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Inferring viral dynamics in chronically HCV infected patients from the spatial distribution of infected hepatocytes.

Graw F, Balagopal A, Kandathil AJ, Ray SC, Thomas DL, Ribeiro RM, Perelson AS - PLoS Comput. Biol. (2014)

Bottom Line: We found that individual clusters on biopsy samples range in size from 4-50 infected cells.In addition, the HCV RNA content in a cluster declines from the cell that presumably founded the cluster to cells at the maximal cluster extension.Further, we do not find a relationship between the cluster size and the estimated cluster expansion time.

View Article: PubMed Central - PubMed

Affiliation: Los Alamos National Laboratory, Theoretical Biology and Biophysics, Los Alamos, New Mexico, United States of America; Center for Modeling and Simulation in the Biosciences, Heidelberg University, Heidelberg, Germany.

ABSTRACT
Chronic liver infection by hepatitis C virus (HCV) is a major public health concern. Despite partly successful treatment options, several aspects of intrahepatic HCV infection dynamics are still poorly understood, including the preferred mode of viral propagation, as well as the proportion of infected hepatocytes. Answers to these questions have important implications for the development of therapeutic interventions. In this study, we present methods to analyze the spatial distribution of infected hepatocytes obtained by single cell laser capture microdissection from liver biopsy samples of patients chronically infected with HCV. By characterizing the internal structure of clusters of infected cells, we are able to evaluate hypotheses about intrahepatic infection dynamics. We found that individual clusters on biopsy samples range in size from 4-50 infected cells. In addition, the HCV RNA content in a cluster declines from the cell that presumably founded the cluster to cells at the maximal cluster extension. These observations support the idea that HCV infection in the liver is seeded randomly (e.g. from the blood) and then spreads locally. Assuming that the amount of intracellular HCV RNA is a proxy for how long a cell has been infected, we estimate based on models of intracellular HCV RNA replication and accumulation that cells in clusters have been infected on average for less than a week. Further, we do not find a relationship between the cluster size and the estimated cluster expansion time. Our method represents a novel approach to make inferences about infection dynamics in solid tissues from static spatial data.

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Cluster structure and age of infection.(A) Factors influencing the observed viral landscape in a cluster including (i) viral transmission, (ii) the viral eclipse phase, and (iii) intracellular viral replication. (B, C) Relationship between the maximal cluster extension and the age of the assumed founder cell of the cluster (B) and the time until this cluster extension was possibly reached,  (C), i.e., the difference between the age of the assumed founder cell and cells that were more recently added to the cluster. Estimates were obtained using the model on intracellular HCV replication discussed in the text. The mean and the 2.5% and 97.5% percentiles of 10,000 bootstrap replicates for each individual cluster are shown. (D) Comparison of the average fractional decrease in intracellular HCV RNA, , between the founder cell and the surrounding cells of a cluster comprising 9 cells. Expansion of individual foci was simulated in a 2D-grid with different assumptions for the average duration of the eclipse phase , and the probability for viral transmission, . We simulated 1000 individual foci and selected all foci showing clusters comprising 9 cells with radial spread. The average fractional decrease is calculated relative to the amount of viral RNA within the founder cell of the cluster. The mean and 95%-percentiles are shown. For a detailed description of the simulation environment see Supporting Information (Text S3).
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pcbi-1003934-g004: Cluster structure and age of infection.(A) Factors influencing the observed viral landscape in a cluster including (i) viral transmission, (ii) the viral eclipse phase, and (iii) intracellular viral replication. (B, C) Relationship between the maximal cluster extension and the age of the assumed founder cell of the cluster (B) and the time until this cluster extension was possibly reached, (C), i.e., the difference between the age of the assumed founder cell and cells that were more recently added to the cluster. Estimates were obtained using the model on intracellular HCV replication discussed in the text. The mean and the 2.5% and 97.5% percentiles of 10,000 bootstrap replicates for each individual cluster are shown. (D) Comparison of the average fractional decrease in intracellular HCV RNA, , between the founder cell and the surrounding cells of a cluster comprising 9 cells. Expansion of individual foci was simulated in a 2D-grid with different assumptions for the average duration of the eclipse phase , and the probability for viral transmission, . We simulated 1000 individual foci and selected all foci showing clusters comprising 9 cells with radial spread. The average fractional decrease is calculated relative to the amount of viral RNA within the founder cell of the cluster. The mean and 95%-percentiles are shown. For a detailed description of the simulation environment see Supporting Information (Text S3).

Mentions: Several aspects of viral replication and transmission dynamics should influence the observed HCV RNA profile within a cluster of infected cells. These include the rate at which neighboring cells get infected, the average time it takes for a cell to start viral replication, the rate at which the virus replicates, the rate at which intracellular HCV RNA is degraded, and the lifespan of infected cells (Figure 4A).


Inferring viral dynamics in chronically HCV infected patients from the spatial distribution of infected hepatocytes.

Graw F, Balagopal A, Kandathil AJ, Ray SC, Thomas DL, Ribeiro RM, Perelson AS - PLoS Comput. Biol. (2014)

Cluster structure and age of infection.(A) Factors influencing the observed viral landscape in a cluster including (i) viral transmission, (ii) the viral eclipse phase, and (iii) intracellular viral replication. (B, C) Relationship between the maximal cluster extension and the age of the assumed founder cell of the cluster (B) and the time until this cluster extension was possibly reached,  (C), i.e., the difference between the age of the assumed founder cell and cells that were more recently added to the cluster. Estimates were obtained using the model on intracellular HCV replication discussed in the text. The mean and the 2.5% and 97.5% percentiles of 10,000 bootstrap replicates for each individual cluster are shown. (D) Comparison of the average fractional decrease in intracellular HCV RNA, , between the founder cell and the surrounding cells of a cluster comprising 9 cells. Expansion of individual foci was simulated in a 2D-grid with different assumptions for the average duration of the eclipse phase , and the probability for viral transmission, . We simulated 1000 individual foci and selected all foci showing clusters comprising 9 cells with radial spread. The average fractional decrease is calculated relative to the amount of viral RNA within the founder cell of the cluster. The mean and 95%-percentiles are shown. For a detailed description of the simulation environment see Supporting Information (Text S3).
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC4230741&req=5

pcbi-1003934-g004: Cluster structure and age of infection.(A) Factors influencing the observed viral landscape in a cluster including (i) viral transmission, (ii) the viral eclipse phase, and (iii) intracellular viral replication. (B, C) Relationship between the maximal cluster extension and the age of the assumed founder cell of the cluster (B) and the time until this cluster extension was possibly reached, (C), i.e., the difference between the age of the assumed founder cell and cells that were more recently added to the cluster. Estimates were obtained using the model on intracellular HCV replication discussed in the text. The mean and the 2.5% and 97.5% percentiles of 10,000 bootstrap replicates for each individual cluster are shown. (D) Comparison of the average fractional decrease in intracellular HCV RNA, , between the founder cell and the surrounding cells of a cluster comprising 9 cells. Expansion of individual foci was simulated in a 2D-grid with different assumptions for the average duration of the eclipse phase , and the probability for viral transmission, . We simulated 1000 individual foci and selected all foci showing clusters comprising 9 cells with radial spread. The average fractional decrease is calculated relative to the amount of viral RNA within the founder cell of the cluster. The mean and 95%-percentiles are shown. For a detailed description of the simulation environment see Supporting Information (Text S3).
Mentions: Several aspects of viral replication and transmission dynamics should influence the observed HCV RNA profile within a cluster of infected cells. These include the rate at which neighboring cells get infected, the average time it takes for a cell to start viral replication, the rate at which the virus replicates, the rate at which intracellular HCV RNA is degraded, and the lifespan of infected cells (Figure 4A).

Bottom Line: We found that individual clusters on biopsy samples range in size from 4-50 infected cells.In addition, the HCV RNA content in a cluster declines from the cell that presumably founded the cluster to cells at the maximal cluster extension.Further, we do not find a relationship between the cluster size and the estimated cluster expansion time.

View Article: PubMed Central - PubMed

Affiliation: Los Alamos National Laboratory, Theoretical Biology and Biophysics, Los Alamos, New Mexico, United States of America; Center for Modeling and Simulation in the Biosciences, Heidelberg University, Heidelberg, Germany.

ABSTRACT
Chronic liver infection by hepatitis C virus (HCV) is a major public health concern. Despite partly successful treatment options, several aspects of intrahepatic HCV infection dynamics are still poorly understood, including the preferred mode of viral propagation, as well as the proportion of infected hepatocytes. Answers to these questions have important implications for the development of therapeutic interventions. In this study, we present methods to analyze the spatial distribution of infected hepatocytes obtained by single cell laser capture microdissection from liver biopsy samples of patients chronically infected with HCV. By characterizing the internal structure of clusters of infected cells, we are able to evaluate hypotheses about intrahepatic infection dynamics. We found that individual clusters on biopsy samples range in size from 4-50 infected cells. In addition, the HCV RNA content in a cluster declines from the cell that presumably founded the cluster to cells at the maximal cluster extension. These observations support the idea that HCV infection in the liver is seeded randomly (e.g. from the blood) and then spreads locally. Assuming that the amount of intracellular HCV RNA is a proxy for how long a cell has been infected, we estimate based on models of intracellular HCV RNA replication and accumulation that cells in clusters have been infected on average for less than a week. Further, we do not find a relationship between the cluster size and the estimated cluster expansion time. Our method represents a novel approach to make inferences about infection dynamics in solid tissues from static spatial data.

Show MeSH
Related in: MedlinePlus