Biology subjects

Bailey, I.

Publications and source records attributed to Bailey, I..

3 recordsLinked to original sources

bioRxiv2026

Proximity proteomics reveals a role for IFI16 during human coronavirus infection

Viruses rely on the infected host cell to ensure successful replication and propagation of infection. This is achieved through interactions between virus-encoded proteins and proteins expressed in infected cells. All human coronaviruses (HCoVs) encode 16 non-structural proteins (NSPs) which exhibit some level of similarity in identity and function among the HCoVs. To identify host proteins that are potential interacting partners of HCoV NSPs, we utilized split-TurboID along with mass spectrometry and identified IFN-{gamma}-inducible protein-16 (IFI16) as a proximal partner of SARS-CoV-2 NSP8 and NSP10. To investigate the significance of the association between the NSP8/NSP10 complex and IFI16, we utilized CRISPR-Cas9 to knockout and CRISPRi to knockdown IFI16 in A549 cells and demonstrated that loss or reduced expression of IFI16 leads to a decrease in human coronavirus infection. We further demonstrated that there is reduced viral RNA replication and viral protein synthesis upon loss of IFI16. Interestingly, the loss of IFI16 results in reduced expression of type I IFNs. Taken together, these data suggests that IFI16 promotes human coronavirus infection, and the role IFI16 plays in coronavirus replication is independent of its role as a regulator of type I IFN gene expression.

microbiology↗

bioRxiv2025

Interstrain Recombinants of Human Cytomegalovirus Reveals Complex Genetic Correlates and Epistasis Influencing Glycoprotein Display, Virion Infectivity and Spread Characteristics.

Most of the nucleotide diversity in the human cytomegalovirus (HCMV) genome is due to approximately 17 genes with 2-14 alleles each. These allelic genes are interspersed among longer stretches of highly conserved sequences with signatures of extensive recombination that would shuffle the allelic genes into a vast number of allelic haplotypes. Bacterial artificial chromosome clones derived from 3 independent clinical isolates (TB40/e (TB), TR and Merlin (ME)) display dramatic differences in the abundance of entry-mediating glycoproteins gH/gL/gO and gH/gL/UL128-131, virion infectivity and efficiency of cell-free and cell-to-cell modes of spread. Of these, TB and ME are the most phenotypically different and share only 2 of the 17 allelic genes. A set of recombinant HCMV was generated by coinfecting cells with TB and ME and restriction fragment length polymorphism (RFLP) analyses demonstrated complex crossover patterns. Most recombinants were either "TB-like" with much more gH/gL/gO than gH/gL/UL128-131, or "ME-like" with much more gH/gL/UL128-131. This correlated with a TB or ME UL128 sequence, consistent with a G/T polymorphism affecting UL128 pre-mRNA splicing. One recombinant had a gH/gL/gO:gH/gL/UL128-131 ratio of 0.8, suggesting genetic determinants beyond UL128. Virion infectivity correlated with TB versus ME-like glycoprotein display, but intragroup variability indicated additional factors and variability in spread efficiency and the contribution of cell-free and cell-to-cell spread modes indicated an influence of characteristics beyond virion infectivity. Results suggest that the relationships among these three phenotypes are not strictly causal and that all three phenotypes are genetically complex and influenced by epistasis among polymorphic loci across the genome. IMPORTANCEThe emerging picture of the genetic diversity of HCMV in vivo prompts a reevaluation of how in vitro characterized viral phenotypes, such as the abundance of the various glycoproteins displayed on the virion envelope and tendency towards cell-free or direct cell-to-cell spread, reflect viral characteristics in vivo. A small sampling of the in vivo genetic diversity of HCMV has been examined in the laboratory and the genetic correlates of in vitro phenotypes are unclear. Engineered mutations can yield different phenotypic effects when introduced on to different genetic backgrounds, suggesting complex epistasis among polymorphic loci across the genome. By generating a set of recombinants derived from two phenotypically and genotypically distinct parental clones, this work offers an approach to characterize complex genetic correlates of viral phenotypes, which in turn may enhance efforts to link genomics data with in vivo viral behavior and clinical outcomes.

microbiology↗

bioRxiv2023

A scalable, GMP-compatible, autologous organotypic cell therapy for Dystrophic Epidermolysis Bullosa

BackgroundGene editing in induced pluripotent stem (iPS) cells has been hailed to enable new cell therapies for various monogenetic diseases including dystrophic epidermolysis bullosa (DEB). However, manufacturing, efficacy and safety roadblocks have limited the development of genetically corrected, autologous iPS cell-based therapies. MethodsWe developed Dystrophic Epidermolysis Bullosa Cell Therapy (DEBCT), a new generation GMP-compatible (cGMP), reproducible, and scalable platform to produce autologous clinical-grade iPS cell-derived organotypic induced skin composite (iSC) grafts to treat incurable wounds of patients lacking type VII collagen (C7). DEBCT uses a combined high-efficiency reprogramming and CRISPR-based genetic correction single step to generate genome scar- free, COL7A1 corrected clonal iPS cells from primary patient fibroblasts. Validated iPS cells are converted into epidermal, dermal and melanocyte progenitors with a novel 2D organoid differentiation protocol, followed by CD49f enrichment and expansion to minimize maturation heterogeneity. iSC product characterization by single cell transcriptomics was followed by mouse xenografting for disease correcting activity at 1 month and toxicology analysis at 1-6 months. Culture-acquired mutations, potential CRISPR-off targets, and cancer-driver variants were evaluated by targeted and whole genome sequencing. FindingsiPS cell-derived iSC grafts were reproducibly generated from four recessive DEB patients with different pathogenic mutations. Organotypic iSC grafts onto immune-compromised mice developed into stable stratified skin with functional C7 restoration. Single cell transcriptomic characterization of iSCs revealed prominent holoclone stem cell signatures in keratinocytes and the recently described Gibbin-dependent signature in dermal fibroblasts. The latter correlated with enhanced graftability. Multiple orthogonal sequencing and subsequent computational approaches identified random and non-oncogenic mutations introduced by the manufacturing process. Toxicology revealed no detectable tumors after 3-6 months in DEBCT- treated mice. InterpretationDEBCT successfully overcomes previous roadblocks and represents a robust, scalable, and safe cGMP manufacturing platform for production of a CRISPR-corrected autologous organotypic skin graft to heal DEB patient wounds.

bioengineering↗