Single-cell RNA-seq landscape midbrain cell responses to red spotted grouper nervous necrosis virus infection

Author summary NNV is one of the most contagious and economically devastating viruses of marine fish, which lead to severe central nervous system (CNS) damage. Because of the functional diversity and highly complex anatomical and cellular composition of the CNS, it is hard to identify the specific type of cell targeted by NNV, and to decipher the host immune response. In this study, we conducted single-cell RNA-seq analysis of the midbrain of healthy and RGNNV-infected fish and identified 35 transcriptionally distinct cell subtypes, including 28 neuronal and seven non-neuronal cell types. An evaluation of the subpopulations of immune cells revealed that macrophages were enriched in RGNNV-infected fish, and the transcriptional profiles of macrophages indicated an acute cytokine and inflammatory response. Unsupervised pseudotime analysis of immune cells showed that microglia transformed into M1-type activated macrophages to produce cytokines to reduce the damage to nerve tissue caused by the virus. Finally, we found that RGNNV targeted GLU1 and GLU3 neuronal cells, and we screened for genes that cause GLU1 and GLU3 cell vacuole morphology changes and death. These data provided a comprehensive transcriptional perspective of the grouper midbrain and the basis for further research on how viruses infect the teleost CNS. Viral nervous necrosis (VNN) is an acute and serious fish disease caused by nervous necrosis virus (NNV) which has been reported massive mortality in more than fifty teleost species worldwide. VNN causes damage of necrosis and vacuolation to central nervous system (CNS) cells in fish. It is difficult to identify the specific type of cell targeted by NNV, and to decipher the host immune response because of the functional diversity and highly complex anatomical and cellular composition of the CNS. In this study, we found that the red spotted grouper NNV (RGNNV) mainly attacked the midbrain of orange-spotted grouper (Epinephelus coioides). We conducted single-cell RNA-seq analysis of the midbrain of healthy and RGNNV-infected fish and identified 35 transcriptionally distinct cell subtypes, including 28 neuronal and 7 non-neuronal cell types. An evaluation of the subpopulations of immune cells revealed that macrophages were enriched in RGNNV-infected fish, and the transcriptional profiles of macrophages indicated an acute cytokine and inflammatory response. Unsupervised pseudotime analysis of immune cells showed that microglia transformed into M1-type activated macrophages to produce cytokines to reduce the damage to nerve tissue caused by the virus. We also found that RGNNV targeted neuronal cell types was GLU1 and GLU3, and we found that the key genes and pathways by which causes cell cytoplasmic vacuoles and autophagy significant enrichment, this may be the major route viruses cause cell death. These data provided a comprehensive transcriptional perspective of the grouper midbrain and the basis for further research on how viruses infect the teleost CNS.

Automated summary

The study uncovered that RGNNV primarily targeted the midbrain of orange-spotted grouper, leading to neuronal damage. Single-cell RNA-seq analysis identified 35 cell subtypes, with enriched macrophages in infected fish showing acute inflammatory responses. Pseudotime analysis revealed the transformation of microglia into activated macrophages to reduce nerve tissue damage caused by the virus.