Rôles fonctionnels de la ligase de l’ubiquitine ITCH dans l’endocytose dépendante de la clathrine du récepteur du facteur de croissance épidermique

ITCH est une ligase de l’ubiquitine impliquée dans différents processus cellulaires. Elle contient une région riche en prolines (PRR, proline rich region) qui lui permet de lier le domaine SH3 (Src homology 3) d’Endophiline et d’autres protéines à domaine SH3. Plusieurs de ces protéines sont impliquées dans l’endocytose clathrine-dépendante de récepteurs tel le récepteur du facteur de croissance épidermique (EGFR, epidermal growth factor receptor). Après activation, l’EGFR est internalisé dans des vésicules enrobées de Clathrine et un complexe protéique formé par CBL, CIN85 et Endophiline participe à cet évènement. ITCH lie l’ubiquitine à CBL et à Endophiline pour vraisemblablement modifier leurs fonctions, ce qui suggère un lien direct entre cette ligase et l’endocytose de l’EGFR. Afin de déterminer le rôle d’ITCH dans ce processus, plusieurs expériences furent réalisées. Premièrement, la modalité de liaison entre la ligase ITCH et les protéines à domaine SH3 a été étudiée en détails. Une série de mutations dans la région PRR d’ITCH nous a aidé à identifier trois résidus arginines (R252, R255, R258) nécessaires pour son interaction avec Endophiline et d’autres protéines à domaine SH3. Deuxièmement, des lignées cellulaires HeLa et Cos7 furent modifiées génétiquement par CRISPR pour empêcher l’expression d’ITCH. Ces lignées cellulaires knockout furent caractérisées et utilisées dans un essai d’endocytose de l’EGFR, puis examinées par spectrométrie de masse. L’internalisation d’EGFR fut suivie en microscopie confocale à l’aide d’un ligand EGF fluorescent -/- dans les deux types de cellules ITCH . En absence d’ITCH, nous observons une diminution significative du niveau d’EGF internalisé par rapport aux cellules parentales. La surexpression d’ITCH dans les cellules ITCH-/- rétablit l’internalisation normale de l’EGF, confirmant l’implication d’ITCH dans le processus, mais la surexpression des formes mutantes de ITCH incapable de lier Endophiline ou catalytiquement inactive ne rétablit pas l’internalisation de l’EGF. Ces résultats nous permettent de conclure que l’interaction ITCH-Endophiline et la fonction catalytique de ITCH sont nécessaires pour l’endocytose de l’EGFR. Ensemble, ces deux fonctions de ITCH régulent le trafic endocytique de l’EGFR. De plus, les cellules ITCH-/- montrent un délai de dégradation de l’EGFR phosphorylé ainsi qu’une prolongation du temps d’activation de la kinase MAPK (mitogen-activated protein kinase). Finalement, pour explorer l’influence de l’absence d’ITCH sur ses substrats et partenaires moléculaires nous avons effectué une comparaison protéomique des partenaires d’interaction et des protéines ubiquitylées à partir des lysats cellulaires ITCH-/- et WT. Les résultats ont montré que le manque d’expression de la ligase ITCH altère la présence peptidique des protéines liées à la signalisation de l’EGFR, à la voie protéolytique dépendante de l'ubiquitine et à l’adhésion cellulaire. Cette étude révèle pour une première fois que la protéine ITCH est requise pour l’endocytose dépendante de la Clathrine de l’EGFR.ITCH is a ubiquitin ligase involved in various cellular processes including endocytosis. It contains a proline rich region (PRR) which allows it to bind the SH3 domain of endophilin and other SH3 domain-containing proteins involved in Clathrin-mediated endocytosis (CME). CME is an important regulatory mechanism for growth factor receptor activity. The epidermal growth factor receptor (EGFR) is actively internalized in Clathrin-coated vesicles after activation. This endocytosis is facilitated by a protein complex formed by CBL, CIN85 and Endophilin. ITCH is known to ubiquitinate both CBL and endophilin, providing a potential functional link between the ligase and receptor internalization. In order to determine the role of ITCH in this process, several experiments were performed. First, the mapping of molecular binding sites between the ligase ITCH and SH3 domain proteins has been studied in detail. A series of mutations in the PRR region of ITCH helped us identify three arginine residues (R252, R255, R258) as necessary for its interaction with endophilin and all the tested SH3-domain containing proteins. Secondly, HeLa and Cos7 cell lines were genetically modified by CRISPR to prevent ITCH expression. These knockout cell lines were characterized for use in an EGFR endocytosis assay and for mass spectrometry analysis. EGFR internalization was monitored by confocal microscopy using fluorescent EGF ligand in both ITCH-/- cell types. In the absence of ITCH, a significant decrease in the level of internalized EGF compared to parental cells is visible. Overexpression of WT ITCH in the knockout cells restores normal internalization of EGF, confirming the involvement of ITCH in the process. Overexpression of Endophilin-binding defective or catalytically inactive ITCH does not restore the internalization of EGF in ITCH-/- cells. These results show that the ITCH- Endophilin interaction as well as the catalytic function of ITCH are necessary for the endocytosis of EGFR. In addition, ITCH-/- cells show a delay in the degradation of phosphorylated EGFR accompanied with an extended period of mitogen-activated protein kinase (MAPK) activation. In a last set of experiments, we explored the influence of the absence of ITCH on its substrates and molecular partners. We performed a proteomic comparison of ITCH-binding partners and potential substrates using the ITCH-/- and WT cell lysates. The results showed that the lack of ITCH expression alters the peptide count of proteins mainly related to EGFR signaling, theubiquitin-dependent proteolytic pathway and cell adhesion. This study shows for the first time that the protein ITCH is required for the clathrin-dependent endocytosis of EGFR

Identification of high-performing antibodies for Apolipoprotein E for use in Western Blot and immunoprecipitation [version 3; peer review: 1 approved, 2 approved with reservations]

Apolipoprotein E is a secreted protein involved in mediating lipid distribution and metabolism among cells of specific tissues. The dysregulation of Apolipoprotein E can disturb cholesterol homeostasis, resulting in several diseases, including cardiovascular disease and Alzheimer’s disease. The therapeutic potential of Apolipoprotein E against these diseases demonstrates the importance of providing high-quality antibodies for this protein to the scientific community. In this study, we characterized fourteen Apolipoprotein E commercial antibodies for Western Blot and immunoprecipitation, using a standardized experimental protocol based on comparing read-outs in knockout cell lines and isogenic parental controls. We identified many high-performing antibodies and encourage readers to use this report as a guide to select the most appropriate antibody for their specific needs

The identification of high-performing antibodies for Coiled-coil-helix-coiled-coil-helix domain containing protein 10 (CHCHD10) for use in Western Blot, immunoprecipitation and immunofluorescence [version 2; peer review: 2 approved, 1 approved with reservations]

CHCHD10 is a mitochondrial protein, implicated in the regulation of mitochondrial morphology and cristae structure, as well as the maintenance of mitochondrial DNA integrity. Recently discovered to be associated with amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) in its mutant form, the scientific community would benefit from the availability of validated anti-CHCHD10 antibodies. In this study, we characterized four CHCHD10 commercial antibodies for Western Blot, immunoprecipitation, and immunofluorescence using a standardized experimental protocol based on comparing read-outs in knockout cell lines and isogenic parental controls. As this study highlights high-performing antibodies for CHCHD10, we encourage readers to use it as a guide to select the most appropriate antibody for their specific needs

A guide to selecting high-performing antibodies for human Midkine for use in Western blot and immunoprecipitation [version 4; peer review: 2 approved]

Midkine is a secreted protein that acts as a growth factor or cytokine involved in cell survival and inflammatory processes. It accumulates in amyloid plaques, which are hallmarks of Alzheimer’s Disease (AD). The reproducibility of Midkine research would be enhanced if the community had access to well-characterized anti-Midkine antibodies. In this study, we characterized 8 commercial Midkine antibodies for Western blot and immunoprecipitation, using a standardized experimental protocol based on comparing read-outs in a knockout cell line and isogenic parental control. These studies are part of a larger, collaborative initiative seeking to address the antibody reproducibility issue by characterizing commercially available antibodies for human proteins and publishing the results openly as a resource for the scientific community. While use of antibodies and protocols vary between laboratories, we encourage readers to use this report as a guide to select the most appropriate antibodies for their specific needs

A guide to selecting high-performing antibodies for human Midkine for use in Western blot and immunoprecipitation [version 3; peer review: 2 approved]

Midkine is a secreted protein that acts as a growth factor or cytokine involved in cell survival and inflammatory processes. It accumulates in amyloid plaques, which are hallmarks of Alzheimer’s Disease (AD). The reproducibility of Midkine research would be enhanced if the community had access to well-characterized anti-Midkine antibodies. In this study, we characterized 8 commercial Midkine antibodies for Western blot and immunoprecipitation, using a standardized experimental protocol based on comparing read-outs in a knockout cell line and isogenic parental control. These studies are part of a larger, collaborative initiative seeking to address the antibody reproducibility issue by characterizing commercially available antibodies for human proteins and publishing the results openly as a resource for the scientific community. While use of antibodies and protocols vary between laboratories, we encourage readers to use this report as a guide to select the most appropriate antibodies for their specific needs

The identification of high-performing antibodies for RNA-binding protein FUS for use in Western Blot, immunoprecipitation, and immunofluorescence [version 2; peer review: 2 approved]

RNA-binding protein Fused-in Sarcoma (FUS) plays an essential role in various cellular processes. Mutations in the C-terminal domain region, where the nuclear localization signal (NLS) is located, causes the redistribution of FUS from the nucleus to the cytoplasm. In neurons, neurotoxic aggregates are formed as a result, contributing to neurogenerative diseases. Well-characterized anti-FUS antibodies would enable the reproducibility of FUS research, thereby benefiting the scientific community.  In this study, we characterized ten FUS commercial antibodies for Western Blot, immunoprecipitation, and immunofluorescence using a standardized experimental protocol based on comparing read-outs in knockout cell lines and isogenic parental controls. We identified many high-performing antibodies and encourage readers to use this report as a guide to select the most appropriate antibody for their specific needs

Acquired pure megakaryocytic aplasia successfully treated with cyclosporine

Acquired pure megakaryocytic aplasia is a rare hematological disorder characterized by thrombocytopenia with absent or markedly reduced megakaryocytes in the bone marrow. We report a case of a 25-year-old male diagnosed as acquired pure megakaryocytic aplasia. Treatment with prednisone and intravenous immunoglobulin failed, but he was successfully treated with cyclosporine, with complete remission after 90 days and normal platelet count maintained thereafter

A guide to selecting high-performing antibodies for Rab1A and Rab1B for use in Western Blot, immunoprecipitation and immunofluorescence [version 2; peer review: 2 approved]

Rab1 is a highly conserved small GTPase that exists in humans as two isoforms: Rab1A and Rab1B, sharing 92% sequence identity. These proteins regulate vesicle trafficking between the endoplasmic reticulum (ER) and Golgi and within the Golgi stacks. Rab1A and Rab1B may be oncogenes, as they are frequently dysregulated in various human cancers. Moreover, they contribute to the progression of Parkinson’s disease. The availability of high-quality antibodies specific for Rab1A or Rab1B is essential to understand the distinct functions of these Rab1 proteins in both health and diseaseand to enhance the reproducibility of research involving these proteins. In this study, we characterized seven antibodies targeting Rab1A and five antibodies targeting Rab1B for Western Blot, immunoprecipitation, and immunofluorescence using a standardized experimental protocol based on comparing read-outs in knockout cell lines and isogenic parental controls. These studies are part of a much larger, collaborative initiative seeking to address the antibody reproducibility issue by characterizing commercially available antibodies for human proteins and publishing the results openly as a valuable resource for the scientific community. While uses of antibodies and protocols vary between laboratories, we encourage readers to use this report as a guide to select the most appropriate antibodies for their specific needs

Antibody Characterization Report for Spondin-1

<p>This report presents a guide to selecting high-quality commercial antibodies against Spondin-1 by immunoblot (Western blot) and immunoprecipitation, using a knockout based validation approach. Work reported in this study was supported in part by the Emory-Sage-SGC TREAT-AD center established by the National Institutes of Aging under the award number U54AG065187. </p&gt