The Endogenous Retroviral Transcriptome in Melanoma
endogenous retroviruses (HERVs) are retroviral sequences passed from parent to offspring
in a Mendelian fashion. Due to relatively recent endogenization and correlation to human
illness, interest in the HERV-K (HML-2) subclade has increased. Expression of HML-2 -
specific transcripts and proteins in melanoma cell lines was first discovered about a
decade ago. Since there are a... read moret least 96 known HML-2 proviruses within the human genome,
others have studied the HML-2 transcriptome in melanoma to identify the proviral
sequences responsible for such expression. More recently, cDNA cloning frequency was
used to detect HML-2 expression in melanoma cell lines and patient samples. Though they
were able to detect the expression of several proviruses, cDNA cloning frequency is not
as sensitive as RNA-sequencing and therefore they could have missed the expression of
poorly expressed proviruses or the expression of rare proviruses. Furthermore,
determining transcriptional mechanisms responsible for HML-2 expression in melanoma
using cDNA cloning frequency data would be difficult while one could easily do this
using a stranded library. Due to the potential role of expressed rare HML-2 proviruses
in cancer etiology, and to understand transcriptional mechanisms responsible for HML-2
expression in melanoma, I submitted cellular RNA from five melanoma cell lines and three
primary melanocyte populations for RNA-seq. I detected five proviruses that were
uniquely expressed in melanoma compared to primary melanocytes. 7q22.2 was the highest
expressing provirus followed by 3q12.3, which based on comparison to breast cancer and
Tera-1s was only detected in cancerous cell lines. Most proviruses that were expressed
in melanoma were young, human specific, and were mostly located in extragenic regions
and driven by sense transcription. Two proviruses - 7p22.1a and 7p22.1b - contain intact
ORFs for Env, yet I was unable to detect the presence of Env in whole cell lysate.
Furthermore, three proviruses were capable of LTR-driven transcription in some of my
melanoma cell lines which appears to be partially driven by transcription factor binding
to LTRs. In conclusion, this work expands upon the known HML-2 transcriptome in melanoma
while offering a larger view on HML-2 expression in cancer. It also shows one potential
cause of HML-2 expression in melanoma and identifies the potential proviruses
responsible for previous HML-2 protein production. Future work should include analyzing
the effect epigenetic regulation has on HML-2 expression in cancer. Furthermore, future
work should focus on analyzing patient samples to identify unique proviruses expressed
in cancer so HML-2 expression can be evaluated for potential therapeutic and diagnosis
Thesis (Ph.D.)--Tufts University, 2018.
Submitted to the Dept. of Genetics.
Advisor: John Coffin.
Committee: Philip Hinds, Naomi Rosenberg, Jack Lenz, and Ralph Isberg.
Keyword: Genetics.read less