Biology subjects

Qin, Y.

Publications and source records attributed to Qin, Y..

At least 73 records · Page 4Linked to original sources

bioRxiv2024

Efficient Gene Editing and Overexpression of Gametophyte Transformation in a Model Fern

The clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-related nuclease (Cas) system allows precise and easy editing of genes in many plant species. However, this system has not yet been applied to any fern species due to the complex characteristics of fern genomes, genetics and physiology. Here, we established, for the first time, a protocol for gametophyte-based screening single-guide RNAs (sgRNAs) with high efficiency for CRISPR/Cas-mediated gene editing in a model fern species, Ceratopteris richardii. We utilized the C. richardii Actin promoter to drive sgRNA expression and enhanced CaMV 35S promoter to drive the expression of Streptococcus pyogenes Cas9 in this CRISPR-mediated editing system, which was employed to successfully edit a few genes (e.g., nucleotidase/phosphatase 1, CrSAL1; Cryptochrome 4, CRY4) and CrPDS, encoding a phytoene desaturase protein that resulted in an albino phenotype in C. richardii. Knockout of CrSAL1 resulted in significantly reduced stomatal conductance (gs), leaf transpiration rate (E), stomatal/pore length, and abscisic acid (ABA)-induced reactive oxygen species (ROS) accumulation in guard cells. Moreover, CrSAL1 overexpressing plants showed significantly increased net photosynthetic rate (A), gs, E and intrinsic water use efficiency (iWUE) as well as most of the stomatal traits and ROS production in guard cells compared to those in the wild-type (WT) plants. Taken together, the optimized CRISPR/Cas9 system provides a useful tool for functional genomics in a model fern species, allowing the exploration of fern gene functions for evolutionary biology, herbal medicine discovery and agricultural applications.

plant biology↗

bioRxiv2024

Classification and functional characterization of regulators of intracellular STING trafficking identified by genome-wide optical pooled screening

STING is an innate immune sensor that traffics across many cellular compartments to carry out its function of detecting cyclic di-nucleotides and triggering defense processes. Mutations in factors that regulate this process are often linked to STING-dependent human inflammatory disorders. To systematically identify factors involved in STING trafficking, we performed a genome-wide optical pooled screen and examined the impact of genetic perturbations on intracellular STING localization. Based on subcellular imaging of STING protein and trafficking markers in 45 million cells perturbed with sgRNAs, we defined 464 clusters of gene perturbations with similar cellular phenotypes. A higher-dimensional focused optical pooled screen on 262 perturbed genes which assayed 11 imaging channels identified 73 finer phenotypic clusters. In a cluster containing USE1, a protein that mediates Golgi to ER transport, we found a gene of unknown function, C19orf25. Consistent with the known role of USE1, loss of C19orf25 enhanced STING signaling. Other clusters contained subunits of the HOPS, GARP and RIC1-RGP1 complexes. We show that HOPS deficiency delayed STING degradation and consequently increased signaling. Similarly, GARP/RIC1-RGP1 loss increased STING signaling by delaying STING exit from the Golgi. Our findings demonstrate that genome-wide genotype-phenotype maps based on high-content cell imaging outperform other screening approaches, and provide a community resource for mining for factors that impact STING trafficking as well as other cellular processes observable in our dataset.

systems biology↗

bioRxiv2024

CROPseq-multi: a versatile solution for multiplexed perturbation and decoding in pooled CRISPR screens

Forward genetic screens seek to dissect complex biological systems by systematically perturbing genetic elements and observing the resulting phenotypes. While standard screening methodologies introduce individual perturbations, multiplexing perturbations improves the performance of single-target screens and enables combinatorial screens for the study of genetic interactions. Current tools for multiplexing perturbations are limited by technical challenges and do not offer compatibility across diverse screening methodologies, including enrichment, single-cell sequencing, and optical pooled screens. Here, we report the development of CROPseq-multi (CSM), a CROPseq1-inspired lentiviral system to multiplex Streptococcus pyogenes (Sp) Cas9-based perturbations with versatile readout compatibility and high performance for both perturbation and barcode identification. CSM has equivalent per-guide activity to CROPseq and low lentiviral recombination frequencies. Dual-guide CSM libraries are constructed in a single, facile molecular cloning step that facilitates the use of unique molecular identifiers. CSM is compatible with enrichment screening methodologies, single-cell RNA-sequencing readouts, and optical pooled screens. For optical pooled screens, an optimized and multiplexed in situ detection protocol improves barcode counts 10-fold (for mRNA detection), enables detection of recombination events, and reduces the number of sequencing cycles required for decoding by 3-fold relative to CROPseq. CROPseq-multi-v2 (CSMv2) adds compatibility for detection methods based on T7 RNA polymerase in vitro transcription2-5. CSM provides a single system for CRISPR screens that is compatible with individual and combinatorial perturbations, diverse SpCas9-based perturbation technologies, and multiple high-content, single-cell phenotypic readouts.

genomics↗

bioRxiv2024

Diverse cell death signature based subtypes predict the prognosis and immune characteristics within glioma

BackgroundCell death plays an essential role in the pathogenesis, progression, drug resistance and recurrence of glioma. Although multiple cell death pathways are involved in glioma development, there is lack of a stratification and prognostic modelling for glioma based on the integration of diverse genes for cell deaths. MethodsIn this study, 1254 diverse cell death (DCD)-related genes were assessed using the ConsensusClusterPlus assessment to identify DCD patterns in glioma. CIBERSORT, ssGSEA, and ESTIMATE algorithms were applied to evaluate immune microenvironment differences between subtypes. LASSO Cox regression was used to screen prognosis-related DCD genes, and a risk score model was constructed. TMB, TIDE, immune infiltration, and immunotherapy response was analyzed to evaluate the immune characteristics. ResultsTwo DCD-related subgroups named Clusters 1 and 2, with distinct DCD levels, immune characteristics, and prognoses, were determined from glioma samples. A DCD-based risk score model was developed to assess DCD levels in glioma patients and divide patients into high- and low-risk groups. We found this risk model can be used as an independent prognostic factor for glioma patients. Notably, glioma patients with low risk scores exhibited subdued DCD activity, prolonged survival, and a favorable disposition towards benefiting from immune checkpoint blockade therapies. ConclusionsThis study established a novel signature classification and a risk model by comprehensively analyzing patterns of various DCDs to stratify glioma patients and to predict the prognosis and immune characteristics of glioma. We provided a theoretical basis for the clinical application of DCD-related genes in glioma prognosis and immunotherapy.

bioinformatics↗

bioRxiv2024

Pathway-enhanced Transformer-based model for robust enumeration of cell types from the cell-free transcriptome

Analyzing cell types of origin of cell-free RNA can enhance the resolution of liquid biopsies, thereby deepening the understanding of molecular and cellular changes in development and disease processes. Existing deconvolution methods typically rely on meticulously curated gene expression profiles or employ deep neural network with vast and complex solution spaces that are difficult to interpret. These approaches overlook the synergistic and co-expression effects among genes in biological signaling pathways, compromising their generalizability and robustness. we developed Deconformer, a Transformer-based deconvolution model that integrates biological signaling pathways at the embedding stage, to address these issues. Compared to popular methods on multiple datasets, Deconformer demonstrates superior performance and robustness, and is capable of tracking the developmental process of the fetal and placenta. Additionally, pathway-level interpretability of Deconformer offers new insights into crosstalk, dependencies, and other interactions within cell-free RNA pathways, supporting further biological discoveries. We posit that Deconformer represents a significant advancement in the precise analysis of the cell-free transcriptome. It holds the promise of describing disease progression and severity with a new level of accuracy, focusing on the contributions of originating cell types and their pathway dependencies. This model has the potential to catalyze the development of non-invasive diagnostic tools and enhance our understanding of the underlying biology of diseases.

bioinformatics↗

bioRxiv2024

Self-amplifying ROS-sensitive SN38 Dimeric Prodrug nanoparticles for Combined Chemotherapy and Ferroptosis in Cancer Treatment

Chemotherapy drugs are often limited by their own clinical shortcomings and serious adverse consequences. To solve these problems, we developed a self-amplifying reactive oxygen species (ROS)-sensitive dimeric prodrug nanoparticles, namely SN38-CA@FC NPs for tumor treatment. A ROS-sensitive 7-ethyl-10-hydroxycamptothecin (SN38) prodrug (SN38-CA) was synthesized by a thioacetal linker between SN38 and the ROS generator cinnamaldehyde (CA). The subsequent release of SN38 inflicts DNA damage, exerting chemotherapeutic effects, while the liberated CA intensifies ferroptosis through Fenton reaction-mediated disruption of the redox balance. This dual-action strategy not only leverages chemotherapy but also induces ferroptosis, establishing a synergistic therapeutic paradigm. The system is uniquely characterized by a positive feedback loop where ROS instigates the release of SN38/CA, which in turn promotes further ROS production. In experimental evaluations, this combination therapy exhibited potent antitumor activity against both A549 and LLC cancer cell lines, as well as in xenograft LLC-bearing C57BL/6 mouse models. Collectively, our findings introduce a transformative Nano-Drug Delivery System (NDDS) that holds significant promise for advancing cancer chemotherapy and ferroptosis-based therapies.

cancer biology↗

bioRxiv2023

Astrocyte CB1 receptors are required for inhibitory maturation and ocular dominance plasticity in the mouse visual cortex

Summary and IntroductionNeuronal circuits are shaped by experience. This happens much more readily in the young compared to the adult brain. The unique learning capacity of the young brain is regulated through postnatal critical periods, during which the ability of neuronal networks to re-wire is greatly enhanced1. Endocannabinoids, which signal through the cannabinoid CB1 receptor (CB1R), regulate several forms of neuronal plasticity2. In the developing neocortex, CB1Rs play a key role in the maturation of inhibitory circuits. For example, interfering with CB1R signaling during development disrupts inhibitory maturation in the prefrontal cortex3. In developing primary visual cortex (V1), endocannabinoid-mediated plasticity at inhibitory synapses regulates the maturation of inhibitory synaptic transmission, shifting synapses from an immature state characterized by strong short-term depression to a mature state with reduced short-term depression4,5. This maturation step correlates with the timing of the critical period. While CB1Rs were originally thought to reside mainly on presynaptic axon terminals, recent studies have highlighted an unexpected role for astrocytic CB1Rs in endocannabinoid mediated plasticity6-8. Here, we investigate the impact of cell-type specific removal of CB1Rs from interneurons or astrocytes on development of inhibitory synapses and network plasticity of V1. We show that removing CB1Rs from astrocytes interferes with maturation of inhibitory synaptic transmission in V1. In addition, it strongly reduces ocular dominance (OD) plasticity during the critical period. In contrast, removing interneuron CB1Rs leaves these processes intact. Our results reveal an unexpected role of astrocytic CB1Rs in critical period plasticity in V1, and highlight the involvement of glial cells in the plasticity and synaptic maturation of sensory circuits.

neuroscience↗

bioRxiv2023

A Day in the Life of Arabidopsis: 24-Hour Time-lapse Single-nucleus Transcriptomics Reveal Cell-type specific Circadian Rhythms

Functional circadian clock is fundamental to the adaptation and survival of organisms. In land plants, the comprehensive profiling of circadian gene expression at the single-cell level is largely unknown partly due to the challenges in obtaining precisely-timed single cells from plant cells embedded within cell walls. To bridge this gap, we employed single-nucleus RNA sequencing (snRNA-seq) on twelve seedling samples collected at 2-hour intervals over a 24-hour day in Arabidopsis, yielding a total of over 130,000 nuclei. From this data, we found that three cell clusters in the shoot share a coherent rhythm, while more than 3,000 genes display cell-type specific rhythmic expression. Only 19 genes are oscillating in more than ten different cell types, and the majority of them are well-documented core oscillators, suggesting the snRNA-seq circadian data could be used to identify key circadian regulators in a broad range of plant systems. Our data provides the first comprehensive resource for plant circadian rhythms at the single-cell level (hosted at https://zhailab.bio.sustech.edu.cn/sc_circadian).

plant biology↗

bioRxiv2023

De novo lipogenesis pathway is a vulnerability in IDH1 mutant glioma

Histone deacetylases (HDACs) have a wide range of targets and can rewire both the chromatin and lipidome of cancer cells. In this study, we show that valproic acid (VPA), a brain penetrant anti-epileptic and histone deacetylase inhibitor, inhibits the growth of IDH1 mutant tumors in vivo and in vitro, with at least some selectivity over IDH1 wild type tumors. Surprisingly, genes upregulated by VPA showed no change in chromatin accessibility at the promoter, but there was a correlation between VPA downregulated genes and diminished promoter chromatin accessibility. VPA inhibited the transcription of lipogenic genes and these lipogenic genes showed significant decrease in promoter chromatin accessibility only in the IDH1 MT glioma cell lines tested. VPA targeted a key lipogenic gene, fatty acid synthase (FASN), via inhibition of the mTOR pathway and both VPA and a selective FASN inhibitor TVB-2640 rewired the lipidome and promoted apoptosis in an IDH1 MT but not in an IDH1 WT glioma cell line. We further find HDACs are involved in the regulation of lipogenic genes and in particular HDAC6 is important for regulation of FASN in IDH1 MT glioma. Finally, we show that FASN knockdown alone and VPA in combination with FASN knockdown significantly improved the survival of mice in a IDH1 MT primary orthotopic xenograft model in vivo. We conclude that targeting fatty acid metabolism through HDAC inhibition and/or FASN inhibition may be a novel therapeutic option in IDH1 mutant gliomas.

cancer biology↗

bioRxiv2023

Methyl-TWAS: A powerful method for in silico transcriptome-wide association studies (TWAS) using long-range DNA methylation

In silico transcriptome-wide association studies (TWAS) are commonly used to test whether expression of specific genes is linked to a complex trait. However, genotype-based in silico TWAS such as PrediXcan, exhibit low prediction accuracy for a majority of genes because genotypic data lack tissue- and disease-specificity and are not affected by the environment. Because methylation is tissue-specific and, like gene expression, can be modified by environment or disease status, methylation should predict gene expression with more accuracy than SNPs. Therefore, we propose Methyl-TWAS, the first approach that utilizes long-range methylation markers to impute gene expression for in silico TWAS through penalized regression. Methyl-TWAS 1) predicts epigenetically regulated/associated expression (eGReX), which incorporates tissue-specific expression and both genetically- (GReX) and environmentally-regulated expression to identify differentially expressed genes (DEGs) that could not be identified by genotype-based methods; and 2) incorporates both cis- and trans- CpGs, including various regulatory regions to identify DEGs that would be missed using cis-methylation only. Methyl-TWAS outperforms PrediXcan and two other methods in imputing gene expression in the nasal epithelium, particularly for immunity-related genes and DEGs in atopic asthma. Methyl-TWAS identified 3,681 (85.2%) of the 4,316 DEGs identified in a previous TWAS of atopic asthma using measured expression, while PrediXcan could not identify any gene. Methyl-TWAS also outperforms PrediXcan for expression imputation as well as in silico TWAS in white blood cells. Methyl-TWAS is a valuable tool for in silico TWAS, leveraging a growing body of publicly available genome-wide DNA methylation data for a variety of human tissues.

bioinformatics↗

bioRxiv2023

Stomatal maturomics: identifying genes regulating guard cell maturation and function formation from single-cell transcriptomes

Stomata play critical roles in gas exchange and immunity to pathogens. While many genes regulating early stomatal development up to the production of young guard cells (GCs) have been described in Arabidopsis, much less is known about how young GCs develop into mature functional stomata. Here we performed a maturomics study on stomata, with "maturomics" defined as omics analysis of the maturation process of a tissue or organ. We developed an integrative scheme to analyze three public stomata-related single-cell RNA-seq datasets and identified a list of 586 genes that were specifically up-regulated in all three datasets during stomata maturation and function formation. The list, termed sc_586, is enriched with known regulators of stomatal maturation and functions. We selected two candidate G2-like TFs genes, MYS1 and MYS2, from the list to investigate their roles in stomata. Our results showed that these two genes redundantly regulate the size and hoop rigidity of mature GCs, and their double mutations caused mature GCs to have severe defects in regulating their stomatal apertures. Our analysis thus provides a valuable gene list for studying GC maturation and function formation.

plant biology↗

bioRxiv2023

ERas-Null Mice Generated Directly from Embryonic Stem Cells in a Lipid-rich Medium Enable the Discovery of A Novel Role in Craniofacial Development

Generating mice entirely from embryonic stem cells (ESCs) via tetraploid complementation, termed all-ESC mice, is considered the gold standard for pluripotency testing. In this study, we examined the effects of our newly reported lipid-rich 2i/LIF medium (2iLA) on ESCs for genetic engineering. As a proof of principle, we targeted the ERas gene using the 2iLA medium, since ERas-null mice displayed no noticeable phenotype in a previously developed mouse model through chimeras. We demonstrated that the 2iLA medium effectively supports the creation of both male and female ERas-null all-ESC mice, emphasizing the advantages of this culture medium. Unexpectedly, we observed that ERas-null all-ESC mice produced with the 2iLA medium exhibited a non-Mendelian lethal craniofacial anomaly, which can be mitigated by using the lipid-free 2i/LIF medium. Our findings not only highlight the potential of the 2iLA medium for gene targeting but also reveal a novel lipid-associated role of the ERas gene in craniofacial development. Our system offers a unique alternative for studying developmental gene functions unachievable with traditional methods and provides a novel platform for the rapid construction of mouse models. Graphic AbstractAll-ESC pups from wild-type (WT) ESCs cultured in lipid-rich 2iLA medium are normal. In contrast, both male and female ERas-null isogenic all-ESC pups produced from ESCs in 2iLA medium display a non-Mendelian craniofacial anomaly. This phenotype is alleviated when the ESCs are grown in a lipid-free 2iL medium. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=195 SRC="FIGDIR/small/565209v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@c2dd48org.highwire.dtl.DTLVardef@14dbd07org.highwire.dtl.DTLVardef@b54a86org.highwire.dtl.DTLVardef@2fcdd5_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2023

Data-driven optimization yielded a highly-efficient CRISPR/Cas9 system for gene editing in Arabidopsis

The CRISPR/Cas9 technology is widely used for plant gene editing. In Arabidopsis, the early CRISPR/Cas9 systems using constitutive promoters to drive Cas9 expression usually have low heritable mutation efficiencies in the T1 generation. Germ cell-specific or cell division-specific promoters, like EC1.2en-EC1.1p fusion, YAO and CDC45, have been used as alternatives to direct Cas9 expression, but the efficiency of getting nonchimeric mutations is still not high. To further improve gene editing efficiency, we used gene co-expression network analysis to identify NUC1 as a candidate promoter for driving Cas9 expression. NUC1 has expression patterns similar to YAO, but expresses at a much higher level. We constructed a CRISPR/Cas9 system pHY07 that uses the NUC1 promoter to drive Cas9 and carries the mCherry protein as a fluorescent marker for selecting transgenic seeds. Using this system to edit the GL2 gene, we obtained apparently nonchimeric mutations in 55% of the T1 transgenic plants. Among the Cas9-free T2 plants 99% harbored mutations that are stably inherited from the previous generation. Therefore, our system exhibited extremely high editing efficiency, and through fluorescent screening of transgenic seeds, it become easy to obtain Cas9-free and stable genetic mutants in the T2 generation.

plant biology↗

bioRxiv2023

PfAgo-based dual signal amplification biosensor for rapid and highly sensitive detection of alkaline phosphatase activity

Developing rapid and highly sensitive methods for alkaline phosphatase (ALP) activity analysis is significant for the clinical diagnosis and treatment of diseases. Here, a Pyrococcus furiosus Argonaute (PfAgo)-based biosensor is presented for ALP activity detection in which the ALP-catalyzed hydrolysis of 3-phosphate-modified functional DNA activates the strand displacement amplification, and the amplicon -mediates the fluorescent reporter cleavage as a guide sequence of PfAgo. Under the dual amplification mode of PfAgo-catalyzed multiple-turnover cleavage activity and pre-amplification technology, the developed method was successfully applied in ALP activity analysis with a detection limit (LOD) of 0.0013 U L-1 (3{sigma}) and a detection range of 0.0025 U L-1 to 1 U L-1 within 90 min. The PfAgo-based method exhibits satisfactory analytic performance in the presence of the potential interferents and in complex human serum samples. The proposed method shows several advantages, such as rapid, highly sensitive, low-cost, and easy operation, and has great potential in disease evolution fundamental studies and clinical diagnosis applications.

biochemistry↗

bioRxiv2023

High red/far-red ratio promotes root colonization of Serratia plymuthica A21-4 in tomato by root exudates-stimulated chemotaxis and biofilm formation

Effective colonization on plant roots is a prerequisite for plant growth promoting rhizobacterias (PGPR) to exert beneficial activities. Light is essential for plant growth, development and stress response. However, how light modulates root colonization of PGPR remains unclear. Here, we found that high red/far red(R/FR) light promoted and low R/FR light inhibited the colonization and growth enhancement of Serratia plymuthica A21-4 on tomato. Non-targeted metabolomic analysis of root exudates collected from different R/FR ratio treated tomato seedlings with A21-4 inoculation by ultra performance liquid chromatography-tandem mass spectrometry showed that 64 primary metabolites including amino acids, sugars and organic acids in high R/FR light-grown plants significantly increased compared with those determined for low R/FR light-grown plants. Among them, 7 amino acids, 1 organic acid and 1 sugar obviously induced the chemotaxis and biofilm formation of A21-4 compared to the control. Furthermore, exogenous addition of five artificial root exudate compontents (leucine, methionine, glutamine, 6-aminocaproic acid and melezitose) regained and further increased the colonization and growth promoting ability of A21-4 in tomato under low R/FR light and high R/FR light, respectively, indicating their involvement in high R/FR light-regulated the interaction of tomato root and A21-4. Taken together, our results, for the first time, clearly demonstrate that high R/FR light-induced root exudates play a key role in chemotaxis, biofilm formation and root colonization of A21-4. This study provides new insights into the interactions of plant-PGPR under different light conditions and can help promote the combined application of light supplementation and PGPR to facilitate crop growth and health in green agricultural production.

microbiology↗

bioRxiv2023

Cryo-EM structure of TMEM63C suggests it functions as a monomer

The TMEM63 family proteins (A, B, and C), calcium-permeable channels in animals that are preferentially activated by hypo-osmolality, have been implicated in various physiological functions. Deficiency of these channels would cause many diseases including hearing loss. However, their structures and physiological roles are not yet well understood. In this study, we determined the cryo-EM structure of the mouse TMEM63C at 3.56 [A], and revealed structural differences compared to its plant orthologues OSCAs. Further structural guided mutagenesis and electrophysiological studies demonstrated the important roles of the coupling of TM0 and TM6 in channel activity. Additionally, we confirmed that the physiological state of TMEM63C is monomer, while TMEM63B is a mix of monomer and dimer in cells, suggesting that oligomerization is a novel regulatory mechanism for TMEM63 proteins.

biophysics↗

bioRxiv2023

Participant-derived cell line transcriptomic analyses and mouse studies reveal a role for ZNF335 in plasma cholesterol statin response

BackgroundStatins lower circulating low-density lipoprotein cholesterol (LDLC) levels and reduce cardiovascular disease risk. Though highly efficacious in general, there is considerable inter-individual variation in statin efficacy that remains largely unexplained. MethodsTo identify novel genes that may modulate statin-induced LDLC lowering, we used RNA-sequencing data from 426 control- and 2 M simvastatin-treated lymphoblastoid cell lines (LCLs) derived from European and African American ancestry participants of the Cholesterol and Pharmacogenetics (CAP) 40 mg/day 6-week simvastatin clinical trial (ClinicalTrials.gov Identifier: NCT00451828). We correlated statin-induced changes in LCL gene expression with plasma LDLC statin response in the corresponding CAP participants. For the most correlated gene identified (ZNF335), we followed up in vivo by comparing plasma cholesterol levels, lipoprotein profiles, and lipid statin response between wild-type mice and carriers of a hypomorphic (partial loss of function) missense mutation in Zfp335 (the mouse homolog of ZNF335). ResultsThe statin-induced expression changes of 147 human LCL genes were significantly correlated to the plasma LDLC statin responses of the corresponding CAP participants in vivo (FDR=5%). The two genes with the strongest correlations were zinc finger protein 335 (ZNF335 aka NIF-1, rho=0.237, FDR-adj p=0.0085) and CCR4-NOT transcription complex subunit 3 (CNOT3, rho=0.233, FDR-adj p=0.0085). Chow-fed mice carrying a hypomorphic missense (R1092W; aka bloto) mutation in Zfp335 had significantly lower non-HDL cholesterol levels than wild type C57BL/6J mice in a sex combined model (p=0.04). Furthermore, male (but not female) mice carrying the Zfp335R1092W allele had significantly lower total and HDL cholesterol levels than wild-type mice. In a separate experiment, wild-type mice fed a control diet for 4 weeks and a matched simvastatin diet for an additional 4 weeks had significant statin-induced reductions in non-HDLC (-43{+/-}18% and -23{+/-}19% for males and females, respectively). Wild-type male (but not female) mice experienced significant reductions in plasma LDL particle concentrations, while male mice carrying Zfp335R1092W allele(s) exhibited a significantly blunted LDL statin response. ConclusionsOur in vitro and in vivo studies identified ZNF335 as a novel modulator of plasma cholesterol levels and statin response, suggesting that variation in ZNF335 activity could contribute to inter-individual differences in statin clinical efficacy.

genomics↗

bioRxiv2023

RAPSYN-Mediated Neddylation of BCR-ABL Alternatively Determines the Fate of Philadelphia Chromosome-positive Leukemia

Philadelphia chromosome-positive (Ph+) leukemia is a fatal hematological malignancy. Although standard treatments with tyrosine kinase inhibitors (TKI) have achieved remarkable success in prolonging patient survival, intolerance, relapse and TKI resistance remain serious issues for patients with Ph+ leukemia. Here, we report a new leukemogenic process in which RAPSYN and BCR-ABL co-occur in Ph+ leukemia, and RAPSYN mediates the neddylation of BCR-ABL. Consequently, neddylated BCR-ABL enhances the stability by competing its c-CBL-mediated degradation. Furthermore, SRC phosphorylates RAPSYN to activate its NEDD8 E3 ligase activity, promoting BCR-ABL stabilization and disease progression. Moreover, in contrast to in vivo ineffectiveness of PROTAC-based degraders, depletion of RAPSYN expression or its ligase activity decreased BCR-ABL stability and, in turn, inhibited tumor formation and growth. Collectively, these findings represent an alternative to tyrosine kinase activity for the oncoprotein and leukemogenic cells and generate a rationale of targeting RAPSYN-mediated BCR-ABL neddylation for the treatment of Ph+ leukemia.

cancer biology↗