Biology subjects

Wang, G.

Publications and source records attributed to Wang, G..

At least 199 records · Page 11Linked to original sources

bioRxiv2024

Predicting Spatially Resolved Gene Expression via Tissue Morphology using Adaptive Spatial GNNs

MotivationSpatial transcriptomics technologies, which generate a spatial map of gene activity, can deepen the understanding of tissue architecture and its molecular underpinnings in health and disease. However, the high cost makes these technologies difficult to use in practice. Histological images co-registered with targeted tissues are more affordable and routinely generated in many research and clinical studies. Hence, predicting spatial gene expression from the morphological clues embedded in tissue histological images, provides a scalable alternative approach to decoding tissue complexity. ResultsHere, we present a graph neural network based framework to predict the spatial expression of highly expressed genes from tissue histological images. Extensive experiments on two separate breast cancer data cohorts demonstrate that our method improves the prediction performance compared to the state-of-the-art, and that our model can be used to better delineate spatial domains of biological interest. Availabilityhttps://github.com/song0309/asGNN/

bioinformatics↗

bioRxiv2024

Targeting PRMT3 Impairs Methylation and Oligomerization of HSP60 to Boost Anti-Tumor Immunity by Activating cGAS/STING Signaling

Hepatocellular carcinoma (HCC) is a highly lethal cancer for which current available treatment options have limited efficacy. Immunotherapy has emerged as a promising therapeutic option for HCC, yet resistance to immunotherapy is a major challenge. Here, we uncover protein arginine methyltransferase 3 (PRMT3) as a novel driver of immunotherapy resistance in HCC. We show that PRMT3 expression is induced by activated T cells in response to immune checkpoint blockade (ICB) via an interferon-gamma (IFN{gamma})-STAT1 signaling pathway, and that high PRMT3 expression inversely correlates with tumor-infiltrating CD8+ T cells and predicts poor response to ICB in HCC patients. We demonstrate that genetic depletion and pharmacological inhibition of PRMT3 induce a profound influx of T cells into tumors and activate anti-tumor immunity to suppress HCC progression. Mechanistically, we demonstrate that PRMT3 methylates HSP60, a mitochondrial chaperone protein, at R446, and that this novel post-translational modification is required for HSP60 oligomerization and maintaining mitochondrial homeostasis. We reveal that targeting PRMT3-dependent HSP60-R446 methylation boosts anti-tumor immunity by disrupting mitochondrial function, increasing mitochondrial DNA (mtDNA) leakage, and activating the cGAS/STING pathway, a key innate immune sensor of cytosolic DNA. Importantly, we provide genetic and pharmacologic evidence that targeting PRMT3 enhances anti-PD1 efficacy and anti-tumor immunity in HCC mouse models. Our study identifies PRMT3 as a potential biomarker and therapeutic target to overcome immunotherapy resistance in HCC.

cancer biology↗

bioRxiv2024

Pi-PrimeNovo: An Accurate and Efficient Non-Autoregressive Deep Learning Model for De Novo Peptide Sequencing

Peptide sequencing via tandem mass spectrometry (MS/MS) is fundamental in proteomics data analysis, playing a pivotal role in unraveling the complex world of proteins within biological systems. In contrast to conventional database searching methods, deep learning models excel in de novo sequencing peptides absent from existing databases, thereby facilitating the identification and analysis of novel peptide sequences. Current deep learning models for peptide sequencing predominantly use an autoregressive generation approach, where early errors can cascade, largely affecting overall sequence accuracy. And the usage of sequential decoding algorithms such as beam search suffers from the low inference speed. To address this, we introduce{pi} -PrimeNovo, a non-autoregressive Transformer-based deep learning model designed to perform accurate and efficient de novo peptide sequencing. With the proposed novel architecture,{pi} -PrimeNovo achieves significantly higher accuracy and up to 69x faster sequencing compared to the state-of-the-art methods. This remarkable speed makes it highly suitable for computation-extensive peptide sequencing tasks such as metaproteomic research, where{pi} -PrimeNovo efficiently identifies the microbial species-specific peptides. Moreover,{pi} -PrimeNovo has been demonstrated to have a powerful capability in accurately mining phosphopeptides in a non-enriched phosphoproteomic dataset, showing an alternative solution to detect low-abundance post-translational modifications (PTMs). We suggest that this work not only advances the development of peptide sequencing techniques but also introduces a transformative computational model with wide-range implications for biological research.

bioinformatics↗

bioRxiv2024

Production and functional verification of 8-gene (GGTA1, CMAH, β4GalNT2, hCD46, hCD55, hCD59, hTBM, hCD39)-edited donor pigs for xenotransplantation

Gene-edited pig-to-human xenotransplantation continues to make breakthroughs and is expected to enter clinic to solve the global shortage of donor organs. However, which gene combination is suitable for which organ transplantation remains unclear. In this study, we utilized CRISPR/Cas9 gene editing technology, PiggyBac transposon system and somatic cell cloning to construct GTKO/CMAHKO/{beta}4GalNT2KO/hCD46/hCD55/hCD59/hCD39/hTBM 8 gene-edited cloned (GEC) donor pigs, and performed pig to non-human primate (NHP) transplantation to evaluate the effectiveness of these GEC pigs. The multiple vectors were co-transfected into fetal fibroblasts of Diannan miniature pig with O blood type, and 25 colonies were screened out, and one of them carried GGTA1, CMAH and {beta}4GalNT2 biallelic knockout and integration of hCD46, hCD55, hCD59, hTBM and hCD39 genes, which was used as a donor cell for cloning, and a 33-day-old viable fetus was obtained. The fetus was identified and confirmed for normal karyotype and the absence of three xenogeneic antigens -Gal, Neu5Gc and Sda, and expression of hCD46, hCD55, hCD59, hTBM and hCD39 genes, then the recloning was carried out and 28 cloned piglets were obtained by natural delivery. Molecular identification at DNA, mRNA and protein levels showed that 8 gene editing (GE) was successful in these GEC piglets. Moreover, antigen-antibody binding assay and complement-dependent cytotoxicity assay demonstrated that 8GE effectively reduced the immune incompatibility and kidney xenograft survived up to 15 and 17 days into two NHPs, respectively. During this period, the recipient serum antibodies IgA and IgM, complements C3 and C4, coagulation indicators PT, APTT, TT and FIB, as well as most electrolytes and liver function indicators remained relatively stable. The 24-hour urine output and serum creatinine remained normal at a period of post-transplantation. These results indicated that the 8GEC pigs effectively alleviated immune rejection and exerted life-supporting kidney function in the recipient.

genetics↗

bioRxiv2024

Personalized transcriptome signatures in a cardiomyopathy stem cell biobank

BACKGROUNDThere is growing evidence that pathogenic mutations do not fully explain hypertrophic (HCM) or dilated (DCM) cardiomyopathy phenotypes. We hypothesized that if a patients genetic background was influencing cardiomyopathy this should be detectable as signatures in gene expression. We built a cardiomyopathy biobank resource for interrogating personalized genotype phenotype relationships in human cell lines. METHODSWe recruited 308 diseased and control patients for our cardiomyopathy stem cell biobank. We successfully reprogrammed PBMCs (peripheral blood mononuclear cells) into induced pluripotent stem cells (iPSCs) for 300 donors. These iPSCs underwent whole genome sequencing and were differentiated into cardiomyocytes for RNA-seq. In addition to annotating pathogenic variants, mutation burden in a panel of cardiomyopathy genes was assessed for correlation with echocardiogram measurements. Line-specific co-expression networks were inferred to evaluate transcriptomic subtypes. Drug treatment targeted the sarcomere, either by activation with omecamtiv mecarbil or inhibition with mavacamten, to alter contractility. RESULTSWe generated an iPSC biobank from 300 donors, which included 101 individuals with HCM and 88 with DCM. Whole genome sequencing of 299 iPSC lines identified 78 unique pathogenic or likely pathogenic mutations in the diseased lines. Notably, only DCM lines lacking a known pathogenic or likely pathogenic mutation replicated a finding in the literature for greater nonsynonymous SNV mutation burden in 102 cardiomyopathy genes to correlate with lower left ventricular ejection fraction in DCM. We analyzed RNA-sequencing data from iPSC-derived cardiomyocytes for 102 donors. Inferred personalized co-expression networks revealed two transcriptional subtypes of HCM. The first subtype exhibited concerted activation of the co-expression network, with the degree of activation reflective of the disease severity of the donor. In contrast, the second HCM subtype and the entire DCM cohort exhibited partial activation of the respective disease network, with the strength of specific gene by gene relationships dependent on the iPSC-derived cardiomyocyte line. ADCY5 was the largest hubnode in both the HCM and DCM networks and partially corrected in response to drug treatment. CONCLUSIONSWe have a established a stem cell biobank for studying cardiomyopathy. Our analysis supports the hypothesis the genetic background influences pathologic gene expression programs and support a role for ADCY5 in cardiomyopathy.

genomics↗

bioRxiv2024

Exploring differences between depression and bipolar disorder through the urinary proteome

How to differentiate the diagnosis of depression and bipolar disorder has always been an important problem that needs to be solved urgently in clinical practice. In this study, from the perspective of urine proteomics, urine samples of similar age were collected from two hospitals to investigate the candidate biomarkers for differentiating the diagnosis of depression and bipolar disorder using both group analysis and one-to-many analysis(1 patient: many control samples). The experimental results of the paired group analysis showed that 108 differential proteins were identified in the depressed group compared to the bipolar group under strict screening conditions with screening criteria of FC [≥] 2 or [≤] 0.5 and a two-tailed unpaired t-test of P < 0.01, with an average of 3.7 randomly generated differential proteins, and a confidence level of 96.6 % for the correlation between these proteins and the disease difference. In the one-to-many analysis, 24 differential proteins were co-identified by the samples of 13 depressed patients, 16 of which showed a completely consistent trend of expression changes in all depressed patients studied, and 6 of which were associated with immunoglobulins; 41 differential proteins were co-identified by the samples of 12 depressed patients out of 13, and 19 of which showed a completely consistent trend of expression change in the These results reflect the strong consistency of differential proteins between the two groups of patients. 12 or more samples from depressed patients were enriched for differential proteins related to multiple biological processes and signaling pathways associated with the immune system, which is consistent with previous studies: immune mechanisms may be one of the pathogenetic mechanisms of major depression and that drugs with major immune targets can improve depressive symptoms. In the future, it may be possible to observe the immune status of patients with depression to provide direction and basis for the precise treatment of depression. The results of this paper show that urine proteomics can differentiate between depression and bipolar disorder, suggest possible mechanisms and potential targets for the treatment of depression and bipolar disorder, and provide a tool for future differential diagnosis and precision treatment of the diseases.

biochemistry↗

bioRxiv2024

SAMP: Identifying Antimicrobial Peptides by an Ensemble Learning Model Based on Proportionalized Split Amino Acid Composition

AbstractIt is projected that 10 million deaths could be attributed to drug-resistant bacteria infections in 2050. To address this concern, identifying new-generation antibiotics is an effective way. Antimicrobial peptides (AMPs), a class of innate immune effectors, have received significant attention for their capacity to eliminate drug-resistant pathogens, including viruses, bacteria, and fungi. Recent years have witnessed widespread applications of computational methods especially machine learning (ML) and deep learning (DL) for discovering AMPs. However, existing methods only use features including compositional, physiochemical, and structural properties of peptides, which cannot fully capture sequence information from AMPs. Here, we present SAMP, an ensemble random projection (RP) based computational model that leverages a new type of features called Proportionalized Split Amino Acid Composition (PSAAC) in addition to conventional sequence-based features for AMP prediction. With this new feature set, SAMP captures the residue patterns like sorting signals at around both the N-terminus and the C-terminus, while also retaining the sequence order information from the middle peptide fragments. Benchmarking tests on different balanced and imbalanced datasets demonstrate that SAMP consistently outperforms existing state-of-the-art methods, such as iAMPpred and AMPScanner V2, in terms of accuracy, MCC, G-measure and F1-score. In addition, by leveraging an ensemble RP architecture, SAMP is scalable to processing large-scale AMP identification with further performance improvement, compared to those models without RP. To facilitate the use of SAMP, we have developed a Python package freely available at https://github.com/wan-mlab/SAMP.

bioinformatics↗

bioRxiv2024

Rampant transcription replication conflict creates therapeutic vulnerability in extrachromosomal DNA containing cancers

Extrachromosomal DNA (ecDNA) presents a major challenge for precision medicine, contributing to poor survival for patients with oncogene-amplified tumours. EcDNA renders tumours resistant to targeted treatments by facilitating massive transcription of oncogenes and rapid genome evolution. At present, there are no ecDNA- specific treatments. Here we show that enhancing transcription replication conflict enables targeted elimination of ecDNA-containing cancers, exposing an actionable vulnerability. Stepwise analyses of ecDNA transcription reveal landscapes of pervasive RNA transcription and associated single-stranded DNA, leading to excessive transcription replication conflicts and replication stress (RS) compared to chromosomal loci. Nucleotide incorporation onto growing DNA strands is markedly slower on ecDNA, and RS is significantly higher in ecDNA-containing tumours regardless of cancer type or oncogene cargo. Replication Protein A2 phosphorylated on serine 33, a mediator of DNA damage repair that binds single-stranded DNA, shows elevated localization on ecDNA in a transcription dependent manner, along with increased DNA double strand breaks, and activation of the S-phase checkpoint kinase, CHK1. Genetic or pharmacological CHK1 inhibition abrogates the DNA replication check point, causing extensive and preferential tumour cell death in ecDNA-containing tumours as they enter S-phase. To exploit this vulnerability, we develop a highly selective, potent, and bioavailable oral CHK1 inhibitor, BBI-2779, and demonstrate that it preferentially kills ecDNA-containing tumour cells. In a gastric cancer model containing FGFR2 on ecDNA, BBI-2779, suppresses tumour growth and prevents ecDNA-mediated acquired resistance to the pan-FGFR inhibitor infigratinib, resulting in potent and sustained tumour regression in mice. These results reveal transcription-replication conflict as an ecDNA-generated vulnerability that can be targeted as an ecDNA-directed therapy and suggest that synthetic lethality of excess can be exploited as a strategy for treating cancer.

cancer biology↗

bioRxiv2024

Aeromonas hydrophila CobQ is a new type of NAD+- and Zn2+-independent protein lysine deacetylase in prokaryotes

Protein N--lysine acetylation (Kac) modifications play crucial roles in diverse physiological and pathological functions in cells. In prokaryotic cells, there are only two types of lysine deacetylases (KDACs) that are Zn2+- or NAD+-dependent. In this study, we reported a protein, AhCobQ, in Aeromonas hydrophila ATCC 7966 that presents NAD+- and Zn2+-independent KDAC activity. Furthermore, its KDAC activity is located in an unidentified domain (from 195-245 aa). Interestingly, AhCobQ has no homology with current known KDACs, and no homologous protein was found in eukaryotic cells. A protein substrate analysis showed that AhCobQ has specific protein substrates in common with other known KDACs, indicating that these KDACs can dynamically co-regulate the states of Kac proteins. Microbiological methods employed in this study affirmed AhCobQs positive regulation of isocitrate dehydrogenase (ICD) enzymatic activity at the K388 site, implicating AhCobQ in the modulation of bacterial enzymatic activities. In summary, our findings present compelling evidence that AhCobQ represents a distinctive type of KDAC with significant roles in bacterial biological functions. SummaryThe lack of exploration of new lysine acetylases and deacetylases (KDACs) and their protein substrates in prokaryotic cells has become a bottleneck in the functional study of lysine acetylation modifications. In this study, we reported a novel Zn2+- and NAD+-independent KDAC protein, AhCobQ, in Aeromonas hydrophila. Interestingly, this protein does not share homology with current known KDACs, and its KDAC activity is located in an unknown domain for which a homologous protein cannot be found in eukaryotic cells. The following analysis showed that AhCobQ affected the enzymatic activity and protein-protein interaction ability of its protein substrates. In summary, these results extended our understanding of the regulatory mechanism of bacterial lysine acetylation modifications. HighlightsAhCobQ is an NAD+- and Zn2+-independent protein lysine deacetylase. There are no proteins homologous to AhCobQ in eukaryotes. The deacetylase activity of AhCobQ is located in an unknown domain. AhCobQ has specific protein substrates and substrates in common with other lysine deacetylases. AhCobQ positively regulates the enzymatic activity of isocitrate dehydrogenase at its K388 site.

microbiology↗

bioRxiv2024

Transcriptional Determinism and Stochasticity Contribute to the Complexity of Autism Associated SHANK Family Genes

Precision of transcription is critical because transcriptional dysregulation is disease causing. Traditional methods of transcriptional profiling are inadequate to elucidate the full spectrum of the transcriptome, particularly for longer and less abundant mRNAs. SHANK3 is one of the most common autism causative genes. Twenty-four Shank3 mutant animal lines have been developed for autism modeling. However, their preclinical validity has been questioned due to incomplete Shank3 transcript structure. We applied an integrative approach combining cDNA-capture and long-read sequencing to profile the SHANK3 transcriptome in human and mice. We unexpectedly discovered an extremely complex SHANK3 transcriptome. Specific SHANK3 transcripts were altered in Shank3 mutant mice and postmortem brains tissues from individuals with ASD. The enhanced SHANK3 transcriptome significantly improved the detection rate for potential deleterious variants from genomics studies of neuropsychiatric disorders. Our findings suggest the stochastic transcription of genome associated with SHANK family genes.

genetics↗

bioRxiv2024

Validation of Enhancer Regions in Primary Human Neural Progenitor Cells using Capture STARR-seq

Genome-wide association studies (GWAS) and expression analyses implicate noncoding regulatory regions as harboring risk factors for psychiatric disease, but functional characterization of these regions remains limited. We performed capture STARR-sequencing of over 78,000 candidate regions to identify active enhancers in primary human neural progenitor cells (phNPCs). We selected candidate regions by integrating data from NPCs, prefrontal cortex, developmental timepoints, and GWAS. Over 8,000 regions demonstrated enhancer activity in the phNPCs, and we linked these regions to over 2,200 predicted target genes. These genes are involved in neuronal and psychiatric disease-associated pathways, including dopaminergic synapse, axon guidance, and schizophrenia. We functionally validated a subset of these enhancers using mutation STARR-sequencing and CRISPR deletions, demonstrating the effects of genetic variation on enhancer activity and enhancer deletion on gene expression. Overall, we identified thousands of highly active enhancers and functionally validated a subset of these enhancers, improving our understanding of regulatory networks underlying brain function and disease.

neuroscience↗

bioRxiv2024

Zinc Alpha-2-Glycoprotein (ZAG/AZGP1) secreted by triple-negative breast cancer promotes tumor microenvironment fibrosis.

Obesity is a predisposition factor for breast cancer, suggesting a localized, reciprocal interaction between breast cancer cells and the surrounding mammary white adipose tissue. To investigate how breast cancer cells alter the composition and function of adipose tissue, we screened the secretomes of ten human breast cancer cell lines for the ability to modulate the differentiation of adipocyte stem and progenitor cells (ASPC). The screen identified a key adipogenic modulator, Zinc Alpha-2-Glycoprotein (ZAG/AZGP1), secreted by triple-negative breast cancer (TNBC) cells. TNBC-secreted ZAG inhibits adipogenesis and instead induces the expression of fibrotic genes. Accordingly, depletion of ZAG in TNBC cells attenuates fibrosis in white adipose tissue and inhibits tumor growth. Further, high expression of ZAG in TNBC patients, but not other clinical subtypes of breast cancer, is linked to poor prognosis. Our findings suggest a role of TNBC-secreted ZAG in promoting the transdifferentiation of ASPCs into cancer-associated fibroblasts to support tumorigenesis.

cancer biology↗

bioRxiv2024

Targeting GFPT2 to reinvigorate immunotherapy in EGFR-mutated NSCLC

In the evolving field of cancer immunotherapy, EGFR-mutated NSCLC presents a significant challenge, demonstrating marked innate resistance to established treatments. An effective method to counter this resistance remains elusive. Through comprehensive genetic and pharmacological analyses across various models, we have identified glutamine fructose-6-phosphate transaminase 2 (GFPT2) as a key facilitator of immune evasion in EGFR-mutated NSCLC. Mechanistically, under EGFR mutation condition, GFPT2 expression, which is typically low in normal tissues, is highly induced via EGFR/IRE1/Xbp1s signaling axis, leading to a significant increase in intracellular UDP-GlcNAc and consequently, an altered N-glycosylation profile. GFPT2 escalates the expression and glycosylation of PD-L1, PVR and CD276, bolstering their interactions with CD8+T cells, and amplifies CD73 glycosylation, thereby intensifying adenosine-mediated CD8+T cells suppression. These actions collectively reduce tumor cell vulnerability to CD8+T cell-mediated death. Moreover, GFPT2 regulates EGFR glycosylation, which consequentially modulates the EGFR-dependent secretion of CXCL10 and VEGF, thus impeding CD8+T cell infiltration within tumors. We further identified a GFPT2 isoform-specific inhibitor that potentiates PD-1 blockade therapy beyond that of existing strategy, corroborated by results in xenografts and patient-derived organoids. Together, these findings illuminate the promising therapeutic potential of GFPT2 as a metabolic checkpoint, offering an innovative approach to invigorate immunotherapy in NSCLC with EGFR mutations.

cancer biology↗

bioRxiv2024

Dark-based Optical Sectioning assists Background Removal in Fluorescence Microscopy

A fundamental challenge in fluorescence microscopy is the defocused background caused by scattering light, optical aberration, or limited axial resolution. Severe defocus backgrounds will submerge the in-focus information and cause artifacts in the following processing. Here, we leverage a priori knowledge about dark channels of biological structures and dual frequency separation to develop a single-frame defocus removal algorithm. It stably improves the signal-to-background ratio and structural similarity index measure of images by approximately 10-fold, and recovers in-focus signal with 85% accuracy, even when the defocus background is 50 times larger than in-focus information. Our Dark-based optical sectioning approach (Dark sectioning) is fully compatible with various microscopy techniques, such as wide-filed microscopy, polarized microscopy, laser-scanning / spinning-disk confocal microscopy, stimulated emission depletion microscopy, lightsheet microscopy, and light-field microscopy. It also complements reconstruction or processing algorithms such as deconvolution, structure illumination microscopy, and super-resolution optical fluctuation imaging.

bioinformatics↗

bioRxiv2024

Transcriptome sequencing and bioinformatics analysis of kidney tissue in a tree shrew model of calcium oxalate nephrolithiasis

BackgroundKidney stones, predominantly composed of calcium oxalate, are a prevalent and recurrent urological condition. Given their high incidence and recurrence rates, understanding their pathogenesis and identifying effective treatment strategies are imperative. MethodsIn this study, we established a calcium oxalate nephrolithiasis model using tree shrews, a primate-like animal species. When compared to commonly used rodent models (rats and mice), the tree shrew model demonstrated superior reproducibility and relevance. And leveraging transcriptome sequencing and comprehensive bioinformatics analysis. Resultswe identified 1,927 differentially expressed genes, including 1,450 upregulated and 476 downregulated genes. Furthermore, we annotated these genes to 41 KEGG enriched pathways and 1,413 GO enrichments, encompassing 1276 Biological Processes, 72 Cellular Components, and Molecular Functions. Notably, we prioritized the top 50 core genes that could potentially underlie the pathogenesis of calcium oxalate nephrolithiasis. ConclusionsOur findings establish the tree shrew as a relevant model for studying kidney stone formation and provide valuable insights into the underlying molecular mechanisms. These insights hold promise for the development of novel therapeutic strategies to address this significant health burden.

genomics↗

bioRxiv2024

Architecture of the spinach plastid-encoded RNA polymerase

The plastid-encoded RNA polymerase (PEP) serves as the principal transcription machinery within chloroplasts and is responsible for transcribing over 80% of primary plastid transcripts. Plant PEP is composed of a prokaryotic-like multisubunit core enzyme known as the PEP core, supplemented by newly evolved PEP-associated proteins (PAPs). In this study, we present the cryo-electron microscopy (cryo-EM) structure of a PEP complex derived from spinach (Spinacia oleracea). Our structural analysis unveils the presence of 14 PAPs closely associated with the PEP core complex consisting of 5 subunits, forming an irregular-shaped supercomplex. We provide a detailed depiction of the PEP core subunits and the 14 PAPs, elucidating their precise spatial arrangement and interactions. This research offers a crucial structural basis for future investigations into the functions and regulatory mechanisms governing plastid transcription.

biochemistry↗

bioRxiv2024

Turnover of RNA-binding Proteins and MicroRNAs by intrinsically disordered region-directed ZSWIM8 ubiquitin ligase during brain development

Widely present in mammalian proteomes, intrinsically disordered regions (IDRs) in proteins play important biological functions by conferring structural flexibility and mediating biomolecular interactions. IDR-containing proteins, including many RNA-binding proteins (RBPs), are prone to misfolding and aggregation and must be constantly monitored. Here we show that the conserved ZSWIM8-type Cullin-RING ubiquitin ligase (CRLZSWIM8) is a master regulator of such proteins during brain development. ZSWIM8 selects its substrates via an IDR-dependent mechanism, and deletion of ZSWIM8 causes aberrant accumulation of numerous RBPs including AGO2 and ELAV1 in neonatal brains. Furthermore, AGO2 ubiquitination by ZSWIM8 is triggered by microRNA binding, leading to target-directed microRNA degradation (TDMD) of MiR7. Dysregulation of MiR7 in the absence of ZSWIM8 results in defects in oligodendrocyte maturation and functions. Together, our findings have demonstrated that, by utilizing variable target-recognition strategies, ZSWIM8 controls the abundance of conformationally flexible RBPs and miRNA metabolism that are essential for brain development. TeaserA conserved ubiquitin ligase controls the quality of disordered proteins to ensure brain development.

developmental biology↗

bioRxiv2024

Supercontinuum intrinsic fluorescence imaging heralds free view of living systems

Optimal imaging strategies remain underdeveloped to maximize information for fluorescence microscopy while minimizing the harm to fragile living systems. Taking hint from the supercontinuum generation in ultrafast laser physics, we generated supercontinuum fluorescence from untreated unlabeled live samples before nonlinear photodamage onset. Our imaging achieved high-content cell phenotyping and tissue histology, identified bovine embryo polarization, quantified aging-related stress across cell types and species, demystified embryogenesis before and after implantation, sensed drug cytotoxicity in real-time, scanned brain area for targeted patching, optimized machine learning to track small moving organisms, induced two-photon phototropism of leaf chloroplasts under two-photon photosynthesis, unraveled microscopic origin of autumn colors, and interrogated intestinal microbiome. The results enable a facility-type microscope to freely explore vital molecular biology across life sciences.

bioengineering↗