Gene-expression profiling of SLK-knockout NeuNDL-transformed cell lines
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ABSTRACT:
PROVIDER: PRJNA527975 | ENA |
REPOSITORIES: ENA
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Project description:Subconfluent cycling cells from immortalized SLK-expressing and knockout NeuNDL-derived cells were profiled across multiple passages to identify differentially regulated genes in the absence of SLK using an Affymetrix Mouse Gene 2.0 ST array
2019-03-20 | GSE128514 | GEO
Project description:Human SLK cells were infected with wildtype (wt) and LANA knockout (KO) Kaposi's sarcoma-associated herpesvirus (KSHV), separately for 3 days. Cellular gene expression changes were identified upon the wild type and LANA KO KSHV virus infection compared to the uninfected SLK cells using the human gene expression microarray U133plus2.0. 2 independent biological replicates from uninfected SLK cells, wild type KSHV infected SLK cells at 72hrs post-infection (hpi) , and LANA KO infected SLK cells at 72 hrs post-infection were collected and RNA was prepared for microarray analysis.
2016-08-01 | E-GEOD-78282 | biostudies-arrayexpress
Project description:Human SLK cells were infected with wildtype (wt) and LANA knockout (KO) Kaposi's sarcoma-associated herpesvirus (KSHV), separately for 3 days. Cellular gene expression changes were identified upon the wild type and LANA KO KSHV virus infection compared to the uninfected SLK cells using the human gene expression microarray U133plus2.0.
2016-08-01 | GSE78282 | GEO
Project description:RNA-seq data from wildtype, STAT5A-knockout and STAT5B-knockout BCR/ABLp185+ transformed mouse bone marrow cell lines
| PRJNA496473 | ENA
Project description:[original title] Mock or latently infected KSHV cells (BCBL, SLK and HFF) vs common reference (mixture of RNA from both infected and uninfected cells). Expression profiling of latently infected cells using a custom tiling microarray. SLK and HFF cells were infected and selected for rKSHV.219. Mock infected SLK and HFF cells served as controls for each of these two stably infected cells, respectively. BJAB cells served as uninfected controls for the BCBL-1 cells. Biological replicates were harvested and analyzed.
2010-03-24 | GSE20443 | GEO
Project description:SLK controls the cytoskeleton, cell adhesion and migration. Analysis of a protein kinase phosphorylation site dataset showed that podocyte adhesion proteins – paxillin, vinculin and talin-1 may be potential SLK substrates. The project examines if these adhesion proteins are substrates of SLK.
2024-01-22 | PXD046962 | Pride
Project description:[original title] Mock or latently infected KSHV cells (BCBL, SLK and HFF) vs common reference (mixture of RNA from both infected and uninfected cells). Expression profiling of latently infected cells using a custom tiling microarray. SLK and HFF cells were infected and selected for rKSHV.219. Mock infected SLK and HFF cells served as controls for each of these two stably infected cells, respectively. BJAB cells served as uninfected controls for the BCBL-1 cells. Biological replicates were harvested and analyzed. Two condition experiment: mock infected vs. latently infected cells. Three cell types.
2010-06-05 | E-GEOD-20443 | biostudies-arrayexpress
Project description:Transcription factors (TFs) have long been aspirational therapeutic targets for the treatment of diseases, as their dysregulation is a common mechanism for altered cell states. Despite this, many TFs implicated in disease havedisordered structures and lack canonical binding pockets, rendering them non-trivial targets for small moleculebased therapies. Directly inhibiting TF function has proven difficult, but indirect inhibition by targeting the effector molecules that modulate TF function is a promising, yet underexplored, alternative approach. Here we report a strategy for capturing cancer-specific protein-protein interactions using context-dependent µMap photoproximity labeling. Using an intein-based method for catalyst conjugation in biochemically intact nuclei, we demonstrate that we can capture unique protein interactomes of c-Myc in healthy and cancerous prostate cell lines, and that these unique interactors can be mined to identify druggable vulnerabilities. We find that a cancerspecific c-Myc interactor, STE20 like kinase (SLK), selectively promotes c-Myc stabilization at the protein level, drives epithelial morphology, and is essential for tumorigenesis, validating it as a viable therapeutic target. Mechanistically, this stabilization is driven by SLK-mediated phosphorylation of c-Myc at serine 329, which antagonizes GSK3β-dependent phosphorylation of the c-Myc phosphodegron and effectively increases the stability of c-Myc. This cancer-selective interaction is enabled by a change in SLK splicing that promotes nuclear localization of the long isoform, rather than changes at the protein or total RNA level. Furthermore, analysis of cancer patient data shows a strong correlation between the SLK long splice isoform and expression of c-Myc targets across multiple tumor types. Importantly, the SLK-c-Myc interaction is validated in cancer cell lines from diverse tissues, suggesting this novel regulatory axis is broadly operative across human cancer.
2026-05-17 | GSE330346 | GEO
Project description:Transcription factors (TFs) have long been aspirational therapeutic targets for the treatment of diseases, as their dysregulation is a common mechanism for altered cell states. Despite this, many TFs implicated in disease have disordered structures and lack canonical binding pockets, rendering them non-trivial targets for small molecule-based therapies. Directly inhibiting TF function has proven difficult, but indirect inhibition by targeting the effector molecules that modulate TF function is a promising, yet underexplored, alternative approach. Here we report a strategy for capturing cancer-specific protein-protein interactions using context-dependent µMap photoproximity labeling. Using an intein-based method for catalyst conjugation in biochemically intact nuclei, we demonstrate that we can capture unique protein interactomes of c-Myc in healthy and cancerous prostate cell lines, and that these unique interactors can be mined to identify druggable vulnerabilities. We find that a cancer-specific c-Myc interactor, STE20 like kinase (SLK), selectively promotes c-Myc stabilization at the protein level, drives epithelial morphology, and is essential for tumorigenesis, validating it as a viable therapeutic target. Mechanistically, this stabilization is driven by SLK-mediated phosphorylation of c-Myc at serine 329, which antagonizes GSK3β-dependent phosphorylation of the c-Myc phosphodegron and effectively increases the stability of c-Myc. This cancer-selective interaction is enabled by a change in SLK splicing that promotes nuclear localization of the long isoform, rather than changes at the protein or total RNA level. Furthermore, analysis of cancer patient data shows a strong correlation between the SLK long splice isoform and expression of c-Myc targets across multiple tumor types. Importantly, the SLK-c-Myc interaction is validated in cancer cell lines from diverse tissues, suggesting this novel regulatory axis is broadly operative across human cancer.
2026-05-17 | GSE330345 | GEO
Project description:Transcription factors (TFs) have long been aspirational therapeutic targets for the treatment of diseases, as their dysregulation is a common mechanism for altered cell states. Despite this, many TFs implicated in disease have disordered structures and lack canonical binding pockets, rendering them non-trivial targets for small molecule-based therapies. Directly inhibiting TF function has proven difficult, but indirect inhibition by targeting the effector molecules that modulate TF function is a promising, yet underexplored, alternative approach. Here we report a strategy for capturing cancer-specific protein-protein interactions using context-dependent µMap photoproximity labeling. Using an intein-based method for catalyst conjugation in biochemically intact nuclei, we demonstrate that we can capture unique protein interactomes of c-Myc in healthy and cancerous prostate cell lines, and that these unique interactors can be mined to identify druggable vulnerabilities. We find that a cancer-specific c-Myc interactor, STE20 like kinase (SLK), selectively promotes c-Myc stabilization at the protein level, drives epithelial morphology, and is essential for tumorigenesis, validating it as a viable therapeutic target. Mechanistically, this stabilization is driven by SLK-mediated phosphorylation of c-Myc at serine 329, which antagonizes GSK3β-dependent phosphorylation of the c-Myc phosphodegron and effectively increases the stability of c-Myc. This cancer-selective interaction is enabled by a change in SLK splicing that promotes nuclear localization of the long isoform, rather than changes at the protein or total RNA level. Furthermore, analysis of cancer patient data shows a strong correlation between the SLK long splice isoform and expression of c-Myc targets across multiple tumor types. Importantly, the SLK-c-Myc interaction is validated in cancer cell lines from diverse tissues, suggesting this novel regulatory axis is broadly operative across human cancer.
2025-09-16 | GSE307813 | GEO