Biology subjects

Zhang, Q.

Publications and source records attributed to Zhang, Q..

At least 127 records · Page 7Linked to original sources

bioRxiv2026

Base-resolution DNA methylome of human MDS hematopoietic stem cell reveals TET2-GFI1 epigenetic axis repressing MDS

Dysfunctional hematopoietic stem cells (HSCs) drive the initiation of myelodysplastic syndromes (MDS), yet the genome-wide DNA methylation landscape in MDS primitive HSCs and its mechanistic contribution to disease pathogenesis remain poorly defined. Here, we establish single-base resolution DNA methylomes of bone marrow HSCs from MDS patients and healthy donors. We uncover widespread hypermethylation within CpG islands, alongside hypomethylation in repetitive elements such as Alu. Differentially methylated regions (DMRs) are enriched for genes involved in cancer-related pathways, as well as extrinsic signaling pathways and intrinsic transcriptional networks essential for HSC function. Among these, we identify GFI1 and BMI1 as key targets of DNA methylation dysregulation in MDS. Notably, using either MDS or Tet2-deficient mouse model, we demonstrate that loss of Tet2, a frequently mutated epigenetic regulator in MDS, induces promoter hypermethylation and transcriptional repression of Gfi1, contributing to expansion of the MDS or aged hematopoietic stem and progenitor cell pool. Our study not only charts the base-resolution DNA methylome of human MDS HSCs but also reveals a TET2-GFI1 axis that safeguards HSC homeostasis. These findings provide mechanistic insight into how aberrant DNA methylation drives HSC dysfunction in MDS and offer an epigenomic resource for discovering novel regulators and therapeutic targets at the stem cell level.

immunology↗

bioRxiv2026

A T-cell engager platform induces deep plasma cell depletion in autoimmune dry eye

Bispecific T cell engagers (TCEs) have transformed targeted immunotherapy but remain constrained by ex vivo manufacturing and systemic delivery, limiting their application in autoimmune disorders. Here, we introduce the first in vivo TCE platform, utilizing a T cell-targeted integration-deficient lentiviral vector (T-IDLE) to reprogram endogenous T cells into engineered T cells secreting BCMAxCD3 TCEs (STCEs) directly in vivo. In murine Sjogrens syndrome-associated dry eye model, a single intravenous administration of T-IDLESTCE achieved deep and sustained depletion of plasmablasts and plasma cells, reversing lacrimal gland inflammation and restoring tear production without detectable off-target transduction. Longitudinal studies in cynomolgus monkeys confirmed translational promise, demonstrating potent plasma cell clearance and favorable safety profiles over 12 weeks post-vector dosing. Mechanistic analyses demonstrated attenuation of Th1/Th17-mediated inflammation and controlled cytokine responses, accompanied by negligible vector integration in non-T cell lineages, thereby substantiating the safety profile of the integration-deficient design. This first-in-class in vivo TCE approach represents a manufacturing-free, scalable immunotherapy strategy for autoantibody-mediated diseases.

bioengineering↗

bioRxiv2026

Living Cells Employ Ubiquitin-Proteasomal System and Nucleotide Excision Repair Pathways to Remove Reactive Oxygen Species-Induced DNA-Protein Crosslinks (ROS-DPCs).

Oxidative DNA damage caused by endogenous reactive oxygen species (ROS) is a key driver of mutagenesis, cellular dysfunction, and aging, contributing to diseases like cancer, neurodegeneration, rheumatoid arthritis, cardiovascular disorders, and diabetes. Although more than 20 oxidative base lesions have been identified, ROS-induced DNA-protein crosslinks (DPCs) are poorly characterized. ROS-DPCs are unusually bulky and highly toxic lesions that accumulate in metabolically active tissues with age, but their identities, biological consequences, and repair in living cells have remained elusive. In the present work, we characterized ROS-DPCs in human fibrosarcoma (HT1080) cells treated with hydrogen peroxide (H2O2) and elucidated the mechanisms of their removal. Mass spectrometry-based proteomics has identified over 100 cellular proteins that participated in DPC formation, most of which are involved in DNA metabolism. Our data further reveal that DNA replication and transcription facilitate DPC detection and identify a critical role of the ubiquitin-proteasomal system (UPS), replication-coupled activity of SPRTN metalloprotease, and nucleotide excision repair (NER) in removing ROS-induced DPCs. ROS-DPC formation was blocked by pretreatment with metabolically stable and cell-permeable glutathione (GSH) analog ({Psi}-GSH), suggesting a possible therapeutic strategy for preventing diseases associated with increased ROS levels. KEY POINTSMass spectrometry-based proteomics identified over 100 proteins participating in DNA-protein cross-links in human cells treated with ROS Our work reveals the mechanisms through which living cells recognize and remove ROS-DPCs Our study demonstrates the potential of a glutathione analog to prevent ROS-DPC formation GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=75 SRC="FIGDIR/small/704426v2_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@61ea7dorg.highwire.dtl.DTLVardef@69c420org.highwire.dtl.DTLVardef@1cb28aeorg.highwire.dtl.DTLVardef@dbc8d7_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2026

Detection of Somatic Point Mutations Directly from Spatial Transcriptomics Enables in vivo Spatiotemporal Lineage Tracing

Spatial transcriptomics reveals tissue organization but lacks in vivo lineage-tracing methods applicable to humans. We introduce SpaceTracer, a computational framework that accurately detects somatic single-nucleotide variants (SNVs) directly from spatial transcriptomics data. By leveraging naturally occurring somatic SNVs, SpaceTracer reconstructs cellular phylogenies within native tissue architecture, enabling the mapping of lineage spread, migration, lineage-coupled expression changes and lineage-aware local interactions. Applied to human cutaneous squamous cell carcinoma, it traced tumor initiation and progressions, uncovered widespread pre-invasive migration of dedifferentiated epithelial cells and characterized mutant B cells migrating from tertiary lymphoid structures (TLS) into the tumor boundary. The framework also reconstructed developmental lineages across multiple tissues and identified tissue-resident mutant immune cells. SpaceTracer thus provides a perturbation-free platform for high-resolution spatiotemporal lineage tracing, offering a transformative tool for elucidating complex biological systems--especially tumor-immune ecosystems--with direct implications for advancing cancer immunotherapy.

bioinformatics↗

bioRxiv2026

Extracting large-scale neural activity with Suite2p

Neural recordings using optical methods have improved dramatically. For example, we demonstrate here recordings of over 100,000 neurons from the mouse cortex obtained with a standard commercial microscope. To process such large datasets, we developed Suite2p, a collection of efficient algorithms for motion correction, cell detection, activity extraction and quality control. We also developed new approaches to benchmark performance on these tasks. Our GPU-accelerated non-rigid motion correction substantially outperforms alternative methods, while running over five times faster. For cell detection, Suite2p outperforms the CNMF algorithm in Caiman and Fiola, finding more cells and producing fewer false positives, while running in a fraction of the time. We also introduce quality control steps for users to evaluate performance on their own data, while offering alternative algorithms for specialized types of recordings such as those from one-photon and voltage imaging.

neuroscience↗

bioRxiv2026

MtDNA heteroplasmy controls tumor immune reprogramming through mitochondrial translation

Mitochondrial DNA (mtDNA) mutations are among the most frequent genetic alterations in human cancers, yet their molecular mechanisms in shaping tumor progression and metastasis under physiological conditions remain poorly understood. Here, we show that mtDNA heteroplasmy acts as a tumor cell-intrinsic rheostat that orchestrates fate decisions between progression and suppression. Moderate heteroplasmy induces a ribosomal storm of mitochondrial translation and ribosome biogenesis, driven by leucyl-tRNA synthetase 2 (LARS2). This response enhances metabolic fitness and licenses the secretion of S100A8/A9, enabling tumor cells to actively remodel the immune microenvironment through recruitment of myeloid-derived suppressor cells and exclusion of CD8 T cells, thereby promoting immune evasion and metastatic progression. In contrast, high heteroplasmy impairs tumorigenesis due to oxidative phosphorylation collapse. Disruption of LARS2, mitochondrial translation, or S100A9 signalling abrogates tumor progression. Our findings establish mtDNA heteroplasmy as a key regulator of cancer evolution, linking mitochondrial genetic variation to immune modulation, and reveal the LARS2-mitochondrial translation-S100A8/A9 axis as a therapeutically targetable programme within the pro-tumorigenic window of mtDNA heteroplasmy.

cancer biology↗

bioRxiv2026

Peroxisome dysfunction alters metabolism of photoreceptor outer segments in human retinal pigment epithelium

Peroxisomes are ubiquitous organelles that compartmentalize metabolic reactions including lipid catabolism and cellular detoxification. Pathogenic variants in PEX1 and PEX6 disrupt essential peroxisome functions and cause profound neurodegenerative diseases called peroxisome biogenesis disorders (PBDs). Despite retinal degeneration and blindness occurring frequently in PBDs, precisely how impaired peroxisome activity disrupts retinal function remains to be fully explored. To address this, we differentiated PEX1-/-, PEX6-/-, and wildtype human induced pluripotent stem cells into retinal pigment epithelium (iRPE) to study the consequences of peroxisome dysfunction in this disease-relevant cell type. Despite exhibiting impaired peroxisome matrix protein import, PEX1-/- and PEX6-/-iRPE had comparable morphology, tight junctions, and expression of proteins characteristic of RPE compared to wildtype iRPE. Targeted lipid profiling revealed reduced docosahexaenoic acid, a polyunsaturated fatty acid (PUFA) essential for retinal function, and elevated lipid species exclusively metabolized by peroxisomes in PEX1-/- and PEX6-/- iRPE. Following a photoreceptor outer segment (POS) challenge, PEX1-/- and PEX6-/- iRPE demonstrated disrupted PUFA retroconversion and lipid droplet accumulation. Additionally, PEX1-/- and PEX6-/-iRPE had impaired rhodopsin degradation, lysosomal dysfunction, and reduced transepithelial electrical resistance. These findings suggest that dysregulated POS metabolism in the RPE is a potential mechanism driving retinal degeneration in patients with PBDs. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/701576v2_ufig1.gif" ALT="Figure 1"> View larger version (99K): org.highwire.dtl.DTLVardef@bf2389org.highwire.dtl.DTLVardef@b62e1forg.highwire.dtl.DTLVardef@8e0b21org.highwire.dtl.DTLVardef@17cb332_HPS_FORMAT_FIGEXP M_FIG C_FIG Schematic summarizing the consequences of PEX1 and PEX6 knockout on iRPE biology, including the presence of import-incompetent peroxisomes, impaired {omega}3 and {omega}6 fatty acid retroconversion, lipid droplet accumulation, and defective photoreceptor outer segment phagocytosis.

cell biology↗

bioRxiv2026

Small brown planthopper infestation enhances it reproduction and insecticide tolerance by manipulating glucose distribution and levels in rice

The evolutionary arms race between plants and insects involves not only direct defense and counter-defense but also sophisticated resource manipulation. However, how herbivorous insects respond to host nutritional signals to modulate their fitness traits remains unclear. This study investigates how the small brown planthopper (SBPH, Laodelphax striatellus) manipulates host plant carbohydrate allocation, and to elucidate the molecular mechanisms by which the acquired glucose enhances SBPH fecundity and insecticide tolerance. Using molecular, pharmacological, and biochemical approaches, we found that SBPH infestation induced systemic carbohydrate reallocation in rice, elevating whole-plant glucose levels by promoting aerial accumulation while depleting root reserves. Host-derived glucose enhanced SBPH fecundity by activating the target of rapamycin (TOR) pathway, upregulating juvenile hormone (JH) signaling, and increasing vitellogenin production. For imidacloprid tolerance, glucose boosted glutathione S-transferase (GST) activity via two synergistic mechanisms: by upregulating glutamate cysteine ligase (GCL) to increase glutathione synthesis, and transcriptionally via the glucose-TOR-JH axis to induce LsGSTe1 (SBPH epsilon class GST) and LsGSTo1 (SBPH omega class GST) expression. Our findings establish host-derived glucose as a central signaling molecule that SBPH utilizes to modulate conserved pathways for simultaneous optimization of reproduction and insecticide resistance. This reveals a multifaceted nutrient-responsive mechanism in insect pests and identifies the glucose-TOR-JH axis as critical molecular targets for developing nutrient-based pest control strategies, such as disrupting insect nutrient-sensing pathways or modulating host carbohydrate metabolism. HighlightsO_LISBPH infestation elevates whole-plant glucose levels by promoting aerial accumulation while suppressing root abundance. C_LIO_LISBPH-induced glucose in the rice aerial tissues boosts reproduction of SBPH via TOR-JH-Vg pathway. C_LIO_LISBPH-induced glucose in the rice aerial tissues enhances imidacloprid tolerance of SBPH through GCL-GSH-GST and TOR-JH-GST axis. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=152 SRC="FIGDIR/small/701313v2_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@39e084org.highwire.dtl.DTLVardef@1c310cborg.highwire.dtl.DTLVardef@1838575org.highwire.dtl.DTLVardef@1aedebe_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2026

Disrupted TRiC allostery and conformational equilibrium by LCA-linked mutations: structural and functional insights

The eukaryotic chaperonin TRiC/CCT is essential for proteostatis, yet the molecular basis of its subunit-specific pathologies remains poorly understood. Here, we elucidate the molecular mechanism of Leber Congenital Amaurosis (LCA), a severe hereditary retinal dystrophy arised from mutations in the CCT2 subunit of TRiC. By integrating cryo-electron microscopy, biochemistry, and proteomics, we demonstrate that LCA-associated mutations (T400P and R516H in CCT2) disrupt TRiCs critical intra-molecular and intra-ring allosteric network and impair its functional cycle, drastically reducing the population of the folding-active closed state. Unexpectedly, we captured a fully folded endogenous -tubulin within the mutant TRiC chamber, revealing a unique CCT8 C-terminal tail involved folding pathway, distinct from {beta}-tubulin. Furthermore, cellular proteomics revealed that TRiC dysfunction causes a specific downregulation of essential SLC membrane transporters. We propose that the loss of these transporters is likely catastrophic for metabolically demanding tissues like the retina and developing embryo. Our work provides a direct mechanistic link between TRiC structural defects and LCA pathology, offering a new framework for understanding etiology of chaperonopathies.

biochemistry↗

bioRxiv2026

Cortico-basal ganglia dynamics of global and selective response inhibition in humans

Response inhibition is an important cognitive control mechanism, which enables flexible behavior by stopping inappropriate actions. Intracranial recordings across species have identified a neural circuit that implements response inhibition via the subthalamic nucleus of the basal ganglia. However, this work has been limited to simple tasks, in which unequivocal, salient "stop"-signals require the inhibition of all ongoing responses. Notably, response inhibition in the real world is substantially different. Real-world response inhibition is selective: it occurs only after specific salient signals ( stimulus-selectivity) and stops only specific movements, while others continue ( response-selectivity). If and how the fronto-subthalamic system implements selective inhibition is largely unknown. Here, we recorded subthalamic local field potentials and scalp-EEG in humans performing a novel, selective inhibition task. Salient signals either required stopping all initiated responses (global inhibition), stopping only some responses (response-selective inhibition), or continuing all responses - i.e., ignoring the signal (which ensures stimulus-selectivity). All three signals initially triggered a common fronto-subthalamic inhibitory process, signified by a rapid increase in {beta}-burst activity. During global inhibition, subthalamic {beta}-bursting subsequently increased above baseline, persisting for over a second. During response-selective inhibition, this activity was delayed, which enabled a second bout of disinhibition and allowed appropriate responses to continue. Throughout this period, frontal cortical and subthalamic {beta}-band activity was tightly coupled. This shows that selective inhibition is implemented through rapid, context-dependent engagement and release of fronto-subthalamic inhibition. Moreover, subthalamic activity lasted substantially longer than assumed by classic behavioral-computational models. This supports recent theoretical models that assume protracted response inhibition during action-stopping.

neuroscience↗

bioRxiv2026

Isolation and Characterisation of Hair Follicle-Derived Melanocytes

Melanocytes are unique population of cells which produce melanin pigment. However, the property of melanocytes from hair follicle and epidermis, particularly, their molecular signatures remained largely unknown. In this study, we investigated the properties of epidermis and hair follicle melanocytes by biochemical and molecular biological assays. We found that epidermal melanocytes are differentiated and mature form of hair follicle melanocytes, and they are potentially related. Irradiation with NB-UVB did not induce cell death of hair follicle melanocytes as observed in epidermal melanocytes, but activate hair follicle melanocytes, promote proliferation and migration. In situ study suggested that after UVB irradiation, root sheath of hair follicles, particularly proximity of interfollicular epidermis and hair bulb become darker, suggesting migration and maturation of hair follicle melanocytes after UVB irradiation, rather than cell death. This observation provides hints and evidence to the relationship between hair follicle and epidermal melanocytes, helps to explain the contradiction of melanocytes cell death after UVB irradiation and the use of UVB in treatment of vitiligo lesion, as well as the perifollicular repigmentation phenomenon observed in vitiligo lesion after NB-UVB phototherapy.

cell biology↗

bioRxiv2026

Single-cell transcriptomic landscapes reveal cell-type-specific regulatory mechanisms of nutrient accumulation and transport in wheat grain

To elucidate the transcriptional regulatory mechanisms underlying wheat grain development, we constructed single-cell transcriptomic atlases of wheat grains at 4 and 8 days after pollination (DAP) using single-nucleus RNA sequencing. A total of 58,546 high-quality nuclei were clustered into 16 distinct cell populations representing all major seed tissues, including the embryo, aleurone layer, transfer cells, endosperm, inner pericarp, seed coat, and embryo surrounding region. Comparative analysis revealed a dynamic transcriptional reprogramming from growth-related pathways at DAP 4 to nutrient accumulation at DAP 8, which coincided with shifts in the expression of hormone signaling and organ development genes, as well as starch and storage protein genes. Pseudotime trajectory analysis identified two major differentiation branches, highlighting distinct roles in nutrient storage and support. Notably, the transcription factor TaMADS58 was found to regulate pericarp cell number while simultaneously enhancing protein content and processing quality. Concurrently, TaJEKLL, specifically expressed in nucellar projection cells, was demonstrated to influence nucellar projection development and nutrient transport. Natural variation in TaMADS58 and TaJEKLL revealed their potential to decouple yield from quality traits, offering promising applications for crop improvement. Collectively, this study provides a high-resolution single-cell resource for wheat seed biology and demonstrates that investigating gene expression with spatiotemporal precision at the single-cell level can facilitate the discovery of key genes for precisely regulating individual traits.

plant biology↗

bioRxiv2026

'Zipper' Grammar of CTD Governs the Spatial Programing of the Transcription Cycle of RNA Polymerase II

RNA polymerase II transcribes all protein-coding genes in eukaryotes, with its C-terminal domain (CTD) acting as a regulatory platform throughout the transcription cycle. Despite its simple sequence, the conserved heptad repeats encode a regulatory grammar critical for transcription initiation, elongation, and termination. Using structural analysis, single-molecule imaging, and synthetic CTD-engineered Pol II constructs, we defined the minimal sequence requirements across transcriptional stages. We show that while SP motifs are essential phosphorylation sites, flanking residues tolerate variability. In contrast, the periodic positioning of tyrosine residues is indispensable for pre-initiation complex (PIC) assembly through interactions with the Mediator, which are disrupted upon Ser5 phosphorylation triggering promoter escape. This supports a "zipper" model where sequential tyrosine engagement stabilizes PIC assembly and progressive phosphorylation propels Pol II escape. Site-specific Ser2/5 phosphorylation orchestrates 3-end processing factor recruitment. These findings redefine the functional grammar of the Pol II CTD and explain how a low-complexity sequence achieves regulatory specificity.

cell biology↗

bioRxiv2025

Dose-dependent NFI regulation of progenitor lifespan and output underlying human neocortical malformation

Nuclear Factor I (NFI) misexpressions in humans are associated with severe brain malformations, yet the underlying mechanisms remain poorly understood. Here we show that NFIs regulate the broad lineage progression and lifespan of radial glial progenitors (RGPs), and consequently neocortical development in a dose-dependent manner. Human cerebral organoids carrying patient-mimicking NFI mutations exhibit expression level-dependent bidirectional impairments in RGP temporal development, coinciding with patient phenotypes. In mouse models, selective removal of NFIs leads to a dramatic protraction of RGP lineage progression and lifespan, excessive progeny output, and neocortical overgrowth and abnormal folding, whereas overexpression of NFIs accelerates RGP lineage progression, resulting in developmental stage-dependent precocious productions of diverse neural progenies. Moreover, NFIs exhibit a positive auto-regulation and progressive increase in expression, and regulate distinct temporal-specific targets underlying RGP lineage progression. These results suggest that NFIs act as evolutionarily conserved key global temporal regulators of RGP lineage progression and neocortical development. HIGHLIGHTSO_LINFIs affect human RGP temporal development coinciding with patient phenotypes. C_LIO_LINFI removal protracts RGP lineage progression and lifespan with excessive progeny output. C_LIO_LINFI overexpression accelerates RGP lineage progression with precocious progeny output. C_LIO_LINFIs regulate distinct temporal-specific targets underlying RGP lineage progression. C_LI

neuroscience↗

bioRxiv2025

Probing Critical Injury Thresholds for Maladaptive Epithelial Injury and Repair Processes with Photoresponsive Bioinspired Synthetic Basement Membrane

Microinjuries to the lung epithelium are hypothesized to initiate maladaptive processes that lead to fibrosis. Human in vitro models remain a great need for studying this injury-initiation process for mechanistic understanding and therapeutic development. We established a photoresponsive synthetic extracellular matrix (ECM) inspired by the basement membrane that enables triggered injuries of defined size and frequency for probing cellular responses. The synthetic matrix integrated a photolabile bis-coumarin linker for light-triggered injury and relevant integrin-binding peptides for cell function. Bio-orthogonal chemistry was used to create hydrogel-based ECMs with tunable elasticity in transwells, which are traditionally used for epithelial cell culture. Integrin-binding peptide combinations synergistically promoted model epithelial cell layer formation with increased E-cadherin expression and barrier function. An accessible photomasking approach was established for selectively photodegrading the synthetic matrix with cytocompatible visible light and achieving different injury depths and widths. Following a critical injury size, cell responses recapitulated key features of dysregulated re-epithelialization with decreased E-cadherin, proliferation, and barrier function and increased apoptosis. This work provides a new materials-based tool for probing injury and repair processes with tunable control of both the ECM and injury to it with opportunities for future mechanistic and therapeutic insights to address maladaptive wound healing processes.

bioengineering↗

bioRxiv2025

Genome assembly and population genomic analysis of Aegilops caudata uncover a rich source for disease and insect pest resistance for wheat improvement

Aegilops caudata L. is a rich source of resistance genes to major wheat pathogens and pests, yet its complex genome structure and lack of a reference sequence have hindered genetic analysis, gene discovery, and introgression. Here, we report a high-quality genome sequence assembly of Ae. caudata accession S740-69, integrated with optical mapping to precisely delineate introgressed segments from structurally altered genomic regions in wheat-Ae. caudata translocation lines carrying a novel stem rust resistance gene. Resequencing and phenotyping of 95 diverse accessions, coupled with k-mer-based association mapping, enabled population-level identification of several novel loci for resistance to wheat pests and diseases, such as greenbug and stem rust. Virus-induced gene silencing confirmed Aecau6C01G127270 (SrAect1) as the first functionally characterized stem rust resistance gene from Ae. caudata. This new genomic framework provides a foundation for systematic mining of resistance genes in this species and their efficient introgression into wheat.

genomics↗

bioRxiv2025

Neocortical temporal patterning by a two-layered regulatory network

In the developing neocortex, a diverse array of neurons with defined types and abundances are systematically generated by a limited population of radial glial progenitors (RGPs) as they undergo successive fate changes. The molecular regulation behind this intricate temporal patterning remains elusive. We undertook in-depth single-cell multi-omics analyses, discovering a two-layered regulatory framework at the core of this process. Central to this are global temporal regulators positioned above a temporal network, consisting of series of transcriptional factor (TF) hub groups under sequential state transitions. This temporal network operates not by restricting TF expressions to discrete temporal windows, but through coordinated transcriptional and chromatin-accessibility dynamics that modulate transient TF regulatory activity. Moreover, global temporal regulators specify the duration of each cascading stage and, consequently, the number of progenies generated at each stage. Loss of global temporal regulators protracts RGP lineage progression, whereas their increased activity accelerates it. These findings suggest a two-layer temporal regulatory system controlling RGP lineage progression and neural progeny output duality in mammalian neocortical development.

neuroscience↗

bioRxiv2025

Tuning the open-close equilibrium of Cereblon with small molecules influences protein degradation

Most PROTACs and molecular glue degraders currently approved or in clinical trials recruit Cereblon (CRBN) as the ubiquitin E3 ligase. Upon binding ligands and molecular glues, CRBN undergoes a significant structural rearrangement from an open to closed state, defined by the positioning of the thalidomide-binding domain (TBD) with respect to the Lon domain. However, the exact molecular basis for this ligand-induced conformational change and its implication to neo-substrate degradation remain elusive. During our campaign to discover novel CRBN binders, we found hits exhibiting distinct biophysical behaviour from classical thalidomide-based ligands. By combining orthogonal biophysical methods of differential scanning fluorimetry, isothermal titration calorimetry, and small-angle X-ray scattering, supported by X-ray crystallography and cryo-EM structures of ligand-bound complexes, we classify CRBN binders between those that can induce CRBN closure, and those that cannot. Mutational studies identify key residues in the CRBN ligand binding pocket and N-terminal belt that are essential for the Lon and TBD domains to come together in the closed state. Finally, we show that the probability to yield active degrader molecules is greatly influenced by whether binders can or cannot induce CRBN closure. Together, our study reveals new molecular insights into the structural basis for how CRBN open-closed equilibrium is directly modulated by compound binding and impact target degradability by CRBN, with important implications to the design of PROTACs and molecular glue degraders.

biochemistry↗