Biology subjects

Ahn, J. J.

Publications and source records attributed to Ahn, J. J..

6 recordsLinked to original sources

bioRxiv2026

Defining the molecular interaction between influenza hemagglutinin and MHC-II

The hemagglutinin (HA) of some influenza viruses can interact with major histocompatibility complex class II (MHC-II), but how these proteins interact is unclear. Here we demonstrate that diverse H5 HAs can use MHC-II to enter cells, with avian MHC-II enabling more efficient entry than human MHC-II for most H5 HAs. To define the molecular interface, we use pseudovirus deep mutational scanning to measure how mutations to H5 HA affect its interaction with tufted duck MHC-II, and identify mutations that restrict HA to exclusively MHC-II or sialic acid receptors. We leverage identification of H5 HA mutations that increase binding to tufted duck MHC-II to determine a 4.8 [A] cryo-EM model of the complex. To support the structural model, we measure how all mutations to tufted duck MHC-II affect its interaction with H5 HA, and find the alpha chain is the dominant determinant but beta chain sites near the peptide-binding groove also contribute. To generalize these findings, we use deep mutational scanning to show that a H7 HA interacts with MHC-II similarly to H5 HA. Finally, we show that H1, H2, H3, and H9 HAs interact with avian or human MHC-II, although interactions vary among strains that evolved in different hosts.

microbiology↗

bioRxiv2026

Influenza hemagglutinin subtypes have different sequence constraints despite sharing extremely similar structures

Hemagglutinins (HA) from different influenza A virus subtypes share as little as [~]40% amino acid identity, yet their protein structure and cell entry function are highly conserved. Here we examine the extent that sequence constraints on HA differ across three subtypes. To do this, we first use pseudovirus deep mutational scanning to measure how all amino-acid mutations to an H7 HA affect its cell entry function. We then compare these new measurements to previously described measurements of how all mutations to H3 and H5 HAs affect cell entry function. We find that [~]50% of HA sites display substantially diverged preferences for different amino acids across the HA subtypes. The sites with the most divergent amino-acid preferences tend to be buried and have biochemically distinct wildtype amino acids in the different HA subtypes. We provide an example of how rewiring the interactions among contacting residues has dramatically shifted which amino acids are tolerated at specific sites. Overall, our results show how proteins with the same structure and function can become subject to very different site-specific evolutionary constraints as their sequences diverge.

evolutionary biology↗

bioRxiv2025

Neuropathological hallmarks during the chronic phase of ischemic stroke in mice and humans

BackgroundImprovements in acute stroke treatment, including endovascular thrombectomy and critical care management, have increased survival rates post-stroke. However, stroke remains a leading cause of long-term disability and many survivors have significant neurological and cognitive deficits. Despite this, the chronic neurological sequelae and underlying secondary injury mechanisms induced by ischemic stroke remain understudied. MethodsThis study examined long-term neurobehavioral recovery and neuropathology at 2- and 6- months post-stroke in young (12-week-old) male C57Bl/6 mice after a 60-minute transient middle cerebral artery occlusion (MCAO) or sham surgery. Behavioral testing included the open field test (OFT), novel object recognition test (NORT), fear conditioning (FC), nesting activity, and tail suspension. Post-mortem brain samples from patients with chronic ischemic stroke were also assessed. Immunohistochemistry (IHC) was performed to assess demyelination (MBP), neuronal apoptosis (TUNEL), and A{beta}42 in human brains. Flow cytometric analysis was performed to assess microglial phenotypes, the chronic neuroimmune landscape, and to evaluate senescent-like phenotypes (SA-{beta}Gal and lipofuscin). Transcriptomic profiling was performed using RNA isolated from the ipsilateral hemisphere in stroke mice. ResultsExperimental stroke caused progressive cognitive and motor decline up to 6 months post-MCAO. IHC and flow cytometric analyses revealed a significant increase in TUNEL-positive neurons, cortical and hippocampal gliosis, white matter degradation, senescent cell accumulation, and altered microglial function. IHC analysis of postmortem human brains shows significantly increased levels of microgliosis, senescent cells and amyloid burden. Transcriptomic analysis revealed that pathways involving apoptosis, microglial activation and the complement pathway were chronically upregulated after stroke. ConclusionOur findings demonstrate that ischemic stroke induces a non-resolving microglial response and accelerated inflamm-aging in the brain, evidenced by premature senescence and elevated production of cytokines within the chronic infarct microenvironment. Senescent-like phenotypes and chronic neurodegenerative disease signatures may contribute to the progressive worsening of cognitive function post-stroke. These results suggest that chronic, ongoing neurodegeneration occurs late after stroke, even in younger mice. Mitigating these detrimental changes may offer viable targets for delayed treatment strategies for stroke.

neuroscience↗

bioRxiv2024

Deep mutational scanning of H5 hemagglutinin to inform influenza virus surveillance

H5 influenza is a potential pandemic threat. Previous studies have identified molecular phenotypes of the viral hemagglutinin (HA) protein that contribute to pandemic risk, including cell entry, receptor preference, HA stability, and reduced neutralization by polyclonal sera. Here we use pseudovirus deep mutational scanning to measure how all mutations to a clade 2.3.4.4b H5 HA affect each phenotype. We identify mutations that allow HA to better bind 2-6-linked sialic acids, and show that some viruses already carry mutations that stabilize HA. We also identify recent viral strains with reduced neutralization to sera elicited by candidate vaccine virus. Overall, the systematic nature of deep mutational scanning combined with the safety of pseudoviruses enables comprehensive characterization of mutations to inform surveillance of H5 influenza.

microbiology↗

bioRxiv2024

MEK signaling represents a viable therapeutic vulnerability of KRAS-driven somatic brain arteriovenous malformations

Brain arteriovenous malformations (bAVMs) are direct connections between arteries and veins that remodel into a complex nidus susceptible to rupture and hemorrhage. Most sporadic bAVMs feature somatic activating mutations within KRAS, and endothelial-specific expression of the constitutively active variant KRASG12D models sporadic bAVM in mice. By leveraging 3D-based micro-CT imaging, we demonstrate that KRASG12D-driven bAVMs arise in stereotypical anatomical locations within the murine brain, which coincide with high endogenous Kras expression. We extend these analyses to show that a distinct variant, KRASG12C, also generates bAVMs in predictable locations. Analysis of 15,000 human patients revealed that, similar to murine models, bAVMs preferentially occur in distinct regions of the adult brain. Furthermore, bAVM location correlates with hemorrhagic frequency. Quantification of 3D imaging revealed that G12D and G12C alter vessel density, tortuosity, and diameter within the mouse brain. Notably, aged G12D mice feature increased lethality, as well as impaired cognition and motor function. Critically, we show that pharmacological blockade of the downstream kinase, MEK, after lesion formation ameliorates KRASG12D-driven changes in the murine cerebrovasculature and may also impede bAVM progression in human pediatric patients. Collectively, these data show that distinct KRAS variants drive bAVMs in similar patterns and suggest MEK inhibition represents a non-surgical alternative therapy for sporadic bAVM.

molecular biology↗

bioRxiv2020

Rapid Establishment of Tracheal Stenosis in Pigs Using Endotracheal Tube Cuff Overpressure and Electrocautery

BackgroundCentral airway obstruction can be caused by cancer, tracheal intubation, or tuberculosis, among others. If surgery is contraindicated, bronchoscopic therapy may be performed. Bronchoscopic treatment for airway obstruction is continuously evolving. In particular, attempts to overcome the current shortcomings of airway stents (stent migration, mucostasis, and granulation tissue formation) are currently ongoing. To apply a new airway stent to humans, preclinical studies in an appropriate animal model is needed. Canine and porcine tracheas have been used as animal airway stenosis models. However, existing models take a long time to develop (3-8 weeks) and have a disadvantage that the mechanism of stenosis is different from that in humans. PurposeTo establish a new and fast tracheal stenosis model in pigs using a combination of cuff overpressure intubation and electrocautery. MethodsFourteen pigs were divided into three groups: tracheal cautery (TC) group (n = 3), cuff overpressure intubation (COI) group (n = 3), and COI-TC combination group (n = 8). Cuff overpressure (200/400/500 mmHg) was applied using a 9-mm internal diameter endotracheal tube. Tracheal cautery (40/60 watts) was performed using a rigid bronchoscopic electrocoagulator. After intervention, the pigs were observed for 3 weeks and bronchoscopy was performed every 7 days. When the cross-sectional area decreased by > 50%, it was judged that tracheal stenosis was established. ResultsThe time for tracheal stenosis was 14 days in the TC group and 7 days in the COI-TC combination group. In the COI group, no stenosis occurred. In the COI-TC group, electrocautery (40 watts) immediately after intubation for > 1 hour with a cuff pressure of 200 mmHg or more resulted in sufficient tracheal stenosis within 7 days. Moreover, the degree of tracheal stenosis increased in proportion to the cuff pressure and tracheal intubation time. ConclusionsThe combined use of cuff overpressure and electrocautery helped to establish tracheal stenosis in pigs rapidly. This animal model was technically simple and reproducible, and used a mechanism similar to that in human tracheal stenosis. It is expected to help develop new treatments for airway stenosis

physiology↗