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Tie J, Kinde I, Wang Y, Wong HL, Roebert J, Christie M, Tacey M, Wong R, Singh M, Karapetis CS, Desai J, Tran B, Strausberg RL, Diaz LA, Papadopoulos N, Kinzler KW, Vogelstein B, Gibbs P. Circulating tumor DNA as an early marker of therapeutic response in patients with metastatic colorectal cancer. Ann Oncol 2015; 26:1715-22. [PMID: 25851626 DOI: 10.1093/annonc/mdv177] [Citation(s) in RCA: 459] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 03/20/2015] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Early indicators of treatment response in metastatic colorectal cancer (mCRC) could conceivably be used to optimize treatment. We explored early changes in circulating tumor DNA (ctDNA) levels as a marker of therapeutic efficacy. PATIENTS AND METHODS This prospective study involved 53 mCRC patients receiving standard first-line chemotherapy. Both ctDNA and CEA were assessed in plasma collected before treatment, 3 days after treatment and before cycle 2. Computed tomography (CT) scans were carried out at baseline and 8-10 weeks and were centrally assessed using RECIST v1.1 criteria. Tumors were sequenced using a panel of 15 genes frequently mutated in mCRC to identify candidate mutations for ctDNA analysis. For each patient, one tumor mutation was selected to assess the presence and the level of ctDNA in plasma samples using a digital genomic assay termed Safe-SeqS. RESULTS Candidate mutations for ctDNA analysis were identified in 52 (98.1%) of the tumors. These patient-specific candidate tissue mutations were detectable in the cell-free DNA from the plasma of 48 of these 52 patients (concordance 92.3%). Significant reductions in ctDNA (median 5.7-fold; P < 0.001) levels were observed before cycle 2, which correlated with CT responses at 8-10 weeks (odds ratio = 5.25 with a 10-fold ctDNA reduction; P = 0.016). Major reductions (≥10-fold) versus lesser reductions in ctDNA precycle 2 were associated with a trend for increased progression-free survival (median 14.7 versus 8.1 months; HR = 1.87; P = 0.266). CONCLUSIONS ctDNA is detectable in a high proportion of treatment naïve mCRC patients. Early changes in ctDNA during first-line chemotherapy predict the later radiologic response.
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Affiliation(s)
- J Tie
- Division of Systems Biology and Personalised Medicine, Walter and Eliza Hall Institute of Medical Research, Melbourne Department of Medical Oncology, Western Hospital, Melbourne Department of Medical Oncology, The Royal Melbourne Hospital, Melbourne Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Melbourne, Australia
| | - I Kinde
- Ludwig Center for Cancer Genetics and Therapeutics, Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, USA
| | - Y Wang
- Ludwig Center for Cancer Genetics and Therapeutics, Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, USA
| | - H L Wong
- Division of Systems Biology and Personalised Medicine, Walter and Eliza Hall Institute of Medical Research, Melbourne Department of Medical Oncology, The Royal Melbourne Hospital, Melbourne Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Melbourne, Australia Faculty of Medicine, Nursing and Health Sciences, Monash University, Eastern Health Clinical School, Melbourne
| | | | - M Christie
- Division of Systems Biology and Personalised Medicine, Walter and Eliza Hall Institute of Medical Research, Melbourne Department of Medical Oncology, The Royal Melbourne Hospital, Melbourne Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Melbourne, Australia
| | - M Tacey
- Melbourne EpiCentre, Department of Medicine, The University of Melbourne, Melbourne
| | - R Wong
- Faculty of Medicine, Nursing and Health Sciences, Monash University, Eastern Health Clinical School, Melbourne
| | - M Singh
- Andrew Love Cancer Centre, Barwon Health, Geelong
| | - C S Karapetis
- Department of Medical Oncology, Flinders University, Adelaide, Australia
| | - J Desai
- Division of Systems Biology and Personalised Medicine, Walter and Eliza Hall Institute of Medical Research, Melbourne Department of Medical Oncology, The Royal Melbourne Hospital, Melbourne Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Melbourne, Australia
| | - B Tran
- Division of Systems Biology and Personalised Medicine, Walter and Eliza Hall Institute of Medical Research, Melbourne Department of Medical Oncology, Western Hospital, Melbourne Department of Medical Oncology, The Royal Melbourne Hospital, Melbourne Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Melbourne, Australia
| | | | - L A Diaz
- Ludwig Center for Cancer Genetics and Therapeutics, Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, USA
| | - N Papadopoulos
- Ludwig Center for Cancer Genetics and Therapeutics, Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, USA
| | - K W Kinzler
- Ludwig Center for Cancer Genetics and Therapeutics, Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, USA
| | - B Vogelstein
- Ludwig Center for Cancer Genetics and Therapeutics, Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, USA
| | - P Gibbs
- Division of Systems Biology and Personalised Medicine, Walter and Eliza Hall Institute of Medical Research, Melbourne Department of Medical Oncology, Western Hospital, Melbourne Department of Medical Oncology, The Royal Melbourne Hospital, Melbourne Faculty of Medicine Dentistry and Health Sciences, The University of Melbourne, Melbourne, Australia Ludwig Institute for Cancer Research, New York, USA Ludwig Institute for Cancer Research, Melbourne, Australia
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Christie M, Jorissen RN, Mouradov D, Sakthianandeswaren A, Li S, Day F, Tsui C, Lipton L, Desai J, Jones IT, McLaughlin S, Ward RL, Hawkins NJ, Ruszkiewicz AR, Moore J, Burgess AW, Busam D, Zhao Q, Strausberg RL, Simpson AJ, Tomlinson IPM, Gibbs P, Sieber OM. Different APC genotypes in proximal and distal sporadic colorectal cancers suggest distinct WNT/β-catenin signalling thresholds for tumourigenesis. Oncogene 2013; 32:4675-82. [PMID: 23085758 PMCID: PMC3787794 DOI: 10.1038/onc.2012.486] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2012] [Revised: 08/20/2012] [Accepted: 09/04/2012] [Indexed: 01/05/2023]
Abstract
Biallelic protein-truncating mutations in the adenomatous polyposis coli (APC) gene are prevalent in sporadic colorectal cancer (CRC). Mutations may not be fully inactivating, instead producing WNT/β-catenin signalling levels 'just-right' for tumourigenesis. However, the spectrum of optimal APC genotypes accounting for both hits, and the influence of clinicopathological features on genotype selection remain undefined. We analysed 630 sporadic CRCs for APC mutations and loss of heterozygosity (LOH) using sequencing and single-nucleotide polymorphism microarrays, respectively. Truncating APC mutations and/or LOH were detected in 75% of CRCs. Most truncating mutations occurred within a mutation cluster region (MCR; codons 1282-1581) leaving 1-3 intact 20 amino-acid repeats (20AARs) and abolishing all Ser-Ala-Met-Pro (SAMP) repeats. Cancers commonly had one MCR mutation plus either LOH or another mutation 5' to the MCR. LOH was associated with mutations leaving 1 intact 20AAR. MCR mutations leaving 1 vs 2-3 intact 20AARs were associated with 5' mutations disrupting or leaving intact the armadillo-repeat domain, respectively. Cancers with three hits had an over-representation of mutations upstream of codon 184, in the alternatively spliced region of exon 9, and 3' to the MCR. Microsatellite unstable cancers showed hyper-mutation at MCR mono- and di-nucleotide repeats, leaving 2-3 intact 20AARs. Proximal and distal cancers exhibited different preferred APC genotypes, leaving a total of 2 or 3 and 0 to 2 intact 20AARs, respectively. In conclusion, APC genotypes in sporadic CRCs demonstrate 'fine-tuned' interdependence of hits by type and location, consistent with selection for particular residual levels of WNT/β-catenin signalling, with different 'optimal' thresholds for proximal and distal cancers.
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Affiliation(s)
- M Christie
- Ludwig Colon Cancer Initiative Laboratory, Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Victoria, Australia
- Department of Surgery, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - R N Jorissen
- Ludwig Colon Cancer Initiative Laboratory, Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - D Mouradov
- Ludwig Colon Cancer Initiative Laboratory, Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - A Sakthianandeswaren
- Ludwig Colon Cancer Initiative Laboratory, Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - S Li
- Ludwig Colon Cancer Initiative Laboratory, Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - F Day
- Ludwig Colon Cancer Initiative Laboratory, Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Victoria, Australia
- Department of Surgery, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - C Tsui
- Ludwig Colon Cancer Initiative Laboratory, Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - L Lipton
- Ludwig Colon Cancer Initiative Laboratory, Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Victoria, Australia
- Department of Surgery, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Royal Melbourne Hospital, Parkville, Victoria, Australia
- Department of Medical Oncology, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - J Desai
- Ludwig Colon Cancer Initiative Laboratory, Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Victoria, Australia
- Department of Medical Oncology, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - I T Jones
- Department of Colorectal Surgery, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - S McLaughlin
- Department of Colorectal Surgery, Western Hospital, Footscray, Victoria, Australia
| | - R L Ward
- Lowy Cancer Research Centre, Prince of Wales Clinical School, University of New South Wales, Sydney, New South Wales, Australia
| | - N J Hawkins
- Department of Pathology, School of Medical Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - A R Ruszkiewicz
- Pathology Department, Institute of Medical and Veterinary Science, Adelaide, South Australia, Australia
| | - J Moore
- Department of Colorectal Surgery, Royal Adelaide Hospital, Adelaide, South Australia, Australia
| | - A W Burgess
- Epithelial Biology Laboratory, Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - D Busam
- J Craig Venter Institute, Rockville, MD, USA
| | - Q Zhao
- J Craig Venter Institute, Rockville, MD, USA
| | - R L Strausberg
- Department of Neurosurgery, Ludwig Collaborative Laboratory for Cancer Biology and Therapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Ludwig Institute for Cancer Research Ltd, New York, NY, USA
| | - A J Simpson
- Department of Neurosurgery, Ludwig Collaborative Laboratory for Cancer Biology and Therapy, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Ludwig Institute for Cancer Research Ltd, New York, NY, USA
| | - I P M Tomlinson
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, Oxford, OX, UK
| | - P Gibbs
- Ludwig Colon Cancer Initiative Laboratory, Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Victoria, Australia
- Department of Surgery, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Royal Melbourne Hospital, Parkville, Victoria, Australia
- Department of Medical Oncology, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - O M Sieber
- Ludwig Colon Cancer Initiative Laboratory, Ludwig Institute for Cancer Research, Royal Melbourne Hospital, Parkville, Victoria, Australia
- Department of Surgery, Faculty of Medicine, Dentistry and Health Sciences, University of Melbourne, Royal Melbourne Hospital, Parkville, Victoria, Australia
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Lawniczak MKN, Emrich SJ, Holloway AK, Regier AP, Olson M, White B, Redmond S, Fulton L, Appelbaum E, Godfrey J, Farmer C, Chinwalla A, Yang SP, Minx P, Nelson J, Kyung K, Walenz BP, Garcia-Hernandez E, Aguiar M, Viswanathan LD, Rogers YH, Strausberg RL, Saski CA, Lawson D, Collins FH, Kafatos FC, Christophides GK, Clifton SW, Kirkness EF, Besansky NJ. Widespread divergence between incipient Anopheles gambiae species revealed by whole genome sequences. Science 2010; 330:512-4. [PMID: 20966253 DOI: 10.1126/science.1195755] [Citation(s) in RCA: 223] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
The Afrotropical mosquito Anopheles gambiae sensu stricto, a major vector of malaria, is currently undergoing speciation into the M and S molecular forms. These forms have diverged in larval ecology and reproductive behavior through unknown genetic mechanisms, despite considerable levels of hybridization. Previous genome-wide scans using gene-based microarrays uncovered divergence between M and S that was largely confined to gene-poor pericentromeric regions, prompting a speciation-with-ongoing-gene-flow model that implicated only about 3% of the genome near centromeres in the speciation process. Here, based on the complete M and S genome sequences, we report widespread and heterogeneous genomic divergence inconsistent with appreciable levels of interform gene flow, suggesting a more advanced speciation process and greater challenges to identify genes critical to initiating that process.
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Affiliation(s)
- M K N Lawniczak
- Division of Cell and Molecular Biology, Imperial College London, South Kensington Campus, London SW7 2AZ, UK
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4
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Chain PSG, Grafham DV, Fulton RS, Fitzgerald MG, Hostetler J, Muzny D, Ali J, Birren B, Bruce DC, Buhay C, Cole JR, Ding Y, Dugan S, Field D, Garrity GM, Gibbs R, Graves T, Han CS, Harrison SH, Highlander S, Hugenholtz P, Khouri HM, Kodira CD, Kolker E, Kyrpides NC, Lang D, Lapidus A, Malfatti SA, Markowitz V, Metha T, Nelson KE, Parkhill J, Pitluck S, Qin X, Read TD, Schmutz J, Sozhamannan S, Sterk P, Strausberg RL, Sutton G, Thomson NR, Tiedje JM, Weinstock G, Wollam A, Detter JC. Genomics. Genome project standards in a new era of sequencing. Science 2009; 326:236-7. [PMID: 19815760 DOI: 10.1126/science.1180614] [Citation(s) in RCA: 286] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- P S G Chain
- U.S. Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA.
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Abstract
The cost of sequencing and genotyping is aggressively decreasing, enabling pervasive personalized genomic screening for drug reactions. Drug-metabolizing genes have been characterized sufficiently to enable practitioners to go beyond simplistic ethnic characterization and into the precisely targeted world of personal genomics. We examine six drug-metabolizing genes in J. Craig Venter and James Watson, two Caucasian men whose genomes were recently sequenced. Their genetic differences underscore the importance of personalized genomics over a race-based approach to medicine. To attain truly personalized medicine, the scientific community must aim to elucidate the genetic and environmental factors that contribute to drug reactions and not be satisfied with a simple race-based approach.
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Affiliation(s)
- P C Ng
- J. Craig Venter Institute, Rockville, Maryland, USA.
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6
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Abstract
This overview presents vectors and host strains that are available to direct gene expression in S. cerevisiae, including information on promoters, vector maintenance and copy number, transcription terminators, and selectable markers. Challenges to the expression of foreign proteins are also covered, including attainment of desired production yield, production of protein with appropriate post-translational modifications, conformation and function, and secretion to the extracellular medium.
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7
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Leethanakul C, Knezevic V, Patel V, Amornphimoltham P, Gillespie J, Shillitoe EJ, Emko P, Park MH, Emmert-Buck MR, Strausberg RL, Krizman DB, Gutkind JS. Gene discovery in oral squamous cell carcinoma through the Head and Neck Cancer Genome Anatomy Project: confirmation by microarray analysis. Oral Oncol 2003; 39:248-58. [PMID: 12618197 DOI: 10.1016/s1368-8375(02)00107-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The near completion of the human genome project and the recent development of novel, highly sensitive high-throughput techniques have now afforded the unique opportunity to perform a comprehensive molecular characterization of normal, precancerous, and malignant cells, including those derived from squamous carcinomas of the head and neck (HNSCC). As part of these efforts, representative cDNA libraries from patient sets, comprising of normal and malignant squamous epithelium, were generated and contributed to the Head and Neck Cancer Genome Anatomy Project (HN-CGAP). Initial analysis of the sequence information indicated the existence of many novel genes in these libraries [Oral Oncol 36 (2000) 474]. In this study, we surveyed the available sequence information using bioinformatic tools and identified a number of known genes that were differentially expressed in normal and malignant epithelium. Furthermore, this effort resulted in the identification of 168 novel genes. Comparison of these clones to the human genome identified clusters in loci that were not previously recognized as being altered in HNSCC. To begin addressing which of these novel genes are frequently expressed in HNSCC, their DNA was used to construct an oral-cancer-specific microarray, which was used to hybridize alpha-(33)P dCTP labeled cDNA derived from five HNSCC patient sets. Initial assessment demonstrated 10 clones to be highly expressed (>2-fold) in the normal squamous epithelium, while 14 were highly represented in the malignant counterpart, in three of the five patient sets, thus suggesting that a subset of these newly discovered transcripts might be highly expressed in this tumor type. These efforts, together with other multi-institutional genomic and proteomic initiatives are expected to contribute to the complete understanding of the molecular pathogenesis of HNSCCs, thus helping to identify new markers for the early detection of preneoplastic lesions and novel targets for pharmacological intervention in this disease.
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Affiliation(s)
- C Leethanakul
- Oral and Pharyngeal Cancer Branch, National Institute of Dental and Craniofacial Research, 30 Convent Drive, Building 30, Room 212, Bethesda, MD 20892-4340, USA
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8
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Strausberg RL, Camargo AA, Riggins GJ, Schaefer CF, de Souza SJ, Grouse LH, Lal A, Buetow KH, Boon K, Greenhut SF, Simpson AJG. An international database and integrated analysis tools for the study of cancer gene expression. Pharmacogenomics J 2003; 2:156-64. [PMID: 12082587 DOI: 10.1038/sj.tpj.6500103] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2002] [Revised: 02/21/2002] [Accepted: 02/27/2002] [Indexed: 11/10/2022]
Abstract
Researchers working collaboratively in Brazil and the United States have assembled an International Database of Cancer Gene Expression. Several strategies have been employed to generate gene expression data including expressed sequence tags (ESTs), serial analysis of gene expression (SAGE), and open reading-frame expressed sequence tags (ORESTES). The database contains six million gene tags that reflect the gene expression profiles in a wide variety of cancerous tissues and their normal counterparts. All sequences are deposited in the public databases, GenBank and SAGEmap. A suite of informatics tools was designed to facilitate in silico analysis of the gene expression datasets and are available through the NCI Cancer Genome Anatomy Project web site (http://cgap.nci.nih.gov).
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Abstract
The Cancer Genome Anatomy Project (CGAP) was designed and implemented to provide public datasets, material resources and informatics tools to serve as a platform to support the elucidation of the molecular signatures of cancer. This overview of CGAP describes the status of this effort to develop resources based on gene expression, polymorphism identification and chromosome aberrations, and we describe a variety of analytical tools designed to facilitate in silico analysis of these datasets.
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Affiliation(s)
- R L Strausberg
- Cancer Genomics Office, National Cancer Institute, Bethesda, MD 20892, USA.
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Lal A, Peters H, St Croix B, Haroon ZA, Dewhirst MW, Strausberg RL, Kaanders JH, van der Kogel AJ, Riggins GJ. Transcriptional response to hypoxia in human tumors. J Natl Cancer Inst 2001; 93:1337-43. [PMID: 11535709 DOI: 10.1093/jnci/93.17.1337] [Citation(s) in RCA: 233] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND The presence of hypoxic regions within solid tumors is associated with a more malignant tumor phenotype and worse prognosis. To obtain a blood supply and protect against cellular damage and death, oxygen-deprived cells in tumors alter gene expression, resulting in resistance to therapy. To investigate the mechanisms by which cancer cells adapt to hypoxia, we looked for novel hypoxia-induced genes. METHODS The transcriptional response to hypoxia in human glioblastoma cells was quantified with the use of serial analysis of gene expression. The time course of gene expression in response to hypoxia in a panel of various human tumor cell lines was measured by real-time polymerase chain reaction. Hypoxic regions of human carcinomas were chemically marked with pimonidazole. Immunohistochemistry and in situ hybridization were used to examine gene expression in the tumor's hypoxic regions. RESULTS From the 24 504 unique transcripts expressed, 10 new hypoxia-regulated genes were detected-all induced, to a greater extent than vascular endothelial growth factor, a hypoxia-induced mitogen that promotes blood vessel growth. These genes also responded to hypoxia in breast and colon cancer cells and were activated by hypoxia-inducible factor 1, a key regulator of hypoxic responses. In tumors, gene expression was limited to hypoxic regions. Induced genes included hexabrachion (an extracellular matrix glycoprotein), stanniocalcin 1 (a calcium homeostasis protein), and an angiopoietin-related gene. CONCLUSIONS We have identified the genes that are transcriptionally activated within hypoxic malignant cells, a crucial first step in understanding the complex interactions driving hypoxia response. Within our catalogue of hypoxia-responsive genes are novel candidates for hypoxia-driven angiogenesis.
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Affiliation(s)
- A Lal
- Department of Pathology, Duke University Medical Center, Durham, NC 27710, USA
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12
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Abstract
The Cancer Genome Anatomy Project (CGAP) has built informational, technological, and physical resources to interface genomics with basic and clinical cancer research. The CGAP web site (http://cgap.nci.nih.gov) provides informatics tools for in silico analysis of the CGAP datasets as well as information for accessing each of the CGAP resources. Published in 2001 by John Wiley & Sons, Ltd.
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13
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Abstract
The Cancer Genome Anatomy Project (CGAP) is a collaborative network of cancer researchers with a common goal: to decipher the genetic changes that occur during cancer formation and progression. The project brings together several recent technologies capable of high-throughput analysis to help achieve this goal. Automated sequencing of cDNA libraries is a primary focus and is geared towards providing a comprehensive and annotated set of human and mouse transcribed sequences. This effort includes full-length transcript sequence generated by CGAP's new Mammalian Gene Collection initiative. Single nucleotide polymorphisms (SNPs) within human gene sequences (Genetic Annotation Initiative) and chromosomal rearrangements within cancer cells (Cancer Chromosome Aberration Project) are also being cataloged as part of CGAP. Finally, to help determine gene expression patterns related to cancer, CGAP provides a quantitative catalog of data through its SAGEmap initiative. The genome and genetic analysis tools listed in this review are all freely distributed by CGAP (http://cgap.nci.nih.gov/) without restriction.
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Affiliation(s)
- G J Riggins
- Duke University Medical Center, Durham, NC 27710, USA.
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14
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Emmert-Buck MR, Strausberg RL, Krizman DB, Bonaldo MF, Bonner RF, Bostwick DG, Brown MR, Buetow KH, Chuaqui RF, Cole KA, Duray PH, Englert CR, Gillespie JW, Greenhut S, Grouse L, Hillier LW, Katz KS, Klausner RD, Kuznetzov V, Lash AE, Lennon G, Linehan WM, Liotta LA, Marra MA, Munson PJ, Ornstein DK, Prabhu VV, Prang C, Schuler GD, Soares MB, Tolstoshev CM, Vocke CD, Waterston RH. Molecular profiling of clinical tissues specimens: feasibility and applications. J Mol Diagn 2001; 2:60-6. [PMID: 11272889 PMCID: PMC1906897 DOI: 10.1016/s1525-1578(10)60617-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- M R Emmert-Buck
- Pathogenetics Unit, Laboratory of Pathology, National Cancer Institute, Bethesda, Maryland, USA.
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15
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BAC Resource Consortium T, Cheung VG, Nowak N, Jang W, Kirsch IR, Zhao S, Chen XN, Furey TS, Kim UJ, Kuo WL, Olivier M, Conroy J, Kasprzyk A, Massa H, Yonescu R, Sait S, Thoreen C, Snijders A, Lemyre E, Bailey JA, Bruzel A, Burrill WD, Clegg SM, Collins S, Dhami P, Friedman C, Han CS, Herrick S, Lee J, Ligon AH, Lowry S, Morley M, Narasimhan S, Osoegawa K, Peng Z, Plajzer-Frick I, Quade BJ, Scott D, Sirotkin K, Thorpe AA, Gray JW, Hudson J, Pinkel D, Ried T, Rowen L, Shen-Ong GL, Strausberg RL, Birney E, Callen DF, Cheng JF, Cox DR, Doggett NA, Carter NP, Eichler EE, Haussler D, Korenberg JR, Morton CC, Albertson D, Schuler G, de Jong PJ, Trask BJ. Integration of cytogenetic landmarks into the draft sequence of the human genome. Nature 2001; 409:953-8. [PMID: 11237021 PMCID: PMC7845515 DOI: 10.1038/35057192] [Citation(s) in RCA: 203] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We have placed 7,600 cytogenetically defined landmarks on the draft sequence of the human genome to help with the characterization of genes altered by gross chromosomal aberrations that cause human disease. The landmarks are large-insert clones mapped to chromosome bands by fluorescence in situ hybridization. Each clone contains a sequence tag that is positioned on the genomic sequence. This genome-wide set of sequence-anchored clones allows structural and functional analyses of the genome. This resource represents the first comprehensive integration of cytogenetic, radiation hybrid, linkage and sequence maps of the human genome; provides an independent validation of the sequence map and framework for contig order and orientation; surveys the genome for large-scale duplications, which are likely to require special attention during sequence assembly; and allows a stringent assessment of sequence differences between the dark and light bands of chromosomes. It also provides insight into large-scale chromatin structure and the evolution of chromosomes and gene families and will accelerate our understanding of the molecular bases of human disease and cancer.
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Affiliation(s)
| | - V. G. Cheung
- grid.239552.a0000 0001 0680 8770Department of Pediatrics, University of Pennsylvania, The Children's Hospital of Philadelphia, 3516 Civic Center Boulevard, ARC 516, Philadelphia, 19104 Pennsylvania USA
| | - N. Nowak
- grid.240614.50000 0001 2181 8635Roswell Park Cancer Institute, Elm and Carleton Street, Buffalo, 14263 New York USA
| | - W. Jang
- grid.419234.90000 0004 0604 5429National Center for Biotechnology Information, National Library of Medicine, Building 38A/Room 8N805, Bethesda, 20894 Maryland USA
| | - I. R. Kirsch
- grid.420086.80000 0001 2237 2479National Cancer Institute, NIH, Building 10/Room 12N214, Bethesda, 20889-5105 Maryland USA
| | - S. Zhao
- grid.469946.0The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, 20850 Maryland USA
| | - X.-N. Chen
- grid.50956.3f0000 0001 2152 9905Departments of Pediatrics and Human Genetics, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, 90048 California USA
| | - T. S. Furey
- grid.205975.c0000 0001 0740 6917Computer Science Department, University of California Santa Cruz, 1156 High Street, Santa Cruz, 95064-1077 California USA
| | - U.-J. Kim
- grid.20861.3d0000000107068890Department of Biology, California Institute of Technology, Mail Code 147-75, Pasadena, 91125 California USA ,Present Address: PanGenomics, 6401 Foothill Boulevard, Tujunga, California 91024 USA
| | - W.-L. Kuo
- grid.266102.10000 0001 2297 6811University of California San Francisco Cancer Center, Box 0808, San Francisco, 94143-0808 California USA
| | - M. Olivier
- grid.168010.e0000000419368956Stanford University, Genome Lab, Mail Code 5120, Stanford, 94305-5120 California USA
| | - J. Conroy
- grid.240614.50000 0001 2181 8635Roswell Park Cancer Institute, Elm and Carleton Street, Buffalo, 14263 New York USA
| | - A. Kasprzyk
- Sanger Center, Wellcome Trust Genome Campus, Hinxton, CB10 1SA Cambridge UK
| | - H. Massa
- grid.270240.30000 0001 2180 1622Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North C3-168, P.O. Box 19024, Seattle, 98109-1024 Washington USA
| | - R. Yonescu
- grid.420086.80000 0001 2237 2479National Cancer Institute, NIH, Building 10/Room 12N214, Bethesda, 20889-5105 Maryland USA
| | - S. Sait
- grid.240614.50000 0001 2181 8635Roswell Park Cancer Institute, Elm and Carleton Street, Buffalo, 14263 New York USA
| | - C. Thoreen
- grid.34477.330000000122986657Department of Molecular Biotechnology, University of Washington, Box 357730, Seattle, 98195-7730 Washington USA ,grid.38142.3c000000041936754XPresent Address: Harvard Medical School, Cell Biology, 240 Longwood Avenue, Cambridge, Massachusetts 02115 USA
| | - A. Snijders
- grid.266102.10000 0001 2297 6811University of California San Francisco Cancer Center, Box 0808, San Francisco, 94143-0808 California USA
| | - E. Lemyre
- grid.62560.370000 0004 0378 8294Departments of Obstetrics and Gynecology and Pathology, Brigham and Women's Hospital, Amory Lab Building 3rd floor, Boston, 02115 Massachusetts USA
| | - J. A. Bailey
- grid.67105.350000 0001 2164 3847Department of Human Genetics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, 44106 Ohio USA
| | - A. Bruzel
- grid.239552.a0000 0001 0680 8770Department of Pediatrics, University of Pennsylvania, The Children's Hospital of Philadelphia, 3516 Civic Center Boulevard, ARC 516, Philadelphia, 19104 Pennsylvania USA
| | - W. D. Burrill
- Sanger Center, Wellcome Trust Genome Campus, Hinxton, CB10 1SA Cambridge UK
| | - S. M. Clegg
- Sanger Center, Wellcome Trust Genome Campus, Hinxton, CB10 1SA Cambridge UK
| | - S. Collins
- grid.34477.330000000122986657Department of Molecular Biotechnology, University of Washington, Box 357730, Seattle, 98195-7730 Washington USA
| | - P. Dhami
- Sanger Center, Wellcome Trust Genome Campus, Hinxton, CB10 1SA Cambridge UK
| | - C. Friedman
- grid.270240.30000 0001 2180 1622Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North C3-168, P.O. Box 19024, Seattle, 98109-1024 Washington USA
| | - C. S. Han
- grid.148313.c0000 0004 0428 3079Joint Genome Institute-Los Alamos National Laboratory, MS M888 B-N1, P.O. Box 1663, Los Alamos, 87545 New Mexico USA
| | - S. Herrick
- grid.62560.370000 0004 0378 8294Departments of Obstetrics and Gynecology and Pathology, Brigham and Women's Hospital, Amory Lab Building 3rd floor, Boston, 02115 Massachusetts USA
| | - J. Lee
- grid.20861.3d0000000107068890Department of Biology, California Institute of Technology, Mail Code 147-75, Pasadena, 91125 California USA
| | - A. H. Ligon
- grid.62560.370000 0004 0378 8294Departments of Obstetrics and Gynecology and Pathology, Brigham and Women's Hospital, Amory Lab Building 3rd floor, Boston, 02115 Massachusetts USA
| | - S. Lowry
- grid.184769.50000 0001 2231 4551Joint Genome Institute-Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 84-171, Berkeley, 94720 California USA
| | - M. Morley
- grid.239552.a0000 0001 0680 8770Department of Pediatrics, University of Pennsylvania, The Children's Hospital of Philadelphia, 3516 Civic Center Boulevard, ARC 516, Philadelphia, 19104 Pennsylvania USA
| | - S. Narasimhan
- grid.239552.a0000 0001 0680 8770Department of Pediatrics, University of Pennsylvania, The Children's Hospital of Philadelphia, 3516 Civic Center Boulevard, ARC 516, Philadelphia, 19104 Pennsylvania USA
| | - K. Osoegawa
- grid.240614.50000 0001 2181 8635Roswell Park Cancer Institute, Elm and Carleton Street, Buffalo, 14263 New York USA ,grid.414016.60000 0004 0433 7727Children's Hospital Oakland Research Institute, 747 52nd Street, Oakland, 94609 California USA
| | - Z. Peng
- grid.184769.50000 0001 2231 4551Joint Genome Institute-Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 84-171, Berkeley, 94720 California USA
| | - I. Plajzer-Frick
- grid.184769.50000 0001 2231 4551Joint Genome Institute-Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 84-171, Berkeley, 94720 California USA
| | - B. J. Quade
- grid.62560.370000 0004 0378 8294Departments of Obstetrics and Gynecology and Pathology, Brigham and Women's Hospital, Amory Lab Building 3rd floor, Boston, 02115 Massachusetts USA
| | - D. Scott
- grid.184769.50000 0001 2231 4551Joint Genome Institute-Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 84-171, Berkeley, 94720 California USA
| | - K. Sirotkin
- grid.419234.90000 0004 0604 5429National Center for Biotechnology Information, National Library of Medicine, Building 38A/Room 8N805, Bethesda, 20894 Maryland USA
| | - A. A. Thorpe
- Sanger Center, Wellcome Trust Genome Campus, Hinxton, CB10 1SA Cambridge UK
| | - J. W. Gray
- grid.266102.10000 0001 2297 6811University of California San Francisco Cancer Center, Box 0808, San Francisco, 94143-0808 California USA
| | - J. Hudson
- grid.418190.50000 0001 2187 0556Research Genetics, 2130 Memorial Parkway, Huntsville, 35801 Alabama USA
| | - D. Pinkel
- grid.266102.10000 0001 2297 6811University of California San Francisco Cancer Center, Box 0808, San Francisco, 94143-0808 California USA
| | - T. Ried
- grid.420086.80000 0001 2237 2479National Cancer Institute, NIH, Building 10/Room 12N214, Bethesda, 20889-5105 Maryland USA
| | - L. Rowen
- grid.64212.330000 0004 0463 2320Institute for Systems Biology, 4225 Roosevelt Way NE, Suite 200, Seattle, 98105-6099 Washington USA
| | - G. L. Shen-Ong
- grid.420086.80000 0001 2237 2479National Cancer Institute, NIH, Building 10/Room 12N214, Bethesda, 20889-5105 Maryland USA ,Present Address: Gene Logic, Inc., 708 Quince Orchard Road, Gaithersburg, Maryland 20878 USA
| | - R. L. Strausberg
- grid.420086.80000 0001 2237 2479National Cancer Institute, NIH, Building 10/Room 12N214, Bethesda, 20889-5105 Maryland USA
| | - E. Birney
- Sanger Center, Wellcome Trust Genome Campus, Hinxton, CB10 1SA Cambridge UK
| | - D. F. Callen
- grid.1694.aDepartment of Cytogenetics and Molecular Genetics, Women's and Children's Hospital, 72 King William Road, North Adelaide, 5006 South Australia Australia
| | - J.-F. Cheng
- grid.184769.50000 0001 2231 4551Joint Genome Institute-Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Mail Stop 84-171, Berkeley, 94720 California USA
| | - D. R. Cox
- grid.168010.e0000000419368956Stanford University, Genome Lab, Mail Code 5120, Stanford, 94305-5120 California USA
| | - N. A. Doggett
- grid.148313.c0000 0004 0428 3079Joint Genome Institute-Los Alamos National Laboratory, MS M888 B-N1, P.O. Box 1663, Los Alamos, 87545 New Mexico USA
| | - N. P. Carter
- Sanger Center, Wellcome Trust Genome Campus, Hinxton, CB10 1SA Cambridge UK
| | - E. E. Eichler
- grid.67105.350000 0001 2164 3847Department of Human Genetics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, 44106 Ohio USA
| | - D. Haussler
- grid.205975.c0000 0001 0740 6917Computer Science Department, Howard Hughes Medical Institute, University of California Santa Cruz, 1156 High Street, Santa Cruz, 95064–1077 California USA
| | - J. R. Korenberg
- grid.50956.3f0000 0001 2152 9905Departments of Pediatrics and Human Genetics, Cedars-Sinai Medical Center, 8700 Beverly Boulevard, Los Angeles, 90048 California USA
| | - C. C. Morton
- grid.62560.370000 0004 0378 8294Departments of Obstetrics and Gynecology and Pathology, Brigham and Women's Hospital, Amory Lab Building 3rd floor, Boston, 02115 Massachusetts USA
| | - D. Albertson
- grid.266102.10000 0001 2297 6811University of California San Francisco Cancer Center, Box 0808, San Francisco, 94143-0808 California USA
| | - G. Schuler
- grid.419234.90000 0004 0604 5429National Center for Biotechnology Information, National Library of Medicine, Building 38A/Room 8N805, Bethesda, 20894 Maryland USA
| | - P. J. de Jong
- grid.240614.50000 0001 2181 8635Roswell Park Cancer Institute, Elm and Carleton Street, Buffalo, 14263 New York USA ,grid.414016.60000 0004 0433 7727Children's Hospital Oakland Research Institute, 747 52nd Street, Oakland, 94609 California USA
| | - B. J. Trask
- grid.270240.30000 0001 2180 1622Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North C3-168, P.O. Box 19024, Seattle, 98109-1024 Washington USA
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16
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Schaefer C, Grouse L, Buetow K, Strausberg RL. A new cancer genome anatomy project web resource for the community. Cancer J 2001; 7:52-60. [PMID: 11269648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Abstract
The National Cancer Institute's Cancer Genome Anatomy Project (CGAP) is developing publicly accessible information, technology, and material resources that provide a platform for the interface of cancer research and genomics. CGAP's efforts have focused toward (1) building and annotating catalogues of genes expressed during cancer development, (2) identifying polymorphisms in those genes, and (3) developing resources for the molecular characterization of cancer-related chromosomal aberrations. To date, CGAP has produced more than 1,000,000 expressed sequence tags, approximately 3,300,000 serial analysis of gene expression tags, and identified more than 10,000 human gene-based single-nucleotide polymorphisms. To enhance access to these datasets by the research community, a new Cancer Genome Project web site (http://cgap.nci.nih.gov/) is being introduced. The web site includes genomic data for humans and mice, including transcript sequence, gene expression patterns, single-nucleotide polymorphisms, clone resources, and cytogenetic information. Descriptions of the methods and reagents used in deriving the CGAP datasets are also provided. An extensive suite of informatics tools facilitates queries and analysis of the CGAP data by the community. One of the newest features of the CGAP web site is an electronic version of the Mitelman Database of Chromosome Aberrations in Cancer.
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Affiliation(s)
- C Schaefer
- Center for Bioinformatics, National Cancer Institute, Bethesda, Maryland 20892-2590, USA
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17
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Loging WT, Lal A, Siu IM, Loney TL, Wikstrand CJ, Marra MA, Prange C, Bigner DD, Strausberg RL, Riggins GJ. Identifying potential tumor markers and antigens by database mining and rapid expression screening. Genome Res 2000; 10:1393-402. [PMID: 10984457 PMCID: PMC310902 DOI: 10.1101/gr.138000] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Genes expressed specifically in malignant tissue may have potential as therapeutic targets but have been difficult to locate for most cancers. The information hidden within certain public databases can reveal RNA transcripts specifically expressed in transformed tissue. To be useful, database information must be verified and a more complete pattern of tissue expression must be demonstrated. We tested database mining plus rapid screening by fluorescent-PCR expression comparison (F-PEC) as an approach to locate candidate brain tumor antigens. Cancer Genome Anatomy Project (CGAP) data was mined for genes highly expressed in glioblastoma multiforme. From 13 mined genes, seven showed potential as possible tumor markers or antigens as determined by further expression profiling. Now that large-scale expression information is readily available for many of the commonly occurring cancers, other candidate tumor markers or antigens could be located and evaluated with this approach.
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Affiliation(s)
- W T Loging
- Duke University Medical Center, Durham, North Carolina 27710, USA
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18
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Abstract
We have constructed a public gene expression data repository and online data access and analysis, WWW and FTP sites for serial analysis of gene expression (SAGE) data. The WWW and FTP components of this resource, SAGEmap, are located at http://www.ncbi.nlm.nih. gov/sage and ftp://ncbi.nlm.nih.gov/pub/sage, respectively. We herein describe SAGE data submission procedures, the construction and characteristics of SAGE tags to gene assignments, the derivation and use of a novel statistical test designed specifically for differential-type analyses of SAGE data, and the organization and use of this resource.
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Affiliation(s)
- A E Lash
- National Center for Biotechnology Information, National Institutes of Health, Bethesda, MD 20894 USA.
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19
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20
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Shillitoe EJ, May M, Patel V, Lethanakul C, Ensley JF, Strausberg RL, Gutkind JS. Genome-wide analysis of oral cancer--early results from the Cancer Genome Anatomy Project. Oral Oncol 2000; 36:8-16. [PMID: 10889913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
The Cancer Genome Anatomy Project (CGAP) is a large cooperative effort sponsored by the US National Institutes of Health designed to find, catalog and annotate genes that are expressed during cancer development. In the past 2 years, the CGAP has sequenced over 700,000 clones from approximately 140 cDNA libraries, resulting in the identification of over 30,000 new human genes. As a first step in applying this project to oral cancer we entered four cell lines--two from oral cancer, one from primary oral keratinocytes, and one from oral keratinocytes which had been immortalized by human papillomavirus. Libraries of cDNA were made and sequenced and the data were deposited in GenBank. The expressed genes were then identified where possible. The cell lines, and the total number of expressed genes that were cloned from each were: HN3 (oral cancer), 263 genes; HN4 (oral cancer), 550 genes; HN5 (primary keratinocytes), 237 genes; HN6 (immortalized keratinocytes), 408 genes. The total number of different genes that were found was 1160. A total of 38 new genes, of unknown function, were discovered. The data presented here represent a beginning of the application of the CGAP technology to oral cancer. Even though the data are still quite incomplete, they already represent a large quantity of new information and clones of potential utility to the oral cancer community, and provide a glimpse of the data sets to be forthcoming from the Project. It must therefore be expected that there will soon be a large expansion in the volume of data regarding the genetics of oral cancer. Those who study this disease must be prepared to develop new methods of analysis and storage for handling the oncoming volumes of information.
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Affiliation(s)
- E J Shillitoe
- Department of Microbiology and Immunology, SUNY College of Medicine, Syracuse 13210, USA.
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21
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Lal A, Lash AE, Altschul SF, Velculescu V, Zhang L, McLendon RE, Marra MA, Prange C, Morin PJ, Polyak K, Papadopoulos N, Vogelstein B, Kinzler KW, Strausberg RL, Riggins GJ. A public database for gene expression in human cancers. Cancer Res 1999; 59:5403-7. [PMID: 10554005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/14/2023]
Abstract
A public database, SAGEmap, was created as a component of the Cancer Genome Anatomy Project to provide a central location for depositing, retrieving, and analyzing human gene expression data. This database uses serial analysis of gene expression to quantify transcript levels in both malignant and normal human tissues. By accessing SAGEmap (http://www.ncbi.nlm.nih.gov/SAGE) the user can compare transcript populations between any of the posted libraries. As an initial demonstration of the database's utility, gene expression in human glioblastomas was compared with that of normal brain white matter. Of the 47,174 unique transcripts expressed in these two tissues, 471 (1.0%) were differentially expressed by more than 5-fold (P<0.001). Classification of these genes revealed functions consistent with the biological properties of glioblastomas, in particular: angiogenesis, transcription, and cell cycle related genes.
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Affiliation(s)
- A Lal
- Department of Pathology, Duke University Medical Center, Durham, North Carolina 27710, USA
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22
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Abstract
The Mammalian Gene Collection (MGC) project is a new effort by the NIH to generate full-length complementary DNA (cDNA) resources. This project will provide publicly accessible resources to the full research community. The MGC project entails the production of libraries, sequencing, and database and repository development, as well as the support of library construction, sequencing, and analytic technologies dedicated to the goal of obtaining a full set of human and other mammalian full-length (open reading frame) sequences and clones of expressed genes.
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Affiliation(s)
- R L Strausberg
- National Cancer Institute, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
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23
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Abstract
In April, the Merck Genome Research Institute and the National Cancer Institute's Cancer Genome Anatomy Project, both supporters of functional genomics technology development and research, brought together a group of 27 scientists working at the forefront of this new field. Here we report on the presentations, discussions, and outcomes from this highly interactive and stimulating meeting held at the Banbury Center.
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24
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Krizman DB, Wagner L, Lash A, Strausberg RL, Emmert-Buck MR. The Cancer Genome Anatomy Project: EST sequencing and the genetics of cancer progression. Neoplasia 1999; 1:101-6. [PMID: 10933042 PMCID: PMC1508126 DOI: 10.1038/sj.neo.7900002] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
As the process of tumor progression proceeds from the normal cellular state to a preneoplastic condition and finally to the fully invasive form, the molecular characteristics of the cell change as well. These characteristics can be considered a molecular fingerprint of the cell at each stage of progression and, analogous to fingerprinting a criminal, can be used as markers of the progression process. Based on this premise, the Cancer Genome Anatomy Project was initiated with the broad goal of determining the comprehensive molecular characterization of normal, premalignant, and malignant tumor cells, thus making a reality the identification of all major cellular mechanisms leading to tumor initiation and progression ([Strausberg, R.L., Dahl, C.A., and Klausner, R.D. (1997). "New opportunities for uncovering the molecular basis of cancer." Nat. Genet., 16: 415-516.], www.ncbi.nlm.nih.gov/ncicgap/). The expectation of determining the genetic fingerprints of cancer progression will allow for 1) correlation of disease progression with therapeutic outcome; 2) improved evaluation of disease treatment; 3) stimulation of novel approaches to prevention, detection, and therapy; and 4) enhanced diagnostic tools for clinical applications. Whereas acquiring the comprehensive molecular analysis of cancer progression may take years, results from initial, short-term goals are currently being realized and are proving very fruitful.
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Affiliation(s)
- D B Krizman
- Cancer Genome Anatomy Project, Office of the Director, National Cancer Institute, Bethesda, MD, USA.
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25
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Affiliation(s)
- R L Strausberg
- National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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27
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Bhogal BS, Miller GA, Anderson AC, Jessee EJ, Strausberg S, McCandliss R, Nagle J, Strausberg RL. Potential of a recombinant antigen as a prophylactic vaccine for day-old broiler chickens against Eimeria acervulina and Eimeria tenella infections. Vet Immunol Immunopathol 1992; 31:323-35. [PMID: 1589958 DOI: 10.1016/0165-2427(92)90019-m] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A genetically engineered Eimeria tenella antigen (GX3262), produced as a fusion protein with beta-galactosidase and identified with a monoclonal antibody, induced partial but significant protection in young broiler chickens against experimental E. tenella and Eimeria acervulina infections. The antigen appears to share a T-helper cell epitope with the parasite as evidenced by (a) booster inoculation with either the recombinant antigen or with a small number of live oocysts enhanced the protective immunity in GX3262 primed chickens, and (b) ability of the antigen to induce in vitro stimulation of T-cells from chickens immunized with antigen or parasite. These observations suggest the feasibility of a single vaccination of 1 or 2-day-old broilers with GX3262 to induce an acceptable degree of protective immunity. The implications of the observations reported here are far reaching in terms of a practical coccidiosis vaccine for poultry, and show for the first time that 1-day-old broiler chickens can be efficiently vaccinated with a recombinant antigen against one or more species of Eimeria.
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Affiliation(s)
- B S Bhogal
- Department of Molecular Biology, A.H. Robins Research Laboratories, Richmond, VA 23220
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28
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Abstract
The DOPA-rich polyphenolic protein secreted by the marine mussel Mytilus edulis establishes key chemical linkages in a water-resistant adhesive. Molecular cloning of the gene for this remarkable protein reveals its primary structure as one of the most repetitive proteins identified in the animal kingdom. Expression and purification of polyphenolic proteins from recombinant yeast have provided sufficient material to demonstrate adhesivity of these polypeptides in the laboratory. Adhesive tests reveal a water-resistant bonding capacity of the protein that is dependent on in vitro modification of tyrosine residues to DOPA and the subsequent oxidation to quinone.
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Affiliation(s)
- D R Filpula
- Genex Corporation, Gaithersburg, Maryland 20877
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29
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Abstract
There are many naturally occurring adhesive proteins which have potential for application in medicine and dentistry. Cloning and expression of their genes enables the modes of action of these proteins to be better understood and increases their availability for practical applications. This article concentrates on the adhesive protein from the blue mussel Mytilus edulis but also describes medical adhesives based on fibrin isolated from human blood.
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30
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Danforth HD, Augustine PC, Ruff MD, McCandliss R, Strausberg RL, Likel M. Genetically engineered antigen confers partial protection against avian coccidial parasites. Poult Sci 1989; 68:1643-52. [PMID: 2622819 DOI: 10.3382/ps.0681643] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
A fusion protein of beta-galactosidase and Eimeria tenella produced in a recombinant Escherichia coli strain was injected into chickens and elicited partial protection against an oral challenge with Eim. tenella parasites. The fusion protein contained a 31 kilodalton (kD) coccidial antigen designated as 5401. The DNA sequencing of the 5401 antigen-coding sequence revealed that this protein segment was highly negatively charged and strongly hydrophilic, and contained an amino-acid sequence repeated five times. A dose-titration study showed that immunizing chickens with a single subcutaneous injection of the 5401 antigen at 1,200 to 4,800 nanograms (ng)/bird in Freund's complete adjuvant decreased lesion scores, mortality, and feed conversions compared to unimmunized, challenged controls. Using the 1,200 and 2,400 ng/bird of the 5401 antigen, group weight gains were higher than for the unimmunized, challenged birds. In three other trials using the 5401 antigen at 2,400 ng/bird with light, medium, and heavy coccidial infections, significant protection was evidenced by reduced lesion scores, increased individual weight gains, or both. In addition, feed conversions were reduced when compared with unimmunized controls or birds immunized with a noncoccidial protein E. coli extract. Western blot analysis of sporozoite preparations with serum from 5401-immunized birds labeled two antigenic bands of 66 and less than 200 kD. These results indicate that the coccidial proteins produced in E. coli are potentially effective immunogens for protecting chickens against avian coccidiosis.
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Affiliation(s)
- H D Danforth
- United States Department of Agriculture, Agricultural Research Service, Beltsville, Maryland 20705
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31
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Miller GA, Bhogal BS, McCandliss R, Strausberg RL, Jessee EJ, Anderson AC, Fuchs CK, Nagle J, Likel MH, Strasser JM. Characterization and vaccine potential of a novel recombinant coccidial antigen. Infect Immun 1989; 57:2014-20. [PMID: 2659532 PMCID: PMC313835 DOI: 10.1128/iai.57.7.2014-2020.1989] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
A cDNA clone derived from sporulated oocysts of Eimeria tenella and encoding the expression product GX3262 was identified using a monoclonal antibody raised against Eimeria acervulina sporozoites. The cDNA fragment containing the coccidial antigen gene was cloned in bacteriophage lambda gt11, transferred to a plasmid, and introduced into Escherichia coli for analysis of the gene products. The strain carrying the plasmid produced GX3262 as part of a fusion protein consisting of the first 1,006 amino acids of E. coli beta-galactosidase and 112 amino acids of the E. tenella protein of approximately 12 kilodaltons. Partially purified antigen, heat-killed recombinant bacterin, and live E. coli containing the recombinant coccidial antigen were used to immunize 1-week-old or newly hatched broiler chicks. Several immunization protocols were utilized, including boosts with partially purified beta-galactosidase-GX3262, bacterin, or small numbers of live E. tenella oocysts. After challenge with an experimental E. tenella infection, the birds were evaluated by scoring cecal lesions to determine the level of protection. The greatest degree of protection was seen after only a single immunization of 2-day-old birds with a live recombinant E. coli preparation. The results presented here identify GX3262 as a potential candidate coccidial vaccine antigen and provide evidence for the first time that newly hatched chickens can be successfully vaccinated with a recombinant antigen.
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Affiliation(s)
- G A Miller
- Molecular Biology Department, A. H. Robins Co., Richmond, Virginia 23220
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32
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Filpula D, Vaslet CA, Levy A, Sykes A, Strausberg RL. Nucleotide sequence of gene for phenylalanine ammonia-lyase from Rhodotorula rubra. Nucleic Acids Res 1988; 16:11381. [PMID: 3205749 PMCID: PMC339031 DOI: 10.1093/nar/16.23.11381] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- D Filpula
- Genex Corporation, Gaithersburg, MD 20877
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33
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Vaslet CA, Strausberg RL, Sykes A, Levy A, Filpula D. cDNA and genomic cloning of yeast phenylalanine ammonia-lyase genes reveal genomic intron deletions. Nucleic Acids Res 1988; 16:11382. [PMID: 3205750 PMCID: PMC339032 DOI: 10.1093/nar/16.23.11382] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Affiliation(s)
- C A Vaslet
- Genex Corporation, Gaithersburg, MD 20877
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34
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Abstract
Alleles of the var1 locus on yeast mtDNA determine the apparent size of the mitochondrial translation product, var1 polypeptide. We have analyzed most of the different var1 alleles in our collection, which number at least 15, and have developed procedures and a genetic rationale for determining their origin and predicting their behavior in crosses. The var1 alleles are characterized by two genetically defined segments, designated a and b, which can move from one var1 allele to another by asymmetric gene conversion. We show that the a segment behaves as an entity in recombination; it is either present in or absent from different var1 alleles. The b segment usually, but not always, recombines as an entity; in some cases, only portions of the b segment recombine by gene conversion. Thus, the total number of electrophoretically resolvable var1 species we observe is explained by the assortment of a, b, and partial b segments. Each segment recombines at a characteristic frequency; however, one example is presented which shows that the recipient can modulate the frequency of gene conversion. Finally, we show that, like the 21S rDNA region (omega), there is polarity of gene conversion within var1.
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Vincent RD, Perlman PS, Strausberg RL, Butow RA. Physical mapping of genetic determinants on yeast mitochondrial DNA affecting the apparent size of the Var 1 polypeptide. Curr Genet 1980; 2:27-38. [DOI: 10.1007/bf00445691] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/1980] [Indexed: 10/26/2022]
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36
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37
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Abstract
Different molecular weight forms of the protein product of the yeast mitochondrial gene var 1 are shown at arise by a process of asymmetric gene conversion. These different forms can be accounted by two DNA segments, 36 and 57 base pairs long, present in one allelic form of the var 1 structural gene, which can be inserted independently and at different frequencies into other var 1 alleles.
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Strausberg RL, Perlman PS. The effect of zygotic bud position on the transmission of mitochondrial genes in Saccharomyces cerevisiae. Mol Gen Genet 1978; 163:131-44. [PMID: 355844 DOI: 10.1007/bf00267404] [Citation(s) in RCA: 53] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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39
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Perlman PS, Douglas MG, Strausberg RL, Butow RA. Localization of genes for variant forms of mitochondrial proteins on mitochondrial DNA of Saccharomyces cerevisiae. J Mol Biol 1977; 115:675-94. [PMID: 338916 DOI: 10.1016/0022-2836(77)90109-7] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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40
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Abstract
A protocol is introduced for probing the organization and regulation of expression of the yeast mitochondrial genome, termed "zygotic gene rescue." The procedure is based on the notion that genes retained on mitochondrial DNA of on the notion that genes retained on mitochondrial DNA of petites can be expressed in zygotes of a cross between petite and wild type. To test the validity of this notion, we have taken advantage of our ability to discriminate, by mobility differences on sodium dodecyl sulfate/polyacrylamide gels, different forms of the product of alleles of the mitochondrial gene, varI. In petite strains that have retained the varI gene, its characteristic product appears in zygotes 4-5 hr after mating; no product is observed in petite strains deleted in the varI locus. Our studies indicate that (i) expression in the zygote of the varI gene in the petite genome is not exclusively the result of recombination with mitochondrial DNA of the wild-type tester, and (ii) the varI gene is probably reiterated in the petite mitochondrial genome. The strength of the technique of zygotic gene rescue in the analysis of the mitochondrial genome is discussed.
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