Biology subjects

Ly, H.

Publications and source records attributed to Ly, H..

4 recordsLinked to original sources

bioRxiv2025

Identification of a novel biological role of arenavirus NP exonuclease (exoN) activity in a safe Pichinde virus model

Arenaviruses such as Lassa virus (LASV) and Junin virus (JUNV) can cause lethal hemorrhagic fever diseases with no FDA-approved vaccines or effective therapeutics. The arenaviral nucleoprotein (NP) contains an exoribonuclease (exoN) domain that suppresses type I interferon (IFN-I) production by degrading pathogen-associated molecular-pattern (PAMP) RNAs. The biological roles of NP exoN during viral infection have not been well characterized for highly pathogenic arenaviruses, largely due to biosafety constraints and challenges in generating viable NP exoN mutants. We previously developed a recombinant tri-segmented viral vector (rP18tri) based on non-pathogenic Pichinde virus (PICV), which allows functional studies of transgenes during arenavirus infection in a BSL-2 setting. In this study, we introduced point mutations at individual catalytic residues to abolish PICV NP exoN activity and generated exoN-deficient rP18tri(NPm) reporter viruses. These mutants failed to replicate in IFN-competent A549 cells, accompanied by strong IFN-I induction. Expression of wild-type (WT) JUNV NP, but not its exoN-deficient mutant, in the rP18tri(NPm)-G backbone restored single-cycle infectivity and suppressed IFN-I induction. Furthermore, exoN-deficient viruses produced disproportionately high levels of defective virion particles relative to virion RNA from infected A549 cells, a defect that was rescued by expression of WT JUNV NP but not the exoN-deficient NP as a transgene. Together, these data demonstrate an essential role of NP exoN in IFN-I suppression and identify a novel biological function of NP exoN in promoting the production of infectious virion particles in IFN-competent cells. ImportanceArenaviruses, such as Junin virus (JUNV), can cause severe viral hemorrhagic fever in humans, with no FDA-approved vaccines or effective therapeutics. Arenaviral nucleoprotein (NP) contains an exoribonuclease domain (exoN), which helps to evade the host immune system by blocking the production of type I interferons (IFNs). However, the biological role of NP exoN in arenavirus infection is not well understood. In this study, we used a recombinant, tri-segmented non-pathogenic Pichinde virus (PICV) with NP exoN mutations as a safe and infectious arenavirus vector to express JUNV NP as a transgene. We found that JUNV NP exoN plays a key role in suppressing IFN-I responses and discovered a previously unrecognized function of exoN in producing infectious virion particles in IFN-competent cells. These findings improve our understanding of arenavirus infection and identify NP exoN as a promising target for developing new antiviral therapies.

microbiology↗

bioRxiv2024

Recombinant Pichinde reporter virus as a safe and suitable surrogate for high-throughput antiviral screening against highly pathogenic arenaviruses

Several arenaviruses, such as the Old World (OW) Lassa virus (LASV) and the New World (NW) Junin virus (JUNV), can cause severe and lethal viral hemorrhagic fevers in humans. Currently, no vaccines or specific antiviral therapies are FDA-approved for treating arenavirus infections. One major challenge for the development of new therapeutic candidates against these highly pathogenic viruses is that they are BSL-3/4 pathogens that need to be handled in high biocontainment laboratories. In this work, a recombinant non-pathogenic New World arenavirus, Pichinde virus (rPICV), was used for the development of a high-throughput screening (HTS) assay in the BSL-2 laboratory for the screening and identification of small molecule inhibitors against arenaviruses. The rPICV is a replication-competent virus expressing the firefly luciferase reporter gene in the infected cells proportionally to the infection rate. rPICV infection was optimized for an automated HTS in 384-well format with robust Z' scores, high signal-to-background ratios, and low intrinsic variance. Screening an established library allowed for the identification of five top hit compounds, which included ribavirin, a known inhibitor of arenaviral RNA synthesis, showing good potency and selectivity in inhibiting rPICV replication. The antiviral activity of the top hit compounds was further validated against another recombinant arenavirus, the OW lymphocytic choriomeningitis virus (rLCMV) and against laboratory strains of LASV (Josiah) and JUNV (Romero). The use of rPICV in the HTS-based antiviral assay under BSL-2 condition has proven to be safe and suitable for the identification of broad-spectrum small molecule inhibitors against highly pathogenic arenaviruses.

microbiology↗

bioRxiv2024

Balancing Locality and Reconstruction in Protein Structure Tokenizer

The structure of a protein is crucial to its biological function. With the expansion of available protein structures, such as those in the AlphaFold Protein Structure Database (AFDB), there is an increasing need for efficient methods to index, search, and generate these structures. Additionally, there is a growing interest in integrating structural information with models from other modalities, such as protein sequence language models. We present a novel VQ-VAE-based protein structure tokenizer, AIDO.StructureTokenizer (AIDO.St), which is a pretrained module for protein structures in an AI-driven Digital Organism [1]. AIDO.StructureTokenizer is a 300M parameter model consisting of an equivariant encoder to discretize input structures into tokens, and an invariant decoder to reconstruct the inputs from these tokens. In addition to evaluating structure reconstruction ability, we also compared our model to Foldseek, ProToken, and ESM3 in terms of protein structure retrieval ability. Through our experiments, we discovered an intriguing trade-off between the encoders locality and retrieval ability and the decoders reconstruction ability. Our results also demonstrate that a better balance between retrieval and reconstruction enables a better alignment between the structure tokens and a protein sequence language model, resulting in better structure prediction accuracy. Models and code are available through ModelGenerator in https://github.com/genbio-ai/AIDO and on Hugging Face.

bioinformatics↗

bioRxiv2023

Cancer cells co-evolve with retrotransposons to mitigate viral mimicry

Overexpression of repetitive elements is an emerging hallmark of human cancers1. Diverse repeats can mimic viruses by replicating within the cancer genome through retrotransposition, or presenting pathogen-associated molecular patterns (PAMPs) to the pattern recognition receptors (PRRs) of the innate immune system2-5. Yet, how specific repeats affect tumor evolution and shape the tumor immune microenvironment (TME) in a pro- or anti-tumorigenic manner remains poorly defined. Here, we integrate whole genome and total transcriptome data from a unique autopsy cohort of multiregional samples collected in pancreatic ductal adenocarcinoma (PDAC) patients, into a comprehensive evolutionary analysis. We find that more recently evolved Short Interspersed Nuclear Elements (SINE), a family of retrotransposable repeats, are more likely to form immunostimulatory double-strand RNAs (dsRNAs). Consequently, younger SINEs are strongly co-regulated with RIG-I like receptor associated type-I interferon genes but anti-correlated with pro-tumorigenic macrophage infiltration. We discover that immunostimulatory SINE expression in tumors is regulated by either Long Interspersed Nuclear Elements 1 (LINE1/L1) mobility or ADAR1 activity in a TP53 mutation dependent manner. Moreover, L1 retrotransposition activity tracks with tumor evolution and is associated with TP53 mutation status. Altogether, our results suggest pancreatic tumors actively evolve to modulate immunogenic SINE stress and induce pro-tumorigenic inflammation. Our integrative, evolutionary analysis therefore illustrates, for the first time, how dark matter genomic repeats enable tumors to co-evolve with the TME by actively regulating viral mimicry to their selective advantage.

cancer biology↗