Biology subjects

Jordi, S.

Publications and source records attributed to Jordi, S..

3 recordsLinked to original sources

bioRxiv2026

Genetic modification of primary airway epithelial cell cultures defines MX1 as a barrier for zoonotic influenza A viruses in the human respiratory epithelium

The antiviral innate immune response is a major species barrier that emerging viruses must overcome to infect and transmit efficiently in new hosts. In humans, the interferon-stimulated MX1 gene encodes the antiviral MX1 protein, which restricts zoonotic influenza A viruses (IAVs). Resistance to MX1 is considered a key feature of human-adapted IAVs and a potential determinant of zoonotic and pandemic risk. However, MX1-mediated restriction and viral escape have mostly been investigated in cell lines and animal models, which incompletely recapitulate virus-host interactions in the human airway epithelium, representing the primary site of IAV replication. Although primary human airway epithelial cell (hAEC) cultures, such as airway organoids and air-liquid interface (ALI) cultures, provide a physiologically relevant model, their use in studying MX1 restriction has been limited by challenges in achieving efficient and reliable genetic modification. Here, we used engineered virus-like particles (eVLPs) to deliver Cas9-sgRNA ribonucleoprotein complexes into primary hAECs and disrupt MX1 expression. This approach generated MX1-knockout airway organoids and organoid-derived hAEC ALI cultures with >90% genomic-level editing efficiency and near-complete loss of MX1 protein, while preserving epithelial differentiation at the air-liquid interface. MX1 knockout in hAEC ALI cultures had only a minor effect on the replication kinetics of the human-adapted H1N1pdm09 strain. By contrast, MX1 knockout markedly impaired interferon lambda-mediated restriction of the zoonotic bovine H5N1/Texas and avian H7N9/Anhui strains, resulting in viral titers up to 3-4 logs TCID50 higher than in MX1-competent cultures. These findings provide direct evidence that MX1 restricts zoonotic IAVs in primary human airway epithelium. Our study establishes a biologically relevant platform for assessing the sensitivity of emerging IAVs to a key antiviral host factor and thereby informs evaluations into their zoonotic and pandemic risk.

microbiology↗

bioRxiv2026

Genetically modified primary airway-epithelial cell culture models to study virus-host interactions of emerging respiratory viruses

Airway epithelial cell (AEC) cultures such as air-liquid interface cultures or airway organoids are widely used to study emerging respiratory virus infection in a physiologically representative model system of the human respiratory epithelium. Loss-of-function studies in AEC culture systems offer a unique opportunity to better understand viral disease mechanisms of emerging viruses in the human host, may reveal biologically relevant host-factor dependencies that can be therapeutically targeted, or identify human host barriers of cross-species transmission of emerging viruses that can inform risk assessment. In this chapter, we describe the generation of knockout (KO) AECs using engineered virus-like particles (eVLPs). These particles transiently deliver the Cas9-gRNA ribonucleoprotein (RNP) complex into target cells, enabling efficient genome editing of any gene of interest. We detail the production, quantification, and application of eVLPs for gene editing in AECs, alongside an optimized protocol for AEC expansion and differentiation at the air-liquid interface that is compatible with genetically modified cells. Finally, we describe procedures for infecting KO AECs with emerging respiratory viruses. Together, these protocols provide a robust workflow for generating renewable KO AEC cultures in less than two months, facilitating the functional characterization of host factors that influence viral infection of the airway epithelium.

microbiology↗

bioRxiv2025

Emergent spatial structure in the gut microbiota is driven by bacterial growth and gut contractions

Spatial structure can determine function and evolution of bacterial communities. The gut microbiota is known to be spatially structured longitudinally along the many meters of the gastrointestinal tract, but micro-scale structure in the gut lumen has not been extensively explored. In samples from mice and humans, we show that upper large-intestinal content behaves as a non-Newtonian fluid that changes its viscoelastic properties under the force of gut contractions. This phenomenon is sufficient to explain micro-scale bacterial clustering in the murine cecum, resulting from growth within the gel-like structure of cecum content, and periodic disruption due to peristalsis-driven shear-thinning and clearance. Shear-thinning can also explain the surprising observation that fed beads enter the tip of the mouse cecum by flow along the epithelial cell layer before being mixed into the cecum content. Our study shows mechanistically how spatial structure in the gut emerges through the interplay of microbial and host physiology and highlights the possibility of host control over gut microbiota distribution via gut contractions. One sentence summaryWe show how spatial structure emerges in the gut microbiota through bacterial growth in the matrix of gut content.

systems biology↗