Biology subjects

Luan, H.

Publications and source records attributed to Luan, H..

14 recordsLinked to original sources

bioRxiv2026

Centered cross-context perturbation transfer on the public 2025 Virtual Cell Challenge benchmark

Predicting transcriptional responses across cellular contexts requires transferring both expression direction and differential-expression priority. We developed a compact numerical method that combines public perturbation summaries with a differential-expression kernel fitted to H1 CRISPRi training targets. The method centers an independent KOLF2.1J source on known training targets, transfers its response signs and magnitude ranks, and uses isotonic regression to render predicted expression means. We evaluated the frozen model retrospectively on the released public TEST100 of the 2025 Virtual Cell Challenge, using an external KOLF source released in 2026. The model achieved DES 0.371834, PDS 0.8614, and MAE 0.302206. With reconstructed historical anchors, its composite score was 0.341344, compared with the archived champion score of 0.340052, a difference of +0.001292. The comparison showed higher DES and lower PDS, with zero normalized MAE contributions for both methods. Source centering also improved development PDS across all three TRAIN folds and official VALIDATION. These results demonstrate a practical numerical approach to cross-context perturbation transfer and differential-expression ranking.

bioinformatics↗

bioRxiv2026

An immune world model with multi-agent orchestration for peptide vaccines

Peptide-vaccine design requires a connection between vaccine-induced priming and recognition of the antigen naturally displayed by a tumor. We present an immune world model that preserves this connection through separate vaccine and tumor branches, endpoint-specific evidence and multi-agent orchestration. Native-recognition constraints held an altered peptide despite its higher presentation score, and targeted perturbations removed antigen-dependent benefit when required tumor-recognition conditions were absent. Public dendritic-cell data distinguished donor from antigen-source transfer: a context ranker achieved Recall@20 of 0.483 and 0.333 under the respective holdouts. Structure-informed receptor prediction added candidate-ranking evidence while preserving functional constraints and matched scenario trajectories. An assay observation model further concentrated a cross-presentation coefficient around its known value in a synthetic conditioning experiment. Together, these results establish a computational framework for linking molecular predictions, native-target requirements and conditional immune dynamics. The framework provides a reproducible basis for choosing peptide-vaccine candidates and the experiments needed to resolve their biological dependencies.

bioinformatics↗

bioRxiv2026

Orai1 is required for Ca2+-dependent plasma membrane repair and mechanoadaptation

Ca2+-dependent repair of plasma membrane breaches is essential for animal cell viability. An initial passive influx of extracellular Ca2+ triggers the formation of a protein plug that rapidly seals breaches. However, the mechanism of extracellular Ca2+ requirement for subsequent repair remains undefined. EHD2 protein stabilizes the plasma membrane caveolae, which sustain membrane repair, and maintains high surface levels of the caveolae-resident Ca2+ channel Orai1. We establish the requirement of both Orai1 and EHD2 for repair of plasma membrane lesions induced by mechanical injury or by a model bacterial pore-forming toxin. We demonstrate rapid EHD2 recruitment and Orai1-mediated Ca2+ entry at plasma membrane sites of localized mechanical stimulus, the latter requiring EHD2 and CAV1. EHD2 and Orai1 are necessary for mechanosensitive YAP/TAZ-TEAD activation and positive feedback for CAV1 expression that promotes membrane repair. Our studies establish EHD2 and Orai1 as novel components of mammalian plasma membrane repair and mechanoadaptation.

cell biology↗

bioRxiv2025

Characterization Eclosion Hormone Receptor function reveals differential hormonal control of ecdysis during Drosophila development.

Neuromodulators and peptide hormones play important roles in regulating animal behavior. A well-studied example is ecdysis, which is used by insects to shed their exoskeleton at the end of each molt. Ecdysis is initiated by Ecdysis Triggering Hormone (ETH) and Eclosion Hormone (EH), which interact via positive feedback to coordinate the sequence of behavioral and physiological changes that cause exoskeleton shedding. Whereas the cell types targeted by ETH are well characterized, those targeted by EH have remained largely unknown due to limited characterization of the EH receptor (EHR). A gene encoding an EHR has been described in the oriental fruit fly, B. dorsalis, and in the desert locust, Schistocerca gregaria. However, little is known in these species about its expression pattern and its precise role at ecdysis, and no other insect EHRs are known. Here we analyze CG10738, the Drosophila ortholog of the B. dorsalis gene encoding EHR, and show that expressing it in cells confers sensitivity to EH. In addition, mutations of CG10738 specifically disrupt ecdysis, phenocopying the knockout of the EH gene. Together, these results indicate that CG10738 encodes the Drosophila EHR. As in B. dorsalis, EHR is expressed in the ETH-producing Inka cells; in addition, it is expressed in many known targets of ETH, including the neurons responsible for the secretion of other ecdysis-related peptides, such as CCAP and EH itself. Our results from targeted knockdown and rescue experiments reveal that EHR is required for ecdysis in diverse cell types and that the role of EHR in different targets differs with developmental stage. Our findings indicate extensive convergence of EH and ETH signaling and provide an exemplar of the complex mechanisms by which hormones control animal behavior. AUTHOR SUMMARYHormones and neuromodulators are important regulators of animal behavior. In insects, one of the best studied behaviors influenced by hormones is ecdysis, which allows the animal to shed the remains of its exoskeleton at the end of each molt. Ecdysis is controlled by two key hormones: Ecdysis Triggering Hormone (ETH) and Eclosion Hormone (EH). Whereas most targets of ETH have been identified, those of EH have remained largely unknown due to the limited characterization of its receptor, EHR. Previous studies identified a gene encoding EHR in the oriental fruit fly, Bactrocera dorsalis, and in the desert locust, Schistocerca gregaria, but little is known about its expression pattern or its precise role. Here, we show that CG10738 encodes the Drosophila EHR. We found that EHR is expressed in ETH-producing Inka cells, in neurons that secrete other ecdysis-related peptides, in addition to other neuronal classes and non-neuronal cells. Targeted knockdown and rescue experiments revealed that EHR is essential for ecdysis in various cell types, and that its role can vary depending on the developmental stage. Our findings reveal that the role of EH at ecdysis is complex and provides insights into how hormones and neuromodulators regulate animal behavior.

neuroscience↗

bioRxiv2024

Accurate Multiple Sequence Alignment of Ultramassive Genome Sets

With ever increasing sequencing efficiency, there is a pressing need to tackle a presently intractable task of accurate multiple sequence alignment (MSA) for ultramassive genome sets of millions and beyond. Additionally, efficient graph and probabilistic representations for downstream analysis are in dire lack. In light of these challenges, we develop a set of essentially linearly scalable algorithms, including that for constructing directed acyclic graphs, for training tiled profile hidden Markov models and for conducting alignment on such graphs. The power of these algorithms is demonstrated by both significantly improved accuracy and tremendous acceleration of SAR-CoV-2 MSA by three observed to five projected orders of magnitude for genome set sizes ranging from 40,000 to 4 million when compared with widely utilized MAFFT. Future application to other viral species and extension to more complex genomes will prove this algorithm set as a cornerstone for the coming era of ultramassive genome sets.

bioinformatics↗

bioRxiv2023

Split-intein Gal4 provides intersectional genetic labeling that is fully repressible by Gal80

The split-Gal4 system allows for intersectional genetic labeling of highly specific cell-types and tissues in Drosophila. However, the existing split-Gal4 system, unlike the standard Gal4 system, cannot be repressed by Gal80, and therefore cannot be controlled temporally. This lack of temporal control precludes split-Gal4 experiments in which a genetic manipulation must be restricted to specific timepoints. Here, we describe a new split-Gal4 system based on a self-excising split-intein, which drives transgene expression as strongly as the current split-Gal4 system and Gal4 reagents, yet which is fully repressible by Gal80. We demonstrate the potent inducibility of "split-intein Gal4" in vivo using both fluorescent reporters and via reversible tumor induction in the gut. Further, we show that our split-intein Gal4 can be extended to the drug-inducible GeneSwitch system, providing an independent method for intersectional labeling with inducible control. We also show that the split-intein Gal4 system can be used to generate highly cell-type specific genetic drivers based on in silico predictions generated by single cell RNAseq (scRNAseq) datasets, and we describe a new algorithm ("Two Against Background" or TAB) to predict cluster-specific gene pairs across multiple tissue-specific scRNA datasets. We provide a plasmid toolkit to efficiently create split-intein Gal4 drivers based on either CRISPR knock-ins to target genes or using enhancer fragments. Altogether, the split-intein Gal4 system allows for the creation of highly specific intersectional genetic drivers that are inducible/repressible. Significance statementThe split-Gal4 system allows Drosophila researchers to drive transgene expression with extraordinary cell type specificity. However, the existing split-Gal4 system cannot be controlled temporally, and therefore cannot be applied to many important areas of research. Here, we present a new split-Gal4 system based on a self-excising split-intein, which is fully controllable by Gal80, as well as a related drug-inducible split GeneSwitch system. This approach can both leverage and inform single-cell RNAseq datasets, and we introduce an algorithm to identify pairs of genes that precisely and narrowly mark a desired cell cluster. Our split-intein Gal4 system will be of value to the Drosophila research community, and allow for the creation of highly specific genetic drivers that are also inducible/repressible.

genetics↗

bioRxiv2023

Role of GD2 and its biosynthetic enzyme GD3 synthase in prostate cancer tumorigenesis

While better management of loco-regional prostate cancer (PC) has greatly improved survival, advanced PC remains a major cause of cancer deaths. Identification of novel targetable pathways that contribute to tumor progression in PC could open new therapeutic options. The di-ganglioside GD2 is a target of FDA-approved antibody therapies in neuroblastoma, but the role of GD2 in PC is unexplored. Here, we show that GD2 is expressed in a small subpopulation of PC cells in a subset of patients and a higher proportion of metastatic tumors. Variable levels of cell surface GD2 expression were seen on many PC cell lines, and the expression was highly upregulated by experimental induction of lineage progression or enzalutamide resistance in CRPC cell models. GD2high cell fraction was enriched upon growth of PC cells as tumorspheres and GD2high fraction was enriched in tumorsphere-forming ability. CRISPR-Cas9 knockout (KO) of the rate-limiting GD2 biosynthetic enzyme GD3 Synthase (GD3S) in GD2high CRPC cell models markedly impaired the in vitro oncogenic traits and growth as bone-implanted xenograft tumors and reduced the cancer stem cell (CSC) and epithelial-mesenchymal transition (EMT) marker expression. Our results support the potential role of GD3S and its product GD2 in promoting PC tumorigenesis by maintaining cancer stem cells and suggest the potential for GD2 targeting in advanced PC.

cancer biology↗

bioRxiv2023

Multifunctional Materials Strategies for Enhanced Safety of Wireless, Skin-Interfaced Bioelectronic Devices

Many recently developed classes of wireless, skin-interfaced bioelectronic devices rely on conventional thermoset silicone elastomer materials, such as poly(dimethylsiloxane) (PDMS), as soft encapsulating structures around collections of electronic components, radio frequency antennas and, commonly, rechargeable batteries. In optimized layouts and device designs, these materials provide attractive features, most prominently in their gentle, noninvasive interfaces to the skin even at regions of high curvature and large natural deformations. Past work, however, overlooks opportunities for developing variants of these materials for multimodal means to enhance the safety of the devices against failure modes that range from mechanical damage to thermal runaway. This paper presents a self-healing PDMS dynamic covalent matrix embedded with chemistries that provide thermochromism, mechanochromism, strain-adaptive stiffening, and thermal insulation, as a collection of attributes relevant to safety. Demonstrations of this materials system and associated encapsulation strategy involve a wireless, skin-interfaced device that captures mechanoacoustic signatures of health status. The concepts introduced here can apply immediately to many other related bioelectronic devices.

bioengineering↗

bioRxiv2023

EHD1-dependent traffic of IGF-1 receptor to the cell surface is essential for Ewing sarcoma tumorigenesis and metastasis

Overexpression of EPS15 Homology Domain containing 1 (EHD1) has been linked to tumorigenesis but whether its core function as a regulator of intracellular traffic of cell surface receptors plays a role in oncogenesis remains unknown. We establish that EHD1 is overexpressed in Ewing sarcoma (EWS), with high EHD mRNA expression specifying shorter patient survival. ShRNA and CRISPR-knockout with mouse Ehd1 rescue established a requirement of EHD1 for tumorigenesis and metastasis. RTK antibody arrays identified the IGF-1R as a target of EHD1 regulation in EWS. Mechanistically, we demonstrate a requirement of EHD1 for endocytic recycling and Golgi to plasma membrane traffic of IGF-1R to maintain its surface expression and downstream signaling. Conversely, EHD1 overexpression-dependent exaggerated oncogenic traits require IGF-1R expression and kinase activity. Our findings define the RTK traffic regulation as a proximal mechanism of EHD1 overexpression-dependent oncogenesis that impinges on IGF-1R in EWS, supporting the potential of IGF-1R and EHD1 co-targeting.

cancer biology↗

bioRxiv2022

EHD2 overexpression promotes tumorigenesis and metastasis in triple-negative breast cancer by regulating store-operated calcium entry

With nearly all cancer deaths a result of metastasis, elucidating novel pro-metastatic cellular adaptations could provide new therapeutic targets. Here, we show that overexpression of the EPS15-Homology Domain-containing 2 (EHD2) protein in a large subset of breast cancers (BCs), especially the triple-negative (TNBC) and HER2+ subtypes, correlates with shorter patient survival. The mRNAs for EHD2 and Caveolin-1/2, structural components of caveolae, show co-overexpression across breast tumors, predicting shorter survival in basal-like BC. EHD2 shRNA knockdown and CRISPR-Cas9 knockout of EHD2, together with mouse EHD2 rescue, in TNBC cell line models demonstrate a major positive role of EHD2 in promoting tumorigenesis and metastasis. Mechanistically, we link these roles of EHD2 to store-operated calcium entry (SOCE), with EHD2-dependent stabilization of plasma membrane caveolae ensuring high cell surface expression of the SOCE-linked calcium channel Orai1. The novel EHD2-SOCE oncogenic axis represents a potential therapeutic target in EHD2 and CAV1/2-overexpressing BC.

cancer biology↗

bioRxiv2021

The adenosine analogue prodrug ATV006 is orally bioavailable and has potent preclinical efficacy against SARS-CoV-2 and its variants

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which causes the COVID-19 pandemic, is rapidly evolving. Due to the limited efficacy of vaccination in prevention of SARS-CoV-2 transmission and continuous emergence of variants of concern (VOC), including the currently most prevalent Delta variant, orally bioavailable and broadly efficacious antiviral drugs are urgently needed. Previously we showed that adenosine analogue 69-0 (also known as GS-441524), possesses potent anti-SARS-CoV-2 activity. Herein, we report that esterification of the 5-hydroxyl moieties of 69-0 markedly improved the antiviral potency. The 5-hydroxyl-isobutyryl prodrug, ATV006, showed excellent oral bioavailability in rats and cynomolgus monkeys and potent antiviral efficacy against different VOCs of SARS-CoV-2 in cell culture and three mouse models. Oral administration of ATV006 significantly reduced viral loads, alleviated lung damage and rescued mice from death in the K18-hACE2 mouse model challenged with the Delta variant. Moreover, ATV006 showed broad antiviral efficacy against different mammal-infecting coronaviruses. These indicate that ATV006 represents a promising oral drug candidate against SARS-CoV-2 VOCs and other coronaviruses.

microbiology↗

bioRxiv2019

Cre-assisted Fine-mapping of Neural Circuits using Orthogonal Split Inteins

Summary:Genetic methods for targeting small numbers of neurons of a specific type are critical for mapping the brain circuits underlying behavior. Existing methods can provide exquisite targeting precision in favorable cases, but for many cases alternative techniques will be required. Here, we introduce a new step-wise combinatorial method for sequentially refining neuronal targeting: Depending on the restriction achieved at the first step, a second step can be easily implemented to further refine expression. For both steps, the new method relies on two independent intersections. The primary intersection targets neurons based on their developmental origins (i.e. lineage) and terminal identities, while the second intersection limits the number of lineages represented in the primary intersection by selecting lineages with overlapping activity of two distinct enhancers during neurogenesis. Our method relies critically on two libraries of 134 transgenic fly lines that express fragments of a split Cre recombinase under the control of distinct neuroblast enhancers. The split Cre fragments are fused to non-interacting pairs of split inteins, which ensure reconstitution of full-length and active Cre when all fragments are expressed in the same cell. Our split Cre system, together with its open source libraries, represent off-the-shelf components that should facilitate the targeting and characterization of brain circuits in Drosophila. Our methodology may also prove useful in other genetic model organisms.

neuroscience↗

bioRxiv2019

Manure substitution of chemical fertilizer affect soil microbial community diversity, structure and function in greenhouse vegetable production systems

Soil microbial community and enzyme activities together affect various ecosystem functions of soils. Fertilization, as important agricultural management practices, are known to modify soil microbial characteristics; however, inconsistent results have been reported. The aim of this research therefore was to make a comparative study of the effects of different fertilization patterns (No N inputs (No N), 100% chemical fertilizer-N (CN) inputs (4/4CN) and different substitution rates of CN by organic manure-N (MN) (3/4CN+1/4MN, 2/4CN+2/4MN and 1/4CN+3/4MN)) on soil physicochemical properties, enzyme activities and microbial attributes in a GVP of Tianjin, China. Manure substitution of chemical fertilizer, especially at higher substitution rate (2/4CN+2/4MN and 1/4CN+3/4MN), improved soil physicochemical properties (higher soil organic C (SOC) and nutrient contents; lower bulk densities), promoted microbial growth (higher total phospholipid fatty acids and microbial biomass C contents) and activity (higher soil hydrolase activities). Manure addition caused a remarkable increase of the fungi/bacteria ratio and a distinct shift in the fungal (bacterial) community to greater abundance of arbuscular mycorrhizal fungi (G+ bacteria) compared with saprotrophic fungi (G- bacteria). These changes drove shifts toward fungal-dominated soil microbial communities and then optimized microbial community structure. Also, manure application increased soil biodiversity (microbial community and enzyme function), indicated by increased Shannon-Wiener diversity. Redundancy analysis indicated that the most possible mechanism of the impacts of different fertilization patterns on soil microbial characteristics may be the mediation of SOC and nutrient (N) availability (especially SOC) in this GVP of China. In conclusion, manure substitution of chemical fertilizer, especially at higher substitution rate, was more efficient for improving soil quality and biological functions.

microbiology↗

bioRxiv2018

Quality control-based signal drift correction and interpretations of metabolomics/proteomics data using random forest regression

Large-scale mass spectrometry-based metabolomics and proteomics study requires the long-term analysis of multiple batches of biological samples, which often accompanied with significant signal drift and various inter- and intra- batch variations. The unwanted variations can lead to poor inter- and intra-day reproducibility, which is a hindrance to discover real significance. We developed a novel quality control-based random forest signal correction algorithm, being ensemble learning approach to remove inter- and intra- batches of unwanted variations at feature-level. Our evaluation based on real samples showed the developed algorithm improved the data precision and statistical accuracy for metabolomics and proteomics, which was superior to other common correction methods. We have been able to improve its performance for interpretations of large-scale metabolomics and proteomics data, and to allow the improvement of the data precision for uncovering the real biologically differences.

bioinformatics↗