ZenoFishDb v1.1: A Database for Xenotransplantation Studies in Zebrafish

Abstract

Rapidly accumulating literature has proven feasibility of the zebrafish xenograft models in cancer research. Nevertheless, online databases for searching the current zebrafish xenograft literature are in great demand. Herein, we have developed a manually curated database, called ZenoFishDb v1.1 (https://konulab.shinyapps.io/ zenofishdb), based on R Shiny platform aiming to provide searchable information on ever increasing collection of zebrafish studies for cancer cell line transplantation and patient-derived xenografts (PDXs). ZenoFishDb v1.1 user interface contains four modules: DataTable, Visualization, PDX Details, and PDX Charts. The DataTable and Visualization pages represent xenograft study details, including injected cell lines, PDX injections, molecular modifications of cell lines, zebrafish strains, as well as technical aspects of the xenotransplantation procedures in table, bar, and/or pie chart formats. The PDX Details module provides comprehensive information on the patient details in table format and can be searched and visualized. Overall, ZenoFishDb v1.1 enables researchers to effectively search, list, and visualize different technical and biological attributes of zebrafish xenotransplantation studies particularly focusing on the new trends that make use of reporters, RNA interference, overexpression, or mutant gene constructs of transplanted cancer cells, stem cells, and PDXs, as well as distinguished host modifications.

Lvsiyujins A–G, new sesquiterpenoids, fromCurcuma phaeocaulisValeton root tuber and their preliminary pharmacological property assessment based on ADME evaluation, molecular docking andin vitroexperiments

“…13,14 A large amount of literature studies has proven the practicability of zebrafish xenograft models in cancer research. 15,16 Drug-like properties can be jointly evaluated by Lipinski's ''rule of five'', Veber's rule, and ADME (absorption, distribution, metabolism, and excretion) profiling, which could provide insight into the future clinical application of compounds. 17,18 In addition, molecular docking can virtually screen the activity of compounds by docking with the target and has become a popular and practical method in the field of medical research.…”

“…The cytotoxicity assay and zebrafish xenograft model were used to evaluate the anticancer activity of the ethanol extract from the root tuber of C. phaeocaulis (CP), and promising results were obtained. Sixteen sesquiterpenoids were isolated from CP; among them, there were seven new sesquiterpenoids, lvsiyujins A-G (1-7), and nine known sesquiterpenoids (8)(9)(10)(11)(12)(13)(14)(15)(16) (Fig. 1).…”

XePhIR: the zebrafish xenograft phenotype interactive repository

“…The need for a platform of this kind is also evidenced by the recent initiative by Targen et al. 2020, who created a zebrafish xenograft metadata repository ( 9 ). However, zebrafish research is often driven by image-based quantification analyses.…”

Giloy Ghanvati (Tinospora cordifolia (Willd.) Hook. f. and Thomson) Reversed SARS-CoV-2 Viral Spike-Protein Induced Disease Phenotype in the Xenotransplant Model of Humanized Zebrafish

“…Zebrafish (Danio rerio) has been a reliable model for infectious diseases and studying the immune function in response to the introduction of human viruses (Sullivan and Kim, 2008;Van Dycke et al, 2019). The similarities in the immune cells, cytokines, and the presence of various receptors that are required for host-pathogen interactions makes the correlation of zebrafish research to humans, very much relevant (Targen et al, 2020). Xeno-transplantation was achieved by introducing human lung epithelial A549 cells into the swim bladder of the fish (Shen et al, 2020).…”