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Ethical Issues of Genomes, Genetics, and Genetic Engineering 1 Examples of Questions that can now be raised as a result of HGP • Genetic testing, health insurance, and privacy – heart attack gene recently found in Iowa family (would you want this known?, would your descendents?) – Genetic marker for IQ (Gattaca) – Deafness -- may be increase in IQ • Genetic engineering • Cloning and therapeutic cloning – primates, pigs, fish? • Basic research in virulent or infectious organisms (anthrax) • Stem cell research – Economic and moral issues – Offshore? 2 Genetic Engineering • Definition: alteration of genetic code by “artificial means” – Examples? (within the system?): • dog breeds • corn selectively bred for 1000’s of years – More “artificial” • goats with spider gene to create spider silk in milk • GFP (green fluorescent protein – jellyfish) into many different organisms (trypanosomes, zebrafish) and luciferase – More practically, in medicine (gene therapy) • introduction of a normal copy of a gene for a diseased, missing, or non-functional gene • insulin 3 Gene Therapy Challenges • Have to know and understand the cause – “You cannot fix something unless you know it is broken.” • Safety and unexpected consequences • Delivery method. – How do you get a “good” copy of a gene to replace a “bad” copy of a gene in all tissues of an organ? – Engineering challenge 4 Genetic Engineering • Ethical and legal issues – is it appropriate to splice “unnatural” genes into organisms? • Concern is that this could lead to a catastrophe – – – – "environmental" damage? "un-natural" organisms (infectious organism) good news is that it has not happened yet bad news is that an absence of evidence is not evidence of absence. – lateral gene transfer: the transfer of genes between organisms – there is evidence that suggests gene transfer has occurred between organisms (mitochondria in humans) 5 Case Study: Genetic Engineering (Gene Therapy) • Cavazzana-Calvo M, Hacein-Bey S, de Saint Basile G, Gross F, Yvon E, Nusbaum P, Selz F, Hue C, Certain S, Casanova JL, Bousso P, Deist FL, Fischer A., “Gene therapy of human severe combined immunodeficiency (SCID)-X1 disease.” Science. 2000 Apr 28;288(5466):669-72. 6 SCID-X1 - Overview • severe combined immunodeficiency X1 (SCIDX1, aka IL2RG) www.ensembl.org • X-linked inherited disorder • OMIM – disease information – www.ncbi.nih.gov/entrez/query.fcgi?db=OMIM • recessive disorder – consequences for males VS females 7 Male VS Female SCIDX1 SCIDX1 X Y X X 8 SCID-X1 • 1-2 in 100,000 (30-40% of all SCID in US) medicine.ucsd.edu/peds/Pediatric%20Links/Links/AllergyImmunology/T%20Cell%20Immunodefici encies%20Ped%20Clin%20of%20NA%20Dec%202000.htm • characterized by block in early T and “natural killer” (NK) lymphocyte cell differentiation • caused by mutations in “gama-C” gene, aka SCIDX1 • usually fatal in first year of life • severe infections (no immune response) • The Boy in the Plastic Bubble 9 SCIDX1 • bone marrow transplant can be successful, but requires compatible donor (applies to less than 1/3 of cases) 10 SCIDX1 Gene Therapy • retro virus (modified murine/mouse RNA virus) as vector – delivery method – alternative delivery methods??? • implantation of devices 11 Modify the virus so that it infects, but does not replicate. http://www.accessexcellence.org/AB/GG/retrovirus.gif 12 SCIDX1 Therapy • Anticipated that transformed lymphoid progenitor cells will have selective advantage – transmits “survival” and “proliferative” signals to progenitor cells • known that wild-type retroviruses can contribute to cancerous changes if insertion perturbs a gene – “insertional oncogenesis” • accepted as unlikely but possible risk 13 SCIDX1 Therapy • Initial study – 2 boys in France – removed bone marrow – modified vector • inserted gama-C gene • disabled reproductive capability of virus – “infected” bone marrow “ex-vivo” – virus inserts into genome carrying therapeutic gene – re-implanted infected bone marrow (and all progeny cells) which should supplant the defective cells 14 SCIDX1 Therapy • 747 analogy – human body is complex system, components, networks, control, regulation, feedback, etc. – know a component is non-functional, but have incomplete understanding of relationship to the rest of the system 15 Results • April 2000 – – – – – – skin lesions disappeared both left protective isolation after 95 days at home for 10 and 11 months normal growth and motor development no side effects study expanded to 3rd recipient, with similar results 16 Results (Part 2) • Sustained correction of X-linked severe combined immunodeficiency by ex vivo gene therapy -- NEJM • April 18th, 2002 – 2.5 years – no adverse results – “Ex vivo gene therapy with gamma(c) can safely correct the immune deficiency of patients with X-linked severe combined immunodeficiency.” • • • • This is outstanding!!! Paving the way for other disorders Multiple studies underway, including US $250 M per year on genome (US) well spent 17 Gene Therapy Challenges Revisited • Have to know and understand the cause – SCIDX gene defective • Safety and unexpected consequences – “Appears to be okay*.” • Delivery method. – How do you get a “good” copy of a gene to replace a “bad” copy of a gene in all tissues of an organ? – Engineering challenge – Answer: borrow an existing mechanism from nature -- the retrovirus 18 Results (Part 3) • 3 years • 10/11 successfully treated • October, 2002 – “French gene therapy group reports on the adverse event in a clinical trial of gene therapy for X-linked severe combined immune deficiency (X-SCID)” – Journal of Gene Medicine – 30 months after treatment – leukemia – chemotherapy – history of leukemia in family 19 Results (Part 4) • January 14, 2003 – Report of a second serious adverse event in a clinical trail of gene therapy for X-linked severe combined immune deficiency (X-SCID) – Journal of Gene Medicine – 3 year-old (2 years, 9 months after treatment) – leukemia (no history) – chemo – study halted • 30 studies in US halted by FDA • 3 years better than nothing? (what percentage?) 20 What Happened? • Mapping integration site – appears to have integrated near LMO-2 gene in both individuals (in tumors) – still under review • Other groups have shown that the AIDS virus tends to insert in genes that are actively expressed – theory -- DNA has to be unpackaged to express genes, and viruses may rely on this mechanism for integration 21 Take Home Messages • Recent advances in science is forcing policy makers to try and make difficult decisions – Genetic engineering – Cloning – Stem cell research • Important to understand the basics of the science in making these decisions • Many of the policies have yet to be determined and may significantly influence basic science, research, the economy, and human health – example: stem cell research ban prior to Clinton administration 22 Where's the Bioinformatics? • Groups have started exploring different vectors – – – – – – – identify integration sites know the vector sequence may design "primers" to "amplify" vector read resulting sequence directly align to human genome – and "see" where it integrates manually – may do 10, 50? 100? 800 23 Analysis Pipeline Perl Sequence Read Quality Processing BLAST Sequence Characteristics Statistics and Reports Genome Indices Acquire Gene Positions (Ensembl) 24 Other Efforts 25 26 Ali, Bainbridge 27 End 28 NIH RoadMap • toolbox (small molecules) – procedure for when interesting target or marker is identified – currently, academic labs don't have the resources to pursue targets – "open source" drug discovery 29