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Ct of PROTAC #89, which targets an endogenously SNAP-tagged clathrin light chain, on the HAP1 cell proteome

ABSTRACT: We would like to investigate what effect degradation of the clathrin light chain has on the HAP1 proteome. We therefore tagged the clathrin light chain (CLC) in HAP1 cells endogenously with a SNAP-tag via CRISPaint. The degradation of the SNAP-tagged protein is induced by the addition of a SNAP-PROTAC (PROTAC #89). The proteomes of a short (6 h) and long (24 h) treatment with PROTAC #89 are compared against the corresponding DMSO controls using LFQ.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Chronic Myeloid Leukemia Cell Line

SUBMITTER: Farnusch Kaschani

LAB HEAD: Farnusch Kaschani

PROVIDER: PXD049283 | Pride | 2025-05-06

REPOSITORIES: Pride

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	ACE_0719_JS01.raw	Raw
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Publications

Induced degradation of SNAP-fusion proteins.

Pol Savina Abraham SA Liljenberg Sara S Barr Jack J Simon Gina G Wong-Dilworth Luis L Paterson Danielle L DL Berishvili Vladimir P VP Bottanelli Francesca F Kaschani Farnusch F Kaiser Markus M Pettersson Mariell M Hellerschmied Doris D

RSC chemical biology 20241021

Self-labeling protein tags are an efficient means to visualize, manipulate, and isolate engineered fusion proteins with suitable chemical probes. The SNAP-tag, which covalently conjugates to benzyl-guanine and -chloropyrimidine derivatives is used extensively in fluorescence microscopy, given the availability of suitable SNAP-ligand-based probes. Here, we extend the applicability of the SNAP-tag to targeted protein degradation. We developed a set of SNAP PROteolysis TArgeting Chimeras (SNAP-PROT ...[more]

PMID: 39444693

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Project description:We used CRISPR/Cas9 to intoroduce frame-shifting mutations into the ABCC1 and ABCB1 genes and treated HAP1 WT cells with varying concentrations of the MZ1 PROTAC. To measure the transcriptional response to both genetic and chemical perturbances, we performed RNA-seq and quantified gene expression levels.

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Proteomics analysis of a new Cas9-targeting PROTAC molecule

Project description:Scientists have developed several methods to control the activity of Cas protein in a timely way and hence reduce off-target effects, including anti-CRISPR proteins and small molecule inhibitors. The PROTAC is a new conception of using the natural ubiquitin-proteasome system to degrade the protein of interest in drug design and development. Here, we engineered Cas proteins (Cas9, Cas12, and Cas13) by inserting a Phe-Cys-Pro-Phe (FCPF) amino acid sequence (also known as the π-clamp system) and demonstrate that the modified CasFCPF proteins could be labeled in live cells by perfluoroaromatics carrying FITC fluorophore or were degraded by perfluoroaromatics-functionalized PROTAC (PROTAC-FCPF). Proteome-wide analysis of PROTAC-FCPF-mediated Cas9FCPF protein degradation revealed high target specificity, suggesting a wide application of chemically induced proximity in combination with site-specific protein modification in the regulation of protein stability, activity and functionality.

2022-10-18 | PXD022199 | Pride

Analysis of the methylation state of K510, K514 and K515 of human EZH2 within recombinant PRC2

Project description:Using mass-spectrometry, we are seeking to determine the extent of methylation of EZH2 K510, K514 and K515 in the above mentioned recombinant PRC2 variants, answering the question whether recombinant mutant PRC2 is automethylated to the same or similar extent as the wt PRC2 complex.

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Proteogenomics uncovers critical elements of host response in bovine soft palate epithelial cells following in vitro infection with foot-and-mouth disease virus (FMDV)

Project description:The pathogen and host factors that contribute to the establishment of foot-and-mouth disease virus (FMDV) persistence are currently not understood. Using primary bovine soft palate multilayers in combination with RNA sequencing, we analyzed the transcriptional responses during acute and persistent FMDV infection.

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UBR4 KO analysis with TMT labeling

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Macrocycle-based PROTACs selectively degrade cyclophilin A and inhibit HIV-1 and HCV

Project description:We have designed and characterised antiviral PROteolysis TArgeting Chimeras (PROTACs) targeting the human protein cyclophilin A (CypA), a host cofactor for unrelated viruses including human immunodeficiency virus (HIV) and hepatitis C virus (HCV). The PROTAC warheads are based on fully synthetic macrocycles derived from sanglifehrin A, which are structurally different from the classical Cyp inhibitor, cyclosporin A. Our Cyp-PROTACs decrease CypA levels in cell lines and primary human cells, and this degradation is via a PROTAC mechanism. These molecules have high specificity for CypA illustrated by proteomics experiments. Critically, CypA degradation facilitates improved antiviral activity against HIV-1 in primary human CD4+ T cells compared to the non-PROTAC parental inhibitor, at limiting inhibitor concentrations. Similarly, we observe antiviral activity against HCV replicon in a hepatoma cell line. We propose that CypA targeting PROTACs inhibit viral replication potently, and anticipate reduced evolution of viral resistance and broad efficacy against unrelated viruses. Furthermore, they provide powerful tools for probing cyclophilin biology.

2024-11-29 | PXD057024 | Pride

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2024-05-24 | PXD040156 | Pride

Innate lymphoid cell development requires TOX-dependent generation of a common ILC progenitor

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