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human embryo kidney hek293 cells  (ATCC)


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    ATCC human embryo kidney hek293 cells
    (A) Cartoon of the PROTAC dTAG-13 depicting how it recruits the CUL4A CRBN E3 ligase complex to ubiquitylate dTAG-PPP2CA for its degradation through the ubiquitin-proteasome pathway. (B) Homozygous dTAG/dTAG PPP2CA knock-in <t>HEK293</t> cells were treated with DMSO, dTAG-13 (100 nM) or MG-132 (20 µM) as indicated for 16 h prior to lysis. Extracts (30 µg protein) were resolved by SDS-PAGE, and transferred to PVDF membranes, which were immunoblotted with the indicated antibodies. (C) Volcano plot showing changes in abundance of proteins identified in dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO control. Indicated are components of the PP2A holoenzyme complexes that are degraded by dTAG-13 significantly compared to DMSO control. (D) A quantitative analysis of PPP2CA protein levels from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 or DMSO from across individual replicates as indicated. (E) Volcano plot showing changes in ubiquitylated proteins identified from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO in the absence of MG-132 treatment. (F) As in (E) except that the data is represented as a trend plot. Ubiquitylated proteins with most differences (lower or higher) in abundance are indicated. (G-I) The abundance of PPP2CA-K21 (G), PPP2CA-K29 (H), and PPP2CA-K8 (I) ubiquitylation in dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO from individual replicates.
    Human Embryo Kidney Hek293 Cells, supplied by ATCC, used in various techniques. Bioz Stars score: 99/100, based on 22441 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/human+embryo+kidney+hek293+cells/293/bio_rxiv__2025__05__27__656291-201-8-13
    Average 99 stars, based on 22441 article reviews
    human embryo kidney hek293 cells - by Bioz Stars, 2026-10
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    1) Product Images from "Data-independent acquisition (DIA) approach for comprehensive ubiquitinome profiling in targeted protein degradation"

    Article Title: Data-independent acquisition (DIA) approach for comprehensive ubiquitinome profiling in targeted protein degradation

    Journal: bioRxiv

    doi: 10.1101/2025.05.27.656291

    (A) Cartoon of the PROTAC dTAG-13 depicting how it recruits the CUL4A CRBN E3 ligase complex to ubiquitylate dTAG-PPP2CA for its degradation through the ubiquitin-proteasome pathway. (B) Homozygous dTAG/dTAG PPP2CA knock-in HEK293 cells were treated with DMSO, dTAG-13 (100 nM) or MG-132 (20 µM) as indicated for 16 h prior to lysis. Extracts (30 µg protein) were resolved by SDS-PAGE, and transferred to PVDF membranes, which were immunoblotted with the indicated antibodies. (C) Volcano plot showing changes in abundance of proteins identified in dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO control. Indicated are components of the PP2A holoenzyme complexes that are degraded by dTAG-13 significantly compared to DMSO control. (D) A quantitative analysis of PPP2CA protein levels from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 or DMSO from across individual replicates as indicated. (E) Volcano plot showing changes in ubiquitylated proteins identified from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO in the absence of MG-132 treatment. (F) As in (E) except that the data is represented as a trend plot. Ubiquitylated proteins with most differences (lower or higher) in abundance are indicated. (G-I) The abundance of PPP2CA-K21 (G), PPP2CA-K29 (H), and PPP2CA-K8 (I) ubiquitylation in dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO from individual replicates.
    Figure Legend Snippet: (A) Cartoon of the PROTAC dTAG-13 depicting how it recruits the CUL4A CRBN E3 ligase complex to ubiquitylate dTAG-PPP2CA for its degradation through the ubiquitin-proteasome pathway. (B) Homozygous dTAG/dTAG PPP2CA knock-in HEK293 cells were treated with DMSO, dTAG-13 (100 nM) or MG-132 (20 µM) as indicated for 16 h prior to lysis. Extracts (30 µg protein) were resolved by SDS-PAGE, and transferred to PVDF membranes, which were immunoblotted with the indicated antibodies. (C) Volcano plot showing changes in abundance of proteins identified in dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO control. Indicated are components of the PP2A holoenzyme complexes that are degraded by dTAG-13 significantly compared to DMSO control. (D) A quantitative analysis of PPP2CA protein levels from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 or DMSO from across individual replicates as indicated. (E) Volcano plot showing changes in ubiquitylated proteins identified from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO in the absence of MG-132 treatment. (F) As in (E) except that the data is represented as a trend plot. Ubiquitylated proteins with most differences (lower or higher) in abundance are indicated. (G-I) The abundance of PPP2CA-K21 (G), PPP2CA-K29 (H), and PPP2CA-K8 (I) ubiquitylation in dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO from individual replicates.

    Techniques Used: Ubiquitin Proteomics, Knock-In, Lysis, SDS Page, Control

    A. Volcano plot showing changes in proteins identified from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO in the presence of MG-132. B. Volcano plot showing changes in ubiquitylated peptides identified from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO in the presence of MG-132.
    Figure Legend Snippet: A. Volcano plot showing changes in proteins identified from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO in the presence of MG-132. B. Volcano plot showing changes in ubiquitylated peptides identified from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO in the presence of MG-132.

    Techniques Used: Knock-In

    (A) Volcano plot representing changes in global ubiquitylated sites in dTAG/dTAG PPP2CA knock-in HEK293 cells treated for 15 min with dTAG-13 compared to DMSO controls. Sites identified on PPP2CA upon dTAG-13 treatment are indicated. (B) As in (A) except that dTAG-13 was applied for 30 min. (C) As in (A) except that dTAG-13 was applied for 60 min. (D) The changes in abundance of the indicated ubiquitylated peptides that were identified on PPP2CA after 15 min, 30 min and 60 min of dTAG-13 treatment compared to DMSO treatment. (E) The 3D-structure of the PPP2CA rendered from the Integrator-PP2A complex (PDB: 7CUN) with annotations of dTAG-13-induced ubiquitylation sites on PPP2CA in red.
    Figure Legend Snippet: (A) Volcano plot representing changes in global ubiquitylated sites in dTAG/dTAG PPP2CA knock-in HEK293 cells treated for 15 min with dTAG-13 compared to DMSO controls. Sites identified on PPP2CA upon dTAG-13 treatment are indicated. (B) As in (A) except that dTAG-13 was applied for 30 min. (C) As in (A) except that dTAG-13 was applied for 60 min. (D) The changes in abundance of the indicated ubiquitylated peptides that were identified on PPP2CA after 15 min, 30 min and 60 min of dTAG-13 treatment compared to DMSO treatment. (E) The 3D-structure of the PPP2CA rendered from the Integrator-PP2A complex (PDB: 7CUN) with annotations of dTAG-13-induced ubiquitylation sites on PPP2CA in red.

    Techniques Used: Knock-In

    (A) HEK293 cells were treated with DMSO, SGK3-PROTAC1 (100 nM) or MG-132 (20 µM) as indicated for 16 h prior to lysis. Extracts (30 µg protein) were resolved by SDS-PAGE, and transferred to PVDF membranes, which were immunoblotted with the indicated antibodies. (B) Volcano plot showing global changes in the proteome abundance from HEK293 cells treated with SGK3-PROTAC1 compared to DMSO control in the absence of MG-132. (C) Volcano plot representing global changes in the abundance of ubiquitylated peptides from HEK293 cells treated with SGK3-PROTAC1 compared to DMSO control in presence of MG-132. The ubiquitylated SGK3 peptides that were identified and show significant increase upon SGK3-PROTAC1 treatment are indicated. (D) The trends in abundance of all identified ubiquitylated peptides from SGK3 from HEK293 cells treated with SGK3-PROTAC1+MG-132 compared to DMSO+MG-132 controls are indicated. (E) All ubiquitylation sites on SGK3 identified in (D) shown on the 3D-structure of SGK3 (PDB: 6EDX).
    Figure Legend Snippet: (A) HEK293 cells were treated with DMSO, SGK3-PROTAC1 (100 nM) or MG-132 (20 µM) as indicated for 16 h prior to lysis. Extracts (30 µg protein) were resolved by SDS-PAGE, and transferred to PVDF membranes, which were immunoblotted with the indicated antibodies. (B) Volcano plot showing global changes in the proteome abundance from HEK293 cells treated with SGK3-PROTAC1 compared to DMSO control in the absence of MG-132. (C) Volcano plot representing global changes in the abundance of ubiquitylated peptides from HEK293 cells treated with SGK3-PROTAC1 compared to DMSO control in presence of MG-132. The ubiquitylated SGK3 peptides that were identified and show significant increase upon SGK3-PROTAC1 treatment are indicated. (D) The trends in abundance of all identified ubiquitylated peptides from SGK3 from HEK293 cells treated with SGK3-PROTAC1+MG-132 compared to DMSO+MG-132 controls are indicated. (E) All ubiquitylation sites on SGK3 identified in (D) shown on the 3D-structure of SGK3 (PDB: 6EDX).

    Techniques Used: Lysis, SDS Page, Control

    A. Volcano plot representing global changes in the abundance of ubiquitylated peptides from HEK293 cells treated with SGK3-PROTAC1 compared to DMSO control in the absence of MG-132. (B) Volcano plot showing global changes in the proteome abundance from HEK293 cells treated with SGK3-PROTAC1 compared to DMSO control in the presence of MG-132.
    Figure Legend Snippet: A. Volcano plot representing global changes in the abundance of ubiquitylated peptides from HEK293 cells treated with SGK3-PROTAC1 compared to DMSO control in the absence of MG-132. (B) Volcano plot showing global changes in the proteome abundance from HEK293 cells treated with SGK3-PROTAC1 compared to DMSO control in the presence of MG-132.

    Techniques Used: Control

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    Cell Culture:

    Article Title: Photosensitized and Photothermal Stimulation of Cellular Membranes by Organic Thin Films and Nanoparticles.
    Article Snippet: .. The human embryo kidney (HEK293) cells (from ATCC) and human epithelial adenocarcinoma (Hela) cell lines were cultured in Dulbecco’s modified Eagle Medium (DMEM) supplemented with 2 mM L-glutamine. .. The SV40 immortalized human microglial cells were cultured at 37°C/5% CO2 in RPMI-1640 with sodium bicarbonate (Sigma-Aldrich).

    Article Title: Klotho preservation by Rhein promotes toll-like receptor 4 proteolysis and attenuates lipopolysaccharide-induced acute kidney injury.
    Article Snippet: Renal anti-aging protein Klotho exhibits impressive properties of anti-inflammation and renal protection, however is suppressed early after renal injury, making Klotho restoration an attractive strategy of treating renal inflammatory disorders.. Here, we reported that Klotho is enriched in macrophages and Klotho preservation by Rhein, an anthraquinone derived from medicinal plant rhubarb, attenuates lipopolysaccharide (LPS)-induced acute inflammation essentially via promoting toll-like receptor 4 (TLR4) degradation.. LPS-induced pro-inflammatory NF-κB signaling and cytokine expressions coincided with Klotho repression and toll-like receptor 4 (TLR4) elevation in macrophages, renal epithelial cells, and acutelyinflamed kidney.

    Article Title: Use of SU8 as a stable and biocompatible adhesion layer for gold bioelectrodes
    Article Snippet: .. Human Embryo Kidney (HEK293) cells, obtained from ATCC, were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum, 2 mM L-glutamine, 100 μg/ml penicillin, and 100 μg/ml streptomycin (Life Technologies). ..

    Article Title: Photosensitized and Photothermal Stimulation of Cellular Membranes by Organic Thin Films and Nanoparticles
    Article Snippet: .. The human embryo kidney (HEK293) cells (from ATCC) and human epithelial adenocarcinoma (Hela) cell lines were cultured in Dulbecco’s modified Eagle Medium (DMEM) supplemented with 2 mM l -glutamine. .. The SV40 immortalized human microglial cells were cultured at 37°C/5% CO 2 in RPMI-1640 with sodium bicarbonate (Sigma-Aldrich).

    Modification:

    Article Title: Photosensitized and Photothermal Stimulation of Cellular Membranes by Organic Thin Films and Nanoparticles.
    Article Snippet: .. The human embryo kidney (HEK293) cells (from ATCC) and human epithelial adenocarcinoma (Hela) cell lines were cultured in Dulbecco’s modified Eagle Medium (DMEM) supplemented with 2 mM L-glutamine. .. The SV40 immortalized human microglial cells were cultured at 37°C/5% CO2 in RPMI-1640 with sodium bicarbonate (Sigma-Aldrich).

    Article Title: Klotho preservation by Rhein promotes toll-like receptor 4 proteolysis and attenuates lipopolysaccharide-induced acute kidney injury.
    Article Snippet: Renal anti-aging protein Klotho exhibits impressive properties of anti-inflammation and renal protection, however is suppressed early after renal injury, making Klotho restoration an attractive strategy of treating renal inflammatory disorders.. Here, we reported that Klotho is enriched in macrophages and Klotho preservation by Rhein, an anthraquinone derived from medicinal plant rhubarb, attenuates lipopolysaccharide (LPS)-induced acute inflammation essentially via promoting toll-like receptor 4 (TLR4) degradation.. LPS-induced pro-inflammatory NF-κB signaling and cytokine expressions coincided with Klotho repression and toll-like receptor 4 (TLR4) elevation in macrophages, renal epithelial cells, and acutelyinflamed kidney.

    Article Title: Use of SU8 as a stable and biocompatible adhesion layer for gold bioelectrodes
    Article Snippet: .. Human Embryo Kidney (HEK293) cells, obtained from ATCC, were cultured in Dulbecco’s Modified Eagle Medium (DMEM) supplemented with 10% fetal calf serum, 2 mM L-glutamine, 100 μg/ml penicillin, and 100 μg/ml streptomycin (Life Technologies). ..

    Article Title: Photosensitized and Photothermal Stimulation of Cellular Membranes by Organic Thin Films and Nanoparticles
    Article Snippet: .. The human embryo kidney (HEK293) cells (from ATCC) and human epithelial adenocarcinoma (Hela) cell lines were cultured in Dulbecco’s modified Eagle Medium (DMEM) supplemented with 2 mM l -glutamine. .. The SV40 immortalized human microglial cells were cultured at 37°C/5% CO 2 in RPMI-1640 with sodium bicarbonate (Sigma-Aldrich).

    Stable Transfection:

    Article Title: Data-independent acquisition (DIA) approach for comprehensive ubiquitinome profiling in targeted protein degradation
    Article Snippet: .. The cell lines used in this study were: human embryo kidney HEK293 cells (ATCC, CRL-1573), HEK293-FT cells (Invitrogen, Cat# R70007), HEK293-derived QBI-293 (Clone 4.0) cell line stably expressing full length human Tau (T40-2N4R) carrying the P301L mutation with a GFP-tag at the C-terminus and dTAG/dTAG PPP2CA knock-in HEK293 cells generated using CRISPR/Cas9 genome editing . .. All cells were cultured in DMEM (Life Technologies) supplemented with 10% (v/v) foetal bovine serum (FBS, Thermo Fisher Scientific), 2 mM L-glutamine (Lonza), 100 U/mL penicillin (Lonza) and 0.1 mg/mL streptomycin (Lonza).

    Article Title: Pivotal role for the ESCRT-II complex subunit EAP30/SNF8 in IRF3-dependent innate antiviral defense
    Article Snippet: .. PH5CH8 non-neoplastic hepatocytes (provided by Nobuyuki Kato, Okayama University, Japan) [ ], human hepatoma Huh7.5-TLR3 and Huh7-TLR3 cells that were stably reconstituted for the expression of human TLR3 (developed in this laboratory) [ , ], and human embryo kidney HEK293 cells (obtained from American Type Culture Collection), were maintained as described previously [ , , ]. ..

    Expressing:

    Article Title: Data-independent acquisition (DIA) approach for comprehensive ubiquitinome profiling in targeted protein degradation
    Article Snippet: .. The cell lines used in this study were: human embryo kidney HEK293 cells (ATCC, CRL-1573), HEK293-FT cells (Invitrogen, Cat# R70007), HEK293-derived QBI-293 (Clone 4.0) cell line stably expressing full length human Tau (T40-2N4R) carrying the P301L mutation with a GFP-tag at the C-terminus and dTAG/dTAG PPP2CA knock-in HEK293 cells generated using CRISPR/Cas9 genome editing . .. All cells were cultured in DMEM (Life Technologies) supplemented with 10% (v/v) foetal bovine serum (FBS, Thermo Fisher Scientific), 2 mM L-glutamine (Lonza), 100 U/mL penicillin (Lonza) and 0.1 mg/mL streptomycin (Lonza).

    Article Title: EML4-ALK-mediated activation of the JAK2-STAT pathway is critical for non-small cell lung cancer transformation
    Article Snippet: .. Human embryo kidney (HEK293) cells do not express STAT6 and the human lung adenocarcinoma cell line H2228, expressing STAT6 and harboring the EML4-ALK variant 3 fusion gene, were obtained from the American Type Culture Collection. ..

    Article Title: Pivotal role for the ESCRT-II complex subunit EAP30/SNF8 in IRF3-dependent innate antiviral defense
    Article Snippet: .. PH5CH8 non-neoplastic hepatocytes (provided by Nobuyuki Kato, Okayama University, Japan) [ ], human hepatoma Huh7.5-TLR3 and Huh7-TLR3 cells that were stably reconstituted for the expression of human TLR3 (developed in this laboratory) [ , ], and human embryo kidney HEK293 cells (obtained from American Type Culture Collection), were maintained as described previously [ , , ]. ..

    Mutagenesis:

    Article Title: Data-independent acquisition (DIA) approach for comprehensive ubiquitinome profiling in targeted protein degradation
    Article Snippet: .. The cell lines used in this study were: human embryo kidney HEK293 cells (ATCC, CRL-1573), HEK293-FT cells (Invitrogen, Cat# R70007), HEK293-derived QBI-293 (Clone 4.0) cell line stably expressing full length human Tau (T40-2N4R) carrying the P301L mutation with a GFP-tag at the C-terminus and dTAG/dTAG PPP2CA knock-in HEK293 cells generated using CRISPR/Cas9 genome editing . .. All cells were cultured in DMEM (Life Technologies) supplemented with 10% (v/v) foetal bovine serum (FBS, Thermo Fisher Scientific), 2 mM L-glutamine (Lonza), 100 U/mL penicillin (Lonza) and 0.1 mg/mL streptomycin (Lonza).

    Knock-In:

    Article Title: Data-independent acquisition (DIA) approach for comprehensive ubiquitinome profiling in targeted protein degradation
    Article Snippet: .. The cell lines used in this study were: human embryo kidney HEK293 cells (ATCC, CRL-1573), HEK293-FT cells (Invitrogen, Cat# R70007), HEK293-derived QBI-293 (Clone 4.0) cell line stably expressing full length human Tau (T40-2N4R) carrying the P301L mutation with a GFP-tag at the C-terminus and dTAG/dTAG PPP2CA knock-in HEK293 cells generated using CRISPR/Cas9 genome editing . .. All cells were cultured in DMEM (Life Technologies) supplemented with 10% (v/v) foetal bovine serum (FBS, Thermo Fisher Scientific), 2 mM L-glutamine (Lonza), 100 U/mL penicillin (Lonza) and 0.1 mg/mL streptomycin (Lonza).

    Generated:

    Article Title: Data-independent acquisition (DIA) approach for comprehensive ubiquitinome profiling in targeted protein degradation
    Article Snippet: .. The cell lines used in this study were: human embryo kidney HEK293 cells (ATCC, CRL-1573), HEK293-FT cells (Invitrogen, Cat# R70007), HEK293-derived QBI-293 (Clone 4.0) cell line stably expressing full length human Tau (T40-2N4R) carrying the P301L mutation with a GFP-tag at the C-terminus and dTAG/dTAG PPP2CA knock-in HEK293 cells generated using CRISPR/Cas9 genome editing . .. All cells were cultured in DMEM (Life Technologies) supplemented with 10% (v/v) foetal bovine serum (FBS, Thermo Fisher Scientific), 2 mM L-glutamine (Lonza), 100 U/mL penicillin (Lonza) and 0.1 mg/mL streptomycin (Lonza).

    CRISPR:

    Article Title: Data-independent acquisition (DIA) approach for comprehensive ubiquitinome profiling in targeted protein degradation
    Article Snippet: .. The cell lines used in this study were: human embryo kidney HEK293 cells (ATCC, CRL-1573), HEK293-FT cells (Invitrogen, Cat# R70007), HEK293-derived QBI-293 (Clone 4.0) cell line stably expressing full length human Tau (T40-2N4R) carrying the P301L mutation with a GFP-tag at the C-terminus and dTAG/dTAG PPP2CA knock-in HEK293 cells generated using CRISPR/Cas9 genome editing . .. All cells were cultured in DMEM (Life Technologies) supplemented with 10% (v/v) foetal bovine serum (FBS, Thermo Fisher Scientific), 2 mM L-glutamine (Lonza), 100 U/mL penicillin (Lonza) and 0.1 mg/mL streptomycin (Lonza).

    Variant Assay:

    Article Title: EML4-ALK-mediated activation of the JAK2-STAT pathway is critical for non-small cell lung cancer transformation
    Article Snippet: .. Human embryo kidney (HEK293) cells do not express STAT6 and the human lung adenocarcinoma cell line H2228, expressing STAT6 and harboring the EML4-ALK variant 3 fusion gene, were obtained from the American Type Culture Collection. ..



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    Microbix Inc human embryo kidney cell line hek293
    Figure 2. TAT-mPiC fusion protein internalization and processing. (A) Three cell lines (HeLa, <t>HEK293,</t> and HepG2) were incubated with the TAT-mPiC fusion protein for 2.5 h, whole cell lysates from cells with or without the addition of the fusion protein were analyzed by Western blot. (B) Hek293-MitoGFP cells were incubated with TAT-PiCA-cherry fusion protein (20 µg/mL) for 3 h and a fluorescence microscope was used to obtain images. White arrows indicate yellow spots where MitoGFP and TAT-PiCA-cherry overlap. The white boxes indicate the region of interest, which is enlarged in the inset to highlight colocalization. (C) HeLa cells were incubated for 3 h with the fusion protein then the mitochondria were isolated and sub- fractionated and analyzed by Western blot. (D) Isolated mitochondrial inner membranes of treated HeLa cells were incubated for different time periods and protein treatment doses and analyzed by Western blot. IM—mitochondrial inner membrane, Mat—mitochondrial matrix, OM—mitochondrial outer membrane, Cyto—cytoplasm, WCE—Whole cell lysate. Red arrow—42 kDa full length fusion protein, green dashed rectangle—endogenous mPiC protein, green arrow—the 34 kDa processed exogenous mPiC protein.
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    (A) Cartoon of the PROTAC dTAG-13 depicting how it recruits the CUL4A CRBN E3 ligase complex to ubiquitylate dTAG-PPP2CA for its degradation through the ubiquitin-proteasome pathway. (B) Homozygous dTAG/dTAG PPP2CA knock-in HEK293 cells were treated with DMSO, dTAG-13 (100 nM) or MG-132 (20 µM) as indicated for 16 h prior to lysis. Extracts (30 µg protein) were resolved by SDS-PAGE, and transferred to PVDF membranes, which were immunoblotted with the indicated antibodies. (C) Volcano plot showing changes in abundance of proteins identified in dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO control. Indicated are components of the PP2A holoenzyme complexes that are degraded by dTAG-13 significantly compared to DMSO control. (D) A quantitative analysis of PPP2CA protein levels from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 or DMSO from across individual replicates as indicated. (E) Volcano plot showing changes in ubiquitylated proteins identified from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO in the absence of MG-132 treatment. (F) As in (E) except that the data is represented as a trend plot. Ubiquitylated proteins with most differences (lower or higher) in abundance are indicated. (G-I) The abundance of PPP2CA-K21 (G), PPP2CA-K29 (H), and PPP2CA-K8 (I) ubiquitylation in dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO from individual replicates.

    Journal: bioRxiv

    Article Title: Data-independent acquisition (DIA) approach for comprehensive ubiquitinome profiling in targeted protein degradation

    doi: 10.1101/2025.05.27.656291

    Figure Lengend Snippet: (A) Cartoon of the PROTAC dTAG-13 depicting how it recruits the CUL4A CRBN E3 ligase complex to ubiquitylate dTAG-PPP2CA for its degradation through the ubiquitin-proteasome pathway. (B) Homozygous dTAG/dTAG PPP2CA knock-in HEK293 cells were treated with DMSO, dTAG-13 (100 nM) or MG-132 (20 µM) as indicated for 16 h prior to lysis. Extracts (30 µg protein) were resolved by SDS-PAGE, and transferred to PVDF membranes, which were immunoblotted with the indicated antibodies. (C) Volcano plot showing changes in abundance of proteins identified in dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO control. Indicated are components of the PP2A holoenzyme complexes that are degraded by dTAG-13 significantly compared to DMSO control. (D) A quantitative analysis of PPP2CA protein levels from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 or DMSO from across individual replicates as indicated. (E) Volcano plot showing changes in ubiquitylated proteins identified from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO in the absence of MG-132 treatment. (F) As in (E) except that the data is represented as a trend plot. Ubiquitylated proteins with most differences (lower or higher) in abundance are indicated. (G-I) The abundance of PPP2CA-K21 (G), PPP2CA-K29 (H), and PPP2CA-K8 (I) ubiquitylation in dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO from individual replicates.

    Article Snippet: The cell lines used in this study were: human embryo kidney HEK293 cells (ATCC, CRL-1573), HEK293-FT cells (Invitrogen, Cat# R70007), HEK293-derived QBI-293 (Clone 4.0) cell line stably expressing full length human Tau (T40-2N4R) carrying the P301L mutation with a GFP-tag at the C-terminus and dTAG/dTAG PPP2CA knock-in HEK293 cells generated using CRISPR/Cas9 genome editing .

    Techniques: Ubiquitin Proteomics, Knock-In, Lysis, SDS Page, Control

    A. Volcano plot showing changes in proteins identified from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO in the presence of MG-132. B. Volcano plot showing changes in ubiquitylated peptides identified from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO in the presence of MG-132.

    Journal: bioRxiv

    Article Title: Data-independent acquisition (DIA) approach for comprehensive ubiquitinome profiling in targeted protein degradation

    doi: 10.1101/2025.05.27.656291

    Figure Lengend Snippet: A. Volcano plot showing changes in proteins identified from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO in the presence of MG-132. B. Volcano plot showing changes in ubiquitylated peptides identified from dTAG/dTAG PPP2CA knock-in HEK293 cells treated with dTAG-13 compared to DMSO in the presence of MG-132.

    Article Snippet: The cell lines used in this study were: human embryo kidney HEK293 cells (ATCC, CRL-1573), HEK293-FT cells (Invitrogen, Cat# R70007), HEK293-derived QBI-293 (Clone 4.0) cell line stably expressing full length human Tau (T40-2N4R) carrying the P301L mutation with a GFP-tag at the C-terminus and dTAG/dTAG PPP2CA knock-in HEK293 cells generated using CRISPR/Cas9 genome editing .

    Techniques: Knock-In

    (A) Volcano plot representing changes in global ubiquitylated sites in dTAG/dTAG PPP2CA knock-in HEK293 cells treated for 15 min with dTAG-13 compared to DMSO controls. Sites identified on PPP2CA upon dTAG-13 treatment are indicated. (B) As in (A) except that dTAG-13 was applied for 30 min. (C) As in (A) except that dTAG-13 was applied for 60 min. (D) The changes in abundance of the indicated ubiquitylated peptides that were identified on PPP2CA after 15 min, 30 min and 60 min of dTAG-13 treatment compared to DMSO treatment. (E) The 3D-structure of the PPP2CA rendered from the Integrator-PP2A complex (PDB: 7CUN) with annotations of dTAG-13-induced ubiquitylation sites on PPP2CA in red.

    Journal: bioRxiv

    Article Title: Data-independent acquisition (DIA) approach for comprehensive ubiquitinome profiling in targeted protein degradation

    doi: 10.1101/2025.05.27.656291

    Figure Lengend Snippet: (A) Volcano plot representing changes in global ubiquitylated sites in dTAG/dTAG PPP2CA knock-in HEK293 cells treated for 15 min with dTAG-13 compared to DMSO controls. Sites identified on PPP2CA upon dTAG-13 treatment are indicated. (B) As in (A) except that dTAG-13 was applied for 30 min. (C) As in (A) except that dTAG-13 was applied for 60 min. (D) The changes in abundance of the indicated ubiquitylated peptides that were identified on PPP2CA after 15 min, 30 min and 60 min of dTAG-13 treatment compared to DMSO treatment. (E) The 3D-structure of the PPP2CA rendered from the Integrator-PP2A complex (PDB: 7CUN) with annotations of dTAG-13-induced ubiquitylation sites on PPP2CA in red.

    Article Snippet: The cell lines used in this study were: human embryo kidney HEK293 cells (ATCC, CRL-1573), HEK293-FT cells (Invitrogen, Cat# R70007), HEK293-derived QBI-293 (Clone 4.0) cell line stably expressing full length human Tau (T40-2N4R) carrying the P301L mutation with a GFP-tag at the C-terminus and dTAG/dTAG PPP2CA knock-in HEK293 cells generated using CRISPR/Cas9 genome editing .

    Techniques: Knock-In

    (A) HEK293 cells were treated with DMSO, SGK3-PROTAC1 (100 nM) or MG-132 (20 µM) as indicated for 16 h prior to lysis. Extracts (30 µg protein) were resolved by SDS-PAGE, and transferred to PVDF membranes, which were immunoblotted with the indicated antibodies. (B) Volcano plot showing global changes in the proteome abundance from HEK293 cells treated with SGK3-PROTAC1 compared to DMSO control in the absence of MG-132. (C) Volcano plot representing global changes in the abundance of ubiquitylated peptides from HEK293 cells treated with SGK3-PROTAC1 compared to DMSO control in presence of MG-132. The ubiquitylated SGK3 peptides that were identified and show significant increase upon SGK3-PROTAC1 treatment are indicated. (D) The trends in abundance of all identified ubiquitylated peptides from SGK3 from HEK293 cells treated with SGK3-PROTAC1+MG-132 compared to DMSO+MG-132 controls are indicated. (E) All ubiquitylation sites on SGK3 identified in (D) shown on the 3D-structure of SGK3 (PDB: 6EDX).

    Journal: bioRxiv

    Article Title: Data-independent acquisition (DIA) approach for comprehensive ubiquitinome profiling in targeted protein degradation

    doi: 10.1101/2025.05.27.656291

    Figure Lengend Snippet: (A) HEK293 cells were treated with DMSO, SGK3-PROTAC1 (100 nM) or MG-132 (20 µM) as indicated for 16 h prior to lysis. Extracts (30 µg protein) were resolved by SDS-PAGE, and transferred to PVDF membranes, which were immunoblotted with the indicated antibodies. (B) Volcano plot showing global changes in the proteome abundance from HEK293 cells treated with SGK3-PROTAC1 compared to DMSO control in the absence of MG-132. (C) Volcano plot representing global changes in the abundance of ubiquitylated peptides from HEK293 cells treated with SGK3-PROTAC1 compared to DMSO control in presence of MG-132. The ubiquitylated SGK3 peptides that were identified and show significant increase upon SGK3-PROTAC1 treatment are indicated. (D) The trends in abundance of all identified ubiquitylated peptides from SGK3 from HEK293 cells treated with SGK3-PROTAC1+MG-132 compared to DMSO+MG-132 controls are indicated. (E) All ubiquitylation sites on SGK3 identified in (D) shown on the 3D-structure of SGK3 (PDB: 6EDX).

    Article Snippet: The cell lines used in this study were: human embryo kidney HEK293 cells (ATCC, CRL-1573), HEK293-FT cells (Invitrogen, Cat# R70007), HEK293-derived QBI-293 (Clone 4.0) cell line stably expressing full length human Tau (T40-2N4R) carrying the P301L mutation with a GFP-tag at the C-terminus and dTAG/dTAG PPP2CA knock-in HEK293 cells generated using CRISPR/Cas9 genome editing .

    Techniques: Lysis, SDS Page, Control

    A. Volcano plot representing global changes in the abundance of ubiquitylated peptides from HEK293 cells treated with SGK3-PROTAC1 compared to DMSO control in the absence of MG-132. (B) Volcano plot showing global changes in the proteome abundance from HEK293 cells treated with SGK3-PROTAC1 compared to DMSO control in the presence of MG-132.

    Journal: bioRxiv

    Article Title: Data-independent acquisition (DIA) approach for comprehensive ubiquitinome profiling in targeted protein degradation

    doi: 10.1101/2025.05.27.656291

    Figure Lengend Snippet: A. Volcano plot representing global changes in the abundance of ubiquitylated peptides from HEK293 cells treated with SGK3-PROTAC1 compared to DMSO control in the absence of MG-132. (B) Volcano plot showing global changes in the proteome abundance from HEK293 cells treated with SGK3-PROTAC1 compared to DMSO control in the presence of MG-132.

    Article Snippet: The cell lines used in this study were: human embryo kidney HEK293 cells (ATCC, CRL-1573), HEK293-FT cells (Invitrogen, Cat# R70007), HEK293-derived QBI-293 (Clone 4.0) cell line stably expressing full length human Tau (T40-2N4R) carrying the P301L mutation with a GFP-tag at the C-terminus and dTAG/dTAG PPP2CA knock-in HEK293 cells generated using CRISPR/Cas9 genome editing .

    Techniques: Control

    Figure 2. TAT-mPiC fusion protein internalization and processing. (A) Three cell lines (HeLa, HEK293, and HepG2) were incubated with the TAT-mPiC fusion protein for 2.5 h, whole cell lysates from cells with or without the addition of the fusion protein were analyzed by Western blot. (B) Hek293-MitoGFP cells were incubated with TAT-PiCA-cherry fusion protein (20 µg/mL) for 3 h and a fluorescence microscope was used to obtain images. White arrows indicate yellow spots where MitoGFP and TAT-PiCA-cherry overlap. The white boxes indicate the region of interest, which is enlarged in the inset to highlight colocalization. (C) HeLa cells were incubated for 3 h with the fusion protein then the mitochondria were isolated and sub- fractionated and analyzed by Western blot. (D) Isolated mitochondrial inner membranes of treated HeLa cells were incubated for different time periods and protein treatment doses and analyzed by Western blot. IM—mitochondrial inner membrane, Mat—mitochondrial matrix, OM—mitochondrial outer membrane, Cyto—cytoplasm, WCE—Whole cell lysate. Red arrow—42 kDa full length fusion protein, green dashed rectangle—endogenous mPiC protein, green arrow—the 34 kDa processed exogenous mPiC protein.

    Journal: International journal of molecular sciences

    Article Title: Rescue of the First Mitochondrial Membrane Carrier, the mPiC, by TAT-Mediated Protein Replacement Treatment.

    doi: 10.3390/ijms26094379

    Figure Lengend Snippet: Figure 2. TAT-mPiC fusion protein internalization and processing. (A) Three cell lines (HeLa, HEK293, and HepG2) were incubated with the TAT-mPiC fusion protein for 2.5 h, whole cell lysates from cells with or without the addition of the fusion protein were analyzed by Western blot. (B) Hek293-MitoGFP cells were incubated with TAT-PiCA-cherry fusion protein (20 µg/mL) for 3 h and a fluorescence microscope was used to obtain images. White arrows indicate yellow spots where MitoGFP and TAT-PiCA-cherry overlap. The white boxes indicate the region of interest, which is enlarged in the inset to highlight colocalization. (C) HeLa cells were incubated for 3 h with the fusion protein then the mitochondria were isolated and sub- fractionated and analyzed by Western blot. (D) Isolated mitochondrial inner membranes of treated HeLa cells were incubated for different time periods and protein treatment doses and analyzed by Western blot. IM—mitochondrial inner membrane, Mat—mitochondrial matrix, OM—mitochondrial outer membrane, Cyto—cytoplasm, WCE—Whole cell lysate. Red arrow—42 kDa full length fusion protein, green dashed rectangle—endogenous mPiC protein, green arrow—the 34 kDa processed exogenous mPiC protein.

    Article Snippet: HeLa cervical carcinoma cells (ATCCCCL-2), HEK293 human embryo kidney cells (ATCC-CRL-1573), HepG2 hepatocellular carcinoma cells (ATCC-HB-8065), BJ normal fibroblasts (ATCC-CRL-2522), and Hek293MitoGFP (our engineered cells as described in [35]) cells were grown in DMEM medium supplemented with 10% fetal bovine serum (FBS; Merck, Darmstadt, Germany), 2 mM L-glutamine (Sartorius, Göttingen, Germany), 100 units/mL penicillin, 100 μg/mL streptomycin. (Penicillin-Streptomycin Solution 100X; Biowest, Rue de la Caille, Nuaillé, France).

    Techniques: Incubation, Western Blot, Fluorescence, Microscopy, Isolation, Membrane