Prognostic Value Of TP53 Mutations Research Articles

Integrative analysis of TP53 mutations in lung adenocarcinoma for immunotherapies and prognosis

BackgroundThe TP53 tumor suppressor gene is one of the most mutated genes in lung adenocarcinoma (LUAD) and plays a vital role in regulating the occurrence and progression of cancer. We aimed to elucidate the association between TP53 mutations, response to immunotherapies and the prognosis of LUAD.MethodsGenomic, transcriptomic, and clinical data of LUAD were downloaded from The Cancer Genome Atlas (TCGA) dataset. Gene ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, gene set enrichment analysis (GSEA). Gene set variation analysis (GSVA) were performed to determine the differences in biological pathways. A merged protein–protein interaction (PPI) network was constructed and analyzed. MSIpred was used to analyze the correlation between the expression of the TP53 gene, tumor mutation burden (TMB) and tumor microsatellite instability (MSI). CIBERSORT was used to calculate the abundance of immune cells. Univariate and multivariate Cox regression analyses were used to determine the prognostic value of TP53 mutations in LUAD.ResultsTP53 was the most frequently mutated in LUAD, with a mutational frequency of 48%. GO and KEGG enrichment analysis, GSEA, and GSVA results showed a significant upregulation of several signaling pathways, including PI3K-AKT mTOR (P < 0.05), Notch (P < 0.05), E2F target (NES = 1.8, P < 0.05), and G2M checkpoint (NES = 1.7, P < 0.05). Moreover, we found a significant correlation between T cells, plasma cells, and TP53 mutations (R2 < 0.01, P = 0.040). Univariate and multivariate Cox regression analyses revealed that the survival prognosis of LUAD patients was related to TP53 mutations (Hazard Ratio (HR) = 0.72 [95% CI, 0.53 to 0.98], P < 0.05), cancer status (P < 0.05), and treatment outcomes (P < 0.05). Lastly, the Cox regression models showed that TP53 exhibited good power in predicting three- and five-year survival rates.ConclusionsTP53 may be an independent predictor of response to immunotherapy in LUAD, and patients with TP53 mutations have higher immunogenicity and immune cell infiltration.

Transplant Outcomes for TP53 AML and MDS in a Contemporary Era

Background:TP53 gene mutations are detected in approximately 10%-20% of patients with de novo myelodysplastic syndromes (MDS) or acute myeloid leukemia (AML) and 30%-40% of patients with therapy-related disease. TP53 mutated MDS/AML are associated with a dismal prognosis when treated with intensive chemotherapy alone. Even after allogeneic stem cell transplant (SCT), TP53 mutated MDS and AML patients are shown to have low survival rates. In this single center retrospective analysis, we aimed to investigate the prognostic value of TP53 mutations in patients with MDS/AML that undergo SCT and to identify other variables such as conditioning regimen, use of post-transplant maintenance, donor selection or hematopoietic cell transplantation-specific comorbidity index (HCT-CI) had any impact on the post-transplant outcomes. Methods: Patients with a diagnosis of MDS or AML who received first SCT between January 2013 through April 2022 with available pre-transplant genetic profile obtained from next generation sequencing of genes, and confirmed to have TP53 mutation, were included in the retrospective analysis. Disease risk factors were categorized by the revised International Prognostic Scoring System (R-IPSS) for MDS and European Leukemia Net (ELN)for MDS and AML respectively. When using ELN classification, cytogenetic and molecular data was used as instructed other than TP53 to able to identify different risk groups for SCT outcomes. Primary outcome of interest was risk of relapse-free survival (RFS). MDS and AML patients were analyzed separately. Results: Within the study period, 181 patients (60 MDS and 121 AML) were eligible to be included in this analysis. As shown in the table 1, the study cohort with TP53 mutation was a high risk one; disease risk groups were very-high and high by IPSS-R in 78.4% of MDS, and adverse risk by ELN in 78.5%% of AML patients, respectively. Median age was 66 and 59 in MDS and AML patients and HCT-CI was >2 at SCT in 75% of MDS and 64.5% of AML patients respectively. In MDS patients, median RFS was 8.4 months with 1-year estimate of 44.7% (Figure 1a). By univariate analyses, none of the disease and transplant related characteristics were found to have a prognostic impact on RFS. In AML patients, median RFS was 5.7 months with 1-year estimate of 27.4%. By univariate analyses, as shown in Table 1, adverse risk category by ELN, complete remission without count recovery (CRi/p), advanced disease at transplant and HCT-CI >2 were significant predictors of decreased RFS. The use of post-transplant maintenance was shown to improve RFS. Multivariate regression (MV) in AML patients revealed that adverse risk by ELN (HR=3.6, CI=1.9-6.8, p<0.001), disease status at SCT other than CR1/CR2 (HR=2.1, CI=1.4-3.3, p<0.001) and HCT-CI >2 (HR=1.9, CI=1.9-6.9, p<0.001) were poor risk factors for worse RFS. Maintenance treatment lost its significance to improve RFS with MV (HR=0.76; CI=0.47-1.24, p=0.3). Based on MV, 3 mutually exclusive risk groups for RFS were identified (Figure 1b). The best group included patients with favorable/intermediate risk by ELN, with no more than one other risk factor (CRi/p or advanced disease at SCT or HCT-CI >2) with 1-year RFS of 80%. On the other hand, patients with adverse risk by ELN, transplanted in CRi/p or with advanced disease and had HCT-CI>2 represented a very poor group with 1-year RFS of 0%. Adverse risk ELN patients had slightly better RFS if they had only one other high-risk feature with 1-year estimate of 20%. Overall survival at 1-year in MDS and AML patients were 57.3% and 36.4% respectively. The cause of death was relapse of disease in 65% of MDS and 63% in AML patients. Median time to relapse was 135 days, and incidence of disease relapse was very high as 31.2% at 6 months and 49.5% at 1-year in MDS and 30% at 6 months and 47.9% at 1-year in AML patients. Conclusion: TP53 mutated MDS and AML patients continue to represent one of the worst prognostic groups for outcome expectations after transplant. In our analysis, the conditioning regimen, stem cell source and use of post-transplant maintenance therapies did not lead to improved outcomes. On the other hand, among AML patient, we were able to identify a subgroup with favorable outcomes indicating that other disease related characteristics need to be taken into account while planning transplant in this population. Innovative strategies to improve outcomes are urgently needed for TP53 mutated MDS and AML patient. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Prognostic Impact of Monoallelic Versus Biallelic TP53 Alterations in Intensively-Treated Adults AML Patients: A Retrospective Study from the ALFA Group

Introduction:TP53 is a key tumor suppressor gene involved in apoptotic pathways, metabolism functions, preservation of genomic balance and DNA repairs. TP53 locus is subject to mutations, deletions and copy-neural loss of heterozygosity. TP53 mutations are associated with a reduced overall survival and are assigned to the ELN 2017 adverse-risk group. Recent studies have suggested a worse prognostic impact of biallelic TP53 alterations compared to monoallelic TP53 mutations in myelodysplastic syndromes (Bernard et al, Nat. Medicine, 2020). Whether TP53 allelic state impairs the prognostic in intensively-treated acute myeloid leukemia (AML) patients and may refine the treatment strategy has not been addressed. Here, we analysed TP53 alterations in newly diagnosed AML patients (pts) from 3 prospective Acute Leukemia French Association (ALFA) trials. Methods: A total of 983 adult AML pts enrolled in ALFA-0701 (NCT00927498), ALFA-0702 (NCT00932412) and ALFA-1200 (NCT01966497) trials were retrospectively screened for TP53 alterations by high throughput sequencing and conventional cytogenetics. Pts displaying at least two TP53 mutations or one TP53 mutation associated with either TP53 locus deletion or TP53 locus copy-neutral loss of heterozygosity (CN-LOH) were assigned as biallelic TP53 alteration patients. TP53 locus CN-LOH were approximated based on variant allele frequencies and copy number analysis. Survival was analysed with multivariate Cox models stratified on the trial. Results: Eighty-three patients had TP53 mutations (8%; ALFA-0701: n=21, ALFA-0702: n=28; ALFA-1200: n=34), including 14 pts with monoallelic and 69 pts with biallelic TP53 alterations respectively. Median age of TP53 mutated patients was 62 years (IQR: 57-68). Leukocytes counts and bone marrow blast counts at diagnosis were lower in TP53 mutated patients (3.0 G/L vs. 8.7 G/L, p<0.0001; 40% vs. 58%, p=0.002, respectively). Median variant allele frequency of TP53 mutations was 43% (IQR: 21-69). As compared to TP53 wildtype AML, TP53 mutated pts more often harbored complex karyotype (n=69 (86%) vs n=51 (6%), p<0.0001) and monosomal karyotype (n=65 (81%) vs n=32 (4%), p<0.0001). The median number of additional mutations was 2 (IQR: 0-3). TP53 mutations were associated with mutations in signalling genes (NF1, NRAS, PTPN11, KRAS, FLT3, KIT and JAK2) in 33 pts (40%). Overall, 43 TP53 mutated AML patients (52%) achieved complete remission (CR)/complete remission without platelet recovery (CRp) after one or two courses of induction whereas 684 TP53-wt patients (76%) were in CR/CRp at that time (p<0.0001). TP53 mutations were associated with a significantly reduced OS and DFS in multivariate analysis including age and WBC count (2-year OS, 11% vs 56%, HR: 3.48, 95% CI: 2.71-4.47, p<0.0001; 2-year DFS, 12% vs 50%, HR: 2.97, 95% CI: 2.12-4.16, p<0.0001, respectively). Among TP53 mutated AML, biallelic TP53 alterations were associated with worse OS compared to monoallelic TP53 alterations (2-year OS, 4% vs 43%, HR: 4.13, 95% CI: 1.87-9.13, p=0.0004 in multivariate analysis accounting for age and WBC count). Interestingly, outcome of the 2017 ELN risk stratification intermediate group was not different to that of monoallelic TP53 pts (2-year OS, 43% for monoallelic TP53 pts vs 53%, HR: 1.07, 95% CI: 0.55-2.07, p=0.84). In pts with biallelic TP53 alterations, presence of signalling mutations was associated with a worse survival in a multivariate analysis accounting for age and WBC (HR: 1.82, 95% CI: 1.06-3.11, p=0.03). Conclusion: Allelic status refines the prognostic value of TP53 mutations in AML. While monoallelic TP53 alterations display similar outcome to that of the ELN 2017 intermediate risk group, biallelic TP53 alterations dramatically impair patient outcome. Patients with biallelic TP53 alterations may be good candidates for new first-line treatment strategies. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal

Dose-adjusted EPOCH and rituximab for the treatment of double expressor and double-hit diffuse large B-cell lymphoma: impact of TP53 mutations on clinical outcome

Diffuse large B-cell lymphoma (DLBCL) is a heterogeneous disease, including one-third of cases overexpressing MYC and BCL2 proteins (double expressor lymphoma, DEL) and 5-10% of patients with chromosomal rearrangements of MYC, BCL2 and/or BCL-6 (double/triple-hit lymphomas, DH/TH). TP53 mutations are detected in 20-25% of DEL. We report the efficacy of dose-adjusted EPOCH and rituximab (DA-EPOCH-R) in a series of 122 consecutive patients, including DEL (n=81, 66%), DEL-MYC (n=9, 7%), DEL-BCL2 (n=13, 11%), or high-grade lymphomas (DH/TH) (n=19, 16%). Central nervous system (CNS) prophylaxis included intravenous methotrexate (n=66), intrathecal chemotherapy (IT) (n=40) or no prophylaxis (n=16). Sixty-seven patients (55%) had highintermediate or high International Prognostic Index (IPI) and 30 (25%) had high CNS-IPI. The 2-year progression-free survival (PFS) and overall survival (OS) for the entire study population were 74% and 84%, respectively. There was a trend for inferior OS for DH/TH (2-year OS: 66%, P=0.058) as compared to all the others. The outcome was significantly better for the IPI 0-2 versus IPI 3-5 (OS: 98% vs. 72%, P=0.002). DA-EPOCH-R did not overcome the negative prognostic value of TP53 mutations: 2-year OS of 62% versus 88% (P=0.036) were observed for mutated as compared to wild-type cases, respectively. Systemic CNS prophylaxis conferred a better 2-year OS (94%) as compared to IT or no prophylaxis (76% and 65%, respectively; P=0.008). DA-EPOCH-R treatment resulted in a favorable outcome in patients with DEL and DEL with single rearrangement, whereas those with multiple genetic alterations such as DEL-DH/TH and TP53 mutated cases still have an inferior outcome.

Clinical spectrum and prognostic value of TP53 mutations in circulating tumor DNA from breast cancer patients in China.

Background TP53 mutations are common in breast cancer. There is currently no large‐scale cohort study to investigate the TP53 landscape in breast cancer patients from China. The predictive value of TP53 mutations for the efficacy of human epidermal growth factor receptor 2 (HER2)‐targeted therapy in breast cancer remains controversial. In the present study, we aimed to analyze the clinical spectrum and prognostic value of TP53 mutations in circulating tumor DNA (ctDNA) from breast cancer patients in China.MethodsWe retrospectively analyzed the clinical data and TP53 mutation features in ctDNA samples from 804 patients with metastatic breast cancer. TP53 mutations were detected by target region capture‐based next‐generation sequencing. The relationship between TP53 mutation status and disease‐free survival (DFS) was analyzed in 444 patients with metastatic breast cancer. Moreover, the relationship between TP53 mutation status and progression‐free survival (PFS) was analyzed in 55 HER2‐positive patients treated with first‐line trastuzumab‐based therapy. Kaplan‐Meier analysis was performed to estimate the survival curves of the different subgroups, and the log‐rank test was used to compare the curves. A Cox regression model was used to estimate multivariable‐adjusted hazard ratios and their 95% confidence intervals (CIs) associated with the DFS and PFS.ResultsAmong the 804 investigated patients, 431 (53.6%) patients harbored TP53 mutations. TP53 mutations were differentially distributed among different molecular subtypes of breast cancer (P < 0.05). Patients with TP53 mutations had a shorter DFS than those with wild‐type TP53 (hazard ratio = 1.32, 95% CI = 1.09‐1.61, P = 0.005). TP53 mutations in exons 5‐8 were associated with worse outcome (hazard ratio = 1.50, 95% CI = 1.11‐2.03, P = 0.009). However, TP53 mutation status was not significantly associated with PFS in HER2‐positive patients who received first‐line trastuzumab‐based therapy (P = 0.966). Interestingly, in the taxane combination group, patients with TP53 mutations exhibited longer PFS than those without TP53 mutations (hazard ratio = 0.08, 95% CI = 0.02‐0.30, P < 0.001). However, in the non‐taxane combination group, patients with TP53 mutations displayed shorter PFS than those with wild‐type TP53 (hazard ratio = 4.84, 95% CI = 1.60‐14.66, P = 0.005).Conclusions TP53 mutations in exons 5‐8 may be an independent prognostic marker for short DFS in patients with metastatic breast cancer. TP53 mutations had opposite effects on trastuzumab‐treated patients treated with and without taxanes.

The Prognostic Value of TP53 Mutations Depends on Clinical Backgrounds in Pediatric Patients with Acute Lymphoblastic Leukemia

IntroductionTP53 mutations in relapsed cases with pediatric acute lymphoblastic leukemia have been implicated in poor clinical outcomes. However, the prevalence and clinical significance of TP53 mutations at diagnosis have not been fully investigated. Such knowledge is essential for the care of patients, because treatment intensity is tailored to predictive prognosis, where increased attention has been directed toward de-escalation of treatment for the problem of long term effects and second malignancies in childhood cancer survivors.MethodsMutation status of TP53 was detected by targeted-capture sequencing of TP53 coding regions in 1,003 children with B-precursor ALL who had been treated in either of the two prospective clinical trials, JACLS (Japan Association of Childhood Leukemia Study) ALL-02 and TCCSG (Tokyo Children's Cancer Study Group) L04-16. Detection of common fusion genes, including BCR-ABL, ETV6-RUNX1, MLL-AF4, MLL-ENL, MLL-AF9, and TCF3-PBX1, were performed using qPCR assays. We designed SNP baits to analyze copy number status of chromosome 17, and also captured 662 probes tiling the entire IgH enhancer locus to identify IGH-DUX4 rearrangement.ResultIn total, 36 different non-silent coding TP53 mutations were identified in 30 (3%) patients, including 22 missense, 7 frameshift indel, 5 in-frame indel, and 2 nonsense mutations. All missense mutations were found in the core DNA-binding domain (n=21), except for one mutation, which affected the tetramerization motif. Variant allele frequencies (VAF) of TP53 mutations varied from 3% to 97% with 14 mutations showing < 10% VAFs. Showing a significant correlation with mutated TP53 (Odds ratio 20: 95%CI 6.4-61, P<0.001), loss of heterozygosity affecting the TP53 locus was observed in 11 (37%) cases and caused by del(17p) in most cases (n=10). We next evaluated clinical features of TP53-mutated cases. TP53 was most frequently mutated in Hypodiploid ALL (33% n=3), followed by MLL rearrangement (12% n=4), IGH-DUX4 (9% n=5), Others (3% n=8), TCF3-PBX1 (2% n=2), Hyperdiploid (2% n=6), and ETV6-RUNX1 (n=2 0.9%). TP53 mutations were not associated with age or white blood cell count at diagnosis. However, significantly more patients were categorized into National Cancer Institute (NCI) high risk (HR) category (Odds ratio 2.4: 95%CI 1.1-5.3, P = 0.03) and TP53 mutation was associated with a significantly shorter overall survival (OS) among NCI-HR patients (n = 16; HR for death, 6.3; 95% CI, 3.1-13; P<0.001). Five-year OS of NCI-HR patients with TP53 mutations was 44%, suggesting that early treatment intensification or alternative treatment strategies are warranted for these patients. TP53 mutations were also associated with a shorter OS in MLL rearrangement and IGH-DUX4 ALL. Particularly, 67% (n=4/6) of cases with any cause of death harbored TP53 mutation in IGH-DUX4 ALL. In contrast, TP53 mutation was not associated with shorter overall survival in NCI-SR cases. In Hyperdiploid ALL, 5 out of 6 cases with TP53 mutations were categorized into the NCI-SR category and were all alive. Prognostic impact of TP53 mutation was also investigated using recursive partitioning to generate a hierarchical prognostic model for OS by incorporating genetic subgroups and the NCI risk criteria. This model also demonstrated that the NCI risk criteria was the most important prognostic variable and TP53 mutation was used for stratification of patients only in the NCI-HR category.ConclusionTP53 mutations at diagnosis are common in Hypodiploid ALL and also found in a substantial fraction of MLL rearrangement and IGH-DUX4 ALL, where the mutations predict a poor prognosis. TP53 mutation is also found in NCI-SR cases but may not be associated with poor prognosis. [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

Clinical Implications of TP53 Mutations in Adult Patients with Newly Diagnosed Acute Lymphoblastic Leukemia (ALL) Treated with the Hypercvad-Based Regimens

Introduction -TP53 is the most extensively studied gene in cancer and is associated with a poor outcome. The clinical implication of TP53 gene mutations in adult ALL has not been evaluated.Methods - We screened for TP53 mutations in 119 newly diagnosed patients with ALL who were treated with HCVAD-based regimens (2012-2016) and evaluated the predictive and prognostic value of TP53mutations. Bone marrow samples underwent targeted amplicon-based next-generation sequencing (NGS) based mutation analysis.Results - Among 119 patients with adult ALL, we identified 23 patients (19%, 22 B-cell; 1 T-cell) with TP53 mutations (TP53mut); 96 had wild type TP53 (TP53wt; 83 B-cell; 13 T-cell). BCR/ABL1 rearrangement was noted in 2/23 TP53mut ALL and 43/96 TP53wt ALL (p=0.001). Of the 23 patients with TP53mut, 20 were missense, 2 were nonsense mutations and 1 was an insertion/ deletion, spanning exons 2-10. The most common pattern of amino acid substitution,in 10 of the 23 patients, was a substitution of arginine to histidine or proline on different codons. The median TP53 mutant allelic frequency was 42.2% (range, 1.4 - 93.8). Seven patients (30%) with TP53mut had concurrent mutations: NRAS in 2, BRAF, NOTCH1, TET2, DNMT3A, and EZH2 - 1 each. Among patients with TP53wt, 40 patients (42%) had mutations in other genes: 9 JAK2, 7 NRAS, 5 KRAS, 5 NOTCH1, 3 IDH2, 2 each with DNMT3A, ASXL1, FLT3, PTPN11, and 1 with TET2. The clinical characteristics, pattern of mutations, response to therapy, and outcomes of patients with TP53mut ALL (n=23) vs. TP53wt ALL(n=96) were compared (Table 1 and Figure-1). Patients with TP53mutALL were significantly older at presentation (median age 60 years [24-81] versus 46 years [18-81]; p=0.01) and had significantly lower platelet counts (29 x 109 /L versus 45 x 109/L; p=0.01) and lower peripheral blood blast percentages (10% versus 43%; p=0.005). Distribution of chromosomal aberrations was significantly different among the two groups: t(9;22) was observed at a much lower rate in TP53mut ALL, while hyper and hypodiploidy were more commonly encountered in TP53mut ALL There was no significant difference in the complete remission (83% in TP53mut ALL versus 91% in TP53wt ALL, p=0.25) and minimal residual disease (66% in TP53mut ALL versus 59% in TP53wt ALL, p=0.23) rates between the 2 groups. Overall, the median follow-up was 11.3 months (range, 0.2 to 41 months). There was no statistically significant difference in outcome between patients with and without TP5mutation. (Figure -1 A-B). The 3-year event-free (EFS) and overall survival (OS) rates were 45% and 42% in patients with TP53mutand 46% and 59% in those with TP53wt. The median EFS was 18 and 26.7 months (p=0.37) respectively. The median OS was 27.5 and 37.2 months (p=0.20), respectively. Furthermore, no significant difference was observed when only patients with Philadelphia-negative B-ALL were assessed.Conclusions -TP53 mutations are seen in about 19% of adult with newly diagnosed ALL. Patients tend to be older with higher incidence of hypodiploidy. TP53 mutations had no significant negative impact on outcome in patients treated with Hyper-CVAD based regimens. Further studies are underway at our institution to expand the cohort and identify the relevance of TP53mutations in adult ALL in the era of novel chemoimmunotherapy.*3 patients in TP53 - Mutated group had 1 patient each with miscellaneous/insufficient metaphases/ not done while 6 patients had miscellaneous aberrations and 4 with insufficient metaphases TP53wild type respectively [Display omitted] [Display omitted] DisclosuresKonopleva:Calithera: Research Funding; Cellectis: Research Funding. Jain:Incyte: Research Funding; Abbvie: Research Funding; Pharmacyclics: Consultancy, Honoraria, Research Funding; ADC Therapeutics: Consultancy, Honoraria, Research Funding; Novimmune: Consultancy, Honoraria; Pfizer: Consultancy, Honoraria, Research Funding; Infinity: Research Funding; Servier: Consultancy, Honoraria; BMS: Research Funding; Seattle Genetics: Research Funding; Genentech: Research Funding; Celgene: Research Funding; Novartis: Consultancy, Honoraria. Wierda:Novartis: Research Funding; Gilead: Research Funding; Genentech: Research Funding; Acerta: Research Funding; Abbvie: Research Funding. O'Brien:Janssen: Consultancy, Honoraria; Pharmacyclics, LLC, an AbbVie Company: Consultancy, Honoraria, Research Funding. Cortes:ARIAD: Consultancy, Research Funding; BMS: Consultancy, Research Funding; Novartis: Consultancy, Research Funding; Pfizer: Consultancy, Research Funding; Teva: Research Funding. Jabbour:ARIAD: Consultancy, Research Funding; Pfizer: Consultancy, Research Funding; Novartis: Research Funding; BMS: Consultancy.

Clinical implications of TP53 mutations in myelodysplastic syndromes treated with hypomethylating agents.

We screened TP53 mutations in 168 MDS patients who were treated with HMA and evaluated predictive and prognostic value of TP53 mutations. Overall response to HMA was not different based on TP53 mutation status (45% vs. 32% in TP53-mutated and wild type [WT], respectively, P = 0.13). However, response duration was significantly shorter in TP53-mutated patients compared to WT patients (5.7 months vs. 28.5 months, P = 0.003). Longitudinal analysis of TP53 mutations after HMA showed that TP53 mutations almost always persisted at times of disease progression. TP53-mutated patients showed significantly worse overall survival (OS) compared to WT patients (9.4 months vs. 20.7 months, P <0.001). Further, TP53 mutations distinguished prognosis in the subgroup of patients with complex karyotype and Revised International Prognostic Scoring System (IPSS-R) defined very high-risk disease. Multivariate analysis showed that TP53 mutation status is significantly prognostic for OS after adjusting prognostic effect from other factors. The current study provides evidence that TP53 mutations are independently prognostic in MDS patients treated with HMA. While TP53-mutated MDS patients initially respond well to HMA, their duration of response is significantly shorter than WT patients. Novel strategies to improve duration of response in TP53-mutated MDS are urgently needed.

TP53 Mutations and Survival in Osteosarcoma Patients: A Meta-Analysis of Published Data.

Several research groups have examined the association between TP53 mutations and prognosis in human osteosarcoma. However, the results were controversial. The purpose of this study was to evaluate the prognostic value of TP53 mutations in osteosarcoma patients. A meta-analysis was conducted with all eligible studies which quantitatively evaluated the relationship between TP53 mutations and clinical outcome of osteosarcoma patients. Eight studies with a total of 210 patients with osteosarcoma were included in this meta-analysis. The risk ratio (RR) with a 95% confidence interval (95% CI) was calculated to assess the effect of TP53 mutations on 2-year overall survival. The quantitative synthesis of 8 published studies showed that TP53 mutations were associated with 2-year overall survival in osteosarcoma patients. These data suggested that TP53 mutations had an unfavorable impact on 2-year overall survival when compared to the counterparts with wild type (WT) TP53 (RR: 1.79; 95% CI: 1.12 to 2.84; P = 0.01; I 2 = 0%). There was no between-study heterogeneity. TP53 mutations are an effective prognostic marker for survival of patients with osteosarcoma. However, further large-scale prospective trials should be performed to clarify the prognostic value of TP53 mutations on 3- or 5-year survival in osteosarcoma patients.

P-023 Incidence and prognostic value of TP53 mutations in IPSS low and INT 1 (lower risk) MDS with del 5q

Bivalent H3K4me3 and H3K27me3 chromatin domains in embryonic stem cells keep active developmental regulatory genes expressed at very low levels and poised for activation. Here, we show an alternative and previously unknown bivalent modified histone signature in lineage-committed mesenchymal stem cells and preadipocytes that pairs H3K4me3 with H3K9me3 to maintain adipogenic master regulatory genes (Cebpa and Pparg) expressed at low levels yet poised for activation when differentiation is required. We show lineage-specific gene-body DNA methylation recruits H3K9 methyltransferase SETDB1, which methylates H3K9 immediately downstream of transcription start sites marked with H3K4me3 to establish the bivalent domain. At the Cebpa locus, this prevents transcription factor C/EBPβ binding, histone acetylation, and further H3K4me3 deposition and is associated with pausing of RNA polymerase II, which limits Cebpa gene expression and adipogenesis.

Incidence and Prognostic Value of TP53 Mutations in Lower Risk MDS with Del 5q.

AbstractAbstract 2809 Background:TP53 gene mutations, frequent in AML and MDS with complex karyotype, have recently been found in about 20% of lower risk MDS with del 5q, where they possibly conferred resistance to lenalidomide (LEN), and a higher risk of AML progression (Jadersten, JCO, 2011). We assessed the incidence and prognostic value of TP53 mutations in 79 lower risk MDS with del 5q, treated or not with LEN, and analysed in early disease phase or after progression to higher risk MDS or AML. Methods:IPSS low and int 1 (Lower) risk MDS with del 5q were analysed at diagnosis or onset of LEN (“early phase”) and/or after progression to IPSS high or int 2 (higher) risk MDS or AML. LEN was administered at 5 or 10 mg/d during 16 weeks, and continued in erythroid responders until relapse or disease progression.TP53 mutations were detected by the functional FASAY technique, assessing the transcriptional activity of p53 by co-transfecting an open gap repair plasmid with the product of amplification of TP53 from patients in yeasts whose growth is dependent on p53 functionality. The detection limit of this technique is around 10–15% (Flaman, PNAS 1995). Mutations found by FASAY were confirmed by direct sequencing, using Sanger method and /or (more recently) high sensitivity (1%) Next Generation Sequencing (NGS) by pyrosequencing (GS Junior System-Roche, with the IRON II plate design). Results:79 lower risk MDS with del 5q from 6 French centers of the GFM were analyzed, including 62 at diagnosis or onset of LEN (“early phase”), and 17 after progression to higher risk MDS or AML (5 of the latter were also retrospectively analysed on early phase samples).Overall, 28 (35%) of the 79 patients had TP53 mutation, including 16 (26%) of the 62 pts analyzed at early phase and 12 (70%) of the 17 evaluated after higher risk MDS or AML progression (p= 0.001).The 62 early phase pts had marrow blasts <5% and 5–9% in 91 and 9% of the cases, isolated del 5q, del 5q+1 and del5q+>1 (complex karyotype) in 84, 14 and 2% of the cases, and IPSS low and int 1 in 80 and 20% of the cases, respectively. No significant difference was found between mutated and non mutated cases for baseline characteristics including gender, age, WHO classification, cytogenetic complexity and IPSS. In the 5 pts analysed after progression where early phase samples were available, who all had received LEN, 4 had TP53 mutation at progression. In all of them, TP53 mutation was already detectable during early phase. However, the percentage of mutated colonies found by FASAY increased with progression, from 18 to 75%, 26 to 55%, 12 to 87% and 13 to 23%, respectively, showing an increase of the size of the mutated clone at progression.Among the 43 pts analyzed in early phase who received LEN (we excluded the 5 pts analysed after progression where early phase samples were available, to avoid bias), 36 (84 %) had isolated del 5q, 6 (14%) del 5q+1, and 1 (2%) had complex karyotype. IPSS was low in 73% and int-1 in 27%. 12/43 (28%) had TP53 mutation. 63% of the 43 pts achieved erythroid response, and 9 (47%) of the 19 pts evaluable at erythroid response achieved cytogenetic response. Erythroid response was seen in 45% mutated vs 71% non mutated cases (p= 0.258). Cytogenetic response was seen in 1/8(12%) mutated vs 8/11 (73%) non mutated cases (p=0.020). In those 43 pts who received LEN, the cumulative incidence (CI) of AML evolution, with death as a competitive event, did not significantly differ between patients with or without TP53 mutation (3 year CI of 35% vs 30%, p=0.33). Finally, in those pts, TP53 mutational status had no significant impact on OS (median 49 months in mutated pts vs not reached in non mutated pts, p=0.48, figure 1). Conclusion:We confirm the presence of TP53 mutations in about 25 % of lower risk MDS with del 5q analysed in early disease phase. TP53 mutations, in those patients, were not correlated with other baseline parameters. When treated with LEN, mutated cases had similar hematological response, lower cytogenetic response but no significant difference in progression to higher risk MDS or AML and survival compared to non mutated cases. The high incidence of TP 53 mutations at progression to higher risk MDS/AML (70%), and the increase in the TP53 mutated clone size observed during progression in pts with a baseline mutation support the pathophysiological importance of TP53 mutations in disease progression in lower risk MDS with del 5q. [Display omitted] Disclosures:No relevant conflicts of interest to declare.

Prognostic Value of TP53 Gene Mutations in Higher Risk MDS Treated with Azacitidine

AbstractAbstract 1706▪▪This icon denotes a clinically relevant abstract Background:TP53 gene mutations in MDS and AML are, with the exception of cases of isolated del 5q, generally associated with complex karyotype, often including del (17p) (with loss of the remaining TP53 allele) and with poor overall outcome (Fenaux, BJH, 1992; Bejar, NEJM, 2011). They are, in MDS and AML, more specifically generally associated with resistance to chemotherapy, including anthracycline-Ara C combinations and low-dose AraC (Wattel, Blood, 1994), but their correlation with treatment outcome with hypomethylating agents has not been studied. Our aim was to assess the prognostic value of TP53 mutations for response to Azacitidine (AZA) in higher risk MDS, AML with 20–30% blasts or advanced CMML (corresponding to the EU label for AZA). Methods:Patients were treated with AZA (75 mg/m2/d, generally during 7 days every 4 weeks) in 2 centers of the Groupe Francophone des Myélodysplasies. TP53 mutations were detected by the functional FASAY technique, which assesses the transcriptional activity of p53 by co-transfecting an open gap repair plasmid with the product of amplification of TP53 from patients in yeasts whose growth is dependent on the functionality of p53. The detection limit of this technique is around 10–15% (Flaman et al, PNAS 1995). The presence of mutations was subsequently confirmed by direct sequencing using the Sanger method and, more recently, by a Next-Generation Sequencing (NGS) assay using pyrosequencing (GS Junior System, Roche with the IRON II plate design). Results:72 pts treated with AZA (median n° of cycles of AZA received 4, range 1–7) were analyzed, including 34 MDS according to WHO classification (IPSS high: 9, int2: 13, int1: 6, undetermined: 6), 33 AML with 20–30% blasts and 5 advanced CMML. According to IPSS, karyotype was favorable in 27%, intermediate in 13% and unfavorable in 60% of the pts, including 47% of complex karyotypes.Response to AZA (according to IWG 2006 criteria) was observed overall in 51% of the pts, including 34% CR, 6% PR, 4% marrow CR, 7% stable disease with HI. Median overall survival (OS) from onset of AZA was 15.6 months, possibly explained by the 47% of complex karyotypes.29 (40%) patients had a TP53 mutation, detected by FASAY technique and subsequently confirmed by Sanger sequencing or NGS (no false positive with FASAY technique was observed). 22 of the 34 (67%) patients with complex karyotype had a TP53 mutation. In the 7 patients with TP53 mutation without complex karyotype, 3 pts had isolated del(5q), 2 had del (17p) (isolated in 1 pt, with del (20q) in 1 pt), 1 had pentasomy 11 and 1 had +8, del(20q). Ten (77%) of the 13 cases with chromosome 17 rearrangement leading to del (17p) were TP53 mutated.Overall Response to AZA (41% vs 57%, p= 0.227) and CR rate (21% vs 42%, p= 0.073) did not significantly differ between TP53 mutated and wild-type patients. Nevertheless, OS was negatively influenced by the presence of TP53 mutation (median 13 vs 21 months, p= 0.0022, figure 1), complex cytogenetics (median 14 vs 18 months, p=0.0120), WHO AML diagnosis (median 13 vs 21 months for WHO-MDS or CMML, p= 0.0014). By multivariate analysis, marrow blast % (HR 1.03 (1.01–1.05) (p<10-4)) and TP53 mutational status (HR 2.29 (1.06–4.97) p=0.035) were the only 2 factors retaining statistical significance for OS. When the analysis was restricted to WHO MDS and CMML patients, only the presence of TP53 mutation was associated with worse OS in multivariate analysis (HR=4.08 (1.31– 12.7), p=0.015)). Conclusion:In higher risk MDS (and AML with 20–30% blasts and advanced CMML) patients treated with AZA, the presence of TP53 mutation appears to constitute an independent prognostic parameter of poorer survival. [Display omitted] Disclosures:No relevant conflicts of interest to declare.

Abstract 1983: TP53 mutations in hepatocellular carcinoma: Association with survival and stem cell-like gene expression traits

Abstract PURPOSE Mutations of TP53, a tumor suppressor gene, are associated with prognosis of many cancers. However, the prognostic value of TP53 mutations in hepatocellular carcinoma (HCC) is still unclear, largely because of the enormous heterogeneity in the geographic and etiological backgrounds of the HCC patients. Here, we analyzed the prognostic values of TP53 mutations. Gene expression profiling analysis was performed to evaluate the effect of TP53 mutations at the molecular level. PATIENTS AND METHODS TP53 mutations were investigated in a total of 409 HCC patients including Chinese (n=336) and Caucasian (n=73) patients using direct sequencing method. RESULTS A total of 125 TP53 mutations were found in Chinese HCC patients (37.2 %). HCC patients harboring TP53 mutations showed shorter overall survival compared to patients with wild-type TP53 (Hazard ratio [HR], 1.86; 95% confidence interval [CI], 1.37-2.52; P&amp;lt;0.001). The hotspot mutations at R249S and V157F were significantly associated with worse prognosis in both univariate (HR, 2.11; 95% CI, 1.51-2.94; P&amp;lt;0.001) and multivariate analyses (HR, 1.79; 95% CI, 1.29-2.51; P&amp;lt;0.001). In addition, gene expression profile analysis revealed the expression of stem cell-like traits in TP53 mutated tumors. This finding was validated in breast and lung cancers with TP53 mutations. CONCLUSION TP53 mutations, particularly hotspot mutations, are associated with poor prognosis in HCC. The acquisition of stem cell-like gene expression traits may contribute to the aggressive behavior of the TP53 mutated tumors. 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 1983.

The Prognostic Value of TP53 Mutations in Chronic Lymphocytic Leukemia Is Independent of Del17p13: Implications for Overall Survival and Chemorefractoriness

Del17p13 predicts poor outcome and chemorefractoriness in chronic lymphocytic leukemia (CLL). Conversely, it is unknown whether TP53 mutations carry any prognostic value independent of del17p13. We tested the independent prognostic value of TP53 mutations in CLL. The study was based on a consecutive series of 308 CLL. DNA sequencing of TP53 exons 2 to 10 and del17p13 interphase fluorescence in situ hybridization were done at CLL diagnosis. Study end points were survival and chemorefractoriness. At diagnosis, TP53 mutations (n = 32) occurred in 31 of 308 (10.0%) patients. Of all CLL showing TP53 disruption by either mutation and/or deletion (n = 44), 10 cases (22.7%) showed TP53 mutations in the absence of del17p13. Multivariate analysis selected TP53 mutations (hazard ratio, 3.20; P = 0.002) as an independent predictor of overall survival after adjustment for del17p13. Also, multivariate analysis selected TP53 mutations (hazard ratio, 3.97; P < 0.001) as an independent predictor of chemorefractoriness after adjustment for del17p13. Compared with cases without TP53 alterations, CLL harboring any type of TP53 disruption (mutation only, del17p13 only, or both mutation and del17p13) uniformly displayed a high prevalence of unfavorable prognosticators and poor outcome. Analysis of sequential CLL samples showed the acquisition of new or additional TP53 alterations at the time of chemorefractoriness. These data show that (a) TP53 mutations are an independent predictor of short survival and chemorefractoriness, and (b) that CLL presenting with TP53 mutations without del17p13 fare as poorly as CLL carrying del17p13. Because CLL harboring TP53 mutations without del17p13 are currently not recognized by conventional diagnostic strategies, these results may be relevant for a comprehensive prognostic characterization of CLL.

The Prognostic Value of TP53 Mutations in Chronic Lymphocytic Leukemia (CLL) Is Independent of del17p13: Implications for Overall Survival and Chemorefractoriness

CLL harboring del17p13 displays a dismal prognosis and a high risk of chemorefractoriness. We tested whether TP53 inactivation through mutation harbors the same prognostic role as del17p13 on 308 consecutive CLL. TP53 mutation status was assessed at diagnosis by direct sequencing of TP53 exons 2–10. Thirty-two TP53 mutations were observed in 31/308 (10.0%) CLL. Among 26 missense mutations, the median residual transactivation activity compared to germline TP53 was 8.9% (25th–75th percentile: 0.6–13.0%), and was ≤20% in 22/26 (84.6%) mutations. All microdeletions and microinsertions (4/32; 12.5%) led to frameshift. One non-sense mutation introduced a stop codon at position 213, and one mutation affected the 3′ splicing site of exon 8. Despite the statistical association between TP53 mutations and del17p13 in the whole cohort, the overlap between the two genetic lesions was restricted to a fraction of patients. By combining results of FISH and TP53 mutation analysis, 44/297 (14.8%) CLL carried TP53 inactivation: 18/44 (40.9%) showed TP53 mutation paired to del17p13; 10/44 (22.7%) showed TP53 mutations in the absence of del17p13; and 16/44 (36.3%) showed del17p13 in the absence of TP53 mutations. Univariate log-rank analysis identified both TP53 mutations and del17p13 as risk factors for short overall survival (OS). Median OS for patients with TP53 mutations was 79.6 months (5-year OS 66.2%), whereas median OS for patients without TP53 mutations was not reached and the 5-year OS was 85.2% (p<.001). Multivariate analysis selected TP53 mutations (HR 3.20; p=.002), along with age >65 years (HR 4.98; p<.001) and advanced Binet stage (HR 3.01; p<.001), as independent predictors of OS after adjustment for del17p13 and other potentially confounding biological and clinical covariates. Univariate log-rank analysis identified both TP53 mutations and del17p13 as risk factors of short time to chemorefractoriness. Median time to chemorefractoriness for patients with TP53 mutations was 6.3 months versus 72.7 months for patients without TP53 mutations (p<.001). Multivariate analysis selected TP53 mutations (HR 3.97; p<.001) as independent predictor of short time to chemorefractoriness after adjustment for del17p13 and other potentially confounding covariates. OS and time to chemorefractoriness did not differ between CLL harboring TP53 mutations in the absence of del17p13 and CLL harboring del17p13. Patients harboring TP53 mutations only and patients harboring both TP53 mutation and del17p13 were characterized by short time to chemorefractoriness compared to patients without any TP53 alteration or to patients harboring del17p13 only (p<.05). CLL that at diagnosis harbored del17p13 without TP53 mutations showed a significantly longer time to chemorefractoriness compared to CLL who at diagnosis carried both del17p13 and TP53 mutations (median: 55.2 months vs 5.5 months, respectively; p=.003). Notably, at diagnosis, the percentage of deleted nuclei was significantly lower in CLL harboring del17p13 only (median: 45.0%, 25th–75th percentiles: 7.3–67.4%) compared to CLL with both del17p13 and TP53 mutations (median: 66.5%, 25th–75th percentiles: 52.1–77.9%, respectively) (p=.020). The value of TP53 mutations in predicting chemorefractoriness was also assessed in patients who had been exposed to fludarabine (n=88). Multivariate analysis selected TP53 mutations as the sole independent predictor of short time to fludarabine refractoriness (HR 6.72; p<.001). Sequential samples were available for 14 CLL who had no TP53 abnormalities at diagnosis and who later developed chemorefractoriness. At the time of chemorefractoriness, TP53 abnormalities were acquired in 5/14 (35.7%) cases. The implications of this study are threefold:mutation in the absence of del17p13 is the sole mechanism of TP53 inactivation in 20% CLL harboring TP53 disruption;TP53 mutations carry the same prognostic relevance as del17p13 in terms of CLL progression, survival and risk of chemorefractoriness;because of the practical implications for choice of therapy, screening for TP53 mutations, in addition to del17p13 assessment, should be included in the initial prognostic assessment of CLL.

Mutational Status of the TP53 Gene as a Predictor of Response and Survival in CLL Patients with and without 17p Deletion

Background: Deletion of 17p in chronic lymphocytic leukaemia (CLL) is associated with resistance to conventional therapy and a poor clinical outcome. Though TP53 mutations have been described in some of these cases, the extent to which they occur in CLL patients and their clinical implications remain unclear. We investigated the prognostic value of TP53 mutations in the clinical course of CLL patients.Methods: We analysed 529 CLL samples from the UK LRF CLL4 clinical trial (Chlorambucil vs Fludarabine±Cyclophosphamide) for the presence of TP53 mutations and their association with response to treatment, progression-free survival (PFS) and overall survival (OS). We also investigated the correlation between TP53 mutations and other well-known prognostic indicators in CLL including stage, chromosomal aberrations, VH mutational status and CD38 and ZAP-70 expression.Results: Mutations of TP53 were found in 44 of 529 patients overall (8.3%). TP53 mutations were present in 26 out of 32 (81%) patients with 17p deletion in >20% of cells (p<0.0001). TP53 mutations were also present at lower frequencies in samples with no 17p deletion (13/446; 2.9%) or with <20% of cells with 17p deletion (4/47; 8.5%). Overall response rates were significantly better in patients without TP53 mutations compared to those with mutations (82% vs 34%; p<0.0001), including complete or nodular partial responses in 42% of patients without TP53 patients compared to only 10% of patients with mutations (p<0.0001). TP53 mutations were associated with significantly poorer OS; 36% (95% CI 22–51) at 3 years versus 79% (95% CI 75–83) for patients without mutations, p<0.00001 (Figure 1a). Similarly, PFS was significantly shorter for patients with TP53 mutations (3 year PFS: 9% [95% CI: 1–18]) compared to those without (34% [95% CI 30–38], p<0.00001; Figure 1b). CLL patients with TP53 haploinsufficiency -either TP53 mutation or >20% of 17p deletion- define a subgroup with intermediate prognosis (3 year OS: 52% [95% CI 32–73]) compared to those with neither (80% [95% CI 76–83]) or both (23% [95% CI 7–39]) (p(trend)<0.00001, Figure 2). There was no significant association between TP53 mutations and age, stage, VH mutations, CD38 expression, ZAP-70 expression or any other chromosomal abnormality other than 17p deletion.Conclusions: Our data shows that TP53 mutations are associated with a poor outcome in CLL patients regardless of the deletion of 17p. Furthermore, the clinical significance of 17p deletion seems to be tightly linked to the presence of mutations in the remaining TP53 allele, and these patients with no wild-type TP53 genes have the lowest OS and PFS rates. Finally, the group of CLL patients with TP53 haploinsufficiency (either by mutation or deletion in >20% of the cells) presents an intermediate prognosis and will be further investigated. [Display omitted] [Display omitted] [Display omitted]

Mutations in TP53 are a prognostic factor in colorectal hepatic metastases undergoing surgical resection

The aim of this study was to analyze the prognostic value of TP53 mutations in a consecutive series of patients with hepatic metastases (HMs) from colorectal cancer undergoing surgical resection. Ninety-one patients with liver metastases from colorectal carcinoma were included. Mutational analysis of TP53, exons 4-10, was performed by single-strand conformation polymorphism and sequencing. P53 and P21 protein immunostaining was assessed. Multivariate Cox models were adjusted for gender, number of metastasis, resection margin, presence of TP53 mutations and chemotherapy treatment. Forty-six of 91 (50.05%) metastases showed mutations in TP53, observed mainly in exons 5-8, although 14.3% (n = 13) were located in exons 9 and 10. Forty percent (n = 22) were protein-truncating mutations. TP53 status associated with multiple (> or =3) metastases (65.6%, P = 0.033), advanced primary tumor Dukes' stage (P = 0.011) and younger age (<57 years old, P = 0.03). Presence of mutation associated with poor prognosis in univariate (P = 0.017) and multivariate Cox model [hazard ratio (HR) = 1.80, 95% confidence interval (CI) = 1.07-3.06, P = 0.028]. Prognostic value was maintained in patients undergoing radical resection (R0 series, n = 79, P = 0.014). Mutation associated with a worse outcome in chemotherapy-treated patients (HR = 2.54, 95% CI = 1.12-5.75, P = 0.026). The combination of > or =3 metastases and TP53 mutation identified a subset of patients with very poor prognosis (P = 0.009). P53 and P21 protein immunostaining did not show correlation with survival. TP53 mutational status seems to be an important prognostic factor in patients undergoing surgical resection of colorectal cancer HMs.

LOH rather than genotypes of TP53 codon 72 is associated with disease-free survival in primary breast cancer

Mutations in the TP53 gene are a well-documented strong prognostic factor in breast cancer. A prognostic value of the Arg72Pro polymorphism of the TP53 gene is more contradictory. We assessed TP53 mutations and genotypes of the Arg72Pro polymorphism in a study including 204 Danish women. Patients with mutations in the TP53 gene had a significant reduction in disease-free survival of breast cancer (p < 0.0001). Genotypes of the Arg72Pro polymorphism were neither significantly associated with TP53 mutations nor with disease-free survival (p = 0.4). Among heterozygous patients a reduction in disease-free survival was found for patients with LOH and retention of the Pro allele as compared to patients with LOH and retention of the Arg allele and patients with no LOH (p = 0.05). In conclusion, we find a highly significant prognostic value of TP53 mutations but find a possible prognostic value of the Arg72Pro polymorphism only related to LOH.