2nd Edition of Cell & Gene Therapy World Conference 2026

Abstract

Background: Flaviviruses such as Dengue virus (DENV), Zika virus (ZIKV) and West Nile Virus (WNV) continue to pose public health risks.  Diagnostics approaches based on nucleic acid testing and serology, are limited by transient viremia and antibody cross-reactivity, underscoring the need for developing orthogonal detection strategies.  Human induced pluripotent stem cells (hiPSCs) provide a biologically relevant human cell substrate for studying virus-host interactions and are also widely used in the development and manufacture of cell and gene therapy products. Because viral infection impacts cellular state, which can affect product quality and patient safety, it is important to understand how clinically relevant viruses perturb hiPSC biology and to develop sensitive tools to detect such perturbations. Here, we evaluated whether untargeted metabolomics could capture virus-specific metabolic remodeling in hiPSCs and thereby distinguish DENV and ZIKV infections, with the goal of identifying metabolic signatures that may inform improved detection strategies. Methodology: For acute infection, hiPSCs were infected with ZIKV-MR766 or DENV3 at a multiplicity of infection (MOI) of 1, and samples were collected at 0, 8-, 24-, 48-, and 96-hour post-infection (hpi). For long-term infection (LTI), hiPSCs were infected with ZIKV-PRV, DENV2, or DENV3 (MOI 1) and serially passaged for 75 days. Metabolomic profiling was performed using liquid chromatography-mass spectrometry (LC-MS) and data was analyzed with MZmine for peak extraction. Statistical analyses were conducted in R, with significant features identified based on false discovery rate (FDR) adjusted p-values >< 0.05 and fold changes >1.25 or <0.75. Results: LC-MS–based profiling revealed virus-specific metabolic reprogramming during both acute and LTI. DENV3 induced early and sustained activation of metabolic features, while ZIKV-MR766 triggered transient suppression. LTI with DENV2, DENV3, or ZIKV-PRV resulted in durable and virus-specific metabolic reprogramming, with ZIKV-PRV exhibiting the greatest divergence from uninfected controls. Despite strain-specific differences, conserved alterations were observed in amino acids, lipids, and nucleosides, including consistent regulation of tryptophan, glutamate, and thiamine. Functional interrogation of tryptophan metabolism revealed a regulatory role in infection outcomes. Conclusions: Untargeted metabolomics discriminated against DENV and ZIKV infected hiPSCs from uninfected controls and identified conserved, functionally relevant metabolic nodes linked to infection phenotypes. These findings support metabolomics as a complementary, host-response-based approach that may inform development of orthogonal signatures for differentiating closely related viral infections and regulatory science efforts, including characterization of virus-host interactions in human cell substrates and development of additional tools to assess biological risk to cell and gene therapies.