Skip to main content
SpringerLink
Log in

Genomics and Proteomics

  • Chapter
  • First Online:
Experimental and Clinical Metastasis

  • 759 Accesses

Abstract

Understanding the specific changes that occurl in the DNA, RNA, and proteins of cancerous cells may allow for the identification of markers for early cancer detection, prevention and in the development of molecular-targeted treatments. Gene expression profiling is a powerful tool that allows for the evaluation of thousands of genes simultaneously and can provide insight into the complex interactions between genes in biologic specimen (Fingleton, Cancer Genomics–Proteomics 4:211–221, 2007). Proteomic tools have enabled the analysis of thousands of proteins and the identification of disease-specific proteins (Hudler et al, Clinical and Experimental Metastasis 27:441–451, 2010). These tools have the potential to lead to clinical applications such as improved diagnosis, an understanding specific tumor behavior, prognosis indicators and prediction of response to different treatment modalities.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Log in via an institution
Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Abramovitz M, Leyland-Jones B (2006) A systems approach to clinical oncology: focus on breast cancer. Proteome Sci 4:5

    Google Scholar 

  • Adam BL et al (2002) Serum protein fingerprinting coupled with a pattern-matching algorithm distinguishes prostate cancer from benign prostate hyperplasia and healthy men. Cancer Res 62:3609–3614

    PubMed  CAS  Google Scholar 

  • Alaiya A, Al-Mohanna M, Linder S (2005) Clinical cancer proteomics: promises and pitfalls. J Proteome Res 4:1213–1222. doi:10.1021/pr050149f

    Article  PubMed  CAS  Google Scholar 

  • Altshuler D, Daly MJ, Lander ES (2008) Genetic mapping in human disease. Science 322, 881–888. doi:322/5903/881 [pii] 10.1126/science.1156409

    Article  PubMed  CAS  Google Scholar 

  • Bayani J, Squire JA (2004) Fluorescence in situ hybridization (FISH). Curr Protoc Cell Biol Chapter 22, Unit 22 24, doi:10.1002/0471143030.cb2204s23

    Google Scholar 

  • Brazma A et al (2001) Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet 29:365–371

    Article  PubMed  CAS  Google Scholar 

  • Calin GA et al (2002) Frequent deletions and down-regulation of micro-RNA genes miR15 and miR16 at 13q14 in chronic lymphocytic leukemia. Proc Natl Acad Sci U S A 99:15524–15529. doi:10.1073/pnas.242606799 242606799 [pii]

    Article  PubMed  CAS  Google Scholar 

  • Chaerkady R, Pandey A (2008) Applications of proteomics to lab diagnosis. Ann Rev Pathol 3:485–498

    Article  CAS  Google Scholar 

  • Caprioli RM (2005) Deciphering protein molecular signatures in cancer tissues to aid in diagnosis, prognosis, and therapy. Cancer Res 65:10642–10645. doi:65/23/10642 [pii] 10.1158/0008–5472.CAN-04–3581

    Article  PubMed  CAS  Google Scholar 

  • Chung CH, Levy S, Chaurand P, Carbone DP (2007) Genomics and proteomics: emerging technologies in clinical cancer research. Crit Rev Oncol Hematol 61:1–25. doi:S1040–8428(06)00109–0 [pii] 10.1016/j.critrevonc.2006.06.005

    Article  PubMed  Google Scholar 

  • Conway C et al (2009) Gene expression profiling of paraffin-embedded primary melanoma using the DASL assay identifies increased osteopontin expression as predictive of reduced relapse-free survival. Clin Cancer Res 15:6939–6946

    Article  PubMed  CAS  Google Scholar 

  • Cornish TJ, Cotter RJ (1993) A curved-field reflectron for improved energy focusing of product ions in time-of-flight mass spectrometry. Rapid Commun Mass Spectrom 7:P1037–P1040. doi:10.1002/rcm.1290071114

    Article  Google Scholar 

  • Couzin J (2008) MicroRNAs make big impression in disease after disease. Science 319:1782–1784. doi:319/5871/1782 [pii] 10.1126/science.319.5871.1782

    Article  PubMed  CAS  Google Scholar 

  • DeRisi J et al (1996) Use of a cDNA microarray to analyse gene expression patterns in human cancer. Nat Genet 14, 457–460. doi:10.1038/ng1296–457

    Article  PubMed  CAS  Google Scholar 

  • Dumur CI et al (2008) Interlaboratory performance of a microarray-based gene expression test to determine tissue of origin in poorly differentiated and undifferentiated cancers. J Mol Diagn 10:67–77. doi:jmoldx.2008.070099 [pii] 10.2353/jmoldx.2008.070099

    Article  PubMed  CAS  Google Scholar 

  • Fenn JB, Mann M, Meng CK, Wong SF, Whitehouse CM (1989) Electrospray ionization for mass spectrometry of large biomolecules. Science 246:64–71

    Article  PubMed  CAS  Google Scholar 

  • Fingleton B (2007) Molecular targets in metastasis: lessons from genomic approaches. Cancer Genom Proteom 4:211–221

    CAS  Google Scholar 

  • Foulkes WD (2008) Inherited susceptibility to common cancers. N Engl J Med 359:2143–2153. doi:359/20/2143 [pii] 10.1056/NEJMra0802968

    Article  PubMed  CAS  Google Scholar 

  • Futreal PA et al (2004) A census of human cancer genes. Nat Rev Cancer 4:177–183. doi:10.1038/nrc1299 nrc1299 [pii]

    Article  PubMed  CAS  Google Scholar 

  • Gonzalez-Angulo AM, Hennessy BT, Mills GB (2010) Future of personalized medicine in oncology: a systems biology approach. J Clin Oncol 28:2777–2783. doi:JCO.2009.27.0777 [pii] 10.1200/JCO.2009.27.0777

    Article  PubMed  CAS  Google Scholar 

  • Goswami RS et al (2010) Optimization and analysis of a quantitative real-time PCR-based technique to determine microRNA expression in formalin-fixed paraffin-embedded samples. BMC Biotechnol 10:47. doi:1472–6750-10–47 [pii] 10.1186/1472–6750-10–47

    Article  PubMed  Google Scholar 

  • Greenman C et al (2007) Patterns of somatic mutation in human cancer genomes. Nature 446:153–158. doi:nature05610 [pii] 10.1038/nature05610

    Article  PubMed  CAS  Google Scholar 

  • Harris TJ, McCormick F (2010) The molecular pathology of cancer. Nature rev 7:251–265

    CAS  Google Scholar 

  • Henzel WJ et al(1993) Identifying proteins from two-dimensional gels by molecular mass searching of peptide fragments in protein sequence databases. Proc Natl Acad Sci U S A 90:5011–5015

    Article  PubMed  CAS  Google Scholar 

  • Hirschhorn JN (2009) Genomewide association studies–illuminating biologic pathways. N Engl J Med 360. 1699–1701. doi:NEJMp0808934 [pii] 10.1056/NEJMp0808934

    Google Scholar 

  • Hu Z et al (2006) The molecular portraits of breast tumors are conserved across microarray platforms. BMC Genomics 7:96. doi:1471–2164-7–96 [pii] 10.1186/1471–2164-7–96

    Google Scholar 

  • Hanash S (2003) Disease proteomics. Nature 422:226–232, doi:10.1038/nature01514 nature01514 [pii]

    Article  PubMed  CAS  Google Scholar 

  • Hudler P, Gorsic M, Komel R (2010) Proteomic strategies and challenges in tumor metastasis research. Clin Exp Metastasis 27:441–451. doi:1007/s10585–010-9339–7

    Article  PubMed  CAS  Google Scholar 

  • Iwadate Y (2008) Clinical proteomics in cancer research-promises and limitations of current two-dimensional gel electrophoresis. Curr Med Chem 15:2393–2400

    Article  PubMed  CAS  Google Scholar 

  • Jeffrey SS, Lonning PE, Hillner BE (2005) Genomics-based prognosis and therapeutic prediction in breast cancer. J Natl Compr Canc Netw 3:291–300

    PubMed  Google Scholar 

  • Jr GW et al (1999) Proteinchip® surface enhanced laser desorption/ionization (SELDI) mass spectrometry: a novel protein biochip technology for detection of prostate cancer biomarkers in complex protein mixtures. Prostate Cancer Prostatic Dis 2:264–276.doi:10.1038/sj.pcan.4500384 4500384 [pii]

    Article  PubMed  Google Scholar 

  • Kubota K, Kosaka T, Ichikawa K (2009) Shotgun protein analysis by liquid chromatography-tandem mass spectrometry. Methods Mol Biol Clifton NJ 519:483–494. doi:10.1007/978–1-59745–281-6_32

    CAS  Google Scholar 

  • Lilley KS, Friedman DB (2004) All about DIGE: quantification technology for differential-display 2D-gel proteomics. Expert Rev Proteomics 1:401–409. doi:10.1586/14789450.1.4.401

    Article  PubMed  CAS  Google Scholar 

  • Lu J et al (2005) MicroRNA expression profiles classify human cancers. Nature 435:834–838. doi:nature03702 [pii] 10.1038/nature03702

    Article  PubMed  CAS  Google Scholar 

  • Mann M, Hojrup P, Roepstorff P (1993) Use of mass spectrometric molecular weight information to identify proteins in sequence databases. Biol Mass Spectrom 22:338–345. doi:10.1002/bms.1200220605

    Article  PubMed  CAS  Google Scholar 

  • Mann M, Hendrickson RC, Pandey A (2001) Analysis of proteins and proteomes by mass spectrometry. Annu Rev Biochem 70:437–473. doi:70/1/437 [pii] 10.1146/annurev.biochem.70.1.437

    Article  PubMed  CAS  Google Scholar 

  • Manolio TA, Brooks LD, Collins FS (2008) A HapMap harvest of insights into the genetics of common disease. J Clin Invest 118:1590–1605. doi:10.1172/JCI34772

    Article  PubMed  CAS  Google Scholar 

  • Mardis ER (2008a) The impact of next-generation sequencing technology on genetics. Trends Genet 24:133–141

    Article  CAS  Google Scholar 

  • Mardis ER (2008b) Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 9:387–402. doi:10.1146/annurev.genom.9.081307.164359

    Article  CAS  Google Scholar 

  • Merchant M, Weinberger SR (2000) Recent advancements in surface-enhanced laser desorption/ionization-time of flight-mass spectrometry. Electrophoresis 21:1164–1177. doi:10.1002/(SICI)1522–2683(20000401)21:6 < 1164::AID-ELPS1164 > 3.0.CO;2–0 [pii] 10.1002/(SICI)1522–2683(20000401)21:6 < 1164::AID-ELPS1164 > 3.0.CO;2–0

    Article  PubMed  CAS  Google Scholar 

  • Minden JS, Dowd SR, Meyer HE, Stuhler K (2009) Difference gel electrophoresis. Electrophoresis 30 (Suppl 1):S156–161. doi:10.1002/elps.200900098

    Google Scholar 

  • Monzon FA, Koen TJ (2010) Diagnosis of metastatic neoplasms: molecular approaches for identification of tissue of origin. Arch Pathol Lab Med 134:216–224

    PubMed  CAS  Google Scholar 

  • Motoyama A, Yates JR 3rd (2008) Multidimensional LC separations in shotgun proteomics. Anal Chem 80:7187–7193, doi:10.1021/ac8013669

    Article  PubMed  CAS  Google Scholar 

  • Ornstein DK et al (2004) Serum proteomic profiling can discriminate prostate cancer from benign prostates in men with total prostate specific antigen levels between 2.5 and 15.0 ng/ml. J Urol 172:1302–1305. doi:00005392–200410000-00019 [pii]

    Article  PubMed  CAS  Google Scholar 

  • Parikh AA, Johnson JC, Merchant NB (2008) Genomics and proteomics in predicting cancer outcomes. Surg Oncol Clin N Am 17:257–277 (vii)

    Article  PubMed  Google Scholar 

  • Papadopoulos N, Kinzler KW, Vogelstein B (2006) The role of companion diagnostics in the development and use of mutation-targeted cancer therapies. Nat Biotechnol 24:985–995. doi:nbt1234 [pii] 10.1038/nbt1234

    Article  PubMed  CAS  Google Scholar 

  • Perou CM et al (2000) Molecular portraits of human breast tumours. Nature 406:747–752. doi:10.1038/35021093

    Article  PubMed  CAS  Google Scholar 

  • Petricoin EF, Zoon KC, Kohn EC, Barrett JC, Liotta LA (2002a) Clinical proteomics: translating benchside promise into bedside reality. Nat Rev Drug Discov 1:683–695. doi:10.1038/nrd891 nrd891 [pii]

    Article  CAS  Google Scholar 

  • Petricoin EF 3rd et al (2002b) Serum proteomic patterns for detection of prostate cancer. J Natl Cancer Inst 94:1576–1578

    Article  CAS  Google Scholar 

  • Pleasance ED et al (2010) A comprehensive catalogue of somatic mutations from a human cancer genome. Nature 463:191–196. doi:nature08658 [pii] 10.1038/nature08658

    Article  PubMed  CAS  Google Scholar 

  • Pushkarev D, Neff NF, Quake SR (2009) Single-molecule sequencing of an individual human genome. Nat Biotechnol 27:847–852

    Article  PubMed  CAS  Google Scholar 

  • Quackenbush J (2002) Microarray data normalization and transformation. Nat Genet 32 (Suppl):496–501, doi:10.1038/ng1032 ng1032 [pii]

    Google Scholar 

  • Quackenbush J (2006) Microarray analysis and tumor classification. N Engl J Med 354:2463–2472. doi:354/23/2463 [pii] 10.1056/NEJMra042342

    Article  PubMed  CAS  Google Scholar 

  • Quackenbush J (2009) Data reporting standards: making the things we use better. Genome Med 1:111. doi:gm111 [pii] 10.1186/gm111

    Google Scholar 

  • Ramaswamy S et al (2001) Multiclass cancer diagnosis using tumor gene expression signatures. Proc Natl Acad Sci U S A 98:15149–15154. doi:10.1073/pnas.211566398 211566398 [pii]

    Article  PubMed  CAS  Google Scholar 

  • Ramaswamy S, Golub TR (2002) DNA microarrays in clinical oncology. J Clin Oncol 20:1932–1941

    PubMed  CAS  Google Scholar 

  • Ramaswamy S, Perou CM (2003) DNA microarrays in breast cancer: the promise of personalised medicine. Lancet 361:1576–1577. doi:S0140–6736(03)13322–3 [pii] 10.1016/S0140–6736(03)13322–3

    Article  PubMed  Google Scholar 

  • Roboz J (2005) Mass spectrometry in diagnostic oncoproteomics. Cancer Invest 23:465–478

    Article  PubMed  CAS  Google Scholar 

  • Rosenblatt KP et al (2004) Serum proteomics in cancer diagnosis and management. Annu Rev Med 55:97–112

    Article  PubMed  CAS  Google Scholar 

  • Schena M, Shalon D, Davis RW, Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467–470

    Article  PubMed  CAS  Google Scholar 

  • Shi L et al (2006) The Microarray quality control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements. Nat Biotechnol 24:1151–1161

    Article  PubMed  CAS  Google Scholar 

  • Simpkins F, Czechowicz JA, Liotta L, Kohn EC (2005) SELDI-TOF mass spectrometry for cancer biomarker discovery and serum proteomic diagnostics. Pharmacogenomics 6:647–653. doi:10.2217/14622416.6.6.647

    Article  PubMed  CAS  Google Scholar 

  • Sorlie T et al (2003) Repeated observation of breast tumor subtypes in independent gene expression data sets. Proc Natl Acad Sci U S A 100:8418–8423. doi:10.1073/pnas.09326921000932692100 [pii]

    Article  PubMed  CAS  Google Scholar 

  • Spellman PT et al (2002) Design and implementation of microarray gene expression markup language (MAGE-ML). Genome Biol 3:Research0046

    Google Scholar 

  • Stratton M (2008) Genome resequencing and genetic variation. Nat Biotechnol 26:65–66. doi:nbt0108–65 [pii] 10.1038/nbt0108–65

    Article  PubMed  CAS  Google Scholar 

  • Stratton MR, Campbell PJ, Futreal PA (2009) The cancer genome. Nature 458:719–724. doi:nature07943 [pii] 10.1038/nature07943

    Article  PubMed  CAS  Google Scholar 

  • Sugimura H et al (2010) Fluorescence in situ hybridization analysis with a tissue microarray: ‘FISH and chips’ analysis of pathology archives. Pathol Int 60:543–550. doi:PIN2561 [pii] 10.1111/j.1440–1827.2010.02561.x

    Article  PubMed  Google Scholar 

  • Tanas MR, Goldblum JR (2009) Fluorescence in situ hybridization in the diagnosis of soft tissue neoplasms: a review. Adv Anat Pathol 16:383–391. doi:10.1097/PAP.0b013e3181bb6b86 00125480–200911000-00002 [pii]

    Article  PubMed  CAS  Google Scholar 

  • Tothill RW et al (2005) An expression-based site of origin diagnostic method designed for clinical application to cancer of unknown origin. Cancer Res 65:4031–4040

    Article  PubMed  CAS  Google Scholar 

  • Turnbull C et al (2010) Genome-wide association study identifies five new breast cancer susceptibility loci. Nat Genet 42:504–507. doi:ng.586 [pii] 10.1038/ng.586

    Article  PubMed  CAS  Google Scholar 

  • Van Prooijen-Knegt AC et al (1982) In situ hybridization of DNA sequences in human metaphase chromosomes visualized by an indirect fluorescent immunocytochemical procedure. Exp Cell Res 141:397–407

    Article  PubMed  Google Scholar 

  • Volpi EV, Bridger JM (2008) FISH glossary: an overview of the fluorescence in situ hybridization technique. Biotechniques 45:385–386, 388, 390 passim. doi:000112811 [pii] 10.2144/000112811

    Article  PubMed  CAS  Google Scholar 

  • Waddell N et al (2010) Gene expression profiling of formalin-fixed, paraffin-embedded familial breast tumours using the whole genome-DASL assay. J Pathol 221:452–461. doi:10.1002/path.2728

    PubMed  CAS  Google Scholar 

  • Wang X et al (2005) Autoantibody signatures in prostate cancer. N Engl J Med 353:1224–1235. doi:353/12/1224 [pii] 10.1056/NEJMoa051931

    Article  PubMed  CAS  Google Scholar 

  • Weksberg R et al (2005) A method for accurate detection of genomic microdeletions using real-time quantitative PCR. BMC Genomics 6:180. doi:1471–2164-6–180 [pii] 10.1186/1471–2164-6–180

    Article  PubMed  Google Scholar 

  • Wong SC et al (2009) Advanced proteomic technologies for cancer biomarker discovery. Expert Rev Proteomics 6:123–134. doi:10.1586/epr.09.1

    Article  PubMed  CAS  Google Scholar 

  • Yates JR 3rd, Speicher S, Griffin PR, Hunkapiller T (1993) Peptide mass maps: a highly informative approach to protein identification. Anal Biochem 214:397–408. doi:S0003–2697(83)71514–9 [pii] 10.1006/abio.1993.1514

    Article  PubMed  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

  1. Department of Pathology, Henry C Witelson Ocular Pathology Laboratory and Department of Dermatology, McGill University, Montreal, QC, Canada

    Dominique Fausto de Souza M.D.

Authors
  1. Dominique Fausto de Souza M.D.
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Dominique Fausto de Souza M.D. .

Editor information

Editors and Affiliations

  1. Centre for Genomic Regulation, N/A, Barcelona, N/A, Spain

    Julia V. Burnier

  2. , Ophthalmology, Pathology, Medicine & Onc, McGill University Health Centre, University Street 3775, Montreal, H3A 2B4, Québec, Canada

    Miguel N. Burnier, Jr.

Rights and permissions

Reprints and permissions

Copyright information

© 2013 Springer Science+Business Media New York

About this chapter

Cite this chapter

Fausto de Souza, D. (2013). Genomics and Proteomics. In: Burnier, J., Burnier, Jr., M. (eds) Experimental and Clinical Metastasis. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-3685-0_22

Download citation

Publish with us

Policies and ethics

Search

Navigation