bioRxiv Science⌕ Search

Biology subjects

Zhou, D.

Publications and source records attributed to Zhou, D..

At least 37 records · Page 2Linked to original sources

Autism associated Cntnap2 deletion disrupts vestibular sensory signaling and spatial cognition in mice

Autism spectrum disorder (ASD) is frequently accompanied by sensory and motor abnormalities, including impaired balance, postural control, and spatial orientation, that are often attributed largely to altered central circuitry. Emerging evidence, however, suggests that peripheral sensory dysfunction can also shape ASD related behavioral phenotypes. Here, we tested whether loss of the ASD associated gene Cntnap2/Caspr2 alters vestibular signaling in Cntnap2-/- mice. Developmental transcriptomic analysis showed that Cntnap2 is expressed in vestibular sensory organs and increases during the first postnatal month, coincident with vestibular pathway maturation. Vestibular sensory evoked potentials revealed reduced response amplitudes and prolonged latencies in Cntnap2-/- mice, indicating impaired peripheral afferent responses to transient linear acceleration. Cntnap2-/- mice also showed delayed contact righting, reduced ocular counter roll, and increased hindlimb slips and compensatory tail excursions during balance beam walking, whereas rotational vestibulo-ocular reflex gain and phase were preserved. These vestibular and balance abnormalities were accompanied by reduced novel arm preference in the Y maze and severe impairment of Barnes maze acquisition, consistent with impaired spatial learning. Together, these findings identify Cntnap2/Caspr2 as a regulator of vestibular sensory signaling and support a model in which disrupted peripheral vestibular input, likely acting together with central effects of Cntnap2 loss, contributes to sensorimotor and spatial cognitive phenotypes relevant to ASD.

neuroscience↗

Targeting melanosome pH is an effective method for the treatment of oculocutaneous albinism

Oculocutaneous albinism (OCA) is a genetic condition associated with impaired visual acuity and increased skin cancer risk. When OCA is due to defects in melanosome ion transport, abnormally acidic conditions in the melanosome lumen inhibit tyrosinase, the critical pigment synthetic enzyme. Hence, a therapeutic approach that optimizes melanosome pH to increase pigment production presents a potential treatment for OCA and a method for decreasing skin cancer risk. Here, we report that reduction in sAC (ADCY10) activity via naturally occurring human variants in ADCY10 restores OCA pigmentation, and sAC inhibition increases melanin synthesis in both human and mouse OCA models. These findings demonstrate that targeting melanosome pH is an effective, previously untapped therapeutic strategy for OCA and elevated skin cancer risk.

physiology↗

Brain Organoids, Lessons from Fetal Neocortex Formation, and Rational Design for Quality Control

Recent widespread adoption of cerebral organoid protocols has led to many new studies assessing the human-specific features of neural diseases. However, not all organoid studies employ proper quality control, which limits the physiological relevance of their findings. Here, we discuss the stages of in vivo neocortex formation and how those stages are recapitulated in organoid protocols. We then present the first guide for real-time operator removal of maldeveloped organoids in shaking culture. Finally, we show preliminary work on an organoid imaging and mesofluidic control platform for automated quality control of organoid development. Taken together, this approach for assessing the morphological features of organoids will improve the rigor and reproducibility of organoid studies, increase effect sizes of physiologically relevant disease etiology, and pave the way for cortical organoid GMP in high-throughput. Clinical RelevanceThis establishes high-throughput, visual brain organoid quality control for disease studies and preclinical testing.

neuroscience↗

Levosimendan inhibits HIV-1 infection in myeloid cells in the RIOK1-dependent manner

Despite of the highly potent antiretroviral therapies, HIV-1 establishes persistent infection and causes chronic inflammation in AIDS patients. Beyond CD4+ T cells, HIV-1 infects myeloid cells, including circulating monocytes and tissue-resident macrophages, and integrates with host genomes to form stable viral reservoirs. To achieve a functional HIV cure, latency-promoting agents (LPAs) have been developed for the "block-and-lock" strategy to reinforce deep HIV-1 latency and permanently silence proviruses. However, most LPAs have been tested mainly in CD4+ T cells, and their efficacy in myeloid cells remains unclear. In this study, we reported that levosimendan (LSM), a drug approved for clinic use to treat heart failures, is able to inhibit HIV lytic infection and reactivation in myeloid cells. LSM blocked viral lytic reactivation in HIV-1 latently infected monocytic cells (TH89GFP, U1) and microglial cells (HC69). LSM also inhibited HIV infection in human induced pluripotent stem cell (iPSC) derived microglia (iMG), primary human resident liver macrophages (Kupffer cells) as well as human monocyte-derived macrophages (MDMs). Furthermore, we demonstrated that overexpression of a predicted drug target of LSM, the conserved serine/threonine kinase RIOK1 (RIO kinase 1), overcomes LSMs anti-HIV effect. Overall, our studies concluded that LSM is a promising LPA to inhibit HIV-1 infection in myeloid cells in the RIOK1-dependent manner.

microbiology↗

Z-TAC enables custom and combinatorial degradation of cell surface proteins

Cell-surface degrader platforms typically require target-specific engineering and have therefore been applied to a relatively small set of protein targets. Here we report Z-TAC, a strategy that enables plug-and-play conversion of existing IgG antibodies into cell-surface protein degraders. Across multiple targets from distinct protein families, Z-TAC induced efficient and sustained degradation of both individual receptors and receptor combinations. For a multi-pass membrane receptor lacking selective antagonists, Z-TAC mediated complete receptor degradation and functional inhibition, demonstrating the ability of this platform to overcome the limitations of conventional pharmacological approaches. This study delineates a generalizable and scalable strategy for functional perturbation of the cell-surface proteome.

bioengineering↗

Farnesoid X receptor-dependent microbiome-bile acid signaling mediates obstructive sleep apnea-induced atherosclerosis

Intermittent hypoxia and hypercapnia (IHC), a hallmark of obstructive sleep apnea (OSA), accelerates atherosclerosis, yet the underlying mechanisms remain unclear. The gut microbiota and metabolites, specifically bile acids, change with IHC and thus the bile acid receptor farnesoid X receptor (FXR) might mediate IHC-induced atherosclerosis. In this study, ApoE-/- and ApoE-/- FXR-/- mice were exposed to IHC or room air and fed with a high-fat, high-cholesterol diet for 10 weeks. Markers of atherosclerosis, fecal microbiome, and metabolome were then examined via Sudan IV staining, absolute abundance shotgun metagenomics, and untargeted liquid chromatography tandem mass spectrometry (LC-MS/MS). IHC markedly increased aortic atherosclerosis in ApoE-/-mice, an increase that was abolished by FXR deficiency. In addition, IHC reshaped gut microbial composition, promoting enrichment of bile acid-modifying taxa and increasing levels of microbial hydroxysteroid dehydrogenase (hsdh). The bile acid pool was also remodeled and associated with aortic atherosclerosis via FXR-dependent metabolic signals in ApoE-/- mice. Knockout of FXR disrupted microbiome shift under IHC and uncoupled microbial bile acid metabolism from vascular lesion development, thereby protecting against aortic atherosclerosis. These findings show that FXR has a central role in linking IHC, microbial bile acid metabolism, and cardiovascular pathology.

microbiology↗

A lateral linker histone binding mode scaffolds dinucleosome stacking in chromatin fibers

Linker histones are essential for chromatin compaction, yet how they contribute to higher-order fiber assembly remains poorly understood. Here, we determined cryo-electron microscopy structures of Arabidopsis dodeca-nucleosome fibers containing distinct H2A/H3 variants and linker histone H1.3, revealing a noncanonical binding mode that a laterally positioned H1.3 connects the acidic patch of one nucleosome and the DNA of the neighboring nucleosome, thereby scaffolding dinucleosomes into two-start chromatin fibers. This noncanonical binding mode is structurally conserved when H1.3 is replaced by Gallus gallus H5. Furthermore, incorporation of H2A.W and H3.3 further induces back-to-back fiber dimerization. Cryo-electron tomography and in vivo cross-linking mass spectrometry analyses support the physiological relevance of H1 lateral engagement. Our findings establish that linker histones act as active architectural scaffolds in higher-order chromatin organization.

molecular biology↗

A Multi-Dataset Transcriptomic Analysis Unravels Core Mechanisms Involving Vitamin D Metabolism and Inflammatory Pathways for Frailty Diagnosis.

Frailty is a prevalent geriatric syndrome, and the shortage of objective biomarkers restricts its early diagnosis and intervention. This study aimed to identify robust molecular signatures and diagnostic markers for frailty using bioinformatics analyses of multiple independent datasets. Two transcriptome datasets (GSE144304, n=80; GSE287726, n=70) were obtained from the GEO database. We performed differential gene expression analysis, GO, KEGG and GSEA enrichment, and machine learning (70% training / 30% validation) to screen and validate core biomarkers. Numerous shared differentially expressed genes were identified. Vitamin D metabolism, ABC transporter, and inflammatory/immune pathways were consistently enriched and confirmed by GSEA. Machine learning models based on these signatures showed favorable diagnostic performance. Our study demonstrates that vitamin D metabolic disorders and chronic inflammation are core molecular features of frailty. The identified biomarkers provide new strategies for basic research, early clinical diagnosis, and therapeutic target development for frailty.

bioinformatics↗

Anti-inflammatory and pro-proliferative effects of fasudil in human trisomy 21 neural progenitor cells

Down syndrome (DS) results from trisomy for human chromosome 21 and is the most frequent genetic cause of intellectual disability. No effective treatments currently exist that improve neurodevelopment and cognition. Atypical brain development in individuals with DS is apparent before birth, which suggests that the optimal time to begin administration of therapies is prenatally. Human neural progenitor cell (NPC) cultures provide a tractable in vitro model system to examine the effects of trisomy 21 (T21) on neurodevelopment and to measure the effects of pharmacological interventions. Here we report the results of preclinical studies evaluating 24 candidate therapies. RNA-Seq analyses found that euploid and T21 NPCs showed different transcriptomic responses to five candidate pharmacotherapies. The Rho-associated coiled-coil kinase (ROCK) inhibitor fasudil increased proliferation of T21 NPCs, reduced expression of inflammatory pathway genes in T21 NPCs, and reduced markers of inflammation in LPS-stimulated microglia model systems. These results demonstrate that fasudil can alter multiple T21-associated abnormalities in a beneficial manner, suggesting that fasudil warrants further study as a candidate prenatal pharmacotherapy for DS.

pharmacology and toxicology↗

Unravelling genome-wide mosaic microsatellite mutations at single-cell resolution

Short tandem repeats (STRs), or microsatellites, are highly mutable genomic elements that modulate gene regulations and are implicated in a range of human diseases. However, detecting mosaic STR mutations at single-cell resolution remains challenging due to both technical and biological complexities. To address this, we developed BayesMonSTR, a robust algorithm that enables accurate detection of mosaic STR mutations. Using this tool in single-cell analysis of human tissues, we reveal an accumulation of longer mosaic STR insertions and deletions (indels) in aging mitotic and post-mitotic cells. Strikingly, prefrontal cortex (PFC) neurons accumulate a higher burden of STR mutations than B cells or lung epithelium, with aged neurons exhibiting a particularly pronounced increase in longer STR deletions. These mutations are enriched at transcription start sites (TSSs) and active enhancers of highly expressed genes. Our work establishes a foundation for genome-wide, hypothesis-free discovery of disease-associated mosaic STR mutations and reveals a previously unexplored landscape of mosaic STR variation in development and aging.

bioinformatics↗

Inhibition of KDM5A/B promotes antitumor innate immune responses in HHV-8/KSHV2 positive B-cell lymphomas

Summary/AbstractHistone methylation is a dynamic and reversible epigenetic modification that critically controls the progression of human diseases, including infections and cancers. Here we reported that histone lysine demethylases (KDMs) in the KDM5 family KDM5A/B play profound roles in suppressing lytic reactivation of oncogenic human herpesvirus 8 (HHV-8), i.e., Kaposis sarcoma-associated herpesvirus (KSHV), as well as antiviral/antitumor innate immune responses in KSHV-infected B-cell lymphomas. We showed that KSHV lytic replication decreases KDM5A/B protein stability by enhancing their K-48 linked polyubiquitination while KDM5A/B depletion facilitates KSHV lytic reactivation. Mechanistic studies illustrated that KDM5A/B associate with KSHV LANA protein and dampen its chromatin association at both KSHV viral lytic promoter and promoters of antitumor immune-responsive genes (IRGs). In comparisons to normal B cells, KDM5A/B expression significantly increased in B-cell lymphoma cells, including KSHV-positive primary effusion lymphoma (PEL). We demonstrated that KDM5A/B inhibition remarkably induces both KSHV lytic reactivation and innate immune responses in PEL cells, resulting in a strong viral oncolytic effect, both in vitro in cell cultures and in vivo using a PEL xenograft mouse model. Overall, our studies identified the novel functions of KDM5A/B to silence KSHV lytic replication and antiviral/antitumor innate immune responses, which can be blocked to benefit the treatment of KSHV-associated B-cell lymphomas that are usually aggressive and difficult to treat.

microbiology↗

Inhalable Polymeric Nanoparticle Vaccine for Lysosome-targeting Co-delivery of Antigen and Adjuvant with Enhanced Immunoprotection

Conventional subunit vaccines suffer from premature clearance and poor synchronization of antigen and adjuvant, limiting coordinated immune activation. Here, we develop an amphipathic polymer (YAXA) with acid-labile imine bonds for acid-sensitive degradation and terminal NHS-activated esters for antigen conjugation. YAXA is co-assembled with hydrophobic TLR7 agonist 3M-052 and conjugated to protein antigen, forming nanoparticle vaccine YM3.7. Following aerosolized intratracheal inoculation into the lung, YM3.7 is efficiently internalized by antigen-presenting cell and trafficked into lysosome, where acidic conditions trigger its dissociation and co-release of antigen and adjuvant. This spatiotemporally synchronized delivery promotes robust immune activation, including cell maturation, germinal center formation, systemic and lung-resident B/T cell response, and IgG/sIgA production. In lethal pneumonia models induced by either Pseudomonas aeruginosa or Staphylococcus aureus, YM3.7 markedly improves survival over conventional antigen and adjuvant mixture. This study presents an inhalable nanoparticle platform that coordinately activates innate, humoral, mucosal, and cellular immunity for enhanced protection.

immunology↗

Molecular Imaging of the TGF-β Activating Integrin αvβ6 Detects Chronic Lung Allograft Dysfunction

TGF-{beta}-activating integrins promote solid-organ fibrosis, suggesting their use as a molecular marker of disease. Chronic lung allograft dysfunction (CLAD), a progressive fibrotic complication that limits lung transplant survival, is driven by intragraft TGF-{beta} activation. However, the expression patterns of TGF-{beta}-activating integrins remain undefined in lung transplants. Single-cell RNA sequencing in a mouse CLAD model revealed high levels of the TGF-{beta}-activating integrin v{beta}6, which was mainly localized to fibrosis-associated Krt8+ transitional alveolar cells (AT1/2), while tolerant transplants lacked both v{beta}6 expression and Krt8+AT1/2 cells. Molecular imaging with a newly developed positron emission tomography radiotracer specific for v{beta}6, [64Cu]Cu-DOTA-A20-K16R, showed significantly higher uptake in CLAD versus tolerant transplants. In contrast, [64Cu]Cu-DOTA-A20-K16R allograft uptake was reduced by treatments that lowered v{beta}6 expression and CLAD severity. Finally, [64Cu]Cu-DOTA-A20-K16R autoradiographic analysis on human explanted lungs with CLAD showed elevated activity that correlated with v{beta}6 expression. Collectively, these findings demonstrate the potential utility of v{beta}6 molecular imaging to detect CLAD pathogenesis.

immunology↗

The combination of BCL-xL PROTAC and mTOR inhibitor sensitizes pancreatic ductal adenocarcinoma to KRASG12D inhibitor treatment by enhancing apoptosis induction

Pancreatic ductal adenocarcinoma (PDAC) is a highly aggressive cancer with a five-year survival rate of approximately 13%, partly because of limited treatment options and resistance to therapies. Although the recently discovered KRAS G12D inhibitor MRTX1133 has shown promise for PDAC treatment in preclinical studies, its clinical efficacy as a single agent is expected to be limited, as is the case with KRAS G12C inhibitors. Therefore, in this study, we evaluated potential combination strategies to enhance the therapeutic effect of MRTX1133. We rationally combined MRTX1133 with the BCL-xL proteolysis-targeting chimera (PROTAC) DT2216 and the mTOR inhibitor everolimus, which significantly potentiated the anti-tumor activity of MRTX1133 in multiple G12D-mutated PDAC cells in vitro by enhancing apoptosis induction. Mechanistically, MRTX1133 treatment increased BIM and decreased NOXA levels, while the combination of DT2216/everolimus was shown to simultaneously enhance BIM release and stabilize NOXA. In vivo, DT2216/everolimus combination significantly potentiated the anti-tumor activity of MRTX1133 in AsPC1 PDAC xenograft model. Furthermore, the triple combination of MRTX1133, DT2216, and everolimus effectively overcame acquired resistance to MRTX1133 in AsPC1 cells in vitro and in xenograft model. Collectively, our findings suggest that the single-agent efficacy of MRTX1133 is limited by apoptosis inhibition, and that its combination with DT2216/everolimus can enhance apoptosis and potentially overcome resistance in KRAS G12D-mutated PDAC. SIGNIFICANCEKRAS inhibitors, including KRAS G12D inhibitor MRTX1133, are promising therapeutics against KRAS-mutated pancreatic ductal adenocarcinoma (PDAC), but drug resistance limits their efficacy. Our study reveals that robust induction of apoptosis using a combination of BCL-xL PROTAC degrader and an mTOR inhibitor, significantly enhances MRTX1133 efficacy in PDAC models without increasing toxicity to normal tissues.

cancer biology↗

Photoinitiator-Free, Visible Light-Crosslinking Hydrogel with Tuneable Properties for 3D Bioprinting

Light-mediated crosslinking of polymers is widely employed in the preparation of hydrogels for biofabrication and tissue engineering, since photo-crosslinking enables the spatiotemporal control over the gelation processes. Nevertheless, a critical bottleneck persists: most photo-crosslinking reactions rely on the use of photo-initiator, and ultraviolet or short-visible-wavelength light activation, which suffers from potential photodamage and poor penetration. Here we present a photoinitiator-free hydrogel system based on gelatin functionalized with acrylamidylpyrene groups (Gel-Pyr) able to undergo crosslinking via visible-light-induced [2+2] cycloaddition. Gel-Pyr solution exhibits rapid gelation kinetics, tuneable mechanical properties, facile temporal control over photocrosslinking, and long-term structural stability (>30 days) in cell culture conditions. Rheological analyses reveal pronounced shear-thinning behaviour at room temperature, enabling extrusion-based 3D bioprinting of multilayered constructs with high structural fidelity. Fine strand resolution (<400 {micro}m) is achieved in bioprinted crosshatch structures, enabling sufficient nutrient diffusion for cell support. Compared with gelatin methacryloyl (GelMA), Gel-Pyr significantly reduces photocrosslinking-induced oxidative stress and apoptosis in encapsulated bone-marrow mesenchymal stem cells (BM-MSCs), supporting >80% viability over 7 days. By eliminating UV exposure and lowering free radical generation, this visible-light-responsive hydrogel platform offers a facile and cytoprotective alternative to other hydrogel systems. Table of ContentA visible light-crosslinkable, initiator-free gelatin-based hydrogel (Gel-Pyr) is developed using acrylamidylpyrene functionalization. This system enables rapid crosslinking under cytocompatible reaction conditions and offers excellent printability, tuneable mechanics, and long-term stability. Gel-Pyr supports high cell viability, reduced oxidative stress and precision bioprinting, positioning it as a promising platform for tissue engineering and in vitro biofabrication. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=178 SRC="FIGDIR/small/691472v3_ufig1.gif" ALT="Figure 1"> View larger version (54K): org.highwire.dtl.DTLVardef@1abe2b4org.highwire.dtl.DTLVardef@1b09b5borg.highwire.dtl.DTLVardef@1a786b1org.highwire.dtl.DTLVardef@17c06b5_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

Integrated multiomics reveals inflammation-driven excessive erythrocytosis in subjects with Monge's disease

Monges disease, or Chronic Mountain Sickness (CMS), is a chronic high-altitude disorder characterized by hypoxia-induced excessive erythrocytosis (EE), elevating the risk of stroke and myocardial infarction. Using RNA-seq and ATAC-seq, we profiled iPSC-derived erythroid cells from CMS and non-CMS subjects under normoxia and hypoxia to identify statistically significant, disease-associated transcriptional and chromatin accessibility changes. RNA-seq revealed induction of inflammatory, stress, and erythropoiesis programs in CMS even under normoxia, including robust activation of JAK/STAT signaling, upregulation of heme metabolism and VEGF, and accelerated erythrocyte lineage commitment alongside repression of Notch and WNT/{beta}-catenin. Hypoxia amplified this dysregulated state, and critically, activated NF{kappa}B-driven inflammatory signaling together with canonical HIF targets. ATAC-seq revealed pronounced hypoxia-induced changes, with increased accessibility within inflammatory and erythrocyte lineage genes occurring concomitantly with decreased accessibility within pluripotency and ectodermal lineage genes. Pharmacological NF{kappa}B inhibition in CMS cells significantly reduced EE (p-value <0.0001), whereas NF{kappa}B activation in non-CMS cells was sufficient to drive EE (p-value <0.01), confirming the causal role inferred by our multiomics analyses. Collectively, our multiomics and functional experiments substantiate a coordinated chromatin-transcription paradigm favoring an inflammatory axis that, through hypoxia-driven NF{kappa}B activation, accelerates stress-induced erythroid commitment and underlies EE in CMS.

genetics↗

RNA viruses in water shape the viromes of shrimp and fish in aquaculture systems

Aquatic environments host immense RNA viral diversity, yet the extent to which waterborne viruses influence the virome of aquatic animals remains unclear. Here, we conducted a comprehensive longitudinal metatranscriptomic analysis of water, shrimp, and fish across multiple culture stages in aquaculture systems. We identified 3,211 RNA viruses spanning 21 viral supergroups, with 97.4% representing novel species. Water exhibited the greatest viral diversity (3,093 species), followed by shrimp (1,280) and fish (398), with most viruses detected in shrimp and fish also detected in water. Diversity analyses revealed increasing richness and significant compositional shifts in 92 high-abundance viruses (>1,000 RPM) across culture stages. Viral abundance in aquatic animals was strongly correlated with that in water, and the temporal trajectories of the 16 most abundant viruses were closely synchronized between water and shrimp. Furthermore, 337 virus species were shared among shrimp and two fish species, of which 309 were present in water. These findings demonstrated that RNA viruses in water shape the composition and dynamics of aquatic animal viromes, underscoring the importance of water virome surveillance and management for disease prevention in shrimp aquaculture.

microbiology↗

PHOX2B polyalanine repeat mutation has a profound impact on the transcriptome of neuronal progenitor cells in Haddad syndrome

Mutation in paired-like homeobox 2B (PHOX2B) is used as the diagnostic marker of Haddad syndrome (HS). The mutant gene/protein afflict neural crest cells during embryonic development which leads to congenital central hypoventilation syndrome (CCHS) and Hirschsprungs disease (HSCR). Previous studies on HS and CCHS have mainly focused on the conformational dynamics of the mutant protein and have remained controversial. Here we performed RNA-sequencing on the patient derived neuroepithelial stem cells (NESCs), pertinent to the neurodevelopmental phenotype in HS, and found that the PHOX2B-PARM has a profound impact on the transcriptional profile of the cells. The single copy of PHOX2B-PARM in heterozygote cells were leading to >10 fold differentially expressed genes. In the patient cells there was a significant enrichment of genes related to neuronal development and synapse organization mainly driven by L1CAM interactions and synaptogenesis signaling pathway. Our result not only highlight the use of a suitable model of HS but also provide a clear path for future experimental validation and downstream targets with potential therapeutic values.

neuroscience↗