Biology subjects

Sun, W.

Publications and source records attributed to Sun, W..

At least 181 records · Page 10Linked to original sources

bioRxiv2023

Spatial and single-cell transcriptomics reveal neuron-astrocyte interplay in long-term memory

Memory encodes past experiences, thereby enabling future plans. The basolateral amygdala (BLA) is a center of salience networks that underlie emotional experience and thus plays a key role in long-term fear memory formation1, 2. Here we used spatial and single-cell transcriptomics to illuminate the cellular and molecular architecture of the role of the basolateral amygdala in long-term memory. We identified transcriptional signatures in subpopulations of neurons and astrocytes that were memory-specific and persisted for weeks. These transcriptional signatures implicate neuropeptide signaling, mitogen-activated protein kinase (MAPK), brain-derived neurotrophic factor (BDNF), cAMP response element-binding protein (CREB), ubiquitination pathways, and synaptic connectivity in long-term memory. We also discovered that a neuronal sub-population, defined by increased Penk expression and decreased Tac expression, constitutes the most prominent component of the BLAs memory engram. These transcriptional changes were observed both with single-cell RNAseq and with single-molecule spatial transcriptomics in intact slices, thereby providing a rich spatial map of a memory engram. The spatial data enabled us to show that this neuronal subpopulation further interacts with spatially related astrocytes that are essential for memory consolidation, indicating that neurons require interactions with astrocytes to encode long term memory.

neuroscience↗

bioRxiv2023

Urine proteomic characterization of active and recovered COVID-19 patients

BackgroundThe molecular changes in COVID-19 patients have been reported in many studies. However, there were limited attention has been given to the disease sequelae in the recovered COVID-19 patients. MethodsHere, we profiled the urine proteome of a cohort of 29 COVID-19 patients in their disease onset and recovery period, including mild, severe, and fatal patients and survivors who recovered from mild or severe symptoms. ResultsThe molecular changes in the COVID-19 onset period suggest that viral infections, immune response changes, multiple organ damage, cell injury, coagulation system changes and metabolic changes are associated with COVID-19 progression. The patients who recovered from COVID-19 still exhibited an innate immune response, coagulation system changes and central nervous system changes. We also proposed four potential biomarkers to monitor the whole progression period of COVID-19. ConclusionsOur findings provide valuable knowledge about the potential molecular pathological changes and biomarkers that can be used to monitor the whole period of COVID-19.

biochemistry↗

bioRxiv2023

ADAM10 mediates macroglial cell fate decisions in the developing brain

ADAMs (a disintegrin and metalloproteinase) are transmembrane proteins with cell adhesion and protease activities that contain disintegrin and metalloproteinase domains. ADAM10, a member of the ADAM family, is widely expressed in the brain. There are >40 substrates reported for ADAM10, including Notch, Delta-like ligand-1 (Dll1), and N-cadherin. To date, however, its function in the brain has been largely unknown. We used genetic manipulation to delete Adam10 specifically from glial progenitors in developing brains and observed that conditional knockout mice showed locomotor abnormalities. They all died within 4 months with apparent defects in the cerebellum. By comprehensively analyzing data from bulk RNA sequencing, single-cell RNA sequencing, and staining of the cerebellum, we found that ADAM10 promoted astrocyte generation under physiological conditions. Upon the removal of Adam10 in glial progenitors, the production of oligodendrocytes vastly increased, whereas the generation of astrocytes was substantially inhibited. Our results showed that ADAM10 plays a critical role in macroglial cell fate decisions during brain development.

neuroscience↗

bioRxiv2023

Syntaxin of plants 32 regulates pollen wall development and pollen tube cell wall integrity via controlling secretory pathway

Pollen tubes (PTs) elongate in a polar way to deliver sperm cells to the ovule. Pollen wall development and PT cell wall integrity (CWI) maintenance are critical for PT growth and double fertilization. Pollen wall development mainly relies on secretion of exine precursors in tapetum. RALF4/19-ANX/BUPS-MRI and RALF4/19-LRX-AUN are two distinct signaling pathways but converge to fine-tune CWI during PT growth. Here, we discovered that atsyp32+/-, AtSYP32 RNAi and AtSYP3132 RNAi lines were male sterile. The tapetum development in these lines were disturbed, and the pollen wall structure was impaired resulting in pollen grain and tube bursting and less PTs navigated to micropyles. Strikingly, there were numerous ectopic secretory vesicles retained in pollen cytoplasm, and the abundance or distribution of polysaccharides and AGPs altered significantly in PTs of the mutants and RNAi lines. AtSYP32 interacted with the vesicle transport regulators SEC31B, SEC22 and BET12, the PT CWI regulators RALF19 and LRX11, and the XyG xylosyltransferase XXT5, in the Golgi apparatus. Transcription of some genes related to pollen wall biosynthesis and PT CWI maintenance were seriously affected by AtSYP32 downregulation. Our findings illustrate that AtSYP32 plays essential roles in pollen wall development and PT CWI maintenance via controlling secretory pathway. IN A NUTSHELLO_ST_ABSBackgroundC_ST_ABSPollen wall is the most complex cell wall. Pollen wall development mainly relies on secretion of precursors of exine and pollen coat in tapetal cells. Pollen tubes (PTs) grow in a polar way to deliver sperm cells to the ovule. Maintenance of PT cell wall integrity (CWI) is critical for PT elongation and double fertilization. RALF4/19 ligands interact with BUPS-ANX receptors, signaling it in an autocrine manner to maintain CWI during PT elongation. RALF4/19-LRX-AUN pathway is distinct with RALF4/19-ANX/BUPS-MRI pathway but they converge to fine-tune CWI during PT growth. Biosynthesis of PT cell wall involves multiple subcellular compartments and vesicle transport pathways. Golgi apparatus acts as a hub in vesicle trafficking. Golgi-syntaxin AtSYP31 and AtSYP32 regulate pollen development by controlling intra-Golgi transport and Golgi morphology QuestionWhat is AtSYP32 role in pollen wall and tapetum development? Who are the AtSYP32 partners that regulate secretion of cell wall biosynthesis materials? FindingsWe found that no homozygote progeny was obtained from self-pollinated atsyp32+/- alleles due to pollen sterile. The tapetum development and degeneration in atsyp32+/- mutants was severely delayed, and the pollen wall and PT wall structure were impaired. Strikingly, there were numerous ectopic secretory vesicles retained in pollen cytoplasm in atsyp32+/- mutants, and the abundance or distribution of PT wall polysaccharides and AGPs altered obviously. AtSYP32 interacted with the vesicle transport regulators SEC31B, SEC22 and BET12, the PT CWI regulators RALF19 and LRX11, and XyG xylosyltransferase XXT5, in the Golgi. All these highlight that AtSYP32 regulates pollen wall development and maintenance of PT CWI via controlling secretory pathway. Next stepsThe biological significances and the molecular mechanisms of AtSYP32 interacting with XXT5, RALF19 and LRX11 are elusive but thought-provoking. We are going to clarify the mechanisms.

molecular biology↗

bioRxiv2023

Anti-CRISPR AcrIIC5 is a dsDNA mimic that inhibits type II-C Cas9 effectors by blocking PAM recognition

Anti-CRISPR proteins are encoded by phages to inhibit the CRISPR-Cas systems of the hosts. AcrIIC5 inhibits several naturally high-fidelity type II-C Cas9 enzymes, including orthologs from Neisseria meningitidis (Nme1Cas9) and Simonsiella muelleri (SmuCas9). Here, we solve the structure of AcrIIC5 in complex with Nme1Cas9 and sgRNA. We show that AcrIIC5 adopts a novel fold to mimic the size and charge distribution of double-stranded DNA, and uses its negatively charged grooves to bind and occlude the protospacer adjacent motif (PAM) binding site in the target DNA cleft of Cas9. AcrIIC5 is positioned into the crevice between the WED and PI domains of Cas9, and one end of the anti-CRISPR interacts with the phosphate lock loop and a linker between the RuvC and BH structural domains. We employ biochemical and mutational analyses to build a model for AcrIIC5s mechanism of action, and identify residues on both the anti-CRISPR and Cas9 that are important for their interaction and inhibition. Together, the structure and mechanism of AcrIIC5 reveal convergent evolution among disparate anti-CRISPR proteins that use a DNA-mimic strategy to inhibit diverse CRISPR-Cas surveillance complexes, and provide new insights into a tool for potent inhibition of type II-C Cas9 orthologs.

biochemistry↗

bioRxiv2023

Decoding the genetic and chemical basis of sexual attractiveness in parasitic wasps

Attracting and securing potential mating partners is of fundamental importance for successfully initiating reproduction and thus assuring the passing of genes to the next generation. Therefore, signaling sexual attractiveness is expected to be tightly coordinated in communication systems synchronizing senders and receivers. Chemical signaling has permeated through all taxa of life as the earliest and most wide-spread form of communication and is particularly prevalent in insects. However, it has been notoriously difficult to decipher how exactly information related to sexual signaling is encoded in complex chemical profiles. Similarly, our knowledge of the genetic basis of sexual signaling is very limited and usually restricted to a few case studies with comparably simple pheromonal communication mechanisms. The present study jointly addresses these two knowledge gaps by characterizing a single gene simultaneously impacting sexual attractiveness and complex chemical surface profiles in parasitic wasps. Knocking down a fatty acid synthase gene in female wasps dramatically reduces their sexual attractiveness coinciding with a drastic decrease in male courtship and copulation behavior. Concordantly, we found a striking shift of methyl-branching patterns in the female surface pheromonal compounds, which we subsequently demonstrate to be the main cause for the greatly reduced male response. Intriguingly, this suggests a potential coding mechanism for sexual attractiveness mediated by specific methyl-branching patterns, whose genetic underpinnings are not well understood despite their high potential for encoding information. Our study sheds light on how biologically relevant information can be encoded in complex chemical profiles and on the genetic basis of sexual attractiveness. Significance StatementUnraveling the genetic basis of chemical signaling is one of the most prevalent yet challenging topics in functional genetics and animal communication studies. Here we present the characterization of a biosynthetic gene in parasitoid wasps that simultaneously impacts sexual attractiveness as well as majorly shifts complex surface pheromone compositions. The shifted pattern primarily constitutes up- and down-regulated methyl-branched compounds with very distinct branching positions. Therefore, these findings immediately suggest a potential coding mechanism for sexual attractiveness in complex chemical profiles. This advances our understanding of how genetic information can be translated into biologically relevant chemical information and reveals that sexual attractiveness can have a comparably simple genetic basis.

genetics↗

bioRxiv2022

Cataloguing and profiling of the gut virome in Chinese populations uncover extensive viral signatures across common diseases

The gut viral community has been linked to human physiology and health, but our knowledge of its genetic and functional contents and disease dependence is far from complete. Here, we collected 11,327 bulk or viral metagenomes from fecal samples from large-scale Chinese populations to establish a Chinese gut virus catalogue (cnGVC) comprising 67,096 nonredundant viral genomes. This catalogue included [~]70% of novel viruses that are not represented in existing gut viral databases, and allowed us to characterize the functional diversity and specificity of the gut virome. Using cnGVC, we 1) profiled the gut virome in large-scale populations and evaluated their sex- and age-related variations, 2) investigated the diversity and compositional patterns of the gut virome across common diseases by analyzing 6,314 bulk metagenomes spanning 28 disease or unhealthy statuses, and 3) identified a large number of universal viral signatures of diseases and validated their predictive ability for health status. Overall, our resources and results would contribute to the grand effort of expanding the knowledge of the human gut virome and addressing a full picture of the associations between viruses and common diseases.

microbiology↗

bioRxiv2022

M-Band Wavelet-Based Imputation of scRNA-seq Matrix and Multi-view Clustering of Cell

Wavelet analysis has been recognized as a cutting-edge and promising tool in the fields of signal processing and data analysis. However, application of wavelet-based method in single-cell RNA sequencing (scRNA-seq) data is little known. Here, we present M-band wavelet-based imputation of scRNA-seq matrix and multi-view clustering of cells (WIMC). We applied integration of M-band wavelet analysis and uniform manifold approximation and projection (UMAP) to a panel of single cell sequencing datasets by breaking up the data matrix into a trend (low frequency or low resolution) component and (M-1) fluctuation (high frequency or high resolution) components. We leverage a non-parametric wavelet-based imputation algorithm of sparse data that integrates M-band wavelet transform for recovering dropout events of scRNA-seq datasets. Our method is armed with multi-view clustering of cell types, identity, and functional states, enabling missing cell types visualization and new cell types discovery. Distinct to standard scRNA-seq workflow, our wavelet-based approach is a new addition to resolve the notorious chaotic sparsity of scRNA-seq matrix and to uncover rare cell types with a fine-resolution. Author summaryWe develop M-band wavelet-based imputation of scRNA-seq matrix and multi-view clustering of cells. Our new approach integrates M-band wavelet analysis and UMAP to a panel of single cell sequencing datasets via breaking up the data matrix into a trend (low frequency or low resolution) component and (M - 1) fluctuation (high frequency or high resolution) components. Our method enables us to efficiently impute sparse scRNA-seq data matrix and to examine multi-view clustering of cell types, identity, and functional states, potentializing missing cell types recovery, fine rare cell types discovery, as well as functional cell states exploration.

bioinformatics↗

bioRxiv2022

Robust and High-Throughput Analytical Flow Proteomics Analysis of Cynomolgus Monkey and Human Matrices with Zeno SWATH Data Independent Acquisition

Modern mass spectrometers routinely allow deep proteome coverage in a single experiment. These methods are typically operated at nano and micro flow regimes, but they often lack throughput and chromatographic robustness, which is critical for large-scale studies. In this context, we have developed, optimized and benchmarked LC-MS methods combining the robustness and throughput of analytical flow chromatography with the added sensitivity provided by the Zeno trap across a wide range of cynomolgus monkey and human matrices of interest for toxicological studies and clinical biomarker discovery. SWATH data independent acquisition (DIA) experiments with Zeno trap activated (Zeno SWATH DIA) provided a clear advantage over conventional SWATH DIA in all sample types tested with improved sensitivity, quantitative robustness and signal linearity as well as increased protein coverage by up to 9-fold. Using a 10-min gradient chromatography, up to 3,300 proteins were identified in tissues at 2 {micro}g peptide load. Importantly, the performance gains with Zeno SWATH translated into better biological pathway representation and improved the ability to identify dysregulated proteins and pathways associated with two metabolic diseases in human plasma. Finally, we demonstrate that this method is highly stable over time with the acquisition of reliable data over the injection of 1,000+ samples (14.2 days of uninterrupted acquisition) without the need for human intervention or normalization. Altogether, Zeno SWATH DIA methodology allows fast, sensitive and robust proteomic workflows using analytical flow and is amenable to large-scale studies. This work provides detailed method performance assessment on a variety of relevant biological matrices and serves as a valuable resource for the proteomics community.

biochemistry↗

bioRxiv2022

Immunity to seasonal coronavirus spike proteins does not protect from SARS-CoV-2 challenge in a mouse model but has no detrimental effect on protection mediated by COVID-19 mRNA vaccination

Seasonal coronaviruses have been circulating widely in the human population for many years. With increasing age, humans are more likely to have been exposed to these viruses and to have developed immunity against them. It has been hypothesized that this immunity to seasonal coronaviruses may provide partial protection against infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and it has also been shown that coronavirus disease 2019 (COVID-19) vaccination induces a back-boosting effects against the spike proteins of seasonal betacoronaviruses. In this study, we tested if immunity to the seasonal coronavirus spikes from OC43, HKU1, 229E or NL63 would confer protection against SARS-CoV-2 challenge in a mouse model, and whether pre-existing immunity against these spikes would weaken the protection afforded by mRNA COVID-19 vaccination. We found that mice vaccinated with the seasonal coronavirus spike proteins had no increased protection as compared to the negative controls. While a negligible back-boosting effect against betacoronavirus spike proteins was observed after SARS-CoV-2 infection, there was no negative original antigenic sin-like effect on the immune response and protection induced by SARS-CoV-2 mRNA vaccination in animals with pre-existing immunity to seasonal coronavirus spike proteins. ImportanceThe impact that immunity against seasonal coronaviruses has on both susceptibility to SARS-CoV-2 infection as well as on COVID-19 vaccination is unclear. This study provides insights into both questions in a mouse model of SARS-CoV-2.

microbiology↗

bioRxiv2022

Gap-free nuclear and mitochondrial genomes of Ustilaginoidea virens strain JS60-2, a fungal pathogen causing rice false smut

Rice false smut (RFS), caused by Ustilaginoidea virens, has become a major disease in recent years, and mycotoxins produced by U. virens often threaten food safety. To study fungal pathogenesis and identify potential targets for developing new fungicides, gap-free nuclear and complete mitochondrial genomes of U. virens JS60-2 were sequenced and assembled. Using the second and third generation sequencing data, we assembled a 38.02-Mb genome that consists of seven contigs with the contig N50 being 6.32-Mb. In total, 8,486 protein-coding genes were annotated in the genome, including 21 secondary metabolism gene clusters. We also assembled the complete mitochondrial genome, which is 102,498 bp, with 28% GC content. The JS60-2 genomes assembled in this study will facilitate research on U. virens and contribute to RFS control.

genomics↗

bioRxiv2022

A novel brain penetrant PDGFRα inhibitor HY-008 is effective against glioblastoma

BackgroundGlioblastoma multiforme (GBM) is the most common primary intracranial malignant tumor in adults, with poor prognosis and high recurrence. Routine treatments of GBM show unsatisfactory efficiency in improving patients survival because of limited area of surgical resection and drug resistance. New therapeutic agents are needed to improve GBM treatment efficiency, but the blood-brain barrier (BBB) permeability is a major hurdle. Here, we report HY-008 as a promising therapeutic drug targeting PDGFR signaling with high BBB permeability and efficient inhibiting effects both in vitro and in vivo. MethodsThrough structural modification and medicinal chemistry efforts, HY-007 and HY-008 were developed. The brain and plasma pharmacokinetic profiles of these two compounds were assessed. The inhibitory efficiency of HY-007 and HY-008 on GBM cell survival and PDGFR signaling were evaluated. The efficacy of HY-007 and HY-008 as a single agent or HY-008 in combination with temozolomide (TMZ) was investigated using transformed mouse astrocyte and glioma stem-like cell (GSC) orthotopic xenograft models. ResultsHY-007 and HY-008 both had good brain permeability and desirable PK profiles with mild hERG inhibition, while HY-008 is more brain permeable than HY-007. In vitro, HY-007 and HY-008 both significantly inhibited viability of the established GBM cells with PDGF-A overexpression and transformed mouse astrocytes with PDGF-A/PDGFR overexpression by targeting the PDGFR signaling activated Erk1/2 and Akt. In vivo, HY-007 and HY-008 both effectively inhibited orthotopic GBM tumor xenograft growth and prolonged the survival of mice, and HY-008 showed less toxicity and better therapeutic effect. In addition, HY-008 increased sensitivity of TMZ, exhibited treatment efficiency both as a single agent and in combination with TMZ, providing significant survival benefits for GBM tumor xenograft-bearing mice. ConclusionsOur data demonstrate that HY-008 is a promising therapeutic agent in GBM treatment and a combination HY-008 with TMZ could serves as a potential efficient therapeutic option for improving GBM clinical treatment.

cancer biology↗

bioRxiv2022

Heterosynaptic Plasticity of the Visuo-auditory Projection Requires Cholecystokinin released from Entorhinal Cortex Afferents

The entorhinal cortex is involved in establishing enduring visuo-auditory associative memory in the neocortex. Here we explored the mechanisms underlying this synaptic plasticity related to projections from the visual and entorhinal cortices to the auditory cortex, using optogenetics of dual pathways. High-frequency laser stimulation (HFLS) of the visuo-auditory projection did not induce long-term potentiation (LTP). However, after pairing with sound stimulus, the visuo-auditory inputs were potentiated following either infusion of cholecystokinin (CCK) or HFLS of the entorhino-auditory CCK-expressing projection. Combining retrograde tracing and RNAscope in situ hybridization, we show that CCK expression is higher in entorhinal cortex neurons projecting to the auditory cortex than in those originating from the visual cortex. In the presence of CCK, potentiation in the neocortex occurred when the pre-synaptic input arrived 200 ms before post-synaptic firing, even after just five trials of pairing. Behaviorally, inhibition of CCK signaling blocked the generation of associative memory. Our results indicate that neocortical visuo-auditory association is formed through heterosynaptic plasticity, which depends on release of CCK in the neocortex mostly from entorhinal afferents.

neuroscience↗

bioRxiv2022

Transcription coactivator OCA-B/Pou2af1 is necessary and sufficient to promote T cell-intrinsic CD4 memory

The molecular mechanisms leading to the establishment of immunological memory are inadequately understood, limiting the development of effective vaccines and durable anti-tumor immune therapies. Here we show that ectopic OCA-B expression is sufficient to improve antiviral memory recall responses, while having minimal effects on primary effector responses. At peak viral response short lived effector T cell populations are expanded but show increased Gadd45b and Socs2 expression, while memory precursor effector cells show increased expression of Bcl2, Il7r and Tcf7 on a per-cell basis. Using an OCA-B mCherry reporter mouse line, we observe high OCA-B expression in CD4+ TCM cells. We show that early in viral infection, endogenously elevated OCA-B expression prospectively identifies memory precursor cells with increased survival capability and memory recall potential. Cumulatively, the results demonstrate that OCA-B is both necessary and sufficient to promote CD4 T cell memory in vivo and can be used to prospectively identify memory precursor cells. SignificanceCD4+ T cell memory is incompletely defined and memory progenitors difficult to identify. Here, we show that expression of the OCA-B transcription coactivator in CD4+ T cells is necessary and sufficient to drive productive memory. Using a novel mCherry reporter mouse line, we show that OCA-B expression enriches for responding effector cells with elevated memory potential. The results show that OCA-B expression in T cells is sufficient to promote CD4+ memory formation and marks memory precursor cells.

immunology↗

bioRxiv2022

Positional cues underlie cell fate specification during branching morphogenesis of the embryonic mammary epithelium

How cells coordinate morphogenetic cues and fate specification during development is a fundamental question at the basis of tissue formation. Lineage tracing studies have demonstrated that many stratified epithelia, including the mammary gland, first arise from multipotent stem cells, which are progressively replaced by distinct pools of unipotent progenitors that maintain tissue homeostasis postnatally. The lack of specific markers for early fate specification in the mammary gland has prevented the delineation of the features and spatial localization of lineage-committed progenitors that co-exist with multipotent stem cells (MaSCs) during tissue development. Here, using single-cell RNA-sequencing across 4 stages of embryonic development, we reconstructed the differentiation trajectories of multipotent mammary stem cells towards basal and luminal fate. Our data revealed that MaSCs can already be resolved into distinct populations exhibiting lineage commitment at the time coinciding with the first sprouting events of mammary branching morphogenesis (E15.5). By visualizing gene expression across our developmental atlas, we provide novel molecular markers for committed and multipotent MaSCs, and define their spatial distribution within the developing tissue. Furthermore, we show that the mammary embryonic mesenchyme is composed of two spatially-restricted cell populations, representing the sub-epithelial and dermal mesenchyme. Mechanistically, we explored the communication between different subsets of mesenchymal and epithelial cells, using time-lapse analysis of mammary embryonic explant cultures, and reveal that mesenchymal-produced FGF10 accelerates embryonic mammary branching morphogenesis without affecting cell proliferation. Altogether, our data elucidate the spatiotemporal signals underlying lineage specification of multipotent mammary stem cells and uncover the paracrine interactions between epithelial and mesenchymal cells that guide mammary branching morphogenesis.

developmental biology↗

bioRxiv2022

Stability of SARS-CoV-2 in cold-chain transportation environments and the efficacy of disinfection measures

Cold-chain environment could extend the survival duration of SARS-CoV-2 and increases the risk of transmission. However, the effect of clod-chain environmental factors and packaging materials on SARS-CoV-2 stability and the efficacy of intervention measures to inactivate SARS-CoV-2 under cold-chain environment remains uncertain. This study aimed to unravel cold-chain environmental factors that preserved the stability of SARS-CoV-2 and disinfection measures against SARS-CoV-2 under the cold-chain environment. The spike gene of SARS-CoV-2 isolated from Wuhan hu-1 was used to construct the SARS-CoV-2 pseudovirus and used as model of the SARS-CoV-2 virus. The decay rate of SARS-CoV-2 pseudovirus in the cold-chain environment, various types of packaging material surfaces i.e., PE plastic, stainless steel, Teflon and cardboard, and in frozen seawater was investigated. The influence of LED visible light(wavelength 450 nm-780 nm) and airflow movement on the stability of SARS-CoV-2 pseudovirus at -18{degrees} C were subsequently assessed. The results show that SARS-CoV-2 pseudovirus decayed more rapidly on porous cardboard surface compared with the non-porous surfaces including PE plastic, stainless steel and Teflon. Compared with 25{degrees} C, the decay rate of SARS-CoV-2 pseudovirus was significantly lower at low temperature. Seawater preserved viral stability both at -18{degrees} C and repeated freeze-thawing cycles compared with deionized water. LED visible light illumination and airflow movement environment at -18{degrees} C reduced the SARS-CoV-2 pseudovirus stability. In conclusion, our results indicate cold-chain temperature and seawater as risk factors for SARS-CoV-2 transmission and LED visible light illumination and airflow movement as possible disinfection measures of SARS-CoV-2 under the cold-chain environment. ImportanceIt is widely recognized that low temperature is a condition for maintaining virus vitality, and cold-chain transportation spreads the events of the SARS-CoV-2 were reported. This study provides that the decay rate of the SARS-CoV-2 pseudovirus at low temperatures varies on different packaging materials, and salt ions present in frozen foods such as seafood may protect virus survival. These results provide evidence for the possibility of SARS-CoV-2 transmission through cold-chain transport and also suggest the importance for disinfection of items. However, the commonly used disinfection methods of ultraviolet radiation and chemical reagents are generally not suitable for the disinfection of frozen food. Our study shows LED visible light illumination and airflow movement as possible disinfection measures of SARS-CoV-2 under the cold-chain environment. This has implications for reducing the long-distance transmission of the virus through cold-chain transportation.

microbiology↗

bioRxiv2022

Isoform-specific Disruption of the TP73 Gene Reveals a Critical Role for TAp73gamma in Tumorigenesis via Leptin

TP73, a member of the p53 family, is expressed as TAp73 and {Delta}Np73 along with multiple C-terminal isoforms (-{eta}). {Delta}Np73 is primarily expressed in neuronal cells and necessary for neuronal development. Interestingly, while TAp73 is a tumor suppressor and predominantly expressed in normal cells, TAp73 is found to be frequently altered in human cancers, suggesting a role of TAp73 C-terminal isoforms in tumorigenesis. To test this, the TCGA SpliceSeq database was searched and showed that exon 11 (E11) exclusion occurs frequently in several human cancers. We also found that p73 to p73{gamma} isoform switch resulting from E11 skipping occurs frequently in human prostate cancers and dog lymphomas. To determine whether p73 to p73{gamma} isoform switch plays a role in tumorigenesis, CRISPR technology was used to generate multiple cancer cell lines and a mouse model in that Trp73 E11 is deleted. Surprisingly, we found that in E11-deificient cells, p73{gamma} becomes the predominant isoform and exerts oncogenic activities by promoting cell proliferation and migration. In line with this, E11-deficient mice were more prone to obesity and B-cell lymphomas, indicating a unique role of p73{gamma} in lipid metabolism and tumorigenesis. Additionally, we found that E11-deficient mice phenocopies Trp73-deficient mice with short lifespan, infertility, and chronic inflammation. Mechanistically, Mechanistically, we showed that Leptin, a pleiotropic adipocytokine involved in energy metabolism and oncogenesis, was highly induced by p73{gamma}, necessary for p73{gamma}-mediated oncogenic activity, and associated with p73 to {gamma} isoform switch in human prostate cancer and dog lymphoma. Finally, we showed that E11-knockout promoted, whereas knockdown of p73{gamma} or Leptin suppressed, xenograft growth in mice. Our study indicates that the p73{gamma}-Leptin pathway promotes tumorigenesis and alters lipid metabolism, which may be targeted for cancer management.

cancer biology↗

bioRxiv2022

The highly conserved RNA-binding specificity of nucleocapsid protein facilitates the identification of drugs with broad anti-coronavirus activity

The binding of SARS-CoV-2 nucleocapsid (N) protein to both the 5'- and 3'-ends of genomic RNA has different implications arising from its binding to the central region during virion assembly. However, the mechanism underlying selective binding remains unknown. Herein, we performed the high-throughput RNA-SELEX (HTR-SELEX) to determine the RNA-binding specificity of the N proteins of various SARS-CoV-2 variants as well as other {beta}-coronaviruses and showed that N proteins could bind two unrelated sequences, both of which were highly conserved across all variants and species. Interestingly, both these sequence motifs are virtually absent from the human transcriptome; however, they exhibit a highly enriched, mutually complementary distribution in the coronavirus genome, highlighting their varied functions in genome packaging. Our results provide mechanistic insights into viral genome packaging, thereby increasing the feasibility of developing drugs with broad-spectrum anti-coronavirus activity by targeting RNA binding by N proteins.

molecular biology↗