The IARC TP53 Mutation Database compiles all TP53 gene variations identified in human populations and tumor samples. Data are compiled from the peer-reviewed literature and from generalist databases. The following datasets are available: # TP53 somatic mutations in sporadic cancers # TP53 germline mutation in familial cancers # Common TP53 polymorphisms identified in human populations # Functional and structural properties of P53 mutant proteins # TP53 gene status in human cell-lines # Mouse-models with engineered TP53 The database includes various annotations on the predicted or experimentally assessed functional impact of mutations, clinicopathologic characteristics of tumors and demographic and life-style information on patients. The database is meant to be a source of information on TP53 mutations for a broad range of scientists and clinicians who work in different research areas: # Basic research, to study the structural and functional aspects of the p53 protein # Molecular pathology of cancer, to understand the clinical significance of mutations identified in cancer patients # Molecular epidemiology of cancer, to analyze the links between specific exposures and mutation patterns and to make inferences about possible causes of cancer # Molecular genetics, to analyze genotype/phenotype relationships

IARC database characteristics of germline TP53 mutations observed in both IARC and in this study (families with more than 10 confirmed carriers in the IARC database are in bold).

PurposeLung cancer is the deadliest known cancer in the world, with the highest number of mutations in proto-oncogenes and tumor suppressor genes. Therefore, this study was conducted to determine the status of hotspot regions in DDR2 and KRAS genes for the first time, as well as in TP53 gene, in lung cancer patients within the Iranian population.Experimental designThe mutations in exon 2 of KRAS, exon 18 of DDR2, and exons 5–6 of TP53 genes were screened in lung cancer samples, including non-small cell lung cancer (NSCLC) and small cell lung cancer (SCLC) using PCR and sequencing techniques.ResultsAnalysis of the KRAS gene showed only a G12C variation in one large cell carcinoma (LCC) patient, whereas variants were not found in adenocarcinoma (ADC) and squamous cell carcinoma (SCC) cases. The Q808H variation in the DDR2 gene was detected in one SCC sample, while no variant was seen in the ADC and LCC subtypes. Variations in the TP53 gene were seen in all NSCLC subtypes, including six ADC (13.63%), seven SCC (15.9%) and two LCC (4.54%). Forty-eight variants were found in the TP53 gene. Of these, 15 variants were found in coding regions V147A, V157F, Q167Q, D186G, H193R, T211T, F212L and P222P, 33 variants in intronic regions rs1625895 (HGVS: c.672+62A>G), rs766856111 (HGVS: c.672+6G>A) and two new variants (c.560-12A>G and c.672+86T>C).ConclusionsIn conclusion, KRAS, DDR2, and TP53 variants were detected in 2%, 2.17% and 79.54% of all cases, respectively. The frequency of DDR2 mutation is nearly close to other studies, while KRAS and TP53 mutation frequencies are lower and higher than other populations, respectively. Three new putative pathogenic variants, for the first time, have been detected in Iranian patients with lung cancer, including Q808H in DDR2, F212L, and D186G in coding regions of TP53. In addition, we observed five novel benign variants, including Q167Q, P222P and T211T in coding sequence, and c.560-12A>G and c.672+86T>C, in intronic region of TP53. Mutations of KRAS and DDR2 were found in LCC and SCC subtypes, respectively, whereas mutations of TP53 were seen in SCC and ADC subtypes with higher frequencies and LCC subtype with lower frequency. Therefore, Iranian lung cancer patients can benefit from mutational analysis before starting the conventional treatment. A better understanding of the biology of these genes and their mutations will be critical for developing future targeted therapies.

High-grade ovarian serous carcinomas (HGSC) are characterized by TP53 mutations and non-random patterns of chromosomal anomalies, where the nature of the TP53 mutation may correlate with clinical outcome. However, the frequency of common somatic genomic events occurring in HGSCs from demographically defined populations has not been explored. Whole genome SNP array, and TP53 mutation, gene and protein expression analyses were assessed in 87 confirmed HGSC samples with clinical correlates from French Canadians, a population exhibiting strong founder effects, and results were compared with independent reports describing similar analyses from unselected populations. TP53 mutations were identified in 91% of HGSCs. Anomalies observed in more than 50% of TP53 mutation-positive HGSCs involved gains of 3q, 8q and 20q, and losses of 4q, 5q, 6q, 8p, 13q, 16q, 17p, 17q, 22q and Xp. Nearly 400 regions of non-overlapping amplification or deletion were identified, where 178 amplifications and 98 deletions involved known genes. The subgroup expressing mutant p53 protein exhibited significantly prolonged overall and disease-free survival as compared with the p53 protein null subgroup. Interestingly, a comparative analysis of genomic landscapes revealed a significant enrichment of gains involving 1q, 8q, and 12p intervals in the subgroup expressing mutant p53 protein as compared with the p53 protein null subgroup. Although the findings show that the frequency of TP53 mutations and the genomic landscapes observed in French Canadian samples were similar to those reported for samples from unselected populations, there were differences in the magnitude of global gains/losses of specific chromosomal arms and in the spectrum of amplifications and deletions involving focal regions in individual samples. The findings from our comparative genomic analyses also support the notion that there may be biological differences between HGSCs that could be related to the nature of the TP53 mutation.

Whole-genome sequence (WGS) analysis of tumors from 22 TP53 mutation carriers. We observed somatic mutations affecting Wnt, PI3K/AKT signaling, epigenetic modifiers and homologous recombination genes as well as mutational signatures associated with prior chemotherapy. We identified near-ubiquitous early loss of heterozygosity of TP53, with gain of the mutant allele. This occurred earlier in these tumors compared to tumors with somatic TP53 mutations, suggesting the timing of this mark may distinguish germline from somatic TP53 mutations. Phylogenetic trees of tumor evolution, reconstructed from bulk and multi-region WGS, revealed that LFS tumors exhibit comparatively limited heterogeneity. Overall, our study delineates early copy number gains of mutant TP53 as a characteristic mutational process in LFS tumorigenesis, likely arising very early in life or in utero.years prior to tumor diagnosis.

Mutations #1–4 have been previously reported as somatic mutations in other tumour types at the IARC TP53 database. Mutation #2 was not carried by the patient blood, meaning it was a somatic mutation. The others could not be evaluated in blood, as it was not available for analysis. PA =  pleomorphic adenoma; PLGA =  polymorphous low grade adenocarcinoma; CaexPA =  Carcinoma ex-pleomorphic adenoma; ACC =  adenoid cystic carcinoma; MEC =  mucoepidermoid carcinoma. WT =  wild-type.

Contains 1. significantly differentially expressed genes between eTN and eFP ("FP_TN"), 2. significantly differentially expressed genes between eTN and eTP ("TP_TN"), 3. the pathway overrepresentations for 2-3. ("Reactome_table_FP_TN", "Reactome_table_TP_TN", "MSIGDBHALLMARK_TP_TN", "MSIGDBHALLMARK_FP_TN")

AC: adenocarcinoma.SCC: squamous cell carcinoma.

Supplementary Tables S1-S6

SNV: Single Nucleotide Variation.†: Case that had two mutations together with TP53 loss.*Cases identified by deep-sequencing.¥Mutations found in Li Fraumeni patients (IARC TP53 Database, R17).Cases of diffuse anaplastic WT with TP53 mutations.

TP53 Mutations as Drivers of Chordoma Progression and Hallmarks of Aggressive Chordoma

Methods

For the original dataset FFPE-derived DNA from three tumor samples of DC, one PDC, and 32 CCs was analyzed for the coding sequence of 664 cancer-related genes using the SeqCap EZ Custom Enrichment Kit (Roche, Basel, Switzerland). A complete list of genes is presented in details previously. One additional sample of primary CC and recurrent DC, DNA from a blood sample, as well as primary and recurrent tumors (CC and DC, respectively) from one patient, was subjected to whole-exome sequencing (WES). Exome enrichment was performed using the Agilent SureSelectXT Reagent Kit and Agilent SureSelect Human All ExonV6 (Cat No. G9611B). A sequencing library was constructed using the Novogene NGS DNA Library Prep Set (Cat No.PT004). Libraries were sequenced using the paired end 150 bp mode on Illumina NovaSeq X Plus instrument (Illumina, San Diego, CA). The procedures were performed by an NGS service provider, Novogene.

For the replication dataset, publically available data from Bai et al. were downloaded.

Whole-Genome Sequencing, panel sequencing, and WES datasets were aligned to the GRCh38p11 human reference genome, utilizing BWA. For WGS and WES data, somatic single nucleotide variants and small insertions/deletions were called using Strelka and Manta. Copy number alterations were identified and analyzed using the FACETS R package and samples with low tumor purity were rejected (ten WGS samples).

For panel sequencing data, given the absence of matched normal controls, variant calling was performed using Scalpel and bcftools. Variant annotation was subsequently conducted with vcf2maf, incorporating the Variant Effect Predictor (VEP). Variants were filtered at a minimum of 14x coverage and a Variant Allele Frequency (VAF) of at least 0.2, with a ratio of VAF in tumor to normal control of at least 4. For samples without a normal control, common variants were rejected, and SNPs were manually checked for benign variation.

Data

• Table with somatic mutations from the ZJ case (ZJsomatic.zip)
• Table with copy-number events from the ZJ case (ZJsegments.csv)
• Table with somatic mutations from the mutation panel (PanelSomatic.zip)
• Table with somatic mutations from the Bai et al. (BaiSomatic.zip)

Germline mutations in BRCA1, BRCA2 and TP53 genes have been identified as one of the most important disease-causing issues in young breast cancer patients worldwide. The specific defective biological processes that trigger germline mutation-associated and -negative tumors remain unclear. To delineate an initial portrait of Brazilian early-onset breast cancer, we performed an investigation combining both germline and tumor analysis. Germline screening of the BRCA1, BRCA2, CHEK2 (c.1100delC) and TP53 genes was performed in 54 unrelated patients <35 y; their tumors were investigated with respect to transcriptional and genomic profiles as well as hormonal receptors and HER2 expression/amplification. Germline mutations were detected in 12 out of 54 patients (22%) [7 in BRCA1 (13%), 4 in BRCA2 (7%) and one in TP53 (2%) gene]. A cancer familial history was present in 31.4% of the unrelated patients, from them 43.7% were carriers for germline mutation (37.5% in BRCA1 and in 6.2% in the BRCA2 genes). Fifty percent of the unrelated patients with hormone receptor-negative tumors carried BRCA1 mutations, percentage increasing to 83% in cases with familial history of cancer. Over-representation of DNA damage-, cellular and cell cycle-related processes was detected in the up-regulated genes of BRCA1/2-associated tumors, whereas cell and embryo development-related processes were over-represented in the up-regulated genes of BRCA1/2-negative tumors, suggesting distinct mechanisms driving the tumorigenesis. An initial portrait of the early-onset breast cancer patients in Brazil was generated pointing out that hormone receptor-negative tumors and positive familial history are two major risk factors for detection of a BRCA1 germline mutation. Additionally, the data revealed molecular factors that potentially trigger the tumor development in young patients.

Background: Somatic CDKN2A and TP53 mutations are recurrent events in melanoma, occurring in 13.3% and 15.1% of cases respectively and are associated with poorer outcomes. It is unclear what effect somatic CDKN2A and TP53 mutations have on the clinical outcomes of patients treated with checkpoint inhibitors. Methods: All patients with cutaneous melanoma or melanoma of unknown primary who received checkpoint inhibitor therapy and underwent genomic profiling with the 50-gene Mayo Clinic solid tumor targeted cancer gene panel were included. Patients were stratified according to the presence or absence of mutations in BRAF, NRAS, CDKN2A, and TP53. Patients without mutations in any of these genes were termed quadruple wild type (Quad WT ). Clinical outcomes including median time to progression (TTP), median overall survival (OS), 6-month and 12-month OS, 6-month and 12-month without progression, ORR and disease control rate (DCR) were analyzed according to the mutational status of CDKN2A, TP...

High-grade serous ovarian cancer (HGSOC) is the most aggressive histological type of epithelial ovarian cancer, which is characterized by a high frequency of somatic TP53 mutations. We performed exome analyses of tumors and matched normal tissues of 34 Japanese patients with HGSOC and observed a substantial number of patients without TP53 mutation (24%, 8/34). Combined with the results of copy number variation analyses, we subdivided the 34 patients with HGSOC into subtypes designated ST1 and ST2. ST1 showed intact p53 pathway and was characterized by fewer somatic mutations and copy number alterations. In contrast, the p53 pathway was impaired in ST2, which is characterized by abundant somatic mutations and copy number alterations. Gene expression profiles combined with analyses using the Gene Ontology resource indicate the involvement of specific biological processes (mitosis and DNA helicase) that are relevant to genomic stability and cancer etiology. In particular we demonstrate the presence of a novel subtype of patients with HGSOC that is characterized by an intact p53 pathway, with limited genomic alterations and specific gene expression profiles.

BackgroundTP53 gene mutation is one of the most common mutations in human bladder cancer (BC) and has been implicated in the progression and prognosis of BC.MethodsRNA sequencing data and TP53 mutation data in different populations and platforms were downloaded from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) database to determine and validate a TP53-associated immune prognostic signature (TIPS) based on differentially expressed immune-related genes (DEIGs) between muscle-invasive bladder cancer (MIBC) patients with and without TP53 mutations.ResultsA total of 99 DEIGs were identified based on TP53 mutation status. TIPS including ORM1, PTHLH, and CTSE were developed and validated to identify high-risk prognostic group who had a poorer prognosis than low-risk prognostic group in TCGA and GEO database. The high-risk prognostic group were characterized by a higher abundance of regulatory T cells, myeloid-derived suppressor cells, and tumor-associated macrophages than the low-risk prognostic group. Moreover, they exhibited a lower abundance of CD56bright NK cells, higher expression of CTLA4, LAG3, PDCD1, TIGIT, and HAVCR2, as well as being more likely to respond to anti–PD-1, and neoadjuvant chemotherapy than the low-risk prognostic group. Based on TIPS and other clinical characteristics, a nomogram was constructed for clinical use.ConclusionTIPS derived from TP53 mutation status is a potential prognostic signature or therapeutic target but additional prospective studies are necessary to confirm this potential.

Contains 1. significantly differentially expressed genes between samples with high and low gleason grade ("Gleason_high_low"), 2. the pathway overrepresentations for these genes ("MSigDB_Gleason_HL", "Reactome_Gleason_HL"), 3. the overlapping genes between "Gleason_high_low" and "TP TN" from Suppl. Data 1 ("Gleason_HL_overlap TP_TN"), 4. the pathway overrepresentations for genes from (3) ("reactome_GLHL_TP_TN", "MSigDB_GLHL_TP_TN")

Myxoid/round-cell liposarcoma (MLS/RCLS) is characterized by either the fusion gene FUS-DDIT3 or the less commonly occurring EWSR1-DDIT3 and most cases carry few or no additional cytogenetic changes. There are conflicting reports concerning the status and role of TP53 in MLS/RCLS. Here we analysed four MLS/RCLS derived cell lines for TP53 mutations, expression and function. Three SV40 transformed cell lines expressed normal TP53 proteins. Irradiation caused normal posttranslational modifications of TP53 and induced P21 expression in two of these cell lines. Transfection experiments showed that the FUS-DDIT3 fusion protein had no effects on irradiation induced TP53 responses. Ion Torrent AmpliSeq screening, using the Cancer Hotspot panel, showed no dysfunctional or disease associated alleles/mutations. In conclusion, our results suggest that most MLS/RCLS cases carry functional TP53 genes and this is consistent with the low numbers of secondary mutations observed in this tumor entity.

Somatic variation is a major type of genetic variation contributing to human diseases, including cancer. The functional impact of many somatic variants including missense variants remains unclear, hindering the translation of such variation information into clinical applications. We previously developed a protein structural-based method, Ramachandran plot-molecular dynamics simulations (RP-MDS), to predict the function of germline missense variants based on their effects on protein structure stability, which produced successful predictions of the deleterious germline missense variants in multiple cancer-related genes. We reasoned that somatic missense variants and germline missense variants should have similar effects on the stability of the protein structure. In this study, we applied our protein structural-based approach, RP-MDS, to provide a comprehensive classification of the somatic missense variants in TP53. We analyzed 397 somatic missense variants and showed that 195 (49.1%) variants were deleterious due to their disruptions to p53 structure. The results were furthered validated by using a p53 - p21 promoter - green fluorescent protein (GFP) reporter gene assay. Our study demonstrated that deleterious somatic missense variants can be identified by referring to their effects on protein structural stability.

Despite of multitude investigations no reliable prognostic immunohistochemical biomarkers in GIST have been established so far with added value to predict the recurrence risk of high risk GIST besides mitotic count, primary location and size. In this study, we analyzed the prognostic relevance of eight cell cycle and apoptosis modulators and of TP53 mutations for prognosis in GIST with high risk of recurrence prior to adjuvant treatment with imatinib. In total, 400 patients with high risk for GIST recurrence were randomly assigned for adjuvant imatinib either for one or for three years following laparotomy. 320 primary tumor samples with available tumor tissue were immunohistochemically analyzed prior to treatment for the expression of cell cycle regulators and apoptosis modulators cyclin D1, p21, p16, CDK4, E2F1, MDM2, p53 and p-RB1. TP53 mutational analysis was possible in 245 cases. A high expression of CDK4 was observed in 32.8% of all cases and was associated with a favorable recurrence free survival (RFS), whereas high expression of MDM2 (12.2%) or p53 (35.3%) was associated with a shorter RFS. These results were independent from the primary KIT or PDGFRA mutation. In GISTs with higher mitotic counts was a significantly increased expression of cyclin D1, p53 and E2F1. The expression of p16 and E2F1 significantly correlated to a non-gastric localization. Furthermore, we observed a significant higher expression of p21 and E2F1 in KIT mutant GISTs compared to PDGFRA mutant and wt GISTs. The overall frequency of TP53 mutations was low (n = 8; 3.5%) and could not be predicted by the immunohistochemical expression of p53. In summary, mutation analysis in TP53 plays a minor role in the subgroup of high-risk GIST before adjuvant treatment with imatinib. Strong expression of MDM2 and p53 correlated with a shorter recurrence free survival, whereas a strong expression of CDK4 correlated to a better recurrence free survival.

Background We have previously reported that glycerol acts as a chemical chaperone to restore the expression of WAF1 in some human cancer cell lines bearing mutant p53. Since the expression of WAF1 is up-regulated by activated wildtype p53, glycerol appears to restore wtp53 function. The aim of the present study is to examine the restoration of heat-induced p53-dependent apoptosis by glycerol in human glioblastoma cells (A-172) transfected with a vector carrying a mutant p53 gene (A-172/mp53 cells) or neo control vector (A-172/neo cells).

   Results
   A-172/mp53 cells showed heat resistance compared with A-172/neo cells but A-172/mp53 cells in turn became heat sensitive when pre-treated with glycerol before heat treatment. The accumulation of Bax in the A-172/mp53 cells was induced by heating with glycerol pre-treatment, but not without it, whereas the accumulation in the A-172/neo cells was induced in both cases. Furthermore, mp53 extracted from heated cells came to bind to the sequence specific region after heating combined with glycerol pre-treatment. The phosphorylation of mp53 at serine15 was suppressed by an inhibitor of the phosphatidylinositol 3-kinase (PI3-K) family.


   Conclusion
   These results suggest that glycerol is effective in inducing conformational change of phosphorylated p53 and restoring mp53 to wtp53 function, leading to enhanced heat sensitivity through the induction of apoptosis. This novel tool for enhancement of heat sensitivity in cancer cells bearing mp53 may be applicable for p53-targeted hyperthermia, because mutation or inactivation of p53 is observed in approximately 50% of human cancers.