Microarray Technologies in the Diagnosis and Treatment of Head and Neck Cancer

Microarray Technologies in the Diagnosis and Treatment of Head and Neck Cancer

No Results

No Results

processing….

Since the draft sequence of the human genome was published in 2001, [1] the Cancer Genome Anatomy Project index of tumor genes has classified more than 40,000 genes directly or indirectly involved in one or more cancers. [2, 3] Conventional techniques of gene investigation in cancer rely on the identification of single genetic alterations associated with disease. This has proven to be both time consuming and cost ineffective. The introduction of complementary DNA (cDNA) microarray technology in 1995 has helped to facilitate the identification and classification of DNA sequence information and the assignment of functions to these new genes by allowing investigators to analyze expression of thousands of genes simultaneously in a single experiment. [4]

Microarrays are a significant advance because of their small size and are therefore useful when one wants to survey a large number of genes quickly or when the study sample is small. Microarrays may be used to assay gene expression within a single sample or to compare gene expression in 2 different cell types or tissue samples, such as in healthy versus diseased tissue. [20] Because a microarray can be used to examine the expression of hundreds or thousands of genes at once, it promises to revolutionize the way gene expression is examined.

DNA microarrays are simply platforms that consist of small solid supports onto which the sequences from thousands of different genes are attached at fixed locations. The technology allows evaluation of many gene transcripts at one time. The individual DNA strands are called probes. The supports themselves are usually glass microscope slides but can also be silicon chips or nylon membranes. The DNA is printed, spotted, or actually synthesized directly onto the support (see image below.)

Messenger RNA (mRNA) from the sample of interest can serve as a template for producing complementary DNA (cDNA) in the presence of a reverse transcriptase enzyme. This cDNA can then be fluorescently labeled and hybridized to the target gene sequences on the microarray. Because the locations of the probes are known, the intensity and pattern of the labeled mRNA can be used to measure the expression of the targeted gene. A confocal scanner then reads the fluorescent intensity of each hybridized sequence in the array. The scanner that records the intensity value is linked to digital image analysis software, which produces a color-coded image of the array, and a quantitative value is recorded for each target gene. The intensity of fluorescence is analyzed and correlates with expression of the gene.

The data produced from a microarray experiment typically constitute a long list of measurements of spot intensities and intensity ratios, generated either by a pair-wise comparison of 2 samples or by a comparison of several samples with a common control. The challenge is to sort through these data to find meaningful results. Because of the complexity of the data sets generated by microarray experiments, the use of data-analysis software is essential. Several commercial and public data-analysis tools have been developed for this purpose.

The 2 most common microarray technologies in use are the oligonucleotide microarrays and the robotically spotted complementary DNA (cDNA) microarrays. [19] Both technologies use hybridization of labeled nucleic acid transcripts to measure the gene expression.

Oligonucleotide microarrays are manufactured by Affymetrix (Santa Clara, Calif) using photolithographic techniques. [5] They consist of a glass surface onto which oligonucleotides consisting of 25 bases are built a single nucleotide at a time. The chemical addition of nucleotides is controlled by exposing certain strands to light while masking others. This process is repeated to build specific oligonucleotide sequences. Each chip contains thousands of probe sets, each representing single genes. Each probe set consists of 16-20 probe pairs that represent specific coding regions for a given gene. The oligonucleotide sequence on the array should be complementary and specific to the messenger RNA (mRNA) being investigated.

This technique was first developed at Stanford University by robotically spotting purified cDNA samples onto a glass slide or nylon membrane. [6] The sequences are amplified by polymerase chain reaction and printed onto the slide using robotic techniques. These DNA probes are transferred as intact DNA strands, compared with individual bases of oligonucleotide microarrays.

This technique uses 2 fluorescent labels. Cy3 fluoresces green when exposed to light, while Cy5 fluoresces red. The mRNA samples are reverse-transcribed to cDNA using fluorescently labeled nucleotides. These are then combined to the microarray, and the target cDNA is hybridized to the corresponding probe on the microarray. The nonhybridized DNA is washed off the slide, and the intensity of fluorescence is measured.

DNA microarrays are relatively new techniques in the field of oncology and are used to better understand and diagnose various malignancies. Its use is promising in the advancement of tumor detection and therapeutics. In recent years, the use of microarray technology has been of great interest in head and neck squamous cell carcinoma (HNSCCa). Despite the advancement of the diagnosis and treatment of HNSCCa, survival has not improved. [18]

Microarrays may eventually help in the understanding of the disease and ultimately lead to improvements in diagnosis, treatment, and outcome. [7] Furthermore, the quantitative and qualitative aspect of microarrays may eventually be exploited to screen for molecular markers of head and neck cancer. [8, 9] Ideally, their use will aid in the identification of progression from dysplasia to invasive carcinoma, distant metastisis, and clinically important outcome measures. Numerous expression studies of HNSCCa have been performed. [8, 10, 11, 12, 13, 14, 15, 16]

Currently, there is much heterogeneity within large amounts of data available, which leads to contradictory findings between studies. In their review, Choi et al [17] identified simultaneous up- or down-regulation of genes encoding for cell cycle regulation, matrix metalloproteinases, inflammatory response mediators, enzymes of the mevalonate pathway, or ribosomal proteins.

Belbin et al [10] used complementary DNA (cDNA) microarrays that contained 9216 clones to measure global patterns of gene expression in HNSCCa. Through the use of statistical analysis, they identified 375 differentially expressed genes, which divided 17 patients with head and neck tumors into 2 clinically distinct subgroups based on gene-expression patterns. The results of their analysis demonstrated that gene-expression profiling can be used as a predictor of outcome and highlighted pathways, meriting exploration for possible links to outcome in HNSCCa.

Using cDNA subtractive methodology in conjunction with microarray technology to screen for HNSCCa-specific genes, Villaret et al [11] were able to identify 9 known genes that were significantly overexpressed in HNSCCa compared with healthy tissue specimens. In addition, they found 4 previously unidentified genes that were overexpressed in a subset of tumors.

Using a cDNA array of 588 known human cancer-related genes and 9 housekeeping genes, Leethanakul et al [12] demonstrated a consistent decrease in the expression of differentiation markers, such as cytokeratins, and an increase in the expression of numerous signal-transducing and cell-cycle regulatory molecules, as well as growth and angiogenic factors and tissue-degrading proteases. The authors also found that most HNSCCas over-express members of the Wnt and Notch growth and differentiation regulatory system, suggesting that the Wnt and Notch pathways may contribute to squamous cell carcinogenesis.

Spectral karyotyping (SKY), comparative genomic hybridization (CGH), and microarrays were used by Squire et al [13] to identify consensus regions of chromosomal imbalance and structural rearrangement in HNSCCa. [13] The authors were able to demonstrate recurrent chromosomal alterations using CGH and SKY and to correlate them to expression array analysis.

Sok et al [8] used hierarchical clustering analysis to reveal that the gene-expression profiles obtained from a panel of 12,000 genes could distinguish tumor from nonmalignant tissues. [8] Gene expression changes were reproducibly observed in 227 genes, representing previously identified factors associated with neoplasia. Furthermore, significant expression of the collagen type XI alpha-1 gene and a novel gene were reproducibly observed in all 9 tumors, whereas these genes were virtually undetectable in their corresponding, adjacent nonmalignant tissues.

Despite strides in prevention and advances in treatment, cancer of the head and neck remains a disease of considerable morbidity and mortality. The use of complementary DNA (cDNA) microarray technology to explore gene expression on a global level is rapidly evolving. Although microarray technology is still in its infancy, further investigation may prove helpful in the diagnosis, prognosis, and management of head and neck cancer.

Lander ES, Linton LM, Birren B, et al. Initial sequencing and analysis of the human genome. Nature. 2001 Feb 15. 409(6822):860-921. [Medline].

Strausberg RL. The Cancer Genome Anatomy Project: new resources for reading the molecular signatures of cancer. J Pathol. 2001 Sep. 195(1):31-40. [Medline].

Strausberg RL, Buetow KH, Emmert-Buck MR, Klausner RD. The cancer genome anatomy project: building an annotated gene index. Trends Genet. 2000 Mar. 16(3):103-6. [Medline].

Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 1995 Oct 20. 270(5235):467-70. [Medline].

Lipshutz RJ, Fodor SP, Gingeras TR, Lockhart DJ. High density synthetic oligonucleotide arrays. Nat Genet. 1999 Jan. 21(1 Suppl):20-4. [Medline].

Eisen MB, Brown PO. DNA arrays for analysis of gene expression. Methods Enzymol. 1999. 303:179-205. [Medline].

Warner GC, Reis PP, Makitie AA, et al. Current applications of microarrays in head and neck cancer research. Laryngoscope. 2004 Feb. 114(2):241-8. [Medline].

Sok JC, Kuriakose MA, Mahajan VB, Brown PO. Tissue-specific gene expression of head and neck squamous cell carcinoma in vivo by complementary DNA microarray analysis. Arch Otolaryngol Head Neck Surg. 2003 Jul. 129(7):760-70. [Medline].

Sahu N, Grandis JR. New advances in molecular approaches to head and neck squamous cell carcinoma. Anticancer Drugs. 2011 Aug. 22(7):656-64. [Medline]. [Full Text].

Belbin TJ, Singh B, Barber I, et al. Molecular classification of head and neck squamous cell carcinoma using cDNA microarrays. Cancer Res. 2002 Feb 15. 62(4):1184-90. [Medline].

Villaret DB, Wang T, Dillon D, et al. Identification of genes overexpressed in head and neck squamous cell carcinoma using a combination of complementary DNA subtraction and microarray analysis. Laryngoscope. 2000 Mar. 110(3 Pt 1):374-81. [Medline].

Leethanakul C, Patel V, Gillespie J, et al. Distinct pattern of expression of differentiation and growth-related genes in squamous cell carcinomas of the head and neck revealed by the use of laser capture microdissection and cDNA arrays. Oncogene. 2000 Jun 29. 19(28):3220-4. [Medline].

Squire JA, Bayani J, Luk C, et al. Molecular cytogenetic analysis of head and neck squamous cell carcinoma: By comparative genomic hybridization, spectral karyotyping, and expression array analysis. Head Neck. 2002 Sep. 24(9):874-87. [Medline].

Szczepanski MJ, Deleo AB, Luczak M, et al. PRAME expression in head and neck cancer correlates with markers of poor prognosis and might help in selecting candidates for retinoid chemoprevention in pre-malignant lesions. Oral Oncol. 2012 Aug 31. [Medline].

Nankivell PC, Williams H, Bartlett JM, Mehanna H. Validation of tissue microarrays in oral epithelial dysplasia using a novel virtual-array technique. J Clin Pathol. 2012 Dec. 65(12):1084-7. [Medline].

Sepiashvili L, Hui A, Ignatchenko V, et al. Potentially Novel Candidate Biomarkers for Head and Neck Squamous Cell Carcinoma Identified Using an Integrated Cell Line-based Discovery Strategy. Mol Cell Proteomics. 2012 Nov. 11(11):1404-15. [Medline]. [Full Text].

Choi P, Chen C. Genetic expression profiles and biologic pathway alterations in head and neck squamous cell carcinoma. Cancer. 2005 Sep 15. 104(6):1113-28. [Medline].

Zivicova V, Gal P, Mifkova A, et al. Detection of Distinct Changes in Gene-expression Profiles in Specimens of Tumors and Transition Zones of Tenascin-positive/-negative Head and Neck Squamous Cell Carcinoma. Anticancer Res. 2018 Mar. 38 (3):1279-90. [Medline]. [Full Text].

Michna A, Schotz U, Selmansberger M, et al. Transcriptomic analyses of the radiation response in head and neck squamous cell carcinoma subclones with different radiation sensitivity: time-course gene expression profiles and gene association networks. Radiat Oncol. 2016 Jul 26. 11:94. [Medline]. [Full Text].

Karim S, Mirza Z, Chaudhary AG, Abuzenadah AM, Gari M, Al-Qahtani MH. Assessment of Radiation Induced Therapeutic Effect and Cytotoxicity in Cancer Patients Based on Transcriptomic Profiling. Int J Mol Sci. 2016 Feb 19. 17 (2):250. [Medline].

Ryan S Jackson, MD Assistant Professor, Department of Otolaryngology-Head and Neck Surgery, Washington University in St Louis School of Medicine

Ryan S Jackson, MD is a member of the following medical societies: Alpha Omega Alpha, American Academy of Otolaryngology-Head and Neck Surgery, American Medical Association

Disclosure: Nothing to disclose.

Tapan A Padhya, MD Professor and Vice Chairman, Director, Division of Head and Neck Oncology, Department of Otolaryngology-Head and Neck Surgery, University of South Florida College of Medicine

Disclosure: Nothing to disclose.

Francisco Talavera, PharmD, PhD Adjunct Assistant Professor, University of Nebraska Medical Center College of Pharmacy; Editor-in-Chief, Medscape Drug Reference

Disclosure: Received salary from Medscape for employment. for: Medscape.

Karen H Calhoun, MD, FACS, FAAOA Professor, Department of Otolaryngology-Head and Neck Surgery, Ohio State University College of Medicine

Karen H Calhoun, MD, FACS, FAAOA is a member of the following medical societies: American Academy of Facial Plastic and Reconstructive Surgery, American Head and Neck Society, Association for Research in Otolaryngology, Southern Medical Association, American Academy of Otolaryngic Allergy, American Academy of Otolaryngology-Head and Neck Surgery, American College of Surgeons, American Medical Association, American Rhinologic Society, Society of University Otolaryngologists-Head and Neck Surgeons, Texas Medical Association

Disclosure: Nothing to disclose.

Arlen D Meyers, MD, MBA Professor of Otolaryngology, Dentistry, and Engineering, University of Colorado School of Medicine

Arlen D Meyers, MD, MBA is a member of the following medical societies: American Academy of Facial Plastic and Reconstructive Surgery, American Academy of Otolaryngology-Head and Neck Surgery, American Head and Neck Society

Disclosure: Serve(d) as a director, officer, partner, employee, advisor, consultant or trustee for: Cerescan;RxRevu;Cliexa;Preacute Population Health Management;The Physicians Edge<br/>Received income in an amount equal to or greater than $250 from: The Physicians Edge, Cliexa<br/> Received stock from RxRevu; Received ownership interest from Cerescan for consulting; for: Rxblockchain;Bridge Health.

Benoit J Gosselin, MD, FRCSC Associate Professor of Surgery, Dartmouth Medical School; Director, Comprehensive Head and Neck Oncology Program, Norris Cotton Cancer Center; Staff Otolaryngologist, Division of Otolaryngology-Head and Neck Surgery, Dartmouth-Hitchcock Medical Center

Benoit J Gosselin, MD, FRCSC is a member of the following medical societies: American Head and Neck Society, American Academy of Facial Plastic and Reconstructive Surgery, North American Skull Base Society, American Academy of Otolaryngology-Head and Neck Surgery, American Medical Association, American Rhinologic Society, Canadian Medical Association, Canadian Society of Otolaryngology-Head & Neck Surgery, College of Physicians and Surgeons of Ontario, New Hampshire Medical Society, Ontario Medical Association

Disclosure: Nothing to disclose.

Perminder S Parmar, MD Staff Physician, Department of Otolaryngology, New York Eye and Ear Infirmary

Perminder S Parmar, MD is a member of the following medical societies: American Academy of Facial Plastic and Reconstructive Surgery and American Academy of Otolaryngology-Head and Neck Surgery

Disclosure: Nothing to disclose.

James M Pearson, MD Director, Pearson Facial Plastic Surgery, Beverly Hills/Hermosa Beach, CA

James M Pearson, MD is a member of the following medical societies: American Academy of Facial Plastic and Reconstructive Surgery, American Academy of Otolaryngology-Head and Neck Surgery, California Medical Association, and Los Angeles County Medical Association

Disclosure: Nothing to disclose.

Stimson P Schantz, MD Head, Department of Otolaryngology, Division of Head and Neck Surgery, New York Eye and Ear Infirmary

Stimson P Schantz, MD is a member of the following medical societies: American Academy of Otolaryngology-Head and Neck Surgery, American Association for Cancer Research, American College of Surgeons, American Laryngological Rhinological and Otological Society, American Medical Association, American Society for Head and Neck Surgery, New York Head and Neck Society, Society of Surgical Oncology, and Society of University Surgeons

Disclosure: Nothing to disclose.

Microarray Technologies in the Diagnosis and Treatment of Head and Neck Cancer

Research & References of Microarray Technologies in the Diagnosis and Treatment of Head and Neck Cancer|A&C Accounting And Tax Services
Source