Biology subjects

Sun, H.

Publications and source records attributed to Sun, H..

At least 199 records · Page 11Linked to original sources

bioRxiv2024

Comparative transcriptome analysis provides insights into the resistance regulation mechanism and inhibitory effect of fungicide phenamacril in Fusarium asiaticum

Fusarium asiaticum is a destructive phytopathogenic fungus that causes Fusarium head blight of wheat (FHB), leading to serious yield and economic losses to cereal crops worldwide. Our previous studies indicated that target-site mutations (K216R/E, S217P/L, or E420K/G/D) of Type I myosin FaMyo5 conferred high resistance to phenamacril. Here, we first constructed a sensitive strain H1S and point mutation resistant strains HA, HC and H1R. Then we conducted comparative transcriptome analysis of these strains in F. asiaticum after 1 g{middle dot}mL-1 and 10 g{middle dot}mL-1 phenamacril treatment. Results indicated that 2135 genes were differentially expressed (DEGs) among the sensitive and resistant strains. Among them, the DEGs encoding ammonium transporter MEP1/MEP2, nitrate reductase, copper amine oxidase 1, 4-aminobutyrate aminotransferase, amino-acid permease inda1, succinate-semialdehyde dehydrogenase, 2, 3-dihydroxybenzoic acid decarboxylase, etc., were significantly up-regulated in all the phenamacril-resistant strains. Compared to the control group, a total of 1778 and 2097 DEGs were identified in these strains after 1 g{middle dot}mL-1 and 10 g{middle dot}mL-1 phenamacril treatment, respectively. These DEGs involved in 4-aminobutyrate aminotransferase, chitin synthase 1, multiprotein-bridging factor 1, transcriptional regulatory protein pro-1, amino-acid permease inda1, ATP-dependent RNA helicase DED, acetyl-coenzyme A synthetase, sarcoplasmic/endoplasmic reticulum calcium ATPase 2, etc., showed significantly down-regulated expression in phenamacril-sensitive strain but not in resistant strains after phenamacril treatment. In addition, cyanide hydratase, mating-type protein MAT-1, putative purine nucleoside permease, plasma membrane protein yro2, etc., showed significantly co-down-regulated expression in all the strains after phenamacril treatment. Taken together, This study provide deep insights into the resistance regulation mechanism and inhibitory effect of fungicide phenamacril and these new annotated proteins or enzymes are worth for the discovery of new fungicide targets. Author summaryFungicide phenamacril resistance occur in F. asiaticum and the resistance regulation mechanis are systematic and complex. Here, we conducted comparative transcriptome analysis of a sensitive strain H1S and point mutation resistant strains HA, HC and H1R in F. asiaticum after 1 g{middle dot}mL-1 and 10 g{middle dot}mL-1 phenamacril treatment. Among these annotated proteins or enzymes, amino-acid permease inda1, 1, 4-aminobutyrate aminotransferase, chitin synthase 1, multiprotein-bridging factor 1, ATP-dependent RNA helicase DED, acetyl-coenzyme A synthetase, sarcoplasmic/endoplasmic reticulum calcium ATPase 2, cyanide hydratase, mating-type protein MAT-1, putative purine nucleoside permease, plasma membrane protein yro2, etc., were involved in the resistance regulation mechanism and inhibitory effect of fungicide phenamacril. Our paper provides a reference basis for the study of drug resistance in other microorganisms. In addition, the relevant proteins or enzymes annotated in our study also have reference value for the discovery of new fungicide targets.

pathology↗

bioRxiv2024

Shrimp Hemocyanin elicits a potent humoral response in mammals and is favorable to hapten conjugation

Conjugation to a carrier protein is essential to give rise to the antigenicity of hapten, which is a small molecule and cannot induce an immune response by itself alone. Three carrier proteins e.g. KLH (Keyhole Limpet Hemocyanin), BSA (Bovine Serum Albumin), and OVA (Ovalbumin) were used mostly. KLH is advantageous to the others, majorly owing to its strong immunogenicity and limited usage in other biological assays. However, the solubility of KLH is not as well as the others, especially after hapten conjugation. Besides, the high market price of KLH results in high costs in vaccine and antibody development. Here, we extracted the shrimp hemocyanin (SHC) from Penaeus vannamei (P. vannamei) with a production yield of > 1 g proteins (98 % pure) per 1 kg shrimp. Compared to KLH, the peptide-SHC conjugates exhibit higher solubility after hapten conjugation. Furthermore, compared with KLH, SHC induces comparable antibody production efficiency in mammals, with or without conjugation. Finally, rabbit polyclonal antibodies or mouse monoclonal antibodies were generated by immunizing SHC-peptide conjugates, and their applications in western blot, immunofluorescence and immunohistochemistry were confirmed. Therefore, we demonstrated that SHC may be used as a substitute for KLH in future antibody and vaccine development.

bioengineering↗

bioRxiv2024

Skeletal Muscle Stem Cells Modulate Niche Function in Duchenne Muscular Dystrophy through YY1-CCL5 Axis

Stem cell activity is known to be tightly regulated by both intrinsic and extrinsic pathways but less is known about whether and how stem cells modulate their niche microenvironment. Adult skeletal muscle stem cells (MuSCs) are indispensable for muscle regeneration and also tightly regulated by macrophages (MPs) and fibro-adipogenic progenitors (FAPs) in the niche. Deregulated MuSC/MP/FAP interactions and the ensuing inflammation and fibrosis are hallmarks of dystrophic muscle. Here in this study we demonstrate that intrinsic deletion of transcription factor YY1 in MuSCs exacerbates dystrophic pathologies by altering the cellular composition and heterogeneity of MPs and FAPs. Further analysis reveals that the YY1 loss induces the expression of immune genes in MuSCs, including Ccl5. Augmented secretion of CCL5 from MuSCs promotes the recruitment of MPs via CCL5/CCR5 mediated crosstalk, which subsequently hinders the apoptosis and clearance of FAPs through elevated TGF{beta}1 accumulation. Maraviroc mediated pharmacological blockade of the CCL5/CCR5 axis effectively mitigates muscle dystrophy and improves muscle performance. Lastly, we further demonstrate that YY1 represses Ccl5 transcription in MuSCs by directly binding to its enhancer thus facilitating promoter-enhancer looping. Altogether, our study has demonstrated the previously unappreciated role of MuSCs in actively shaping their niche microenvironment through secreting immunomodulatory cytokines, and has also provided novel insight into the therapeutic intervention of muscle dystrophy.

cell biology↗

bioRxiv2024

The majority of somatic mutations in fruit trees are layer-specific

BackgroundAll plant tissues and organs develop from meristems. Plant meristems are structured organs consisting of distinct layers of stem cells. Somatic mutations occurring in one of these layers can propagate into large sectors of the plant. However, the frequency and characteristics of meristematic mutations that form the basis of somaclonal phenotypic variation remain unclear. ResultsHere, we analysed the frequency and distribution of somatic mutations in an individual Apricot tree. For this, we sequenced the genomes of fruit samples corresponding to distinct meristematic cell layers selected across the entire tree. Most somatic mutations (>90%) were specific to individual layers. Genotyping the somatic mutations in leaves sampled next to the fruits confirmed their meristematic origin. Interestingly, layer 1 (epidermis) had a higher mutation load than layer 2 (mesocarp), implying differential mutational dynamics between the layers. The somatic mutations followed the branching pattern of the tree. These factors led to the unexpected observation that the layer 1 samples from different branches were more similar to each other than to layer 2 samples of the same branch. Further, using single-cell RNA sequencing, we demonstrated that the layer-specific mutant alleles could only be found in the transcripts of the respective, layer-specific cell clusters and could form the basis for somaclonal phenotypic variation. ConclusionsHere, we analyzed the prevalence and distribution of somatic mutations with meristematic origin. Our insights into the yet unexplored layer-specificity of such somatic mutations outlined how they can be identified and how they impact the breeding of clonally propagated crops.

genomics↗

bioRxiv2024

FveDAD2 negatively regulates branch crowns by affecting abscisic acid metabolism through FveHB7 in woodland strawberry

Strigolactones (SLs) are a significant hormone in plant growth response, crucial for regulating branching. DECREASED APICAL DOMINANCE2 (DAD2) is a novel receptor of SL. Here, FveDAD2 in woodland strawberries (Fragaria vesca) as the receptor for SL was identified, and three FveDAD2-RNAi transgenic lines that exhibited the phenotype of multi-branched crowns and smaller fruits were obtained. Gene expression, phenotypic analysis, and yeast assays were used to investigate the function of FveDAD2 in regulating branch crowns in strawberries. Like the alpha/beta hydrolase D14, FveDAD2 interacts with FveSMXL7 and depends on SL. Furthermore, the yeast single-hybrid, GUS activity assay, and LUC assay results demonstrate that FveSMXL7 binds to the promoter of FveHB7 and repress its transcription. FveHB7, a homeobox transcription factor, negatively regulates the transcription of FveABA8OH1, which encodes the enzyme that catabolizes abscisic acid (ABA). ABA contents were reduced in the shoot tips of the FveDAD2-RNAi lines, while treating wide-type plants with 20 M ABA significantly suppressed the number of branches. In conclusion, we discovered a novel pathway of SL signaling to regulate branching through ABA. One-sentence summaryFveDAD2 negatively regulates branch crowns by affecting abscisic acid levels by interacting with FveSMXL7 to regulate the expression of FveABA8OH1 via the transcription factor FveHB7.

molecular biology↗

bioRxiv2023

MERITS: a web-based integrated MycobacterialPE/PPE protein database

MotivationPE/PPE proteins, highly abundant in the Mycobacterium genome, play a vital role in virulence and immune modulation. Understanding their functions is key to comprehending the internal mechanisms of Mycobacterium. However, a lack of dedicated resources has limited research into PE/PPE proteins. ResultsAddressing this gap, we introduce MERITS, a comprehensive 3D structure database specifically designed for PE/PPE proteins. MERITS hosts 22,353 non-redundant PE/PPE proteins, encompassing details like physicochemical properties, subcellular localisation, post-translational modification sites, protein functions, and measures of antigenicity, toxicity, and allergenicity. MERITS also includes data on their secondary and tertiary structure, along with other relevant biological information. MERITS is designed to be user-friendly, offering interactive search and data browsing Features to aid researchers in exploring the potential functions of PE/PPE proteins. MERITS is expected to become a crucial resource in the field, aiding in developing new diagnostics and vaccines by elucidating the sequence-structure-functional relationships of PE/PPE proteins. Availability and implementationMERITS is freely accessible at http://merits.unimelb-biotools.cloud.edu.au/.

bioinformatics↗

bioRxiv2023

Aerosolized α1 adrenoreceptor antagonism does not affect experimentally induced lung fibrosis in animal models

Pulmonary Fibrosis is a progressive and incurable condition that complicates many disease states. Adrenergic hyperinnervation and accumulation of fibroblasts expressing 1- adrenoreceptors have been implicated in this process. Previous studies have demonstrated that systemic treatment with an 1-adrenoreceptors antagonist attenuates fibrotic endpoints in lung fibrosis models. In an attempt to develop a lung targeted therapy, we determined whether 1- adrenoreceptors antagonism delivered via inhaled administration of terazosin exerts antifibrotic benefits in experimentally induced lung fibrosis. C57/BL6 mice treated with bleomycin, or a doxycycline inducible line of transgenic mice with lung specific overexpression of the bioactive form of the human TGF{beta}1 (TGF{beta}1-Tg+ model), received nebulized terazosin at varying doses on a therapeutic schedule following the induction of fibrosis and were sacrificed at 21 days. Airway inflammation, fibrotic endpoints, and lung function were evaluated. 1-adrenoreceptors antagonism delivered via this method did not impact airway inflammation as indicated by bronchoalveolar lavage cell counts, and there was no significant difference observed in soluble collagen content. There was similarly no significant difference in respiratory mechanics with terazosin administration. These data show that inhaled delivery of the 1-adrenoreceptors antagonist terazosin by this method is ineffective at treating fibrosis in these models and suggest that alternative dosing schedules or delivery methods may be more fruitful avenues of investigation. Further exploration of these findings may provide new therapeutic options and illuminate mechanisms through which adrenergic innervation and 1-adrenoreceptors mediate fibrosis in the adult mammalian lung.

pathology↗

bioRxiv2023

Sysrecon: A systematic data-driven tool for genome-scale metabolic reconstructions

Genome-scale metabolic reconstructions contain the information about metabolism, which understands organisms molecular mechanisms better. Different reconstruction procedures are developed to achieve high-quality GSMRs of organisms; however, the descriptions of procedures are vague, meaning that they cannot be qualitatively reproduced, even contradictory, and different published reconstructions may involve different steps. This indicates that there is no unified strategy to quantify the steps in GSMRs. To resolve the problem, we created a R package, Sysrecon, to quantitatively and qualitatively describe the steps of GSMRs in the literature. Sysrecon disassembles GSMR into 93 steps, which are compiled after the comprehensive textual analysis of metabolic reconstructions. Then, Sysrecon decomposes each step of the reconstruction procedure into three components: step content, step conversion, and database and tools. When building a GSMR, Sysrecon creates a template procedure that includes a list of pipeline steps, the description of the information conversion in the steps, and the database and tools that may be used to facilitate the conversion. Because each steps conversion is defined by a formula, the entire GSMR can be dismantled into many step blocks. The reconstruction procedure is therefore transformed into an adaptable automated assembly line that can be customized and tailored to settings of different organisms. To the best of our knowledge, Sysrecon is the first computational tool that dynamically constructs the GSMRs pipeline and provides a framework for defining reconstruction steps and can be used as a basis for the development of high-quality GSMRs.

systems biology↗

bioRxiv2023

Not dasycladalean alga, but an Odyssey of the earliest Phanerozoic animal reef-builders

The compacted macrofossil Protomelission? sp. from the early Cambrian Xiaoshiba Lagerstatte was recently ascribed to early dasycladalean green algae and used to disprove the bryozoan affinity of coeval phosphatized microfossils, which made the puzzling question whether the bryozoans originated in early Cambrian pending again. Our new analyses of multiple specimens which are conspecific with Protomelission? from the Chengjiang Lagerstatte indicate that they are not dasycladaleans but one of the three groups of archaeocyath-like sponges that atypically inhabited siliciclastic substrates. All the archaeocyath-like fossils share the same preservation mode and exhibit archaeocyath-type external skeletal features. Particularly, the Protomellision?-like fossils preserve structures indicative of archaeocyath aquiferous system and ontogeny. They represent the first recognized one-walled archaeocyath sponges in South China and evidence the niche expansion of archaeocyaths on their way of global radiation from Siberia, 518 million years ago. The origin of the bryozoans remains a mystery.

paleontology↗

bioRxiv2023

KGRACDA: A Model Based on Knowledge Graph from Recursion and Attention Aggregation for CircRNA-disease Association Prediction

CircRNA has been found to exhibit with human diseases, rendering the investigation of the circRNA-disease association (CDA) of significant importance. Deep learning provides a novel avenue for predicting CDA, however, due to the limited availability of comprehensive CDA datasets, most existing methods operate by directly reasoning over triplets of embedded entities and relations, neglecting the explicit capture local depth information. In this study, we propose a novel approach called Knowledge Graph-Enhanced Recursive Aggregation for CDA (KGRACDA), which enables the querying of explicit local structures surrounding triplets, thereby serving as crucial evidence for predicting CDA. First, we construct a comprehensive CDA knowledge graph utilizing a large-scale, multi-source heterogeneous dataset. Subsequently, we develop a graph neural network using recursive techniques and employ attention aggregation to generate CDA prediction scores. Experimental results demonstrate that KGRACDA surpasses other state-of-the-art methods by explicitly capturing local depth information related to CDA. To improve the convenience of CDA prediction, we have updated an interactive web platform named HNRBase v2.0, which provides rich visualization of circRNA data, and allows users to easily download data and predict CDA using KGRACDA. The code and datasets are publicly available at https://github.com/maoyuanma/KGRACDA.

bioinformatics↗

bioRxiv2023

UBE2N is essential for maintenance of skin homeostasis and suppression of inflammation

UBE2N, a Lys63-ubiquitin conjugating enzyme, plays critical roles in embryogenesis and immune system development and function. However, its roles in adult epithelial tissue homeostasis and pathogenesis are unclear. We generated conditional mouse models that deleted Ube2n in skin cells in a temporally and spatially controlled manner. We found that Ube2n- knockout (KO) in the adult skin keratinocytes induced a range of inflammatory skin defects characteristic of psoriatic and actinic keratosis. These included eczematous inflammation, epidermal and dermal thickening, parakeratosis, and increased immune cell infiltration, as well as signs of edema and blistering. Single cell transcriptomic analyses and RT-qPCR showed that Ube2n KO keratinocytes expressed elevated myeloid cell chemo-attractants such as Cxcl1 and Cxcl2 and decreased the homeostatic T lymphocyte chemo-attractant, Ccl27a. Consistently, the infiltrating immune cells of Ube2n-KO skin were predominantly myeloid-derived cells including neutrophils and M1-like macrophages that were highly inflammatory, as indicated by expression of Il1{beta} and Il24. Pharmacological blockade of the IL-1 receptor associated kinases (IRAK1/4) alleviated eczema, epidermal and dermal thickening, and immune infiltration of the Ube2n mutant skin. Together, these findings highlight a key role of keratinocyte-UBE2N in maintenance of epidermal homeostasis and skin immunity and identify IRAK1/4 as potential therapeutic target for inflammatory skin disorders.

pathology↗

bioRxiv2023

Multi-task machine learning reveals the neuroanatomy fingerprint of mental processing

Mental processing delineates the functions of human mind encompassing a wide range of motor, sensory, emotional, and cognitive processes, each of which is underlain by the neuroanatomical substrates. Identifying accurate representation of functional neuroanatomy substrates of mental processing could inform understanding of its neural mechanism. The challenge is that it is unclear whether a specific mental process possesses a functional neuroanatomy fingerprint, i.e., a unique and reliable pattern of functional neuroanatomy that underlies the mental process. To address this question, we utilized a multi-task deep learning model to disentangle the functional neuroanatomy fingerprint of seven different and representative mental processes including Emotion, Gambling, Language, Motor, Relational, Social, and Working Memory. Results based on the functional magnetic resonance imaging data of two independent cohorts of 1235 subjects from the US and China consistently show that each of the seven mental processes possessed a functional neuroanatomy fingerprint, which is represented by a unique set of functional activity weights of whole-brain regions characterizing the degree of each region involved in the mental process. The functional neuroanatomy fingerprint of a specific mental process exhibits high discrimination ability (93% classification accuracy and AUC of 0.99) with those of the other mental processes, and is robust across different datasets and using different brain atlases. This study provides a solid functional neuroanatomy foundation for investigating the neural mechanism of mental processing. One-Sentence SummaryThere exists a functional neuroanatomy fingerprint to underlie the mental process.

bioinformatics↗

bioRxiv2023

Pervasive RNA Binding Protein Enrichment on TAD Boundaries Regulates TAD Organization

Mammalian genome is hierarchically organized by CTCF and cohesin through loop extrusion mechanism to facilitate the organization of topologically associating domains (TADs). Mounting evidence suggests additional factors/mechanisms exist to orchestrate TAD formation and maintenance. In this study, we investigate the potential role of RNA binding proteins (RBPs) in TAD organization. By integrated analyses of global RBP binding and 3D genome mapping profiles from both K562 and HepG2 cells, our study unveils the prevalent enrichment of RBPs on TAD boundaries and define boundary associated RBPs (baRBPs). We also characterize chromatin features of baRBP binding and uncover clustering among baRBPs and with transcription factors (TFs). Moreover, we found that baRBP binding is correlated with enhanced TAD insulation strength and in a CTCF independent manner. Further analyses revealed that baRBP binding is associated with nascent promoter transcription thus RBP/transcription may synergistically demarcate TADs. Additional experimental testing was performed using RBFox2 as a paradigm. Knockdown of RBFox2 in K562 cells causes remarkable TAD reorganization and boundary loss. Moreover, we found RBFox2 enrichment on TAD boundaries is a conserved phenomenon in C2C12 myoblast (MB) cells. RBFox2 is down-regulated and its bound boundaries are remodeled during MB differentiation into myotubes (MTs). Knockout of Rbfox2 in MBs also causes significant boundary reorganization. Finally, transcriptional inhibition in C2C12 cells indeed decreases RBFox2 binding and disrupts TAD boundary insulation. Altogether, our findings demonstrate that RBPs can play active role in modulating TAD organization through co-transcriptional association and synergistic action with nascent promoter transcripts.

bioinformatics↗

bioRxiv2023

Hammerhead-type FXR agonists induce an eRNA FincoR that ameliorates nonalcoholic steatohepatitis in mice

The nuclear receptor, Farnesoid X Receptor (FXR/NR1H4), is increasingly recognized as a promising drug target for metabolic diseases, including nonalcoholic steatohepatitis (NASH). Protein coding genes regulated by FXR are well known, but whether FXR also acts through regulation of long non-coding RNAs (lncRNAs), which vastly outnumber protein-coding genes, remains unknown. Utilizing RNA-seq and GRO-seq analyses in mouse liver, we found that FXR activation affects the expression of many RNA transcripts from chromatin regions bearing enhancer features. Among these we discovered a previously unannotated liver-enriched enhancer-derived lncRNA (eRNA), termed FincoR. We show that FincoR is specifically induced by the hammerhead-type FXR agonists, including GW4064 and tropifexor. CRISPR/Cas9-mediated liver-specific knockdown of FincoR in dietary NASH mice reduced the beneficial effects of tropifexor, an FXR agonist currently in clinical trials for NASH and primary biliary cholangitis (PBC), indicating that that amelioration of liver fibrosis and inflammation in NASH treatment by tropifexor is mediated in part by FincoR. Overall, our findings highlight that pharmacological activation of FXR by hammerhead-type agonists induces a novel eRNA, FincoR, contributing to the amelioration of NASH in mice. FincoR may represent a new drug target for addressing metabolic disorders, including NASH.

physiology↗

bioRxiv2023

Accelerating protein engineering with fitness landscape modeling and reinforcement learning

Protein engineering holds significant promise for designing proteins with customized functions, yet the vast landscape of potential mutations versus limited lab capacity constrains the discovery of optimal sequences. To address this, we present the {micro}Protein framework, which accelerates protein engineering by combining {micro}Former, a deep learning model for accurate mutational effect prediction, with {micro}Search, a reinforcement learning algorithm designed to efficiently navigate the protein fitness landscape using {micro}Former as an oracle. {micro}Protein leverages single mutation data to predict optimal sequences with complex, multi-amino acid mutations through its modeling of epistatic interactions and a multi-step search strategy. Except from state-of-the-art performance on benchmark datasets, {micro}Protein identified high-gain-of-function multi-point mutants for the enzyme {beta}-lactamase, surpassing the highest known activity level, in wet-lab, trained solely on single mutation data. These results demonstrate {micro}Proteins capability to discover impactful mutations across vast protein sequence space, offering a robust, efficient approach for protein optimization.

synthetic biology↗

bioRxiv2023

Universal Digital High Resolution Melt for the detection of pulmonary mold infections

BackgroundInvasive mold infections (IMIs) such as aspergillosis, mucormycosis, fusariosis, and lomentosporiosis are associated with high morbidity and mortality, particularly in immunocompromised patients, with mortality rates as high as 40% to 80%. Outcomes could be substantially improved with early initiation of appropriate antifungal therapy, yet early diagnosis remains difficult to establish and often requires multidisciplinary teams evaluating clinical and radiological findings plus supportive mycological findings. Universal digital high resolution melting analysis (U-dHRM) may enable rapid and robust diagnosis of IMI. This technology aims to accomplish timely pathogen detection at the single genome level by conducting broad-based amplification of microbial barcoding genes in a digital polymerase chain reaction (dPCR) format, followed by high-resolution melting of the DNA amplicons in each digital reaction to generate organism-specific melt curve signatures that are identified by machine learning. MethodsA universal fungal assay was developed for U-dHRM and used to generate a database of melt curve signatures for 19 clinically relevant fungal pathogens. A machine learning algorithm (ML) was trained to automatically classify these 19 fungal melt curves and detect novel melt curves. Performance was assessed on 73 clinical bronchoalveolar lavage (BAL) samples from patients suspected of IMI. Novel curves were identified by micropipetting U-dHRM reactions and Sanger sequencing amplicons. ResultsU-dHRM achieved an average of 97% fungal organism identification accuracy and a turn-around-time of 4hrs. Pathogenic molds (Aspergillus, Mucorales, Lomentospora and Fusarium) were detected by U-dHRM in 73% of BALF samples suspected of IMI. Mixtures of pathogenic molds were detected in 19%. U-dHRM demonstrated good sensitivity for IMI, as defined by current diagnostic criteria, when clinical findings were also considered. ConclusionsU-dHRM showed promising performance as a separate or combination diagnostic approach to standard mycological tests. The speed of U-dHRM and its ability to simultaneously identify and quantify clinically relevant mold pathogens in polymicrobial samples as well as detect emerging opportunistic pathogens may provide information that could aid in treatment decisions and improve patient outcomes.

microbiology↗

bioRxiv2023

Three-dimensional visualization of blood vessels in human gliomas based on tissue clearing and deep learning

Gliomas, with their intricate and aggressive nature, call for a detailed visualization of their vasculature. While many studies lean towards 2D imaging of thin sections, this method often overlooks the full spatial heterogeneity inherent to tumors. To overcome this limitation, our study melded state-of-the-art techniques, encompassing tissue clearing technology, 3D confocal microscopy imaging, and deep learning-aided vessel extraction, resulting in a comprehensive 3D visualization of glioma vasculature in intact human tissue. Specifically, we treated formalin-fixed thick human glioma tissue sections (500 m) with OPTIClear for transparency and subsequently performed immunofluorescent labeling using CD31. Using confocal microscopy, we obtained 3D images of the glioma vasculature. For vessel extraction, we employed a specialized 3D U-Net, enriched with image preprocessing and post-processing methods, and benchmarked its performance against the Imaris software. Our findings indicated that OPTIClear-enabled tissue clearing yielded a holistic 3D representation of immunolabeled vessels in clinical human glioma samples. Impressively, our deep learning technique outshined the traditional Imaris approach in terms of accuracy and efficiency in vessel extraction. Further, discernible variations in vascular metrics, such as mean diameter, branching point count, and volume ratio, were observed between low-grade and high-grade gliomas. In essence, our innovative blend of tissue clearing and deep learning not only enables enhanced 3D visualization of human glioma vasculature but also underscores morphological disparities across glioma grades, potentially influencing pathological grading, therapeutic strategies, and prognostic evaluations.

neuroscience↗

bioRxiv2023

Differential chromatin accessibility and transcriptional dynamics define breast cancer subtypes and their lineages

Breast cancer is a heterogeneous disease, and treatment is guided by biomarker profiles representing distinct molecular subtypes. Breast cancer arises from the breast ductal epithelium, and experimental data suggests breast cancer subtypes have different cells of origin within that lineage. The precise cells of origin for each subtype and the transcriptional networks that characterize these tumor-normal lineages are not established. In this work, we applied bulk, single-cell (sc), and single-nucleus (sn) multi-omic techniques as well as spatial transcriptomics and multiplex imaging on 61 samples from 37 breast cancer patients to show characteristic links in gene expression and chromatin accessibility between breast cancer subtypes and their putative cells of origin. We applied the PAM50 subtyping algorithm in tandem with bulk RNA-seq and snRNA-seq to reliably subtype even low-purity tumor samples and confirm promoter accessibility using snATAC. Trajectory analysis of chromatin accessibility and differentially accessible motifs clearly connected progenitor populations with breast cancer subtypes supporting the cell of origin for basal-like and luminal A and B tumors. Regulatory network analysis of transcription factors underscored the importance of BHLHE40 in luminal breast cancer and luminal mature cells, and KLF5 in basal-like tumors and luminal progenitor cells. Furthermore, we identify key genes defining the basal-like (PRKCA, SOX6, RGS6, KCNQ3) and luminal A/B (FAM155A, LRP1B) lineages, with expression in both precursor and cancer cells and further upregulation in tumors. Exhausted CTLA4-expressing CD8+ T cells were enriched in basal-like breast cancer, suggesting altered means of immune dysfunction among breast cancer subtypes. We used spatial transcriptomics and multiplex imaging to provide spatial detail for key markers of benign and malignant cell types and immune cell colocation. These findings demonstrate analysis of paired transcription and chromatin accessibility at the single cell level is a powerful tool for investigating breast cancer lineage development and highlight transcriptional networks that define basal and luminal breast cancer lineages.

cancer biology↗