lec 23 - gene therapy II (guo)

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delivering genes to patient cells overview

  1. to deliver a gene to patient cells we can use: 1) viruses or 2) non-viral methods

  2. when using viruses, first we haev to find a way to get the desired gene into the virus

  3. to get the desired gene into viruses, we use specifically engineered eukaryotic cells grow in the lab. these cells are engineered with genes (called gene sequences) that express viral proteins → b/c they supply viral proteins, they are called packaging cells

    1. scientists grow eukaryotic cells and then modify these cells to give them genes that make viral proteins (gag/pol, env; tools to make virus structure) → these cells now produce the viral proteins needed to build the virus but they do NOT have the full viral genome → b/c these cells package the viral proteins to help assemble the virus they are called packaging cells

  4. if we transfer the desired gene linked to the correct packaging sequences (called cis sequences) into the packaging cells, the packaging cells will start making viruses carrying the desired gene. such viruses that carry the desired gene are called vector virus

  5. finally the vector viruses that carry the desired gene can be collected and used to infect target cells from the patient; upon infection, the vector virus will deliver the desired gene to the target cell

<ol><li><p>to deliver a gene to patient cells we can use: 1) viruses or 2) non-viral methods</p></li><li><p>when using viruses, first we haev to find a way to get the desired gene into the virus</p></li><li><p>to get the desired gene into viruses, we use specifically engineered eukaryotic cells grow in the lab. these cells are engineered with genes (called <strong>gene sequences</strong>) that express viral proteins → b/c they supply viral proteins, they are called <strong>packaging cells</strong></p><ol><li><p>scientists grow eukaryotic cells and then modify these cells to give them genes that make viral proteins (gag/pol, env; tools to make virus structure) → these cells now produce the viral proteins needed to build the virus but they do NOT have the full viral genome → b/c these cells package the viral proteins to help assemble the virus they are called packaging cells</p></li></ol></li><li><p>if we transfer the desired gene linked to the correct packaging sequences (called <strong>cis sequences</strong>) into the packaging cells, the packaging cells will start making viruses carrying the desired gene. such viruses that carry the desired gene are called <strong>vector virus</strong></p></li><li><p>finally the vector viruses that carry the desired gene can be collected and used to infect target cells from the patient; upon infection, the vector virus will deliver the desired gene to the target cell</p></li></ol><p></p>
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vector virus production and infection

packaging cell with trans/cis parts → replication-incompetent vector virus → gene delivery into target cells of patients by infection

<p>packaging cell with trans/cis parts → replication-incompetent vector virus → gene delivery into target cells of patients by infection</p><p></p>
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non-viral gene delivery systems

liposomes

  • spherical vesicles composed of synthetic lipid bilayers that miimc the structure of biological membranes

  • cationic (pos charge) lipids used for transferring DNA (neg charge) into cells

  • the transgene is packaged in vitro with the liposomes and used directly for delivering the DNA to a suitable target tissue in vivo

  • lipid coating protects the DNA in vivo and binds to cells

  • packaged DNA enters into cells by direct fusion

  • efficiency of transfer is relatively low and the introduced foreign gene does NOT integrate into hosts genome

  • high liposome and DNA concentrations required but both are relatively easy and cheap to manufacture in large amounts

<p>liposomes</p><ul><li><p>spherical vesicles composed of <strong>synthetic lipid bilayers</strong> that miimc the structure of biological membranes</p></li><li><p><strong>cationic (pos charge) lipids</strong> used for transferring <strong>DNA (neg charge) </strong>into cells</p></li><li><p>the transgene is packaged <em>in vitro</em> with the liposomes and used directly for delivering the DNA to a suitable target tissue <em>in vivo</em></p></li><li><p>lipid coating protects the DNA <em>in vivo</em> and binds to cells</p></li><li><p>packaged DNA enters into cells by <strong>direct fusion</strong></p></li><li><p><strong>efficiency of transfer is relatively low and the introduced foreign gene does NOT integrate into hosts genome</strong></p></li><li><p><strong>high liposome and DNA concentrations required</strong> but both are relatively easy and cheap to manufacture in large amounts</p></li></ul><p></p>
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improved targeting of liposomes

  • PEGylated liposomes

    • PEG (improved PK/PD) improves the half life of liposomes

  • transferrin-conjugated liposome

    • transferrin can binds transferrin receptors found on human cells

  • antibody modified liposomes

    • antibody coating for specificity

  • adding a sendai (HVJ) viral proteins

    • allows DNA to escape the endosome intact by disrupting endosomal membrane

  • DNA binding proteins (HMG-1 high mobility group 1 protein)

    • to target foreign DNA into nucleus

  • nuclear localizing sequence (NLS) within DNA

  • as a wide range of DNA encoding both small or large proteins can be accommodated → liposomes offer very versatile option for gene delivery

<ul><li><p><strong>PEGylated liposomes</strong></p><ul><li><p>PEG (improved PK/PD) improves the half life of liposomes</p></li></ul></li><li><p><strong>transferrin-conjugated liposome</strong></p><ul><li><p>transferrin can binds <strong>transferrin receptors</strong> found on human cells</p></li></ul></li><li><p><strong>antibody modified liposomes</strong></p><ul><li><p>antibody coating for <strong>specificity </strong></p></li></ul></li><li><p><strong>adding a sendai (HVJ) viral proteins</strong></p><ul><li><p>allows DNA to escape the endosome intact by disrupting endosomal membrane</p></li></ul></li><li><p><strong>DNA binding proteins </strong>(HMG-1 high mobility group 1 protein)</p><ul><li><p>to target foreign DNA into nucleus</p></li></ul></li><li><p>nuclear localizing sequence (<strong>NLS</strong>) within DNA</p></li><li><p>as a <strong>wide range of DNA</strong> encoding both small or large proteins can be accommodated → <strong>liposomes offer very versatile option for gene delivery</strong></p></li></ul><p></p>
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nanoparticles for gene delivery: polymer-based nanomaterial for gene delivery

  • electrostatic interactions between DNA + polymer allow nanocomplexes to be formed with DNA → protects DNA from degradation

  • PGA (poly-glycolic acid) = FDA approved for drug delivery

  • poly (lactic-co-glycolic acid) → can potentially be used for gene delivery also

  • benefits

    • increasing transfection efficiency

    • navigating through the multiple biological barriers

<ul><li><p><strong>electrostatic interactions</strong> between DNA + polymer allow nanocomplexes to be formed with DNA → protects DNA from degradation</p></li><li><p><strong>PGA (poly-glycolic acid) = FDA approved for drug delivery</strong></p></li><li><p>poly (lactic-co-glycolic acid) → <strong>can potentially be used for gene delivery also</strong></p></li><li><p>benefits</p><ul><li><p>increasing transfection efficiency</p></li><li><p>navigating through the multiple biological barriers</p></li></ul></li></ul><p></p>
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naked DNA

  • muscle cells were first shown to be able to take up naked DNA and express proteins

  • 99% of injected DNA is degraded by extracellular nucleases

  • large amounts of DNA required

  • very low gene transfer efficiency leads to low and transient protein expression

  • NOT immunogenic

  • useful when the effect of the expressed protein is naturally amplified (such as to activate immune system via cytokines or antigens)

    • basically when even small amounts of protein can have a big effect

  • increase transduction efficiency by electric impulse or ‘gene gun’

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biolistic gene gun

  • uses kinetic energy to deliver nucleic acids inside cells

  • DNA is coated on gold or tungsten particles

  • 5-10% transduction efficiency

  • only be used for exposed targets such as skin for local transfection that can withstand pressure

  • NOT useful for deep tissues

  • e.g. skeletal myotubules that are hard to transduce with viral vectors due to lack of receptors can be transfected with gene guns

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summary of viral and non-viral gene delivery system

viral vectors

  • pros

    • high transfection efficiency

    • natural tropism → ability to infect different cell types

    • evolved mechanisms for endosomal escape

      • viruses have evolved ways to avoid being destroyed inside cell’s endosomes

    • natural transportation mechanism of DNA into nucleus

  • cons

    • strong immune rxns against vial proteins prohibit multiple admins

    • possibility of chromosomal inserting and proto-oncogene activation

    • complicated synthesis process

    • toxicity, risk of contamination of live virus

    • limitation of gene size

non-viral vectors

  • pros

    • low immunogenicity

    • can be made to be non-toxic

    • easy to synthesis → quality control for mass production

    • potentially targetable

    • NO limit on plasmid size

    • No integration → can be admin as drugs

  • cons

    • low transfection efficacy

    • NO natural tropism, endosomal escape or nuclear transport mechanisms

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process of clinical trials

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clinical trials of gene therapy

  • 1972 → concept of gene therapy considered as form of treatment

  • 1975 → first organ cell for therapy isolated from fetus

  • 1985 → studies report safe use of fetal organ cell in patient

  • 1990 → first gene therapy trial in humans

  • 1999 → death of jesse gelsinger in AAV therapy trial

  • 2003 → first gene therapy clinical trial for parkinson’s disease is initiated

  • 2012 → jennifer doudna and emmanuelle charpentier developed the CRISPR-cas9 gene editing system

  • 2017 → FDA approved first gene therapy in U.S.; kymriah, CAR-T cell therapy, was approved

  • 2023 → first CRISPR therapy seeking FDA approval

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gene therapy clinical trials approved or initiated 1989-2023

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total number of gene therapy trials currently

3900

  • most in phase I

<p><strong>3900</strong></p><ul><li><p>most in phase I</p></li></ul><p></p>
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gene types transferred in gene therapy clinical trials

  • mostly receptor followed by antigen

<ul><li><p>mostly receptor followed by antigen</p></li></ul><p></p>
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indications addressed by gene therapy clinical trials

mostly cancer

<p>mostly cancer</p>
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clinical application — case studies

  • parkinsons

  • restenoisis

  • cancer

  • severe combine immune deficiency (SCID) (bubble boy disease)

  • retinal disorders

  • CFR

  • hemophilia genetic defects

<ul><li><p>parkinsons</p></li><li><p>restenoisis</p></li><li><p>cancer</p></li><li><p>severe combine immune deficiency (SCID) (bubble boy disease)</p></li><li><p>retinal disorders</p></li><li><p>CFR</p></li><li><p>hemophilia genetic defects</p></li></ul><p></p>
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clinical feature of ADA-SCID (adenosine deaminase deficiency)

  • ADA deficiency = cause of approx 20% of severe combined immunodeficiency (SCID)

  • pts have multiple severe opportunistic infections usually beginning in infancy

  • inherited as autosomal recessive condition

  • rare, <1/100,000 births

  • usually fatal in 1st year of life if untreated

  • selective toxicity to lymphocytes from accumulation of metabolites of deoxyadenosine, esp dATP

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rational for considering ADA-SCID for initial gene therapy trials

  • normal human ADA gene had been cloned

  • a single gene defect leads to loss of enzymatic function

  • HLA-matched allogenic bone marrow transplantation completely corrects the disease

  • treatment for those patients who lack HLA-matched bone marrow donors is with recombinant ADA protein

  • corrected cells have selective growth advantage in vivo

  • small amount of ADA activity is sufficient to correct disease

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first human gene therapy trial - 1990

  • 2 girls (4 and 9) with ADA-SCID = first gene therapy recipients

  • ADA gene delivered into patient lymphocytes using retroviral vectors; ex vivo therapy

  • patients continued to receive ADA protein replacement therapy

  • immune systems restored

  • process

    • remove ADA-deficient lymphocytes from SCID patient → culture the cells in a lab

    • infect the cells with a retrovirus that contains the normal ADA gene

    • no selection procedure

    • reinfuse the ADA-gene-corrected lymphocytes back into the SCID patient

  • both girls had the transgene years after treatment and exhibited robust immune systems

<ul><li><p>2 girls (4 and 9) with ADA-SCID = <strong>first gene therapy recipients</strong></p></li><li><p>ADA gene delivered into patient lymphocytes using <strong>retroviral vectors; ex vivo therapy</strong></p></li><li><p>patients continued to receive ADA protein replacement therapy</p></li><li><p>immune systems restored</p></li><li><p>process</p><ul><li><p>remove ADA-deficient lymphocytes from SCID patient → culture the cells in a lab</p></li><li><p>infect the cells with a retrovirus that contains the normal ADA gene</p></li><li><p><strong>no selection procedure</strong></p></li><li><p>reinfuse the ADA-gene-corrected lymphocytes back into the SCID patient</p></li></ul></li><li><p><strong>both girls had the transgene years after treatment and exhibited robust immune systems</strong></p></li></ul><p></p>
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a case study for failed gene therapy clinical trials

  • jeese gelsinger, relatively fit 18yr old with ornithine transcarbamylase deficiency (OTC) died on sep 17,1999 in a gene therapy trial at upenn, 4 days after he was administered a massive dosage of 38 trillion genetically altered adenovirus particles carrying the OTC gene directly into the hepatic artery in the liver

  • what went wrong?

    • the vector invaded organs other than the intended target

    • only 1% of the transferred genes reached the target cells

    • harsh immune response was triggered (may be an undetected genetic condition or a latent parvovirus infection)

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X-linked severe combined immunodeficiency (SCID)

  • 40-50% of SCID cases

  • caused by deficiency in y subunit of cytokine IL-2 receptor (IL2RG gene)

  • the y subunit of IL-2 receptor is also called common y chain (cy) as it is a subunit common to the receptors for 5 other cytokines also:

    • IL-4

    • IL-7

    • IL-9

    • IL-15

    • IL-21

  • received an infusion of autologous bone marrow-derived CD34+ cells transduced with the y chain-IL2R containing retroviral vector

  • gene therapy caused 4 patients to develop leukemia 2-4 years after treatment

  • possible reasons for leukemia development

    • something about the vector virus made it integrate at oncogenic sites (LMO2)

    • the transferred gene IL2RG itself is oncogenic

    • genetic background of patient makes them predisposed to cancer (siblings of some patients developed cancer)

<ul><li><p>40-50% of SCID cases</p></li><li><p>caused by deficiency in <strong>y subunit of cytokine IL-2 receptor (IL2RG gene)</strong></p></li><li><p>the y subunit of IL-2 receptor is also called common y chain (cy) as it is a subunit common to the receptors for 5 other cytokines also:</p><ul><li><p>IL-4</p></li><li><p>IL-7</p></li><li><p>IL-9</p></li><li><p>IL-15</p></li><li><p>IL-21</p></li></ul></li><li><p>received an infusion of autologous bone marrow-derived CD34+ cells transduced with the y chain-IL2R containing <strong>retroviral vector</strong></p></li><li><p><strong>gene therapy caused 4 patients to develop leukemia 2-4 years after treatment</strong></p></li><li><p>possible reasons for leukemia development</p><ul><li><p>something about the vector virus made it <strong>integrate at oncogenic sites (LMO2)</strong></p></li><li><p>the transferred gene <strong>IL2RG itself is oncogenic</strong></p></li><li><p><strong>genetic background of patient</strong> makes them predisposed to cancer (siblings of some patients developed cancer)</p></li></ul></li></ul><p></p>
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cystic fibrosis (CFR)

  • effects 1 in 3300 caucasians and 1/25 are carriers (most common hereditary disease in caucasians)

  • gene

    • CFTR

  • name of protein

    • cystic fibrosis transmembrane conductance regulator

  • locus

    • 7q31.2

  • size

    • CFTR gene consists of 27 exons (coding regions)

    • gene (total # of bps of exons + introns) is over 250,000 bps (250 kbp)

    • after introns are spliced out, mRNA = 6100 bps long and is translated into the 1480 AA sequence of CFTR protein

  • protein function

    • normal CFTR protein is a channel protein found in membranes of epithelial cells

  • major symptoms

    • impaired lung function

    • chronic respiratory infections

    • airway inflammation

  • CFTR gene codes for an ABC transporter class ion channel proteins that conducts chloride and thiocyanate ions across epithelial cell membranes

    • mutations of the CFTR gene affecting Cl- ion channel function → lead to dysregulation of epithelial fluid transport in the lung, pancreas and other organs → results in CFR

<ul><li><p><strong>effects 1 in 3300 caucasians and 1/25 are carriers (most common</strong> hereditary disease in caucasians)</p></li><li><p>gene</p><ul><li><p>CFTR</p></li></ul></li><li><p>name of protein</p><ul><li><p>cystic fibrosis transmembrane conductance regulator</p></li></ul></li><li><p>locus</p><ul><li><p>7q31.2</p></li></ul></li><li><p>size</p><ul><li><p>CFTR gene consists of 27 exons (coding regions)</p></li><li><p>gene (total # of bps of exons + introns) is over 250,000 bps (<strong>250 kbp)</strong></p></li><li><p>after introns are spliced out, <strong>mRNA = 6100 bps</strong> long and is translated into the <strong>1480 AA</strong> sequence of CFTR protein</p></li></ul></li><li><p>protein function</p><ul><li><p>normal CFTR protein is a <strong>channel protein</strong> found in membranes of epithelial cells</p></li></ul></li><li><p>major symptoms</p><ul><li><p>impaired lung function</p></li><li><p>chronic respiratory infections</p></li><li><p>airway inflammation</p></li></ul></li><li><p>CFTR gene codes for an <strong>ABC transporter</strong> class <strong>ion channel</strong> proteins that conducts <strong>chloride</strong> and <strong>thiocyanate</strong> ions across <strong>epithelial cell membranes</strong></p><ul><li><p>mutations of the CFTR gene affecting Cl- ion channel function → lead to dysregulation of epithelial fluid transport in the lung, pancreas and other organs → results in CFR</p></li></ul></li></ul><p></p>
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why is CFR an ideal candidate for gene therapy?

  • single gene defect

  • recessive condition (heterozygotes normal, suggesting no gene dosing effects, means small changes in gene expression are unlikely to cause harm)

  • main pathology = lung which is accessible for treatment

  • progressive disease with virtually normal phenotype at birth thereby providing a therapeutic window from symptom to treatment

  • protein replacement therapy in lungs NOT available and may NOT be possible for a membrane protein

    • gene therapy might be the only option

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what are the requirements for CFR gene therapy to work?

  • adequate carrying capacity by gene delivery system

  • to be undetectable by the immune system

  • to be non-inflammatory

  • to be safe to patients with pre-existing lung inflammation

  • to have an efficiency sufficient to correct the cystic fibrosis phenotype

  • to have long duration of expression or the ability to be safely re-administered

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gene therapy for CFR

  • first trials in NY in 1993 using adenoviral vector were unsuccessful due to significant immune rxns and inflammation in the lungs

  • clinical trial currently ongoing by the UK cystic fibrosis gene therapy consortium: CFTR gene introduced via aerosol to lungs using cationic liposomes

    • 136 patients aged 12 and above were randomly assigned to either nebulised pGM169/GL67A (gene therapy) or saline (placebo) at monthly intervals over 1 year; lung function was evaluated using a common clinical measure FEV1 (amount of air you can force from your lungs in one second)

    • clinical trials reached its primary endpoint with patients who received therapy having a significant if modest benefit in lung function compared with the gene therapy, FEV was 3.7% greater compared to placebo

    • trial is the first ever to show that repeated doses of a gene therapy can have a meaningful effect on the disease and change the lung function of patients

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hemophilia B (christmas disease)

  • X linked genetic disorder

  • affects 1/100,000 male births

  • abnormal bleeding due to defective coagulation factor IX

  • mutation in factor IX now know to be cause of ‘royal disease’

  • queen victoria and many of her descendants carried what was once called ‘royal disease’

<ul><li><p>X linked genetic disorder</p></li><li><p>affects 1/100,000 male births</p></li><li><p>abnormal bleeding due to defective coagulation factor IX</p></li><li><p>mutation in <strong>factor IX</strong> now know to be cause of ‘royal disease’</p></li><li><p>queen victoria and many of her descendants carried what was once called ‘royal disease’</p></li></ul><p></p>
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gene therapy for hemophilia B

  • classification (factor IX activity)

    • normal → 100% (factor IX activity) → 5 mg/mL (factor Ix concentration)

    • mild → 5-50% → >250 ng/mL → bleed as result of surgery or major injury

    • moderate → 1-5% → 50-250 ng/mL → bleed less frequently, once a month

    • severe → <1% → <50 ng/mL → bleed 1-2 times per week, spontaneous, no reason

  • 40% of cases are severe

  • effective care can be achieved with levels of 85-100 ng/mL factor IX in blood; in other words → symptoms can be significantly reduced by expression of only 1.5-2% of normal levels of factor IX

  • factor IX cDNA gene = 1.5 kbp

<ul><li><p>classification (factor IX activity)</p><ul><li><p>normal → 100% (factor IX activity) → 5 mg/mL (factor Ix concentration)</p></li><li><p>mild → 5-50% → &gt;250 ng/mL → bleed as result of surgery or major injury</p></li><li><p>moderate → 1-5% → 50-250 ng/mL → bleed less frequently, once a month</p></li><li><p>severe → &lt;1% → &lt;50 ng/mL → bleed 1-2 times per week, spontaneous, no reason</p></li></ul></li><li><p>40% of cases are severe</p></li><li><p>effective care can be achieved with levels of 85-100 ng/mL factor IX in blood; in other words → <strong>symptoms can be significantly reduced by expression of only 1.5-2% of normal levels of factor IX</strong></p></li><li><p>factor IX cDNA gene = <strong>1.5 kbp</strong></p></li></ul><p></p>
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current treatment for factor IX deficiency

  • infusion of factor IX protein IV

    • concentrated from donated human blood

    • improved manufacturing and production of rfactorIX has reduced complications of contaminations associated with using a blood product

  • factor IX half life → 18-24 hrs

  • in america, infusions given usually only in management of crisis situations

  • can cost up to $20 million over the lifetime of a patient

  • gene therapy which obviates IV infusions would advance care both clinically and economically

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long-term expression of factor IX after gene therapy using AAV

  • AAV normally delivers a single-stranded DNA version of the therapeutic gene

  • after virus infects the target cell, cell has to synthesize the 2nd DNA strand to make it double stranded before gene can be used → second strand synthesis is slow (rate limiting step)

  • solution

    • self-complementary adeno-associated virus vector (sc-AAV)

    • instead of delivering just 1 DNA strand, sc-AAV delivers both strands already connected together → once inside the cell, the 2 strands fold and bind to form double stranded DNA quickly → allows the therapeutic gnee to start working faster and more efficiently

    • although very efficient gene deliver vehicles, sc-AAV vectors can deliver genes that are maximally only ~2.3-2.4 kbp in size (half the size of regular AAV vectors)

<ul><li><p>AAV normally delivers a single-stranded DNA version of the therapeutic gene</p></li><li><p>after virus infects the target cell, cell has to synthesize the 2nd DNA strand to make it double stranded before gene can be used → <strong>second strand synthesis is slow (rate limiting step)</strong></p></li><li><p>solution</p><ul><li><p><strong>self-complementary adeno-associated virus vector (sc-AAV)</strong></p></li><li><p>instead of delivering just 1 DNA strand, sc-AAV delivers both strands already connected together → once inside the cell, the 2 strands fold and bind to form double stranded DNA quickly → allows the therapeutic gnee to start working faster and more efficiently</p></li><li><p>although very efficient gene deliver vehicles, sc-AAV vectors can deliver genes that are maximally only <strong>~2.3-2.4 kbp</strong> in size (half the size of regular AAV vectors)</p></li></ul></li></ul><p></p>
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hemophilia A

  • most common type of hemophilia

  • 5x more common than hemophilia B

  • X-linked disorder

  • factor VIII gene near factor IX on X chromosome

  • gene (cDNA) = ~9kbp

  • good target for gene therapy as even a low level of secreted protein expression can prevent symptoms

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other applications of gene therapy

  1. hereditary blindness: leber’s congenital amaurosis (LCA)

    • caused by mutation in RPE65 gene

    • eye disorder that primarily affects the retina

    • 4 independent clinical trials with AAV2-containing RPE65 reported improvement in vision with none being associated with vector-related adverse events

  2. lysosomal storage diseases

    • more than 50 diseases are considered lysosomal storage disorders

    • most common: gaucher disease, fabry disease, hunter syndrome, hurler syndrome, tay-sachs disease, pompe disease

    • rare, inherited conditions occur when the body does NOT produce the enzymes needed to help break down certain substances such as fats, sugars or proteins

  3. parkinsons

    • cell death in brain region called ‘substantia negra’

    • responsible for making neurotransmitter dopamine

    • currently treated with exogenous dopamine systemically which inefficiently crosses BBB and has side effects

    • gene transduction of tyrosine hydroxylase → enzyme that synthesizes dopamine

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strategy for the rationality in the gene therapy trials in parkinson’s

  • parkinsons has a complex pathophysiology that is by no means fully understood and involves multiple brain structures and signaling pathways

  • 3 broad approaches to selection of a therapeutic target

    • restoration of dopamine synthesis in the dorsal striatum

    • modulation of activity in the basal ganglia downstream of the striatum

    • modification of disease progression by neuroprotection

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vectors associated with gene therapy for parkinsons

  • over-expression of GDNF (glial cell line-derived neurotrophic factor) mediated by lentiviral vector has conferred some protection of the nigrostriatal dopamine terminal against toxic insults

  • ad-GDNF can protect dopaminergic neurons and improve dopamine-dependent behavioral function in young rats with progressive 6-OHDA lesions of the nigrostriatal projection

  • AAV-2 when administered locally transduced only neurons within the CNS and is particularly efficient in brain regions known to be involved in the pathophysiology of parkinsons such as globus pallidus and substatia nigra

  • long term safety and tolerability of prosavin, lentiviral vector based gene therapy

    • dose escalation, open-label → phase 1/2 trial

    • phase 3 trial → called exPDite-2 study, expected to begin in the first half of 2025, will enroll 102 pts to assess efficacy and safety over 78 weeks

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gene therapy for treatment of cardiac disease

  • endovascular surgery = innovative, less invasive procedure used to treat problems affecting the blood vessels

    • blocked artery is opened using a stent → keeps artery open, restoring blood flow

    • over time, >50% of patients, artery narrows again in process called restenosis = common adverse event of endovascular procesdures

<ul><li><p><strong>endovascular</strong> surgery = innovative, less invasive procedure used to treat problems affecting the blood vessels</p><ul><li><p>blocked artery is opened using a stent → keeps artery open, restoring blood flow</p></li><li><p>over time, &gt;50% of patients, artery narrows again in process called <strong>restenosis = common adverse event of endovascular procesdures</strong></p></li></ul></li></ul><p></p>
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gene-eluting stents for preventing coronary restenosis

  • stent coated with PLGA-nanoparticles containing vascular endothelial growth factor (VEGF) gene in animal model system

    • keeps artery OPEN

  • other potential genes to treat restenosis

    • PCNA (proliferating cell nuclear antigen)

    • NOS (nitric oxide synthase)

<ul><li><p>stent coated with PLGA-nanoparticles containing vascular endothelial growth factor (<strong>VEGF</strong>) gene in <strong>animal</strong> model system</p><ul><li><p>keeps artery OPEN</p></li></ul></li><li><p>other potential genes to treat restenosis</p><ul><li><p><strong>PCNA</strong> (proliferating cell nuclear antigen)</p></li><li><p><strong>NOS</strong> (nitric oxide synthase)</p></li></ul></li></ul><p></p>
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gene therapy in cancer

  1. engineer T cells to recognize tumor antigens like CEA, NY-ESO-1, CD19

  2. immunopotentiating genes (IL2, B7, GM-CSF) introduced into tumor cells to increase immune rxn to tumor

  3. restoring tumor suppressor genes like p53, BRCA1, Rb that are mutated in cancer cells

  4. anti-sense therapy to turn OFF oncogenes/replication genes

  5. suicide genes → implant herpes simplex thymidine kinase into tumor cells

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immunotherapy: CAR T cell therapy

enhance the natural cancer-fighting ability of patients’ own T cells

  • sample of patients T cells is collected and mixed with viruses carry several specific genes

  • viruses deliver these genes to the T cells nuclei where they are incorporated into the cell’s DNA

  • the genes cause the T cells to express a special protein called a chimeric antigen receptor, or CAR, on their surface

  • CAR directs the T cell to the tumor cell using a specific ‘address’ and the CAR T cell is then equipped to rapidly destroy the cancer cell

  • when the CAR T cells are infused into the patient → they seek out tumor cells and then proliferate to generate many more cancer-killing cells

<p><strong>enhance the natural cancer-fighting ability of patients’ own T cells</strong></p><ul><li><p>sample of patients T cells is collected and mixed with viruses carry several specific genes</p></li><li><p>viruses deliver these genes to the T cells nuclei where they are incorporated into the cell’s DNA</p></li><li><p>the genes cause the T cells to express a special protein called a chimeric antigen receptor, or CAR, on their surface</p></li><li><p>CAR directs the T cell to the tumor cell using a specific ‘address’ and the CAR T cell is then equipped to rapidly destroy the cancer cell</p></li><li><p>when the CAR T cells are infused into the patient → they seek out tumor cells and then proliferate to generate many more cancer-killing cells</p></li></ul><p></p>
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targeted gene therapy using suicide gene

  • normal cell

    • prodrug activator gene (e.g. herpes simplex thymidine kianse) is OFF b.c the tumor specific promoter is inactive in normal cells → gene is NOT transcribed → prodrug (e.g. ganciclovir) NOT metabolized → NO cell death

  • tumor cell

    • tumor specific promoter is ON → turns the prodrug activator gene ON → enzyme converts prodrug to toxic metabolite → cell death

  • basic concept of suicide gene therapy = introduction of viral or bacterial genes into tumor cells which convert a non-toxic prodrug → toxic one

  • gene-directed enzyme-producing therapy (GDEPT) → uses a gene taken from the cancer cell and then modified with other genes to form enzymes that are harmless to healthy cells but in cancer cells will activate the prodrug to turn into toxic metabolite that will kill cancer cells

  • virus-directed enzyme-prodrug therapy → uses a virus, such as herpes simplex or cold virus, as the carrier, or vector, to deliver the modified genes to cancer cells

<ul><li><p>normal cell</p><ul><li><p>prodrug activator gene (e.g. <strong>herpes simplex thymidine kianse</strong>) is OFF b.c the tumor specific promoter is <strong>inactive</strong> in normal cells → gene is NOT transcribed → prodrug (<strong>e.g. ganciclovir</strong>) NOT metabolized → NO cell death</p></li></ul></li><li><p>tumor cell</p><ul><li><p>tumor specific promoter is ON → turns the prodrug activator gene ON → enzyme converts prodrug to toxic metabolite → cell death</p></li></ul></li><li><p><strong>basic concept of suicide gene therapy</strong> = introduction of viral or bacterial genes into tumor cells which convert a non-toxic prodrug → toxic one</p></li><li><p><strong>gene-directed enzyme-producing therapy (GDEPT) → </strong>uses a gene taken from the cancer cell and then modified with other genes to form enzymes that are harmless to healthy cells but in cancer cells will activate the prodrug to turn into toxic metabolite that will kill cancer cells</p></li><li><p><strong>virus-directed enzyme-prodrug therapy</strong> → uses a virus, such as herpes simplex or cold virus, as the carrier, or vector, to deliver the modified genes to cancer cells</p></li></ul><p></p>
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suicide gene therapy

  • mode → induces tumor lysis by tumor-specific delivery of prodrug-activating genes

  • examples

    • HSV-tk/GCV

    • CD/5-FC

  • advantages

    • requires short-term gene expression

    • safety in clinical trials

    • ‘bystander’ tumor killing via gap-junction delivery of drug

    • enhances sensitivity to conventional therapy

  • limitations

    • limited spatial distribution of gene transfer vectors

    • poor gene-transfer efficiency into tumor cells in vivo

    • inability to target dispersed tumor cells

  • cytosine deaminase gene (CD) of escherechia coli = converts the pro-drug 5-fluorocytosine (5-FC) → 5-fluorouracil (5-FU)

  • herpes simplex virus thymidine kinase gene (HSC-tk) = converts ganciclovir (GCV) to ganciclovir monophosphate, converted by the cancer cells’ enzymes to ganciclovir triphosphate

  • suicide gene therapy has demonstrated limited clinical efficacy for treatment of malignant glioma (aggressive brain tumor)

<ul><li><p>mode → induces tumor lysis by tumor-specific delivery of prodrug-activating genes</p></li><li><p>examples</p><ul><li><p>HSV-tk/GCV</p></li><li><p>CD/5-FC</p></li></ul></li><li><p>advantages</p><ul><li><p>requires short-term gene expression</p></li><li><p>safety in clinical trials</p></li><li><p>‘bystander’ tumor killing via gap-junction delivery of drug</p></li><li><p>enhances sensitivity to conventional therapy</p></li></ul></li><li><p>limitations</p><ul><li><p>limited spatial distribution of gene transfer vectors</p></li><li><p>poor gene-transfer efficiency into tumor cells <em>in vivo</em></p></li><li><p>inability to target dispersed tumor cells</p></li></ul></li><li><p>cytosine deaminase gene (<strong>CD</strong>) of escherechia coli = converts the pro-drug <strong>5-fluorocytosine (5-FC) → 5-fluorouracil (5-FU)</strong></p></li><li><p>herpes simplex virus thymidine kinase gene (<strong>HSC-tk) </strong>= converts ganciclovir (<strong>GCV</strong>) to <strong>ganciclovir monophosphate</strong>, converted by the cancer cells’ enzymes to <strong>ganciclovir triphosphate</strong></p></li><li><p><strong>suicide gene therapy has demonstrated limited clinical efficacy for treatment of malignant glioma (aggressive brain tumor)</strong></p></li></ul><p></p>
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advances in gene editing technologies

  • in vivo CRISPR editing

    • researchers have begun editing genes directly inside the human body

    • for instance, intellia therapeutics and regeneron pharmaceuticals have developed treatemnts that use lipid nanoparticles to deliver CRISPR components to the liver, targeting diseases like transthyretin amyloidosis

    • early results show significant reductions in disease causing proteins

  • base and prime editing

    • next generation CRISPR techniques such as base and prime editing allow for precise correction of a single-letter genetic mutations WITHOUT cutting the DNA

    • these methods are being explored for treating conditions like progeria and other monogenic diseases → offers potential for safer and more accurate therapies

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CRISPR technology

  • simple yet powerful tool for editing genomes, allows researchers to easily alter DNA sequences and modify gene function

  • components of the CRISPR-Cas9 system

    • 2 core components

      • RNA guided DNA endonuclease Cas9

      • chimeric single guide RNA (sgRNA)

    • the sgRNA, which has an invariant scaffold region and a spacer region, is derived from CRISPR RNA (crRNA) and transactivating crRNA (tracrRNA)

    • sgRNA binds to Cas9 and directs it to the locus of interest by a 20-nt guide sequence via base pairing to the genomic target

    • the target sequence in genomic DNA paired to sgRNA sequenced is immediately followed by either NGG or NAG trinucleotide for S. pyogenes-derived cas9 (other cas9 orthologues recognize different PAM) called the protospacer adjacent motif (PAM)

      • Cas9 only cuts DNA if the target site is followed by a special PAM sequence, which for the common cas0 form s. pyrogenes is NGG or NAG

    • PAM is located on the immediate 3’ end of the sgRNA recognition sequence but is NOT a part of the 20-nt guide sequence within sgRNA

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mechanism of CRISPR-cas9 mediated genome engineering

  • cas9 enzyme uses sgRNA with a 20-nt guide to find and bind the matching sequence in the genomic DNA → once bound, cas9 cuts both strands at that location using:

    • HNH → cuts one strand

    • RuvC → cuts other strand

    • result = double strnad break

  • cell repairs the break in one of 2 ways

    • nonhomologous end joining (NHEJ)

      • quick fix, NO template needed

      • cells glue the broken ends together but introduces random mutations

        • small insertion

        • small deletion

        • substitution

      • can disrupt the function of a gene

    • homology directed repair (HDR)

      • precise fix, requires a template

      • scientists provide a piece of donor DNA containing the desired sequence

      • cell copies this donor DNA into the broken site

      • precise gene editing or gene knock in

<ul><li><p>cas9 enzyme uses sgRNA with a 20-nt guide to find and bind the matching sequence in the genomic DNA → once bound, cas9 cuts both strands at that location using:</p><ul><li><p>HNH → cuts one strand</p></li><li><p>RuvC → cuts other strand</p></li><li><p>result = double strnad break</p></li></ul></li><li><p>cell repairs the break in one of 2 ways</p><ul><li><p>nonhomologous end joining (NHEJ)</p><ul><li><p>quick fix, NO template needed</p></li><li><p>cells glue the broken ends together but introduces <strong>random mutations</strong></p><ul><li><p>small insertion</p></li><li><p>small deletion</p></li><li><p>substitution</p></li></ul></li><li><p>can disrupt the function of a gene</p></li></ul></li><li><p>homology directed repair (HDR)</p><ul><li><p>precise fix, requires a template</p></li><li><p>scientists provide a piece of donor DNA containing the desired sequence</p></li><li><p>cell copies this donor DNA into the broken site</p></li><li><p>precise gene editing or gene knock in</p></li></ul></li></ul></li></ul><p></p>
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CRISPR technology: potential applications and advantage

  • altering specific genetic loci thru insertions, deletions, point mutations, and sequence inversions

  • treating and preventing the spread of diseases and improving crops

  • transform medicine, enabling us to NOT only treat but also prevent many diseases

  • system was recently modified to act as a genome regulator by tethering effector domains to Cas9 or guide-RNA and as a visualization tool by fusing with marker molecules

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CRISPR: potential disadvantages

  • philosophical dilemma

    • ethical concerns about germline gene editing which are responsible for passing genes on to the next generation

  • safety

    • accuracy

      • off target effects lack of specificity in targeting and incomplete targeting

      • particularly important issue when it comes to the use of technology for applications directed towards human health

    • another issues is that once an organism, such as plant or insect, is modified, they are difficult to distinguish from the wild-type and once released into the environment could endanger biodiversity

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CRISPR engineering of T cells in cancer patients

  • steps in cycle

    • collect T cells

    • CRISPR used to make 3 main changes

      • PD-1 knockout → PD-1 normally turns OFF T cells and tumors exploit this

      • TCR knockout → to prevent T cells from accidentally attacking normal tissues

      • insert new TCR (lentivirus vector) → recognizes cancer-specific antigen and helps T cells find and kill cancer cells

    • return edited T cells into patient

      • stay active → b/c PD-1 is gone

      • only target cancer → new TCR

      • avoid attacking healthy cells → OG TCR removed

  • disrupts 3 genes (TRAC, TRBC, and PDCD1)

  • cancer targeting transgene, NY-ESO-1, introduced to recognize tumors

<ul><li><p>steps in cycle</p><ul><li><p>collect T cells</p></li><li><p>CRISPR used to make 3 main changes</p><ul><li><p>PD-1 knockout → PD-1 normally turns OFF T cells and tumors exploit this </p></li><li><p>TCR knockout → to prevent T cells from accidentally attacking normal tissues</p></li><li><p>insert new TCR (lentivirus vector) → recognizes cancer-specific antigen and helps T cells find and kill cancer cells</p></li></ul></li><li><p>return edited T cells into patient</p><ul><li><p>stay active → b/c PD-1 is gone</p></li><li><p>only target cancer → new TCR</p></li><li><p>avoid attacking healthy cells → OG TCR removed</p></li></ul></li></ul></li><li><p>disrupts 3 genes (TRAC, TRBC, and PDCD1)</p></li><li><p>cancer targeting transgene, NY-ESO-1, introduced to recognize tumors</p></li></ul><p></p>
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cancer vaccine

this approach involves:

  • collecting tumor cells from patient

  • engineering them with genes that cause them to be conspicuous (immune system can detect them easier) to the immune system

  • re-infusing altered cancer cells into pt along with immune-stimulating compound

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potential complications of gene therapy and strategies to mitigate risk

  • problem

    • solution

  • gene silencing — repression of promoter

    • use endogenous cellular promoters, avoid viral-derived regulatory sequences

  • genotoxicity — complications arising from insertional mutagenesis

    • use vectors with safer integration profile (e.g. self inactivating lentiviral vectors)

    • sequence-specific integration (e.g. genome editing)

  • phenotoxicity — complications arising from overexpression or ectopic expression of teh transgene

    • control transgene expression spatially (e.g. endogenous, tissue-specific promoters) and temporally (on/off switch)

  • immunotoxicity — harmful immune response to either the vector or transgene

    • carefully monitor T cell reactivity to the vector and transgene to initiate immune suppression if needed

  • risk of horizontal transmission — shedding of infectious vector into the environment

    • monitor vector shedding in preclinical models when developing novel vectors

  • risk of vertical transmission — germline transmission of donated DNA

    • use of barrier contraceptive methods until vector shedding is negative

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approved gene therapies worldwide

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major gene therapy approvals (2023-2024)

  • casgevy

    • first CRISPR based gene therapy in the U.S> for sickle cell disease

    • approved for transfusion-dependent beta thalassemia in Jan 2024

    • edits the BCL11A gene in a patients stem cells to boost fetal hemoglobin production → reducing disease symptoms

  • roctavian

    • approved by FDA in june 2023

    • one-time gene therapy for severe hemophilia A

    • delivers a functional copy of the factor VIII gene using AAV vector → enables patients to produce their own clotting factor

  • hemgenix

    • approved in nov 2022

    • treats hemophilia B

    • AAV vector to deliver factor IX gene → reducing need for regular infusions

  • vyjuvek

    • approved may 2023

    • first topical gene therapy

    • treats wounds in pts with dystrophic epidermolysis bullosa

    • employs a modified herpes simplex virus to deliver COL7A1 gene directly to skin cells

<ul><li><p>casgevy </p><ul><li><p>first CRISPR based gene therapy in the U.S&gt; for sickle cell disease</p></li><li><p>approved for transfusion-dependent beta thalassemia in Jan 2024 </p></li><li><p>edits the BCL11A gene in a patients stem cells to boost fetal hemoglobin production → reducing disease symptoms</p></li></ul></li><li><p>roctavian</p><ul><li><p>approved by FDA in june 2023</p></li><li><p>one-time gene therapy for severe hemophilia A</p></li><li><p>delivers a functional copy of the factor VIII gene using AAV vector → enables patients to produce their own clotting factor</p></li></ul></li><li><p>hemgenix</p><ul><li><p>approved in nov 2022</p></li><li><p>treats hemophilia B</p></li><li><p>AAV vector to deliver factor IX gene → reducing need for regular infusions</p></li></ul></li><li><p>vyjuvek</p><ul><li><p>approved may 2023</p></li><li><p>first topical gene therapy</p></li><li><p>treats wounds in pts with dystrophic epidermolysis bullosa</p></li><li><p>employs a modified herpes simplex virus to deliver COL7A1 gene directly to skin cells</p></li></ul></li></ul><p></p>
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upcoming cell and gene therapies that FDA are reviewing

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gene therapy: ethical and social issues

  • who decides which traits are normal adn which constitute a disability or disorder?

  • will the host cost of gene therapy make it available only to wealthy?

  • could the widespread use of gene therapy make society less accepting of people who are different?

  • is it ethical to allow ppl to use gene therapy to enhance basic human traits such as height, intelligence and athletic ability?