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Ahmed FE. Development of novel diagnostic and prognostic molecular markers for sporadic colon cancer. Expert Rev Mol Diagn 2014; 5:337-52. [PMID: 15934812 DOI: 10.1586/14737159.5.3.337] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Gene expression studies are informative about changes in colon cancer, increase understanding of the biology of tumorigenesis and aid in developing diagnostic and prognostic markers. In this review, expression techniques used to examine the multistage process of colon cancer are discussed. Many genes have been found to differ in expression between normal and tumorigenic states, as early as the seemingly normal colonic crypts. The clinical usefulness of markers varies with stage, ethnicity and anatomic location of colon cancer. Thus, combinations of markers can be used to develop an approach to molecularly screen and follow the progression of this prevalent cancer.
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Affiliation(s)
- Farid E Ahmed
- The Brody School of Medicine at East Carolina University, Department of Radiation Oncology, Leo W. Jenkins Cancer Center, Greenville, NC 27858, USA.
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Costa AFD, Gomes-Ruiz AC, Rabelo ÉM. Identification of gender-regulated genes in Ancylostoma braziliense by real-time RT-PCR. Vet Parasitol 2008; 153:277-84. [DOI: 10.1016/j.vetpar.2008.02.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2007] [Revised: 02/07/2008] [Accepted: 02/09/2008] [Indexed: 12/16/2022]
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3
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Haddad GE, Saunders LJ, Crosby SD, Carles M, del Monte F, King K, Bristow MR, Spinale FG, Macgillivray TE, Semigran MJ, Dec GW, Williams SA, Hajjar RJ, Gwathmey JK. Human cardiac-specific cDNA array for idiopathic dilated cardiomyopathy: sex-related differences. Physiol Genomics 2008; 33:267-77. [DOI: 10.1152/physiolgenomics.00265.2007] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Idiopathic dilated cardiomyopathy (IDCM) constitutes a large portion of patients with heart failure of unknown etiology. Up to 50% of all transplant recipients carry this clinical diagnosis. Female-specific gene expression in IDCM has not been explored. We report sex-related differences in the gene expression profile of ventricular myocardium from patients undergoing cardiac transplantation. We produced and sequenced subtractive cDNA libraries, using human left ventricular myocardium obtained from male transplant recipients with IDCM and nonfailing human heart donors. With the resulting sequence data, we generated a custom human heart failure microarray for IDCM containing 1,145 cardiac-specific oligonucleotide probes. This array was used to characterize RNA samples from female IDCM transplant recipients. We identified a female gene expression pattern that consists of 37 upregulated genes and 18 downregulated genes associated with IDCM. Upon functional analysis of the gene expression pattern, deregulated genes unique to female IDCM were those that are involved in energy metabolism and regulation of transcription and translation. For male patients we found deregulation of genes related to muscular contraction. These data suggest that 1) the gene expression pattern we have detected for IDCM may be specific for this disease and 2) there is a sex-specific profile to IDCM. Our observations further suggest for the first time ever novel targets for treatment of IDCM in women and men.
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Affiliation(s)
- Georges E. Haddad
- Department of Physiology and Biophysics, College of Medicine, Howard University, Washington, District of Columbia
| | | | - Seth D. Crosby
- Microarray Core Facility, Washington University Medical School, St. Louis, Missouri
| | - Maria Carles
- Gwathmey, Incorporated, Cambridge, Massachusetts
| | - Federica del Monte
- Cardiovascular Research Center, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Kindra King
- Gwathmey, Incorporated, Cambridge, Massachusetts
| | - Michael R. Bristow
- Division of Cardiology, School of Medicine, University of Colorado Health Sciences Center, Denver, Colorado
| | - Francis G. Spinale
- Cardiothoracic Surgery, Medical University of South Carolina, Charleston, South Carolina
| | | | - Marc J. Semigran
- Cardiology Division, Gray/Bigelow, Massachusetts General Hospital, Boston
| | - G. William Dec
- Cardiology Division, Gray/Bigelow, Massachusetts General Hospital, Boston
| | - Steven A. Williams
- Department of Biological Sciences, Smith College, Northampton, Massachusetts
| | - Roger J. Hajjar
- Cardiovascular Research Center, Mount Sinai School of Medicine, New York, New York
| | - Judith K. Gwathmey
- Gwathmey, Incorporated, Cambridge, Massachusetts
- Boston University School of Medicine, Cambridge, Massachusetts
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Abstract
Advances in tumor immunology are supporting the clinical implementation of several immunological approaches to cancer in the clinical setting. However, the alternate success of current immunotherapeutic regimens underscores the fact that the molecular mechanisms underlying immune-mediated tumor rejection are still poorly understood. Given the complexity of the immune system network and the multidimensionality of tumor/host interactions, the comprehension of tumor immunology might greatly benefit from high-throughput microarray analysis, which can portrait the molecular kinetics of immune response on a genome-wide scale, thus accelerating the discovery pace and ultimately catalyzing the development of new hypotheses in cell biology. Although in its infancy, the implementation of microarray technology in tumor immunology studies has already provided investigators with novel data and intriguing new hypotheses on the molecular cascade leading to an effective immune response against cancer. Although the general principles of microarray-based gene profiling have rapidly spread in the scientific community, the need for mastering this technique to produce meaningful data and correctly interpret the enormous output of information generated by this technology is critical and represents a tremendous challenge for investigators, as outlined in the first section of this book. In the present Chapter, we report on some of the most significant results obtained with the application of DNA microarray in this oncology field.
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Affiliation(s)
- Simone Mocellin
- Clinica Chirurgica II, Dipartimento di Scienze Oncologiche e Chirurgiche, University of Padova, Via Giustiniani 2, Italy.
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Carles A, Millon R, Cromer A, Ganguli G, Lemaire F, Young J, Wasylyk C, Muller D, Schultz I, Rabouel Y, Dembélé D, Zhao C, Marchal P, Ducray C, Bracco L, Abecassis J, Poch O, Wasylyk B. Head and neck squamous cell carcinoma transcriptome analysis by comprehensive validated differential display. Oncogene 2006; 25:1821-31. [PMID: 16261155 DOI: 10.1038/sj.onc.1209203] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Head and neck squamous cell carcinoma (HNSCC) is common worldwide and is associated with a poor rate of survival. Identification of new markers and therapeutic targets, and understanding the complex transformation process, will require a comprehensive description of genome expression, that can only be achieved by combining different methodologies. We report here the HNSCC transcriptome that was determined by exhaustive differential display (DD) analysis coupled with validation by different methods on the same patient samples. The resulting 820 nonredundant sequences were analysed by high throughput bioinformatics analysis. Human proteins were identified for 73% (596) of the DD sequences. A large proportion (>50%) of the remaining unassigned sequences match ESTs (expressed sequence tags) from human tumours. For the functionally annotated proteins, there is significant enrichment for relevant biological processes, including cell motility, protein biosynthesis, stress and immune responses, cell death, cell cycle, cell proliferation and/or maintenance and transport. Three of the novel proteins (TMEM16A, PHLDB2 and ARHGAP21) were analysed further to show that they have the potential to be developed as therapeutic targets.
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Affiliation(s)
- A Carles
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS/INSERM/ULP, 67404 Illkirch Cedex, France
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Mocellin S, Provenzano M, Rossi CR, Pilati P, Nitti D, Lise M. DNA array-based gene profiling: from surgical specimen to the molecular portrait of cancer. Ann Surg 2005; 241:16-26. [PMID: 15621987 PMCID: PMC1356842 DOI: 10.1097/01.sla.0000150157.83537.53] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Cancer is a heterogeneous disease in most respects, including its cellularity, different genetic alterations, and diverse clinical behaviors. Traditional molecular analyses are reductionist, assessing only 1 or a few genes at a time, thus working with a biologic model too specific and limited to confront a process whose clinical outcome is likely to be governed by the combined influence of many genes. The potential of functional genomics is enormous, because for each experiment, thousands of relevant observations can be made simultaneously. Accordingly, DNA array, like other high-throughput technologies, might catalyze and ultimately accelerate the development of knowledge in tumor cell biology. Although in its infancy, the implementation of DNA array technology in cancer research has already provided investigators with novel data and intriguing new hypotheses on the molecular cascade leading to carcinogenesis, tumor aggressiveness, and sensitivity to antiblastic agents. Given the revolutionary implications that the use of this technology might have in the clinical management of patients with cancer, principles of DNA array-based tumor gene profiling need to be clearly understood for the data to be correctly interpreted and appreciated. In the present work, we discuss the technical features characterizing this powerful laboratory tool and review the applications so far described in the field of oncology.
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Affiliation(s)
- Simone Mocellin
- Surgery Branch, Department of Oncological and Surgical Sciences, University of Padova, Italy.
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Mocellin S, Wang E, Panelli M, Pilati P, Marincola FM. DNA array-based gene profiling in tumor immunology. Clin Cancer Res 2005; 10:4597-606. [PMID: 15269130 DOI: 10.1158/1078-0432.ccr-04-0327] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Recent advances in tumor immunology have fostered the clinical implementation of different immunotherapy modalities. However, the alternate success of such regimens underscores the fact that the molecular mechanisms underlying tumor immune rejection are still poorly understood. Given the complexity of the immune system network and the multidimensionality of tumor-host interactions, the comprehension of tumor immunology might greatly benefit from high-throughput DNA array analysis, which can portray the molecular kinetics of immune response on a genome-wide scale, thus accelerating the accumulation of knowledge and ultimately catalyzing the development of new hypotheses in cell biology. Although in its infancy, the implementation of DNA array technology in tumor immunology studies has already provided investigators with novel data and intriguing hypotheses on the cascade of molecular events leading to an effective immune response against cancer. Although the principles of DNA array-based gene profiling techniques have become common knowledge, the need for mastering this technique to produce meaningful data and correctly interpret this enormous output of information is critical and represents a tremendous challenge for investigators. In the present work, we summarize the main technical features and critical issues characterizing this powerful laboratory tool and review its applications in the fascinating field of cancer immunogenomics.
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Affiliation(s)
- Simone Mocellin
- Department of Oncological and Surgical Sciences, University of Padova, Padua, Italy.
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