Uddin Md Jashim, Thompson Brandon, Leslie Jhansi L, Fishman Casey, Sol-Church Katia, Kumar Pankaj, Petri William A
Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia School of Medicine, Charlottesville, Virginia, USA.
Arcus Biosciences, Hayward, California, USA.
mBio. 2024 Mar 13;15(3):e0333823. doi: 10.1128/mbio.03338-23. Epub 2024 Feb 20.
Innate lymphoid cells (ILCs) play a critical role in maintaining intestinal health in homeostatic and diseased conditions. During infection (CDI), IL-33 activates ILC2 to protect from colonic damage and mortality. The function of IL-33 and ILC is tightly regulated by the intestinal microbiota. We set out to determine the impact of antibiotic-induced disruption of the microbiome on ILC function. Our goal was to understand antibiotic-induced changes in ILC function on susceptibility to colitis in a mouse model. We utilized high-throughput single-cell RNAseq to investigate the phenotypic features of colonic ILC at baseline, after antibiotic administration with or without IL-33 treatment. We identified a heterogeneous landscape of colonic ILCs with gene signatures of inflammatory, anti-inflammatory, migratory, progenitor, plastic, and antigen-presenting ILCs. Antibiotic treatment decreased ILC2 while coordinately increasing ILC1 and ILC3 phenotypes. Notably, Ifng, Ccl5, and Il23r ILC increased after antibiotics. IL-33 treatment counteracted the antibiotic effect by downregulating ILC1 and ILC3 and activating ILC2. In addition, IL-33 treatment markedly induced the expression of type 2 genes, including Areg and Il5. Finally, we identified amphiregulin, produced by ILC2, as protective during infection. Together, our data expand our understanding of how antibiotics induce susceptibility to colitis through their impact on ILC subsets and function.IMPORTANCE infection (CDI) accounts for around 500,000 symptomatic cases and over 20,000 deaths annually in the United States alone. A major risk factor of CDI is antibiotic-induced dysbiosis of the gut. Microbiota-regulated IL-33 and innate lymphoid cells (ILCs) are important in determining the outcomes of infection. Understanding how antibiotic and IL-33 treatment alter the phenotype of colon ILCs is important to identify potential therapeutics. Here, we performed single-cell RNAseq of mouse colon ILCs collected at baseline, after antibiotic treatment, and after IL-33 treatment. We identified heterogeneous subpopulations of all three ILC subtypes in the mouse colon. Our analysis revealed several potential pathways of antibiotic-mediated increased susceptibility to intestinal infection. Our discovery that Areg is abundantly expressed by ILCs, and the protection of mice from CDI by amphiregulin treatment, suggests that the amphiregulin-epidermal growth factor receptor pathway is a potential therapeutic target for treating intestinal colitis.
固有淋巴细胞（ILCs）在维持稳态和患病状态下的肠道健康中发挥着关键作用。在艰难梭菌感染（CDI）期间，白细胞介素-33（IL-33）激活ILC2以保护结肠免受损伤和死亡。IL-33和ILC的功能受到肠道微生物群的严格调控。我们着手确定抗生素诱导的微生物群破坏对ILC功能的影响。我们的目标是了解在小鼠模型中抗生素诱导的ILC功能变化对结肠炎易感性的影响。我们利用高通量单细胞RNA测序来研究基线时、给予抗生素后以及给予或不给予IL-33治疗后的结肠ILC的表型特征。我们确定了具有炎症、抗炎、迁移、祖细胞、可塑性和抗原呈递ILC基因特征的结肠ILC的异质性格局。抗生素治疗减少了ILC2，同时协同增加了ILC1和ILC3表型。值得注意的是，抗生素治疗后Ifng、Ccl5和Il23r ILC增加。IL-33治疗通过下调ILC1和ILC3并激活ILC2来抵消抗生素的作用。此外，IL-33治疗显著诱导了包括Areg和Il5在内的2型基因的表达。最后，我们确定了由ILC2产生的双调蛋白在感染期间具有保护作用。总之，我们的数据扩展了我们对抗生素如何通过影响ILC亚群和功能诱导结肠炎易感性的理解。重要性仅在美国，艰难梭菌感染（CDI）每年就导致约50万例有症状病例和超过2万例死亡。CDI的一个主要危险因素是抗生素诱导的肠道生态失调。微生物群调节的IL-33和固有淋巴细胞（ILCs）在决定艰难梭菌感染的结果中很重要。了解抗生素和IL-33治疗如何改变结肠ILC的表型对于确定潜在的治疗方法很重要。在这里，我们对在基线、抗生素治疗后和IL-33治疗后收集的小鼠结肠ILC进行了单细胞RNA测序。我们确定了小鼠结肠中所有三种ILC亚型的异质性亚群。我们的分析揭示了抗生素介导的肠道感染易感性增加的几种潜在途径。我们发现双调蛋白由ILCs大量表达，并且用双调蛋白治疗可保护小鼠免受CDI，这表明双调蛋白-表皮生长因子受体途径是治疗肠道结肠炎的潜在治疗靶点。
