Biology subjects

Shi, J.

Publications and source records attributed to Shi, J..

At least 127 records · Page 7Linked to original sources

bioRxiv2024

Human TRPV4 engineering yields an ultrasound-sensitive actuator for sonogenetics

AbstractSonogenetics offers non-invasive and cell-type specific modulation of cells genetically engineered to express ultrasound-sensitive actuators. Finding an ion channel to serve as sonogenetic actuator it critical for advancing this promising technique. Here, we show that ultrasound can activate human TRP channel hTRPV4. By screening different hTRPV4 variants, we identify a mutation F617L that increases mechano-sensitivity of this channel to ultrasound, while reduces its sensitivity to hypo-osmolarity, elevated temperature, and agonist. This altered sensitivity profile correlates with structural differences in hTRPV4-F617L compared to wild-type channels revealed by our cryo-electron microscopy analysis. We also show that hTRPV4-F617L can serve as a sonogenetic actuator for neuromodulation in freely moving mice. Our findings demonstrate the use of structure-guided mutagenesis to engineer ion channels with tailored properties of ideal sonogenetic actuators.

biophysics↗

bioRxiv2024

DDX3 regulates the cap-independent translation of the Japanese encephalitis virus via its interactions with PABP1 and the untranslated regions of the viral genome

The translation of global cellular proteins is almost completely repressed in cells with flavivirus infection, while viral translation remains efficient. The mechanisms of flaviviruses evade host translational shutoff are largely unknown. Here, we identified viral elements and host factors associated with JEV evasion of host shutoff. JEV 5'UTR lacked IRES or IRES-like activity, while noncapped 5'UTR initiated translation in the presence of 3'UTR. Furthermore, the elements DB2 and sHP-SL within 3'UTR were involved in the regulation of cap-independent translation, which is conserved in the genus Orthoflavivirus. By RNA affinity purification and mass spectrometry analysis, cellular DDX3 and PABP1 were identified as key factors in regulating cap-independent translation of JEV via their interactions with DB2 and sHP-SL RNA structures. Mechanistically, we revealed that DDX3 could bind to both 5'UTR and 3'UTR of the JEV genome to establish a closed-loop architecture, recruit eIF4G/eIF4A to form the DDX3/PABP1/eIF4G/eIF4A tetrameric complex via its interaction with PABP1, thereby recruiting 43S PIC to the 5'-end of the JEV genome to start translation. Our findings demonstrated a noncanonical translation strategy employed by JEV and further revealed the regulatory roles of DDX3 and PABP1 in this mechanism. These results expand our knowledge of the translation initiation regulation in flaviviruses under the state of host translational shutoff, which provides a conserved antiviral target against orthoflavivirus.

microbiology↗

bioRxiv2024

Shaping the mechanical properties of a gelatin hydrogel interface via amination

Injuries to musculoskeletal interfaces, such as the tendon-to-bone insertion of the rotator cuff, present significant physiological and clinical challenges for repair due to complex gradients of structure, composition, and cellularity. Advances in interface tissue engineering require stratified biomaterials able to both provide local instructive signals to support multiple tissue phenotypes while also reducing the risk of strain concentrations and failure at the transition between dissimilar materials. Here, we describe adaptation of a thiolated gelatin (Gel-SH) hydrogel via selective amination of carboxylic acid subunits on the gelatin backbone. The magnitude and kinetics of HRP-mediated primary crosslinking and carbodiimide-mediated secondary crosslinking reactions can be tuned through amination and thiolation of carboxylic acid subunits on the gelatin backbone. We also show that a stratified biomaterial comprised of mineralized (bone-mimetic) and non-mineralized (tendon-mimetic) collagen scaffold compartments linked by an aminated Gel-SH hydrogel demonstrate improved mechanical performance and reduced strain concentrations. Together, these results highlight significant mechanical advantages that can be derived from modifying the gelatin macromer via controlled amination and thiolation and suggest an avenue for tuning the mechanical performance of hydrogel interfaces within stratified biomaterials.

bioengineering↗

bioRxiv2024

Structural insights into inhibitor mechanisms on immature HIV-1 Gag lattice revealed by high-resolution in situ single-particle cryo-EM

HIV-1 inhibitors, such as Bevirimat (BVM) and Lenacapavir (LEN), block the production and maturation of infectious virions. However, their mechanisms remain unclear due to the absence of high-resolution structures for BVM complexes and LENs structural data being limited to the mature capsid. Utilizing perforated virus-like particles (VLPs) produced from mammalian cells, we developed an approach to determine in situ cryo-electron microscopy (cryo-EM) structures of HIV-1 with inhibitors. This allowed for the first structural determination of the native immature HIV-1 particle with BVM and LEN bound inside the VLPs at high resolutions. Our findings offer a more accurate model of BVM engaging the Gag lattice and, importantly, demonstrate that LEN not only binds the mature capsid but also targets the immature lattice in a distinct manner. The binding of LEN induces a conformational change in the capsid protein (CA) region and alters the architecture of the Gag lattice, which may affect the maturation process. These insights expand our understanding of the inhibitory mechanisms of BVM and LEN on HIV-1 and provide valuable clues for the design of future inhibitors.

biochemistry↗

bioRxiv2024

Continual integration of single-cell multimodal data with MIRACLE

Single-cell sequencing technologies have revolutionized our understanding of cellular heterogeneity and facilitated the construction of multi-omics cell atlases via data integration. However, updating these atlases with new data conventionally requires reintegration of all data and is computationally intensive, hindering timely updates and dynamic adjustments in biological and medical research. To address this challenge, we present Multimodal Integration with Continual Learning (MIRACLE), a novel online learning framework for the adaptive and efficient integration of single-cell multimodal data. MIRACLE employs dynamic architectures and data rehearsal strategies to support continual learning, allowing diverse data to be integrated while minimizing information loss over time. Our evaluations demonstrate that MIRACLE achieves accurate online integration with reduced computational requirements, effectively updating and expanding atlases with new cross-tissue and cross-modal data, and precisely identifying novel cell types and transferring labels across datasets. MIRACLE provides an efficient and flexible tool for single-cell community to integrate, share and explore biological knowledge from single-cell multimodal data.

bioinformatics↗

bioRxiv2024

Genome-wide A to G and C to T Mutations Induced by Functional TadA Variants in Escherichia coli

The fusion expression of DNA replication-related proteins with nucleotide deaminase enzymes promotes random mutations in bacterial genomes, thereby increasing genetic diversity among population. Most previous studies have focused on cytosine deaminase, which produces only C[->]T mutations, significantly limiting the variety of mutation types. In this study, we developed a fusion expression system by combining DnaG (RNA primase) with adenine deaminase TadA-8e (DnaG-TadA) in Escherichia coli, which is capable of rapidly introducing A[->]G mutations into the E. coli genome, resulting in a 664-fold increase in terms of mutation rate. Additionally, we engineered a dual-functional TadA variant, TadAD, and then fused it with DnaG. This construct introduced both C[->]T and A[->]G mutations into the E. coli genome, with the mutation rate further increased by 370-fold upon co-expression with an uracil glycosylase inhibitor (DnaG-TadAD-UGI). We applied DnaG-TadA and DnaG-TadAD-UGI systems to the adaptive laboratory evolution for Cd2+ and kanamycin resistance, achieving an 8.0 mM Cd2+ and 200 g/mL kanamycin tolerance within just 17 days and 132 hours, respectively. Compared to conventional evolution methods, the final tolerance levels were increased by 320% and 266%, respectively. Our work offers a novel strategy for random mutagenesis in E. coli and potentially other prokaryotic species. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=98 SRC="FIGDIR/small/610230v1_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@176e445org.highwire.dtl.DTLVardef@848b7corg.highwire.dtl.DTLVardef@1e190b9org.highwire.dtl.DTLVardef@1e47b44_HPS_FORMAT_FIGEXP M_FIG C_FIG For TOC only

synthetic biology↗

bioRxiv2024

A Hybrid Type I and II Polyketide Synthases Yields Distinct Aromatic Polyketides

Bacterial aromatic polyketides are compounds with multiple aromatic rings synthesized by bacterial type II polyketide synthases (PKSs), some of which have been developed into clinical drugs. Compounds containing aromatic polyketides synthesized by a hybrid type I and type II PKSs are extremely rare. Here, we report the discovery of a gene cluster encoding both modular type I PKS, type II PKS and KAS III through extensive bioinformatics analysis, leading to the characterization of the hybrid polyketide, spirocycline A. The structure of spirocycline A is unprecedented among all aromatic polyketides, featuring a unique starter unit, four spirocycles, and forming a dimer. Biosynthetic studies indicate that the starter unit of this molecule is synthesized by type I PKS in collaboration with two trans-acting ketoreductase (KR) and enoylreductase (ER). It is then transferred by KAS III to the type II PKS system, which then synthesizes the tricyclic aromatic polyketide backbone. The subsequent formation of the spirocycle and dimerization is carried out by four redox enzymes encoded in the gene cluster. Overall, the discovery of spirocycline A provides a new approach for identifying novel aromatic polyketides and offers potential enzymatic tools for the bioengineering of these hybrid polyketides. Table of Contents O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=82 SRC="FIGDIR/small/610196v1_ufig1.gif" ALT="Figure 1"> View larger version (11K): org.highwire.dtl.DTLVardef@5a7efaorg.highwire.dtl.DTLVardef@14665d5org.highwire.dtl.DTLVardef@c7b8f2org.highwire.dtl.DTLVardef@3f1e6c_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

Targeting Liver Epsins Ameliorates Dyslipidemia in Atherosclerosis

BackgroundThe low-density lipoprotein receptor (LDLR) in the liver plays a crucial role in clearing low-density lipoprotein cholesterol (LDL-C) from the bloodstream. This process takes place mainly in the liver. Under atherogenic conditions, Proprotein Convertase Subtilisin/Kexin Type 9 (PCSK9), secreted by the liver, binds to LDLR on hepatocytes, preventing its recycling and enhancing its lysosomal degradation. This process reduces LDL-C clearance, promoting hypercholesterolemia. Epsins, a family of ubiquitin-binding endocytic adaptors, are key regulators of atherogenesis in lesional cells, including endothelial cells and macrophages. Given epsins canonical role in regulating endocytosis of cell surface receptors, we aimed to determine whether and how liver epsins contribute to PCSK9-mediated LDLR endocytosis and degradation, thereby impairing LDL-C clearance and accelerating atherosclerosis. MethodsLiver-specific epsin knockout (Liver-DKO) atherosclerotic models were generated in ApoE-/- and PCSK9-AAV8-induced atheroprone mice fed on a Western diet. We utilized single-cell RNA sequencing, along with molecular, cellular, and biochemical analyses, to investigate the physiological role of liver epsins in PCSK9-mediated LDLR degradation. Additionally, we explored the therapeutic potential of nanoparticle-encapsulated siRNAs targeting epsins 1 and 2 in ApoE-/- mice with established atherosclerosis. ResultsWestern diet (WD)-induced atherosclerosis was significantly attenuated in ApoE-/-/Liver-DKO mice compared with ApoE-/- controls, as well as in PCSK9-AAV8-induced Liver-DKO mice compared with PCSK9-AAV8-induced wild-type (WT) mice accompanied by reductions in blood cholesterol and triglyceride levels. Mechanistically, single-cell RNA sequencing of hepatocytes and aortas isolated from atherosclerotic ApoE-/- and ApoE-/-/Liver-DKO mice revealed epsin-deficient Ldlrhi hepatocytes with diminished lipogenic potential. Notably, pathway analysis of hepatocytes showed increased LDL particle clearance and enhanced LDLR-cholesterol interactions under WD treatment in ApoE-/-/Liver-DKO mice compared with ApoE-/- controls, correlating with decreased plasma LDL-C levels. Furthermore, pathway analysis of the aortas showed attenuated inflammation and endothelial activation, coupled with reduced lipid uptake, and enhanced cholesterol efflux under WD treatment in ApoE-/-/Liver-DKO mice compared with ApoE-/- controls. Moreover, the absence of liver epsins led to an upregulation of LDLR protein expression in hepatocytes. We further demonstrated that epsins bind LDLR via the ubiquitin-interacting motif (UIM), enabling PCSK9-mediated LDLR degradation. Depleting epsins abolished this degradation, thereby preventing atheroma progression. Lastly, targeting liver epsins with nanoparticle-encapsulated epsins siRNAs effectively ameliorates dyslipidemia and inhibits atherosclerosis progression. These results are consistent with findings showing an increased epsin1 and epsin2 expression in atherosclerotic cardiovascular disease patients. ConclusionsLiver epsins drive atherogenesis by promoting PCSK9-mediated LDLR degradation, thereby elevating circulating LDL-C levels and heightening lesional inflammation. As such, targeting epsins in the liver represents a promising therapeutic strategy to mitigate atherosclerosis by preserving LDLR and enhancing LDL-C clearance in the liver.

cell biology↗

bioRxiv2024

Targeting Interferon-Driven Inflammatory Memory Prevents Epigenetic Evolution of Cancer Immunotherapy Resistance

Acquired resistance is a growing obstacle to durable responses after cancer immune checkpoint blockade (ICB). The mechanisms by which heterogeneous tumors evolve under immunotherapy pressure and strategies targeting key populations to prevent relapse are poorly understood. We show that chronic interferon (IFN) enables a subpopulation of cancer cells to acquire inflammatory memory and express memory ISGs, a subset of IFN-stimulated genes enriched for immune evasion properties, leading to subclonal epigenetic evolution of ICB-resistant states. Inflammatory memory is epigenetically encoded through chronic virus mimicry - feedforward MDA5 signaling likely activated by endogenous retroelements. While JAK inhibitors can improve ICB response, combining them with TBK1 inhibitors collapses this feedforward mechanism, erasing inflammatory memory and preventing differentiation into resistance states. Across human cancers, small subpopulations of memory ISG-expressing cells are prevalent and coupled to T cell exhaustion, suggesting inflammatory memory may be a common mechanism of acquired resistance targetable by JAK plus TBK1 inhibition.

immunology↗

bioRxiv2024

Targeting NOTCH2-JAG1 juxtacrine signaling reverses macrophage-mediated tumor resistance to taxol

Taxanes are widely used in chemotherapy, but primary and acquired resistance limit the clinical efficacy. Studies have shown tumor interaction with macrophages in the tumor microenvironment (TME) plays a significant role in taxane resistance, yet therapeutic strategies that directly deplete or repolarize macrophages are challenging and with considerable risk of side effects. Here we uncovered that tumor-macrophage interaction can be selectively targeted by inhibiting post-mitotic NOTCH2-JAG1 juxtacrine signaling in the TME, which strongly sensitizes paclitaxel response. Using translatome profiling, we found significant NOTCH2 upregulation during paclitaxel-induced prolonged mitosis. NOTCH2 was subsequently activated in the post-mitotic G1 phase by JAG1 expressed on the neighboring macrophages and tumor cells, which promoted tumor cell survival and upregulated cytokines that recruited JAG1-expressing macrophages, thus generating a positive feedback loop that further enhanced the pro-tumor NOTCH2 activity. By targeting this NOTCH2-JAG1 axis using NOTCH2 shRNA or a pan-NOTCH inhibitor, macrophage recruitment and paclitaxel resistance were significantly attenuated in multiple mouse tumor models of ovarian cancer. Clinical samples from paired primary and recurrent ovarian cancer patients also showed significant correlation of higher NOTCH2 expression with worse prognosis. Our results thus point to combining NOTCH2 inhibitor with taxane as an effective therapeutic strategy to selectively disrupt tumor-macrophage interaction in the TME and overcome macrophage-mediated taxane resistance in NOTCH2-positive tumors.

cancer biology↗

bioRxiv2024

The fully activated open state of KCNQ1 controls the cardiac 'fight-or-flight' response

The cardiac KCNQ1+KCNE1 (IKs) channel regulates heart rhythm in both normal and stress conditions. Under stress, the {beta}-adrenergic stimulation elevates the intracellular cAMP level, leading to KCNQ1 phosphorylation by protein kinase A and increased IKs, which shortens action potentials to adapt to accelerated heart rate. An impaired response to the {beta}-adrenergic stimulation due to KCNQ1 mutations is associated with the occurrence of a lethal congenital long QT syndrome (type 1, also known as LQT1). However, the underlying mechanism of {beta}-adrenergic stimulation of IKs remains unclear, impeding the development of new therapeutics. Here we find that the unique properties of KCNQ1 channel gating with two distinct open states are key to this mechanism. KCNQ1s fully activated open (AO) state is more sensitive to cAMP than its intermediate open (IO) state. By enhancing the AO state occupancy, the small molecules ML277 and C28 are found to effectively enhance the cAMP sensitivity of the KCNQ1 channel, independent of KCNE1 association. This finding of enhancing AO state occupancy leads to a potential novel strategy to rescue the response of IKs to {beta}-adrenergic stimulation in LQT1 mutants. The success of this approach is demonstrated in cardiac myocytes and also in a high-risk LQT1 mutation. In conclusion the present study not only uncovers the key role of the AO state in IKs channel phosphorylation, but also provides a new target for anti-arrhythmic strategy. Significance statementThe increase of IKs potassium currents with adrenalin stimulation is important for "fight-or-flight" responses. Mutations of the IKs channel reducing adrenalin responses are associated with more lethal form of the type-1 long-QT syndrome (LQT). The alpha subunit of the IKs channel, KCNQ1 opens in two distinct open states, the intermediate-open (IO) and activated-open (AO) states, following a two-step voltage sensing domain (VSD) activation process. We found that the AO state, but not the IO state, is responsible for the adrenalin response. Modulators that specifically enhance the AO state occupancy can enhance adrenalin responses of the WT and LQT-associated mutant channels. These results reveal a mechanism of state dependent modulation of ion channels and provide an anti-arrhythmic strategy.

biophysics↗

bioRxiv2024

Identification of BiP as a temperature sensor mediating temperature-induced germline sex reversal

Besides regulation by karyotype, sex determination is also modulated by environmental cues like temperature, but the involving temperature-transduction mechanism remains elusive. Moreover, while sex determination was traditionally seen as dictated exclusively by either karyotype or temperature, recent observations suggest these factors can co-regulate sex, posing a mechanistic mystery. Here, we discovered that certain wild-isolated and mutant C. elegans strains displayed genotypic-germline-sex-determination (GGSD) but with a temperature override. We found that ER chaperone BiP transduces temperature into germline-sex-governing signal and enables the co-existence of GGSD and temperature-dependent-germline-sex-determination (TGSD). Mechanistically, BiP availability is reduced at warmer temperatures through detecting increased ER-protein-folding burden, which promotes male-germline-fate through ERAD-mediated downregulation of the oocyte-fate driving factor, TRA-2. Remarkably, we can induce a switch between GGSD and TGSD by manipulating this newly-discovered process. Functionally, TGSD facilitates C. elegans hermaphrodites in maintaining brood size at warmer temperatures. Moreover, BiP also acts in germline-sex-determination in a dioecious nematode. Collectively, our findings identify thermosensitive BiP as a conserved temperature sensor in TGSD and provide mechanistic insights into the fascinating transition of GGSD and TGSD.

developmental biology↗

bioRxiv2024

Cyclophilin A Facilitates HIV-1 DNA Integration

Cyclophilin A (CypA) promotes HIV-1 infection by facilitating reverse transcription, nuclear entry and by countering the antiviral activity of TRIM5. These multifunctional roles of CypA are driven by its binding to the viral capsid. Interestingly, recent studies suggest that the HIV-1 capsid lattice enters the nucleus of an infected cell and uncoats just before integration. Therefore, we tested whether CypA-capsid interaction regulates post-nuclear entry steps of infection, particularly integration. First, we challenged CypA-expressing (CypA+/+) and CypA-depleted (CypA-/-) cells with HIV-1 particles and quantified the resulting levels of provirus. Surprisingly, CypA-depletion significantly reduced integration, an effect that was independent of CypAs effect on reverse transcription, nuclear entry, and the presence or absence of TRIM5. Additionally, cyclosporin A, an inhibitor that disrupts CypA-capsid binding, inhibited HIV-1 integration in CypA+/+ cells but not in CypA-/- cells. Accordingly, HIV-1 capsid mutants (G89V and P90A) deficient in CypA binding were also blocked at integration in CypA+/+ cells but not in CypA-/- cells. Then, to understand the mechanism, we assessed the integration activity of HIV-1 preintegration complexes (PICs) extracted from infected cells. The PICs from CypA-/- cells had lower activity in vitro compared to those from CypA+/+ cells. PICs from cells depleted for CypA and TRIM5 also had lower activity, suggesting that CypAs effect on PIC activity is independent of TRIM5. Finally, addition of CypA protein significantly stimulated the integration activity of PICs extracted from both CypA+/+ and CypA-/-cells. Collectively, these results suggest that CypA promotes HIV-1 integration, a previously unknown role of this host factor. ImportanceHIV-1 capsid interaction with host cellular factors is essential for establishing a productive infection. However, the molecular details of such virus-host interactions are not fully understood. Cyclophilin A (CypA) is the first host protein identified to specifically bind to the HIV-1 capsid. Now it is established that CypA promotes reverse transcription and nuclear entry steps of HIV-1 infection. In this report, we show that CypA promotes HIV-1 integration by binding to the viral capsid. Specifically, our results demonstrate that CypA promotes HIV-1 integration by stimulating the activity of the viral preintegration complex and identifies a novel role of CypA during HIV-1 infection. This new knowledge is important because recent reports suggest that an operationally intact HIV-1 capsid enters the nucleus of an infected cell.

microbiology↗

bioRxiv2024

Transcriptional reprogramming deploys a compartmentalized "timebomb" in Catharanthus roseus to fend off chewing herbivores

The evolutionary arms-race between plants and insects has led to key adaptive innovations that drive diversification. Alkaloids are well-documented anti-herbivory compounds in plant chemical defenses, but how these specialized metabolites are allocated to cope with both biotic and abiotic stresses concomitantly is largely unknown. To examine how plants prioritize their metabolic resources responding to herbivory and cold, we integrated dietary toxicity bioassay in insects with co-expression analysis, hierarchical clustering, promoter assay, and protein-protein interaction in plants. Catharanthus roseus, a medicinal plant known for its insecticidal property against chewing herbivores, produces two terpenoid indole alkaloid monomers, vindoline and catharanthine. Individually, they exhibited negligible toxicity against Manduca sexta, a chewing herbivore; their condensed product, anhydrovinblastine, however, was highly toxic. Such unique insecticidal mode of action demonstrates that terpenoid indole alkaloid "timebomb" can only be activated when the two spatially isolated monomeric precursors are dimerized by herbivory. Without initial selection pressure and apparent fitness costs, this adaptive chemical defense against herbivory is innovative and sustainable. The biosynthesis of insecticidal terpenoid indole alkaloids is induced by herbivory but suppressed by cold. Here, we identified a transcription factor, Herbivore Induced Vindoline-gene Expression (HIVE), that coordinates the production of terpenoid indole alkaloids in response to herbivory and cold stress. The HIVE-mediated transcriptional reprogramming allows this herbaceous perennial to allocate their metabolic resources for chemical defense at a normal temperature, when herbivory pressure is high, but switches to cold tolerance under a cooler temperature, when insect infestation is secondary.

plant biology↗

bioRxiv2024

Potent and broadly neutralizing antibodies against sarbecoviruses elicited by single ancestral SARS-CoV-2 infection

Monoclonal antibody (mAb) therapeutics hold promise for both preventing and treating infectious diseases, especially among vulnerable populations. However, the emergence of various variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) presents challenges for current mAb treatments, emphasizing the need for more potent and broadly neutralizing antibodies. In this study, we employed an unbiased screening approach to discover broadly neutralizing antibodies and successfully isolated two mAbs from individuals with only exposure to ancestral SARS-CoV-2. One of these antibodies, CYFN1006-1, exhibited robust cross-neutralization against a spectrum of SARS-CoV-2 variants, including the latest JN.1 and KP.2 variants, with consistent IC50 values ranging from [~]1 to 5 ng/mL. Notably, it also displayed broad neutralization activity against SARS-CoV and related sarbecoviruses, such as WIV1, SHC014, RaTG13, and GD-Pangolin. Structural analysis revealed that these mAbs target shared hotspot but mutation-resistant epitopes, with their Fabs locking the RBD in the "down" conformation through interactions with adjacent Fabs and RBDs, and cross-linking Spike trimers into di-trimers to block viral infection. In vivo studies conducted in a JN.1-infected hamster model validated the protective efficacy of CYFN1006-1, emphasizing its therapeutic potential. These findings suggest that, through meticulous approaches, rare antibodies with cross-neutralization activities against SARS-CoV-2 and related sarbecoviruses can be identified from individuals with exclusively ancestral virus exposure.

microbiology↗

bioRxiv2024

LncCE: Landscape of Cellular-Elevated LncRNAs in Single Cells Across Normal and Cancer Tissues

Long non-coding RNAs (lncRNAs) have emerged as significant players for maintaining the morphology and function of tissues or cells. The precise regulatory effectiveness of lncRNA is closely associated with the spatial expression patterns across tissues and cells. Here, we proposed the Cellular-Elevated LncRNA (LncCE) database to systematically explore cellular-elevated (CE) lncRNAs across normal and cancer tissues in single cells. LncCE encompasses 87,946 CE lncRNAs of 149 cell types by analyzing 181 single-cell RNA sequencing (scRNA-seq) datasets, involved in 20 fetal normal tissues, 59 adult normal tissues, as well as 32 adult and 5 pediatric cancer tissues.Two main search options were provided via a given lncRNA name or a cell type. The output results emphasize both qualitative and quantitative expression features of lncRNAs across different cell types, co-expression with protein-coding genes as well as their involved in biological functions. For cancers, LncCE particularly provided quantitative figures for exhibiting their expression changes compared to control samples and clinical associations with patient overall survivals. Together, LncCE offers an extensive, quantitative and user-friendly interface to investigate cellular-elevated expression atlas for lncRNAs across normal and cancers tissues at single-cell level. The LncCE database is available at http://bio-bigdata.hrbmu.edu.cn/LncCE.

cancer biology↗

bioRxiv2024

The novel role of Kallistatin in linking metabolic syndromes and cognitive memory deterioration by inducing amyloid-β plaques accumulation and tau protein hyperphosphorylation

Accumulation of amyloid {beta} (A{beta}) peptides and hyperphosphorylated tau proteins in the hippocampus triggers cognitive memory decline in Alzheimers disease (AD). The incidence and mortality of sporadic AD were tightly associated with diabetes and hyperlipidemia, while the exact linked molecular is uncertain. Here, we reported that serum Kallistatin concentrations were meaningfully higher in AD patients, with a higher concentration of fasting blood glucose and triglyceride. In addition, the constructed Kallistatin-transgenic (KAL-TG) mice defined its cognitive memory impairment phenotype and lower LTP in hippocampal CA1 neurons accompanied by increased A{beta} deposition and tau phosphorylation. Mechanistically, Kallistatin could directly bind to the Notch1 receptor and thereby upregulate BACE1 expression by inhibiting PPAR{gamma} signaling, resulting in A{beta} cleavage and production. Besides, Kallistatin could promote the phosphorylation of tau by activating GSK-3{beta}. Fenofibrate, a hypolipidemic drug, could alleviate cognitive memory impairment by down-regulating A{beta} and tau phosphorylation of KAL-TG mice. Collectively, our data clarified a novel mechanism for A{beta} accumulation and tau protein hyperphosphorylation regulation by Kallistatin, which might play a crucial role in linking metabolic syndromes and cognitive memory deterioration, and suggested that fenofibrate might have the potential for treating metabolism-related AD. HighlightsO_LIKallistatin-transgenic (KAL-TG) mice defined its cognitive memory impairment phenotype accompanied by increased A{beta} deposition and tau phosphorylation. C_LIO_LIKallistatin could directly bind to the Notch1 receptor and thereby upregulate BACE1 expression by inhibiting PPAR{gamma} signaling. C_LIO_LIFenofibrate could alleviate cognitive memory impairment and down-regulate the serum Kallistatin level. C_LI

neuroscience↗

bioRxiv2024

Structural insights into transcription regulation of the global virulence factor PhoP from Mycobacterium tuberculosis

Mycobacterium tuberculosis (Mtb), remaining as the leading cause of the worldwide threat Tuberculosis, relies heavily on its transcriptional reprogramming of diverse stress genes to swiftly adapt to adverse environments and ensure infections. The global virulence factor PhoP plays a pivotal role in coordinating transcription activation or repression of the essential phosphate-nitrogen metabolic remodeling genes. However, what defines PhoP to deferentially act as an activator or a repressor remains largely unexplored. Here, we determine one cryo-EM structure of Mtb RNAP-promoter open complex, three cryo-EM structures of PhoP-dependent transcription activation complexes (PhoP-TACs) consisting of Mtb RNA polymerase (RNAP), different number of PhoP molecules binding to different types of well-characterized consensus promoters, and one cryo-EM structure of Mtb PhoP-dependent transcription repression complex (PhoP-TRC) comprising of Mtb RNAP, PhoP, the nitrogen metabolism regulator GlnR and their co-regulated promoter. Structural comparisons reveal phosphorylation of PhoP is required for stabilization of PhoP-TACs, PhoP specifically recognizes promoters as novel tandem dimers and recruits RNAP through extensively interacting with its conserved {beta} flap and {sigma}AR4 domains. Strikingly, the distinct promoter spacer length and PhoP-GlnR interactions in PhoP-TRC constrain the upstream DNA into a distinct topology and retain PhoP in a novel dragging repression mode. Collectively, these data highlight the dual regulatory mechanisms of PhoP-dependent transcription regulation in governing stress adaptation. These findings provide structural basis for developing potential anti-tuberculosis drugs and/or interventions.

microbiology↗