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Pifer PM, Yang L, Kumar M, Xie T, Frederick M, Hefner A, Beadle B, Molkentine D, Molkentine J, Dhawan A, Abdelhakiem M, Osman AA, Leibowitz BJ, Myers JN, Pickering CR, Sandulache VC, Heymach J, Skinner HD. FAK Drives Resistance to Therapy in HPV-Negative Head and Neck Cancer in a p53-Dependent Manner. Clin Cancer Res 2024; 30:187-197. [PMID: 37819945 PMCID: PMC10767302 DOI: 10.1158/1078-0432.ccr-23-0964] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 07/21/2023] [Accepted: 10/09/2023] [Indexed: 10/13/2023]
Abstract
PURPOSE Radiation and platinum-based chemotherapy form the backbone of therapy in human papillomavirus (HPV)-negative head and neck squamous cell carcinoma (HNSCC). We have correlated focal adhesion kinase (FAK/PTK2) expression with radioresistance and worse outcomes in these patients. However, the importance of FAK in driving radioresistance and its effects on chemoresistance in these patients remains unclear. EXPERIMENTAL DESIGN We performed an in vivo shRNA screen using targetable libraries to identify novel therapeutic sensitizers for radiation and chemotherapy. RESULTS We identified FAK as an excellent target for both radio- and chemosensitization. Because TP53 is mutated in over 80% of HPV-negative HNSCC, we hypothesized that mutant TP53 may facilitate FAK-mediated therapy resistance. FAK inhibitor increased sensitivity to radiation, increased DNA damage, and repressed homologous recombination and nonhomologous end joining repair in mutant, but not wild-type, TP53 HPV-negative HNSCC cell lines. The mutant TP53 cisplatin-resistant cell line had increased FAK phosphorylation compared with wild-type, and FAK inhibition partially reversed cisplatin resistance. To validate these findings, we utilized an HNSCC cohort to show that FAK copy number and gene expression were associated with worse disease-free survival in mutant TP53, but not wild-type TP53, HPV-negative HNSCC tumors. CONCLUSIONS FAK may represent a targetable therapeutic sensitizer linked to a known genomic marker of resistance.
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Affiliation(s)
- Phillip M. Pifer
- Department of Radiation Oncology, University of Pittsburgh, UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania
| | - Liangpeng Yang
- Department of Experimental Radiation Oncology, University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - Manish Kumar
- Department of Biochemistry, All India Institute of Medical Sciences (AIIMS), Bilaspur, Himachal Pradesh, India
| | - Tongxin Xie
- Department of Head and Neck Surgery, University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - Mitchell Frederick
- Department of Otolaryngology-Head and Neck Surgery, Baylor College of Medicine, Houston, Texas
| | - Andrew Hefner
- Department of Radiation Oncology, University of Pittsburgh, UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania
| | - Beth Beadle
- Department of Radiation Oncology, Stanford University, Stanford, California
| | - David Molkentine
- Department of Radiation Oncology, University of Pittsburgh, UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania
| | - Jessica Molkentine
- Department of Radiation Oncology, University of Pittsburgh, UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania
| | - Annika Dhawan
- Department of Radiation Oncology, University of Pittsburgh, UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania
| | - Mohamed Abdelhakiem
- Department of Radiation Oncology, University of Pittsburgh, UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania
| | - Abdullah A. Osman
- Department of Head and Neck Surgery, University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - Brian J. Leibowitz
- Department of Radiation Oncology, University of Pittsburgh, UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania
| | - Jeffrey N. Myers
- Department of Head and Neck Surgery, University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - Curtis R. Pickering
- Department of Head and Neck Surgery, University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - Vlad C. Sandulache
- Department of Otolaryngology-Head and Neck Surgery, Baylor College of Medicine, Houston, Texas
| | - John Heymach
- Department of Thoracic and Head and Neck Medical Oncology, University of Texas, MD Anderson Cancer Center, Houston, Texas
| | - Heath D. Skinner
- Department of Radiation Oncology, University of Pittsburgh, UPMC Hillman Cancer Center, Pittsburgh, Pennsylvania
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2
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Treating Head and Neck Cancer in the Age of Immunotherapy: A 2023 Update. Drugs 2023; 83:217-248. [PMID: 36645621 DOI: 10.1007/s40265-023-01835-2] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/03/2023] [Indexed: 01/17/2023]
Abstract
Most patients diagnosed with head and neck squamous cell carcinoma (HNSCC) will present with locally advanced disease, requiring multimodality therapy. While this approach has a curative intent, a significant subset of these patients will develop locoregional failure and/or distant metastases. The prognosis of these patients is poor, and therapeutic options other than palliative chemotherapy are urgently needed. Epidermal growth factor receptor (EGFR) overexpression is an important factor in the pathogenesis of HNSCC, and a decade ago, the EGFR targeting monoclonal antibody cetuximab was approved for the treatment of late-stage HNSCC in different settings. In 2016, the anti-programmed death-1 (PD-1) immune checkpoint inhibitors nivolumab and pembrolizumab were both approved for the treatment of patients with recurrent or metastatic HNSCC with disease progression on or after platinum-containing chemotherapy, and in 2019, pembrolizumab was approved for first-line treatment (either as monotherapy in PD-L1 expressing tumors, or in combination with chemotherapy). Currently, trials are ongoing to include immune checkpoint inhibition in the (neo)adjuvant treatment of HNSCC as well as in novel combinations with other drugs in the recurrent/metastatic setting to improve response rates and survival and help overcome resistance mechanisms to immune checkpoint blockade. This article provides a comprehensive review of the management of head and neck cancers in the current era of immunotherapy.
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Rodriguez CP, Kang H, Geiger JL, Burtness B, Chung CH, Pickering CR, Fakhry C, Le QT, Yom SS, Galloway TJ, Golemis E, Li A, Shoop J, Wong S, Mehra R, Skinner H, Saba NF, Flores ER, Myers JN, Ford JM, Karchin R, Ferris RL, Kunos C, Lynn JM, Malik S. Clinical Trial Development in TP53-Mutated Locally Advanced and Recurrent and/or Metastatic Head and Neck Squamous Cell Carcinoma. J Natl Cancer Inst 2022; 114:1619-1627. [PMID: 36053203 PMCID: PMC9745425 DOI: 10.1093/jnci/djac163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 05/03/2022] [Accepted: 06/15/2022] [Indexed: 01/11/2023] Open
Abstract
TP53 mutation is the most frequent genetic event in head and neck squamous cell carcinoma (HNSCC), found in more than 80% of patients with human papillomavirus-negative disease. As mutations in the TP53 gene are associated with worse outcomes in HNSCC, novel therapeutic approaches are needed for patients with TP53-mutated tumors. The National Cancer Institute sponsored a Clinical Trials Planning Meeting to address the issues of identifying and developing clinical trials for patients with TP53 mutations. Subcommittees, or breakout groups, were tasked with developing clinical studies in both the locally advanced and recurrent and/or metastatic (R/M) disease settings as well as considering signal-seeking trial designs. A fourth breakout group was focused on identifying and standardizing biomarker integration into trial design; this information was provided to the other breakout groups prior to the meeting to aid in study development. A total of 4 concepts were prioritized to move forward for further development and implementation. This article summarizes the proceedings of the Clinical Trials Planning Meeting with the goal of developing clinical trials for patients with TP53-mutant HNSCC that can be conducted within the National Clinical Trials Network.
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Affiliation(s)
| | - Hyunseok Kang
- Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Jessica L Geiger
- Department of Hematology and Medical Oncology, Cleveland Clinic Foundation, Cleveland, OH, USA
| | | | - Christine H Chung
- Department of Head and Neck-Endocrine Oncology, Moffit Cancer Center, Tampa, FL, USA
| | - Curtis R Pickering
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Carole Fakhry
- Division of Head and Neck Surgery, Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University, Baltimore, MD, USA
| | - Quynh Thu Le
- Department of Radiation Oncology-Radiation Therapy, Stanford University, Palo Alto, CA, USA
| | - Sue S Yom
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
| | - Thomas J Galloway
- Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Erica Golemis
- Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
| | - Alice Li
- Kaiser Permanente Oakland, Oakland, CA, USA
| | | | - Stuart Wong
- Division of Neoplastic Diseases, Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Ranee Mehra
- Division of Hematology/Oncology, Department of Medicine, University of Maryland, Baltimore, MD, USA
| | - Heath Skinner
- Department of Radiation Oncology, University of Pittsburgh, Pittsburgh, PA, USA
| | - Nabil F Saba
- Department of Hematology and Medical Oncology, Emory University, Atlanta, GA, USA
| | - Elsa R Flores
- Department of Molecular Oncology, Moffit Cancer Center, Tampa, FL, USA
| | - Jeffrey N Myers
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - James M Ford
- Department of Medicine, Stanford University, Palo Alto, CA, USA
| | - Rachel Karchin
- Department of Oncology, Johns Hopkins University, Baltimore, MD, USA
| | - Robert L Ferris
- Department of Otolaryngology, University of Pittsburgh, Pittsburgh, PA, USA
| | | | - Jean M Lynn
- National Institutes of Health, Bethesda, MD, USA
| | - Shakun Malik
- National Institutes of Health, Bethesda, MD, USA
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4
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Michikawa C, Torres-Saavedra PA, Silver NL, Harari PM, Kies MS, Rosenthal DI, Le QT, Jordan RC, Duose DY, Mallampati S, Trivedi S, Luthra R, Wistuba II, Osman AA, Lichtarge O, Foote RL, Parvathaneni U, Hayes DN, Pickering CR, Myers JN. Evolutionary Action Score of TP53 Analysis in Pathologically High-Risk Human Papillomavirus-Negative Head and Neck Cancer From a Phase 2 Clinical Trial: NRG Oncology Radiation Therapy Oncology Group 0234. Adv Radiat Oncol 2022; 7:100989. [PMID: 36420184 PMCID: PMC9677209 DOI: 10.1016/j.adro.2022.100989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 05/04/2022] [Indexed: 12/15/2022] Open
Abstract
Purpose An evolutionary action scoring algorithm (EAp53) based on phylogenetic sequence variations stratifies patients with head and neck squamous cell carcinoma (HNSCC) bearing TP53 missense mutations as high-risk, associated with poor outcomes, or low-risk, with similar outcomes as TP53 wild-type, and has been validated as a reliable prognostic marker. We performed this study to further validate prior findings demonstrating that EAp53 is a prognostic marker for patients with locally advanced HNSCC and explored its predictive value for treatment outcomes to adjuvant bio-chemoradiotherapy. Methods and Materials Eighty-one resection samples from patients treated surgically for stage III or IV human papillomavirus-negative HNSCC with high-risk pathologic features, who received either radiation therapy + cetuximab + cisplatin (cisplatin) or radiation therapy + cetuximab + docetaxel (docetaxel) as adjuvant treatment in a phase 2 study were subjected to TP53 targeted sequencing and EAp53 scoring to correlate with clinical outcomes. Due to the limited sample size, patients were combined into 2 EAp53 groups: (1) wild-type or low-risk; and (2) high-risk or other. Results At a median follow-up of 9.8 years, there was a significant interaction between EAp53 group and treatment for overall survival (P = .008), disease-free survival (P = .05), and distant metastasis (DM; P = .004). In wild-type or low-risk group, the docetaxel arm showed significantly better overall survival (hazard ratio [HR] 0.11, [0.03-0.36]), disease-free survival (HR 0.24, [0.09-0.61]), and less DM (HR 0.04, [0.01-0.31]) than the cisplatin arm. In high-risk or other group, differences between treatments were not statistically significant. Conclusions The docetaxel arm was associated with better survival than the cisplatin arm for patients with wild-type or low-risk EAp53. These benefits appear to be largely driven by a reduction in DM.
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Affiliation(s)
- Chieko Michikawa
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas,Department of Maxillofacial Surgery, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Pedro A. Torres-Saavedra
- NRG Oncology Statistics and Data Management Center, American College of Radiology, Philadelphia, Pennsylvania
| | - Natalie L. Silver
- Cleveland Clinic, Head and Neck Institute/Lerner Research Institute, Cleveland, Ohio
| | - Paul M. Harari
- Department of Human Oncology, University of Wisconsin School of Medicine and Public Health, Madison, Wisconsin
| | - Merrill S. Kies
- Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David I. Rosenthal
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Quynh-Thu Le
- Department of Radiation Oncology, Stanford University Medical Center, Stanford, California
| | - Richard C. Jordan
- NRG Oncology Biospecimen Bank and University of California, San Francisco, San Francisco, California
| | | | | | - Sanchit Trivedi
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Rajyalakshmi Luthra
- Department of Hematopathology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | | | - Abdullah A. Osman
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Olivier Lichtarge
- Departments of Molecular and Human Genetics, Pharmacology, and Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, Texas
| | - Robert L. Foote
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota
| | - Upendra Parvathaneni
- Radiation Oncology Center, University of Washington Medical Center, Seattle, Washington
| | - D. Neil Hayes
- Division of Medical Oncology, The University of Tennessee Health Science Center, Memphis, Tennessee
| | - Curtis R. Pickering
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jeffrey N. Myers
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas,Corresponding author: Jeffrey N. Myers, MD, PhD
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5
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Deneka AY, Baca Y, Serebriiskii IG, Nicolas E, Parker MI, Nguyen TT, Xiu J, Korn WM, Demeure MJ, Wise-Draper T, Sukari A, Burtness B, Golemis EA. Association of TP53 and CDKN2A Mutation Profile with Tumor Mutation Burden in Head and Neck Cancer. Clin Cancer Res 2022; 28:1925-1937. [PMID: 35491653 PMCID: PMC9186806 DOI: 10.1158/1078-0432.ccr-21-4316] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 01/21/2022] [Accepted: 02/23/2022] [Indexed: 01/31/2023]
Abstract
PURPOSE Head and neck squamous cell carcinoma (HNSCC) is a frequently devastating cancer that affects more than a half million people annually worldwide. Although some cases arise from infection with human papillomavirus (HPV), HPV-negative HNSCC is more common, and associated with worse outcome. Advanced HPV-negative HNSCC may be treated with surgery, chemoradiation, targeted therapy, or immune checkpoint inhibition (ICI). There is considerable need for predictive biomarkers for these treatments. Defects in DNA repair capacity and loss of cell-cycle checkpoints sensitize tumors to cytotoxic therapies, and can contribute to phenotypes such as elevated tumor mutation burden (TMB), associated with response to ICI. Mutation of the tumor suppressors and checkpoint mediators TP53 and CDKN2A is common in HPV-negative HNSCC. EXPERIMENTAL DESIGN To gain insight into the relation of the interaction of TP53 and CDKN2A mutations with TMB in HNSCC, we have analyzed genomic data from 1,669 HPV-negative HNSCC tumors with multiple criteria proposed for assessing the damaging effect of TP53 mutations. RESULTS Data analysis established the TP53 and CDKN2A mutation profiles in specific anatomic subsites and suggested that specific categories of TP53 mutations are more likely to associate with CDKN2A mutation or high TMB based on tumor subsite. Intriguingly, the pattern of hotspot mutations in TP53 differed depending on the presence or absence of a cooccurring CDKN2A mutation. CONCLUSIONS These data emphasize the role of tumor subsite in evaluation of mutational profiles in HNSCC, and link defects in TP53 and CDKN2A to elevated TMB levels in some tumor subgroups.
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Affiliation(s)
- Alexander Y. Deneka
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111
| | | | - Ilya G. Serebriiskii
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111;,Kazan Federal University, 420000, Kazan, Russian Federation
| | - Emmanuelle Nicolas
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111
| | - Mitchell I. Parker
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111;,Drexel University College of Medicine, Philadelphia, PA 19102
| | - Theodore T. Nguyen
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111;,Drexel University College of Medicine, Philadelphia, PA 19102
| | | | | | - Michael J. Demeure
- Precision Medicine Program, Hoag Family Cancer Institute, Newport Beach, CA
| | - Trisha Wise-Draper
- Department of Internal Medicine, Division of Hematology/Oncology, University of Cincinnati, Cincinnati, OH
| | - Ammar Sukari
- Department of Oncology, Karmanos Cancer Institute/Wayne State University, Detroit, Michigan, USA
| | - Barbara Burtness
- Section of Medical Oncology, Department of Internal Medicine, and Yale Cancer Center, Yale University School of Medicine, New Haven, CT 06520
| | - Erica A. Golemis
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, PA 19111;,Lewis Katz School of Medicine, Department of Cancer and Cellular Biology, Philadelphia, PA 19140,Correspondence should be directed to: Erica A. Golemis, Fox Chase Cancer Center, 333 Cottman Ave, Philadelphia, PA 19111 USA, , (215) 728-2860
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6
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Nathan CA, Khandelwal AR, Wolf GT, Rodrigo JP, Mäkitie AA, Saba NF, Forastiere AA, Bradford CR, Ferlito A. TP53 mutations in head and neck cancer. Mol Carcinog 2022; 61:385-391. [PMID: 35218075 DOI: 10.1002/mc.23385] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2021] [Revised: 11/30/2021] [Accepted: 12/02/2021] [Indexed: 12/12/2022]
Abstract
Head and neck squamous cell carcinomas (HNSCCs) arising in the mucosal linings of the upper aerodigestive tract are highly heterogeneous, aggressive, and multifactorial tumors affecting more than half a million patients worldwide each year. Classical etiological factors for HNSCC include alcohol, tobacco, and human papillomavirus (HPV) infection. Current treatment options for HNSCCs encompass surgery, radiotherapy, chemotherapy, or combinatorial remedies. Comprehensive integrative genomic analysis of HNSCC has identified mutations in TP53 gene as the most frequent of all somatic genomic alterations. TP53 mutations are associated with either loss of wild-type p53 function or gain of functions that promote invasion, metastasis, genomic instability, and cancer cell proliferation. Interestingly, disruptive TP53 mutations in tumor DNA are associated with aggressiveness and reduced survival after surgical treatment of HNSCC. This review summarizes the current evidence and impact of TP53 mutations in HNSCC.
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Affiliation(s)
- Cherie-Ann Nathan
- Department of Otolaryngology-Head and Neck Surgery, Louisiana State University-Health Shreveport, Shreveport, Louisiana, USA
| | - Alok R Khandelwal
- Department of Otolaryngology-Head and Neck Surgery, Louisiana State University-Health Shreveport, Shreveport, Louisiana, USA
| | - Gregory T Wolf
- Department of Otolaryngology-Head and Neck Surgery, University of Michigan Health System, Ann Arbor, Michigan, USA
| | - Juan P Rodrigo
- Department of Otorhinolaryngology-Head and Neck Surgery, Hospital Universitario Central de Asturias, Oviedo, Spain
| | - Antti A Mäkitie
- Department of Otorhinolaryngology-Head and Neck Surgery, University of Helsinki and HUS Helsinki University Hospital, Helsinki, Finland
| | - Nabil F Saba
- Department of Hematology and Medical Oncology, Emory University, Atlanta, Georgia, USA
| | - Arlene A Forastiere
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Carol R Bradford
- Department of Otolaryngology-Head and Neck Surgery, The Ohio State University Wexner Medical Center, Columbus, Ohio, USA
| | - Alfio Ferlito
- International Head and Neck Scientific Group, Padua, Italy
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7
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The genomic landscape of lung adenocarcinoma—insights towards personalized medicine. PROCEEDINGS OF THE INDIAN NATIONAL SCIENCE ACADEMY 2021. [DOI: 10.1007/s43538-021-00054-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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8
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van Harten AM, Brakenhoff RH. Targeted Treatment of Head and Neck (Pre)Cancer: Preclinical Target Identification and Development of Novel Therapeutic Applications. Cancers (Basel) 2021; 13:2774. [PMID: 34204886 PMCID: PMC8199752 DOI: 10.3390/cancers13112774] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/14/2022] Open
Abstract
Head and neck squamous cell carcinomas (HNSCC) develop in the mucosal lining of the upper-aerodigestive tract. In carcinogen-induced HNSCC, tumors emerge from premalignant mucosal changes characterized by tumor-associated genetic alterations, also coined as 'fields' that are occasionally visible as leukoplakia or erythroplakia lesions but are mostly invisible. Consequently, HNSCC is generally diagnosed de novo at more advanced stages in about 70% of new diagnosis. Despite intense multimodality treatment protocols, the overall 5-years survival rate is 50-60% for patients with advanced stage of disease and seems to have reached a plateau. Of notable concern is the lack of further improvement in prognosis despite advances in treatment. This can be attributed to the late clinical presentation, failure of advanced HNSCC to respond to treatment, the deficit of effective targeted therapies to eradicate tumors and precancerous changes, and the lack of suitable markers for screening and personalized therapy. The molecular landscape of head and neck cancer has been elucidated in great detail, but the absence of oncogenic mutations hampers the identification of druggable targets for therapy to improve outcome of HNSCC. Currently, functional genomic approaches are being explored to identify potential therapeutic targets. Identification and validation of essential genes for both HNSCC and oral premalignancies, accompanied with biomarkers for therapy response, are being investigated. Attentive diagnosis and targeted therapy of the preceding oral premalignant (preHNSCC) changes may prevent the development of tumors. As classic oncogene addiction through activating mutations is not a realistic concept for treatment of HNSCC, synthetic lethality and collateral lethality need to be exploited, next to immune therapies. In recent studies it was shown that cell cycle regulation and DNA damage response pathways become significantly altered in HNSCC causing replication stress, which is an avenue that deserves further exploitation as an HNSCC vulnerability for treatment. The focus of this review is to summarize the current literature on the preclinical identification of potential druggable targets for therapy of (pre)HNSCC, emerging from the variety of gene knockdown and knockout strategies, and the testing of targeted inhibitors. We will conclude with a future perspective on targeted therapy of HNSCC and premalignant changes.
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Affiliation(s)
- Anne M. van Harten
- Cancer Center Amsterdam, Otolaryngology-Head and Neck Surgery, Tumor Biology & Immunology Section, Vrije Universiteit Amsterdam, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands; or
- Sidney Kimmel Cancer Center, Department of Cancer Biology, Thomas Jefferson University, Philadelphia, PA 19107, USA
| | - Ruud H. Brakenhoff
- Cancer Center Amsterdam, Otolaryngology-Head and Neck Surgery, Tumor Biology & Immunology Section, Vrije Universiteit Amsterdam, Amsterdam UMC, 1081 HV Amsterdam, The Netherlands; or
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9
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Jin Y, Qin X. Significance of TP53 mutation in treatment and prognosis in head and neck squamous cell carcinoma. Biomark Med 2021; 15:15-28. [PMID: 33427498 DOI: 10.2217/bmm-2020-0400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/09/2022] Open
Abstract
Background: TP53 is ranked as the most common mutated gene in head and neck squamous cell carcinoma (HNSCC). Results: The status of TP53 mutation was investigated on International Cancer Genome Consortium and The Cancer Genome Atlas database and TP53-related differentially expressed genes were screened out from transcriptome data and mutation information. A TP53-related prognostic gene signature (TIMP4, ONECUT2, CGNL1, DMRTA2 and NKX2.3) was constructed based on Cox regression analysis and LASSO algorithm. Univariate and multivariate analyses were carried out to identify promising prognosticators for HNSCC. Conclusion: Our findings provide a well-rounded landscape of TP53 mutation in HNSCC and pave the groundwork for developing innovative and effective cancer treatment methods for HNSCC.
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Affiliation(s)
- Yu Jin
- Department of General Dentistry, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, PR China.,Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai 200000, PR China
| | - Xing Qin
- Department of Oral & Maxillofacial-Head & Neck Oncology, Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200011, PR China.,Shanghai Key Laboratory of Stomatology & Shanghai Research Institute of Stomatology, National Clinical Research Center of Stomatology, Shanghai 200000, PR China
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10
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Xavier GM, Guimarães ALS, de Carvalho Fraga CA, Guimarães TA, de Souza MG, Jones KM, Farias LC. Pathways Related to the Anti-Cancer Effects of Metabolites Derived from Cerrado Biome Native Plants: An Update and Bioinformatics Analysis on Oral Squamous Cell Carcinoma. Protein Pept Lett 2020; 28:735-749. [PMID: 33302827 DOI: 10.2174/0929866527999201209221012] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/14/2020] [Accepted: 10/20/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND Oral cancer is a significant health problem worldwide. Oral squamous cell carcinoma (OSCC) is a malignant neoplasm of epithelial cells that mostly affects different anatomical sites in the head and neck and derives from the squamous epithelium or displays similar morphological characteristics. Generally, OSCC is often the end stage of several changes in the stratified squamous epithelium, which begin as epithelial dysplasia and progress by breaking the basement membrane and invading adjacent tissues. Several plant-based drugs with potent anti-cancer effects are considered inexpensive treatments with limited side effects for cancer and other diseases. OBJECTIVE The aim of this review is to explore whether some Brazilian plant extracts or constituents exhibit anti-tumorigenic activity or have a cytotoxic effect on human oral carcinoma cells. METHODS Briefly, OSCC and several metabolites derived from Brazilian plants (i.e., flavonoids, vinblastine, irinotecan, etoposide and paclitaxel) were used as keywords to search the literature on PubMed, GenBank and GeneCards. RESULTS The results showed that these five chemical compounds found in Cerrado Biome plants exhibit anti-neoplastic effects. Evaluating the compounds revealed that they play a main role in the regulation of cell proliferation. CONCLUSION Preserving and utilising the biodiversity of our planet, especially in unique ecosystems, such as the Cerrado Biome, may prove essential to preserving and promoting human health in modern contexts.
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11
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Gleber-Netto FO, Neskey D, Costa AFDM, Kataria P, Rao X, Wang J, Kowalski LP, Pickering CR, Dias-Neto E, Myers JN. Functionally impactful TP53 mutations are associated with increased risk of extranodal extension in clinically advanced oral squamous cell carcinoma. Cancer 2020; 126:4498-4510. [PMID: 32797678 DOI: 10.1002/cncr.33101] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 05/24/2020] [Accepted: 06/20/2020] [Indexed: 11/10/2022]
Abstract
BACKGROUND The treatment of advanced oral squamous cell carcinoma (OSCC) is a clinical challenge because it is unclear which therapeutic approaches are the best for this highly heterogeneous group of patients. Because TP53 mutations are the most common genetic event in these tumors, the authors investigated whether they could represent an ancillary biomarker in the management of advanced OSCC. METHODS The TP53 gene was sequenced in 78 samples from patients with advanced OSCC who received treatment at 2 institutions located in the United States and Brazil. TP53 mutations were classified according to an in-silico impact score (the evolutionary action score of p53 [EAp53]), which identifies mutations that have greater alterations of p53 protein function (high-risk). Associations between TP53 mutation status/characteristics and clinicopathologic characteristics were investigated. The relevant findings were validated in silico by analyzing 197 samples from patients with advanced OSCC from The Cancer Genome Atlas. RESULTS No differences in clinical outcomes were detected between patients with TP53-mutant and wild-type TP53 disease. However, patients who had tumors carrying high-risk TP53 mutations had a significantly increased risk of developing extranodal extension (ENE) compared with those who had wild-type TP53-bearing tumors. The increased chances of detecting ENE among patients who had high-risk TP53 mutations was validated among patients with advanced OSCC from The Cancer Genome Atlas cohort. CONCLUSIONS High-risk TP53 mutations are associated with an increased chance of detecting ENE in patients with advanced OSCC. Because ENE is 1 of the major factors considered for OSCC patient management, TP53 mutation status may represent a potential ancillary biomarker for treatment decisions regarding postoperative adjuvant therapy.
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Affiliation(s)
- Frederico O Gleber-Netto
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - David Neskey
- Department of Otolaryngology, Head and Neck Surgery, Medical University of South Carolina, Charleston, South Carolina.,Department of Cell and Molecular Pharmacology and Developmental Therapeutics, Medical University of South Carolina, Charleston, South Carolina
| | - Ana Flávia de Mattos Costa
- Laboratory of Medical Genomics, International Research Center, AC Camargo Cancer Center, Sao Paulo, Brazil
| | - Pranav Kataria
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Xiayu Rao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jing Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Luiz Paulo Kowalski
- Department of Head and Neck Surgery and Otorhinolaryngology, AC Camargo Cancer Center, Sao Paulo, Brazil
| | - Curtis R Pickering
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas.,The University of Texas Graduate School of Biomedical Sciences, Houston, Texas
| | - Emmanuel Dias-Neto
- Laboratory of Medical Genomics, International Research Center, AC Camargo Cancer Center, Sao Paulo, Brazil
| | - Jeffrey N Myers
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas.,The University of Texas Graduate School of Biomedical Sciences, Houston, Texas
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12
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Matsuda S, Mafune A, Kohda N, Hama T, Urashima M. Associations among smoking, MGMT hypermethylation, TP53-mutations, and relapse in head and neck squamous cell carcinoma. PLoS One 2020; 15:e0231932. [PMID: 32324779 PMCID: PMC7179834 DOI: 10.1371/journal.pone.0231932] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 04/02/2020] [Indexed: 01/04/2023] Open
Abstract
Background Epigenetic silencing of the O6-methylguanine-DNA methyltransferase (MGMT) DNA repair enzyme via promoter hypermethylation (hmMGMT) may increase mutations in the TP53 oncosuppressor gene and contribute to carcinogenesis. The effects of smoking, which is a risk factor for head and neck squamous cell carcinoma (HNSCC), were investigated to determine whether they up- or down-regulate hmMGMT. Additionally, the impact of hmMGMT and disruptive TP53-mutations on relapse was investigated in patients with HNSCC. Methods This study included 164 patients with HNSCC who were negative for both p16 protein expression and human papilloma virus infection. The association of smoking and hmMGMT was investigated using multiple logistic regression analysis. Competing risk regression was used to evaluate the effects of hmMGMT and TP53-mutations in exon 2 to 11 on relapse of HNSCC. Results hmMGMT was observed in 84% of the 164 patients. TP53-mutations, specifically, G:C>A:T transition, were more frequent in patients with hmMGMT (32%) than in those without hmMGMT (8%). The frequency of disruptive TP53-mutations was not significantly different between groups. Compared with nonsmoking, heavy smoking of 20 pack-years or more was significantly associated with decreased hmMGMT (adjusted odds ratio, 0.08; 95% CI, 0.01 to 0.56; P = 0.01). Patients who had both hmMGMT and disruptive TP53-mutations showed a significantly higher relapse rate than all other patients (subdistribution hazard ratio, 1.77; 95% CI, 1.07 to 2.92; P = 0.026). Conclusions It was found that hmMGMT was suppressed by heavy smoking, and hmMGMT combined with disruptive TP53-mutations may indicate a poor prognosis in patients with HNSCC.
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Affiliation(s)
- Shinichi Matsuda
- Division of Molecular Epidemiology, The Jikei University School of Medicine, Tokyo, Japan
- Real World Data Science Department, Chugai Pharmaceutical Co. Ltd., Tokyo, Japan
| | - Aki Mafune
- Division of Molecular Epidemiology, The Jikei University School of Medicine, Tokyo, Japan
- Division of Kidney and Hypertension, Department of Internal Medicine, The Jikei University School of Medicine, Tokyo, Japan
| | - Nagisa Kohda
- Division of Molecular Epidemiology, The Jikei University School of Medicine, Tokyo, Japan
| | - Takanori Hama
- Division of Molecular Epidemiology, The Jikei University School of Medicine, Tokyo, Japan
- Department of Oto-Rhino-laryngology, The Jikei University School of Medicine, Tokyo, Japan
| | - Mitsuyoshi Urashima
- Division of Molecular Epidemiology, The Jikei University School of Medicine, Tokyo, Japan
- * E-mail:
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13
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Lee JW, Parameswaran J, Sandoval-Schaefer T, Eoh KJ, Yang DH, Zhu F, Mehra R, Sharma R, Gaffney SG, Perry EB, Townsend JP, Serebriiskii IG, Golemis EA, Issaeva N, Yarbrough WG, Koo JS, Burtness B. Combined Aurora Kinase A (AURKA) and WEE1 Inhibition Demonstrates Synergistic Antitumor Effect in Squamous Cell Carcinoma of the Head and Neck. Clin Cancer Res 2019; 25:3430-3442. [PMID: 30755439 DOI: 10.1158/1078-0432.ccr-18-0440] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 01/17/2019] [Accepted: 02/07/2019] [Indexed: 11/16/2022]
Abstract
PURPOSE Human papillomavirus (HPV)-negative head and neck squamous cell carcinomas (HNSCC) commonly bear disruptive mutations in TP53, resulting in treatment resistance. In these patients, direct targeting of p53 has not been successful, but synthetic lethal approaches have promise. Although Aurora A kinase (AURKA) is overexpressed and an oncogenic driver, its inhibition has only modest clinical effects in HPV-negative HNSCC. We explored a novel combination of AURKA and WEE1 inhibition to overcome intrinsic resistance to AURKA inhibition.Experimental Design: AURKA protein expression was determined by fluorescence-based automated quantitative analysis of patient specimens and correlated with survival. We evaluated treatment with the AURKA inhibitor alisertib (MLN8237) and the WEE1 inhibitor adavosertib (AZD1775), alone or in combination, using in vitro and in vivo HNSCC models. RESULTS Elevated nuclear AURKA correlated with worse survival among patients with p16(-) HNSCC. Alisertib caused spindle defects, G2-M arrest and inhibitory CDK1 phosphorylation, and cytostasis in TP53 mutant HNSCC FaDu and UNC7 cells. Addition of adavosertib to alisertib instead triggered mitotic entry and mitotic catastrophe. Moreover, in FaDu and Detroit 562 xenografts, this combination demonstrated synergistic effects on tumor growth and extended overall survival compared with either vehicle or single-agent treatment. CONCLUSIONS Combinatorial treatment with adavosertib and alisertib leads to synergistic antitumor effects in in vitro and in vivo HNSCC models. These findings suggest a novel rational combination, providing a promising therapeutic avenue for TP53-mutated cancers.
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Affiliation(s)
- Jong Woo Lee
- Section of Medical Oncology, Department of Internal Medicine and Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - Janaki Parameswaran
- Section of Medical Oncology, Department of Internal Medicine and Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - Teresa Sandoval-Schaefer
- Section of Medical Oncology, Department of Internal Medicine and Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - Kyung Jin Eoh
- Section of Medical Oncology, Department of Internal Medicine and Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - Dong-Hua Yang
- Biosample Repository, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Fang Zhu
- Department of Biostatistics, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Ranee Mehra
- Department of Medical Oncology, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Roshan Sharma
- Section of Medical Oncology, Department of Internal Medicine and Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - Stephen G Gaffney
- Department of Biostatistics, Yale University School of Public Health, New Haven, Connecticut
| | - Elizabeth B Perry
- Department of Biostatistics, Yale University School of Public Health, New Haven, Connecticut
| | - Jeffrey P Townsend
- Department of Biostatistics, Yale University School of Public Health, New Haven, Connecticut
| | - Ilya G Serebriiskii
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Erica A Golemis
- Molecular Therapeutics Program, Fox Chase Cancer Center, Philadelphia, Pennsylvania
| | - Natalia Issaeva
- Section of Otolaryngology, Department of Surgery, Yale University School of Medicine, New Haven, Connecticut
| | - Wendell G Yarbrough
- Section of Otolaryngology, Department of Surgery, Yale University School of Medicine, New Haven, Connecticut
- Department of Pathology, Yale University School of Medicine, New Haven, Connecticut
| | - Ja Seok Koo
- Section of Medical Oncology, Department of Internal Medicine and Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut
| | - Barbara Burtness
- Section of Medical Oncology, Department of Internal Medicine and Yale Cancer Center, Yale University School of Medicine, New Haven, Connecticut.
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14
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van Ginkel JH, de Leng WWJ, de Bree R, van Es RJJ, Willems SM. Targeted sequencing reveals TP53 as a potential diagnostic biomarker in the post-treatment surveillance of head and neck cancer. Oncotarget 2018; 7:61575-61586. [PMID: 27528217 PMCID: PMC5308673 DOI: 10.18632/oncotarget.11196] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 07/28/2016] [Indexed: 02/07/2023] Open
Abstract
Head and neck squamous cell carcinomas (HNSCC) form a large heterogeneous group of tumors and have a relatively poor outcome in advanced cases. Revealing the underlying genetic mutations in HNSCC facilitates the development of diagnostic biomarkers, which might lead to improved diagnosis and post treatment surveillance. We retrospectively analyzed mutational hotspots using targeted next-generation sequencing (NGS) of 239 HNSCC tumor samples in order to examine the mutational profile of HNSCC. Furthermore, we assessed prevalence, co-occurrence, and synonymy of gene mutations in (matched) tumor samples. TP53 was found mutated the most frequent with mutation rates of up to 83% in all tumors, compared to mutation rates of between 0 and 21% of CDKN2A, PIK3CA, HRAS, CDK4, FBXW7 and RB1. Mutational co-occurrence predominantly existed between TP53 and PIK3CA, TP53 and CDKN2A, and HRAS and PIK3CA. Mutational synonymy between primary tumor and associated metastasis and recurrence was present in respectively 88% and 89%. TP53 mutations were concordantly mutated in 95% of metastases and in 91% of recurrences. This indicates TP53 mutations to be highly prevalent and concordant in primary tumors and associated locoregional metastases and recurrences. In turn, this provides ground for further investigating the use of TP53 mutations as diagnostic biomarkers in HNSCC patients.
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Affiliation(s)
- Joost H van Ginkel
- Department of Oral and Maxillofacial Surgery, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Wendy W J de Leng
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Remco de Bree
- Department of Head and Neck Surgical Oncology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Robert J J van Es
- Department of Oral and Maxillofacial Surgery, University Medical Center Utrecht, Utrecht, The Netherlands.,Department of Head and Neck Surgical Oncology, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Stefan M Willems
- Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands
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15
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El Baroudi M, Machiels JP, Schmitz S. Expression of SESN1, UHRF1BP1, and miR-377-3p as prognostic markers in mutated TP53 squamous cell carcinoma of the head and neck. Cancer Biol Ther 2017; 18:775-782. [PMID: 28886272 DOI: 10.1080/15384047.2017.1373212] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Abstract
The tumor suppressor gene TP53 is the most frequently mutated gene in human papillomavirus (HPV)-negative head and neck squamous cell carcinoma (HNSCC). It represents a known transcription factor that controls different microRNAs (miRNA) and target genes involved in the regulation of cellular stress, apoptosis and response to DNA damage. We used The Cancer Genome Atlas database to investigate the difference in transcriptome and proteome levels between mutated and wild-type TP53 HPV-negative HNSCC. Using different databases and an extensive literature review, we built the transcriptional and post-transcriptional network regulated by TP53. TP53 mutation was associated with poor overall survival in 203 HPV-negative patients compared to 40 patients with TP53 wild-type tumors. Using the enrichment analysis, we found that UHRF1BP1 and SESN1 mRNA were linked to prognosis in the TP53 mutated group. This is also the case for miR-377-3p, an important miRNA regulator of SESN1. Our study shows that SESN1 mRNA, UHRF1BP11 mRNA and miRNA-377-3p levels are prognostically relevant in HPV-negative HNSCC patients. This finding may help with patient stratification and the development of potential new therapeutic targets to treat patients with HNSCC.
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Affiliation(s)
- Mariama El Baroudi
- a Department of Medical Oncology, Institut de Recherche Expérimentale et Clinique (IREC)-Pole MIRO , Université Catholique de Louvain , Brussels , Belgium
| | - Jean-Pascal Machiels
- a Department of Medical Oncology, Institut de Recherche Expérimentale et Clinique (IREC)-Pole MIRO , Université Catholique de Louvain , Brussels , Belgium.,b Institut Roi Albert II, Department of Medical Oncology and Head and Neck Surgery , Cliniques Universitaires Saint-Luc and Institut de Recherche Clinique et Expérimentale (Pole MIRO), Université catholique de Louvain , Brussels , Belgium
| | - Sandra Schmitz
- a Department of Medical Oncology, Institut de Recherche Expérimentale et Clinique (IREC)-Pole MIRO , Université Catholique de Louvain , Brussels , Belgium.,b Institut Roi Albert II, Department of Medical Oncology and Head and Neck Surgery , Cliniques Universitaires Saint-Luc and Institut de Recherche Clinique et Expérimentale (Pole MIRO), Université catholique de Louvain , Brussels , Belgium
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16
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Tamura M, Ishizawa M, Isojima T, Özen S, Oka A, Makishima M, Kitanaka S. Functional analyses of a novel missense and other mutations of the vitamin D receptor in association with alopecia. Sci Rep 2017; 7:5102. [PMID: 28698609 PMCID: PMC5505967 DOI: 10.1038/s41598-017-05081-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 05/23/2017] [Indexed: 01/08/2023] Open
Abstract
Hereditary 1,25-dihydroxyvitamin D-resistant rickets (HVDRR) is a rare disorder, caused by bialellic mutations of the vitamin D receptor (VDR) gene, sometimes associated with alopecia. The aim of this study is to elucidate the mechanism of functional disruption of a novel mutation, detected in a patient with HVDRR, comparing to other mutations with or without alopecia. The patient was a 2-year-old girl with alopecia, who was clinically diagnosed as HVDRR. Genetic analysis revealed a novel homozygous mutation, S360P, located in ligand binding domain (LBD). The mutation was predicted as not disease causing by Polyphen2 and SIFT. But the transcriptional activity of S360P was disrupted as well as other reported mutations, Q152X (located in the hinge lesion), and R274L, H305Q (located in LBD). Following assays revealed no ligand binding affinity, no interaction with cofactors or RXR and no functioning of nuclear localization signals. Our results provide an additional evidence for the previous findings suggesting that DNA binding by the VDR/RXR heterodimer is essential for the function of the VDR in hair development. In conclusion, we identified a novel missense mutation of VDR causing HVDRR with alopecia. Functional analyses revealed that the single amino acid substitution could disrupt the function of the protein.
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Affiliation(s)
- Mayuko Tamura
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.,The Japan Society for the Promotion of Science, Tokyo, Japan
| | - Michiyasu Ishizawa
- Division of Biochemistry, Department of Biochemical Sciences, Nihon University School of Medicine, Tokyo, Japan
| | - Tsuyoshi Isojima
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Samim Özen
- Department of Pediatric Endocrinology, School of Medicine, Ege University, Izmir, Turkey
| | - Akira Oka
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Makoto Makishima
- Division of Biochemistry, Department of Biochemical Sciences, Nihon University School of Medicine, Tokyo, Japan
| | - Sachiko Kitanaka
- Department of Pediatrics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
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17
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Reeb J, Hecht M, Mahlich Y, Bromberg Y, Rost B. Predicted Molecular Effects of Sequence Variants Link to System Level of Disease. PLoS Comput Biol 2016; 12:e1005047. [PMID: 27536940 PMCID: PMC4990455 DOI: 10.1371/journal.pcbi.1005047] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 07/04/2016] [Indexed: 11/19/2022] Open
Abstract
Developments in experimental and computational biology are advancing our understanding of how protein sequence variation impacts molecular protein function. However, the leap from the micro level of molecular function to the macro level of the whole organism, e.g. disease, remains barred. Here, we present new results emphasizing earlier work that suggested some links from molecular function to disease. We focused on non-synonymous single nucleotide variants, also referred to as single amino acid variants (SAVs). Building upon OMIA (Online Mendelian Inheritance in Animals), we introduced a curated set of 117 disease-causing SAVs in animals. Methods optimized to capture effects upon molecular function often correctly predict human (OMIM) and animal (OMIA) Mendelian disease-causing variants. We also predicted effects of human disease-causing variants in the mouse model, i.e. we put OMIM SAVs into mouse orthologs. Overall, fewer variants were predicted with effect in the model organism than in the original organism. Our results, along with other recent studies, demonstrate that predictions of molecular effects capture some important aspects of disease. Thus, in silico methods focusing on the micro level of molecular function can help to understand the macro system level of disease. The variations in the genetic sequence between individuals affect the gene-product, i.e. the protein differently. Some variants have no measurable effect (are neutral), while others affect protein function. Some of those effects are so severe they cause so called monogenic Mendelian diseases, i.e. diseases triggered by a single letter change. Some in silico methods predict the molecular impact of sequence variation. However, both experimental and computational analyses struggle to generalize from the effect upon molecular protein function to the effect upon the organism such as a disease. Here, we confirmed that methods predicting molecular effects correctly capture the type of effects causing Mendelian diseases in human and introduced a data set for animal diseases that was also captured by predictions methods. Predicted effects were less when in silico testing human variants in an animal model (here mouse). This is important to know because “mouse models” are common to study human diseases. Overall, we provided some evidence for a link between the molecular level and some type of disease.
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Affiliation(s)
- Jonas Reeb
- Department of Informatics, Bioinformatics & Computational Biology—i12, Technische Universität München, Garching/Munich, Germany
- TUM Graduate School, Center of Doctoral Studies in Informatics and its Applications (CeDoSIA), Technische Universität München, Garching, Germany
- * E-mail:
| | - Maximilian Hecht
- Department of Informatics, Bioinformatics & Computational Biology—i12, Technische Universität München, Garching/Munich, Germany
| | - Yannick Mahlich
- Department of Informatics, Bioinformatics & Computational Biology—i12, Technische Universität München, Garching/Munich, Germany
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, United States of America
- Institute for Advanced Study (TUM-IAS), Garching/Munich, Germany
| | - Yana Bromberg
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, New Jersey, United States of America
- Institute for Advanced Study (TUM-IAS), Garching/Munich, Germany
| | - Burkhard Rost
- Department of Informatics, Bioinformatics & Computational Biology—i12, Technische Universität München, Garching/Munich, Germany
- Institute for Advanced Study (TUM-IAS), Garching/Munich, Germany
- Institute for Food and Plant Sciences WZW, Technische Universität München, Weihenstephan, Freising, Germany
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18
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Beck TN, Kaczmar J, Handorf E, Nikonova A, Dubyk C, Peri S, Lango M, Ridge JA, Serebriiskii IG, Burtness B, Golemis EA, Mehra R. Phospho-T356RB1 predicts survival in HPV-negative squamous cell carcinoma of the head and neck. Oncotarget 2016; 6:18863-74. [PMID: 26265441 PMCID: PMC4662460 DOI: 10.18632/oncotarget.4321] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2015] [Accepted: 05/22/2015] [Indexed: 11/25/2022] Open
Abstract
Locally advanced squamous cell carcinoma of the head and neck (SCCHN) that is not associated with human papillomavirus (HPV) has a poor prognosis in contrast to HPV-positive disease. To better understand the importance of RB1 activity in HPV-negative SCCHN, we investigated the prognostic value of inhibitory CDK4/6 phosphorylation of RB1 on threonine 356 (T356) in archival HPV-negative tumor specimens from patients who underwent surgical resection and adjuvant radiation. We benchmarked pT356RB1 to total RB1, Ki67, pT202/Y204ERK1/2, and TP53, as quantified by automatic quantitative analysis (AQUA), and correlated protein expression with tumor stage and grade. High expression of pT356RB1 but not total RB1 predicted reduced overall survival (OS; P = 0.0295), indicating the potential relevance of post-translational phosphorylation. Paired analysis of The Cancer Genome Atlas (TCGA) data for regulators of this RB1 phosphorylation identified loss or truncating mutation of negative regulator CDKN2A (p16) and elevated expression of the CDK4/6 activator CCND1 (cyclin D) as also predicting poor survival. Given that CDK4/6 inhibitors have been most effective in the context of functional RB1 and low expression or deletion of p16 in other tumor types, these data suggest such agents may merit evaluation in HPV-negative SCCHN, specifically in cases associated with high pT356RB1.
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Affiliation(s)
- Tim N Beck
- Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, USA.,Molecular and Cell Biology and Genetics, Drexel University College of Medicine, Philadelphia, PA, USA
| | - John Kaczmar
- Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, USA.,Medical Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Elizabeth Handorf
- Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Anna Nikonova
- Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Cara Dubyk
- Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Suraj Peri
- Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Miriam Lango
- Surgical Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - John A Ridge
- Surgical Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
| | - Ilya G Serebriiskii
- Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, USA.,Department of Biochemistry, Kazan Federal University, Kazan, Russia
| | - Barbara Burtness
- Department of Internal Medicine, Yale University School of Medicine and Yale Cancer Center, New Haven, CT, USA
| | - Erica A Golemis
- Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, USA.,Molecular and Cell Biology and Genetics, Drexel University College of Medicine, Philadelphia, PA, USA
| | - Ranee Mehra
- Molecular Therapeutics, Fox Chase Cancer Center, Philadelphia, PA, USA.,Medical Oncology, Fox Chase Cancer Center, Philadelphia, PA, USA
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19
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Abstract
Head and neck squamous cell carcinoma (HNSCC) is the sixth most common cancer worldwide and is frequently impervious to curative treatment efforts. Similar to other cancers associated with prolonged exposure to carcinogens, HNSCCs often have a high burden of mutations, contributing to substantial inter- and intra-tumor heterogeneity. The heterogeneity of this malignancy is further increased by the rising rate of human papillomavirus (HPV)-associated (HPV+) HNSCC, which defines an etiological subtype significantly different from the more common tobacco and alcohol associated HPV-negative (HPV-) HNSCC. Since 2011, application of large scale genome sequencing projects by The Cancer Genome Atlas (TCGA) network and other groups have established extensive datasets to characterize HPV- and HPV+ HNSCC, providing a foundation for advanced molecular diagnoses, identification of potential biomarkers, and therapeutic insights. Some genomic lesions are now appreciated as widely dispersed. For example, HPV- HNSCC characteristically inactivates the cell cycle suppressors TP53 (p53) and CDKN2A (p16), and often amplifies CCND1 (cyclin D), which phosphorylates RB1 to promote cell cycle progression from G1 to S. By contrast, HPV+ HNSCC expresses viral oncogenes E6 and E7, which inhibit TP53 and RB1, and activates the cell cycle regulator E2F1. Frequent activating mutations in PIK3CA and inactivating mutations in NOTCH1 are seen in both subtypes of HNSCC, emphasizing the importance of these pathways. Studies of large patient cohorts have also begun to identify less common genetic alterations, predominantly found in HPV- tumors, which suggest new mechanisms relevant to disease pathogenesis. Targets of these alterations including AJUBA and FAT1, both involved in the regulation of NOTCH/CTNNB1 signaling. Genes involved in oxidative stress, particularly CUL3, KEAP1 and NFE2L2, strongly associated with smoking, have also been identified, and are less well understood mechanistically. Application of sophisticated data-mining approaches, integrating genomic information with profiles of tumor methylation and gene expression, have helped to further yield insights, and in some cases suggest additional approaches to stratify patients for clinical treatment. We here discuss some recent insights built on TCGA and other genomic foundations.
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Affiliation(s)
- Tim N Beck
- Program in Molecular Therapeutics, Fox Chase Cancer Center, 333 Cottman Ave, Philadelphia, PA 19111, USA.,Program in Molecular and Cell Biology and Genetics, Drexel University College of Medicine, Philadelphia, PA 19129, USA
| | - Erica A Golemis
- Program in Molecular Therapeutics, Fox Chase Cancer Center, 333 Cottman Ave, Philadelphia, PA 19111, USA.,Program in Molecular and Cell Biology and Genetics, Drexel University College of Medicine, Philadelphia, PA 19129, USA
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20
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Fransson Å, Glaessgen D, Alfredsson J, Wiman KG, Bajalica-Lagercrantz S, Mohell N. Strong synergy with APR-246 and DNA-damaging drugs in primary cancer cells from patients with TP53 mutant High-Grade Serous ovarian cancer. J Ovarian Res 2016. [PMID: 27179933 DOI: 10.1186/s13048-016-0239-6] [] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mutation in the tumor suppressor gene TP53 is an early event in the development of high-grade serous (HGS) ovarian cancer and is identified in more than 96 % of HGS cancer patients. APR-246 (PRIMA-1(MET)) is the first clinical-stage compound that reactivates mutant p53 protein by refolding it to wild type conformation, thus inducing apoptosis. APR-246 has been tested as monotherapy in a Phase I/IIa clinical study in hematological malignancies and prostate cancer with promising results, and a Phase Ib/II study in combination with platinum-based therapy in ovarian cancer is ongoing. In the present study, we investigated the anticancer effects of APR-246 in combination with conventional chemotherapy in primary cancer cells isolated from ascitic fluid from 10 ovarian, fallopian tube, or peritoneal cancer patients, 8 of which had HGS cancer. METHODS Cell viability was assessed with fluorometric microculture cytotoxicity assay (FMCA) and Combination Index was calculated using the Additive model. p53 status was determined by Sanger sequencing and single strand conformation analysis, and p53 protein expression by western blotting. RESULTS We observed strong synergy with APR-246 and cisplatin in all tumor samples carrying a TP53 missense mutation, while synergistic or additive effects were found in cells with wild type or TP53 nonsense mutations. Strong synergy was also observed with carboplatin or doxorubicin. Moreover, APR-246 sensitized TP53 mutant primary ovarian cancer cells, isolated from a clinically platinum-resistant patient, to cisplatin; the IC50 value of cisplatin decreased 3.6 fold from 6.5 to 1.8 μM in the presence of clinically relevant concentration of APR-246. CONCLUSION These results suggest that combination treatment with APR-246 and DNA-damaging drugs could significantly improve the treatment of patients with TP53 mutant HGS cancer, and thus provide strong support for the ongoing clinical study with APR-246 in combination with carboplatin and pegylated liposomal doxorubicin in patients with recurrent HGS cancer.
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Affiliation(s)
| | | | | | - Klas G Wiman
- Karolinska Institutet Dept. of Oncology-Pathology, Cancer Center Karolinska (CCK), Stockholm, Sweden
| | - Svetlana Bajalica-Lagercrantz
- Karolinska University Hospital, Stockholm, Sweden.,Karolinska Institutet Dept. of Oncology-Pathology, Cancer Center Karolinska (CCK), Stockholm, Sweden
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Fransson Å, Glaessgen D, Alfredsson J, Wiman KG, Bajalica-Lagercrantz S, Mohell N. Strong synergy with APR-246 and DNA-damaging drugs in primary cancer cells from patients with TP53 mutant High-Grade Serous ovarian cancer. J Ovarian Res 2016. [PMID: 27179933 DOI: 10.1186/s13048-016-0239-6]+[] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mutation in the tumor suppressor gene TP53 is an early event in the development of high-grade serous (HGS) ovarian cancer and is identified in more than 96 % of HGS cancer patients. APR-246 (PRIMA-1(MET)) is the first clinical-stage compound that reactivates mutant p53 protein by refolding it to wild type conformation, thus inducing apoptosis. APR-246 has been tested as monotherapy in a Phase I/IIa clinical study in hematological malignancies and prostate cancer with promising results, and a Phase Ib/II study in combination with platinum-based therapy in ovarian cancer is ongoing. In the present study, we investigated the anticancer effects of APR-246 in combination with conventional chemotherapy in primary cancer cells isolated from ascitic fluid from 10 ovarian, fallopian tube, or peritoneal cancer patients, 8 of which had HGS cancer. METHODS Cell viability was assessed with fluorometric microculture cytotoxicity assay (FMCA) and Combination Index was calculated using the Additive model. p53 status was determined by Sanger sequencing and single strand conformation analysis, and p53 protein expression by western blotting. RESULTS We observed strong synergy with APR-246 and cisplatin in all tumor samples carrying a TP53 missense mutation, while synergistic or additive effects were found in cells with wild type or TP53 nonsense mutations. Strong synergy was also observed with carboplatin or doxorubicin. Moreover, APR-246 sensitized TP53 mutant primary ovarian cancer cells, isolated from a clinically platinum-resistant patient, to cisplatin; the IC50 value of cisplatin decreased 3.6 fold from 6.5 to 1.8 μM in the presence of clinically relevant concentration of APR-246. CONCLUSION These results suggest that combination treatment with APR-246 and DNA-damaging drugs could significantly improve the treatment of patients with TP53 mutant HGS cancer, and thus provide strong support for the ongoing clinical study with APR-246 in combination with carboplatin and pegylated liposomal doxorubicin in patients with recurrent HGS cancer.
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Affiliation(s)
| | | | | | - Klas G Wiman
- Karolinska Institutet Dept. of Oncology-Pathology, Cancer Center Karolinska (CCK), Stockholm, Sweden
| | - Svetlana Bajalica-Lagercrantz
- Karolinska University Hospital, Stockholm, Sweden.,Karolinska Institutet Dept. of Oncology-Pathology, Cancer Center Karolinska (CCK), Stockholm, Sweden
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Fransson Å, Glaessgen D, Alfredsson J, Wiman KG, Bajalica-Lagercrantz S, Mohell N. Strong synergy with APR-246 and DNA-damaging drugs in primary cancer cells from patients with TP53 mutant High-Grade Serous ovarian cancer. J Ovarian Res 2016; 9:27. [PMID: 27179933 PMCID: PMC4868029 DOI: 10.1186/s13048-016-0239-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/05/2016] [Indexed: 12/19/2022] Open
Abstract
Background Mutation in the tumor suppressor gene TP53 is an early event in the development of high-grade serous (HGS) ovarian cancer and is identified in more than 96 % of HGS cancer patients. APR-246 (PRIMA-1MET) is the first clinical-stage compound that reactivates mutant p53 protein by refolding it to wild type conformation, thus inducing apoptosis. APR-246 has been tested as monotherapy in a Phase I/IIa clinical study in hematological malignancies and prostate cancer with promising results, and a Phase Ib/II study in combination with platinum-based therapy in ovarian cancer is ongoing. In the present study, we investigated the anticancer effects of APR-246 in combination with conventional chemotherapy in primary cancer cells isolated from ascitic fluid from 10 ovarian, fallopian tube, or peritoneal cancer patients, 8 of which had HGS cancer. Methods Cell viability was assessed with fluorometric microculture cytotoxicity assay (FMCA) and Combination Index was calculated using the Additive model. p53 status was determined by Sanger sequencing and single strand conformation analysis, and p53 protein expression by western blotting. Results We observed strong synergy with APR-246 and cisplatin in all tumor samples carrying a TP53 missense mutation, while synergistic or additive effects were found in cells with wild type or TP53 nonsense mutations. Strong synergy was also observed with carboplatin or doxorubicin. Moreover, APR-246 sensitized TP53 mutant primary ovarian cancer cells, isolated from a clinically platinum-resistant patient, to cisplatin; the IC50 value of cisplatin decreased 3.6 fold from 6.5 to 1.8 μM in the presence of clinically relevant concentration of APR-246. Conclusion These results suggest that combination treatment with APR-246 and DNA-damaging drugs could significantly improve the treatment of patients with TP53 mutant HGS cancer, and thus provide strong support for the ongoing clinical study with APR-246 in combination with carboplatin and pegylated liposomal doxorubicin in patients with recurrent HGS cancer.
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Affiliation(s)
| | | | | | - Klas G Wiman
- Karolinska Institutet Dept. of Oncology-Pathology, Cancer Center Karolinska (CCK), Stockholm, Sweden
| | - Svetlana Bajalica-Lagercrantz
- Karolinska University Hospital, Stockholm, Sweden.,Karolinska Institutet Dept. of Oncology-Pathology, Cancer Center Karolinska (CCK), Stockholm, Sweden
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Sandulache VC, Chen Y, Skinner HD, Lu T, Feng L, Court LE, Myers JN, Meyn RE, Fuller CD, Bankson JA, Lai SY. Acute Tumor Lactate Perturbations as a Biomarker of Genotoxic Stress: Development of a Biochemical Model. Mol Cancer Ther 2015; 14:2901-8. [PMID: 26376962 DOI: 10.1158/1535-7163.mct-15-0217] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 09/07/2015] [Indexed: 12/15/2022]
Abstract
Ionizing radiation is the primary nonsurgical treatment modality for solid tumors. Its effectiveness is impacted by temporal constraints such as fractionation, hypoxia, and development of radioresistant clones. Biomarkers of acute radiation response are essential to developing more effective clinical algorithms. We hypothesized that acute perturbations in tumor lactate levels act as a surrogate marker of radiation response. In vitro experiments were carried out using validated human-derived cell lines from three histologies: anaplastic thyroid carcinoma (ATC), head and neck squamous cell carcinoma (HNSCC), and papillary thyroid carcinoma (PTC). Cellular metabolic activity was measured using standard biochemical assays. In vivo validation was performed using both an orthotopic and a flank derivative of a previously established ATC xenograft murine model. Irradiation of cells and tumors triggered a rapid, dose-dependent, transient decrease in lactate levels that was reversed by free radical scavengers. Acute lactate perturbations following irradiation could identify hypoxic conditions and correlated with hypoxia-induced radioresistance. Mutant TP53 cells and cells in which p53 activity was abrogated (shRNA) demonstrated a blunted lactate response to irradiation, consistent with a radioresistant phenotype. Lactate measurements therefore rapidly detected both induced (i.e., hypoxia) and intrinsic (i.e., mutTP53-driven) radioresistance. We conclude that lactate is a quantitative biomarker of acute genotoxic stress, with a temporal resolution that can inform clinical decision making. Combined with the spatial resolution of newly developed metabolic imaging platforms, this biomarker could lead to the development of truly individualized treatment strategies.
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Affiliation(s)
- Vlad C Sandulache
- Bobby R. Alford Department of Otolaryngology-Head and Neck Surgery, Baylor College of Medicine, Houston, Texas. Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Yunyun Chen
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Heath D Skinner
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Tongtong Lu
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Lei Feng
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Laurence E Court
- Department of Radiation Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Jeffrey N Myers
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Raymond E Meyn
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Clifton D Fuller
- Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - James A Bankson
- Department of Imaging Physics, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Stephen Y Lai
- Department of Head and Neck Surgery, The University of Texas MD Anderson Cancer Center, Houston, Texas. Department of Molecular and Cellular Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas.
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Burtness B. Complexity in the Gastric Cancer Genome and a Biomarker-Driven Trial of Poly (ADP-Ribose) Polymerase Inhibition in Gastric Cancer. J Clin Oncol 2015; 33:3845-6. [PMID: 26282638 DOI: 10.1200/jco.2015.62.8487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
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25
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Comparison of predicted and actual consequences of missense mutations. Proc Natl Acad Sci U S A 2015; 112:E5189-98. [PMID: 26269570 DOI: 10.1073/pnas.1511585112] [Citation(s) in RCA: 157] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Each person's genome sequence has thousands of missense variants. Practical interpretation of their functional significance must rely on computational inferences in the absence of exhaustive experimental measurements. Here we analyzed the efficacy of these inferences in 33 de novo missense mutations revealed by sequencing in first-generation progeny of N-ethyl-N-nitrosourea-treated mice, involving 23 essential immune system genes. PolyPhen2, SIFT, MutationAssessor, Panther, CADD, and Condel were used to predict each mutation's functional importance, whereas the actual effect was measured by breeding and testing homozygotes for the expected in vivo loss-of-function phenotype. Only 20% of mutations predicted to be deleterious by PolyPhen2 (and 15% by CADD) showed a discernible phenotype in individual homozygotes. Half of all possible missense mutations in the same 23 immune genes were predicted to be deleterious, and most of these appear to become subject to purifying selection because few persist between separate mouse substrains, rodents, or primates. Because defects in immune genes could be phenotypically masked in vivo by compensation and environment, we compared inferences by the same tools with the in vitro phenotype of all 2,314 possible missense variants in TP53; 42% of mutations predicted by PolyPhen2 to be deleterious (and 45% by CADD) had little measurable consequence for TP53-promoted transcription. We conclude that for de novo or low-frequency missense mutations found by genome sequencing, half those inferred as deleterious correspond to nearly neutral mutations that have little impact on the clinical phenotype of individual cases but will nevertheless become subject to purifying selection.
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Rettig EM, Chung CH, Bishop JA, Howard JD, Sharma R, Li RJ, Douville C, Karchin R, Izumchenko E, Sidransky D, Koch W, Califano J, Agrawal N, Fakhry C. Cleaved NOTCH1 Expression Pattern in Head and Neck Squamous Cell Carcinoma Is Associated with NOTCH1 Mutation, HPV Status, and High-Risk Features. Cancer Prev Res (Phila) 2015; 8:287-95. [PMID: 25633867 DOI: 10.1158/1940-6207.capr-14-0366] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 01/15/2015] [Indexed: 12/21/2022]
Abstract
The Notch pathway is frequently altered in head and neck squamous cell carcinomas (HNSCC); however, the clinical significance of NOTCH1 dysregulation is poorly understood. This study was designed to characterize expression of the transcriptionally active NOTCH1 intracellular domain (NICD1) in HNSCCs and evaluate its association with NOTCH1 mutation status and clinical parameters. IHC for NICD1 was performed on 79 previously sequenced archival HNSCCs with known NOTCH1 mutation status. Three distinct immunohistochemical staining patterns were identified: positive/peripheral (47%), positive/nonperipheral (34%), and negative (19%). NICD1 expression was associated with NOTCH1 mutation status (P < 0.001). Most NOTCH1-wild-type tumors were peripheral (55%), whereas mutated NOTCH1 tumors were most commonly negative (47%). Nonperipheral tumors were more likely than peripheral tumors to have extracapsular spread [adjusted odds ratio (aOR), 16.01; 95% confidence interval (CI), 1.92-133.46; P = 0.010] and poor differentiation (aOR, 5.27; 95% CI, 0.90-30.86; P = 0.066). Negative staining tumors tended to be poorly differentiated (aOR, 24.71; 95% CI, 1.53-399.33; P = 0.024) and were less likely to be human papillomavirus (HPV) positive (aOR, 0.043; 95% CI, 0.001-1.59; P = 0.087). NOTCH1 mutagenesis was significantly associated with HPV status, with NOTCH1-wild-type tumors more likely to be HPV positive than NOTCH1-mutated tumors (aOR, 19.06; 95% CI, 1.31-276.15; P = 0.031). TP53 disruptive mutations were not associated with NICD1 expression or NOTCH1 mutation. In conclusion, NICD1 is expressed in three distinct patterns in HNSCC that are significantly associated with high-risk features. These findings further support a dual role for NOTCH1 as both tumor suppressor and oncogene in HNSCC. Further research is necessary to clarify the role of NOTCH1 in HNSCC and understand the clinical and therapeutic implications therein.
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MESH Headings
- Biomarkers, Tumor
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/metabolism
- Carcinoma, Squamous Cell/pathology
- Carcinoma, Squamous Cell/virology
- Female
- Follow-Up Studies
- Head and Neck Neoplasms/genetics
- Head and Neck Neoplasms/metabolism
- Head and Neck Neoplasms/pathology
- Head and Neck Neoplasms/virology
- Humans
- Immunoenzyme Techniques
- Male
- Middle Aged
- Mutation/genetics
- Neoplasm Invasiveness
- Neoplasm Recurrence, Local/genetics
- Neoplasm Recurrence, Local/metabolism
- Neoplasm Recurrence, Local/pathology
- Neoplasm Recurrence, Local/virology
- Neoplasm Staging
- Papillomaviridae/genetics
- Papillomavirus Infections/genetics
- Papillomavirus Infections/metabolism
- Papillomavirus Infections/pathology
- Papillomavirus Infections/virology
- Prognosis
- Receptor, Notch1/genetics
- Receptor, Notch1/metabolism
- Retrospective Studies
- Risk Factors
- Tumor Suppressor Protein p53
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Affiliation(s)
- Eleni M Rettig
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Christine H Chung
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland. Sidney Kimmel Comprehensive Cancer Center, Baltimore, Maryland. Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Justin A Bishop
- Department of Pathology, Johns Hopkins School of Medicine, Johns Hopkins Medicine, Baltimore, Maryland
| | - Jason D Howard
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Rajni Sharma
- Department of Pathology, Johns Hopkins School of Medicine, Johns Hopkins Medicine, Baltimore, Maryland
| | - Ryan J Li
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Christopher Douville
- Johns Hopkins Institute for Computational Medicine and Department of Biomedical Engineering, Baltimore, Maryland
| | - Rachel Karchin
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland. Johns Hopkins Institute for Computational Medicine and Department of Biomedical Engineering, Baltimore, Maryland
| | - Evgeny Izumchenko
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - David Sidransky
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Wayne Koch
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Joseph Califano
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland. Milton J. Dance Jr. Head and Neck Center, Greater Baltimore Medical Center, Baltimore, Maryland
| | - Nishant Agrawal
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland. Johns Hopkins University School of Medicine Ludwig Center for Cancer Genetics and Therapeutics, Baltimore, Maryland.
| | - Carole Fakhry
- Department of Otolaryngology-Head and Neck Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland. Milton J. Dance Jr. Head and Neck Center, Greater Baltimore Medical Center, Baltimore, Maryland. Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland.
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