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Uroog L, Zeya B, Imtiyaz K, Ahmad Wani R, Moshahid Alam Rizvi M. FBXW7 polymorphism asserts susceptibility to colorectal cancer. Gene 2024; 901:148181. [PMID: 38244948 DOI: 10.1016/j.gene.2024.148181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Revised: 01/05/2024] [Accepted: 01/17/2024] [Indexed: 01/22/2024]
Abstract
FBXW7, belonging to the F-Box protein family, is considered a candidate cancer susceptibility gene. Our findings indicate that single nucleotide polymorphisms (SNPs) in the FBXW7 gene are linked to cancer risk, strengthening FBXW7's role in the pathogenesis of colorectal cancer. Our case-control study comprised of 450 patients diagnosed with colorectal cancer (CRC) and an equal number of 450 healthy subjects. FBXW7 SNPs rs2255137C>T and rs6842544C>T were genotyped using PCR-Restriction Fragment Length Polymorphism (PCR-RFLP) and Single-Stranded Conformation Polymorphism (SSCP) techniques and further cross-checked by direct sequencing. Linkage disequilibrium and haplotype analyses of these SNPs were also assessed. The in-silico approach was used to reveal the functional analysis between the nonsynonymous variation (rs6842544) and CRC followed by its validation at the protein level by western blotting and reverse transcription-PCR. A significant association of colorectal cancer was detected with rs6842544 SNP. However, there was no association between FBXW7 rs2255137 polymorphism and CRC. The homozygous individuals carrying the C variant in FBXW7 rs6842544 showed a slightly higher risk for colorectal cancer (OR = 1.590, 95%CI = 0.39 ∼ 2.89, p = 0.011). The haplotype CC identified in this study seemed to be associated with good prognosis (OR = 1.22, 95% CI = 1.00 ∼ 1.47, p = 0.0013) whereas the TT haplotype was found to reduce the CRC risk (OR = 0.642, 95%CI = 0.48 ∼ 0.84, p = 0.039). In-silico prediction proposed that the variant R133G is responsible for the lower expression of FBXW7. Additionally, the expression profiling of FBXW7 nonsynonymous SNP was significantly lower in primary CRC tissues than in the paired non-cancerous tissues at protein and mRNA levels. The study indicates that the FBXW7 rs6842544 is associated with the risk of development of CRC and could serve as a molecular biological marker to screen high-risk groups for CRC.
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Affiliation(s)
- Laraib Uroog
- Genome Biology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Bushra Zeya
- Genome Biology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Khalid Imtiyaz
- Genome Biology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India
| | - Rauf Ahmad Wani
- Department of General Surgery, SKIMS, Srinagar, Jammu and Kashmir, India
| | - M Moshahid Alam Rizvi
- Genome Biology Lab, Department of Biosciences, Jamia Millia Islamia, New Delhi 110025, India.
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2
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Fan J, Bellon M, Ju M, Zhao L, Wei M, Fu L, Nicot C. Clinical significance of FBXW7 loss of function in human cancers. Mol Cancer 2022; 21:87. [PMID: 35346215 PMCID: PMC8962602 DOI: 10.1186/s12943-022-01548-2] [Citation(s) in RCA: 47] [Impact Index Per Article: 23.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/22/2022] [Indexed: 12/13/2022] Open
Abstract
FBXW7 (F-Box and WD Repeat Domain Containing 7) (also referred to as FBW7 or hCDC4) is a component of the Skp1-Cdc53 / Cullin-F-box-protein complex (SCF/β-TrCP). As a member of the F-box protein family, FBXW7 serves a role in phosphorylation-dependent ubiquitination and proteasome degradation of oncoproteins that play critical role(s) in oncogenesis. FBXW7 affects many regulatory functions involved in cell survival, cell proliferation, tumor invasion, DNA damage repair, genomic instability and telomere biology. This thorough review of current literature details how FBXW7 expression and functions are regulated through multiple mechanisms and how that ultimately drives tumorigenesis in a wide array of cell types. The clinical significance of FBXW7 is highlighted by the fact that FBXW7 is frequently inactivated in human lung, colon, and hematopoietic cancers. The loss of FBXW7 can serve as an independent prognostic marker and is significantly correlated with the resistance of tumor cells to chemotherapeutic agents and poorer disease outcomes. Recent evidence shows that genetic mutation of FBXW7 differentially affects the degradation of specific cellular targets resulting in a distinct and specific pattern of activation/inactivation of cell signaling pathways. The clinical significance of FBXW7 mutations in the context of tumor development, progression, and resistance to therapies as well as opportunities for targeted therapies is discussed.
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Affiliation(s)
- Jingyi Fan
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Guangdong Esophageal Cancer Institute; Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong Province, China.,Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, China.,Liaoning Province, China Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, 110122, Liaoning Province, China
| | - Marcia Bellon
- Department of Pathology and Laboratory Medicine, Center for Viral Pathogenesis, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS, 66160, USA
| | - Mingyi Ju
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, China.,Liaoning Province, China Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, 110122, Liaoning Province, China
| | - Lin Zhao
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, China.,Liaoning Province, China Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, 110122, Liaoning Province, China
| | - Minjie Wei
- Department of Pharmacology, School of Pharmacy, China Medical University, Shenyang, 110122, China.,Liaoning Province, China Liaoning Key Laboratory of Molecular Targeted Anti-Tumor Drug Development and Evaluation, Liaoning Cancer Immune Peptide Drug Engineering Technology Research Center, Key Laboratory of Precision Diagnosis and Treatment of Gastrointestinal Tumors, Ministry of Education, China Medical University, Shenyang, 110122, Liaoning Province, China
| | - Liwu Fu
- State Key Laboratory of Oncology in South China; Collaborative Innovation Center for Cancer Medicine, Guangdong Esophageal Cancer Institute; Sun Yat-sen University Cancer Center, Guangzhou, 510060, Guangdong Province, China.
| | - Christophe Nicot
- Department of Pathology and Laboratory Medicine, Center for Viral Pathogenesis, University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS, 66160, USA.
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3
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Leichsenring J, Horak P, Kreutzfeldt S, Heining C, Christopoulos P, Volckmar A, Neumann O, Kirchner M, Ploeger C, Budczies J, Heilig CE, Hutter B, Fröhlich M, Uhrig S, Kazdal D, Allgäuer M, Harms A, Rempel E, Lehmann U, Thomas M, Pfarr N, Azoitei N, Bonzheim I, Marienfeld R, Möller P, Werner M, Fend F, Boerries M, Bubnoff N, Lassmann S, Longerich T, Bitzer M, Seufferlein T, Malek N, Weichert W, Schirmacher P, Penzel R, Endris V, Brors B, Klauschen F, Glimm H, Fröhling S, Stenzinger A. Variant classification in precision oncology. Int J Cancer 2019; 145:2996-3010. [DOI: 10.1002/ijc.32358] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Accepted: 04/08/2019] [Indexed: 02/06/2023]
Affiliation(s)
- Jonas Leichsenring
- Institute of Pathology, University Hospital Heidelberg Heidelberg Germany
| | - Peter Horak
- National Center for Tumor Diseases (NCT) Heidelberg Heidelberg Germany
- German Cancer Consortium (DKTK) Heidelberg Germany
| | - Simon Kreutzfeldt
- National Center for Tumor Diseases (NCT) Heidelberg Heidelberg Germany
- German Cancer Consortium (DKTK) Heidelberg Germany
| | - Christoph Heining
- National Center for Tumor Diseases (NCT) Dresden Germany
- University Hospital Carl Gustav Carus Dresden Germany
| | - Petros Christopoulos
- Thoraxklinik Heidelberg Germany
- Translational Lung Cancer Research Heidelberg (TLCR‐H)German Center for Lung Research (DZL) Giessen Germany
| | - Anna‐Lena Volckmar
- Institute of Pathology, University Hospital Heidelberg Heidelberg Germany
| | - Olaf Neumann
- Institute of Pathology, University Hospital Heidelberg Heidelberg Germany
| | - Martina Kirchner
- Institute of Pathology, University Hospital Heidelberg Heidelberg Germany
| | - Carolin Ploeger
- Institute of Pathology, University Hospital Heidelberg Heidelberg Germany
| | - Jan Budczies
- Institute of Pathology, University Hospital Heidelberg Heidelberg Germany
| | | | | | | | - Sebastian Uhrig
- German Cancer Research Center (DKFZ) Heidelberg Germany
- Faculty of BiosciencesHeidelberg University Heidelberg Germany
| | - Daniel Kazdal
- Institute of Pathology, University Hospital Heidelberg Heidelberg Germany
| | - Michael Allgäuer
- Institute of Pathology, University Hospital Heidelberg Heidelberg Germany
| | - Alexander Harms
- Institute of Pathology, University Hospital Heidelberg Heidelberg Germany
| | - Eugen Rempel
- Institute of Pathology, University Hospital Heidelberg Heidelberg Germany
| | - Ulrich Lehmann
- Institute of Pathology, Hannover Medical School Hanover Germany
| | - Michael Thomas
- Thoraxklinik Heidelberg Germany
- Translational Lung Cancer Research Heidelberg (TLCR‐H)German Center for Lung Research (DZL) Giessen Germany
| | - Nicole Pfarr
- Institute of Pathology, Technische Universität München Munich Germany
| | - Ninel Azoitei
- Clinic of Internal Medicine IUniversity Hospital Ulm Ulm Germany
| | - Irina Bonzheim
- Institute of Pathology, University Hospital Tübingen Tübingen Germany
| | | | - Peter Möller
- Institute of Pathology, University Hospital Ulm Ulm Germany
| | - Martin Werner
- Institute of Pathology, Medical Center, University of Freiburg Breisgau Germany
| | - Falko Fend
- Institute of Pathology, University Hospital Tübingen Tübingen Germany
| | - Melanie Boerries
- German Cancer Consortium (DKTK) Heidelberg Germany
- German Cancer Research Center (DKFZ) Heidelberg Germany
- Institute of Molecular Medicine and Cell ResearchUniversity of Freiburg Freiburg Germany
- MIRACUM Consortium of the Medical Informatics Initiative Freiburg Germany
| | - Nikolas Bubnoff
- German Cancer Consortium (DKTK) Heidelberg Germany
- German Cancer Research Center (DKFZ) Heidelberg Germany
- Department of Hematology, Oncology and Stem Cell Transplantation, Medical Center, Faculty of MedicineUniversity of Freiburg Freiburg Germany
- Department of Hematology and OncologyMedical Center, University of Schleswig‐Holstein Lübeck Germany
| | - Silke Lassmann
- Institute of Pathology, Medical Center, University of Freiburg Breisgau Germany
| | - Thomas Longerich
- Institute of Pathology, University Hospital Heidelberg Heidelberg Germany
- Heidelberg‐Göttingen‐Hannover Medizininformatik (HiGHmed) Konsortium Heidelberg Germany
| | - Michael Bitzer
- Department of Internal Medicine IUniversity Hospital Tübingen Tübingen Germany
| | | | - Nisar Malek
- Department of Internal Medicine IUniversity Hospital Tübingen Tübingen Germany
| | - Wilko Weichert
- Institute of Pathology, Technische Universität München Munich Germany
| | - Peter Schirmacher
- Institute of Pathology, University Hospital Heidelberg Heidelberg Germany
- German Cancer Consortium (DKTK) Heidelberg Germany
| | - Roland Penzel
- Institute of Pathology, University Hospital Heidelberg Heidelberg Germany
| | - Volker Endris
- Institute of Pathology, University Hospital Heidelberg Heidelberg Germany
| | - Benedikt Brors
- National Center for Tumor Diseases (NCT) Heidelberg Heidelberg Germany
- German Cancer Consortium (DKTK) Heidelberg Germany
- German Cancer Research Center (DKFZ) Heidelberg Germany
| | | | - Hanno Glimm
- National Center for Tumor Diseases (NCT) Dresden Germany
| | - Stefan Fröhling
- National Center for Tumor Diseases (NCT) Heidelberg Heidelberg Germany
- German Cancer Consortium (DKTK) Heidelberg Germany
- DKFZ‐Heidelberg Center for Personalized Oncology (HIPO) Heidelberg Germany
| | - Albrecht Stenzinger
- Institute of Pathology, University Hospital Heidelberg Heidelberg Germany
- DKFZ‐Heidelberg Center for Personalized Oncology (HIPO) Heidelberg Germany
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4
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FBXW7 in Cancer: What Has Been Unraveled Thus Far? Cancers (Basel) 2019; 11:cancers11020246. [PMID: 30791487 PMCID: PMC6406609 DOI: 10.3390/cancers11020246] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/07/2019] [Accepted: 02/11/2019] [Indexed: 12/14/2022] Open
Abstract
: The FBXW7 (F-box with 7 tandem WD40) protein encoded by the gene FBXW7 is one of the crucial components of ubiquitin ligase called Skp1-Cullin1-F-box (SCF) complex that aids in the degradation of many oncoproteins via the ubiquitin-proteasome system (UPS) thus regulating cellular growth. FBXW7 is considered as a potent tumor suppressor as most of its target substrates can function as potential growth promoters, including c-Myc, Notch, cyclin E, c-JUN, and KLF5. Its regulators include p53, C/EBP-δ, Numb, microRNAs, Pin 1, Hes-5, BMI1, Ebp2. Mounting evidence has indicated the involvement of aberrant expression of FBXW7 for tumorigenesis. Moreover, numerous studies have also shown its role in cancer cell chemosensitization, thereby demonstrating the importance of FBXW7 in the development of curative cancer therapy. This comprehensive review emphasizes on the targets, functions, regulators and expression of FBXW7 in different cancers and its involvement in sensitizing cancer cells to chemotherapeutic drugs.
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Xiao Y, Yin C, Wang Y, Lv H, Wang W, Huang Y, Perez-Losada J, Snijders AM, Mao JH, Zhang P. FBXW7 deletion contributes to lung tumor development and confers resistance to gefitinib therapy. Mol Oncol 2018; 12:883-895. [PMID: 29633504 PMCID: PMC5983212 DOI: 10.1002/1878-0261.12200] [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: 12/26/2017] [Revised: 01/31/2018] [Accepted: 02/01/2018] [Indexed: 11/26/2022] Open
Abstract
Gefitinib, an epidermal growth factor receptor–tyrosine kinase inhibitor (EGFR‐TKI), is an effective treatment for non‐small‐cell lung cancer (NSCLC) with EGFR activating mutations, but inevitably, the clinical efficacy is impeded by the emergence of acquired resistance. The tumor suppressor gene FBXW7 modulates chemosensitivity in various human cancers. However, its role in EGFR‐TKI therapy in NSCLC has not been well studied. Here, we demonstrate that the mice with deficient Fbxw7 have greater susceptibility to urethane‐induced lung tumor development. Through analysis of The Cancer Genome Atlas data, we show that deletion of FBXW7 occurs in 30.9% of lung adenocarcinomas and 63.5% of lung squamous cell carcinomas, which significantly leads to decrease in FBXW7 mRNA expression. The reduction in FBXW7 mRNA level is associated with poor overall survival in lung cancer patients. FBXW7 knockdown dramatically promotes epithelial–mesenchymal transition, migration, and invasion in NSCLC cells. Moreover, with silenced FBXW7, EGFR‐TKI‐sensitive cells become resistant to gefitinib, which is reversed by the mammalian target of rapamycin inhibitor, rapamycin. Furthermore, xenograft mouse model studies show that FBXW7 knockdown enhances tumorigenesis and resistance to gefitinib. Combination of gefitinib with rapamycin treatment suppresses tumor formation of gefitinib‐resistant (GR) FBXW7‐knockdown cells. In conclusion, our findings suggest that loss of FBXW7 promotes NSCLC progression as well as gefitinib resistance and combination of gefitinib and rapamycin may provide an effective therapy for GR NSCLC.
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Affiliation(s)
- Yi Xiao
- Department of Biochemistry and Molecular Biology, Shandong University School of Basic Medical Sciences, Jinan, China
| | - Chunli Yin
- Department of Biochemistry and Molecular Biology, Shandong University School of Basic Medical Sciences, Jinan, China
| | - Yuli Wang
- Department of Clinical Laboratory, The Second Hospital of Shandong University, Jinan, China
| | - Hanlin Lv
- Department of Biochemistry and Molecular Biology, Shandong University School of Basic Medical Sciences, Jinan, China
| | - Wenqing Wang
- Department of Biochemistry and Molecular Biology, Shandong University School of Basic Medical Sciences, Jinan, China
| | - Yurong Huang
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, CA, USA
| | - Jesus Perez-Losada
- Instituto de Biología Molecular y Celular del Cáncer (IBMCC), Instituto Mixto Universidad de Salamanca/CSIC, IBSAL, Salamanca, Spain
| | - Antoine M Snijders
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, CA, USA
| | - Jian-Hua Mao
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, CA, USA
| | - Pengju Zhang
- Department of Biochemistry and Molecular Biology, Shandong University School of Basic Medical Sciences, Jinan, China
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Liu H, Wang K, Fu H, Song J. Low expression of the ubiquitin ligase FBXW7 correlates with poor prognosis of patients with colorectal cancer. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2018; 11:413-419. [PMID: 31938126 PMCID: PMC6957979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 10/30/2017] [Indexed: 06/10/2023]
Abstract
FBXW7 is a potential tumor suppressor that regulates ubiquitination and proteolysis of multiple targets such as cyclin E, c-Myc, c-Jun and Notch. However, little knows about the correlation between FBXW7 and prognosis of patients with colorectal cancer (CRC). In this study, we detected FBXW7 expression in CRC tissue microarray which includes 568 cases cancer tissue and their paired adjacent non-cancerous tissues. We found that FBXW7 expression was significantly reduced in CRC tissues versus paired normal colon tissues (P < 0.001). Moreover, low FBXW7 expression was significantly associated with increased lymph node metastasis (P < 0.001) and advanced TNM stage (P < 0.001). Besides, the low expression of FBXW7 indicated the poor prognosis in CRC patients for both overall and disease-free cumulative survival (P < 0.001 and P = 0.003, respectively). Multivariate Cox regression analysis showed that low FBXW7 expression was an independent unfavorable prognostic factor of CRC (hazard ratio = 0.45, P = 0.001). In conclusion, we can indicate that FBXW7 may play essential roles in the progression of CRC and function as an independent prognostic marker for clinical diagnosis and therapy treatment of patients with CRC.
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Affiliation(s)
- Hao Liu
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical UniversityXuzhou, Jiangsu Province, China
| | - Kai Wang
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical UniversityXuzhou, Jiangsu Province, China
| | - Haixiao Fu
- Department of General Surgery, The Affiliated Hospital of Xuzhou Medical UniversityXuzhou, Jiangsu Province, China
| | - Jinhui Song
- Department of General Surgery, Maigaoqiao Hospital of NanjingNanjing, Jiangsu Province, China
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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.
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Guyard A, Danel C, Théou-Anton N, Debray MP, Gibault L, Mordant P, Castier Y, Crestani B, Zalcman G, Blons H, Cazes A. Morphologic and molecular study of lung cancers associated with idiopathic pulmonary fibrosis and other pulmonary fibroses. Respir Res 2017; 18:120. [PMID: 28619094 PMCID: PMC5472872 DOI: 10.1186/s12931-017-0605-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 06/07/2017] [Indexed: 01/26/2023] Open
Abstract
BACKGROUND Primitive lung cancers developed on lung fibroses are both diagnostic and therapeutic challenges. Their incidence may increase with new more efficient lung fibrosis treatments. Our aim was to describe a cohort of lung cancers associated with idiopathic pulmonary fibrosis (IPF) and other lung fibrotic disorders (non-IPF), and to characterize their molecular alterations using immunohistochemistry and next-generation sequencing (NGS). METHODS Thirty-one cancer samples were collected from 2001 to 2016 in two French reference centers for pulmonary fibrosis - 18 for IPF group and 13 for non-IPF group. NGS was performed using an ampliseq panel to analyze hotspots and targeted regions in 22 cancer-associated genes. ALK, ROS1 and PD-L1 expressions were assessed by immunohistochemistry. RESULTS Squamous cell carcinoma was the most frequent histologic subtype in the IPF group (44%), adenocarcinoma was the most frequent subtype in the non-IPF group (62%). Forty-one mutations in 13 genes and one EGFR amplification were identified in 25 samples. Two samples had no mutation in the selected panel. Mutations were identified in TP53 (n = 20), MET (n = 4), BRAF (n = 3), FGFR3, PIK3CA, PTEN, STK11 (n = 2), SMAD4, CTNNB1, DDR2, ERBB4, FBXW7 and KRAS (n = 1) genes. No ALK and ROS1 expressions were identified. PD-L1 was expressed in 10 cases (62%) with only one (6%) case >50%. CONCLUSIONS This extensive characterization of lung fibrosis-associated cancers evidenced molecular alterations which could represent either potential therapeutic targets either clues to the pathophysiology of these particular tumors. These findings support the relevance of large molecular characterization of every lung fibrosis-associated cancer.
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Affiliation(s)
- Alice Guyard
- Département de Pathologie, Hôpital Bichat-Claude Bernard, Assistance Publique-Hôpitaux de Paris, 46 rue Henri Huchard, 75018, Paris, France
| | - Claire Danel
- Département de Pathologie, Hôpital Bichat-Claude Bernard, Assistance Publique-Hôpitaux de Paris, 46 rue Henri Huchard, 75018, Paris, France
| | - Nathalie Théou-Anton
- Département de Génétique, Hôpital Bichat-Claude Bernard, Assistance Publique-Hôpitaux de Paris, 46 rue Henri Huchard, 75018, Paris, France
| | - Marie-Pierre Debray
- Service de Radiologie, Hôpital Bichat-Claude Bernard, Assistance Publique-Hôpitaux de Paris, 46 rue Henri Huchard, 75018, Paris, France
| | - Laure Gibault
- Service de Pathologie, Hôpital Européen Georges Pompidou, Assistance Publique-Hôpitaux de Paris, 20 rue Leblanc, 75015, Paris, France
| | - Pierre Mordant
- Service de chirurgie vasculaire et thoracique, Hôpital Bichat-Claude Bernard, Assistance Publique-Hôpitaux de Paris, 46 rue Henri Huchard, 75018, Paris, France
| | - Yves Castier
- Service de chirurgie vasculaire et thoracique, Hôpital Bichat-Claude Bernard, Assistance Publique-Hôpitaux de Paris, 46 rue Henri Huchard, 75018, Paris, France
| | - Bruno Crestani
- Service de Pneumologie A, Hôpital Bichat-Claude Bernard, Assistance Publique-Hôpitaux de Paris, 46 rue Henri Huchard, 75018, Paris, France
- INSERM U1152, DHU FIRE, Labex Inflamex, Université Paris- Diderot, Paris, France
| | - Gérard Zalcman
- Service d'Oncologie Thoracique, CIC1425/CLIP2 Paris-Nord, Université Paris-Diderot, Hôpital Bichat-Claude Bernard, AP-HP, 46 rue Henri Huchard, 75018, Paris, France
- INSERM U830, Institut Curie, Paris, France
| | - Hélène Blons
- Department of Biochemistry, Pharmacogenetic and Molecular Oncology Unit, Hôpital Européen Georges Pompidou, Assistance Publique - Hôpitaux de Paris, INSERM UMR-S1147, Université Sorbonne Paris Cité, Paris, France
| | - Aurélie Cazes
- Département de Pathologie, Hôpital Bichat-Claude Bernard, Assistance Publique-Hôpitaux de Paris, 46 rue Henri Huchard, 75018, Paris, France.
- INSERM U1152, DHU FIRE, Labex Inflamex, Université Paris- Diderot, Paris, France.
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9
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Ye M, Zhang Y, Zhang X, Zhang J, Jing P, Cao L, Li N, Li X, Yao L, Zhang J, Zhang J. Targeting FBW7 as a Strategy to Overcome Resistance to Targeted Therapy in Non–Small Cell Lung Cancer. Cancer Res 2017; 77:3527-3539. [PMID: 28522751 DOI: 10.1158/0008-5472.can-16-3470] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 03/27/2017] [Accepted: 05/10/2017] [Indexed: 11/16/2022]
Affiliation(s)
- Mingxiang Ye
- Department of Pulmonary Medicine, Xijing Hospital, Xi'an, China
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
| | - Yong Zhang
- Department of Pulmonary Medicine, Xijing Hospital, Xi'an, China
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
| | - Xinxin Zhang
- Department of Pulmonary Medicine, Xijing Hospital, Xi'an, China
| | - Jianbin Zhang
- Department of Occupational and Environmental Health, School of Public Health, Fourth Military Medical University, Xi'an, China
| | - Pengyu Jing
- Department of Thoracic Surgery, Tangdu Hospital, Fourth Military Medical University, Xi'an, China
| | - Liang Cao
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
| | - Nan Li
- Department of Pulmonary Medicine, Xijing Hospital, Xi'an, China
| | - Xia Li
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
| | - Libo Yao
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China
| | - Jian Zhang
- State Key Laboratory of Cancer Biology, Department of Biochemistry and Molecular Biology, Fourth Military Medical University, Xi'an, China.
| | - Jian Zhang
- Department of Pulmonary Medicine, Xijing Hospital, Xi'an, China.
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10
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Gallo LH, Ko J, Donoghue DJ. The importance of regulatory ubiquitination in cancer and metastasis. Cell Cycle 2017; 16:634-648. [PMID: 28166483 PMCID: PMC5397262 DOI: 10.1080/15384101.2017.1288326] [Citation(s) in RCA: 108] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Revised: 01/20/2017] [Accepted: 01/24/2017] [Indexed: 12/26/2022] Open
Abstract
Ubiquitination serves as a degradation mechanism of proteins, but is involved in additional cellular processes such as activation of NFκB inflammatory response and DNA damage repair. We highlight the E2 ubiquitin conjugating enzymes, E3 ubiquitin ligases and Deubiquitinases that support the metastasis of a plethora of cancers. E3 ubiquitin ligases also modulate pluripotent cancer stem cells attributed to chemotherapy resistance. We further describe mutations in E3 ubiquitin ligases that support tumor proliferation and adaptation to hypoxia. Thus, this review describes how tumors exploit members of the vast ubiquitin signaling pathways to support aberrant oncogenic signaling for survival and metastasis.
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Affiliation(s)
- L. H. Gallo
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - J. Ko
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
| | - D. J. Donoghue
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA, USA
- Moores UCSD Cancer Center, University of California San Diego, La Jolla, CA, USA
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11
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Ivanov M, Laktionov K, Breder V, Chernenko P, Novikova E, Telysheva E, Musienko S, Baranova A, Mileyko V. Towards standardization of next-generation sequencing of FFPE samples for clinical oncology: intrinsic obstacles and possible solutions. J Transl Med 2017; 15:22. [PMID: 28137276 PMCID: PMC5282851 DOI: 10.1186/s12967-017-1125-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 01/19/2017] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Next generation sequencing has a potential to revolutionize the management of cancer patients within the framework of precision oncology. Nevertheless, lack of standardization decelerated entering of the technology into the clinical testing space. Here we dissected a number of common problems of NGS diagnostics in oncology and introduced ways they can be resolved. METHODS DNA was extracted from 26 formalin fixed paraffin embedded (FFPE) specimens and processed with the TrueSeq Amplicon Cancer Panel (Illumina Inc, San Diego, California) targeting 48 cancer-related genes and sequenced in single run. Sequencing data were comparatively analyzed by several bioinformatics pipelines. RESULTS Libraries yielded sufficient coverage to detect even low prevalent mutations. We found that the number of FFPE sequence artifacts significantly correlates with pre-normalization concentration of libraries (rank correlation -0.81; p < 1e-10), thus, contributing to sample-specific variant detection cut-offs. Surprisingly, extensive validation of EGFR mutation calls by a combination of aligners and variant callers resulted in identification of two false negatives and one false positive that were due to complexity of underlying genomic change, confirmed by Sanger sequencing. Additionally, the study of the non-EGFR amplicons revealed 33 confirmed unique mutations in 17 genes, with TP53 being the most frequently mutated. Clinical relevance of these finding is discussed. CONCLUSIONS Reporting of entire mutational spectrum revealed by targeted sequencing is questionable, at least until the clinically-driven guidelines on reporting of somatic mutations are established. The standardization of sequencing protocols, especially their data analysis components, requires assay-, disease-, and, in many cases, even sample-specific customization that could be performed only in cooperation with clinicians.
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Affiliation(s)
- Maxim Ivanov
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow Region, 141700 Russia
- Atlas Biomed Group, Moscow, 121069 Russia
- Institute of Chemical Biology and Fundamental Medicine of SB RAS, Novosibirsk, 630090 Russia
| | - Konstantin Laktionov
- N.N. Blokhin Russian Cancer Research Center, Ministry of Health of the Russian Federation, Kashirskoe sh. 24, Moscow, 115478 Russia
| | - Valery Breder
- N.N. Blokhin Russian Cancer Research Center, Ministry of Health of the Russian Federation, Kashirskoe sh. 24, Moscow, 115478 Russia
| | - Polina Chernenko
- N.N. Blokhin Russian Cancer Research Center, Ministry of Health of the Russian Federation, Kashirskoe sh. 24, Moscow, 115478 Russia
| | - Ekaterina Novikova
- Federal State Budgetary Institution Russian Scientific Center of Roentgenoradiology (RSCRR) of the Ministry of Healthcare of the Russian Federation (Russian Scientific Center of Roentgenoradiology), Moscow, 117485 Russia
| | - Ekaterina Telysheva
- Federal State Budgetary Institution Russian Scientific Center of Roentgenoradiology (RSCRR) of the Ministry of Healthcare of the Russian Federation (Russian Scientific Center of Roentgenoradiology), Moscow, 117485 Russia
| | | | - Ancha Baranova
- Moscow Institute of Physics and Technology (State University), Dolgoprudny, Moscow Region, 141700 Russia
- Atlas Biomed Group, Moscow, 121069 Russia
- Research Centre for Medical Genetics, Moscow, 115478 Russia
- Center for the Study of Chronic Metabolic and Rare Diseases, School of System Biology, George Mason University, Fairfax, VA USA
| | - Vladislav Mileyko
- Atlas Biomed Group, Moscow, 121069 Russia
- Institute of Chemical Biology and Fundamental Medicine of SB RAS, Novosibirsk, 630090 Russia
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12
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Dhir M, Choudry HA, Holtzman MP, Pingpank JF, Ahrendt SA, Zureikat AH, Hogg ME, Bartlett DL, Zeh HJ, Singhi AD, Bahary N. Impact of genomic profiling on the treatment and outcomes of patients with advanced gastrointestinal malignancies. Cancer Med 2016; 6:195-206. [PMID: 28028924 PMCID: PMC5269696 DOI: 10.1002/cam4.992] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Revised: 09/28/2016] [Accepted: 11/12/2016] [Indexed: 12/14/2022] Open
Abstract
The impact of genomic profiling on the outcomes of patients with advanced gastrointestinal (GI) malignancies remains unknown. The primary objectives of the study were to investigate the clinical benefit of genomic‐guided therapy, defined as complete response (CR), partial response (PR), or stable disease (SD) at 3 months, and its impact on progression‐free survival (PFS) in patients with advanced GI malignancies. Clinical and genomic data of all consecutive GI tumor samples from April, 2013 to April, 2016 sequenced by FoundationOne were obtained and analyzed. A total of 101 samples from 97 patients were analyzed. Ninety‐eight samples from 95 patients could be amplified making this approach feasible in 97% of the samples. After removing duplicates, 95 samples from 95 patients were included in the further analysis. Median time from specimen collection to reporting was 11 days. Genomic alteration‐guided treatment recommendations were considered new and clinically relevant in 38% (36/95) of the patients. Rapid decline in functional status was noted in 25% (9/36) of these patients who could therefore not receive genomic‐guided therapy. Genomic‐guided therapy was utilized in 13 patients (13.7%) and 7 patients (7.4%) experienced clinical benefit (6 PR and 1 SD). Among these seven patients, median PFS was 10 months with some ongoing durable responses. Genomic profiling‐guided therapy can lead to clinical benefit in a subset of patients with advanced GI malignancies. Attempting genomic profiling earlier in the course of treatment prior to functional decline may allow more patients to benefit from these therapies.
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Affiliation(s)
- Mashaal Dhir
- Division of Surgical Oncology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, 15232
| | - Haroon A Choudry
- Division of Surgical Oncology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, 15232
| | - Matthew P Holtzman
- Division of Surgical Oncology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, 15232
| | - James F Pingpank
- Division of Surgical Oncology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, 15232
| | - Steven A Ahrendt
- Division of Surgical Oncology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, 15232
| | - Amer H Zureikat
- Division of Surgical Oncology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, 15232
| | - Melissa E Hogg
- Division of Surgical Oncology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, 15232
| | - David L Bartlett
- Division of Surgical Oncology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, 15232
| | - Herbert J Zeh
- Division of Surgical Oncology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, 15232
| | - Aatur D Singhi
- Division of Gastrointestinal Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, 15232
| | - Nathan Bahary
- Division of Oncology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, 15232
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13
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Yang H, Lu X, Liu Z, Chen L, Xu Y, Wang Y, Wei G, Chen Y. FBXW7 suppresses epithelial-mesenchymal transition, stemness and metastatic potential of cholangiocarcinoma cells. Oncotarget 2016; 6:6310-25. [PMID: 25749036 PMCID: PMC4467439 DOI: 10.18632/oncotarget.3355] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Accepted: 01/17/2015] [Indexed: 12/11/2022] Open
Abstract
Epithelial-mesenchymal transition (EMT) plays a fundamental role in cancer metastasis. The ubiquitin ligase FBXW7, a general tumor suppressor in human cancer, has been implicated in diverse cellular processes, however, its role in cholangiocarcinoma (CCA) metastasis has not been identified. Here, we report a crucial role of FBXW7 in CCA metastasis by regulating EMT. Loss of FBXW7 expression was detected in CCA cells and clinical specimens. Clinicopathological analysis revealed a close correlation between FBXW7 deficiency and metastasis, TNM stage and differentiation in intrahepatic CCA and perihilar CCA. Moreover, FBXW7 silencing in CCA cells dramatically promoted EMT, stem-like capacity and metastasis both in vitro and in vivo. Conversely, FBXW7 overexpression attenuated these processes. Mechanistically, treatment with rapamycin, a mTOR inhibitor, inhibited EMT, stem-like capacity and metastasis induced by FBXW7 silencing both in vitro and in vivo. Furthermore, the expression of EMT regulating transcription factors, snail, slug and ZEB1, were also decreased markedly with rapamycin treatment. In addition, silencing ZEB1 inhibited EMT and metastasis of both CCA cells and FBXW7 deficient CCA cells, which implicated the potential role of ZEB1 in FBXW7/mTOR signaling pathway related CCA metastasis. In conclusion, our findings defined a pivotal function of FBXW7 in CCA metastasis by regulating EMT.
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Affiliation(s)
- Hui Yang
- Department of Hepatobiliary Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Xiaofei Lu
- Department of Hepatobiliary Surgery, Qilu Hospital of Shandong University, Jinan, China.,Department of General Surgery, Jinan Central Hospital of Shandong University, Jinan, China
| | - Ziming Liu
- Department of Emergency Medicine, Jinan Fifth People's Hospital, Jinan, China
| | - Lili Chen
- Department of Pathology, Jinan Fourth People's Hospital, Jinan, China
| | - Yunfei Xu
- Department of Hepatobiliary Surgery, Qilu Hospital of Shandong University, Jinan, China
| | - Yuli Wang
- Department of Anatomy and Key Laboratory of Experimental Teratology, Ministry of Education, Shandong University School of Medicine, Jinan, China
| | - Guangwei Wei
- Department of Anatomy and Key Laboratory of Experimental Teratology, Ministry of Education, Shandong University School of Medicine, Jinan, China
| | - Yuxin Chen
- Department of Hepatobiliary Surgery, Qilu Hospital of Shandong University, Jinan, China
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14
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Abstract
Rapidly accumulating data indicate that F-box/WD repeat-containing protein 7 (Fbxw7) is one of the most frequently mutated genes in human cancers and regulates a network of crucial oncoproteins. These studies have generated important new insights into tumorigenesis and may soon enable therapies targeting the Fbxw7 pathway. We searched PubMed, Embase, and ISI Web of Science databases (1973-2015, especially recent 5 years) for articles published in the English language using the key words "Fbxw7," "Fbw7," "hCDC4," and "Sel-10," and we reviewed recent developments in the search for Fbxw7. Fbxw7 coordinates the ubiquitin-dependent proteolysis of several critical cellular regulators, thereby controlling essential processes, such as cell cycle, differentiation, and apoptosis. Fbxw7 contains 3 isoforms (Fbxw7α, Fbxw7β, and Fbxw7γ), and they are differently regulated in subtract recognition. Besides those, Fbxw7 activity is controlled at different levels, resulting in specific and tunable regulation of the abundance and activity of its substrates in a variety of human solid tumor types, including glioma malignancy, nasopharyngeal carcinoma, osteosarcoma, melanoma as well as colorectal, lung, breast, gastric, liver, pancreatic, renal, prostate, endometrial, and esophageal cancers. Fbxw7 is strongly associated with tumorigenesis, and the mechanisms and consequences of Fbxw7 deregulation in cancers may soon enable the development of novel therapeutic approaches.
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Affiliation(s)
- Jun Cao
- From the Zhejiang Cancer Research Institute (JC, Z-QL); and Department of Surgical Oncology, Zhejiang Province Cancer Hospital, Zhejiang Cancer Center, Hangzhou, China (JC, M-HG)
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15
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Ali SM, Pal SK, Wang K, Palma NA, Sanford E, Bailey M, He J, Elvin JA, Chmielecki J, Squillace R, Dow E, Morosini D, Buell J, Yelensky R, Lipson D, Frampton GM, Howley P, Ross JS, Stephens PJ, Miller VA. Comprehensive Genomic Profiling of Advanced Penile Carcinoma Suggests a High Frequency of Clinically Relevant Genomic Alterations. Oncologist 2015; 21:33-9. [PMID: 26670666 DOI: 10.1634/theoncologist.2015-0241] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 07/31/2015] [Indexed: 12/26/2022] Open
Abstract
BACKGROUND Advanced penile squamous cell carcinoma (PSCC) is associated with poor survival due to the aggressiveness of the disease and lack of effective systemic therapies. Comprehensive genomic profiling (CGP) was performed to identify clinically relevant genomic alterations (CRGAs). MATERIALS AND METHODS DNA was extracted from 40 μm of formalin-fixed, paraffin-embedded sections in patients with advanced PSCC. CGP was performed on hybridization-captured, adaptor ligation-based libraries to a mean coverage depth of 692× for 3,769 exons of 236 cancer-related genes plus 47 introns from 19 genes frequently rearranged in cancer. CRGAs were defined as genomic alterations (GAs) linked to targeted therapies on the market or under evaluation in mechanism-driven clinical trials. RESULTS Twenty male patients with a median age of 60 years (range, 46-87 years) were assessed. Seventeen (85%) cases were stage IV and three cases (15%) were stage III. CGP revealed 109 GAs (5.45 per tumor), 44 of which were CRGAs (2.2 per tumor). At least one CRGA was detected in 19 (95%) cases, and the most common CRGAs were CDKN2A point mutations and homozygous deletion (40%), NOTCH1 point mutations and rearrangements (25%), PIK3CA point mutations and amplification (25%), EGFR amplification (20%), CCND1 amplification (20%), BRCA2 insertions/deletions (10%), RICTOR amplifications (10%), and FBXW7 point mutations (10%). CONCLUSION CGP identified CRGAs in patients with advanced PSCC, including EGFR amplification and PIK3CA alterations, which can lead to the rational administration of targeted therapy and subsequent benefit for these patients. IMPLICATIONS FOR PRACTICE Few treatment options exist for patients with advanced penile squamous cell carcinoma (PSCC). Outcomes are dismal with platinum-based chemotherapy, with median survival estimated at 1 year or less across multiple series. Biological studies of patients with PSCC to date have principally focused on human papillomavirus status, but few studies have elucidated molecular drivers of the disease. To this end, comprehensive genomic profiling was performed in a cohort of 20 patients with advanced PSCC. Findings of frequent mutations in CDKN2A, NOTCH1, PIK3CA, and EGFR (all in excess of 20%) point to potential therapeutic avenues. Trials of targeted therapies directed toward these mutations should be explored.
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Affiliation(s)
- Siraj M Ali
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA; Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, California, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA; Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, New York, USA
| | - Sumanta K Pal
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA; Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, California, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA; Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, New York, USA
| | - Kai Wang
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA; Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, California, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA; Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, New York, USA
| | - Norma A Palma
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA; Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, California, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA; Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, New York, USA
| | - Eric Sanford
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA; Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, California, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA; Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, New York, USA
| | - Mark Bailey
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA; Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, California, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA; Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, New York, USA
| | - Jie He
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA; Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, California, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA; Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, New York, USA
| | - Julia A Elvin
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA; Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, California, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA; Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, New York, USA
| | - Juliann Chmielecki
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA; Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, California, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA; Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, New York, USA
| | - Rachel Squillace
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA; Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, California, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA; Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, New York, USA
| | - Edward Dow
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA; Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, California, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA; Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, New York, USA
| | - Deborah Morosini
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA; Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, California, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA; Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, New York, USA
| | - Jamie Buell
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA; Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, California, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA; Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, New York, USA
| | - Roman Yelensky
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA; Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, California, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA; Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, New York, USA
| | - Doron Lipson
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA; Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, California, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA; Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, New York, USA
| | - Garrett M Frampton
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA; Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, California, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA; Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, New York, USA
| | - Peter Howley
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA; Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, California, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA; Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, New York, USA
| | - Jeffrey S Ross
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA; Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, California, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA; Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, New York, USA
| | - Philip J Stephens
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA; Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, California, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA; Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, New York, USA
| | - Vincent A Miller
- Foundation Medicine, Inc., Cambridge, Massachusetts, USA; Department of Medical Oncology, City of Hope Comprehensive Cancer Center, Duarte, California, USA; Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, USA; Department of Pathology and Laboratory Medicine, Albany Medical College, Albany, New York, USA
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16
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Squillace RM, Frampton GM, Stephens PJ, Ross JS, Miller VA. Comparing two assays for clinical genomic profiling: the devil is in the data. Onco Targets Ther 2015; 8:2237-42. [PMID: 26346763 PMCID: PMC4556029 DOI: 10.2147/ott.s88908] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
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17
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Gleeson FC, Kipp BR, Voss JS, Campion MB, Minot DM, Tu ZJ, Klee EW, Sciallis AP, Graham RP, Lazaridis KN, Henry MR, Levy MJ. Endoscopic ultrasound fine-needle aspiration cytology mutation profiling using targeted next-generation sequencing: personalized care for rectal cancer. Am J Clin Pathol 2015; 143:879-88. [PMID: 25972331 DOI: 10.1309/ajcpu3j7fgayqbrl] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
OBJECTIVES In an era of precision medicine, our aim was to determine the frequency and theranostic potential of mutations identified in malignant lymph nodes (LNs) sampled by endoscopic ultrasound fine-needle aspiration (EUS FNA) of patients with rectal cancer by targeted next-generation sequencing (NGS). METHODS The NGS Ion AmpliSeq Cancer Hotspot Panel v2 (Life Technologies, Carlsbad, CA) and MiSeq (Illumina, San Diego, CA) sequencers were used to sequence and assess for 2,800 or more possible mutations in 50 established cancer-associated genes. RESULTS Among 102 patients, 89% had 194 pathogenic alterations identified in 19 genes. The identification of KRAS, NRAS, or BRAF mutations suggests that 42% are likely nonresponders to anti-epidermal growth factor receptor therapy. Among KRAS, NRAS, or BRAF wild-type patients, alterations in eight genes linked to alternative therapies were identified in 44%. CONCLUSIONS Our data demonstrate the successful ability to apply a single multiplex test to allow multigene mutation detection from malignant LN cytology specimen DNA collected by EUS FNA.
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Affiliation(s)
- Ferga C. Gleeson
- Divison of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
| | | | - Jesse S. Voss
- Department of Anatomic Pathology, Mayo Clinic, Rochester, MN
| | | | | | - Zheng J. Tu
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | - Eric W. Klee
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN
| | | | | | - Konstantinos N. Lazaridis
- Divison of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
- Center for Individualized Medicine, Mayo Clinic, Rochester, MN
| | | | - Michael J. Levy
- Divison of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN
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