TP53-mutant Patients Research Articles

Clinical Utility of Molecular Profiling in Higher Risk MDS Treated with Azacitidine: Can We Tailor Therapy Accordingly?

▪Background Hypomethylating agent (HMA) therapy represents the standard of care for patients with higher risk myelodysplastic syndromes although only 50% of patients respond to treatment. Recent evidence from molecular profiling through next-generation sequencing (NGS) in myeloid diseases has been conflicting as to the value of somatic mutations as a biomarker for response to HMA. TET2 mutations, predominantly in the absence of ASXL1 mutations (or variant allele frequency (VAF) < 10%), have been shown to predict HMA response in MDS and chronic myelomonocytic leukemia (CMML) (Itzykson et al., 2011; Bejar et al., 2014 (80% decitabine)) while DNMT3A mutations predict response to frontline HMA treatment in acute myeloid leukemia (AML) (Coombs et al., 2016). Therefore, our goal was to identify molecular predictors of response and outcomes to azacitidine in myeloid malignancies.Patients and Methods Genetically profiled higher-risk MDS, CMML and oligoblastic AML (20-30% blasts) cases were retrospectively identified from the Moffitt Cancer Center MDS database. We evaluated gene mutations associated with DNA methylation (TET2, DNMT3A, IDH1, IDH2, and WT1) and up to 19 additional genes. NGS was performed prior to the initiation of HMA in all patients. The lower limit of VAF detection was set at 5% and the minimum depth of coverage at each position was 500X. Clinical variables and outcomes of MDS patients were characterized at the time of sample procurement. Fisher's exact and t-tests were used for comparative analyses. Kaplan-Meier curves were used to estimate overall survival and analyzed from the date of mutation identification. Multivariate Cox regression models were created to adjust for clinical characteristics.Results From May 2013 to February 2016, a total of 77 patients with NGS for somatic mutations prior to HMA therapy were identified with a median age of 70 years and male predominance (66%). Of the cohort, 97% of patients (n=75) were treated with azacitidine with 17% of patients (n=13) proceeding to allogeneic hematopoietic stem cell transplant (AHSCT). A total of 86% of patients (n=66) had at least one pathogenic mutation. Mutations in DNA methylation occurred in 43% of patients (n=33) while TET2 mutation without clonal ASXL1 mutations occurred in 13% of patients (n=10). At a median follow up 17 months, the median OS of the entire cohort was 12.5 months. Patients with a DNA methylation mutation had a median OS that was not reached (NR) vs a median OS of 11.5 months in wildtype (WT) patients (HR 0.38, 95% CI 0.21 to 0.75; P = 0.005), which remained significant when censoring patients at time of AHSCT (P = 0.002). TP53 mutant (MT) patients (n=14, 18% of cohort) had a median OS of 7.9 months vs 15.4 months in WT patients (HR 3.69, 95% CI 3.04 to 28.8; P = 0.0001). The presence of DNA methylation or TP53 mutation in comparison to wildtype patients significantly stratified prognosis in azacitidine treated patients (Figure 1A, P = 0.0001). In multivariable analysis incorporating age and revised international prognostic scoring system (IPSS-R) category, DNA methylation (HR 0.45, 95% CI 0.21 to 0.96; P = 0.04) and TP53 (HR 2.34, 95% CI 1.04 to 5.26; P = 0.04) mutation status remained predictive for survival. Notably, response rates in DNA methylation mutant patients were similar to WT patients (40% versus 42%) with no difference in treatment duration. However, the overall response rate of TET2 MT/ASXL1 WT patients was 70% versus 36% in the rest of the cohort (P =0.08) and 0% in TET2 MT/ASXL1 MT patients (0/6, P =0.01) with a significantly longer duration of treatment in the TET2 MT/ASXL1 WT cohort (median number of cycles 7.5 versus 4; P = 0.002). Additionally, TET2 MT/ASXL1 WT patients had longer survival (median OS NR vs 12.2 months; P = 0.047). When censoring for transplant, the impact of TET2 MT/ASXL1 WT genoptype was significantly strengthened with 70% of patients alive past 15 months (median OS NR vs 9.9 months; HR 0.24, 95% CI 0.19 to 0.75; P = 0.007; Figure 1B).Conclusion In patients with myeloid malignancies, molecular profiling via NGS can predict outcomes to azacitidine therapy. Patients with mutations of DNA methylation have improved OS whereas OS is poor in TP53 MT patients. Most importantly, TET2 MT/ASXL1 WT identifies a genotypic subgroup with particularly good outcomes when treated with HMA without AHSCT and potentially challenges the early timing of AHSCT for higher risk patients and this molecular profile. [Display omitted] DisclosuresPadron:Novartis: Honoraria; Incyte: Research Funding; CTI: Honoraria, Research Funding; KALOBIOS: Research Funding. Vaupel:Genoptix, a Novartis Company: Employment. Hall:Genoptix, a Novartis Company: Employment. Komrokji:Celgene: Membership on an entity's Board of Directors or advisory committees, Research Funding; Novartis: Consultancy, Speakers Bureau; Boehringer-Ingelheim: Research Funding; Incyte: Consultancy.

TP53 Alterations Correlate with Response to VEGF/VEGFR Inhibitors: Implications for Targeted Therapeutics.

TP53 tumor-suppressor gene mutations are among the most frequent abnormalities in cancer, affecting approximately 40% of patients. Yet, there is no accepted way to target these alterations in the clinic. At the same time, antagonists of VEGFR or its ligand are best-selling oncology drugs, with multiple, expensive compounds approved. Although only a subset of patients benefit from these antiangiogenesis agents, no relevant biomarker has been identified. Interestingly, TP53 mutations upregulate VEGF-A and VEGFR2. We prospectively enrolled 500 patients, to be interrogated by comprehensive genomic profiling (CGP) (next-generation sequencing, 236 genes), and to be matched, whenever possible, with targeted agents. Herein, we analyze outcomes based on VEGF/VEGFR inhibitor treatment and presence of TP53 mutations. Of the 500 patients, 188 (37.6%; with ≥1 alteration) were treated; 106 (56% of 188) had tumors that harbored TP53 mutations. VEGF/VEGFR inhibitor therapy was independently associated with improvement in all outcome parameters [rate of stable disease (SD) ≥6 months/partial and complete remission (PR/CR); (31% versus 7%; TP53-mutant patients (who received no other molecular-matched agents) treated with versus without VEGF/VEGFR inhibitors), time-to-treatment failure, and overall survival (multivariate analysis: all P ≤ 0.01)] for the patients harboring TP53-mutant cancers, but improvement was not seen in any of these parameters for patients with TP53 wild-type neoplasms. We conclude that TP53 mutations predict sensitivity to VEGF/VEGFR inhibitors in the clinic. TP53 alterations may therefore be a ready biomarker for treatment with antiangiogenesis agents, a finding of seminal importance across the cancer field. Mol Cancer Ther; 15(10); 2475-85. ©2016 AACR.

A Primary Study of the Gene Mutations in Predicting Treatment Response to Decitabine in Patients with MDS

BackgroundTo analyze whether some distinct gene mutations could predict treatment response to Hypomethylation Agent---Decitabine.Patients and MethodsTargeted next-generation sequencing was performed on reported 30 recurrently mutated genes for 106 MDS patients before they accepted Decitabine therapy. For those who presented satisfactory response (CR) or poor response (NR or PD), their gene sequencing were repeated after Decitabine therapy to analyze the alteration of the gene mutation.ResultsThe overall response rate was 67.0%, with 26.4% patients (28 cases) achieving CR. The median survival of patients who achieved CR was longer than those who just achieved NR/PD (22 months VS 14 months, p =0.021). Among the 14 TP53 mutant patients, ten achieved CR (71.4%). Moreover, two of 3 BCOR mutant patients (66.7%) and three of 5 KIF20B mutant patient (60.0%) also achieved CR. Zero of the patients who were with IDH1/2(n=11), GATA2 (n=5), SETBP1 (n=5), EZH2 (n=3) or CEBPa (n=1) mutations could get CR response (Figure1). On the other hand, total five of the 8 PTPRD mutant patients (62.5%) and five of 11 ASXL1mutant patients did not responded to Decitabine. In addition, 16 among the 28 CR patients accepted the target sequencing after the stop of decitabine therapy. Ten of the 16 patients showed decreased number of mutant genes (Table1). Besides, the TP53 mutation was completely fade away in five of 7 patients after Decitabine treatment (Table 2). Finally, the TP53 mutant and wild type of MDS patients achieved comparable overall survival, suggesting decitabine treatment could significantly alter the prognostic impact of adverse genetic alterations.ConclusionSome gene mutation (specially TP53) seemed predictive for Decitabine response. Further studies with large samples are needed to identify it.Table 1The number of mutant genes on CR patients before and after Decitabie therapySampleNumber of mutationsresponseBeforeAfterSample 58632CRSample 96732CRSample 176142CRSample 161923CRSample 186474CRSample 185431CRSample 181832CRSample 152224CRSample 203822CRSample 205521CRSample 70231CRSample 82820CRSample 136100CRSample 100221CRSample 191712CRSample 115400CRTable 2Status of TP53 mutation after hypomethylating agents in CR patients.SampleBeforeAfterresponseSample 586TP53/8/D242HTP53-WTCRSample 967TP53/6/R174LTP53-WTCRSample 1864TP53/8/R244HTP53/8/R244HCRSample 1854TP53/4/W91TP53-WTCRSample 2038TP53/8/F231STP53/8/F231SCRSample 2055TP53/6/R196*TP53-WTCRSample 1002TP53/8/R234HTP53-WTCR [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

A Final Report: Phase I/II Study of Sequential Azacitidine and Lenalidomide in Patients with Higher-Risk Myelodysplastic Syndrome (MDS) and Acute Myeloid Leukemia (AML)

▪Hypomethylating agents (HMAs) are currently the front-line therapeutic choice for patients with higher risk MDS, and also frequently employed in elderly AML or in AML patients not otherwise eligible for standard intensive therapy. A number of combination strategies are under development to improve the results of HMA monotherapy. Given the single-agent activity of both azacitidine (AZA) and lenalidomide (LEN) in patients with MDS and AML, a scientific rationale exists to explore this therapeutic combination strategy. Previous studies have evaluated the combination of AZA and lenalidomide in this population with encouraging results, using lenalidomide at doses ranging from 5 to 50mg daily over 5 to 28 days per cycle. The optimal dose and schedule for this combination remains unknown.We report our completed Phase I/II study of sequential AZA and lenalidomide in 88 patients with high-risk MDS and AML. Phase I eligibility included relapsed/refractory AML or MDS patients with bone marrow blasts >10%. Phase II eligibility included untreated high-risk MDS, or AML with 20-30% blasts. All subjects were registered into the RevAssist® program. Median age was 67 (range 32–88). Per WHO criteria, there were 42 MDS patients (48%), 3 (3%) with CMML-2, 20 (23%) with RAEB-T (i.e. 20-30% bone marrow blasts), and 23 patients (26%) with AML (>30% blasts). All subjects received 75mg/m²/day AZA days 1-5 of each 28-day cycle. LEN was administered orally for 5 or 10 days, starting on day 6 per cycle. 28 patients in the Phase I and 60 in the Phase II portion were treated. In the Phase I portion, 7 levels of LEN were evaluated with the following doses and schedules: 10mg x 5 days (n=5), 15mg x 5 days (n=3), 20mg x 5 days (n=3), 25mg x 5 days (n=3), 50mg x 5 days (n=4), 75mg x 5 days (n=3), and 75mg x 10 days (n=7). The initial Phase II starting dose was LEN 50mg daily x 10 days, however due to myelosuppression and infections with repeated cycles in the first 20 Phase II subjects, the Phase II dose was amended to LEN 25mg daily x 5 days, and another 40 patients were evaluated.In the entire cohort, overall response rate (ORR) was 35% (31/88) (15 CR; 16 CR with incomplete count recovery (CRi)), with median overall survival (OS) of 33 weeks (range 1-172). Phase I ORR was 14% (4/28) and Phase II ORR was 45% (27/60). Of the 40 patients receiving the optimal Phase II dose, ORR was 55% (22/40), with 75 week median OS. In responding patients (n=31), the median response duration was 29 weeks (range 2 - 127 weeks), with a median overall survival that has not been reached with a median follow-up time of 57 weeks (Figure 1). 13 of the 31 responding patients (42%) proceeded with stem cell transplant, of which 10 patients continue in a sustained remission. In a cohort of 25 molecularly annotated patients (Table 1), 5 of 9 (56%) TP53-mutant patients, all with complex cytogenetics, achieved CR/CRi. By multivariate analysis, treatment was associated with worse OS in patients with bone marrow blasts > 30% (HR 4.5, 95% CI 2.4 – 8.5, p < 0.001), complex cytogenetics (HR 3.4, 95% CI 1.8 – 6.2, p < 0.001), and lenalidomide dose (HR 2.2, 95% CI 1.1-4.4, p = 0.03).In conclusion, we identify the combination of AZA 75mg/m²/day on days 1-5 with 25mg LEN on days 6-10 over a 28-day cycle as an effective front-line regimen for high-risk MDS and AML with up to 30% blasts. Responses are rapid with a median of 2 cycles for response, durable, and treatment with this dosing schedule is well tolerated. [Display omitted] [Display omitted] DisclosuresGarcia-Manero:Celgene: Research Funding.

Genomic Profiling Combining DNA and RNA Analysis of 112 Formalin-Fixed Paraffin-Embedded Diffuse Large B Cell Lymphoma Specimens Identifies a High Frequency of Clinically Relevant Genomic Alterations

Background: A variety of next-generation sequencing methods have been used to investigate the genomic landscape of primary lymphoma patient samples, including whole-genome, whole-exome, and RNA sequencing. In diffuse large B cell lymphoma (DLBCL), sequencing studies identified numerous genomic alterations (GAs) of potential clinical relevance, but the distribution and frequency of GAs have not been precisely determined. Discrepancies in existing data likely arise from variability in types of specimens examined, sequencing technologies employed, and depth of coverage utilized to identify GAs. In this study, we performed comprehensive DNA/RNA sequencing of genes known to be important across the spectrum of hematologic malignancies in order to determine the nature and prevalence of GAs with potential diagnostic, prognostic, or therapeutic implications in a cohort of 112 well-annotated clinical DLBCL cases.Methods: We performed hybridization capture of 405 cancer-related genes and 31 genes commonly rearranged in cancer (FoundationOne Heme) and 265 frequently rearranged genes for RNA-seq applied to ³50ng of DNA and sequenced to high, uniform coverage. Genomic alterations, including short variants (small indels and base substitutions), rearrangements, and copy number alterations, were determined. All captured libraries were sequenced to high depth (Illumina HiSeq), averaging >500x for DNA and >20,000,000 total pairs for RNA, to enable the sensitive and specific detection of GAs. Significant non-synonomous variants were identified as mutations from the COSMIC database, amplifications of established oncogenes, or homozygous deletions and/or clear loss-of-function mutations of known tumor suppressors.Results: GAs with diagnostic, prognostic, or therapeutic relevance were identified in 96% of cases, with a median of 5 (range 0 to 12) alterations per sample. Figure 1 shows the frequencies of different GAs. De novo DLBCL tended to exhibit fewer GAs (median 4) than relapsed/refractory (median 6) or transformed disease (median 6) (p=0.179; Wilcoxon rank sum). Compared with reported frequencies ranging from 5 to 44%, we detected alterations in CREBBP/EP300 in 21% of cases, with CREBBP mutations preferentially found in germinal-center B cell-like (GCB) compared to non-GCB DLBCL (26% vs. 8%; p=0.02; Pearson’s chi-squared). Although previously described only in Burkitt lymphoma, we identified mutations in ID3 (L70P, P98R, Q100P) and TCF3 (N551K) in GCB-phenotype DLBCL cases with aggressive pathologic features and no MYC expression by IHC. Additional novel findings included alterations of genes involved in cellular metabolism in 18% of cases, including one IDH2 R172M mutation and two cases with SDHA L649fs* truncating mutations. We also identified several mutations more commonly found in solid tumors and leukemias, including BRAF V600E and KRAS G13D. With respect to genomic rearrangements, combined DNA/RNA capture and sequencing detected translocations/fusions in MYC, BCL2, and BCL6, which were concordant with cytogenetics/FISH analysis. We also identified rearrangements involving TBXL1XR1-P63, NOTCH2, SOCS1, and ETV6. Copy number alterations were detected in 26 different genes, including amplifications of CD274/PDCD1LG2 (PD-L1/PD-L2) (n=4) that were restricted to non-GCB cases. Alterations in TP53 were more frequently observed in transformed (42%) and relapsed/refractory (26%) compared to de novo DLBCL (12%; p=0.007; Pearson’s chi-squared). TP53 mutations predicted for lack of response to chemotherapy, with chemo-refractory disease occurring in 48% of TP53-mutant patients compared to 10% of patients with intact TP53 (p=0.0004; Fisher’s exact). Truncating mutations or deletions of RB1, albeit rare (5% of cases), were the most significant negative prognostic factor and were associated with therapeutic resistance and poor overall survival.Conclusions: Our results demonstrate the utility of comprehensive combined DNA/RNA next-generation sequencing as a promising method to identify clinically relevant GAs in clinical lymphoma specimens. This streamlined approach has the potential to combine multiple molecular and cytogenetic tests into a single platform. Future efforts will be directed at incorporating this approach both retrospectively and prospectively into clinical trials to identify predictive biomarkers to guide therapeutic decisions. [Display omitted] DisclosuresIntlekofer:Foundation Medicine, Inc: Consultancy. Levine:Foundation Medicine, Inc: Consultancy. Zelenetz:Foundation Medicine, Inc: Consultancy. Dogan:Foundation Medicine, Inc: Consultancy. Palomba:Foundation Medicine, Inc: Consultancy. van den Brink:Foundation Medicine, Inc: Consultancy. Brennan:Foundation Medicine, Inc: Employment. Young:Foundation Medicine, Inc: Employment. He:Foundation Medicine: Employment. Nahas:Foundation Medicine, Inc: Employment. Yelensky:Foundation Medicine, Inc: Employment. Otto:Foundation Medicine, Inc: Employment. Lipson:Foundation Medicine, Inc: Employment. Stephens:Foundation Medicine, Inc: Employment. Miller:Foundation Medicine, Inc: Employment. Younes:Foundation Medicine, Inc: Consultancy.

CSNK1E/CTNNB1 Are Synthetic Lethal To TP53 in Colorectal Cancer and Are Markers for Prognosis

Two genes are called synthetic lethal (SL) if their simultaneous mutations lead to cell death, but each individual mutation does not. Targeting SL partners of mutated cancer genes can kill cancer cells specifically, but leave normal cells intact. We present an integrated approach to uncovering SL pairs in colorectal cancer (CRC). Screening verified SL pairs using microarray gene expression data of cancerous and normal tissues, we first identified potential functionally relevant (simultaneously differentially expressed) gene pairs. From the top-ranked pairs, ~20 genes were chosen for immunohistochemistry (IHC) staining in 171 CRC patients. To find novel SL pairs, all 169 combined pairs from the individual IHC were synergistically correlated to five clinicopathological features, e.g. overall survival. Of the 11 predicted SL pairs, MSH2-POLB and CSNK1E-MYC were consistent with literature, and we validated the top two pairs, CSNK1E-TP53 and CTNNB1-TP53 using RNAi knockdown and small molecule inhibitors of CSNK1E in isogenic HCT-116 and RKO cells. Furthermore, synthetic lethality of CSNK1E and TP53 was verified in mouse model. Importantly, multivariate analysis revealed that CSNK1E-P53, CTNNB1-P53, MSH2-RB1, and BRCA1-WNT5A were independent prognosis markers from stage, with CSNK1E-P53 applicable to early-stage and the remaining three throughout all stages. Our findings suggest that CSNK1E is a promising target for TP53-mutant CRC patients which constitute ~40% to 50% of patients, while to date safety regarding inhibition of TP53 is controversial. Thus the integrated approach is useful in finding novel SL pairs for cancer therapeutics, and it is readily accessible and applicable to other cancers.

Relationship of RAS and TP53 predictive value for cetuximab (C) benefit: Results of the EXPERT-C trial.

447 Background: We previously reported that TP53 status may predict C benefit in patients with locally advanced rectal cancer treated with neoadjuvant chemotherapy and chemoradiotherapy (CRT) and this effect appeared to be independent of KRAS. Recent studies indicate that NRAS mutations and KRAS mutations beyond exons 2-3 may also preclude benefit from anti-EGFRs. We analyzed whether the predictive value of TP53 in EXPERT-C was independent of RAS. Methods: 164 patients received 4 cycles of CAPOX followed by CRT, surgery, and 4 cycles of adjuvant CAPOX (n=81) or the same regimen plus C (CAPOX-C, n=83) and were analyzed for KRAS (exons 2-3) and NRAS (exon 3). TP53 mutations (exons 4-9) were screened for by CE-SSCA. KRAS (exon 4) and NRAS (exons 2 and 4) mutations were screened for by bi-directional Sanger sequencing. Progression-free survival (PFS) and overall survival (OS) were estimated with Kaplan-Meier methods and log-rank analysis was used to compare the treatment arms. The interaction between treatment and TP53 was adjusted for prognostic variables and RAS in a multivariate model. Results: 75/144 (52%) eligible patients had a TP53 mutation. 81/86 patients with known KRAS (exons 2-3) and NRAS (exon 3) wild-type (WT) status were analyzed for the remaining RAS mutations. Of these, 11 (13%) had tumours with mutation in KRAS exon 4 (11%) or NRAS exons 2/4 (2%). Overall, 75/144 (52%) patients were RAS WT (CAPOX, n=39; CAPOX-C, n=36). After a median follow-up of 65 months, no difference in PFS (HR 1.21, p=0.59) and OS (HR 0.97, p=0.94) was observed between TP53 mutant patients treated with CAPOX or CAPOX-C. In TP53 WT patients, the addition of C was associated with a statistically significant improvement in PFS (HR 0.23, p=0.02) and OS (HR 0.16, p=0.02). A significant interaction between TP53 status and C effect was found (PFS, p=0.029; OS, p=0.036). In multivariate analyses, this interaction remained significant even after adjusting for RAS status (PFS, p=0.026; OS, p=0.033). Conclusions: In EXPERT-C, the value of TP53 as predictive biomarker for C benefit was independent of RAS. The value of monoallelic vs. biallelic TP53 inactivation will be presented at the meeting.