DNA Microarrays Examining Gene Expression

Prof. GrossBiology 4 DNA MicroArrays DNA MicroArrays use hybridization technology to examine gene expression DNA MicroArrays use hybridization technology to examine gene expression Attach different DNAs onto a slide as a grid of small spots, one for each gene - up to 50,000 per slide Attach different DNAs onto a slide as a grid of small spots, one for each gene - up to 50,000 per slide Hybridize a mixture of fluorescently labeled cDNAs extracted from cells after different treatments - control is green and experimental is red Hybridize a mixture of fluorescently labeled cDNAs extracted from cells after different treatments - control is green and experimental is red Examine expression patterns by looking at levels of fluorescence for all genes in array Examine expression patterns by looking at levels of fluorescence for all genes in array

Prof. GrossBiology 4 DNA MicroArray Hybridization Data increased expression decreased expression mRNAs at lower levels in treated cells are green, those at higher levels in treated cells are red, those that are unchanged are yellow. each spot corresponds to a different gene

Prof. GrossBiology 4 Some Uses of DNA MicroArrays Rapid scanning of DNA or RNA populations Rapid scanning of DNA or RNA populations Used for identifying bacterial infections in hospitals Used for identifying bacterial infections in hospitals Used in research on molecular biology of gene expression Used in research on molecular biology of gene expression Stanford MicroArray Database (SMD) - gene expression information and extensive database of results Stanford MicroArray Database (SMD) - gene expression information and extensive database of resultsSMD

Prof. GrossBiology 4 Tumor Subgroup Clusters Perou, et al Nature 406:747 (2000)

Prof. GrossBiology 4 Tumor Clusters basal expression Erb-B2+ normal breast-like Luminal epithelial/ER+ Perou, et al Nature 406:747 (2000)

Prof. GrossBiology 4 Tumor Portraits Breast tumors are histologically diverse and differ in their responsiveness to treatments Breast tumors are histologically diverse and differ in their responsiveness to treatments The expression profiles provided a distinctive molecular portrait of each tumor subtype The expression profiles provided a distinctive molecular portrait of each tumor subtype Gene expression patterns in two tumor samples from the same individual were more similar to each other than either was to any other sample Gene expression patterns in two tumor samples from the same individual were more similar to each other than either was to any other sample Sets of co-expressed genes (portraits) were identified that were correlated with specific features or physiological variation Sets of co-expressed genes (portraits) were identified that were correlated with specific features or physiological variation Metastases and primary tumors had similar expression profiles Metastases and primary tumors had similar expression profiles Can lead to more effective chemotherapy decisions Can lead to more effective chemotherapy decisions Perou, et al Nature 406:747 (2000)

Prof. GrossBiology 4 Pharmacogenomics examine expression profile of patient examine expression profile of patient compare to known profiles compare to known profiles determine most effective treatment for this particular allele determine most effective treatment for this particular allele designing drugs for individuals designing drugs for individuals

Prof. GrossBiology 4 Some Questions If pharmacogenomics tests are not done prior to treatment, can doctor/drug company be sued? If pharmacogenomics tests are not done prior to treatment, can doctor/drug company be sued? If tests are expensive, and patients pay for them, is this a kind of “economic” discrimination? If tests are expensive, and patients pay for them, is this a kind of “economic” discrimination? If patient pays for test is she/he “hiding” information from insurance company and subject to having policy cancelled? If patient pays for test is she/he “hiding” information from insurance company and subject to having policy cancelled? If insurance company pays for test do they have a right to the results? If insurance company pays for test do they have a right to the results? From a business perspective, doesn’t it make sense for an insurance company to pay for the tests since it might result in avoidance of cancer (a big bill!)? From a business perspective, doesn’t it make sense for an insurance company to pay for the tests since it might result in avoidance of cancer (a big bill!)? Discover of “accidental” information in a gene expression profile analysis of a patient – should the patient be told? Discover of “accidental” information in a gene expression profile analysis of a patient – should the patient be told?