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A systematic p53 mutation library links differential functional impact to cancer mutation pattern and evolutionary conservation

ABSTRACT: The TP53 gene is frequently mutated in human cancer. Research has focused predominantly on six major “hotspot” codons, accounting for only ~30% of cancer-associated p53 mutations. To comprehensively characterize the consequences of the p53 mutation spectrum, we created a synthetically designed library and measured the functional impact of ~10,000 DNA-binding domain (DBD) p53 variants in human cells in culture and in vivo. Our results highlight the differential outcome of distinct p53 mutations in human patients and elucidate the selective pressure driving p53 conservation throughout evolution. Furthermore, while loss of anti-proliferative functionality largely correlates with the occurrence of cancer-associated p53 mutations, we observe that selective gain-of-function may further favor particular mutants in vivo. Finally, when combined with additional acquired p53 mutations, seemingly neutral TP53 SNPs may modulate phenotypic outcome and presumably tumor progression.

ORGANISM(S): Homo sapiens

PROVIDER: GSE115072 | GEO | 2018/06/21

REPOSITORIES: GEO

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Domain-specific p53 mutants activate EGFR by distinct mechanisms exposing tissue-independent therapeutic vulnerabilities

Project description:Mis-sense mutations affecting TP53 promote carcinogenesis both by inactivating its tumor suppressive functions, and by conferring aberrant pro-carcinogenic activities. We report here that mis-sense mutants in the p53 DNA-binding domain (DBD) and the transactivation domain (TAD) unexpectedly activate pro-carcinogenic epidermal growth factor receptor (EGFR) signaling via distinct, previously unrecognized molecular mechanisms. DBD- and TAD-specific TP53 mutants exhibited different cellular localization patterns and induced distinct gene expression profiles. Combining mass spectrometry with drug compound screens, we identified EGFR as a major signaling factor that is stabilized by TAD and DBD mutants in the cytosolic and nuclear compartments respectively, in a tissue-independent manner. Mechanistically, TAD mutants promote EGFR-mediated signaling by enhancing EGFR interaction with AKT via DDX31 in the cytosol. Conversely, DBD mutants maintain EGFR activity in the nucleus, by blocking EGFR interaction with the phosphatase SHP1, triggering upregulation of c-Myc and Cyclin D1 levels. Therapeutically, the sensitivity of DBD mutants to EGFR inhibition is enhanced by increasing the affinity of EGFR for SHP1, while that of TAD mutants can be induced by concurrent inhibition of AKT, mTOR or PI3K signaling. Thus, our findings suggest that gain-of-function, mis-sense mutations affecting two different p53 domains promote carcinogenesis by enhancing EGFR signaling via distinctive mechanisms. Our findings imply that cancer cells bearing domain-specific mutations may have distinct and exploitable therapeutic vulnerabilities.

2023-02-17 | PXD031725 | JPOST Repository

Distinct gain of function mechanism for the hot-spot mutant p53R175H

Project description:TP53 (p53) is the most commonly mutated gene in human cancers, and p53 missense mutations are present in more than 40% of all human tumors. Most p53 mutations are located within the DNA binding domain, including hotspot mutations R175H, R248W, and R273H. To elucidate the precise mechanism by which p53 missense mutants execute their gain-of-functions (GOFs) in vivo, we used a proteomic screen to identify any protein that recognizes the p53 DNA-binding domain (DBD) in a manner dependent on its mutation status. To do so, we first purified the potential binding proteins associated with the p53 DBD through multi-step affinity chromatography from a SFB-p53 H1299 stable cell line. The affinity-purified SFB-p53 interacting proteins were detected by liquid chromatography mass spectrometry/mass spectrometry (LC–MS/MS) and revealed a few cellular proteins that have been reported to interact with the DNA binding domain of p53, such as TP53BP1, USP28, and Sirt1. Interestingly, we also identified many new interacting proteins from the same complex.

2023-02-17 | PXD039886 | Pride

Transcriptional consequences of wild-type and missense mutant p53 in isogenic human acute myeloid leukemia (AML) cell lines

Project description:TP53, encoding for the tumor suppressor p53, is the most frequently mutated gene in human cancer. The selective pressures shaping its mutational spectrum, dominated by missense mutations, have remained enigmatic, and neomorphic gain-of-function (GOF) activities have been implicated. We generated isogenic human leukemia cell lines of the most common TP53 missense mutations using CRISPR/Cas9. Functional, DNA binding, and transcriptional analyses revealed loss-of-function (LOF) without GOF effects of missense mutations. Comprehensive mutational scanning of p53 single amino acid variants demonstrated that DNA-binding domain missense variants exert dominant-negative effects (DNE). In mice, DNE of p53 missense variants confer a selective advantage on hematopoietic cells upon DNA damage in vivo. Clinical outcomes in acute myeloid leukemia patients showed no evidence of GOF for TP53 missense mutations. These findings establish dominant-negativity as the primary unit of selection for TP53 missense mutations in myeloid malignancies.

2019-08-30 | GSE131592 | GEO

Genome-wide binding of wild-type and missense mutant p53 in isogenic human acute myeloid leukemia (AML) cell lines

2019-08-30 | GSE131484 | GEO

Mis-splicing Drives Loss of Function of p53E224D Point Mutation

Project description:Background: Tp53 is the most commonly mutated gene in cancer. Canonical Tp53 DNA damage response pathways are well characterized and classically thought to underlie the tumor suppressive effect of Tp53. Challenging this dogma, mouse models have revealed that p53 driven apoptosis and cell cycle arrest are dispensable for tumor suppression. Here, we investigated the inverse context of a p53 mutation predicted to drive expression of canonical targets, but is detected in human cancer. Methods: We established a novel mouse model with a single base pair mutation (GAG>GAC, p53E221D) in the DNA-Binding domain that has wild-type function in screening assays, but is paradoxically found in human cancer in Li Fraumeni syndrome. Using mouse p53 E221D and the the analogous human p53E224D mutant, we evaluated expression, transcriptional activation, and tumor suppression in vitro and in vivo. Results: Expression of human p53E224D from cDNA translated to a fully functional p53 protein. However, p53 E221D/E221D RNA transcribed from the endogenous locus is mis-spliced resulting in nonsense mediated decay. Moreover, fibroblasts derived from p53 E221D/E221D mice do not express a detectable protein product. Mice homozygous for p53 E221D exhibited increased tumor penetrance and decreased life expectancy compared to p53 WT animals. Conclusions: Mouse p53 E221D and human p53 E224D mutations lead to splice variation and a biologically relevant p53 loss of function in vitro and in vivo.

2024-07-28 | GSE239745 | GEO

A molecular signature of normal breast epithelial and stromal cells from Li-Fraumeni syndrome mutation carriers

Project description:Specific changes in gene expression during cancer initiation should enable discovery of biomarkers for risk assessment, early detection and targets for chemoprevention. It has been previously demonstrated that altered mRNA and proteome signatures of morphologically normal cells bearing a single inherited âhitâ in a tumor suppressor gene parallel many changes observed in the corresponding sporadic cancer. Here, we report on the global gene expression profile of morphologically normal, cultured primary breast epithelial and stromal cells from Li-Fraumeni syndrome (LFS) TP53 mutation carriers. Our analyses identified multiple changes in gene expression in both morphologically normal breast epithelial and stromal cells associated with TP53 haploinsufficiency, as well as interlocking pathways. Notably, a dysregulated p53 signaling pathway was readily detectable. Pharmacological intervention with the p53 rescue compounds CP-31398 and PRIMA-1 provided further evidence in support of the central role of p53 in affecting these changes in LFS cells and treatment for this cancer. Because loss of signaling mediated by TP53 is associated with the development and survival of many human tumors, identification of gene expression profiles in morphologically normal cells that carry âone-hitâ p53 mutations may reveal novel biomarkers, enabling the discovery of potential targets for chemoprevention of sporadic tumors as well. compare gene expression from different cell types

2010-10-21 | E-GEOD-23994 | biostudies-arrayexpress

Splicing Correction as a Therapeutic Approach for Acetylation-Defective p53 K120R mutation

Project description:The TP53 c.359A>G mutation severely impairs expression of the major TP53 transcript variant encoding p53 K120R by creating a new splicing donor site. Antisense morpholino oligomer (AMO) targeting the mutation site restored normal splicing and expression of the major variant. Despite the recovery of mutant TP53 mRNA levels, the functional restoration as the tumor suppressor of p53 K120R was unclear. Given that p53 exerts its tumor suppressor function through regulation of target genes that mediate growth arrest or apoptosis, the p53 K120R mutant exhibits impaired transcriptional regulation of CDKN1A, a key target gene in growth arrest, while maintaining normal induction of the pro-apoptotic BBC3 gene. Consequently, the p53 K120R mutant protein demonstrates a phenotype characterized by defective cell growth arrest but retained apoptotic induction capacity, suggesting that the p53 K120R mutant protein may retain some tumor suppressor functionality. In addition, Lysine 120 provides a critical acetylation site linked to p53 activation. Although other studies of the oncogenic effects of p53 K120R highlight the relevance of acetylation for tumor suppression, our findings indicate that targeting mutant TP53 mRNA is a prerequisite for restoration of p53 function. In particular, despite the presence of mutations, it showed sufficient corrective effect to restore p53 functions, including apoptosis induction. In conclusion, this study highlights the potential of AMO-mediated splice correction as a therapeutic approach for TP53 mutations.

2024-12-06 | GSE274604 | GEO

Mouse Homolog of a Human TP53 Germline Mutation Reveals a Lipolytic Activity of p53

Project description:The physiological effects of the many germline mutations of TP53, encoding the tumor suppressor protein p53, are poorly understood. Here, we report generating a p53 R178C knockin mouse modeling the human TP53 R181C mutation that is notable for its prevalence and prior molecular characterization. Consistent with its weak cancer penetrance in humans, homozygous p53178C/C mice showed a modest increase in tumorigenesis but, surprisingly, were lean with decreased body fat content. They displayed evidence of increased lipolysis and upregulation of fatty acid metabolism in their inguinal white adipose tissue (iWAT). Gene expression and chromatin immunoprecipitation sequencing (ChIP-Seq) analyses showed that the mutant p53 bound and transactivated Beta-3-Adrenergic Receptor (ADRB3), a gene that is known to promote lipolysis and is associated with obesity. The current study reveals that a germline mutation of p53 can affect fat metabolism which can impact cancer development.

2020-01-21 | GSE132715 | GEO

TP53 c.1000G>C; p.G334R is an Ashkenazi Jewish predominant mutation associated with a low penetrance Li-Fraumeni Syndrome

Project description:Multiple family members with cancer or individuals with multiple primary cancers are indicative of potential genetic etiology1. Germline mutations in TP53 cause a rare high penetrance cancer syndrome, Li Fraumeni Syndrome (LFS)2. We identified a TP53 tetramerization domain (TD) missense mutation c.1000G>C;p.G334R, in a family with LFS-associated cancers. Twenty-one additional probands were identified, and available tumors showed biallelic somatic inactivation of TP53. The majority of families were of Ashkenazi Jewish descent, and the TP53 c.1000G>C allele was found on a commonly inherited haplotype. While classical p53 target gene activation was maintained in p.G334R mutant cell lines treated with Nutlin-3a, a subset of p53 target genes, including PCLO, PLTP, PLXNB3 and LCN15, showed defective transactivation. Structural analysis demonstrated thermal instability of the mutant TD, and the G334R mutant protein showed increased preponderance of mutant conformation protein. TP53 c.1000G>C;p.G334R is a rare AJ-predominant mutation associated with low penetrance Li-Fraumeni Syndrome

2020-07-24 | GSE143741 | GEO

Effect of TP53 missense mutation R172H on the single cell gene expression of pre-neoplastic mouse mammary gland

Project description:Mutations in the TP53 gene are the most common genetic alterations in breast cancer. To investigate at a single cell level what is the gene expression network that is regulated by mutant p53 at a non-tumoral stage, we employed a pre-neoplastic mouse model harboring the germline hotspot missense mutation R172H. We thus performed scRNAseq of cells derived from the normal mammary glands of mice harboring wt or mutant p53.

2023-10-06 | GSE239706 | GEO

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