Induction of protein degradation is emerging as a powerful strategy to modulate protein functions and alter cellular signaling pathways. Proteolysis-targeting chimeras (PROTACs) have been used to degrade a range of diverse proteins in vitro and in vivo. Here we present a type of photo-caged PROTACs (pc-PROTACs) to induce degradation activity with light. Photo-removable blocking groups were added to a degrader of Brd4, and the resulting molecule pc-PROTAC1 showed potent degradation activity in live cells only after light irradiation. Furthermore, this molecule efficiently degraded Brd4 and induced expected phenotypic changes in zebrafish. Additionally, this approach was successfully applied to construct pc-PROTAC3 of BTK. Thus, a general strategy to induce protein degradation with light was established to augment the chemists' toolbox to study disease-relevant protein targets. Communication pubs.acs.org/JACS

Classic T cell subsets are defined by a small set of cell surface markers, while single-cell RNA sequencing (scRNA-seq) clusters cells using genome-wide gene expression profiles. The relationship between scRNA-seq clustered populations (scCPops) and cell surface marker–defined classic T cell subsets remains unclear. In this article, we integrated six bead-enriched T cell subsets with 62,235 single-cell transcriptomes from human PBMCs and clustered them into nine scCPops. Bead-enriched CD4+/CD45RA+/CD25− naive T and CD8+/CD45RA+ naive T cells were mainly clustered into their scCPop counterparts, while cells from the other T cell subsets were assigned to multiple scCPops, including mucosal-associated invariant T cells and NKT cells. The multiple T cell subsets forming one scCPop exhibit similar expression patterns, but not vice versa, indicating scCPop is a more homogeneous cell population with similar cell states. Interestingly, we discovered and named IFN signaling–associated gene (ISAG) high T (ISAGhi T) cells, a T cell subpopulation that highly expressed ISAGs. We further enriched ISAGhi T cells from human PBMCs by FACS of BST2 for scRNA-seq analyses. The ISAGhi T cell cluster disappeared on t-distributed stochastic neighbor embedding plot after removing ISAGs, whereas the ISAGhi T cell cluster showed up by analysis of ISAGs alone, indicating ISAGs are the major contributor of the ISAGhi T cell cluster. BST2+ and BST2− T cells showing different efficiencies of T cell activation indicate that a high level of ISAGs may contribute to quick immune responses.

Mutations in LRRK2 are genetically linked to Parkinson's disease (PD) but its normal biological function is largely unknown. Sheng et al. recently reported that deletion of the WD40 domain of LRRK2 in zebrafish specifically causes PD-like loss of neurons and behavior defect. However, our similar early study and recent confirming experiments using the same reagents reported by Sheng et al. failed to reproduce the phenotype of the loss of dopaminergic neurons, although the mRNA of LRRK2 was molecularly disrupted. Our study suggests that function of LRRK2 and its usefulness to generate zebrafish PD model needs further evaluation.

Background: Zebrafish tyrosine hydroxylase 2 (th2) has been considered as a marker of dopaminergic (DA) neurons in the investigation of DA neuron development and the pathological mechanism of Parkinson disease. Results: th2 is required for the synthesis of serotonin in vivo and has tryptophan hydroxylase activity in vitro. Conclusion: th2 should be considered as a marker gene of serotonergic neurons. Significance: This result facilitates the elucidation of zebrafish neural circuitry.

The RNA helicase DHX33 has been shown to be a critical regulator of cell proliferation and growth. However, the underlying mechanisms behind DHX33 function remain incompletely understood. We present original evidence in multiple cell lines that DHX33 transcriptionally controls the expression of genes involved in the cell cycle, notably cyclin, E2F1, cell division cycle (CDC), and minichromosome maintenance (MCM) genes. DHX33 physically associates with the promoters of these genes and controls the loading of active RNA polymerase II onto these promoters. DHX33 deficiency abrogates cell cycle progression and DNA replication and leads to cell apoptosis. In zebrafish, CRISPR-mediated knockout of DHX33 results in downregulation of cyclin A2, cyclin B2, cyclin D1, cyclin E2, cdc6, cdc20, E2F1, and MCM complexes in DHX33 knockout embryos. Additionally, we found the overexpression of DHX33 in a subset of non-small-cell lung cancers and in Ras-mutated human lung cancer cell lines. Forced reduction of DHX33 in these cancer cells abolished tumor formation in vivo. Our study demonstrates for the first time that DHX33 acts as a direct transcriptional regulator to promote cell cycle progression and plays an important role in driving cell proliferation during both embryo development and tumorigenesis.

Glycogen synthase kinase 3 (GSK3) is an essential component of the Wnt signaling pathway and plays important roles in regulating cell proliferation, differentiation, and apoptosis. As GSK3 is abnormally upregulated in several diseases including type II diabetes, Alzheimer's disease and cancer, it has been regarded as a potential drug target. During zebrafish development, inhibition of GSK3 leads to ectopic activation of the Wnt pathway, resulting in a headless embryo. Using this phenotype as an assay we screened a chemical library of 4000 compounds and identified one novel compound, 3F8, which specifically inhibits eye and forebrain formation in zebrafish embryos, resembling a typical Wnt overexpression phenotype. Cell reporter assays, chemical informatics analysis and in vitro kinase experiments revealed that 3F8 is a selective GSK3 inhibitor, which is more potent than SB216763, a commonly used GSK3 inhibitor. Based on the structure of 3F8, a new generation of compounds inhibiting GSK3 was synthesized and validated by biological assays. Together, 3F8 and its derivatives could be useful as new reagents and potential therapeutic candidates for GSK3 related diseases.

Bisphenol S (BPS), an alternative for bisphenol A (BPA) that is present in thermal paper and numerous consumer products, has been linked to estrogenic, cytotoxic, genotoxic, neurotoxic, and immunotoxic responses. However, the mechanisms of BPS toxicity remain poorly understood. Here, following exposure to environmentally relevant concentrations ranging from 0.1 to 100 μg/L BPS, transcriptional changes evaluated by enriched gene ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Ingenuity Pathway Analysis (IPA) predicted cardiac disease and impairment of immune function in zebrafish at the embryo-to-larvae stage. Consistent with impacts predicted by transcriptional changes, significant sublethal impacts were observed ranging from reduced heart rate [8.7 ± 2.4% reductions at 100 μg/L BPS treatment; P < 0.05] to abnormal cardiac morphology [atrial/ventricle area significantly increased; 36.2 ± 9.6% at 100 μg/L BPS treatment; P < 0.05]. RNA-sequencing analysis results also indicated changes in nitric oxide synthetase (NOS2) and interleukin 12 (IL12) after BPS treatment, which was confirmed at the protein level. Increased expression of other cytokine genes was observed in larvae, suggesting inflammatory responses may be contributing to cardiac impairment by BPS. BPS caused cardiotoxicity, which temporally corresponded with inflammatory responses as predicted from RNA sequencing and confirmed at the protein and cellular levels of biological organization. Additional study is needed to find causal linkages between these responses.

A ngiogenesis is necessary for the vascularization of a tumor, providing essential nourishment for tumor growth, and the progression and metastasis of cancer cells. 1 Although tremendous efforts and resources have been dedicated to discovering angiogenesis inhibitors, very few candidates have been approved by FDA for therapeutic applications. Currently, Avastin (bevacizumab), a humanized monoclonal antibody, and Macugen (Pegaptanib), a pegylated oligonucleotide aptamer, both directed against vascular endothelial growth factor (VEGF) pathway, are two of the approved drugs for clinical use. There is still a great need to develop small molecule drugs for antiangiogenesis purpose. One approach to broaden the discovery platform is to identify antiangiogenic activities from existing drugs that have well defined toxicity and pharmacokinetics. Once a known drug is demonstrated to inhibit angiogenesis, it would move into the clinic trails more rapidly. Because most known drugs have well defined structures and defined biological targets, it is also possible to further improve the compound structure or select the target as a new entry point for angiogenesis-based studies and therapies. Currently there are more than 2000 known drugs that can be used for re-purposing applications. It would be desirable to have a single in vivo assay allowing rapid screening of a large number of compounds for new activities such as angiogenesis inhibition. Recently, the zebrafish has been shown to be a useful model organism for this type of approach. 2,3 Zebrafish blood vessels form by angiogenic sprouting and appear to use the same pathways necessary for blood vessel growth in mammals. 4 Using transgenic embryos expressing GFP in vessels, the embryonic blood vessels in live zebrafish can be directly visualized in multiwell plates for rapidly screening compounds affecting blood vessel formation and patterning. 5 This approach is highly effective and specific as was shown by the effect of previously known antiangiogenic compounds, such as SU6668 and SU5416, on embryonic blood vessel formation of zebrafish. 5 To identify clinically applicable drugs for antiangiogenesis we screened a library of 1120 compounds consisting of 85% FDA approved drugs (Prestwick Chemical, Inc) for inhibition of blood vessels. Live transgenic zebrafish embryos expressing GFP in vascular endothelial cells under the control of flk (also known as the VEGF receptor 2 gene) regulatory sequences were directly visualized under a fluorescent microscope to reveal drug-induced alteration of fluorescent blood vessels. 5 An initial screen of the drugs (at 10 mol/L concentration with 3 embryos in 200 L fish water per well of 96-well duplicate plates) identified several drugs that exhibited certain degree of inhibition of blood vessels but had no other detrimental effects on general embryonic development. Here we report one of the inhibitors, mycophenolic acid (MPA, Figure, A), for its efficacy and the subsequent target validation studies.MPA is an immuno-suppressive drug that is wi...