Biology subjects

Zhang, H.

Publications and source records attributed to Zhang, H..

At least 721 records · Page 40Linked to original sources

bioRxiv2023

INTEGRATED GLOBAL CHICKEN REFERENCE PANEL FROM 13,187 CHICKEN GENOMES

Chickens are a crucial source of protein for humans and a popular model animal for bird research. Despite the emergence of imputation as a reliable genotyping strategy for large populations, the lack of a high-quality chicken reference panel has hindered progress in chicken genome research. To address this issue, here we introduce the first phase of the 100 K Global Chicken Reference Panel Project (100 K GCRPP). The project includes 13,187 samples and provides services for varied applications on its website (http://farmrefpanel.com/GCRP/). Currently, two panels are available: a Comprehensive Mix Panel (CMP) for domestication diversity research and a Commercial Breed Panel (CBP) for breeding broilers specifically. Evaluation of genotype imputation quality showed that CMP had the highest imputation accuracy compared to imputation using existing chicken panel in animal SNPAtlas, whereas CBP performed stably in the imputation of commercial populations. Additionally, we found that genome-wide association studies using GCRP-imputed data, whether on simulated or real phenotypes, exhibited greater statistical power. In conclusion, our study indicates that the GCRP effectively fills the gap in high-quality reference panels for chickens, providing an effective imputation platform for future genetic and breeding research.

bioinformatics↗

bioRxiv2023

Inhibition of KLK8 promotes pulmonary endothelial repair by restoring VE-cadherin/Akt/FOXM1 pathway

The tissue kallikrein-related peptidases (KLKs) are secreted serine proteases deeply involved in angiogenesis. However, whether KLKs are involved in the regulation of endothelial regeneration during sepsis remains unknown. By comparing the mRNA levels of 15 KLKs, we found that KLK8 was the highest induced KLK member in lung tissues or primary isolated mouse lung vascular endothelial cells (MLVECs) exposed to lipopolysaccharide (LPS). Adenovirus-mediated overexpression of KLK8 caused endothelial hyperpermeability both in vitro and in vivo. Inhibition of KLK8, by either gene knockout or KLK8 neutralizing antibodies, alleviated sepsis-induced endothelial hyperpermeability, acute lung injury and mortality. Mechanistically, transcription profiling of KLK8-overexpressed endothelial cells revealed a central role of forkhead box M1 (FOXM1) downregulation in mediating the pro-injury and anti-proliferation effects of KLK8. KLK8 cleaved VE-cadherin and consequently suppressed FOXM1 expression by inactivation of the VE-cadherin/Akt pathway. KLK8 deficiency or blockade rescued VE-cadherin/Akt/FOXM1 pathway, thus promoting endothelium regeneration. This study reveals a critical role for KLK8-induced inactivation of VE-cadherin/Akt/FOXM1 pathway in mediating the impairment of endothelial regeneration and the consequent lung vascular leakiness in response to sepsis. HighlightsO_LIUpregulated KLK8 mediates lung endothelial barrier dysfunction during sepsis C_LIO_LIKLK8 inactivates VE-cadherin/Akt/FOXM1, thus impairing endothelium regeneration C_LIO_LIKLK8 deficiency or blockade rescues VE-cadherin/Akt/FOXM1 signaling pathway C_LIO_LIKLK8 deficiency or blockade promotes endothelium regeneration during sepsis C_LIO_LIKLK8 deficiency or blockade attenuates sepsis-induced acute lung injury and mortality C_LI

physiology↗

bioRxiv2023

Decision Characteristics Underlying Non-Suicidal Self-Injury in Patients with Major Depressive Disorder

BackgroundNon-suicidal self-injury (NSSI) behavior is significantly prevalent in both adolescents and psychiatric populations, particularly in individuals with major depressive disorder (MDD). NSSI can be considered a result of risky decision-making in response to negative emotions, where individuals choose self-harm over other less harmful alternatives, suggesting a potential decision-making deficit in those engaging in NSSI. This study delves into the complex relationship between NSSI and depression severity in decision-making and its cognitive underpinnings. MethodsWe assessed decision behaviors in 57 MDD patients with NSSI, 42 MDD patients without NSSI and 142 healthy controls using the Balloon Analogue Risk Task, which involves risk-taking, learning, and exploration in uncertain scenarios. Using computational modeling, we dissected the nuanced cognitive dimensions influencing decision behaviors. A novel statistical method was developed to elucidate the interaction effects between NSSI and depression severity. ResultsContrary to common perceptions, we found that individuals with NSSI behaviors were typically more risk-averse. Meanwhile, there was a complex interaction between NSSI and depression severity in shaping risk-taking behaviors. As depressive symptoms intensified, these individuals with NSSI began to perceive less risk and behave more randomly. ConclusionsThis research provides new insights into the cognitive aspects of NSSI and depression, highlighting the importance of considering the influence of comorbid mental disorders when investigating the cognitive underpinnings of such behaviors, especially in the context of prevalent cross-diagnostic phenomena like NSSI behaviors.

neuroscience↗

bioRxiv2023

Structure basis for recognition of 26RFa by the pyroglutamylated RFamide peptide receptor

The neuropeptide 26RFa, a member of the RF-amide peptide family, activates the pyroglutamylated RF-amide peptide receptor (QRFPR), a class A GPCR. The 26RFa/QRFPR system plays critical roles in energy homeostasis, making QRFPR an attractive drug target for treating obesity, diabetes, and eating disorders. However, the lack of structural information has hindered our understanding of the peptide recognition and regulatory mechanism of QRFPR, impeding drug design efforts. In this study, we determined the cryo-EM structure of the Gq-coupled QRFPR bound to 26RFa. The structure reveals a unique assembly mode of the receptor extracellular regions and the peptide N-terminus and elucidates the recognition mechanism of the C-terminal heptapeptide of 26RFa within the transmembrane binding pocket of QRFPR. The study also clarifies the similarities and distinctions in the binding pattern of the RF-amide moiety in five RF-amide peptides and the RY-amide segment in neuropeptide Y. These findings deepen our understanding of the RF-amide peptides recognition, aiding in the rational design of drugs targeting QRFPR and other RF-amide receptors.

biophysics↗

bioRxiv2023

Neuronal connectivity, behavioral, and transcriptional alterations associated with the loss of MARK2

Neuronal connectivity is essential for adaptive brain responses and can be modulated by dendritic spine plasticity and the intrinsic excitability of individual neurons. Dysregulation of these processes can lead to aberrant neuronal activity, which has been associated with numerous neurological disorders including autism, epilepsy, and Alzheimers disease. Nonetheless, the molecular mechanisms underlying aberrant neuronal connectivity remains unclear. We previously found that the serine/threonine kinase Microtubule Affinity Regulating Kinase 2 (MARK2), also known as Partitioning Defective 1b (Par1b), is important for the formation of dendritic spines in vitro. However, despite its genetic association with several neurological disorders, the in vivo impact of MARK2 on neuronal connectivity and cognitive functions remains unclear. Here, we demonstrate that loss of MARK2 in vivo results in changes to dendritic spine morphology, which in turn leads to a decrease in excitatory synaptic transmission. Additionally, loss of MARK2 produces substantial impairments in learning and memory, anxiety, and social behavior. Notably, MARK2 deficiency results in heightened seizure susceptibility. Consistent with this observation, RNAseq analysis reveals transcriptional changes in genes regulating synaptic transmission and ion homeostasis. These findings underscore the in vivo role of MARK2 in governing synaptic connectivity, cognitive functions, and seizure susceptibility.

neuroscience↗

bioRxiv2023

Golgi-associated retrograde protein (GARP) complex recruits retromer to trans-Golgi network for FgKex2 and FgSnc1 recycling, necessary for development and pathogenicity of Fusarium graminearum

In eukaryotic cells, the retromer complex plays a crucial role in orchestrating the sorting and retrograde transport of cargo proteins from endosomes to the trans-Golgi network (TGN). Despite its significance, the molecular details of this intracellular trafficking process remain unclear. Here, we identified a Golgi-associated retrograde protein (GARP) complex as a mediator of vesicular transport, facilitating the recruitment of the retromer complex to TGN to exert its functions. The GARP complex is mainly localized to the TGN, where it interacts with the retromer complex. This interaction is evolutionarily conserved across different species. Furthermore, we identified FgKex2 and Fgsnc1 as cargo proteins in the GARP/retromer-mediated recycling pathway. Loss of GARP or retromer results in a complete mis-sorting of FgKex2 and FgSnc1 to the vacuolar degradation pathway, which affects the growth, development, toxisome biogenesis, and pathogenicity of F. graminearum. In summary, we assert that GARP facilitates the recruitment of retromer from endosomes to the TGN, orchestrating the recycling of FgKex2 and FgSnc1. This is integral to sustaining continuous growth, development and contributes significantly to the pathogenicity of F. graminearum.

microbiology↗

bioRxiv2023

Role of Dusp5 KO on Vascular Properties of Middle Cerebral Artery in Rats

Vascular aging influences hemodynamics, elevating risks for vascular diseases and dementia. We recently demonstrated that knockout (KO) of Dusp5 enhances cerebral and renal hemodynamics and cognitive function. This improvement correlates with elevated pPKC and pERK1/2 levels in the brain and kidneys. Additionally, we observed that Dusp5 KO modulates the passive mechanical properties of cerebral and renal arterioles, associated with increased myogenic tone at low pressure, enhanced distensibility, greater compliance, and reduced stiffness. The present study evaluates the structural and mechanical properties of the middle cerebral artery (MCA) in Dusp5 KO rats. We found that vascular smooth muscle cell layers and the collagen content in the MCA wall are comparable between Dusp5 KO and control rats. The internal elastic lamina in the MCA of Dusp5 KO rats exhibits increased thickness, higher autofluorescence intensity, smaller fenestrae areas, and fewer fenestrations. Despite an enhanced myogenic response and tone of the MCA in Dusp5 KO rats, other passive mechanical properties, such as wall thickness, cross-sectional area, wall-to-lumen ratio, distensibility, incremental elasticity, circumferential wall stress, and elastic modulus, do not significantly differ between strains. These findings suggest that while Dusp5 KO has a limited impact on altering the structural and mechanical properties of MCA, its primary role in ameliorating hemodynamics and cognitive functions is likely attributable to its enzymatic activity on cerebral arterioles. Further research is needed to elucidate the specific enzymatic mechanisms and explore potential clinical applications in the context of vascular aging.

physiology↗

bioRxiv2023

MARK1 regulates dendritic spine morphogenesis and cognitive functions in vivo

Dendritic spines play a pivotal role in synaptic communication and are crucial for learning and memory processes. Abnormalities in spine morphology and plasticity are observed in neurodevelopmental and neuropsychiatric disorders, yet the underlying signaling mechanisms remain poorly understood. The microtubule affinity regulating kinase 1 (MARK1) has been implicated in neurodevelopmental disorders, and the MARK1 gene shows accelerated evolution in the human lineage suggesting a role in cognition. However, the in vivo role of MARK1 in synaptogenesis and cognitive functions remains unknown. Here we show that forebrain-specific conditional knockout (cKO) of Mark1 causes defects in dendritic spine morphogenesis in hippocampal CA1 pyramidal neurons with a significant reduction in spine density. In addition, we found that MARK1 cKO mice show defects in spatial learning in the Morris Water Maze and reduced anxiety-like behaviors in the Elevated Plus Maze. Furthermore, we found loss of MARK1 causes synaptic accumulation of GKAP and GluR2. Taken together, our data show a novel role for MARK1 in regulating dendritic spine morphogenesis and cognitive functions in vivo.

neuroscience↗

bioRxiv2023

Towards ultra-low-cost smartphone microscopy

The outbreak of COVID-19 exposed the inadequacy of our technical tools for home health surveillance, and recent studies have shown the potential of smartphones as a universal optical microscopic imaging platform for such applications. However, most of them use laboratory-grade optomechanical components and transmitted illuminations to ensure focus tuning capability and imaging quality, which keeps the cost of the equipment high. Here we propose an ultra-low-cost solution for smartphone microscopy. To realize focus tunability, we designed a seesaw-like structure capable of converting large displacements on one side into small displacements on the other (reduced to [~]9.1%), which leverages the intrinsic flexibility of 3D printing materials. We achieved a focus-tuning accuracy of [~] 5 {micro}m, which is 40 times higher than the machining accuracy of the 3D-printed lens holder itself. For microscopic imaging, we use an off-the-shelf smartphone camera lens as the objective and the built-in flashlight as the illumination. To compensate for the resulting image quality degradation, we developed a learning-based image enhancement method. We use the CycleGAN architecture to establish the mapping from smartphone microscope images to benchtop microscope images without pairing. We verified the imaging performance on different biomedical samples. Except for the smartphone, we kept the full costs of the device under 4 USD. We think these efforts to lower the costs of smartphone microscopes will benefit their applications in various scenarios, such as point-of-care testing, on-site diagnosis, and home health surveillance. Research highlightsWe propose a solution for ultra-low-cost smartphone microscopy. Utilizing the flexibility of 3D-printed material, we can achieve focusing accuracy of [~] 5 {micro}m. Such a low-cost device will benefit point-of-care diagnosis and home health surveillance.

bioengineering↗

bioRxiv2023

AP-2α/AP-2β transcription factors are key regulators of epidermal homeostasis

AP-2 transcription factors regulate ectodermal development but their roles for epidermal homeostasis in the adult skin are unknown. We find that AP-2 is the predominant AP-2 family member in adult epidermis, followed by AP-2{beta}. Through inactivation of AP-2, AP-2{beta}, or both in keratinocytes we assessed the effects of a gradient of epidermal AP-2 activity on skin function. We find that (1) loss of AP-2{beta} in keratinocytes is compensated for by AP-2, (2) loss of AP-2 impairs terminal keratinocyte differentiation and hair morphogenesis, and (3) the combined loss of AP-2/AP-2{beta} results in more severe skin and hair abnormalities. Keratinocyte differentiation defects precede a progressive neutrophilic skin inflammation. Inducible inactivation of AP-2/AP-2{beta} in the adult phenocopies these manifestations. Transcriptomic analyses of epidermis lacking AP-2 or AP-2/AP-2{beta} in keratinocytes demonstrate a terminal keratinocyte differentiation defect with upregulation of alarmin keratins and of several immune pathway regulators. Moreover, our analyses suggest a key role of loss of AP-2-dependent gene expression of CXCL14 and KRT15 as an early pathogenic event towards the manifestation of skin inflammation. Thus, AP-2/AP-2{beta} are critical regulators of epidermal homeostasis in the adult skin.

cell biology↗

bioRxiv2023

Deciphering the Biosynthetic Potential of Microbial Genomes Using a BGC Language Processing Neural Network Model

Microbial secondary metabolites are usually synthesized by colocalized genes termed biosynthetic gene clusters (BGCs). A large portion of BGCs remain undiscovered in microbial genomes and metagenomes, representing a pressing challenge in unlocking the full potential of natural product diversity. In this work, we propose BGC-Prophet, a language model based on the transformer encoder that captures the distant location-dependent relationships among biosynthetic genes, allows accurately and efficiently identifies known BGCs and extrapolates novel BGCs among the microbial universe. BGC-Prophet is the first ultrahigh-throughput (UHT) method that is several orders of magnitude faster than existing tools such as DeepBGC, enabling pan-phylogenetic screening and whole-metagenome screening of BGCs. By analyzing 85,203 genomes and 9,428 metagenomes, new insights have been obtained about the diversity of BGCs on genomes from the majority of bacterial and archaeal lineages. The profound enrichment of BGCs in microbes after important geological events have been revealed: Both the Great Oxidation and Cambrian Explosion events led to a surge in BGC diversity and abundance, particularly in polyketides. These findings suggest that it is a general but constantly evolving approach for microbes to produce secondary metabolites for their adaptation in the changing environment. Taken together, BGC-Prophet enables accurate and fast detection of BGCs on a large scale, holds great promise for expanding BGC knowledge, and sheds light on the evolutionary patterns of BGCs for possible applications in synthetic biology. HighlightsO_LIBGC-Prophet shows superior performance to existing tools in terms of accuracy and speed. C_LIO_LIBGC-Prophet is the first ultrahigh-throughput (UHT) method that enables pan-phylogenetic screening and whole-metagenome screening of BGCs. C_LIO_LIBGC-Prophet builds the comprehensive profile of BGCs on 85,203 genomes and 9,428 metagenomes from the majority of bacterial and archaeal lineages. C_LIO_LIBGC-Prophet reveals the profound enrichment pattern of BGCs after important geological events. C_LI

bioinformatics↗

bioRxiv2023

Epigenetic reader ZMYND11 noncanonical function restricts HNRNPA1-mediated stress granule formation and oncogenic activity

ZMYND11 encodes an epigenetic reader of histone methylation, functioning as a transcriptional corepressor. However, whether and how ZMYND11 contributes to cancer progression and therapy remains unclear. Here we report that ZMYND11 downregulation is prevalent in cancers and profoundly correlates with adverse prostate cancer patient outcomes. Depletion of ZMYND11 promotes tumor cell growth, migration and invasion in vitro as well as tumor formation and metastasis in vivo. Mechanistically, we find that ZMYND11 exhibits tumor suppressive roles through recognizing arginine-194-methylated HNRNPA1 dependent on its MYND domain, thereby squeezing HNRNPA1 in nucleus and inhibiting the formation of stress granules in cytoplasm. Furthermore, ZMYND11 antagonizes HNRNPA1-driven high PKM2/PKM1 ratio and counteracts PKM2-induced aggressive tumor phenotype. Remarkably, ZMYND11 recognition of HNRNPA1 could be disrupted by pharmaceutical inhibition of arginine methyltransferase PRMT5 while ZMYND11 low-expressing tumors are sensitive to the treatment of PRMT5 inhibitors. Collectively, our study unravels a novel and noncanonical function of ZMYND11 as the nonhistone methyl reader and discovers a mechanism for the requirement of arginine-methylation-mediated ZMYND11-HNRNPA1 association to restrict tumor progression and offers cancer therapeutic targets and potential biomarkers.

cancer biology↗

bioRxiv2023

ChemXTree: A Tree-enhanced Classification Approach to Small-molecule Drug Discovery

The rapid advancement of machine learning, particularly deep learning, has propelled significant strides in drug discovery, offering novel methodologies for molecular property prediction. However, despite these advancements, existing approaches often face challenges in effectively extracting and selecting relevant features from molecular data, which is crucial for accurate predictions. Our work introduces ChemXTree, a novel graph-based model that integrates tree-based algorithms to address these challenges. By incorporating a Gate Modulation Feature Unit (GMFU) for refined feature selection and a differentiable decision tree in the output layer. Extensive evaluations on benchmark datasets, including MoleculeNet and eight additional drug databases, have demonstrated ChemXTrees superior performance, particularly in feature optimization. Permutation experiments and ablation studies further validate the effectiveness of GMFU, positioning ChemXTree as a significant advancement in molecular informatics, capable of rivaling state-of-the-art models.

bioinformatics↗

bioRxiv2023

Use of TSAR, Thermal Shift Analysis in R, to identify Folic Acid as a Molecule that Interacts with HIV-1 Capsid

The thermal shift assay (TSA) is a versatile biophysical technique for studying protein-ligand interactions in vitro. Here, we report a free, open-source software tool, TSAR ("Thermal Shift Analysis in R"), to expedite the analysis of TSA data. The TSAR package incorporates multiple workflows that facilitate TSA analyses, returns publication-ready graphics, and includes an optional graphic user interface. The package is available at https://bioconductor.org/packages/TSAR/. Applying TSAR, we screened two chemical libraries and found multiple molecules that potentially interact in vitro with the capsid protein (CA) of human immunodeficiency virus type 1 (HIV-1). First, a library of vitamins exemplifies the different graphic outputs of TSAR, and we report a change in the 50% melting temperature ({Delta}Tm) for folic acid-treated CA hexamers (CAHEX). Since HIV-1 CAHEX interacts with host-derived acids like inositol hexaphosphate (IP6) or dNTPs, a second library was screened containing 96 organic, acidic metabolites; multiple anionic ligands caused a {Delta}Tm for CAHEX. Subsequent investigation of these interactions includes biolayer interferometry, antiviral activity against pseudotyped HIV-1, and endogenous reverse transcriptase assays that were used to validate and investigate the biological impact of these native ligands that thermally-stabilize CAHEX. One compound hit, gallic acid, exhibited anti-HIV-1 activity as previously reported, and we show interacts with CAHEX as a potentially novel mechanism. Overall, the TSAR package facilitated quick analysis of TSA data from multiple libraries to help identify a biologically relevant hit, gallic acid, as a molecule that can inhibit HIV-1 replication and targets CAHEX. ImportanceThe TSAR package is freely available (AGPL-3) and is designed for both experienced or new R users, having command-line code for handling large and challenging datasets while also including an optional GUI that enables easy use by non-programmers. This is the first TSA analysis program written in R, a free and open-source language; TSAR simplifies TSA analysis while maintaining diverse visualization options for small-to-large libraries and multidimensional analysis. Additionally, we report multiple endogenous metabolites that potentially interact with the HIV-1 capsid protein hexamers (CAHEX) in vitro, including folic acid, gallic acid, and multiple others, primarily from the tricarboxylic acid (TCA) cycle. Various methods validate gallic acid interactions with CAHEX, leading to a novel suggested mechanism of action, and in-line with previous reports, this metabolite has potential for natural-based treatments of HIV-1. Further, we advance the understanding of the potential mechanism(s) for HIV-1 inhibition by gallic acid treatment.

biochemistry↗

bioRxiv2023

Well-Paired-Seq2: High-Throughput and High-Sensitivity Strategy for Characterizing Low RNA-Content Cell/Nucleus Transcriptomes

High-throughput single-cell RNA sequencing (scRNA-seq) is recognized as a powerful technology for disentangling the heterogeneity of cellular states. However, the Poisson-dependent cell capture and low sensitivity in scRNA-seq methods pose challenges for throughput and for samples with low RNA-content. Herein, to address these challenges, we developed Well-Paired-Seq2 (WPS2) based on size-exclusion and locally quasi-static hydrodynamic principles to realize high efficiency of cell utilization, single cell/bead pairing, and cell-free RNA removal. WPS2 exploits molecular crowding effect, tailing activity enhancement in reverse transcription, and homogeneous enzymatic reaction in the initial bead-based amplification to achieve 3116 genes and 8447 transcripts. With an average of [~]20,000 reads per cell, WPS2 detected 1420 more genes and 4864 more transcripts than our previous Well-Paired-Seq. Using WPS2, we overcame the Poisson limit for the capture of both cells and beads and accurately characterized transcriptomes of low RNA-content single cells and nuclei with high sensitivity. WPS2 was further applied to comprehensively profile transcriptomes from frozen clinical samples. We found that clear cell renal cell carcinoma (ccRCC) has a complex microenvironment, and that chromophobe renal cell carcinoma (chRCC) exhibits abundant copy number variations (CNVs). In addition, metanephric adenoma (MA) was characterized at single-cell level for the first time and some potentially specific markers were revealed. With the advantages of high sensitivity, high throughput, and high fidelity, we anticipate that WPS2 will be broadly applicable in basic and clinical research.

genetics↗

bioRxiv2023

Development of attenuated coxsackievirus B3 vectored intranasal pre-emptive pan-coronavirus vaccine

SARS-CoV-2 has the ability to evade immunity, resulting in breakthrough infections even after vaccination. Similarly, zoonotic coronaviruses pose a risk of spillover to humans. There is an urgent need to develop a pre-emptive pan-coronavirus vaccine that can induce systemic and mucosal immunity. Here, we employed a combination of immune-informatics approaches to identify shared immunodominant linear B- and T-cell epitopes from SARS-CoV-2 variants of concern (VOCs) and variants of interest (VOIs), as well as zoonotic coronaviruses. Epitope-guided vaccine were designed and the attenuated coxsackievirus B3 vectored intranasal vaccines rCVB3-EPI and rCVB3-RBD-trimer were constructed. The immunogenicity of these candidate vaccines was evaluated using Balb/c mice. The results demonstrated effective immune responses, including the production of SARS-CoV-2-specific IgG and sIgA antibodies, as well as T cell-mediated responses. However, further verification is required to assess cross-reactivity with various variants. Our intranasal pre-emptive pan-coronavirus vaccine design framework offers an appealing candidate for future vaccine development.

microbiology↗

bioRxiv2023

MitoTracer facilitates the identification of informative mitochondrial mutations for precise lineage reconstruction

Mitochondrial (MT) mutations serve as natural genetic markers for inferring clonal relationships using single cell sequencing data. However, the fundamental challenge of MT mutation-based lineage tracing is automated identification of informative MT mutations. Here, we introduced an open-source computational algorithm called "MitoTracer", which accurately identified clonally informative MT mutations and inferred evolutionary lineage from scRNA-seq or scATAC-seq samples. We benchmarked MitoTracer using the ground-truth experimental lineage sequencing data and demonstrated its superior performance over the existing methods measured by high sensitivity and specificity. MitoTracer is compatible with multiple single cell sequencing platforms. Its application to a cancer evolution dataset revealed the genes related to primary BRAF-inhibitor resistance from scRNA-seq data of BRAF-mutated cancer cells. Overall, our work provided a valuable tool for capturing real informative MT mutations and tracing the lineages among cells. TeaserMitoTracer enables automatically and accurately discover informative mitochondrial mutations for lineage tracing.

bioinformatics↗

bioRxiv2023

An automated archival single-nucleus total RNA sequencing platform mapping integrative and retrospective cell atlas of gliomas

Single-cell RNA sequencing (scRNA-seq) has dramatically transformed biomedical research within laboratory settings. It has been extensively employed to investigate the heterogeneity and plasticity of glioma, the most prevalent brain tumor. However, the clinical diagnosis and treatment of glioma remain complex and challenging, highlighting the need for comprehensive cancer research. Currently available scRNA-seq platforms are insufficient to fulfill the demands posed by large-scale clinical applications. Here, we present an automated high-throughput single-nucleus total RNA sequencing platform, known as AAsnRandom-seq. This platform integrates automated single-nucleus isolation and droplet barcoding systems with the random primer-based scRNA-seq chemistry, designed to accommodate a diverse range of sample types. The performance and versatility of AAsnRandom-seq are validated using over one hundred clinical FFPE and frozen samples. AAsnRandom-seq was applied to archival FFPE samples of various glioma subtypes, including rare clinical samples, and matched primary-recurrent glioblastomas (GBMs), delving into the comprehensive molecular characteristic of glioma at single-cell level. Abundant non-coding RNAs (ncRNAs) with distinct expression profiles within different glioma clusters are detected. Promising recurrence-related targets and pathways are identified from the matched primary-recurrent GBMs. AAsnRandom-seq holds significant application value on large-scale integrative and retrospective clinical research using archived specimens.

bioengineering↗