Single cell transcriptomics reveals cell type specific features of developmentally regulated responses to lipopolysaccharide between birth and 5 years

James F Read; Michael Serralha; Jesse D Armitage; Muhammad Munir Iqbal; Mark N Cruickshank; Alka Saxena; Deborah H Strickland; Jason Waithman; Patrick G Holt; Anthony Bosco

doi:10.3389/fimmu.2023.1275937

Single cell transcriptomics reveals cell type specific features of developmentally regulated responses to lipopolysaccharide between birth and 5 years

Front Immunol. 2023 Oct 17:14:1275937. doi: 10.3389/fimmu.2023.1275937. eCollection 2023.

Authors

James F Read^{1

2}, Michael Serralha², Jesse D Armitage^{2

3}, Muhammad Munir Iqbal⁴, Mark N Cruickshank³, Alka Saxena⁴, Deborah H Strickland^{2

5}, Jason Waithman³, Patrick G Holt^{2

5}, Anthony Bosco^{1

6}

Affiliations

¹ Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, United States.
² Telethon Kids Institute, The University of Western Australia, Perth, WA, Australia.
³ School of Biomedical Sciences, The University of Western Australia, Nedlands, Western Australia, Australia.
⁴ Genomics WA, Joint Initiative of Telethon Kids Institute, Harry Perkins Institute of Medical Research and The University of Western Australia, Nedlands, WA, Australia.
⁵ UWA Centre for Child Health Research, The University of Western Australia, Nedlands, WA, Australia.
⁶ Department of Immunobiology, The University of Arizona College of Medicine, Tucson, AZ, United States.

Abstract

Background: Human perinatal life is characterized by a period of extraordinary change during which newborns encounter abundant environmental stimuli and exposure to potential pathogens. To meet such challenges, the neonatal immune system is equipped with unique functional characteristics that adapt to changing conditions as development progresses across the early years of life, but the molecular characteristics of such adaptations remain poorly understood. The application of single cell genomics to birth cohorts provides an opportunity to investigate changes in gene expression programs elicited downstream of innate immune activation across early life at unprecedented resolution.

Methods: In this study, we performed single cell RNA-sequencing of mononuclear cells collected from matched birth cord blood and 5-year peripheral blood samples following stimulation (18hrs) with two well-characterized innate stimuli; lipopolysaccharide (LPS) and Polyinosinic:polycytidylic acid (Poly(I:C)).

Results: We found that the transcriptional response to LPS was constrained at birth and predominantly partitioned into classical proinflammatory gene upregulation primarily by monocytes and Interferon (IFN)-signaling gene upregulation by lymphocytes. Moreover, these responses featured substantial cell-to-cell communication which appeared markedly strengthened between birth and 5 years. In contrast, stimulation with Poly(I:C) induced a robust IFN-signalling response across all cell types identified at birth and 5 years. Analysis of gene regulatory networks revealed IRF1 and STAT1 were key drivers of the LPS-induced IFN-signaling response in lymphocytes with a potential developmental role for IRF7 regulation.

Conclusion: Additionally, we observed distinct activation trajectory endpoints for monocytes derived from LPS-treated cord and 5-year blood, which was not apparent among Poly(I:C)-induced monocytes. Taken together, our findings provide new insight into the gene regulatory landscape of immune cell function between birth and 5 years and point to regulatory mechanisms relevant to future investigation of infection susceptibility in early life.

Keywords: cord blood; interferon; lipopolysaccharide; poly(I:C); proinflammatory; scRNA-Seq; single cell genomics; toll-like receptors.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Gene Expression Regulation
Humans
Infant, Newborn
Lipopolysaccharides* / metabolism
Lipopolysaccharides* / pharmacology
Monocytes
Poly I-C / metabolism
Poly I-C / pharmacology
Signal Transduction
Transcriptome*

Substances

Lipopolysaccharides
Poly I-C

Grants and funding

The author(s) declare financial support was received for the research, authorship, and/or publication of this article. This work was funded by National Health and Medical Research Council (NHMRC) project grant #1129996.