Th2 immune responses induced by helminth infection reprogram multilineage progenitors to produce successive waves of neutrophils, basophils, and eosinophils

Abstract Helminths are parasitic worm pathogens known to induce innate acquired type 2 immune responses that lead to the accumulation of granulocytes in peripheral tissues. N. brasiliensis is a natural rat nematode parasite used in mouse models to elicit this immune response. Infective larvae are injected into the skin, migrate to the lung within 24–48 hours, are coughed up at 48–72 hours, and mature in the intestines in 5–6 days. Though much is known about the cytokine signaling and recruitment of granulocytes, little is known about the source of these cells. Their short half-life suggests a role for multi-lineage progenitors in the bone marrow. To test this, we exploited CITE-seq, flow cytometry, and machine learning on mouse bone marrow to build a reference atlas of transcriptional and immunophenotypic states of hematopoietic stem and progenitor cells (HSPCs). We generated an InfinityFlow object from millions of HSPCs and integrated these values with CITE-seq ADT values to allow transfer of transcriptionally defined clusters to flow cytometry-defined immunophenotypes. This enabled the generation of unsupervised gating srategies for isolation and functional validation of transcriptionally defined developmental stages. We then applied scRNA-seq and flow cytometry along a time course of N. brasiliensis infection in mice to characterize bone marrow HSPC responses to Th2-mediated immune effectors. We identified a multilineage progenitor that expands and transcriptionally reprograms at 72 hrs after infection and leads to the production of successive waves of neutrophils, basophils, and eosinophils on days 3, 7, and 10, respectively. Thus, worm infection stimulates Th2 responses that call to the marrow to specify granulocyte production.