Biology subjects

Cui, C. S.

Publications and source records attributed to Cui, C. S..

3 recordsLinked to original sources

bioRxiv2026

Spatial pharmaco-multiomics reveals drug distribution, metabolic niches, and spatially constrained resistance in medulloblastoma

Single-cell and spatial transcriptomic studies have provided insights into the developmental origins and intratumoural heterogeneity of SHH medulloblastoma (SHH-MB) and suggested how targeted drugs such as CDK4/6 inhibitors remodel tumour ecosystems, yet the interplay between local drug exposure, metabolism, cell state, and drug resistance remains poorly understood. Here we developed a same-section spatial pharmaco-multiomics framework that integrates MALDI-MSI-based spatial metabolomics with Visium whole-transcriptome profiling and high-resolution Xenium imaging to map palbociclib distribution, metabolite landscapes, and transcriptional programs within the same histological contexts of an SHH-MB PDOX model and primary human tumours. Palbociclib-rich tumour bulk exhibited broad suppression of E2F-driven proliferation and a shift toward neuronal differentiation, corroborating and extending prior findings. In contrast, drug-poor tumour-brain interfaces and perivascular regions retained E2F-high proliferative states and were enriched for mesenchymal-like stromal cells and ECM-remodelling genes, indicating anatomically constrained reservoirs of tolerance. Spatial metabolomics linked these interface niches to ganglioside (GM2) and sphingomyelin enrichment, while differentiated, drug-exposed regions displayed phosphatidylcholine, phosphatidic-acid signatures consistent with neuronal maturation. Integrated pathway analysis further revealed a "mitochondrial tuning" program, with upregulation of histidine, folate/one-carbon, CoA, and lipoate metabolism with redox and oxidative-phosphorylation support. These signatures were specific to therapy-exposed border cells. Rare palbociclib-positive, E2F-high resistant spots additionally exhibited mitotic checkpoint and DNA-repair signatures, implying a drug-induced resistance axis independent of scarcity. Together, our study provides a generalisable same-section spatial pharmaco-multiomics pipeline and a spatially resolved model of CDK4/6 response, nominating interface-focused metabolic and cell-intrinsic vulnerabilities for combination therapy.

cancer biology↗

bioRxiv2025

Molecular mechanism of naturally-encoded signaling-bias at the complement anaphylatoxin receptors

The conceptual framework of biased signaling has revolutionized our understanding of GPCR signaling and regulatory paradigms, and greatly impacted the efforts focused on the discovery of GPCR-targeted therapeutics. However, the mechanistic basis of biased signaling remains primarily defined based on synthetic ligands and receptor mutants with relatively limited progress in understanding naturally-encoded signaling-bias. Here, we present fundamental molecular and structural insights into naturally-encoded signaling-bias at the complement anaphylatoxin C5a receptors namely, C5aR1 and C5aR2. We first discover that C5a-d-Arg, the naturally-occurring version of C5a lacking the terminal arginine, exhibits robust G-protein signaling-bias at C5aR1, characterised by attenuated {beta}arr recruitment. This signaling-bias manifests in both cytokine release from primary human immune cells, and in vivo, during neutrophil mobilization. We combine the cryo-EM structures of C5a/C5a-d-Arg-C5aR1 complexes with MD simulation, site-directed mutagenesis, and cellular experiments to elucidate that the G-protein-bias exhibited by C5a-d-Arg results from a distinct orientation of TM7 and helix 8 in C5aR1 leading to inefficient GRK recruitment and receptor phosphorylation. Next, we determine the first cryo-EM structures of C5aR2, a naturally-encoded {beta}-arrestin-biased receptor, in an apo state, complexed with the natural agonists C5a and C5a-d-Arg, and three peptide agonists including a first-in-class, newly discovered C5aR2-selective agonist, R8Y. These structural snapshots reveal key differences between the binding of C5a and C5a- d-Arg to C5aR1 and C5aR2, and provide a molecular basis of functional specialization at these two receptors. Moreover, the structural insights also allow us to decipher the molecular basis of naturally-encoded signaling-bias at C5aR2 originating from a shallower cytoplasmic interface with hydrophobic interior pocket that is not permissive to efficient G-protein-coupling and activation. Finally, we also engineer and characterize loss-of-function and gain-of-function variants of C5aR1 and C5aR2, which in turn corroborate and validate the structural observations presented here. Collectively, our findings offer crucial insights into previously lacking molecular mechanisms of the naturally-encoded signaling-bias at GPCRs, which have broad implications not only for the general framework of biased-signaling, but also for novel therapeutic design.

biochemistry↗

bioRxiv2025

Molecular fingerprints of a convergent mechanism orchestrating diverse ligand recognition and species-specific pharmacology at the complement anaphylatoxin receptors

Complement anaphylatoxin receptors (C3aR and C5aR1) are prototypical G protein-coupled receptors (GPCRs) playing crucial physiological roles in innate immunity by combating pathogenic infections and orchestrating inflammatory responses. They continue to be important therapeutic targets for multiple disorders including autoimmune diseases, acute and chronic inflammation, and allergy-related conditions. Recent structural coverage has provided important insights into their activation and signaling, however, confounding observations in the literature related to ligand efficacy and functional responses, especially in different model systems, present a major challenge for drug discovery efforts. Here, we systematically and comprehensively profile a broad set of natural and synthetic ligands at C3aR and C5aR1 and discover a previously unanticipated level of functional specialization in terms of species-specific pharmacology and receptor activation. Taking a lead from this, we determine seventeen cryo-EM structures of different ligand-receptor-G-protein complexes and uncover distinct orientation of agonists between the human and mouse receptors despite an overlapping positioning in the orthosteric binding pocket. Combined with extensive mutagenesis and functional assays, these structural snapshots allow us to decode and validate a convergent molecular mechanism involving a "Five-Point-Switch" in these receptors that orchestrates the recognition and efficacy of diverse agonists. We also identify species-specific differences at the level of phosphorylation patterns encoded in the carboxyl-terminus of these receptors and directly visualize their impact on {beta}arr binding and activation using cryo-EM structures. Interestingly, we observe that {beta}arrs engage with the mouse C5aR1 using a variation of previously discovered P-X-P-P phosphorylation motif via a "Sliding-Mechanism" and also exhibit distinct oligomeric state for the human vs. mouse receptors. Taken together, this study elucidates functional specialization at the complement anaphylatoxin receptors and underlying molecular mechanisms, offering a previously lacking framework with direct and immediate implications for the development of novel therapeutics.

biochemistry↗