1 / 36

Predictive Biomarkers for tailoring drug therapy

Predictive Biomarkers for tailoring drug therapy. Outline. What is a predictive biomarker and why are they important? How does genomics facilitates the search for predictive biomarkers? Are there any examples of clinically useful predictive biomarkers?. 1. What is a predictive biomarker?.

ostinmannual
Download Presentation

Predictive Biomarkers for tailoring drug therapy

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Predictive Biomarkers for tailoring drug therapy

  2. Outline • What is a predictive biomarker and why are they important? • How does genomics facilitates the search for predictive biomarkers? • Are there any examples of clinically useful predictive biomarkers?

  3. 1. What is a predictive biomarker?

  4. Predictive Biomarkers Biomarker: A gene, protein, or other change that heralds a biomedical phenotype before that phenotype Is clinically apparent. Biomarkers used for: Diagnosing Disease Establishing Disease Risk Establishing Drug Response Establishing Drug Toxicity Predicting Drug Response Predicting Drug Toxicity

  5. What is the most valuable Predicitive Biomarker today?

  6. Discuss LDL High LDL (low density lipoprotein) levels indicate individuals At high risk of artherosclerotic plaque formation. Artherosclerotic plaque formation leads to thrombosis (stroke) and Embolism (heart attack) Stroke and heart attach are the major killers in the world The use of LDL as a biomarker of heart disease has led to the explosion of the statins: multi-billion cholesterol reducing drugs.

  7. Functional Genomics: Genome-wide biomarker drug discovery

  8. 2. How genomics is facilitating the search for predictive biomarkers?

  9. Using the sequence information to probe the transcriptome of the Cell Transcriptome: the set of all expressed genes (mRNAs) inside a cell. Different types of technology used to probe the transcriptome: SAGE (serial analysis of gene expression) Strategy: isolated mRNA is reversed-transcribed to cDNA, digested into fragments, randomly ligated into clones, and the clones are sequenced. Relative abundance of different mRNAs within a single pool are reflected in the sequenced clones. DNA microarrays Strategy: mRNA is reversed transcribed to cDNA, labeled with fluorescent probe, And hybridized to complementary strand DNA attached to glass slides. By comparing hybridizationn of two samples, relative abundance of mRNA between samples can be determined Affymetrix GeneChips. Same as DNA microarrays, except that cDNA is transcribed to cRNA in vitro, which is labeled with fluorescent probes.oligonucleotides are chemically synthesized on chip and the presence/absence of genes is determined based on hybridization between sets of perfectly matched and mismatched probes.

  10. SAGE: Serial Analysis of Gene Expression gtac AAAA gtac AAAA gtac AAAA gtac AAAA gtac AAAA Cut and tag AAAA gtac Total cell mRNA Concatenate ATTGCGTACCCCgtacTTGAGAACCCgtacATTGCGTACCCCgtacGCCCAATTCATTTAgtacATTGCGTACCCCgtacAAAACCCCTTTTT Sequence

  11. Differential Analysis of Gene Expression with SAGE Normal Sample Disease Sample Gene A B C D E F A B C D E F 5 3 12 4 1 12 # SAGETags 4 2 10 5 1 4 Y=x 1SD 2SD

  12. Probe Preparation and labeling for hybridization experiments • Fluorescent probes prepared from two mRNA sources to be compared • Cy-dCTP nucleotides added to the cDNA synthesis reaction • Cy3 (green)-control sample • Cy5 (red)-experimental sample

  13. Synthetic oligonucleotide arrays: Affymetrix Gene Chips PM MM

  14. Differential Analysis of Gene Expression with GeneChip Normal Sample (Red) Disease Sample(Green) Gene A B C D E F A B C D E F 5 3 12 4 1 12 PM-MM 4 2 10 5 1 4 Y=x 1SD 2SD

  15. Spotted arrays: cDNA microarrays • Oligonucleotides are obtained by PCR amplification of cDNA templates and have an amine linking group on 5’ end • Glass slides are chemically treated (aldehyde) to be reactive to the group on the 5’ of the oligo • A microdroplet of PCR product is placed on slide with use of metal pin. Schiff base reaction links oligo to slide surface via covalent bond.

  16. Differential Analysis of Gene Expression with Microarrays Normal Sample (Red) Disease Sample(Green) Gene A B C D E F A B C D E F 5 3 12 4 1 12 Fluorescence 4 2 10 5 1 4 Y=x 1SD 2SD

  17. How transcriptome analysis offers insights into potential biomarkers Differential gene expression in normal tissues (relating the expression of specific genes to suceptibility Of certain tissue to specific diseases (e.g. retinal degeneration). Differential gene expression in disease states. (comparing normal and disease tissues; class prediction; class Identification.) Gene expression in model systems (comparing drugs to mutations, human to mice, cells to Living tissues) Gene expression in pathogens Gene expression in response to drugs (drug target identification, drug classification; drug activity, Drug metabolism)

  18. Proteomics –Finding Protein Biomarkers 30,000 genes >200,000 proteins

  19. The Basic Technique: Sodium dodecyl sulfate- polyacrylamide Gel electrophoresis (SDS-PAGE)

  20. Basic Technique 2: Isoelectric focusing

  21. 2D gel electrophoresis: Isoelectric focusing x SDS PAGE SDS Isoelectric focusing PAGE

  22. Comparative analysis of 2D gels from different samples

  23. Mass Spec sequencing: ID proteins according to fragment masses 292-145= 147 1022-875 = 147

  24. 3. How are predictive biomarkers making their way into the clinic?

  25. BIOMARKERS USED IN CANCER THERAPY The two-hit hypothesis: Cancer cells need to acquire both gain-of-function (“oncogenic”) and loss-of-function (“tumor suppressor”) Mutations to become cancerous Oncogene:gain of function Tumor suppressor: loss Of function

  26. Oncogenic mutation mechanisms DNA Chromosomal rearrangement Deletion or point mutation in coding sequence Gene amplification DNA mRNA protein

  27. HERCEPTIN • Herceptin® (Trastuzumab) is the first targeted, humanized antibody for treatment of women with HER2 (human epidermal growth factor receptor 2) positive metastatic breast cancer. Herceptin is designed to target and block the function of HER2. • HER2 positive metastatic breast cancer have a more aggressive disease, greater likelihood of recurrence, poorer prognosis and approximately half the life expectancy of women with HER2 negative breast cancer. • The U.S. Food and Drug Administration (FDA) approved Herceptin in September 1998 in combination with paclitaxel for treatment of patients with metastatic breast cancer whose tumors overexpress the HER2 protein and who have not received chemotherapy for their metastatic disease. • Herceptin is one of the few therapies, and the only humanized antibody, that has demonstrated a survival benefit indicated for metastatic breast cancer

  28. Herceptin- Antibodies block HER2

  29. Clinical Trial Results • Data showed that patients receiving Herceptin with chemotherapy survived for a median of 25.1 months compared to 20.3 months for patients in the Phase III trial receiving chemotherapy alone, a difference of 24 percent. • In addition to survival, when used in combination with chemotherapy, Herceptin was shown to improve overall response rates from 29 percent in women treated with chemotherapy alone to 45 percent with Herceptin added -- a 64 percent increase. The median time to disease progression increased from 4.5 months in the chemotherapy alone group to 7.2 months in the Herceptin plus chemotherapy group -- a 63 percent increase. • Additionally, the duration of response of women treated with Herceptin with chemotherapy was 8.3 months, compared to 5.8 months for those women receiving chemotherapy alone. • In the trial evaluating Herceptin alone, 14 percent of 222 women who had failed one or two prior chemotherapy regimens had objective tumor responses with tumor shrinkage of 50 percent or greater.1

  30. Other example: Targeted Inhibitors of BCR-ABL oncogene • Chronic Myelogenous Leukemia: a biphasic disease • a. chronic phase (associated with t(9;22) translocation.) • b. blast crisis (fatal for 85% of Patients) • . • Allogeneic bone marrow transplantation was the only curative treatment available but is only applicable to a minority of patients (15-20%). • A recent advance in the treatment has been the introduction of the Bcr-Abl inhibitor STI571 (Gleevec)

  31. Diagnosis: t(9;22) Karyotype analysis FISH: FLUORESCENCE IN SITU HYBRIDIZATION NORMAL MUTANT

  32. Gleevec binds Bcr-Abl protein target Rational design: STI-571 bound to ABL (PDB: 1IEP)

  33. Gleevec clinical results Initially, 90% Remission with GLEEVEC with recurrence due to resistance (mediated by BCR-ABL mutations) Anti BCR-ABL cocktails to fight off resistant cells. Ability to target c-kit kinase has led to additional application: gastric cancer. Current market value over 1 billion dollars.

  34. Transcriptome Analysis for Personalized Therapy Collect tumor sample from patient Perform transcriptome analysis of tumor sample relative to control sample (gene expression profiles) Treat tumor Establish sets of genes that are up or down-regulated in responsive vs. non responsive tumors Use those genes to predict outcome or Guide treatment decisions

  35. Molecular classification of lung cancers with DNA microarrays

More Related