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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Affymetrix Clariom D transcriptome profiling of TP73 isoforms TAp73alpha and DNp73beta in melanoma cell SK-MEL-29

ABSTRACT: The abundance of isoforms of p73 in clinical samples is indicative for the patient's survival and the aggressiveness of the tumor, also in cell culture. On the basis of the well-etablished Sk-Mel-29 cell line model, we over-expressed two isoforms by transduction of a respective adenoviral vector.

ORGANISM(S): Homo sapiens

SUBMITTER: Steffen Möller

PROVIDER: E-MTAB-14704 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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TAp73α drives cancer metastasis via PPI-mediated derepression of the neuronal HDAC2/REST-GABBR2 axis.

Murr Nico N Richter Christin C Gupta Shailendra K SK Hammer Elke E Trakooljul Nares N Stoll Anja A Möller Steffen S Neumann Lukas E LE Pützer Brigitte M BM Spitschak Alf A

Cancer letters 20250610

Metastasis is the leading cause of death in patients with malignant melanoma, yet the molecular and transcriptional mechanisms remain elusive. This study reveals a crucial role of the p53 homolog, TAp73α, in promoting melanoma metastasis. Using multi-omics approaches combining transcriptomics, proteomics, cistromics and 3D modeling, we discovered a paradigm-shifting mechanism by which TAp73α binds directly to HDAC2, disassembles the HDAC2/REST repressor complex and aberrantly triggers activation ...[more]

PMID: 40505831

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Binding of full length p73 (TAp73alpha) and cancer-specific variant (DNp73beta) to genome of melanoma cell line SK-Mel-29

Project description:All p73 isoforms share an identical DNA-binding domain. These CUT&RUN datasets for TAp73α, DNp73β, and a GFP control illustrate the isoform-specific differences in genomic binding. As no antibodies are currently available that selectively recognize individual p73 variants, the data were generated following overexpression of the individual variant.

2026-03-30 | E-MTAB-15709 | biostudies-arrayexpress

p53 isoforms have a high aggregation propensity, interact with chaperones and lack binding to p53 interaction partners

Project description:The p53 transcription factor family consists of the three members p53, p63 and p73. Both p63 and p73 exist in different isoforms that are well characterized. Recently, isoforms have also been identified for p53 and it has been proposed that they are responsible for increased cancer metastasis. In contrast to the p63 and p73 isoforms, which do not contain truncations in folded domains, most of the p53 isoforms contain only parts of either the DNA binding domain or the oligomerization domain. To better understand the effect of p53 isoforms in cancer we provide here a comprehensive characterization. With the exception of the Δ40p53α isoform none of the other variants can bind to DNA with high affinity and none can upregulate transcription. Probing with antibodies, DARPins and other interaction partners confirmed that isoforms harboring deletions in the DNA binding domain cannot interact specifically with them, but instead are bound to chaperones and other factors known to interact with misfolded proteins. Expression of isoforms with deletions in the DNA binding domain results in upregulation of cellular chaperones. If the expression level surpasses a threshold, the chaperone system can no longer keep these isoforms soluble resulting in aggregation and co-aggregation with other factors.

2025-08-26 | PXD045655 | Pride

p53 isoforms have a high aggregation propensity, interact with chaperones and lack binding to p53 interaction partners

Project description:The p53 transcription factor family consists of the three members p53, p63 and p73. Both p63 and p73 exist in different isoforms that are well characterized. Isoforms have also been identified for p53 and it has been proposed that they are responsible for increased cancer metastasis. In contrast to the p63 and p73 isoforms, which do not contain truncations in folded domains, most of the p53 isoforms contain only parts of either the DNA binding domain or the oligomerization domain. To better understand the effect of p53 isoforms in cancer we provide here a comprehensive biochemical characterization. With the exception of the Δ40p53α isoform none of the other variants can bind to DNA with high affinity and none can upregulate transcription. Probing with antibodies, DARPins and other interaction partners confirmed that isoforms harboring deletions in the DNA binding domain cannot interact specifically with them, but instead are bound to chaperones and other factors known to interact with misfolded proteins. Expression of isoforms with deletions in the DNA binding domain results in upregulation of cellular chaperones. If the expression level surpasses a threshold, the chaperone system can no longer keep these isoforms soluble resulting in aggregation and co-aggregation with other factors.

2025-06-03 | PXD058245 | Pride

Piezo1 Activation Prevents Spheroid Formation by Malignant Melanoma SK-MEL-2 Cells.

Project description: Not available

| S-EPMC10648948 | biostudies-literature

Binding of full length p73 (TAp73alpha) and cancer-specific variant (DNp73beta) to genome of melanoma cell line SK-Mel-29

Project description:Binding of full length p73 (TAp73alpha) and cancer-specific variant (DNp73beta) to genome of melanoma cell line SK-Mel-29

| PRJEB100610 | ENA

CBFB cooperates with p53 to maintain TAp73 expression and suppress breast cancer

Project description:The goal of this study is to use H3K4me3 signal to mark the promoter regions of the p73 gene. The p73 gene expresses TAp73 and DNp73 isoforms, which use two different promoters. H3K4me3 is generally associated with the promoter of a gene and, therefore, can be used to mark the promoters for TAp73 and DNp73.

2021-04-16 | GSE169716 | GEO

Whole-transcriptomic Profile of SK-MEL-3 Melanoma Cells Treated with the Histone Deacetylase Inhibitor: Trichostatin A.

Project description: Not available

| S-EPMC6199573 | biostudies-literature

HA-tagged FOXM1 isoforms

Project description:HA-tagged FOXM1 isoforms

| PRJEB24594 | ENA

Transcription profiling of human H1299 cellls transformed with different p73/p53 constructs shows C-terminal diversity within the p53 family accounts for differences in DNA binding and transcriptional activity

Project description:The p53 family is known as a family of transcription factors with functions in tumor suppression and development. Whereas the central DNA binding domain is highly conserved among the three family members p53, p63 and p73, the C-terminal domains (CTDs) are diverse and subject to alternative splicing and post-translational modification. Here we demonstrate that the CTDs strongly influence DNA binding and transcriptional activity. While p53 and the p73 isoform p73ï§ have basic CTDs and form weak sequence-specific protein-DNA complexes, the major p73 isoforms ï¡, ï¢ and ï¤ have neutral CTDs and bind DNA strongly. A basic CTD has been previously shown to enable sliding along the DNA backbone and to facilitate the search for binding sites in the complex genome. Our experiments, however, reveal that a basic CTD also reduces protein-DNA complex stability, intranuclear mobility, promoter occupancy in vivo, transgene activation and induction of cell cycle arrest or apoptosis. A basic CTD in p53 and p73ï§ therefore provides both positive and negative regulatory functions presumably to enable rapid switching of protein activity in response to stress. In contrast, most p73 isoforms exhibit constitutive DNA binding activity consistent with a predominant role in developmental control. Experiment Overall Design: Infection of H1299 cell with different p73/p53 constructs by adenoviral system

2008-10-18 | E-GEOD-8660 | biostudies-arrayexpress

Proteomic response of SK-MEL-2 cells to polymyxin B

Project description:SK-MEL-2 cell line belongs to series of melanoma cell lines established from patient-derived tumor samples, which is usually applied in the melanin-related mechanism studies. TMT-labeling quantitative proteomics which is the state-of-art LC-MS/MS technique for protein quantitation, in this study, was applied to reveal the overall response of proteins involved in the polymyxin B-induced melanogenesis in SK-MEL-2 cells, in order to provide a possible clue at the cellular level for understanding mechanisms of polymyxin B-induced skin hyperpigmentation in clinics.

2022-03-22 | PXD030206 | Pride

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