Table_2_Single-Cell Transcriptome Profiling of Immune Cell Repertoire of the Atlantic Cod Which Naturally Lacks the Major Histocompatibility Class II System.pdf

The Atlantic cod’s unusual immune system, entirely lacking the Major Histocompatibility class II pathway, has prompted intriguing questions about what mechanisms are used to combat bacterial infections and how immunological memory is generated. By single-cell RNA sequencing we here report an in-depth characterisation of cell types found in immune tissues, the spleen and peripheral blood leukocytes of Atlantic cod. Unbiased transcriptional clustering revealed eleven distinct immune cell signatures. Resolution at the single cell level enabled characterisation of the major cell subsets including the cytotoxic T cells, B cells, erythrocytes, thrombocytes, neutrophils, and macrophages. Additionally, to our knowledge we are the first to uncover cell subsets in Atlantic cod which may represent dendritic cells, natural killer-like cells, and a population of cytotoxic cells expressing GATA-3, a master transcription factor of T helper 2 cells. We further identify putative gene markers for each cluster and describe the relative proportions of each cell type in the spleen and peripheral blood leukocytes. Of the major haematopoietic cell populations, the lymphocytes make up 55 and 68% of the spleen and peripheral blood leukocytes respectively, while the myeloid cells make up 45 and 32%. By single-cell analysis, this study provides the most detailed molecular and cellular characterisation of the immune system of the Atlantic cod so far.

大西洋鳕鱼拥有极为特殊的免疫系统，其完全缺失主要组织相容性复合体II类通路（Major Histocompatibility class II pathway），这引发了一系列引人深思的科学疑问：该物种依靠何种机制抵御细菌感染，以及免疫记忆究竟如何形成。本研究借助单细胞RNA测序（single-cell RNA sequencing），对大西洋鳕鱼免疫组织——脾脏与外周血白细胞中的细胞类型展开了深度表征。无偏倚转录组聚类分析揭示了11种独特的免疫细胞特征。凭借单细胞分辨率，本研究得以鉴定包括细胞毒性T细胞、B细胞、红细胞、血栓细胞、嗜中性粒细胞与巨噬细胞在内的主要细胞亚群。此外，据我们所知，本研究首次在大西洋鳕鱼中发现了潜在的树突状细胞、自然杀伤样细胞亚群，以及一群表达GATA-3的细胞毒性细胞——GATA-3是T辅助2细胞的核心转录因子。本研究还为每个细胞簇鉴定了候选基因标记物，并明确了脾脏与外周血白细胞中各类细胞的相对占比。在主要造血细胞群中，淋巴细胞分别占脾脏与外周血白细胞总量的55%与68%，髓系细胞则分别占45%与32%。本研究通过单细胞分析，实现了目前为止对大西洋鳕鱼免疫系统最为详尽的分子与细胞层面表征。