Biology subjects

He, D.

Publications and source records attributed to He, D..

At least 19 recordsLinked to original sources

bioRxiv2026

An iris-like pore for protein import into peroxisomes

Peroxisomes are ubiquitous, membrane-bound organelles that house essential metabolic enzymes imported from the cytosol in a folded and sometimes oligomeric state. Mobile receptors, such as PEX5, ferry cargo through a tyrosine/glycine (YG)-rich selective phase formed by PEX13 within the membrane, but how folded proteins of different sizes cross the membrane remains unknown. Here we report structures of the channel that mediates cargo import. Twelve PEX13 molecules assemble into a pore formed by a ring of tilted amphipathic helices in alternating orientations. Hydrophobic faces contact the lipid bilayer, whereas hydrophilic faces line the pore containing the YG phase. Pairs of oppositely oriented helices can slide relative to neighboring pairs and thereby alter the helix tilt angle, enabling iris-like dilation of the pore from ~52 Angstrom in the resting state to ~70 Angstrom, sufficient to accommodate the PEX5 receptor carrying small cargo. Translocation of the largest cargo requires further widening to ~100 Angstrom, a state supported by AlphaFold modeling and disulfide crosslinking. Our findings suggest that the channel provides an adaptive conduit for folded proteins of varying sizes, a mechanism distinct from other known modes of protein translocation.

cell biology↗

bioRxiv2026

NHE1 sustains leukemia-propagating capacity and mitochondrial fitness in T-cell acute lymphoblastic leukemia

Leukemia-propagating cells (LPCs) sustain T-cell acute lymphoblastic leukemia (T-ALL) and are thought to contribute to disease progression and relapse. However, the lack of reliable LPC markers has hindered efforts to identify their vulnerabilities. We screened 786 FDA-approved compounds using a zebrafish transplantation assay that directly measures leukemia-propagating activity. Amiloride markedly reduced functional LPC frequency (p < 0.0001) without significantly delaying leukemia onset at higher transplantation doses. Because amiloride inhibits the sodium-hydrogen exchanger NHE1, we investigated its role in T-ALL. NHE1 knockdown reduced self-renewal-associated colony formation by >70% human T-ALL cells, with only modest increases in apoptosis. Transcriptomic and proteomic analyses revealed extensive molecular remodeling, including reduced abundance of proteins involved in mitochondrial respiration and translation. Amiloride treatment and NHE1 knockdown impaired mitochondrial respiration and reduced mitochondrial content, while NHE1 knockdown also decreased mitochondrial membrane potential. Metabolomic profiling revealed alterations in TCA cycle intermediates and broader cellular metabolism. In mouse xenografts, NHE1 knockdown reduced leukemia involvement in the bone marrow and spleen despite similar overall leukemia progression and survival. Together, these findings implicate NHE1 as a previously unrecognized regulator of T-ALL leukemia-propagating activity, reveal unexpected contributions of this ion exchanger to mitochondrial fitness and leukemia involvement in hematopoietic tissues, and support further investigation of NHE1 as a potential therapeutic target in T-ALL.

cancer biology↗

bioRxiv2026

Co-targeting KRAS and BCL-2 induces pyroptosis and antitumor tertiary lymphoid structures

Mutant KRAS drives lung tumorigenesis through both cell-intrinsic and cell-extrinsic mechanisms, yet mutation subtype-specific differences in metabolic regulation and immune evasion remain incompletely understood. Here we show that the KRAS G12D mutation, particularly in the KRAS/STK11 co-mutant (KL) context, is associated with poor prognosis and a suppressed immune microenvironment characterized by impaired antigen presentation. At the cell-intrinsic level, G12D exhibits weakened interaction with hexokinase 1 (HK1), reduced spare respiratory capacity, and diminished mitochondrial stress resistance compared with G12C. Based on this mitochondrial vulnerability, we screened a panel of clinically available agents that induce mitochondrial stress and identified that co-targeting KRAS and BCL-2 synergistically triggers GSDME-mediated pyroptosis predominantly in G12D tumors. This combination further induces functional tertiary lymphoid structures (TLS) in vivo. Immune cell depletion experiments further demonstrate that the antitumor efficacy is dramatically dependent on B cells. Moreover, this treatment strategy induced membrane attack complex (MAC) deposition in situ and elicited memory antitumor responses. Collectively, these findings establish that combined KRAS and BCL-2 inhibition elicits pyroptosis and TLS formation, leading to B-cell-dependent in situ and memory antitumor immunity, providing a mechanistic rationale for targeting mitochondrial-immune crosstalk in KRAS G12D-mutant lung cancer.

cancer biology↗

bioRxiv2026

An engineered IdeS variant with enhanced activity and performance for IgG degradation

IgG-degrading enzymes have emerged as innovative therapeutic agents for treating conditions driven by pathogenic antibodies. Here, we used structure-guided rational design to engineer IdeSM33, a double mutant (K167R/D226E) of the IgG-specific bacterial protease IdeS from Streptococcus pyogenes, with improved catalytic efficiency. Biolayer interferometry revealed a fourfold increase in binding affinity relative to wild-type IdeS (IdeSWT). This enhancement is likely attributable to mutations that strengthen hydrogen bonding at the enzyme-IgG Fc interface. In vitro, IdeSM33 has higher performance than IdeSWT in cleaving serum IgG. In vivo studies in rabbits demonstrated that IdeSM33 effectively depleted circulating IgG and showed better performance at a dose of 0.005 mg/kg than the IdeSWT. Although doses greater than 0.2 mg/kg demonstrated higher plasma concentrations of IdeS and a larger AUClast, they did not show a significant enhancement in the pharmacodynamics of IgG degradation. Importantly, a single dose of IdeSM33 (0.2 mg/kg) potently degraded binding and neutralizing antibodies against AAV9 within 1-2 days and restored hepatic AAV9 transduction in pre-immunized animals. Together, these findings highlight IdeSM33 as a potent and safe engineered enzyme with therapeutic potential for autoimmune disorders, transplant rejection, and overcoming pre-existing humoral immunity in gene therapy.

bioengineering↗

bioRxiv2026

Chiral methionine oxidation reagents reveal stereospecific proteome modifications

Life is predicated on chirality, a molecular asymmetry akin to the left and right versions of human hands. Here we show that privileged protein residues are predisposed for chiral regulation. We developed enantiomeric oxaziridine reagents that systematically identify pro-(S) and pro-(R) methionine oxidation sites across proteomes that can be erased by stereospecific methionine sulfoxide reductase enzymes A and B, respectively. These probes reveal that chiral regulation of methionine oxidation-reduction processes can allosterically regulate protein function, as shown in cell and murine models of oxidative stress where selective (R)-methionine sulfoxide formation on M69 of biphenyl hydrolase-like protein leads to hydrolase inhibition and amplification of proteome N-homocysteinylation modifications. This work introduces a platform for characterizing sites of asymmetric methionine oxidation and the functional consequences concomitant with an individual chiral single-atom modification.

biochemistry↗

bioRxiv2026

Magnetically activatable insect viral vectors promote anticancer immunity through spatially confined gene disruption

Precise control of genome editing activity in vivo remains a major barrier to the clinical translation of CRISPR-based therapeutics, as current approaches cannot reliably restrict editing activity to target tissues 1,2,3. Here we show that a magnetically gated baculoviral CRISPR platform enables spatial control of genome editing activity 4. By coupling magnetic activation of viral transduction at target sites with complement-mediated inactivation of circulating vectors, this system functionally confines genome editing activity to defined spatial contexts, effectively decoupling editing activity from biodistribution. We further show that spatially confined genome editing can be coupled with endogenous antiviral sensing to drive coordinated immune modulation within tumours. In a syngeneic murine tumour model, local administration combined with magnetic activation restricts genome editing to tumours without detectable editing in major organs, remodels dendritic cell and CD8{square} T cell states, suppresses tumour growth, and extends survival. Together, these findings establish a generalizable strategy for spatial control of genome editing and localized immunomodulation in cancer.

bioengineering↗

bioRxiv2025

ZAKα is a sensor of mRNA stasis at the ribosomal exit channel

Despite a growing interest in the ribotoxic stress response (RSR), it remains unknown how the upstream p38 and JNK-activating MAP3 kinase ZAK senses translational impairment. Combining Alphafold3 prediction and RNA crosslinking and immunoprecipitation (CLIP), we uncover that ZAK dynamically monitors the mRNA exit channel of elongating ribosomes for mRNA stasis. This is accomplished by ZAK via its direct interactions with the ribosomal proteins RACK1 and RPS27 as well as with the 18S rRNA helix-26. In this conformation, four mRNA-binding peptides in ZAK span across the path of ribosome-exiting mRNA. Progressive elongation effectively threads ZAK off the ribosome, while mRNA stasis stabilizes the interaction allowing for kinase activation. Prolonged binding of ZAK to slow-elongating, stalled and collided ribosomes is associated with sequestration of the inhibitory SAM domain on RACK1, allowing for transient ZAK dimerization, activation loop trans-autophosphorylation and RSR activation. We propose that compromised ribosome processivity constitutes a common ribotoxic stress signal and that ZAK is a ribosome collision-agnostic sensor of such perturbations.

molecular biology↗

bioRxiv2025

mTORC1-Dependent Regulation of the CCL24-CCR3 Axis Controls Granuloma Formation and Maintenance in Sarcoidosis

Sarcoidosis is a chronic granulomatous disease marked by persistent inflammation and immune cell aggregation, yet its molecular underpinnings remain incompletely understood, hindering the development of effective targeted therapies. Here, we report that deletion of TSC1 or TSC2 in mice using a Fsp1-Cre leads to spontaneous formation of sarcoid-like granulomas, driven by hyperactivation of the mTORC1 pathway in fibroblasts and interstitial macrophages. Through inflammatory cytokine/chemokine array, we identified CCL24, a chemokine ligand for CCR3, as a key immunoregulatory molecule downregulated in both our murine model and sarcoid cohort plasma. Mechanistically, mTORC1 suppresses CCL24 expression via aberrant STAT3 signaling in fibroblasts and promotes CCR3 expression in interstitial macrophages, uncovering a novel regulatory axis in granuloma formation and maintenance. Pharmacological inhibition using rapamycin and azithromycin markedly attenuated granuloma burden and normalized CCL24-CCR3 signaling, underscoring the therapeutic relevance of this axis. Together, our study establishes a mechanistic link between mTORC1 activation, CCL24-CCR3 dysregulation, and granuloma persistence, offering not only a new insight into molecular mechanisms in sarcoidosis but also identifying promising targets for clinical intervention.

immunology↗

bioRxiv2025

QCatch: A framework for quality control assessment and analysis of single-cell sequencing data

MotivationSingle-cell sequencing data analysis requires robust quality control (QC) to mitigate technical artifacts and ensure reliable downstream results. While tools like alevin-fry and simpleaf (and augmented execution context for the alevin-fry), offer flexibility and computational efficiency to process single-cell data, this ecosystem will further benefit from a standardized QC reporting tailored for its outputs. ResultsWe introduce QCatch, a Python-based command-line tool that generates comprehensive and interactive HTML QC reports designed specifically for single-cell quantification results. Taking the output directory of alevin-fry or simpleaf as the input, QCatch is able to perform essential processing steps, like cell calling, and generate detailed QC reports that contain informative visualizations and statistics, including unique molecular identifier (UMI) count distributions, sequencing saturation estimates, and splicing status information, for QC assurance. Built for seamless integration into downstream analysis workflows, QCatch exports the processed results in a richly-annotated H5AD format file, a widely used data format common among many downstream single-cell data analysis tools. AvailabilityThe source code and documentation of QCatch are available on GitHub at https://github.com/COMBINE-lab/QCatch. QCatch can be installed via both Bioconda and PyPI.

bioinformatics↗

bioRxiv2025

PLK1-mediated phosphorylation of PHGDH reprograms serine metabolism in advanced prostate cancer

Metabolic reprogramming is a hallmark of cancer, enabling tumor cells to meet their increased biosynthetic and energetic demands. While cells possess the capacity for de novo serine biosynthesis, most transformed cancer cells heavily depend on exogenous serine uptake to sustain their growth, yet the regulatory mechanisms driving this metabolic dependency remain poorly understood. Here, we uncover a novel mechanism by which Polo-like kinase 1 (PLK1), often overexpressed in prostate cancer, orchestrates a metabolic shift in serine and lipid metabolism through the phosphorylation of phosphoglycerate dehydrogenase (PHGDH), the rate-limiting enzyme of the serine synthesis pathway (SSP). We demonstrate that PLK1 phosphorylates PHGDH at three specific sites (S512, S513, S517), leading to a marked reduction in its protein level and enzymatic activity. This downregulation of SSP forces cancer cells to increase their reliance on exogenous serine uptake via the ASCT2 transporter, which, in turn, fuels the biosynthesis of lipids, including sphingolipids essential for tumor growth and survival. Targeting the SSP, serine uptake, or downstream lipid biosynthetic pathways may offer promising therapeutic avenues in PLK1-high advanced cancers.

cancer biology↗

bioRxiv2025

A Rapid and Highly Sensitive CRISPR Assay Utilizing Cas12a Orthologs for the Detection of Novel Duck Reovirus

The novel duck reovirus (NDRV) disease presents a significant threat to the poultry industry due to the absence of effective therapeutic measures. As a result, there is an urgent need to develop innovative rapid diagnostic methods for early virus detection. In this study, we developed a Rapid Visual CRISPR Assay to detect the NDRV S3 gene using novel Cas12a orthologs. Specifically, we compared the performance of two candidates, Gs12-16 and Gs12-18, in detecting the NDRV S3 gene to identify a highly sensitive and efficient CRISPR-based diagnostic method. Our results demonstrated that both Gs12-16 and Gs12-18 exhibited strong cis- and trans-cleavage activities for classical "TTTV" protospacer adjacent motif (PAM)-containing targets in vitro, although they required different reaction temperatures. Notably, Gs12-18 showed relatively higher activity for dsDNA targets compared to Gs12-16, indicating that Gs12-18 is more suitable for CRISPR-based nucleic acid detection applications. To leverage these properties, we integrated Gs12-18 with loop-mediated isothermal amplification (LAMP) technology to establish a LAMP-CRISPR/Gs12-18-mediated method for detecting the NDRV S3 gene. This approach enables highly sensitive and visually detectable on-site identification of the NDRV S3 gene, achieving a sensitivity of 38 copies per reaction. Our LAMP-CRISPR/Gs12-18-based method can be utilized for highly sensitive detection of NDRV nucleic acids.

synthetic biology↗

bioRxiv2025

Multimodal brain cell atlas across the adult macaque lifespan

High-throughput single-cell omics of non-human primate tissues present a remarkable opportunity to study primate brain aging. Here, we introduce a transcriptomic and chromatin accessibility landscape of 1,985,317 cells from eight brain regions of 13 cynomolgus female monkeys spanning adult lifespan including exceptionally old individuals up to 29-years old. This dataset uncovers dynamic molecular changes in critical brain functions such as synaptic communication and axon myelination, exhibiting a high degree of cell type and brain region specificity. We identify the multicellular networks of the pons and medulla as a previously unrecognized hotspot for aging. Furthermore, comparative analyses with human neurodegeneration datasets highlight both shared and distinct mechanisms contributing to aging and disease. In addition, we uncover transcription factors implicated in monkey brain aging and pinpoint aging-regulated loci linked to longevity and neurodegeneration. This spatiotemporal atlas will advance our understanding of primate brain aging and its broader implications for health and disease.

neuroscience↗

bioRxiv2025

Mapping the ISR Landscape in Cognitive Disorders via single-cell multi-omics

Persistent activation of the integrated stress response (ISR) is a major driver of cognitive decline in both neurodevelopmental and neurodegenerative disorders. Using a new mouse model (Ppp1r15bR658C mice) that mimics the persistent ISR activation and cognitive decline observed in humans, we generated the first single-cell ISR atlas of the brain. By integrating single-cell RNA-seq and single-cell ATAC-seq with proteomics, we discovered that distinct brain cell types respond differently to persistent ISR activation and elicit cell-type-specific ISR programs. Interestingly, chromatin accessibility analyses revealed that the ISR downstream factor ATF4 is a key ISR effector in GABAergic neurons, while AP-1 (JUNB) is implicated in glutamatergic neurons. More importantly, selective deletion of ATF4 in GABAergic neurons--but not in glutamatergic neurons--impacts ISR-mediated cognitive decline in Ppp1r15bR658C mice, demonstrating that different neuronal subtypes rely on unique ISR downstream effectors to regulate mnemonic processes. Furthermore, we defined a comprehensive molecular signature of persistent ISR activation, which we showed could serve as a biomarker for cognitive dysfunction across neurodevelopmental, neurodegenerative disorders and normal aging. This multi-omic framework provides a key platform for exploring and validating new scientific hypotheses, significantly advancing our understanding of ISR-related brain disorders.

neuroscience↗

bioRxiv2025

China Autism Brain Imaging Consortium: Charting Brain Growth in Chinese Children with Autism

Autism Spectrum Disorder (ASD) is a lifelong neurodevelopmental condition characterized by atypical brain growth. While advances in neuroimaging and openly sharing large-sample datasets such as the Autism Brain Imaging Data Exchange (ABIDE) have improved understanding of ASD, most studies focus on adolescents and adults, with early brain development-critical for diagnosis and intervention-remaining underexplored. Existing research predominantly involves Western samples, offering limited insight and generalizability into non-Caucasian populations. We introduce the China Autism Brain Imaging Consortium (CABIC) (https://php.bdnilab.com/resources/), a grassroots effort by researchers across the country to aggregate previously collected multi-site structural MRI datasets and phenotypic information from 1,451 autistic children and 1,119 typically developing children, covering an age range from early childhood to school age (1.0 - 12.92 years). Here, we present this resource and depict brain growth charts to push forward a more comprehensive understanding of the brain development in Chinese autism children. We constructed brain growth charts that reveal a developmental shift in autistic children, transitioning from early overgrowth to delayed maturation. Regional analyses identified distinct atypical trajectories across specific brain regions. Individual deviation scores quantified inter-subject variability, characterizing the heterogeneity of brain development in ASD. Comparative analyses between CABIC and ABIDE highlighted differences potentially attributable to ethnicity and culture, advancing our understanding of cross-population neurodevelopmental diversity. CABIC MRI datasets will be shared publicly to foster investigation of the potential neural mechanisms underlying ASD in non-Western populations and support efforts toward precision medicine for autistic individuals across diverse backgrounds.

neuroscience↗

bioRxiv2024

Leveraging Persistent Homology of Eye Movements for Neural Disorder Screening

Abnormal ocular behaviors are associated with numerous neural disorders, detectable through specific eye movement patterns. Eye tracking--a non-invasive, accessible method--has thus been investigated as a tool for the automated diagnosis of these disorders. However, traditional eye movement feature extraction methods have limitations and are not universally applicable across diverse tasks. In this study, we present a novel feature extraction approach using Persistent Homology, a topological data analysis technique, to capture spatial and temporal topological features from eye movement data. Topological features retain multiple theoretical properties, making them robust for identifying abnormal eye movements and broadly applicable across tasks. By using only spatio-temporal topological features, our approach demonstrated promising performance in screening dyslexia and ADHD with a simple shallow perceptron classifier containing one or two hidden layers. These results support the informative validity of topological features as well as the efficacy of our proposed methods for extracting them.

bioinformatics↗

bioRxiv2024

Airway applied IVT mRNA vaccine needs specific sequence design and high standard purification that removes devastating dsRNA contaminant

The development of next-generation mucosal mRNA vaccines is promising but extremely challenging. Major efforts have been focused on optimizing delivery systems, whereas it is still unknown whether the intrinsic quality of IVT mRNA significantly impacts the potency of airway inoculated mRNA vaccines. Here, we systematically demonstrate the mucosal mRNA vaccine requires a higher standard of purification and tailor-designed sequence to fulfil its potency compared to the parenteral route inoculated counterpart. We found double strand RNA (dsRNA) contaminants are prone to trigger innate immunoreaction in the airway that activates the mRNA degradation mechanism, thereby diminishing the mRNA expression and subsequent antigen-specific immune responses. To address these challenges, we developed a strategy that combines optimized untranslated regions (UTRs) screened from endogenous genes of pulmonary cells with affinity chromatography-based purification which removes almost all the dsRNA contaminants. The optimized mRNA administered via the airway route not only demonstrates superior protein expression (30-fold increase) and reduces inflammation in the lung, but also promotes robust immunity comprising significantly elevated systemic, cellular, and mucosal immune responses, which is in stark contrast to intramuscular injected counterpart that displays less pronounced benefits. Our findings offer new insight into the development of mucosal mRNA therapeutics from an overlooked but crucial perspective of optimizing mRNA components.

synthetic biology↗

bioRxiv2024

Evolution of the Spatial transcriptomic landscape during the progression of high-grade pancreatic intraductal papillary mucinous neoplasms to invasive cancer

Intraductal papillary mucinous neoplasms (IPMN) is one of the known precancerous lesions. Patients prognosis is aggravated as IPMN transforms into invasive Pancreatic Ductal Adenocarcinoma (PDAC). The molecular mechanisms underlying this progression lack effective experimental models and urgently need to be elaborated. We performed spatial transcriptomics (ST) on fresh tissue samples from the same patient including normal pancreas, high-grade IPMN, and invasive PDAC, and described the step-by-step development of transcriptional landscape including clone evolution and adjacent TME feature variation. Our findings identified the master transcript factors and critical signaling pathways promoting IPMN progression to invasive PDAC. Additionally, both IPMN and PDAC harbored the ELF3, MYC, and KLF4 amplification. The Spatial CNV profile demonstrated significant heterogeneity among PDAC in their spatial distribution compared to IPMN, with seven distinct subclones showing diverse functions, such as hypoxia, oxidative phosphorylation, and epithelial-mesenchymal Transition. We observed a marked shift in the immune landscape, with the depletion of CD4+ T-cells and dendritic cells and an increase in immune-suppressive M2 macrophages in invasive PDAC, indicating a transition to an immune-evasive microenvironment. Additionally, cancer-associated fibroblasts (CAFs), particularly myofibroblastic CAFs, were enriched adjacent to invasive PDAC, suggesting their active role in tumor progression. By leveraging spatial transcriptomic analysis, our study provides comprehensive insights into the intricate molecular landscape that underlies the progression of IPMNs to invasive PDAC. These findings not only enhance our understanding of this complex process but also offer valuable knowledge for early diagnosis and intervention. HighlightsO_LISpatial CNV analysis reveals clonal evolution and distinct subclones in PDAC. C_LIO_LIKey drivers like ELF3, MYC, and KLF4 are amplified in both IPMN and invasive PDAC. C_LIO_LIImmune landscape shifts from pro-inflammatory in IPMN to immune-evasive in PDAC. C_LIO_LIEnrichment of myofibroblastic CAFs suggests their role in tumor progression C_LI

cancer biology↗

bioRxiv2024

Trust or doubt? Neural resonance based on facial expressions in a deception game reflected by frontal EEG activities.

Current understanding of the neural mechanisms underlying facial trustworthiness perception is primarily based on studies using static facial stimuli. However, real-life social interactions are dynamic and complex, and the neural processes involved in such naturalistic contexts remain largely unexplored. In this study, we analyzed EEG data collected during a deception game involving two participants: a player and an observer engaged in real-time interaction. The player either followed instructions or made spontaneous decisions to lie or tell the truth, while the observer judged whether to trust the player based solely on their facial expressions. We examined observers behavioral data, event-related potentials, and interhemispheric EEG asymmetries in both signal magnitude and instantaneous phase. The results revealed a significant effect of trustworthiness on hemispheric asymmetry in the observers centroparietal phase activities between 1500-3000 ms post-stimulus. Subsequent frequency-based analysis revealed that this asymmetry in phase progression was primarily driven by lateralized signal frequency. These findings suggest that the perception of facial trustworthiness involves dynamic hemispheric lateralization. Whereas previous studies using static face stimuli indicate rapid trustworthiness perception, our findings suggest that trustworthiness perception can be modulated by persistent and dynamical affective processing in real-time social contexts.

neuroscience↗