Biology subjects

Cheng, C.

Publications and source records attributed to Cheng, C..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Astrocyte cell-surface proteomics identified CD44 as an OPN/SPP1 receptor regulating lipid metabolism and glial crosstalk in Alzheimer s disease

Abstract/SummaryThe development of {beta}-amyloid (A{beta}) pathology in Alzheimers disease (AD) is accompanied by profound changes in astrocytes and microglia. How these responses are orchestrated by cell surface proteins, key mediators of cell-cell communication, remain unclear. Using in situ astrocyte cell-surface proteome profiling in 5xFAD mice, we identified a set of dysregulated surface proteins induced by A{beta} pathology, including CD44. CD44 was selectively upregulated in plaque-adjacent astrocytes and interacted with osteopontin (OPN), encoded by the disease-associated microglia gene Spp1, to promote lipid accumulation, and this effect is {gamma}-secretase dependent. Astrocytic CD44 in turn regulated Spp1 expression and microglial activity. Conditional deletion of Cd44 in adult astrocytes of 5xFAD mice attenuated glial reactivity, reduced A{beta} pathology, and improved cognition. These findings define a plaque-proximal OPN-CD44 axis that controls astrocyte lipid metabolism and glial activity, positioning CD44 as a surface-accessible therapeutic target in AD.

neuroscience↗

bioRxiv2025

Cross-Species Cortical Geometry Reveals Conserved Gradients Across Primates and Human-Specific Expansion

The primate cerebral cortex, characterized by its complex structural geometry, underlies advanced cognitive functions and represents a defining feature distinguishing primates from other mammals. However, cross-species patterns of cortical geometry and the links between human cortical geometry and transcriptional architecture remain poorly understood. We developed a geometry-based cross-species cortical alignment framework to systematically investigate the similarities and differences in structural connectivity and cortical expansion characteristics among macaques, chimpanzees, and humans, and additionally explored the transcriptional underpinnings of human cortical geometry. Our analysis revealed conserved spatial patterns of cortical geometric features across species, providing the foundation for constructing a cross-species structural common space to support the alignment framework. We found that primary sensory, somatomotor, and face-selective regions exhibited high structural connectivity similarity across species, whereas prefrontal and parietal association cortices displayed significant divergence. We also identified disproportionate cortical expansion in the default mode network, with a consistent expansion trend across different evolutionary lineages in primates. Furthermore, neuroimage-transcription analysis indicated that cortical geometric features were correlated with transcriptional profiles enriched in neurodevelopmental and connectivity-related pathways. These results highlight a conserved yet hierarchically differentiated organization of the cerebral cortex in primates, providing new insights into the biological basis of human brain evolution.

neuroscience↗

bioRxiv2025

Differential Tissue Coupled Powering for Battery-Free Injectable Electroceuticals

Electroceutical implants that deliver targeted neural stimulation have shown therapeutic potential for a wide range of neurological and peripheral disorders, yet wirelessly powering ultra-miniaturized, fully injectable systems remains a critical challenge. Here we report a Thread-like Injectable Neural TechnologY (TINY), powered via a differential tissue-coupled powering (DTCP) scheme. DTCP employs mid-frequency differential potentials applied across external electrodes on a compact, wearable transmitter to deliver energy through tissue to an ultra-miniaturized, thread-like implant that integrates a custom ASIC and PEDOT-coated receiver and stimulation electrodes. Benchtop experiments in agar phantoms characterize the power-transfer efficiency (PTE) and reveal that PTE increases with implant length while maintaining strong tolerance to angular misalignment. In vivo tests in rat hindlimbs further demonstrate wireless activation of the sciatic nerve through tissue at centimeter-scale depths, confirming effective transcutaneous energy delivery for neurostimulation. A 20-day implantation study shows stable positioning of the device with minimal tissue response, indicating excellent chronic compatibility. These findings address long-standing challenges in wirelessly powering injectable electroceuticals and establish DTCP as a scalable and alignment-robust powering strategy for future minimally invasive neuromodulation therapies.

bioengineering↗

bioRxiv2025

Vaccine Elicitation of HIV-1 Neutralizing Antibodies Against Both V2 Apex and Fusion Peptide in Rhesus Macaques

Broadly neutralizing antibodies targeting multiple sites of HIV-1 Env vulnerability can be induced by infection, but simultaneous elicitation of neutralizing antibodies (NAbs) against multiple epitopes has not yet been achieved by vaccination. In this study, we designed a dual-epitope vaccine targeting both fusion peptide (FP) and V2 apex and evaluated its capacity to induce NAbs against both epitopes in rhesus macaques. This vaccine combined an FP conjugate with a cocktail of engineered Env trimers with enhanced V2 apex recognition and increased antigen retention in lymph nodes. Immunization of macaques with the dual-epitope vaccine elicited >1000-fold higher autologous tier 2-neutralization titers than the wildtype Env trimer and enhanced heterologous NAb breadth. Both FP and V2-apex monoclonal antibodies (mAb) were isolated from immunized macaques and showed heterologous neutralization with genetic and structural signatures that were similar to well-characterized FP and V2 apex bNAbs, although the V2 apex mAbs showed incomplete maturation. These results demonstrate proof-of-concept for simultaneous vaccine elicitation of NAbs against multiple sites of Env vulnerability, which will likely be critical for an effective HIV-1 vaccine. HIGHLIGHTSO_LIDesigned a dual-epitope vaccine targeting both fusion peptide (FP) and V2 apex C_LIO_LIV2-SET Env trimer conferred higher binding of V2 apex bNAbs, longer retention in draining lymph nodes, and >1000-fold higher induction of autologous neutralization titers compared with wildtype Env trimer C_LIO_LIDual-epitope vaccine enhanced serum tier 2 neutralization breadth C_LIO_LIDual-epitope vaccine elicited FP- and V2 apex-specific neutralizing mAbs with genetic signatures similar to well-characterized FP and V2 apex bNAbs C_LI

immunology↗

bioRxiv2025

Rat somatic genome editing enables ER+ breast cancer modeling

Genetically engineered mouse models have advanced cancer research but often fail to capture key features of certain human tumors. Rats, with distinct physiology and tumor biology, offer a powerful alternative, yet their use has been constrained by technical barriers to genome editing. Here, we report efficient somatic genome editing in rats, enabling both Indel and substitution mutations. We then apply this approach to model estrogen receptor (ER)-positive breast cancer, which accounts for [~]70% of human cases but remains poorly represented in mice. The resulting rat tumors reproduce hallmarks of human ER+ breast cancer, including ductal histology, hormone responsiveness, and immune-microenvironmental features. By contrast, identical genetic alterations in mice failed to yield ER+ tumors, underscoring critical species differences in tumorigenesis. Together, this work establishes a versatile platform for rapid generation of clinically relevant rat tumor models, opening new avenues to dissect tumor biology, therapeutic response, and immune interactions in previously inaccessible cancer subtypes.

cancer biology↗

bioRxiv2025

Contribution of endothelial Piezo1 in mechanically induced muscle hypertrophy

Piezo1 proteins form nonselective cation channels with key roles in endothelial responses to mechanical forces. Here we reveal that endothelial Piezo1 regulates skeletal muscle hypertrophy following mechanical overload. Using a conditional endothelial cell-specific deletion of Piezo1 in adult mice, we assessed the role of endothelial Piezo1 in mechanical overload-induced muscle hypertrophy in the extensor digitorum longus. Endothelial Piezo1 deletion blunted muscle hypertrophy following mechanical overload despite normal baseline vascularisation, as evidenced by a lack of increase in muscle mass and abolished myofibre growth. Despite being required for optimal muscle growth, endothelial Piezo1 was dispensable for muscle regeneration after injury. In line with this, the reduced muscle growth following mechanical overload was not associated with impaired myonuclear accretion. We suggest that endothelial Piezo1 participates in a myofibre partnership that regulates skeletal muscle growth in response to mechanical overload.

physiology↗

bioRxiv2025

GASPS: A Multi-Omics Framework for Defining Genomic Aberration-Driven Signatures and Predicting Patient Outcomes in Lung Cancer

Lung cancer is the most common cause of cancer-related death worldwide. Recent advancements in targeted therapies and immunotherapies have achieved remarkable success. However, patient responses to treatments with lung cancer vary substantially. The mutation status of driver genes can direct personalized treatment, but their prognostic value and treatment efficacy are limited. In this study, we developed a statistical framework named Genomic Aberration-Derived Signature for Patient Stratification (GASPS) to characterize the transcriptomic deregulation of driver genomic aberrations and stratify patients. By applying GASPS to The Cancer Genome Atlas Lung Adenocarcinoma (TCGA-LUAD) data, we developed gene signatures for 38 driver genomic aberrations, including gene mutations, amplifications, and deletions. These signatures were applied to independent lung cancer transcriptomic datasets containing a total of 2,226 patient samples. Our results indicated that these driver gene signatures are much more prognostic than their corresponding genomic mutations. Interestingly, the two EGFR-related signatures characterizing EGFR mutation and amplification, respectively, exhibited contrasting associations with prognosis, treatment response, and immune infiltration in the tumor microenvironment. Moreover, the STK11 mutation signature, rather than the mutation status, was found to be predictive of the response and long-term benefit of patients treated with immune checkpoint blockade therapy in lung cancer. This framework is readily applicable to most cancer types using existing data to improve prognostic risk assessment and treatment efficacy by guiding personalized therapies.

bioinformatics↗

bioRxiv2025

Cross-ancestry information transfer framework improves protein abundance prediction and protein-trait association identification

Genetics-informed proteome-wide association studies (PWAS) provide an effective way to map the complex molecular landscape of biological mechanisms for complex diseases. PWAS relies on an ancestry-matched reference panel to model protein expression using genetic variants as features and determine the proteins impact on phenotype. However, reference panels from underrepresented populations remain relatively limited. In this study, we developed an analytic framework that borrows information from potentially multiple ancestries to boost the protein abundance prediction accuracy in an underrepresented population. We illustrate the frameworks utility and reproducibility through application to PWAS in East Asians: BioBank Japan (BBJ), Korean Genome and Epidemiology Study (KoGES), and Taiwan Biobank (TWB). An ensemble of information-sharing approaches was integrated to build the Multi-Ancestry-based Best-performing Model (MABM). MABM substantially improved the prediction performance with higher performance observed in both cross-validation and an external validation dataset (Tongji-Huaxi-Shuangliu Birth Cohort). Leveraging the BBJ, we identified three times as many significant PWAS associations with MABM as with the baseline Lasso model. Notably, 47.5% of the MABM specific associations were reproduced in independent East Asian datasets with concordant effect sizes. Furthermore, MABM enhanced gene/protein prioritization for downstream functional validation by (1) confirming a greater number of well-established gene/protein-trait associations and (2) identifying previously uncharacterized trait-associated genes. The benefits of MABM were further validated in additional ancestries and demonstrated in brain tissue-based PWAS, underscoring its broad applicability. Our findings close critical gaps in multi-omics research, develop a new reference resource of genetic models of protein abundance, and facilitate trait-relevant protein discovery in underrepresented populations.

genomics↗

bioRxiv2025

Minimal immune cell subset differences in a cohort of close contacts of tuberculosis index cases

Understanding the perturbations in immune response across the spectrum of TB infection is still unclear. In this study, we followed a cohort of close contacts of pulmonary TB patients with serial QFT testing at 0, 3, 6, and 12 months, and stratified them into six subgroups: QFT-increasing (low/high), QFT converters (QFT- to QFT+), QFT+ stable, and QFT- individuals. Despite these distinct QFT trajectories, we observed minimal differences in immune cell frequencies, activation profiles, and T helper subset distributions among the QFT subgroups, suggesting limited immunological stratification based on QFT dynamics alone. Ex vivo immune phenotyping, including analysis of CD4, CD8, and NKT cell frequencies, memory T cell subsets, and activated T cells (HLA-DRCD38), failed to distinguish between QFT subgroups. Antigen-specific CD4 T cell responses assessed by the activation-induced marker (AIM) assay were elevated in QFT+ compared to QFT- individuals. These findings suggest that blood-based immune profiling may not capture subtle immunological transitions among QFT converters or individuals with increasing QFT responses. In contrast, individuals with active TB (ATB) showed clear immune perturbations. ATB patients at diagnosis exhibited significantly elevated frequencies of antigen-specific CD4 T cells, increased activated T cells, and higher frequencies of intermediate monocytes and NK cells compared to QFT+/QFT- contacts. Many of these immune features declined with treatment, indicating therapy-associated immune resolution. Additionally, shifts in T helper subsets and effector memory populations were observed over the course of treatment. These results suggest that while ex vivo immune profiling can robustly distinguish active TB from non-diseased states, it lacks the resolution to differentiate QFT subgroups based on QFT dynamics alone. This could reflect either immunological similarity among close contacts regardless of QFT status or limitations of blood-based phenotyping in detecting early or subclinical immune shifts. Our study highlights the challenge of immunologically distinguishing QFT-defined subgroups within close contacts using conventional ex vivo profiling approaches.

immunology↗

bioRxiv2025

Gene signatures characterizing driver mutations in lung squamous carcinoma are predictive of the progression of pre-cancer lesions

Patients with lung squamous cell carcinoma (LUSC) are often diagnosed at advanced stages, limiting opportunities for early intervention. LUSC develops through a multistep progression from low-grade lesions to high-grade lesions, including carcinoma in situ (CIS), of which approximately half progress to invasive cancer while the other half regress. Although frequent mutations and copy number alterations have been documented in LUSC and observed in precursor lesions, their prognostic significance in precancerous stages remains largely unexplored. In this study, we leveraged gene expression data from LUSC tumors in The Cancer Genome Atlas (TCGA) to derive transcriptional signatures corresponding to 34 key driver genomic aberrations, including mutations, amplifications, and deletions. These tumor-derived gene signatures were then applied to precancerous lesion datasets to assess their ability to characterize developmental stages and predict progression risk. We found that many of these signatures increased progressively across lesion stages, reflecting their roles in early tumorigenesis. In particular, several signatures accurately predicted which CIS lesions would progress to invasive cancer. Furthermore, these signature scores were more strongly associated with patient prognosis in LUSC than the presence of genomic aberrations alone. We also examined the relationship between driver-associated signatures and the tumor immune microenvironment. Signature scores were significantly correlated with immune features such as immune cell infiltration and immune checkpoint gene expression, including CD274 (PD-L1). Interestingly, these associations varied across lesion stages, indicating dynamic immune interactions during cancer evolution. Together, our findings demonstrate that tumor-derived driver gene expression signatures provide valuable insight into the biology and progression risk of precancerous lesions, offering potential utility for early detection and intervention strategies in LUSC. Novelty and ImpactIn this study, we developed gene expression signatures using lung squamous cell carcinoma (LUSC) transcriptomic and genomic data and apply them to characterize precancerous lesions. These signatures showed high performance in predicting the progression risk of carcinoma in situ (CIS), offering a valuable tool for personalized prevention and early intervention in LUSC. These findings have the potential to improve early lung cancer detection and provide new insights into the tumor microenvironment in the context of precancer evolution of LUSC.

bioinformatics↗

bioRxiv2025

Antisense oligonucleotides targeting Valosin-containing protein improve muscle pathology and molecular defects in cell and mouse models of multisystem proteinopathy.

Valosin-containing protein (VCP) related disease, also known as multisystem proteinopathy 1 (MSP1), is an autosomal dominant disease caused by gain-of-function pathogenic variants of the VCP gene. The disease is associated with inclusion body myopathy, early-onset Pagets disease of bone, frontotemporal dementia, and familial amyotrophic lateral sclerosis. There is currently no treatment for this progressive disease associated with early demise resulting from proximal limb girdle and respiratory muscle weakness. We hypothesize that regulating VCP hyperactivity to normal levels can reduce the disease pathology. In this study, we assessed the effect of antisense oligonucleotides (ASOs) specifically targeting the human VCP gene in the patient (R155H) iPSC-derived skeletal muscle progenitor cells (SMPCs). ASOs were well tolerated up to a concentration of 5 {micro}M, and significantly reduced VCP protein expression in the SMPCs by 48% (95% CI [39-56]). We also treated the transgenic mouse model of VCP disease with the overexpressed humanized VCP gene severe A232E pathogenic variant with weekly subcutaneous ASO injections starting from 6 months of age for 3 months. In the skeletal muscle of transgenic mice, ASOs resulted in 30% (95%CI [27-32]) knockdown of VCP protein compared to control ASO. The ASO-mediated reduction of VCP expression in muscle tissue was associated with improvement in autophagy flux and reduction in TDP-43 expression, hallmarks of VCP disease. In addition, ASO-treated VCP A232E mice showed improvements in functional tests of muscle strength, such as rotarod and inverted screen test compared to mice treated with control ASO. These results suggest that targeting VCP could be beneficial in preventing the progression of the VCP myopathy and hold promise for the treatment of patients with VCP MSP1.

molecular biology↗

bioRxiv2025

Cell cycle dysregulation of globally important SAR11 bacteria resulting from environmental perturbation

Genome streamlining is hypothesized to occur in bacteria as an adaptation to resource-limited environments, but can result in gene losses affecting fundamental aspects of cellular physiology. The most abundant marine microorganisms, SAR11 (order Pelagibacterales), exhibit canonical genome streamlining, but the consequences of this genotype on core cellular processes like cell division remain unexplored. Here, analysis of 470 SAR11 genomes revealed widespread absence of key cell cycle control genes. Growth experiments demonstrated that although SAR11 bacteria maintain a normal cell cycle under oligotrophic conditions, they exhibit growth inhibition and aneuploidy when exposed to nutrient enrichment, carbon source shifts, or temperature stress. Detailed growth measurements and antibiotic inhibition experiments showed that these phenotypes resulted from cell division disruption with continuing DNA replication, leading to heterogeneous subpopulations of normal and polyploid cells. This vulnerability raises questions about microbial genome evolution and the evolutionary trade-offs between adaptations to stable nutrient-limited conditions and physiological resilience.

microbiology↗

bioRxiv2025

Deciphering the microbial landscape of lower respiratory tract in health and respiratory diseases

The microbiota plays an important role in maintaining lung homeostasis and the development of respiratory diseases. However, there have not been detailed characteristics of lung microbiome in health and respiratory diseases. Bronchoalveolar lavage fluid of 43 healthy individuals, 23 COVID patients, and 28 non-small cell lung cancer patients was conducted to characterize microbial diversity and function by metagenomic sequencing. We identified 196 species in health lung after removing low abnudance species. The most abundant species were Staphylococcus aureus, Salmonella enterica, and Klebsiella pneumoniae. Keystone species were identified through co-network analysis, such as Granulicatella adiacens and Mogibacterium diversum. To further explore the microbial function in the healthy lung, we obtained 56 non-redundant metagenome-assembled genomes (MAGs) and subsequently classified them into nine phyla. Metabolism and genetic information processing exhibit high abundance, including bacterial secretion systems, protein export, and Staphylococcus aureus infection, indicating a close correlation between microbiota and the host. Furthermore, the microbiome pairwise distances of non-small cell lung cancer (NSCLC) participants were more similar to those of the healthy group than those of individuals with COVID-19. Rothia dentocariosa, Corynebacterium kefirresidentii, Sphingobium yanoikuyae were enriched in the healthy group, while Schaalia odontolytica, Actinomyces graevenitzii, and Rothia mucilaginosa was enriched in the NSCLC group. Overall, this study provides a comprehensive overview of the diversity and gene function of the lung microbiome, which will facilitate future studies of microbiota associated with respiratory diseases in humans.

microbiology↗

bioRxiv2025

A high-throughput immunopeptidome platform for MHC II alleles to characterize antigen-specific CD4 + T cells

CD4+ T cells play a pivotal role in adaptive immunity, recognizing peptide antigens presented by MHC II molecules during infections and tumor development. Identifying immunodominant MHC II epitopess is essential for understanding CD4+ T cell responses; however, current methods such as mass spectrometry, suffer from low sensitivity and throughput, while computational algorithms show variable accuracy. To overcome these challenges, we developed EliteMHCII, a high-throughput immunopeptidome profiling platform that identifies antigen-derived MHC II epitopes and measures peptide binding affinity across 24 globally common MHC II alleles. Using EliteMHCII, we assessed the immunodominant epitopes of the SARS-CoV-2 RBD protein. Validation in vaccinated individuals and humanized mouse models revealed a strong correlation between high-affinity peptides and robust CD4+ T cell responses, while low-affinity peptides failed to elicit responses. Therefore, our immunopeptidome profiling platform, EliteMHCII, serves as a rapid, high throughput, feasible platform for CD4+ T cell epitope discovery at a global populational level in the context of infectious diseases and cancer immunotherapy.

biochemistry↗

bioRxiv2025

Ventral Hippocampus and NAc Core, but not Shell activity is required for well-learned instrumental memory destabilization

While there is increasing evidence that instrumental memories undergo destabilization and reconsolidation, little is known about the underlying neural mechanisms of these processes. Here, we focussed on instrumental memory destabilization, and the functional involvement therein of the nucleus accumbens core and shell regions, as well as the ventral hippocampus. In male rats, and using a previously established destabilization reminder procedure, we infused the GABA receptor agonists baclofen/muscimol at the time of memory reminder. We found infusions into the core but not shell impaired well-learned instrumental memory destabilization, protecting against MK-801-induced reconsolidation impairment. Moreover, infusion of baclofen/muscimol into the ventral hippocampus resulted in the same protective effect. These results suggest that the NAc core, but not the shell or vHPC, is involved in the destabilization of well-learned instrumental memory, potentially through a vHPC-NAc core projection.

animal behavior and cognition↗

bioRxiv2025

CCN1 forms a complex with GPC4 and heparin to fine-tune signaling activities for embryonic cortical neural stem cell maintenance

Radial glial cells (RGCs) are the neural stem cells (NSCs) in the developing brain, capable of self-renewing and generating neurons and glia in order. The developmental behaviors of NSCs are determined by extrinsic factors from the NSC niche, together with intrinsic factors. Here, we show that Cellular Communication Network 1 (CCN1), a secreted matricellular protein, is an autocrine factor derived from RGCs in the embryonic telencephalon. Loss of Ccn1 in RGCs leads to accelerated lineage progression of RGCs, and causes premature cell cycle exit and neuronal differentiation, resulting in a reduction in NSC pool size, and in turn, at the expense of the perinatal gliogenesis. Mechanistically, CCN1 interacts with an RGC-expressed membrane protein GPC4, one of the heparan sulfate proteoglycans (HSPGs), and is required for GPC4 to maintain NSCs through the Sonic Hedgehog (Shh) signaling pathway, depending on the binding of heparin to CCN1. Our work provides a potential mechanism for the dynamic and sophisticated interconnections of niche components that meet the needs of context-dependent maintenance, differentiation, and fate determination of NSCs.

developmental biology↗

bioRxiv2025

Targeted Protein Degradation of NUDT5 Reveals an Unexpected Non-Enzymatic Role in 6-Thioguanine-Mediated Toxicity

6-Thioguanine (6-TG), an FDA-approved antimetabolite drug, is widely used in the treatment of leukemia. Its cellular effects require metabolic activation and are regulated through interactions with various proteins such as NUDT15, which catalyzes the hydrolysis of the active 6-TG metabolites 6-thio-deoxyGTP (6-thio-dGTP) and 6-thio-GTP. Recent genome-wide CRISPR loss-of-function studies have identified another NUDIX hydrolase, NUDT5, as a crucial mediator of 6-TG toxicity. Here, we present the development and characterization of potent and selective NUDT5 degraders, guided by a cell-based assay screening strategy. These degraders, in conjunction with orthogonal CRISPR knock-out and reconstitution experiments, reveal a novel and unexpected, non-enzymatic role for NUDT5 in modulating the cellular response to 6-TG. Depletion of NUDT5 protein is antagonistic to NUDT15 inhibition, suggesting a distinct mode-of-action with potential implications for patient therapy.

cell biology↗

bioRxiv2025

Functional profiling reveals a non-enzymatic role of NUDT5 in repressing purine de novo synthesis

Folate metabolism is intricately linked to purine de novo synthesis through the incorporation of folate-derived one-carbon units into the purine scaffold. Here, we investigate the chemical and genetic dependencies caused by mutations in the folate enzyme MTHFD1 and discover a key role for Nudix hydrolase 5 (NUDT5) in regulating purine de novo synthesis. Through genetic knockout and development of a selective chemical NUDT5 degrader, we uncover an unprecedented scaffolding role rather than NUDT5 enzymatic activity is responsible for this phenotype. We find that NUDT5 interacts with the rate-limiting enzyme of purine de novo synthesis, PPAT, to repress the pathway in response to elevated purine levels. Our findings establish NUDT5 as an important regulator of purine de novo synthesis and elucidate its role in mediating sensitivities to 6-thioguanine in cancer treatment and to adenosine in MTHFD1 deficiency.

molecular biology↗