Biology subjects

Zhu, C.

Publications and source records attributed to Zhu, C..

At least 109 records · Page 6Linked to original sources

bioRxiv2024

Local optogenetic NMYII activation within the zebrafish neural rod results in long-range, asymmetric force propagation

How do cellular forces propagate through tissue to allow large-scale morphogenetic events? To investigate this question, we used an in vivo optogenetic approach to reversibly manipulate actomyosin contractility at depth within the developing zebrafish neural rod. Contractility was induced along the lateral cortices of a small patch of developing neural epithelial progenitor cells, resulting in a shortening of these cells along their mediolateral axis. Imaging the immediate response of surrounding tissue uncovered a long-range, tangential, and elastic tissue deformation along the anterior-posterior axis. Unexpectedly, this was highly asymmetric, propagating in either the anterior or the posterior direction in response to local gradients in optogenetic activation. The degree of epithelialisation did not have a significant impact on the extent of force propagation via lateral cortices. We also uncovered a dynamic oscillatory expansion and contraction of the tissue along the anterior-posterior axis, with wavelength within the range of rhombomere length. Together, this study shows dynamic and wave-like propagation of force along the anterior-posterior axis. It also suggests that cell generated forces are actively propagated over long distances within the tissue, and that local anisotropies in tissue organisation and contractility are sufficient to drive directional force propagation.

developmental biology↗

bioRxiv2024

Precision-dependent modulation of social attention

Social attention, guided by cues like gaze direction, is crucial for effective social interactions. However, how dynamic environmental context modulates this process remains unclear. Integrating a hierarchical Bayesian model with fMRI, this study investigated how individuals adjusted attention based on the predictions about cue validity (CV). Thirty-three participants performed a modified Posner location-cueing task with varying CV. Behaviorally, individuals allocation of social attention was finely tuned to the precision (inverse variance) of CV predictions, with the predictions being updated by precision-weighted prediction errors (PEs) about the occurrence of target locations. Neuroimaging results revealed that the interaction between allocation of social attention and CV influenced activity in regions involved in spatial attention and/or social perception, such as the temporoparietal junction (TPJ), frontal eye field (FEF), superior temporal sulcus (STS), and inferior parietal sulcus (IPS). Precision-weighted PEs about target locations specifically modulated activity in the TPJ, STS, and primary visual cortex (V1), underscoring their roles in refining attentional predictions. Dynamic causal modeling (DCM) further demonstrated that enhanced absolute precision-weighted PEs about target locations strengthened the effective connectivity from V1 and STS to TPJ, emphasizing their roles in conveying residual error signals from low-level sensory areas to high-level critical attention areas. These findings elucidated how the precision of contextual predictions dynamically modulated social attention, offering insights into the computational and neurocognitive mechanisms of context-dependent social attention.

neuroscience↗

bioRxiv2024

Metapipeline-DNA: A Comprehensive Germline & Somatic Genomics Nextflow Pipeline

SummaryThe price, quality and throughout of DNA sequencing continue to improve. Algorithmic innovations have allowed inference of a growing range of features from DNA sequencing data, quantifying nuclear, mitochondrial and evolutionary aspects of both germline and somatic genomes. To automate analyses of the full range of genomic characteristics, we created an extensible Nextflow meta-pipeline called metapipeline-DNA. Metapipeline-DNA analyzes targeted and whole-genome sequencing data from raw reads through pre-processing, feature detection by multiple algorithms, quality-control and data- visualization. Each step can be run independently and is supported robust software engineering including automated failure-recovery, robust testing and consistent verifications of inputs, outputs and parameters. Metapipeline-DNA is cloud-compatible and highly configurable, with options to subset and optimize each analysis. Metapipeline-DNA facilitates high-scale, comprehensive analysis of DNA sequencing data. AvailabilityMetapipeline-DNA is an open-source Nextflow pipeline under the GPLv2 license and is available at https://github.com/uclahs-cds/metapipeline-DNA.

bioinformatics↗

bioRxiv2024

Potent LILRB1 D1D2-containing antibodies inhibit RIFIN-mediated immune evasions

The spread of drug-resistant malaria parasites presents a major challenge to global efforts in malaria control, increasing the urgency for new treatments and vaccines. A promising approach involves developing antibodies that can counteract the parasites immune evasion mechanisms. In this study, we designed a receptor-containing antibody, targeting the D1D2 domain of the LILRB1 receptor, using a structure-based rational approach. We began with the MDB1 antibody as a scaffold and replaced the LILRB1-D3D4 insertion domain with D1D2.v, a high-affinity variant optimized through yeast surface display. The modified D1D2.v-IgG efficiently blocked the interaction between RIFIN#1 (from PF3D7_1254800) and LILRB1, thereby reversing the inhibition of NK cell activity caused by RIFIN#1. To further enhance this effect, we developed NK-biAb, a bispecific antibody based on D1D2.v-IgG that targets both RIFIN#1 and NKG2D receptors. NK-biAb exhibited superior biological performance compared to D1D2.v-IgG alone. These findings provide a clear framework for designing antibodies that target immune evasion in malaria, potentially guiding the development of more effective treatments and vaccines.

biochemistry↗

bioRxiv2024

Successive pattern in winter wheat main stem structure modeling

1.With the rise of research on functional structural plant models (FSPMs), it is particularly important to realistically describe the structural traits of a plant. In 3D FSPMs, the true structural information of the canopy can make the models estimation of functional traits more accurate. Since canopy is the medium of the crop stands that sense and respond to the external environment, accurate estimation of detailed organ sizes in crop canopy is crucial, and current FSPMs still need to be improved. Here the structure of wheat (Triticum aestivum) was measured in detail at the phytomer level. Dataset was built which covers a set of [~]100 cultivars and 11 site-year under various field managements such as sowing density, inter-row, nitrogen fertilizer and sowing date. The relationships of successive phytomer sizes were quantified and the variance was analyzed for each independent experiment, only site was found as a significant impact factor. A conceptual model based on the successive pattern was proposed and validated for detailed final phytomer sizes. Then we coupled the meteorology data - the ratio of average daily gross radiation and temperature during the emergence and architecture mature with the model. The validation has taken place three times to emphasize models independent of cultivars, sites dependent and the ability of model parameters deriving from environmental factors, respectively. The results revealed the feasibility of the newly built wheat main stem structure model with the R2 higher than 0.85. Compared with ADEL-Wheat and Sirius Quality, the model achieved better performance in blade width and blade area estimation. According to the concise and easily acquired parameters of this model, it has potential for high throughput phenotyping detail wheat canopy structure. Previous work on the relationship between blade width and circumference of apex shoot in maize illustrated that the cell number was the most likely explanation for this pattern, which means the same work holds for similar crops.

developmental biology↗

bioRxiv2024

Vortex light field microscopy: 3D spectral single-molecule imaging with a twist

We introduce vortex light field microscopy (VLFM), a novel method for snapshot 3D spectral single-molecule localization microscopy. Inspired by the azimuthal phase profile of optical vortices, we place an azimuthally oriented prism array immediately after the microlens array in a Fourier light field microscope (FLFM). This innovative arrangement causes the axial position and spectral peak for a point emitter to be encoded in the radial and azimuthal displacement of point-spread-function (PSF) respectively. This enables simultaneous detection of 3D position and emission peak of individual fluorophores with 25 nm spatial precision and 3 nm spectral precision over a 4 m depth of field (DOF). We illustrate the spectral scalability of our method by performing four-color 3D single particle tracking of freely diffusing fluorescent beads, and two-color 3D dSTORM imaging of microtubules and mitochondria in fixed COS-7 cells, without the need for spectrally distinct fluorophores.

biophysics↗

bioRxiv2024

Origin and stepwise improvement of vertebrate lungs

Lungs, essential for terrestrial vertebrates and present in bony fishes but absent in cartilaginous fishes, provide an ideal model for studying organ origination. Our study analyzed single-cell RNA sequencing data from mature and developing vertebrate lungs, revealing substantial similarities in cell composition, developmental trajectories and gene expression pattern across species. Notably, most lung-related genes are also present in cartilaginous fishes, indicating that gene presence alone does not guarantee lung development. We identified thousands of lung regulatory elements specific to bony fishes, with higher concentrations around genes such as tbx4 and the hoxb gene cluster. These regulatory changes might contribute to lung emergence as well as the unique co-expression patterns in lung epithelial cells, such as those related to pulmonary surfactants and cell morphology. Our research also revealed that AT1 cells are specific to mammals, and we identified a mammal-specific gene, sfta2. Knockout experiments demonstrated that sfta2 deletion causes severe respiratory defects in mice, underscoring its critical role in specialized mammalian lungs. In conclusion, our results demonstrate that the origin and evolution of lungs are driven by a complex interplay of regulatory network modifications and the emergence of new genes, underscoring the multifaceted nature of organ evolution.

evolutionary biology↗

bioRxiv2024

Peri-centrosomal localization of small interfering RNAs in C. elegans

The centrosome is the microtubule-organizing center and a crucial part of cell division. Centrosomal RNAs (cnRNAs) have been reported to enable precise spatiotemporal control of gene expression during cell division in many species. Whether and how cnRNAs exist in C. elegans are unclear. Here, using the nuclear RNAi Argonaute protein NRDE-3 as a reporter, we observed potential peri-centrosome localized small interfering (si)RNAs in C. elegans. NRDE-3 was previously shown to associate with pre-mRNAs and pre-rRNAs via a process involving the presence of complementary siRNAs. We generated a GFP-NRDE-3 knock-in transgene through CRISPR/Cas9 technology and observed that NRDE-3 formed peri-centrosomal foci neighboring the tubulin protein TBB-2, other centriole proteins and pericentriolar material (PCM) components in C. elegans embryos. The peri-centrosomal accumulation of NRDE-3 depends on RNA-dependent RNA polymerase (RdRP)-synthesized 22G siRNAs and the PAZ domain of NRDE-3, which is essential for siRNA binding. Mutation of eri-1, ergo-1, or drh-3 significantly increased the percentage of pericentrosome-enriched NRDE-3. At the metaphase of the cell cycle, NRDE-3 was enriched in both the peri-centrosomal region and the spindle. Moreover, the integrity of centriole proteins and pericentriolar material (PCM) components is also required for the peri-centrosomal accumulation of NRDE-3. Therefore, we concluded that siRNAs could accumulate in the peri-centrosomal region in C. elegans and suggested that the peri-centrosomal region may also be a platform for RNAi-mediated gene regulation.

genetics↗

bioRxiv2024

An Artificial Intelligence Model for Profiling the Landscape of Antigen-binding Affinities of Massive BCR Sequencing Data

The interaction between antigens and antibodies (B cell receptors, BCRs) is the key step underlying the function of the humoral immune system in cancers and other biological contexts. The capability to profile the landscape of antigen-binding affinities of a vast number of BCRs will provide a powerful tool to reveal novel insights at unprecedented levels and will yield powerful tools for translational development. However, current experimental approaches for detecting antibody-antigen interactions are costly and time-consuming, and can only achieve low-to-mid throughput. On the other hand, bioinformatics tools in the field of antibody informatics mostly focus on optimization of antibodies given known binding antigens, which is a very different research question and of limited scope. In this work, we developed an innovative Artificial Intelligence tool, Cmai, to address the prediction of binding between antibodies and antigens that can be scaled to high-throughput sequencing data. We devised a biomarker metric based on the output from Cmai applied to high-throughput BCR sequencing data to predict the landscape of the antigen-binding affinities of the BCRs. We found that extracellular antigens on malignant tumor cells are inducing B cell infiltrations, and the infiltrating B cells have a greater tendency to co-localize with tumor cells expressing these antigens. We further found that the abundance of tumor antigen-targeting antibodies is predictive of immune-checkpoint inhibitor (ICI) treatment response. On the other hand, we found that, during immune-related adverse events (irAEs) caused by ICI treatment, humoral immunity is preferentially responsive to intracellular antigens from the organs affected by the irAEs. Overall, we developed a powerful tool for elucidating the antigen binding landscape of BCR repertoires, and it shall also propell antibody-centric translational applications for cancers and other diseases.

immunology↗

bioRxiv2024

The UPRER governs the cell-specific response of human dopaminergic neurons to mitochondrial stress

Mitochondrial dysfunction is thought to be central to the pathophysiology of Parkinsons disease. The preferential vulnerability of dopaminergic (DA) neurons of the substantia nigra pars compacta to mitochondrial stress may underlie their massive degeneration and the occurrence of motor symptoms. Using LUHMES-derived DA neurons, we demonstrated that inhibition of the mitochondrial electron transport chain resulted in a severe alteration of mitochondrial turnover, pushing the balance towards mitochondrial loss, a reduction of the maturation status of the DA population and an increased proportion of apoptotic cells. PERK-mediated Unfolded Protein Response of the Endoplasmic Reticulum (UPRER) emerged as the key coordinator of the stress response, governing the inactivation of the mitochondrial UPR (UPRmt), the initiation of mitophagy and the cell-specific expression of long non-coding RNAs (lncRNAs). Importantly, we discovered novel lncRNAs specifically expressed in human DA neurons upon stress. Among them, we showed that lnc-SLC6A15-5 contributes to the resumption of translation after mitochondrial stress. SummaryThe Unfolded Protein Response of the Endoplasmic Reticulum is induced upon stress in human dopaminergic neurons and modulates mitochondrial homeostasis and transcriptional programs including expression of long non-coding RNAs (lncRNAs). We discovered a lncRNA involved in translation resumption after stress.

neuroscience↗

bioRxiv2024

Transcranial Brain Atlas Based on Photon Measurement Density Function in a Triple-Parameter Standard Channel Space

Functional near-infrared spectroscopy (fNIRS) is a widely used transcranial brain imaging technique in neuroscience research. Nevertheless, its lack of anatomical information poses challenges for designing appropriate optode montage and localizing fNIRS signals to underlying anatomical regions. The photon measurement density function (PMDF) is often employed to address these issues, as it accurately measures the sensitivity of a fNIRS signal channel to perturbations of absorption coefficients at any brain locations. However, existing PMDF-based localization methods have two limitations: a limited channel space, and PMDF estimation based on single standard head models, which differ anatomically from individual subjects. To overcome these limitations, this study proposes a continuous fNIRS standard channel space and constructs a PMDF-based transcranial brain atlas (PMDF-TBA) by calculating PMDFs based on MRI images of 48 adults. PMDF-TBA contains group-averaged sensitivities of channels to gray matter and brain regions of atlases, such as Brodmann, AAL2, and LPBA40. Through leave-one-out cross-validation, we evaluated the prediction ability of PMDF-TBA for sensitivity of unseen individuals and found that it outperformed PMDFs based on single standard head models. Thus, PMDF-TBA serves as a more generalizable fNIRS spatial localization tool. Therefore, PMDF-TBA can be utilized to optimize optode montage design, improve channel sensitivity to target brain regions, and assist in the source localization of fNIRS data, thereby promoting the application of fNIRS in neuroscience research.

neuroscience↗

bioRxiv2024

HIF1α controls adipose tissue growth through metabolic rechanneling

Excessive expansion of white adipose tissue occurs when energy intake exceeds demand. It creates a state of relative hypoxia that is directly linked to activation of the hypoxia-inducible factor (HIF) in obese human subjects and mouse models of obesity. Whether HIF1 function is important for the development of basal adiposity and diet-induced obesity remains unclear. In the present study, we genetically ablated Hif1 in adipocytes and analyzed the corresponding mice for both basal and diet-induced obesity-associated visceral white adipose tissue mass as well as parameters of systemic glucose homeostasis and peripheral insulin sensitivity. We found that inactivation of Hif1 in mouse adipocytes inhibited basal adiposity and suppressed nutrient-overload-induced adipose tissue growth. These changes in adiposity were associated with improved systemic glucose homeostasis and peripheral insulin sensitivity. Mechanistically, Hif1 mediated effects on adipocyte metabolism by re-routing glycolytic intermediates into the glycerolipid shunt, leading to increased de novo triacylglyceride synthesis in hypertrophic adipocytes. Our results have established key roles for HIif1 in controlling adipocyte growth and metabolism and adipose tissue expansion under basal conditions and in response to a high-fat diet, highlighting the central role of hypoxia and HIF1 in the development of obesity. Article HighlightsO_LIHif1 function is critical for basal adipose tissue mass expansion, and is also required for fat accumulation in response to high fat diet. C_LIO_LICo-option and co-activation of the glycerolipid biosynthetic pathway by glycolysis is an important modulator of visceral adiposity. C_LIO_LIThese findings reveal an important role of Hif1 in the adipose tissue through the coupling of glycolysis and lipid anabolism in response to HFD, which may provide a potential therapeutic target for type 2 diabetes in the future. C_LI

cell biology↗

bioRxiv2024

The dual resistance mechanism of CYP325G4 and CYP6AA9 in Culex pipiens pallens legs according to transcriptome and proteome analysis

Mosquitoes within the Culex pipiens complex play a crucial role in human disease transmission. Insecticides, especially pyrethroids, are used to control these vectors. Mosquito legs are the main entry point and barrier for insecticides to gain their neuronal targets. However, the resistance mechanism in mosquito legs is unclear. Herein, we employed transcriptomic analyses and isobaric tags for relative and absolute quantitation techniques to investigate the resistance mechanism, focusing on Cx. pipiens legs. We discovered 2346 differentially expressed genes (DEGs) between deltamethrin-resistant (DR) and deltamethrin-sensitive (DS) mosquito legs, including 41 cytochrome P450 genes. In the same comparison, we identified 228 differentially expressed proteins (DEPs), including six cytochrome P450 proteins). Combined transcriptome and proteome analysis revealed only two upregulated P450 genes, CYP325G4 and CYP6AA9. The main clusters of DEGs and DEPs were associated with metabolic processes, such as cytochrome P450-mediated metabolism of drugs and xenobiotics. Transcription analysis revealed high CYP325G4 and CYP6AA9 expression in the DR strain at 72 hours post-eclosion compared with that in the DS strain, particularly in the legs. Mosquitoes knocked down for CYP325G4 were more sensitive to deltamethrin than the controls. CYP325G4 knockdown reduced the expression of several chlorinated hydrocarbon (CHC)-related genes, which altered the cuticle thickness and structure. Conversely, CYP6AA9 knockdown increased CHC gene expression without altering cuticle thickness and structure. P450 activity analysis demonstrated that CYP325G4 and CYP6AA9 contributed to metabolic resistance in the midgut and legs. This study identified CYP325G4 as a novel mosquito deltamethrin resistance factor, being involved in both metabolic and cuticular resistance mechanisms. The previously identified CYP6AA9 was investigated for its involvement in metabolic resistance and potential cuticular resistance in mosquito legs. These findings enhance our comprehension of resistance mechanisms, identifying P450s as promising targets for the future management of mosquito vector resistance, and laying a theoretical groundwork for mosquito resistance management. Author SummaryCulex pipiens mosquitoes are the primary vector of the filamentous nematode, Wuchereria bancrofti and also involved in the transmission of other pathogens, such as West Nile virus (WNV), avian malarias, and avian pox virus. Insecticides, particularly pyrethroids, continue to be the primary method to control these significant vectors. Worryingly, resistance to insecticides has become widespread and is rapidly intensifying in Culex mosquitoes throughout China, posing a threat to the efficacy of insecticides. Legs are the main sites of contact with ITNs and sprayed insecticides, and the insecticides have to penetrate the leg cuticle to reach their targets.Therefore, the resistance mechanisms in mosquito legs deserve further investigation. Several reports have found a certain amount of P450 in insect legs. Unfortunately, none of the above reports have conducted further functional studies on P450s in the legs. Here, we have identified two P450 enzymes, CYP325G4 and CYP6AA9, through the integrated analysis of transcriptomics and proteomics. CYP325G4 enriched in the cuticle of resistant mosquitoes might possess a dual resistance mechanism involving metabolic resistance and cuticle resistance. CYP6AA9 was slightly different, possibly exerting metabolic resistance as its main function and also being involved in cuticle synthesis. Understanding the dual resistance mechanism of P450s in the metabolism of pyrethroid insecticides will have an important role in optimizing vector control strategies.

physiology↗

bioRxiv2024

Deconvolution of polygenic risk score in single cells unravels cellular and molecular heterogeneity of complex human diseases

Polygenic risk scores (PRSs) are commonly used for predicting an individuals genetic risk of complex diseases. Yet, their implication for disease pathogenesis remains largely limited. Here, we introduce scPRS, a geometric deep learning model that constructs single-cell-resolved PRS leveraging reference single-cell chromatin accessibility profiling data to enhance biological discovery as well as disease prediction. Real-world applications across multiple complex diseases, including type 2 diabetes (T2D), hypertrophic cardiomyopathy (HCM), and Alzheimers disease (AD), showcase the superior prediction power of scPRS compared to traditional PRS methods. Importantly, scPRS not only predicts disease risk but also uncovers disease-relevant cells, such as hormone-high alpha and beta cells for T2D, cardiomyocytes and pericytes for HCM, and astrocytes, microglia and oligodendrocyte progenitor cells for AD. Facilitated by a layered multi-omic analysis, scPRS further identifies cell-type-specific genetic underpinnings, linking disease-associated genetic variants to gene regulation within corresponding cell types. We substantiate the disease relevance of scPRS-prioritized HCM genes and demonstrate that the suppression of these genes in HCM cardiomyocytes is rescued by Mavacamten treatment. Additionally, we establish a novel microglia-specific regulatory relationship between the AD risk variant rs7922621 and its target genes ANXA11 and TSPAN14. We further illustrate the detrimental effects of suppressing these two genes on microglia phagocytosis. Our work provides a multi-tasking, interpretable framework for precise disease prediction and systematic investigation of the genetic, cellular, and molecular basis of complex diseases, laying the methodological foundation for single-cell genetics.

genetics↗

bioRxiv2024

Successful Gene Editing of Apolipoprotein E4 to E3 in Brain of Alzheimer Model MiceAfter a Single IV Dose of Synthetic Exosome-Delivered CRISPR

BackgroundThe gene for apolipoprotein E4 (ApoE4 E4) confers an increased risk for development and lowers the age of onset of Alzheimers disease (AD), and is a highly suitable target for CRISPR-based editing because ApoE4 differs from ApoE3 by a single nucleotide polymorphism in the codon for residue 112 that codes for arginine (CGC) in E4 and cysteine (TGC) in E3. Editing of E4 to E3 could lower the risk of AD or ameliorate E4-related AD phenotypes. For AD, in order to deliver CRISPR components across the blood-brain barrier to the brain, we have developed a delivery platform termed Synthetic Exosomes (SEs) - microfluidically-synthesized deformable nanovesicles approximately the size of natural exosomes that have the ability to cross the BBB and deliver cargo to the brain. Here, we describe our use of SEs carrying CRISPR to successfully edit E4 to E3 in brain tissue of an E4-expressing mouse model. MethodsSeveral CRISPR guide RNAs (gRNA) and Cytosine Base Editor (CBE) mRNAs were synthesized by chemical and in vitro transcription syntheses, respectively. Four combinations of gRNA and CBE mRNA were tested in vitro for their relative activity to edit the E4 (cytosine) to E3 (thymine) in E4-expressing neuroblastoma (E4-N2A) and human Kelly neuroblastoma cells, to assess which combination produced the highest E4 to E3 base editing efficiency. The CRISPR RNA combination with the highest efficiency was encapsulated in SEs and injected intravenously (IV) via the tail vein into an AD model E4-expressing (E4-5XFAD) transgenic mouse; as a negative control, an E4-5XFAD mouse was injected with empty SEs. Five days after injection, mice were euthanized and brain, liver, and buffy coat (white blood cells (WBC)) collected to determine the editing of E4 to E3 measured by Next Generation Sequencing. In addition, E3 mRNA was measured in the brain and liver and compared to the %E3 gene editing. ResultsThe highest gRNA+CBE mRNA editing efficiency was [~]50% in E4-N2A cells and the same gRNA+CBE combination delivered in SEs to Kelly neuroblastoma cells showed 6.5% editing efficiency. In the E4-5XFAD mouse in vivo, five days after IV delivery of a single dose of the highest-activity SE-CRISPR gRNA+CBE mRNA, the percent of E4 edited to E3 was 0.14% in brain, 0.8% in liver, and 0.36% in WBCs. As evidence of functional editing, SE-CRISPR-treated mice had 0.03% E3 mRNA in brain and 0.09% E3 mRNA in liver. ConclusionsWhile this level of ApoE4 to E3 editing achieved five days after a single IV injection of SE-CRISPR is small, it provides initial in vivo proof-of-concept that the ApoE4 gene can be successfully edited, and editing results in functional expression of ApoE3 mRNA. The findings presented herein supports further optimization of the SE-CRISPR approach to increase the level of editing in brain as part of clinical development of SE-CRISPR as a powerful novel therapeutic approach for AD.

neuroscience↗

bioRxiv2024

Loss of VHL-mediated pRb regulation promotes clear cell renal cell carcinoma

The von Hippel-Lindau (VHL) tumor suppressor is a component of E3 ubiquitin ligase complexes that target cellular substrates for proteasome-mediated degradation. VHL inactivation by genetic aberrations is observed in most sporadic cases of clear cell renal cell carcinoma (ccRCC). VHL loss leads to constitutive stabilization of E3 ligase targets, including hypoxia inducible factor (HIF), in VHL-associated tumors. HIF stabilization upon VHL loss promotes transactivation of hypoxia responsive genes, which contributes to ccRCC development. However, several HIF-independent VHL targets have also been implicated in the promotion of tumorigenesis. Using proximity labeling to identify proteasomal VHL interactors, we identified retinoblastoma protein (pRb) as a novel substrate of VHL. Mechanistically, VHL interacts with pRb in an oxygen-sensitive manner, promoting its ubiquitin-mediated degradation. Concordantly, VHL-inactivation results in pRb hyperstabilization. Functionally, the hyperstabilization of pRb in ccRCC promoted tumorigenesis in vitro and in mouse models. We also show that downstream transcriptional changes induced by pRb hyperstabilization may contribute to ccRCC tumor development. Together, our findings reveal a novel VHL-related pathway which can be therapeutically targeted to inhibit ccRCC tumor development.

cancer biology↗

bioRxiv2024

moPepGen: Rapid and Comprehensive Proteoform Identification

Proteogenomics is limited by challenges of modeling the complexities of gene expression. We create moPepGen, a graph-based algorithm that comprehensively generates non-canonical peptides in linear time. moPepGen works with multiple technologies, in multiple species and on all types of genetic and transcriptomic data. In human cancer proteomes, it enumerates previously unobservable noncanonical peptides arising from germline and somatic genomic variants, noncoding open reading frames, RNA fusions and RNA circularization.

bioinformatics↗

bioRxiv2024

Exploring the repository of de novo designed bifunctional antimicrobial peptides through deep learning

Antimicrobial peptides (AMPs) are attractive candidates to combat antibiotic resistance for their capability to target bio-membranes and restrict a wide range of pathogens. It is a daunting challenge to discover novel AMPs due to their sparse distributions in a vast peptide universe, especially for peptides that demonstrate potencies for both bacterial membranes and viral envelopes. Here we establish a de novo AMP design framework by bridging a deep generative module and a graph-encoding activity regressor. The generative module learns hidden grammars of AMP features and produces candidates sequentially pass antimicrobial predictor and antiviral classifiers. We discover 16 bifunctional AMPs and experimentally validated their abilities to inhibit a spectrum of pathogens in vitro and in animal models. Notably, P076 is a highly potent bactericide with the minimal inhibitory concentration of 0.21 M against multidrug-resistant A. baumannii, while P002 broadly inhibits five enveloped viruses. Our study provides feasible means to uncover sequences that simultaneously encode antimicrobial and antiviral activities, thus bolstering the function spectra of AMPs to combat a wide range of drug-resistant infections.

microbiology↗