Aldersey Johanna E, Abernathy Jason W, Beck Benjamin H, Lange Miles D
ARS Research Participation Program, Oak Ridge Institute for Science and Education (ORISE), Oak Ridge, TN, United States.
Aquatic Animal Health Research Unit, Agricultural Research Service (ARS), United States Department of Agriculture, Auburn, AL, United States.
Front Immunol. 2025 Mar 17;16:1547193. doi: 10.3389/fimmu.2025.1547193. eCollection 2025.
Catfish production is the primary aquaculture sector in the United States, and the key cultured species is channel catfish (). The major causes of production losses are pathogenic diseases, and the spleen, an important site of adaptive immunity, is implicated in these diseases. To examine the channel catfish immune system, single-nuclei transcriptomes of sorted and captured IgM cells were produced from adult channel catfish. Three channel catfish (~1 kg) were euthanized, the spleen dissected, and the tissue dissociated. The lymphocytes were isolated using a Ficoll gradient and IgM cells were then sorted with flow cytometry. The IgM cells were lysed and single-nuclei libraries generated using a Chromium Next GEM Single Cell 3' GEM Kit and the Chromium X Instrument (10x Genomics) and sequenced with the Illumina NovaSeq X Plus sequencer. The reads were aligned to the reference assembly (Coco_2.0) using Cell Ranger, and normalization, cluster analysis, and differential gene expression analysis were carried out with Seurat. Across the three samples, approximately 753.5 million reads were generated for 18,686 cells. After filtering, 10,637 cells remained for the cluster analysis. The cluster analysis identified 16 clusters which were classified as B cells (10,276), natural killer-like (NK-like) cells (178), T cells or natural killer cells (45), hematopoietic stem and progenitor cells (HSPC)/megakaryocytes (MK) (66), myeloid/epithelial cells (40), and plasma cells (32). The B cell clusters were further defined as different populations of mature B cells, cycling B cells, and plasma cells. The plasma cells highly expressed and we demonstrated that the secreted form of the transcript was largely being expressed by these cells. This atlas provides insight into the gene expression of IgM immune cells in channel catfish. The atlas is publicly available and could be used garner more important information regarding the gene expression of splenic immune cells.
鲶鱼养殖是美国主要的水产养殖部门，主要养殖品种是沟鲶（Ictalurus punctatus）。产量损失的主要原因是致病性疾病，而脾脏作为适应性免疫的重要部位，与这些疾病有关。为了研究沟鲶的免疫系统，我们从成年沟鲶中制备了分选并捕获的IgM细胞的单核转录组。选取三条沟鲶（约1千克）实施安乐死，解剖脾脏并解离组织。使用Ficoll梯度分离淋巴细胞，然后通过流式细胞术分选IgM细胞。裂解IgM细胞，使用Chromium Next GEM单细胞3' GEM试剂盒和Chromium X仪器（10x Genomics）生成单核文库，并使用Illumina NovaSeq X Plus测序仪进行测序。使用Cell Ranger将读取的序列与参考基因组组装（Coco_2.0）进行比对，并使用Seurat进行标准化、聚类分析和差异基因表达分析。在三个样本中，共为18,686个细胞生成了约7.535亿条读取序列。经过筛选，剩余10,637个细胞用于聚类分析。聚类分析确定了16个簇，分别归类为B细胞（10,276个）、自然杀伤样（NK样）细胞（178个）、T细胞或自然杀伤细胞（45个）、造血干细胞和祖细胞（HSPC）/巨核细胞（MK）（66个）、髓样/上皮细胞（40个）和浆细胞（32个）。B细胞簇进一步细分为成熟B细胞、循环B细胞和浆细胞的不同群体。浆细胞高表达 ，并且我们证明转录本的分泌形式主要由这些细胞表达。该图谱提供了对沟鲶IgM免疫细胞基因表达的深入了解。该图谱已公开，可用于获取有关脾脏免疫细胞基因表达的更多重要信息。
