Biology subjects

Zhang, M.

Publications and source records attributed to Zhang, M..

At least 271 records · Page 15Linked to original sources

bioRxiv2024

Molecular mechanisms of dynamics-mediated effects of pathogenic missense mutations on Menin protein function

Understanding how disease-causing missense mutations (DCMMs) affect protein function is fundamental. The traditional structure-function paradigm for proteins has evolved into a structure-dynamics-function model, as dynamics is increasingly recognized as a key regulator of protein function. Consequently, it is essential to incorporate dynamics into the once heavily emphasized structure-function framework to explain the effects of DCMMs. Although research in this area is emerging, evidence supporting a definitive role of dynamics in mediating DCMM effects on protein function remains limited. In this study, we used Menin--a mutation-prone scaffold protein involved in various pathologies--as a model system to explore how DCMMs affect Menins function. By performing molecular dynamics (MD) simulations on 24 clinically confirmed DCMMs, we showed that DCMMs do not necessarily destabilize protein stability. Instead, they induce similar dynamic changes in the protein. The consequences of DCMMs on Menins function were further assessed through umbrella sampling of the Menin-JunD protein protein interaction (PPI). We found that DCMMs attenuate this interaction and disrupt a highly conserved JunD dissociation pathway in wild-type (WT) Menin. The underlying mechanism was revealed through allosteric analysis, which showed that, despite being located far from the JunD binding site, DCMMs uniformly disturbed the coupling between residue E179 and the binding pocket. Additionally, forced maintenance of E197-pocket coupling restored the impaired Menin-JunD PPI in DCMMs. Together, these data demonstrate that DCMMs alter Menins function through dynamics, with allostery playing a crucial role. This study further supports the incorporation of dynamics into the traditional "structure-function" diagram to better explain the effects of DCMMs.

biophysics↗

bioRxiv2024

A Palette of Bridged Bicycle-Strengthened Fluorophores

Organic fluorophores are the keystone of advanced biological imaging. The vast chemical space of fluorophores has been extensively explored in seek of molecules with ideal properties. However, within the current molecular constraints, there appears to be a trade-off between high brightness, robust photostability, and tunable biochemical properties. Herein we report a general strategy to systematically boost the performance of donor-acceptor-type fluorophores by leveraging SO2 and O-substituted azabicyclo[3.2.1] octane auxochromes. These bicyclic heterocycles give rise to a collection of Bridged dyes (BD) spanning the UV and visible range with top-notch quantum efficiencies, enhanced water solubility, and tunable cell-permeability. Notably, these azabicyclic fluorophores showed remarkable photostability than its tetramethyl or azatidine analogue, at the same time completely resistant to oxidative photobluing rendered by the Bredts rule. Functionalized BD dyes are tailored for applications in single-molecule imaging, super-resolution imaging (STED and SIM) in fixed or live mammalian cells and plant cells, and live zebrafish imaging or chemigenetic voltage imaging. Synergizing with advanced imaging methods, the bridge bicycle dyes represent a versatile palette for biological researches.

biophysics↗

bioRxiv2024

Telomere-to-Telomere Genome Assembly Uncovers Wolbachia-Driven Sex-Specific Demography and Challenges Fisher's Principle in a Sawfly

Wolbachia, a widespread endosymbiotic bacterium, can reshape the evolutionary fates of its insect hosts by distorting reproduction and altering population dynamics. Despite extensive laboratory research, its long-term effects on host evolution in nature remain poorly understood, particularly regarding genetic mechanisms underlying changes in sex determination and reproduction. Here, we report the first telomere-to-telomere (T2T) genome assembly of the sawfly Analcellicampa danfengensis and the complete genome of it symbiotic Wolbachia. Comparative population genomics of six closely related Analcellicampa species revealed that Wolbachia-infected populations experience marked changes in sex-specific demography. While uninfected species maintain balanced genetic features between males and females, infected species show a persistent reduction in male effective population size alongside a stable or even growing female population, ultimately driving males toward extinction. Genomic scans identified positively selected genes associated with reproductive functions, sensory perception, neural development, and longevity, suggesting that Wolbachia manipulates critical host biological pathways to promote its transmission. These findings provide direct genomic evidence that Wolbachia acts as a powerful evolutionary force, reshaping host genomes in a way that disrupts Fishers principle, ultimately driving female-biased demography and the extinction of males at evolutionary timescales. This work provides deeper insights into host- endosymbiont coevolution and has important implications for evolutionary theory and pest management strategies.

evolutionary biology↗

bioRxiv2024

Echidna: A Bayesian framework for quantifying gene dosage effect impacting phenotypic plasticity

Phenotypic plasticity, the ability of cells to adapt their behavior in response to genetic or environmental changes, is a fundamental biological process that drives cellular diversity in both normal and pathological contexts, including in tumor evolution. While chromosomal instability and somatic copy number alterations (CNAs) are known to influence cellular states, it remains difficult to separate genetic from cell non-autonomous mechanisms that govern transcriptional variability. Here, we present Echidna, a Bayesian hierarchical model that integrates single-cell RNA sequencing (scRNA-seq) and bulk whole-genome sequencing (WGS) data to quantify the impact of CNAs on gene expression dynamics. By jointly inferring clone-specific CNA profiles and uncovering clonal dependencies, Echidna bridges genomic and transcriptomic landscapes within and across multiple time points, enabling the decoupling of gene dosage effects from cell-extrinsic factors on phenotypic plasticity. Applying Echidna to patient tumor specimens, we demonstrate its superior performance in clonal reconstruction and derive insights into resistance mechanisms.

bioinformatics↗

bioRxiv2024

Oncogenic RAS Induces a Distinctive Form of Non-Canonical Autophagy Mediated by the P38-ULK1-PI4KB Axis

Cancer cells with RAS mutations exhibit enhanced autophagy, essential for their proliferation and survival, making it a potential target for therapeutic intervention. However, the regulatory differences between RAS-induced autophagy and physiological autophagy remain poorly understood, complicating the development of cancer-specific anti-autophagy treatments. In this study, we identified a form of non-canonical autophagy induced by oncogenic KRAS expression, termed RAS-induced non-canonical autophagy via ATG8ylation (RINCAA). RINCAA involves distinct autophagic factors compared to those in starvation-induced autophagy and incorporates non-autophagic components, resulting in the formation of non-canonical autophagosomes with multivesicular/multilaminar structures labeled by ATG8 family proteins (e.g., LC3 and GABARAP). We have designated these structures as RAS-induced multivesicular/multilaminar bodies of ATG8ylation (RIMMBA). A notable feature of RINCAA is the substitution of the class III PI3K in canonical autophagy for PI4KB. We identified a regulatory P38-ULK1-PI4KB-WIPI2 signaling cascade governing this process, where ULK1 phosphorylation at S317, S479, S556, and S758 activates PI4KB. This activation involves PI4KB phosphorylation at S256 and T263, initiating PI4P production, ATG8ylation, and non-canonical autophagy. Importantly, elevated PI4KB phosphorylation at S256 and T263 was observed in RAS-mutated cancer cells and colorectal cancer specimens. Inhibition of PI4KB S256 and T263 phosphorylation led to a reduction in RINCAA activity and tumor growth in both xenograft and KPC models of pancreatic cancer, suggesting that ULK1-mediated PI4KB-Peptide-1 phosphorylation could represent a promising therapeutic target for RAS-mutated cancers.

cell biology↗

bioRxiv2024

Transgenic augmentation of erythroferrone in mice ameliorates anemia in adenine-induced chronic kidney disease

Anemia is a common and disabling complication of chronic kidney disease (CKD). Current therapies can be burdensome, and full correction of anemia is limited by cardiovascular side effects. New approaches that may offer additional therapeutic options are needed. We explored the anti-anemic effects of erythroferrone, an erythroid hormone that induces iron mobilization by suppressing the master iron-regulatory hormone hepcidin. In a preclinical murine model of adenine-induced CKD, transgenic augmentation of erythroferrone mobilized iron, increased hemoglobin concentrations by approximately 2 g/dl, and modestly improved renal function without affecting systemic or renal inflammation, fibrosis, or markers of mineral metabolism. This study supports the concept that therapeutic augmentation of erythroferrone is a promising approach for alleviating CKD-associated anemia.

pathology↗

bioRxiv2024

The Cardioprotective Effect of Ischemic Postconditioning is Mediated by Inhibiting RAP2C-MAP4K4 Pathway

BackgroundIschemic postconditioning (PostC) serves as a vital defense for cardiomyocytes against the deleterious effects of ischemia/reperfusion (I/R) injury, the beneficial effects could be further enhanced through pharmacological strategies. Our prior research demonstrated upregulated expression of the GTP-binding protein RAP2C in H9C2 cells post hypoxia-reoxygenation (H/R). The cardioprotective effects of RAP2C and underlying mechanisms are unclear. We therefore explored the role of RAP2C in PostC-induced cardioprotection against I/R injury. MethodsOpen-chest rat I/R and primary cultured cardiomyocytes H/R models were used. RAP2C and MAP4K4 expression was detected by immunohistochemistry and Western blotting. The BioGRID and STRING databases were tapped to predict the RAP2C-MAP4K4 binding, which was confirmed by co-immunoprecipitation and immunofluorescence. ResultsResults indicated that I/R and H/R upregulated the protein levels of RAP2C, MAP4K4, phospho-JNK, phospho-P38, and phospho-ERK, concomitant with increased apoptosis. PostC mitigated these effects. The pro-apoptotic impacts and the activation of the MAPK pathway induced by H/R were attenuated by RAP2C knockdown and intensified by RAP2C overexpression. H/R increased the interaction between RAP2C and MAP4K4, and PostC attenuated this effect. MAP4K4 knockdown reduced the pro-apoptotic and MAPK-activating effects induced by both RAP2C overexpression and hypoxia/reoxygenation (H/R). ConclusionsThese results demonstrate that PostC reduces cardiomyocyte apoptosis via modulating RAP2C/MAP4K4 pathways, suggesting their potential as therapeutic targets for the treatment of ischemic heart disease.

cell biology↗

bioRxiv2024

TET knockout cells transit between pluripotent states and exhibit precocious germline entry

TET1, TET2 and TET3 are DNA demethylases with critical roles in development and differentiation. To assess the contributions of TET proteins to cell function during early development, single and compound knockouts of Tet genes in mouse pluripotent embryonic stem cells (ESCs) were generated. Here we show that TET proteins are not required to transit between naive, formative and primed pluripotency. Moreover, ESCs with double-knockouts of Tet1 and Tet2 or triple-knockouts of Tet1, Tet2 and Tet3 are phenotypically indistinguishable. These TET-deficient ESCs exhibit differentiate defects; they fail to activate somatic gene expression and retain expression of pluripotency transcription factors. Therefore, TET1 and TET2, but not TET3 act redundantly to facilitate somatic differentiation. Importantly however, TET-deficient ESCs can differentiate into primordial germ cell-like cells (PGCLCs), and do so at high efficiency in the presence or absence of PGC-promoting cytokines. Moreover, acquisition of a PGCLC transcriptional programme occurs more rapidly in TET-deficient cells. These results establish that TET proteins act at the juncture between somatic and germline fates: without TET proteins, epiblast cell differentiation defaults to the germline.

developmental biology↗

bioRxiv2024

Natural variations of TaMYB7-A1 regulate PHS resistance and specify wheat geographic adaptation

Crop domestication tended to select against seed dormancy for uniform germination--raising risks of undesirable pre-harvest sprouting (PHS) -- but regulation of seed dormancy and PHS in wheat are grossly under-characterized. Here, we identified wheat PHS resistance loci by GWAS. TaMYB7-A1 confers PHS resistance by elevating ABA signaling and seed dormancy in grains. Three TaMYB7-A1 haplotypes (Hap-1/2/3) contrast in PHS resistance, with Gly23 and Gly92 crucial for binding to and activating TaABI5 in Hap-1/3. A MITE transposon in the TaMYB7-A1Hap-1 promoter likely recruited the TaAZF1-TaABI4 module to boost expression, resulting in strong PHS resistance. TaMYB7-A1Hap-1 originated from wild einkorn and was integrated into hexaploid wheat through introgression into wild emmer. Different haplotypes of TaMYB7-A1, in conjunction with alleles of other major PHS resistance genes, is pivotal in shaping wheats adaptability to rainfall conditions in China, US and Europe during the harvest season. Introduction of TaMYB7-A1Hap-1 into elite cultivars confers PHS resistance without yield defects. Thus, artificial and natural selection across diverse climates regions have collectively shaped wheat adaptation and enabled rational delivery of improved lines tailored to local cropping needs.

plant biology↗

bioRxiv2024

Low-frequency Cortical Activity Reflects Context-dependent Parsing of Word Sequences

During speech listening, it has been hypothesized that the brain builds representations of large linguistic structures such as sentences, which are captured by neural activity tracking the rhythm of these structures. Nevertheless, it has been concerned that the brain may only encode words, and neural activity tracking structures may be confounded by neural activity tracking the predictability or syntactic properties of individual words. Here, to disentangle the neural responses to sentences and words, we design word sequences that are parsed into different sentences in different contexts. By analyzing neural activity recorded by magnetoencephalography, we find that low-frequency neural activity strongly depends on the context - The difference between MEG responses to the same word sequence in two contexts yields a low-frequency signal, most strongly generated in the superior temporal gyrus, which precisely tracks sentences. The predictability and syntactic properties of words can partly explain the neural response in each context but cannot explain the difference between contexts. In summary, low-frequency neural activity encodes sentences and can reliably reflect how the same word sequence is parsed in different contexts.

neuroscience↗

bioRxiv2024

YY1 Enhances the Stability of HIF-1α Protein by Interacting with NUSAP1 in Macrophages within the Prostate Cancer Microenvironment

Immune checkpoint therapy for prostate cancer (PCa) has failed in clinical trials; however, the precise underlying mechanisms involved remain elusive. PCa, a classic "immune-cold" tumor, is characterized by an immunosuppressive tumor microenvironment. Within this milieu, macrophages, the predominant immune cell population, have a propensity to infiltrate the hypoxic zones of tumors. In a previous study, we showed that Yin Yang 1 (YY1) is highly expressed in macrophages in PCa tissues. Here, through multiplexed imaging mass cytometry (IMC) of a PCa tissue microarray, we further demonstrate that YY1+ macrophages aggregate in hypoxic areas of tumors and that hypoxia promotes the phase separation of YY1 in the nucleus by increasing YY1 tyrosine phosphorylation in macrophages. Furthermore, YY1 binds to NUSAP1 and promotes the SUMOylation of HIF-1, which promotes phase separation and stabilization of the HIF-1 protein. We also demonstrated that either treatment with a small molecule inhibitor (tenapanor) to decrease the YY1-NUSAP1-HIF-1 interaction or myeloid-specific YY1 gene knockout impairs subcutaneous PCa tumor formation. Furthermore, we present a first-generation tetrahedral DNA nanostructure (TDN) based on the proteolysis targeting chimera (PROTAC) technique, named YY1-DcTAC, which targets and degrades YY1 in tumor-associated macrophages. In a PCa mouse model, YY1-DcTAC exhibited prolonged drug efficacy, robust macrophage-specific responsiveness, potent antitumor effects, and increased CD8+ T cell tumor infiltration. In summary, our findings underscore the pivotal role of YY1 within the hypoxia/HIF-1 pathway in tumor-associated macrophages and affirm the therapeutic potential of targeting YY1 for treating PCa.

cancer biology↗

bioRxiv2024

C9orf72 expansion creates the unstable folate-sensitive fragile site FRA9A

The hyper-unstable Chr9p21 locus, harbouring the interferon gene cluster, oncogenes and C9orf72, is linked to multiple diseases. C9orf72 (GGGGCC)n expansions (C9orf72Exp) are associated with incompletely penetrant amyotrophic lateral sclerosis, frontotemporal dementia and autoimmune disorders. C9orf72Exp patients display hyperactive cGAS-STING-linked interferon immune and DNA damage responses, but the source of immuno-stimulatory or damaged DNA is unknown. Here, we show C9orf72Exp in pre-symptomatic and ALS-FTD patient cells and brains cause the folate- sensitive chromosomal fragile site, FRA9A. FRA9A centers on >33kb of C9orf72 as highly-compacted chromatin embedded in an 8.2Mb fragility zone spanning 9p21, encompassing 46 genes, making FRA9A one of the largest fragile sites. C9orf72Exp cells show chromosomal instability, heightened global- and Chr9p-enriched sister-chromatid exchanges, truncated-Chr9s, acentric-Chr9s and Chr9-containing micronuclei, providing endogenous sources of damaged and immunostimulatory DNA. Cells from one C9orf72Exp patient contained highly-rearranged FRA9A-expressing Chr9 with Chr9-wide dysregulated gene expression. Somatic C9orf72Exp repeat instability and chromosomal fragility are sensitive to folate-deficiency. Age-dependent repeat instability, chromosomal fragility, and chromosomal instability can be transferred to CNS and peripheral tissues of transgenic C9orf72Exp mice, implicating C9orf72Exp as the source. Our results highlight unappreciated effects of C9orf72 expansions that trigger vitamin-sensitive chromosome fragility, adding structural variations to the disease-enriched 9p21 locus, and likely elsewhere. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=94 SRC="FIGDIR/small/620312v2_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@154b23borg.highwire.dtl.DTLVardef@1814a6dorg.highwire.dtl.DTLVardef@13d713eorg.highwire.dtl.DTLVardef@d5d994_HPS_FORMAT_FIGEXP M_FIG C_FIG

genetics↗

bioRxiv2024

A circuit model for transsaccadic space updating and mislocalization

We perceive a stable, continuous world despite drastic changes of retinal images across saccades. However, while persistent objects in daily life appear stable across saccades, stimuli flashed around saccades can be grossly mislocalized. We address this puzzle with our recently proposed circuit model for perisaccadic receptive-field (RF) remapping in LIP and FEF. The model uses center/surround connections to store a relevant stimulus retinal location in memory as a population activity. This activity profile is updated across each saccade by directional connections gated by the corollary discharge (CD) of the saccade command. The updating is a continuous backward (against the saccade) shift of the population activity (equivalent to continuous forward remapping of the RFs), whose cumulative effect across the saccade is a subtraction of the saccade vector. The model explains forward and backward translational mislocalization for stimuli flashed around the saccade onset and offset, respectively, as insufficient and unnecessary cumulative updating after the saccade, caused by the sluggish CD time course and visual response latency. We confirm the model prediction that for perisaccadic RFs measured with flashes before the saccades, the final forward remapping magnitudes after the saccades are smaller for later flashes. We discuss the possibility that compressive mislocalization results from a brief reduction of attentional remapping and repulsion. Although many models of RF remapping, transsaccadic updating, and perisaccadic mislocalization have been proposed, our work unifies them into a single circuit mechanism and suggests that the brain uses "unaware" decoders which do not distinguish between different origins of neurons activities.

neuroscience↗

bioRxiv2024

Assembling Ruthenium Complexes to Form Ruthenosome Unleashing Ferritinophagy-mediated Tumor Suppression

AbstactWe introduce ruthenosomes, a fusion of liposomal and reactive oxygen species (ROS)-generating properties meticulously engineered as potent ferroptosis inducers (FINs), marking a significant advancement in metallodrug design for cancer therapy. Formed through the self-assembly of oleate-conjugated ruthenium complexes, these ruthenosomes exhibit exceptional cellular uptake, selectively accumulating in mitochondria and causing substantial disruption. This targeted mitochondrial damage significantly elevates ROS levels, triggering autophagy and selectively activating ferritinophagy. Together, these processes sensitize cancer cells to ferroptosis. In vivo, ruthenosomes effectively suppress colorectal tumor growth, underscoring their therapeutic potential. Our study pioneers a design strategy that transforms ruthenium complexes into liposome-like structures capable of inducing ferroptosis independent of light activation. By leveraging ruthenosomes as multifunctional nanocarriers, this research offers a versatile and powerful platform for ROS-mediated, ferroptosis-driven cancer cell eradication.

biochemistry↗

bioRxiv2024

Biocontrol efficiency and mechanism of novel Streptomyces luomodiensis SCA4-21 against banana Fusarium wilt

The soil-borne fungi Fusarium oxysporum f. sp. cubense tropical race 4 (Foc TR4) causes banana Fusarium wilt, which seriously threats global banana production. Biocontrol has been considered viable alternative method to manage banana Fusarium wilt. In previous study, we found that novel S. luomodiensis SCA4-21 exhibited antifungal activity. Here, we revealed that the extracts of strain SCA4-21 significantly inhibited the growth of Foc TR4 hyphae and spore germination, severely disrupting the ultrastructure of Foc TR4 hyphal cells and spore morphology. These extracts also exhibited broad-spectrum antifungal activity against eight other phytopathogenic fungi. Furthermore, we demonstrated that strain SCA4-21 produce 32 volatile organic compounds, including five antifungal compounds. In a pot experiment, we discovered that the inoculation of strain SCA4-21 significantly inhibited the infection of Foc TR4 in banana seedling corms, achieving a biocontrol efficiency of 59.3%, and promoted the growth of banana seedlings. Additionally, this inoculation significantly enhanced the abundances of beneficial bacterial genera Streptomyces, Bacillus, Sphingomonas, and Massilia, as well as fungal genera Mortierella, Purpureocillium, Gibellulopsis, and Xenomyrothecium, while significantly reduced the abundances of pathogenic bacteria genus Pantoea and fungal genus Fusarium, in the banana rhizosphere soil. Moreover, the inoculation of strain SCA4-21 significantly increased the enrichment of pathways such as carbohydrate metabolism, amino acid metabolism, and metabolism of terpenoids and polyketides. Therefore, we postulated that strain SCA4-21 may synergistically combat banana Fusarium wilt by producing antifungal compounds and enriching beneficial bacteria and fungi. Our findings present a promising biocontrol agent for the management of banana Fusarium wilt. IMPORTANCEBanana (Musa spp.) is one of the most popular fruit crops and the fourth largest food crop in developing countries within tropical and subtropical regions. However, the emergence and rapid spread of strain Foc TR4 seriously hinder the development of banana industry. Currently, there is no effective control measure available. Biological control holds potential due to its safety and effectiveness. Here, we found that the extracts of S. luomodiensis SCA4-21 exhibited significant inhibitory effects on the hyphal growth and spore germination of Foc TR4, as well as severe destructive effects on its cell morphology and ultrastructure, and broad-spectrum antifungal activity. We also discovered that the inoculation of strain SCA4-21 significantly inhibited the infection of Foc TR4 in banana seedling corms, reduced the incidence index of banana Fusarium wilt, promoted the growth of banana seedlings, and enhances beneficial microbes and metabolic pathways, suggesting that strain SCA4-21 is a promising biocontrol agent.

physiology↗

bioRxiv2024

Real-Time Visualization of Protein Microenvironment Changes with High Spatial Resolution in Live Cells via Site-Specific Incorporation of Rotor-Based Fluorescent Noncanonical Amino Acids

Traditional methods, such as the use of fluorescent protein fusions and environment-sensitive fluorophores, have limitations when studying protein microenvironment changes at the finest spatial resolution. These techniques often rely on bulky proteins or tags restricted to the N- or C-terminus, which can disrupt the natural behavior of the target protein and dramatically limit the ability of their method to investigate noninvasively microenvironment effects. To overcome these challenges, we have developed an innovative strategy to visualize microenvironment changes of protein substructures in real-time by genetically incorporating environment-sensitive noncanonical amino acids (ncAAs) containing rotor-based fluorophores (RBFs) at specific positions within a protein of interest. Through computational redesign of aminoacyl-tRNA synthetase, we successfully incorporated these rotor-based ncAAs into various proteins in mammalian cells. By site-specifically placing these ncAAs in distinct regions of proteins, we detected microenvironmental changes of several different protein domains during events such as aggregation, clustering, aggregation disassembly, and cluster dissociation.

biochemistry↗

bioRxiv2024

Decipher Fundamental Atomic Interactions to Unify Generative Molecular Docking and Design

Understanding molecular interactions is essential to structural biology and drug discovery. Despite the progress of AI models in revealing and exploiting the interaction mechanisms for various applications, they are predominantly tailored to specific tasks without fully exploiting the underlying transferability across molecular data and tasks. Here, we present PocketXMol, an atom-level generative foundation model to decipher fundamental atomic interactions for general protein-pocket-interacting molecular tasks. It adopts a novel unified generative framework with an innovative task prompt mechanism and an exclusive atom-level representation, making it applicable to diverse tasks covering structure prediction and design of small molecules and peptides, without requiring fine-tuning. PocketXMol was compared to 55 baseline models across 13 typical tasks, achieving state-of-the-art performance in 11 tasks and remaining competitive in the others. We successfully utilized PocketXMol to design novel small molecules that inhibit caspase-9 with efficacy comparable to that of commercial pan-caspase inhibitors. Furthermore, we employed PocketXMol to design PD-L1-binding peptides, demonstrating a success rate substantially higher than random library screening. Three representative peptides underwent further experiments, which validated the cellular specificity and confirmed their potential for molecular probing and therapeutics. PocketXMol presents a powerful and versatile tool with promising prospects for future applications and will have a profound impact on AI-aided drug discovery.

bioinformatics↗

bioRxiv2024

Tunable, self-contained gene dosage control via proteolytic cleavage of CRISPR-Cas systems

The ability to modulate gene expression through modular and universal genetic tools like CRISPR-Cas has greatly advanced gene therapy for therapeutics and basic science. Yet, the inherent stochasticity of delivery methods cause variation in target gene expression at the single-cell level, limiting their applicability in systems that require more precise expression. Thus, we implement a modular incoherent feedforward loop based on proteolytic cleavage of Cas to reduce gene expression variability against the variability of vector delivery. We target a genome-integrated marker and demonstrate dosage control of gene activation and repression, post-delivery tuning, and RNA-based compatibility of the system. To illustrate therapeutic relevance, we target the gene RAI1, the haploinsufficiency and triplosensitivity of which cause two autism-related syndromes. We demonstrate dosage-controlled gene activation for both human and mouse Rai1 via viral delivery to patient-derived cell lines and mouse cortical neurons. Overall, we established a robust dosage control circuit for uniform gene expression, beneficial for basic and translational research.

synthetic biology↗