Biology subjects

Xie, J.

Publications and source records attributed to Xie, J..

At least 145 records · Page 8Linked to original sources

bioRxiv2023

Short-chain carboxylates facilitate the counting of yeasts in Sub-high temperature Daqu.

Sub-high temperature Daqu is a traditional solid fermenting agent that produces Chinese strong-aroma Baijiu. It is abundant in various microorganisms, including bacteria, yeasts, molds, and actinomycetes, of which yeasts play a crucial role in ethanol production and flavor formation. Counting yeasts in Daqu is difficult due to the interference of molds and bacteria. Antibiotics are employed to inhibit bacterial growth, but there is no effective way to suppress molds without affecting the growth of yeasts. In this study, short-chain carboxylates (C1-C6) were added to the culture medium at various pH conditions to investigate their effects on the growth of molds and yeasts. Results showed that they have distinct inhibitory effects in a pH-and concentration-dependent manner. A few of these tested short-chain carboxylates effectively suppress mold growth in agar plates without affecting yeast growth. Herein, a simple and feasible method for improving the efficiency of yeast isolation and counting in Daqu has been proposed, which may be useful for studying yeasts from complex habitats.

microbiology↗

bioRxiv2023

EFEMP1 contributes to light-dependent ocular growth in zebrafish

Myopia (short-sightedness) is the most common ocular disorder. It generally develops after over-exposure to aberrant visual environments, disrupting emmetropization mechanisms that should match eye growth with optical power. A pre-screening of strongly associated myopia-risk genes identified through human genome-wide association studies implicates efemp1 in myopia development, but how this gene impacts ocular growth remains unclear. Here, we modify efemp1 expression specifically in the retina of zebrafish. We found that under normal lighting, efemp1 mutants developed axial myopia, enlarged eyes, reduced spatial vision and altered retinal function. However, under myopia-inducing dark-rearing, compared to control fish, mutants remained emmetropic and showed changes in retinal function. Efemp1 modification changed the expression of efemp1, egr1, tgfb1a, vegfab and rbp3 genes in the eye, and changes the inner retinal distributions of myopia-associated EFEMP1, TIMP2 and MMP2 proteins. Efemp1 modification also impacted dark-rearing-induced responses of vegfab and wnt2b genes and above-mentioned myopia-associated proteins. Together, we provided robust evidence that light-dependent ocular growth is regulated by efemp1. SummaryThis study shows that retina-specific modification of efemp1 expression in zebrafish results in myopic eye, and impacts responses to myopia-inducing dark-rearing in eye growth, retinal function, and myopia-associated molecular expression and distribution, implicating light-dependent regulation of efemp1 in ocular development.

neuroscience↗

bioRxiv2023

Cell shape anisotropy enhances cytoplasm viscoelastic resistance to stabilize mitotic spindle position during early embryo development

Cell geometry is a key parameter for the regulation of mitotic spindle positioning during early embryo development and tissue morphogenesis. To date, however, we still lack an understanding for how intracellular forces that position, orient or hold mitotic spindles depend on cell geometry. Here, we used in vivo magnetic tweezers to directly measure the forces that maintain the mitotic spindle in the center of sea urchin cells that adopt different shapes during early embryo development. We found that spindles are held by viscoelastic forces that progressively increase in amplitude as cells become more elongated during early development. By coupling direct cell shape manipulations and in vivo force measurements, we establish how spindle associated forces increase in dose dependence with cell shape anisotropy. Cytoplasm flow analysis and hydrodynamic simulations suggest that this geometry-dependent mechanical enhancement results from a stronger hydrodynamic coupling between the spindle and cell boundaries, which dampens cytoplasm flows and spindle mobility as cells become more elongated. These findings establish how cell shape affects spindle associated forces, and suggest a novel mechanism for shape-sensing and division positioning mediated by intracellular hydrodynamics with functional implications for early embryo morphogenesis.

cell biology↗

bioRxiv2023

Structure-Aware Dual-Target Drug Design through Collaborative Learning of Pharmacophore Combination and Molecular Simulation

Dual-target drug design has gained significant attention in the treatment of complex diseases, such as cancers and autoimmune disorders. A widely employed design strategy is combining pharmacophores to incorporate the knowledge of structure-activity relationships of both targets. Unfortunately, it often struggles with long and expensive trial and error, because protein pockets of two targets impose complex structural constraints on the pharmacophore combination. In this study, we propose AIxFuse, a structure-aware dual-target drug design method that learns pharmacophore fusion patterns to satisfy the dual-target structural constraints simulated by molecular docking. We utilize two self-play reinforcement learning (RL) agents to learn pharmacophore selection and fusion by comprehensive feedback including dual-target molecular docking scores. Collaboratively, the molecular docking scores are learned by active learning (AL). Through collaborative RL and AL, AIxFuse learns to generate molecules with multiple desired properties. AIxFuse is shown to outperform state-of-the-art methods in generating dual-target drugs against glycogen synthase kinase-3 beta (GSK3{beta}) and c-Jun N-terminal kinase 3 (JNK3). When applied to another task against retinoic acid receptor-related orphan receptor{gamma} -t (ROR{gamma}t) and dihydroorotate dehydrogenase (DHODH), AIxFuse exhibits consistent performance while compared methods suffer performance drops, leading to a 5 times outperformance in success rate. Docking studies demonstrate that AIxFuse can generate molecules concurrently satisfying the binding mode required by both targets. Further free energy perturbation calculation indicates that the generated candidates have promising binding free energies against both targets. Significance StatementComplex diseases like cancers and autoimmune disorders are mostly caused by multiple genes. Designing dual-target drugs against two target proteins simultaneously can achieve synergistic effects and alleviate drug resistance. In this study, we present AIxFuse, which to our knowledge is the first structure-aware dual-target drug design method that learns pharmacophore fusion patterns to satisfy the dual-target structural constraints simulated by molecular docking. AIxFuse exhibits superior performance to previous state-of-the-art methods on comprehensive benchmarks. By generating diverse drug candidates with promising dualtarget binding free energies and other desired properties, AIxFuse holds promising prospects for accelerating the development of novel dual-target drugs for long-term therapeutic of complex diseases.

pharmacology and toxicology↗

bioRxiv2023

Establishment and comprehensive characterization of a novel dark-reared zebrafish model for myopia studies

PurposeMyopia is predicted to impact approximately 5 billion people by 2050, necessitating mechanistic understanding of its development. Myopia results from dysregulated genetic mechanisms of emmetropization, caused by over-exposure to aberrant visual environments; however, these genetic mechanisms remain unclear. Recent human genome-wide association studies have identified a range of novel myopia-risk genes. To facilitate large-scale in vivo mechanistic examination of gene-environment interactions, this study aims to establish a myopia model platform that allows efficient environmental and genetic manipulations. MethodsWe established an environmental zebrafish myopia model by dark-rearing. Ocular biometrics including relative ocular refraction were quantified using optical coherence tomography images. Spatial vision was assessed using optomotor response (OMR). Retinal function was analyzed via electroretinography (ERG). Myopia-associated molecular contents or distributions were examined using RT-qPCR or immunohistochemistry. ResultsOur model produces robust phenotypic changes, showing myopia after 2 weeks of dark-rearing, which were recoverable within 2 weeks after returning animals to normal lighting. 2-week dark-reared zebrafish have reduced spatial-frequency tuning function. ERG showed reduced photoreceptor and bipolar cell function (a- and b-waves) after only 2 days of dark-rearing, which worsened after 2 weeks of dark-rearing. We also found dark-rearing-induced changes to expression of myopia-risk genes, including egr1, vegfaa, vegfab, rbp3, gjd2a and gjd2b, inner retinal distribution of EFEMP1, TIMP2 and MMP2, as well as transiently reduced PSD95 density in the inner plexiform layer. ConclusionsCoupled with the gene editing tools available for zebrafish, our environmental myopia model provides an excellent platform for large-scale investigation of gene-environment interactions in myopia development.

neuroscience↗

bioRxiv2023

CLAIR: An integrated lipid database across multiple crop species

Oilseed crops, which are rich in plant lipids, provide essential fatty acids for human consumption and serve as major sources of biofuels and essential raw materials for the chemical industry. As a result of population growth and ecological changes, the demand for vegetable oil is increasingly outpacing supply. A comprehensive understanding of the genes involved in lipid metabolism in oilseed crops and the regulatory relationships among these genes is essential for improving oil content. However, current studies on lipid metabolism genes rely heavily on a decade-old database of genes involved in lipid metabolism in Arabidopsis thaliana. To address this issue, we mined the literature, integrated data from various databases and studies, and aligned homologs of lipid metabolism genes from nine oilseed crops to construct a comprehensive set of lipid metabolism genes in plants. Using this approach, we identified 221 additional lipid metabolism genes. In addition, we created a user-friendly lipid database called CLAIR (Crop Lipid-Associated Information Resource) by integrating and mining multi-omics data from nine major oil crops. The database is available at http://www.clipair.cn/. These resources should facilitate further research and exploration of lipid metabolism in oil crops, ultimately contributing to improved oil production.

plant biology↗

bioRxiv2023

A machine learning-based approach to identify reliable gold standards for protein complex composition prediction

Co-Fractionation Mass Spectrometry (CFMS) enables the discovery of protein complexes and the systems-level analyses of multimer dynamics that facilitate responses to environmental and developmental conditions. A major challenge in the CFMS analyses, and other omics approaches in general, is to conduct validation experiments at scale and develop precise methods to evaluate the performance of the analyses. For protein complex composition predictions, CORUM is commonly used as a source of known complexes; however, the subunit pools in cell extracts are very rarely in the assumed fully assembled states. Therefore, a fundamental conflict exists between the assumed multimerization of the CORUM "gold standards" and the CFMS experimental datasets to be evaluated. In this paper, we develop a machine learning-based "small world" data analysis method. This method uses size exclusion chromatography profiles of predicted CORUM complex subunits to identify relatively rare instances of fully assembled complexes, as well as bona fide stable CORUM subcomplexes. Our method involves a two-stage machine learning approach that is designed to leverage evolutionarily conserved sequences among CORUM subunits and integrate it with size exclusion chromatography profile data from CFMS experiments. The generated gold standards are evaluated by both statistical significance and size comparison between calculated and predicted complexes. We expect these gold standards to serve as improved benchmarks to assess the overall reliability of CFMS-based protein complex composition predictions.

bioinformatics↗

bioRxiv2023

Targeting CD45 by gene-edited CAR-T cells for leukemia eradication and hematopoietic stem cell transplantation preconditioning

Hematopoietic stem cell transplantation (HSCT) is widely used to treat patients with life-threatening hematologic and immune system disorders. The currently used nontargeted chemo-/radiotherapy conditioning regimens cause tissue injury and induce an array of immediate and delayed adverse effects, which limits the use of this potentially curative treatment. The growing demand to replace canonical conditioning regimens has led to the development of alternative approaches based on antibody-drug conjugates, naked antibodies and CAR T cells. Here, we propose a preconditioning strategy based on targeting CD45 on hematopoietic cells with CAR45 T cells. To avoid fratricide of CD45 CAR T cells, targeted genomic disruption of the CD45 gene was performed in human CD45 CAR T cells in combination with dasatinib treatment. CD45{Delta}CAR45 T cells showed impressive activity in terms of target cell elimination in vitro and depletion of tumor cells in vivo or human hematopoietic cells in humanized immunodeficient mice engrafted with human blood-derived HSCs. CD45{Delta}CAR45 NK cells also exhibited potent killing activity against tumor cell lines and human hematopoietic cells. Therefore, fratricide-resistant CAR45 T and NK cells have the potential to provide the benefits of full myeloablative conditioning and therapy for hematologic malignancies. Thus, we provide the proof of concept for the generation and preclinical efficacy of CAR T cells directed against CD45-expressing cells.

molecular biology↗

bioRxiv2023

The Aspergillus fumigatus maiA gene contributes to cell wall homeostasis and fungal virulence.

In this study, two distinct in vitro infection models of Aspergillus fumigatus, using murine macrophages (RAW264.7) and human lung epithelial cells (A549), were employed to identify the genes important for fungal adaptation during infection. Transcriptomic analyses of co-incubated Aspergillus uncovered 140 fungal genes up-regulated in common between both models that, when compared with a previously published in vivo transcriptomic study, allowed the identification of 13 genes consistently up-regulated in all three infection conditions. Among them, the maiA gene, responsible for a critical step in the L-phenylalanine degradation pathway, was identified. Disruption of maiA resulted in a mutant strain unable to complete the Phe degradation pathway, leading to an excessive production of pyomelanin when this amino acid served as the sole carbon source. Moreover, the disruption mutant exhibited noticeable cell wall abnormalities, with reduced levels of {beta}-glucans within the cell wall. the maiA-1 mutant strain induced reduced inflammation in primary macrophages and displayed significantly lower virulence in a neutropenic mouse model of infection. This is the first study linking the A. fumigatus maiA gene to fungal cell wall homeostasis and virulence.

microbiology↗

bioRxiv2023

The fatty liver disease-causing protein PNPLA3-I148M alters lipid droplet-Golgi dynamics

Non-alcoholic fatty liver disease (NAFLD), recently renamed metabolic dysfunction-associated steatotic liver disease (MASLD), is a progressive metabolic disorder that begins with aberrant triglyceride accumulation in the liver and can lead to cirrhosis and cancer. A common variant in the gene PNPLA3, encoding the protein PNPLA3-I148M, is the strongest known genetic risk factor for MASLD to date. Despite its discovery twenty years ago, the function of PNPLA3, and now the role of PNPLA3-I148M, remain unclear. In this study, we sought to dissect the biogenesis of PNPLA3 and PNPLA3-I148M and characterize changes induced by endogenous expression of the disease-causing variant. Contrary to bioinformatic predictions and prior studies with overexpressed proteins, we demonstrate here that PNPLA3 and PNPLA3-I148M are not endoplasmic reticulum-resident transmembrane proteins. To identify their intracellular associations, we generated a paired set of isogenic human hepatoma cells expressing PNPLA3 and PNPLA3-I148M at endogenous levels. Both proteins were enriched in lipid droplet, Golgi, and endosomal fractions. Purified PNPLA3 and PNPLA3-I148M proteins associated with phosphoinositides commonly found in these compartments. Despite a similar fractionation pattern as the wild-type variant, PNPLA3-I148M induced morphological changes in the Golgi apparatus, including increased lipid droplet-Golgi contact sites, which were also observed in I148M-expressing primary human patient hepatocytes. In addition to lipid droplet accumulation, PNPLA3-I148M expression caused significant proteomic and transcriptomic changes that resembled all stages of liver disease. Cumulatively, we validate an endogenous human cellular system for investigating PNPLA3-I148M biology and identify the Golgi apparatus as a central hub of PNPLA3-I148M-driven cellular change. Significance StatementFatty liver disease affects nearly a quarter of the worlds population and has both environmental and genetic risk factors. A mutation in the gene PNPLA3 that converts Ile 148 to Met is the strongest known genetic risk factor for developing fatty liver disease. Using a series of techniques to track endogenous PNPLA3 and PNPLA3-I148M biogenesis and localization, we reveal new insights into how the mutation changes cellular dynamics. Although previous reports focus on its role on lipid droplets, we reveal that PNPLA3-I148M also functions at the Golgi apparatus, an organelle critical for protein transport into and out of the cell and lipid signaling. PNPLA3-I148M causes altered Golgi morphology and drives changes reminiscent of liver disease.

cell biology↗

bioRxiv2023

DiffDec: Structure-Aware Scaffold Decoration with an End-to-End Diffusion Model

In molecular optimization, one popular way is R-groups decoration on molecular scaffolds, and many efforts have been put to generate R-groups based on deep generative models. However, these methods mostly use information of known binding ligands, without fully utilizing target structure information. In this study, we proposed a new method, DiffDec, to involve three-dimensional pocket constraints by a modified diffusion technique for optimizing molecules through molecular scaffold decoration. For an end-to-end generation of R-groups with different sizes, we designed a novel fake atom mechanism. DiffDec was shown able to generate structure-aware R-groups, and simultaneously generate multiple R-groups for one scaffold on different growth anchors. The growth anchors could be provided by users or automatically determined by our model. DiffDec achieved R-group recovery rates of 69.67% and 45.34% in the single and multiple R-group decoration tasks, respectively, and these values were significantly higher than competing methods (37.33% and 26.85%). According to the molecular docking study, our decorated molecules obtained better average binding affinity than baseline methods. The docking pose analysis revealed that DiffDec could decorate scaffolds with R-groups that exhibited improved binding affinities and more favourable interactions with the pocket. These results demonstrated the potential and applicability of DiffDec in real-world scaffold decoration for molecular optimization.

bioinformatics↗

bioRxiv2023

PRIME-BSPre: A genome-wide protein-RNA binding sites prediction method based on templates

Identification of RNA binding sites that potentially interact with RNA-binding proteins facilitates a comprehensive analysis of protein-RNA interactions and enables further investigation into the mechanisms underlying RNA splicing and modification. However, the current experimental data remains limited in comparison to the vast family of RBPs, and deep learning prediction methods are inadequate for those RBPs lacking sufficient interaction data for training. Therefore, we present PRIME-BSPre, a genome-wide method for predicting protein-RNA binding sites based on templates that incorporate both RNA sequence and secondary structure as well as the tertiary structure of corresponding RBPs. We have successfully benchmarked our method on the human genome, demonstrating excellent prediction performance on RBP datasets beyond our library and robustness across cell lines. Additionally, we are pioneers in introducing the low Shannon entropy algorithm to describe binding preferences of RNA motifs. Our predicted results further support the hypothesis that RBPs preferentially bind RNA motifs with low complexity.

bioinformatics↗

bioRxiv2023

Generalization of deep learning models for predicting spatial gene expression profiles using histology images: A breast cancer case study

Spatial transcriptomics is a breakthrough technology that enables spatially-resolved measurement of molecular profiles in tissues, opening the opportunity for integrated analyses of morphology and transcriptional profiles through paired imaging and gene expression data. However, the high cost of generating data has limited its widespread adoption. Predicting gene expression profiles from histology images only can be an effective and cost-efficient in-silico spatial transcriptomics solution but is computationally challenging and current methods are limited in model performance. To advance research in this emerging and important field, this study makes the following contributions. We first provide a systematic review of deep learning methods for predicting gene expression profiles from histology images, highlighting similarities and differences in algorithm, model architecture, and data processing pipelines. Second, we performed extensive experiments to evaluate the generalization performance of the reviewed methods on several spatial transcriptomics datasets for breast cancer, where the datasets are generated using different technologies. Lastly, we propose several ideas for model improvement and empirically investigate their effectiveness. Our results shed insight on key features in a neural network model that either improve or not the performance of in-silico spatial transcriptomics, and we highlight challenges in developing algorithms with strong generalization performance. Key MessagesO_LIWe comprehensively compared the performance of existing methods for predicting spatial gene expression profiles from histology images C_LIO_LIWe assessed the roles of different algorithms, model architectures, and data processing pipelines to model performance C_LIO_LIWe performed extensive experiments to evaluate the generalization of the models on in-distribution and out-of-distribution spatial transcriptomics datasets C_LIO_LIWe proposed several strategies for improving existing models and empirically investigated their effectiveness C_LI

bioinformatics↗

bioRxiv2023

Role of C2-domain protein CAR1 in the plasma membrane ABA signaling response

Plasma membrane (PM)-associated abscisic acid (ABA) signal transduction is an important component of ABA signaling. The C2-domain ABA-related (CAR) proteins have been reported to play a crucial role in recruiting ABA receptor PYR1/PYL/RCAR (PYLs) to the PM. However, the molecular details of the involvement of CAR proteins in membrane-delimited ABA signal transduction remain unclear. Here, the GUS-tagged materials for all Arabidopsis CAR members were used to comprehensively visualize the extensive expression patterns of the CAR family genes. Based on the specificity of CAR1s response to ABA, we determined to use it as a target to study the function of CAR proteins in PM-associated ABA signaling. Single-particle tracking showed that ABA affected the spatiotemporal dynamics of CAR1. The presence of ABA prolonged the dwell time of CAR1 on the membrane and showed faster lateral mobility. Surprisingly, we verified that CAR1 could directly recruit Hypersensitive to ABA1 (HAB1) and SNF1-related protein kinase 2.2 (SnRK2.2) to the PM at both the bulk and single-molecule levels. Furthermore, PM localization of CAR1 was demonstrated to be related to membrane microdomains. Collectively, our study revealed that CARs recruited the three main components of ABA signaling to the PM to respond positively to ABA. This study deepens our understanding of ABA signal transduction.

biophysics↗

bioRxiv2023

The sterol C-24 methyltransferase encoding gene, erg6, is essential for viability of Aspergillus species.

Ergosterol is a critical component of fungal plasma membranes. Although many currently available antifungal compounds target the ergosterol biosynthesis pathway for antifungal effect, current knowledge regarding ergosterol synthesis remains incomplete for filamentous fungal pathogens like Aspergillus fumigatus. Here, we show for the first time that the lipid droplet-associated sterol C-24 methyltransferase, Erg6, is essential for A. fumigatus viability. We further show that this essentiality extends to additional Aspergillus species, including A. lentulus, A. terreus, and A. nidulans. Neither the overexpression of a putative erg6 paralog, smt1, nor the exogenous addition of ergosterol could rescue erg6 deficiency. Importantly, Erg6 downregulation results in a dramatic decrease in ergosterol and accumulation in lanosterol and is further characterized by diminished sterol-rich plasma membrane domains (SRDs) at hyphal tips. Unexpectedly, erg6 repressed strains demonstrate wild-type susceptibility against the ergosterol-active triazole and polyene antifungals. Finally, repressing erg6 expression reduced fungal burden accumulation in a murine model of invasive aspergillosis. Taken together, our studies suggest that Erg6, which shows little homology to mammalian proteins, is potentially an attractive antifungal drug target for therapy of Aspergillus infections. IMPORTANCEA. fumigatus is the most common pathogen that causes invasive aspergillosis, a life-threatening fungal infection with more than 300,000 cases reported annually. Available antifungals to treat Aspergillus-related infection are limited to three drug classes targeting the plasma membrane (ergosterol) or the cell wall, each of which suffer from either host toxicity or rising resistance levels. As ergosta-type sterols are absent in mammalian cells but are essential for fungal viability, the ergosterol biosynthesis pathway remains an enticing target for the development of new antifungals. Although ergosterol biosynthesis has been well studied in model yeast, only a few genes have been genetically characterized in A. fumigatus. Here, we characterize Erg6, one of the fungus-specific sterol biosynthesis genes, as an essential gene in Aspergillus species. We further provide in vivo evidence of the importance of Erg6 for establishment of invasive aspergillosis. Given the importance of Erg6 in other fungal systems for growth, stress resistance, and virulence, our study suggests that development of Erg6 inhibitors may be a promising strategy for developing novel broad-spectrum antifungals.

microbiology↗

bioRxiv2023

Melatonin alleviates valproic acid-induced neural tube defects by modulating Src/PI3K/ERK signaling and oxidative stress

Neural tube defects (NTDs) represent a developmental disorder of the nervous system that can lead to significant disability in children and impose substantial social burdens. Valproic acid (VPA), a widely prescribed first-line antiepileptic drug for epilepsy and various neurological conditions, has been associated with a fourfold increase in the risk of NTDs when used during pregnancy. Consequently, urgent efforts are required to identify innovative prevention and treatment approaches for VPA-induced NTDs. Studies have demonstrated that the disruption in the delicate balance between cell proliferation and apoptosis is a crucial factor contributing to NTDs induced by VPA. Encouragingly, our current data reveal that melatonin (MT) exerts significant inhibition on apoptosis while promoting the restoration of neuroepithelial cells proliferation impaired by VPA. Moreover, further investigations demonstrate that MT substantially reduces the incidence of neural tube malformations resulting from VPA exposure, primarily achieved by suppressing apoptosis through the modulation of intracellular reactive oxygen species levels. In addition, the Src/PI3K/ERK signaling pathway appears to play a pivotal role in VPA-induced NTDs, with a significant inhibition observed in the affected samples. Notably, MT treatment successfully reinstates the Src/PI3K/ERK signals, thereby offering a potential underlying mechanism for MTs protective effects against VPA-induced NTDs. In summary, our current study substantiates the considerable protective potential of MT in mitigating VPA-triggered NTDs, thereby offering valuable strategies for the clinical management of VPA-related birth defects.

developmental biology↗

bioRxiv2023

Proteomic analysis revealed the function of PoElp3 in development, pathogenicity and autophagy through the tRNA-mediated translation efficiency in the rice blast fungus

The Elongator complex is conserved in a wide range of species and plays crucial roles in diverse cellular processes. We have previously shown that the Elongator protein PoELp3 was involved in the asexual development, pathogenicity, and autophagy of the rice blast fungus. In this study, we further revealed that PoElp3 functions via tRNA-mediated protein integrity. Phenotypic analyses revealed that overexpression of two of the tRNAs, tK(UUU) and tQ(UUG) could rescue the defects in {Delta}Poelp3 strain. TMT-based proteomic and transcriptional analyses demonstrated that 386 proteins were down-regulated in {Delta}Poelp3 strain compared with wild type strain Guy11, in a transcription-independent manner. Codon usage assays revealed an enrichment of Glutamine CAA-biased mRNA in the 386 proteins compared with the 70-15 genome. In addition to those reported previously, we also found that PoErp9, a sphingolipid C9-methyltransferase, was down-regulated in the {Delta}Poelp3 strain. Through an ILV2-specific integration of PoERP9-GFP into the wild type and {Delta}Poelp3 strain, we were able to show that PoErp9 was positively regulated by PoElp3 translationally but not transcriptionally. Functional analyses revealed that PoErp9 was involved in the fungal growth, conidial development, pathogenicity, and TOR-related autophagy homeostasis in P. oryzae. Taken together, our results suggested that PoElp3 acts through the tRNA-mediated translational efficiency to regulate asexual development, pathogenicity, and autophagy in the rice blast fungus.

pathology↗

bioRxiv2023

Comprehensive multi-platform tyrosine kinase profiling reveals novel actionable FGFR aberrations across pediatric and AYA sarcomas

No targeted agents are approved for pediatric sarcomas. Tyrosine kinase (TK) inhibitors represent attractive therapeutic candidates, however, beyond rare TK-activating fusions or mutations, predictive biomarkers are lacking. RNA overexpression of TKs is more commonly observed in pediatric sarcomas, however, an unresolved question is when upregulated TK expression is associated with kinase activation and signaling dependence. We explored the TK molecular landscape of 107 sarcoma patients from the ZERO Childhood Cancer precision medicine program using whole genomic and transcriptomic sequencing. Phosphoproteomic analyses of tyrosine phosphorylation (pY) and functional in vitro and in vivo assays were also performed in cell lines and patient-derived xenografts (PDXs). Our integrated analysis shows that although novel genomic driver lesions are rare, they are present and therapeutically actionable in selected patients as exemplified by a novel LSM1-FGFR1 fusion identified in an osteosarcoma patient. We further show that in certain contexts, TK expression data can be used to indicate TK pathway activity and predict TK-inhibitor sensitivity. We exemplify the utility of FGFR-inhibitors in PAX3-FOXO1 fusion-positive rhabdomyosarcomas (FP-RMS) mediated by high FGFR4 and FGF8 RNA expression levels, and overt activation of FGFR4 (FGFR4_pY). We demonstrate marked tumor growth inhibition in all FP-RMS PDXs treated with single agent FGF401 (FGFR4-specific inhibitor) and single agent lenvatinib (multi-kinase FGFR-inhibitor). Clinical benefit of lenvatinib in a relapsed metastatic FP-RMS patient further exemplifies that FGFR-inhibitors deserve additional investigation in FP-RMS patients. Statement of significanceOur multi-omic interrogation of sarcomas in the ZERO Childhood Cancer program illustrates how an RNA-expression biomarker signature (FGFR4+/FGF8+) in association with FGFR4 activation identifies that PAX3-FOXO1-positive rhabdomyosarcoma patients could benefit from FGFR-inhibitors.

cancer biology↗