Biotechnology and Bioinformatics: Medicine

1. Biotechnology and Bioinformatics: Medicine • Essential Idea: Biotechnology can be used in the diagnosis and treatment of disease.

2. TOK • There have been cases around the world where subjects have died as a consequence of participating in a gene therapy research protocol. How is the decision to proceed with risky procedures made? • What constitutes an acceptable level of risk for allowing humans to be involved in scientific research?

3. ELISA Tests • Pathogens can be detected using a variety of molecular techniques. • One popular method is to use an ELISA test. “ELISA” stands for Enzyme Linked Immunosorbant Assay. • This method allows for rapid detection of a specific disease that allows for quick treatment of an affected individual. www.bio-rad.com

4. ELISA Test • ELISA tests involve multiple steps: • In the first step, the sample in question is placed into a sample well plate and then washed out. Some of the sample will adhere to the sides of the well plate. http://technologyinscience.blogspot.com/2011/12/elisa-protocol-types-of-elisa.html#.VgtFsrRVhBc

5. ELISA Test • A primary antibody is then added to the well plate which will bind to any of the antigens in the original sample. http://technologyinscience.blogspot.com/2011/12/elisa-protocol-types-of-elisa.html#.VgtFsrRVhBc

6. ELISA Test • The wells are then washed again. • A secondary antibody which has an enzyme attached to it is then added to the well plate. • The secondary antibody (along with the enzyme) will then bind to the primary antibody which was bound to the antigen. http://technologyinscience.blogspot.com/2011/12/elisa-protocol-types-of-elisa.html#.VgtFsrRVhBc

7. ELISA Test • An enzyme substrate is then added to the wells. This substrate will react with any enzyme present and indicate a positive result from the original sample. http://technologyinscience.blogspot.com/2011/12/elisa-protocol-types-of-elisa.html#.VgtFsrRVhBc

8. Metabolomics • Metabolomics is a rapidly expanding field of study dedicated to the detection of metabolites in biological systems. • Metabolites that indicate disease can be detected in blood and urine. http://www.intechopen.com/books/calcific-aortic-valve-disease/proteomics-and-metabolomics-in-aortic-stenosis-studying-healthy-valves-for-a-better-understanding-of

9. Metabolomics • For instance, urine samples can be used to detect breast and ovarian cancer. • If these cancers are detected at an early stage, the 5-year survivability rates exceed 90%. http://www.metabolon.com/technology/about-metabolomics.aspx

10. Metabolomics • PKU is a metabolic disorder that results in severe intellectual disability caused by elevated serum phenylalanine levels. • The primary cause is phenylalanine hydroxylase deficiency. • Blood tests can be used to detect phenylalanine levels, and appropriate clinical steps can then be taken to manage the disease.

11. Marker Genes • Some people are predisposed to a genetic disease based upon the whether or not a family member has been afflicted with the disease. • Tests can be run to determine whether or not you will inherit the disease. • These tests look for genetic markers.

12. Marker Genes • For instance, Huntington’s disease is a neurodegenerative disorder that affects some people in mid-life. • Those who get it usually die within a few years of diagnosis. • It is a dominant gene. Thus, if a mother or father have it, you have a 50/50 chance of inheriting it.

13. Marker Genes • Tests can be run to look for markers in the genome to determine the likelihood of developing the disease.

14. DNA Microarrays • DNA microarrays enable scientists to study multiple genes in one experiment. • This is very useful due to the tremendous numbers of genes found within organisms. https://commons.wikimedia.org/wiki/File:DNA_microarray.svg

15. DNA Microarrays • DNA microarrays have many uses, but some of the common ones include: • Measuring changes in the expression levels of genes (expression analysis). • Detecting single nucleotide polymorphisms. • Determining the genotype of an organism. https://mla-lima.wikispaces.com/Southern+Blotting+and+DNA+Microarray

16. DNA Microarrays • For example, when gene expression is being monitored with a microarray, thousands of genes can be simultaneously monitored. • The results can be used to compare the level of gene expression in diseased tissue to that of a normal tissue. • This can help to improve treatment methods/options. http://cisncancer.org/research/how_cancer_is_studied/background/research_technology_02.html

17. DNA Microarrays • DNA microarrays can also be used to detect predisposition to disease. • The information gathered can be used to inform individuals about environmental factors that may trigger certain genetic diseases.

18. PCR Uses • PCR can be used to detect a wide variety of biomolecules. • It can be used in crime scene analysis, tissue typing, and disease outbreak/diagnosis, among many other things. • We used it in class to detect the presence of GMOs in foods. www.thermofisher.com

19. PCR and Influenza Detection • PCR is widely used to detect and track new strains of influenza. • Due to the rapid, sensitive, and specific assay that is followed, governmental agencies are given the opportunity to quickly respond to emerging threats, and take the appropriate measures to protect citizens. http://path.upmc.edu/virology/s-01.htm

20. Tumor Cell Tracking • Tracking experiments are used by researchers to gain information about proteins, their interaction within the cellular environment, and what the localization of these proteins within the cell can tell them. • Advances in biotechnology have also enabled researchers to use tracking experiments to track tumor cells using transferrin linked to luminescent probes. https://www.mskcc.org/blog/new-imaging-agent-could-improve-prostate-diagnosis-and-treatment

21. Tumor Cell Tracking • Transferrin is an iron-binding blood plasma glycoprotein normally present in the bloodstream and binds to fast-growing cells such as tumor cells (as well as fast dividing normal cells). • Its main job is to control the level of free iron in body fluids. http://biologie.ens-lyon.fr/ressources/bibliographies/m1-12-13-biosci-reviews-curis-c-1c-m.xml

22. Tumor Cell Tracking • Scientists are using PET scans to track transferrin uptake in tumor cells. • With this strategy, they can assess the speed at which the iron is taken up by the cells to monitor how rapidly the tumor may be growing. • This allows for early disease detection before any tumor growth can be seen with conventional imaging techniques. https://www.mskcc.org/blog/new-imaging-agent-could-improve-prostate-diagnosis-and-treatment

23. Tumor Cell Tracking • Here’s how it works: • Scientists have developed a way to couple transferrin to a radionuclide called zirconium-89. • Transferrin is rapidly taken up by actively dividing cells, and zirconium-89 is easily detected by a PET scan. http://www.nature.com/nm/journal/v18/n10/full/nm.2935.html?WT.ec_id=NM-201210

24. Tumor Cell Tracking • These two tools produce very high quality images that enable researchers to better understand and design treatments for cancer patients. https://en.wikipedia.org/wiki/Positron_emission_tomography

25. Gene Therapy and Viral Vectors • Viral vectors are used in gene therapy. • Gene therapy is a method of inserting a gene into an organism that does not have it. • The gene must be inserted into a spot on the chromosome where it will be actively expressed. • The gene must also be inserted into a cell that can be transplanted into the organism where it can proliferate and take up long term residence.

26. SCID • SCID (severe combined immunodeficiency) is a disease in which the patient cannot make antibodies nor can mount a cell-mediated response to an antigen. • It is a disease of young children because most children get infected with an illness that kills them. http://labs.pathology.med.nyu.edu/feske-lab/research/immunodeficiency

27. SCID • About 25% of all patients are the result of being homozygous recessive for a defective gene coding for adenosine deaminase. • This faulty purine metabolism creates a situation that is toxic to T and B cells--cells needed for proper immune system function. http://primaryimmune.org/about-primary-immunodeficiencies/relevant-info/inheritance/

28. SCID Treatment Options • Raise the child in a bubble. • Regular bone marrow transplants. • This can pose problems if the donor is infected. • Regular injections of ADA (adenosine deaminase). • Insertion of ADA genes with a retrovirus as a form of gene therapy. http://www.worldmag.com/2014/12/with_breakthrough_parents_can_finally_hug_and_kiss_their_bubble_babies

29. Gene Therapy for SCID--How it Works. • First you need to identify and clone a normal copy of the ADA gene. • The gene then needs to be inserted into the DNA of one of the patient’s own cells. This is done with a retrovirus and reverse transcriptase. • The gene needs to be inserted into a spot where it will be adequately expressed (transcribed and translated) thus producing reasonable amounts of enzyme. • Treating the cells in tissue culture so they multiply, and then returning them to the patient.

30. Gene Therapy for SCID • To get the DNA into the cell, a retrovirus is used as the vector. This makes use of an envelope protein enabling the virus to infect the human cell. • RNA copies of the human ADA gene can then be incorporated into the retroviral genome using a packaging cell. http://learn.genetics.utah.edu/content/genetherapy/gtsuccess/

31. Gene Therapy for SCID • Packaging cells are: • cells that express an RNA copy of the (ADA) gene, • cells that have an RNA copy of the retroviral genes to assist in the copying of the genes which need to be expressed, • cells that contain inverted repeats to assist with the insertion of the DNA into the DNA of the target cell. • Packaging cells lack the genes necessary for critical viral replication. • They become proviruses that replicate as the cell divides. http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/G/GeneTherapy.html

32. Gene Therapy for SCID • Retroviruses are often altered and used for gene therapy. • Researchers insert the desired gene(s) into the virus and then remove the coding regions for the genes needed by the virus to replicate itself. • Thus, these viruses are capable of infecting their target cell, but are unable to continue their destructive life cycle. http://learn.genetics.utah.edu/content/genetherapy/gtsuccess/

33. Gene Therapy for SCID • If the gene is inserted correctly, in this case the ADA gene, the cells begin synthesizing the enzyme needed to produce adenosine deaminase and the patient’s immune system begins to function normally. http://www.mun.ca/biology/scarr/Somatic_Therapy_for_SCID.htm

34. Gene Therapy for SCID • Gene therapy for SCID involves some risks: • 4 of the 10 patients undergoing SCID gene therapy developed leukemia as a result of the ADA gene being inserted near an oncogene. • 2 of the 4 patients were successfully treated. • Other methods of gene insertion have also been explored.

35. Gene Therapy for SCID • Using adeno-associated viruses, for example, have been shown to be much safer because they always integrate in the same spot on a chromosome and are designed to insert in spots not known to cause problems. https://en.wikipedia.org/wiki/Gene_therapy