Biology subjects

Liao, A.

Publications and source records attributed to Liao, A..

8 recordsLinked to original sources

bioRxiv2026

An interferon-like off-switch in invertebrates: Vago4 downregulates Domeless to restrain JAK/STAT signaling

Whether invertebrates possess a functional interferon (IFN)-like system remains controversial, as canonical IFN ligands and their receptors are absent from invertebrate genomes. Although Vago proteins in Drosophila and shrimp are compelling functional analogs of IFN, direct evidence for a canonical cytokine-receptor axis and, importantly, for how such signaling is restrained to prevent excessive immune activation, has been lacking. Here, we identify Vago4 as a bona fide ligand of Domeless, the canonical type I cytokine receptor upstream of JAK/STAT signaling. Vago4 binds the extracellular CBM1 and CBM2 domains of Domeless, triggering receptor endocytosis followed by lysosomal trafficking and K27-linked ubiquitination-dependent proteasomal degradation. This ligand-induced receptor downregulation serves as a negative feedback mechanism that restrains excessive JAK/STAT activation. During acute Vibrio infection, Vago4 silencing accelerated shrimp mortality, whereas recombinant Vago4 alleviated inflammatory lesions and oxidative stress, enhanced phagocytosis, and improved survival, phenocopying JAK or STAT knockdown. Thus, by downregulating Domeless, Vago4 limits immunopathology and defines an IRF-Vago4-Domeless-JAK/STAT IFN-like axis in invertebrates, offering new insight into the evolution of IFN-mediated immune regulation.

immunology↗

bioRxiv2025

EnrichSci: Transcript-guided Targeted Cell Enrichment for Scalable Single-Cell RNA Sequencing

Large-scale single-cell atlas efforts have revealed many aging-or disease-associated cell types, yet these populations are often underrepresented in heterogeneous tissues, limiting detailed molecular and dynamic analyses. To address this, we developed EnrichSci--a highly scalable, microfluidics-free platform that combines Hybridization Chain Reaction RNA FISH with combinatorial indexing to profile single -nucleus transcriptomes of targeted cell types with full gene-body coverage. When applied to profile oligodendrocytes in the aging mouse brain, EnrichSci uncovered aging-associated molecular dynamics across distinct oligodendrocyte subtypes, revealing both shared and subtype-specific gene expression changes. Additionally, we identified aging-associated exon-level signatures that are missed by conventional gene-level analyses, highlighting post-transcriptional regulation as a critical dimension of cell-state dynamics in aging. By coupling transcript-guided enrichment with a scalable sequencing workflow, EnrichSci provides a versatile approach to decode dynamic regulatory landscapes in diverse cell types from complex tissues.

genomics↗

bioRxiv2025

Uncovering Convergent Cell State Dynamics Across Divergent Genetic Perturbations Through Single-Cell High-Content CRISPR Screening

High-throughput genomic studies have uncovered associations between diverse genetic alterations and disease phenotypes; however, elucidating how perturbations in functionally disparate genes give rise to convergent cellular states remains challenging. Here, we present PerturbFate, a high-throughput, cost-effective, combinatorial-indexing single-cell platform that enables systematic interrogation of massively parallel CRISPR perturbations across the full spectrum of gene regulation, from chromatin remodeling and nascent transcription to steady-state transcriptomic phenotypes. Using PerturbFate, we profiled over 300,000 cultured melanoma cells to characterize multi-modal phenotypic and gene regulatory responses to perturbations in more than 140 Vemurafenib resistance-associated genes. We uncovered a shared dedifferentiated cell state marked by convergent transcription factor (TF) activity signatures across diverse genetic perturbations. Combined inhibition of cooperative TF hubs effectively reversed cellular adaptation to Vemurafenib treatment. We further dissected phenotypic responses to perturbations in Mediator Complex components, linking module-specific biochemical properties to convergent gene activations. Together, we reveal common regulatory nodes that drive similar phenotypic outcomes across distinct genetic perturbations. We also delineate how perturbations in functionally unrelated genes reshape cell state. PerturbFate thus establishes a versatile platform for identifying key molecular regulators by anchoring multi-modal regulatory dynamics to disease-relevant phenotypes.

genomics↗

bioRxiv2024

High resolution deep mutational scanning of the melanocortin-4 receptor enables target characterization for drug discovery

Deep Mutational Scanning (DMS) is an emerging method to systematically test the functional consequences of thousands of sequence changes to a protein target in a single experiment. Because of its utility in interpreting both human variant effects and protein structure-function relationships, it holds substantial promise to improve drug discovery and clinical development. However, applications in this domain require improved experimental and analytical methods. To address this need, we report novel DMS methods to precisely and quantitatively interrogate disease-relevant mechanisms, protein-ligand interactions, and assess predicted response to drug treatment. Using these methods, we performed a DMS of the melanocortin-4 receptor (MC4R), a G protein-coupled receptor (GPCR) implicated in obesity and an active target of drug development efforts. We assessed the effects of >6,600 single amino acid substitutions on MC4Rs function across 18 distinct experimental conditions, resulting in >20 million unique measurements. From this, we identified variants that have unique effects on MC4R-mediated Gs- and Gq-signaling pathways, which could be used to design drugs that selectively bias MC4Rs activity. We also identified pathogenic variants that are likely amenable to a corrector therapy. Finally, we functionally characterized structural relationships that distinguish the binding of peptide versus small molecule ligands, which could guide compound optimization. Collectively, these results demonstrate that DMS is a powerful method to empower drug discovery and development.

synthetic biology↗

bioRxiv2024

Context- and sex-dependent links between sire sexual success and offspring pathogen resistance

Sexual selection has been proposed to promote genetic variants that improve resistance to pathogens (a special case of the "good genes" hypothesis). Yet, experimental tests of this hypothesis are scarce and equivocal. It is often assumed that additive genetic correlation between sexual traits and pathogen resistance is generated by their shared dependence on genetically variable "condition" of the organism. However, an alternative scenario posits condition-independent genetic variation in pathogen resistance; individuals more resistant to currently prevalent pathogens remain healthier and can invest more in sexual traits, but this advantage disappears in the absence of pathogens. Here, we tested whether Drosophila melanogaster males that are more sexually competitive (in terms of paternity share) sire offspring that are more resistant to the fungal pathogen Metarhizium brunneum. Furthermore, to investigate the importance of epidemiological context, we exposed sires to either an infection or a sham treatment before mating, to test whether the sire-offspring relationship depends on the presence of pathogens during sexual selection. We found that the relationship between sires sexual success and offspring pathogen resistance not only depended on sires exposure to the pathogen, but also on offspring sex. Sires that were more sexually successful in the absence of the pathogen had less resistant offspring whereas no relationship was detected for sires that competed for paternity after pathogen exposure. For daughters, the relationship tended to be negative irrespective of sires pathogen exposure. In no case was a positive correlation predicted by the "good genes" hypothesis detected. Thus, while sexual selection may act on genes affecting resistance in a context- and sex-dependent manner, we found no circumstances under which it promoted resistance. Lay SummarySexual selection has been debated in relation to natural selection for decades. The "good genes" hypothesis which posits a positive genetic correlation between sexual success and non-sexual fitness, is often considered as a mechanism aligning sexual selection and natural selection. Scientists have long wondered if genetic variants that make individuals more sexually successful also enhance their ability to fight against pathogens, testing a special version of "good genes". However, evidence is mixed. Two key mechanisms linking sexual success and pathogen resistance have been proposed: the "condition- dependent" scenario, where general health improve both sexual traits and pathogen resistance, and the "context-dependent" scenario, where resistance to specific pathogens benefits sexual success only in certain environments. Few studies distinguish between these two mechanisms. This study examines both scenarios in Drosophila melanogaster, finding that the relationship between a sires mating success and offspring pathogen resistance to the fungal pathogen Metarhizium brunneum depends on sires pathogen exposure prior to measurement of sexual success and offspring sex. These findings challenge the "good genes" hypothesis and emphasize the necessity of including context in sexual selection studies.

evolutionary biology↗

bioRxiv2022

A global view of aging and Alzheimer's pathogenesis-associated cell population dynamics and molecular signatures in the human and mouse brains

Conventional single-cell genomics approaches are limited by throughput and thus may have failed to capture aspects of the molecular signatures and dynamics of rare cell types associated with aging and diseases. Here, we developed EasySci, an extensively improved single-cell combinatorial indexing strategy, for investigating the age-dependent dynamics of transcription and chromatin accessibility across diverse brain cell types. We profiled [~]1.5 million single-cell transcriptomes and [~]400,000 single-cell chromatin accessibility profiles across mouse brains spanning different ages, genotypes, and both sexes. With a novel computational framework designed for characterizing cellular subtypes based on the expression of both genes and exons, we identified > 300 cell subtypes and deciphered their underlying molecular programs and spatial locations especially for rare cell types (e.g., pinealocytes, tanycytes). Leveraging these data, we generated a global readout of age-dependent changes at cell subtype resolution, providing insights into cell types that expand (e.g., rare astrocytes and vascular leptomeningeal cells in the olfactory bulb, reactive microglia, and oligodendrocytes) or are depleted (e.g., neuronal progenitors, neuroblasts, committed oligodendrocyte precursors) as age progresses. Furthermore, we explored cell-type-specific responses to genetic perturbations associated with Alzheimers disease (AD) and identified rare cell types depleted (e.g., mt-Cytb+, mt-Rnr2+ choroid plexus epithelial cells) or enriched (e.g., Col25a1+, Ndrg1+ interbrain and midbrain neurons) in both AD models. Key findings are consistent between males and females, validated across the transcriptome, chromatin accessibility, and spatial analyses. Finally, we profiled a total of 118,240 single-nuclei transcriptomes from twenty-four post-mortem human brain samples derived from control and AD patients, revealing highly cell-type-specific and region-specific gene expression changes associated with AD pathogenesis. Critical AD-associated gene signatures were validated in both human and mice. In summary, these data comprise a rich resource for exploring cell-type-specific dynamics and the underlying molecular mechanisms in normal and pathological mammalian aging.

genomics↗

bioRxiv2021

Essential Role of Placenta Derived Interferon Stimulated Gene 20 Against ZIKA Virus Infection

Zika virus is a positive-sense single-stranded RNA virus, which can be transmitted across the placenta and leads to adverse effects on fetal development during pregnancy. The severity of these complications highlights the importance of prevention and treatment. However, no vaccines or drugs are currently available. In this study, we characterized the IFN{beta}-mediated antiviral response in trophoblast cells in order to identify critical components that are necessary for the successful control of viral replication; and determined whether we could use the components of the IFN-induced response as a replacement therapy for ZIKA viral infection during pregnancy. We identified and characterized interferon stimulated gene 20 (ISG20), playing a central role in controlling Zika infection in trophoblast cells, and successfully established a recombinant ISG20-Fc protein that effectively decrease viral titers in vitro and in vivo by maintaining its exonuclease activity and displaying immune modulatory functions. Therefore, rISG20-Fc is a promising anti-viral/immune modulatory approach for the control and prevention of RNA viral infections such as ZIKA virus.

immunology↗

bioRxiv2019

Aurora B-dependent Ndc80 Degradation Regulates Kinetochore Composition in Meiosis

The kinetochore complex is a conserved machinery that connects chromosomes to spindle microtubules. During meiosis, the kinetochore is restructured to accommodate a specialized chromosome segregation pattern. In budding yeast, meiotic kinetochore remodeling is mediated by the temporal changes in the abundance of a single subunit called Ndc80. We have previously described the regulatory events that control the timely synthesis of Ndc80. Here, we report that Ndc80 turnover is also tightly regulated in meiosis: Ndc80 degradation is active in meiotic prophase, but not in metaphase I. Ndc80 degradation depends on the ubiquitin ligase APCAma1 and is mediated by the proteasome. Importantly, Aurora B-dependent Ndc80 phosphorylation, a mark that has been previously implicated in correcting erroneous microtubule-kinetochore attachments, is essential for Ndc80 degradation in a microtubule-independent manner. The N-terminus of Ndc80, including a 27-residue sequence and Aurora B phosphorylation sites, is both necessary and sufficient for kinetochore protein degradation. Finally, defects in Ndc80 turnover predispose meiotic cells to chromosome mis-segregation. Our study elucidates the mechanism by which meiotic cells modulate their kinetochore composition through regulated Ndc80 degradation, and demonstrates that Aurora B-dependent regulation of kinetochores extends beyond altering microtubule attachments.

genetics↗