Proteinchip - Engineering Seminar

INTRODUCTION

Imagine a device no bigger than a credit card that could extract your DNA from a drop of blood and map your entire genetic code while you wait. Within a short period of time the proneness to any illness or disease could be mapped and studied. This is not a snippet from a fiction movie. Biologists and engineers will have ONE working in just a few years, because the tool that makes it possible, a genetic microarray known as the " DNA chip ", already exists. Able to scrutinize tens of thousands of genes at once, the DNA chip's astonishing abilities are astounding biologists."Using these chips, people can in one afternoon confirm work that takes several years using conventional gene-sequencing processes".

The chips aren't just about increased speed. Using them, researchers can do things that were previously almost impossible, such as, uncovering the genetic machinations behind the complex biochemistry of organisms. With a yeast cell, for example, virtually all of its 6200 genes can be represented on just four chips. It is then possible to take "snapshots" that reveal which genes are active, which are dormant and how these patterns change during the organism's life cycle. The chips would radically change our ability to discover drugs, infectious processes and even disease processes that we didn't know about before. What silicon chips did for computers, DNA chips may do for biological research. Systems Biology will be the challenge of the 21st century and the best and most efficient way to understand the biology of systems will be to use tools such as these chips.

The similarities between silicon chips and their gene-oriented counterparts begin with the way they are made. Like computer chips, most DNA chips are produced by computer-controlled micro printing. In computer chips, the process lays down microscopic circuits and switches; in DNA chips, it puts down the stuff of genes. The DNA microarrays have been utilized to examine the changes in gene expression and to generate a database of patterns of gene expression or gene expression changes associated with a certain phenotype or physiological state. Upon separation of the proteins, the resulting gel will be stained and analyzed by computer software to provide quantitative results on fold-induction or repression of protein expression between samples, such as diseased and non-diseased states or control and drug-treated samples. ProteinChip Software automatically writes out ProteinChip data sets for compatibility with protein and protein fragment databases . The computer analyzes the forces of attraction and repulsion between atoms, depending on their positions, distances, and angles. It shuffles through all the possible arrangements to arrive at the most stable three-dimensional configuration

In a few years, the human genome project will be complete and biologists will have a rough idea of the average genetic make-up of a human being. But specific variations from the normal are often crucial in determining a person's susceptibility to disease or their response to drugs. Chips will enable doctors to take a quick snapshot of a person's genes to see which treatment is the best and which drugs to avoid. The DNA chip will be a powerful tool for understanding patterns of gene expression in cells. A gene expresses itself when it acts as a template to make its own distinctive protein. The strength of a gene's expression depends on how much of that protein it causes to be made. Having an eaSj .-.a. "3 measure the strength of a gene's expression would be extremely useful to biologists. But the chip has no memory or processing capability, but engineers can measure inductance, capacitance, impedance or resistance across the device.

As the demand for DNA chips and the computers that read the results grow, the cost of both should plummet in the near future. Chips now cost as much as $ 2000 each to make and some of the equipment needed to make and read them is TEN times more expensive than the chip. The DNA chips are set to revolutionize every aspect of biology and within three to five years, virtually every scientist will have access to these chips at an affordable price low enough to rival that of disposable needles for syringes. The biopchips markets will continue to increase in the next decade because medicine will demand tailor-made medical services using these chips as powerful tools. The competition in the development of DNA and protein chips will become more intense worldwide.

MAKING OF THE CHIPS

The chips are made by first coating a surface like glass or silica with a sticky chemical. Then at precise locations, nucleotides are attached. These include the four "bases" adenine (A), cytosine (C), guanine (G) and thymine (T). The nucleotides are then linked to form short chains with different sequences. Some chipmakers build the chip first and then stick them on to the surface, while others build them onsite by adding molecules one by one. When finished, the microarray is dotted with nucleotides, ranging from just a few dozens to tens of thousands of short strands of nucleotides.

This repertoire of sequences lets the DNA chip do its work -searching out specific sequences from an organism's genome. The method works because DNA consists of two strands along which "A" on one strand always binds with "T" on the other and "C" on one strand always binds with "G" on the other. This gives the double helix a "complementary nature".

To pick out a gene, the strings on the DNA chip don't have to be too long. A typical gene may contain 10 000 pairs of nucleotides, or more. But within a gene's chain there's usually a short sequence, no more than 25 bases long, unique to that gene. By encoding that short, unique chain on a chip geneticists can represent the whole gene. This shorthand makes the entire process manageable. Thus it is a computer chip that contains inorganic silicon, organic protein molecules, and microfluidic channels. The protein biochip, which uses the proteins to identify specific molecules, is designed to be used in handheld devices that will quickly detect low levels of harmful or therapeutic chemicals and microbes. The biochip contains tiny channels that allow fluids to pass by proteins that are attached to the chip using a process that leverages the proteins' naturally occurring electrical charges. In creating the protein chips, the scientists used a contact-printing robot developed earlier by HHMI investigator Patrick O. Brown at Stanford University. The robot precisely delivers tiny droplets of liquid protein—each the width of a human hair—to microscope slides. The robot placed liquid protein samples on microscope slides at a density of 1,600 spots per square centimeter. The protein samples were made to adhere to the glass slides by coating the slides with an aldehyde-containing reagent that attaches to primary amines, chemicals that are commonly found in proteins. The scientists also took measures to prevent evaporation and denaturation of the proteins, thereby ensuring that the proteins on the slide would retain their natural shape and activity.

A supercomputer was originally developed to simulate elementary particles in high-energy physics to help determine the structures and functions of proteins, including, for example, the 30,000 or so proteins encoded by the human genome. Structural information will help scientists better understand proteins' role in disease and health, and may lead to new diagnostic and therapeutic agents.

Unlike typical parallel processors, the 10,000 processors in this supercomputer (called Quantum Chromodynamics on a Chip, or QCDOC, for its original application in physics) each contain their own memory and the equivalent of a 24-lane superhighway for communicating with one another in six dimensions. This configuration allows the supercomputer to break the task of deciphering the three-dimensional arrangement of a protein's atoms — 100,000 in a typical protein — into smaller chunks of 10 atoms per processor. Working together, the chips effectively cut the computing time needed to solve a protein's structure by a factor of 1000, says James Davenport, a physicist at Brookhaven. This would reduce the time for a simulation from approximately 20 years to 1 week.

"The computer analyzes the forces of attraction and repulsion between atoms, depending on their positions, distances, and angles. It shuffles through all the possible arrangements to arrive at the most stable three-dimensionai configuration," The technique is complementary to other methods of protein-structure determination, such as x-ray crystallography — where the pattern of x-rays scattering off atoms in crystallized proteins is used to determine structure. It will be particularly useful for proteins that are impossible or difficult to crystallize, such as those that control the movement of molecules across the cellular membrane. The high-speed analysis will also allow scientists to study how proteins change as they interact or undergo other biochemical processes, which will give them more information about the proteins' functions than available from structural studies alone.

The ProteinChip system includes arrays and reagents consumed in the process, the chip reader, software to analyze results, and a proprietary database to enable comparisons between phenomic and genomic data. Known proteins are analyzed using functional assays that are on the chip. For example, chip surfaces can contain enzymes, receptor proteins, or antibodies that enable researchers to conduct protein-protein interaction studies, ligand binding studies, or immunoassays. With state-of-the-art ion optic and laser optic technologies, the ProteinChip system detects proteins ranging from small peptides of less than 1000 Da up to proteins of 300 kDa and calculates the mass based on time-of-flight (TOF).

Ciphergen's ProteinChip System is comprised of a ProteinChip Reader integrated with ProteinChip Software and a personal computer to analyze proteins captured on ProteinChip Arrays. The ProteinChip System detects and accurately calculates the mass of compounds ranging from small molecules and peptides of less than 1000 Da up to proteins of 500 kDa or more based on measured time-of-flight. The System is compact enough to fit into almost any lab space, allowing researchers direct access to precision mass analysis of important peptides and proteins from complex biological samples.

PARTS OF CHIP

PROTEINCHIP ARRAYS

Ciphergen's ProteinChip Arrays distinguish this technology from other mass spectrometry-based analytical systems. ProteinChip Arrays provide a variety of surface chemistries that allow researchers to optimize protein capture and analysis. The surface chemistries of the arrays include a series of classic chromatographic chemistries and specialized affinity capture surfaces. Classic chromatographic surfaces include normal phase for generic protein binding; hydrophobic surfaces for reversed-phase capture; cation- and anion-exchange surfaces; and immobilized metal affinity capture (IMAC) for metal-binding proteins. Specific proteins of interest can be covalently immobilized on pre-activated surface arrays, enabling customized experiments to investigate antibody-antigen, DNA-protein, receptor-ligand, and other molecular interactions.

Five surface types of 8 array ProteinChips

THE PROTEINCHIP READER

The ProteinChip Reader is a laser desorption/ionization time-of-flight mass spectrometer that uses state-of-the-art ion optic and laser optic technology. The laser optics maximize ion extraction efficiency over the greatest possible sample area, and thus increase analytical sensitivity and reproducibility. The Reader's ion optics incorporate a four-stage, time-lag-focusing ion lens assembly that provides precise, accurate molecular weight determination with excellent mass sensitivity.

THE PROTEINCHIP SOFTWARE

Ciphergen's ProteinChip Software controls all aspects of the ProteinChip Reader and facilitates data collection and analysis. The software uses a Microsoft Windows NT interface, and contains numerous features, including automatic reading of ProteinChip Arrays; multiple spectrum comparison for differential protein display and biomarker discovery; several alternative viewing formats for data; and a user-friendly interface.

Pre-loaded calibration standard values for ProteinChip Kits and a series of wizard-like prompts make experiment setup accurate and efficient. Built-in analysis tools detect peaks automatically, compare spectra, and present your data in a variety of formats designed to simplify analysis and interpretation. The ProteinChip System offers two prime software applications to help you get excellent results: ProteinChip Software and Biomarker Patterns™ Software.

ProteinChip Software

ProteinChip Software controls ProteinChip instrumentation, guides experiment set-up, keeps data organized, and makes analysis straightforward. Pre-loaded calibration standard values for ProteinChip Kits and a series of wizard-like prompts make experiment setup accurate and efficient. Built-in analysis tools detect peaks automatically, compare hundreds of spectra, and present your data in a variety of formats designed to simplify analysis and interpretation: trace view, gel view, map view, difference map, and 3-D overlay.

The Biomarker Wizard analyzes and compares multiple mass spectra to identify potential biomarkers. ProteinChip Software automatically writes out ProteinChip data sets for compatibility with protein and protein fragment databases, and Ciphergen's sophisticated Biomarker Patterns software.The ProteinChip Software has several powerful capabilities including:

- Database capabilities

Differential protein expression analysis

Biomarker identification

Automated ProteinChip Reader operation

Data export to Biomarker Patterns™ Software

Biomarker Patterns™ Software

Biomarker Patterns Software finds hidden correlations to sample phenotypes identified by SELDI protein profiles. The software discovers patterns and presents the results in an easy-to-interpret tree model. The results also include assignment scores of clinical sensitivity {percentage of positive cases) and specificity (percentage of negative cases).

Once generated, the model can be used to classify "unknowns" or it can be updated with additional sample data to increase its predictive power. Patterns consisting of multiple biomarkers, such as those discovered by Biomarker Patterns Software, can provide statistically superior predictive value and clinical utility for diagnosis, patient stratification and drug response monitoring.

Biomarker Wizard

The ProteinChip Biomarker Wizard™ analyzes and compares multiple mass spectra to identify potential biomarkers. In addition, ProteinChip Software automatically writes out ProteinChip data sets for compatibility with protein and protein fragment databases, and Ciphergen's sophisticated Biomarker Patterns' Software.

Automatic determination of candidate biomarkers

The Biomarker Wizard is a utility that helps you identify biomarkers by analyzing multiple sample profiles and automatically grouping similar peaks. Using the Biomarker Wizard, you can:

Evaluate statistical data for differential protein expression in sample sets .   Sort candidate peaks by the relative differences in expression level

The ProteinChip Software automates biomarker analysis and provides a choice of views for easy data interpretation. The basic Trace View displays SELDI protein profiles. The horizontal axis indicates molecular weight; the vertical axis indicates abundance. The Gel View translates profiles to simulate gel lane images for easy viewing and interpretation. The Biomarker Wizard identifies clusters and displays them for differential protein expression.

DISEASE SPECIFICITY

The chips can also specialize in specific maladies, replicating the handful of specific genes implicated in a particular illness from arthritis to HIV. For example, Larry Brody and Joseph Hacia at the National Institutes of Health, near Washington DC are studying the human BRCA1 and BRCA2 genes, which are implicated in hereditary breast cancer. When breast cancer runs in a family, as many as 80% of the women affected show mutations in either or both of these genes. The mutations make a women's chance of developing the disease as high as 85%.

The two scientists are testing chips that lay out the complete sequence of "health/1 BRCA1 and BRCA2 genes - 5000 and 10 000 base pairs, respectively. The researchers flood a chip with a sample of BRCA genes from a woman whose family has a history of the disease. If her genetic sample matches point by point, i.e. if complementary sequences bind to all the strings on the microarray, she has normal BRCA genes and a clean bill of life. If there are mismatches, that is, one or more strings don't find complementary partners, she's at a risk of developing the disease.

"Without the chips, it's relatively easy to screen for a mutation when you know what to look for. But the problem is that BRCA1 has more than 500 known mutations and more are being found out all the time. Most researchers feel that using conventional methods, one tends to study only those locations, where a variation is expected. But, by using DNA chips, you can get the entire data report of a DNA sample and easily determine the place of variation and also the factors, which could have influenced the variation.

This capability should help to tailor medicines to the specific genetic character of any one individual. In a few years, the human genome project will be complete and biologists will have a rough idea of the average genetic make-up of a human being. But specific variations from the normal are often crucial in determining a person's susceptibility to disease or their response to drugs. Chips will enable doctors to take a quick snapshot of a person's genes to see which treatment is the best and which drugs to avoid.

The DNA chip will be a powerful tool for understanding patterns of gene expression in cells. A gcne expresses itself when it acts as a template to make its own distinctive protein. The strength of a gene's expression depends on how much of that protein it causes to be made. Having an easy way to measure the strength of a gene's expression would be extremely useful to biologists.

But a gene doesn't make its own proteins directly. Instead, the cell extracts the information needed to make a protein and dispatches it to protein making areas in the form of RNA. The amount of protein manufactured is directly proportional to the translation of RNA's. So, by measuring the amount of RNA in a sample, researchers can easily figure out the amounts of protein being produced.

MANAGING THE DATA

After detection comes interpretation, which means bioinformatics. "The need for bioinformatics in particular and software in general in proteomics ranges from image analysis to managing ail the data that are generated and performing quality control on the data," BioDiscovery's Shams says.

Companies such as Accelrys, BioDiscovery, and MDL Information

Systems have developed suites of bioinformatic software to manage the storage and retrieval of data from protein microarray experiments, to mine those data sets, and to explore relationships among the data. BioDiscovery, meanwhile, has partnered with Prolinx to develop integrated software for analyzing protein microarrays. Why did they link up? "BioDiscovery is a leading software provider for gene expression and imaging analysis. Prolinx made protein chips," Shams explains. "It made a lot of sense to bring our experiences together."

To interpret their protein microarray data most effectively, researchers need meaningful access to the hundreds of databases worldwide that house textual and other information on proteins, DNA, and other biomolecules. To facilitate those efforts, MiraiBio has developed an internet-based data mining system that it calls DNASIS Genelndex. It enables researchers to query more than 20 public and commercial databases for DNA and protein sequences; by doing so they can narrow their searches and complete them as thoroughly as possible. And by integrating text mining technology and data related to life sciences, DNASIS Genelndex provides a new approach for data searches that permits life scientists to discover previously untapped knowledge.

Protein microarrays may have made slow progress toward acceptance by proteomics researchers until now, but continuing improvements make them increasingly compelling. "Protein chip surfaces, formats, materials, methods, and reagents are still emerging," NNI's Schroen says. "So it's an exciting time to be involved in this field."

USAGE OF CHIPS

To use the chip, a physician or lab technician extracts a sample of an organism's DNA from a bit of blood or tissue. The DNA is purified, replicated, split into single strands and finally cut up by enzymes into small pieces. Each piece in this DNA hash is then tagged with a fluorescent molecule. At the moment, lab technicians do this work, but all these processes could soon be carried out in computer-controlled reaction chambers squeezed onto the same chip as the microarrays.

This mixture is then washed over the chip. If a DNA strand in the hash meets a complementary counterpart on the chip, the matching sections zip together to form a double strand. The better the match, more the bonds between the strands, and stronger the join. The array is then flushed with a chemical solution that breaks apart all b: the best-matched double strands. In theory, the pair that remain are perfect fits. In practice, however, there is a 5% error rate. So a typical chip has built-in redundancies - additional test sites with the same unique DNA fragment, each offering a second opinion on the results of the others.

When the flushing is complete, a computer reads the location of any fluorescent tags shining from the chip's surface and matches those locations to its record of the nucleotide chains deposited at those points. The result - a full catalogue display of all the genetic ingredients. Ciphergen's ProteinChip System offers sophisticated software solutions for acquiring organizing, and analyzing SELDI data. Developed in conjunction with the ProteinChip Reader, ProteinChip Software provides a user-friendly tool that allows simple, straightforward data acquisition and rapid, automated analysis of multiple experiments on a array.

Data Acquisition

Obtaining data using the ProteinChip reader is easy with Ciphergen's ProteinChip Software. The system provides a series of prompts that guide input of Protocol parameters for reading the ProteinChip Array. Once defined, the Protocols can be saved and used repeatedly for subsequent, similar experiments.

After establishing the desired Protocol and inserting a ProteinChip Array into the Reader, one simply clicks on the "Read" button to collect data; the Reader automatically identifies the masses of proteins from all samples present on a array.As the array is read, mass data is displayed as a spectrum trace that represents all the detected sample proteins.

Data Views

To enhance the appearance and facilitate interpretation of the protein mass data collected, ProteinChip Software offers various presentation formats or data views. Data collected from a ProteinChip Array experiment can be reformatted at any time simply by accessing the original data file and clicking a few buttons on-screen.

Trace View: A standard spectral view for mass spectrometry or chromatography, Trace View depicts the quantity of protein reaching the detector at each particular molecular weight.

Map View: In this view only the peak height and mass information are retained from the Trace View, yielding a cleaner image and enabling proteins with nearly identical molecular weights to be more easily seen.

Difference Map: The Difference Map compares two or more spectra,conveniently highlighting unique proteins and proteins which are up- or down-regulated between samples. Protein profiles (spectra) from any two samples may compared visually, for example, spectra from aliquots of the same sample run on two chemically distinct ProteinChip Array surfaces. This type of analysis allows rapid determination of the surface binding properties of proteins of interest.

Get View: Sometimes it is easier to visually compare a large number of samples using the Gel View where each mass from the Trace View is converted into a grayscale image based on the height of each peak. Gel View images resemble those seen by biologists from electrophoretic (agarose or acrylamide) gels.

3-D Overlays: For comparison of several spectra, the 3-D overlay allows assessment of several spectra together to study subtle changes in relative peak heights. This data view style is particularly useful for studying the progression of a disease or the effects of drug administration over time.

Data Vt'ewj

The ProteinChip Software automates biomaraer analysis and provide* a choice Of views for easy data interpretation.

The bask Tract View display* SELDI protein profiler The horizontal axis indicate! molecular weight; the vertical axis indicates abundance.

The Cel View translates iirofiles to simulate gel lane images for easy viewing and Interpretation.

The Peak Map View displays differential protein expression.

Data Analysis

The ProteinChip System offers powerful software capabilities for straightforward data interpretation. Built-in analysis tools detect peaks automatically, compare spectra, and present your data in a variety of formats designed to simplify analysis and interpretation.

The ProteinChip Biomarker Wizard analyzes and compares multiple mass spectra to identify potential biomarkers. Biomarker Wizard also automatically writes out data sets for further analysis in Ciphergen's Biomarker Patterns™ Software, a sophisticated multivariate analysis program for identifying hidden correlations and patterns from SELDI protein profiles.

Scientists often compare the binding of proteins to a key matching with a lock. By attaching these biological "keys" to computer chips, scientists believe they will be able to detect specific microbes, disease cells and harmful or therapeutic chemicals quickly and cheaply.

The yeast ORFs were cloned into a double tagged yeast GAL1 expression    vector via a recombination strategy and verified for correct identities by sequencing.

Each pure plasmid construct was then reintroduced into a yeast strain for large-scale protein purification. Yeast cultures were grown in a 96-well format and induced by addition of galactose. After the high-throughput purification step, the purified proteins were aliquoted and stored in a glycerol buffer at "C80jaC before printing. Using a high precision microarrayer, 6566 protein samples can be double-spotted onto 80 slides in a single experiment.

ADVANTAGES

1. Protein chips could detect cancer earlier.

2.Protein Chip Improves SARS Testing.

3. Protein-coated chip sniffs out bacteria.

4. protein-chip technology in molecular diagnostics

DISADVANTAGES AND LIMITATIONS

Although very promising, the current protein chips technology has a number of drawbacks that limit its application. First, the capture protein-analyte reaction in the current design is a solid-phase reaction and limited by the diffusion rate of the analytes toward the solid-liquid interface. Further, the fluorescence detection is limited to the use of conventional organic dyes, which suffers from weak signal intensity, photobleaching and self-quenching. To solve these problems, we have been developing a novel protein chip based on filtration assay, and detect the signal using the superior phycobiliprotein dyes. Our initial results have demonstrated that using a novel filtration-based assay the detection kinetic rate can be increased by 10 fold or more compared with the current protein-chip design.

However, techniques to enable efficient and highly parallel identification, measurement, and analysis of proteins remain a bottleneck. A platform technology that makes collection and analysis of proteomic data as accessible as genomic data has yet to be developed. Sensitive and highly parallel technologies analogous to the nucleic acid biochip, for example, do not exist for protein analysis.

CONCLUSION

Protein array technology allows high-throughput screening for gene expression and molecular interactions. Protein arrays appear as new and versatile tools in functional genomics, enabling the translation of gene expression patterns of normal and diseased tissues into protein product catalog. Protein function, such as enzyme activity, antibody specificity, and other ligand-receptor interactions and binding of nucleic acids or small molecules can be analyzed on a whole-genome level.

As the array technology develops, an ever-increasing variety of formats become available (e.g., nanoplates, patterned arrays, three-dimensional pads, flat-surface spot arrays, microfluidic chips), and proteins can be arrayed onto different surfaces (e.g., membrane filters, polystyrene film, glass, silane, gold). Various techniques are being developed for producing arrays, and robot-controlled, pin-based, or ink-jet printing heads are the preferred tools for manufacturing protein arrays. CCD cameras or laser scanners are used for signal detection; atomic force microscopy and mass spectrometry are upcoming options. The emerging future array systems will be used for high-throughput functional annotation of gene products. In addition, their involvements in molecular pathways and their response to medical treatment will become the doctor's indispensable diagnostic tools.