High-throughput tissue analysis
Related Terms
Bioinformatics, DNA, DNA chip, FISH, fluorescence in situ hybridization, genome, high-throughput tissue analysis, IHC, immunohistochemistry, microarray, PCR, polymerase chain reaction, RNA, targeted therapies, tissue microarray, TMA, transcriptome.
Background
Tissue microarray, also called microarray, is one of many techniques developed to explore the inner workings of the living cell and the function of genes. It is used to identify individual ribonucleic acid (RNA) molecules in cells.
Genes are made of DNA, which is a very large molecule composed of a string of smaller chemicals called nucleotides held together by a chain of 5-carbon sugars called ribose. RNA is similar to DNA in that it comprises a string of nucleotides held together by a chain of ribose molecules. Each nucleotide in RNA corresponds to a similar nucleotide in DNA. RNA communicates the genetic information from DNA to the proteins that are produced in the cell. Proteins are both the building blocks of living tissue and the builders that do the work.
A microarray is a system that can identify many RNA molecules at a time by fixing them with specific matching molecules or markers in a wax matrix. There can be many hundreds of these markers in a single array, one for each RNA molecule that might be in the sample to be analyzed.
Although all cells in a living creature contain the entire genome of that creature, only a few are at work at any given time. A genome is the entire set of genes possessed by an organism. Knowing which genes are active gives insight into what cells are doing, whether the work is good, as in healthy functioning, or destructive as in disease. RNA comes only from the active DNA, so the set of RNA molecules in a cell indicates what the cell is doing. The active DNA is called the transcriptome of the cell.
Methods
Before a microarray assay can be done, a sample must be amplified because there is generally not enough material in a typical specimen. To get enough of a sample from a few cells, the ribonucleic acid (RNA) must be multiplied hundreds of times by a process called polymerase chain reaction (PCR). PCR is a method of using a cell's mechanics in the laboratory to multiply pieces of RNA.
When an amplified sample specimen from a cell washes through the wax matrix of a microarray, RNA molecules stick only to specific markers. At the end of the test, only markers that have their target RNA stuck to them glow under ultraviolet light. Because each marker is known, the RNA stuck to it can be identified.
The exact structure of many RNA molecules is known. It is therefore possible to create unique matching molecules that will combine with specific RNA molecules like connecting two sides of a zipper. The matching molecule can be made to glow under ultraviolet light by attaching a molecular component that glows.
Once a cell's RNA is known, researchers can know what the cell is doing. For example, if the cell is supposed to be making a hormone, the mechanism for making that hormone should be producing RNA. If it is a cancer cell, it will be making chemicals to promote its growth and spread beyond its normal boundaries. If it is an infecting organism, it will be making various chemicals that promote infection.
Microarrays are also used to identify DNA and proteins. The identification of DNA and the proteins it produces tells researchers what the cell is capable of doing and what it is doing at any moment in time. If the cell is cancerous, the reason why it has become a cancer can be determined. If it is an infectious organism, the reason why it causes infection can be determined.
Research
Cancer is the most active area of research using tissue microarray technology. Cancer cells make too many of some proteins, not enough of others, and several they shouldn't be making at all. This combination of abnormal functions allows the cancer to grow and spread. Once the abnormal proteins are identified using tissue microarray technology, a search for ways to correct the abnormalities can be focused, or "targeted."
Many so-called targeted therapies have already been developed and tested successfully in humans with various types of cancer. Many others are being developed. For example, a drug called imatinib (Gleevec?) is being used to treat leukemia. Bevacizumab (Avastin?) is being used to treat lung cancer, and trastuzumab (Herceptin?) is being used to treat breast cancer. Tissue microarray technology is one of the more common ways of identifying molecular targets for these therapies.
Genetic research using tissue microarray technology is also improving food crops and livestock. For example, Monsanto has created a strain of corn resistant to the herbicide Roundup?, and efforts are in progress to improve milk production and speed maturation of meat-producing animals.
Researchers using genetic techniques such as tissue microarray technology are working on converting organic waste such as weeds and sawdust into ethanol fuel for cars by transforming cellulose to glucose and then fermenting it.
Implications
Molecular biology is a new and highly complex science. It has already produced effective cancer treatments, healthier food crops, and a remarkably deeper understanding of the mechanics of life and disease. Microarray is one of many techniques used in this new science. The main advantage of microarray technology is the quantity of molecules it can identify in a single run. Microarray is a powerful tool for identifying the abnormal functions of the tissues involved in many diseases.
There are other similar techniques for identifying specific gene products, but none can identify nearly as many at a single time. These tests, called immunohistochemistry and fluorescence in situ hybridization, are used to characterize certain cancers because they identify effective treatments.
Limitations
As with all new technologies, progress is slow, costs are high, and the time from discovery to therapy can be long. In terms of human disease, there are technical issues such as the quantity of tissue required to run a test and the long road from initial RNA identification to safe and effective drugs safe for human use.
Future research
Chronic diseases: Patients with chronic diseases such as arthritis have already benefited from microarray technology with targeted therapies such as etanercept and infliximab. The use of microarray technology in studying other chronic diseases such as Alzheimer's is yielding greater understanding of possible approaches to prevention and treatment.
Energy: New energy sources such as ethanol from sawdust and weeds will soon be in production. Microarray technology is one of the principal methods used to identify promising genes and gene products that can be used to create biofuels.
Pollution: Abatement of environmental pollutants is possible with such advances as genetically altered bacteria that eat petroleum. Microarray technology is one of the principal methods used to identify promising genes and gene products that can be used for pollution control.
Author information
This information has been edited and peer-reviewed by contributors to the Natural Standard Research Collaboration (www.naturalstandard.com).
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