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Gene expression

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Related terms
Background
Methods
Research
Implications
Limitations
Safety
Future research
Author information
Bibliography

Related Terms
  • Activator, baseline expression, down-regulation, expression profile, expression profiling, expression signals, gene expression, gene expression profiling, gene signatures, gene transcription, genetic profiling, genome expression, inducible gene, messenger RNA expression, MAGE, microarray and gene expression, microarrays, mRNA, oligonucleotide array, over-expression, probe, promotion, protein expression profile, repression, SAGE, serial analysis of gene expression, transcript expression, transcript profiling, transcription, transcription factors, under-expression, up-regulation.

Background
  • Genes, the basic units of heredity, are found in all cells of the body and are made of DNA (the carrier of genetic information). The genes in a genome (the set of complete genetic material) do not affect cell function until they are "expressed."
  • Gene expression is the process by which heritable information contained in a gene is made into a functional gene product. The process of gene expression involves the production of a protein or a functional RNA from its gene. Every living cell that produces protein from DNA contains an expression system that typically contains a DNA source and the material to transcribe the DNA into messenger RNA (mRNA; RNA that serves as a template for protein synthesis) and translate the mRNA into protein.
  • Two major stages are required for gene expression, gene transcription and gene translation. Gene transcription is the process by which the gene's DNA sequence is copied into mRNA to produce an RNA molecule (a primary transcript) with the virtually identical sequence as the gene.
  • Gene translation is the process by which transcribed mRNA guides the creation of proteins from amino acids. Information is passed from DNA as mRNA is converted into a series of amino acids bound together with peptide bonds (a type of bond between two molecules), which involves a translation from one code, nucleotide sequence to another code, and an amino acid sequence (languages used by molecules within a cell to communicate to each other).
  • Transcription factors turn on or turn off the genes they control by binding to promoters (the DNA segment that controls gene expression) and enhancers (the region of DNA that involved in initiating transcription).
  • Regulation of gene expression is the influence of the cell on the amount, timing, and appearance of the functional product of a gene. The cell employs gene regulation to dictate structure and function, and gene regulation is the foundation of cell differentiation, as well as the versatility and adaptability of the organism. This is due to the profound effect that control of the timing, location, and amount of gene expression has on the function of the gene in the organism.
  • There is great variation in the way genes are expressed in the human genome. Genes that are essential for basic cell functions are expressed in all cells all of the time. Other genes, such as those that encode muscle proteins in muscle cells are only expressed in those specific cell types. Some genes are activated or inhibited by circulating signals, such as hormones.

Methods
  • Measurement of mRNA levels:
  • Microarrays: A microarray is a method to analyze gene expression that uses a small membrane or glass slide containing gene samples in a prearranged pattern. A microarray uses the ability of mRNA to bind specifically to the DNA template from which it came. An array containing many DNA samples can determine expression levels of hundreds or thousands of genes within a cell by measuring the amount of mRNA bound to each site on the array. The amount of mRNA bound to the specific microarray sites is measured to produce the cells gene expression profile. Microarrays are very useful in measuring gene expression with large numbers of genes or small sample sizes
  • Northern blotting: With Northern blotting, RNA is transferred onto a matrix (objects arranged in rows and columns) and the presence of a specific RNA molecule is detected by DNA-RNA hybridization (a DNA/RNA combination that is heated and then cooled). Northern blotting remains the gold-standard to detect and measure mRNA levels because it allows a direct comparison of the mRNA abundance between samples on a single membrane. The advantages of Northern blots include wide acceptance, the relative ease of the procedure, and their versatility. The disadvantages include the need to use radioactive agents, the lengthy process, and the quality of the data being negatively affected by even slight imperfections in the RNA sample.
  • Oligonucleotide chips: Oligonucleotides are short fragments of a single-stranded DNA. Oligonucleotide chips provide a method to use gene sequence information from parallel experiments to monitor large numbers of gene expression measurements. Small glass plates with thousands of oligonucleotide probes attached to their surfaces are used. Since the oligonucleotides are synthesized directly onto the surface, very large numbers of mRNAs can be probed at the same time.
  • Polymerase chain reaction(PCR): PCR amplifies, or copies, small DNA segments and is considered vital for molecular and genetic analyses since studies of isolated pieces of DNA are nearly impossible without PCR amplification. PCR amplifies DNA segments by generating multiple copies using DNA polymerase enzymes (enzymes that build new DNA strands) under controlled conditions. A single copy of the DNA segment or gene can be cloned into millions of copies, which is visualized using dyes and other techniques.
  • For example, PCR was used in the Human Genome Project (HGP), a research program designed to map out all of the genes that make up human beings. PCR is capable of producing very precise measurements of the exact number of copies of mRNA in a given volume of tissue. The accuracy of the data obtained by this method makes it the first choice, although the required equipment and material is costly.
  • Reverse transcriptase polymerase chain reaction (RT-PCR): Reverse transcriptase is an enzyme that converts RNA into DNA, and this technique reverse-transcribes (the process of making DNA using RNA as a template and reverse transcriptase as a catalyst) mRNA into cDNA (DNA synthesized from an RNA template using reverse transcriptase), then increases the cDNA to measurable levels with PCR to measure gene expression.
  • Serial analysis of gene expression (SAGE): SAGE is a method of large-scale gene expression analysis that can potentially generate the entire list of mRNAs present within a cell population at a given time. SAGE captures RNAs, "rewrites" them into DNA, and cuts a small tag, termed a sequence tag, from each one. SAGE combines the sequence tags into long molecules called concatemers. A computer program reads these molecules, counts and analyzes them, and provides a list of the genes they belong to.
  • Measurement of protein levels:
  • Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE): Proteins differ from each other in terms of mass and charge, and 2D-PAGE uses these properties to separate proteins in a sample. 2D-PAGE separates proteins on a two-dimensional sheet of gel, first in one direction based on their electrical level by applying a voltage across the gel, and then in the other direction based on their molecular weight. A two-dimensional image with many protein spots is produced, with the intensity of each spot related to the amount of the specific protein present. 2D-PAGE is able to isolate the major proteins in a sample and compare protein levels in related samples.
  • Western blot: Western blots measure the levels of production of a given protein in a particular tissue or at a specific developmental stage, and are used to determine the molecular weight of a protein and to measure amounts of the protein in different samples. The proteins are separated by gel electrophoresis (a method to separate large molecules from a mixture of similar molecules), and then transferred to a sheet of special blotting paper that contains a generic protein, such as a milk protein. An antibody that has an enzyme or dye attached to it is then added to the solution, which is able to bind to its specific protein and allows for visualization.

Research
  • Non-small cell lung cancer (NSCLC): NSCLC comprises 85-90% of lung cancers and forms in the lung tissue, usually in the cells lining the air passages. A new system of classifying NSCLC has been achieved through research involving gene expression, which has provided an important understanding of how NSCLC is caused and maintained. Potential biomarkers, or chemical compounds associated with specific diseases, have been identified through research on gene expression and may be useful in diagnosis, screening, and assessing treatment effectiveness. These breakthroughs in understanding the molecular biology of NSCLC are expected to lead to improved patient outcomes from more effective treatments.
  • Breast cancer: Microarray technology, which allows the simultaneous study of the expression of thousands of genes, has identified subgroups of breast cancer in terms of treatment response. This may lead to greater accuracy in predicting disease and treatment outcomes and a better understanding of the disease process and progression, potentially impacting the management of breast cancer patients.
  • Melanoma: Melanoma is the most serious and aggressive form of skin cancer. Gene expression profiling with a series of patients with melanoma found an expression signature of 254 genes with predictive significance. Most of these genes were associated with tumor thickness, emphasizing the importance of thickness in disease prognosis. Immunohistochemistry (a method for locating proteins in tissue cells by using antibodies) found three new markers of disease prediction (mini-chromosome maintenance proteins 3, 4 and 6). Because several of the genes related to disease progression encode molecules that are the target of anti-cancer therapies, the results may hopefully contribute to the treatment of end-stage melanoma.

Implications
  • Research involving gene expression can potentially provide a better understanding of the factors that underlie the causation, disease process and drug effectiveness with a variety of medical conditions. This knowledge may ultimately improve patient outcomes.
  • Gene expression has the potential to aid in the development of more effective drugs by uncovering gene regulatory and biochemical pathways, and to help researchers understand how these pathways are disrupted by disease and altered by drugs.
  • Advances in understanding the molecular mechanisms of action of anti-cancer drugs may lead to improvement of current drug therapies and the identification of new targets.

Limitations
  • A limitation with gene expression analysis is related to the large number of variables to a small number of observations have added further constraints. This increases the potential of finding "false positives" that are due to chance.
  • Gene expression profiling is unlikely to provide biochemical information on the functional activities of proteins

Safety




Future research
  • Many questions regarding gene expression remain to be studied. Microarray analysis can help investigate relatively unexplored areas of gene expression. Some of these areas include how gene expression changes during the different stages of cell development, how post-transcription mechanisms control the target mRNA, how DNA affects gene expression, and what exactly makes up the gene regulatory networks that control cell function.
  • Gene expression profiling is changing the understanding of breast cancer biology by identifying subgroups of these patients. This knowledge may allow a better selection of patients in need of additional treatment following the primary therapy and may help in the development of tailored treatment approaches.

Author information
  • This information has been edited and peer-reviewed by contributors to the Natural Standard Research Collaboration (www.naturalstandard.com).

Bibliography
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  6. National Human Genome Research Institute (NHGRI). .
  7. Natural Standard: The Authority on Integrative Medicine. .
  8. Petty RD, Nicolson MC, Kerr KM, et al. Gene expression profiling in non-small cell lung cancer: from molecular mechanisms to clinical application. Clin Cancer Res. 2004;10(10):3237-48.
  9. Weichselbaum RR, Kufe DW, Hellman S, et al. Radiation-induced tumour necrosis factor-alpha expression: clinical application of transcriptional and physical targeting of gene therapy. Lancet Oncol. 2002;3(11):665-71.
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  11. Winnepenninckx V, van den Oord JJ. Gene expression profiling and clinical outcome in melanoma: in search of novel prognostic factors. Expert Rev Anticancer Ther. 2007;7(11):1611-31.

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The information in this monograph is intended for informational purposes only, and is meant to help users better understand health concerns. Information is based on review of scientific research data, historical practice patterns, and clinical experience. This information should not be interpreted as specific medical advice. Users should consult with a qualified healthcare provider for specific questions regarding therapies, diagnosis and/or health conditions, prior to making therapeutic decisions.

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