Biology subjects

Hou, X.

Publications and source records attributed to Hou, X..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

The inactivation of DHHC7 in mouse liver promotes diet-induced obesity through a hepatic Prg4-GPR146 axis

The liver secretes hepatokines that coordinate whole-body metabolism. Posttranslational lipidation of signaling proteins by DHHC palmitoyltransferases controls membrane targeting and signaling, yet the role of hepatic palmitoylation in systemic metabolic regulation is largely unexplored. Using an inducible, liver-specific DHHC7 knockout (D7LKO) mouse, we report that loss of DHHC7 in hepatocytes potentiates adenylyl cyclase-PKA-CREB signaling through reducing palmitoylation of inhibitory G protein subunit (Gi), leading to transcriptional elevation and secretion of proteoglycan 4 (Prg4). Elevated circulating Prg4 acts on adipocytes by binding GPR146 via Prg4s N-terminal SMB domain, suppressing adipocyte PKA substrate phosphorylation and hormone-sensitive lipase (HSL) Ser563 phosphorylation, thereby impairing lipolysis. Under high-fat diet (HFD) feeding, D7LKO mice and mice with adenoviral hepatic Prg4 overexpression develop pronounced obesity characterized by increasing brown, subcutaneous, and visceral fat mass and adipocyte hypertrophy; strikingly, these animals show little impairment in glucose tolerance or circulating triglycerides but display elevated plasma cholesterol. Conditioned medium containing Prg4 recapitulates suppression of adipocyte HSL phosphorylation in vitro, and SMB-deleted Prg4 fails to bind GPR146 or inhibit HSL phosphorylation. Our findings define a liver palmitoylation- hepatokine axis that controls adipose lipolysis and predisposes to diet-induced fat accumulation, establishing Prg4-GPR146 as a mechanistic link between hepatic signaling and adipose energy mobilization.

physiology↗

bioRxiv2025

Diverse infections transcriptionally reprogram the intestinal epithelium and epithelial-immune cell interactions

The distal small intestine plays vital roles in host physiology by regulating nutrient and fluid homeostasis. Despite being impacted in Crohns disease and a major target for a range of infections, we know relatively little about the complexity of cellular responses and cell-cell communication in the ileum during infection. Single cell and spatial transcriptomics have emerged as powerful technologies to study tissue heterogeneity in the gut, but these tools have focused on the large intestine, in part due to the accessibility of this tissue for biopsies and its importance in cancer. Here we present GutPath, an atlas of over 500,000 single cells with RNA and protein expression profiles for 91 cell states in the ileum across diverse infectious archetypes. We show that GutPath accurately captures established immune responses to infection while revealing pathogen-specific responses in enterocytes. To highlight the discovery potential of this atlas, we identify a novel enterocyte cell state present during Yersinia pseudotuberculosis infection that is spatially linked to bacterial load and tissue pathology. GutPath establishes a much-needed resource for the immunology community that will accelerate the study of the transcriptional diversity of cellular landscapes in the small intestine.

immunology↗

bioRxiv2025

Revisiting Humidity Ramp Protocols for Assessing Human Heat Tolerance

BackgroundHumidity ramp protocols are widely used to estimate human heat tolerance limits, yet reported critical environmental limits (CELs) vary markedly across studies. Whether this variability reflects true physiological differences or systematic methodological artifacts related to ramp design remains unresolved. MethodsWe combined first-order thermal modeling with controlled physiological trials to examine how ramp temporal structure (step dwell time) influences apparent rectal temperature (Tcr) inflection points. Twenty-six healthy young adults completed randomized trials at 42 {degrees}C under two protocols: an aggressive-ramp (30-min equilibration followed by humidity increases every 5 min) and a slow-ramp (4-h equilibration followed by hourly humidity increments). CELs derived from ramp protocols were further evaluated using prolonged fixed-condition exposures in independent cohorts (n=14 per sex). ResultsShort-step dwell times ({Delta}t/{tau} <<1) prevented rectal temperature from approaching its step-specific equilibrium, resulting in kinetically constrained, non-equilibrium dynamics and earlier Tcr inflection points. Consequently, aggressive-ramp protocols yielded substantially lower CELs than slow-ramp protocols in both sexes ({approx}3.5 {degrees}C difference). CELs derived from the slow ramp closely matched those obtained from prolonged fixed-condition exposures, whereas aggressive ramps misclassified physiologically compensable conditions as uncompensable. ConclusionRapid humidity increments systematically underestimate heat tolerance because environmental forcing outpaces physiological response kinetics. Accurate CEL determination requires either prolonged fixed-condition exposures (benchmark approach) or sufficiently slow ramps that allow near-equilibrium responses ({Delta}t/{tau} {gtrsim}0.3-0.5).

physiology↗

bioRxiv2025

Hemin Inhibits the Activation of STING in Macrophages by Inducing HO-1, Promoting Endometriosis Development

IntroductionEndometriosis (EMS) is an estrogen-dependent inflammatory disorder characterized by immune dysregulation. This condition profoundly affects the quality of life and reproductive health of nearly 200 million women of reproductive age worldwide and poses significant clinical challenges due to lack of diagnosis tools and effective treatment. Peritoneal macrophages play a central role in promoting the initiation and progression of EMS. Bioinformatics studies have indicated that the STimulator of INterferon Gene (STING) was downregulated in the macrophages in EMS, and this influenced their polarization and functional. However, the specific contribution of STING pathway alterations to EMS pathogenesis remains unclear. MethodsWe integrated scRNA-seq data from EMS patients and healthy controls-including lesions, eutopic endometrium, non-lesional tissue, and peritoneal fluid from EMS patients and healthy controls(n = 19,291 total samples)-to analyze macrophage STING expression and function. Mouse EMS model was generated by injecting uterus fragments into WT or STING-/- mice. Peritoneal fluid was collected and macrophage proportions and subtypes were assessed via flow cytometry. Macrophages were depleted in STING-/- mice prior to EMS induction to evaluate their role in disease progression. In vitro, hemin was used to treat macrophages to investigate how heme oxygenase-1 (HO-1) modulates the STING pathway, assessed through immunoblotting, co-immunoprecipitation, ELISA, and multiplex immunofluorescence. ResultsBioinformatic analysis revealed that macrophages within the EMS lesions are primarily derived from peritoneal macrophages and exhibit decreased STING expression, which correlated negatively with HO-1. STING-/- mice developed more numerous and larger EMS lesions, accompanied by a decreased proportion of large peritoneal macrophages and an increase in small peritoneal macrophages. A marked elevation in M2-type macrophages within the lesions was detected in STING-/- mice. In vitro, hemin-induced HO-1 suppressed STING pathway activation in macrophages. Mechanistically, HO-1 inhibited the translocation of STING from the endoplasmic reticulum to the Golgi, thereby suppressing STING signaling and facilitating EMS. ConclusionMacrophages are essential for lesion formation in STING-/- mice. In vitro, hemin promotes EMS progression via HO-1 - mediated suppression of the STING pathway. Our findings identify the heme-HO-1-STING axis as a key immunomodulatory pathway in EMS and suggest its potential as a therapeutic target. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=157 SRC="FIGDIR/small/683839v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@6901beorg.highwire.dtl.DTLVardef@1f18d44org.highwire.dtl.DTLVardef@1716f6forg.highwire.dtl.DTLVardef@4ae22d_HPS_FORMAT_FIGEXP M_FIG Graphical abstract (Created in BioRender.com) Retrograde menstruation leads to the accumulation of heme in the peritoneal cavity, which upregulates HO-1 expression in peritoneal macrophages. HO-1 inhibits the translocation of STING from the endoplasmic reticulum to the Golgi apparatus in macrophages, thereby suppressing the STING pathway and promoting the development and progression of EMS. The progression of EMS, in turn, reinforces this mechanism, creating a self-sustaining vicious cycle. C_FIG

immunology↗

bioRxiv2025

Prolactin links psychological stress to psoriasis via a fibroblast-chemokine pathway

Psoriasis is a chronic inflammatory skin disease that forms a vicious cycle with psychological stress. Whether and how the hypothalamic-pituitary (HP) axis-mediated neuroendocrine system regulates psoriasis remains obscure. Here, we report elevated levels of the pituitary hormone prolactin (PRL) in both psoriasis patients and imiquimod (IMQ)-induced psoriasis mice. Mechanistically, PRL acts on dermal PRLR-expressing fibroblasts to promote the production of the chemokines CCL2 and CCL7, which then recruit monocytes/macrophages into psoriatic lesional skin, thereby activating local IL-17A-producing T cells. Accordingly, pharmacological targeting of PRL signaling inhibits the recruitment of monocytes/macrophages, decreases the frequency of IL-17A-producing T cells, and alleviates IMQ-induced psoriasis in mice. In summary, our results delineate a mechanism by which the neuroendocrine hormone PRL aggravates psoriasis and highlight a potential therapeutic strategy of inhibiting PRL-PRLR signaling, particularly in psoriasis patients experiencing psychological stress.

immunology↗

bioRxiv2025

Comprehensive analysis of metabolic reprogramming-related gene signaturesmetabolic reprogramming related gene signature for predicting ovarian cancer prognosis, immune landscape, and potential treatment options

Ovarian cancer (OV) is the most lethal gynecologic malignancy. Metabolic reprogramming is a distinctive feature of cancer and is associated with tumorigenesis and progression. It could be a potential therapeutic target for cancer treatments and a biomarker for assessing cancer prognosis. In this study, we identified metabolic reprogramming-related differentially expressed genes (MRRDEGs) in OV through differential gene expression analysis and conducted a comprehensive characterization of these MRRDEGs. Based on the MRRDEGs, we constructed an effective prognostic risk model including five model genes for OV. The risk score was a valid independent prognostic factor that could more accurately predict the survival of OV patients. It could classify OV patients into distinct risk groups with significant differences in survival. We observed significant differences between risk groups in biological pathway activity, immune cell infiltration patterns, and immunotherapy responses. Specifically, the low-risk group demonstrated superior immunotherapy response compared to the high-risk group. These findings significantly advance our understanding of the relationship between metabolic reprogramming and OV pathogenesis, progression, prognosis, and immunotherapy response, laying a foundation for developing novel biomarkers and therapeutic targets in the future and providing an important reference for the formulation of precision medicine strategies.

bioinformatics↗

bioRxiv2025

Human ribosome interactions reframe neomycin toxicity

Aminoglycosides such as neomycin are clinically limited by toxicity, commonly attributed to the inhibition of mitoribosomes. Here, we re-evaluate this mechanism by integrating Cryo-EM and functional assays to assess neomycins binding potential in vitro with its cellular engagement and functional consequences. Cryo-EM revealed extensive multi-site binding of neomycin on both human mitochondrial and cytosolic ribosomes in vitro, including conserved regions of the decoding center. In contrast, ribosomes isolated from neomycin-treated cells show markedly remodeled occupancy patterns, with no detectable neomycin bound to the mitoribosomes and reduced occupancy at a subset of cytosolic ribosome sites. However, neomycin remained functionally active in cells, inducing widespread stop-codon readthrough while having minimal effects on global mitochondrial and cytosolic protein synthesis. These findings reveal a disconnect between structural binding potential and cellular target engagement and identify disruption of translational fidelity, rather than global translational inhibition, as a major cellular consequence of neomycin exposure.

biochemistry↗

bioRxiv2025

Long-term independent use of an intracortical brain-computer interface for speech and cursor control

Brain-computer interfaces (BCIs) can provide naturalistic communication and digital access to people with severe paralysis by decoding neural activity associated with attempted speech and movement. Recent work has demonstrated highly accurate intracortical BCIs for speech and cursor control, but two critical capabilities needed for practical viability were unmet: independent at-home operation without researcher assistance, and reliable long-term performance supporting accurate speech and cursor decoding. Here, we demonstrate the independent and near-daily use of a multimodal BCI with novel brain-to-text speech and computer cursor decoders by a man with paralysis and severe dysarthria due to amyotrophic lateral sclerosis (ALS). Over nearly two years, the participant used the BCI for more than 3,800 cumulative hours to maintain rich interpersonal communication with his family and friends, independently control his personal computer, and sustain full-time employment - despite being paralyzed. He communicated 183,060 sentences - totaling 1,960,163 words - at an average rate of 56.1 words per minute. He labeled 92.3% of sentences as being decoded at least mostly correctly. In formal quantifications of performance where he was asked to say words presented on a screen, attempted speech was consistently decoded with over 99% word accuracy (125,000 word vocabulary). The participant also used the speech BCI as keyboard input and the cursor BCI as mouse input to control his personal computer, enabling him to send text messages, emails, and to browse the internet. These results demonstrate that intracortical BCIs have the potential to support independent use in the home, marking a critical step toward practical assistive technology for people with severe motor impairment.

neuroscience↗

bioRxiv2025

The CATION CALCIUM EXCHANGER 4 (CCX4) regulates LRX1-related root hair development through Ca2+ homeostasis

Calcium, as a cellular second messenger, is essential for plant growth. A tip-focused Ca2+ gradient in polarized cells is considered to drive cell expansion. The cell wall polysaccharide pectin is a major Ca2+ binding structure and Ca2+ homeostasis is influenced by the cell wall architecture. LRR-extensin (LRX) proteins are extracellular regulators of cell wall development that are anchored in the cell wall by their extensin domain. The extensin-less LRX1{Delta}E14 variant of the root hair-expressed LRX1 of Arabidopsis induces a dominant-negative effect resulting in aberrant root hairs. In an effort to identify the underlying mechanism of the root hair defect caused by LRX1{Delta}E14, we isolated a suppressor of dominant-negative effect mutant, sune42. It codes for the CATION CALCIUM EXCHANGER 4 (CCX4) that localizes to the Golgi apparatus and was shown to have Ca2+ transport activity. A detailed investigation of the Ca2+ dynamics revealed that LRX1{Delta}E14 coincides with a defect in tip-focused cytoplasmic Ca2+ oscillation, and this effect is alleviated by the sune42 mutation. Additionally, reducing Ca2+ availability influences the LRX1{Delta}E14-induced root hair defect. We conclude that sune42 suppresses the root hair defect in LRX1{Delta}E14 through modulating cytoplasmic Ca2+ dynamics, pointing at the importance of the Golgi apparatus for cellular Ca2+ homeostasis.

plant biology↗

bioRxiv2025

Error encoding in human speech motor cortex

Humans monitor their actions, including detecting errors during speech production. This self-monitoring capability also enables speech neuroprosthesis users to recognize mistakes in decoded output upon receiving visual or auditory feedback. However, it remains unknown whether neural activity related to error detection is present in the speech motor cortex. In this study, we demonstrate the existence of neural error signals in speech motor cortex firing rates during intracortical brain-to-text speech neuroprosthesis use. This activity could be decoded to enable the neuroprosthesis to identify its own errors with up to 86% accuracy. Additionally, we observed distinct neural patterns associated with specific types of mistakes, such as phonemic or semantic differences between the persons intended and displayed words. These findings reveal how feedback errors are represented within the speech motor cortex, and suggest strategies for leveraging these additional cognitive signals to improve neuroprostheses.

neuroscience↗

bioRxiv2025

Encoding of speech modes and loudness in ventral precentral gyrus

The ability to vary the mode and loudness of speech is an important part of the expressive range of human vocal communication. However, the encoding of these behaviors in the ventral precentral gyrus (vPCG) has not been studied at the resolution of neuronal firing rates. We investigated this in two participants who had intracortical microelectrode arrays implanted in their vPCG as part of a speech neuroprosthesis clinical trial. Neuronal firing rates modulated strongly in vPCG as a function of attempted mimed, whispered, normal or loud speech. At the neural ensemble level, mode/loudness and phonemic content were encoded in distinct neural subspaces. Attempted mode/loudness could be decoded from vPCG with an accuracy of 94% and 89% for two participants respectively, and corresponding neural preparatory activity could be detected hundreds of milliseconds before speech onset. We then developed a closed-loop loudness decoder that achieved 94% online accuracy in modulating a brain-to-text speech neuroprosthesis output based on attempted loudness. These findings demonstrate the feasibility of decoding mode and loudness from vPCG, paving the way for speech neuroprostheses capable of synthesizing more expressive speech.

neuroscience↗

bioRxiv2025

Chimpanzee and human ApoE isoforms differ in the stimulation of neurite differentiation consistent with structural predictions with relevance to brain development and aging

BackgroundAmong anthropoids, humans uniquely possess ApoE isoforms that modulate Alzheimers disease (AD) risk and brain aging. While chimpanzee and human ApoE4 share R112 and R158, chimps do not exhibit advanced AD. A key difference is T61 in chimps versus R61 in humans, structurally resembling ApoE3. ObjectiveWe examined how astrocyte-derived ApoE isoforms impact neuronal morphology and used structural modeling to explore functional divergence. MethodsNeonatal rat hippocampal neurons were cultured with astrocyte-conditioned media (ACM) from mice expressing human ApoE3, ApoE4, or chimpanzee ApoE. Neuronal outgrowth was quantified after 72 hours. ResultsChimpanzee ACM increased neurite number by 30% over human ApoE isoforms. However, chimpanzee ACM resembled ApoE4 functionally, producing 40% shorter neurites and spines. Structural modeling supported greater similarity to ApoE4. ConclusionsChimpanzee ApoE is structurally and functionally more similar to ApoE4 than ApoE3, revealing evolutionary distinctions relevant to AD risk and neurodevelopment.

neuroscience↗

bioRxiv2025

Inhibiting glucocorticoid receptors enhances adult spinal cord neural stem cell activity and improves outcomes in spinal cord injury

The internal microenvironment plays a critical role in the proliferation and differentiation of endogenous neural stem/progenitor cells (NSPCs). A big change in the spinal cord injury (SCI) microenvironment is the elevated level of glucocorticoids. In this study, we examined the impact of glucocorticoids on endogenous NSPCs in the adult mouse spinal cord. Our findings reveal that adult spinal cord NSPCs express glucocorticoid receptors, but not mineralocorticoid receptors. Glucocorticoids were found to significantly inhibit the proliferation and neurosphere formation of NSPCs via activation of glucocorticoid receptors, and they also impaired their differentiation. Importantly, the glucocorticoid receptor inhibitor CORT125281 was shown to enhance motor function in a traumatic SCI model in mice. Treatment with CORT125281 increased the number of NSPCs at the injury site in vivo. Flow cytometry and RNA sequencing analyses indicated that glucocorticoids induce NSPC arrest in the G1/G0 phase through the p53 signaling pathway. Glucocorticoids increased the expression of cell-cycle regulatory genes p15, p16, p18, and p27 in adult spinal cord NSPCs. In summary, our data suggest that glucocorticoids elevation following SCI suppresses the proliferation of endogenous NSPCs via glucocorticoid receptor activation. Targeting glucocorticoid receptors with specific inhibitors may represent a novel therapeutic strategy to promote recovery after spinal cord injury.

neuroscience↗

bioRxiv2025

Single-Cell Epigenomics Uncovers Heterochromatin Instability and Transcription Factor Dysfunction during Mouse Brain Aging

The mechanisms regulating transcriptional changes in brain aging remain poorly understood. Here, we use single-cell epigenomics to profile chromatin accessibility and gene expression across eight brain regions in the mouse brain at 2, 9, and 18 months of age. In addition to a significant decline in progenitor cell populations involved in neurogenesis and myelination, we observed widespread and concordant changes of transcription and chromatin accessibility during aging in glial and neuronal cell types. These alterations are accompanied by dysregulation of master transcription factors and a shift toward stress-responsive programs driven by AP-1, indicating a progressive loss of cell identity with aging. We also identify region- and cell-type-specific heterochromatin decay, characterized by increased accessibility at H3K9me3-marked domains, activation of transposable elements, and upregulation of long non-coding RNAs, particularly in glutamatergic neurons. Together, these results reveal age-related disruption of heterochromatin maintenance and transcriptional programs, identify vulnerable brain regions and cell types, and pinpoint key molecular pathways altered in brain aging. HighlightsO_LISingle-cell multimodal profiling across eight brain regions reveals coordinated chromatin and transcriptional shifts during aging C_LIO_LIAge-related depletion of progenitor cells coincides with dysregulation of key developmental transcription factors C_LIO_LICell identity maintenance is compromised with the decline of master transcription factors C_LIO_LIHeterochromatin destabilization accompanied by activation of AP-1, transposable elements, pseudogene families, and long non-coding RNAs C_LI

genomics↗

bioRxiv2025

Single cell resolution of an epigenetic signature of persister tumor cell

Cancer can recur when a subset of tumor cells, denoted here as persister cells, are able to survive therapy and re-enter the cell cycle. The precise mechanisms that confer the persister state and whether it is characteristic of a subgroup of cells or arises from multiple cellular lineages remain poorly understood. We hypothesize that an epigenetic signature underlies the drug-tolerant persister state, characterized by transcriptional and chromatin accessibility changes that promote survival of residual cancer following chemotherapy. To identify clinically relevant features of persister cells in untreated tumors and residual disease, we performed single-cell multiomic profiling (snRNA+snATAC) on a cohort of non-malignant fallopian tube, treatment-naive, and neoadjuvant chemotherapy (NACT)-treated high-grade serous ovarian cancer (HGSOC) samples. We identified differences in gene expression and open chromatin between naive and residual patient tumors following chemotherapy. Although only a small proportion of the differentially expressed genes enriched in residual HGSOC overlapped with established gene sets for chemo-response and patient prognosis, the epigenomic analysis revealed activity of several DNA-binding factors that are both enriched upon chemotherapy and also high in resistant tumors prior to treatment. From this analysis, we identified an epigenetic signature that precedes expression and defines the persister state. This epigenetic signature also correlated with chemotherapy sensitivity and resistance using patient-derived xenograft models of HGSOC. Gene regulatory networks driven by the persister signature are involved in the activation of oncogenic pathways, including changes to the cell cycle promoting quiescence and stress response. Further study of the persister cells identified by this epigenetic signature may increase understanding of the mechanisms underlying persister cell survival and reveal new vulnerabilities that could be exploited to delay or prevent cancer recurrence.

genomics↗

bioRxiv2025

Proteomic Analysis of PTEN-Deficient Cells Reveals Src-Mediated Upregulation of EphA2 and Therapeutic Potential of Dual Inhibition

Loss of the tumor suppressor PTEN is frequently observed in various cancers and promotes tumorigenesis by activating the PI3K-AKT pathway. However, the effectiveness of therapies targeting this pathway is limited by complex signaling crosstalk and compensatory mechanisms. Here, we employed quantitative proteomic and phosphoproteomic analyses using MCF10A PTEN knockout models to comprehensively map the signaling alterations induced by PTEN loss. Our analyses revealed that PTEN deficiency not only activates canonical PI3K-AKT signaling but also induces widespread changes in cytoskeleton organization, cell cycle regulation, and central carbon metabolism. PTEN loss also substantially elevates the activity of a variety of tyrosine kinases, including Src kinase and EphA2, a receptor tyrosine kinase (RTK) implicated in cancer progression. Mechanistic studies demonstrated that Src activation, rather than the canonical AKT signaling pathway, drives the upregulation of the receptor tyrosine kinase EphA2. The activation of the noncanonical tyrosine kinase signaling renders AKT inhibition alone insufficient in PTEN-deficient cancers. Importantly, combined treatment with the FDA-approved AKT inhibitor capivasertib and the Src inhibitor dasatinib synergistically induced apoptosis and suppressed the tumor cell growth in various PTEN-deficient cell lines as well as in three-dimensional cultures of endometrial cancer patient-derived xenograft models. Our study reveals that PTEN loss drives oncogenic signaling via dual activation of PI3K-AKT and tyrosine kinase pathways. Specifically, Src-mediated upregulation of EphA2 in PTEN-deficient cells highlights a therapeutic vulnerability that can be exploited by combined AKT and Src inhibition. This approach addresses the resistance associated with AKT inhibition alone and enhances therapeutic efficacy in PTEN-deficient cancers, supporting its potential application in targeted combination therapies.

cancer biology↗

bioRxiv2025

CHIEF: An Attention-based Ensemble Learning Framework for Functional Protein Design

Protein de novo design is a longstanding challenge in biological field due to the multifaceted physicochemical properties and complexities of proteins. Several deep learning models have emerged for protein de novo design. However, each model exhibits distinct strengths and limitations because of the differences in training strategies or neural network architectures. Therefore, improving the effectiveness of protein design, particularly for functional protein, requires further improvement. To tackle this challenge, we developed CHIEF (Chimera Ensemble Inverse Folding), an attention-based ensemble framework that integrates five pretrained base models (ProteinMPNN-vanilla, ProteinMPNN-soluble, ESM-IF, Frame2seq and PiFold) to leverage their complementary strengths and mitigate limitations. Compared with the base models, CHIEF significantly improved the sequence recovery rate by 16.6-28.0%, while reducing the prediction perplexity by 22.7-34.6%. CHIEF also exhibited superior protein-designing capacity in variable sequence- and structure-based metrics and in large and complex proteins. CHIEF dynamically captured the semantic information from base models in a context-dependent manner and was minimally affected by the ablation of each base model. More importantly, CHIEF demonstrates real-world applicability to design functional malate dehydrogenase (MDH), achieving a 100% success rate. In summary, our study develops an ensemble deep learning model that improves the efficacy of protein sequence design, and will be a valuable platform for protein engineering and drug development.

bioengineering↗

bioRxiv2025

Infectome Analysis of Small Mammals in Southern China Reveals Ecological Associations and Emerging Threats from Diverse Pathogens

Small mammals harbor a diverse array of zoonotic pathogens. To date, however, metagenomic surveys of these species have primarily focused on viral diversity, with limited attention paid to bacteria and eukaryotic pathogens. Additionally, the ecological determinants of pathogen diversity within these mammals have not been systematically examined. Herein, we employed a metatranscriptomics approach to survey the pathogen infectome of 2,408 individual samples, representing lung, liver, and gut tissues from 858 animals collected throughout Guangdong province, China, with a study design that accounted for host species, tissue, season, and geographic location. We identified 76 pathogen species, including 29 RNA viruses, 12 DNA viruses, 5 bacteria, and 30 eukaryotic pathogens, 33 of which were newly discovered. Tissue distribution analysis revealed distinct organotropisms, suggesting varied transmission routes, while host distribution analysis showed that each animal carried an average of one pathogen, with 10 pathogens widely distributed among mammalian orders. Our characterization of the geographic and seasonal patterns revealed that pathogen richness was primarily influenced by region, host species, and season, while pathogen composition was largely shaped by host genetic distance. Collectively, these data provide the first comprehensive insight into the dynamics of the pathogen infectome in these key mammalian disease reservoirs, highlighting the major factors driving pathogen diversity and transmission.

microbiology↗