mouse models. By eliminating purpose-specific model training and providing a raw-image-informed accessible workflow, CASTLE offers a scalable framework for interpretable, cross-species behavioral phenotyping.

neuroscience↗

bioRxiv2025

Airway microbiome-host transcriptome networks link microbial dysbiosis to survival outcomes and therapeutic opportunities in severe COVID-19

The lower respiratory tract microbiome may critically influence outcomes in severe COVID-19, yet remains understudied. We analyzed bronchoalveolar lavage fluid from 86 severe patients requiring mechanical ventilation, stratified into two groups. We identified 213 bacteria with differential abundance, 11 bacteria associated with differentially expressed genes, and 39 of them were associated with patient survival. The more serious group exhibited reduced microbial network complexity, suggesting ecosystem disruption. To explore therapeutic potential, we employed our previously published model and predicted that compounds like palbociclib, XMD-1499, RS-17053, and RS-504393 may shift host gene expression favoring beneficial microbial signatures. These results highlight an important link between microbial dysbiosis and COVID-19 severity, offering promising directions for microbiome-informed therapeutic strategies. Our findings underscore the importance of the lung microbiome in modulating host responses and clinical outcomes, and suggest that modulating microbial-host interactions may serve as a novel adjunctive approach in the treatment of severe COVID-19. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=101 SRC="FIGDIR/small/661228v1_ufig1.gif" ALT="Figure 1"> View larger version (39K): org.highwire.dtl.DTLVardef@2fc879org.highwire.dtl.DTLVardef@1128d5dorg.highwire.dtl.DTLVardef@fef0eaorg.highwire.dtl.DTLVardef@17aa499_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

bioRxiv2025

Unmasking Human T Cell Receptor Germline Diversity: 335 Novel Alleles Identified in 47 Pangenome Reference Individuals Using the gAIRR Suite

The adaptive immune receptor repertoire (AIRR), composed of V(D)J-recombined T cell receptors (TR) and immunoglobulins (IG), is central to adaptive immunity. Accurate AIRR profiling depends on a comprehensive and diverse germline gene set encoding AIRR (gAIRR). Furthermore, gAIRR alleles themselves are associated with immune-related phenotypes and diseases. However, for TR genes, the IMGT database - the primary gAIRR reference - has not been updated since 2020 and lacks sufficient population diversity and complete flanking sequences. To address these limitations, we investigated 47 high-quality genomes from the Human Pangenome Reference Consortium (HPRC) using the gAIRR Suite and identified 335 novel TR alleles - 305 TRV and 30 TRJ - representing 91.6% and 30.9% increases over IMGT records. All novel alleles were crosschecked using two orthogonal pipelines. We also established a comprehensive flanking sequence database, including recombination signal sequences (RSS). We have made all resources publicly available to support immunogenomics research and clinical applications.

genomics↗

bioRxiv2023

Graph-KIR: Graph-based KIR Copy Number Estimation and Allele Calling Using Short-read Sequencing Data

MotivationThe Killer-cell Immunoglobulin-like Receptor (KIR) is a highly polymorphic region in the human genome, associated with autoimmune diseases and organ transplantation. The sequences of KIR genes are highly similar among star alleles as well as in between individual genes, with the copy number of each KIR gene typically ranging from 0 to 4. In this study, we introduce a tool Graph-KIR that aims to estimate the copy number of genes and to call full-resolution (7-digit) KIR alleles from a whole genome sequencing (WGS) sample. ResultsGraph-KIR, unlike most KIR tools, is capable of independently typing KIR alleles per sample with no reliance on the distribution of any framework gene in a cohort. In a set of 100 simulated samples, Graph-KIR demonstrated 100% accuracy in copy number estimation and high accuracy of allele typing: 91.2% at 7-digit resolution, 97.0% at 5-digit resolution, 97.2% at 3-digit resolution, and 99.6% at gene-level resolution. Graph-KIR outperforms existing tools such as PINGs WGS version (91.9% accuracy) and T1K (84.6% accuracy) at 5-digit resolution. By analyzing the results on 44 HPRC samples, Graph-KIR achieves an accuracy of 85.0%, better than PINGs WGS version (75.5% accuracy) at 5-digit resolution. The release of Graph-KIR adds another valuable tool to assist users in accurately estimating copy numbers and calling alleles of KIR genes from WGS samples, ensuring reliable performance. AvailabilityThe Graph-KIR and paper-related pipeline codes are available at https://github.com/linnil1/KIR_graph.

bioinformatics↗

bioRxiv2023

Genetic Diversity and Structural Complexity of the Killer-Cell Immunoglobulin-Like Receptor Gene Complex: A Comprehensive Analysis using Human Pangenome Assemblies

The killer-cell immunoglobulin-like receptor (KIR) gene complex, a highly polymorphic region of the human genome that encodes proteins involved in immune responses, poses strong challenges in genotyping due to its remarkable genetic diversity and structural intricacy. Accurate analysis of KIR alleles, including their structural variations, is crucial for understanding their roles in various immune responses. Leveraging the high-quality genome assemblies from the Human Pangenome Reference Consortium (HPRC), we present a novel bioinformatic tool, the Structural KIR annoTator (SKIRT), to investigate gene diversity and facilitate precise KIR allele analysis. We applied SKIRT on 47 HPRC-phased assemblies and identified a recurrent novel KIR2DS4/3DL1 fusion gene in the paternal haplotype of HG02630 and maternal haplotype of NA19240. Additionally, SKIRT accurately identifies eight structural variants and 17 novel nonsynonymous alleles, all of which were independently validated using short-read data or quantitative polymerase chain reaction. Our study has discovered a total of 570 novel alleles, among which eight haplotypes harbor at least one KIR gene duplication, six haplotypes have lost at least one framework gene, and 75 out of 94 haplotypes (79.8%) carry at least five novel alleles, thus confirming KIR genetic diversity. These findings are pivotal in providing insights into KIR gene diversity and serve as a solid foundation for understanding the functional consequences of KIR structural variations. High-resolution genome assemblies offer unprecedented opportunities to explore polymorphic regions that are challenging to investigate using short-read sequencing methods. The SKIRT pipeline emerges as a highly efficient tool, enabling the comprehensive detection of the complete spectrum of KIR alleles within human genome assemblies.

genomics↗

bioRxiv2022

Equilibrative Nucleoside Transporter 3 is an IFN-stimulated Gene that Facilitates Viral Genome Release

An increasing body of evidence emphasizes the role of metabolic reprogramming in immune cells to fight off infections. However, little is known about the regulation of metabolite transporters that facilitate and support metabolic demands. In this study, we found that equilibrative nucleoside transporter 3 (ENT3) expression is part of the innate immune response, and is rapidly upregulated upon bacterial and viral infection. The transcription of ENT3 is directly under the regulation of IFN-induced signaling, positioning this metabolite transporter as an Interferon-stimulated gene (ISG). Moreover, we unveil that several viruses, including SARS-CoV2, require ENT3 to facilitate their entry into the cytoplasm. The removal or suppression of ENT3 expression is sufficient to significantly decrease viral replication in vitro and in vivo.

immunology↗

bioRxiv2021

Thymic macrophages consist of two populations with distinct localization and origin

Tissue-resident macrophages are essential to protect from pathogen invasion and maintain organ homeostasis. The ability of thymic macrophages to engulf apoptotic thymocytes is well appreciated, but little is known about their ontogeny, maintenance, and diversity. Here, we characterized the surface phenotype and transcriptional profile of these cells and defined their expression signature. Thymic macrophages were most closely related to spleen red pulp macrophages and Kupffer cells and shared the expression of the transcription factor SpiC with these cells. Single-cell RNA sequencing showed that the macrophages in the adult thymus are composed of two populations distinguished by the expression of Timd4 and Cx3cr1. Remarkably, Timd4+ cells were located in the cortex, while Cx3cr1+ macrophages were restricted to the medulla and the cortico-medullary junction. Using shield chimeras, transplantation of embryonic thymuses, and genetic fate mapping, we found that the two populations have distinct origins. Timd4+ thymic macrophages are of embryonic origin, while Cx3cr1+ macrophages are derived from adult hematopoietic stem cells. Aging has a profound effect on the macrophages in the thymus. Timd4+ cells underwent gradual attrition, while Cx3cr1+ cells slowly accumulated with age and, in older mice, were the dominant macrophage population in the thymus. Altogether, our work defines the phenotype, origin, and diversity of thymic macrophages.

immunology↗

bioRxiv2021

Rapid synaptic plasticity contributes to a learned conjunctive code of position and choice-related information in the hippocampus

To successfully perform goal-directed navigation, animals must know where they are and what they are doing--e.g., looking for water, bringing food back to the nest, or escaping from a predator. Hippocampal neurons code for these critical variables conjunctively, but little is known about how this where/what code is formed or flexibly routed to other brain regions. To address these questions, we performed intracellular whole-cell recordings in mouse CA1 during a cued, two-choice virtual navigation task. We demonstrate that plateau potentials in CA1 pyramidal neurons rapidly strengthen synaptic inputs carrying conjunctive information about position and choice. Plasticity-induced response fields were modulated by cues only in animals previously trained to collect rewards based on these cues. Thus, we reveal that gradual learning is required for the formation of a conjunctive population code, upstream of CA1, while plateau-potential-induced synaptic plasticity in CA1 enables flexible routing of the code to downstream brain regions.

neuroscience↗

bioRxiv2021

Synthetic dysmobility screen unveils an integrated STK40-YAP-MAPK system driving cell migration

Integrating signals is essential for cell survival, leading to the concept of synthetic lethality. However, how signaling is integrated to control cell migration remains unclear. By conducting a "two-hit" screen, we revealed the synergistic reduction of cell migration when serine-threonine kinase 40 (STK40) and mitogen-activated protein kinase (MAPK) were simultaneously suppressed. Single-cell analyses showed that STK40 knockdown reduced cell motility and coordination by strengthening focal adhesion (FA) complexes. Furthermore, STK40 knockdown reduced translocation of yes-associated protein (YAP) into the nucleus, while MAPK inhibition further weakened YAP activities in the nucleus to disturb FA remodeling. Altogether, we unveiled an integrated STK40-YAP-MAPK system regulating cell migration, and introduced "synthetic dysmobility" as a novel strategy to collaboratively control cell migration. One Sentence SummaryBlocking collaborative pathways within the integrated signaling network synergistically disrupts the migration of cells.

cell biology↗

bioRxiv2020

Profiling Germline Adaptive Immune Receptor Repertoire with gAIRR Suite

Genetic profiling of germline adaptive immune receptor repertoire (AIRR), including T cell receptor (TR) and immunoglobulin (IG), is imaginably relevant to numerous immune-related conditions, but currently insurmountable due to high genetic complexity. Our gAIRR Suite comprises three modules. gAIRR-seq, a probe capture-based targeted sequencing pipeline, profiles AIRR from individual DNA samples. gAIRR-call and gAIRR-annotate call alleles from gAIRR-seq reads and annotate whole-genome assemblies respectively. We gAIRR-seqed TRV and TRJ of seven Genome in a Bottle (GIAB) DNA samples with 100% accuracy, and discovered novel alleles. We also gAIRR-seqed and gAIRR-called a subject from both the peripheral blood mononuclear cells (PBMC) and oral mucosal cells. The calling results from these two cell types have a high concordance (99% for all known AIRR alleles). We gAIRR-annotated 36 genomes to cumulatively unearth 325 novel TRV alleles and 29 novel TRJ alleles. We could further profile the flanking sequences, including the recombination signal sequence (RSS). We validated two structural variants for HG002. We uncovered substantial conflicts of AIRR genes in references GRCh37 and GRCh38. The gAIRR Suite can potentially benefit future genetic study and clinical applications of various immune-related phenotypes.

genomics↗