Prevalence Of TP53 Mutations Research Articles

Structure-based predictions broadly link transcription factor mutations to gene expression changes in cancers.

Thousands of unique mutations in transcription factors (TFs) arise in cancers, and the functional and biological roles of relatively few of these have been characterized. Here, we used structure-based methods developed specifically for DNA-binding proteins to systematically predict the consequences of mutations in several TFs that are frequently mutated in cancers. The explicit consideration of protein–DNA interactions was crucial to explain the roles and prevalence of mutations in TP53 and RUNX1 in cancers, and resulted in a higher specificity of detection for known p53-regulated genes among genetic associations between TP53 genotypes and genome-wide expression in The Cancer Genome Atlas, compared to existing methods of mutation assessment. Biophysical predictions also indicated that the relative prevalence of TP53 missense mutations in cancer is proportional to their thermodynamic impacts on protein stability and DNA binding, which is consistent with the selection for the loss of p53 transcriptional function in cancers. Structure and thermodynamics-based predictions of the impacts of missense mutations that focus on specific molecular functions may be increasingly useful for the precise and large-scale inference of aberrant molecular phenotypes in cancer and other complex diseases.

Circulating tumor DNA and circulating tumor cells in metastatic triple negative breast cancer patients.

Circulating tumor DNA (ctDNA) is a new circulating tumor biomarker which might be used as a prognostic biomarker in a way similar to circulating tumor cells (CTCs). Here, we used the high prevalence of TP53 mutations in triple negative breast cancer (TNBC) to compare ctDNA and CTC detection rates and prognostic value in metastatic TNBC patients. Forty patients were enrolled before starting a new line of treatment. TP53 mutations were characterized in archived tumor tissues and in plasma DNA using two next generation sequencing (NGS) platforms in parallel. Archived tumor tissue was sequenced successfully for 31/40 patients. TP53 mutations were found in 26/31 (84%) of tumor samples. The same mutation was detected in the matched plasma of 21/26 (81%) patients with an additional mutation found only in the plasma for one patient. Mutated allele fractions ranged from 2 to 70% (median 5%). The observed correlation between the two NGS approaches (R(2) = 0.903) suggested that ctDNA levels data were quantitative. Among the 27 patients with TP53 mutations, CTC count was ≥1 in 19 patients (70%) and ≥5 in 14 patients (52%). ctDNA levels had no prognostic impact on time to progression (TTP) or overall survival (OS), whereas CTC numbers were correlated with OS (p = 0.04) and marginally with TTP (p = 0.06). Performance status and elevated LDH also had significant prognostic impact. Here, absence of prognostic impact of baseline ctDNA level suggests that mechanisms of ctDNA release in metastatic TNBC may involve, beyond tumor burden, biological features that do not dramatically affect patient outcome.

Analysis of the molecular and clinicopathologic features of surgically resected lung adenocarcinoma in patients under 40 years old.

The youthful lung cancer may constitute an entity with distinct clinicopathologic characteristics and a controversial prognosis compared with the older counterpart. Whether the youthful lung cancer has the exclusively distinct molecular features has not been well investigated. Thirty-six resected lung adenocarcinomas from young patients under 40 years old were analyzed concurrently for mutations in EGFR, KRAS, HER2, BRAF, AKT1, ALK, RET, TP53 and LKB1 and enrolled as the younger group. Their molecular and clinicopathologic characteristics were compared with those of 87 adenocarcinoma cases from patients above 40 years old which were collected as the older group. The comparable overall survival (OS) (P=0.942), more early adenocarcinomas (P=0.033), more wedge resections (P<0.001) and fewer smokers (P=0.004) were seen in the younger group, when compared with the clinicopathologic characteristics in the older group. Nineteen EGFR mutations (52.8%), 3 KRAS mutations (8.3%), 2 EML4-ALK fusions (5.6%) and 1 KIF5b-RET fusion (2.8%) were identified in the younger group. The difference of oncogenic mutations between the two groups was statistically insignificant (P=0.396). Twenty-six TP53 mutations (72.2%) and 4 LKB1 mutations (11.1%) were found in the younger group. When compared with the old patients, young patients showed a higher prevalence of TP53 mutations (P<0.001) and a comparable prevalence of LKB1 mutations (P=0.951). The youthful lung cancer unequivocally presented the distinct clinicopathologic characteristics including more early adenocarcinomas and fewer smokers. It showed the similar oncogenic characteristics and higher prevalence of TP53 mutations compared with the older counterpart.

Targeted sequencing using a 47 gene multiple myeloma mutation panel (M(3) P) in -17p high risk disease.

We constructed a multiple myeloma (MM)-specific gene panel for targeted sequencing and investigated 72 untreated high-risk (del17p) MM patients. Mutations were identified in 78% of the patients. While the majority of studied genes were mutated at similar frequency to published literature, the prevalence of TP53 mutation was increased (28%) and no mutations were found in FAM46C. This study provides a comprehensive insight into the mutational landscape of del17p high-risk MM. Additionally, our work demonstrates the practical use of a customized sequencing panel, as an easy, cheap and fast approach to characterize the mutational profile of MM.

TP53 Mutations Detected By Next-Generation Deep-Sequencing In Patients With Myelodysplastic Syndrome and Isolated Deletion (5q): Results From a German Multicenter Trial

BackgroundBeside cytogenetic aberrations, additional gene mutations are powerful predictors of outcome in myeloid diseases. Moreover, myelodysplastic syndromes with isolated deletion (5q) (MDS del(5q)) have been regarded as one of the most favorable entities among MDS. However, a substantial proportion of MDS del(5q) patients experience transformation into AML soon after diagnosis (Germing et al. Leukemia. 2012;26:1286-1292). Mutations of TP53 gene have early been recognized as an unfavorable prognostic biomarker in MDS in general and recent data suggest a role of TP53 mutations in the transformation of MDS del(5q) into AML. Lenalidomid (Len) is now approved in the US as well as in Europe for the treatment of MDS del(5q) it is of particular interest whether Lenalidomide can alter the course of pretreatment TP53 mutated MDS del(5q). MethodsThe Le-Mon-5 trial investigated the safety and efficacy of Len in patients with MDS and isolated deletion (5q). All patients gave their written informed consent to the clinical trial and to additional molecular genetic analyses. Bone marrow aspirates were performed at screening prior treatment initiation and during follow-up every 6 months. Only freshly extracted, high-quality DNA from ficollized mononuclear cells was used for next-generation deep-sequencing analysis. For generation of PCR amplicon libraries TP53 oligonucleotide primer plate assays were used and technically validated within the IRON-II (Interlaboratory Robustness Of Next generation sequencing) research study network. Amplicon deep-sequencing of TP53 (exons 4-11) was performed on a Roche 454 GS Junior system. Mean coverage of sequenced exons was about 800-fold allowing an approximate detection sensitivity of 2% mutational burden. ResultsCentral cytological, histological and cytogenetic review was performed in all patients establishing the diagnosis of MDS with isolated deletion (5q). A total of 68 patients (male: n=9) were analyzed with a median age of 71 years (range 41-88 years). TP53 mutations prior to treatment initiation with Len were found in 7 patients (10%). Mean mutation frequency was 38%. Notably, we did not find mutation frequencies lower than 15%. Of 4 evaluable patients, three patients became transfusion independent within 4 months of Len treatment. Of 2 patients we had follow-up samples available. Both patients showed no difference with regard to the mutation frequency after a follow-up of 4 and 17 months on Len treatment (27% and 51%, respectively). Noteworthy, one the two patients achieved a complete cytogenetic remission despite maintaining his TP53 mutation frequency. ConclusionUsing freshly extracted DNA we achieved high-quality NGS results with a high mean coverage of the relevant coding region of TP53. However, prevalence of TP53 mutations in our patient cohort was lower as compared to previously published data and we did not find low-level allele burdens as published by other groups, which might be due to the different sample sources used. Transfusion independence as well as cytogenetic remissions can be achieved in patients with TP53 mutations who are treated with Lenalidomide. Disclosures:Platzbecker:Celgene: Honoraria. Giagounidis:Celgene: Consultancy, Honoraria. Götze:Celgene Corp.: Honoraria. Haase:Celgene: Honoraria, Membership on an entity's Board of Directors or advisory committees, Research Funding. Kohlmann:MLL Munich Leukemia Laboratory: Employment. Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Bug:Celgene: Honoraria, Research Funding. Hofmann:Celgene: Research Funding. Germing:Celgene: Honoraria, Research Funding. Nolte:Celgene: Honoraria, Research Funding.

Response To Azacitidine Is Independent Of TP53 Mutations In Higher-Risk Myelodysplastic Syndromes (MDS) and Secondary Acute Myeloid Leukemia (sAML)

IntroductionHigher-risk myelodysplastic syndromes (MDS) progress to secondary acute myeloid leukemia (sAML) within months. Treatment with azacitidine (AZA) has been shown to prolong survival and delay progression to sAML. TP53 mutations are found in MDS with abnormal chromosome 5 or complex karyotype and are associated with poor prognosis. In particular, TP53 mutations confer resistance to lenalidomide in low-risk MDS with del(5q). However, whether TP53 mutations also influence response to AZA is unclear. Therefore, we analyzed the prevalence of TP53 mutations in a cohort of 100 patients with higher-risk MDS or sAML treated with AZA and correlated this to outcome. Patients and Methods100 cases of higher risk MDS (IPSS INT-2 or High, n= 53), MDS/MPN (n= 8) or sAML (≥ 20% marrow blasts, n= 39) were included who had received at least one complete cycle of AZA (75 mg/m2 d1-7 q28) and for whom a bone marrow biopsy was available before the start of treatment. Presence of TP53 mutations was determined by immunohistochemistry [Iwasaki et al, Pathol Int 2008; Jädersten et al, JCO 2011; Kulasekararaj et al, Br J Haematol 2013]. Staining was defined as positive if ≥5% of CD34+ cells showed strong nuclear staining. In addition, 37 randomly selected cases were confirmed by sensitive next-generation amplicon deep-sequencing, demonstrating good correlation between both methods. Response to AZA was determined using IWG2006 criteria. Kaplan-Meier curves were estimated from the first day of AZA treatment with the log-rank test to determine significance. Patients who subsequently underwent allogeneic transplantation were censored at that date. ResultsThirty-five patients (35%) had TP53 mutations. Both TP53 positive and negative cohorts were balanced in age (median 71 years) and number of administered AZA cycles (median 5/4, TP53 positive/negative, respectively). Of the TP53 positive patients, 68% had higher-risk MDS, 6% had MDS/MPN and 26% had sAML. Significantly more patients diagnosed with sAML had unmutated TP53 (46%, p=0.046). With regard to cytogenetics, only 23% of patients with TP53 mutations showed a good risk karyotype (KT) according to IPSS cytogenetic risk classification whereas 74% were diagnosed with poor risk KT. A closer look at the TP53 positive patients with poor risk cytogenetics revealed involvement of chromosome 5 aberrations in 77% compared to 33% in wild-type TP53 patients (p < 0.001). Of all 100 patients a total of 18 fulfilled the criteria for monosomal KT and 14 of these harbored TP53 mutations (77%, p < 0.001). There was no difference in pretreatment absolute neutrophil count or hemoglobin value in patients with or without TP53 mutations. The pretreatment median platelet count in TP53 mutated patients was significantly higher than in patients with wild-type TP53 (90 G/l vs. 43 G/l, respectively, p=0.021). The overall response rate (ORR) for patients with and without TP53 mutations treated with AZA was 74% (26/35) and 68% (44/65), respectively (n.s.). Quality of response did not show any differences between cohorts. However, hematologic improvement was significantly more frequent in patients with MDS and TP53 mutations than in MDS with wild-type TP53 (46% vs. 14%, p=0.015). Patients with complex KT and TP53 mutations responded as well as patients with wild-type TP53 to treatment with AZA (ORR 65% versus 53%, respectively, n.s.). Regarding the subgroup of patients with any kind of chromosome 5 abnormality within the complex KT group, there was a better ORR to AZA but no statistical significance between those with TP53 mutations compared to those with wild-type TP53 (75% vs. 43%, respectively). A similar result with respect to ORR was seen in the subgroup of patients with monosomal KT and the presence or absence TP53 mutations (ORR: 64% vs. 25%, respectively, n.s.). The median OS of the total cohort was 288 days, with a median OS of 212 days for TP53 positive patients and 353 days for TP53 negative patients (p = 0.731). ConclusionTP53 mutations in higher-risk MDS and sAML are frequent and predominantly associated with complex karyotype involving chromosome 5 abnormalities. In our cohort of 100 patients treated with AZA, the presence of TP53 mutations did not negatively impact on response to epigenetic therapy. However, although this analysis was not created for survival assessment it confirms the very poor survival for higher-risk MDS and sAML patients with TP53 mutations, in spite of response to AZA. Disclosures:Haferlach:MLL Munich Leukemia Laboratory: Employment, Equity Ownership. Germing:Celgene: Honoraria, Research Funding. Platzbecker:Celgene Corp: Honoraria. Götze:Celgene Corp: Honoraria.

Hepatocellular carcinoma and liver cirrhosis TP53 mutation analysis reflects a moderate dietary exposure to aflatoxins in Espírito Santo State, Brazil

The close relationship between aflatoxins and 249ser TP53 gene mutation (AGG to AGT, Arg to Ser) in hepatocellular carcinoma (HCC) makes this mutation an indirect indicator of dietary contamination with this toxin. We have examined the prevalence of codon 249 TP53 mutation in 41 HCC and 74 liver cirrhosis (without HCC) cases diagnosed at the HUCAM University Hospital in Vitoria, Espírito Santo State, Brazil. DNA was extracted from paraffin sections and from plasma. The mutation was detected by DNA amplification, followed by restriction endonuclease digestion and confirmed by direct sequencing. DNA restriction showed 249ser mutation in 16 HCC and 13 liver cirrhosis, but sequencing confirmed mutations in only 6 HCC and 1 liver cirrhosis. In addition, sequencing revealed 4 patients with mutations at codon 250 (250ser and 250leu) in HCC cases. The prevalence of TP53 mutation was 10/41 (24.3%) in HCC and 1/74 (1.4%) in liver cirrhosis. No relationship between the presence of mutations and the etiology of HCC was observed. TP53 exon 7 mutations, which are related to aflatoxins exposure, were found at 14.6% (249ser), 7.3% (250leu) and 2.4% (250ser) in 41 cases of HCC and 1.4% in 74 liver cirrhosis (without HCC) cases, suggesting a moderate dietary exposure to aflatoxins in the Espírito Santo State, Brazil.

Prevalence of TP53 germ line mutations in young Pakistani breast cancer patients

Women from Pakistan and India are more often diagnosed with early-onset breast cancer than Caucasian women. Given that only 12% of Pakistani women diagnosed with breast cancer at or before 30 years of age have previously been shown to harbor germ line mutations in the breast cancer susceptibility genes BRCA1 and BRCA2, the genetic causes of the majority of early-onset cases are unexplained. Since germ line mutations in the tumor suppressor gene TP53 predispose women to early-onset breast cancer, we assessed the prevalence of TP53 mutations in 105 early-onset breast cancer patients from Pakistan, who had previously been found to be negative for BRCA1 and BRCA2 germ line mutations. The patient group included 67 women diagnosed with early-onset breast cancer at or before age 30 with no family history of breast or ovarian cancer (EO30NFH group) and 38 women diagnosed with breast cancer at or before age 40 with one or more first- or second-degree relatives with breast or ovarian cancer (EO40FH group). Mutation analysis of the complete TP53 coding region was performed using denaturing high-performance liquid chromatography analysis, followed by DNA sequencing of variant fragments. One deleterious mutation, c.499-500delCA in exon 5, was identified in the 105 breast cancer patients (1%). This mutation is novel in the germ line and has not been described in other populations. It was detected in a 28-year-old patient with no family history of breast or ovarian cancer. This mutation is rare as it was not detected in additional 157 recently recruited non-BRCA1 and non-BRCA2-associated early-onset breast cancer patients. Our findings show that TP53 mutations may account for a minimal portion of early-onset breast cancer in Pakistan.

P1-09-03: Prevalence of Germline TP53 Mutations in Young Women with HER2−Positive Breast Cancer.

Abstract Background: Li Fraumeni syndrome is a rare inherited cancer susceptibility condition associated with germline mutations in the TP53 gene, in which breast cancer (BC) is the most frequent tumor. The prevalence of TP53 mutations in population-based series of very young onset BC (&amp;lt;30 years at diagnosis) ranges from &amp;lt;1% to approximately 7%1-4. Recent data show that BC in patients carrying a germline TP53 mutation are commonly HER2 amplified (63-83%)5-7. In this study, we assessed the prevalence of germline TP53 mutations in women with HER2 positive BC diagnosed age ≤ 50 years. Material &amp; Methods: We identified 347 women with invasive HER2 positive BC diagnosed at age ≤ 50 years using the Clinical Operations and Research Information System (CORIS) at the Dana Farber Cancer Institute. Information on age at diagnosis, histology, hormone receptor and HER2 status as well as personal and family cancer history was confirmed from medical records. 129 patients were excluded for various reasons, including a cancer diagnosis prior to the BC and a documented BRCA1/2 mutation. A combination of Exon Grouping Analysis (EGAN) and Sanger sequencing for detection of TP53 mutations in exons 2–11 including surrounding intronic sequence was performed on 218 germline DNA samples. Multiplex Ligation-dependent Probe Amplification (MLPA) analysis for the detection of TP53 deletions or duplications is ongoing. Results: A germline TP53 mutation was identified in 4 women diagnosed at age ≤ 50 years (1.8%, 95%CI 0.5−4.6). At BC diagnosis, they were 23, 32, 44 and 50 years. Two BC were ER+/PR+, HER2+ and 2 were ER-/PR-, HER2+. Estimate of prevalence of germline TP53 mutations by age at BC diagnosis are: age ≤ 35, 2/41 (4.9%, 95%CI 0.6−16.6), and age ≤ 45 3/168 (1.8%, 95%CI 0.4−5.1). Among the women with germline TP53 mutations, 2 met the Chompret criteria8 and none the classic LFS criteria. Discussion: TP53 mutations were identified in a cohort of women with HER2+ BC at young age. As expected, the frequency is higher in younger women, but mutations were seen in all age groups that were evaluated. None of these women met classic LFS criteria by family history. Consideration of TP53 testing should be given to women diagnosed below age 35 who are negative for BRCA1/2 mutations regardless of family history. Analysis of other series will be helpful in reaching more stable estimates of the prevalence of mutation carriers among patients with HER2+ BC at young age. 1. Sidransky D et al. Cancer Res. 1992; 52:2984–2986. 2. Borresen AL et al. Cancer Res.1992; 52:3234–3236. 3. Lalloo F et al. Lancet 2003; 361:1101–02 4. Gonzalez KD et al. J Clin Oncol 2009;27(8):1250–6 5. Wilson JR et al. J Med Genet 2010;47(11):771–774. 6. Melhem-Bertrandt A et al: San Antonio Breast Cancer Symposium 2010: P3-12-01. 7. Masciari S et al: J Clin Oncol 29: 2011 (suppl; abstr 1519) 8. Tinat J et al. J Clin Oncol. 2009;27(26):e108–9 Citation Information: Cancer Res 2011;71(24 Suppl):Abstract nr P1-09-03.

Genome-Wide Analysis of Primary Plasma-Cell Leukemia Identifies Recurrent Imbalances Associated with Transcriptional Profile Alterations

Abstract 2878Primary plasma-cell leukemia (pPCL) is an aggressive, rare variant of plasma cell (PC) dyscrasia characterized by extra-medullary proliferation of PCs, high genomic instability and very poor prognosis. The present study was aimed at investigating global genomics in 17 pPCL recruited in an open-label, exploratory, single-arm, two-stage study from the GIMEMA myeloma network designed to evaluate the safety and antitumor activity of lenalidomide in combination with low dose dexamethasone as first-line therapy in pPCL. All the samples were characterized for the main chromosomal aberrations by Fluorescence In-Situ Hybridization (FISH). Specifically, 13q and 17p deletions have been identified in 13 (76.5%) and 6 (35.3%) cases, respectively; the presence of t(11;14) translocation was found in 7 patients (41.2%), t(4;14) in 2 (11.8%) and t(14;16) in 7 (41.2%). To better define the chromosomal alterations of this set of patients, we further investigated them by means of Human Mapping 250K Nsp SNP-array (Affymetrix). SNP-array data were fully concordant with FISH results as regards 13q and 17p deletions in the analyzed patients. Among the copy number alterations identified by mapping analysis the most frequently gained chromosomal region was represented by 1q (9 cases, 52.9%); 1p, 8p, 14q, and 16q arms were affected by loss of DNA material in more than 40% of cases. Moreover, four patients showed gain at 7q (23.5%), one case displayed a near tetraploid karyotype and another one had a hyperdiploid-like pattern. Most of the minimally altered regions identified on the different chromosomes encompassed genes that have been reported to be deregulated in PC dyscrasia, such as CDKN2C (mapped to 1p32.3), FAM46C (1p12), CKS1B (1q21.2), PARK2 (6q26), PPP2R2A (8p21.2), RB1 and MIR-15A/16-1 (13q14.2), TRAF3 (14q32.32), CYLD (16q12.1), WWOX (16q23.3-q24.1), and TP53 (17p13.1). The mutational analysis of the most frequently mutated exons (5–9) of TP53 gene revealed the presence of coding mutations in 4 patients (23.5%), three of which carried a monoallelic deletion including the gene locus. This supports the knowledge that the prevalence of TP53 mutations increases in more advanced disease and is strongly associated with hemizygosity. Genome-wide profiling data were then integrated with the transcriptional profiles generated on Gene 1.0 ST array (Affymetrix). Our analysis (Wilcoxon rank-sum test at a P <0.001) identified 134 transcripts whose expression levels strongly correlated with the occurrence of allelic imbalances, all of them in the previously described altered regions; specifically, 42 mapped to gained regions on 1q (40/134=29.9%) and 7q (1.5%), and 92 mapped to deleted regions on 1p (10.4%), 6q (6.7%), 8p (10.4%), 13q (9.7%), 14q (18.7%), 16q (6.0%) and 17p (6.7%). Enriched categories in functional annotation analysis are protein metabolism, transport, catabolic processes as the proteasome ubiquitination pathway (PSMC6, PSMA3, PSMB4 and PSMD4), and telomere organization and maintenance (PINX1, PARP1 and WRN). Overall, our data highlighted a wide gene-dosage effect, suggesting that genomic structural abnormalities in pPCL closely reflect in expression imbalances. Disclosures:No relevant conflicts of interest to declare.

TP53 mutations, human papilloma virus DNA and inflammation markers in esophageal squamous cell carcinoma from the Rift Valley, a high-incidence area in Kenya

BackgroundSquamous Cell Carcinoma of Esophagus is one of the most common malignancies in both men and women in eastern and south-eastern Africa. In Kenya, clinical observations suggest that this cancer is frequent in the Rift Valley area. However, so far, there has been no report on the molecular characteristics of esophageal squamous cell carcinoma (ESCC) in this area.ResultsWe have analyzed TP53 mutations, the presence of human papilloma virus (HPV) DNA and expression of inflammation markers Cyclooxygenase 2 (Cox-2) and Nitrotyrosine (NTyR) in 28 cases (13 males and 15 females) of archived ESCC tissues collected at the Moi Teaching and Referral Hospital in Eldoret, Kenya. Eleven mutations were detected in TP53 exons 5 to 8 (39%). All ESCC samples were negative for HPV 16, 18, 26, 31, 33, 35, 39, 45, 51, 52, 53, 56, 58, 59, 66, 68, 70, 73 and 82. Immunohistochemical analysis of Cox-2 and NTyR showed a low proportion of positive cases (17.4% and 39.1%, respectively). No association between the above markers and suspected risk factors (alcohol or tobacco use, hot tea drinking, use of charcoal for cooking) was found.ConclusionOur findings suggest that mechanisms of esophageal carcinogenesis in eastern Africa might be different from other parts of the world. Low prevalence of TP53 mutation compared with other intermediate or high incidence areas of the world highlights this hypothesis. Our data did not support a possible ole of HPV in this series of cases. Further studies are needed to assess and compare the molecular patterns of ESCC from Kenya with those of high-incidence areas such as China or Central Asia.

Abstract 5538: Sarcomas in TP53 germline mutation carriers

Abstract Sarcoma plays a central role in Li-Fraumeni syndrome (LFS) definition. Germline mutations in TP53 gene underlie this rare familial syndrome and are detected in over 80% of LFS patients. The International Agency for Research on Cancer (IARC) maintains a database of germline TP53 mutations that collects published data on LFS and related syndromes and provides baseline information about TP53 mutation prevalence and phenotype in these patients. We analyzed the characteristics of germline TP53 germline mutations in LFS and related syndrome patients with sarcoma using the IARC TP53 Database. The prevalence of individual sarcoma types and their age/gender distribution in TP53 mutation carriers were compared to sporadic sarcomas in Caucasians obtained by SEER registry analysis using the SEERStat program. Sarcoma represented 25% of all tumors diagnosed in TP53 carriers in this study. We confirmed young age of sarcoma onset among carriers, with 95.6% of cases diagnosed before the age of fifty years, as opposed to 38.3% of sporadic cancer. Carriers had increased risk for osteosarcoma in both children/adolescents and adults (OR=1.41, 95% CI=1.02-1.94, and OR=4.61, 95% CI=2.72-7.83), while increased risk for rhabdomyosarcoma was confined to carriers younger than 5 years (OR=11.6, 95%CI=6.1-21.9, p&amp;lt;0.00001). Analysis of the association of mutations with specific sarcoma types revealed that mutations in the oligomerization domain (codon 344 and 337) increased the risk of leiomyosarcoma (OR=10.1, 95% CI=3.4-29.9). Analysis of codons most frequently mutated in sarcoma showed that four codons (220, 275, 282, 344) were associated with 3-fold increased risk of sarcoma, compared to other cancers in TP53 carriers. In conclusion, this study provided further evidence for genotype-phenotype correlations in germline TP53 mutations carriers. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 102nd Annual Meeting of the American Association for Cancer Research; 2011 Apr 2-6; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2011;71(8 Suppl):Abstract nr 5538. doi:10.1158/1538-7445.AM2011-5538

TP53 genetic alterations in Arab breast cancer patients: Novel mutations, pattern and distribution.

Breast cancer remains a worldwide public health concern. The incidence and mortality of breast cancer varies significantly in ethnically and geographically distinct populations. In the Kingdom of Saudi Arabia (KSA) breast cancer has shown an increase in incidence and is characterized by early onset and aggressiveness. The tumor suppressor TP53 gene is a crucial genetic factor that plays a significant role in breast carcinogenesis. Furthermore, studies have shown a correlation between certain p53 mutations and response to therapy in breast cancer. In the present study, TP53 mutations were identified by direct sequencing of the gene (exons 4-9) from 119 breast cancer tissues. The prevalence of TP53 mutations in Arab breast cancer patients living in the KSA is among the highest in the world (40%). Notably, 73% of the patients whose tumors harbored p53 mutations were less than 50 years of age. Furthermore, for the first time, we identified 7 novel mutations and 16 mutations in breast cancer tissues. Notably, all the novel point mutations were found in exon 4, wherein 29% of the mutations were localized. Furthermore, an excess of G:C→A:T transitions (49%) at non-CpG sites was noted, suggesting exposure to particular environmental carcinogens such as N-nitroso compounds. The results indicate that the TP53 gene plays a significant role in breast carcinogenesis and the early onset of the disease among Arab female individuals.

Associations between polymorphisms in DNA repair genes and TP53 mutations in non-small cell lung cancer

This study was conducted to identify genetic factors predisposing to TP53 mutations in patients with non-small cell lung cancer (NSCLC). A comprehensive panel of potentially functional single nucleotide polymorphisms (SNPs) in DNA repair genes was evaluated in relation to TP53 mutations. Thirty-seven SNPs in 28 DNA repair genes were genotyped by a sequenome mass spectrometry-based genotyping assay in 173 NSCLCs and the associations with TP53 mutations in the entire coding exons (exons 2–11), including splicing sites of the gene, were analyzed. Four SNPs (XPA rs1800975, OGG1 rs1052133, ADPRT rs1136410, and NBS1 rs1805794) were significantly associated with the prevalence of TP53 mutations in multivariate analysis for each SNP. When the 4 SNPs were combined, the prevalence of TP53 mutations was increased as the number of bad genotypes increased (Ptrend=0.001). Patients with 3 and 4 bad genotypes had a significantly higher frequency of TP53 mutations than those with 0–1 bad genotypes (adjusted odds ratio=5.18, 95% confidence interval=1.51–17.81, P=0.01 and adjusted odds ratio=18.26, 95% confidence interval=2.87–116.09, P=0.002, respectively). These findings suggest that the 4 SNPs may modulate the occurrence of TP53 mutations and contribute to lung carcinogenesis. However, larger studies are required to confirm our findings in other ethnic populations.

TP53 Mutations are infrequent in newly diagnosed chronic lymphocytic leukemia

TP53 mutations in the absence of 17p-deletion correlate with rapid disease progression and poor survival in chronic lymphocytic leukemia (CLL). Herein, we determined the TP53 mutation frequency in 268 newly diagnosed CLL patients from a population-based material. Overall, we detected TP53 mutations in 3.7% of patients ( n = 10), where 7/10 cases showed a concomitant 17p-deletion, confirming the high prevalence of TP53 mutation in 17p-deleted patients. Only 3 (1.1%) of the newly diagnosed patients in our cohort thereby carried TP53 mutations without 17p-deletion, a frequency that is much lower than previous reports on referral cohorts (3–6%). Our findings imply that TP53 mutations are rare at CLL onset and instead may arise during disease progression.

Abstract 1120: Low prevalence of TP53 mutations in pediatric rhabdomyosarcoma

Abstract The tumor suppressor gene TP53 is the most commonly mutated gene in human cancer. Mutations in TP53 in rhabdomyosarcoma (RMS) have been associated with aggressive tumors and poor prognosis, however, reported prevalence of mutations in these tumors varied with smaller series reporting larger prevalence. Apart from gene mutations, p53 function can also be attenuated by overexpression of MDM2. Most recent report suggested extremely low prevalence of TP53 mutations and MDM2 amplifications (Taylor et al., 2000). We had 40 embryonal and 40 alveolar RMS tumor samples available for TP53 mutations/MDM2 amplification analyses, the largest series analyzed thus far. Half of the available samples were histopathology slides and the other half were frozen tumor tissue. The average age of slides was 13 years, therefore only 24 out of 40 slide DNA samples were of sufficient quality/quantity to complete direct sequencing of TP53 exons 4-9, limiting our results to 64 samples. MDM2 amplification was analyzed by differential PCR using dopamine gene as control. TP53 sequencing detected only one single mutation, p. D259Y, and six polymorphisms (Table 1).Table 1.Mutations and polymorphisms in TP53 gene in 64 pediatric embryonal and alveolar RMS. DiagnosisAgeGenderRacePrimary siteStageGene Variation*Protein ChangeMutationsERMS1MWhiteRight thighN/Ag.13412G&amp;gt;Tp. D259YPolymorphismsERMS0MBlackRight ankleN/Ag.14077T&amp;gt;CN/A ERMS4FBlackBladder2g.12708A&amp;gt;Gp. R213R ARMS4MAsianButtockN/Ag.12708A&amp;gt;Gp. R213R ARMS6MWhiteForearmN/Ag.12708A&amp;gt;Gp. R213R ERMS6FWhiteUterusN/Ag.12708A&amp;gt;Gp. R213R ARMS9FWhiteParotid mass1g.11370C&amp;gt;Tp. P47S* nucleotide number based on GenBank sequence NC_000017.9 No distinct pattern between TP53 mutation/polymorphisms was associated with any RMS subtype. Likewise, no MDM2 amplifications were observed. In conclusion, we confirm the extremely low prevalence of TP53 mutations/MDM2 amplifications in pediatric RMS (1.25% and 0% respectively). The possible inactivation of p53 function by other mechanisms thus remains to be elucidated. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 1120.

Driver mutations in TP53 are ubiquitous in high grade serous carcinoma of the ovary

Numerous studies have tested the association between TP53 mutations in ovarian cancer and prognosis but these have been consistently confounded by limitations in study design, methodology, and/or heterogeneity in the sample cohort. High-grade serous (HGS) carcinoma is the most clinically important histological subtype of ovarian cancer. As these tumours may arise from the ovary, Fallopian tube or peritoneum, they are collectively referred to as high-grade pelvic serous carcinoma (HGPSC). To identify the true prevalence of TP53 mutations in HGPSC, we sequenced exons 2–11 and intron–exon boundaries in tumour DNA from 145 patients. HGPSC cases were defined as having histological grade 2 or 3 and FIGO stage III or IV. Surprisingly, pathogenic TP53 mutations were identified in 96.7% (n = 119/123) of HGPSC cases. Molecular and pathological review of mutation-negative cases showed evidence of p53 dysfunction associated with copy number gain of MDM2 or MDM4, or indicated the exclusion of samples as being low-grade serous tumours or carcinoma of uncertain primary site. Overall, p53 dysfunction rate approached 100% of confirmed HGPSCs. No association between TP53 mutation and progression-free or overall survival was found. From this first comprehensive mapping of TP53 mutation rate in a homogeneous group of HGPSC patients, we conclude that mutant TP53 is a driver mutation in the pathogenesis of HGPSC cancers. Because TP53 mutation is almost invariably present in HGPSC, it is not of substantial prognostic or predictive significance. Copyright © 2010 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.

TP53, EGFR, and KRAS mutations in relation to VHL inactivation and lifestyle risk factors in renal-cell carcinoma from central and eastern Europe

Renal-cell carcinomas (RCC) are frequent in central and eastern Europe and the reasons remain unclear. Molecular mechanisms, except for VHL, have not been much investigated. We analysed 361 RCCs (334 clear-cell carcinomas) from a multi-centre case-control study for mutations in TP53 (exons 5–9 in the whole series and exons 4 and 10 in a pilot subset of 60 tumours) and a pilot 50 tumours for mutations in EGFR (exons 18–21) or KRAS (codon 12) in relation to VHL status. TP53 mutations were detected in 4% of clear-cell cases, independently of VHL mutations. In non-clear-cell carcinomas, they were detected in 11% of VHL-wild-type tumours and in 0% of tumours with VHL functional mutations. No mutations were found in EGFR or KRAS. We conclude that mutations in TP53, KRAS, or EGFR are not major contributors to the RCC development even in the absence of VHL inactivation. The prevalence of TP53 mutations in relation to VHL status may differ between clear-cell and other renal carcinomas.

TP53 and EGFR mutations in combination with lifestyle risk factors in tumours of the upper aerodigestive tract from South America

Cancers of the upper aerodigestive tract [(UADT): oral cavity, pharynx, larynx and oesophagus] have high incidence rates in some parts of South America. Alterations in the TP53 gene are common in these cancers. In our study, we have estimated the prevalence and patterns of TP53 mutations (exons 4-10) in 236 UADT tumours from South America in relation to lifestyle risk factors, such as tobacco smoking and alcohol drinking. Moreover, we have conducted a pilot study of EGFR mutations (exons 18-21) in 45 tumours from the same population. TP53 mutation prevalence was high: 59% of tumours were found to carry mutant TP53. We found an association between TP53 mutations and tobacco smoking and alcohol drinking. The mutation rate increased from 38% in never-smokers to 66% in current smokers (P-value for trend = 0.09). G:C>T:A transversions were found only in smokers (15%). Alcohol drinkers carried more G:C>A:T transitions (P = 0.08). Non-exposed individuals were more probable to carry G:C>A:T transitions at CpG sites (P = 0.01 for never-smokers and P < 0.001 for never-drinkers). EGFR mutations were found in 4% of cases. Inactivation of TP53 by mutations is a crucial molecular event in the UADT carcinogenesis and it is closely related to exposure to lifestyle risk factors. EGFR mutations do not appear to be a common event in UADT carcinogenesis in this population.

Relationship between TP53 tumour suppressor gene mutations and smoking-related bulky DNA adducts in a lung cancer study population from Hungary

Lung cancer rate in Hungary is one of the highest in the world among men and also very high among women, for reasons not clearly understood yet. The aim of the study was to explore characteristics of DNA damage and TP53 gene mutations in lung cancer from Hungary. Tissue samples from 104 lung resections for lung cancer patients, both men and women, operated on for non-small cell lung cancer, specifically, primary squamous cell carcinoma or adenocarcinoma were studied. Of the cases, 37% smoked up to the surgery, 24% stopped smoking within 1 year before the surgery, 26% stopped smoking more than a year before the surgery and 13% never smoked. TP53 mutations were detected by denaturant gradient gel electrophoresis, automated capillary electrophoresis single-strand conformation polymorphism and sequencing. Bulky DNA adduct levels were determined by (32)P-post-labelling in non-tumorous lung tissue. In total, 45% (47/104) of the cases carried TP53 mutation. The prevalence of TP53 mutations was statistically significantly associated with duration of smoking, tumour histology and gender. Smokers had approximately twice as high bulky adduct level as the combined group of former- and never-smokers (10.9 +/- 6.5 versus 5.5 +/- 3.4 adducts/10(8) nucleotides). The common base change G --> T transversion (8/43; 19%) was detected exclusively in smokers. For the first time, we demonstrate that most carriers of G --> T transversions had also a high level of bulky DNA adducts in their non-tumourous lung tissue. Our study provides evidence for a high burden of molecular alterations occurring concurrently in the lung of lung cancer patients.