Research in the Burns Lab

Interspersed repeats and genetic variation
Specific types of transposons are active in humans, and our lab was one of the first to develop strategies to map insertion sites of these elements in the human genome. Our observations underscored that transposons are major sources of genetic structural variation in human populations (Cell, 2010). Over the next decade, catalogs of commonly-occurring mobile element insertion alleles grew, and our group led efforts to identify those variants that may be relevant to disease risk by integrating information about these insertions with findings of genome wide association studies (GWAS) (PNAS, 2017). Our group has since developed experimental systems to show that inherited transposable element insertion alleles can affect gene expression and mRNA splicing, demonstrating molecular mechanisms for how transposons may impact phenotypes. Together, these avenues have shown that we each inherit a unique compliment of transposon insertions – thousands of LINE-1, Alu, SVA, and ERV alleles – and that a specific subset of these have phenotypic effects.
See our review: Nature Reviews Genetics (2019).

Questions going forward:
What is the landscape of transposon expression in normal and diseased tissues?
Do functional variants of transposon insertions modify disease risk or disease phenotypes?
Do inherited LINE-1 loci contribute to somatic mosaicism and genome instability in non-cancerous tissues and in precancerous lesions? 

LINE-1 ORF1p expression as a cancer biomarker
Our laboratory has had a long-standing interest in transposable element expression in human malignancies. Many cancers undergo epigenetic changes that permit the expression of otherwise silenced transposable elements. Here, we are best known for our research on Long INterspersed Element-1 (LINE-1, L1), the only protein-coding retrotransposon active in modern humans. We were the first to develop and commercialize a monoclonal antibody to detect the LINE-1-encoded RNA-binding protein, open reading frame 1 protein (ORF1p). Using this reagent, we showed that LINE-1 expression is a hallmark of human cancers, including many of the most common and lethal forms of these diseases (Am J Path, 2014).

Questions going forward:
Does ORF1p in the peripheral blood have utility as a cancer biomarker?
What pathways limit LINE-1 expression and what epigenetic drugs affect LINE-1 expression?
For any given tumor type, what are the clinical pathological correlates of LINE-1 expression (e.g., histologic subtype, genetic alterations, features of the tumor microenvironment, responsiveness to therapy)? 
What mechanisms determine the relative ratio of ORF1p and ORF2p? 

LINE-1 as a mutagen in cancers
We have shown that cancers that express ORF1p have somatically-acquired insertions of genomic LINE-1 sequences that distinguish tumor genomes from a patient’s constitutional genetic make-up. We have led collaborations to map somatically-acquired LINE-1 insertion sites in pancreatic (Nature Medicine, 2015) and ovarian cancers (PNAS, 2017) and participated in larger efforts to identify somatically-acquired insertions as part of the International Cancer Genome Consortium (Nature Genetics, 2020). Together, these studies have shown that LINE-1 expression is commonplace in human cancers, and that it contributes to genome instability.
See our review: Nature Reviews Cancer (2017).

Questions going forward:
Does retrotransposition directly produce cancer-driving mutations?
Does LINE-1 expression promote tumor suppressor gene loss by changing selective pressures on cells?
Is LINE-1 activation responsible for structural alterations in cancer genomes and are there specific mutational signatures associated with this activity?

Mechanisms of retrotransposition and repair
Because so many cancers express LINE-1, we tested whether LINE-1 expression was pro-growth. Paradoxically, we find that LINE-1 hinders cell growth in experimental systems. Moreover, cell fitness screens show LINE-1 expression makes cells especially vulnerable to loss of replication-coupled DNA repair pathways, and sensitive to DNA-damaging chemotherapies and DNA-repair inhibitors (Nature Structural and Molecular Biology, 2020). We're now studying how cells cope with retrotransposition-associated DNA damage, and how compromising these pathways may be leveraged for cancer therapeutics. 

Questions going forward: 
Does retrotransposition represent a significant source of endogenous replication stress?
In specific cancer contexts, how does LINE-1 expression affect drug susceptibility and resistance? 
How can we recapitulate steps in retrotransposition and repair of LINE-1 insertion intermediates in vitro? 
What mechanisms underlie other molecular dependencies we see in cells expressing transposable elements? 
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