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Kamble P, Nagar PR, Bhakhar KA, Garg P, Sobhia ME, Naidu S, Bharatam PV. Cancer pharmacoinformatics: Databases and analytical tools. Funct Integr Genomics 2024; 24:166. [PMID: 39294509 DOI: 10.1007/s10142-024-01445-5] [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: 07/29/2024] [Revised: 08/26/2024] [Accepted: 09/03/2024] [Indexed: 09/20/2024]
Abstract
Cancer is a subject of extensive investigation, and the utilization of omics technology has resulted in the generation of substantial volumes of big data in cancer research. Numerous databases are being developed to manage and organize this data effectively. These databases encompass various domains such as genomics, transcriptomics, proteomics, metabolomics, immunology, and drug discovery. The application of computational tools into various core components of pharmaceutical sciences constitutes "Pharmacoinformatics", an emerging paradigm in rational drug discovery. The three major features of pharmacoinformatics include (i) Structure modelling of putative drugs and targets, (ii) Compilation of databases and analysis using statistical approaches, and (iii) Employing artificial intelligence/machine learning algorithms for the discovery of novel therapeutic molecules. The development, updating, and analysis of databases using statistical approaches play a pivotal role in pharmacoinformatics. Multiple software tools are associated with oncoinformatics research. This review catalogs the databases and computational tools related to cancer drug discovery and highlights their potential implications in the pharmacoinformatics of cancer.
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Affiliation(s)
- Pradnya Kamble
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Punjab, India
| | - Prinsa R Nagar
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Punjab, India
| | - Kaushikkumar A Bhakhar
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Punjab, India
| | - Prabha Garg
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Punjab, India
| | - M Elizabeth Sobhia
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Punjab, India
| | - Srivatsava Naidu
- Center of Biomedical Engineering, Indian Institute of Technology Ropar, Rupnagar, Punjab, India
| | - Prasad V Bharatam
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Punjab, India.
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, S.A.S. Nagar, Punjab, India.
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Evaluation of Methylation Profiles of An Epidermal Growth Factor Receptor Gene in a Head and Neck Squamous Cell Carcinoma Patient Group. Balkan J Med Genet 2021; 23:65-72. [PMID: 33816074 PMCID: PMC8009575 DOI: 10.2478/bjmg-2020-0025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Upregulation of the epidermal growth factor receptor (EGFR) gene has shown an important impact on the development of head and neck cancers due to its important regulation role on multiple cell signaling pathways. The aim of this study was to investigate the methylation pattern of the promoter region of the EGFR gene between head and neck squamous cell carcinoma (HNSCC) patients and a control group. Forty-seven unrelated HNSCC patients, clinically diagnosed at the Department of Otorhinolaryngology, Dışkapı Yıldırım Beyazıt Training and Research Hospital, Ankara, Turkey, and 48 unrelated healthy volunteers from different geographic regions of Turkey, were included in this study. Methylation status of the promoter region of the EGFR gene was detected by methylation-specific-polymerase chain reaction (MS-PCR). The correlation between EGFR gene promoter methylation profiles and clinical characteristics were examined using the χ2 test. Methylation was observed in 79.0% of HNSCC patients, whereas this ratio was 90.0% in healthy individuals. The results show that promoter region methylation of the EGFR gene was not associated with HNSCC development in the studied Turkish patient group. In addition, the methylation status of the EGFR gene promoter was not found to be related to age, gender or tumor stage.
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Deshmukh P, Nair P, Trivedi A, Thomas J. Oral cancer and genomics. JOURNAL OF THE INTERNATIONAL CLINICAL DENTAL RESEARCH ORGANIZATION 2021. [DOI: 10.4103/jicdro.jicdro_23_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
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Teixeira A, DaCunha DC, Barros L, Caires HR, Xavier CPR, Ferreira ICFR, Vasconcelos MH. Eucalyptus globulus Labill. decoction extract inhibits the growth of NCI-H460 cells by increasing the p53 levels and altering the cell cycle profile. Food Funct 2019; 10:3188-3197. [PMID: 31165800 DOI: 10.1039/c8fo02466a] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Eucalyptus globulus Labill. is a widespread evergreen plant belonging to the Myrtaceae family. Several species of Eucalyptus are known to have a plethora of medicinal properties, particularly anti-tumor activity, which prompts the study of the chemical composition and bioactivity of extracts from this plant. Hereby, the main aims of this work were to (i) profile the phenolic compounds in E. globulus extracts prepared by decoction and infusion; (ii) test the cell growth inhibitory activity of E. globulus decoction and infusion, in three human tumor cell line models: colorectal, pancreatic and non-small cell lung cancer (HCT-15, PANC-1 and NCI-H460, respectively); and (iii) study the mechanism of action of the most potent extract in the most sensitive cell line. Our work demonstrated that both the decoction and infusion preparations revealed the presence of phenolic acids, flavonoids and gallotannins, the last group being the most abundant polyphenols found, especially two digalloyl-glucosides. Both extracts inhibited the growth of all the tumor cell lines tested. The decoction extract was the most potent in inhibiting the NCI-H460 cell growth (lower GI50 determined by sulforhodamine B assay), which could be due to its higher content of phenolic compounds. Hence, the effect of the decoction extract on the NCI-H460 cells was further investigated. For this, cell viability (by Trypan blue exclusion assay), the cell cycle profile and apoptosis (by flow cytometry), cell proliferation (by bromodeoxyuridine assay) and protein expression (by western blot) were analyzed. Two different concentrations of the extract (52 μg mL-1 and 104 μg mL-1, corresponding to GI50 and 2 × GI50 concentration) were tested in these studies. Remarkably, the E. globulus decoction extract caused a dose-dependent decrease in the NCI-H460 cell number, which was correlated with a cell cycle arrest in the G0/G1 phase, a decrease in cell proliferation and an increase in the expression of p53, p21 and cyclin D1 proteins. Interestingly, no differences were found in the levels of ds-DNA damage and in the levels of apoptosis. This work highlights the relevance of the Eucalyptus globulus Labill. extract as a source of bioactive compounds with potential anti-tumor activity.
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Affiliation(s)
- Alexandra Teixeira
- i3S - Instituto de Investigação e Inovação em Saúde da Universidade do Porto, Rua Alfredo Allen 208, Porto 4200-135, Portugal.
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Blesa JR, Prieto-Ruiz JA, Hernández-Yago J. Conformation-Sensitive Gel Electrophoresis as an Ideal High-Throughput Strategy for Accurate Detection of Sequence Variations in DNA: Screening hTomm and hTimm Genes. ACTA ACUST UNITED AC 2016; 9:621-4. [PMID: 15475482 DOI: 10.1177/1087057104266390] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Conformation-sensitive gel electrophoresis is a heteroduplex-based method that is particularly well suited to high-throughput analyses. Its simplicity makes it amenable to various adaptations and modifications to enhance its applicability to genome-wide mutation scans. Technical aspects that markedly improve the conformation-sensitive gel electrophoresis performance by combining high throughput and high resolution of the bands facilitating the interpretation of the results are described here. The authors report some of the results they have obtained in the screening of the exon 1 of human Timm8A gene as an example of the suitability of the conformation-sensitive gel electrophoresis–based protocol that has been adapted to optimize its throughput, speed, and simplicity in the recognition of both heterozygous and homozygous DNA mutations. The higher throughput is achieved by using 12 batches per gel. The length of the gel is sufficient for an adequate well-to-read distance for each batch that allows a clear distinction and resolution of the conformation-sensitive gel electrophoresis bands. Standardization of the procedure using multichannel pipettes reduces the preparation time of the 96-well PCRs to 10 min and also accelerates the gel loading. The resulting bands give high-quality images, allowing easy detection of known as well as novel mutations.
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Affiliation(s)
- José Rafael Blesa
- Fundación Valenciana de Investigaciones Biomédicas, Instituto de Investigaciones Citológicas, Amadeo de Saboya, 4, 46010 Valencia, Spain.
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Tan M, Myers JN, Agrawal N. Oral cavity and oropharyngeal squamous cell carcinoma genomics. Otolaryngol Clin North Am 2013; 46:545-66. [PMID: 23910469 DOI: 10.1016/j.otc.2013.04.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Recent technological advances now permit the study of the entire cancer genome, which can elucidate complex pathway interactions that are not apparent at the level of single genes. In this review, the authors describe innovations that have allowed for whole-exome/genome analysis of genetic and epigenetic alterations and of changes in gene expression. Studies using next-generation sequencing, array comparative genomic hybridization, methylation arrays, and gene expression profiling are reviewed, with a particular focus on findings from recent whole-exome sequencing projects. A discussion of the implications of these data on treatment and future goals for cancer genomics is included.
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Affiliation(s)
- Marietta Tan
- Department of Otolaryngology, Head and Neck Surgery, Johns Hopkins University School of Medicine, 601 North Caroline Street, Baltimore, MD 21287, USA
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Abstract
Melanoma is the deadliest form of skin cancer and is increasing in incidence. Recent treatment advances have been made, but there remains a need for continued development of effective therapy options, as treatment rarely leads to cure. Many melanomas contain somatic mutations involved in tumor pathogenesis. Accurate identification of these mutations is necessary to stratify patients for the purpose of treatment and potential for clinical trials, given the absence or presence of a specific mutation. There are a number of techniques available that will identify genetic mutations and genomic aberrations present within melanoma tumor samples which are reviewed here. The type of mutation and sample number will drive selection of a given mutation detection strategy. The strengths and weaknesses, along with limitations, of the various methods will also be discussed. The discovery of somatic mutations integral in melanoma will increase our understanding of tumor pathogenesis and should facilitate identification of mutations relevant to clinical treatment decisions, advancing progress toward personalized medicine.
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Characterization of the DNA copy-number genome in the blood of cutaneous T-cell lymphoma patients. J Invest Dermatol 2011; 132:188-97. [PMID: 21881587 DOI: 10.1038/jid.2011.254] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Cutaneous T-cell lymphoma (CTCL) is a heterogeneous non-Hodgkin's lymphoma that may variably involve the skin, lymph nodes, and peripheral blood. Malignant burden ranges from cutaneous patches and plaques with little evidence of blood involvement to erythroderma often in association with frank leukemia, as in Sézary syndrome. Toward a better understanding of the pathogenesis of this CD4+ T-cell malignancy, we conducted a high-resolution genomic analysis combining DNA (23 samples) and mRNA (12 samples) data of peripheral blood isolates from CTCL patients across a spectrum of stages. Strikingly, even patients with limited involvement, e.g., normal CD4 counts, contained significant copy-number alterations. Defining genomic characteristics of CTCL blood involvement included gains on 8q and 17q, and deletions on 17p and chromosome 10. A consensus analysis of 108 leukemic CTCL samples demonstrated global similarities among patients with varied blood involvement, narrowing 38 of 62 loci. Toward an annotated framework for in vitro testing, we also characterized genomic alterations in five CTCL cell lines (HH, HUT78, PNO, SeAx, and Sez4), revealing intact core features of leukemic CTCL. Together, these studies produce the most comprehensive view of the leukemic CTCL genome to date, with implications for pathogenesis, molecular classification, and potential future therapeutic developments.
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Wang Y, Yang D, Cogdell D, Hu L, Xue F, Broaddus R, Zhang W. Genomic characterization of gene copy-number aberrations in endometrial carcinoma cell lines derived from endometrioid-type endometrial adenocarcinoma. Technol Cancer Res Treat 2010; 9:179-89. [PMID: 20218740 DOI: 10.1177/153303461000900207] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Endometrial carcinoma is one of the most common cancers in women. A limited number of endometrial carcinoma cell lines are available for studies of signal transduction pathways and experimental therapeutics in vitro. However, these cell lines have not been comprehensively characterized. In this study, we used genome-wide microarray-based comparative genomic hybridization (aCGH) technology to characterize five of the more commonly used endometrial cancer cell lines. We detected DNA copy-number gains in chromosomal regions 2q, 3p, 3q, 5q, 7p, 17q, and 19q in all five cell lines. Other common sites of copy-number gains, which were detected in four of five cell lines, included segments of chromosomes 1, 6, 8, 9, 11, 12, and 16. In all five cell lines, we found DNA copy-number losses in regions 3p, 10p, 10q, 11q, 11p, 14q, 15q, 18p, and 21q. Other common sites of genetic aberrations included segments of chromosomes 1, 2, 4, 5, 6, 16, 20, and 22. The genes involved in the copy-number alterations included the oncogenes PIK3CA (3q26.3), K-ras (12p12.1), R-ras (19q13.3-qter), Raf-1 (3p25), EGFR (7p12), Akt1 (14q32.32), and Akt2 (19q13.1-q13.2). A pathway analysis showed that genes in the PI3K and Wnt pathways are commonly affected. Our characterization of genomic alterations in these five commonly used endometrial cancer cell lines provides valuable genomic information for research that focuses on these key oncogenic pathways in endometrial cancer.
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Affiliation(s)
- Yingmei Wang
- Department of Pathology, The University of Texas M. D. Anderson Cancer Center, Houston Texas, USA
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Bae JS, Choi JS, Baik SH, Park WC, Song BJ, Kim JS, Lim Y, Jung SS. Genomic alterations of primary tumor and blood in invasive ductal carcinoma of breast. World J Surg Oncol 2010; 8:32. [PMID: 20409316 PMCID: PMC2865462 DOI: 10.1186/1477-7819-8-32] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2009] [Accepted: 04/21/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genomic alterations are important events in the origin and progression of various cancers, with DNA copy number changes associated with progression and treatment response in cancer. Array CGH is potentially useful in the identification of genomic alterations from primary tumor and blood in breast cancer patients. The aim of our study was to compare differences of DNA copy number changes in blood and tumor tissue in breast cancer. METHODS DNA copy number changes in blood were compared to those in tumor tissue using array-comparative genomic hybridization in samples obtained from 30 breast cancer patients. The relative degree of chromosomal changes was analyzed using log2 ratios and data was validated by real-time polymerase chain reaction. RESULTS Forty-six regions of gains present in more than 30% of the tissues and 70 regions of gains present in more than 30% of blood were identified. The most frequently gained region was chromosome 8q24. In total, agreement of DNA copy numbers between primary tumor and blood was minimal (Kappa = 0.138, p < 0.001). CONCLUSION Although there was only a slight agreement of DNA copy number alterations between the primary tumor and the blood samples, the blood cell copy number variation may have some clinical significance as compared to the primary tumor in IDC breast cancer patients.
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Affiliation(s)
- Ja Seong Bae
- Department of Surgery, The Catholic University, Seoul, Korea
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Kotliarov Y, Bozdag S, Cheng H, Wuchty S, Zenklusen JC, Fine HA. CNAReporter: a GenePattern pipeline for the generation of clinical reports of genomic alterations. BMC Med Genomics 2010; 3:11. [PMID: 20380730 PMCID: PMC2872651 DOI: 10.1186/1755-8794-3-11] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2009] [Accepted: 04/09/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genomic copy number alterations are widely associated with a broad range of human tumors and offer the potential to be used as a diagnostic tool. Especially in the emerging era of personalized medicine medical informatics tools that allow the fast visualization and analysis of genomic alterations of a patient's genomic profile for diagnostic and potential treatment purposes increasingly gain importance. RESULTS We developed CNAReporter, a software tool that allows users to visualize SNP-specific data obtained from Affymetrix arrays and generate PDF-reports as output. We combined standard algorithms for the analysis of chromosomal alterations, utilizing the widely applied GenePattern framework. As an example, we show genome analyses of two patients with distinctly different CNA profiles using the tool. CONCLUSIONS Glioma subtypes, characterized by different genomic alterations, are often treated differently but can be difficult to differentiate pathologically. CNAReporter offers a user-friendly way to visualize and analyse genomic changes of any given tumor genomic profile, thereby leading to an accurate diagnosis and patient-specific treatment.
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Affiliation(s)
- Yuri Kotliarov
- Neuro-Oncology Branch, National Cancer Institute, National Institutes of Neurological Disorder and Stroke, National Institutes of Health, Bethesda, MD 20892, USA
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Kong SY, Kang S. Epstein-Barr virus-transformation of B-cell lines in ovarian cancer patients: feasibility of genomic storage for unlimited use. J Gynecol Oncol 2009; 20:243-5. [PMID: 20041102 DOI: 10.3802/jgo.2009.20.4.243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2009] [Accepted: 10/21/2009] [Indexed: 11/30/2022] Open
Abstract
OBJECTIVE The aim of the current study is to test whether immortalized B-lymphocyte cell line via Ebstein-Barr virus (EBV) transformation is feasible and can be an unlimited source of genome wide study. METHODS We obtained peripheral whole blood from 5 ovarian cancer patients and immortalized the B-cell lines using EBV transformation. The success rate was analyzed and the bio-identity of the genome was performed using human leukocyte antigen (HLA) identity test. RESULTS EBV transformation was successful in all 5 cases (95% confidence interval, 46.3% to 100%). After cryopreservation of EBV-transformed B-cell lines and subsequent thawing, we observed that all cell lines were viable and proliferative. To check bio-identity, HLA-A, B, and DR were tested between the genome of the original samples and the transformed samples. The HLA typing revealed that all observed HLA-A, B, and DR type was identical in 5 cases before and after EBV-transformation. CONCLUSION The current results suggest that EBV-transformation of peripheral blood is an efficient tool in genome banking. The EBV-transformed B-cell lines may be a valuable resource of genome in multi-center translational research by the Korean Gynecologic Oncology Group.
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Affiliation(s)
- Sun-Young Kong
- Hematologic Malignancy Branch & Department of Laboratory Medicine, Center for Clinical Services, Goyang, Korea
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Saito S, Morita K, Hirano T. High frequency of common DNA copy number abnormalities detected by bacterial artificial chromosome array comparative genomic hybridization in 24 breast cancer cell lines. Hum Cell 2009; 22:1-10. [PMID: 19222606 DOI: 10.1111/j.1749-0774.2008.00061.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Breast cancer is a widespread disease in Japan and across the world. Breast cancer cells, as well as most other types of cancer cells, have diverse chromosomal aberrations. Clarifying the character of these chromosomal aberrations should contribute to the development of more suitable therapies, along with the predictions of metastasis and prognosis. Twenty-four breast cancer cell lines were analyzed by bacterial artificial chromosome (BAC) array comparative genomic hybridization (CGH). The array slide contained duplicate spots of 4030 BAC clone DNAs covering the entire human genome with 1 Mbp resolution. In all 24 breast cancer cell lines, frequent and significant amplifications as well as deletions were detected by BAC array CGH. Common DNA copy number gains, detected in 60% (above 15 cell lines) of the 24 breast cancer cell lines were found in 76 BAC clones, located at 1q, 5p, 8q, 9p, 16p, 17q, and 20q. Moreover, common DNA copy number loss was detected in 136 BAC clones, located at 1q, 2q, 3p, 4p, 6q, 8p, 9p, 11p, 13q, 17p, 18q, 19p, Xp, and Xq. The DNA copy number abnormalities found included abnormality of the well-known oncogene cMYC (8q24.21); however, most of them were not reported to relate to breast cancer. BAC array CGH has great potential to detect DNA copy number abnormalities, and has revealed that breast cancer cell lines have substantial heterogeneity.
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Affiliation(s)
- Soichiro Saito
- Applied Gene Technology Research Group, Research Institute for Cell Engineering, National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki, Japan
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Ahn JY, Seo K, Weinberg O, Boyd SD, Arber DA. A comparison of two methods for screening CEBPA mutations in patients with acute myeloid leukemia. J Mol Diagn 2009; 11:319-23. [PMID: 19525338 DOI: 10.2353/jmoldx.2009.080121] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The goal of the study was to compare the performance of a fluorescence-based multiplex PCR fragment analysis to a direct sequencing method for detecting CEBPA mutations in patients with acute myeloid leukemia. Thirty-three samples were selected from a larger study of 107 cases of acute myeloid leukemia by screening for CEBPA mutations by sequence analysis. Of ten identified mutations, six (insertions and deletions) were detected by both sequencing and fragment methods. The fragment analysis method did not detect the remaining four base substitutions because the method cannot detect changes that result in identically sized products. The multiplex PCR fragment length analysis method therefore failed to detect substitution mutations accounting for 40% of total CEBPA mutations in our patient set. Our results indicate that fragment length analysis should not be used in isolation, and that direct sequencing is required to evaluate CEBPA gene mutational status in acute myeloid leukemia. A combination of the two assays may offer some advantages, chiefly in permitting more sensitive detection by fragment length analysis of insertions and deletions.
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Affiliation(s)
- Jeung-Yeal Ahn
- Department of Pathology,Stanford University School of Medicine, Stanford, California.
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Overdevest JB, Theodorescu D, Lee JK. Utilizing the molecular gateway: the path to personalized cancer management. Clin Chem 2009; 55:684-97. [PMID: 19246616 DOI: 10.1373/clinchem.2008.118554] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
BACKGROUND Personalized medicine is the provision of focused prevention, detection, prognostic, and therapeutic efforts according to an individual's genetic composition. The actualization of personalized medicine will require combining a patient's conventional clinical data with bioinformatics-based molecular-assessment profiles. This synergistic approach offers tangible benefits, such as heightened specificity in the molecular classification of cancer subtypes, improved prognostic accuracy, targeted development of new therapies, novel applications for old therapies, and tailored selection and delivery of chemotherapeutics. CONTENT Our ability to personalize cancer management is rapidly expanding through biotechnological advances in the postgenomic era. The platforms of genomics, proteomics, single-nucleotide polymorphism profiling and haplotype mapping, high-throughput genomic sequencing, and pharmacogenomics constitute the mechanisms for the molecular assessment of a patient's tumor. The complementary data derived during these assessments is processed through bioinformatics analysis to offer unique insights for linking expression profiles to disease detection, tumor response to chemotherapy, and patient survival. Together, these approaches permit improved physician capacity to assess risk, target therapies, and tailor a chemotherapeutic treatment course. SUMMARY Personalized medicine is poised for rapid growth as the insights provided by new bioinformatics models are integrated with current procedures for assessing and treating cancer patients. Integration of these biological platforms will require refinement of tissue-processing and analysis techniques, particularly in clinical pathology, to overcome obstacles in customizing our ability to treat cancer.
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Affiliation(s)
- Jonathan B Overdevest
- Departments of Molecular Physiology and Biological Physics; and Public Health Sciences, University of Virginia Health Sciences Center, Charlottesville, VA 22908, USA
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Greshock J, Cheng J, Rusnak D, Martin AM, Wooster R, Gilmer T, Lee K, Weber BL, Zaks T. Genome-wide DNA copy number predictors of lapatinib sensitivity in tumor-derived cell lines. Mol Cancer Ther 2008; 7:935-43. [PMID: 18413807 DOI: 10.1158/1535-7163.mct-07-2072] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
A common aim of pharmacogenomic studies that use genome-wide assays on panels of cancers is the unbiased discovery of genomic alterations that are associated with clinical outcome and drug response. Previous studies of lapatinib, a selective dual-kinase inhibitor of epidermal growth factor receptor (EGFR) and HER2 tyrosine kinases, have shown predictable relationships between the activity of these target genes and response. Under the hypothesis that additional genes may play a role in drug sensitivity, a predictive model for lapatinib response was constructed from genome-wide DNA copy number data from 24 cancer cell lines. An optimal predictive model which consists of aberrations at nine distinct genetic loci, includes gains of HER2, EGFR, and loss of CDKN2A. This model achieved an area under the receiver operating characteristic curve of approximately 0.85 (80% confidence interval, 0.70-0.98; P < 0.01), and correctly classified the sensitivity status of 8 of 10 head and neck cancer cell lines. This study shows that biomarkers predictive for lapatinib sensitivity, including the previously described copy number gains of EGFR and HER2, can be discovered using novel genomic assays in an unbiased manner. Furthermore, these results show the utility of DNA copy number profiles in pharmacogenomic studies.
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Affiliation(s)
- Joel Greshock
- Translational Medicine Oncology, GlaxoSmithKline, 1250 South Collegeville Road, UP 4W-4230, Collegeville, PA 19426, USA
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Lin WM, Baker AC, Beroukhim R, Winckler W, Feng W, Marmion JM, Laine E, Greulich H, Tseng H, Gates C, Hodi FS, Dranoff G, Sellers WR, Thomas RK, Meyerson M, Golub TR, Dummer R, Herlyn M, Getz G, Garraway LA. Modeling genomic diversity and tumor dependency in malignant melanoma. Cancer Res 2008; 68:664-73. [PMID: 18245465 PMCID: PMC10493008 DOI: 10.1158/0008-5472.can-07-2615] [Citation(s) in RCA: 245] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The classification of human tumors based on molecular criteria offers tremendous clinical potential; however, discerning critical and "druggable" effectors on a large scale will also require robust experimental models reflective of tumor genomic diversity. Here, we describe a comprehensive genomic analysis of 101 melanoma short-term cultures and cell lines. Using an analytic approach designed to enrich for putative "driver" events, we show that cultured melanoma cells encompass the spectrum of significant genomic alterations present in primary tumors. When annotated according to these lesions, melanomas cluster into subgroups suggestive of distinct oncogenic mechanisms. Integrating gene expression data suggests novel candidate effector genes linked to recurrent copy gains and losses, including both phosphatase and tensin homologue (PTEN)-dependent and PTEN-independent tumor suppressor mechanisms associated with chromosome 10 deletions. Finally, sample-matched pharmacologic data show that FGFR1 mutations and extracellular signal-regulated kinase (ERK) activation may modulate sensitivity to mitogen-activated protein kinase/ERK kinase inhibitors. Genetically defined cell culture collections therefore offer a rich framework for systematic functional studies in melanoma and other tumors.
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Affiliation(s)
- William M. Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School
- Department of Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School
- The Broad Institute of M.I.T. and Harvard
| | - Alissa C. Baker
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School
- Department of Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School
| | - Rameen Beroukhim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School
- Department of Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School
- The Broad Institute of M.I.T. and Harvard
| | - Wendy Winckler
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School
- Department of Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School
- The Broad Institute of M.I.T. and Harvard
| | - Whei Feng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School
- Department of Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School
- The Broad Institute of M.I.T. and Harvard
| | | | - Elisabeth Laine
- Department of Dermatology, University of Zurich Hospital, Zürich, Switzerland
| | - Heidi Greulich
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School
- Department of Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School
- The Broad Institute of M.I.T. and Harvard
| | - Hsiuyi Tseng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School
- Department of Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School
| | | | - F. Stephen Hodi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School
| | - Glenn Dranoff
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School
| | - William R. Sellers
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Roman K. Thomas
- Max Planck Institute for Neurological Research with Klaus Joachim Zulch Laboratories of the Max Planck Society and the Medical Faculty of the University of Cologne
- Center for Integrated Oncology and Department I for Internal Medicine, University of Cologne, Cologne, Germany
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School
- Department of Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School
- Department of Pathology, Harvard Medical School, Boston, Massachusetts
- The Broad Institute of M.I.T. and Harvard
| | - Todd R. Golub
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School
- Department of Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School
- The Broad Institute of M.I.T. and Harvard
| | - Reinhard Dummer
- Department of Dermatology, University of Zurich Hospital, Zürich, Switzerland
| | - Meenhard Herlyn
- Cancer Biology Division, Wistar Institute, Philadelphia, Pennsylvania
| | - Gad Getz
- Department of Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School
- The Broad Institute of M.I.T. and Harvard
| | - Levi A. Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School
- Department of Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School
- The Broad Institute of M.I.T. and Harvard
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18
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Greshock J, Feng B, Nogueira C, Ivanova E, Perna I, Nathanson K, Protopopov A, Weber BL, Chin L. A Comparison of DNA Copy Number Profiling Platforms. Cancer Res 2007; 67:10173-80. [DOI: 10.1158/0008-5472.can-07-2102] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
The accurate mapping of recurring DNA copy number aberrations (CNAs), a hallmark feature of the cancer genome, has facilitated the discovery of tumor suppressor genes and oncogenes. Microarray-based assays designed to detect these chromosomal copy number alterations on a genome-wide and high-resolution scale have emerged as a cornerstone technology in the genomic era. The diversity of commercially available platforms prompted a systematic comparison of five copy number profiling assays for their ability to detect 2-fold copy number gain and loss (4n or 1n, respectively) as well as focal high-amplitude CNAs. Here, using a collection of established human melanoma cell lines, we defined the reproducibility, absolute signals, signal to noise, and false-positive and false-negative rates for each of the five assays against ground truth defined by spectral karyotyping, in addition to comparing the concordance of CNA detection by two high-resolution Agilent and Affymetrix microarray platforms. Our analyses concluded that the Agilent's 60-mer oligonucleotide microarray with probe design optimized for genomic hybridization offers the highest sensitivity and specificity (area under receiver operator characteristic curve >0.99), whereas Affymetrix's single nucleotide polymorphism microarray seems to offer better detection of CNAs in gene-poor regions. Availability of these comparison results should guide study design decisions and facilitate further computational development. [Cancer Res 2007;67(21):10173–80]
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Affiliation(s)
- Joel Greshock
- 1Translational Medicine, GlaxoSmithKline, King of Prussia, Pennsylvania
| | - Bin Feng
- 2Center for Applied Cancer Science, the Belfer Institute for Innovative Cancer Science and
| | | | - Elena Ivanova
- 2Center for Applied Cancer Science, the Belfer Institute for Innovative Cancer Science and
| | - Ilana Perna
- 2Center for Applied Cancer Science, the Belfer Institute for Innovative Cancer Science and
| | - Katherine Nathanson
- 5Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Alexei Protopopov
- 2Center for Applied Cancer Science, the Belfer Institute for Innovative Cancer Science and
| | - Barbara L. Weber
- 1Translational Medicine, GlaxoSmithKline, King of Prussia, Pennsylvania
| | - Lynda Chin
- 2Center for Applied Cancer Science, the Belfer Institute for Innovative Cancer Science and
- 3Department of Medical Oncology, Dana-Farber Cancer Institute
- 4Department of Dermatology, Harvard Medical School, Boston, Massachusetts; and
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19
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Jönsson G, Staaf J, Olsson E, Heidenblad M, Vallon-Christersson J, Osoegawa K, de Jong P, Oredsson S, Ringnér M, Höglund M, Borg A. High-resolution genomic profiles of breast cancer cell lines assessed by tiling BAC array comparative genomic hybridization. Genes Chromosomes Cancer 2007; 46:543-58. [PMID: 17334996 DOI: 10.1002/gcc.20438] [Citation(s) in RCA: 154] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
A BAC-array platform for comparative genomic hybridization was constructed from a library of 32,433 clones providing complete genome coverage, and evaluated by screening for DNA copy number changes in 10 breast cancer cell lines (BT474, MCF7, HCC1937, SK-BR-3, L56Br-C1, ZR-75-1, JIMT1, MDA-MB-231, MDA-MB-361, and HCC2218) and one cell line derived from fibrocystic disease of the breast (MCF10A). These were also characterized by gene expression analysis and found to represent all five recently described breast cancer subtypes using the "intrinsic gene set" and centroid correlation. Three cell lines, HCC1937 and L56BrC1 derived from BRCA1 mutation carriers and MDA-MB-231, were of basal-like subtype and characterized by a high frequency of low-level gains and losses of typical pattern, including limited deletions on 5q. Four estrogen receptor positive cell lines were of luminal A subtype and characterized by a different pattern of aberrations and high-level amplifications, including ERBB2 and other 17q amplicons in BT474 and MDA-MB-361. SK-BR-3 cells, characterized by a complex genome including ERBB2 amplification, massive high-level amplifications on 8q and a homozygous deletion of CDH1 at 16q22, had an expression signature closest to luminal B subtype. The effects of gene amplifications were verified by gene expression analysis to distinguish targeted genes from silent amplicon passengers. JIMT1, derived from an ERBB2 amplified trastuzumab resistant tumor, was of the ERBB2 subtype. Homozygous deletions included other known targets such as PTEN (HCC1937) and CDKN2A (MDA-MB-231, MCF10A), but also new candidate suppressor genes such as FUSSEL18 (HCC1937) and WDR11 (L56Br-C1) as well as regions without known genes. The tiling BAC-arrays constitute a powerful tool for high-resolution genomic profiling suitable for cancer research and clinical diagnostics.
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Affiliation(s)
- Göran Jönsson
- Department of Oncology, University Hospital, Lund, Sweden
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20
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Jaeger J, Koczan D, Thiesen HJ, Ibrahim SM, Gross G, Spang R, Kunz M. Gene expression signatures for tumor progression, tumor subtype, and tumor thickness in laser-microdissected melanoma tissues. Clin Cancer Res 2007; 13:806-15. [PMID: 17289871 DOI: 10.1158/1078-0432.ccr-06-1820] [Citation(s) in RCA: 180] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE To better understand the molecular mechanisms of malignant melanoma progression and metastasis, gene expression profiling was done of primary melanomas and melanoma metastases. EXPERIMENTAL DESIGN Tumor cell-specific gene expression in 19 primary melanomas and 22 melanoma metastases was analyzed using oligonucleotide microarrays after laser-capture microdissection of melanoma cells. Statistical analysis was done by random permutation analysis and support vector machines. Microarray data were further validated by immunohistochemistry and immunoblotting. RESULTS Overall, 308 genes were identified that showed significant differential expression between primary melanomas and melanoma metastases (false discovery rate<or=0.05). Significantly overrepresented gene ontology categories in the list of 308 genes were cell cycle regulation, mitosis, cell communication, and cell adhesion. Overall, 47 genes showed up-regulation in metastases. These included Cdc6, Cdk1, septin 6, mitosin, kinesin family member 2C, osteopontin, and fibronectin. Down-regulated genes included E-cadherin, fibroblast growth factor binding protein, and desmocollin 1 and desmocollin 3, stratifin/14-3-3sigma, and the chemokine CCL27. Using support vector machine analysis of gene expression data, a performance of >85% correct classifications for primary melanomas and metastases was reached. Further analysis showed that subtypes of primary melanomas displayed characteristic gene expression patterns, as do thin tumors (<or=1.0 mm Breslow thickness) compared with intermediate and thick tumors (>2.0 mm Breslow thickness). CONCLUSIONS Taken together, this large-scale gene expression study of malignant melanoma identified molecular signatures related to metastasis, melanoma subtypes, and tumor thickness. These findings not only provide deeper insights into the pathogenesis of melanoma progression but may also guide future research on innovative treatments.
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Affiliation(s)
- Jochen Jaeger
- Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
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21
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Arriola E, Lambros MBK, Jones C, Dexter T, Mackay A, Tan DSP, Tamber N, Fenwick K, Ashworth A, Dowsett M, Reis-Filho JS. Evaluation of Phi29-based whole-genome amplification for microarray-based comparative genomic hybridisation. J Transl Med 2007; 87:75-83. [PMID: 17170740 DOI: 10.1038/labinvest.3700495] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
For the optimal performance of high throughput genomic technologies sufficient yields of high-quality DNA are crucial. Following microdissection, most samples fail to produce sufficient quantities of DNA for genome-wide experiments. Various PCR-based amplification methods have been used, but these usually produce nonuniform representations of the genome. Bacteriophage Phi29 DNA polymerase random-primed DNA amplification is based on isothermal multiple displacement amplification. We sought to define the genome representation of this method in a bacterial artificial chromosome microarray comparative genomic hybridisation (aCGH) platform. Test genomic female DNA was amplified using Phi29 amplification at four different starting concentrations (0.5, 5, 10 and 50 ng). These products were combined with unamplified and amplified genomic female DNA as reference. In addition, 50 ng of DNA from five microdissected breast cancer frozen samples, were amplified using the same method. Three combinations were performed: unamplified test with unamplified reference, amplified test with unamplified reference and both amplified tumour and reference DNA. aCGH was performed with an in-house 16 K BAC platform (a resolution of approximately 100 Kb). Pearson's correlation tests and hierarchical clustering were performed to compare the profiles obtained. aCGH profiles obtained with amplified test and unamplified reference female genomic DNA showed copy number biases throughout the genome. These biases were more conspicuous with smaller amounts of starting material and mapped to regions of known copy number polymorphisms. When similar concentrations of test and reference DNA were amplified, the biases were significantly reduced, rendering accurate profiles. For the tumours, representative profiles were obtained when both test and reference DNA were amplified. Phi29 amplification induces copy number biases and unamplified material remains the gold standard for copy number analysis. For accurate results using Phi29 amplification, samples subjected to aCGH analysis should be combined with reference DNA amplified with the same method, using similar amounts of starting template.
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Affiliation(s)
- Edurne Arriola
- The Breakthrough Breast Cancer Research Centre, Institute of Cancer Research, London, UK
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22
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Garraway LA, Weir BA, Zhao X, Widlund H, Beroukhim R, Berger A, Rimm D, Rubin MA, Fisher DE, Meyerson ML, Sellers WR. "Lineage addiction" in human cancer: lessons from integrated genomics. COLD SPRING HARBOR SYMPOSIA ON QUANTITATIVE BIOLOGY 2006; 70:25-34. [PMID: 16869735 DOI: 10.1101/sqb.2005.70.016] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Genome-era advances in the field of oncology endorse the notion that many tumors may prove vulnerable to targeted therapeutic avenues once their salient molecular alterations are elucidated. Accomplishing this requires both detailed genomic characterization and the ability to identify in situ the critical dependencies operant within individual tumors. To this end, DNA microarray platforms such as high-density single-nucleotide polymorphism (SNP) arrays enable large-scale cancer genome characterization, including copy number and loss-of-heterozygosity analyses at high resolution. Clustering analyses of SNP array data from a large collection of tumor samples and cell lines suggest that certain copy number alterations correlate strongly with the tissue of origin. Such lineage-restricted alterations may harbor novel cancer genes directing genesis or progression of tumors from distinct tissue types. We have explored this notion through combined analysis of genome-scale data sets from the NCI60 cancer cell line collection. Here, several melanoma cell lines clustered on the basis of increased dosage at a region of chromosome 3p containing the master melanocyte regulator MITF. Combined analysis of gene expression data and additional functional studies established MITF as an amplified oncogene in melanoma. MITF may therefore represent a nodal point within a critical lineage survival pathway operant in a subset of melanomas. These findings suggest that, like oncogene addiction, "lineage addiction" may represent a fundamental tumor survival mechanism with important therapeutic implications.
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Affiliation(s)
- L A Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA
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23
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Abstract
Although cell-lineage and differentiation models dominate tumour classification and treatment, the recognition that cancer is also a genomic disease has prompted a reconfiguration of cancer taxonomies according to molecular criteria. Recent evidence indicates that a synthesis of lineage-based and genetic paradigms might offer new insights into crucial and therapeutically pliable tumour dependencies. For example, MITF (microphthalmia-associated transcription factor), which is a master regulator of the melanocyte lineage, might become a melanoma oncogene when deregulated in certain genetic contexts. MITF and other lineage-survival genes therefore implicate lineage dependency (or lineage addiction) as a newly recognized mechanism that is affected by tumour genetic alterations.
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Affiliation(s)
- Levi A Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA.
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24
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Esteban MA, Harten SK, Tran MG, Maxwell PH. Formation of primary cilia in the renal epithelium is regulated by the von Hippel-Lindau tumor suppressor protein. J Am Soc Nephrol 2006; 17:1801-6. [PMID: 16775032 DOI: 10.1681/asn.2006020181] [Citation(s) in RCA: 119] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
Growing evidence points to defects in the primary cilium as a critical mechanism underlying renal cyst development. Inactivation of the VHL gene is responsible for the autosomal dominant condition von Hippel-Lindau (VHL) disease and is implicated in most sporadic clear cell renal carcinomas. Manifestations of VHL disease include cysts in several organs, particularly in the kidney. Here it is shown that VHL inactivation is associated with abrogation of the primary cilium in renal cysts of patients with VHL disease and in VHL-defective cell lines. Complementation of VHL-defective clear cell renal carcinoma cell lines with wild-type VHL restored primary cilia. Moreover, it is shown that the effects of VHL on the primary cilium are mediated substantially via hypoxia-inducible factor. The effect of VHL status on the primary cilium provides a potential mechanism for renal cyst development in VHL disease and may help in the understanding of how VHL acts as a tumor suppressor.
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Affiliation(s)
- Miguel A Esteban
- Renal Laboratory, Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK
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25
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Berger R. [Human cytogenetics. From 1956 to 2006]. ACTA ACUST UNITED AC 2006; 55:1-12. [PMID: 16697121 DOI: 10.1016/j.patbio.2006.04.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2006] [Accepted: 04/05/2006] [Indexed: 01/24/2023]
Abstract
The correct enumeration of human chromosomes, only established in 1956, has marked the starting point of the modern cytogenetics. The introduction of banding techniques, then of in situ hybridization techniques, and now of genomic microarray technology allowed a dramatic development of cytogenetics of which the main applications to basic and medical research are evoked in this review.
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Affiliation(s)
- R Berger
- Hôpital Necker-Enfants-Malades, EMI 0210 Inserm, 149, rue de Sèvres, 75743 Paris cedex 15, France.
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26
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Naylor TL, Greshock J, Wang Y, Colligon T, Yu QC, Clemmer V, Zaks TZ, Weber BL. High resolution genomic analysis of sporadic breast cancer using array-based comparative genomic hybridization. Breast Cancer Res 2005; 7:R1186-98. [PMID: 16457699 PMCID: PMC1410746 DOI: 10.1186/bcr1356] [Citation(s) in RCA: 160] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2005] [Revised: 08/26/2005] [Accepted: 10/24/2005] [Indexed: 11/19/2022] Open
Abstract
Introduction Genomic aberrations in the form of subchromosomal DNA copy number changes are a hallmark of epithelial cancers, including breast cancer. The goal of the present study was to analyze such aberrations in breast cancer at high resolution. Methods We employed high-resolution array comparative genomic hybridization with 4,134 bacterial artificial chromosomes that cover the genome at 0.9 megabase resolution to analyze 47 primary breast tumors and 18 breast cancer cell lines. Results Common amplicons included 8q24.3 (amplified in 79% of tumors, with 5/47 exhibiting high level amplification), 1q32.1 and 16p13.3 (amplified in 66% and 57% of tumors, respectively). Moreover, we found several positive correlations between specific amplicons from different chromosomes, suggesting the existence of cooperating genetic loci. Queried by gene, the most frequently amplified kinase was PTK2 (79% of tumors), whereas the most frequently lost kinase was PTK2B (hemizygous loss in 34% of tumors). Amplification of ERBB2 as measured by comparative genomic hybridization (CGH) correlated closely with ERBB2 DNA and RNA levels measured by quantitative PCR as well as with ERBB2 protein levels. The overall frequency of recurrent losses was lower, with no region lost in more than 50% of tumors; the most frequently lost tumor suppressor gene was RB1 (hemizygous loss in 26% of tumors). Finally, we find that specific copy number changes in cell lines closely mimicked those in primary tumors, with an overall Pearson correlation coefficient of 0.843 for gains and 0.734 for losses. Conclusion High resolution CGH analysis of breast cancer reveals several regions where DNA copy number is commonly gained or lost, that non-random correlations between specific amplicons exist, and that specific genetic alterations are maintained in breast cancer cell lines despite repeat passage in tissue culture. These observations suggest that genes within these regions are critical to the malignant phenotype and may thus serve as future therapeutic targets.
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Affiliation(s)
- Tara L Naylor
- Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Joel Greshock
- Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Yan Wang
- Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - Theresa Colligon
- Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - QC Yu
- Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | | | - Tal Z Zaks
- Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
- GlaxoSmithKline, King of Prussia, PA 19406, USA
| | - Barbara L Weber
- Abramson Family Cancer Research Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
- GlaxoSmithKline, King of Prussia, PA 19406, USA
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27
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Little SE, Vuononvirta R, Reis-Filho JS, Natrajan R, Iravani M, Fenwick K, Mackay A, Ashworth A, Pritchard-Jones K, Jones C. Array CGH using whole genome amplification of fresh-frozen and formalin-fixed, paraffin-embedded tumor DNA. Genomics 2005; 87:298-306. [PMID: 16271290 DOI: 10.1016/j.ygeno.2005.09.019] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2005] [Accepted: 09/21/2005] [Indexed: 11/18/2022]
Abstract
The ability to utilize formalin-fixed, paraffin-embedded (FFPE) archival specimens reliably for high-resolution molecular genetic analysis would be of immense practical application in the study of human disease. We have evaluated the ability of the GenomePlex whole genome amplification (WGA) kit to amplify frozen and FFPE tissue for use in array CGH (aCGH). GenomePlex gave highly representative data compared with unamplified controls both from frozen material (Pearson's R(2) = 0.898) and from FFPE (R(2) = 0.883). Artifactual amplification observed using DOP-PCR at chromosomes 1p, 3, 13q, and 16p was not seen with GenomePlex. Highly reproducible aCGH profiles were obtained using as little as 5 ng starting material from FFPE (R(2) = 0.918). This WGA method should readily lend itself to the determination of DNA copy number alterations from small fresh-frozen and FFPE clinical tumor specimens, although some care must be taken to optimize the DNA extraction procedure.
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Affiliation(s)
- Suzanne E Little
- Paediatric Oncology, Institute of Cancer Research/Royal Marsden NHS Trust, Sutton, Surrey SM2 5NG, UK
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28
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Abstract
Information obtained from animal models (mostly mice and rats) has contributed substantially to the development of treatments for human cancers. However, important interspecies differences have to be taken into account when considering the mechanisms of cancer development and extrapolating the results from mice to humans. Comparative studies of cancer in humans and animal models mostly focus on genetic factors. This review discusses the bio-epidemiological aspects of cancer manifestation in humans and rodents that have been underrepresented in the literature.
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Affiliation(s)
- Vladimir N Anisimov
- Department of Carcinogenesis and Oncogerontology, N.N. Petrov Research Institute of Oncology, Pesochny-2, St. Petersburg 197758, Russia.
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29
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30
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Abstract
The implementation and integration of systems biology approaches with the emerging nanosciences and microchip technology will revolutionize profoundly molecular imaging and fuel the drive toward a more predictive and individualized health care. In combination with informatics platforms, key gene and protein targets will be identified, and serve as more effective targets for diagnostic and therapeutic interventions. Drug development also will be expedited by the judicious selection of more appropriate molecular biomarkers that will serve as objective end points of treatment efficacy, in addition to facilitating the development of new target-specific therapeutics. Finally, with the more widespread proliferation of high-field magnets and advancements in imaging hardware; acquisition methods; and novel,"smart" MR agents, the ability to achieve higher resolution analyses of tumor biology, cell track-ing, and gene expression will be realized more fully. Although radiologists will continue to serve as diagnostic consultants and assist in management decisions, the contributions from new developments in the biologic and molecular sciences will significantly alter the scope of our profession. Radiologists will be required to participate more actively in the individualized care of the patient and cultivate a deeper understanding of the underlying molecular basis of disease and molecular pharmacology for facilitating selection of the most appropriate combination of imaging studies that address biologically relevant questions. These radical changes in our profession will necessitate the re-education and emergence of a small cadre of professionals that is educated broadly in multiple scientific disciplines, and demonstrate expertise in clinical care and the basic sciences. The optimistic view is that this already is happening.
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Affiliation(s)
- Michelle Bradbury
- Department of Radiology, Memorial Sloan Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA.
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31
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32
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Margolin AA, Greshock J, Naylor TL, Mosse Y, Maris JM, Bignell G, Saeed AI, Quackenbush J, Weber BL. CGHAnalyzer: a stand-alone software package for cancer genome analysis using array-based DNA copy number data. Bioinformatics 2005; 21:3308-11. [PMID: 15905276 DOI: 10.1093/bioinformatics/bti500] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
SUMMARY This synopsis provides an overview of array-based comparative genomic hybridization data display, abstraction and analysis using CGHAnalyzer, a software suite, designed specifically for this purpose. CGHAnalyzer can be used to simultaneously load copy number data from multiple platforms, query and describe large, heterogeneous datasets and export results. Additionally, CGHAnalyzer employs a host of algorithms for microarray analysis that include hierarchical clustering and class differentiation. AVAILABILITY CGHAnalyzer, the accompanying manual, documentation and sample data are available for download at http://acgh.afcri.upenn.edu. This is a Java-based application built in the framework of the TIGR MeV that can run on Microsoft Windows, Macintosh OSX and a variety of Unix-based platforms. It requires the installation of the free Java Runtime Environment 1.4.1 (or more recent) (http://www.java.sun.com).
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Affiliation(s)
- Adam A Margolin
- Abramson Family Cancer Research Institute, University of Pennsylvania, Philadelphia, PA 19104, USA
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33
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Abstract
Ductal lavage is a minimally-invasive procedure that permits sampling of breast ductal fluids for cytopathologic analysis. The technique is performed with topical anesthesia and involves cannulation of any fluid-yielding nipple orifice with a specially-designed catheter for lavage and aspiration of the ductal system. The procedure is used for women who have clinical evidence of increased breast cancer risk; if atypia is detected, it may strengthen a woman's interest in committing to a risk-reducing strategy or a chemoprevention trial. The technology also is being used as a tool in ongoing translational research studies.
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Affiliation(s)
- Aeisha Rivers
- Department of Surgery, St. Joseph's Hospital and Medical Center, Ann Arbor, MI, USA
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34
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Hibbs K, Skubitz KM, Pambuccian SE, Casey RC, Burleson KM, Oegema TR, Thiele JJ, Grindle SM, Bliss RL, Skubitz APN. Differential gene expression in ovarian carcinoma: identification of potential biomarkers. THE AMERICAN JOURNAL OF PATHOLOGY 2004; 165:397-414. [PMID: 15277215 PMCID: PMC1618570 DOI: 10.1016/s0002-9440(10)63306-8] [Citation(s) in RCA: 175] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Ovarian cancer remains the fifth leading cause of cancer death for women in the United States. In this study, the gene expression of 20 ovarian carcinomas, 17 ovarian carcinomas metastatic to the omentum, and 50 normal ovaries was determined by Gene Logic Inc. using Affymetrix GeneChip HU_95 arrays containing approximately 12,000 known genes. Differences in gene expression were quantified as fold changes in gene expression in ovarian carcinomas compared to normal ovaries and ovarian carcinoma metastases. Genes up-regulated in ovarian carcinoma tissue samples compared to more than 300 other normal and diseased tissue samples were identified. Seven genes were selected for further screening by immunohistochemistry to determine the presence and localization of the proteins. These seven genes were: the beta8 integrin subunit, bone morphogenetic protein-7, claudin-4, collagen type IX alpha2, cellular retinoic acid binding protein-1, forkhead box J1, and S100 calcium-binding protein A1. Statistical analyses showed that the beta8 integrin subunit, claudin-4, and S100A1 provided the best distinction between ovarian carcinoma and normal ovary tissues, and may serve as the best candidate tumor markers among the seven genes studied. These results suggest that further exploration into other up-regulated genes may identify novel diagnostic, therapeutic, and/or prognostic biomarkers in ovarian carcinoma.
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MESH Headings
- Adenocarcinoma, Papillary/genetics
- Adenocarcinoma, Papillary/metabolism
- Adenocarcinoma, Papillary/secondary
- Adult
- Aged
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Cystadenocarcinoma, Serous/genetics
- Cystadenocarcinoma, Serous/metabolism
- Cystadenocarcinoma, Serous/secondary
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Humans
- Immunoenzyme Techniques
- Middle Aged
- Oligonucleotide Array Sequence Analysis
- Ovarian Neoplasms/genetics
- Ovarian Neoplasms/metabolism
- Ovarian Neoplasms/pathology
- Ovary/metabolism
- Peritoneal Neoplasms/genetics
- Peritoneal Neoplasms/metabolism
- Peritoneal Neoplasms/secondary
- RNA, Neoplasm/genetics
- RNA, Neoplasm/metabolism
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Affiliation(s)
- Kathleen Hibbs
- Department of Laboratory Medicine and Pathology, University of Minnesota, MMC 609, 420 Delaware St. S.E., Minneapolis, MN 55455, USA
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35
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Mundle SD, Sokolova I. Clinical implications of advanced molecular cytogenetics in cancer. Expert Rev Mol Diagn 2004; 4:71-81. [PMID: 14711351 DOI: 10.1586/14737159.4.1.71] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The field of cytogenetics has already entered the molecular era and a rapid expansion of its contribution is seen in genomic disease management. Among the evolving advanced molecular techniques, with an impeccable balance of high specificity, sensitivity and assay rapidity, fluorescence in situ hybridization has made its home in routine clinical laboratory. Today, its clinical application is vivid in every phase of disease management of a number of malignancies. The rapid growth in the knowledge of specific associations between distinct chromosomal abnormalities and different types of cancers will necessitate simultaneous detection of multiple abnormalities using multicolor/multiplex fluorescence in situ hybridization tests more often in the near future. Also, as the human genome sequence is ascertained, genome-wide screening with microarray technology will gain eminence in the clinical scenario, yield better solutions and bring the concept of personalized medicine in cancer closer to reality than ever before.
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Robert J. [Pharmacogenetics and pharmacogenomics of cancers]. ACTA ACUST UNITED AC 2004; 52:332-7. [PMID: 15261376 DOI: 10.1016/j.patbio.2003.09.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2003] [Accepted: 09/05/2003] [Indexed: 10/26/2022]
Abstract
Sequencing the human genome brings new tools for the individualisation of cancer chemotherapy, firstly thanks to the identification of polymorphisms of genes involved in anticancer drug metabolism or activity (Pharmacogenetics), and secondly thanks to the determination of tumour gene expression profiles and their relationship to chemosensitivity and chemoresistance (Pharmacogenomics). A few functional polymorphisms have been known for a long time (thiopurine methyltransferase, glutathion S-transferases), but several new ones have been identified recently, at the level of the genes encoding drug targets (thymidylate synthase), at the level of DNA repair enzymes (XPD) or at the level of transport proteins (MDR1). On the other hand, the research of correlations between gene expression profiles and chemosensitivity has been performed on the in vitro models of the National Cancer Institute and may allow crucial improvements in the identification of patients who would best take advantage of a specific chemotherapy. Clinical trials, first on a retrospective basis, then on a prospective one, are implemented to validate this approach.
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Affiliation(s)
- J Robert
- Institut Bergonié et université Victor-Segalen, 229, cours de l'Argonne, 33076 Bordeaux, France.
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Abstract
The emerging and rapidly growing field of molecular and genomic imaging is providing new opportunities to directly visualize the biology of living organisms. By combining our growing knowledge regarding the role of specific genes and proteins in human health and disease, with novel ways to target these entities in a manner that produces an externally detectable signal, it is becoming increasingly possible to visualize and quantify specific biological processes in a non-invasive manner. All the major imaging modalities are contributing to this new field, each with its unique mechanisms for generating contrast and trade-offs in spatial resolution, temporal resolution and sensitivity with respect to the biological process of interest. Much of the development in molecular imaging is currently being carried out in animal models of disease, but as the field matures and with the development of more individualized medicine and the molecular targeting of new therapeutics, clinical translation is inevitable and will likely forever change our approach to diagnostic imaging. This review provides an introduction to the field of molecular imaging for readers who are not experts in the biological sciences and discusses the opportunities to apply a broad range of imaging technologies to better understand the biology of human health and disease. It also provides a brief review of the imaging technology (particularly for x-ray, nuclear and optical imaging) that is being developed to support this new field.
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Affiliation(s)
- Simon R Cherry
- Department of Biomedical Engineering, University of California, Davis, CA, USA.
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Singletary SE, Dowlatshahi K, Dooley W, Hollenbeck ST, Kern K, Kuerer H, Newman LA, Simmons R, Whitworth P. Minimally invasive operation for breast cancer. Curr Probl Surg 2004; 41:394-447. [PMID: 15114298 DOI: 10.1016/j.cpsurg.2003.12.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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39
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Heng HHQ, Stevens JB, Liu G, Bremer SW, Ye CJ. Imaging genome abnormalities in cancer research. CELL & CHROMOSOME 2004; 3:1. [PMID: 14720303 PMCID: PMC331418 DOI: 10.1186/1475-9268-3-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2003] [Accepted: 01/13/2004] [Indexed: 02/09/2023]
Abstract
Increasing attention is focusing on chromosomal and genome structure in cancer research due to the fact that genomic instability plays a principal role in cancer initiation, progression and response to chemotherapeutic agents. The integrity of the genome (including structural, behavioral and functional aspects) of normal and cancer cells can be monitored with direct visualization by using a variety of cutting edge molecular cytogenetic technologies that are now available in the field of cancer research. Examples are presented in this review by grouping these methodologies into four categories visualizing different yet closely related major levels of genome structures. An integrated discussion is also presented on several ongoing projects involving the illustration of mitotic and meiotic chromatin loops; the identification of defective mitotic figures (DMF), a new type of chromosomal aberration capable of monitoring condensation defects in cancer; the establishment of a method that uses Non-Clonal Chromosomal Aberrations (NCCAs) as an index to monitor genomic instability; and the characterization of apoptosis related chromosomal fragmentations caused by drug treatments.
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Affiliation(s)
- Henry HQ Heng
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI, USA
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI, USA
| | - Joshua B Stevens
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Guo Liu
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Steven W Bremer
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
| | - Christine J Ye
- Center for Molecular Medicine and Genetics, Wayne State University School of Medicine, Detroit, MI, USA
- SeeDNA Biotech Inc, Windsor, Ontario, Canada
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Rook MS, Delach SM, Deyneko G, Worlock A, Wolfe JL. Whole genome amplification of DNA from laser capture-microdissected tissue for high-throughput single nucleotide polymorphism and short tandem repeat genotyping. THE AMERICAN JOURNAL OF PATHOLOGY 2004; 164:23-33. [PMID: 14695315 PMCID: PMC1602222 DOI: 10.1016/s0002-9440(10)63092-1] [Citation(s) in RCA: 77] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 09/22/2003] [Indexed: 11/20/2022]
Abstract
Genome-wide screening of genetic alterations between normal and cancer cells, as well as among subgroups of tumors, is important for establishing molecular mechanism and classification of cancer. Gene silencing through loss of heterozygosity is widely observed in cancer cells and detectable by analyzing allelic loss of single nucleotide polymorphism and/or short tandem repeat markers. To use minute quantities of DNA that are available through laser capture microdissection (LCM) of cancer cells, a whole genome amplification method that maintains locus and allele balance is essential. We have successfully used a ø29 polymerase-based isothermal whole genome amplification method to amplify LCM DNA using a proteinase K lysis procedure coupled with a pooling strategy. Through single nucleotide polymorphism and short tandem repeat genotype analysis we demonstrate that using pooled DNA from two or three separate amplification reactions significantly reduces any allele bias introduced during amplification. This strategy is especially effective when using small quantities of source DNA. Although a convenient alkaline lysis DNA extraction procedure provided satisfactory results from using 1500 to 3000 LCM cells, proteinase K digestion was superior for lower cell numbers. Accurate genotyping is achieved with as few as 100 cells when both proteinase K extraction and pooling are applied.
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Frühwald MC. DNA methylation patterns in cancer: novel prognostic indicators? AMERICAN JOURNAL OF PHARMACOGENOMICS : GENOMICS-RELATED RESEARCH IN DRUG DEVELOPMENT AND CLINICAL PRACTICE 2003; 3:245-60. [PMID: 12930158 DOI: 10.2165/00129785-200303040-00003] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
DNA methylation is an epigenetic phenomenon influencing the normal function of DNA and its scaffolding proteins. Especially in cancer, aberrant methylation patterns may contribute to the disease process by the induction of point mutations, activation of inactive genes through hypomethylation of promoters, and transcriptional inactivation through a complex interplay with histone acetylation and other inhibitory mechanisms. Aberrant methylation patterns have been evaluated as tools in the management of patients with cancer. The predictive value, the therapeutic manipulation and the prognostic significance of aberrantly methylated gene loci have been tested in hematological as well as in solid neoplasias in adults and children. A seemingly insurmountable wealth of data has been generated, however, data on clinical associations are sometimes presented in an almost incautious fashion. Nevertheless, some genes like p15INK4B in myelodysplastic syndrome (MDS) and p16INK4A in some lung cancer subtypes have been shown to confer a certain prognosis. In selected cases the data have been confirmed by independent studies. Assays have been developed that can be used by almost any clinical laboratory (e.g. methylation-specific PCR) for the rapid and affordable screening of tumors for aberrant methylation. The study of aberrant methylation patterns has successfully entered the arena of relevant clinical applications. Importantly, methylation does not only hold the potential for being 'just another' biomarker, but also, as it can be reverted chemically, it is a phenomenon that holds great promise for therapeutic exploitation.
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Affiliation(s)
- Michael C Frühwald
- Department of Pediatric Hematology and Oncology, University Children's Hospital Muenster, Albert-Schweitzer-Strasse 33, Muenster, Germany.
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Ley TJ, Minx PJ, Walter MJ, Ries RE, Sun H, McLellan M, DiPersio JF, Link DC, Tomasson MH, Graubert TA, McLeod H, Khoury H, Watson M, Shannon W, Trinkaus K, Heath S, Vardiman JW, Caligiuri MA, Bloomfield CD, Milbrandt JD, Mardis ER, Wilson RK. A pilot study of high-throughput, sequence-based mutational profiling of primary human acute myeloid leukemia cell genomes. Proc Natl Acad Sci U S A 2003; 100:14275-80. [PMID: 14614138 PMCID: PMC283582 DOI: 10.1073/pnas.2335924100] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In this pilot study, we used primary human acute myeloid leukemia (AML) cell genomes as templates for exonic PCR amplification, followed by high-throughput resequencing, analyzing approximately 7 million base pairs of DNA from 140 AML samples and 48 controls. We identified six previously described, and seven previously undescribed sequence changes that may be relevant for AML pathogenesis. Because the sequencing templates were generated from primary AML cells, the technique favors the detection of mutations from the most dominant clones within the tumor cell mixture. This strategy represents a viable approach for the detection of potentially relevant, nonrandom mutations in primary human cancer cell genomes.
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Affiliation(s)
- Timothy J Ley
- Department of Medicine, Siteman Cancer Center, Washington University School of Medicine, St. Louis, MO 63110, USA.
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Ahluwalia R, Freimuth R, McLeod HL, Marsh S. Use of Pyrosequencing to Detect Clinically Relevant Polymorphisms in Dihydropyrimidine Dehydrogenase. Clin Chem 2003; 49:1661-4. [PMID: 14500593 DOI: 10.1373/49.10.1661] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Ranjeet Ahluwalia
- Washington University School of Medicine, Division of Oncology, St. Louis, MO 63110, USA
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Abstract
BACKGROUND Leiomyosarcomas (LMS) are a common subtype of soft tissue sarcoma. The molecular causes of the disease remain unclear. METHODS In the current study, gene expression in LMS, leiomyomas, and normal myometrium was examined. RNA was prepared and gene expression was determined using microarray analysis arrays containing approximately 12,000 known genes and 48,000 expressed sequence tags (ESTs). RESULTS A number of genes were found to be differentially expressed in these sample sets, and six genes including cyclin-dependent kinase inhibitor 2A, diaphanous (Drosophila homolog) 3, doublecortin, calpain 6, interleukin-17B, and proteolipid 1 were found to be overexpressed in LMS compared with normal myometrium and 18 other tissues. Sets of genes were identified whose expression could be used to cluster samples with either LMS, leiomyomas, or normal myometrium. CONCLUSIONS The authors concluded that differences in gene expression can be detected between LMS and leiomyomas, normal myometrium, and other tissues, and that these changes in gene expression may yield clues with regard to the pathophysiology of leiomyosarcoma.
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Affiliation(s)
- Keith M Skubitz
- Department of Medicine, University of Minnesota Medical School and the Masonic Cancer Center, MMC 286, University Hospital, 420 Delaware Street SE, Minneapolis, MN 55455, USA.
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45
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Cheng C, Kimmel R, Neiman P, Zhao LP. Array rank order regression analysis for the detection of gene copy-number changes in human cancer. Genomics 2003; 82:122-9. [PMID: 12837263 DOI: 10.1016/s0888-7543(03)00122-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
cDNA microarray technology has been applied to the detection of DNA copy-number changes in malignant tumors. Test and control genomic DNA samples are differentially labeled and cohybridized to a spotted cDNA microarray. The ratio of test to control fluorescence intensities for each spot reflects relative gene copy number. The low signal-to-noise ratios of this assay and the variable levels of gene amplification and deletion among tumors hamper the detection of deviations from the diploid complement. We describe a regression-based statistical method to test for altered copy number on each gene and apply the technique to copy-number profiles in 10 thyroid tumors. We show that a novel transformation of fluorescence ratios into array rank order efficiently normalizes the heterogeneity among copy-number profiles and improves the reproducibility of the results. Array rank order regression analysis enhances the detection of consistent changes in gene copy number in solid tumors by cDNA microarray-based comparative genome hybridization.
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Affiliation(s)
- Chun Cheng
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109, USA
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46
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Bañez LL, Prasanna P, Sun L, Ali A, Zou Z, Adam BL, McLeod DG, Moul JW, Srivastava S. Diagnostic potential of serum proteomic patterns in prostate cancer. J Urol 2003; 170:442-6. [PMID: 12853795 DOI: 10.1097/01.ju.0000069431.95404.56] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
PURPOSE The serum prostate specific antigen test has been widely used in the last decade as an effective screening tool for prostate cancer (CaP). However, the high false-positive rate of the serum prostate specific antigen test necessitates the development of more accurate diagnostic and prognostic biomarkers for CaP. Promising diagnostic potential of serum protein patterns detected by surface enhanced laser desorption/ionization time of flight mass spectrometry for CaP has recently been reported. Independent evaluation of this new technology is warranted to realize its translational utility. We determined whether serum protein profiling by surface enhanced laser desorption/ionization time of flight mass spectrometry and a decision tree algorithm classification system could accurately discriminate between patients with CaP and unaffected individuals. MATERIALS AND METHODS Proteomic spectra of crude serum were generated using the Ciphergen ProteinChip System and pattern detection was performed using Biomarker Patterns Software (Ciphergen Biosystems, Inc., Fremont, California). A total of 106 patients with CaP and 56 controls were randomly allocated to a training set and a test set. The training set, which consisted of 44 patients with cancer and 30 controls, was used to build a decision tree algorithm. The test set, which consisted of 62 patients with cancer and 26 controls, was used in blinded fashion to validate the decision tree. RESULTS Accuracy of classification using the test set was 67% and 42% for the weak cation exchange array and the copper metal affinity capture array, respectively. Combined spectral data from the weak cation exchange and copper metal affinity capture arrays generated an algorithm that achieved 85% sensitivity and 85% specificity for the detection of CaP. CONCLUSIONS These preliminary findings support recent observations that complex protein profiles have promising potential for the early detection of CaP and warrant future studies with streamlined technology. Furthermore, the combined effect of using 2 array types can greatly enhance the ability of protein profile patterns, suggesting the potential usefulness of alternative approaches to evaluate this new emerging technology.
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Affiliation(s)
- Lionel L Bañez
- Department of Surgery, Uniformed Armed Services University of the Health Sciences, Bethesda, Maryland, USA
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47
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Wunderlich V. JMM---past and present. Chromosomes and cancer: Theodor Boveri's predictions 100 years later. J Mol Med (Berl) 2002; 80:545-8. [PMID: 12226736 DOI: 10.1007/s00109-002-0374-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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48
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Buetow KH, Klausner RD, Fine H, Kaplan R, Singer DS, Strausberg RL. Cancer Molecular Analysis Project: weaving a rich cancer research tapestry. Cancer Cell 2002; 1:315-8. [PMID: 12086845 DOI: 10.1016/s1535-6108(02)00065-x] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The Cancer Molecular Analysis Project (CMAP) of the NCI is integrating diverse cancer research data to elucidate fundamental etiologic processes, enable development of novel therapeutic approaches, and facilitate the bridging of basic and clinical science.
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Affiliation(s)
- Kenneth H Buetow
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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