Biology subjects

Xu, W.

Publications and source records attributed to Xu, W..

At least 145 records · Page 8Linked to original sources

bioRxiv2024

Heterotrimeric Collagen Helix with High Specificity of Assembly Results in a Rapid Rate of Folding

The most abundant natural collagens form heterotrimeric triple helices. Synthetic mimics of collagen heterotrimers have been found to fold slowly, even compared to the already slow rates of homotrimeric helices. These prolonged folding rates are not understood and have not been studied. This work compares three heterotrimeric collagen mimics stabilities, specificities and folding rates. One of these was designed through a computational-assisted approach, resulting in a well-controlled composition and register, in addition to providing increased amino acid diversity and excellent specificity. The crystal structure of this heterotrimer elucidates the composition, register and geometry of pairwise cation-{pi} and axial and lateral salt bridges. Complementary experimental methods of circular dichroism and NMR suggest the folding paradigm is frustrated by unproductive, competing heterotrimer species and these species must completely unwind to the monomeric state before refolding into the thermodynamically favored assembly. This collagen heterotrimer, which displays the best reported thermal specificity, was also found to fold much faster (hours vs days) than comparable, well-designed systems. The heterotrimeric collagen folding rate was observed to be both concentration and temperature-independent, suggesting a complex, multi-step mechanism. These results suggest heterotrimer folding kinetics are dominated by frustration of the energy landscape caused by competing triple helices.

biophysics↗

bioRxiv2024

Gene2role: a role-based gene embedding method for comparative analysis of signed gene regulatory networks

MotivationUnderstanding the dynamics of gene regulatory networks (GRNs) across various cellular states is crucial for deciphering the underlying mechanisms governing cell behavior and functionality. However, current comparative analytical methods, which often focus on simple topological information such as the degree of genes, are limited in their ability to fully capture the similarities and differences among the complex GRNs. ResultsWe present Gene2role, a gene embedding approach that leverages multi-hop topological information from genes within signed GRNs. Initially, we demonstrated the effectiveness of Gene2role in capturing the intricate topological nuances of genes using GRNs inferred from four distinct data sources. Then, applying Gene2role to integrated GRNs allowed us to identify genes with significant topological changes across cell types or states, offering a fresh perspective beyond traditional differential gene expression analysis. Additionally, we quantified the stability of gene modules between two cellular states by measuring the changes in the gene embeddings within these modules. In conclusion, our method augments the existing toolkit for probing the dynamic regulatory landscape, thereby opening new avenues for understanding gene behavior and interaction patterns across cellular transitions.

bioinformatics↗

bioRxiv2024

An epilepsy-associated CILK1 variant compromises KATNIP regulation and impairs primary cilia and Hedgehog signaling

Mutations in human CILK1 (ciliogenesis associated kinase 1) are linked to ciliopathies and epilepsy. Homozygous point and nonsense mutations that extinguish kinase activity impair primary cilia function, whereas mutations outside the kinase domain are not well understood. Here, we produced a knock-in mouse equivalent of the human CILK1 A615T variant identified in juvenile myoclonic epilepsy (JME). This residue is in the C-terminal region of CILK1 separate from the kinase domain. Mouse embryo fibroblasts (MEF) with either heterozygous or homozygous A612T mutant alleles exhibited a higher ciliation rate, shorter individual cilia and up-regulation of ciliary Hedgehog signaling. Thus, a single A612T mutant allele was sufficient to impair primary cilia and ciliary signaling in MEFs. Gene expression profiles of wild type versus mutant MEFs revealed profound changes in cilia-related molecular functions and biological processes. CILK1 A615T mutant protein was not increased to the same level as the wild type protein when co-expressed with scaffold protein KATNIP (katanin-interacting protein). Our data show that KATNIP regulation of a JME-associated single residue variant of CILK1 is compromised and this impairs the maintenance of primary cilia and Hedgehog signaling.

cell biology↗

bioRxiv2024

Time-lapse Image Super-resolution Neural Network with Reliable Confidence Evaluation for Optical Microscopy

Single image super-resolution (SISR) neural networks for optical microscopy have shown great capability to directly transform a low-resolution (LR) image into its super-resolution (SR) counterpart, enabling low-cost long-term live-cell SR imaging. However, when processing time-lapse data, current SISR models failed to exploit the important temporal dependencies between neighbor frames, often resulting in temporally inconsistent outputs. Besides, SISR models are subject to inference uncertainty that is hard to accurately quantify, therefore it is difficult to determine to what extend can we trust the inferred SR images. Here, we first build a large-scale, high-quality fluorescence microscopy dataset for the time-lapse image super-resolution (TISR) task, and conducted a comprehensive evaluation on two essential components of TISR neural networks, i.e., propagation and alignment. Second, we devised a deformable phase-space alignment (DPA) based TISR neural network (DPA-TISR), which adaptively enhances the cross-frame alignment in the phase domain and outperforms existing state-of-the-art SISR and TISR models. Third, we combined the Bayesian training scheme and Monte Carlo dropout with DPA-TISR, developing Bayesian DPA-TISR, and designed an expected calibration error (ECE)minimization framework to obtain a well-calibrated confidence map along with each output SR image, which reliably implicates potential inference errors. We demonstrate the unique characteristics of Bayesian DPA-TISR underlie the ultralong-term live-cell SR imaging capability with high spatial fidelity, superb temporal consistency, and accurate confidence quantification on a wide variety of bioprocesses.

biophysics↗

bioRxiv2024

Megabarcoding reveals a tale of two very different dark taxa along the same elevational gradient

AbstractOur planet is entering the sixth mass extinction without detailed spatio-temporal distribution and abundance information for most insect species. Particularly lacking is this information for dark taxa although they contain most animal species. This problem can be addressed with high-throughput single specimen barcoding (megabarcoding), but it remain unknown to what extent one dark taxon can be used as a proxy for another because of similar biodiversity patterns. This is here tested and we show that two Diptera taxa (Phoridae, Mycetophilidae) have very different spatio-temporal distributions across the same elevational gradient. We applied COI megabarcoding to samples collected every 14 days over three seasons at six elevations (800 to 1,800 m) in a temperate forest ecosystem in Northern China (Baihua Mountain Reserve). Elevation, precipitation, and temperature were used as environmental variables to understand the data obtained for 17,179 specimens representing 492 mOTUs of Phoridae and 2,281 specimens of 148 mOTUs of Mycetophilidae. Congruent is that the alpha diversity for both taxa increased in the summer and there is evidence for a mid-domain effect and phylogenetic clustering in high elevations. However, the extent and pattern of seasonal variation differed considerably. Phorid communities exhibited shifts between spring, summer and autumn seasons, but surprisingly little difference between elevations. In contrast, mycetophilid communities were structured along the elevational gradient and dependent on precipitation. Our study highlights the urgent need for obtaining detailed spatio-temporal information for the most diverse dark taxa, but also illustrates that these data can be readily obtained with megabarcoding.

ecology↗

bioRxiv2024

A change in the cell wall status initiates the elimination of the nucellus in Arabidopsis

The evolution of the seed habit coincides with a change in the cell fate of the nucellus, the sporophytic tissue responsible for female meiosis. Seeds arose when the nucellus retained the female spores instead of releasing them in the environment. As a consequence, the nucellus was partially eliminated to accommodate the growth of the female gametophyte inside the sporophyte. With the evolution of angiosperm seeds, the process of nucellus elimination was requisitioned to allow the growth of the endosperm, the second fertilization product devoted to store nutrients. Cell elimination differs from most known cell death programs as it leads to the apparent dismantling of the cell wall. Here, we show that nucellus elimination in Arabidopsis is initiated by the lysis of the pectic polysaccharides in the cell wall. This process exposes other cell wall components to possible further degradation and precedes a cell death program that leads to nuclear DNA fragmentation. Both pathways are regulated by TRANSPARENT TESTA 16, a MADS-domain transcription factor that evolved with seed plants. Finally, the causal effect of cell wall modification on nucellus development is demonstrated by inhibiting pectin degradation, thus suggesting that a change in the cell wall status might have driven seed evolution.

plant biology↗

bioRxiv2024

Regulatory Functional Landscape of the HMX1 Gene for Normal Ear Development

Enhancers, through the combinatorial action of transcription factors (TFs), dictate both the spatial specificity and the levels of gene expression, and their aberrations can result in diseases. The association between HMX1 and its downstream enhancer with ear deformities has been previously documented. However, the pathogenic variations and molecular mechanisms underlying the bilateral constricted ear (BCE) malformations remain unclear. This study identifies a copy number variation (CNV) encompassing three enhancers that induces BCE. These enhancers, collectively termed the positional identity hierarchical enhancer cluster (PI-HEC), co-regulate spatiotemporal expression of the HMX1 gene in a coordinated and synergistic mode, each displaying unique activity-location-structure characteristics. A thorough exploration of this regulatory locus reveals that specific motif clusters within the PI-HEC variably modulate its activity and specificity, with the high mobility group (HMG) box combined with Coordinator and homeodomain (HD)-TFs notably influencing them respectively. Our findings based on various types of mouse models, reveal that both aberrant Hmx1 expression in the fibroblasts of the basal pinna, originating from neural crest cells, and ectopic expression in the distal pinna structures contribute to the abnormal development of the outer ear, including the cartilage, muscle, and epidermis tissues. This study deepens our understanding of mammalian ear morphogenesis and sheds light on the complexity of gene expression regulation by enhancers and specific sequence motifs.

developmental biology↗

bioRxiv2024

Assessing Spns2-dependent S1P Transport as a Prospective Therapeutic Target using a New Chemical Probe

S1P (sphingosine 1-phosphate) receptor modulator (SRM) drugs interfere with lymphocyte trafficking by downregulating lymphocyte S1P receptors. While the immunosuppressive activity of SRM drugs has proved useful in treating autoimmune diseases such as multiple sclerosis, that drug class is beset by on-target liabilities such as initial dose bradycardia. The S1P that binds to cell surface lymphocyte S1P receptors is provided by S1P transporters. Mice born deficient in one of these, spinster homolog 2 (Spns2), are lymphocytopenic and have low lymph S1P concentrations. Such observations suggest that inhibition of Spns2-mediated S1P transport might provide another therapeutically beneficial method to modulate immune cell positioning. We report here results using a novel S1P transport blocker (STB), SLF80821178, to investigate the consequences of S1P transport inhibition in rodents. We found that SLF80821178 is efficacious in a multiple sclerosis model but - unlike the SRM fingolimod - neither decreases heart rate nor compromises lung endothelial barrier function. Notably, although Spns2 null mice have a sensorineural hearing defect, mice treated chronically with SLF80821178 have normal hearing acuity. STBs such as SLF80821178 evoke a dose-dependent decrease in peripheral blood lymphocyte counts, which affords a reliable pharmacodynamic marker of target engagement. However, the maximal reduction in circulating lymphocyte counts in response to SLF80821178 is substantially less than the response to SRMs such as fingolimod (50% vs. 90%) due to a lesser effect on T lymphocyte sub-populations by SLF80821178. Finally, in contrast to results obtained with Spns2 deficient mice, lymph S1P concentrations were not significantly changed in response to administration of STBs at doses that evoke maximal lymphopenia, which indicates that current understanding of the mechanism of action of S1P transport inhibitors is incomplete.

pharmacology and toxicology↗

bioRxiv2024

The dynamin-related protein Dyn2 is essential for both apicoplast and mitochondrial fission in Plasmodium falciparum

Dynamins, or dynamin-related proteins (DRPs), are large mechano-sensitive GTPases mediating membrane dynamics or organellar fission/fusion events. Plasmodium falciparum encodes three dynamin-like proteins whose functions are poorly understood. Here, we demonstrate that PfDyn2 mediates both apicoplast and mitochondrial fission. Using super-resolution and ultrastructure expansion microscopy, we show that PfDyn2 is expressed in the schizont stage and localizes to both the apicoplast and mitochondria. Super-resolution long-term live cell microscopy shows that PfDyn2-deficient parasites cannot complete cytokinesis because the apicoplast and mitochondria do not undergo fission. Further, the basal complex or cytokinetic ring in Plasmodium cannot fully contract upon PfDyn2 depletion, a phenotype secondary to physical blockage of undivided organelles in the middle of the ring. Our data suggest that organellar fission defects result in aberrant schizogony, generating unsuccessful merozoites. The unique biology of PfDyn2, mediating both apicoplast and mitochondrial fission, has not been observed in other organisms possessing two endosymbiotic organelles. HighlightsO_LIPfDyn2 is essential for schizont-stage development. C_LIO_LIPfDyn2 mediates both apicoplast and mitochondrial fission. C_LIO_LIDeficiency of PfDyn2 leads to organellar fission failures and blockage of basal complex contraction. C_LIO_LIAddition of apicoplast-derived metabolite IPP does not rescue the growth defects. C_LI

microbiology↗

bioRxiv2024

Experimental evolution of a reduced bacterial chemotaxis network

Chemotaxis allows bacteria to follow chemical gradients by comparing their environment over time and adjusting their swimming behavior accordingly. The chemotaxis signaling pathway is highly conserved among all chemotactic bacteria. The system comprises two modules: one for environmental sensing and signal transduction toward the flagellar motor, and the other for adapting to the constant level of background stimulation and providing short-term memory for temporal comparisons. Previous experimental analysis and mathematical modeling have suggested that all components of the paradigmatic chemotaxis pathways in Escherichia coli are essential. This indicates that it may contain a minimal set of protein components necessary to mediate gradient sensing and behavioral response. To test this assumption, here we subjected strains carrying deletions in chemotaxis genes to experimental laboratory evolution. We observed that the core components of the chemotaxis pathway are indeed essential. However, the absence of individual auxiliary pathway proteins, including the adaptation enzymes that are conserved in a vast majority of bacteria, and the phosphatase, could be compensated for to varying degrees by changes in other pathway components. Our results suggest that the experimental evolution of these deletion strains has led to the emergence of alternative strategies for bacterial chemotaxis, demonstrating the surprisingly rapid evolvability of this signaling network.

microbiology↗

bioRxiv2024

U-FISH: a universal deep learning approach for accurate FISH spot detection across diverse datasets

In the rapidly advancing landscape of fluorescence in situ hybridization (FISH) technologies, there is a critical need for sophisticated yet adaptable methods for spot detection. This study introduces U-FISH, a deep learning approach that significantly improves accuracy and generalization capabilities. Our method utilizes a U-Net model to transform noisy and ambiguous FISH images into a standardized representation with consistent signal characteristics, facilitating efficient spot detection. For the training and evaluation of the U-FISH model, we have constructed a comprehensive dataset comprising over 4,000 images and more than 1.6 million manually annotated spots, sourced from both experimental and simulated environments. Our benchmarks demonstrate that U-FISH outperforms existing methods for FISH spot detection, offering improved versatility by eliminating the need for laborious manual parameter adjustments. This allows for its application across a broad spectrum of datasets and formats. Furthermore, U-FISH is designed for high scalability and is capable of processing 3D data, supporting the latest generation of file formats for large and complex datasets. To promote community adoption and ensure accessibility, we provide a user-friendly interfaces: Napari plugin, web application and command-line interface. The complete training dataset is made publicly available, laying a solid foundation for future research in this field.

bioinformatics↗

bioRxiv2024

Novel Polymycoviruses Are Encapsidated in Filamentous Virions

Polymycoviridae is a new viral family that was established nearly five years ago, but their viral morphologies (naked or encapsidated) remain controversy since only one member namely, Colletotrichum camelliae filamentous virus 1 (CcFV1), was identified as being encapsidated in filamentous virions. Here, three novel dsRNA viruses belonging to the family Polymycoviridae were identified in three phytopathogenic fungal strains and tentatively named Pseudopestalotiopsis camelliae-sinensis polymycovirus 1 (PscPmV1), and Phyllosticta capitalensis polymycovirus 1 (PhcPmV1) and -2 (PhcPmV2), respectively. PscPmV1 and PhcPmVs have five or six genomic dsRNAs, ranging from 1055 to 2405 bp, encoding five or seven putative open reading frames (ORFs), of which ORF1 encodes an RNA-dependent RNA polymerase, ORF5 encodes a P-A-S-rich protein behaving as coat protein (CP); and dsRNAs 4 and 6 encode putative proteins with unknown functions and share no detectable identities with known viral sequences. Upon examination under transmission electron microscopy after purification from fungal mycelia, PscPmV1 and PhcPmVs were found to be encapsidated in filamentous particles, as was a known polymycovirus, Botryosphaeria dothidea RNA virus 1 (BdRV1), which was previously assumed to likely have no conventional virions. The morphology of PscPmV1 was further supported by the observation that its particles could be decorated by polyclonal antibodies against its CP and bound by immuno-gold particles conjugated to the specific CP antibody. Together with CcFV1 and BdRV1, PcsPmV1 PhcPmVs provide strong evidence to support the notion that polymycoviruses are encapsidated in filamentous virions constituted by P-A-S-rich CPs. Moreover, their biological effects on their fungal hosts were assessed. Significance statementPolymycoviridae, a recently established viral family, has raised questions about encapsidation. Here, we identify and characterize three novel polymycoviral dsRNA viruses in phytopathogenic fungal strains, tentatively named Pseudopestalotiopsis camelliae-sinensis polymycovirus 1, and Phyllosticta capitalensis polymycovirus 1 and -2, respectively. These polymycoviruses possess five or six genomic dsRNAs, ranging from 1055 to 2405 bp, with two encoding putative proteins of unknown functions and sharing no detectable identities with known viral sequences. Their morphologies indicate filamentous virions constituted by P-A-S-rich coat proteins, observed using immunosorbent electron microscopy combined with immune-gold labeling techniques. Additionally, Botryosphaeria dothidea RNA virus 1, previously assumed to lack conventional virions, is also shown to be encapsidated in filamentous particles. This study provides new evidence supporting the encapsidation of polymycoviruses into elongated and flexuous virions, significantly contributing to our understanding of the evolutionary particle architecture within the virosphere and expanding our knowledge of viral diversity and evolution.

microbiology↗

bioRxiv2024

HyperGen: Compact and Efficient Genome Sketching using Hyperdimensional Vectors

MotivationGenomic distance estimation is a critical workload since exact computation for whole-genome similarity metrics such as Average Nucleotide Identity (ANI) incurs prohibitive runtime overhead. Genome sketching is a fast and memory-efficient solution to estimate ANI similarity by distilling representative k-mers from the original sequences. In this work, we present HyperGen that improves accuracy, runtime performance, and memory efficiency for large-scale ANI estimation. Unlike existing genome sketching algorithms that convert large genome files into discrete k-mer hashes, HyperGen leverages the emerging hyperdimensional computing (HDC) to encode genomes into quasi-orthogonal vectors (Hypervector, HV) in high-dimensional space. HV is compact and can preserve more information, allowing for accurate ANI estimation while reducing required sketch sizes. In particular, the HV sketch representation in HyperGen allows efficient ANI estimation using vector multiplication, which naturally benefits from highly optimized general matrix multiply (GEMM) routines. As a result, HyperGen enables the efficient sketching and ANI estimation for massive genome collections. ResultsWe evaluate HyperGens sketching and database search performance using several genome datasets at various scales. HyperGen is able to achieve comparable or superior ANI estimation error and linearity compared to other sketch-based counterparts. The measurement results show that HyperGen is one of the fastest tools for both genome sketching and database search. Meanwhile, HyperGen produces memory-efficient sketch files while ensuring high ANI estimation accuracy. AvailabilityA Rust implementation of HyperGen is freely available under the MIT license as an open-source software project at https://github.com/wh-xu/Hyper-Gen. The scripts to reproduce the experimental results can be accessed at https://github.com/wh-xu/experiment-hyper-gen. Contactwexu@ucsd.edu

genomics↗

bioRxiv2024

The segmented flavivirus Alongshan virus reduces mitochondrial mass via degrading STAT2 to suppress innate immune response

Alongshan virus (ALSV) is a newly discovered pathogen of the Flaviviridae family, characterized by a multi-segmented genome distantly related to the canonical flaviviruses. Understanding the pathogenic mechanism of the emerging segmented flavivirus is crucial for the development of intervention strategies. Here we show that ALSV can infect multiple mammalian cells and induces the expression of antiviral genes. Moreover, ALSV is sensitive to IFN-{beta} and possesses the ability to counteract type I IFN response. Mechanistically, ALSVs nonstructural protein NSP1 binds to and degrades human STAT2 through an autophagy pathway in a species-dependent manner, resulting in direct inhibition of the expression of interferon-stimulated genes (ISGs). Specifically, NSP1 methyltransferase domain binds to the key sites of F175/R176 located in coiled-coil domain of STAT2. Moreover, NSP1-mediated degradation of STAT2 results in a reduction in mitochondrial mass by disrupting mitochondrial dynamics to induce mitophagy and inhibiting mitochondrial biogenesis, thereby suppressing the innate immune response. Interestingly, inhibiting mitophagy using 3-Methyladenine and enhancing mitochondrial biogenesis using the PPAR{gamma} agonist pioglitazone can reverse NSP1-mediated inhibition of ISGs, suggesting that promoting mitochondrial mass presents an effective antiviral strategy. Our findings elucidate the intricate regulatory crosstalk between ALSV and the hosts innate immune response, providing valuable insights into the pathogenesis and intervention strategy of emerging segmented flavivirus.

microbiology↗

bioRxiv2024

Avian influenza virus circulation and immunity in a wild urban duck population prior to and during a highly pathogenic H5N1 outbreak

Highly pathogenic avian influenza (HPAI) H5N1 clade 2.3.4.4b viruses were first detected in St. Johns, Newfoundland, Canada in late 2021, with the virus rapidly spreading across the western hemisphere over the next year. To investigate the patterns of avian influenza virus (AIV) infection and immune responses subsequent to the arrival of H5N1, we sampled the wild urban duck population in St. Johns for a period of 16 months after the start of the outbreak and compared these findings to archived samples. Antibody seroprevalence was relatively stable before the outbreak (2011-2014) at 27.6% and 3.9% for anti-AIV (i.e., NP) and H5-specific antibodies, respectively. During the winter of 2022, AIV-NP and H5-specific antibody seroprevalence both reached 100%, signifying a population-wide infection event. As expected, population-level immunity waned over time, and we found that ducks were seropositive for anti- AIV-NP antibodies for around twice as long as for H5-specific antibodies. The population was H5 seronegative to the latter approximately six months after the initial H5N1 incursion. In late February 2023, H5N1 clade 2.3.4.4b viruses were again detected in the duck population as a result of a second incursion into Newfoundland from Eurasia, which resulted in a second population-wide infection event. We observed a clear relationship of increasing antibody levels with decreasing viral RNA loads that allowed for interpretation of the course of infection and immune response in infected individuals and applied these findings to two cases of resampled ducks to infer infection history. Our study highlights the significance of applying both AIV surveillance and seroprevalence monitoring to provide a better understanding of AIV dynamics in wild populations, which may be crucial following the arrival of 2.3.4.4b H5Nx subtypes to assess the threats they pose to both wild and domestic animals, and to humans.

microbiology↗

bioRxiv2024

Restoring O-glycosylation and expression of MUC2 limits progression of colorectal cancer

This study investigated the molecular mechanisms underlying the regulation of MUC2 expression and O-glycosylation modification in colorectal cancer. In addition, the potential of rosiglitazone to inhibit colorectal cancer by improving MUC2 glycosylation to protect intestinal barrier function was explored. In vitro, lectin staining combined with Co-IP assay was used to detect glycosyltransferases regulating MUC2 O-glycosylation. ChIP and Luciferase experiments were used to verify the transcription factors regulating MUC2 expression level. Samples from CRC patients were used to detect differences in multimolecular expression. The AOM/DSS mouse model was used to validate the effect of rosiglitazone on inhibiting colorectal cancer progression. Our results showed that B3GNT6 acts as a glycosyltransferase to enhance the O-glycosylation level of MUC2 and maintain protein stability to resist degradation by StcE secreting from pathogenic bacteria. Furthermore, KLF4 directly promotes the transcription of B3GNT6 and MUC2, which are regulated by PPARg. Rosiglitazone activated PPARg-KLF4-B3GNT6 axis which increased the expression level and glycosylation of MUC2 and further improved the intestinal mucosal barrier function to delay the development of colorectal cancer in mice. These data suggest that O-glycosylation and expression of MUC2 is key to the maintenance of functional intestinal mucosa and rosiglitazone is a potential colorectal cancer therapeutic agent.

cancer biology↗

bioRxiv2024

Dual-targeted nanoparticulate drug delivery systems for enhancing triple-negative breast cancer treatment

The efficacy of DNA-damaging agents, such as the topoisomerase I inhibitor SN38, is often compromised by the robust DNA repair mechanisms in tumor cells, notably homologous recombination (HR) repair. Addressing this challenge, we introduce a novel nano-strategy utilizing binary tumor-killing mechanisms to enhance the therapeutic impact of DNA damage and mitochondrial dysfunction in cancer treatment. Our approach employs a synergistic drug pair comprising SN38 and the BET inhibitor JQ-1. We synthesized two prodrugs by conjugating linoleic acid (LA) to SN38 and JQ-1 via a cinnamaldehyde thioacetal (CT) bond, facilitating co-delivery. These prodrugs co-assemble into a nanostructure, referred to as SJNP, in an optimal synergistic ratio. SJNP was validated for its efficacy at both the cellular and tissue levels, where it primarily disrupts the transcription factor protein BRD4. This disruption leads to downregulation of BRCA1 and RAD51, impairing the HR process and exacerbating DNA damage. Additionally, SJNP releases cinnamaldehyde (CA) upon CT linkage cleavage, elevating intracellular ROS levels in a self-amplifying manner and inducing ROS-mediated mitochondrial dysfunction. Our results indicate that SJNP effectively targets murine triple-negative breast cancer (TNBC) with minimal adverse toxicity, showcasing its potential as a formidable opponent in the fight against cancer.

cancer biology↗

bioRxiv2024

Natural diversity of heat-induced transcription of retrotransposons in Arabidopsis thaliana

Transposable elements (TEs) are major components of plant genomes, profoundly impacting the fitness of their hosts. However, technical bottlenecks have long hindered our mechanistic understanding of TEs. Using RNA-Seq and long-read sequencing with Oxford Nanopore Technologies direct cDNA sequencing, we analyzed the heat-induced transcription of TEs in three natural accessions of Arabidopsis thaliana (Cvi-0, Col-0, and Ler-1). In addition to the well- studied ONSEN retrotransposon family, we identified Copia-35 as a second heat-responsive retrotransposon family with particularly high activity in the relict accession Cvi-0. Our analysis revealed distinct expression patterns of individual TE copies and suggest different mechanisms regulating the GAG protein production in the ONSEN versus Copia-35 families. In addition, analogously to ONSEN, Copia-35 activation led to the upregulation of flanking genes such as AMUP9 and potentially to the quantitative modulation of flowering time. Unexpectedly, our results indicate that for both families, the upregulation of flanking genes is not directly initiated by transcription from their 3 LTRs. These findings highlight the inter- and intraspecific expressional diversity linked to retrotransposon activation under stress, providing insights into their potential roles in plant adaptation and evolution at elevated temperatures.

genomics↗