Single-cell analysis of Kaposi's sarcoma-associated herpesvirus infection in three-dimensional air-liquid interface culture model

The oral cavity is the major site for transmission of Kaposi's sarcoma-associated herpesvirus (KSHV), but how KSHV establishes infection and replication in the oral epithelia remains unclear. Here, we report a KSHV spontaneous lytic replication model using fully differentiated, three-dimensional (3D) oral epithelial organoids at an air-liquid interface (ALI). This model revealed that KSHV infected the oral epithelia when the basal epithelial cells were exposed by damage. Unlike two-dimensional (2D) cell culture, 3D oral epithelial organoid ALI culture allowed high levels of spontaneous KSHV lytic replication, where lytically replicating cells were enriched at the superficial layer of epithelial organoid. Single cell RNA sequencing (scRNAseq) showed that KSHV infection induced drastic changes of host gene expression in infected as well as uninfected cells at the different epithelial layers, resulting in altered keratinocyte differentiation and cell death. Moreover, we identified a unique population of infected cells containing lytic gene expression at the KSHV K2-K5 gene locus and distinct host gene expression compared to latent or lytic infected cells. This study demonstrates an in vitro 3D epithelial organoid ALI culture model that recapitulates KSHV infection in the oral cavity, where KSHV undergoes the epithelial differentiation-dependent spontaneous lytic replication with a unique cell population carrying distinct viral gene expression. While KSHV is the etiologic agent of Kaposi's sarcoma that frequently occurs in AIDS patients, there is not biologically relevant, reproducible in vitro culture system to study KSHV infection and spontaneous lytic replication. Here, we describe that a 3D human oral epithelial ALI culture that can support a robust KSHV infection and spontaneous lytic replication associated with oral epithelial differentiation. scRNAseq analysis identified considerable alteration of host gene expression in both KSHV-infected cells and -uninfected bystander cells. Our study provides insights into the early stages of KSHV infection in oral epithelial cells and serves as a useful blueprint for the investigation of KSHV infection and transmission.

Automated summary

This study presents a spontaneous lytic replication model of KSHV using three-dimensional oral epithelial organoid culture. Unlike traditional two-dimensional cell culture, this three-dimensional model successfully replicates the infection and replication behavior of KSHV in the oral cavity. Single cell RNA sequencing analysis reveals significant host gene expression changes induced by KSHV infection.