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Chinchilla-Tábora LM, Sayagués JM, González-Morais I, Rodríguez M, Ludeña MD. Prognostic Impact of EGFR Amplification and Visceral Pleural Invasion in Early Stage Pulmonary Squamous Cell Carcinomas Patients after Surgical Resection of Primary Tumor. Cancers (Basel) 2022; 14:cancers14092174. [PMID: 35565304 PMCID: PMC9101408 DOI: 10.3390/cancers14092174] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/22/2022] [Accepted: 04/25/2022] [Indexed: 12/04/2022] Open
Abstract
Over the last few decades, an increasing amount of information has been accumulated on biomarkers in non-small cell lung cancer (NSCLC). Despite these advances, most biomarkers have been identified in the adenocarcinoma histological subtype (AC). However, the application of molecular-targeted therapies in the prognosis and treatment of SCC in the clinical setting is very limited, becoming one of the main focus areas in research. Here, we prospectively analyzed the frequency of numerical/structural abnormalities of chromosomes 5, 7, 8, 9, 13 and 22 with FISH in 48 pulmonary SCC patients. From a total of 12 probes, only abnormalities of the 7p12 and 22q12 chromosomal regions were identified as unique genetic variables associated with the prognosis of the disease. The study for these two chromosomal regions was extended to 108 patients with SCC. Overall, chromosome losses were observed more frequently than chromosome gains, i.e., 61% versus 19% of all the chromosome abnormalities detected. The highest levels of genetic amplification were detected for the 5p15.2, 7p12, 8q24 and 22q11 chromosome bands, of which several genes are potentially involved in the pathogenesis of SCC, among others, include the EGFR gene at chromosome 7p12. Patients who displayed EGFR amplification (n = 13; 12%) were mostly older than 65 years (p = 0.07) and exclusively patients in early T-primary tumor stage (pT1−pT2; p = 0.03) with a significantly shortened overall survival (OS) (p ≤ 0.001). Regarding prognosis, the clinical, biological, and histopathologic characteristics of the disease that displayed a significant adverse influence on OS in the univariate analysis included patients older than 65 years (p = 0.02), the presence of lymph node involvement (p = 0.005), metastasis (p = 0.01) and, visceral pleural invasion (VPI) at diagnosis (p = 0.04). EGFR amplification also conferred an adverse impact on patient OS in the whole series (p = 0.02) and especially in patients in early stages (pT1−pT2; p = 0.01). A multivariate analysis of the prognostic factors for OS showed that the most informative combination of independent variables to predict an adverse outcome was the presence of VPI and/or EGFR amplification (p < 0.001). Based on these two variables, a scoring system was built to stratify patients into low- (no adverse features: score 0; n = 69), intermediate- (one adverse feature: score 1; n = 29) and high-risk (two adverse features: score 2; n = 5) groups, with significantly different (p = 0.001) OS rates at 50 months, which were as following: 32%, 28% and 0%, respectively. In the present study, we show that the presence of a high level of 7p12 (EGFR) amplification, exclusively detected in early stage SCC (pT1−pT2), is an independent adverse prognostic factor for OS. The identification of the EGFR gene copy number using FISH techniques may provide a more accurate diagnosis of high-risk populations after the complete resection of the primary tumor. When combined with VPI, three groups of pulmonary SCC were clearly identified that show the extent of the disease. This is of such importance that further prospective studies are necessary in larger series of SCC patients to be classified at the time of diagnosis. This could be achieved with the combined assessment of 7p12 amplification and VPI in primary tumor samples.
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Hu L, Shen D, Liang D, Shi J, Song C, Jiang K, Du S, Cheng W, Ma J, Li S, Bi X, Barr MP, Fang Z, Xu Q, Li W, Piao H, Meng S. Thyroid receptor-interacting protein 13 and EGFR form a feedforward loop promoting glioblastoma growth. Cancer Lett 2020; 493:156-166. [PMID: 32860853 DOI: 10.1016/j.canlet.2020.08.023] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 08/04/2020] [Accepted: 08/20/2020] [Indexed: 11/19/2022]
Abstract
Epidermal growth factor receptor (EGFR) amplification and EGFRvIII mutation drive glioblastoma (GBM) pathogenesis, but their regulation remains elusive. Here we characterized the EGFR/EGFRvIII "interactome" in GBM and identified thyroid receptor-interacting protein 13 (TRIP13), an AAA + ATPase, as an EGFR/EGFRvIII-associated protein independent of its ATPase activity. Functionally, TRIP13 augmented EGFR pathway activation and contributed to EGFR/EGFRvIII-driven GBM growth in GBM spheroids and orthotopic GBM xenograft models. Mechanistically, TRIP13 enhanced EGFR protein abundance in part by preventing Cbl-mediated ubiquitination and proteasomal degradation. Reciprocally, TRIP13 was phosphorylated at tyrosine(Y) 56 by EGFRvIII and EGF-activated EGFR. Abrogating TRIP13 Y56 phosphorylation dramatically attenuated TRIP13 expression-enhanced EGFR signaling and GBM cell growth. Clinically, TRIP13 expression was upregulated in GBM specimens and associated with poor patient outcome. In GBM, TRIP13 localized to cell membrane and cytoplasma and exhibited oncogenic effects in vitro and in vivo, depending on EGFR signaling but not the TRIP13 ATPase activity. Collectively, our findings uncover that TRIP13 and EGFR form a feedforward loop to potentiate EGFR signaling in GBM growth and identify a previously unrecognized ATPase activity-independent mode of action of TRIP13 in GBM biology.
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Affiliation(s)
- Lulu Hu
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, 116044, PR China
| | - Dachuan Shen
- Department of Oncology, Affiliated Zhongshan Hospital of Dalian University, Dalian, PR China
| | - Dapeng Liang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, 116044, PR China
| | - Ji Shi
- Department of Neurosurgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, 110042, PR China
| | - Chunyan Song
- Department of Neuro-oncology, Neurosurgery Center, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, PR China
| | - Ke Jiang
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, 116044, PR China; Department of Medical Oncology, Shanghai Tenth People's Hospital, Tongji University, Shanghai, 200072, PR China
| | - Sha Du
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, 116044, PR China
| | - Wei Cheng
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, 116044, PR China
| | - Jianmei Ma
- College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, PR China
| | - Shao Li
- College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, PR China
| | - Xiaolin Bi
- College of Basic Medical Sciences, Dalian Medical University, Dalian, 116044, PR China
| | - Martin P Barr
- Thoracic Oncology Research Group, Trinity Translational Medicine Institute, Trinity Centre for Health Sciences, St. James's Hospital & Trinity College, Dublin, Ireland
| | - Zhiyou Fang
- Center of Medical Physics and Technology, Hefei Institutes of Physical Science, Chinese Academy of Sciences, Hefei, PR China
| | - Qing Xu
- Department of Medical Oncology, Shanghai Tenth People's Hospital, Tongji University, Shanghai, 200072, PR China.
| | - Wenbin Li
- Department of Neuro-oncology, Neurosurgery Center, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, PR China.
| | - Haozhe Piao
- Department of Neurosurgery, Cancer Hospital of China Medical University, Liaoning Cancer Hospital & Institute, Shenyang, 110042, PR China.
| | - Songshu Meng
- Institute of Cancer Stem Cell, Dalian Medical University, Dalian, 116044, PR China.
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Barón AE, Kako S, Feser WJ, Malinowski H, Merrick D, Garg K, Malkoski S, Pretzel S, Siegfried JM, Franklin WA, Miller Y, Wolf HJ, Varella-Garcia M. Clinical Utility of Chromosomal Aneusomy in Individuals at High Risk of Lung Cancer. J Thorac Oncol 2017. [PMID: 28634123 DOI: 10.1016/j.jtho.2017.06.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
INTRODUCTION Low-dose computed tomography screening for lung cancer has a high false-positive rate with frequent discovery of indeterminate pulmonary nodules. Noninvasive biomarkers are needed to reduce false positives and improve risk stratification. A retrospective longitudinal evaluation was performed to assess chromosomal aneusomy in sputum by fluorescence in situ hybridization (CA-FISH) in four nested case-control studies. METHODS Receiver operating characteristic analysis resulted in two grouped cohorts: a high-risk cohort (Colorado High-Risk Cohort and Colorado Nodule Cohort [68 case patients and 69 controls]) and a screening cohort (American College of Radiology Imaging Network/National Lung Screening Trial and Pittsburgh Lung Screening Study [97 case patients and 185 controls]). The CA-FISH assay was a four-target DNA panel encompassing the EGFR and v-myc avian myelocytomatosis viral oncogene homolog (MYC) genes, and the 5p15 and centromere 6 regions or the fibroblast growth factor 1 gene (FGFR1) and phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha gene (PIK3CA). A four-category scale (normal, probably normal, probably abnormal, and abnormal) was applied. Sensitivity, specificity, and positive and negative likelihood ratios (LRs) (with 95% confidence intervals [CIs]) were estimated for each cohort. RESULTS Sensitivity and specificity were, respectively, 0.67 (95% CI: 0.55-0.78) and 0.94 (95% CI: 0.85-0.98) for high-risk participants and 0.20 (95% CI: 0.13-0.30) and 0.84 (95% CI: 0.78-0.89) for screening participants. The positive and negative LRs were, respectively, 11.66 (95% CI: 4.44-30.63) and 0.34 (95% CI: 0.24-0.48) for high-risk participants and 1.36 (95% CI: 0.81-2.28) and 0.93 (95% CI: 0.83-1.05) for screening participants. CONCLUSION The high positive LR of sputum CA-FISH indicates that it could be a useful adjunct to low-dose computed tomography for lung cancer in high-risk settings. For screening, however, its low positive LR limits clinical utility. Prospective assessment of CA-FISH in the incidentally identified indeterminate nodule setting is ongoing in the Colorado Pulmonary Nodule Biomarker Trial.
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Affiliation(s)
- Anna E Barón
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado.
| | - Severine Kako
- Department of Medicine, Division of Medical Oncology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado; Department of Pathology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - William J Feser
- Department of Biostatistics and Informatics, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Heather Malinowski
- Department of Pathology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Daniel Merrick
- Department of Pathology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Kavita Garg
- Department of Radiology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Stephen Malkoski
- Department of Pulmonary and Critical Care Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Shannon Pretzel
- University of Colorado Cancer Center, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Jill M Siegfried
- Department of Pharmacology, Masonic Cancer Center, University of Minnesota, Minneapolis, Minnesota; Department of Pharmacology and Chemical Biology, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Wilbur A Franklin
- Department of Pathology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - York Miller
- Department of Pulmonary and Critical Care Medicine, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado; Veterans Affairs Medical Center, Denver, Colorado
| | - Holly J Wolf
- Department of Community and Behavioral Health, Colorado School of Public Health, University of Colorado Anschutz Medical Campus, Aurora, Colorado
| | - Marileila Varella-Garcia
- Department of Medicine, Division of Medical Oncology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado; Department of Pathology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado
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Mahas A, Potluri K, Kent MN, Naik S, Markey M. Copy number variation in archival melanoma biopsies versus benign melanocytic lesions. Cancer Biomark 2017; 16:575-97. [PMID: 27002761 DOI: 10.3233/cbm-160600] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
BACKGROUND Skin melanocytes can give rise to benign and malignant neoplasms. Discrimination of an early melanoma from an unusual/atypical benign nevus can represent a significant challenge. However, previous studies have shown that in contrast to benign nevi, melanoma demonstrates pervasive chromosomal aberrations. OBJECTIVE This substantial difference between melanoma and benign nevi can be exploited to discriminate between melanoma and benign nevi. METHODS Array-comparative genomic hybridization (aCGH) is an approach that can be used on DNA extracted from formalin-fixed paraffin-embedded (FFPE) tissues to assess the entire genome for the presence of changes in DNA copy number. In this study, high resolution, genome-wide single-nucleotide polymorphism (SNP) arrays were utilized to perform comprehensive and detailed analyses of recurrent copy number aberrations in 41 melanoma samples in comparison with 21 benign nevi. RESULTS We found statistically significant copy number gains and losses within melanoma samples. Some of the identified aberrations are previously implicated in melanoma. Moreover, novel regions of copy number alterations were identified, revealing new candidate genes potentially involved in melanoma pathogenesis. CONCLUSIONS Taken together, these findings can help improve melanoma diagnosis and introduce novel melanoma therapeutic targets.
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Affiliation(s)
- Ahmed Mahas
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, OH, USA
| | - Keerti Potluri
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, OH, USA
| | - Michael N Kent
- Department of Dermatology, Wright State University Boonshoft School of Medicine, Dayton, OH, USA.,Dermatopathology Laboratory of Central States, Dayton, OH, USA
| | - Sameep Naik
- Dermatopathology Laboratory of Central States, Dayton, OH, USA
| | - Michael Markey
- Department of Biochemistry and Molecular Biology, Wright State University, Dayton, OH, USA
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Galvani E, Sun J, Leon LG, Sciarrillo R, Narayan RS, Tjin Tham Sjin R, Lee K, Ohashi K, Heideman DA, Alfieri RR, Heynen GJ, Bernards R, Smit EF, Pao W, Peters GJ, Giovannetti E. NF-κB drives acquired resistance to a novel mutant-selective EGFR inhibitor. Oncotarget 2015; 6:42717-32. [PMID: 26015408 PMCID: PMC4767465 DOI: 10.18632/oncotarget.3956] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2015] [Accepted: 04/08/2015] [Indexed: 01/22/2023] Open
Abstract
The clinical efficacy of EGFR tyrosine kinase inhibitors (TKIs) in non-small cell lung cancer (NSCLC) harbouring activating EGFR mutations is limited by the emergence of acquired resistance, mostly ascribed to the secondary EGFR-T790M mutation. Selective EGFR-T790M inhibitors have been proposed as a new, extremely relevant therapeutic approach. Here, we demonstrate that the novel irreversible EGFR-TKI CNX-2006, a structural analog of CO-1686, currently tested in a phase-1/2 trial, is active against in vitro and in vivo NSCLC models expressing mutant EGFR, with minimal effect on the wild-type receptor. By integration of genetic and functional analyses in isogenic cell pairs we provide evidence of the crucial role played by NF-κB1 in driving CNX-2006 acquired resistance and show that NF-κB activation may replace the oncogenic EGFR signaling in NSCLC when effective and persistent inhibition of the target is achieved in the presence of the T790M mutation. In this context, we demonstrate that the sole, either genetic or pharmacologic, inhibition of NF-κB is sufficient to reduce the viability of cells that adapted to EGFR-TKIs. Overall, our findings support the rational inhibition of members of the NF-κB pathway as a promising therapeutic option for patients who progress after treatment with novel mutant-selective EGFR-TKIs.
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Affiliation(s)
- Elena Galvani
- Department Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Jing Sun
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University School of Medicine and Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Leticia G. Leon
- Instituto de Tecnologias Biomedicas, Center for Biomedical Research of the Canary Islands, University of La Laguna, Tenerife, Spain
| | - Rocco Sciarrillo
- Department Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
- Department Hematology, VU University Medical Center, Amsterdam, The Netherlands
| | - Ravi S. Narayan
- Department Radiation Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | | | - Kwangho Lee
- Celgene Avilomics Research, Bedford, MA, USA
| | - Kadoaki Ohashi
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University School of Medicine and Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | | | - Roberta R. Alfieri
- Department of Clinical and Experimental Medicine, University of Parma, Parma, Italy
| | - Guus J. Heynen
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - René Bernards
- Division of Molecular Carcinogenesis, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Egbert F. Smit
- Department of Pulmonary Diseases, VU University Medical Center, Amsterdam, The Netherlands
| | - William Pao
- Division of Hematology/Oncology, Department of Medicine, Vanderbilt University School of Medicine and Vanderbilt-Ingram Cancer Center, Nashville, TN, USA
| | - Godefridus J. Peters
- Department Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
| | - Elisa Giovannetti
- Department Medical Oncology, VU University Medical Center, Amsterdam, The Netherlands
- Cancer Pharmacology Lab, AIRC Start-Up Unit, DIPINT, University of Pisa, Pisa, Italy
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Lee HW, Seol HJ, Choi YL, Ju HJ, Joo KM, Ko YH, Lee JI, Nam DH. Genomic copy number alterations associated with the early brain metastasis of non-small cell lung cancer. Int J Oncol 2012; 41:2013-20. [PMID: 23076643 DOI: 10.3892/ijo.2012.1663] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Accepted: 08/16/2012] [Indexed: 11/06/2022] Open
Abstract
Frequent early development of systemic metastasis leads to unfavourable clinical prognosis of non-small cell lung cancer (NSCLC). Although brain metastasis (BM) contributes significantly to morbidity and mortality of NSCLC, relevant driver mechanisms are largely unknown. To elucidate genetic alterations associated with early BM of NSCLC, we retrospectively collected 18 NSCLC cases with BM [12 adenocarcinomas (ADC) and 6 squamous cell carcinomas (SQCC)] whose surgical tissues of both primary and brain metastatic tumors were preserved as formaldehyde-fixed and paraffin-embedded (FFPE) pathological samples. When chromosomal copy number alterations (CNA) of those FFPE samples were analysed by the Molecular Inversion Probe (MIP) technology, the most frequent CNAs detected in primary lung ADCs were gains of 3q, 5p, 5q, 6p, 8q, 9p, 11p, 15q, 17q and losses of 10q and 22q whereas primary lung SQCCs revealed gains in 4q and 12q and loss in 9q. In particular, when comparative MIP was performed in primary 12 ADCs depending on the pattern of BM to uncover predetermining signatures that can predict the risk of BM, selectively amplified regions of primary lung ADCs (5q35, 10q23 and 17q23-24) were identified as significantly associated with the development of early BM within 3 months after first diagnosis of primary tumors. Those regions harbour several candidate genes including NeurL1B, ACTA2, FAS and ICAM2. Although more validation is needed, the genetic signatures elucidated in this study help to identify useful molecular markers defining an NSCLC patient subgroup at risk of early BM, guiding therapeutic decisions.
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Affiliation(s)
- Hye Won Lee
- Cancer Stem Cell Research Center, Sungkyunkwan University School of Medicine, Seoul 135-710, Republic of Korea
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Ribeiro DC, Gleber-Netto FO, Sousa SF, Bernardes VDF, Guimarães-Abreu MHN, Aguiar MCF. Immunohistochemical expression of EGFR in oral leukoplakia: association with clinicopathological features and cellular proliferation. Med Oral Patol Oral Cir Bucal 2012; 17:e739-44. [PMID: 22322523 PMCID: PMC3482515 DOI: 10.4317/medoral.17950] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2011] [Accepted: 11/13/2011] [Indexed: 01/08/2023] Open
Abstract
Objectives: to investigate the immunoexpression of epidermal growth factor receptor (EGFR) in a sample of oral leukoplakias (OL) and to determine the receptor’s association with dysplasia, tobacco consumption, lesion site, and proliferation rate. Although EGFR should be overexpressed in some oral leukoplakias, the factors that may interfere with this expression and the influence of this receptor on epithelial proliferation have yet to be investigated.
Study Design: Samples of oral leukoplakias (48) and of normal oral epithelium (10) were immunohistologically examined for expression of EGFR. Immunohistochemistry for Ki-67, and p27 were also performed in leukoplakias. EGFR expression was associated with clinical and pathological features.
Results: EGFR was positive in 62.5% of the leukoplakias and 50% of normal oral epithelium. The number of EGFR positive OL located in high-risk sites was significantly higher than EGFR positive OL located in low-risk sites. Most of the p27 negative leukoplakias were EGFR positive, and the p27 index in the parabasal layer was diminished in the presence of dysplasia. Positivity for EGFR was not associated with dysplasia, tobacco exposure, or Ki-67.
Conclusion: EGFR is expressed in leukoplakia regardless of dysplasia, but EGFR positivity should be more frequent in lesions sited in areas of high cancer risk. The association between EGFR and p27 may represent an important mechanism in the control of cellular proliferation and malignant progression of oral epithelium and therefore warrants further investigation.
Key words:Oral leukoplakia, EGFR, p27, Ki-67, epithelial dysplasia.
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Affiliation(s)
- Daniela-Cotta Ribeiro
- Department of Oral Pathology and Surgery, School of Dentistry, Universidade Federal de Minas Gerais, Faculdade de Odontologia, Av. Antônio Carlos, 6627 sala 3201, Pampulha 31.270-901, Belo Horizonte, MG, Brazil
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Youn A, Simon R. Estimating the order of mutations during tumorigenesis from tumor genome sequencing data. ACTA ACUST UNITED AC 2012; 28:1555-61. [PMID: 22492649 DOI: 10.1093/bioinformatics/bts168] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
MOTIVATION Tumors are thought to develop and evolve through a sequence of genetic and epigenetic somatic alterations to progenitor cells. Early stages of human tumorigenesis are hidden from view. Here, we develop a method for inferring some aspects of the order of mutational events during tumorigenesis based on genome sequencing data for a set of tumors. This method does not assume that the sequence of driver alterations is the same for each tumor, but enables the degree of similarity or difference in the sequence to be evaluated. RESULTS To evaluate the new method, we applied it to colon cancer tumor sequencing data and the results are consistent with the multi-step tumorigenesis model previously developed based on comparing stages of cancer. We then applied the new method to DNA sequencing data for a set of lung cancers. The model may be a useful tool for better understanding the process of tumorigenesis. AVAILABILITY The software is available at: http://linus.nci.nih.gov/Data/YounA/OrderMutation.zip.
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Affiliation(s)
- Ahrim Youn
- Biometric Research Branch, National Cancer Institute, 9000 Rockville Pike, MSC 7434, Bethesda, MD 20892-7434, USA
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9
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Huang YT, Lin X, Chirieac LR, McGovern R, Wain JC, Heist RS, Skaug V, Zienolddiny S, Haugen A, Su L, Christiani DC. Impact on disease development, genomic location and biological function of copy number alterations in non-small cell lung cancer. PLoS One 2011; 6:e22961. [PMID: 21829676 PMCID: PMC3149069 DOI: 10.1371/journal.pone.0022961] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2011] [Accepted: 07/02/2011] [Indexed: 12/18/2022] Open
Abstract
Lung cancer, of which more than 80% is non-small cell, is the leading cause of cancer-related death in the United States. Copy number alterations (CNAs) in lung cancer have been shown to be positionally clustered in certain genomic regions. However, it remains unclear whether genes with copy number changes are functionally clustered. Using a dense single nucleotide polymorphism array, we performed genome-wide copy number analyses of a large collection of non-small cell lung tumors (n = 301). We proposed a formal statistical test for CNAs between different groups (e.g., non-involved lung vs. tumors, early vs. late stage tumors). We also customized the gene set enrichment analysis (GSEA) algorithm to investigate the overrepresentation of genes with CNAs in predefined biological pathways and gene sets (i.e., functional clustering). We found that CNAs events increase substantially from germline, early stage to late stage tumor. In addition to genomic position, CNAs tend to occur away from the gene locations, especially in germline, non-involved tissue and early stage tumors. Such tendency decreases from germline to early stage and then to late stage tumors, suggesting a relaxation of selection during tumor progression. Furthermore, genes with CNAs in non-small cell lung tumors were enriched in certain gene sets and biological pathways that play crucial roles in oncogenesis and cancer progression, demonstrating the functional aspect of CNAs in the context of biological pathways that were overlooked previously. We conclude that CNAs increase with disease progression and CNAs are both positionally and functionally clustered. The potential functional capabilities acquired via CNAs may be sufficient for normal cells to transform into malignant cells.
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Affiliation(s)
- Yen-Tsung Huang
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Xihong Lin
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Lucian R. Chirieac
- Department of Pathology, Brigham and Women's Hospital, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Ray McGovern
- Department of Biostatistics, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - John C. Wain
- Cancer Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Thoracic Surgery Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
| | - Rebecca S. Heist
- Cancer Center, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Environmental Health, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - Vidar Skaug
- Department of Biological and Chemical Working Environment, National Institute of Occupational Health, Oslo, Norway
| | - Shanbeh Zienolddiny
- Department of Biological and Chemical Working Environment, National Institute of Occupational Health, Oslo, Norway
| | - Aage Haugen
- Department of Biological and Chemical Working Environment, National Institute of Occupational Health, Oslo, Norway
| | - Li Su
- Department of Environmental Health, Harvard School of Public Health, Boston, Massachusetts, United States of America
| | - David C. Christiani
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Department of Environmental Health, Harvard School of Public Health, Boston, Massachusetts, United States of America
- Pulmonary and Critical Care Unit, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- * E-mail:
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10
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Schramm M, Wrobel C, Born I, Kazimirek M, Pomjanski N, William M, Kappes R, Gerharz CD, Biesterfeld S, Böcking A. Equivocal cytology in lung cancer diagnosis: improvement of diagnostic accuracy using adjuvant multicolor FISH, DNA-image cytometry, and quantitative promoter hypermethylation analysis. Cancer Cytopathol 2011; 119:177-92. [PMID: 21413159 DOI: 10.1002/cncy.20142] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Revised: 01/24/2011] [Accepted: 01/25/2011] [Indexed: 11/11/2022]
Abstract
BACKGROUND Sometimes, cytological lung cancer diagnosis is challenging because equivocal diagnoses are common. To enhance diagnostic accuracy, fluorescent in situ hybridization (FISH), DNA-image cytometry, and quantitative promoter hypermethylation analysis have been proposed as adjuncts. METHODS Bronchial washings and/or brushings or transbronchial fine-needle aspiration biopsies were prospectively collected from patients who were clinically suspected of having lung carcinoma. After routine cytological diagnosis, 70 consecutive specimens, each cytologically diagnosed as negative, equivocal, or positive for cancer cells, were investigated with adjuvant methods. Suspicious areas on the smears were restained with the LAVysion multicolor FISH probe set (Abbott Molecular, Des Plaines, Illinois) or according to the Feulgen Staining Method for DNA-image cytometry analysis. DNA was extracted from residual liquid material, and frequencies of aberrant methylation of APC, p16(INK4A) , and RASSF1A gene promoters were determined with quantitative methylation-specific polymerase chain reaction (QMSP) after bisulfite conversion. Clinical and histological follow-up according to a reference standard, defined in advance, were available for 198 of 210 patients. RESULTS In the whole cohort, cytology, FISH, DNA-image cytometry, and QMSP achieved sensitivities of 83.7%, 78%, 79%, and 49.6%, respectively (specificities of 69.8%, 98.2%, 98.2%, and 98.4%, respectively). Subsequent to cytologically equivocal diagnoses, FISH, DNA-image cytometry, and QMSP definitely identified malignancy in 79%, 83%, and 49%, respectively. With QMSP, 4 of 22 cancer patients with cytologically negative diagnoses were correctly identified. CONCLUSIONS Thus, adjuvant FISH or DNA-image cytometry in cytologically equivocal diagnoses improves diagnostic accuracy at comparable rates. Adjuvant QMSP in cytologically negative cases with persistent suspicion of lung cancer would enhance sensitivity.
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Affiliation(s)
- Martin Schramm
- Institute of Cytopathology, Heinrich Heine University, Düsseldorf, Germany
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Katz RL, He W, Khanna A, Fernandez RL, Zaidi TM, Krebs M, Caraway NP, Zhang HZ, Jiang F, Spitz MR, Blowers DP, Jimenez CA, Mehran RJ, Swisher SG, Roth JA, Morris JS, Etzel CJ, El-Zein R. Genetically abnormal circulating cells in lung cancer patients: an antigen-independent fluorescence in situ hybridization-based case-control study. Clin Cancer Res 2010; 16:3976-87. [PMID: 20651054 DOI: 10.1158/1078-0432.ccr-09-3358] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
PURPOSE We performed a study to determine if a fluorescence in situ hybridization (FISH)-based assay using isolated peripheral blood mononuclear cells (PBMCs) with DNA probes targeting specific sites on chromosomes known to have abnormalities in non-small cell lung cancer (NSCLC) cases could detect circulating genetically abnormal cells (CACs). EXPERIMENTAL DESIGN We evaluated 59 NSCLC cases with stage I through IV disease and 24 controls. PBMCs and matched tumors were hybridized with 2 two-color [3p22.1/CEP3 and 10q22.3 (SP-A)/CEP10) and 2 four-color [CEP3, CEP7, CEP17, and 9p21.3 (URO); and EGFR, c-MYC, 6p11-q11, and 5p15.2 (LAV)] FISH probes. Percentages of cytogenetically abnormal cells (CACs) in peripheral blood and in matched tumor specimens were quantified by using an automated fluorescent scanner. Numbers of CACs were calculated based on the percentage of CACs (defined as PBMCs with genetic abnormalities) per milliliter of blood and expressed per microliter of blood. RESULTS Patients with NSCLC had significantly higher numbers of CACs than controls. Mean number of CACs ranged from 7.23 +/- 1.32/microL for deletions of 10q22.3/CEP10 to 45.52 +/- 7.49/microL for deletions of 3p22.1/CEP3. Numbers of CACs with deletions of 3p22.1, 10q22.3, and 9p21.3, and gains of URO, increased significantly from early to advanced stage of disease. CONCLUSIONS We have developed a sensitive and quantitative antigen-independent FISH-based test for detecting CACs in peripheral blood of patients with NSCLC, which showed a significant correlation with the presence of cancer. If this pilot study can be validated in a larger study, CACs may have a role in the management of patients with NSCLC.
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Affiliation(s)
- Ruth L Katz
- Department of Pathology, University of Texas M.D. Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA.
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Taoudi Benchekroun M, Saintigny P, Thomas SM, El-Naggar AK, Papadimitrakopoulou V, Ren H, Lang W, Fan YH, Huang J, Feng L, Lee JJ, Kim ES, Hong WK, Johnson FM, Grandis JR, Mao L. Epidermal growth factor receptor expression and gene copy number in the risk of oral cancer. Cancer Prev Res (Phila) 2010; 3:800-9. [PMID: 20570883 DOI: 10.1158/1940-6207.capr-09-0163] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
UNLABELLED Leukoplakia is the most common premalignant lesion of the oral cavity. Epidermal growth factor receptor (EGFR) abnormalities are associated with oral tumorigenesis and progression. We hypothesized that EGFR expression and gene copy number changes are predictors of the risk of an oral premalignant lesion (OPL) progressing to oral squamous cell carcinoma (OSCC). A formalin-fixed, paraffin-embedded OPL biopsy specimen was collected from each of 162 patients in a randomized controlled clinical trial. We assessed EGFR expression by immunohistochemistry with two METHODS a semiquantitative analysis (145 evaluable specimens) and an automated quantitative analysis (127 evaluable specimens). EGFR gene copy number was assessed by fluorescence in situ hybridization (FISH) in a subset of 49 OPLs with high EGFR expression defined by the semiquantitative analysis. We analyzed EGFR abnormalities for associations with OSCC development. High EGFR expression occurred in 103 (71%) of the 145 OPLs and was associated with a nonsignificantly higher risk of OSCC (P = 0.10). Twenty (41%) of 49 OPLs assessed by FISH had an increased EGFR gene copy number (FISH-positive). Patients with FISH-positive lesions had a significantly higher incidence of OSCC than did patients with FISH-negative (a normal copy number) lesions (P = 0.0007). Of note, 10 of 11 OSCCs that developed at the site of the examined OPL were in the FISH-positive group, leaving only one FISH-negative OPL that did so (P < 0.0001). Our data indicate that an increased EGFR gene copy number is common in and associated with OSCC development in patients with OPLs expressing high EGFR, particularly OSCC developing at the site of a high-expression OPL; they also suggest that EGFR inhibitors may prevent oral cancer in patients with OPLs having an increased EGFR gene copy number.
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Affiliation(s)
- Mohammed Taoudi Benchekroun
- Department of Thoracic/Head and Neck Medical Oncology, The University of Texas M. D. Anderson Cancer Center, Houston, USA
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Kang JU, Koo SH, Kwon KC, Park JW, Kim JM. Identification of novel candidate target genes, including EPHB3, MASP1 and SST at 3q26.2-q29 in squamous cell carcinoma of the lung. BMC Cancer 2009; 9:237. [PMID: 19607727 PMCID: PMC2716371 DOI: 10.1186/1471-2407-9-237] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2009] [Accepted: 07/16/2009] [Indexed: 11/10/2022] Open
Abstract
Background The underlying genetic alterations for squamous cell carcinoma (SCC) and adenocarcinoma (AC) carcinogenesis are largely unknown. Methods High-resolution array- CGH was performed to identify the differences in the patterns of genomic imbalances between SCC and AC of non-small cell lung cancer (NSCLC). Results On a genome-wide profile, SCCs showed higher frequency of gains than ACs (p = 0.067). More specifically, statistically significant differences were observed across the histologic subtypes for gains at 2q14.2, 3q26.2–q29, 12p13.2–p13.33, and 19p13.3, as well as losses at 3p26.2–p26.3, 16p13.11, and 17p11.2 in SCC, and gains at 7q22.1 and losses at 15q22.2–q25.2 occurred in AC (P < 0.05). The most striking difference between SCC and AC was gains at the 3q26.2–q29, occurring in 86% (19/22) of SCCs, but in only 21% (3/14) of ACs. Many significant genes at the 3q26.2–q29 regions previously linked to a specific histology, such as EVI1,MDS1, PIK3CA and TP73L, were observed in SCC (P < 0.05). In addition, we identified the following possible target genes (> 30% of patients) at 3q26.2–q29: LOC389174 (3q26.2),KCNMB3 (3q26.32),EPHB3 (3q27.1), MASP1 and SST (3q27.3), LPP and FGF12 (3q28), and OPA1,KIAA022,LOC220729, LOC440996,LOC440997, and LOC440998 (3q29), all of which were significantly targeted in SCC (P < 0.05). Among these same genes, high-level amplifications were detected for the gene, EPHB3, at 3q27.1, and MASP1 and SST, at 3q27.3 (18, 18, and 14%, respectively). Quantitative real time PCR demonstrated array CGH detected potential candidate genes that were over expressed in SCCs. Conclusion Using whole-genome array CGH, we have successfully identified significant differences and unique information of chromosomal signatures prevalent between the SCC and AC subtypes of NSCLC. The newly identified candidate target genes may prove to be highly attractive candidate molecular markers for the classification of NSCLC histologic subtypes, and could potentially contribute to the pathogenesis of the squamous cell carcinoma of the lung.
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Affiliation(s)
- Ji Un Kang
- Department of Pathology, Columbia University Medical Center, New York, NY, USA.
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Combined therapies for cancer: a review of EGFR-targeted monotherapy and combination treatment with other drugs. J Cancer Res Clin Oncol 2009; 135:1137-48. [DOI: 10.1007/s00432-009-0622-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2008] [Accepted: 06/02/2009] [Indexed: 12/21/2022]
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