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Moving target – retrotransposable elements and cancer

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by Cancer Research UK | In depth

11 July 2023

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The surprisingly large fraction of our genome occupied by retrotransposable elements, together with greater appreciation of their dysregulation in cancer has sparked real interest. However, the links between retrotransposable elements and cancer have a much deeper roots – George Kassiotis gets into their chequered past and how we might utilise these ancient viral infections  


40 years ago Barbara McClintock was awarded a Nobel Prize for her work on mobile genetic elements in Maize. She had discovered transposable elements (TE) – DNA sequences which have the ability to change their position within a genome.

Sometimes called ‘jumping genes’ because of this characteristic genome-hopping, new technologies and approaches are now revealing just how many cellular activities these TEs are involved in. And the varying types and classes of TE discovered have also expanded dramatically – with increasing evidence suggesting retrotransposable elements are of particular importance for cancer research.

What are they?

The class of TE known as retrotransposable elements all have a common characteristic – a unique and obligatory step in their replication cycle.

They are all made up of DNA sequences that are transcribed into RNA. Reverse transcriptase creates a complementary DNA (cDNA) copy of this RNA which is then inserted into a new location in the genome. Once the cDNA copy is inserted into a new location, the cycle can be repeated to make additional copies of the retrotransposable element’s DNA sequence.

The source of many of these retrotransposable elements is thought to be retroviral DNA which has become integrated into the host genome. If this process takes place in a germ cell that goes on to develop into an embryo, the viral DNA copy is inherited by all the cells of the offspring. This means that every cell in the individual’s body carries a new copy of the viral DNA, and because this copy is now in the germline it is passed on from generation to generation, just like any other genetic material.

Over evolutionary time, retrotransposable elements accumulate in the genome of the host species in staggering numbers and become fixed in the population.

This process happens infrequently but continuously. Over evolutionary time, retrotransposable elements accumulate in the genome of the host species in staggering numbers and become fixed in the population.

Collectively, in humans they make up an estimated 42% of the human genome, contrasting with the just over 1% that carries the information to make all our proteins. Not only that, much of the remaining genome may also derive from retrotransposable elements that have disintegrated beyond recognition through accumulated mutations and deletions.

So that, of course, begs a question. Why aren’t we all riddled with retroviral infection? Interestingly, although endogenous retroviruses have the potential to give rise to infectious retroviruses that can be passed on from one cell to another, just like their exogenous counterparts, this ability is thought to have been lost by all current human endogenous retroviruses which seem unable to complete the full replication life-cycle.

The source of endogenous retroviruses can be traced to exogenous retroviruses that have infected our ancestors and have become integrated into our genome.

Despite the commonalties, there are also important distinguishing features between sub-types of retrotransposable elements. Their genomic structure and mechanism of transposition can vary hugely. The genomes of endogenous retroviruses for example, are flanked by regulatory sequences called long terminal repeats (LTRs) and they are collectively referred to as LTR elements. Their genomic structure and replication mechanism is similar to that of exogenous retroviruses, from which they derive. Indeed, the source of endogenous retroviruses can be traced to exogenous retroviruses that have infected our ancestors and have become integrated into our genome.

Non-LTR retrotransposable elements, lack the long terminal repeats found in LTR elements. Sequence homology of their reverse transcriptases suggest a common ancestry of LTR and non-LTR elements, but the precise origins of the latter are still uncertain.

The life cycle of non-LTR elements does not include an extracellular step, meaning they are unable to jump from one cell to another and can only do so to different places in the genome of the same cell. However, importantly, some of these non-LTR elements are still very much active in humans causing frequent transpositions in somatic cells and more rarely in germ cells.

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Do they cause cancer?

Historically, retroviruses – both exogenous and endogenous – have been linked with the development of cancer.

Peyton Rous at Rockefeller University in New York City, made the discovery of the first oncogenic virus in 1916, for which he was later award the Nobel Prize in Physiology or Medicine. The virus named after him, Rous sarcoma virus (RSV), is a retrovirus that causes sarcoma in chickens because it carries an oncogene.

Later work carried out by Michael Bishop and Harold Varmus revealed just how complex the relationship is between retrovirus and host. They found the oncogenes carried by oncogenic retroviruses were in fact captured from the host cell and thereafter carried along by the retrovirus. Insertion of retrovirus DNA copies in the genome of the host cell could activate these oncogenes. This paved the way for the discovery of large number of cellular oncogenes, as well as the network that regulates growth of cells more broadly, a discovery that won them the Nobel Prize in Physiology or Medicine for 1989.

In 1936, John Joseph Bittner at the Jackson Laboratory in Maine described the ‘milk factor’, an oncogenic agent transmitted to newborn mice via their mother’s milk causing mammary tumours. This was another retrovirus, now referred to as mouse mammary tumour virus (MMTV). Several years later, Bentvelzen and Daams at the Netherlands Cancer Institute discovered endogenous copies of MMTV in the mouse germline, directly demonstrating the oncogenic potential of endogenous retroviruses.

The association of endogenous retroviruses with cancer was becoming ever clearer and the discovery of oncogenic retroviruses in mice led to much speculation that similar retroviruses may have been causing cancer in humans

At a similar time, endogenous copies of murine leukaemia virus (MLV) were discovered in laboratory mice by two independent laboratories and of avian leukosis virus (ALV) in domestic fowl by Robin Weiss in London.

The association of endogenous retroviruses with cancer was becoming ever clearer and the discovery of oncogenic retroviruses in mice led to much speculation that similar retroviruses may have been causing cancer in humans. This inspired a thorough, yet fruitless quest in the 1970s for equivalent human “tumour viruses”. The interest diminished in the 1980s, with some scientists referring to the elusive targets as “rumour viruses”.

Unbeknownst to the investigators in the mid-1980s, some of the detections of MMTV DNA in human breast cancer tumours may have been copies of the human endogenous retrovirus K (HERV-K) group, which includes the most recently acquired HML-2 (human MMTV-like-2) subgroup, so named due to its sequence similarity with MMTV.

While human endogenous retroviruses have lost the ability to copy themselves and therefore the ability to cause cancer by insertional mutagenesis, the potential to cause cancer through this mechanism still exists for non-LTR elements. Through retrotransposition, ‘jumping’ non-LTR elements can cause genomic instability. Their insertion into the genome can disrupt or alter the function of important genes, regulatory regions, or chromosomes. This genomic instability could contribute to the development of cancer by promoting the accumulation of additional mutations.

A complex relationship with cancer

Even retrotransposable elements that are no longer able to ‘jump’ may still contribute to the development of cancer or affect its progression.

Retrotransposable elements are not normally permitted to transcribe RNA as a result of epigenetic repression. This repressed state is, however, reversible and often lost in cancer cells, where certain retrotransposable elements become transcriptionally activated, with potentially important consequences. These newly activated elements have the potential to, for example, activate oncogenes or tumour-promoting genes within which they have been integrated. They can also influence the epigenetic regulation of adjacent genes. Aberrant retrotransposable element activity can lead to changes in DNA methylation patterns and histone modifications, which can impact the expression of nearby genes and contribute to cancer development.

Retrotransposable elements can even trigger immune responses, just like those seen in genuine viral infection. The transcription of retrotransposable element-derived sequences in the genome and subsequent translation into proteins can activate the immune system, leading to chronic inflammation. Prolonged inflammation can create a microenvironment conducive to the development and progression of cancer.

However, once again it is a complex relationship, and conversely, by triggering innate and adaptive immunity to their replication intermediates and protein antigens, reactivated retrotransposable elements can enhance the immunogenicity of cancer cells, leading to more effective anti-tumour immune responses.

It is worth noting that not all retrotransposable elements have the same impact, and the role of these elements in cancer is very much an active area of research. The extent to which retrotransposable elements contribute to cancer development may vary depending on the specific element, its location within the genome, the individual’s genetic background, and the type and stage of cancer.

For example, recent studies from my lab highlight both pro-tumour and anti-tumour effects of a single human endogenous retrovirus copy in squamous lung cancer, as well as antibody reactivity against viral envelope glycoproteins in lung adenocarcinoma, particularly in the context of immunotherapy.

Retrotransposable elements have long been implicated in the development of cancer, although the relationship is complex and not fully understood. The accumulating evidence suggests that with evolutionary time, the ability of retrotransposable elements to directly cause cancer is diminishing, whereas their co-option in pathways and mechanism that protect against cancer may be increasing.

Understanding this complex interaction may be the key to turning these old foes into friends.

Author

George Kassiotis

George is a Senior Group Leader and head of the laboratory of Retroviral Immunology at the Francis Crick Institute