151
|
Duffy MJ, Synnott NC, Crown J. Mutant p53 in breast cancer: potential as a therapeutic target and biomarker. Breast Cancer Res Treat 2018; 170:213-219. [PMID: 29564741 DOI: 10.1007/s10549-018-4753-7] [Citation(s) in RCA: 126] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 03/13/2018] [Indexed: 12/21/2022]
Abstract
OBJECTIVE The aim of this article is to discuss mutant p53 as a possible therapeutic target and biomarker for breast cancer. RESULTS TP53 (p53) is the most frequently mutated gene in invasive breast cancer. Although mutated in 30-35% of all cases, p53 is mutated in approximately 80% of triple-negative (TN) tumors (i.e., tumors negative for ER, PR, and HER2). Because of this high prevalence, mutated p53 is both a potential biomarker and therapeutic target for patients with breast cancer, especially for those with the TN subtype. Although several retrospective studies have investigated a potential prognostic and therapy predictive role for mutant p53 in breast cancer, the results to date are mixed. Thus, at present, mutant p53 cannot be recommended as a prognostic or therapy predictive biomarker in breast cancer. In contrast to the multiple reports on a potential biomarker role, few studies had until recently, investigated mutant p53 as a potential target for breast cancer treatment. In the last decade, however, several compounds have become available which can reactivate mutant p53 protein and convert it to a conformation with wild-type properties. Some of these compounds, especially PRIMA-1, APR-246 PK11007, and COTI-2, have been found to exhibit anticancer activity in preclinical models of breast cancer. CONCLUSION Since p53 is mutated in the vast majority of TN breast cancers, compounds such as APR-246, PK11007, and COTI-2 are potential treatments for patients with this subform of the disease. Further research is necessary to identify a potential biomarker role for mutant p53 in breast cancer.
Collapse
Affiliation(s)
- Michael J Duffy
- UCD Clinical Research Centre, St. Vincent's University Hospital, Dublin 4, Ireland. .,UCD School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland.
| | - Naoise C Synnott
- UCD School of Medicine, Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - John Crown
- Department of Medical Oncology, St. Vincent's University Hospital, Dublin, Ireland
| |
Collapse
|
152
|
Yates LR, Desmedt C. Translational Genomics: Practical Applications of the Genomic Revolution in Breast Cancer. Clin Cancer Res 2018; 23:2630-2639. [PMID: 28572257 DOI: 10.1158/1078-0432.ccr-16-2548] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Revised: 03/06/2017] [Accepted: 04/06/2017] [Indexed: 11/16/2022]
Abstract
The genomic revolution has fundamentally changed our perception of breast cancer. It is now apparent from DNA-based massively parallel sequencing data that at the genomic level, every breast cancer is unique and shaped by the mutational processes to which it was exposed during its lifetime. More than 90 breast cancer driver genes have been identified as recurrently mutated, and many occur at low frequency across the breast cancer population. Certain cancer genes are associated with traditionally defined histologic subtypes, but genomic intertumoral heterogeneity exists even between cancers that appear the same under the microscope. Most breast cancers contain subclonal populations, many of which harbor driver alterations, and subclonal structure is typically remodeled over time, across metastasis and as a consequence of treatment interventions. Genomics is deepening our understanding of breast cancer biology, contributing to an accelerated phase of targeted drug development and providing insights into resistance mechanisms. Genomics is also providing tools necessary to deliver personalized cancer medicine, but a number of challenges must still be addressed. Clin Cancer Res; 23(11); 2630-9. ©2017 AACRSee all articles in this CCR Focus section, "Breast Cancer Research: From Base Pairs to Populations."
Collapse
Affiliation(s)
- Lucy R Yates
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, United Kingdom.,Department of Clinical Oncology, Guys and St Thomas' NHS Trust, London, United Kingdom
| | - Christine Desmedt
- Breast Cancer Translational Research Laboratory, Institut Jules Bordet, Université Libre de Bruxelles, Brussels, Belgium.
| |
Collapse
|
153
|
Clinical outcomes based on multigene profiling in metastatic breast cancer patients. Oncotarget 2018; 7:76362-76373. [PMID: 27806348 PMCID: PMC5363515 DOI: 10.18632/oncotarget.12987] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2016] [Accepted: 10/13/2016] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Identifying the clinical impact of recurrent mutations can help define their role in cancer. Here, we identify frequent hotspot mutations in metastatic breast cancer (MBC) patients and associate them with clinical outcomes. PATIENTS AND METHODS Hotspot mutation testing was conducted in 500 MBC patients using an 11 gene (N = 126) and/or 46 or 50 gene (N = 391) panel. Patients were stratified by hormone receptor (HR) and human epidermal growth factor 2 (HER2) status. Clinical outcomes were retrospectively collected. RESULTS Hotspot mutations were most frequently detected in TP53 (30%), PIK3CA (27%) and AKT1 (4%). Triple-negative breast cancer (TNBC) patients had the highest incidence of TP53 (58%) and the lowest incidence of PIK3CA (9%) mutations. TP53 mutation was associated with shorter relapse-free survival (RFS) (median 22 vs 42months; P < 0.001) and overall survival (OS) from diagnosis of distant metastatic disease (median 26 vs 51months; P < 0.001). Conversely, PIK3CA mutation was associated with a trend towards better clinical outcomes including RFS (median 41 vs 30months; P = 0.074) and OS (52 vs 40months; P = 0.066). In HR-positive patients, TP53 mutation was again associated with shorter RFS (median 30 vs 46months; P = 0.017) and OS (median 30 vs 55months; P = 0.001). When multivariable analysis was performed for RFS and OS, TP53 but not PIK3CA mutation remained a significant predictor of outcomes in the overall cohort and in HR-positive patients. CONCLUSIONS Clinical hotspot sequencing identifies potentially actionable mutations. In this cohort, TP53 mutation was associated with worse clinical outcomes, while PIK3CA mutation did not remain a significant predictor of outcomes after multivariable analysis.
Collapse
|
154
|
Luo Y, Huang W, Zhang H, Liu G. Prognostic significance of CD117 expression and TP53 missense mutations in triple-negative breast cancer. Oncol Lett 2018; 15:6161-6170. [PMID: 29616097 PMCID: PMC5876428 DOI: 10.3892/ol.2018.8104] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 11/24/2017] [Indexed: 12/15/2022] Open
Abstract
Triple-negative breast cancer (TNBC) is extremely aggressive and associated with poor prognosis. There are no known predictive or prognostic markers for TNBC. Inhibition of tumor protein P53 (TP53) has been demonstrated to increase the levels of cluster of differentiation 117 (CD117) in human colorectal cancer cells. However, the function of TP53 in the regulation of CD117 in TNBC has, to the best of our knowledge, not been reported. In the present study, the association between the expression of CD117 protein and TP53 mutations was investigated, and their prognostic value in patients with TNBC was assessed. A total of 58 TNBC and 48 non-TNBC breast cancer tissue samples were assessed for the expression of CD117, p53 and TP53 mutations. The marker of proliferation Ki-67 (MKI67) proliferation index and vascular invasion index (obtained by measuring D2-40 and CD34) was investigated via immunohistochemistry, and mutations in exons 4–8 of TP53 were measured using direct sequencing. Associations between CD117 and p53 levels or TP53 mutations and clinical parameters were statistically evaluated. The rates of CD117 or MKI67 positivity, CD117+/TP53 missense mutation+, TP53 missense mutations or recurrence were significantly higher in patients with TNBC than in patients with non-TNBC. In TNBC tissues, the presence of CD117 was associated with TP53 missense mutations (P=0.031), vascular invasion, recurrence and MKI67. CD117+/TP53 missense mutation+ also associated with vascular invasion, recurrence and MKI67. Under univariate analysis, MKI67, vascular invasion, CD117, CD117+/TP53 missense mutation+ and TP53 missense mutations were associated with the overall survival of patients with TNBC. Multivariate analysis revealed that vascular invasion and CD117+/TP53 missense mutation+ in primary tumors were independent prognostic factors in patients with TNBC. In conclusion, CD117+/TP53 missense mutation+ was associated with MKI67, vascular invasion and tumor recurrence in TNBC. The presence of CD117 and TP53 missense mutations together in the primary tumors was an independent prognostic factor for survival of patients with TNBC.
Collapse
Affiliation(s)
- Yanli Luo
- Department of Pathology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, P.R. China
| | - Wentao Huang
- Department of Pathology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, P.R. China
| | - Huizhen Zhang
- Department of Pathology, Shanghai Jiao Tong University Affiliated Sixth People's Hospital, Shanghai 200233, P.R. China
| | - Guang Liu
- Department of Vascular Surgery, Ninth People's Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai 200011, P.R. China
| |
Collapse
|
155
|
Darb-Esfahani S, Denkert C, Stenzinger A, Salat C, Sinn B, Schem C, Endris V, Klare P, Schmitt W, Blohmer JU, Weichert W, Möbs M, Tesch H, Kümmel S, Sinn P, Jackisch C, Dietel M, Reimer T, Loi S, Untch M, von Minckwitz G, Nekljudova V, Loibl S. Role of TP53 mutations in triple negative and HER2-positive breast cancer treated with neoadjuvant anthracycline/taxane-based chemotherapy. Oncotarget 2018; 7:67686-67698. [PMID: 27611952 PMCID: PMC5356512 DOI: 10.18632/oncotarget.11891] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2016] [Accepted: 08/24/2016] [Indexed: 11/27/2022] Open
Abstract
Background TP53 mutations are frequent in breast cancer, however their clinical relevance in terms of response to chemotherapy is controversial. Methods 450 pre-therapeutic, formalin-fixed, paraffin-embedded core biopsies from the phase II neoadjuvant GeparSixto trial that included HER2-positive and triple negative breast cancer (TNBC) were subjected to Sanger sequencing of exons 5-8 of the TP53 gene. TP53 status was correlated to response to neoadjuvant anthracycline/taxane-based chemotherapy with or without carboplatin and trastuzumab/lapatinib in HER2-positive and bevacizumab in TNBC. p53 protein expression was evaluated by immunohistochemistry in the TNBC subgroup. Results Of 450 breast cancer samples 297 (66.0%) were TP53 mutant. Mutations were significantly more frequent in TNBC (74.8%) compared to HER2-positive cancers (55.4%, P < 0.0001). Neither mutations nor different mutation types and effects were associated with pCR neither in the whole study group nor in molecular subtypes (P > 0.05 each). Missense mutations tended to be associated with a better survival compared to all other types of mutations in TNBC (P = 0.093) and in HER2-positive cancers (P = 0.071). In TNBC, missense mutations were also linked to higher numbers of tumor-infiltrating lymphocytes (TILs, P = 0.028). p53 protein overexpression was also linked with imporved survival (P = 0.019). Conclusions Our study confirms high TP53 mutation rates in TNBC and HER2-positive breast cancer. Mutations did not predict the response to an intense neoadjuvant chemotherapy in these two molecular breast cancer subtypes.
Collapse
Affiliation(s)
| | - Carsten Denkert
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin, Germany.,German Cancer Consortium, (DKTK), Berlin, Germany
| | - Albrecht Stenzinger
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany.,Department of Pathology, Center for Integrated Diagnostics (CID), Massachusetts General Hospital, Boston, MA, USA
| | | | - Bruno Sinn
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Christian Schem
- Department of Gynecology and Obstetrics, University Hospital Schleswig-Hostein, Kiel, Germany
| | - Volker Endris
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Peter Klare
- Praxisklinik Krebsheilkunde für Frauen/Brustzentrum, Berlin, Germany
| | - Wolfgang Schmitt
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Jens-Uwe Blohmer
- Department of Gynecology and Obstetrics, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Wilko Weichert
- German Cancer Consortium, (DKTK), Berlin, Germany.,Institute of Pathology, Technical University Munich, Munich, Germany
| | - Markus Möbs
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Hans Tesch
- Center for Hematology and Oncology Bethanien, Frankfurt/Main, Germany
| | | | - Peter Sinn
- Institute of Pathology, University Hospital Heidelberg, Heidelberg, Germany
| | - Christian Jackisch
- Department of Gynecology and Obstetrics, Sana Klinikum Offenbach, Offenbach, Germany
| | - Manfred Dietel
- Institute of Pathology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Toralf Reimer
- Department of Gynecology, Klinikum Südstadt Rostock, Rostock, Germany
| | - Sherene Loi
- Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Michael Untch
- Department of Gynecology and Obstetrics, Helios Klinikum Berlin-Buch, Berlin, Germany
| | | | | | - Sibylle Loibl
- German Breast Group c/o (GBG Forschungs GmbH), Neu-Isenburg, Germany
| |
Collapse
|
156
|
Fountzilas G, Giannoulatou E, Alexopoulou Z, Zagouri F, Timotheadou E, Papadopoulou K, Lakis S, Bobos M, Poulios C, Sotiropoulou M, Lyberopoulou A, Gogas H, Pentheroudakis G, Pectasides D, Koutras A, Christodoulou C, Papandreou C, Samantas E, Papakostas P, Kosmidis P, Bafaloukos D, Karanikiotis C, Dimopoulos MA, Kotoula V. TP53 mutations and protein immunopositivity may predict for poor outcome but also for trastuzumab benefit in patients with early breast cancer treated in the adjuvant setting. Oncotarget 2017; 7:32731-53. [PMID: 27129168 PMCID: PMC5078047 DOI: 10.18632/oncotarget.9022] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 03/28/2016] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND We investigated the impact of PIK3CA and TP53 mutations and p53 protein status on the outcome of patients who had been treated with adjuvant anthracycline-taxane chemotherapy within clinical trials in the pre- and post-trastuzumab era. RESULTS TP53 and PIK3CA mutations were found in 380 (21.5%) and 458 (25.9%) cases, respectively, including 104 (5.9%) co-mutated tumors; p53 immunopositivity was observed in 848 tumors (53.5%). TP53 mutations (p < 0.001) and p53 protein positivity (p = 0.001) were more frequent in HER2-positive and triple negative (TNBC) tumors, while PIK3CA mutations were more frequent in Luminal A/B tumors (p < 0.001). TP53 mutation status and p53 protein expression but not PIK3CA mutation status interacted with trastuzumab treatment for disease-free survival; patients with tumors bearing TP53 mutations or immunopositive for p53 protein fared better when treated with trastuzumab, while among patients treated with trastuzumab those with the above characteristics fared best (interaction p = 0.017 for mutations; p = 0.015 for IHC). Upon multivariate analysis the above interactions remained significant in HER2-positive patients; in the entire cohort, TP53 mutations were unfavorable in patients with Luminal A/B (p = 0.003) and TNBC (p = 0.025); p53 immunopositivity was strongly favorable in patients treated with trastuzumab (p = 0.009). MATERIALS AND METHODS TP53 and PIK3CA mutation status was examined in 1766 paraffin tumor DNA samples with informative semiconductor sequencing results. Among these, 1585 cases were also informative for p53 protein status assessed by immunohistochemistry (IHC; 10% positivity cut-off). CONCLUSIONS TP53 mutations confer unfavorable prognosis in patients with Luminal A/B and TNBC tumors, while p53 immunopositivity may predict for trastuzumab benefit in the adjuvant setting.
Collapse
Affiliation(s)
- George Fountzilas
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece.,Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia.,The University of New South Wales, NSW, Australia
| | - Zoi Alexopoulou
- Department of Biostatistics, Health Data Specialists Ltd, Athens, Greece
| | - Flora Zagouri
- Department of Clinical Therapeutics, "Alexandra" Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - Eleni Timotheadou
- Department of Medical Oncology, "Papageorgiou" Hospital, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloniki, Greece
| | - Kyriaki Papadopoulou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Sotiris Lakis
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Mattheos Bobos
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Christos Poulios
- Department of Pathology, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloniki, Greece
| | | | - Aggeliki Lyberopoulou
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Helen Gogas
- First Department of Medicine, "Laiko" General Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | | | - Dimitrios Pectasides
- Oncology Section, Second Department of Internal Medicine, "Hippokration" Hospital, Athens, Greece
| | - Angelos Koutras
- Division of Oncology, Department of Medicine, University Hospital, University of Patras Medical School, Patras, Greece
| | | | - Christos Papandreou
- Department of Medical Oncology, University Hospital of Larissa, University of Thessaly School of Medicine, Larissa, Greece
| | - Epaminontas Samantas
- Third Department of Medical Oncology, "Agii Anargiri" Cancer Hospital, Athens, Greece
| | | | - Paris Kosmidis
- Second Department of Medical Oncology, Hygeia Hospital, Athens, Greece
| | | | | | | | - Vassiliki Kotoula
- Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece.,Department of Pathology, Aristotle University of Thessaloniki, School of Health Sciences, Faculty of Medicine, Thessaloniki, Greece
| |
Collapse
|
157
|
Mechanical cues control mutant p53 stability through a mevalonate-RhoA axis. Nat Cell Biol 2017; 20:28-35. [PMID: 29255172 DOI: 10.1038/s41556-017-0009-8] [Citation(s) in RCA: 96] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 11/15/2017] [Indexed: 12/14/2022]
Abstract
Tumour-associated p53 missense mutants act as driver oncogenes affecting cancer progression, metastatic potential and drug resistance (gain-of-function) 1 . Mutant p53 protein stabilization is a prerequisite for gain-of-function manifestation; however, it does not represent an intrinsic property of p53 mutants, but rather requires secondary events 2 . Moreover, mutant p53 protein levels are often heterogeneous even within the same tumour, raising questions on the mechanisms that control local mutant p53 accumulation in some tumour cells but not in their neighbours 2,3 . By investigating the cellular pathways that induce protection of mutant p53 from ubiquitin-mediated proteolysis, we found that HDAC6/Hsp90-dependent mutant p53 accumulation is sustained by RhoA geranylgeranylation downstream of the mevalonate pathway, as well as by RhoA- and actin-dependent transduction of mechanical inputs, such as the stiffness of the extracellular environment. Our results provide evidence for an unpredicted layer of mutant p53 regulation that relies on metabolic and mechanical cues.
Collapse
|
158
|
Fujii T, Matsuda N, Kono M, Harano K, Chen H, Luthra R, Roy-Chowdhuri S, Sahin AA, Wathoo C, Joon AY, Tripathy D, Meric-Bernstam F, Ueno NT. Prior systemic treatment increased the incidence of somatic mutations in metastatic breast cancer. Eur J Cancer 2017; 89:64-71. [PMID: 29232568 DOI: 10.1016/j.ejca.2017.11.015] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 11/01/2017] [Accepted: 11/10/2017] [Indexed: 01/10/2023]
Abstract
BACKGROUND Understanding 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. METHODS Archival 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. RESULTS A 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). CONCLUSION Systemic 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.
Collapse
Affiliation(s)
- Takeo Fujii
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Naoko Matsuda
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Miho Kono
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Kenichi Harano
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Huiqin Chen
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Rajyalakshmi Luthra
- Molecular Diagnostic Laboratory, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Sinchita Roy-Chowdhuri
- Department of Pathology, Division of Pathology/Lab Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Aysegul A Sahin
- Department of Pathology, Division of Pathology/Lab Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Chetna Wathoo
- Sheikh Khalifa Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Aron Y Joon
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Debu Tripathy
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Funda Meric-Bernstam
- Sheikh Khalifa Zayed Al Nahyan Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA; Department of Investigational Cancer Therapeutics (Phase I Trials Department), The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
| | - Naoto T Ueno
- Department of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA.
| |
Collapse
|
159
|
Periyasamy M, Singh AK, Gemma C, Kranjec C, Farzan R, Leach DA, Navaratnam N, Pálinkás HL, Vértessy BG, Fenton TR, Doorbar J, Fuller-Pace F, Meek DW, Coombes RC, Buluwela L, Ali S. p53 controls expression of the DNA deaminase APOBEC3B to limit its potential mutagenic activity in cancer cells. Nucleic Acids Res 2017; 45:11056-11069. [PMID: 28977491 PMCID: PMC5737468 DOI: 10.1093/nar/gkx721] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Revised: 07/30/2017] [Accepted: 08/08/2017] [Indexed: 12/28/2022] Open
Abstract
Cancer genome sequencing has implicated the cytosine deaminase activity of apolipoprotein B mRNA editing enzyme catalytic polypeptide-like (APOBEC) genes as an important source of mutations in diverse cancers, with APOBEC3B (A3B) expression especially correlated with such cancer mutations. To better understand the processes directing A3B over-expression in cancer, and possible therapeutic avenues for targeting A3B, we have investigated the regulation of A3B gene expression. Here, we show that A3B expression is inversely related to p53 status in different cancer types and demonstrate that this is due to a direct and pivotal role for p53 in repressing A3B expression. This occurs through the induction of p21 (CDKN1A) and the recruitment of the repressive DREAM complex to the A3B gene promoter, such that loss of p53 through mutation, or human papilloma virus-mediated inhibition, prevents recruitment of the complex, thereby causing elevated A3B expression and cytosine deaminase activity in cancer cells. As p53 is frequently mutated in cancer, our findings provide a mechanism by which p53 loss can promote cancer mutagenesis.
Collapse
Affiliation(s)
- Manikandan Periyasamy
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Anup K. Singh
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Carolina Gemma
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Christian Kranjec
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Raed Farzan
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Damien A. Leach
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Naveenan Navaratnam
- MRC London Institute of Medical Sciences, Imperial College London, Hammersmith Hospital Campus, Du Cane Road, London W12 0NN, UK
| | - Hajnalka L. Pálinkás
- Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Budapest 1111, Hungary
- Laboratory of Genome Metabolism and Repair, Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest 1117, Hungary
| | - Beata G. Vértessy
- Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, Budapest 1111, Hungary
- Laboratory of Genome Metabolism and Repair, Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest 1117, Hungary
| | - Tim R. Fenton
- School of Biosciences, University of Kent, Canterbury, Kent CT2 7NJ, UK
| | - John Doorbar
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Frances Fuller-Pace
- Division of Cancer Research, University of Dundee, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK
| | - David W. Meek
- Division of Cancer Research, University of Dundee, Ninewells Hospital and Medical School, Dundee DD1 9SY, UK
| | - R. Charles Coombes
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Laki Buluwela
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| | - Simak Ali
- Department of Surgery & Cancer, Imperial College London, Hammersmith Hospital Campus, London W12 0NN, UK
| |
Collapse
|
160
|
Synnott NC, Bauer MR, Madden S, Murray A, Klinger R, O'Donovan N, O'Connor D, Gallagher WM, Crown J, Fersht AR, Duffy MJ. Mutant p53 as a therapeutic target for the treatment of triple-negative breast cancer: Preclinical investigation with the anti-p53 drug, PK11007. Cancer Lett 2017; 414:99-106. [PMID: 29069577 DOI: 10.1016/j.canlet.2017.09.053] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 09/27/2017] [Accepted: 09/28/2017] [Indexed: 01/01/2023]
Abstract
The identification of a targeted therapy for patients with triple-negative breast cancer (TNBC) is one of the most urgent needs in breast cancer therapeutics. The p53 gene is mutated in approximately 80% of patients with TNBC, and is a potential therapeutic target for patients with this form of breast cancer. The 2-sulfonylpyrimidine compound, PK11007, preferentially decreases viability in p53-compromised cancer cell lines. We investigated PK11007 as a potential new treatment for TNBC. IC50 values for inhibition of proliferation in a panel of 17 breast cell lines by PK11007 ranged from 2.3 to 42.2 μM. There were significantly lower IC50 values for TNBC than for non-TNBC cell lines (p = 0.03) and for p53-mutated cell lines compared with p53 WT cells (p = 0.003). Response to PK11007 however, was independent of the estrogen receptor (ER) or HER2 status of the cell lines. In addition to inhibiting cell proliferation, PK11007 induced apoptosis in p53 mutant cell lines. Using RNAseq and gene ontology analysis, we found that PK11007 altered the expression of genes enriched in pathways involved in regulated cell death, regulation of apoptosis, signal transduction, protein refolding and locomotion. The observations that PK11007 inhibited cell proliferation, induced apoptosis and altered genes involved in cell death are all consistent with the ability of PK11007 to reactivate mutant p53. Based on our data, we conclude that targeting mutant p53 with PK11007 is a potential approach for treating p53-mutated breast cancer, including the subgroup with TN disease.
Collapse
Affiliation(s)
- Naoise C Synnott
- UCD School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Matthias R Bauer
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Stephen Madden
- Population Health Sciences, Department of Psychology, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Alyson Murray
- UCD School of Medicine, University College Dublin, Dublin 4, Ireland
| | - Rut Klinger
- UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Norma O'Donovan
- National Institute for Cellular Biotechnology (NICB), Dublin City University, Dublin, Ireland
| | - Darran O'Connor
- Department of Molecular & Cellular Therapeutics, Royal College of Surgeons Ireland, Dublin, Ireland
| | - William M Gallagher
- UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin 4, Ireland
| | - John Crown
- Department of Medical Oncology, St Vincent's University Hospital, Dublin 4, Ireland
| | - Alan R Fersht
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Michael J Duffy
- UCD School of Medicine, University College Dublin, Dublin 4, Ireland; UCD Clinical Research Centre, St. Vincent's University Hospital, Dublin 4, Ireland.
| |
Collapse
|
161
|
Russnes HG, Lingjærde OC, Børresen-Dale AL, Caldas C. Breast Cancer Molecular Stratification: From Intrinsic Subtypes to Integrative Clusters. THE AMERICAN JOURNAL OF PATHOLOGY 2017; 187:2152-2162. [PMID: 28733194 DOI: 10.1016/j.ajpath.2017.04.022] [Citation(s) in RCA: 159] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Revised: 04/19/2017] [Accepted: 04/27/2017] [Indexed: 02/08/2023]
Abstract
Breast carcinomas can be stratified into different entities based on clinical behavior, histologic features, and/or by biological properties. A classification of breast cancer should be based on underlying biology, which we know must be determined by the somatic genomic landscape of mutations. Moreover, because the latest generations of anticancer agents are founded on biological mechanisms, a detailed molecular stratification is a requirement for appropriate clinical management. Such stratification, based on genomic drivers, will be important for selecting patients for clinical trials. It will also facilitate the discovery of novel drivers, the study of tumor evolution, and the identification of mechanisms of treatment resistance. Assays for risk stratification have focused mainly on response prediction to existing treatment regimens. Molecular stratification based on gene expression profiling revealed that breast cancers could be classified in so-called intrinsic subtypes (luminal A and B, HER2-enriched, basal-like, and normal-like), which mostly corresponded to hormone receptor and HER2 status, and further stratified luminal tumors based on proliferation. The realization that a significant proportion of the gene expression landscape is determined by the somatic copy number alterations that drive expression in cis led to the newer classification of breast cancers into integrative clusters. This stratification of breast cancers into integrative clusters reveals prototypical patterns of single-nucleotide variants and is associated with distinct clinical courses and response to therapy.
Collapse
Affiliation(s)
- Hege G Russnes
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway; Department of Pathology, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Ole Christian Lingjærde
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway; Department of Computer Science, University of Oslo, Oslo, Norway
| | - Anne-Lise Børresen-Dale
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway; Department of Medicine, University of Oslo, Oslo, Norway
| | - Carlos Caldas
- Department of Oncology, Cancer Research UK Cambridge Institute, Li Ka Shing Centre, University of Cambridge, Cambridge, United Kingdom.
| |
Collapse
|
162
|
Abstract
Endometrial carcinomas (ECs) are heterogeneous at the genetic level. Although TP53 mutations are highly recurrent in serous endometrial carcinomas (SECs), these are also present in a subset of endometrioid endometrial carcinomas (EECs). Here, we sought to define the frequency, pattern, distribution, and type of TP53 somatic mutations in ECs by performing a reanalysis of the publicly available data from The Cancer Genome Atlas (TCGA). A total of 228 EECs (n=186) and SECs (n=42) from the TCGA data set, for which an integrated genomic characterization was performed, were interrogated for the presence and type of TP53 mutations, and for mutations in genes frequently mutated in ECs. TP53 mutations were found in 15% of EECs and 88% of SECs, and in 91% of copy-number-high and 35% of polymerase (DNA directed), epsilon, catalytic subunit (POLE) integrative genomic subtypes. In addition to differences in prevalence, variations in the type and pattern of TP53 mutations were observed between histologic types and between integrative genomic subtypes. TP53 hotspot mutations were significantly more frequently found in SECs (46%) than in EECs (15%). TP53-mutant EECs significantly more frequently harbored a co-occurring PTEN mutation than TP53-mutant SECs. Finally, a subset of TP53-mutant ECs (22%) was found to harbor frameshift or nonsense mutations. Given that nonsense and frameshift TP53 mutations result in distinct p53 immunohistochemical results that require careful interpretation, and that EECs and SECs display different patterns, types, and distributions of TP53 mutations, the use of the TP53/p53 status alone for the differential diagnosis of EECs and SECs may not be sufficient.
Collapse
|
163
|
Wang R, Li X, Zhang H, Wang K, He J. Cell-free circulating tumor DNA analysis for breast cancer and its clinical utilization as a biomarker. Oncotarget 2017; 8:75742-75755. [PMID: 29088906 PMCID: PMC5650461 DOI: 10.18632/oncotarget.20608] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2017] [Accepted: 08/17/2017] [Indexed: 01/05/2023] Open
Abstract
Circulating tumor DNA (ctDNA) in the blood of cancer patients contains much information on genetic and epigenetic profiles associated with cancer development, progression, and response to therapy. Analysis of ctDNA provides an opportunity for non-invasive sampling of tumor DNA repetitiously and therefore advance precision medicine. Recent development in massively parallel sequencing and digital genomic techniques support the analytical and clinical validity of ctDNA as a promising 'liquid biopsy' in human cancer. In this review, we discussed the current status of cell-free ctDNA including ctDNA biology, recently developed techniques for ctDNA detection, breast cancer specific detecting strategies, with a focus on clinical applications of ctDNA-based biomarkers in breast oncology.
Collapse
Affiliation(s)
- Ru Wang
- Department of Breast Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, P.R. China
| | - Xiao Li
- Department of Breast Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, P.R. China
| | - Huimin Zhang
- Department of Breast Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, P.R. China
| | - Ke Wang
- Department of Breast Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, P.R. China
| | - Jianjun He
- Department of Breast Surgery, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, P.R. China
| |
Collapse
|
164
|
Leroy B, Ballinger ML, Baran-Marszak F, Bond GL, Braithwaite A, Concin N, Donehower LA, El-Deiry WS, Fenaux P, Gaidano G, Langerød A, Hellstrom-Lindberg E, Iggo R, Lehmann-Che J, Mai PL, Malkin D, Moll UM, Myers JN, Nichols KE, Pospisilova S, Ashton-Prolla P, Rossi D, Savage SA, Strong LC, Tonin PN, Zeillinger R, Zenz T, Fraumeni JF, Taschner PEM, Hainaut P, Soussi T. Recommended Guidelines for Validation, Quality Control, and Reporting of TP53 Variants in Clinical Practice. Cancer Res 2017; 77:1250-1260. [PMID: 28254861 DOI: 10.1158/0008-5472.can-16-2179] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 11/12/2016] [Accepted: 11/16/2016] [Indexed: 12/21/2022]
Abstract
Accurate assessment of TP53 gene status in sporadic tumors and in the germline of individuals at high risk of cancer due to Li-Fraumeni Syndrome (LFS) has important clinical implications for diagnosis, surveillance, and therapy. Genomic data from more than 20,000 cancer genomes provide a wealth of information on cancer gene alterations and have confirmed TP53 as the most commonly mutated gene in human cancer. Analysis of a database of 70,000 TP53 variants reveals that the two newly discovered exons of the gene, exons 9β and 9γ, generated by alternative splicing, are the targets of inactivating mutation events in breast, liver, and head and neck tumors. Furthermore, germline rearrange-ments in intron 1 of TP53 are associated with LFS and are frequently observed in sporadic osteosarcoma. In this context of constantly growing genomic data, we discuss how screening strategies must be improved when assessing TP53 status in clinical samples. Finally, we discuss how TP53 alterations should be described by using accurate nomenclature to avoid confusion in scientific and clinical reports. Cancer Res; 77(6); 1250-60. ©2017 AACR.
Collapse
Affiliation(s)
- Bernard Leroy
- Sorbonne Université, UPMC Univ Paris 06, Paris, France
| | - Mandy L Ballinger
- Cancer Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia
| | - Fanny Baran-Marszak
- Hôpital Avicenne, Assistance Publique-Hôpitaux De Paris, Bobigny, Service D'H ematologie Biologique, France
| | - Gareth L Bond
- Ludwig Institute for Cancer Research, University of Oxford, Nuffield Department of Clinical Medicine, Old Road Campus Research Building, Oxford, United Kingdom
| | - Antony Braithwaite
- Dept of Pathology, School of Medicine, University of Otago, Dunedin, New Zealand.,Children's Medical Research Institute, University of Sydney, Westmead NSW, Australia
| | - Nicole Concin
- Department of Gynecology and Obstetrics, Innsbruck Medical University, Innsbruck, Austria
| | | | - Wafik S El-Deiry
- Department of Hematology/Oncology and Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Pierre Fenaux
- Service d'hématologie séniors, Hôpital St Louis/Université Paris 7, 1 avenue Claude Vellefaux, Paris, France
| | - Gianluca Gaidano
- Division of Hematology, Department of Translational Medicine, Amedeo Avogadro University of Eastern Piedmont, Novara, Italy
| | - Anita Langerød
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Eva Hellstrom-Lindberg
- Karolinska Institute, Department of Medicine, Center for Hematology and Regenerative Medicine, Karolinska University Hospital, Stockholm, Sweden
| | - Richard Iggo
- Bergonié Cancer Institute University of Bordeaux 229 cours de l'Argonne 33076 Bordeaux, France
| | | | - Phuong L Mai
- Cancer Genetics Program, Magee Womens Hospital, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania
| | - David Malkin
- Division of Hematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Ute M Moll
- Department of Pathology, Stony Brook University, Stony Brook, New York
| | - Jeffrey N Myers
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Kim E Nichols
- Department of Oncology, Division of Cancer Predisposition, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Sarka Pospisilova
- Masaryk University, CEITEC - Molecular Medicine and University Hospital Brno, Department of Internal Medicine - Hematology and Oncology, Brno, Czech Republic
| | - Patricia Ashton-Prolla
- Universidade Federal do Rio Grande do Sul (UFRGS) e Serviço deGenética Médica-HCPA, Rua Ramiro Barcelos, Porto Alegre, Brasil
| | - Davide Rossi
- Division of Hematology, Department of Translational Medicine, Amedeo Avogadro University of Eastern Piedmont, Novara, Italy
| | - Sharon A Savage
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Louise C Strong
- The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Patricia N Tonin
- Departments of Medicine and Human Genetics, McGill University and Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Robert Zeillinger
- Molecular Oncology Group, Department of Obstetrics and Gynaecology, Medical University of Vienna, Vienna, Austria
| | - Thorsten Zenz
- University of Heidelberg, Department of Medicine V, Heidelberg, Germany; Department of Translational Oncology, National Center for Tumor Diseases and German Cancer Research Center (dkfz), Heidelberg, Germany
| | - Joseph F Fraumeni
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, Maryland
| | - Peter E M Taschner
- Generade Centre of Expertise Genomics and University of Applied Sciences Leiden, Leiden, the Netherlands
| | - Pierre Hainaut
- Institut Albert Bonniot, Inserm 823, Université Grenoble Alpes, Rond Point de la Chantourne, La Tronche, France
| | - Thierry Soussi
- Sorbonne Université, UPMC Univ Paris 06, Paris, France. .,Department of Oncology-Pathology, Karolinska Institutet, Cancer Center Karolinska, Stockholm, Sweden.,INSERM, U1138, Centre de Recherche des Cordeliers, Paris, France
| |
Collapse
|
165
|
Dannenfelser R, Nome M, Tahiri A, Ursini-Siegel J, Vollan HKM, Haakensen VD, Helland Å, Naume B, Caldas C, Børresen-Dale AL, Kristensen VN, Troyanskaya OG. Data-driven analysis of immune infiltrate in a large cohort of breast cancer and its association with disease progression, ER activity, and genomic complexity. Oncotarget 2017; 8:57121-57133. [PMID: 28915659 PMCID: PMC5593630 DOI: 10.18632/oncotarget.19078] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 06/17/2017] [Indexed: 02/02/2023] Open
Abstract
The tumor microenvironment is now widely recognized for its role in tumor progression, treatment response, and clinical outcome. The intratumoral immunological landscape, in particular, has been shown to exert both pro-tumorigenic and anti-tumorigenic effects. Identifying immunologically active or silent tumors may be an important indication for administration of therapy, and detecting early infiltration patterns may uncover factors that contribute to early risk. Thus far, direct detailed studies of the cell composition of tumor infiltration have been limited; with some studies giving approximate quantifications using immunohistochemistry and other small studies obtaining detailed measurements by isolating cells from excised tumors and sorting them using flow cytometry. Herein we utilize a machine learning based approach to identify lymphocyte markers with which we can quantify the presence of B cells, cytotoxic T-lymphocytes, T-helper 1, and T-helper 2 cells in any gene expression data set and apply it to studies of breast tissue. By leveraging over 2,100 samples from existing large scale studies, we are able to find an inherent cell heterogeneity in clinically characterized immune infiltrates, a strong link between estrogen receptor activity and infiltration in normal and tumor tissues, changes with genomic complexity, and identify characteristic differences in lymphocyte expression among molecular groupings. With our extendable methodology for capturing cell type specific signal we systematically studied immune infiltration in breast cancer, finding an inverse correlation between beneficial lymphocyte infiltration and estrogen receptor activity in normal breast tissue and reduced infiltration in estrogen receptor negative tumors with high genomic complexity.
Collapse
Affiliation(s)
- Ruth Dannenfelser
- Department of Computer Science, Princeton University, Princeton, New Jersey, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
| | - Marianne Nome
- Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Clinical Molecular Oncology, Division of Medicine, Akershus University Hospital, Ahus, Norway
| | - Andliena Tahiri
- Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Clinical Molecular Oncology, Division of Medicine, Akershus University Hospital, Ahus, Norway
| | - Josie Ursini-Siegel
- Lady Davis Institute for Medical Research, McGill University, Montreal, Quebec, Canada
| | - Hans Kristian Moen Vollan
- Department of Clinical Molecular Oncology, Division of Medicine, Akershus University Hospital, Ahus, Norway
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Vilde D. Haakensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Åslaug Helland
- Department of Oncology, Division for Surgery, Cancer, and Transplantation, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Bjørn Naume
- Department of Oncology, Division for Surgery, Cancer, and Transplantation, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, United Kingdom
| | - Anne-Lise Børresen-Dale
- Department of Clinical Molecular Oncology, Division of Medicine, Akershus University Hospital, Ahus, Norway
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Vessela N. Kristensen
- Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
- Department of Clinical Molecular Oncology, Division of Medicine, Akershus University Hospital, Ahus, Norway
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radium Hospital, Oslo, Norway
| | - Olga G. Troyanskaya
- Department of Computer Science, Princeton University, Princeton, New Jersey, United States of America
- Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, New Jersey, United States of America
- Flatiron Institute, Simons Foundation, New York, New York, United States of America
| |
Collapse
|
166
|
Pruszko M, Milano E, Forcato M, Donzelli S, Ganci F, Di Agostino S, De Panfilis S, Fazi F, Bates DO, Bicciato S, Zylicz M, Zylicz A, Blandino G, Fontemaggi G. The mutant p53-ID4 complex controls VEGFA isoforms by recruiting lncRNA MALAT1. EMBO Rep 2017; 18:1331-1351. [PMID: 28652379 PMCID: PMC5538427 DOI: 10.15252/embr.201643370] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Revised: 05/08/2017] [Accepted: 05/16/2017] [Indexed: 12/21/2022] Open
Abstract
The abundant, nuclear-retained, metastasis-associated lung adenocarcinoma transcript 1 (MALAT1) has been associated with a poorly differentiated and aggressive phenotype of mammary carcinomas. This long non-coding RNA (lncRNA) localizes to nuclear speckles, where it interacts with a subset of splicing factors and modulates their activity. In this study, we demonstrate that oncogenic splicing factor SRSF1 bridges MALAT1 to mutant p53 and ID4 proteins in breast cancer cells. Mutant p53 and ID4 delocalize MALAT1 from nuclear speckles and favor its association with chromatin. This enables aberrant recruitment of MALAT1 on VEGFA pre-mRNA and modulation of VEGFA isoforms expression. Interestingly, VEGFA-dependent expression signatures associate with ID4 expression specifically in basal-like breast cancers carrying TP53 mutations. Our results highlight a key role for MALAT1 in control of VEGFA isoforms expression in breast cancer cells expressing gain-of-function mutant p53 and ID4 proteins.
Collapse
Affiliation(s)
- Magdalena Pruszko
- Department of Molecular Biology, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
- Institute of Biochemistry and Biophysics, PAS, Warsaw, Poland
| | - Elisa Milano
- Oncogenomic and Epigenetic Unit, Italian National Cancer Institute "Regina Elena", Rome, Italy
| | - Mattia Forcato
- Department of Life Sciences, Center for Genome Research, University of Modena and Reggio Emilia, Modena, Italy
| | - Sara Donzelli
- Oncogenomic and Epigenetic Unit, Italian National Cancer Institute "Regina Elena", Rome, Italy
| | - Federica Ganci
- Oncogenomic and Epigenetic Unit, Italian National Cancer Institute "Regina Elena", Rome, Italy
| | - Silvia Di Agostino
- Oncogenomic and Epigenetic Unit, Italian National Cancer Institute "Regina Elena", Rome, Italy
| | - Simone De Panfilis
- Centre for Life Nano Science, Istituto Italiano di Tecnologia, Rome, Italy
| | - Francesco Fazi
- Department of Anatomical, Histological, Forensic & Orthopedic Sciences, Section of Histology & Medical Embryology, Sapienza University of Rome, Rome, Italy
| | - David O Bates
- Division of Cancer and Stem Cells, Cancer Biology, School of Medicine, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Silvio Bicciato
- Department of Life Sciences, Center for Genome Research, University of Modena and Reggio Emilia, Modena, Italy
| | - Maciej Zylicz
- Department of Molecular Biology, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Alicja Zylicz
- Department of Molecular Biology, International Institute of Molecular and Cell Biology in Warsaw, Warsaw, Poland
| | - Giovanni Blandino
- Oncogenomic and Epigenetic Unit, Italian National Cancer Institute "Regina Elena", Rome, Italy
| | - Giulia Fontemaggi
- Oncogenomic and Epigenetic Unit, Italian National Cancer Institute "Regina Elena", Rome, Italy
| |
Collapse
|
167
|
Yotsukura S, Karasuyama M, Takigawa I, Mamitsuka H. Exploring phenotype patterns of breast cancer within somatic mutations: a modicum in the intrinsic code. Brief Bioinform 2017; 18:619-633. [PMID: 27197545 DOI: 10.1093/bib/bbw040] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Indexed: 11/12/2022] Open
Abstract
Triple-negative (TN) breast cancer (BC) patients have limited treatment options and poor prognosis even after extant treatments and standard chemotherapeutic regimens. Linking TN patients to clinically known phenotypes with appropriate treatments is vital. Location-specific sequence variants are expected to be useful for this purpose by identifying subgroups within a disease population. Single gene mutational signatures have been widely reported, with related phenotypes in literature. We thoroughly survey currently available mutations (and mutated genes), linked to BC phenotypes, to demonstrate their limited performance as sole predictors/biomarkers to assign phenotypes to patients. We then explore mutational combinations, as a pilot study, using The Cancer Genome Atlas Research Network mutational data of BC and three machine learning methods: association rules (limitless arity multiple procedure), decision tree and hierarchical disjoint clustering. The study results in a patient classification scheme through combinatorial mutations in Phosphatidylinositol-4,5-Bisphosphate 3-Kinase and tumor protein 53, being consistent with all three methods, implying its validity from a diverse viewpoint. However, it would warrant further research to select multi-gene signatures to identify phenotypes specifically and be clinically used routinely.
Collapse
|
168
|
Tracz-Gaszewska Z, Klimczak M, Biecek P, Herok M, Kosinski M, Olszewski MB, Czerwińska P, Wiech M, Wiznerowicz M, Zylicz A, Zylicz M, Wawrzynow B. Molecular chaperones in the acquisition of cancer cell chemoresistance with mutated TP53 and MDM2 up-regulation. Oncotarget 2017; 8:82123-82143. [PMID: 29137250 PMCID: PMC5669876 DOI: 10.18632/oncotarget.18899] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2016] [Accepted: 06/13/2017] [Indexed: 01/17/2023] Open
Abstract
Utilizing the TCGA PANCAN12 dataset we discovered that cancer patients with mutations in TP53 tumor suppressor and overexpression of MDM2 oncogene exhibited decreased survival post treatment. Interestingly, in the case of breast cancer patients, this phenomenon correlated with high expression level of several molecular chaperones belonging to the HSPA, DNAJB and HSPC families. To verify the hypothesis that such a genetic background may promote chaperone-mediated chemoresistance, we employed breast and lung cancer cell lines that constitutively overexpressed heat shock proteins and have shown that HSPA1A/HSP70 and DNAJB1/HSP40 facilitated the binding of mutated p53 to the TAp73α protein. This chaperone-mediated mutated p53–TAp73α complex induced chemoresistance to DNA damaging reagents, like Cisplatin, Doxorubicin, Etoposide or Camptothecin. Importantly, when the MDM2 oncogene was overexpressed, heat shock proteins were displaced and a stable multiprotein complex comprising of mutated p53-TAp73α-MDM2 was formed, additionally amplifying cancer cells chemoresistance. Our findings demonstrate that molecular chaperones aid cancer cells in surviving the cytotoxic effect of chemotherapeutics and may have therapeutic implications.
Collapse
Affiliation(s)
- Zuzanna Tracz-Gaszewska
- International Institute of Molecular and Cell Biology, Warsaw, Poland.,Institute of Biochemistry and Biophysics, PAS, Warsaw, Poland
| | - Marta Klimczak
- International Institute of Molecular and Cell Biology, Warsaw, Poland.,Postgraduate School of Molecular Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Przemyslaw Biecek
- Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, Warsaw, Poland.,Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Marcin Herok
- International Institute of Molecular and Cell Biology, Warsaw, Poland.,Nencki Institute of Experimental Biology, PAS, Warsaw, Poland
| | - Marcin Kosinski
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland.,Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, Warsaw, Poland
| | | | - Patrycja Czerwińska
- International Institute of Molecular and Cell Biology, Warsaw, Poland.,Laboratory of Gene Therapy, Department of Cancer Immunology, The Greater Poland Cancer Center, Poznan, Poland
| | - Milena Wiech
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Maciej Wiznerowicz
- Laboratory of Gene Therapy, Department of Cancer Immunology, The Greater Poland Cancer Center, Poznan, Poland
| | - Alicja Zylicz
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Maciej Zylicz
- International Institute of Molecular and Cell Biology, Warsaw, Poland
| | | |
Collapse
|
169
|
Yates LR. Intratumoral heterogeneity and subclonal diversification of early breast cancer. Breast 2017; 34 Suppl 1:S36-S42. [PMID: 28666921 DOI: 10.1016/j.breast.2017.06.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Heterogeneity has long been recognized as a feature of some primary breast cancers manifesting as mixed histopathological subtypes or variable expression of the therapeutic targets ER, PgR and HER2. The recent emergence of next generation sequencing (NGS) technologies has revolutionized our understanding of the extent and nature of subclonal diversification. Careful examination of primary breast cancers often reveals multiple genomically distinct subclones that may contain driver alterations that follow spatial patterns of segregation. Subclonality is of clinical relevance as it forms the substrate of selection and can give rise to aggressive clinical features such as invasiveness, metastasis and treatment resistance. However, spatial and temporal intra-tumoral heterogeneity pose fundamental challenges to representative sampling and consequently the feasibility of a personalized medicine approach. Fundamental clinical and biological questions are starting to be addressed by applying NGS to the study of intra-tumoral heterogeneity and the insights that it provides should be used to better inform the prospective design of clinico-genomics trials.
Collapse
Affiliation(s)
- Lucy R Yates
- The Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK; Department of Clinical Oncology, St Thomas' Hospital, Westminster Bridge Road, London, SE1 7EH, UK.
| |
Collapse
|
170
|
Nikkilä J, Kumar R, Campbell J, Brandsma I, Pemberton HN, Wallberg F, Nagy K, Scheer I, Vertessy BG, Serebrenik AA, Monni V, Harris RS, Pettitt SJ, Ashworth A, Lord CJ. Elevated APOBEC3B expression drives a kataegic-like mutation signature and replication stress-related therapeutic vulnerabilities in p53-defective cells. Br J Cancer 2017; 117:113-123. [PMID: 28535155 PMCID: PMC5520199 DOI: 10.1038/bjc.2017.133] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 04/18/2017] [Accepted: 04/24/2017] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Elevated APOBEC3B expression in tumours correlates with a kataegic pattern of localised hypermutation. We assessed the cellular phenotypes associated with high-level APOBEC3B expression and the influence of p53 status on these phenotypes using an isogenic system. METHODS We used RNA interference of p53 in cells with inducible APOBEC3B and assessed DNA damage response (DDR) biomarkers. The mutational effects of APOBEC3B were assessed using whole-genome sequencing. In vitro small-molecule inhibitor sensitivity profiling was used to identify candidate therapeutic vulnerabilities. RESULTS Although APOBEC3B expression increased the incorporation of genomic uracil, invoked DDR biomarkers and caused cell cycle arrest, inactivation of p53 circumvented APOBEC3B-induced cell cycle arrest without reversing the increase in genomic uracil or DDR biomarkers. The continued expression of APOBEC3B in p53-defective cells not only caused a kataegic mutational signature but also caused hypersensitivity to small-molecule DDR inhibitors (ATR, CHEK1, CHEK2, PARP, WEE1 inhibitors) as well as cisplatin/ATR inhibitor and ATR/PARP inhibitor combinations. CONCLUSIONS Although loss of p53 might allow tumour cells to tolerate elevated APOBEC3B expression, continued expression of this enzyme might impart a number of therapeutic vulnerabilities upon tumour cells.
Collapse
Affiliation(s)
- Jenni Nikkilä
- The CRUK Gene Function Laboratory and The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Rahul Kumar
- The CRUK Gene Function Laboratory and The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - James Campbell
- The CRUK Gene Function Laboratory and The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Inger Brandsma
- The CRUK Gene Function Laboratory and The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Helen N Pemberton
- The CRUK Gene Function Laboratory and The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Fredrik Wallberg
- FACS Facility, The Institute of Cancer Research, London SW3 6JB, UK
| | - Kinga Nagy
- Department of Applied Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp 3, Budapest H-1111, Hungary
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok Str. 2, Budapest H-1117, Hungary
| | - Ildikó Scheer
- Department of Applied Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp 3, Budapest H-1111, Hungary
- Institute of Enzymology, RCNS, Hungarian Academy of Sciences, Magyar Tudósok Str. 2, Budapest H-1117, Hungary
| | - Beata G Vertessy
- Department of Applied Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp 3, Budapest H-1111, Hungary
| | - Artur A Serebrenik
- Howard Hughes Medical Institute, Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Valentina Monni
- Howard Hughes Medical Institute, Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Reuben S Harris
- Howard Hughes Medical Institute, Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Stephen J Pettitt
- The CRUK Gene Function Laboratory and The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Alan Ashworth
- The CRUK Gene Function Laboratory and The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| | - Christopher J Lord
- The CRUK Gene Function Laboratory and The Breast Cancer Now Toby Robins Breast Cancer Research Centre, The Institute of Cancer Research, London SW3 6JB, UK
| |
Collapse
|
171
|
Maxwell KN, Soucier-Ernst D, Tahirovic E, Troxel AB, Clark C, Feldman M, Colameco C, Kakrecha B, Langer M, Lieberman D, Morrissette JJD, Paul MR, Pan TC, Yee S, Shih N, Carpenter E, Chodosh LA, DeMichele A. Comparative clinical utility of tumor genomic testing and cell-free DNA in metastatic breast cancer. Breast Cancer Res Treat 2017. [PMID: 28500398 DOI: 10.1007/s10549‐017‐4257‐x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/29/2022]
Abstract
PURPOSE Breast cancer metastases differ biologically from primary disease; therefore, metastatic biopsies may assist in treatment decision making. Commercial genomic testing of both tumor and circulating tumor DNA have become available clinically, but utility of these tests in breast cancer management remains unclear. METHODS Patients undergoing a clinically indicated metastatic tumor biopsy were consented to the ongoing METAMORPH registry. Tumor and blood were collected at the time of disease progression before subsequent therapy, and patients were followed for response on subsequent treatment. Tumor testing (n = 53) and concurrent cell-free DNA (n = 32) in a subset of patients was performed using CLIA-approved assays. RESULTS The proportion of patients with a genomic alteration was lower in tumor than in blood (69 vs. 91%; p = 0.06). After restricting analysis to alterations covered on both platforms, 83% of tumor alterations were detected in blood, while 90% of blood alterations were detected in tumor. Mutational load specific for the panel genes was calculated for both tumor and blood. Time to progression on subsequent treatment was significantly shorter for patients whose tumors had high panel-specific mutational load (HR 0.31, 95% CI 0.12-0.78) or a TP53 mutation (HR 0.35, 95% CI 0.20-0.79), after adjusting for stage at presentation, hormone receptor status, prior treatment type, and number of lines of metastatic treatment. CONCLUSIONS Treating oncologists must distinguish platform differences from true biological heterogeneity when comparing tumor and cfDNA genomic testing results. Tumor and concurrent cfDNA contribute unique genomic information in metastatic breast cancer patients, providing potentially useful biomarkers for aggressive metastatic disease.
Collapse
Affiliation(s)
- Kara N Maxwell
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Danielle Soucier-Ernst
- Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Emin Tahirovic
- Department of Biostatistics and Epidemiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Andrea B Troxel
- Department of Population Health, NYU School of Medicine, New York, NY, USA
| | - Candace Clark
- Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Michael Feldman
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Christopher Colameco
- Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Bijal Kakrecha
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Melissa Langer
- University of Maryland School of Medicine, Baltimore, MD, USA
| | - David Lieberman
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Jennifer J D Morrissette
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Matt R Paul
- Department of Cancer Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Tien-Chi Pan
- Department of Cancer Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Stephanie Yee
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Natalie Shih
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Erica Carpenter
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.,Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Lewis A Chodosh
- Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.,Department of Cancer Biology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.,Department of Medicine, Division of Endocrinology, Diabetes and Metabolism at the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA
| | - Angela DeMichele
- Department of Medicine, Division of Hematology-Oncology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. .,Abramson Cancer Center, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA. .,Department of Biostatistics and Epidemiology, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, USA.
| |
Collapse
|
172
|
Comparative clinical utility of tumor genomic testing and cell-free DNA in metastatic breast cancer. Breast Cancer Res Treat 2017; 164:627-638. [PMID: 28500398 DOI: 10.1007/s10549-017-4257-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 04/17/2017] [Indexed: 01/24/2023]
Abstract
PURPOSE Breast cancer metastases differ biologically from primary disease; therefore, metastatic biopsies may assist in treatment decision making. Commercial genomic testing of both tumor and circulating tumor DNA have become available clinically, but utility of these tests in breast cancer management remains unclear. METHODS Patients undergoing a clinically indicated metastatic tumor biopsy were consented to the ongoing METAMORPH registry. Tumor and blood were collected at the time of disease progression before subsequent therapy, and patients were followed for response on subsequent treatment. Tumor testing (n = 53) and concurrent cell-free DNA (n = 32) in a subset of patients was performed using CLIA-approved assays. RESULTS The proportion of patients with a genomic alteration was lower in tumor than in blood (69 vs. 91%; p = 0.06). After restricting analysis to alterations covered on both platforms, 83% of tumor alterations were detected in blood, while 90% of blood alterations were detected in tumor. Mutational load specific for the panel genes was calculated for both tumor and blood. Time to progression on subsequent treatment was significantly shorter for patients whose tumors had high panel-specific mutational load (HR 0.31, 95% CI 0.12-0.78) or a TP53 mutation (HR 0.35, 95% CI 0.20-0.79), after adjusting for stage at presentation, hormone receptor status, prior treatment type, and number of lines of metastatic treatment. CONCLUSIONS Treating oncologists must distinguish platform differences from true biological heterogeneity when comparing tumor and cfDNA genomic testing results. Tumor and concurrent cfDNA contribute unique genomic information in metastatic breast cancer patients, providing potentially useful biomarkers for aggressive metastatic disease.
Collapse
|
173
|
Fagerholm R, Khan S, Schmidt MK, GarcClosas M, Heikkilä P, Saarela J, Beesley J, Jamshidi M, Aittomäki K, Liu J, Raza Ali H, Andrulis IL, Beckmann MW, Behrens S, Blows FM, Brenner H, Chang-Claude J, Couch FJ, Czene K, Fasching PA, Figueroa J, Floris G, Glendon G, Guo Q, Hall P, Hallberg E, Hamann U, Holleczek B, Hooning MJ, Hopper JL, Jager A, Kabisch M, Investigators KC, Keeman R, Kosma VM, Lambrechts D, Lindblom A, Mannermaa A, Margolin S, Provenzano E, Shah M, Southey MC, Dennis J, Lush M, Michailidou K, Wang Q, Bolla MK, Dunning AM, Easton DF, Pharoah PD., Chenevix-Trench G, Blomqvist C, Nevanlinna H. TP53-based interaction analysis identifies cis-eQTL variants for TP53BP2, FBXO28, and FAM53A that associate with survival and treatment outcome in breast cancer. Oncotarget 2017; 8:18381-18398. [PMID: 28179588 PMCID: PMC5392336 DOI: 10.18632/oncotarget.15110] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 01/01/2017] [Indexed: 01/13/2023] Open
Abstract
TP53 overexpression is indicative of somatic TP53 mutations and associates with aggressive tumors and poor prognosis in breast cancer. We utilized a two-stage SNP association study to detect variants associated with breast cancer survival in a TP53-dependent manner. Initially, a genome-wide study (n = 575 cases) was conducted to discover candidate SNPs for genotyping and validation in the Breast Cancer Association Consortium (BCAC). The SNPs were then tested for interaction with tumor TP53 status (n = 4,610) and anthracycline treatment (n = 17,828). For SNPs interacting with anthracycline treatment, siRNA knockdown experiments were carried out to validate candidate genes.In the test for interaction between SNP genotype and TP53 status, we identified one locus, represented by rs10916264 (p(interaction) = 3.44 × 10-5; FDR-adjusted p = 0.0011) in estrogen receptor (ER) positive cases. The rs10916264 AA genotype associated with worse survival among cases with ER-positive, TP53-positive tumors (hazard ratio [HR] 2.36, 95% confidence interval [C.I] 1.45 - 3.82). This is a cis-eQTL locus for FBXO28 and TP53BP2; expression levels of these genes were associated with patient survival specifically in ER-positive, TP53-mutated tumors. Additionally, the SNP rs798755 was associated with survival in interaction with anthracycline treatment (p(interaction) = 9.57 × 10-5, FDR-adjusted p = 0.0130). RNAi-based depletion of a predicted regulatory target gene, FAM53A, indicated that this gene can modulate doxorubicin sensitivity in breast cancer cell lines.If confirmed in independent data sets, these results may be of clinical relevance in the development of prognostic and predictive marker panels for breast cancer.
Collapse
Affiliation(s)
- Rainer Fagerholm
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Sofia Khan
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Marjanka K. Schmidt
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Montserrat GarcClosas
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Päivi Heikkilä
- Department of Pathology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Jani Saarela
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Finland
| | - Jonathan Beesley
- Department of Genetics, QIMR Berghofer Medical Research Institute, Brisbane, Australia
| | - Maral Jamshidi
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Kristiina Aittomäki
- Department of Clinical Genetics, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| | - Jianjun Liu
- Human Genetics Division, Genome Institute of Singapore, Singapore, Singapore
| | - H. Raza Ali
- Cancer Research UK Cambridge Institute, University of Cambridge, Li Ka Shing Centre, Cambridge, UK
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Irene L. Andrulis
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Canada
| | - Matthias W. Beckmann
- Department of Gynaecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
| | - Sabine Behrens
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Fiona M. Blows
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
- Division of Preventive Oncology, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT), Heidelberg, Germany
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- University Cancer Center Hamburg (UCCH), University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Fergus J. Couch
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Kamila Czene
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Peter A. Fasching
- Department of Gynaecology and Obstetrics, University Hospital Erlangen, Friedrich-Alexander University Erlangen-Nuremberg, Comprehensive Cancer Center Erlangen-EMN, Erlangen, Germany
- David Geffen School of Medicine, Department of Medicine Division of Hematology and Oncology, University of California at Los Angeles, Los Angeles, CA, USA
| | - Jonine Figueroa
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Usher Institute of Population Health Sciences and Informatics, The University of Edinburgh Medical School, Edinburgh, UK
| | - Giuseppe Floris
- Leuven Multidisciplinary Breast Center, Department of Oncology, KULeuven, Leuven Cancer Institute, University Hospitals Leuven
| | - Gord Glendon
- Lunenfeld-Tanenbaum Research Institute of Mount Sinai Hospital, Toronto, Canada
| | - Qi Guo
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
| | - Emily Hallberg
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Ute Hamann
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Maartje J. Hooning
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - John L. Hopper
- Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global health, The University of Melbourne, Melbourne, Australia
| | - Agnes Jager
- Department of Medical Oncology, Family Cancer Clinic, Erasmus MC Cancer Institute, Rotterdam, The Netherlands
| | - Maria Kabisch
- Molecular Genetics of Breast Cancer, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | | | - Renske Keeman
- Netherlands Cancer Institute, Antoni van Leeuwenhoek Hospital, Amsterdam, The Netherlands
| | - Veli-Matti Kosma
- Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Diether Lambrechts
- Vesalius Research Center, VIB, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Oncology, University of Leuven, Leuven, Belgium
| | - Annika Lindblom
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Arto Mannermaa
- Cancer Center of Eastern Finland, University of Eastern Finland, Kuopio, Finland
- Institute of Clinical Medicine, Pathology and Forensic Medicine, University of Eastern Finland, Kuopio, Finland
- Imaging Center, Department of Clinical Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Sara Margolin
- Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Elena Provenzano
- Department of Oncology, University of Cambridge, Addenbrookes Hospital, Cambridge, UK
- Department of Histopathology, Addenbrookes Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
- Cambridge Experimental Cancer Medicine Centre and NIHR Cambridge Biomedical Research Centre, Cambridge, UK
| | - Mitul Shah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Melissa C. Southey
- Department of Pathology, The University of Melbourne, Melbourne, Australia
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Michael Lush
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Kyriaki Michailidou
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
- Department of Electron Microscopy/Molecular Pathology, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Qin Wang
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Manjeet K. Bolla
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Alison M. Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Douglas F. Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Paul D.P . Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | | | - Carl Blomqvist
- Department of Oncology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
- Department of Oncology, University of Örebro, Örebro, Sweden
| | - Heli Nevanlinna
- Department of Obstetrics and Gynecology, Helsinki University Hospital, University of Helsinki, Helsinki, Finland
| |
Collapse
|
174
|
Alexandrova EM, Mirza SA, Xu S, Schulz-Heddergott R, Marchenko ND, Moll UM. p53 loss-of-heterozygosity is a necessary prerequisite for mutant p53 stabilization and gain-of-function in vivo. Cell Death Dis 2017; 8:e2661. [PMID: 28277540 PMCID: PMC5386572 DOI: 10.1038/cddis.2017.80] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 02/02/2017] [Indexed: 11/24/2022]
Abstract
Missense mutations in TP53 comprise >75% of all p53 alterations in cancer, resulting in highly stabilized mutant p53 proteins that not only lose their tumor-suppressor activity, but often acquire oncogenic gain-of-functions (GOFs). GOF manifests itself in accelerated tumor onset, increased metastasis, increased drug resistance and shortened survival in patients and mice. A known prerequisite for GOF is mutant p53 protein stabilization, which itself is linked to aberrant protein conformation. However, additional determinants for mutant p53 stabilization likely exist. Here we show that in initially heterozygous mouse tumors carrying the hotspot GOF allele R248Q (p53Q/+), another necessary prerequisite for mutant p53 stabilization and GOF in vivo is loss of the remaining wild-type p53 allele, termed loss-of-heterozygosity (LOH). Thus, in mouse tumors with high frequency of p53 LOH (osteosarcomas and fibrosarcomas), we find that mutant p53 protein is stabilized (16/17 cases, 94%) and tumor onset is significantly accelerated compared with p53+/− tumors (GOF). In contrast, in mouse tumors with low frequency of p53 LOH (MMTV-Neu breast carcinomas), mutant p53 protein is not stabilized (16/20 cases, 80%) and GOF is not observed. Of note, human genomic databases (TCGA, METABRIC etc.) show a high degree of p53 LOH in all examined tumor types that carry missense p53 mutations, including sarcomas and breast carcinomas (with and without HER2 amplification). These data – while cautioning that not all genetic mouse models faithfully represent the human situation – demonstrate for the first time that p53 LOH is a critical prerequisite for missense mutant p53 stabilization and GOF in vivo.
Collapse
Affiliation(s)
| | - Safia A Mirza
- Department of Pathology, Stony Brook University, Stony Brook, NY, USA
| | - Sulan Xu
- Department of Pathology, Stony Brook University, Stony Brook, NY, USA
| | | | | | - Ute M Moll
- Department of Pathology, Stony Brook University, Stony Brook, NY, USA.,Institute of Molecular Oncology, University of Göttingen, Göttingen, Germany
| |
Collapse
|
175
|
Tonnessen-Murray CA, Lozano G, Jackson JG. The Regulation of Cellular Functions by the p53 Protein: Cellular Senescence. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a026112. [PMID: 27881444 DOI: 10.1101/cshperspect.a026112] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Transformed cells have properties that allow them to survive and proliferate inappropriately. These characteristics often arise as a result of mutations caused by DNA damage. p53 suppresses transformation by removing the proliferative or survival capacity of cells with DNA damage or inappropriate cell-cycle progression. Cellular senescence, marked by morphological and gene expression changes, is a critical component of p53-mediated tumor suppression. In response to stress, p53 can facilitate an arrest and senescence program in cells exposed to stresses such as DNA damage and oncogene activation, preventing transformation. Senescent cells are evident in precancerous adenoma-type lesions, whereas proliferating, malignant tumors have bypassed senescence, either by p53 mutation or inactivation of the p53 pathway by other means. Tumors that have retained wild-type p53 often show a p53-mediated senescence response to chemotherapy. This response is actually detrimental in some tumor types, as senescent cells can drive relapse by persisting and producing cytokines and chemokines through an acquired secretory phenotype.
Collapse
Affiliation(s)
- Crystal A Tonnessen-Murray
- Department of Biochemistry and Molecular Biology, Tulane School of Medicine, New Orleans, Louisiana 70112
| | - Guillermina Lozano
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas 77030
| | - James G Jackson
- Department of Biochemistry and Molecular Biology, Tulane School of Medicine, New Orleans, Louisiana 70112
| |
Collapse
|
176
|
Li D, Marchenko ND. ErbB2 inhibition by lapatinib promotes degradation of mutant p53 protein in cancer cells. Oncotarget 2017; 8:5823-5833. [PMID: 27791982 PMCID: PMC5351592 DOI: 10.18632/oncotarget.12878] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Accepted: 10/13/2016] [Indexed: 11/30/2022] Open
Abstract
Mutations in the p53 tumor suppressor gene are the most prevalent genetic events in human Her2-positive breast cancer and are associated with poor prognosis and survival. Human clinical data and our in vitro and in vivo studies strongly suggest potent oncogenic cooperation between mutant p53 and Her2 (ErbB2). Yet, the translational significance of mutant p53 in Her2 positive breast cancer, especially with respect to Her2-targeted therapies, has not been evaluated. Our previous work identified novel oncogenic activity of mutant p53 whereby mutp53 amplifies ErbB2 signaling via the mutp53-HSF1-ErbB2 feed-forward loop. Here we report that pharmacological interception of this circuit by ErbB2 inhibitor lapatinib downregulates mutant p53 in vitro and in vivo. We found that ErbB2 inhibition by lapatinib inhibits transcription factor HSF1, and its target Hsp90, followed by mutant p53 degradation in MDM2 dependent manner. Thus, our data suggest that mutant p53 sensitizes cancer cells to lapatinib via two complementary mechanisms: mutant p53 mediated amplification of ErbB2 signaling, and simultaneous annihilation of both potent oncogenic drivers, ErbB2 and mutant p53. Hence, our study could provide valuable information for the optimization of therapeutic protocols to achieve superior clinical effects in the treatment of Her2 positive breast cancer.
Collapse
Affiliation(s)
- Dun Li
- Department of Pathology, Stony Brook University, Stony Brook, NY, 11794, USA
- Department of Pharmacology, Boston University School of Medicine, Boston, MA, 02118, USA
| | - Natalia D Marchenko
- Department of Pathology, Stony Brook University, Stony Brook, NY, 11794, USA
| |
Collapse
|
177
|
Silwal-Pandit L, Langerød A, Børresen-Dale AL. TP53 Mutations in Breast and Ovarian Cancer. Cold Spring Harb Perspect Med 2017; 7:cshperspect.a026252. [PMID: 27815305 DOI: 10.1101/cshperspect.a026252] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Breast and ovarian cancers are the second and fifth leading causes of cancer deaths among women. Both breast and ovarian cancers are highly heterogeneous and are presented with diverse morphology, natural history, and response to therapy. In recent years, international efforts have led to extensive molecular characterization of both breast and ovarian tumors and identified biologically and clinically relevant subtypes of the diseases based on these molecular features. The role of TP53 in tumor initiation and progression is context dependent, and abrogation of the TP53 pathway seems to be essential for the development of basal-like breast cancers and high-grade serous ovarian cancers. These subtypes of breast and ovarian cancer show several genomic similarities including high frequency of TP53 mutation, which seems to be an early, initiating, and driving alteration in these cancer subtypes.
Collapse
Affiliation(s)
- Laxmi Silwal-Pandit
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital The Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway
| | - Anita Langerød
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital The Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway
| | - Anne-Lise Børresen-Dale
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital The Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway
| |
Collapse
|
178
|
Dong ZY, Zhong WZ, Zhang XC, Su J, Xie Z, Liu SY, Tu HY, Chen HJ, Sun YL, Zhou Q, Yang JJ, Yang XN, Lin JX, Yan HH, Zhai HR, Yan LX, Liao RQ, Wu SP, Wu YL. Potential Predictive Value of TP53 and KRAS Mutation Status for Response to PD-1 Blockade Immunotherapy in Lung Adenocarcinoma. Clin Cancer Res 2016; 23:3012-3024. [PMID: 28039262 DOI: 10.1158/1078-0432.ccr-16-2554] [Citation(s) in RCA: 676] [Impact Index Per Article: 84.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 12/01/2016] [Accepted: 12/22/2016] [Indexed: 12/30/2022]
Abstract
Purpose: Although clinical studies have shown promise for targeting programmed cell death protein-1 (PD-1) and ligand (PD-L1) signaling in non-small cell lung cancer (NSCLC), the factors that predict which subtype patients will be responsive to checkpoint blockade are not fully understood.Experimental Design: We performed an integrated analysis on the multiple-dimensional data types including genomic, transcriptomic, proteomic, and clinical data from cohorts of lung adenocarcinoma public (discovery set) and internal (validation set) database and immunotherapeutic patients. Gene set enrichment analysis (GSEA) was used to determine potentially relevant gene expression signatures between specific subgroups.Results: We observed that TP53 mutation significantly increased expression of immune checkpoints and activated T-effector and interferon-γ signature. More importantly, the TP53/KRAS comutated subgroup manifested exclusive increased expression of PD-L1 and a highest proportion of PD-L1+/CD8A+ Meanwhile, TP53- or KRAS-mutated tumors showed prominently increased mutation burden and specifically enriched in the transversion-high (TH) cohort. Further analysis focused on the potential molecular mechanism revealed that TP53 or KRAS mutation altered a group of genes involved in cell-cycle regulating, DNA replication and damage repair. Finally, immunotherapeutic analysis from public clinical trial and prospective observation in our center were further confirmed that TP53 or KRAS mutation patients, especially those with co-occurring TP53/KRAS mutations, showed remarkable clinical benefit to PD-1 inhibitors.Conclusions: This work provides evidence that TP53 and KRAS mutation in lung adenocarcinoma may be served as a pair of potential predictive factors in guiding anti-PD-1/PD-L1 immunotherapy. Clin Cancer Res; 23(12); 3012-24. ©2016 AACR.
Collapse
Affiliation(s)
- Zhong-Yi Dong
- Guangdong Lung Cancer Institute, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
- Southern Medical University, Guangzhou, China
| | - Wen-Zhao Zhong
- Guangdong Lung Cancer Institute, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xu-Chao Zhang
- Guangdong Lung Cancer Institute, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jian Su
- Guangdong Lung Cancer Institute, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Zhi Xie
- Guangdong Lung Cancer Institute, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Si-Yang Liu
- Guangdong Lung Cancer Institute, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Hai-Yan Tu
- Guangdong Lung Cancer Institute, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Hua-Jun Chen
- Guangdong Lung Cancer Institute, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yue-Li Sun
- Guangdong Lung Cancer Institute, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Qing Zhou
- Guangdong Lung Cancer Institute, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jin-Ji Yang
- Guangdong Lung Cancer Institute, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Xue-Ning Yang
- Guangdong Lung Cancer Institute, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Jia-Xin Lin
- Guangdong Lung Cancer Institute, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Hong-Hong Yan
- Guangdong Lung Cancer Institute, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Hao-Ran Zhai
- Guangdong Lung Cancer Institute, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
- Southern Medical University, Guangzhou, China
| | - Li-Xu Yan
- Department of Pathology and Laboratory Medicine, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Ri-Qiang Liao
- Guangdong Lung Cancer Institute, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Si-Pei Wu
- Guangdong Lung Cancer Institute, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China
| | - Yi-Long Wu
- Guangdong Lung Cancer Institute, Guangdong General Hospital and Guangdong Academy of Medical Sciences, Guangzhou, China.
- Southern Medical University, Guangzhou, China
| |
Collapse
|
179
|
Tokunaga E, Yamashita N, Tanaka K, Inoue Y, Akiyoshi S, Saeki H, Oki E, Kitao H, Maehara Y. Expression of APOBEC3B mRNA in Primary Breast Cancer of Japanese Women. PLoS One 2016; 11:e0168090. [PMID: 27977754 PMCID: PMC5158016 DOI: 10.1371/journal.pone.0168090] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 11/25/2016] [Indexed: 12/19/2022] Open
Abstract
Recent studies have identified the apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3B (APOBEC3B) as a source of mutations in various malignancies. APOBEC3B is overexpressed in several human cancer types, including breast cancer. In this study, we analyzed APOBEC3B mRNA expression in 305 primary breast cancers of Japanese women using quantitative reverse transcription-PCR, and investigated the relationships between the APOBEC3B mRNA expression and clinicopathological characteristics, prognosis, and TP53 mutations. The expression of APOBEC3B mRNA was detected in 277 tumors and not detected in 28 tumors. High APOBEC3B mRNA expression was significantly correlated with ER- and PR-negativity, high grade and high Ki67 index. The APOBEC3B mRNA expression was highest in the triple-negative and lowest in the hormone receptor-positive/HER2-negative subtypes. The TP53 gene was more frequently mutated in the tumors with high APOBEC3B mRNA expression. High APOBEC3B mRNA expression was significantly associated with poor recurrence-free survival in all cases and the ER-positive cases. These findings were almost consistent with the previous reports from the Western countries. In conclusion, high APOBEC3B mRNA expression was related to the aggressive phenotypes of breast cancer, high frequency of TP53 mutation and poor prognosis, especially in ER-positive tumors.
Collapse
Affiliation(s)
- Eriko Tokunaga
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
- * E-mail: ,
| | - Nami Yamashita
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Kimihiro Tanaka
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Yuka Inoue
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Sayuri Akiyoshi
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Hiroshi Saeki
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Eiji Oki
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Hiroyuki Kitao
- Department of Molecular Oncology, Graduate School of Medical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| | - Yoshihiko Maehara
- Department of Surgery and Science, Graduate School of Medical Sciences, Kyushu University, Maidashi, Higashi-ku, Fukuoka, Japan
| |
Collapse
|
180
|
Jiang T, Shi W, Wali VB, Pongor LS, Li C, Lau R, Győrffy B, Lifton RP, Symmans WF, Pusztai L, Hatzis C. Predictors of Chemosensitivity in Triple Negative Breast Cancer: An Integrated Genomic Analysis. PLoS Med 2016; 13:e1002193. [PMID: 27959926 PMCID: PMC5154510 DOI: 10.1371/journal.pmed.1002193] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Accepted: 10/28/2016] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Triple negative breast cancer (TNBC) is a highly heterogeneous and aggressive disease, and although no effective targeted therapies are available to date, about one-third of patients with TNBC achieve pathologic complete response (pCR) from standard-of-care anthracycline/taxane (ACT) chemotherapy. The heterogeneity of these tumors, however, has hindered the discovery of effective biomarkers to identify such patients. METHODS AND FINDINGS We performed whole exome sequencing on 29 TNBC cases from the MD Anderson Cancer Center (MDACC) selected because they had either pCR (n = 18) or extensive residual disease (n = 11) after neoadjuvant chemotherapy, with cases from The Cancer Genome Atlas (TCGA; n = 144) and METABRIC (n = 278) cohorts serving as validation cohorts. Our analysis revealed that mutations in the AR- and FOXA1-regulated networks, in which BRCA1 plays a key role, are associated with significantly higher sensitivity to ACT chemotherapy in the MDACC cohort (pCR rate of 94.1% compared to 16.6% in tumors without mutations in AR/FOXA1 pathway, adjusted p = 0.02) and significantly better survival outcome in the TCGA TNBC cohort (log-rank test, p = 0.05). Combined analysis of DNA sequencing, DNA methylation, and RNA sequencing identified tumors of a distinct BRCA-deficient (BRCA-D) TNBC subtype characterized by low levels of wild-type BRCA1/2 expression. Patients with functionally BRCA-D tumors had significantly better survival with standard-of-care chemotherapy than patients whose tumors were not BRCA-D (log-rank test, p = 0.021), and they had significantly higher mutation burden (p < 0.001) and presented clonal neoantigens that were associated with increased immune cell activity. A transcriptional signature of BRCA-D TNBC tumors was independently validated to be significantly associated with improved survival in the METABRIC dataset (log-rank test, p = 0.009). As a retrospective study, limitations include the small size and potential selection bias in the discovery cohort. CONCLUSIONS The comprehensive molecular analysis presented in this study directly links BRCA deficiency with increased clonal mutation burden and significantly enhanced chemosensitivity in TNBC and suggests that functional RNA-based BRCA deficiency needs to be further examined in TNBC.
Collapse
Affiliation(s)
- Tingting Jiang
- Department of Medicine, Yale School of Medicine, Yale University, New Haven, Connecticut, United States of America
| | - Weiwei Shi
- Department of Medicine, Yale School of Medicine, Yale University, New Haven, Connecticut, United States of America
| | - Vikram B. Wali
- Department of Medicine, Yale School of Medicine, Yale University, New Haven, Connecticut, United States of America
| | - Lőrinc S. Pongor
- MTA TTK Lendulet Cancer Biomarker Research Group, Research Center for Natural Sciences, Budapest, Hungary
- 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Charles Li
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, Connecticut, United States of America
| | - Rosanna Lau
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Balázs Győrffy
- MTA TTK Lendulet Cancer Biomarker Research Group, Research Center for Natural Sciences, Budapest, Hungary
- 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Richard P. Lifton
- Department of Medicine, Yale School of Medicine, Yale University, New Haven, Connecticut, United States of America
- Department of Genetics, Yale School of Medicine, Yale University, New Haven, Connecticut, United States of America
- Yale Cancer Center, New Haven, Connecticut, United States of America
| | - William F. Symmans
- Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Lajos Pusztai
- Department of Medicine, Yale School of Medicine, Yale University, New Haven, Connecticut, United States of America
- Yale Cancer Center, New Haven, Connecticut, United States of America
| | - Christos Hatzis
- Department of Medicine, Yale School of Medicine, Yale University, New Haven, Connecticut, United States of America
- Yale Cancer Center, New Haven, Connecticut, United States of America
- * E-mail:
| |
Collapse
|
181
|
Maguire SL, Peck B, Wai PT, Campbell J, Barker H, Gulati A, Daley F, Vyse S, Huang P, Lord CJ, Farnie G, Brennan K, Natrajan R. Three-dimensional modelling identifies novel genetic dependencies associated with breast cancer progression in the isogenic MCF10 model. J Pathol 2016; 240:315-328. [PMID: 27512948 PMCID: PMC5082563 DOI: 10.1002/path.4778] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 07/05/2016] [Accepted: 08/02/2016] [Indexed: 12/21/2022]
Abstract
The initiation and progression of breast cancer from the transformation of the normal epithelium to ductal carcinoma in situ (DCIS) and invasive disease is a complex process involving the acquisition of genetic alterations and changes in gene expression, alongside microenvironmental and recognized histological alterations. Here, we sought to comprehensively characterise the genomic and transcriptomic features of the MCF10 isogenic model of breast cancer progression, and to functionally validate potential driver alterations in three-dimensional (3D) spheroids that may provide insights into breast cancer progression, and identify targetable alterations in conditions more similar to those encountered in vivo. We performed whole genome, exome and RNA sequencing of the MCF10 progression series to catalogue the copy number and mutational and transcriptomic landscapes associated with progression. We identified a number of predicted driver mutations (including PIK3CA and TP53) that were acquired during transformation of non-malignant MCF10A cells to their malignant counterparts that are also present in analysed primary breast cancers from The Cancer Genome Atlas (TCGA). Acquisition of genomic alterations identified MYC amplification and previously undescribed RAB3GAP1-HRAS and UBA2-PDCD2L expressed in-frame fusion genes in malignant cells. Comparison of pathway aberrations associated with progression showed that, when cells are grown as 3D spheroids, they show perturbations of cancer-relevant pathways. Functional interrogation of the dependency on predicted driver events identified alterations in HRAS, PIK3CA and TP53 that selectively decreased cell growth and were associated with progression from preinvasive to invasive disease only when cells were grown as spheroids. Our results have identified changes in the genomic repertoire in cell lines representative of the stages of breast cancer progression, and demonstrate that genetic dependencies can be uncovered when cells are grown in conditions more like those in vivo. The MCF10 progression series therefore represents a good model with which to dissect potential biomarkers and to evaluate therapeutic targets involved in the progression of breast cancer. © 2016 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
Collapse
MESH Headings
- Breast Neoplasms/genetics
- Breast Neoplasms/pathology
- Carcinoma, Ductal, Breast/genetics
- Carcinoma, Ductal, Breast/pathology
- Carcinoma, Intraductal, Noninfiltrating/genetics
- Carcinoma, Intraductal, Noninfiltrating/pathology
- Cell Line, Tumor
- Cell Transformation, Neoplastic
- Class I Phosphatidylinositol 3-Kinases
- DNA, Neoplasm/chemistry
- DNA, Neoplasm/genetics
- Disease Progression
- Exome/genetics
- Female
- Gene Expression Regulation, Neoplastic
- Genome
- High-Throughput Nucleotide Sequencing
- Humans
- Models, Biological
- Mutation
- Phosphatidylinositol 3-Kinases/genetics
- Phosphatidylinositol 3-Kinases/metabolism
- Sequence Analysis, DNA
- Spheroids, Cellular
- Transcriptome
- Tumor Suppressor Protein p53/genetics
Collapse
Affiliation(s)
- Sarah L Maguire
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer, The Institute of Cancer Research, London, UK
| | - Barrie Peck
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer, The Institute of Cancer Research, London, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Patty T Wai
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer, The Institute of Cancer Research, London, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - James Campbell
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer, The Institute of Cancer Research, London, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Holly Barker
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer, The Institute of Cancer Research, London, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Aditi Gulati
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer, The Institute of Cancer Research, London, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Frances Daley
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer, The Institute of Cancer Research, London, UK
| | - Simon Vyse
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Paul Huang
- Division of Cancer Biology, The Institute of Cancer Research, London, UK
| | - Christopher J Lord
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer, The Institute of Cancer Research, London, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK
| | - Gillian Farnie
- Institute of Cancer Sciences, University of Manchester, Manchester, UK
| | - Keith Brennan
- Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Rachael Natrajan
- The Breast Cancer Now Toby Robins Research Centre, Division of Breast Cancer, The Institute of Cancer Research, London, UK.
- Division of Molecular Pathology, The Institute of Cancer Research, London, UK.
| |
Collapse
|
182
|
Hainaut P, Pfeifer GP. Somatic TP53 Mutations in the Era of Genome Sequencing. Cold Spring Harb Perspect Med 2016; 6:cshperspect.a026179. [PMID: 27503997 DOI: 10.1101/cshperspect.a026179] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Amid the complexity of genetic alterations in human cancer, TP53 mutation appears as an almost invariant component, representing by far the most frequent genetic alteration overall. Compared with previous targeted sequencing studies, recent integrated genomics studies offer a less biased view of TP53 mutation patterns, revealing that >20% of mutations occur outside the DNA-binding domain. Among the 12 mutations representing each at least 1% of all mutations, five occur at residues directly involved in specific DNA binding, four affect the tertiary fold of the DNA-binding domain, and three are nonsense mutations, two of them in the carboxyl terminus. Significant mutations also occur in introns, affecting alternative splicing events or generating rearrangements (e.g., in intron 1 in sporadic osteosarcoma). In aggressive cancers, mutation is so common that it may not have prognostic value (all these cancers have impaired p53 function caused by mutation or by other mechanisms). In several other cancers, however, mutation makes a clear difference for prognostication, as, for example, in HER2-enriched breast cancers and in lung adenocarcinoma with EGFR mutations. Thus, the clinical significance of TP53 mutation is dependent on tumor subtype and context. Understanding the clinical impact of mutation will require integrating mutation-specific information (type, frequency, and predicted impact) with data on haplotypes and on loss of heterozygosity.
Collapse
Affiliation(s)
- Pierre Hainaut
- University Grenoble Alpes, Institut Albert Bonniot, Institut National de la Santé et de la Recherche Médicale (INSERM), 823 Grenoble, France
| | - Gerd P Pfeifer
- Center for Epigenetics, Van Andel Research Institute, Grand Rapids, Michigan 49503
| |
Collapse
|
183
|
Murnyák B, Hortobágyi T. Immunohistochemical correlates of TP53 somatic mutations in cancer. Oncotarget 2016; 7:64910-64920. [PMID: 27626311 PMCID: PMC5323125 DOI: 10.18632/oncotarget.11912] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Accepted: 09/01/2016] [Indexed: 12/20/2022] Open
Abstract
Despite controversy on the correlation between p53 accumulation and TP53 mutational status, immunohistochemical (IHC) detection of overexpressed protein has long been used as a surrogate method for mutation analysis. The aim of our study was to characterise the IHC expression features of TP53 somatic mutations and define their occurrence in human cancers. A large-scale database analysis was conducted in the IARC TP53 Database (R17); 7878 mutations with IHC features were retrieved representing 60 distinct tumour sites. The majority of the alterations were immunopositive (p <0.001). Sex was known for 4897 mutations showing a female dominance (57.2%) and females carrying negative mutations were significantly younger. TP53 mutations were divided into three IHC groups according to mutation frequency and IHC positivity. Each group had female dominance. Among the IHC groups, significant correlations were observed with age at diagnosis in breast, bladder, liver, haematopoietic system and head & neck cancers. An increased likelihood of false negative IHC associated with rare nonsense mutations was observed in certain tumour sites. Our study demonstrates that p53 immunopositivity largely correlates with TP53 mutational status but expression is absent in certain mutation types.Besides, describing the complex IHC expression of TP53 somatic mutations, our results reveal some caveats for the diagnostic practice.
Collapse
Affiliation(s)
- Balázs Murnyák
- Division of Neuropathology, Institute of Pathology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| | - Tibor Hortobágyi
- Division of Neuropathology, Institute of Pathology, Faculty of Medicine, University of Debrecen, Debrecen, Hungary
| |
Collapse
|
184
|
Santarpia L, Bottai G, Kelly CM, Győrffy B, Székely B, Pusztai L. Deciphering and Targeting Oncogenic Mutations and Pathways in Breast Cancer. Oncologist 2016; 21:1063-78. [PMID: 27384237 PMCID: PMC5016060 DOI: 10.1634/theoncologist.2015-0369] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Accepted: 04/16/2016] [Indexed: 12/27/2022] Open
Abstract
UNLABELLED : Advances in DNA and RNA sequencing revealed substantially greater genomic complexity in breast cancer than simple models of a few driver mutations would suggest. Only very few, recurrent mutations or copy-number variations in cancer-causing genes have been identified. The two most common alterations in breast cancer are TP53 (affecting the majority of triple-negative breast cancers) and PIK3CA (affecting almost half of estrogen receptor-positive cancers) mutations, followed by a long tail of individually rare mutations affecting <1%-20% of cases. Each cancer harbors from a few dozen to a few hundred potentially high-functional impact somatic variants, along with a much larger number of potentially high-functional impact germline variants. It is likely that it is the combined effect of all genomic variations that drives the clinical behavior of a given cancer. Furthermore, entirely new classes of oncogenic events are being discovered in the noncoding areas of the genome and in noncoding RNA species driven by errors in RNA editing. In light of this complexity, it is not unexpected that, with the exception of HER2 amplification, no robust molecular predictors of benefit from targeted therapies have been identified. In this review, we summarize the current genomic portrait of breast cancer, focusing on genetic aberrations that are actively being targeted with investigational drugs. IMPLICATIONS FOR PRACTICE Next-generation sequencing is now widely available in the clinic, but interpretation of the results is challenging, and its impact on treatment selection is often limited. This work provides an overview of frequently encountered molecular abnormalities in breast cancer and discusses their potential therapeutic implications. This review emphasizes the importance of administering investigational targeted therapies, or off-label use of approved targeted drugs, in the context of a formal clinical trial or registry programs to facilitate learning about the clinical utility of tumor target profiling.
Collapse
Affiliation(s)
- Libero Santarpia
- Oncology Experimental Therapeutics, Istituto di Ricovero e Cura a Carattere Scientifico Humanitas Clinical and Research Institute, Milan, Italy
| | - Giulia Bottai
- Oncology Experimental Therapeutics, Istituto di Ricovero e Cura a Carattere Scientifico Humanitas Clinical and Research Institute, Milan, Italy
| | | | - Balázs Győrffy
- 2nd Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Borbala Székely
- 2nd Department of Pathology, Semmelweis University, Budapest, Hungary
| | - Lajos Pusztai
- Yale Cancer Center, School of Medicine, Yale University, New Haven, Connecticut, USA
| |
Collapse
|
185
|
Girotra S, Yeghiazaryan K, Golubnitschaja O. Potential biomarker panels in overall breast cancer management: advancements by multilevel diagnostics. Per Med 2016; 13:469-484. [PMID: 29767597 DOI: 10.2217/pme-2016-0020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Breast cancer (BC) prevalence has reached an epidemic scale with half a million deaths annually. Current deficits in BC management include predictive and preventive approaches, optimized screening programs, individualized patient profiling, highly sensitive detection technologies for more precise diagnostics and therapy monitoring, individualized prediction and effective treatment of BC metastatic disease. To advance BC management, paradigm shift from delayed to predictive, preventive and personalized medical services is essential. Corresponding step forwards requires innovative multilevel diagnostics procuring specific panels of validated biomarkers. Here, we discuss current instrumental advancements including genomics, proteomics, epigenetics, miRNA, metabolomics, circulating tumor cells and cancer stem cells with a focus on biomarker discovery and multilevel diagnostic panels. A list of the recommended biomarker candidates is provided.
Collapse
|
186
|
Ferrari A, Vincent-Salomon A, Pivot X, Sertier AS, Thomas E, Tonon L, Boyault S, Mulugeta E, Treilleux I, MacGrogan G, Arnould L, Kielbassa J, Le Texier V, Blanché H, Deleuze JF, Jacquemier J, Mathieu MC, Penault-Llorca F, Bibeau F, Mariani O, Mannina C, Pierga JY, Trédan O, Bachelot T, Bonnefoi H, Romieu G, Fumoleau P, Delaloge S, Rios M, Ferrero JM, Tarpin C, Bouteille C, Calvo F, Gut IG, Gut M, Martin S, Nik-Zainal S, Stratton MR, Pauporté I, Saintigny P, Birnbaum D, Viari A, Thomas G. A whole-genome sequence and transcriptome perspective on HER2-positive breast cancers. Nat Commun 2016; 7:12222. [PMID: 27406316 PMCID: PMC4947184 DOI: 10.1038/ncomms12222] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 06/12/2016] [Indexed: 02/06/2023] Open
Abstract
HER2-positive breast cancer has long proven to be a clinically distinct class of breast cancers for which several targeted therapies are now available. However, resistance to the treatment associated with specific gene expressions or mutations has been observed, revealing the underlying diversity of these cancers. Therefore, understanding the full extent of the HER2-positive disease heterogeneity still remains challenging. Here we carry out an in-depth genomic characterization of 64 HER2-positive breast tumour genomes that exhibit four subgroups, based on the expression data, with distinctive genomic features in terms of somatic mutations, copy-number changes or structural variations. The results suggest that, despite being clinically defined by a specific gene amplification, HER2-positive tumours melt into the whole luminal-basal breast cancer spectrum rather than standing apart. The results also lead to a refined ERBB2 amplicon of 106 kb and show that several cases of amplifications are compatible with a breakage-fusion-bridge mechanism.
Collapse
Affiliation(s)
- Anthony Ferrari
- Synergie Lyon Cancer, Plateforme de bioinformatique ‘Gilles Thomas' Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
| | - Anne Vincent-Salomon
- Institut Curie, PSL Research University, Département de Pathologie, INSERM U934, 26 rue d'Ulm, 75248 Paris, France
| | - Xavier Pivot
- Centre Hospitalier Universitaire de Minjoz, UMR INSERM 1098, Boulevard A. Fleming, Besançon 25000, France
| | - Anne-Sophie Sertier
- Synergie Lyon Cancer, Plateforme de bioinformatique ‘Gilles Thomas' Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
| | - Emilie Thomas
- Synergie Lyon Cancer, Plateforme de bioinformatique ‘Gilles Thomas' Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
| | - Laurie Tonon
- Synergie Lyon Cancer, Plateforme de bioinformatique ‘Gilles Thomas' Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
| | - Sandrine Boyault
- Plateforme de génomique des cancers, Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
| | - Eskeatnaf Mulugeta
- Institut Curie, UMR 3215 CNRS, Génétique et biologie du développement, Epigénèse et développement des mammifères, U934 Inserm, 26 rue d'Ulm, 75248 Paris, France
| | - Isabelle Treilleux
- Centre Léon Bérard, Département de Pathologie, 28 rue Laënnec, 69008 Lyon, France
| | - Gaëtan MacGrogan
- Département de Biopathologie, Unité Inserm U916, Institut Bergonié, 229 cours de l'Argonne, 33076 Bordeaux, France
| | - Laurent Arnould
- Centre Georges-François Leclerc et CRB Ferdinand Cabanne, 1 rue du Professeur Marion, Inserm U866-UBFC, 21000 Dijon, France
| | - Janice Kielbassa
- Synergie Lyon Cancer, Plateforme de bioinformatique ‘Gilles Thomas' Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
| | - Vincent Le Texier
- Synergie Lyon Cancer, Plateforme de bioinformatique ‘Gilles Thomas' Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
| | - Hélène Blanché
- Centre d'Etude du Polymorphisme Humain (CEPH), Fondation Jean Dausset, 27 rue Juliette Dodu, 75010 Paris, France
| | - Jean-François Deleuze
- Centre d'Etude du Polymorphisme Humain (CEPH), Fondation Jean Dausset, 27 rue Juliette Dodu, 75010 Paris, France
| | - Jocelyne Jacquemier
- Institut Paoli-Calmettes, Département de Pathologie, 232 Boulevard de Sainte-Marguerite, 13009 Marseille, France
| | - Marie-Christine Mathieu
- Institut Gustave Roussy, Comité de Pathologie Mammaire, 114 rue Edouard Vaillant, 94805 Villejuif, France
| | - Frédérique Penault-Llorca
- Centre Jean Perrin, Département de Biopathologie, EA 4677 ERTICa, Université d'Auvergne, 58 rue Montalembert, 63000 Clermont-Ferrand, France
| | - Frédéric Bibeau
- Institut Régional du Cancer de Montpellier (ICM), Département de Pathologie, 208 Avenue des Apothicaires, 34298 Montpellier, France
| | - Odette Mariani
- Institut Curie, PSL Research University, Service de Pathologie, Centre de Ressources Biologiques, BRIF BB-0033-00048, 26 rue d'Ulm, 75248 Paris, France
| | - Cécile Mannina
- Département de Pathologie, Institut Bergonié, 229 cours de l'Argonne, CS 61283, 33076 Bordeaux, France
| | - Jean-Yves Pierga
- Institut Curie, PSL Research University, Département d'Oncologie Médicale, Université Paris Descartes, 26 rue d'Ulm, 75248 Paris, France
| | - Olivier Trédan
- Centre Léon Bérard, Département de Cancérologie Médicale, 28 rue Laënnec, 69008 Lyon, France
| | - Thomas Bachelot
- Centre Léon Bérard, Département de Cancérologie Médicale, 28 rue Laënnec, 69008 Lyon, France
| | - Hervé Bonnefoi
- Department of Medical Oncology, Institut Bergonié Unicancer, University of Bordeaux, INSERM U916, CIC1401, 229 cours de l'Argonne, CS 61283, 33076 Bordeaux, France
| | - Gilles Romieu
- Institut Régional du Cancer de Montpellier (ICM), Oncologie Sénologie, 208 Avenue des Apothicaires, 34298 Montpellier, France
| | - Pierre Fumoleau
- Centre Georges-François Leclerc et CRB Ferdinand Cabanne, 1 rue du Professeur Marion, Inserm U866-UBFC, 21000 Dijon, France
| | - Suzette Delaloge
- Institut Gustave Roussy, Comité de Pathologie Mammaire, 114 rue Edouard Vaillant, 94805 Villejuif, France
| | - Maria Rios
- Centre Alexis Vautrin, Département d'Oncologie Médicale, 6 Avenue de Bourgogne, 54511 Vandoeuvre Les Nancy, France
| | - Jean-Marc Ferrero
- Centre Antoine Lacassagne, Département d'Oncologie Médicale, 33 Avenue de Valombrose, 06189 Nice, France
| | - Carole Tarpin
- Institut Paoli-Calmettes, Département d'Oncologie Médicale, 232 Boulevard de Sainte-Marguerite, 13009 Marseille, France
| | - Catherine Bouteille
- Clinique Mutualiste de Bellevue, Chirurgie Gynécologique et Mammaire, 3 rue le Verrier, 42100 Saint-Etienne, France
| | - Fabien Calvo
- Institut Gustave Roussy, Cancer Core Europe, 39 rue Camille Desmoulins, Villejuif 94805, France
| | - Ivo Glynne Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra, Plaça de la Mercè, 10, 08002 Barcelona, Spain
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), C/Baldiri Reixac 4, 08028 Barcelona, Spain
- Universitat Pompeu Fabra, Plaça de la Mercè, 10, 08002 Barcelona, Spain
| | - Sancha Martin
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Serena Nik-Zainal
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
- East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 9NB, UK
| | | | - Iris Pauporté
- Institut National du Cancer, Département de Recherche Clinique, 52 Avenue Morizet, 92513 Boulogne-Billancourt, France
| | - Pierre Saintigny
- INSERM U1052-CNRS 5286, Cancer Research Center of Lyon, F-69008 Lyon, France
- Université de Lyon, F-69622 Lyon, France
- Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
| | - Daniel Birnbaum
- Département d'Oncologie Moléculaire, Institut Paoli-Calmettes, Centre de Recherche en Cancérologie de Marseille, INSERM, CNRS, Aix-Marseille Université, 232 boulevard de Sainte-Marguerite, 13009 Marseille, France
| | - Alain Viari
- Synergie Lyon Cancer, Plateforme de bioinformatique ‘Gilles Thomas' Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
- Equipe Erable, INRIA Grenoble-Rhône-Alpes, 655 Avenue de l'Europe, 38330 Montbonnot-Saint Martin, France
| | - Gilles Thomas
- Synergie Lyon Cancer, Plateforme de bioinformatique ‘Gilles Thomas' Centre Léon Bérard, 28 rue Laënnec, 69008 Lyon, France
| |
Collapse
|
187
|
Kotoula V, Karavasilis V, Zagouri F, Kouvatseas G, Giannoulatou E, Gogas H, Lakis S, Pentheroudakis G, Bobos M, Papadopoulou K, Tsolaki E, Pectasides D, Lazaridis G, Koutras A, Aravantinos G, Christodoulou C, Papakostas P, Markopoulos C, Zografos G, Papandreou C, Fountzilas G. Effects of TP53 and PIK3CA mutations in early breast cancer: a matter of co-mutation and tumor-infiltrating lymphocytes. Breast Cancer Res Treat 2016; 158:307-21. [PMID: 27369359 DOI: 10.1007/s10549-016-3883-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 06/21/2016] [Indexed: 10/21/2022]
Abstract
The purpose of this study is to investigate whether the outcome of breast cancer (BC) patients treated with adjuvant chemotherapy is affected by co-mutated TP53 and PIK3CA according to stromal tumor-infiltrating lymphocytes (TILs). Paraffin tumors of all clinical subtypes from 1661 patients with operable breast cancer who were treated within 4 adjuvant trials with anthracycline-taxanes chemotherapy were informative for TP53 and PIK3CA mutation status (semiconductor sequencing genotyping) and for stromal TILs density. Disease-free survival (DFS) was examined. TP53 mutations were associated with higher (p < 0.001) and PIK3CA with lower (p = 0.004) TILs in an ER /PgR-specific manner (p < 0.001). Mutations did not affect the favorable DFS of patients with lymphocyte-predominant (LP) BC. Within non-LPBC, PIK3CA-only mutations conferred best, while TP53-PIK3CA co-mutations (6 % of all tumors) conferred worst DFS (HR 0.59; 95 % CI 0.44-0.79; p = 0.001 for PIK3CA-only). TP53-only mutations were unfavorable in patients with lower TILs, while patients with lower TILs performed worse if their tumors carried TP53-only mutations (interaction p = 0.046). Multivariate analysis revealed favorable PIK3CA-only mutations in non-LPBC (HR 0.64; 95 % CI 0.47-0.88; p = 0.007), and unfavorable TP53 mutations in ER/PgRpos/HER2neg (HR 1.55; 95 % CI 1.07-2.24; p = 0.021). Mutations did not interact with TILs in non-LP triple-negative and HER2-positive patients. TP53 and PIK3CA mutations appear to have diverse effects on the outcome of early BC patients, according to whether these genes are co-mutated or not, and for TP53 according to TILs density and ER/PgR-status. These findings need to be considered when evaluating the effect of these two most frequently mutated genes in the context of large clinical trials.
Collapse
Affiliation(s)
- Vassiliki Kotoula
- Department of Pathology, School of Health Sciences, School of Medicine, Faculty of Medicine, Aristotle University of Thessaloniki, Thessaloniki, Greece. .,Faculty of Medicine, Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece.
| | - Vasilios Karavasilis
- Department of Medical Oncology, Papageorgiou Hospital, Faculty of Medicine, School of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Flora Zagouri
- Department of Clinical Therapeutics, Alexandra Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - George Kouvatseas
- Department of Biostatistics, Health Data Specialists Ltd, Athens, Greece
| | - Eleni Giannoulatou
- Victor Chang Cardiac Research Institute, Darlinghurst, NSW, Australia.,The University of New South Wales, Kensington, NSW, Australia
| | - Helen Gogas
- First Department of Medicine, Laiko General Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - Sotiris Lakis
- Faculty of Medicine, Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | | | - Mattheos Bobos
- Faculty of Medicine, Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Kyriaki Papadopoulou
- Faculty of Medicine, Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Eleftheria Tsolaki
- Faculty of Medicine, Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Dimitrios Pectasides
- Oncology Section, Second Department of Internal Medicine, Hippokration Hospital, Athens, Greece
| | - Georgios Lazaridis
- Department of Medical Oncology, Papageorgiou Hospital, Faculty of Medicine, School of Health Sciences, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Angelos Koutras
- Division of Oncology, Department of Medicine, University Hospital, University of Patras Medical School, Patras, Greece
| | - Gerasimos Aravantinos
- Second Department of Medical Oncology, Agii Anargiri Cancer Hospital, Athens, Greece
| | | | | | - Christos Markopoulos
- Second Department of Prop. Surgery, Laiko General Hospital, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - George Zografos
- Breast Unit, National and Kapodistrian University of Athens School of Medicine, Athens, Greece
| | - Christos Papandreou
- Department of Medical Oncology, University Hospital of Larissa, University of Thessaly School of Medicine, Larissa, Greece
| | - George Fountzilas
- Faculty of Medicine, Laboratory of Molecular Oncology, Hellenic Foundation for Cancer Research/Aristotle University of Thessaloniki, Thessaloniki, Greece.,Aristotle University of Thessaloniki, Thessaloniki, Greece
| |
Collapse
|
188
|
Suh KJ, Ryu HS, Lee KH, Kim H, Min A, Kim TY, Yang Y, Moon HG, Han SW, Oh DY, Han W, Park IA, Noh DY, Im SA. Loss of ataxia-telangiectasia-mutated protein expression correlates with poor prognosis but benefits from anthracycline-containing adjuvant chemotherapy in breast cancer. Breast Cancer Res Treat 2016; 158:233-41. [DOI: 10.1007/s10549-016-3869-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Accepted: 06/14/2016] [Indexed: 10/21/2022]
|
189
|
A microscopic landscape of the invasive breast cancer genome. Sci Rep 2016; 6:27545. [PMID: 27283966 PMCID: PMC4901326 DOI: 10.1038/srep27545] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Accepted: 05/20/2016] [Indexed: 01/18/2023] Open
Abstract
Histologic grade is one of the most important microscopic features used to predict the prognosis of invasive breast cancer and may serve as a marker for studying cancer driving genomic abnormalities in vivo. We analyzed whole genome sequencing data from 680 cases of TCGA invasive ductal carcinomas of the breast and correlated them to corresponding pathology information. Ten genetic abnormalities were found to be statistically associated with histologic grade, including three most prevalent cancer driver events, TP53 and PIK3CA mutations and MYC amplification. A distinct genetic interaction among these genomic abnormalities was revealed as measured by the histologic grading score. While TP53 mutation and MYC amplification were synergistic in promoting tumor progression, PIK3CA mutation was found to have alleviated the oncogenic effect of either the TP53 mutation or MYC amplification, and was associated with a significant reduction in mitotic activity in TP53 mutated and/or MYC amplified breast cancer. Furthermore, we discovered that different types of genetic abnormalities (mutation versus amplification) within the same cancer driver gene (PIK3CA or GATA3) were associated with opposite histologic changes in invasive breast cancer. In conclusion, our study suggests that histologic grade may serve as a biomarker to define cancer driving genetic events in vivo.
Collapse
|
190
|
Zardavas D, Piccart-Gebhart M. New generation of breast cancer clinical trials implementing molecular profiling. Cancer Biol Med 2016; 13:226-35. [PMID: 27458530 PMCID: PMC4944544 DOI: 10.20892/j.issn.2095-3941.2015.0099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 02/26/2016] [Indexed: 01/04/2023] Open
Abstract
The implementation of molecular profiling technologies in oncology deepens our knowledge for the molecular landscapes of cancer diagnoses, identifying aberrations that could be linked with specific therapeutic vulnerabilities. In particular, there is an increasing list of molecularly targeted anticancer agents undergoing clinical development that aim to block specific molecular aberrations. This leads to a paradigm shift, with an increasing list of specific aberrations dictating the treatment of patients with cancer. This paradigm shift impacts the field of clinical trials, since the classical approach of having clinico-pathological disease characteristics dictating the patients' enrolment in oncology trials shifts towards the implementation of molecular profiling as pre-screening step. In order to facilitate the successful clinical development of these new anticancer drugs within specific molecular niches of cancer diagnoses, there have been developed new, innovative trial designs that could be classified as follows: i) longitudinal cohort studies that implement (or not) "nested" downstream trials, 2) studies that assess the clinical utility of molecular profiling, 3) "master" protocol trials, iv) "basket" trials, v) trials following an adaptive design. In the present article, we review these innovative study designs, providing representative examples from each category and we discuss the challenges that still need to be addressed in this era of new generation oncology trials implementing molecular profiling. Emphasis is put on the field of breast cancer clinical trials.
Collapse
Affiliation(s)
| | - Martine Piccart-Gebhart
- Medicine Department, Institut Jules Bordet, Université Libre de Bruxelles, Brussels 100, Belgium
| |
Collapse
|
191
|
Seagle BLL, Eng KH, Dandapani M, Yeh JY, Odunsi K, Shahabi S. Survival of patients with structurally-grouped TP53 mutations in ovarian and breast cancers. Oncotarget 2016. [PMID: 26215675 PMCID: PMC4621916 DOI: 10.18632/oncotarget.4080] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
The objective of this study was to determine if ovarian cancer patients with a TP53 mutation grouped by location of the mutation within the p53 protein structure exhibit differential survival outcomes. Data from patients with high grade serous ovarian cancer (HGS OvCa) (N = 316) or breast cancer (BrCa) (N = 981) sequenced by The Cancer Genome Atlas (TCGA) was studied by Kaplan-Meier and Cox proportional hazards survival analysis. A TP53 DNA binding domain (BD) missense mutation (MM) occurred in 58.5% (185/316) of HGS OvCas and 16.8% (165/981) of BrCas. Patients with a TP53 DNA BD MM grouped by structural location had significantly different overall survival (OS) and progression free survival (PFS). Median OS (months) of HGS OvCa patients by structural group were: Sheet-loop-helix stabilizers, 31.1; DNA minor groove residue R248, 33.6; Wild-type, 34.2; all other MMs, 44.5; DNA major groove residues, 84.1, and zinc ion coordinating residues, 87.0 (log-rank p = 0.006). PFS of DNA major groove MM cases was longer than TP53 wild-type cases (19.1 versus 10.1 months, log-rank p = 0.038). HGS OvCa and BrCa patients with structurally-grouped TP53 DNA BD MMs have different survival outcomes.
Collapse
Affiliation(s)
- Brandon-Luke L Seagle
- Department of Obstetrics, Gynecology and Reproductive Sciences, Western Connecticut Health Network, Danbury, CT, USA
| | - Kevin H Eng
- Department of Biostatistics and Bioinformatics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Monica Dandapani
- Department of Obstetrics, Gynecology and Reproductive Sciences, Western Connecticut Health Network, Danbury, CT, USA
| | - Judy Y Yeh
- Department of Obstetrics, Gynecology and Reproductive Sciences, Western Connecticut Health Network, Danbury, CT, USA
| | - Kunle Odunsi
- Department of Gynecologic Oncology, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Shohreh Shahabi
- Division of Gynecologic Oncology, Department of Obstetrics and Gynecology, Prentice Women's Hospital, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| |
Collapse
|
192
|
Manso L, Mourón S, Tress M, Gómez-López G, Morente M, Ciruelos E, Rubio-Camarillo M, Rodriguez-Peralto JL, Pujana MA, Pisano DG, Quintela-Fandino M. Analysis of Paired Primary-Metastatic Hormone-Receptor Positive Breast Tumors (HRPBC) Uncovers Potential Novel Drivers of Hormonal Resistance. PLoS One 2016; 11:e0155840. [PMID: 27195705 PMCID: PMC4873174 DOI: 10.1371/journal.pone.0155840] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Accepted: 05/05/2016] [Indexed: 12/15/2022] Open
Abstract
We sought to identify genetic variants associated with disease relapse and failure to hormonal treatment in hormone-receptor positive breast cancer (HRPBC). We analyzed a series of HRPBC with distant relapse, by sequencing pairs (n = 11) of tumors (primary and metastases) at >800X. Comparative genomic hybridization was performed as well. Top hits, based on the frequency of alteration and severity of the changes, were tested in the TCGA series. Genes determining the most parsimonious prognostic signature were studied for their functional role in vitro, by performing cell growth assays in hormonal-deprivation conditions, a setting that mimics treatment with aromatase inhibitors. Severe alterations were recurrently found in 18 genes in the pairs. However, only MYC, DNAH5, CSFR1, EPHA7, ARID1B, and KMT2C preserved an independent prognosis impact and/or showed a significantly different incidence of alterations between relapsed and non-relapsed cases in the TCGA series. The signature composed of MYC, KMT2C, and EPHA7 best discriminated the clinical course, (overall survival 90,7 vs. 144,5 months; p = 0.0001). Having an alteration in any of the genes of the signature implied a hazard ratio of death of 3.25 (p<0.0001), and early relapse during the adjuvant hormonal treatment. The presence of the D348N mutation in KMT2C and/or the T666I mutation in the kinase domain of EPHA7 conferred hormonal resistance in vitro. Novel inactivating mutations in KMT2C and EPHA7, which confer hormonal resistance, are linked to adverse clinical course in HRPBC.
Collapse
Affiliation(s)
- Luis Manso
- Medical Oncology Department, Hospital 12 de Octubre, Madrid, Spain
| | - Silvana Mourón
- Breast Cancer Clinical Research Unit, CNIO—Spanish National Cancer Research Center, Madrid, Spain
| | - Michael Tress
- Structural Computational Biology Group, CNIO—Spanish National Cancer Research Center, Madrid, Spain
| | - Gonzalo Gómez-López
- Bioinformatics Unit, CNIO—Spanish National Cancer Research Center, Madrid, Spain
| | - Manuel Morente
- Biobank, CNIO—Spanish National Cancer Research Center, Madrid, Spain
| | - Eva Ciruelos
- Breast Cancer Clinical Research Unit, CNIO—Spanish National Cancer Research Center, Madrid, Spain
| | | | | | - Miguel A. Pujana
- Translational Research Laboratory, Catalan Institute of Oncology, Bellvitge Institute for Biomedical Research, Barcelona, Spain
| | - David G. Pisano
- Bioinformatics Unit, CNIO—Spanish National Cancer Research Center, Madrid, Spain
| | - Miguel Quintela-Fandino
- Breast Cancer Clinical Research Unit, CNIO—Spanish National Cancer Research Center, Madrid, Spain
- * E-mail:
| |
Collapse
|
193
|
Swetzig WM, Wang J, Das GM. Estrogen receptor alpha (ERα/ESR1) mediates the p53-independent overexpression of MDM4/MDMX and MDM2 in human breast cancer. Oncotarget 2016; 7:16049-69. [PMID: 26909605 PMCID: PMC4941297 DOI: 10.18632/oncotarget.7533] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Accepted: 01/27/2016] [Indexed: 12/31/2022] Open
Abstract
MDM2 and MDM4 are heterodimeric, non-redundant oncoproteins that potently inhibit the p53 tumor suppressor protein. MDM2 and MDM4 also enhance the tumorigenicity of breast cancer cells in in vitro and in vivo models and are overexpressed in primary human breast cancers. Prior studies have characterized Estrogen Receptor Alpha (ERα/ESR1) as a regulator of MDM2 expression and an MDM2- and p53-interacting protein. However, similar crosstalk between ERα and MDM4 has not been investigated. Moreover, signaling pathways that mediate the overexpression of MDM4 in human breast cancer remain to be elucidated. Using the Cancer Genome Atlas (TCGA) breast invasive carcinoma patient cohort, we have analyzed correlations between ERα status and MDM4 and MDM2 expression in primary, treatment-naïve, invasive breast carcinoma samples. We report that the expression of MDM4 and MDM2 is elevated in primary human breast cancers of luminal A/B subtypes and associates with ERα-positive disease, independently of p53 mutation status. Furthermore, in cell culture models, ERα positively regulates MDM4 and MDM2 expression via p53-independent mechanisms, and these effects can be blocked by the clinically-relevant endocrine therapies fulvestrant and tamoxifen. Additionally, ERα also positively regulates p53 expression. Lastly, we report that endogenous MDM4 negatively regulates ERα expression and forms a protein complex with ERα in breast cancer cell lines and primary human breast tumor tissue. This suggests direct signaling crosstalk and negative feedback loops between ERα and MDM4 expression in breast cancer cells. Collectively, these novel findings implicate ERα as a central component of the p53-MDM2-MDM4 signaling axis in human breast cancer.
Collapse
Affiliation(s)
- Wendy M. Swetzig
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY, USA
- Department of Molecular Pharmacology and Cancer Therapeutics, The University at Buffalo, State University of New York, Buffalo, NY, USA
| | - Jianmin Wang
- Department of Bioinformatics and Biostatistics, Roswell Park Cancer Institute, Buffalo, NY, USA
| | - Gokul M. Das
- Department of Pharmacology and Therapeutics, Roswell Park Cancer Institute, Buffalo, NY, USA
- Department of Molecular Pharmacology and Cancer Therapeutics, The University at Buffalo, State University of New York, Buffalo, NY, USA
| |
Collapse
|
194
|
Jin MS, Park IA, Kim JY, Chung YR, Im SA, Lee KH, Moon HG, Han W, Noh DY, Ryu HS. New insight on the biological role of p53 protein as a tumor suppressor: re-evaluation of its clinical significance in triple-negative breast cancer. Tumour Biol 2016; 37:11017-24. [DOI: 10.1007/s13277-016-4990-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2015] [Accepted: 02/10/2016] [Indexed: 01/04/2023] Open
|
195
|
Zardavas D, Piccart-Gebhart M. Clinical Trials of Precision Medicine through Molecular Profiling: Focus on Breast Cancer. Am Soc Clin Oncol Educ Book 2016:e183-90. [PMID: 25993171 DOI: 10.14694/edbook_am.2015.35.e183] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
High-throughput technologies of molecular profiling in cancer, such as gene-expression profiling and next-generation sequencing, are expanding our knowledge of the molecular landscapes of several cancer types. This increasing knowledge coupled with the development of several molecularly targeted agents hold the promise for personalized cancer medicine to be fully realized. Moreover, an expanding armamentarium of targeted agents has been approved for the treatment of specific molecular cancer subgroups in different diagnoses. According to this paradigm, treatment selection should be dictated by the specific molecular aberrations found in each patient's tumor. The classical clinical trials paradigm of patients' eligibility being based on clinicopathologic parameters is being abandoned, with current clinical trials enrolling patients on the basis of specific molecular aberrations. New, innovative trial designs have been generated to better tackle the multiple challenges induced by the increasing molecular fragmentation of cancer, namely: (1) longitudinal cohort studies with or without downstream trials, (2) studies assessing the clinical utility of molecular profiling, (3) master or umbrella trials, (4) basket trials, (5) N-of-1 trials, and (6) adaptive design trials. This article provides an overview of the challenges for clinical trials in the era of molecular profiling of cancer. Subsequently, innovative trial designs with respective examples and their potential to expedite efficient clinical development of targeted anticancer agents is discussed.
Collapse
Affiliation(s)
- Dimitrios Zardavas
- From the Breast International Group, Brussels, Belgium; Institut Jules Bordet, Brussels, Belgium
| | - Martine Piccart-Gebhart
- From the Breast International Group, Brussels, Belgium; Institut Jules Bordet, Brussels, Belgium
| |
Collapse
|
196
|
Bjaanæs MM, Fleischer T, Halvorsen AR, Daunay A, Busato F, Solberg S, Jørgensen L, Kure E, Edvardsen H, Børresen-Dale AL, Brustugun OT, Tost J, Kristensen V, Helland Å. Genome-wide DNA methylation analyses in lung adenocarcinomas: Association with EGFR, KRAS and TP53 mutation status, gene expression and prognosis. Mol Oncol 2016; 10:330-43. [PMID: 26601720 PMCID: PMC5528958 DOI: 10.1016/j.molonc.2015.10.021] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Revised: 09/25/2015] [Accepted: 10/28/2015] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND DNA methylation alterations are early events in tumorigenesis and important in the regulation of gene expression in cancer cells. Lung cancer patients have in general a poor prognosis, and a deeper insight into the epigenetic landscape in lung adenocarcinoma tumors and its prognostic implications is needed. RESULTS We determined whole-genome DNA methylation profiles of 164 fresh frozen lung adenocarcinoma samples and 19 samples of matched normal lung tissue using the Illumina Infinium 450K array. A large number of differentially methylated CpGs in lung adenocarcinoma tissue were identified, and specific methylation profiles were observed in tumors with mutations in the EGFR-, KRAS- or TP53 genes and according to the patients' smoking status. The methylation levels were correlated with gene expression and both positive and negative correlations were seen. Methylation profiles of the tumor samples identified subtypes of tumors with distinct prognosis, including one subtype enriched for TP53 mutant tumors. A prognostic index based on the methylation levels of 33 CpGs was established, and was significantly associated with prognosis in the univariate analysis using an independent cohort of lung adenocarcinoma patients from The Cancer Genome Atlas project. CpGs in the HOX B and HOX C gene clusters were represented in the prognostic signature. CONCLUSIONS Methylation differences mirror biologically important features in the etiology of lung adenocarcinomas and influence prognosis.
Collapse
Affiliation(s)
- Maria Moksnes Bjaanæs
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital - The Norwegian Radium Hospital, Oslo, Norway; Department of Oncology, Oslo University Hospital - The Norwegian Radium Hospital, Oslo, Norway.
| | - Thomas Fleischer
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital - The Norwegian Radium Hospital, Oslo, Norway; The K.G. Jebsen Censtre for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway.
| | - Ann Rita Halvorsen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital - The Norwegian Radium Hospital, Oslo, Norway.
| | - Antoine Daunay
- Laboratory for Functional Genomics, Fondation Jean Dausset - CEPH, 75010 Paris, France.
| | - Florence Busato
- Laboratory for Epigenetics and Environment (LEE), Centre National de Génotypage, CEA - Institut de Génomique, 91000 Evry, France.
| | - Steinar Solberg
- Department of Cardiothoracic Surgery, Oslo University Hospital-Rikshospitalet, Oslo, Norway.
| | - Lars Jørgensen
- Department of Cardiothoracic Surgery, Oslo University Hospital-Rikshospitalet, Oslo, Norway.
| | - Elin Kure
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital - The Norwegian Radium Hospital, Oslo, Norway.
| | - Hege Edvardsen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital - The Norwegian Radium Hospital, Oslo, Norway.
| | - Anne-Lise Børresen-Dale
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital - The Norwegian Radium Hospital, Oslo, Norway; Institute of Clinical Medicine, Faculty of Medicine, University of Oslo, Norway.
| | - Odd Terje Brustugun
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital - The Norwegian Radium Hospital, Oslo, Norway; Department of Oncology, Oslo University Hospital - The Norwegian Radium Hospital, Oslo, Norway.
| | - Jörg Tost
- Laboratory for Epigenetics and Environment (LEE), Centre National de Génotypage, CEA - Institut de Génomique, 91000 Evry, France.
| | - Vessela Kristensen
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital - The Norwegian Radium Hospital, Oslo, Norway; The K.G. Jebsen Censtre for Breast Cancer Research, Institute for Clinical Medicine, Faculty of Medicine, University of Oslo, Norway; Department of Clinical Molecular Biology and Laboratory Science (EpiGen), Division of Medicine, Akershus University Hospital, Lørenskog, Norway.
| | - Åslaug Helland
- Department of Genetics, Institute for Cancer Research, Oslo University Hospital - The Norwegian Radium Hospital, Oslo, Norway; Department of Oncology, Oslo University Hospital - The Norwegian Radium Hospital, Oslo, Norway.
| |
Collapse
|
197
|
Treatment-induced cell cycle kinetics dictate tumor response to chemotherapy. Oncotarget 2016; 6:7040-52. [PMID: 25749523 PMCID: PMC4466668 DOI: 10.18632/oncotarget.3140] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Accepted: 01/11/2015] [Indexed: 12/31/2022] Open
Abstract
Chemotherapy fails to provide durable cure for the majority of cancer patients. To identify mechanisms associated with chemotherapy resistance, we identified genes differentially expressed before and after chemotherapeutic treatment of breast cancer patients. Treatment response resulted in either increased or decreased cell cycle gene expression. Tumors in which cell cycle gene expression was increased by chemotherapy were likely to be chemotherapy sensitive, whereas tumors in which cell cycle gene transcripts were decreased by chemotherapy were resistant to these agents. A gene expression signature that predicted these changes proved to be a robust and novel index that predicted the response of patients with breast, ovarian, and colon tumors to chemotherapy. Investigations in tumor cell lines supported these findings, and linked treatment induced cell cycle changes with p53 signaling and G1/G0 arrest. Hence, chemotherapy resistance, which can be predicted based on dynamics in cell cycle gene expression, is associated with TP53 integrity.
Collapse
|
198
|
Sheikh A, Hussain SA, Ghori Q, Naeem N, Fazil A, Giri S, Sathian B, Mainali P, Al Tamimi DM. The spectrum of genetic mutations in breast cancer. Asian Pac J Cancer Prev 2016; 16:2177-85. [PMID: 25824734 DOI: 10.7314/apjcp.2015.16.6.2177] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
Breast cancer is the most common malignancy in women around the world. About one in 12 women in the West develop breast cancer at some point in life. It is estimated that 5%-10% of all breast cancer cases in women are linked to hereditary susceptibility due to mutations in autosomal dominant genes. The two key players associated with high breast cancer risk are mutations in BRCA 1 and BRCA 2. Another highly important mutation can occur in TP53 resulting in a triple negative breast cancer. However, the great majority of breast cancer cases are not related to a mutated gene of high penetrance, but to genes of low penetrance such as CHEK2, CDH1, NBS1, RAD50, BRIP1 and PALB2, which are frequently mutated in the general population. In this review, we discuss the entire spectrum of mutations which are associated with breast cancer.
Collapse
Affiliation(s)
- Asfandyar Sheikh
- Dow Medical College, Dow University of Health Sciences, Karachi, Pakistan E-mail :
| | | | | | | | | | | | | | | | | |
Collapse
|
199
|
Di Agostino S, Sorrentino G, Ingallina E, Valenti F, Ferraiuolo M, Bicciato S, Piazza S, Strano S, Del Sal G, Blandino G. YAP enhances the pro-proliferative transcriptional activity of mutant p53 proteins. EMBO Rep 2015; 17:188-201. [PMID: 26691213 DOI: 10.15252/embr.201540488] [Citation(s) in RCA: 148] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2015] [Accepted: 11/19/2015] [Indexed: 01/02/2023] Open
Abstract
Mutant p53 proteins are present in more than half of human cancers. Yes-associated protein (YAP) is a key transcriptional regulator controlling organ growth, tissue homeostasis, and cancer. Here, we report that these two determinants of human malignancy share common transcriptional signatures. YAP physically interacts with mutant p53 proteins in breast cancer cells and potentiates their pro-proliferative transcriptional activity. We found YAP as well as mutant p53 and the transcription factor NF-Y onto the regulatory regions of cyclin A, cyclin B, and CDK1 genes. Either mutant p53 or YAP depletion down-regulates cyclin A, cyclin B, and CDK1 gene expression and markedly slows the growth of diverse breast cancer cell lines. Pharmacologically induced cytoplasmic re-localization of YAP reduces the expression levels of cyclin A, cyclin B, and CDK1 genes both in vitro and in vivo. Interestingly, primary breast cancers carrying p53 mutations and displaying high YAP activity exhibit higher expression levels of cyclin A, cyclin B, and CDK1 genes when compared to wt-p53 tumors.
Collapse
Affiliation(s)
- Silvia Di Agostino
- Translational Oncogenomic Unit, Molecular Medicine Area Regina Elena National Cancer Institute, Rome, Italy
| | - Giovanni Sorrentino
- Laboratorio Nazionale CIB (LNCIB), Area Science Park, Trieste, Italy Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Trieste, Italy
| | - Eleonora Ingallina
- Laboratorio Nazionale CIB (LNCIB), Area Science Park, Trieste, Italy Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Trieste, Italy
| | - Fabio Valenti
- Translational Oncogenomic Unit, Molecular Medicine Area Regina Elena National Cancer Institute, Rome, Italy
| | - Maria Ferraiuolo
- Translational Oncogenomic Unit, Molecular Medicine Area Regina Elena National Cancer Institute, Rome, Italy Molecular Chemoprevention Group, Molecular Medicine Area Regina Elena National Cancer Institute, Rome, Italy
| | - Silvio Bicciato
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Silvano Piazza
- Laboratorio Nazionale CIB (LNCIB), Area Science Park, Trieste, Italy
| | - Sabrina Strano
- Molecular Chemoprevention Group, Molecular Medicine Area Regina Elena National Cancer Institute, Rome, Italy
| | - Giannino Del Sal
- Laboratorio Nazionale CIB (LNCIB), Area Science Park, Trieste, Italy Dipartimento di Scienze della Vita, Università degli Studi di Trieste, Trieste, Italy
| | - Giovanni Blandino
- Translational Oncogenomic Unit, Molecular Medicine Area Regina Elena National Cancer Institute, Rome, Italy
| |
Collapse
|
200
|
Lin CH, Chen IC, Huang CS, Hu FC, Kuo WH, Kuo KT, Wang CC, Wu PF, Chang DY, Wang MY, Chang CH, Chen WW, Lu YS, Cheng AL. TP53 Mutational Analysis Enhances the Prognostic Accuracy of IHC4 and PAM50 Assays. Sci Rep 2015; 5:17879. [PMID: 26671300 PMCID: PMC4680865 DOI: 10.1038/srep17879] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Accepted: 11/06/2015] [Indexed: 02/04/2023] Open
Abstract
IHC4 and PAM50 assays have been shown to provide additional prognostic information for patients with early breast cancer. We evaluated whether incorporating TP53 mutation analysis can further enhance their prognostic accuracy. We examined TP53 mutation and the IHC4 score in tumors of 605 patients diagnosed with stage I-III breast cancer at National Taiwan University Hospital (the NTUH cohort). We obtained information regarding TP53 mutation and PAM50 subtypes in 699 tumors from the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) cohort. We found that TP53 mutation was significantly associated with high-risk IHC4 group and with luminal B, HER2-enriched, and basal-like subtypes. Despite the strong associations, TP53 mutation independently predicted shorter relapse-free survival (hazard ratio [HR] = 1.63, P = 0.007) in the NTUH cohort and shorter breast cancer-specific survival (HR = 2.35, P = <0.001) in the METABRIC cohort. TP53 mutational analysis added significant prognostic information in addition to the IHC4 score (∆ LR-χ(2) = 8.61, P = 0.002) in the NTUH cohort and the PAM50 subtypes (∆ LR-χ(2) = 18.9, P = <0.001) in the METABRIC cohort. We conclude that incorporating TP53 mutation analysis can enhance the prognostic accuracy of the IHC4 and PAM50 assays.
Collapse
Affiliation(s)
- Ching-Hung Lin
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan.,Department of Internal Medicine; National Taiwan University Hospital, Taipei, Taiwan.,Oncology Center, National Taiwan University Hospital Hsin-Chu Branch, Hsin-Chu, Taiwan
| | - I-Chiun Chen
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
| | - Chiun-Sheng Huang
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Fu-Chang Hu
- Graduate Institute of Clinical Medicine and School of Nursing, College of Medicine, National Taiwan University, Taipei, Taiwan.,International-Harvard Statistical Consulting Company, Taipei, Taiwan
| | - Wen-Hung Kuo
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Kuan-Ting Kuo
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Chung-Chieh Wang
- Department of Pathology, National Taiwan University Hospital, Taipei, Taiwan
| | - Pei-Fang Wu
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
| | - Dwan-Ying Chang
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
| | - Ming-Yang Wang
- Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan
| | - Chin-Hao Chang
- Department of Medical Research, National Taiwan University Hospital, Taipei, Taiwan
| | - Wei-Wu Chen
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan
| | - Yen-Shen Lu
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan.,Department of Internal Medicine; National Taiwan University Hospital, Taipei, Taiwan
| | - Ann-Lii Cheng
- Department of Oncology, National Taiwan University Hospital, Taipei, Taiwan.,Department of Internal Medicine; National Taiwan University Hospital, Taipei, Taiwan.,Graduate Institute of Oncology and Cancer Research Centre, College of Medicine, National Taiwan University, Taipei, Taiwan
| |
Collapse
|