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Cystic Fibrosis and Gene TherapyLecture Notes
Biol 100 – K.Marr
• Topics for this Lecture– Gene Therapy as a treatment for Cystic
Fibrosis• Reading assignments in Essential Biology
– Chapter 12: DNA Technology:• Restriction Enzymes (p. 225)• Gel Electrophoresis (p. 229)• PCR (Polymerase Chain Reaction) p. 228• DNA Fingerprinting (pp. 227-230• Human Gene Therapy (pp. 235-236
Optional Reading
• Cystic Fibrosis Foundation: Gene Therapy and CF– http://www.cff.org/about_cf/
gene_therapy_and_cf.cfm
• Center for Gene Therapy and other Genetic Diseases– http://genetherapy.genetics.uiowa.edu/
• Cystic Fibrosis Research Directions– http://www.niddk.nih.gov/health/endo/pubs/cystic/
cystic.htm
• See "Lecture Related Resources and Enrichment" at the class website
What is the hope for people with cystic fibrosis?
Do you want to have a healthy child?1. Screen potential carriers of CF
• E.g. Use DNA Probe
2. Screen for CF gene in embryo • Only implant embryos without CF allele
Do you want a cure for yourself?3. Gene Therapy
• Use a viral vector to insert the normal CFTR gene into the lungs cells of people with CF
• Somatic vs. Germ line gene therapy
• How to use a DNA Probe to Screen for the CF Gene
1. Isolate DNA from patient
2. Heat to separate DNA strands
3. Add labeled probe that has complementary base sequence to mutant gene
4. Add restriction enzymes (cuts DNA into fragments) and separate by gel electrophoresis
Single stranded DNA from patient
DNA probe complementary to mutant gene
Normal Genotype Abnormal Genotype
Probe does not bind to DNA
Probe binds to DNA
a.) DNA and dye are loaded in a well on a gel, and an electric field is placed across the gel.
b.) DNA fragments move through the gel, shorter fragments faster than longer fragments.
c.) Place photographic film over gel to detect DNA labeled with the probe
(+) Electrode attracts negatively charged DNA fragments
GelWell
DNA samples from PCR ofSnowball’s DNA
Direction ofelectric field
Separation of DNA fragments by Gel electrophoresis
Separation of DNA fragments by Gel electrophoresis
• Smaller fragments move faster than larger fragments through the porous gel.
• Use photographic film to locate DNA fragments bound with radioactive probe
Two Kinds of Gene Therapy
Replace defective gene in.....1. Body cells: Somatic Cell Gene Therapy
• Permanent cure for individual
2. Egg cell: Germ line Gene Therapy• Permanent cure for future generations• Banned by most countries!! Why?
Can’t control where gene inserts. Possible Consequences:
Abortive or defective embryos! Why? Could cause cancer! Why?
What’s Necessary for Gene Therapy to Work?
1. Identify the defective gene• e.g. CFTR gene discovered in 1989
2. Use PCR to make copies of good gene• PCR = polymerase chain reaction
3. Get good gene into the right cells (need vector)
• Use a viral vector
4. Get the cells to transcribe and translate the good gene
• Must make the right amount of protein at the right time and get it to the right place
Double-strandedDNA
Single-strandedDNA
taq DNApolymerase
DNA Primers bindto theircomplementarysequence
DNAPolymerase
copies DNA
Thermocyclerheats sampleto near boiling
(~94oC)
Thermocyclerlowerstemperatureto 55 °C
Thermocyclerraisestemperatureto 72 °C
Heat breakshydrogen bonds
and strandsseparate
PCR—what’s needed
1. DNA—only a tiny amount is needed!
2. Heat stable DNA polymerase (e.g. taq DNA polymerase)
3. DNA primers that bind just outside the DNA to clone
4. DNA nucleotides
5. Thermocycler or water baths at 94oC, 55oC and 72oC
The polymerase chain reaction (PCR)—another view
1. heat briefly to 94oC to break hydrogen bonds & separate strands
2 . Cool to 55oC to allow primers to hydrogen bond
3. Taq DNA polymerase adds nucleotides to 3’ end of each primer
Cycle 1 produces 2 DNA molecules
Cycle 2 produces 4 DNA molecules
Cycle 3 produces 8 DNA molecules
Common Vectors used in Gene Therapy
1. Retroviruses (RNA viruses)2. Adenoviruses (DNA viruses)3. Liposomes4. Naked DNA
1. Modified Retroviruses (RNA viruses) (1 of 2)
Advantages
• Good at inserting genes into host chromosome
- Used with partial success treating Gaucher’s disease
- Successfully cured 4 babies of S.C.I.D.S. in early 2000• Severe Combined Immunodeficiency
Syndrome (Bubble Baby)
1. Modified Retroviruses (RNA viruses) (2 of 2)
Disadvantages1. Inserts genes randomly. Possible
Consequences?2. Usually needs an actively dividing host
cell• Therefore, not used for Cystic Fibrosis
3. Modified virus may mutate and cause serious disease.
2. Liposomes
Liposome • hollow sphere surrounded by a lipid bilayer• Place gene of interest inside• Clinical trials underway with the CFTR gene
Advantages• No threat of disease.
Disadvantages• Very inefficient at inserting genes into host
chromosome
3. Modified Adenoviruses—a DNA viruses
Advantages• Most adenoviruses don’t cause serious
disease.• Clinical trials are underway with the CFTR
gene
Disadvantages• Inefficient at inserting genes into host
chromosome
4. Naked DNA
Advantages• No threat of disease
Disadvantages• Very inefficient at inserting genes into host
chromosome
Problems Doing Gene therapy (1 of 2)
Inefficient gene delivery—not suitable for all genetic diseases
1. Most effective if Stem cells are involved• Only to correct a few cells with the gene• E.g. Blood stem cells: SCIDS and Gaucher Disease
2. Less effective or Ineffective if many cells must be corrected
• Brain cells (Tay-Sacs disease, Huntington’s disease)
• Cystic Fibrosis
Problems Doing Gene therapy (2 of 2)
4. Insertion of Gene isn’t always permanent
• e.g. Gaucher Disease: temporary cure until GCase gene “popped” out of chromosome
5. Insertion of gene into genome could disrupt other genes.
• Possible consequences?
6. Some viruses elicit immune response or may cause disease
• E.g. Jesse Gelsinger died in 1999
– Exhibit some but not all characteristics of living organisms
– No cellular Structure
– No cell organelles
– Can’t carry out metabolism or reproduce by itself
– Can only reproduce inside a host cell
• Viruses—genes in packages!
– Very small—about the size of a ribosome
• Viruses sit on the fence between life and nonlife
What is a virus?
Importance of Viruses1. Cause many diseases in plants, animals & humans
• Some viruses are easily controlled with a vaccine
Mumps, Measles, Smallpox, Polio
• Some viruses are difficult to control with a vaccine
Retroviruses (HIV: ssRNA dsDNA)
Common cold, Influenza (Flu), HIV
2. Used as vectors in biotechnology
• Used to insert therapeutic genes into a host cell chromosome
• Use viruses with provirus in life cycle
Measles (ssRNA template for mRNA synthesis)
Measles: a childhood disease that can be prevented with a vaccine
1918 Influenza epidemic (ssRNA template for mRNA synthesis)
>20 million died of the flu during WW I
A new influenza vaccine must be developed yearly
Background: Influenza Virus Structure (1 of 3)
Flu Viruses Currently infecting... • Humans: H1N1, H1N2, and H3N2• Avian Flu Virus: H5N1
1. Flu viruses are named by the type of surface proteinsa. Hemagglutinin
• Helps virus enter cell
• Type A infects humans, birds and pigs
• Type A has ~ 20 different sub types
Background: Influenza Virus Structure (2 of 3)
2. Named for the type of surface proteinsb. Neuraminidase
• Helps virus exit cell
• 9 subtypes
• Currently infecting Humans:
H1N1, H1N2, and H3N2
3. Influenza viral genome• ssRNA• 8 segments (pieces)• One gene per segment
Avian Flu Virus: H5N1• Transmitted from birds to
humans• No evidence of human to
human transmission• Antiviral drugs: Tamiflu
a neuraminidase inhibitor
Consequences of its action?
Background: Influenza Virus Structure (3 of 3)
Genetic Changes in Influenza Viruses
1. Antigenic drift – due to errors in replication and lack of repair mechanism to correct errors
– Results in ___________________ changes
2. Antigenic shift - reassortment of genetic materials when concurrent infection of different strains occurs
– Results in ___________________ changes
Emergence of New Influenza SubtypesAntigenic shift due to genome reassortment within intermediate hosts drives flu epidemics and pandemics
Key
Solid arrows: current transmission pathways
Dashed arrows: possible future transmission pathways
Numbers: sequence of transmission pathways
Antigenic Drift: mutations result in changes to the Hemagglutinin (HA) molecules
Where do the “new flu” viruses come from?
- RNA replication is error prone- New HA types are created frequently- Requires new vaccine every “season”- What is a vaccine?
Vaccines: Protection against viruses1. What is a vaccine?
2. Vaccines stimulate the production of memory cells
• Give long-term protection against a specific antigen
3. Why are vaccines ineffective against the flu virus?
• Why will this year’s flu vaccine be ineffective next year?
4. Why are vaccines effective against DNA viruses?
- e.g. small pox and polio virus
Smallpox
(dsDNA dsDNA)
Smallpox has been irradiated worldwide due to a very successful vaccine
Why are vaccines for DNA viruses so successful?
Emerging viruses
Ebola Virus
Hanta Virus
Both viruses: ssRNA template for mRNA synthesis
Either virus usually results in death within days!
Mottling of Squash and Tobacco by the Mosaic Virus
Viruses can spread easily from cell to cell via the plasmodesmata junctions between cells
Comparing the size of a virus, a bacterium, and a eukaryotic cell
Viral Size
Millions can fit on pinhead
Smaller than a ribosome!
• The first viruses studied were bacteriophages
Bacteriophages: Viruses that attack bacteria
Head
Tail
Tail fiber
DNA of virusBacterialcell
Bacteriophages (phages) have two reproductive cycles
Phage DNA
1
2
3
4
Phage DNA circularizes
New phage DNA andproteins are synthesized
5 Phage DNA inserts into the bacterialchromosome by recombination
Cell lyses,releasing phages
6 Lysogenic bacteriumreproduces normally,replicating the prophageat each cell division
7Occasionally a prophagemay leave the bacterialchromosome
Bacterial chromosome (DNA)
Lytic cycle Lysogenic
cycle
Many cell divisions
• Lytic Cycle and Lysogenic Cycle
• The Herpes viruses and HIV both carry out these to reproductive cycles
Prophage
(a) Virus lands on bacterium.
(b) Virus injects its genes into the cell.
(c) Virus DNA replicates, and directs the synthesis of new virus proteins.
The Lytic Cycle of a Bacteriophage (slide 1 of 2)
(d) Virus particles assemble. (e) Cell bursts, releasing new virus particle.
The Lytic Cycle of a Bacteriophage (slide 2 of 2)
AIDS: Acquired Immunodeficiency Syndrome
HIV infecting a Helper T-Cell
• AIDS—caused by HIV infection
• HIV = Human Immunodeficiency Virus
AIDS around the world (Source: UNAIDS)
Part of the World People with HIV
New HIV cases in
2002
Deaths from Aids in 2002
Children (under 15) with Aids by end of
2002
North America 980,000 45,000 15,000 10,000
Sub-Saharan Africa
29.4m 3.5m 2.4m 2.8m
South & Southeast Asia
6m
India: 3.9 m
700,000 440,000 240,000
Latin America 1.5m 150,000 60,000 45,000
East Asia & Pacific
1.2m 270,000 45,000 4,000
Caribbean 440,000 60,000 42,000 20,000
RNA (2 copies of its genome)
Capsid made of protein
Protein
Lipid envelope
Carbohydrate
Envelope protein
Reverse Transcriptase
The Structure of HIV: A Retrovirus (RNA virus)
Animation of HIV Life Cycle Questions to Address:1. Why does HIV only infect a specific cell type,
T-helper cells (CD-4 cells)?2. What is HIV’s Genetic material?3. What are the roles of Reverse Transcriptase
and protease? 4. Reverse Transcriptase does not “proof read”
like DNA polymerase does.a. What are the consequences?b. Of what adaptive value is this?
HIV 1.) Binding 2.) Fusion 3.) Infection
Envelopeprotein
Capsid
Plasma membrane of T-helper cell
Helper protein
CD4Receptorprotein
Cytoplasm of white blood cell(T-Helper Cell)
RNA
HIV primarily infects T-Helper Cells!• Why does HIV have a narrow host range?
• Why does the virus that causes rabies have a broad host range?
1
23
4
5
6
DNA strand
Viral RNAReverse transcriptase
Cytoplasm
Double-stranded DNA
Viral RNA and proteins
Nucleus
Overview of HIV’s Reproductive Cycle
DNA of host cell
Provirus DNA
What’s happening?
1.
2.
3.
4.
5.
6.
EntryHIV
Reverse transcriptase
Viral RNAcopiedto viral DNA
Viral DNAintegrates intocell chromosomesand makes moreviral RNA
Protease cleaves largeproteins into smaller ones
Synthesisof HIV proteins
HIV envelope proteinscome to cell surface
HIV assemblesand buds from
cell
Viral RNA
Viral RNA
Integrase
Reproductive Cycle of HIV—the details!
1. Reverse Transcriptase Inhibitors Block viral DNA formation from viral RNA
2. DNA base analogs (e.g. AZT, 3TC) Block DNA elongation
3. Protease Inhibitors Block enzymes that process envelope proteins
4. Why use a “Shotgun” approach?
5. Possible future treatments:
• Plug drugs—drugs that plug receptors for HIV on surface of host cell
• Vaccines
Treatments for HIV
Vaccines: Protection against viruses1. What is a vaccine?
2. Vaccines stimulate the production of memory cells
• Give long-term protection against a specific antigen
3. Why are vaccines not effective against retroviruses such as HIV?
4. Why are vaccines effective against DNA viruses?
- e.g. small pox and polio virus
DNA Technology Lecture Notes Biol 100 – K.Marr
• Topic for the next lecture– DNA technology
• Reading assignments in Essential Biology– Viruses: pp. 188-193; – Chapter 12: DNA Technology
Plasmid DNA
Bacterial Chromosome
Bacteria have two types of DNA• Bacterial Chromosome—contains the genes necessary for life
• Plasmid DNA—contains genes that give resistance to antibiotics
Fig. 7.17-1
Extract mRNA
mRNAHuman cell
cDNA
Use reverse transcriptase to
make cDNA
Insert cDNAinto plasmid
Cutplasmids
Transform recombinantplasmids into bacterial cells
PlasmidDNA
Recombinant DNA Technology
(1 of 2)• Bacterial production of
human protein
e.g. insulin, growth hormone
1. Extract the desired mRNA
2. Use reverse transcriptase make complementary DNA (cDNA)
3. Insert cDNA into bacterial plasmid
4. Transform bacteria with recombinant plasmid
• Some, but not all cells contain the recombinant plasmid
Culture therecombinantbacteria
Make radiolabeledprobe for human gene Probe binds
to human genein the colonythat has it
Hybridized probeto colonies
Grow the bacteriacontaining the human gene, then isolate & purify the human protein
Recombinant DNA Technology
(2 of 2)
Steps 5-7:
• Isolation of the bacterial cells that contain the recombinant plasmid
• The use of bacteria to produce insulin and other pharmaceuticals is very expensive!
Using a restriction enzyme and DNA ligase to make recombinant DNA
1. Cut bacterial plasmid DNA with restriction enzyme
2. Add human gene that was cut out by the same restriction enzyme.
Human gene sticks to plasmid by complementary base pairing of “sticky ends”
3. Use DNA ligase to join the strands.
1.) Parental DNA Molecules
Bacterial plasmid DNA Human gene to clone
Discarded
“Restriction enzyme”
How bacterial plasmids are used to clone genes (slide 1 of 2)
2.) Cut Parental DNA Molecules with a Restriction Enzyme
5.) DNA Ligase joins fragments
3.) Mix plasmid and parental DNA molecules
Plasmid DNA Human Gene
4.) Recombinant DNA Molecule
How bacterial plasmids are used to clone genes (slide 2 of 2)
Inject recombinantDNA into goatZygote (fertilized egg)
Human gene of interest
Promoter
Using “Pharm” Animals to Produce Pharmaceuticals (1 of 2)
“Pharm” animal
Transfer the injectedembryo into theuterus of a surrogatemother goat
Test the offspringfor the presenceof the human DNA
Isolate human proteinfrom the milk
Mate the animalswith the human geneand establish ahomozygousbreeding stock
Using “Pharm” Animals to Produce
Pharmaceuticals (2 of 2)
Cystic Fibrosis, Gene Therapy, Viruses and DNA Technology Lecture Notes
Biol 100 – K.Marr
• Topics for the next few lectures– Gene Therapy as a treatment for Cystic
Fibrosis– Biology of Viruses– DNA technology
• Reading assignments in Essential Biology– Viruses: pp. 188-193; – Sabotaging HIV : p. 171; – Chapter 12: DNA Technology