Biology subjects

Xu, R.-G.

Publications and source records attributed to Xu, R.-G..

4 recordsLinked to original sources

bioRxiv2026

From Generalist to Specialist: Evolution of PS2 α-integrins and Implications for Drug Targeting

Integrins are heterodimeric transmembrane receptors that mediate cell-cell and cell- extracellular matrix interactions and play essential roles in development and disease. Within the PS2 -integrin subfamily, four paralogs (IIb, 5, 8, and V) share a conserved RGD-binding motif yet exhibit diverse functional specializations. Integrins have been widely targeted therapeutically for various clinical conditions, though achieving subtype specificity remains a major challenge. Here, we performed an integrative evolutionary analysis of 114 PS2 -integrin sequences across 28 vertebrate species, combining phylogenetic reconstruction, time calibration, ancestral sequence inference, and structural mapping. Our time-calibrated phylogeny indicates that the PS2 lineage originated [~]862 Mya, with diversification of the four paralogs occurring prior to vertebrate radiation. Ancestral state reconstruction reveals that fibronectin and vitronectin binding are ancestral traits, whereas fibrinogen binding and {beta}3 pairing arose independently in the IIb and V lineage. Evolutionary rate analysis shows domain-specific divergence, with the {beta}-propeller acting as a hotspot of evolutionary change, likely driven by combined pressures from ligand binding and {beta}-subunit interaction. These pressures vary across paralogs: IIb exhibits accelerated evolution in ligand-binding regions, while V displays elevated rates in {beta}-subunit interaction domains. Mapping sequence variation onto structural interfaces identifies lineage-specific substitutions underlying functional divergence, including distinct molecular solutions for fibrinogen binding in IIb and V. These findings collectively demonstrate that PS2 -integrins evolved from a generalist ancestor through neofunctionalization and lineage-specific specialization. This work provides an evolutionary framework for identifying subtype-specific functional sites and highlights the potential of evolution-informed strategies to guide the development of more selective integrin-targeting therapeutics.

bioinformatics↗

bioRxiv2024

Multi-parametric thrombus profiling microfluidics detects intensified biomechanical thrombogenesis associated with hypertension and aging

Arterial thrombosis, which represents a critical complication of cardiovascular diseases, is a leading cause of death and disability worldwide with no effective bioassay for clinical prediction. As a symbolic feature of arterial thrombosis, severe stenosis in the blood vessel creates a high-shear, high-gradient flow environment that effectively facilitates platelet aggregation towards vessel occlusion even with platelet amplification loops inhibited. However, no approach is currently available to comprehensively characterize the size, composition and platelet activation status of thrombi forming under this biorheological condition. Here, we present a thrombus profiling assay that monitors the multi-dimensional attributes of thrombi forming in conditions mimicking the physiological scenario of arterial thrombosis. Using this platform, we demonstrate that different receptor-ligand interactions contribute distinctively to the composition and activation status of the thrombus. Our investigation into hypertensive and older individuals reveals intensified biomechanical thrombogenesis and multi-dimensional thrombus profile abnormalities, demonstrating a direct contribution of mechanobiology to arterial thrombosis and endorsing the diagnostic potential of the assay. Furthermore, we identify the hyperactivity of GPIb-integrin IIb{beta}3 mechanosensing axis as a molecular mechanism that contributes to hypertension-associated arterial thrombosis. By studying the interactions between anti-thrombotic inhibitors and hypertension, and the inter-individual variability in personal thrombus profiles, our work reveals a critical need for personalized anti-thrombotic drug selection that accommodates each patients pathological profile.

bioengineering↗

bioRxiv2018

Next generation CRISPR/Cas9 transcriptional activation in Drosophila using flySAM

CRISPR/Cas9-based transcriptional activation (CRISPRa) has recently emerged as a powerful and scalable technique for systematic over-expression genetic analysis in Drosophila melanogaster. We present flySAM, a potent new tool for in vivo CRISPRa, which offers a major improvement over existing strategies in terms of effectiveness, scalability, and ease-of-use. flySAM outperforms existing in vivo CRISPRa strategies, and approximates phenotypes obtained using traditional Gal4-UAS over-expression. Further, because flySAM typically only requires a single sgRNA, it dramatically improves scalability. We use flySAM to demonstrate multiplexed CRISPRa, which has not been previously shown in vivo. In addition, we have simplified the experimental usage of flySAM by creating a single vector encoding both the UAS:Cas9-activator and the sgRNA, allowing for inducible CRISPRa in a single genetic cross. flySAM will thus replace previous CRISPRa strategies as the basis of our growing genome-wide transgenic over-expression resource, TRiP-OE.

genetics↗

bioRxiv2016

The large terminase DNA packaging motor grips DNA with its ATPase domain for cleavage by the flexible nuclease domain

Many viruses use a powerful terminase motor to pump their genome inside an empty procapsid shell during virus maturation. The large terminase (TerL) protein contains both enzymatic activities necessary for packaging in such viruses: the ATPase that powers DNA translocation and an endonuclease that cleaves the concatemeric genome both at initiation and completion of genome packaging. However, how TerL binds DNA during translocation and cleavage is still mysterious. Here we investigate DNA binding and cleavage using TerL from the thermophilic phage P74-26. We report the structure of the P74-26 TerL nuclease domain, which allows us to model DNA binding in the nuclease active site. We screened a large panel of TerL variants for defects in binding and DNA cleavage, revealing that the ATPase domain is the primary site for DNA binding, and is required for nucleolysis. The nuclease domain is dispensable for DNA binding but residues lining the active site guide DNA for cleavage. Kinetic analysis of nucleolysis suggests flexible tethering of the nuclease domains during DNA cleavage. We propose that interactions with the procapsid shell during DNA translocation conformationally restrict the nuclease domain, inhibiting cleavage; TerL release from the procapsid upon completion of packaging unlocks the nuclease domains to cleave DNA.

biochemistry↗