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Biology subjects

Shao, S.

Publications and source records attributed to Shao, S..

At least 19 recordsLinked to original sources

Venetoclax Resistance Creates Canonical Pyroptosis Vulnerability in AML

Venetoclax has transformed acute myeloid leukemia (AML) therapy, yet resistance is almost inevitable. Its diverse, often difficult-to-target drivers frequently converge on monocytic differentiation, a state that survives on MCL1 rather than BCL2. Here, we show that the very cells that escape BCL2 inhibition retain the canonical pyroptosis machinery of normal monocytes. Across 15 bulk and 4 single-cell cohorts, the canonical pyroptosis program was enriched in monocytic AML and monocytic leukemia stem cells, correlated with venetoclax resistance, and associated with inferior survival specifically after venetoclax-based therapy. In 24 cell lines and 142 patient specimens, both DPP8/9 inhibition by Val-boroPro and NLRP3 activation by lipopolysaccharide (LPS) plus nigericin preferentially killed monocytic AML cells through GSDMD-mediated pyroptosis, largely sparing non-monocytic AML and lymphoid leukemias. Venetoclax preferentially depleted primitive AML blasts but enriched a monocytic residuum vulnerable to canonical pyroptosis; combining venetoclax with Val-boroPro achieved deeper ex vivo clearance than either agent alone. In venetoclax-resistant xenografts, Val-boroPro suppressed leukemia progression, and adding venetoclax further reduced leukemia burden and prolonged survival beyond either monotherapy. Thus, venetoclax resistance itself exposes an alternative, druggable cell-death program that can be therapeutically exploited to overcome this resistance.

cancer biology↗

RNF185 destabilizes specific membrane proteins that span all ERAD branches

The endoplasmic reticulum (ER) is the primary site of eukaryotic membrane protein synthesis and quality control, which largely relies on ER-associated degradation (ERAD) to eliminate aberrant nascent proteins. In yeast, two ubiquitin ligases target proteins for ERAD based on aberrancies in substrate transmembrane (ERAD-M), lumenal (ERAD-L), or cytosolic (ERAD-C) domains. How an expanded repertoire of mammalian ERAD factors selects substrates across these classifications is unclear. Here, we show that the human ER-resident RNF185 ubiquitin ligase complex destabilizes a small but specific set of membrane proteins that span all three ERAD branches. Comparisons of three single-pass membrane proteins destabilized by RNF185 identify ERAD-M features in misoriented CHST10, ERAD-C features in unassembled SRPRB, and N-linked glycosylation-dependent ERAD-L features in ATP1B2. Our findings identify RNF185-destabilized membrane proteins with distinct aberrancies that collectively encompass all canonical ERAD substrate classifications and unexpectedly diverse quality control defects.

cell biology↗

TROP2-targeting chimeras (TRTACs) for tumor-selective membrane protein degradation and enhanced drug delivery

Extracellular targeted protein degradation (eTPD) systems typically utilize lysosome-targeting receptors (LTRs) to mediate internalization and lysosomal degradation of extracellular and membrane proteins. While multiple LTRs have been discovered, there remains a compelling need to seek for new LTRs, particularly those with clear clinical relevance, to expand the therapeutic potential of eTPD. Here we report trophoblast cell surface antigen-2 (TROP2), a clinically validated tumor-associated antigen, as a promising tumor-selective LTR. We engineer TROP2-targeting chimeras (TRTACs) by genetically fusing a TROP2-binding nanobody to nanobodies against specific target proteins. We show that TRTACs can induce tumor cell-selective degradation of diverse membrane proteins, including epithelial growth factor receptor (EGFR), human epithelial growth factor receptor 2 (HER2), and programmed death-ligand 1 (PD-L1). The EGFR-targeted TRTAC significantly inhibits tumor cell proliferation and shows potent antitumor activity in vivo. We further design TRTAC-drug conjugates (TRTAC-DCs) by attaching cytotoxic payloads to TRTACs, enabling targeted protein degradation together with enhanced drug delivery. TRTAC-DCs show significantly enhanced activity against HER2- and EGFR-positive tumors both in vitro and in vivo, with minimal toxicity observed in normal tissues. These findings establish TROP2 as a robust LTR and provide a versatile eTPD platform with profound translational potential for tumor treatment.

cell biology↗

Fibroblast-encoded inflammatory memory orchestrates recurrent skin inflammation via NNMT-dependent metabolic remodeling

Chronic skin inflammation frequently recurs at the same anatomical sites after therapy withdrawal, implying stromal cells may encode local inflammatory memory. Here, we identified nicotinamide N-methyltransferase (NNMT) as a central metabolic-epigenetic regulator of fibroblast inflammatory memory enabling psoriasis relapse. Single-cell and spatial transcriptomics revealed that dermal fibroblasts acquire a persistent senescence-associated secretory phenotype (SASP) during inflammation, maintaining pro-inflammatory niche in resolved skin that supports CD 8+CD 103+ tissue-resident memory T cell (Trm) differentiation. Multi-omics profiling demonstrated that NNMT depletes S-adenosylmethionine (SAM), reduces H 3K 27me3 deposition, and permits sustained AP-1 occupancy at SASP gene promoters. Fibroblast-specific NNMT ablation or pharmacologic inhibition suppressed SASP activity, limited Trm accumulation, and prevented both initiation and relapse of skin inflammation in mice. These findings establish NNMT as a stromal regulator linking fibroblast metabolism to durable epigenetic memory and propose its targeting to erase inflammatory memory and achieve long-term remission in psoriasis and related immune-mediated diseases. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/721223v1_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@34b2f4org.highwire.dtl.DTLVardef@1d0bb89org.highwire.dtl.DTLVardef@c8277borg.highwire.dtl.DTLVardef@9825ac_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphic Abstract:C_FLOATNO Proposed mechanism through which NNMT-driven fibroblast SASP facilitates the initiation and recurrence of psoriasis C_FIG

immunology↗

Murine Neutrophil Chemotaxis Following Burn Injury with Poloxamer 188 Treatment in a Microfluidic Platform

This study investigates the effects of Poloxamer 188 (P188) on neutrophil chemotaxis following burn injury in male and female mice using a microfluidic system. Utilizing male and female CD1 mice, we evaluated neutrophil migration towards two chemoattractants, N-formyl-l-methionyl-l-leucyl-l-phenylalanine (fMLP) and Leukotriene B4 (LTB4), and FPR1 and BLT1 G protein-coupled receptors after administering P188. Our findings revealed that P188 significantly increased the migration toward LTB4 in both sexes. Additionally, our findings highlight the upregulation of BLT1 and FPR1 markers due to burn injury in both female and male mice in the Burn vs. Sham groups. These results demonstrate the potential of P188 in modulating neutrophil behavior post-burn injury in therapeutic strategies for inflammation management. This microfluidic platform offers a precise and controlled microenvironment for studying neutrophil chemotaxis post-burn injury with and without P188 treatment.

bioengineering↗

Phenotype-Guided In Silico Molecular Generation Using Large Language Models

Complex diseases often emerge from coordinated, system-level cellular state changes that are difficult to address with target centric drug discovery. Phenotypic drug discovery offers a principled alternative but remains constrained by the cost and scalability of pathologically relevant assays. Here we present GEMGen, a large language model-based framework that performs in silico phenotypic drug discovery by generating small molecules directly from transcriptomic representations of cellular states. GEMGen encodes desired phenotypic transitions as text-based representations of up- and down-regulated gene sets, enabling transferable modeling across experimental platforms and data modalities. Trained on large scale chemical perturbation data, GEMGen robustly identifies phenotype-oriented compounds and mechanistically related but structurally distinct candidates across multiple benchmarks. Applied to signatures induced by genetic perturbations, GEMGen produces small molecules that phenocopy gene knockdown effects and identifies chemically novel inhibitors, including previously unreported KEAP1 inhibitors that activate NRF2 signaling. Extending this approach to a disease relevant model of fibrosis, GEMGen generates compounds that reverse profibrotic transcriptional programs and cellular phenotypes. These results establish a scalable framework for translating transcriptomic phenotypes into candidate therapeutic molecules, enabling systems-level exploration of vast chemical space and offering a complementary in silico counterpart to physical phenotypic drug screens.

cell biology↗

PEI-Coated Microbubble Attachment to Neutrophils: Potential for Radiation Force Assisted Delivery into Tissue

Immunotherapies have advanced cancer treatment; however, their clinical efficacy remains limited for solid tumors due to challenges associated with effectively directing immune cells into the complex tumor microenvironment. Recent developments in Ultrasound Contrast Agent (UCA -- also known as "microbubble") technology have provided novel opportunities to enhance targeted therapeutic delivery. In this study, we introduce an innovative approach of leveraging microbubbles to enhance immune cell targeting by directly attaching microbubbles to immune cells, enabling the targeted delivery and localization of immune cells into solid tumors using radiation force ultrasound (US) application. To create novel microbubble-immune cell conjugates, we created polyethyleneimine (PEI) coated microbubbles and attached them to differentiated HL-60 (dHL-60) cells. These positively charged PEI microbubbles were formulated using azide-DBCO click chemistry between DBCO-labeled microbubbles and the azide functional groups on the PEI polymer. Following this step, we utilized electrostatic interactions to attach our positively charged PEI microbubbles to our negatively charged dHL-60 cells. We conducted viability experiments to assess the compatibility of these designs and verified that cell viability remained greater than 88% four hours after the conjugation process for different ratios of dHL-60 cells to PEI microbubbles. We used microfluidic chemotaxis platforms to quantify the microbubble-conjugated dHL-60 cell migratory behavior, examining parameters including migration velocity and percentage. Additionally, we investigated the impact of ultrasound power on primary human neutrophils to validate the functional responsiveness of these physiologically relevant immune cells. Here we demonstrated the possibility of ultrasound-responsive immune cell constructs as a targeted strategy without loss of function in migration capabilities. The novel PEI microbubble and immune cell conjugates reported in this work will be used to improve future immunotherapy techniques.

bioengineering↗

Exudate-Guided Janus Trilayer Bioelectronic Dressing for Multimodal Sensing and Therapy of Chronic Wounds

Chronic wound treatment remains challenging because conventional dressings and systemic therapies typically lack real-time adaptability to the dynamic changes in the wound microenvironment. Here, we report a breathable self-adhesive multifunctional wound dressing based on a gradient-wettable Janus trilayer fibrous membrane, which integrates real-time biochemical sensing, on-demand drug release, and low-voltage electrical stimulation therapy simultaneously. The dressing features a vertically integrated trilayer architecture with hierarchical partitioning, where the three vertically stacked layers integrate a multiplex electrochemical sensor array (glucose, lactate, pH), a silver-sulfadiazine drug reservoir, and stimulation electrodes. Specifically, a hydrophilic sensing layer, intermediate drug-storage layer, and hydrophobic adhesivelayer are assembled to achieve spatially resolved functionalities. The membranes gradient wettability and asymmetric porous structure enable directional exudate transport, thereby triggering stepwise activation of sensing, drug release, and electrical stimulation in a spatiotemporally controlled manner. The dressing is thin, breathable, stretchable, self-adhesive and biocompatible, enabling conformal contact and stable signal acquisition on deformable skin without tapes. This design ensures continuous bio-signal monitoring while maintaining a favorable wound healing microenvironment. Preclinical tests demonstrate its effectiveness in promoting wound closure, reducing infection, and providing continuous wound status monitoring. This integrated system offers a promising approach for next-generation wound care and regenerative medicine.

bioengineering↗

YAP1 Depletion Enhances TAZ and its Complexation with TEAD4 and AP-1 Heterodimer C-JUN/FOSB to Promote Gastric Cancer Progression and Metastases

BackgroundDysregulation of the Hippo signaling pathway, characterized by aberrant activation of the transcriptional coactivators YAP1 and TAZ, drives tumour progression, immunosuppression and metastasis. Hippo pathway components are emerging therapeutic targets in several solid tumours, however, the expression profiles of Hippo coactivators YAP1, TAZ and their transcriptional factors TEAD1-4 in gastric cancer peritoneal metastases (GCPMs) and their therapeutic value are unknown. ObjectiveTo determine expression status of YAP1, TAZ and TEAD1-4 in GCPMs; and to evaluate whether dual targeting of YAP1 and TAZ provides superior antitumour activity compared with inhibition of either coactivator alone. DesignExpression of YAP1, TAZ and TEAD1-4 was examined in GCPMs by single-cell RNA sequencing and co-immunofluorescent staining. Functional studies using genetic knockout and antisense oligonucleotide (ASO) inhibition of YAP1 or TAZ were performed to assess antineoplastic effects in vitro and in vivo. Co-immunoprecipitation and luciferase reporter assays were used to characterize YAP1/TAZ interactions with TEADs and AP-1 components (JUN and FOSB) and to quantify transcriptional activity. Antitumour efficacy was validated in patient-derived xenograft (PDX) and KP-Luc2 syngeneic models. ResultsYAP1, TAZ, and TEADs1- 4 were highly coexpressed in GCPMs and correlated with poor survival. YAP1 inhibition alone elicited compensatory upregulation of TAZ, while combined inhibition of both coactivators maximally repressed cell proliferation and invasion in vitro, and tumor growth in vivo. Increased TAZ complexation with TEAD4 and AP-1 (c-JUN and FOSB) heterodimer was observed following YAP1 knockdown or pharmacological ASO inhibition. Dual inhibition of YAP1 and TAZ was required to maximally suppress YAP1/TAZ expression and reduce their nuclear accumulation, transactivation of TEAD, and activation of downstream genes. ConclusionsThese findings show that combined YAP1 and TAZ inhibition holds promise for the treatment of GCPMs, a highly lethal disease with an urgent need for novel treatment options. WHAT IS ALREADY KNOWN ON THIS TOPICO_LIGastric cancer with peritoneal metastasis (GCPM), occurring in > 45% of gastric cancer (GC) patients, is a highly lethal malignancy with limited therapeutic options. C_LIO_LIThe Hippo pathway mediator Yes-associated protein 1 (YAP1) is intimately involved in chemoresistance, cancer stemness properties, and the epithelial-to-mesenchymal transition in gastric and other cancers. C_LIO_LIWhile YAP1 represents a promising therapeutic target, clinical trial of YAP1 antisense oligonucleotides has been disappointing. C_LI WHAT THIS STUDY ADDSO_LIHippo coactivators YAP1, TAZ and their main transcription factors TEAD1-4 are markedly upregulated in GCPMs and associated with poor prognosis. C_LIO_LIAntisense targeting of YAP1 results in compensatory upregulation of its paralog TAZ. C_LIO_LIUpon YAP1 depletion, TAZ forms transcriptional complexes with TEAD4 and the AP-1 heterodimer (JUN and FOSB). C_LIO_LIDual targeting of YAP1 and TAZ, by oligonucleotides, achieves maximal suppression of tumour growth in vitro and in vivo. C_LI HOW THIS STUDY MIGHT AFFECT RESEARCH, PRACTICE OR POLICYO_LIThese findings provide a strong mechanistic rationale for co-targeting YAP1 and TAZ as a therapeutic approach in metastatic gastric cancer. C_LIO_LIDual Hippo coactivator inhibition could inform the design of future clinical trials aimed at improving outcomes for patients with GCPMs. C_LI

cancer biology↗

Structures of human organellar SPFH protein complexes

Stomatin, Prohibitin, Flotillin, and HflK/C (SPFH) family proteins are found in all kingdoms of life and in multiple eukaryotic organelles. SPFH proteins assemble into homo- or hetero-oligomeric rings that form domed structures. Most SPFH assemblies also abut a cellular membrane, where they are implicated in diverse functions ranging from membrane organization to protein quality control. However, the precise architectures of different SPFH complexes remain unclear. Here, we report single-particle cryo-EM structures of the endoplasmic reticulum (ER)-resident Erlin1/2 complex and the mitochondrial prohibitin (PHB1/2) complex, revealing assemblies of 13 heterodimers of Erlin1 and Erlin2 and 11 heterodimers of PHB1 and PHB2, respectively. We also describe key interactions underlying the architecture of each complex and conformational heterogeneity of the PHB1/2 complex. Our findings elucidate the distinct stoichiometries and properties of human organellar SPFH complexes and highlight common principles of SPFH complex organization.

molecular biology↗

Non-invasive skin topical delivery of hyaluronan

Hyaluronic acid (HA), a key glycosaminoglycan in the skin extracellular matrix, diminishes with aging, leading to dryness, wrinkles, and loss of elasticity. While subcutaneous HA injection remains the standard treatment, it is invasive and associated with complications. Here, we developed a zwitterionic polymer-based nanogel system (HA/OP) for noninvasive transdermal HA delivery. The nanogels, formed by complexing HA with poly[2-(N-oxide-N,N-diethylamino)ethyl methacrylate] (OP), exhibited pH-responsive behavior, remaining stable at weakly acidic skin surface pH ([~]5) but dissociating in neutral dermal environments. HA/OP nanogels efficiently permeated the stratum corneum via sebum-assisted enrichment and para-corneocyte transport, followed by transcytosis and enhanced paracellular penetration mediated by myosin light-chain kinase (MLCK) upregulation. This enabled deep HA deposition in the dermis and subcutaneous tissue, significantly improving skin hydration and reducing wrinkles in hairless mice without irritation. Our findings present a safe, needle-free strategy for topical HA delivery, addressing a major unmet need in cosmetic and dermatological applications.

bioengineering↗

Structural basis for the midnolin-proteasome pathway and its role in suppressing myeloma

The midnolin-proteasome pathway degrades many nuclear proteins without ubiquitination, but how it operates mechanistically remains unclear. Here, we present structures of the midnolin-proteasome complex, revealing how established proteasomal components are repurposed to enable a unique form of proteolysis. While the proteasomal subunit PSMD2/Rpn1 binds to ubiquitinated or ubiquitin-like proteins, we discover that it also interacts with the midnolin nuclear localization sequence, elucidating how midnolins activity is confined to the nucleus. Likewise, PSMD14/Rpn11, an enzyme that normally cleaves ubiquitin chains, surprisingly functions non-enzymatically as a receptor for the midnolin ubiquitin-like (Ubl) domain, positioning the substrate-binding Catch domain directly above the proteasomal entry site to guide substrates into the proteasome. Moreover, we demonstrate that midnolin downregulation is critical for the survival of myeloma cells by promoting the expression of its transcription factor substrate IRF4. Our findings uncover the mechanisms underlying the midnolin-proteasome pathway and midnolin downregulation as a driver of multiple myeloma.

cell biology↗

Translational activators align mRNAs at the small mitoribosomal subunit for translation initiation

Mitochondrial gene expression is essential for oxidative phosphorylation. Mitochondrial-encoded mRNAs are translated by dedicated mitochondrial ribosomes (mitoribosomes), whose regulation remains elusive. In the bakers yeast Saccharomyces cerevisiae, nuclear-encoded mitochondrial translational activators (TAs) facilitate transcript-specific translation by a yet unknown mechanism. Here, we investigated the function of TAs containing RNA-binding pentatricopeptide repeats (PPRs) using selective mitoribosome profiling and cryo-EM structural analysis. These analyses revealed that TAs exhibit strong selectivity for mitoribosomes initiating on their target transcripts. Moreover, TA-mitoribosome footprints indicated that TAs recruit mitoribosomes proximal to the start codon. Two cryo-EM structures of mRNA-TA complexes bound to post-initiation/pre-elongation-stalled mitoribosomes revealed the general mechanism of TA action. Specifically, the TAs bind to structural elements in the 5 UTR of the client mRNA as well as to the mRNA channel exit to align the mRNA in the small subunit during initiation. Our findings provide a mechanistic basis for understanding how mitochondria achieve transcript-specific translation initiation without relying on general sequence elements to position mitoribosomes at start codons.

molecular biology↗

Fluence rate-dependent kinetics of light-triggered liposomal doxorubicin assessed by quantitative fluorescence-based endoscopic probe

Liposomal doxorubicin (Dox), a treatment option for recurrent ovarian cancer, often suffers from suboptimal biodistribution and efficacy, which might be addressed with precision drug delivery systems. Here, we introduce a catheter-based endoscopic probe designed for multispectral, quantitative monitoring of light-triggered drug release. This tool utilizes red-light photosensitive porphyrin-phospholipid (PoP), which is encapsulated in liposome bilayers to enhance targeted drug delivery. By integrating diffuse reflectance and fluorescence spectroscopy, our approach not only corrects the effects of tissue optical properties but also ensures accurate drug delivery to deep-seated tumors. Pre-liminary results validate the probe effectiveness in controlled settings, highlighting its potential for future clinical adaptation. This study sets the stage for in vivo applications, enabling the exploration of next-generation treatment paradigms for the management of cancer by optimizing chemotherapy administration with precision and control.

bioengineering↗

Structure of the TXNL1-bound proteasome

Proteasomes degrade diverse proteins in different cellular contexts through incompletely defined regulatory mechanisms. Here, we report the cryo-EM structure of thioredoxin-like protein 1 (TXNL1) bound to the 19S regulatory particle of proteasomes via interactions with PSMD1/Rpn2, PSMD4/Rpn10, and PSMD14/Rpn11. These interactions are necessary for the ubiquitin-independent degradation of TXNL1 upon cellular exposure to metal- or metalloid-containing oxidative agents, thereby establishing a structural basis for the stress-induced degradation of TXNL1.

cell biology↗

Spontaneous emergence and drifting of sequential neural activity in recurrent networks

Repeating sequences of neural activity exist across brain regions of different animals are thought to underlie diverse computations. However, their emergence and evolution during ongoing synaptic plasticity remain unclear. To mechanistically understand this process, we investigated the interaction of biologically-inspired activity-dependent synaptic plasticity rules in models of recurrent circuits to produce connectivity structures that support neuronal sequences. Under unstructured inputs, our recurrent networks developed strong unidirectional connections, resulting in spontaneous repeating sequences of spikes. During ongoing plasticity these sequences repeated despite turnover of individual synaptic connections, a process reminiscent of synaptic drift. The turnover process occurred over different timescales, with sequence-promoting connectivity types and motif structures being strengthened while others weakened, leading to sequences with different degrees of volatility. Structured inputs could reinforce or retrain the resulting connectivity structures underlying sequences, enabling stable yet flexible encoding of inputs. Our model unveils the interplay between synaptic plasticity and sequential activity in recurrent networks, providing insights into how the brain might implement reliable and flexible computations.

neuroscience↗

Mechanism of ASF1 Inhibition by CDAN1

Codanin-1 (CDAN1) is an essential and ubiquitous protein named after congenital dyserythropoietic anemia type I (CDA-I), an autosomal recessive disease that manifests from mutations in the CDAN1 or CDIN1 (CDAN1 interacting nuclease 1) gene. CDAN1 interacts with CDIN1 and the paralogous histone H3-H4 chaperones ASF1A (Anti-Silencing Function 1A) and ASF1B, but its function remains unclear. Here, we biochemically and structurally analyze CDAN1 complexes. We find that CDAN1 dimerizes and assembles into cytosolic complexes with CDIN1 and multiple copies of ASF1A/B. Single-particle cryogenic electron microscopy (cryo-EM) structures of CDAN1 complexes identify interactions with ASF1 mediated by two CDAN1 B-domains commonly found in ASF1 binding partners and two helices that mimic histone H3 binding. We additionally observe that one CDAN1 can recruit two ASF1 molecules and that ASF1A and ASF1B have different requirements for CDAN1 engagement. Our findings explain how CDAN1 sequesters and inhibits the chaperone function of ASF1A/B and provide new molecular-level insights into this enigmatic complex.

biochemistry↗

Unique trajectory of gene family evolution from genomic analysis of nearly all known species in an ancient yeast lineage

Gene gains and losses are a major driver of genome evolution; their precise characterization can provide insights into the origin and diversification of major lineages. Here, we examined gene family evolution of 1,154 genomes from nearly all known species in the medically and technologically important yeast subphylum Saccharomycotina. We found that yeast gene family and genome evolution are distinct from plants, animals, and filamentous ascomycetes and are characterized by small genome sizes and smaller gene numbers but larger gene family sizes. Faster-evolving lineages (FELs) in yeasts experienced significantly higher rates of gene losses--commensurate with a narrowing of metabolic niche breadth--but higher speciation rates than their slower-evolving sister lineages (SELs). Gene families most often lost are those involved in mRNA splicing, carbohydrate metabolism, and cell division and are likely associated with intron loss, metabolic breadth, and non-canonical cell cycle processes. Our results highlight the significant role of gene family contractions in the evolution of yeast metabolism, genome function, and speciation, and suggest that gene family evolutionary trajectories have differed markedly across major eukaryotic lineages.

evolutionary biology↗