Display Settings:

Items per page
We are sorry, but NCBI web applications do not support your browser and may not function properly. More information

Results: 10

1.
Figure 5

Figure 5. A single cell may contain episomes with different degrees of resistance to multiple enzymes.. From: Predictors of Hepatitis B Cure Using Gene Therapy to Deliver DNA Cleavage Enzymes: A Mathematical Modeling Approach.

Example of one theoretical cell containing 6, 3, 2 and 1 episomes with 0, 1, 2, and 3 mutations respectively, as well as 3 delivery vectors.

Joshua T. Schiffer, et al. PLoS Comput Biol. 2013 July;9(7):e1003131.
2.
Figure 9

Figure 9. Possible dynamics of HBV cccDNA between vector delivery doses.. From: Predictors of Hepatitis B Cure Using Gene Therapy to Deliver DNA Cleavage Enzymes: A Mathematical Modeling Approach.

(a) Cell death inducing decay of incorporated episome. (b) Episomal degradation. (c) cccDNA expansion despite suppressive antiviral therapy. (d) Hepatocyte replication with equal dispersion of cccDNA molecules between cells. (e) Hepatocyte replication with replication of cccDNA molecules between cells. Only mechanism (c) could increase number of doses needed prior to inactivation while other mechanisms (a, b and d) may allow more rapid cure.

Joshua T. Schiffer, et al. PLoS Comput Biol. 2013 July;9(7):e1003131.
3.
Figure 3

Figure 3. Possible outcomes for a single episome with three possible cleavage sites.. From: Predictors of Hepatitis B Cure Using Gene Therapy to Deliver DNA Cleavage Enzymes: A Mathematical Modeling Approach.

Any cleavage event that renders the molecule replication incompetent is a terminal event for the episome; induced resistance at one site still leaves other potential target sites susceptible to cleavage. Arrow thickness denotes the relative probability of a certain event.

Joshua T. Schiffer, et al. PLoS Comput Biol. 2013 July;9(7):e1003131.
4.
Figure 1

Figure 1. Schematic of gene therapy vector delivery.. From: Predictors of Hepatitis B Cure Using Gene Therapy to Deliver DNA Cleavage Enzymes: A Mathematical Modeling Approach.

(a) There is a probability, Pv = [(σ*m)v * e−(σ*m)]/v!, of different amounts of vector (red) being delivered to and transduced within each cell containing the target virus (green). (b & c) The percentage of cells with different amounts of transduction will vary according to functional multiplicity of infection (fMOI) which is equal to the ratio of transduced delivery vectors to target hepatocytes multiplied by the proportion of vectors which are transduced, or fMOI = m * σ.

Joshua T. Schiffer, et al. PLoS Comput Biol. 2013 July;9(7):e1003131.
5.
Figure 4

Figure 4. Theoretical effects of dosing multiple enzymes concurrently.. From: Predictors of Hepatitis B Cure Using Gene Therapy to Deliver DNA Cleavage Enzymes: A Mathematical Modeling Approach.

If two enzymes targeting separate sites are split among vectors, then “antagonistic potency” may occur: while the likelihood of de novo resistance decreases because fewer episomes are cleaved at only a single site, fewer episomes are targeted overall. “Synergistic potency” is more likely to occur if two enzymes are packaged within the same vector: intracellular dose of enzyme will double leading to fewer unbound episomes and lower probability of resistance due to higher overall binding of episomes at two sites. The possible therapeutic outcomes illustrated in the diagram are one of hundreds of potential outcomes given nine pre-therapy cccDNA molecules per cell, and are intended only as a demonstration of this principle.

Joshua T. Schiffer, et al. PLoS Comput Biol. 2013 July;9(7):e1003131.
6.
Figure 2

Figure 2. Intracellular HBV DNA cleavage enzyme pharmacodynamics.. From: Predictors of Hepatitis B Cure Using Gene Therapy to Deliver DNA Cleavage Enzymes: A Mathematical Modeling Approach.

(a) An HBV infected cell with three cccDNA molecules (green circles), and delivery of DNA cleavage enzyme containing vectors (red viruses) can transition to several states where none, some, or all of the episomes are eliminated and/or become resistant to the cleavage enzyme. Arrow thickness denotes the relative probability of each event. (b) Cleavage enzymes (red wavy lines) may bind HBV cccDNA molecules cooperatively, whereby binding of one enzyme to its target sequence enhances binding of other enzymes to the same target on separate episomes. (c) Cleavage enzymes (multi-colored wavy lines) that target separate regions within episomes (thick colored lines of corresponding color) may bind HBV cccDNA molecules cooperatively, whereby binding of one enzyme to its target sequence enhances binding of other enzymes to separate sequences on the same episome.

Joshua T. Schiffer, et al. PLoS Comput Biol. 2013 July;9(7):e1003131.
7.
Figure 10

Figure 10. Underlying HBV cccDNA dynamics are unlikely to have a significant outcome on therapeutic outcome.. From: Predictors of Hepatitis B Cure Using Gene Therapy to Deliver DNA Cleavage Enzymes: A Mathematical Modeling Approach.

Simulation of HBV inactivation following 10 doses of therapy given every two weeks. Unlike prior simulations, these simulations assume that DNA cleavage activity accrues evenly over a week rather than instantaneously. Parameters reflect high potency (m*σ = 5, d = 0.004, h = 2). Traces represent no cccDNA activity between does (black lines), residual cccDNA replication between doses at rate = 0.01/day (red lines), hepatocyte replication with dispersion of cccDNA between cells (orange lines) and hepatocyte death with concurrent death of episomes (blue lines). Solid lines are cells with susceptible episomes and would represent therapeutic outcomes in the absence of de novo resistance (Ψ = 0). Dotted lines are cells with resistant episomes and would represent therapeutic outcomes with de novo resistance (Ψ = 0.01). Effects on therapeutic outcomes are minimal unless fairly high levels of cccDNA turnover are assumed (red lines) as may occur in the absence of fully suppressive antiviral therapy.

Joshua T. Schiffer, et al. PLoS Comput Biol. 2013 July;9(7):e1003131.
8.
Figure 7

Figure 7. Rapid development of de novo resistance to DNA cleavage enzyme therapy.. From: Predictors of Hepatitis B Cure Using Gene Therapy to Deliver DNA Cleavage Enzymes: A Mathematical Modeling Approach.

(a) Potent regimens with high fMOI (m*σ = 5), high enzyme – DNA binding avidity (d = 0.04), and positive binding cooperativity (h = 2) will allow for high levels of simulated resistance and predominance of resistant episomes following only 2 to 3 doses; a higher resistance rate (5% versus 1%) will promote a higher number of infected cells containing enzyme resistant episomes. (b) Infected cells containing enzyme resistant episomes will ultimately achieve equivalent levels assuming equal resistant rates whether a potent (m*σ = 5, d = 0.004 & h = 2) or less potent (m*σ = 1, d = 1 & h = 2) regimen is used. (c) If successive enzymes are dosed that target different regions within HBV cccDNA episomes, then the number of remaining episomes following multiple doses decreases accordingly; susceptible and resistant replication competent genomes are summed; by 60 days, all remaining episomes are resistant to each of the dosed enzymes (not shown in diagram).

Joshua T. Schiffer, et al. PLoS Comput Biol. 2013 July;9(7):e1003131.
9.
Figure 8

Figure 8. Packaging of multiple cleavage enzymes that target different HBV regions enhances potency and decreases resistance.. From: Predictors of Hepatitis B Cure Using Gene Therapy to Deliver DNA Cleavage Enzymes: A Mathematical Modeling Approach.

Simulation of HBV eradication employing gene therapy following a single dose. Each data point represents number of remaining infected cells (y-axis) after a simulation with one of 36 unique parameter sets. x-axis is functional multiplicity of infection (fMOI). Enzyme-DNA binding avidity is fixed (d = 0.04). Color represents number of enzymes delivered per vector (orange, green and blue = 1,2 & 3 respectively). Hill coefficient is 1, 2 and 5 (square, diamond and circle). The simulation assumes no pre-existing resistance. (a) Addition of multiple DNA cleavage enzymes within single vectors decreases the number of total remaining infected cells, particularly when vector delivery is high and intracellular binding cooperativity is present. (b) Addition of multiple DNA cleavage enzymes within single vectors decreases the number of total remaining infected cells harboring HBV cccDNA with any de novo resistance mutations, or (c) all possible resistance mutations. (d) Percentage of remaining infected cells containing totally resistant genomes following a single dose increases with high delivery, lower number of cleavage enzymes per vector, and higher binding cooperativity.

Joshua T. Schiffer, et al. PLoS Comput Biol. 2013 July;9(7):e1003131.
10.
Figure 6

Figure 6. High vector delivery, effective enzyme-HBV binding and cooperative binding predict effective cccDNA clearance.. From: Predictors of Hepatitis B Cure Using Gene Therapy to Deliver DNA Cleavage Enzymes: A Mathematical Modeling Approach.

All simulations of HBV eradication show results of ten weekly doses of therapy. A single enzyme is used and de novo resistance is ignored. (a) Each data point represents number of remaining infected cells (y-axis) after a simulation with one of 80 unique parameter sets. x-axis is functional multiplicity of infection (fMOI, separated by vertical black lines and not according to scale). Five different values for enzyme-DNA binding dissociation constant (d = 0.008, 0.04, 0.2, 1 & 5) are represented by blue, green, yellow, orange & red respectively; squares, diamonds, circles and triangles represent different values for the Hill coefficient (h = 0.5, 1, 2, 5). High fMOI, low binding dissociation constant and under conditions of moderate delivery and enzyme-DNA binding, high Hill coefficient (cooperative binding), predict high therapeutic potency. (b) Simulations of 10 weekly doses of a potent regimen (fMOI = 5.0, d = 0.04, h = 2, de novo resistance rate (Ψ) = 0) with decreasing fMOI following each dose due to humoral immunity. (σ: blue, green, orange and red represent decreases in fMOI with each dose of 90%, 50%, 10% and 0% respectively). Removal of vectors following each dose decreases effectiveness of therapy. (c & d) Simulations of 10 weekly doses of a potent regimen (fMOI = 5.0, d = 0.04, h = 2, de novo resistance rate (Ψ) = 0) assuming different burdens of infection (line color represents pre-therapy median number of HBV cccDNA molecules/cell) demonstrate relatively similar potency across highly variable densities of infection whether (c) infected cells or (d) total episomes are tracked as measures of therapeutic outcome.

Joshua T. Schiffer, et al. PLoS Comput Biol. 2013 July;9(7):e1003131.

Display Settings:

Items per page

Supplemental Content

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...
Write to the Help Desk