Dual RNA sequencing reveals dendritic cell reprogramming in response to typhoidal Salmonella invasion

Anna Aulicino,Giorgio Napolitani,Esther Mellado,Philip Hublitz,Hal Drakesmith,Ana Sousa Geros,Agne Antanaviciute,Alison Simmons,Rory Bowden,Moustafa Attar,Lorena Preciado-Llanes,Hashem Koohy,Julia Sinz,Marta Jagielowicz,Joe Frost

doi:10.1038/s42003-022-03038-z

Abstract

Salmonella enterica represent a major disease burden worldwide. S. enterica serovar Typhi (S. Typhi) is responsible for potentially life-threatening Typhoid fever affecting 10.9 million people annually. While non-typhoidal Salmonella (NTS) serovars usually trigger self-limiting diarrhoea, invasive NTS bacteraemia is a growing public health challenge. Dendritic cells (DCs) are key professional antigen presenting cells of the human immune system. The ability of pathogenic bacteria to subvert DC functions and prevent T cell recognition contributes to their survival and dissemination within the host. Here, we adapted dual RNA-sequencing to define how different Salmonella pathovariants remodel their gene expression in tandem with that of infected DCs. We find DCs harness iron handling pathways to defend against invading Salmonellas, which S. Typhi is able to circumvent by mounting a robust response to nitrosative stress. In parallel, we uncover the alternative strategies invasive NTS employ to impair DC functions.

Highlights

Salmonella enterica represent a major disease burden worldwide
Dual RNA sequencing of Salmonella-infected monocyte-derived DCs (MoDCs)
We confirmed the presence of live Salmonella within infected cells by sorting MoDCs by their fluorescence phenotype and enumerating intracellular bacteria after cell lysis (Supplementary Fig. 1b)

Summary

Introduction

Salmonella enterica represent a major disease burden worldwide. S. enterica serovar Typhi 1234567890():,; Salmonella enterica serovars are responsible for a wide range of clinical presentations. S. Typhi is a human-restricted pathogen associated with typhoid fever, a disease that affects around 10.9 million people each year globally[1], whilst broad host range S. Dual RNA sequencing (RNA seq) enables simultaneous gene expression profiling of infecting bacteria and infected host cells, capable of defining bacterial and host cross-talk[10,11,12,13,14,15]. Due to the small relative fraction of bacterial mRNA, current methods for dual host–pathogen RNA seq can fail to obtain the required coverage of pathogen transcriptomes necessary to accurately reveal the nature of these complex molecular interactions, in particular in systems where only very low numbers of bacteria are present within the host cell. Our method showed improved accuracy of bacterial gene expression quantification while enabling the discovery of novel aspects of host–pathogen interactions and more robust comparisons due to minimised biases between strains

Methods

Results

Conclusion