# Retrovirus Evolution and Cancer

> **NIH NIH R35** · TUFTS UNIVERSITY BOSTON · 2022 · $922,751

## Abstract

This application seeks continued support for my research program, funded by the NCI for almost 40 years, with
numerous innovative and high-impact contributions to the biology and evolution of retroviruses and their roles
in AIDS and cancer. We will focus on a number of ongoing projects in the laboratory:
 1. HERV-K (HML-2) Polymorphism in humans. HML-2 is the most recently active endogenous retrovirus
group in humans, with 90 or proviruses, of which 11, all noninfectious, were known to be polymorphic in the
population. To test whether active members may be present at low frequency, but remain undetected, we
have developed bioinformatic and laboratory tools to identify and characterize rare - and therefore more recent
and potentially infectious - proviruses in large sequence databases like those from the the “1000 genomes”
project. We have identified a number of new proviruses, rare in the population, one of which appears to be in-
tact. We will determine its potential to encode infectious virus and possible role in cancer.
 2. HML-2 Expression and cancer. To test for a role of HML-2 proviruses in tumor development, we have
developed sequencing, bioinformatic and other tools to study their expression in cancer cell lines and deter-
mine which of the 90 proviruses are expressed and by what mechanism: i.e., whether the differences in ex-
pression between normal and cancer cells are due to cis (e.g., DNA methylation, chromatin structure) or trans
(e.g., transcription factor patterns) effects. We will determine whether this upregulation might lead to reintegra-
tion of new HML-2 proviruses, and whether it has a positive effect on tumor development and growth.
 3. HML-2 expression and HIV infection. HIV-1 infected patients exhibit elevated levels of HML-2 expres-
sion in PBMCs. We are developing the same approaches as in 2 to test the cell and provirus specificity of this
expression in these individuals and whether it plays any role in the development of malignancy.
 4. Evolution of HML-2 receptor specificity. HML-2 has been coevolving with primates for over 20 million
years and has likely been subject to evolutionary forces similar to ALV. We have developed a strategy to iden-
tify its host receptor based on the ability of viruses pseudotyped with HML-2 Env protein to infect cells express-
ing a cDNA library from permissive cells. We will then use the “fossil record” in primate genomes to study the
coevolution of this interaction.
 5. Retrovirus-APOBEC interaction. Prevention of MLV infection of human xenografts in immunodeficient
mice is an issue of importance due the current interest in developing “personalized immune” mice to grow hu-
man tissues for therapeutic purposes. Our strategy is to make the recipient mice globally express a restriction
factor (human APOBEC3g) that will prevent productive infection of the grafted human tumor cell line. We are
also working to understand the differential sensitivity of MLV to human and murine APOBEC proteins.

## Key facts

- **NIH application ID:** 10470889
- **Project number:** 5R35CA200421-07
- **Recipient organization:** TUFTS UNIVERSITY BOSTON
- **Principal Investigator:** JOHN M COFFIN
- **Activity code:** R35 (R01, R21, SBIR, etc.)
- **Funding institute:** NIH
- **Fiscal year:** 2022
- **Award amount:** $922,751
- **Award type:** 5
- **Project period:** 2016-09-20 → 2024-08-31

## Primary source

NIH RePORTER: https://reporter.nih.gov/project-details/10470889

## Citation

> US National Institutes of Health, RePORTER application 10470889, Retrovirus Evolution and Cancer (5R35CA200421-07). Retrieved via AI Analytics 2026-05-23 from https://api.ai-analytics.org/grant/nih/10470889. Licensed CC0.

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