Table_2_Transcriptome Profiling of Atlantic Salmon Adherent Head Kidney Leukocytes Reveals That Macrophages Are Selectively Enriched During Culture.xlsx

The Atlantic salmon (Salmo salar) is an economically important fish, both in aquaculture and in the wild. In vertebrates, macrophages are some of the first cell types to respond to pathogen infection and disease. While macrophage biology has been characterized in mammals, less is known in fish. Our previous work identified changes in the morphology, phagocytic ability, and miRNA profile of Atlantic salmon adherent head kidney leukocytes (HKLs) from predominantly “monocyte-like” at Day 1 of in vitro culture to predominantly “macrophage-like” at Day 5 of culture. Therefore, to further characterize these two cell populations, we examined the mRNA transcriptome profile in Day 1 and Day 5 HKLs using a 44K oligonucleotide microarray. Large changes in the transcriptome were revealed, including changes in the expression of macrophage and immune-related transcripts (e.g. csf1r, arg1, tnfa, mx2), lipid-related transcripts (e.g. fasn, dhcr7, fabp6), and transcription factors involved in macrophage differentiation and function (e.g. klf2, klf9, irf7, irf8, stat1). The in silico target prediction analysis of differentially expressed genes (DEGs) using miRNAs known to change expression in Day 5 HKLs, followed by gene pathway enrichment analysis, supported that these miRNAs may be involved in macrophage maturation by targeting specific DEGs. Elucidating how immune cells, such as macrophages, develop and function is a key step in understanding the Atlantic salmon immune system. Overall, the results indicate that, without the addition of exogenous factors, the adherent HKL cell population differentiates in vitro to become macrophage-like.

大西洋鲑（Salmo salar）是一类在水产养殖与野生种群中均具备重要经济价值的鱼类。在脊椎动物体内，巨噬细胞（macrophage）是最早响应病原体感染与疾病进程的细胞类型之一。尽管哺乳动物的巨噬细胞生物学特性已得到充分解析，但学界对鱼类巨噬细胞的相关认知仍较为有限。本研究团队既往工作发现，体外培养的大西洋鲑贴壁头肾白细胞（head kidney leukocytes, HKLs）的形态学特征、吞噬能力及miRNA（microRNA）表达谱均发生显著改变：培养第1天时，该细胞群体以“单核细胞样”表型为主；至培养第5天时，则转为以“巨噬细胞样”表型为主。为进一步表征这两类细胞群体，本研究采用44K寡核苷酸微阵列技术，对培养第1天与第5天的HKLs开展mRNA转录组谱分析。结果显示转录组发生大范围重塑，涉及巨噬细胞与免疫相关转录本（如csf1r、arg1、tnfa、mx2）、脂代谢相关转录本（如fasn、dhcr7、fabp6），以及参与巨噬细胞分化与功能调控的转录因子（如klf2、klf9、irf7、irf8、stat1）的表达变化。本研究针对培养第5天HKLs中表达发生改变的miRNA，对差异表达基因（differentially expressed genes, DEGs）开展计算机靶标预测分析，并结合基因通路富集分析，结果提示这些miRNA可能通过靶向特定DEGs参与巨噬细胞成熟过程。阐明巨噬细胞等免疫细胞的发育与功能机制，是解析大西洋鲑免疫系统的关键环节。综上，本研究结果表明，在不添加外源性因子的条件下，贴壁HKLs群体可在体外分化为巨噬细胞样细胞。