Jumping ‘DNA parasites’ linked to early stages of tumour formation

(Press-News.org) A study published today in the journal Science reveals how jumping fragments of human DNA, a type of genetic parasite, destabilise the cancer genome. Unstable genomes are a fertile playground for cancer evolution, giving malignant cells more opportunities to grow, adapt and evade treatment. 

The researchers analysed genome sequences from tumours with unusually high activity of LINE-1 (L1) elements, fragments of DNA which copy themselves and paste that copy into other locations within the genome. 

Previously thought to be a source of local mutations that occasionally disrupt individual genes when inserted into the wrong place, the researchers now find evidence that L1 activity can also drive large-scale architectural modifications which seed genomic chaos. 

“Cancer genomes are more influenced by these jumping fragments of DNA parasites than we previously thought,” explains Professor José Tubio, researcher at the Centro de Investigación en Medicina Molecular y Enfermedades Crónicas (CiMUS) at the Universidade de Santiago de Compostela (USC) and coordinator of the study. 

The findings challenge the long-held assumption that L1 activity is a byproduct of an already chaotic cancer genome. Rather than just appearing in late stages of cancer, the study found two in three (65%) L1 events occurred during the early stages of tumour evolution. 

The discovery could help explain how cancer reshapes the genome, and vice versa, at the early stages of the disease, knowledge which could eventually lead to new strategies for early detection and treatment.  

“The next focus should be understanding when and where L1 activity tips the balance and how to target that therapeutically,” says Dr. Bernardo Rodriguez-Martin, Independent Fellow at the Centre for Genomic Regulation in Barcelona and one of the main authors of the study. 

The legacy of ancient ‘DNA parasites’ 

L1 elements are ancient genetic hitchhikers. They are considered parasitic DNA sequences because almost all of them are either neutral or deleterious for the host organism, existing to promote their own replication through a process called retrotransposition. 

For many million years of mammalian evolution, L1 elements have been amplifying in the genome. There are roughly 500,000 copies which make up 17% of the human genome, but most are genomic fossils that lie dormant. On average, each individual has a small fraction of between 150 and 200 L1 elements which can still jump and insert themselves into new genomic locations. 

L1 retrotransposition is known to be a frequent mutational process in different types of cancers, including head and neck, lung and colorectal tumours. Early evidence has shown these events help tumours grow and adapt by producing genomic aberrations affecting cancer genes. 

Exactly how L1 elements disrupt genomes, and to what extent they do so in health or disease has been unclear because much of what scientists could see depended on a technology called short-read DNA sequencing. When reading DNA, short-read technologies struggle to reconstruct how L1 elements alter the genome’s architecture. 

To get around that, the researchers used a new technology called long-read sequencing. For the first time, this allowed them to see the full changes L1 elements make to the structure of the cancer genome, including deletions, translocations and other rearrangements to the DNA sequence. 

One in 40 jumps rewire the genome 

The researchers selected ten tumours with high L1 activity for in-depth sequencing: five head & neck squamous carcinomas, four lung squamous carcinomas and one colorectal adenoma. They found a total of 6,418 retrotransposition events, with variation between cancer types.  

The vast majority of copy and paste events found were insertions. These are instances where L1 elements insert a copy of themselves into the DNA sequence at other locations, altering the genome’s length. These events might interrupt a gene’s function, but most insertions are truncated and so unlikely to jump again. 

Amongst these thousands of cases, the team also identified 152 instances where L1 created large-scale structural rearrangements, with an incidence rate of 1 in 40 for tumours with high L1 activity and 1 in 60 for tumours with lower activity. These changes to the genome’s architecture are much more dramatic and disruptive, making them potentially powerful drivers of cancer development.  

“On paper, 152 might not sound like a huge number. But when you’re looking at just ten tumours, that’s extraordinarily high,” says Rodriguez-Martin. 

The finding matters because it strengthens arguments for using long-read sequencing in cases where standard tests cannot explain a tumour’s behaviour, as short-read sequencing would not detect the possible mechanism of action.  

“Three quarters of these large-scale rearrangements would have flown under the radar of short-read sequencing technologies. However, we expect the price of long-read sequencing to drop by roughly half this year alone, meaning this kind of deep structural analysis won’t remain niche for long,” says Dr. Rodriguez-Martin. 

The structural rearrangements had many different mechanisms of action, including a DNA exchange between chromosomes that has been unknown to science until now. The researchers hypothesise it may be due to two separate L1 events that occur at roughly the same time on different chromosomes, with each swapping around the same amount of DNA in a balanced exchange they call a reciprocal translocation. 

“It's as if two different pages of a book were torn simultaneously and fragments exchanged with each other. L1 elements behave like glue that sticks both pages together," explains Sonia Zumalave, first author of the study. 

New clues about early stages of tumour formation 

A frequent early milestone of tumour formation is a whole genome doubling event, which happens when a cancer cell accidentally duplicates its entire set of chromosomes. Whole genome doubling occurred a median of 4.77 years before the diagnosis of the tumours used in the study. 

The researchers found that most L1 activity preceded the whole genome doubling event, meaning retrotransposition can be an early mutational process. That suggests L1 activity is a bigger contributor to the genomic chaos that precedes cancer formation than previously thought. 

In a side experiment, the study found that the promoters of L1 events are typically less methylated in tumours than in nearby non-tumour tissue, a pattern consistent with the idea that epigenetic changes to the human genome could awaken dormant parasitic DNA sequences. 

There are limitations to the study. Its results are based on a deliberately chosen set of cancers with extreme L1 activity so that the scientists could detect rare mechanisms that would be invisible in samples with lower activity, meaning the findings may not apply to other types of tumours. 

The study was carried out by the Centro de Investigación en Medicina Molecular y Enfermedades Crónicas (CiMUS) at the Universidade de Santiago de Compostela in collaboration with the Centre for Genomic Regulation (CRG) in Barcelona, Université Côte d’Azur in France, the Francis Crick Institute in the United Kingdom, and the University of Texas MD Anderson Cancer Center in the United States. 

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