TY - JOUR

T1 - Fishing Innate Immune System Properties through the Transcriptomic Single-Cell Data of Teleostei

AU - Bobrovskikh, Aleksandr V

AU - Zubairova, Ulyana S

AU - Doroshkov, Alexey V

N1 - Alexey V. Doroshkov thanks the Institute of Cytology and Genetics for providing joint workspace for team coordination (FWNR-2022-0003).

PY - 2023/12/12

Y1 - 2023/12/12

N2 - The innate immune system is the first line of defense in multicellular organisms. Danio rerio is widely considered a promising model for IIS-related research, with the most amount of scRNAseq data available among Teleostei. We summarized the scRNAseq and spatial transcriptomics experiments related to the IIS for zebrafish and other Teleostei from the GEO NCBI and the Single-Cell Expression Atlas. We found a considerable number of scRNAseq experiments at different stages of zebrafish development in organs such as the kidney, liver, stomach, heart, and brain. These datasets could be further used to conduct large-scale meta-analyses and to compare the IIS of zebrafish with the mammalian one. However, only a small number of scRNAseq datasets are available for other fish (turbot, salmon, cavefish, and dark sleeper). Since fish biology is very diverse, it would be a major mistake to use zebrafish alone in fish immunology studies. In particular, there is a special need for new scRNAseq experiments involving nonmodel Teleostei, e.g., long-lived species, cancer-resistant fish, and various fish ecotypes.

AB - The innate immune system is the first line of defense in multicellular organisms. Danio rerio is widely considered a promising model for IIS-related research, with the most amount of scRNAseq data available among Teleostei. We summarized the scRNAseq and spatial transcriptomics experiments related to the IIS for zebrafish and other Teleostei from the GEO NCBI and the Single-Cell Expression Atlas. We found a considerable number of scRNAseq experiments at different stages of zebrafish development in organs such as the kidney, liver, stomach, heart, and brain. These datasets could be further used to conduct large-scale meta-analyses and to compare the IIS of zebrafish with the mammalian one. However, only a small number of scRNAseq datasets are available for other fish (turbot, salmon, cavefish, and dark sleeper). Since fish biology is very diverse, it would be a major mistake to use zebrafish alone in fish immunology studies. In particular, there is a special need for new scRNAseq experiments involving nonmodel Teleostei, e.g., long-lived species, cancer-resistant fish, and various fish ecotypes.

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-85190101006&origin=inward&txGid=b9a63eb166cc75e156bbb6a7b77b676a

UR - https://www.mendeley.com/catalogue/02ce1db0-2dbd-314c-a53e-30d31f8933f3/

U2 - 10.3390/biology12121516

DO - 10.3390/biology12121516

M3 - Review article

C2 - 38132342

VL - 12

JO - Biology

JF - Biology

SN - 2079-7737

IS - 12

M1 - 1516

ER -