uchl5 subcellular localization and protein expression data  (Human Protein Atlas)

Journal: Molecular & Cellular Proteomics : MCP

Article Title: PI3Kα Translocation Mediates Nuclear PtdIns(3,4,5)P 3 Effector Signaling in Colorectal Cancer

doi: 10.1016/j.mcpro.2023.100529

Figure Lengend Snippet: PtdIns(3,4,5)P 3 subcellular localization in a panel of 58 CRC cell lines. A , representative images of immunofluorescence staining for PtdIns(3,4,5)P 3 using a GST-GRP1PH domain reporter showing CRC cell lines with predominant nuclear (DLD1, SW480, CACO2) or membrane (SKCO1, LIM1215, LOVO) PtdIns(3,4,5)P 3 localization. Scale bar represents 10 μm. B , quantification of the PtdIns(3,4,5)P 3 plasma membrane–nuclear distribution across 58 CRC cell lines. Red boxes indicate the presence of a PIK3CA or KRAS mutation. Blue boxes indicate loss of PTEN protein expression. Data show mean ± SEM for five images per cell line with n > 20 cells per image. Statistical significance was determined using the Student’s t test. C , representative images of immunofluorescence staining for PtdIns(3,4,5)P 3 GST-GRP1PH domain reporter in PIP3 mem SKCO1 and PIP3 nuc DLD1 cells for competition assays with soluble PtdIns(3,4,5)P 3 (8.8 μM). Scale bar represents 10 μm. CRC, colorectal cancer; GST, glutathione- S -transferase; PIP3 mem, PtdIns(3,4,5)P 3 plasma membrane–cytoplasmic localization; PIP3 nuc, PtdIns(3,4,5)P 3 nuclear localization; PtdIns(3,4,5)P 3 , phosphatidylinositol-3,4,5-trisphosphate.

Article Snippet: C , bar graph showing nuclear PtdIns(3,4,5)P 3 interactome enrichment for experimentally validated subcellular protein localization data from the Human Protein Atlas.

Techniques: Immunofluorescence, Staining, Membrane, Clinical Proteomics, Mutagenesis, Expressing

Journal: Molecular & Cellular Proteomics : MCP

Article Title: PI3Kα Translocation Mediates Nuclear PtdIns(3,4,5)P 3 Effector Signaling in Colorectal Cancer

doi: 10.1016/j.mcpro.2023.100529

Figure Lengend Snippet: Subcellular distribution of p110ɑ in PIP3 nuc versus PIP3 mem CRC cell lines. A , representative images of immunofluorescence staining for class I PI3K catalytic subunit p110α in seven PIP3 nuc (DLD1, SW480, HT55, CACO2, HCT15, HCT116, HCA7) and seven PIP3 mem (SKCO1, LIM1215, COLO320, SW948, LS513, HCC2998, LOVO) cell lines. Scale bar represents 10 μm. B and C , Western blot and representative images of immunofluorescence staining for siRNA-based knockdown of p110α (PIK3CA) and siRNA negative control (siNEG) in PIP3 nuc DLD1 and PIP3 mem SKCO1 cells. Scale bars represents 10 μm. CRC, colorectal cancer; PIP3 mem, PtdIns(3,4,5)P 3 plasma membrane–cytoplasmic localization; PIP3 nuc, PtdIns(3,4,5)P 3 nuclear localization.

Article Snippet: C , bar graph showing nuclear PtdIns(3,4,5)P 3 interactome enrichment for experimentally validated subcellular protein localization data from the Human Protein Atlas.

Techniques: Immunofluorescence, Staining, Western Blot, Knockdown, Negative Control, Clinical Proteomics, Membrane

Journal: Molecular & Cellular Proteomics : MCP

Article Title: PI3Kα Translocation Mediates Nuclear PtdIns(3,4,5)P 3 Effector Signaling in Colorectal Cancer

doi: 10.1016/j.mcpro.2023.100529

Figure Lengend Snippet: PI3Kα nuclear translocation is mediated by the importin β-dependent nuclear import pathway. Representative images and quantification of p110α subcellular localization in PIP3 nuc DLD1, SW480, and CACO2 cells treated with importazole (40 μM), a selective importin-β inhibitor, over a 6 h time course. Scale bar represents 10 μm. Data show mean ± SEM from five images per condition with n > 20 cells per image. Statistical significance was determined using Student’s t test. ∗ p < 0.05, ∗∗∗ p < 0.001. PIP3 nuc, PtdIns(3,4,5)P 3 nuclear localization.

Article Snippet: C , bar graph showing nuclear PtdIns(3,4,5)P 3 interactome enrichment for experimentally validated subcellular protein localization data from the Human Protein Atlas.

Techniques: Translocation Assay

Journal: Molecular & Cellular Proteomics : MCP

Article Title: PI3Kα Translocation Mediates Nuclear PtdIns(3,4,5)P 3 Effector Signaling in Colorectal Cancer

doi: 10.1016/j.mcpro.2023.100529

Figure Lengend Snippet: Nuclear PtdIns(3,4,5)P 3 interactome characterization for protein domains, nuclear compartmentalization and biological process enrichment. A , bar graph showing nuclear PtdIns(3,4,5)P 3 interactome enrichment for Interpro protein domains. B , PtdIns(3,4,5)P 3 binding affinities of the PH domain of BTK, PH-like domain of SSRP1, PHD-type domain of TRIM28, S/R-rich domain of SRSF1, PIP3-RRM, and RRM-only domains of PSPC1, and PIP3-RRM and RRM-only domains of NONO as determined by biosensor analysis. C , bar graph showing nuclear PtdIns(3,4,5)P 3 interactome enrichment for experimentally validated subcellular protein localization data from the Human Protein Atlas. D , representative images and quantification of colocalization of PtdIns(3,4,5)P 3 GST-GRP1PH domain reporter or p110α with lamin B1, nucleolin, and SC-35 in PIP3 nuc DLD1 cells using immunofluorescence staining. Scale bar represents 10 μm. Data show mean ± SEM from five images per condition with n > 20 cells per image. Colocalization was determined using Mander’s coefficient. E , STRING network showing nuclear PtdIns(3,4,5)P 3 interactome enrichment for putative protein–protein complexes based on high-quality and experimentally validated interactions (confidence score >0.9). F , Western blot of nuclear PtdIns(3,4,5)P 3 interactome candidates SRSF1, Aly, EIF4A3, and SC-35 pulled down with PtdIns(3,4,5)P 3 beads in nuclear fractions of PIP3 nuc DLD1 and SW480 CRC cells. BTK, Bruton tyrosine kinase; CRC, colorectal cancer; GST, glutathione-S-transferase; NONO, non-POU domain containing octamer binding; PH, pleckstrin homology; PHD, plant homeodomain; PtdIns(3,4,5)P3, phosphatidylinositol-3,4,5-trisphosphate; RRM, RNA recognition motif; S/R, serine/arginine; TRIM28, tripartite motif containing 28.

Article Snippet: C , bar graph showing nuclear PtdIns(3,4,5)P 3 interactome enrichment for experimentally validated subcellular protein localization data from the Human Protein Atlas.

Techniques: Binding Assay, Immunofluorescence, Staining, Western Blot

Journal: Patterns

Article Title: Cell-Type-Specific Proteogenomic Signal Diffusion for Integrating Multi-Omics Data Predicts Novel Schizophrenia Risk Genes

doi: 10.1016/j.patter.2020.100091

Figure Lengend Snippet: The Structure of MAPSD MAPSD steps include: creating the protein-protein interaction network followed by adjusting it for subcellular localizations; creating the Markov transition distribution matrix, assembling SCZ signatures from genome, epigenome, and transcriptome sources followed by creating the signal vector and adjust it for different tissues and cell types within them; creating tissue/cell-specific interaction networks, and signal diffusion across all of the dedicated networks to measure the disease signal intensities in unannotated proteins. Each dot on the human body scheme denoted the tissue being evaluated.

Article Snippet: This adjustment is conducted using the subcellular localization data from the Human Protein Atlas ( A).

Techniques: Plasmid Preparation, Diffusion-based Assay

Journal: Patterns

Article Title: Cell-Type-Specific Proteogenomic Signal Diffusion for Integrating Multi-Omics Data Predicts Novel Schizophrenia Risk Genes

doi: 10.1016/j.patter.2020.100091

Figure Lengend Snippet: The List of Cell Types and Tissues Used in This Study (A) The 131 combinations of cell types and tissues. Each color denotes a tissue and the forks for each color represent their corresponding cell types in this study. (B) The list of subcellular domains in this study followed by the number of proteins being expressed in each subcellular domain.

Article Snippet: This adjustment is conducted using the subcellular localization data from the Human Protein Atlas ( A).

Techniques:

Journal: Patterns

Article Title: Cell-Type-Specific Proteogenomic Signal Diffusion for Integrating Multi-Omics Data Predicts Novel Schizophrenia Risk Genes

doi: 10.1016/j.patter.2020.100091

Figure Lengend Snippet: Expression Patterns of MAPSD Brain-Specific Genes at Cell Resolution and Subcellular Domains (A) Frequency of MAPSD original SCZ risk genes at single-cell resolution to be highly expressed in four brain regions. (B) Frequency of MAPSD newly identified SCZ risk genes at single-cell resolution to be highly expressed in four brain regions. (C) Frequency of MAPSD original SCZ risk genes at protein level to be highly expressed in various subcellular domains in five cell types across four different brain regions. (D) Frequency of MAPSD newly identified SCZ risk genes at protein level to be highly expressed in various subcellular domains in five cell types across four different brain regions.

Article Snippet: This adjustment is conducted using the subcellular localization data from the Human Protein Atlas ( A).

Techniques: Expressing