Biology subjects

Guan, J.

Publications and source records attributed to Guan, J..

At least 73 records · Page 4Linked to original sources

bioRxiv2021

RTK-dependent inducible degradation of mutant PI3K alpha drives GDC-0077 (Inavolisib) efficacy

PIK3CA is one of the most frequently mutated oncogenes; the p110 protein it encodes plays a central role in tumor cell proliferation and survival. Small molecule inhibitors targeting the PI3K p110 catalytic subunit have entered clinical trials, with early-phase GDC-0077 (Inavolisib) studies showing anti-tumor activity and a manageable safety profile in patients with PIK3CA-mutant, hormone receptor-positive breast cancer as a single agent or in combination therapy. Despite this, preclinical studies have shown that PI3K pathway inhibition releases negative feedback and activates receptor tyrosine kinase signaling, reengaging the pathway and attenuating drug activity. Here we discover that GDC-0077 and taselisib more potently inhibit mutant PI3K pathway signaling and cell viability through unique HER2-dependent degradation. Both are more effective than other PI3K inhibitors at maintaining prolonged pathway suppression, resulting in enhanced apoptosis and greater efficacy. This unique mechanism against mutant p110 reveals a new strategy for creating inhibitors that specifically target mutant tumors with selective degradation of the mutant oncoprotein and also provide a strong rationale for pursuing PI3K degraders in patients with HER2-positive breast cancer.

cancer biology↗

bioRxiv2021

Sustained Oxygenation Accelerates Diabetic Wound Healing by Simultaneously Promoting Epithelialization and Angiogenesis, and Decreasing Tissue Inflammation

Non-healing diabetic wound is one of the most common complications for diabetic patients. Chronic hypoxia is among the prominent factors that delay the wound healing process. Therefore, sustained oxygenation to alleviate hypoxia is hypothesized to promote diabetic wound healing. Yet it cannot be achieved by current clinical approaches including hyperbaric oxygen therapy. Herein, we developed a sustained oxygenation system consisting of oxygen-release microspheres and a reactive oxygen species (ROS)-scavenging hydrogel. The hydrogel was used to capture the ROS that is elevated in the diabetic wounds, and that may be generated due to oxygen release. The sustainedly released oxygen augmented survival and migration of keratinocytes and dermal fibroblasts; promoted angiogenic growth factor expression, and angiogenesis in the diabetic wounds; and decreased M1 macrophage density. These effects led to a significant increase of wound closure rate. These findings reveal that sustained oxygenation alone without using drugs is capable of healing diabetic wounds.

bioengineering↗

bioRxiv2021

Automatic Multi-functional Integration Program (AMFIP) towards All-optical Mechanobiology Interrogation

Automatic operations of multi-functional and time-lapse live-cell imaging are necessary for biomedical studies of active, multi-faceted, and long-term biological phenomena. To achieve automatic control, most existing solutions often require the purchase of extra software programs and hardware that rely on the manufacturers own specifications. However, these software programs are usually non-user-programmable and unaffordable for many laboratories. Manager is a widely used open-source software platform for controlling many optoelectronic instruments. Due to limited development since its introduction, Manager lacks compatibility with some of the latest microscopy equipment. To address this unmet need, we have developed a novel software-based automation program, titled Automatic Multi-functional Integration Program (AMFIP), as a new Java-based and hardware-independent plugin for Manager. Without extra hardware, AMFIP enables the functional synchronization of Manager, the Nikon NIS-Elements platform, and other 3rd party software to achieve automatic operations of most commercially available microscopy systems, including but not limited to Nikon. AMFIP provides a user-friendly and programmable graphical user interface (GUI), opening the door to expanding the customizability for many hardware and software. Users can customize AMFIP according to their own specific experimental requirements and hardware environments. To verify AMFIPs performance, we applied it to elucidate the relationship between cell spreading and spatial-temporal cellular expression of Yes-associated protein (YAP), a mechanosensitive protein that shuttles between cytoplasm and nucleus upon mechanical stimulation, in an epithelial cell line. We found that the ratio of YAP expression in nucleus and cytoplasm decreases as the spreading area of cells increases, suggesting that the accumulation of YAP in the nucleus decreases throughout the cell spreading processes. In summary, AMFIP provides a new open-source and charge-free solution to integrate multiple hardware and software to satisfy the need of automatic imaging operations in the scientific community.

bioengineering↗

bioRxiv2021

iRGD-liposomes enhance tumor delivery and therapeutic efficacy of antisense oligonucleotide drugs against primary prostate cancer and bone metastasis

Nucleotide-based drugs, such as antisense oligonucleotides (ASOs), have unique advantages in treating human diseases as they provide virtually unlimited ability to target any gene. However, their clinical translation faces many challenges, one of which is poor delivery to the target tissue in vivo. This problem is particularly evident in solid tumors. Here, we functionalized liposomes with a tumor-homing and -penetrating peptide, iRGD, as a carrier of an ASO against androgen receptor (AR) for prostate cancer treatment. The iRGD-liposomes exhibited a high loading efficiency of AR-ASO, and an efficient knockdown of AR gene products was achieved in vitro, including AR splice variants. In vivo, iRGD-liposomes significantly increased AR-ASO accumulation in the tumor tissue and decreased AR expression relative to free ASOs in prostate tumors established as subcutaneous xenografts. Similar results were obtained with intra-tibial xenografts modeling metastasis to bones, the predominant site of metastasis for prostate cancer. In treatment studies, iRGD-liposomes markedly improved the AR-ASO efficacy in suppressing the growth of both subcutaneous xenografts and intra-tibial xenografts. The inhibitory effect on tumor growth was also significantly prolonged by the delivery of the AR-ASO in the iRGD-liposomes. Meanwhile, iRGD-liposomes did not increase ASO accumulation or toxicity in healthy organs. Overall, we provide here a delivery system that can significantly increase ASO accumulation and efficacy in solid tumors. These benefits are achieved without significant side effects, providing a way to increase the antitumor efficacy of ASOs.

cancer biology↗

bioRxiv2020

Integrative Analysis of Phenomic, Genomic, and Transcriptomic to Identify Potential Functional Genes of Yaks in Plain and Plateau

BackgroundThe yak is an important source of livelihood for the people living in the Qinghai-Tibet Plateau. Most genetics detection studies have focused on the comparison between different tissues of different breeds, both living in the Plateau and in the plains. The genetic background and complex regulatory relationship have frequently puzzled researchers. In this study, we divided a population of 10 yaks into two subgroups, namely Plateau (living in the Plateau) and Plain (living in the plains). Phenomic, genomic, and transcriptomic analyses were used to reveal the molecular genetic type in the body weight, slaughter, and beef quality of yaks. ResultsWe found a significant difference (P <0.01) between the third (60 days), fourth (90 days), fifth (120 days), and sixth (150 days) weights of Plateau and plain subpopulations. The difference in body weight was due to differences in kidney weight, meat weight, fur weight, and head weight. However, the beef quality was not significantly different. We identified 540 Differentially Expressed Genes (DEGs). Using weighted gene co-expression network analysis (WGCNA), we have constructed a co-express network, and the modules were strongly related to traits. In the genome-wide association studies (GWAS), we detected significant 156, 52, 33, 15, and 3 signals in the meat weight, head weight, fur weight, liver weight, and the last body weight traits. Based on the epigenome-wide association studies (eWAS) results, we created a link relationship between the DEGs expression level and genotype. ConclusionIn summary, our study demonstrated the effectiveness and representative of multidimensional data from a finite number of yak populations. The study highlights the underlying way, as well as a related network, to yield new information on genome genetics and pathogen-host interactions of both the living Plateau and plain yak populations.

genomics↗

bioRxiv2020

Exploring heteroaromatic rings as a replacement for the labile amide of antiplasmodial pantothenamides

The Plasmodium parasites that cause malaria are adept at developing resistance to antimalarial drugs, necessitating the search for new antiplasmodials. Although several amide analogs of pantothenate (pantothenamides) show potent antiplasmodial activity, hydrolysis by pantetheinases (or vanins) present in blood rapidly inactivates them. We report herein the facile synthesis and biological activity of a small library of pantothenamide analogs in which the labile amide group is replaced with a variety of heteroaromatic rings. Several of the new analogs display antiplasmodial activity in the nanomolar range against P. falciparum and/or P. knowlesi in the presence of pantetheinase. A previously reported triazole and an isoxazole derivative presented here were further characterized and found to possess high selectivity indices, medium or high Caco-2 permeability, and medium or low microsomal clearance in vitro. Although we show here that the two compounds fail to suppress proliferation of P. berghei in vivo, pharmacokinetic and contact time data presented provide a benchmark for the compound profile required to achieve antiplasmodial activity in mice and should facilitate lead optimization.

pharmacology and toxicology↗

bioRxiv2020

Antibody Upstream Sequences Diversity and Its Biological Implications Revealed by Repertoire Sequencing

The sequence upstream of antibody variable region (Antibody Upstream Sequence, or AUS) consists of 5 untranslated region (5 UTR) and two leader regions, L-PART1 and L-PART2. The sequence variations in AUS affect the efficiency of PCR amplification, mRNA translation, and subsequent PCR-based antibody quantification as well as antibody engineering. Despite their importance, the diversity of AUSs has long been neglected. Utilizing the rapid amplification of cDNA ends (5RACE) and high-throughput antibody repertoire sequencing (Rep-Seq) technique, we acquired full-length AUSs for human, rhesus macaque (RM), cynomolgus macaque (CM), mouse, and rat. We designed a bioinformatics pipeline and discovered 2,957 unique AUSs, corresponding to 2,786 and 1,159 unique sequences for 5 UTR and leader, respectively. Comparing with the leader records in the international ImMunoGeneTics (IMGT), while 529 were identical, 313 were with single nucleotide polymorphisms (SNPs), 280 were totally new, and 37 updated the incomplete records. The diversity of AUSs impact on related antibody biology was also probed. Taken together, our findings would facilitate Rep-Seq primer design for capturing antibodies comprehensively and efficiently as well as provide a valuable resource for antibody engineering and the studies of antibody at the molecular level.

bioinformatics↗

bioRxiv2020

SARS-Cov-2-, HIV-1-, Ebola-neutralizing and anti-PD1 clones are predisposed

Antibody repertoire refers to the totality of the superbly diversified antibodies within an individual to cope with the vast array of possible pathogens. Despite this extreme diversity, antibodies of the same clonotype, namely public clones, have been discovered among individuals. Although some public clones could be explained by antibody convergence, public clones in naive repertoire or virus-neutralizing clones from not infected people were also discovered. All these findings indicated that public clones might not occur by random and they might exert essential functions. However, the frequencies and functions of public clones in a population have never been studied. Here, we integrated 2,449 Rep-seq datasets from 767 donors and discovered 5.07 million public clones - ~10% of the repertoire are public in population. We found 38 therapeutic clones out of 3,390 annotated public clones including anti-PD1 clones in healthy people. Moreover, we also revealed clones neutralizing SARS-CoV-2, Ebola, and HIV-1 viruses in healthy individuals. Our result demonstrated that these clones are predisposed in the human antibody repertoire and may exert critical functions during particular immunological stimuli and consequently benefit the donors. We also implemented RAPID - a Rep-seq Analysis Platform with Integrated Databases, which may serve as a useful tool for others in the field.

immunology↗

bioRxiv2020

senSCOPE: Modeling radiative transfer and biochemical processes in mixed canopies combining green and senescent leaves with SCOPE

Semi-arid grasslands and other ecosystems combine green and senescent leaves featuring different biochemical and optical properties, as well as functional traits. Knowing how these properties vary is necessary to understand the functioning of these ecosystems. However, differences between green and senescent leaves are not considered in recent models representing radiative transfer, heat, water and CO2 exchange such as the Soil-Canopy Observation of Photosynthesis and Energy fluxes (SCOPE). Neglecting the contribution of senescent leaves to the optical and thermal signal of vegetation limits the possibilities to use remote sensing information for studying these ecosystems; as well as neglecting their lack of photosynthetic activity increases uncertainty in the representation of ecosystem fluxes. In this manuscript we present senSCOPE as a step towards a more realistic representation of mixed green and senescent canopies. senSCOPE is a modified version of SCOPE model that describes a canopy combining green and senescent leaves with different properties and function. The model relies on the same numerical solutions than SCOPE, but exploits the linear nature of the scattering coefficients to combine optical properties of both types of leaf. Photosynthesis and transpiration only take place in green leaves; and different green and senescent leaf temperatures are used to close the energy balance. Radiative transfer of sun-induced fluorescence (SIF) and absorptance changes induced by the xanthophyll cycle action are also simulated. senSCOPE is evaluated against SCOPE both using synthetic simulations, forward simulations based on observations in a Mediterranean tree-grass ecosystem, and inverting dataset of ground measurements of reflectance factors, SIF, thermal radiance and gross primary production on a heterogeneous and partly senescent Mediterranean grassland. Results show that senSCOPE outputs vary quite linearly with the fraction of green leaf area, whereas SCOPE does not respond linearly to the effective leaf properties, calculated as the weighted average of green and senescent leaf parameters. Inversion results and pattern-oriented model evaluation show that senSCOPE improves the estimation of some parameters, especially chlorophyll content, with respect SCOPE retrievals during the dry season. Nonetheless, inaccurate knowledge of the optical properties of senescent matter still complicates model inversion. senSCOPE brings new opportunities for the monitoring of canopies mixing green and senescent leaves, and for improving the characterization of the optical properties of senescent material.

ecology↗

bioRxiv2019

Light activates the translational regulatory GCN2 kinase via reactive oxygen species emanating from the chloroplast

Cytosolic mRNA translation is subject to global and mRNA-specific controls. Phosphorylation of translation initiation factor eIF2 anchors a reversible switch that represses translation globally. The stress-responsive GCN2 kinase is the only known kinase for eIF2 in Arabidopsis. Here we show that conditions that generate reactive oxygen species (ROS) in the chloroplast, such as dark-light transitions, high light, and the herbicide methyl viologen all rapidly activated the GCN2 kinase, whereas mitochondrial and ER stress did not. In addition, GCN2 activation was light dependent and mitigated by photosynthesis inhibitors and ROS quenchers. Accordingly, seedling growth of multiple gcn2 mutant alleles was retarded under conditions of excess light, implicating the GCN2-eIF2 pathway in responses to light and associated ROS. Once activated, the GCN2 kinase preferentially suppressed the ribosome loading of mRNAs for functions such as mitochondrial ATP synthesis, the chloroplast thylakoids, vesicle trafficking, and translation. The transcriptome of gcn2 mutants was sensitized to abiotic stress, including oxidative stress, as well as innate immune responses. Accordingly, gcn2 displayed defects in immune priming by the fungal elicitor, chitin. In conclusion, we provide evidence that reactive oxygen species produced by the photosynthetic apparatus help to activate the highly conserved GCN2 kinase, leading to eIF2 phosphorylation and thus affecting the status of the cytosolic protein synthesis apparatus.

plant biology↗

bioRxiv2019

Cytoplasmic protein granules organize kinase-mediated RAS signaling

Receptor tyrosine kinase (RTK)-mediated activation of downstream effector pathways such as the RAS GTPase/MAP kinase (MAPK) signaling cascade is thought to occur exclusively from lipid membrane compartments in mammalian cells. Here, we uncover a membraneless, protein granule-based subcellular structure that can organize RTK/RAS/MAPK signaling in cancer. Chimeric (fusion) oncoproteins involving certain RTKs including ALK and RET undergo de novo higher-order assembly into membraneless cytoplasmic protein granules. These pathogenic biomolecular condensates locally concentrate the RAS activating complex GRB2/SOS1 and activate RAS in a lipid membrane-independent manner to initiate MAPK signaling. Formation of membraneless protein granules by RTK oncoproteins is both necessary and sufficient for RAS/MAPK signaling output in cells. Our findings reveal membraneless, higher-order cytoplasmic protein assembly as a distinct subcellular platform to activate RTKs and RAS GTPases and a general principle by which cells can organize oncogenic signaling. HighlightsO_LIRTK oncoproteins can form de novo membraneless cytoplasmic protein granules C_LIO_LIRTK protein granules activate RAS in lipid membrane-independent manner C_LIO_LIHigher-order protein assembly is critical for oncogenic RAS/MAPK signaling C_LIO_LIProtein granules are a distinct subcellular platform for organizing RTK signaling C_LI

cancer biology↗

bioRxiv2019

MATRIEX Imaging: Multi-Area Two-photon Real-time In-vivo Explorer

Two-photon laser scanning microscopy, originally developed since 1990s1, has been widely applied for biomedical research in recent decades, particularly popular among neuroscientists for studying neural functions in vivo2. However, it is typically restricted to one imaging area that is orthogonal to the optical axis. Here, we demonstrate a novel multi-axis optical conjugation method that enables two-photon imaging at single-cell resolution simultaneously in multiple areas at different depths, each of which could have a view diameter of ~200 m and could be largely freely targeted within a zone up to 12-mm diameter. For example, we show simultaneous imaging of neuronal activities in the primary visual cortex (V1), the primary motor cortex (M1) and the hippocampal CA1 region of awake mice. This method can be readily implemented on a single conventional two-photon microscope to enable multi-area exploration of neuronal activities in vivo.

neuroscience↗

bioRxiv2018

Nationwide population genetic screening improves outcomes of newborn screening for hearing loss in China

PurposeConcurrent newborn hearing and genetic screening has been reported, but its benefits have not been statistically proven due to limited sample sizes and outcome data. To fill this gap, we analyzed outcomes of a large number of newborns with genetic screening results.\n\nMethodsNewborns in China were screened for 20 hearing-loss-related genetic variants from 2012-2017. Genetic results were categorized as positive, at-risk, inconclusive, or negative. Hearing screening results, risk factors, and up-to-date hearing status were followed-up via phone interviews.\n\nResultsWe completed genetic screening on one million newborns and followed up 12,778. We found that a positive genetic result significantly indicated a higher positive predictive value of the initial hearing screening (60% vs. 5.0%, P<0.001) and a lower rate of loss-to-follow-up (5% vs. 22%, P<0.001) than an inconclusive one. Importantly, 42% of subjects in the positive group with reported or presymptomatic hearing loss were \"missed\" by conventional hearing screening. Furthermore, genetic screening identified 0.23% of subjects predisposed to preventable ototoxicity.\n\nConclusionOur results demonstrate that limited genetic screening identified additional cases, reduced loss-to-follow-up, and informed families of ototoxicity risks, providing convincing evidence to support integrating genetic screening into universal newborn hearing screening programs.

genetics↗

bioRxiv2018

Overdispersed gene expression characterizes schizophrenic brains

Schizophrenia (SCZ) is a severe, highly heterogeneous psychiatric disorder with varied clinical presentations. The polygenic genetic architecture of SCZ makes identification of causal variants daunting. Gene expression analyses have shown that SCZ may result in part from transcriptional dysregulation of a number of genes. However, most of these studies took the commonly used approach--differential gene expression analysis, assuming people with SCZ are a homogenous group, all with similar expression levels for any given gene. Here we show that the overall gene expression variability in SCZ is higher than that in an unaffected control (CTL) group. Specifically, we applied the test for equality of variances to the normalized expression data generated by the CommonMind Consortium (CMC) and identified 87 genes with significantly higher expression variances in the SCZ group than the CTL group. One of the genes with differential variability, VEGFA, encodes a vascular endothelial growth factor, supporting a vascular-ischemic etiology of SCZ. We also applied a Mahalanobis distance-based test for multivariate homogeneity of group dispersions to gene sets and identified 19 functional gene sets with higher expression variability in the SCZ group than the CTL group. Several of these gene sets are involved in brain development (e.g., development of cerebellar cortex, cerebellar Purkinje cell layer and neuromuscular junction), supporting that structural and functional changes in the cortex cause SCZ. Finally, using expression variability QTL (evQTL) analysis, we show that common genetic variants contribute to the increased expression variability in SCZ. Our results reveal that SCZ brains are characterized by overdispersed gene expression, resulting from dysregulated expression of functional gene sets pertaining to brain development, necrotic cell death, folic acid metabolism, and several other biological processes. Using SCZ as a model of complex genetic disorders with a heterogeneous etiology, our study provides a new conceptual framework for variability-centric analyses. Such a framework is likely to be important in the era of personalized medicine. (313 words)

genetics↗

bioRxiv2018

Live-Cell Imaging Reveals Enhancer-dependent Sox2 Transcription in the Absence of Enhancer Proximity

Enhancers are important regulatory elements that can control gene activity across vast genetic distances. However, the underlying nature of this regulation remains obscured because it has been difficult to observe in living cells. Here, we visualize the spatial organization and transcriptional output of the key pluripotency regulator Sox2 and its essential enhancer Sox2 Control Region (SCR) in living embryonic stem cells (ESCs). We find that Sox2 and SCR show no evidence of enhanced spatial proximity and that spatial dynamics of this pair is limited over tens of minutes. Sox2 transcription occurs in short, intermittent bursts in ESCs and, intriguingly, we find this activity demonstrates no association with enhancer proximity, suggesting that direct enhancer-promoter contacts do not drive contemporaneous Sox2 transcription. Our study establishes a framework for interrogation of enhancer function in living cells and supports an unexpected mechanism for enhancer control of Sox2 expression that uncouples transcription from enhancer proximity.

genetics↗

bioRxiv2018

Local Enrichment of HP1alpha at Telomeres Alters Their Structure and Regulation of Telomere Protection

Enhanced telomere maintenance is evident in malignant cancers. While telomeres are thought to be inherently heterochromatic, detailed mechanisms of how epigenetic modifications impact telomere protection and structures are largely unknown in human cancers. Here we develop a molecular tethering approach to experimentally enrich heterochromatin protein HP1 specifically at telomeres. This results in increased deposition of H3K9me3 at cancer cell telomeres. Telomere extension by telomerase is attenuated, and damage-induced foci at telomeres are reduced, indicating augmentation of telomere stability. Super resolution STORM imaging shows an unexpected increase in irregularity of telomeric structure. Telomere-tethered chromo shadow domain (CSD) mutant I165A of HP1 abrogates both the inhibition of telomere extension and the irregularity of telomeric structure, suggesting the involvement of at least one HP1-ligand in mediating these effects. This work presents a new approach to specifically manipulate the epigenetic status locally at telomeres to uncover insights into molecular mechanisms underlying telomere structural dynamics.

cell biology↗

bioRxiv2018

Computational modeling of social face perception in humans: Leveraging the active appearance model

Face processing plays a central role in human social life. Humans readily infer social traits (e.g. attractiveness and trustworthiness) from a strangers face. Previous attempts to characterize the facial (physiognomic) features underlying social processing have lacked either systematicity or interpretability. Here, we utilize a statistical framework to tackle this problem, by learning a vector space to represent faces, and a linear mapping from this face space into human social trait judgments. Specifically, we obtain a face space by training the Active Appearance Model on large datasets of face images. Based on human evaluations of numerous social traits on these images, we then use regression to find linear combinations of facial features (what we call Linear Trait Axis, or LTA) that best predict human social judgments. Our model achieves state-of-the-art performance in overall predictive accuracy - comparable to the best convolutional neural network and better than human prediction of other human ratings. To interpret the LTAs, we regress them against a large repertoire of geometric features. To understand the relationship between the facial features that underlie different social, emotional, and demographic traits, we present a novel \"dual space analysis\" that characterizes the geometric relationship among LTA vectors. It shows that facial features important for social trait perception are largely distinct from those underlying demographic and emotion perception, contrary to previous suggestions that social trait perception is driven by over-generalization of relatively primitive demographic and emotion perception processes. In addition, we present a novel correlation decomposition analysis that quantifies how correlations in trait judgments (e.g. between attractiveness and babyfacedness) independently arise from (1) shared facial features among traits, and (2) correlation in the distribution of facial features in the human population.

animal behavior and cognition↗

bioRxiv2018

STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of omics data

Single-cell transcriptomic assays have enabled the de novo reconstruction of lineage differentiation trajectories, along with the characterization of cellular heterogeneity and state transitions. Several methods have been developed for reconstructing developmental trajectories from single-cell transcriptomic data, but efforts on analyzing single-cell epigenomic data and on trajectory visualization remain limited. Here we present STREAM, an interactive pipeline capable of disentangling and visualizing complex branching trajectories from both single-cell transcriptomic and epigenomic data.

genomics↗