An Improved Sequencing-Based Bioinformatics Pipeline to Track the Distribution and Clonal Architecture of Proviral Integration Sites

Establishment of immortalized Egyptian Rousettus bat cell lines

The Egyptian Rousettus bat (Rousettus aegyptiacus) is a common fruit bat species that is distributed mainly in Africa and the Middle East. Bats serve as reservoir hosts for numerous pathogens. Human activities, such as hunting bats for food, managing vermin, and causing habitat loss, elevate the likelihood of transmission of bat pathogens to humans and other animals. Consequently, bat cell lines play a crucial role as research materials for investigating viral pathogens. However, the inherent limitation of finite cell division in primary cells necessitates the use of immortalized cells derived from various bat tissues. Herein, we successfully established six fibroblast cell lines derived from an infant bat heart and lungs and an elderly bat heart. Three of the six cell lines, called K4DT cells, were transduced by a combination of cell cycle regulators, mutant cyclin-dependent kinase 4, cyclin D1, and human telomerase reverse transcriptase. The other three cell lines, named SV40 cells, were transfected with simian virus 40 large T antigen. Transgene protein expression was detected in the transduced cells. All three K4DT cell lines and one lung-derived SV40 cell line were virtually immortalized and nearly maintained the normal diploid karyotypes. However, the two other heart-derived SV40 cell lines had aberrant karyotypes and the young bat-derived cell line stopped proliferating at approximately 40 population doublings. These bat cell lines are valuable for studying pathogen genomics and biology.

Meeting FDA Guidance recommendations for replication-competent virus and insertional oncogenesis testing

Integrating vectors are associated with alterations in cellular function related to disruption of normal gene function. This has been associated with clonal expansion of cells and, in some instances, cancer. These events have been associated with replication-defective vectors and suggest that the inadvertent exposure to a replication-competent virus arising during vector manufacture would significantly increase the risk of treatment-related adverse events. These risks have led regulatory agencies to require specific monitoring for replication-competent viruses, both prior to and after treatment of patients with gene therapy products. Monitoring the risk of cell expansion and malignancy is also required. In this review, we discuss the rational potential approaches and challenges to meeting the US FDA expectations listed in current guidance documents.

Diagnosis and Early Prediction of Lymphoma Using High-Throughput Clonality Analysis of Bovine Leukemia Virus-Infected Cells

Bovine leukemia virus (BLV), a retrovirus, infects B cells of ruminants and is integrated into the host genome as a provirus for lifelong infection. After a long latent period, 1% to 5% of BLV-infected cattle develop aggressive lymphoma, enzootic bovine leukosis (EBL). Since the clonal expansion of BLV-infected cells is essential for the development of EBL, the clonality of proviral integration sites could be a molecular marker for diagnosis and early prediction of EBL. Recently, we developed Rapid Amplification of the Integration Site without Interference by Genomic DNA Contamination (RAISING) and an analysis software of clonality value (CLOVA) to analyze the clonality of transgene-integrated cells. RAISING-CLOVA is capable of assessing the risk of adult T-cell leukemia/lymphoma development in human T-cell leukemia virus-I-infected individuals through the clonality analysis of proviral integration sites. Thus, we herein examined the performance of RAISING-CLOVA for the clonality analysis of BLV-infected cells and conducted a comprehensive clonality analysis by RAISING-CLOVA in EBL and non-EBL cattle. RAISING-CLOVA targeting BLV was a highly accurate and reproducible method for measuring the clonality value. The comprehensive clonality analysis successfully distinguished EBL from non-EBL specimens with high sensitivity and specificity. A longitudinal clonality analysis in BLV-infected sheep, an experimental model of lymphoma, also confirmed the effectiveness of RAISING-CLOVA for early detection of EBL development. Therefore, our study emphasizes the usefulness of RAISING-CLOVA as a routine clinical test for monitoring virus-related cancers. IMPORTANCE Bovine leukemia virus (BLV) infection causes aggressive B-cell lymphoma in cattle and sheep. The virus has spread to farms around the world, causing significant economic damage to the livestock industry. Thus, the identification of high-risk asymptomatic cattle before they develop lymphoma can be effective in reducing the economic damage. Clonal expansion of BLV-infected cells is a promising marker for the development of lymphoma. Recently, we have developed a high-throughput method to amplify random integration sites of transgenes in host genomes and analyze their clonality, named as RAISING-CLOVA. As a new application of our technology, in this study, we demonstrate the value of the RAISING-CLOVA method for the diagnosis and early prediction of lymphoma development by BLV infection in cattle. RAISING-CLOVA is a reliable technology for monitoring the clonality of BLV-infected cells and would contribute to reduce the economic losses by EBL development.

Clonality of HIV-1- and HTLV-1-Infected Cells in Naturally Coinfected Individuals

BACKGROUND

Coinfection with human immunodeficiency virus type 1 (HIV-1) and human T-cell leukemia virus type 1 (HTLV-1) diminishes the value of the CD4+ T-cell count in diagnosing AIDS, and increases the rate of HTLV-1-associated myelopathy. It remains elusive how HIV-1/HTLV-1 coinfection is related to such characteristics. We investigated the mutual effect of HIV-1/HTLV-1 coinfection on their integration sites (ISs) and clonal expansion.

METHODS

We extracted DNA from longitudinal peripheral blood samples from 7 HIV-1/HTLV-1 coinfected, and 12 HIV-1 and 13 HTLV-1 monoinfected individuals. Proviral loads (PVL) were quantified using real-time polymerase chain reaction (PCR). Viral ISs and clonality were quantified by ligation-mediated PCR followed by high-throughput sequencing.

RESULTS

PVL of both HIV-1 and HTLV-1 in coinfected individuals was significantly higher than that of the respective virus in monoinfected individuals. The degree of oligoclonality of both HIV-1- and HTLV-1-infected cells in coinfected individuals was also greater than in monoinfected subjects. ISs of HIV-1 in cases of coinfection were more frequently located in intergenic regions and transcriptionally silent regions, compared with HIV-1 monoinfected individuals.

CONCLUSIONS

HIV-1/HTLV-1 coinfection makes an impact on the distribution of viral ISs and clonality of virus-infected cells and thus may alter the risks of both HTLV-1- and HIV-1-associated disease.