TP53 Mutation Rate Research Articles

High-Risk TP53 Mutations Are Associated with Extranodal Extension in Oral Cavity Squamous Cell Carcinoma.

Purpose: Development of extranodal extension (ENE) has been associated with poor survival in patients with oral cavity squamous cell carcinoma (OSCC). Here, we sought to confirm the role of ENE as a poor prognostic factor, and identify genomic and epigenetic markers of ENE in order to develop a predictive model and improve treatment selection.Experimental Design: An institutional cohort (The University of Texas MD Anderson Cancer Center) was utilized to confirm the impact of ENE on clinical outcomes and evaluate the genomic signature of primary and ENE containing tissue. OSCC data from The Cancer Genome Atlas (TCGA) were analyzed for the presence of molecular events associated with nodal and ENE status.Results: ENE was associated with decreased overall and disease-free survival. Mutation of the TP53 gene was the most common event in ENE+ OSCC. The frequency of TP53 mutation in ENE+ tumors was higher compared with ENE- tumors and wild-type (WT) TP53 was highly represented in pN0 tumors. pN+ENE+ patients had the highest proportion of high-risk TP53 mutations. Both primary tumors (PT) and lymph nodes with ENE (LN) exhibited a high rate of TP53 mutations (58.8% and 58.8%, respectively) with no significant change in allele frequency between the two tissue sites.Conclusions: ENE is one of the most significant markers of OSCC OS and DFS. There is a shift toward a more aggressive biological phenotype associated with high-risk mutations of the TP53 gene. Prospective clinical trials are required to determine whether TP53 mutational status can be used for personalized treatment decisions. Clin Cancer Res; 24(7); 1727-33. ©2018 AACR.

Abstract P3-04-09: Integrated analysis of genetic variations in Chinese breast cancer from a single institution

Abstract To investigate the characteristics of somatic mutation or copy number variations in Chinese breast cancer, tumor tissues from 105 patients diagnosed at age from 26 to 81 (median age 48) were assessed by next-generation sequencing technology using a customized panel, including 33 genes of putative tumor suppressors or oncogenes. At least one genetic alteration (including mutations, copy number variations and fusion genes) was observed in 99/105 (94%) samples. Similar to the previous report in TCGA dataset, TP53 (49%) and PIK3CA (43%) were the most frequently mutated genes, which occurred in a significant mutual exclusive manner (p<0.05). Three genes including MYC copy number amplification (35%), FGFR1 (19%) and GATA3 mutation (16%) were altered at the frequency of >10% in our dataset, in which the occurrence of MYC amplification was higher than the TCGA cohort (22%, p<0.05). Importantly, we identified four fusion genes of FGFR1 including one previously reported (TACC1-FGFR1) and three novel fusion ones (MIR1268A-FGFR1, LZTS1-AS1-FGFR1, and LINC01605-FGFR1). Unlike the high prevalence of CCND1 amplification (17%) and CDH1 mutations (13%) in TCGA dataset, genetic variations of CCND1 and CDH1 in our study occurred at a low frequency with 2% and 4%, respectively (p<0.05). In addition, we also identified three novel ESR1 mutations (ESR1 G74R, D230H and M250T) in the untreated patients with early breast cancer. Furthermore, nonnegative matrix factorization (NMF) clustering of genetic variations revealed five distinct molecular classes in our dataset. NMF class I was characterized by a high rate of HR+/ERBB2- tumors (80%) and genetic alterations of FGFR1 (100%). A gain of ERBB2 gene was observed in 93% of NMF class II along with TOP2A amplification in 57% of HR+/ERBB2+ tumors. NMF class III was characterized by a high rate of HR+/ERBB2- (95%) and GATA3 mutations (75%) without TP53 mutation. The characteristics of NMF class IV were the high rate of PIK3CA mutations (95%) and HR+/ERBB2- tumors (75%) along with low rate of TP53 mutations. More HR-/ERBB2- tumors (39%) were observed in NMF class V with a high rate of MYC amplification (82%) and TP53 mutation (89%). Further analysis in the TCGA cohort revealed the patients in NMF class V had the shorter survival time than other clusters. Collectively, we identified several novel genetic variations and generated a preliminary profile of somatic genetic aberrations that could classify Chinese breast cancer in this study, and may represent novel therapeutic targets for molecular subsets of breast cancer. This study was supported in part by National Natural Science Foundation of China (8160111571) and Guangdong Natural Science Foundation (2016A030313768). Citation Format: Liao N, Zhang G-C, Wang Y, Cao L, Li K, Ren C-Y, Wen L-Z, Shi Y, Zhu W, Chen X. Integrated analysis of genetic variations in Chinese breast cancer from a single institution [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P3-04-09.

Abstract P1-16-04: Somatic mutations, clinicopathologic characteristics, and survival in patients with untreated breast cancer with bone-only and non-bone sites of first metastasis

Abstract Background: Bone is the most common site of metastasis of breast cancer, and bone metastasis is associated with a high rate of skeletal-related events, all of which contribute to decreased quality of life and poor outcomes. Biological mechanisms of metastasis to bone may be unique, and identification of distinct signaling pathways and somatic mutations may provide biological insight into or rational targets for treatment of and prevention of bone metastasis. The aims of this study were to compare and contrast somatic mutations, clinicopathologic characteristics, and survival in breast cancer patients with bone only versus non-bone as first metastatic site. Methods: Tumor samples were collected from 389 patients who had metastasis and untreated primary breast cancer. In each sample, 46 or 50 cancer-related genes were selectively amplified and analyzed for mutations by AmpliSeq Ion Torrent next-generation sequencing. We used Fisher's exact test to identify somatic mutations associated with bone-only first metastasis and logistic regression models to identify differences in clinicopathologic characteristics, survival, and somatic mutations between patients with bone-only first metastasis and patients with first metastasis in non-bone sites only (“other-only first metastasis”). Results: Among the 389 patients, the first metastasis was located in bone only in 72 patients (18.5%), non-bone sites only in 223 patients (57.3%), and both in 94 patients (24.2%). Of the cancer-related genes analyzed, the most commonly mutated were TP53 (N=103), PIK3CA (N=79), AKT (N=13), and PTEN (N=2). Compared to patients with other-only first metastasis, patients with bone-only first metastasis had higher rates of hormone-receptor-positive disease, non-triple-negative subtype, and low nuclear grade (grade 1 or 2) (all 3 comparisons, p<0.001); had a lower ratio of cases of invasive ductal carcinoma to cases of invasive lobular carcinoma (p=0.002); and tended to have a higher 5-year overall survival (OS) rate (78.2% [95% confidence interval (CI), 68.6%-89.0%] vs 55.0% [95% CI, 48.1%-62.9%]; p=0.051). However, in the subgroup of patients with TP53 mutation and in the subgroup of patients with PIK3CA mutation, OS did not differ between patients with bone-only and other-only first metastasis (p=0.49 and p=0.68; respectively). In univariate analysis, the rate of TP53 mutation tended to be lower in patients with bone-only first metastasis than in those with other-only first metastasis (15.3% vs 29.1%; p=0.051). In multivariate analysis, TP53 mutation was not significantly associated with site of first metastasis (p=0.54) but was significantly associated with hormone-receptor-negative disease (p<0.001). Conclusions: We did not find associations between somatic mutations and bone-only first metastasis in patients with untreated breast cancer. Patients with bone-only first metastasis have longer OS than patients with other-only first metastasis. More comprehensive molecular analysis may be needed to further understand the factors associated with bone-only metastatic disease in breast cancer. Citation Format: Kono M, Fujii T, Matsuda N, Harano K, Chen H, Wathoo C, Aron JY, Tripathy D, Meric-Bernstam F, Ueno NT. Somatic mutations, clinicopathologic characteristics, and survival in patients with untreated breast cancer with bone-only and non-bone sites of first metastasis [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P1-16-04.

Abstract GS1-05: Tandem duplicator phenotypes define 50% of triple negative breast cancers

Abstract Background. We recently discovered a unique chromotype, the Tandem Duplicator Phenotype (TDP), characterized by hundreds of somatic tandem duplications (TDs) scattered throughout the genome of a large percentage of triple negative breast cancers (TNBCs). Importantly, we observed that the TDP associates with a better response to cisplatin therapy in vitro and in vivo, suggesting that it is a tractable and quantitative biomarker of response to platinum-based therapy. Here, we expand on our initial findings by analyzing Whole-Genome (WG) sequences of over 2,700 tumors. Methods. TD coordinates from WG sequences relative to 2717 tumors were assembled from over 30 independent studies representing several cancer types, including 254 TNBCs. WG sequencing of mouse breast tumors was carried out using standard Illumina protocols. The number, distribution and span-size of somatic TDs from a training set of 992 tumors were used to develop a TDP classifier that identifies highly recurrent but clearly distinct TDP profiles. The TDP classifier was then applied to the remaining tumor sequences. WG mutation and copy number datasets were investigated to identify the genetic drivers associated with each TDP profile, and the genomic consequences of different TDPs were evaluated through identification of genomic hotspots for gene duplication and transection. Results. We describe six different TDPs featuring distinct TD span size distributions, with peaks at 10Kb (group 1), 300Kb (group 2) and 3Mb (group 3), or different combinations of these (mix12, mix13 and mix23). More than half of all TNBC display a TDP. Of these, 55% classify as group 1, 14% as group 2 and 15% as group mix12. Whereas all TDP groups show a higher TP53 mutation rate compared to non-TDP tumors, each TDP profile is characterized by specific additional gene perturbations, with loss of BRCA1 occurring in groups 1, mix12 and mix13; CCNE1 amplification in group 2; and CDK12 mutations in group mix23. We show that different TDPs are subject to the perturbation of specific oncogenic networks resulting from the duplication of oncogenes by larger TDs (>300Kb) or the disruption of tumor suppressors via double transections by shorter TDs (10Kb). Indeed, tumor suppressor genes such as PTEN, RB1 and MLL3 are frequently disrupted by TDs in TNBC TDP group 1 tumors, whereas TNBC TDP group 2 tumors commonly feature duplication of oncogenes such as MYC and MALAT1. Finally, through WG analyses of 18 mouse models (GEMMs) of breast cancer, we provide the first mechanistic evidence of the driving role of conjoint loss of TP53 and BRCA1, but not of BRCA2, in inducing the TDP group 1 profile. Conclusions. Our study shows a definitive genetic induction of one specific form of TDP (group 1) characterized by 10kb TD span. Different TDP profiles are characterized by alternative somatic genetic origins but always couple with disruptive TP53 mutations. The consequences of the massive TD formation in TDP TNBCs suggest a systems strategy to tumor induction involving heterogeneous combinations of oncogenes and tumor suppressors. That these TDP forms, accounting for ˜50% of TNBC, are associated with significant sensitivity to cisplatin suggest that this chromotype may identify TNBC patients who would benefit from upfront platinum-based chemotherapy. Citation Format: Liu ET, Menghi F, Barthel F, Yadav V, Tang M, Ji B, Carter G, Jonkers J, Verhaak R. Tandem duplicator phenotypes define 50% of triple negative breast cancers [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr GS1-05.

Genomic Landscape and Endocrine-Resistant Subgroup in Estrogen Receptor-Positive, Progesterone Receptor-Negative, and HER2-Negative Breast Cancer.

Estrogen receptor-positive, progesterone receptor-negative, and human epidermal growth factor receptor 2 (HER2)-negative (ER+PR-HER2-) breast cancer comprise a special type of breast cancer that constitutes ~10% of all breast cancer patients. ER+PR-HER2- tumor benefits less from endocrine therapy, while its genomic features remain elusive. In this study, we systematically assessed the multiomic landscape and endocrine responsiveness of ER+PR-HER2- breast cancer.Methods: This study incorporated five cohorts. The first and second cohorts were from the Surveillance, Epidemiology, and End Results database (n=130,856) and Molecular Taxonomy of Breast Cancer International Consortium (n=1,055) for analyzing survival outcomes and endocrine responsiveness. The third cohort was from The Cancer Genome Atlas (n=630) for multiomic analysis and endocrine-resistant subgroup exploration. The fourth cohort, from the MD Anderson database (n=92), was employed to assist gene selection. The fifth cohort was a prospective observational cohort from Fudan University Shanghai Cancer Center (n=245) that was utilized to validate the gene-defined subgroup by immunohistochemistry (IHC).Results: Clinically, ER+PR-HER2- tumors showed lower endocrine responsiveness than did ER+PR+HER2- tumors. Genomically, copy number loss or promoter methylation of PR genes occurred in 75% of ER+PR-HER2- tumors, collectively explaining PR loss. ER+PR-HER2- tumors had higher TP53 (30.3% vs. 17.0%) and lower PIK3CA mutation rates (25.8% vs. 42.7%) and exhibited more ZNF703 (21.5% vs. 13.6%) and RPS6KB1 (18.5% vs. 7.8%) amplification events than ER+PR+HER2- tumors. Among ER+PR-HER2- tumors, nearly 20% were of the PAM50-defined non-luminal-like subgroup and manifested lower endocrine sensitivity scores and enriched biosynthesis, metabolism and DNA replication pathways. We further identified the non-luminal-like subgroup using three IHC markers, GATA3, CK5, and EGFR. These IHC-defined non-luminal-like (GATA3-negative, CK5-positive and/or EGFR-positive) tumors received limited benefit from adjuvant endocrine therapy.Conclusion: ER+PR-HER2- breast cancer consists of clinically and genomically distinct groups that may require different treatment strategies. The non-luminal-like subgroup was associated with reduced benefit from endocrine therapy.

Somatic mutations, clinicopathologic characteristics, and survival in patients with untreated breast cancer with bone-only and non-bone sites of first metastasis.

Background: Bone is the most common site of metastasis of breast cancer. Biological mechanisms of metastasis to bone may be different from mechanisms of metastasis to non-bone sites, and identification of distinct signaling pathways and somatic mutations may provide insights on biology and rational targets for treatment and prevention of bone metastasis. The aims of this study were to compare and contrast somatic mutations, clinicopathologic characteristics, and survival in breast cancer patients with bone-only versus non-bone sites of first metastasis.Methods: Primary tumor samples were collected before treatment from 389 patients with untreated primary breast cancer and distant metastasis at diagnosis. In each sample, 46 or 50 cancer-related genes were analyzed for mutations by AmpliSeq Ion Torrent next-generation sequencing. Fisher's exact test was used to identify somatic mutations associated with bone-only first metastasis. Logistic regression models were used to identify differences in detected somatic mutations, clinicopathologic characteristics, and survival between patients with bone-only first metastasis and patients with first metastasis in non-bone sites only (“other-only first metastasis”).Results: Among the 389 patients, 72 (18.5%) had bone-only first metastasis, 223 (57.3%) had other-only first metastasis, and 94 (24.2%) had first metastasis in both bone and non-bone sites. The most commonly mutated genes were TP53 (N=103), PIK3CA (N=79), AKT (N=13), and PTEN (N=2). Compared to patients with other-only first metastasis, patients with bone-only first metastasis had higher rates of hormone-receptor-positive disease, non-triple-negative subtype, and lower grade (grade 1 or 2; Nottingham grading system) (all three comparisons, p<0.001); had a lower ratio of cases of invasive ductal carcinoma to cases of invasive lobular carcinoma (p=0.002); and tended to have a higher 5-year overall survival (OS) rate (78.2% [95% confidence interval (CI), 68.6%-89.0%] vs 55.0% [95% CI, 48.1%-62.9%]; p=0.051). However, in the subgroup of patients with TP53 mutation and in the subgroup of patients with PIK3CA mutation, OS did not differ between patients with bone-only and other-only first metastasis (p=0.49 and p=0.68, respectively). In univariate analysis, the rate of TP53 mutation tended to be lower in patients with bone-only first metastasis than in those with other-only first metastasis (15.3% vs 29.1%; p=0.051). In multivariate analysis, TP53 mutation was not significantly associated with site of first metastasis (p=0.54) but was significantly associated with hormone-receptor-negative disease (p<0.001).Conclusions: We did not find associations between somatic mutations and bone-only first metastasis in patients with untreated breast cancer. Patients with bone-only first metastasis tend to have longer OS than patients with other-only first metastasis. More comprehensive molecular analysis may be needed to further understand the factors associated with bone-only metastatic disease in breast cancer.

PRIMA-1 induces p53-mediated apoptosis by upregulating Noxa in esophageal squamous cell carcinoma with TP53 missense mutation.

TP53 is associated with the resistance of cytotoxic treatment and patient prognosis, and the mutation rate of TP53 in esophageal squamous cell carcinoma (ESCC) is extraordinarily high, at over 90%. PRIMA‐1 (p53 re‐activation and induction of massive apoptosis) has recently been reported to restore the function of mutant TP53; however, its antitumor effect and mechanism in ESCC remain unclear. After evaluating the TP53 mutation status of a panel of 11 ESCC cell lines by Sanger sequencing, we assessed the in vitro effect of PRIMA‐1 administration on cells with different TP53 status by conducting cell viability and apoptosis assays. The expression levels of proteins in p53‐related pathways were examined by Western blotting, while knockdown studies were conducted to investigate the mechanism underlying PRIMA‐1's function. An ESCC xenograft model was further used to evaluate the therapeutic effect of PRIMA‐1 in vivo. PRIMA‐1 markedly inhibited cell growth and induced apoptosis by upregulating Noxa expression in ESCC cell lines with TP53 missense mutations, whereas no apoptosis was induced in ESCC with wild‐type TP53 and TP53 with frameshift and nonsense mutations. Importantly, the knockdown of Noxa canceled the apoptosis induced by PRIMA treatment in ESCC cell lines with TP53 missense mutations. PRIMA‐1 administration, compared with placebo, showed a significant antitumor effect by inducing Noxa in the xenograft model of an ESCC cell line with a TP53 missense mutation. PRIMA‐1 exhibits a significant antitumor effect, inducing massive apoptosis through the upregulation of Noxa in ESCC with TP53 missense mutations.

Prior systemic treatment increased the incidence of somatic mutations in metastatic breast cancer

BackgroundUnderstanding the biology of breast cancer is important for guiding treatment strategies and revealing resistance mechanisms. Our objectives were to investigate the relationship between previous systemic therapy exposure and mutational spectrum in metastatic breast cancer and to identify clinicopathological factors associated with identified frequent somatic mutations. MethodsArchival tissues of patients with metastatic breast cancer were subjected to hotspot molecular testing by next-generation sequencing. The variables that significantly differed (P < 0.05) in univariate analysis were selected to fit multivariate models. Logistic models were fit to estimate the association between mutation status and clinical variables of interest. Five-fold cross-validation was performed to estimate the prediction error of each model. ResultsA total of 922 patients were included in the analysis. In multivariate analysis, previous systemic treatment before molecular testing (N = 186) was associated with a significantly higher rate of TP53 and PIK3CA mutations compared with the lack of systemic treatment (P < 0.001 for both). ConclusionSystemic treatment exposure is an independent risk factor for high rates of TP53 and PIK3CA mutation, which suggests the importance of testing samples after systemic therapy to accurately assess mutations. It is worth testing the gene profile when tumours become resistant to systemic treatments.

Clinical significance of YAP1 activation in head and neck squamous cell carcinoma.

By analyzing the genomic data of head and neck squamous cell cancer (HNSCC), we investigated clinical significance of YAP1 activation. Copy number and mRNA expression of YAP1 were analyzed together to assess clinical relevance of YAP1 activation in HNSCC. The clinical significance of YAP1 activation was further validated in four independent test cohorts. We also assessed the correlation of YAP1 activation with genomic alterations such as copy number alteration, somatic mutation, and miRNA expression. The YAP1-activated (YA) subgroup showed worse prognosis for HNSCC as tested and validated in five cohorts. In a multivariate risk analysis, the YAP1 signature was the most significant predictor of overall survival. The YAP1-inactivated (YI) subgroup was associated with HPV-positive status. In multiplatform analysis, YA tumors had gain of EGFR and SNAI2; loss of tumor-suppressor genes such as CSMD1, CDKN2A, NOTCH1, and SMAD4; and high mutation rates of TP53 and CDKN2A. YI tumors were characterized by gain of PIK3CA, SOX2, and TP63; deletion of 11q23.1; and high mutation rates of NFE2L2, PTEN, SYNE1, and NSD1. YA tumors also showed weaker immune activity as reflected in low IFNG composite scores and YAP1 activity is negatively associated with potential response to treatment of pembrolizumab. In conclusion, activation of YAP1 is associated with worse prognosis of patients with HNSCC and potential resistance to immunotherapy.

Human hepatocellular carcinomas with a periportal phenotype have the lowest potential for early recurrence after curative resection.

Well-differentiated HCCs display mutually exclusive periportal or perivenous zonation programs. Among all HCCs, periportal-type tumors have the lowest intrinsic potential for early recurrence after curative resection. (Hepatology 2017;66:1502-1518).

Somatic Mutations and Ancestry Markers in Hispanic Lung Cancer Patients.

To address the lack of genomic data from Hispanic/Latino (H/L) patients with lung cancer, the Latino Lung Cancer Registry was established to collect patient data and biospecimens from H/L patients. This retrospective observational study examined lung cancer tumor samples from 163 H/L patients, and tumor-derived DNA was subjected to targeted-exome sequencing (>1000 genes, including EGFR, KRAS, serine/threonine kinase 11 gene [STK11], and tumor protein p53 gene [TP53]) and ancestry analysis. Mutation frequencies in this H/L cohort were compared with those in a similar cohort of non-Hispanic white (NHW) patients and correlated with ancestry, sex, smoking status, and tumor histologic type. Of the adenocarcinomas in the H/L cohort (n= 120), 31% had EGFR mutations, versus 17% in the NHW control group (p < 0.001). KRAS (20% versus 38% [p= 0.002]) and STK11 (8% versus 16% [p= 0.065]) mutations occurred at lower frequency, and mutations in TP53 occurred at similar frequency (46% versus 40% [p= 0.355]) in H/L and NHW patients, respectively. Within the Hispanic cohort, ancestry influenced the rate of TP53 mutations (p= 0.009) and may have influenced the rate of EGFR, KRAS, and STK11 mutations. Driver mutations in H/L patients with lung adenocarcinoma differ in frequency from those in NHW patients associated with their indigenous American ancestry. The spectrum of driver mutations needs to be further assessed in the H/L population.

Vulvar Squamous Cell Carcinoma (VSCC) as Two Diseases: HPV Status Identifies Distinct Mutational Profiles Including Oncogenic Fibroblast Growth Factor Receptor 3.

Purpose: Patients with advanced or recurrent invasive vulvar squamous cell carcinoma (VSCC) have limited treatment options and a grave prognosis. Understanding the genomic landscape may facilitate the identification of new therapies and improve clinical outcomes.Experimental Design: A retrospective chart review and molecular analysis of patients with VSCC from 2000 to 2016 was performed at the Ottawa Hospital Research Institute. The presence of oncogenic human papillomavirus (HPV) was determined by nested PCR and amplified DNA was sequenced using the Ion AmpliSeq Cancer Hotspot v2 Panel. The patients were divided into two groups according to HPV status (HPV-positive versus HPV-negative) and clinical outcome correlated with mutation status using descriptive statistics.Results: In 43 VSCC patients, there was a high mutation rate in both HPV-positive (73%) and HPV-negative (90%) disease with the two subgroups expressing distinct genetic profiles. HPV-positive tumors were characterized by oncogenic mutations in PIK3CA (27%), FGFR3 (14%), and PTEN (9%), whereas HPV-negative tumors were found to have mutations in TP53 (57%), HRAS (24%), PI3KCA (19%), and CDKN2A (14%). Mutation S249C in FGFR3 occurred in 14% of HPV-positive tumors. While there were notable differences in the occurrence of TP53, HRAS, PTEN, and FGFR3 mutations according to HPV status, only the rate of TP53 mutations was statistically significant (P = 0.0004). No significant difference in prognosis was found between patients with HPV-positive and HPV-negative VSCC.Conclusions: HPV-positive VSCC is characterized by oncogenic FGFR3 mutations that helps classify this subtype as a separate disease. Inhibitors of FGFR3 merit consideration as a therapeutic strategy in this neglected cancer in women. Clin Cancer Res; 23(15); 4501-10. ©2017 AACR.

Abstract 3855: Excavation of therapeutic targets based on the molecular signature of patient-derived tumor xenografts in gastric cancer

Abstract Objective: The optimal preclinical models in new targeted drug development are patient-derived tumor xenografts (PDXs) models with definite molecular signatures, which will be excavated and validated in this study. Methods: The genomic profiles of 50 PDXs from advanced gastric cancer (AGC) were analyzed by targeted next-generation sequencing. The Epstein-Barr virus (EBV) infection, microsatellite instability (MSI) status, and expressions of EGFR, HER3, c-Met, PTEN and c-Myc were determined by in situ hybridization and immunohistochemisty, respectively. Results: A total of 581 non-synonymous single nucleotide variations (SNV), 513 Indels, and 225 amplifications were identified in 50 PDXs. Pathway analysis revealed recurrent alterations in the MAPK signaling, ErbB signaling, VEGF signaling, mTOR signaling and cell cycle pathway. The ErbB family amplified in 8% (EGFR), 10% (ERBB2), 2% (ERBB3) and 2% (ERBB4) of the 50 PDXs respectively. Meanwhile, several activating mutations in EGFR (L858R and G719S), ERBB3 (P1212S) and ERBB4 (R1174Q) were also detected in our study. Moreover, we detected 7 PDXs harboring PIK3CA activating mutations (E545K, Q546K, H1047R) and 2 PDXs with PTEN loss. Whether PI3K/Akt/mTOR inhibitors could turn over the primary or acquired resistance of anti-HER2 therapies remains further researches. Genes in the cell cycle pathway altered in 70% of the 50 PDXs. The mutation rates of TP53, BRCA1 and BRCA2 were 28%, 8% and 14%. We also detected amplifications of CCNE1, CCND1 and MYC in 16%, 6% and 20% of the xenografts. In this study, 9 PDXs (18%) were EBV positive, with frequent alterations of ARID1A but rare mutations of TP53, and a robust expression of PD-L1. However, we didn’t observe any loss of MMR protein expressions. Conclusions: Several potential therapeutic targets were identified based on the molecular signature of PDXs in advanced gastric cancer, which will provide evidences for drug development. Citation Format: Zuhua Chen, Jing Gao, Lin Shen. Excavation of therapeutic targets based on the molecular signature of patient-derived tumor xenografts in gastric cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3855. doi:10.1158/1538-7445.AM2017-3855

Abstract 1766: Distinct pattern of alterations in tp53 mutated and wild type acute myeloid leukemia (AML) patients

Abstract Background: Mutations in TP53 gene predict a poor prognosis in patients with AML. The reported TP53 mutation rate in AML is low (2.1%) by contrast AML with a complex karyotype (CK) is higher (69-78%) and have a poor outcome. Quite common is to found paired TP53 mutation together and a segmental 17p deletion. Aims: To investigate the frequency, the types of mutations, the associated cytogenetic, the correlation with known molecular alterations and the prognostic role TP53 mutations in adult AML pts. Moreover we would identify genes/pathways that are mainly affected in the mutated TP53 group compared to the wt one. Patients and Methods: 258 adult AML pts with miscellaneous cytogenetic abnormalities and normal karyotype were examined in our Institution for TP53 mutations using several methods, including Sanger sequencing, NGS and HiSeq2000 platform and were correlated with cytogenetic analysis. 124/258 samples were genotyped with SNP arrays (Affymetrix, 3 250K, 43 SNP 6.0, 78 CytoScan HD). Copy Number Alterations (CNAs) analyses were performed using Chromosome Analysis Suite (Affymetrix) and Nexus Copy Number (BioDiscovery) software. Results: Mutation analysis detected TP53 mutations on 39 patients with 48 different types of mutations (32 deleterious point mutations; 4 deletions); nine pts have 2 mutations. We found 34/48 (70%) missense mutations, 5 mutations in the splice sites, 4 deletions ,2 intronic and and 3 others mutations. The mutation rate is of 15.1%. Mostly (28/39) of the TP53 mutated pts (71.8%) had CK while only 11/39 (28.2%) mutated pts have “no CK” (P&amp;gt;0.0001). Alterations of TP53 were significantly associated with poor outcome (OS and EFS p&amp;lt;0.0001). To take advantage of different methodological characteristics, on TP53 locus, we matched two software and cytogenetic analysis results. We identify 16 mutated pts that were also deleted and one pt that presented only a deletion. Therefore 50% of mutated pts present a concomitant deletion. OS of TP53 mutated and deleted pts is statistically inferior respect to muted pts (p&amp;lt;0.0061). Comparing 32 TP53 mutated and 92 TP53 wt pts CNAs results that: a) chromosomes significantly alterated are 5q, 17p, 12p, 16q, 22q13.33 and 7q; b) over 900 genes are differentially involved (all in Loss); c) and that pathway categories mainly enriched are Signal Transduction, Metabolism, Immune System, Transmembrane transport of small molecules, Gene expression, Cell Cycle. Conclusions: Our data demonstrated that TP53 mutations occur in 15.1% of AML with a higher frequency in the subgroup of CK-AML (p&amp;lt;0.0001). They predicted to be deleterious and significantly correlated with worse prognosis especially if TP53 is both mutated and also deleted. For these reasons, TP53 mutation/deletion screening should be recommended. Different pattern of alterations in mutated and wt groups have to be deeper investigated. ELN, AIL, AIRC, progetto Regione-Università 2010-12 (L. Bolondi), FP7 NGS-PTL project. Citation Format: Anna Ferrari, Eugenio Fonzi, Maria Chiara Fontana, Andrea Ghelli Luserna Di Rorà, Marco Manfrini, Antonella Padella, Carmen Baldazzi, Cristina Papayannidis, Giovanni Marconi, Stefania Paolini, Viviana Guadagnuolo, Margherita Perricone, Valentina Robustelli, Enrica Imbrogno, Eugenia Franchini, Claudia Venturi, Elisa Zuffa, Maria Chiara Abbenante, Giorgia Simonetti, Nicoletta Testoni, Emanuela Ottaviani, Martinelli Giovanni. Distinct pattern of alterations in tp53 mutated and wild type acute myeloid leukemia (AML) patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1766. doi:10.1158/1538-7445.AM2017-1766

Gender-related prognostic value and genomic pattern of intra-tumor heterogeneity in colorectal cancer.

Intra-tumor heterogeneity (ITH) is crucial in tumorigenesis and resistance to target therapy. Here, we used mutant-allele tumor heterogeneity (MATH) to measure ITH based on next-generation sequencing data and high MATH was proven as an independent risk prognostic factor in male CRC patients in both a training set of 284 colorectal cancer (CRC) patients with from The Cancer Genome Atlas (TCGA) and a validating set of 187 CRC patients from International Cancer Genome Consortium (ICGC). Further, the genomic pattern according to MATH demonstrated that mutation rates of TP53, IRF5 and KRAS were independently associated with MATH, and the latter two were only significant in male patients. As MATH increased, the fraction of somatic copy number alteration (SCNA) elevated. Moreover, more SCNA events was independently associated with MATH in male than in female. WNT pathway, TGF-β pathway and DNA repair deficiency was enriched in high MATH group and the latter two showed up only in male patients. In summary, we reveal the gender-related prognostic value of MATH and relevant genomic pattern in CRC. Potential mechanisms are provided and it remains to be proven whether they are drivers of subclone formation and ITH. Taking MATH into consideration in clinical trial might contribute to better therapeutic strategies in CRC with researches added on in the future.

Colorectal cancer: Impact of primary tumor location on genetic alterations.

3578 Background: Recent data show that patients with left sided colon tumors (LT) have better survival and respond differently to biologics compared to patients with right-sided tumors (RT), likely due to molecular differences. We sought to examine these differences. Methods: Primary colorectal tumors (n = 1730) with origins clearly defined as RT (cecum to hepatic flexure; n = 273), LT (splenic flexure to sigmoid colon; n = 585), or rectal (RC; n = 872) were examined by NextGen sequencing, protein expression and gene amplification. Tumor mutational load (TML) was calculated in 1001 of these tumors using only somatic nonsynonymous missense mutations. Chi-square was used for comparison. Results: When compared to LT, RT carried a significantly higher rate of BRAF (25% vs 7%; p &lt; 0.0001), PTEN (5.4% vs 1.3%; p = 0.008), and ATM (4% vs 1%; p = 0.04) mutations. RT were likely to have more MSI-high tumors (22% vs 5%; p &lt; 0.0001) and PD-1 overexpression (58% vs 44%; p = 0.01). There were no differences in the rate of KRAS (50% vs 42%; p = 0.07) or NRAS mutations (2.2% vs 3.4%; p = 0.4). When compared to RC, RT had a higher rate of BRAF (25% vs 3%; p = 7E-07), PIK3CA (22% vs 11%; p = 0.001), CTNNB1 (3% vs 0.3%; p = 0.02); ATM (3% vs 1%; p = 0.04), PTEN (5% vs 1%; p = 0.004), and BRCA1 mutations (4% vs 0%; p = 0.02), and a lower rate of TP53 (56% vs 71%; p = 0.001) and APC (53% vs 66%; p = 0.003) mutations. When compared to RC, LT showed higher rates of BRAF (6.7% vs 3.2%; p = 0.04) and CTNNB1 (2.1% vs 0.3%; p = 0.04) mutations, and a higher rate of MSI-high tumors (4.6% vs 0.7%; p = 0.04), whereas RC had a higher rate of KRAS mutation (50% vs 42%; p = 0.04). There were no differences between RT, LT, and RC for the frequency of PD-L1 (2%, 2%, and 1%) or Her-2 (1%, 2%, and 3%) overexpression, although Her-2 amplification was significantly different (1%, 3%, and 5%, RT vs RC; p = 0.03). Mean TML was 12, 11, and 8 mutations/megabase for RT, LT, and RC, respectively (RT vs RC; p = 0.01). There was a correlation between TML and PD-L1 (p = 0.04) and PD-1 (p = 0.01). Conclusions: Tumors arising in the right colon carry genetic alterations that are different from LT as well as RC. However, it appears that CRCs carry a continuum of molecular alterations from the right to the left side, rather than displaying sharp, clear-cut differences.

Abstract P2-02-04: Li-Fraumeni syndrome in females with early onset breast cancer in a Mexican population

Abstract Background: Breast cancer in Mexican patients presents in average 10 year earlier compared to other populations. Among patients with TP53 mutations, breast cancer is the most common malignancy. In this study we aim to determine the rate of TP53 mutations among young Mexican breast cancer patients. Methods: Breast cancer patients younger that 45 were retrospectively identified, only patients without BRCA1/2 mutations were included. Clinical records and pedigrees were reviewed. Next generation sequencing test for TP53 was performed from blood specimens. All pathogenic mutations were confirmed by Sanger sequencing and verified if were included in the IACR TP53 database. Results: Among the 78 patients younger than 45yo evaluated and tested with next generation sequencing, we identified 5 patients with a TP53 mutation (6.4%). All were younger than 36 corresponding to a rate of 9.4% of mutations in this group of individuals (n = 53). Two, not previously described, frameshift mutations were found (c.291delC and c.273dupG) and three missense mutations (c.844C&amp;gt;T, c.517G&amp;gt;A, c.604C&amp;gt;T). A VUS c.672G&amp;gt;A that causes a silent mutation in a splicing-donor site was identified. All patients with a TP53 mutation had locally advanced disease and tumors were high grade and Her2 positive. Conclusions: Among Mexican women younger than 45yo, the rate of TP53 mutations was higher than in other populations where it's estimated to be 1%. Among patients younger than 36 the proportion was even higher. All patients had a family history suggestive of Li-Fraumeni syndrome. The VUS found in our series needs a deeper analysis (family segregation, structure and function of the resulting protein). Our results support the international recommendation of performing molecular testing for TP53 in breast cancer patients younger than 35 years. Identification of patients with TP53 mutation has important prognostic, therapeutic and quality of life implications for the proband in addition of the risk reduction strategies and intensive surveillance recommended in their families. Citation Format: Gallardo-Alvarado LN, Cantu-De Leon DF, Tusie-Luna T, Tusie-Luna I, Diaz-Chavez J, Herrera EM, Chavez-MacGregor M, Bargallo-Rocha E, Villarreal C, Herrera.Montalvo LA, Segura-Kato YX. Li-Fraumeni syndrome in females with early onset breast cancer in a Mexican population [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P2-02-04.

Abstract P1-06-07: Clinical and molecular relevance of intra-tumor genetic heterogeneity in breast cancer: Integrative analysis of data from The Cancer Genome Atlas

Abstract Background: Intra-tumor heterogeneity (ITH) plays a pivotal role in driving breast cancer progression and therapeutic resistance. Emerging evidence has indicated that the extent of genetic heterogeneity may serve as a clinically useful biomarker. While several studies have suggested the prognostic value of ITH in several cancer types, the clinical significance of genetic ITH and molecular portraits that correlated with different ITH levels were poorly understood in breast cancer. The establishment of algorithms estimating genetic ITH based on sequencing of bulk tumor DNA offered us an opportunity to explore the clinical implication of ITH in large breast cancer cohorts and, for the first time, to use integrative genomic analyses to reveal molecular portraits related to intra-tumor genetic heterogeneity. Methods: We assessed 916 female breast cancer patients from The Cancer Genome Atlas. Mutant-allele tumor heterogeneity (MATH) values were calculated from whole-exome sequencing data. We used integers nearest to the tertiles of the MATH values as cutoff points to divide the patients into three groups nearly equal in size. The association between MATH value and clinical characteristics was evaluated, followed by survival analyses in these different MATH groups. We then compared the rates of total non-silent somatic mutations among the different MATH groups, and further determined the mutations independently associated with high MATH by logistic regression adjusting for T classification and clinical subtypes. Similar methods, superadding somatic copy number alteration (SCNA) burden in logistic model, were used to evaluate SCNA events that were significantly associated with high MATH level. Gene enrichment between the high and rest MATH groups was analyzed using Gene Set Enrichment Analysis. Results: The patients were divided into low (MATH value lower than 33), intermediate (MATH between 33 and 46) and high (MATH higher than 46) MATH groups. High T stage, African American race, and triple-negative or basal-like subtype were associated with a higher MATH level (all P&amp;lt;0.001). In hormone receptor-positive and human epidermal growth factor receptor-negative patients, the high MATH group showed a tendency toward a worse overall survival (P=0.052); however, while in triple-negative breast cancer, both high and low MATH indicated a worse outcome (P=0.032). Furthermore, the TP53 mutation rate increased as MATH was elevated (P&amp;lt;0.001), whereas CDH1 mutations were correlated with a lower level of MATH (P=0.002). Several focal and arm-level SCNA events were more common in the high MATH group, including Chr8q24 with only the MYC gene in the “peak” region. Similarly, high MATH was associated with gene set enrichment related to the MYC pathway and proliferation. Conclusion: Our study extended the knowledge concerning the clinical role of ITH in breast cancer, especially the distinct pattern of prognostic values in different clinical subtypes, which may help promote the clinical utilization of genetic ITH. Our attempt at exploring the molecular features related to ITH might provide clues for the source and consequences of ITH, inspiring subsequent experiments investigating the laws underling tumor heterogeneity. Citation Format: Ma D, Jiang Y-Z, Liu X-Y, Liu Y-R, Yu K-D, Shao Z-M. Clinical and molecular relevance of intra-tumor genetic heterogeneity in breast cancer: Integrative analysis of data from The Cancer Genome Atlas [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-06-07.

Clinical and molecular relevance of mutant-allele tumor heterogeneity in breast cancer.

Intra-tumor heterogeneity (ITH) plays a pivotal role in driving breast cancer progression and therapeutic resistance. We used a mutant-allele tumor heterogeneity (MATH) algorithm to measure ITH and explored its correlation with clinical parameters and multi-omics data. We assessed 916 female breast cancer patients from The Cancer Genome Atlas. We calculated the MATH values from whole-exome sequencing data and further investigated their correlation with clinical characteristics, somatic mutations, somatic copy number alterations (SCNAs), and gene enrichment. The patients were divided into low, intermediate, and high MATH groups. High T stage, African American race, and triple-negative or basal-like subtype were associated with a higher MATH level (all P<0.001). In hormone receptor-positive and human epidermal growth factor receptor-negative patients, the high MATH group showed a tendency toward a worse overall survival (P=0.052); Furthermore, the TP53 mutation rate increased as MATH was elevated (P<0.001), whereas CDH1 mutations were correlated with a lower level of MATH (P=0.002). Several focal and arm-level SCNA events were more common in the high MATH group (P<0.05), including Chr8q24 with only the MYC gene in the "peak" region. Similarly, high MATH was associated with gene set enrichment related to the MYC pathway and proliferation. Our integrative analysis reveals the clinical and genetic relevance of ITH in breast cancer. These results also suggest the origin and natural history of clonal evolution and intra-tumor genetic heterogeneity, which warrant further investigation.

Molecular spectrum of KRAS, NRAS, BRAF, PIK3CA, TP53, and APC somatic gene mutations in Arab patients with colorectal cancer: determination of frequency and distribution pattern.

The frequency rates of mutations such as KRAS, NRAS, BRAF, and PIK3CA in colorectal cancer (CRC) differ among populations. The aim of this study was to assess mutation frequencies in the Arab population and determine their correlations with certain clinicopathological features. Arab patients from the Arab Gulf region and a population of age- and sex-matched Western patients with CRC whose tumors were evaluated with next-generation sequencing (NGS) were identified and retrospectively reviewed. The mutation rates of KRAS, NRAS, BRAF, PIK3CA, TP53, and APC were recorded, along with clinicopathological features. Other somatic mutation and their rates were also identified. Fisher's exact test was used to determine the association between mutation status and clinical features. A total of 198 cases were identified; 99 Arab patients and 99 Western patients. Fifty-two point seven percent of Arab patients had stage IV disease at initial presentation, 74.2% had left-sided tumors. Eighty-nine point two percent had tubular adenocarcinoma and 10.8% had mucinous adenocarcinoma. The prevalence rates of KRAS, NRAS, BRAF, PIK3CA, TP53, APC, SMAD, FBXW7 mutations in Arab population were 44.4%, 4%, 4%, 13.1%, 52.5%, 27.3%, 2% and 3% respectively. Compared to 48.4%, 4%, 4%, 12.1%, 47.5%, 24.2%, 11.1% and 0% respectively in matched Western population. Associations between these mutations and patient clinicopathological features were not statistically significant. This is the first study to report comprehensive hotspot mutations using NGS in Arab patients with CRC. The frequency of KRAS, NRAS, BRAF, TP53, APC and PIK3CA mutations were similar to reported frequencies in Western population except SMAD4 that had a lower frequency and higher frequency of FBXW7 mutation.