Biology subjects

Wang, C.

Publications and source records attributed to Wang, C..

At least 451 records · Page 25Linked to original sources

bioRxiv2024

A VgrG2b fragment cleaved by caspase-11/4 promotes Pseudomonas aeruginosa infection through suppressing the NLRP3 inflammasome

The T6SS of Pseudomonas aeruginosa plays an essential role in the establishment of chronic infections. Inflammatory cytokines mediated by inflammasomes are crucial for the body to resist bacterial infections. Here we found that during the infection of P. aeruginosa, non-canonical inflammasome was activated in macrophages, but the activation of downstream NLRP3 inflammasome was inhibited. The VgrG2b of P. aeruginosa is recognized and cleaved by caspase-11, generating a free C-terminal fragment. The VgrG2b C-terminus can bind to NLRP3, inhibiting the activation of the NLRP3 inflammasome by rejecting NEK7 binding to NLRP3. Administrating a specific peptide that inhibits the cleavage of VgrG2b by caspase-11 to mice can significantly improve their survival rate during infection. Our discovery elucidates a mechanism by which P. aeruginosa inhibits host immune response, providing a new approach for the future clinical treatment of P. aeruginosa infections.

immunology↗

bioRxiv2024

Spatial gene expression at single-cell resolution from histology using deep learning with GHIST

The increased use of spatially resolved transcriptomics provides new biological insights into disease mechanisms. However, the high cost and complexity of these methods are barriers to broad clinical adoption. Consequently, methods have been created to predict spot-based gene expression from routinely-collected histology images. Recent benchmarking showed that current methodologies have limited accuracy and spatial resolution, constraining translational capacity. Here, we introduce GHIST, a deep learning-based framework that predicts spatial gene expression at single-cell resolution by leveraging subcellular spatial transcriptomics and synergistic relationships between multiple layers of biological information. We validated GHIST using public datasets and The Cancer Genome Atlas data, demonstrating its flexibility across different spatial resolutions and superior performance. Our results underscore the utility of in silico generation of single-cell spatial gene expression measurements and the capacity to enrich existing datasets with a spatially resolved omics modality, paving the way for scalable multi-omics analysis and new biomarker discoveries.

bioinformatics↗

bioRxiv2024

Characterization of Multicellular Niches Supporting Hematopoietic Stem Cells Within Distinct Zones

Previous studies of hematopoietic stem cells (HSCs) primarily focused on single cell-based niche models, yielding fruitful but conflicting findings1-5. Here we report our investigation on the fetal liver (FL) as the primary fetal hematopoietic site using spatial transcriptomics. Our study reveals two distinct niches: the portal-vessel (PV) niche and the sinusoidal niche. The PV niche, composing N-cadherin (N-cad)HiPdgfr+ mesenchymal stromal cells (MSCs), endothelial cells (ECs), and N-cadLoAlbumin+ hepatoblasts, maintains quiescent and multipotential FL-HSCs. Conversely, the sinusoidal niche, comprising ECs, hepatoblasts and hepatocytes, as well as potential macrophages and megakaryocytes, supports proliferative FL-HSCs biased towards myeloid lineages. Unlike prior reports on the role of Cxcl12, with its depletion from vessel-associated stromal cells leading to 80% of HSCs reduction in the adult bone marrow (BM)6,7, depletion of Cxcl12 via Cdh2CreERT (encoding N-cad) induces altered localization of HSCs from the PV to the sinusoidal niches, resulting in an increase of HSC number but with myeloid-bias. Similarly, we discovered that adult BM encompasses two niches within different zones, each composed of multi-cellular components: trabecular bone area (TBA, or metaphysis) supporting deep-quiescent HSCs, and central marrow (CM, or diaphysis) fostering heterogenous proliferative HSCs. This study transforms our understanding of niches by shifting from single cell-based to multicellular components within distinct zones, illuminating the intricate regulation of HSCs tailored to their different cycling states.

developmental biology↗

bioRxiv2024

Dynamic Localization of Leukemia Stem Cells via CXCL12 Regulates Leukemia Progression

The processes that govern leukemia progression and remission are poorly understood. Our research reveals that the CXCL12 gradient, traditionally associated with LSC quiescence and survival, critically determines LSC localization and associated behavior. Specifically, CXCL12 guides LSCs to either the quiescent niche in the metaphysis, characterized by N-cadherin-expressing mesenchymal stromal cells (N-cad+ MSCs), or the proliferative niche in the central marrow (CM), marked by sinusoidal endothelial cells and associated stromal cells. We identified that the CXCL12 gradient is finely regulated by the interplay between dipeptidyl peptidase 4 (DPP4) on LSCs and glypican-3 (GPC3) on N-cad+ MSCs. DPP4 deactivates CXCL12, while GPC3 inhibits DPP4, resulting in a higher CXCL12 concentration in the metaphysis and a lower concentration in the CM. This differential gradient facilitates leukemia progression by promoting LSC quiescence and survival in the metaphysis versus relative proliferation and apoptosis in the CM. Depletion of Dpp4 from LSCs or Cxcl12 from N-cad+ MSCs disrupts this gradient, mobilizing LSCs from the metaphysis to the CM and significantly hindering leukemia development. Our findings redefine the role of CXCL12 in LSC behavior and provide a clearer understanding of leukemia progression. This novel insight highlights the potential for targeted therapeutic strategies that disrupt the CXCL12 gradient to treat minimal residual LSCs, offering a promising path toward a lasting cure for acute myeloid leukemia (AML).

cancer biology↗

bioRxiv2024

GeneLLM: A Large cfRNA Language Model for Cancer Screening from Raw Reads

We present GeneLLM, a novel large language model that offers a transformative approach to non-invasive cancer detection and biomarker discovery by directly interpreting plasma cell-free RNA (cfRNA) sequences. Unlike traditional annotation-dependent methods, GeneLLM operates without prior knowledge, achieving significantly improved multi-cancer detection accuracy. Critically, GeneLLM identifies novel cfRNAs ( pseudo-biomarkers) originating from previously unannotated genomic regions-overlooked by existing methods-offering new therapeutic targets and insights into intercellular communication. This innovative, cost-effective approach bypasses traditional bioinformatics tools, generating novel pseudo-biomarkers that outperform existing methods even with low-depth sequencing data. Consequently, GeneLLM opens new avenues for biomarker discovery and expands our understanding of the extracellular transcriptomes role in cancer development.

bioinformatics↗

bioRxiv2024

Structure-Mechanics Principles and Mechanobiology of Fibrocartilage Pericellular Matrix: A Pivotal Role of Type V Collagen

The pericellular matrix (PCM) is the immediate microniche surrounding resident cells in various tissue types, regulating matrix turnover, cell-matrix cross-talk and disease initiation. This study elucidated the structure-mechanical properties and mechanobiological functions of the PCM in fibrocartilage, a family of connective tissues that sustain complex tensile and compressive loads in vivo. Studying the murine meniscus as the model tissue, we showed that fibrocartilage PCM contains thinner, random collagen fibrillar networks that entrap proteoglycans, a structure distinct from the densely packed, highly aligned collagen fibers in the bulk extracellular matrix (ECM). In comparison to the ECM, the PCM has a lower modulus and greater isotropy, but similar relative viscoelastic properties. In Col5a1+/D menisci, the reduction of collagen V, a minor collagen localized in the PCM, resulted in aberrant fibril thickening with increased heterogeneity. Consequently, the PCM exhibited a reduced modulus, loss of isotropy and faster viscoelastic relaxation. This disrupted PCM contributes to perturbed mechanotransduction of resident meniscal cells, as illustrated by reduced intracellular calcium signaling, as well as upregulated biosynthesis of lysyl oxidase and tenascin C. When cultured in vitro, Col5a1+/D meniscal cells synthesized a weakened nascent PCM, which had inferior properties towards protecting resident cells against applied tensile stretch. These findings underscore the PCM as a distinctive microstructure that governs fibrocartilage mechanobiology, and highlight the pivotal role of collagen V in PCM function. Targeting the PCM or its molecular constituents holds promise for enhancing not only meniscus regeneration and osteoarthritis intervention, but also addressing diseases across various fibrocartilaginous tissues.

bioengineering↗

bioRxiv2024

Mature and migratory dendritic cells promote immune infiltration and response to anti-PD-1 checkpoint blockade in metastatic melanoma

Immune checkpoint inhibitors (ICIs) have heralded a remarkable shift in cancer care, significantly extending survival for advanced cancer patients. However, despite their remarkable clinical successes, a substantial majority of patients fail to achieve a lasting response to ICIs. To address this challenge and gain insights into the complex landscape of the tumor microenvironment (TME), we conducted an extensive analysis using single-cell RNA sequencing (scRNA; [~]216K cells across 39 samples) and single-nucleus transposase-accessible chromatin sequencing (snATAC; [~]43K cells from 15 samples) in a metastatic melanoma cohort. This systematic approach delineates 14 distinct cell types and 55 cell subtypes, including the identification of 15 transcriptional hallmarks of malignant cells. Through correlation analysis of cell subtype proportions, we unveiled six distinct clusters associated with varying tumor responses. Particularly intriguing was the identification of the mature DC enriched in immunoregulatory molecules (mregDC) subtype exhibiting correlations with naive T and B cells, forming an anti-tumor program that underscores the importance of multiple immune cell types in mediating anti-tumor immunity. Notably, we found that mregDC abundance represents a good prognostic predictor of progression-free survival (PFS) in the context of ICI treatment, and when combined with the TCF7+/- CD8 T cell ratio, it reliably predicts patient PFS across treatments beyond ICI. We validated our findings using an independent cohort of 274 ICI-treated melanoma samples analyzed using tissue-level expression. We next compared mregDCs and conventional dendritic cell types 1 and 2 (cDC1 and cDC2) using transcriptome signature, differentiation trajectory, interactome, cytokine milieu, and epigenome landscape analyses. This comparative analysis shed light on the unique attributes of mregDCs within the TME. Finally, we investigated cell type/subtype-specific genes, pathways, immune response enrichment, and ligand-receptor interactions closely associated with the proportions of mregDCs within the TME. These molecular and cellular insights, with their critical roles in enhancing the immune response against cancer, offer valuable prospects for predicting the efficacy of ICI regimens, and potentially guiding the selection of rational combinatorial therapies.

cancer biology↗

bioRxiv2024

TurboID-mediated surface protein biotinylation to inhibit the growth of Staphylococcus aureus

Staphylococcus aureus (S. aureus) infection is major cause of nosocomial infections. Antibiotic treatment for S. aureus remains the primary solution for managing S. aureus infections, which, however, increases the risk of antibiotic resistance. To broaden the resolutions on S. aureus infection, here we report TurboID-mediated protein proximity technologies to inhibit the growth of S. aureus. To achieve this goal, we utilized synthetic biology techniques to create a fusion protein named N-AgrD-TurboID (Agr-ID). The N-AgrD domain includes auto-inducer peptide (AIP) which combined to the surface AgrC protein on S. aureus. As such, TurboID then catalyzed the production of biotinoyl-5-AMP anhydride, triggering the biotinylation of surface proteins on S. aureus 25923 which were visualized by using fluorescence microscopy after incubating with Alexa Fluor 647-conjugated streptavidin. The biotinylation of surface protein on S. aureus 25923, S. aureus 43300, and S. aureus 6538 (MRSA) also resulted in growth inhibition and impaired colonization. Moreover, the biotinylation on surface protein further inhibited virulence protein production in S. aureus 25923, as indicated by reduced apoptosis of HEK 293T cells after treatment with S. aureus 25923 lysates. Overall, our work reveals that the biotinylation of surface proteins can inhibit the growth and toxicity of S. aureus 25923, S. aureus 43300, and S. aureus 6538 (MRSA), indicating therapeutic potential in clinical treatment.

microbiology↗

bioRxiv2024

PPTC7 acts as an essential co-factor of the SCFFBXL4 ubiquitin ligase complex to restrict BNIP3/BNIP3L-dependent mitophagy

Mitophagy is a selective process that targets damaged, dysfunctional, or superfluous mitochondria for degradation through autophagy. The SCFFBXL4 ubiquitin ligase complex suppresses basal mitophagy by targeting BNIP3 and BNIP3L, two key mitophagy cargo receptors, for ubiquitin-proteasomal degradation. FBXL4 loss-of-function mutations lead to excessive BNIP3/3L-dependent mitophagy, thereby causing a devasting multi-system disorder called mitochondrial DNA depletion syndrome, type 13 (MTDPS13). PPTC7, a mitochondrial matrix phosphatase, is essential for proper mitochondrial function and biogenesis. Here, we show that a proportion of PPTC7 is located on the outer mitochondrial membrane, where it interacts with FBXL4 and BNIP3/3L. PPTC7 decreases BNIP3/3L protein stability in a protein phosphatase activity-independent manner. Using in vitro cell culture and Pptc7 knockout mice models, we demonstrate that PPTC7 deficiency activates high levels of basal mitophagy in a BNIP3/3L-dependent manner. Mechanistically, PPTC7 facilitates SCFFBXL4-mediated ubiquitin-proteasomal degradation of BNIP3/3L. Overall, these findings establish PPTC7 as an essential co-factor of the SCFFBXL4 complex and a suppressor of BNIP3/3L-dependent mitophagy.

cell biology↗

bioRxiv2024

The up-regulation of TGF-beta1 by miRNA-132-3p/WT1 is involved in inducing leukemia cells to differentiate into macrophages

Although it has been shown that abnormal expression of Wilms tumor gene 1 (WT1) is associated with the occurrence of leukemia, the specific mechanism via which it induces leukemia cells to differentiate into macrophages remains poorly understood. Based on the prediction that the microRNA miRNA-132-3p is the miRNA that possibly lies upstream of the WT1 gene, we hypothesized that miRNA-132-3p may participate in the polarization process of macrophages through regulating expression of the WT1 gene. The focus of the present study was therefore to investigate the role of the miRNA-132-3p/WT1 signaling axis in the differentiation of THP-1 leukemia cells into macrophages induced by PMA. The results obtained indicated that, compared with the control group, the proliferation of THP-1 cells was clearly inhibited by PMA, and the cell cycle was arrested at G0/G1 phase, associated with an upregulation of CD11b and CD14 expression. Induced by PMA, the expression level of miRNA-132-3p was increased, WT1 expression was decreased, and the expression level of TGF-{beta}1 was increased. Following transfection with miRNA-132-3p mimics, however, the expression of WT1 in the THP-1 cells was downregulated, with upregulation of the CD11b and CD14 antigens, whereas this downregulation of WT1 mediated by miRNA-132-3p mimics could be reversed by co-transfection with WT1 vector, which was accompanied by downregulation of the CD11b and CD14 antigens. The luciferase activity of the co-transfected miRNA-132-3p mimic + WT1-wild-type (WT) group was found to be statistically significantly lower compared with that of the co-transfected miRNA-132-3p mimic + WT1-mutated (MUT) group. Furthermore, chromatin immunoprecipitation experiments showed that WT1 was able to directly target the promoter of the downstream target gene TGF-{beta}1, which led to the negative modulation of TGF-{beta}1 expression, whereas downregulation of WT1 led to an upregulation of the expression of TGF-{beta}1, which thereby promoted the differentiation of THP-1 cells into macrophages. Taken together, the present study has provided evidence, to the best of the authors knowledge for the first time, that the miRNA-132-3p/WT1/TGF-{beta}1 axis is able to regulate the committed differentiation of leukemia cells into macrophages.

immunology↗

bioRxiv2024

High IL-1β and IL-18 Levels Associate with Gut Barrier Disruption and Monocyte Activation During Chronic SIV Infection with Long-Term Suppressive Antiretroviral Therapy

HIV-induced persistent immune activation is a key mediator of inflammatory comorbidities such as cardiovascular disease (CVD) and neurocognitive disorders. While a preponderance of data indicate that gut barrier disruption and microbial translocation are drivers of chronic immune activation, the molecular mechanisms of this persistent inflammatory state remain poorly understood. Here, utilizing the nonhuman primate model of HIV infection with suppressive antiretroviral therapy (ART), we investigated activation of inflammasome pathways and their association with intestinal epithelial barrier disruption and CVD pathogenesis. Longitudinal blood samples obtained from rhesus macaques with chronic SIV infection and long-term suppressive ART were evaluated for biomarkers of intestinal epithelial barrier disruption (IEBD), inflammasome activation (IL-1{beta} and IL-18), inflammatory cytokines, and triglyceride (TG) levels. Activated monocyte subpopulations and glycolytic potential were investigated in peripheral blood mononuclear cells (PBMCs). Higher plasma levels of IL-1{beta} and IL-18 were observed following the hallmark increase in IEBD biomarkers, intestinal fatty acid-binding protein (IFABP) and LPS-binding protein (LBP), during the chronic phase of treated SIV infection. Further, significant correlations of plasma IFABP levels with IL-1{beta} and IL-18 were observed between 10-12 months of ART. Higher levels of sCD14, IL-6, and GM-CSF, among other inflammatory mediators, were also observed only during the long-term SIV+ART phase along with a trend of increase in frequencies of activated CD14+CD16+ intermediate monocyte subpopulations. Lastly, we found elevated levels of blood TG and higher glycolytic capacity in PBMCs of chronic SIV-infected macaques with long-term ART. The increase in circulating IL-18 and IL-1{beta} following IEBD and their significant positive correlation with IFABP suggest a connection between gut barrier disruption and inflammasome activation during chronic SIV infection, despite viral suppression with ART. Additionally, the increase in markers of monocyte activation, along with elevated TG and enhanced glycolytic pathway activity, indicates metabolic remodeling that could accelerate CVD pathogenesis. Further research is needed to understand mechanisms by which gut dysfunction and inflammasome activation contribute to HIV-associated CVD and metabolic complications, enabling targeted interventions in people with HIV.

immunology↗

bioRxiv2024

Embracing Uncertainty Reshapes the ETHYLENE INSENSITIVE2-Activated Ethylene Signaling Framework

Signal transduction of the gaseous plant hormone ethylene by ETHYLENE INSENSITIVE2 (EIN2) is proposed to be regulated at multiple levels. EIN2 is phosphorylated by CONSTITUTIVE TRIPLE-RESPONSE1 (CTR1), subject to the F-Box proteins [EIN2-TARGETING PROTEIN1 (ETP1) and ETP2]-mediated degradation, and cannot activate ethylene signaling. Ethylene prevents EIN2 phosphorylation and degradation, and EIN2 accumulates and activates the signaling. MAOHUZI3 LIKE1 (MHL1) and MHL2 stabilize EIN2, and the mhl1 mhl2 double mutation confers ethylene insensitivity. Here, we reported that the regulation of EIN2-activated ethylene signaling can be independent of CTR1-mediated phosphorylation, ETP1/ETP2-directed degradation, and MHL1/MHL2-dependent stabilization. Both the etp1 etp2 double mutant and wild type showed identical ethylene dose-response curves, and the nontreated mhl1 mhl2 double mutant displayed substantial growth inhibition. The reported ethylene-insensitive root phenotype of mhl1 mhl2 seedlings requires sucrose and is associated with unknown loci. The ethylene receptor ETHYLENE RESPONSE1 (ETR1) and EIN2 interact at the rough endoplasmic reticulum. We propose that the docking of CTR1 to ETR1 promotes receptor signaling, which inhibits EIN2-activated ethylene signaling. The discrepancy between our findings and the current model is discussed. Our findings may disrupt the knowledge boundary of the present molecular model, developing a niche for findings outside the framework to advance our understanding of ethylene signaling.

plant biology↗

bioRxiv2024

Comprehensive profiling of transcriptional regulation in cartilage reveals pathogenesis of osteoarthritis

Cartilage damage is a leading cause of osteoarthritis (OA) etiology, however, the underlying mechanism governing gene expression regulation in this progress is poorly understood. Here, we described a comprehensive profiling of transcriptional regulation of 235 primary human cartilage samples. We identified 3,352 independent significant expression quantitative trait loci (eQTLs) for 3,109 genes. We explored the candidate casual SNP and its underlying regulatory mechanism using our established functional fine-mapping pipeline by integrating the cartilage-specific ATAC-seq data. We identified 117 causal eQTLs that display allele-specific open chromatin (ASoC) and 547 transcription factor binding-disruption (TBD) eQTLs. We conducted cell type-interaction eQTL (ci-eQTL) analyses based on speculated chondrocyte subtype proportions and revealed the regulation relationship of 120 eQTL-gene pairs showed cell type dependency. Further, by integrating with genome-wide association studies (GWASs) data of OA, we nominated 43 candidate effector genes for OA risk loci. We verified that the T allele of the OA risk variant rs11750646 increased the AR binding affinity to an open chromatin region and promoted the expression of an OA-related gene PIK3R1. Altogether, our findings provide new insights into the unique regulatory landscape of cartilage and elucidate potential mechanisms underlying the OA pathogenesis.

genetics↗

bioRxiv2024

Comparative Analysis of Human-Chimpanzee Divergence in Brain Connectivity and its Genetic Underpinnings

Chimpanzees (Pan troglodytes) are humans closest living relatives, making them the most directly relevant comparison point for understanding human brain evolution. Zeroing in on the differences in brain connectivity between humans and chimpanzees can provide key insights into the specific evolutionary changes that might have occured along the human lineage. However, conducting comparisons of brain connectivity between humans and chimpanzees remains challenging, as cross-species brain atlases established within the same framework are currently lacking. Without the availability of cross-species brain atlases, the region-wise connectivity patterns between humans and chimpanzees cannot be directly compared. To address this gap, we built the first Chimpanzee Brainnetome Atlas (ChimpBNA) by following a well-established connectivity-based parcellation framework. Leveraging this new resource, we found substantial divergence in connectivity patterns across most association cortices, notably in the lateral temporal and dorsolateral prefrontal cortex between the two species. Intriguingly, these patterns significantly deviate from the patterns of cortical expansion observed in humans compared to chimpanzees. Additionally, we identified regions displaying connectional asymmetries that differed between species, likely resulting from evolutionary divergence. Genes associated with these divergent connectivities were found to be enriched in cell types crucial for cortical projection circuits and synapse formation. These genes exhibited more pronounced differences in expression patterns in regions with higher connectivity divergence, suggesting a potential foundation for brain connectivity evolution. Therefore, our study not only provides a fine-scale brain atlas of chimpanzees but also highlights the connectivity divergence between humans and chimpanzees in a more rigorous and comparative manner and suggests potential genetic correlates for the observed divergence in brain connectivity patterns between the two species. This can help us better understand the origins and development of uniquely human cognitive capabilities.

neuroscience↗

bioRxiv2024

Conserved mycobacterial sRNA B11 regulates lipooligosaccharide synthesis at post-transcriptional level

Extractable glycolipids of mycobacteria, such as lipooligosaccharides (LOS), play key roles in responding to environmental stress and altering the host immune response. However, although the biosynthesis of LOS is likely controlled at multiple levels to ensure proper composition of the cell wall, the key regulators are currently unknown. Here, we studied B11, a conserved mycobacterial sRNA, and found that it post-transcriptionally regulates LOS synthesis in Mycobacteria marinum. Deletion of B11 alters the colony morphology and RNA sequencing combined with mass spectrometry identified several genes in the LOS synthesis locus that are regulated by B11. We found that B11 uses the cytosine-rich loops of its rho-independent transcriptional terminator to interact with guanine-tracks adjacent to the ribosome binding sites of its target genes, thereby impeding translation and promoting mRNA degradation by RNase E. These comprehensive functional studies of mycobacterial sRNA B11 demonstrate sRNA-based regulation of cell wall synthesis in mycobacteria. ImportanceDespite being identified for more than a decade, the functional characterization and regulatory mechanisms of mycobacterial sRNAs remain largely unexplored. We present here the most comprehensive functional study of mycobacterial sRNAs to date, employing convincible target screening using multifaceted experimental approaches and phenotype analysis. Our work reveals how synthesis of mycobacterial lipooligosaccharides (LOS), one of the crucial extractable glycolipids involved in environmental stress response and host immune modulation, is regulated at the post-transcriptional level by the conserved sRNA B11. Furthermore, our discovery of a highly conserved sRNA exhibiting distinct functions across mycobacterial species exemplifies divergent functional evolution among sRNAs.

microbiology↗

bioRxiv2024

Contracted anterior-posterior systematic covariance of cortical thickness in early-onset schizophrenia

Background and HypothesisSchizophrenia is a neurodevelopmental condition with alterations in both sensory and association cortical areas. These alterations have been reported to follow structural connectivity patterning, and to occur in a system-level fashion. Here, we investigated whether pathological alterations of schizophrenia originated from an early disruption of cortical organization by using 7-17-years-old individuals with early-onset schizophrenia (EOS). Study DesignWe estimated cortical thickness using T1-weighted structural MRI data from 95 patients with antipsychotic-naive first-episode EOS and 99 typically developing (TD) controls. We then computed structural covariance of cortical thickness and estimated system-level organizational axes by performing nonlinear dimensionality reduction techniques on covariance matrices for the EOS and TD groups. Finally, we tested for group differences between EOS and TD individuals in terms of both structural covariance and covariance distances along the systematic axis. Study ResultsThe first covariance gradient differentiated motor regions from other cortical areas. Similar to the macrostructural axis in adults, the second gradient axis in young TD discriminated anterior from posterior regions and was compressed in EOS patients relative to TD controls. In addition, patients showed increased structural covariance between two ends of the systematic axis, with increased geodesic distance of covarying regions between two ends. ConclusionOur findings revealed a contracted organizational axis of cortical thickness in EOS patients, which was attributed to excessive distally coordinated changes between anterior and posterior regions of the cortex. Taken together, our study suggests a possible early disruption of system-level neurodevelopment in schizophrenia.

pathology↗

bioRxiv2024

Bayesian Occam's Razor to Optimize Models for Complex Systems

Modeling complex biological systems necessitates the integration of vast and multifaceted information spanning various aspects of these systems, and is expected to yield more insights into the system than any of the inputs. Metamodeling, a specialized form of integrative modeling, addresses this by integrating existing models. Developing and optimizing metamodels pose challenges due to the complexities introduced by diverse input models and their inherent uncertainties. In this study, we employ Bayesian formalism to rigorously analyze the propagation of probability throughout the metamodeling process and propose quantitative assessments for it. Building on this, we introduce a method for optimizing metamodeling that adheres to the Bayesian Occams razor rationale, by (i) minimizing model uncertainty; (ii) maximizing model consistency; and (iii) reducing model complexity. To illustrate the benefits of this method, we apply it to the dynamic system of glucose-stimulated insulin secretion in pancreatic {beta}-cells. The optimized metamodel delivers more accurate estimates of impaired {beta}-cell dynamics and function in T2D subjects compared to the non-optimized one, underscoring the critical role of optimization in enhancing both model reliability and applicability. This method is implemented through the Integrative Modeling Platform (IMP), facilitating the development of accurate, precise, and sufficiently simple models for a variety of complex systems.

bioinformatics↗

bioRxiv2024

Modular Design and Scaffold-Synthesis of Multi-Functional Fluorophores for Targeted Cellular Imaging and Pyroptosis

Modified commercial fluorophores are essential tools for optical imaging and biomedical research. Their synthetic modification to incorporate new functions, however, remains a challenging task. Conventional strategies rely on linear synthesis in which a parent framework is gradually extended. We here designed and synthesized a versatile library of functional fluorophores via a scaffold-based Ugi four-component reaction (U-4CR). The adaptability of the scaffold is achieved through modification of starting materials. This allows to use a small range of starting materials for the creation of fluorogenic probes that can detect reactive-oxygen species and where the localization into subcellular organelles or membranes can be controlled. We present reaction yields ranging from 60% to 90% and discovered that some compounds can even function as imaging and therapeutic agents via Fenton chemistry inducing pyroptosis in living cancer cells. Our study underlines the potential of scaffold-based synthesis for versatile creation of functional fluorophores and their applications.

cell biology↗