Search bioRxiv⌕ Search

Biology subjects

Cai, H.

Publications and source records attributed to Cai, H..

At least 55 records · Page 3Linked to original sources
bioRxiv2025

Cross-modal Denoising and Integration of Spatial Multi-omics data with CANDIES

Spatial multi-omics data offer a powerful framework for integrating diverse molecular profiles while maintaining the spatial organization of cells. However, inherent variations in data quality and noise levels across different modalities pose significant challenges to accurate integration and analyses. In this paper, we introduce CANDIES, which leverages a conditional diffusion model and contrastive learning to effectively denoise and integrates spatial multi-omics data. With our innovative model and algorithm designs, CANDIES not only enhances the quality of spatial multi-omics data, but also yields a unified and comprehensive joint representation, thereby empowering many downstream analysis. We conduct extensive evaluations on diverse synthetic and real datasets, including spatial CITE-seq data from human skin biopsy tissue, MISAR-seq data from the mouse brain, spatial ATAC-RNA-seq data from the mouse embryo and 10x visium data from human lymph nodes. CANDIES shows superior performance on various downstream tasks, including denoising, spatial domain identification, spatiotemporal trajectories reconstruction, and spatial association mapping for complex human traits. In particular, we show that CANDIES representations can be integrated with the rich resources from genome-wide association studies (GWASs), allowing the spatial domains to be linked with complex human traits, yielding spatially resolved interpretation of complex traits in their relevant tissues.

bioinformatics↗
bioRxiv2025

Patchy Striatonigral Neurons Modulate Locomotor Vigor in Response to Environmental Valence

Spiny projection neurons (SPNs) in the dorsal striatum play crucial roles in locomotion control and value-based decision-making. SPNs, which include both direct-pathway striatonigral and indirect-pathway striatopallidal neurons, can be further classified into subtypes based on distinct transcriptomic profiles and cell body distribution patterns. However, how these SPN subtypes regulate spontaneous locomotion in the context of environmental valence remains unclear. Using Sepw1-Cre transgenic mice, which label a specific SPN subtype characterized by a patchy distribution of cell bodies in the dorsal striatum, we found that these patchy striatonigral neurons constrain motor vigor in response to valence differentials. In a modified light/dark box test, mice exhibited differential walking speeds between the light and dark zones. Genetic ablation of these patchy SPNs disrupted restful slowing in the dark zone and increased zone discrimination by speed. In vivo recordings linked the activity of these neurons to zone occupancy, speed, and deceleration, with a specific role in mediating deceleration. Furthermore, chemogenetic activation of patchy SPNs--and optical activation of striatonigral neurons in particular--reduced locomotion and attenuated speed-based zone discrimination. These findings reveal that a subtype of patchy striatonigral neurons regulates implicit walking speed selection based on innate valence differentials.

neuroscience↗
bioRxiv2025

Trimethylamine-N-oxide affects cell type-specific pathways and networks in mouse aorta to promote atherosclerotic plaque vulnerability

BackgroundTrimethylamine-N-oxide (TMAO) has been significantly linked to atherosclerosis via several mechanisms, but its direct effect on the atherosclerosis-prone vasculature remains unclear. The objective of this study was to characterize the cell type-dependent and independent effects of TMAO on key vascular cell types involved in atherosclerosis progression in vivo. MethodsWe performed single cell RNA-sequencing (scRNAseq) on aortic athero-prone regions of female Ldlr-/- mice fed control Chow, high-cholesterol (HC), or HC+TMAO diets for three months to identify which aortic cell types, differentially expressed genes, and biological pathways are affected by TMAO. We also modeled cell-cell communications and intracellular gene regulatory networks to identify gene networks perturbed by TMAO feeding. Key genes and pathways were validated using primary human smooth muscle cells exposed to TMAO. Changes in the thickness of lesional fibrous caps in response to TMAO in female Ldlr-/- mice fed HC+TMAO versus HC diets were measured using transgelin immunostaining. ResultsOur scRNAseq analysis revealed that TMAO supplementation upregulated apoptotic gene signatures and downregulated extracellular matrix (ECM) organization and collagen formation genes in a subset of atherosclerosis-specific modulated vascular smooth muscle cells (vSMCs). We also identified "degradation of the ECM" as a top pathway for SMC-derived macrophage DEGs in response to TMAO. Network analyses support that macrophage-vSMC communication mediates ECM remodeling. Using human smooth muscle cells exposed to TMAO in vitro, we confirmed the direct effect of TMAO on regulating collagen and apoptotic genes. In agreement with the changes in these pathways that affect plaque stability, we observed a significant decrease in fibrous cap thickness in mice supplemented with TMAO. ConclusionsOur results reveal the effects of TMAO on vSMCs to promote apoptosis and decrease ECM formation, and on macrophage-mediated ECM degradation in atherosclerotic lesions to in concert enhance plaque instability. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=84 SRC="FIGDIR/small/640205v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@100254org.highwire.dtl.DTLVardef@109155aorg.highwire.dtl.DTLVardef@158d280org.highwire.dtl.DTLVardef@63d544_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIscRNAseq of the aortic athero-prone regions in female Ldlr-/- mice supplemented with TMAO in the diet revealed the effect of TMAO across cell types, particularly in SMC-derived macrophages and atheroprotective modulated vSMCs. C_LIO_LITMAO increases apoptotic gene signatures and reduces ECM organization and collagen formation gene signatures in modulated vSMCs in vivo, and in vitro exposure studies support a direct effect of TMAO on these genes. C_LIO_LIModulated vSMC-specific gene regulatory networks enriched for apoptotic genes and ECM organization genes were organized by intracellular regulators such as Ccl19 and Tnn and extracellular regulators such as Mmp9 and Spp1 from macrophages. C_LIO_LIFibrous cap thickness, a marker of atherosclerotic plaque stability, was significantly reduced in female Ldlr-/- mice fed HC+TMAO versus HC diets for five months. C_LI

physiology↗
bioRxiv2025

Understanding monocyte-driven neuroinflammation in Alzheimers disease using human brain organoid microphysiological systems

Increasing evidence suggests that Alzheimers disease (AD) pathogenesis strongly correlates with neuroinflammation. Peripheral monocytes are crucial components of the human immune system that may play a role in neuroinflammation, but their contribution to AD pathogenesis is largely understudied partially due to the lack of appropriate human models. Here, we present human cortical organoid microphysiological systems (hCO-MPSs) for modeling dynamic AD neuroinflammation mediated by monocytes. By incorporating 3D printed devices into an existing cortical organoid protocol, 96 hCO-MPSs can be established with significantly reduced necrosis and hypoxia as well as enhanced viability within a commonly used 96 well plate, and each hCO-MPS consists of a doughnut-shaped hCO and a 3D printed device per well. Using this approach, monocytes from AD patients exhibit higher infiltration, decreased amyloid-beta (A{beta}) clearance, and stronger inflammatory responses compared to monocytes from age-matched control donors. Moreover, pro-inflammatory effects such as elevated astrocyte activation and neuronal apoptosis were observed to be induced by AD monocytes. Furthermore, the significant increase in the expression of IL1B and CCL3, both at the transcriptional and protein levels, indicated the pivotal role of these cytokine and chemokine in monocyte-mediated AD neuroinflammation. Our findings provide insight for understanding monocytes role in AD pathogenesis, and the user-friendly MPS models we present are compatible with existing laboratory settings, highlighting their potential for modeling neuroinflammation and developing new therapeutics for various neuroinflammatory diseases.

bioengineering↗
bioRxiv2025

Divergent stem cell mechanisms governing the primary body axis and appendage regeneration in the axolotl

Exploring the fundamental mechanisms of organ regeneration is crucial for advancing regenerative medicine. The axolotl tail represents a unique opportunity to study regeneration of the primary axis including segmented muscle, vertebrae and skin. During tail development, muscle stem cells (MuSCs) displayed expected specificity to the muscle lineage. Tail amputation, however, induced expansion of MuSC potential yielding clonal contribution to muscle, connective tissue including cartilage, pericytes, and fibroblasts. This expanded potential was not observed during limb regeneration, and cross-transplantation showed these differences in potential are intrinsic. ScRNA-Seq profiling revealed that tail MuSCs revert to an embryonic mesoderm-like state. Through genetic manipulation involving the over-expression of constitutively active TGF-{beta} receptors or Smad7 (antagonist of TGF-{beta} signaling) in MuSCs, we demonstrated that the levels of TGF-{beta} signal determine the fate outcome of MuSCs to connective tissue lineage or muscle respectively. Our findings illustrate a fundamental difference between regeneration of primary axis versus limb and offers a novel stem cell source for regeneration of axial skeletal tissues.

developmental biology↗
bioRxiv2025

3D-bioprinted marine bacteria for the degradation of bioplastics

The severe, long-lasting harm caused by plastic pollution to marine ecosystems and coastal economies has led to the development of biodegradable plastics; however, their limited decomposition in cold, dark marine environments remains a challenge. Here, we present our newly developed technologies for creating 3D-bioprinted living materials for bioplastic degradation with specific use in marine environments. Our approach integrates halotolerant bioplastic-degrading bacterium Bacillus sp. NRRL B-14911 into alginate-based bio-ink to print an engineered living material (ELM) termed a "bio-sticker." Quantification of bacteria viability reveals that bioprinted marine bacteria survive within bio-stickers for more than three weeks. The rate at which the bio-stickers degrade the bioplastic polyhydroxybutyrate (PHB) can be tuned by altering bio-sticker biomass concentration, bioplastic concentration, or incubation temperature. Bio-stickers that are transferred to a new PHB sample still retain high biodegradation activity, demonstrating their durability. Strain sweep oscillatory tests demonstrate viscoelastic behavior of the bio-stickers. Monotonic tensile tests indicate that the elastic modulus and the adhesion of the bio-stickers are not negatively impacted by bacteria growth or incubation temperature. Our work paves the way for development of ELMs to facilitate the inclusion of bioplastics within the blue economy, promoting the emergence of more sustainable and eco-friendly materials.

synthetic biology↗
bioRxiv2024

McsB regulates CtsR thermosensing through periphery arginine phosphorylation

When cells sense an elevated temperature in the environment, the bacterial master transcription repressor CtsR becomes phosphorylated and inactivated by the arginine kinase McsB to initiate the expression of heat-shock genes. Here, we utilize a fluorescence intensity shift assay (FISA) based on the protein-induced fluorescence enhancement (PIFE) effect to monitor the DNA-CtsR-McsB interactions in real time. Our single-molecule analysis reveals that CtsR binds rapidly and stably to the cognate DNA, and that McsB is able to transiently interact with CtsR in situ of the target DNA. We determine the binding kinetics between McsB and the DNA-bound CtsR by single-molecule real-time binding assays, with kon and koff of 0.75 M-1 s-1 and 0.34 s-1, respectively. This interaction with McsB does not remove CtsR from the DNA, but lowers the temperature threshold for CtsR dissociation and alters its thermosensing behavior. Mass spectrometry, mutational analysis and structural simulation results together suggest that the phosphorylation of several periphery arginine residues on CtsR, which reduces the binding energy of the CtsR-DNA interaction, underlies a plausible molecular mechanism for this effect. Taken together, these results provide insights into how McsB regulates the CtsR-DNA complex and highlight the functional importance of CtsR periphery arginine residues in the bacterial heat-shock response.

biophysics↗
bioRxiv2024

Distinct cortical populations drive multisensory modulation of segregated auditory sources

Auditory perception can be modulated by other sensory stimuli. However, we do not fully understand the neural mechanisms that support multisensory behavior. Here, we recorded spiking activity from the primary auditory cortex (A1) in non-human primates, while they detected a target vocalization that was embedded in a background chorus of vocalizations. We found that a congruent video of a monkey eliciting a vocalization improved the monkeys behavior, relative to their performance when we only presented a static image of the monkey. As a proxy for the functional organization of A1, we compared the contribution of neurons with significant spectrotemporal response fields (STRFs) with those that had non-significant STRFs (nSTRFs). Based on spike-waveform shape and functional connectivity, STRF and nSTRF neurons appeared to belong to distinct neural populations. Consistent with this, we found that although STRF neurons encoded stimulus information through synchronized activity, the population of nSTRF neurons encoded task-related information in the primate A1 more as a structured dynamic process. Together, these findings demonstrate a functional distinction between the behavioral contributions of nSTRF and STRF neurons.

neuroscience↗
bioRxiv2024

Structure-Based Design of Covalent Nanobody Binders for a Thermostable Green Fluorescence Protein

Green fluorescence protein (GFP) lights up almost every aspects of life sciences. An ultra thermostable GFP (TGP), engineered from a coral GFP, offers potential advantages over traditional jellyfish-derived GFP due to its high stability. However, owing to its later discovery, TGP lacks the extensive toolsets available for GFP, such as heavy chain-only antibody binders known as nanobodies. In this study, we have structurally characterized TGP in complex with Sb92, a synthetic nanobody identified from a previous in vitro screening, revealing its precise three-dimensional epitope. This structural insight, alongside the previously characterized Sb44-TGP complex, have allowed us to rationally design disulfide bonds between antigen and antibody for tighter interactions. Using biochemical analyses, we identify two bridged complexes (TGP A18C-Sb44 V100C, TGP E118C-Sb92 S57C), with the TGP-Sb92 disulfide pair showing high resistance to reducing agents. Our study expands the toolkit available for TGP and should encourage its wider applications.

biochemistry↗
bioRxiv2024

Expression variability following gene duplication facilitates gene retention

Genome analyses reveal that gene duplication in eukaryotes is pervasive, providing a primary source for the emergence of new genes. However, the mechanisms dictating early duplicate retention and the emergence of functional biases--such as the enrichment of tandem duplicates in environmental responses--remain unclear. Here, to better understand the mechanisms and factors determining gene retention, we study a frequently overlooked molecular feature--expression variability--as measured by within-line expression variation, termed variability. We demonstrate that, on average, genes with duplicates exhibit higher expression variability than singletons. Furthermore, small-scale duplications (SSDs) and whole-genome duplications (WGDs) display contrasting functional outcomes and time-dependent profiles in expression variability. These findings suggest a potential overarching mechanism that facilitates gene expression divergence, functional gains of environmental responses, and duplicate retention following SSDs.

evolutionary biology↗
bioRxiv2024

Parallel neuroinflammatory pathways to cerebrovascular injury and amyloid-beta in Alzheimer's disease

ImportanceWhile the hallmark pathologies of amyloid-beta (A{beta}) and tau in Alzheimers disease (AD) are well documented and even part of the definition, upstream neuroinflammation is thought to play an important role but remains poorly understood. ObjectivesWe tested whether two distinct neuroinflammatory markers are associated with cerebrovascular injury and A{beta}, and whether these markers are associated with plasma phosphorylated tau (pTau) concentration, medial temporal lobe (MTL) cortical and hippocampal atrophy, and memory deficits. We examined neuroinflammatory markers plasma YKL-40 and GFAP, due to previous conflicting evidence relating YKL-40 and GFAP to AD pathogenic markers. DesignCross-sectional data from a community observational study (Biomarker Exploration in Aging, Cognition, and Neurodegeneration - BEACoN) were included. SettingAll participants were enrolled in a single site, at University of California, Irvine. Participants126 participants were included if they had at least one of the following measures available: neuropsychological data, MRI, A{beta}-PET, or plasma. ExposuresPlasma YKL-40 and plasma glial fibrillary acidic protein (GFAP) levels. Main outcomes and measuresWhite matter hyperintensity (WMH) volume, 18F-florbetapir (FBP) PET mean SUVR, plasma phosphorylated tau (pTau-217) concentration, MTL cortical thickness, hippocampal volume, and memory function assessed by Rey Auditory Verbal Learning Test. Using path analysis, we tested whether higher plasma YKL-40 and GFAP are associated with WMH and A{beta}, and whether these converge to downstream markers of tauopathy, MTL neurodegeneration, and memory deficits. ResultsIn older adults without dementia (N=126, age=70.60+6.29, 62% women), we found that higher plasma YKL-40 concentration was associated with greater WMH volume, while higher plasma GFAP concentration was related to increased FBP SUVR. Further, higher plasma GFAP, WMH and FBP SUVR were independently associated with increased pTau-217. In turn, plasma pTau-217 was associated with reduced MTL cortical thickness and hippocampal volume. Subsequently, only reduced hippocampal volume was related to lower memory function. Conclusions and RelevanceNeuroinflammatory markers contribute to parallel pathways of cerebrovascular injury and A{beta}, which converge to tau-associated neurodegeneration and memory deficits in older adults. These observations underscore the need for a more comprehensive approach to developing an AD framework and treatment strategies. KEY POINTSO_ST_ABSQuestionC_ST_ABSHow does neuroinflammation impact downstream features of cerebrovascular injury and amyloid-beta (A{beta}) in Alzheimers disease? FindingsIn this study of 126 older adults without dementia, we found evidence for two distinct neuroinflammatory pathways that lead to neurodegeneration and memory deficits. One path involves plasma YKL-40 and its impact on cerebrovascular injury, as measured by white matter hyperintensities (WMH) on MRI scans. The other involves plasma glial fibrillary acidic protein (GFAP) and its impact on A{beta} deposition measured via 18F-florbetapir (FBP) PET. Both pathways converged on tauopathy, measured by plasma pTau-217, which was associated with lower medial temporal lobe (MTL) cortical thickness and hippocampal volume, and consequently, memory deficits. MeaningInflammation acts on Alzheimers disease mechanisms via multiple distinct and parallel pathways which converge downstream onto neurodegeneration. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=110 SRC="FIGDIR/small/616579v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@2d3c39org.highwire.dtl.DTLVardef@1ccc453org.highwire.dtl.DTLVardef@6d40bdorg.highwire.dtl.DTLVardef@b543cb_HPS_FORMAT_FIGEXP M_FIG C_FIG Credit: BioRender was used to help create this graphical abstract.

neuroscience↗
bioRxiv2024

A STAG2-PAXIP1/PAGR1 axis suppresses lung tumorigenesis

The cohesin complex is a critical regulator of gene expression. STAG2 is the most frequently mutated cohesin subunit across several cancer types and is a key tumor suppressor in lung cancer. Here, we coupled somatic CRISPR-Cas9 genome editing and tumor barcoding with an autochthonous oncogenic KRAS-driven lung cancer model and show that STAG2 is uniquely tumor suppressive among all core and auxiliary cohesin components. The heterodimeric complex components PAXIP1 and PAGR1 have highly correlated effects with STAG2 in human lung cancer cell lines, are tumor suppressors in vivo, and are epistatic to STAG2 in oncogenic KRAS-driven lung tumorigenesis in vivo. STAG2 inactivation elicits changes in gene expression, chromatin accessibility and 3D genome conformation that impact cancer cell state. Gene expression and chromatin accessibility similarities between STAG2- and PAXIP1-deficient neoplastic cells further relates STAG2-cohesin to PAXIP1/PAGR1. These findings reveal a STAG2-PAXIP1/PAGR1 tumor-suppressive axis and uncover novel PAXIP1-dependent and PAXIP1-independent STAG2-cohesin mediated mechanisms of lung tumor suppression. SUMMARYSTAG2 is a frequently mutated cohesin subunit across several cancers and one of the most important functional suppressors of lung adenocarcinoma. Our findings underscore important roles of STAG2 in suppressing lung tumorigenesis and highlight a STAG2-PAXIP1/PAGR1 tumor-suppressive program that may transcend cancer type.

cancer biology↗
bioRxiv2024

ElixirSeeker: A Machine Learning Framework Utilizing Attention-Driven Fusion of Molecular Fingerprints for the Discovery of Anti-Aging Compounds

Despite the growing interest in anti-aging drug development, high cost and low success rate pose a significant challenge. We present ElixirSeeker, a new machine-learning framework designed to help speed up the discovery of potential anti-aging compounds by utilizing the attention-driven fusion of molecular fingerprints. Our approach integrates molecular fingerprints generated by different algorithms and utilizes XGBoost to select optimal fingerprint lengths. Subsequently, we assign weights to the molecular fingerprints and employ Kernel Principal Component Analysis (KPCA) to reduce dimensionality, integrating different attention-driven methods. We trained the algorithm using DrugAge database. Our comprehensive analyses demonstrate that 64-bit Attention-ElixirFP maintains high predictive accuracy and F1 score while minimizing computational cost. Using ElixirSeeker to screen external compound databases, we identified a number of promising candidate anti-aging drugs. We tested top 6 hits and found that 4 of these compounds extend the lifespan of Caenorhabditis elegans, including Polyphyllin , Medrysone, Thymoquinone and Medrysone. This study illustrates that attention-driven fusion of fingerprints maximizes the learning of molecular activity features, providing a novel approach for high-throughput machine learning discovery of anti-aging molecules.

systems biology↗
bioRxiv2024

A near-complete genome assembly of the bearded dragon Pogona vitticeps provides insights into the origin of Pogona sex chromosomes

BackgroundThe agamid dragon lizard Pogona vitticeps is one of the most popular domesticated reptiles to be kept as pets worldwide. The capacity of breeding in captivity also makes it emerging as a model species for a range of scientific research, especially for the studies of sex chromosome origin and sex determination mechanisms. ResultsBy leveraging the CycloneSEQ and DNBSEQ sequencing technologies, we conducted whole genome and long-range sequencing for a captive-bred ZZ male to construct a chromosome-scale reference genome for P. vitticeps. The new reference genome is [~]1.8 Gb in length, with a contig N50 of 202.5 Mb and all contigs anchored onto 16 chromosomes. Genome annotation assisted by long-read RNA sequencing greatly expanded the P. vitticeps lncRNA catalog. With the chromosome-scale genome, we were able to characterize the whole Z sex chromosome for the first time. We found that over 80% of the Z chromosome remains as pseudo-autosomal region (PAR) where recombination is not suppressed. The sexually differentiated region (SDR) is small and occupied mostly by transposons, yet it aggregates genes involved in male development, such as AMH, AMHR2 and BMPR1A. Finally, by tracking the evolutionary origin and developmental expression of the SDR genes, we proposed a model for the origin of P. vitticeps sex chromosomes which considered the Z-linked AMH as the master sex-determining gene. ConclusionsOur study provides novel insights into the sex chromosome origin and sex determination of this model lizard. The near-complete P. vitticeps reference genome will also benefit future study of amniote evolution and may facilitate genome-assisted breeding.

genomics↗
bioRxiv2024

Autoantigen TRIM21 (Ro52) assembles pro-inflammatory immune complexes following lytic cell death

Sjogrens disease (SjD) causes localised and systemic inflammation due to autoantibody production against intracellular proteins, such as TRIM21/Ro52. TRIM21 is an E3 ubiquitin ligase which binds antibody Fc domains on opsonised pathogens, which have escaped extracellular immunity and entered cytosols; TRIM21 ubiquitinates these, driving their proteasomal degradation. How and why TRIM21 becomes an autoantigen remains unclear. We show that TRIM21 is released upon lytic cell death (pyroptosis/necroptosis) but not apoptosis. Released TRIM21 binds circulating antibody Fc domains, and forms large immune complexes (ICs). These are further enhanced with TRIM21/Ro52 seropositive SjD plasma antibodies, where interactions are mediated via both Fc and F(ab)2 domains. TRIM21-ICs are taken up by macrophages, which in high interferon environments drive pro-inflammatory responses, antigen presentation, and inflammatory and metabolic transcriptional changes. Whilst many cytosolic proteins are released by dead cells, due to its high affinity for antibodies, TRIM21 can generate large ICs. This may perpetuate inflammation and antigen presentation, causing TRIM21 to be highly autoimmunogenic. One Sentence SummaryHow the intracellular protein TRIM21 becomes an autoantigen.

immunology↗
bioRxiv2024

Vascular network-inspired diffusible scaffolds for engineering functional neural organoids

Organoids, three-dimensional in vitro organ-like tissue cultures derived from stem cells, show promising potential for developmental biology, drug discovery, and regenerative medicine. However, the function and phenotype of current organoids, especially neural organoids, are still limited by insufficient diffusion of oxygen, nutrients, metabolites, signaling molecules, and drugs. Herein, we present Vascular network-Inspired Diffusible (VID) scaffolds to fully recapture the benefits of physiological diffusion physics for generating functional organoids and phenotyping their drug response. In a proof-of-concept application, the VID scaffolds, 3D-printed meshed tubular channel networks, support the successful generation of engineered human midbrain organoids almost without necrosis and hypoxia in commonly used well-plates. Compared to conventional organoids, these engineered organoids develop with more physiologically relevant features and functions including midbrain-specific identity, oxygen metabolism, neuronal maturation, and network activity. Moreover, these engineered organoids also better recapitulate pharmacological responses, such as neural activity changes to fentanyl exposure, compared to conventional organoids with significant diffusion limits. Combining these unique scaffolds and engineered organoids may provide insights for organoid development and therapeutic innovation.

bioengineering↗
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

Patch and matrix striatonigral neurons differentially regulate locomotion

Spiny projection neurons (SPNs) in the dorsal striatum play crucial roles in locomotion control and value-based decision-making. SPNs, which include both direct-pathway striatonigral and indirect-pathway striatopallidal neurons, can be further classified into subtypes based on distinct transcriptomic profiles and cell body distribution patterns. However, how these SPN subtypes regulate spontaneous locomotion in the context of environmental valence remains unclear. Using Sepw1-Cre transgenic mice, which label a specific SPN subtype characterized by a patchy distribution of cell bodies in the dorsal striatum, we found that these patchy striatonigral neurons constrain motor vigor in response to valence differentials. In a modified light/dark box test, mice exhibited differential walking speeds between the light and dark zones. Genetic ablation of these patchy SPNs disrupted restful slowing in the dark zone and increased zone discrimination by speed. In vivo recordings linked the activity of these neurons to zone occupancy, speed, and deceleration, with a specific role in mediating deceleration. Furthermore, chemogenetic activation of patchy SPNs--and optical activation of striatonigral neurons in particular--reduced locomotion and attenuated speed-based zone discrimination. These findings reveal that a subtype of patchy striatonigral neurons regulates implicit walking speed selection based on innate valence differentials.

neuroscience↗