Using ScRNA-seq to Reveal Lymphocyte Responses to ALV-J in Bone Marrow Microenvironment

Abstract

Abstract Background: The main tumors in chicken caused by avian leukemia virus (ALV) are leukemia. The bone marrow microenvironment is the genesis of leukemia, but little is known about the state of the chicken bone marrow microenvironment under avian leukemia virus subgroup J (ALV-J) infection. Meanwhile, alterations in the immune status of the bone marrow microenvironment are closely associated with the development of leukemia. Results: In this article, scRNA-seq was used on chicken bone marrow lymphocytes with different states of ALV-J infection to identify marker genes, cell states, and subgroups of lymphocytes. A total of eighteen clusters and their potential marker genes were identified. Among them, eight T cell clusters, two B cell clusters, and five tumor-like cell clusters were identified, whereas three clusters could not be identified. Among ten lymphocyte clusters, double-positive T cells (cluster_2), B1-like B cells (cluster_7), and cytotoxic T cells (cluster_9) responded strongly to ALV-J infection. Their differentially expressed genes were highly enriched in immune-related pathways and viral infection-related pathways, and they accounted for a large proportion and variation in samples with different clinical symptoms of ALV-J infection. The immunosuppressive state of bone marrow microenvironment was stronger after the occurrence of more severe ALV-J infection. Regulatory T cells and CTLA4T cells were more predominant in samples with more severe ALV-J infection. Immunosuppressive factors TGFB1 and IL16 were expressed in multiple clusters, and the expression of TGFB1 and IL16 was higher in samples with more severe ALV-J infection. ALV-J infected all clusters, but in the same cluster of cells, a fraction of cells expressed ALV-J transcripts, whereas the other fraction did not. Meanwhile, in the same cluster of cells expressing ALV-J transcripts, the pathway associated with intracellular antiviral infection, “Signaling by Rho Family GTPases” was activated. By using IPA analysis software, some upstream regulatory elements (MYCand MCYN) responsible for this difference were predicted. Conclusions: Decreased immunocompetence in the bone marrow microenvironment caused by ALV-J maybe associated with occurrence of leukemia. The cells in the same cluster showed different susceptibility to ALV-J. Our results could contribute to the understanding of bone marrow lymphocytes in different infection states of ALV-J.