Unraveling the stereoscopic gene transcriptional landscape of zebrafish using Fish SED,a fish spatial expression database with multispecies scalability

Dear Editor,The expression profile demonstrates how each gene was expressed in the target tissue or cell at a given time.Cell heterogeneity is a biological concept characterized by the presence of numerous cells with varying functions and expression profiles within organ/tissue samples.There is also cell-to-cell signaling,which implies that the extracellular environment and spatial location influence intracellular transcription,resulting in spatial heterogeneity of gene expression within the same cell type.

The immunoregulatory role of fish specific type Ⅱ SOCS via inhibiting metaflammation in the gut-liver axis

SOCS8,also known as CISHb,is a fish-specific type Ⅱ SOCS.Because CISH binds to cytokine receptors and may inhibit STAT5 activation(a substrate of the insulin receptor),SOCS8 may be involved in the control of metaflammation.The socs8-/-zebrafish were created,and both longer trunks and intestinal villi were observed in 1-month-old(mo)fish.Altered mucosal immunity and gut-liver metabolism were also found in socs8-/-fish.Increased intestinal neutrophils and macrophages,together with overexpression of cytokines and T cell markers in this mutant fish,suggested SOCS8's immunoregulating role.During modeling of soybean-induced enteritis using the 3 mo zebrafish,lower expression levels of inflammatory genes but more mucosa barrier disruption were discovered in socs8-/-zebrafish,compared with wide type counterparts.Furthermore,the shrunk villi at 6 mo in socs8-/-fish suggested that the mucosa might have been protected by SOCS8.This is also consistent with the assertion that metaflammation eventually leads to tissue degeneration and premature death.The fact that socs8-/-fish had more hepatic oil droplets compared to their wild-type counterparts suggested SOCS8's role in inhibiting hepatic metaflammation.Transcriptomic analysis as well as 16S rRNA gene sequencing were done on 3 mo socs8-/-fish to methodically reveal the altered immunity and metabolic reprogramming in the gut and liver caused by socs8-/-.The enriched GO terms for the intestinal tract,such as"cytokine-mediated signaling pathway"and"response to external biotic stimulus",as well as KEGG pathways in both gut and liver like"carbon metabolism"and"glycolysis/gluconeogenesis",were consistent with previously revealed pathological clues and improved growth performance at early age,respectively.In addition,the microbiota in the socs8-/-strain had adapted to the host's increased carbohydrate metabolism,as evidenced by higher levels of Bacteroidota.Furthermore,Verrucomicrobiota associated with immunoregulation were found in lower abundance in socs8-/-fish.As a result,current findings indicate that SOCS8 plays immunoregulatory and mucosa-protective roles in the fish gut and liver by inhibiting carbohydrate metabolism.

Fish SCT: a zebrafish-centric database for exploration and visualization of fish single-cell transcriptome

Dear Editor,Using sc RNA-seq technology, researchers may distinguish between different cell types and tissue heterogeneity as well as perform transcriptome investigations at the single-cell level (Regev et al., 2017). A significant amount of single-cell transcriptome data has been produced as a result of the technology’s quick development and widespread adoption.Research on other model species has also gathered a sizable quantity of transcriptome data at the single-cell level.