Biology subjects

Yue, J.

Publications and source records attributed to Yue, J..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

In-situ structures of the Legionella Dot/Icm T4SS identify the DotA-IcmX complex as the gatekeeper for effector translocation

The Dot/Icm machine in Legionella pneumophila is one of the most versatile type IV secretion systems (T4SSs), with a remarkable capacity to translocate over 330 different effector proteins across the bacterial envelope into host cells. At least 27 Dot and Icm proteins are required for assembly and function of the system, yet the architecture and activation mechanism remain poorly understood at the molecular level. Here, we deploy cryo-electron microscopy to reveal in-situ structures of the Dot/Icm machine at near-atomic resolution. Importantly, two proteins essential for effector translocation, DotA and IcmX, form a pentameric protochannel at an inactive state. Upon activation, the DotA-IcmX protochannel undergoes extensive rearrangements to form an extended transenvelope passage capable of transporting effector proteins from the bacterial cytoplasm into host cells as revealed by cryo-electron tomography. Collectively, our findings suggest that the DotA-IcmX complex functions as the gatekeeper for effector translocation of the Dot/Icm T4SS.

molecular biology↗

bioRxiv2025

Targeting PI3K Signaling for Broad Inhibition of β-Coronavirus Infection

The phosphatidylinositol 3-kinase (PI3K) signaling pathway plays a central role in regulating key cellular processes such as survival, metabolism, and immune responses. Aberrant activation of this pathway is associated with tumorigenesis, and several PI3K inhibitors have been developed as anticancer agents. Emerging evidence suggests that viruses, including {beta}-coronaviruses, have evolved mechanisms to exploit host PI3K signaling for their replication and immune evasion. In this study, we evaluated the antiviral efficacy of a panel of PI3K inhibitors against {beta}-coronaviruses, including mouse hepatitis virus (MHV), human OC43 (HuCoV-OC43) and four major SARS-CoV-2 variants using both cell line and organoid models. Our findings reveal that these compounds exhibit low micromolar potency in inhibiting viral replication. Notably, the inhibitor C20 (PWT33597) demonstrated broad-spectrum activity against multiple {beta}-coronaviruses, including SARS-CoV-2, MHV, and HuCoV-OC43, in conventional cell lines as well as in air-liquid interface (ALI)-cultured, differentiated primary human nasal and bronchial epithelial cells. Given that cytokine storm is a major contributor to SARS-CoV-2-related multiorgan failure and mortality, we further explored the impact of PI3K inhibition on host inflammatory responses. We found that MHV infection markedly increased cytokine expression in 17CL-1 fibroblasts and RAW264.7 macrophages. Interestingly, treatment with C20 further amplified cytokine production in this context, suggesting complex immunomodulatory effects that warrant further investigation. Together, our findings support the therapeutic potential of repurposing PI3K inhibitors as broad-spectrum antivirals. These compounds not only suppress viral replication but may also influence host immune responses, providing a promising avenue for intervention against current and emerging coronavirus threats.

microbiology↗

bioRxiv2025

Repetitive mild traumatic brain injury causes neuronal damage in the APP/PS1 mouse model of Alzheimer's disease without an enduring impact on amyloid pathology, sleep, or epileptiform activity

Traumatic Brain Injury (TBI) is a known risk factor for Alzheimers disease and related neurodegenerative diseases. Sleep disturbances and epileptiform abnormalities can appear after TBI and may contribute to the development of neuropathology. In this study, we characterized sleep, epileptiform activity, and neuropathology after repetitive mild traumatic brain injury (rmTBI) in a mouse model of Alzheimers disease. We used the Closed Head Impact Model of Engineered Rotational Acceleration (CHIMERA) to deliver rmTBI or sham (control) treatment to 6-month-old APP/PS1 mice (N=19). One month post-injury, we implanted electroencephalogram (EEG) and electromyographic (EMG) electrodes, recorded for 72 hours, and then collected brain tissue and blood plasma. Our assessment of sleep architecture showed that time spent in vigilance state was not affected by the rmTBI one month post-injury; however, power spectra analysis showed a shift towards higher frequencies in the rmTBI group during non-rapid eye movement (NREM) sleep. Epileptiform activity did not differ between sham and rmTBI. Compared to sham controls, the rmTBI group showed higher neurofilament light (NF-L), but not glial-fibrillary acidic protein (GFAP) in blood plasma and no change in A{beta} pathology. These results indicate sustained neurological injury in the APP/PS1 mice one month after rmTBI without affecting amyloid deposition in the brain. Our study suggests that rmTBI can induce neural injury without causing enduring sleep disruption, seizures, and exacerbation of amyloidosis in the APP/PS1 mouse model.

neuroscience↗

bioRxiv2025

PML1-Mediated Feedforward Loop Through PI3K and MAPK Axes Drives Endocrine Resistance

Treatment of estrogen receptor-positive (ER+) breast cancer is significantly hindered by endocrine resistance. We identified PML1 as a key therapeutic entity that can be targeted to overcome resistance. Endocrine-resistant breast cancer cells share three key characteristics: elevated PML1 protein levels, enhanced activity of PI3K, MAPK, or both signaling pathways, and reduced ER activity. We developed a PML1 gene signature that predicts poor prognosis and correlates strongly with PI3K, MAPK, and endocrine resistance gene signatures, as evident by cellular studies, scRNA-seq analysis, and spatial transcriptomics of endocrine therapy-treated tumors. This signature is present in endocrine-resistant breast cancer cells harboring the Y537S ER mutation. We consistently demonstrate high PML1 protein levels across cells resistant to various treatments, including 4-hydroxytamoxifen, fulvestrant, elacestrant, and CDK4/6 inhibitors. Furthermore, treatments with these therapeutic agents or knockdown of ESR1 mRNA also increase PML1 protein levels. Mechanistically, we show that ER inhibition through fulvestrant treatment activates PI3K and MAPK signaling, which enhance PML1 protein stability and synthesis. PML1 then drives a feedforward loop by stimulating the expression of cytokine and growth factor mRNAs, including CCL5 and HBEGF, further amplifying PI3K and MAPK signaling. Consequently, in endocrine-resistant cells, endocrine therapies, while inactivating ER, paradoxically reinforce this loop through increased PI3K/MAPK activation and PML1 protein accumulation, ultimately compromising therapeutic efficacy. Finally, we demonstrated that arsenic trioxide, an FDA-approved, PML-reducing drug, effectively disrupts this feedforward loop, offering a promising strategy for treating resistant metastatic breast cancer. STATEMENT OF SIGNIFICANCEEndocrine resistance remains a major obstacle in treating estrogen receptor-positive metastatic breast cancer. Our study identifies PML1 as a central mediator of this resistance, revealing how it maintains a self-reinforcing signaling network through PI3K and MAPK pathways by enhancing the production of cytokines and growth factors. The clinical significance of our findings is threefold: we establish PML1 as a biomarker for therapy resistance, demonstrate its mechanistic role in treatment failure, and show that FDA-approved arsenic trioxide can disrupt PML1-driven resistance. These insights provide a direct path to clinical translation, as combining arsenic trioxide with existing therapies could benefit patients with limited treatment options.

cancer biology↗

bioRxiv2025

Decoding cellular transcriptional regulatory networks governing wheat inflorescence development

Wheat inflorescence architecture, particularly spikelet and floret development, is critical for grain yield. To decode the cellular transcriptional regulatory network (cTRN) underlying wheat inflorescence development, we integrated multiple single-cell omics technologies to construct a spatiotemporal atlas of transcriptional and chromatin accessibility dynamics. This comprehensive analysis identified 20 cell types, 7,211 cell type-specific genes and 152,333 cell type-specific accessible chromatin regions (csACRs) in the wheat inflorescence. Trajectory analysis identified two sub-clusters of proliferating cells as the origins of spikelet and floret formation, deviating from the traditional developmental model. Key transcription factors and hormone-related genes in the cTRN, along with the csACRs, providing new targets for modulating wheat inflorescence architecture. Our findings provide a high-resolution resource for crop inflorescence research and establish a paradigm for applying spatiotemporal single-cell omics analysis to plant biology.

plant biology↗

bioRxiv2025

Mitoxantrone inhibits and downregulates ERα through binding at the DBD-LBD interface

Targeting the estrogen receptor (ER or ER) through competitive antagonists, receptor downregulators, or estrogen synthesis inhibition remains the primary therapeutic strategy for luminal breast cancer. We have identified a novel mechanism of ER inhibition by targeting the critical interface between its DNA-binding domain (DBD) and ligand-binding domain (LBD). We demonstrate that mitoxantrone (MTO), a topoisomerase II inhibitor, binds at this previously unexplored DBD-LBD interface. Using comprehensive computational, biophysical, biochemical, and cellular analyses, we show that independent of its DNA damage response activity, MTO binding induces distinct conformational changes in ER, leading to its cytoplasmic redistribution and subsequent proteasomal degradation. Notably, MTO effectively inhibits clinically relevant ER mutations (Y537S and D538G) that confer resistance to current endocrine therapies, outperforming fulvestrant in both in vitro and in vivo assays. Our findings establish domain-domain interaction targeting as a viable therapeutic strategy for ER, with translational implications for other nuclear receptors.

cancer biology↗

bioRxiv2024

Reshaping epigenomic landscapes in facilitating the speciation of bread wheat

Polyploidization is a driving force of wheat evolution and speciation, yet its impact on epigenetic regulation and gene expression remains unclear. Here, we constructed a high-resolution epigenetic landscape across leaves, spikes, and roots of hexaploidy wheat and its tetraploid and diploid relatives. Inter-species stable-expression genes exhibited conserved amino acid sequences under strong purifying selection, while dynamic-expression genes were linked to species-specific adaptation. During hexaploidization, dominant D-subgenome homoeolog expression was suppressed via reduced activating epigenetic signals, converging expression with the A and B subgenomes. Proximal chromatin regions near genes were more stable, whereas distal regions, particularly enhancer-like elements mediated by H3K27ac and H3K4me3, exhibit higher dynamism. Sequence variations in these enhancers lead to differential gene regulation, influencing traits such as spike development. For instance, the two haplotypes of dCRE region of TaDEP-B1 resulted in significant differences in its expression and spikelet numbers. We also observed a coevolution of transcription factors and their binding sites, particularly within the expanded ERF family, which regulates spike morphology. This study highlights the interplay between sequence variation and epigenetic modifications in shaping transcriptional regulation during wheat speciation, offering valuable insights for genetic improvement.

plant biology↗

bioRxiv2024

FGR Src Family Kinase Causes Signaling and Phenotypic Shift Mimicking Retinoic Acid-Induced Differentiation of Leukemic Cells

Retinoic acid (RA) is an embryonic morphogen used in cancer differentiation-therapy. It causes a plethora of changes in gene expression culminating in cell differentiation. We now find that amongst them, expression of the Src-family-kinase, FGR, by itself causes cell differentiation analogous to RA. The historically dominant/classical paradigm for RA mechanism of action is transcriptional activation via binding to the ligand-activated nuclear receptors, RAR/RXR. In the HL-60 human myelo-monocytic leukemia model, an actively proliferating, phenotypically immature, lineage bi-potent NCI-60 cell line, RA causes election of the myeloid lineage and phenotypic maturation with G1/0 growth inhibition. It thereby converts transformed immature proliferating tumor cells to mature growth retarded cells that bear fidelity to non-transformed mature myeloid cells. The present study finds that expression of the FGR SFK(SRC-family-kinase) alone is sufficient to induce differentiation. Akin to RA, the phenotypic conversion manifests as expression of CD38, CD11b, and ROS, as well as the p27(kip1) CDKI (cyclin-dependent-kinase-inhibitor that retards cells in G1/0) characteristic of mature myeloid cells. To pursue mechanistic insight, signaling attributes known to promote RA-induced differentiation were analyzed to see what FGR affected. RA is known to cause expression of FGR which is incorporated into and activates a putative novel cytosolic macromolecular signaling machine(signalsome) that propels differentiation. RA enhances the abundance of signalsome constituents, their associations, and their phosphorylation. The signalsome contains connected nodes that appear as a spine to which the other components are connected. The apparent "nodes" are RAF, LYN, FGR, SLP-76 and CBL. All of these become enriched in the nucleus after RA-treatment. NUMB and VAV appear to provide further scaffolding functions enhanced by RA. RAF in the nucleus complexes with a RARE (retinoic acid-response-element) in the promoter of the blr1 gene, which encodes a serpentine G-protein-coupled-receptor. blr1 transcriptional activation by RA depends on RAF binding. BLR1 expression is necessary to propel RA-induced differentiation, although by itself is not sufficient to cause phenotypic differentiation. Analyzing this signaling process revealed that expression of FGR mimics RA-induced enhancement of the signalsome nodes, enhancing expression of RAF and its phosphorylation, and causing BLR1 expression. Interestingly, for cd38 and blr1, FGR apparently causes expression of genes targeted by RAR/RXR even without RA. FGR thus appears to cause signaling events and phenotypic shift characteristic of RA. In sum, the data indicate that FGR is the "trigger" for RA-induced differentiation. Given the historical perception of FGR as a pro-proliferation, transforming-viral-oncogene, this is a surprising paradigm shift.

molecular biology↗

bioRxiv2024

The AP2/ERF transcription factor HcERF5 confers drought tolerance via ABA-mediated signaling in kenaf

The APETALA2/ethylene response factor (AP2/ERFs) are pivotal in regulating abiotic stress responses in plants. However, the specific role of ERFs in kenafs response to drought stress remains unclear. In this study, a transcription factors HcERF5 was isolated from kenaf and its role in drought stress tolerance was analyzed. HcERF5 was found to localize in both nucleus and cytoplasm and could be significantly induced by polyethylene glycol-6000 (PEG-6000) and abscisic acid (ABA) in kenaf seedlings. In transgenic Arabidopsis expressing the HcERF5 promoter-driven {beta}-glucuronidase (GUS), strong GUS activity was observed in roots, stems, and leaves. Overexpression of HcERF5 in Arabidopsis enhanced seed germination rates under drought or ABA stress and improved drought tolerance in seedlings by increasing antioxidant enzyme activities, whereas aterf5 knockout lines exhibited the opposite trend. Additionally, HcERF5 overexpressing Arabidopsis showed significantly increased drought tolerance and reduced sensitivity to ABA. Furthermore, virus-induced gene silencing (VIGS) of HcERF5 in kenaf reduced drought tolerance, as evidenced by decreased antioxidant enzyme activity, increased stomatal aperture, and elevated levels of malondialdehyde (MDA), reactive oxygen species (ROS), and proline under drought stress. RNA-seq analysis further revealed that HcERF5 directly regulated ABA signaling pathway. Yeast-two-hybrid (Y2H) assays revealed 29 proteins that interact with HcERF5. Among them, the expression of downstream drought stress-related genes HcPRK, HcRD22, HcMAP2, HcCAB, HcCS, and HcCCoAOMT3 were significantly reduced in HcERF5-silenced plants. Overall, this study highlights the significant potential of HcERF5 in enhancing drought tolerance in kenaf. HighlightO_LIHcERF5 overexpression enhanced drought tolerance in kenaf, however silencing increased drought sensitivity. C_LIO_LIHcERF5 regulates ABA synthesis and increases kenaf stomatal conductance and density under drought stress. C_LIO_LIHcERF5 regulates plant hormone signal transduction, MAPK signalling, and phenylpropanoid biosynthesis in kenaf under drought stress. C_LIO_LIProtein interaction revealed HcERF5 interacts with six stress-response genes. C_LI

molecular biology↗

bioRxiv2024

Enhancing Transcriptome Mapping with Rapid PRO-seq Profiling of Nascent RNA

Precision nuclear run-on (PRO) sequencing (PRO-seq) is a powerful technique for mapping polymerase active sites with nucleotide resolution and measuring newly synthesized transcripts at both promoters and enhancer elements. The current PRO-seq protocol is time-intensive, technically challenging, and requires a large amount of starting material. To overcome these limitations, we developed rapid PRO-seq (rPRO-seq) which utilizes pre-adenylated single-stranded DNAs (AppDNA), a dimer blocking oligonucleotide (DBO), on-bead 5 RNA end repair, and column-based purification. These modifications enabled efficient transcriptome mapping within a single day ([~]12 hours) increasing ligation efficiency, abolished adapter dimers, and reduced sample loss and RNA degradation. We demonstrate the reproducibility of rPRO-seq in measuring polymerases at promoters, gene bodies, and enhancers as compared to original PRO-seq protocols. Additionally, rPRO-seq is scalable, allowing for transcriptome mapping with as little as 25,000 cells. We apply rPRO-seq to study the role of Integrator in mouse hematopoietic stem and progenitor cell (mHSPC) homeostasis, identifying Ints11 as an essential component of transcriptional regulation and RNA processing in mHSPC homeostasis. Overall, rPRO-seq represents a significant advance in the field of nascent transcript analyses and will be a valuable tool for generating patient-specific genome-wide transcription profiles with minimal sample requirements.

molecular biology↗

bioRxiv2024

Covalent DNA-Encoded Library Workflow Drives Discovery of SARS-CoV-2 Non-structural Proteins Inhibitors

The global coronavirus disease 2019 (COVID-19) pandemic persists, with the ongoing mutation of the virus. Consequently, the development of inhibitors with diverse binding modes and mechanisms of action, along with the elucidation of novel binding sites is of paramount importance. The 3-chymotrypsin-like protease (3CLpro) and papain-like protease (PLpro) are two validated cysteine proteases that cleave the viral polyprotein and are essential for viral replication. In this study, we utilized covalent DNA-Encoded libraries (CoDELs) workflow to identify two series of triazine-based covalent inhibitors targeting 3CLpro and PLpro. Molecular docking facilitated the identification of optimization pathways, further refined through medicinal chemistry efforts, leading to the development of the non-peptide 3CLpro inhibitor LU9, which exhibited an IC50 value of 0.34 M, and crystal structure of LU10 revealed a unique binding mode within the active site. Additionally, the X-ray cocrystal structure of SARS-CoV-2 PLpro with XD5 uncovered a previously unexplored binding site, adjacent to the catalytic pocket, providing an opportunity for further development of PLpro inhibitors. Overall, these novel compounds serve as valuable chemical probes for target validation and represent promising drug candidates for the continued development of SARS-CoV-2 antivirals.

biochemistry↗

bioRxiv2024

Generalizable Quantum Computing Pipeline for Real World Drug Discovery

Quantum computing, with its superior computational capabilities compared to classical approaches, holds the potential to revolutionize numerous scientific domains, including pharmaceuticals. However, the application of quantum computing for drug discovery has primarily been limited to proof-of-concept studies, which often fail to capture the intricacies of real-world drug development challenges. In this study, we diverge from conventional investigations by developing an advanced quantum computing pipeline tailored to address genuine drug design problems. Our approach underscores the pragmatic application of quantum computation and propels it towards practical industrial adoption. We specifically construct our versatile quantum computing pipeline to address two critical tasks in drug discovery: the precise determination of Gibbs free energy profiles for prodrug activation involving covalent bond cleavage, and the accurate simulation of covalent bond interactions. This work serves as a pioneering effort in benchmarking quantum computing against veritable scenarios encountered in drug design, especially the covalent bonding issue present in both of the case studies, thereby transitioning from theoretical models to tangible applications. Our results demonstrate the potential of a quantum computing pipeline for integration into real world drug design workflows.

bioinformatics↗

bioRxiv2023

GABRD promotes the progression of breast cancer through CDK1-dependent cell cycle regulation

PurposeY-aminobutyric acid (GABA) is an important inhibitory amino acid neurotransmitter that exerts its biological function by binding to GABA receptors, which not only play an important role in neuromodulation, but also involved in regulating the development of tumors. Gamma-aminobutyric acid type A receptor subunit delta (GABRD) encodes the {delta} subunit of GABAA receptor, its impact on breast cancer has not been clearly studied. This study is aiming to reveal the relationship between GABRD and breast cancer development. MethodsWe performed a tissue microarray to quantify GABRD expression levels in tumor tissue and paracarcinoma tissue. The regulation of GABRD in the proliferation, migration, and apoptosis of breast cancer was examined by a loss-of-function study. A GeneChip microarray was used to probe GABRD for potential downstream molecules. The interaction between GABRD and CDK1 was verified by a set of functional tests and rescue experiments as well as coimmunoprecipitation. ResultsGABRD was expressed at significantly higher levels in tumor tissues and was associated with advanced tumor progression. Silencing GABRD resulted in a significant decrease in proliferation and migration and an increase in apoptosis of breast cancer. GABRD regulated the cell cycle by directly interacting with CDK1, which was identified as an important downstream target. ConclusionGABRD is the breast cancer-related gene and highlights the importance of the GABRD-CDK1 axis in regulating breast cancer proliferation, which provides potential for the development of novel therapeutics.

cancer biology↗

bioRxiv2023

Multi-omics Comparison among Populations of Three Plant Sources of Amomi Fructus

Amomi Fructus (Sharen, AF) is a traditional Chinese medicine (TCM) from three source species (or subspecies) including Wurfbainia villosa var. villosa (WVV), W. villosa var. xanthioides (WVX) or W. longiligularis (WL). Among them, WVV has been transplanted from its top-geoherb region Guangdong to its current main production area Yunnan for more than 50 years in China. However, the genetic and transcriptomic differentiation among multiple AF source (sub)species and between the origin and transplanted populations of WVV is unknown. In our study, the observed overall higher expression of terpenoid biosynthesis genes in WVV than that of WVX supplied possible evidence for the better pharmacological effect of WVV. We also screened ten candidate borneol dehydrogenase (BDH) genes that potentially catalyzed borneol into camphor in WVV. The BDH genes may experience independent evolution after acquiring the ancestral copies and the followed tandem duplications might account for the abundant camphor content in WVV. Furthermore, four populations of WVV, WVX and WL are genetically differentiated and the gene flow from WVX to WVV in Yunnan contributed to the increased genetic diversity in the introduced population (WVV-JH) compared to its top-geoherb region (WVV-YC), which showed the lowest genetic diversity and might undergo genetic degradation. In addition, TPS and BDH genes were selected among populations of multiple AF source (sub)species and between the top-geoherb and non-top-geoherb regions, which might explain the metabolite difference of these populations. Our findings provide important guidance for the conservation, genetic improvement, industrial development of the three source (sub)species, and identifying top-geoherbalism with molecular markers and proper clinical application of AF.

evolutionary biology↗

bioRxiv2022

Multi-omics analyses of single cell-derived colorectal cancer organoids reveal intratumor heterogeneity and immune response diversity

Colorectal cancer (CRC) organoids have similar genomic and functional characteristics to the original specimens. They have become a novel and promising tumor model. However, systematic research of heterogeneity and evolution based on tumor organoids and unbiased evaluation of CD4+ T cell-mediated tumor recognition is presently lacking. Here, we study the variability in genomic characterization and single-cell transcriptome between different tumor organoid clones derived from the same CRC patient. While clone-specific differences in driver gene mutations and cancer stem cell (CSC) subpopulations were observed, inter-clone heterogeneity was even more prevalent. Using single-cell RNA sequencing, we found that compared with bulk organoids, CRC organoid clones are mainly composed of cancer stem cells and transiently-amplifying cells (TACs), but no epithelial-mesenchymal transition (EMT)-like (S100A4+CDH1-) cells. In addition, we study the phenotypic characteristics and TCR properties of tumor-reactive CD4+ T cells by coupling the organoid-TILs co-culture model, single-cell profiling, and recognition testing of candidate TCRs. We found that the proliferating CD4+ T cells increased significantly from 7.1% to 35.4%, and the TCR clonotypes increased from 110 to 1043 after co-culture with organoids. Moreover, 4 of 10 (40%) candidate TCRs with a significant increase in clone abundance exhibited tumor recognition. These results provide evidence that the proliferating CD4+ T cells with clonal expansion after co-culture with tumor organoids are the potential tumor-reactive T cells. Collectively, we reconstructed intra-patient heterogeneity in single cell-derived organoid models and characterized the phenotypic characteristics and functional properties of tumor-reactive CD4+ T cells.

cancer biology↗

bioRxiv2022

Altered tau in rTg4510 mice after a single interfaced CHIMERA traumatic brain injury

Traumatic brain injury (TBI) in an established risk factor for neurodegenerative disease. In this report, we used the Closed Head Injury Model of Engineered Rotational Acceleration (CHIMERA) to study the effects of a single moderate-severe TBI in rTg4510 mice, a mouse model of tauopathy. Fifteen male rTg4510 mice were impacted at 4.0J at 4-mo of age using interfaced CHIMERA and compared to sham controls. Immediately after injury, moderate-severe TBI induced significant mortality (7/15; 47%), and a prolonged duration of loss of righting reflex. At 2-mo post-injury, surviving mice displayed significant histological evidence of microgliosis (Iba1) and axonal injury (Neurosilver). Western blotting showed that TBI mice had a reduced p-GSK-3{beta} (S9):GSK-3{beta} ratio, suggesting greater tau kinase activity. However, tauopathy in surviving TBI mice showed a divergent response, with 3/8 mice having a very low level of tau protein in brain lysates (i.e. lower than sham), and were thus analyzed separately from the other 5/8 TBI mice that maintained the expected level of total tau. Compared to sham controls, TBI mice with normal tau levels had increased p-tau (PHF1 and AT8), increased autophagolysosome accumulation (p62 and Cathepsin D) and decreased hippocampal size. These findings were not observed in TBI mice with low total tau levels. These observations suggest that TBI leads to chronic white matter injury and altered GSK-3{beta} activity. However, post-injury tauopathy and autophagolysosome accumulation diverged in surviving mice through mechanisms that remain to be defined.

neuroscience↗

bioRxiv2022

Identification of a small chemical as a lysosomal calcium mobilizer and characterization of its ability to inhibit autophagy and viral infection

We previously identified GADPH as one of the cyclic adenosine diphosphoribose (cADPR)s binding proteins and found that GADPH participates in cADPR-mediated Ca2+ release from ER via RyRs. Based on the simulated cADPR-GAPDH complex structure, we performed the structure-based drug screening, identified several small chemicals with high docking scores to cADPRs binding pocket in GAPDH, and showed that two of these compounds, C244 and C346, are potential cADPR antagonists. We further synthesized several analogs of C346, and found that its analog, G42, also mobilized Ca2+ release from lysosomes. G42 alkalized lysosomal pH, and inhibited autophagosome-lysosome fusion. Moreover, G42 markedly inhibited Zika virus (ZIKV, a flavivirus) or murine hepatitis virus (MHV, a {beta}-coronavirus) infections of host cells. These results suggest that G42 inhibits virus infection, likely by triggering lysosomal Ca2+ mobilization and inhibiting autophagy.

microbiology↗

bioRxiv2022

CRISPR-induced exon skipping of β-catenin reveals tumorigenic mutants driving distinct subtypes of liver cancer

CRISPR/Cas9-driven cancer modeling studies are based on disruption of tumor suppressor genes (TSGs) by small insertions or deletions (indels) that lead to frame-shift mutations. In addition, CRISPR/Cas9 is widely used to define the significance of cancer oncogenes and genetic dependencies in loss-of function studies. However, how CRISPR/Cas9 influences gain-of-function oncogenic mutations is elusive. Here, we demonstrate that single guide RNA targeting exon 3 of {beta}-catenin results in exon skipping and generates gain-of-function isoforms in vivo. CRISPR/Cas9-mediated exon skipping of {beta}-catenin induces liver tumor formation in synergy with YAPS127A in mice. We define two distinct exon skipping-induced tumor subtypes with different histological and transcriptional features. Notably, ectopic expression of two exon-skipped {beta}-catenin transcript isoforms together with YAPS127A phenocopies the two distinct subtypes of liver cancer. Moreover, we identify similar {beta}-catenin exon skipping events in hepatocellular carcinoma (HCC) patients. Collectively, our findings advance our understanding of {beta}-catenin-related tumorigenesis and reveal that CRISPR/Cas9 can be repurposed, in vivo, to study gain-of-function mutations of oncogenes in cancer.

cancer biology↗