Mitochondrial DNA in cancer: small genome, big impact

In April, we shared the story of a paper from Dr Payam Gammage, shedding light on the role of mitochondrial DNA mutations in cancer. Here, Payam explains in his own words the importance of mitochondria in cancer and the impact this could one day have on cancer care.

Gammage head 2020 067Mitochondria are in vogue, with devotees ranging from exercise physiologists and sports scientists to molecular biologists and clinicians all coalescing around these unusual organelles.

Given their position as a metabolic and energetic hub, as well as their central role in controlling cell death, mitochondria are also an area of focus for many cancer scientists. However, one essential facet of mitochondrial biology in cancer has remained underexplored; mitochondrial DNA (mtDNA).

A physically and heritably distinct piece of DNA that is passed down the generations through the maternal line, mtDNA exists only inside mitochondria. Recent work from my lab at the Cancer Research UK Beatson Institute, in collaboration with scientists at the Memorial Sloan Kettering Cancer Center in the US led by Dr Ed Reznik, has revealed the substantial impact mutations in mtDNA can have in cancer. Understanding this could offer up new indicators of disease prognosis and provide a new focus for future therapeutics.

Mitochondria – a trans-kingdom enigma

At the molecular level, the components of mammalian mitochondria are assembled from viruses, bacteria and eukaryotes. As such, the organelle we see in human cells today is a trans-kingdom mixture that doesn’t fully resemble any of its ancestors.

Human mtDNA is a small genome, only 16,569 base pairs long. In keeping with its bacterial ancestry, mtDNA is also circular and multicopy – with hundreds to thousands of copies present in every cell. mtDNA is very genetically compact and encodes only 13 proteins, all of which are core subunits of the oxidative phosphorylation (OXPHOS) complexes.

These OXPHOS complexes, found only within mitochondria, are unique in human biology as they are the only cellular structures formed of proteins encoded by genes from the two separate genomes. The nuclear DNA provides around 90% of the required proteins for OXPHOS, and the mtDNA provides the remaining 10%.

A new view of cancer?

Now, OXPHOS is not the only way to generate energy and building blocks for cells. A huge cancer research effort has gone into detailing the ways in which cancer cells can be rewired to survive and undergo rapid cell growth.

One of these metabolic changes is a much-discussed phenomenon known as the Warburg effect, where tumours generate large amounts of lactate by preferentially utilising glucose as a fuel source, despite being in conditions where their mitochondria could pick up the slack. Otto Warburg, and many since, have suggested that the altered metabolism associated with this effect, and other forms of metabolic dysfunction, are a driver of cancer initiation and progression. However, consensus on this view has never been reached in the cancer research community and these metabolic changes are often seen as a consequence of cancer rather than a potential cause.

In light of recent developments, this view may need to evolve. While anecdotal evidence of mtDNA mutations arising in tumours has been around for nearly two decades, in the last five years or so several studies using large scale sequencing data concluded that roughly 60% of tumours bear mutations of mtDNA (1,2,3). While these studies lacked statistical power and clinical insight, such clear links between a highly abundant and plausible source of mitochondrial dysfunction and cancer had never been made previously. There was a growing temptation amongst some to view these tumours as isolated groups of cells with both cancer and severe mitochondrial disease.

In a paper recently published in Nature Metabolism, my lab and colleagues from Memorial Sloan Kettering Cancer Center, detail the patterns underlying mtDNA mutations, the impacts these mutations have on tumours and the clinical implications of this in colorectal cancer (CRC) patients (4). In agreement with previous studies, we found that around 60% of tumours contain one or more mtDNA mutations. We also found highly recurrent mutations occurring across all tumours at specific stretches of DNA where a single DNA base is repeated, known as a homopolymer. This is significant because recurrence is an indicator of selective pressure – it implies the mutation confers an advantage to the cancer.

We also calculated a comparative mutation rate for all known cancer-associated genes, which included mtDNA genes. Surprisingly, this led us to the conclusion that mtDNA genes are among the most mutated genes in all cancer, with 25 of the top 30 most mutated genes being encoded in mtDNA. While comparing mtDNA and nuclear DNA does have its limitations – a relative understanding of these mutations can give us a sense of context and proportion when considering cancer genetics. Additionally, we showed that the mutational burden in mtDNA is unrelated to the mutational burden in the nucleus. This is important, because nuclear DNA mutational burden in many tumours is associated with their response to, among other things, immune-targeted therapies. It’s easy to see how mitochondrial mutational status could be harnessed to better allocate such treatments, if not allow development of mitochondria-targeted immunotherapies which may have advantages over current immunotherapy targets. Intriguingly, we saw that the burden of mutations in mtDNA was spread unevenly across the OXPHOS complexes. This hints at how tumours might harness specific forms of mitochondrial dysfunction, while struggling to survive with others and could inform future therapeutic approaches.

Mutations confer survival benefit

The mutations we detected in mtDNA are not arising late in tumour development but are present in stage 1 tumours at a comparable rate to stage 3 tumours. They also cause a distinct change in the way the nuclear DNA of the tumour cell is expressed. Increases in nuclear encoded OXPHOS genes and decreases in genes associated with innate immunity have been linked with diverse mtDNA mutations across nearly all cancers studied. Importantly, we found a substantial survival benefit for CRC patients whose tumours bear mtDNA mutations, with a decreased risk of death of 57-93% for the majority of those in this category.

Cells shutterstock 1130063729This potentially holds significant immediate implications for CRC patient care, however, it also raises many other questions: will this impact be seen in other cancers or just CRC? What are the precise differences between mtDNA mutant vs non-mutant cancer, beyond the mtDNA changes? Do some approaches to therapy for these patients work better or worse because of this? Beyond these specific, immediate questions, do mtDNA mutations actually cause or predispose cells to becoming cancerous, and how has this been missed for so long?

A lot of clinical and laboratory work needs to be done to address these. However, some issues are easier to address. For example, in what now seems to be a major misstep, mtDNA has been actively excluded from analysis of sequenced tumours as a matter of course, mostly owing to technical issues that arise when mtDNA is included in the data. This is an unfortunate but likely reason for their relevance to cancer being overlooked.

For much of the history of cancer research, and with good reason, scientists have focused heavily on nuclear DNA. These efforts have led to cancer being seen by many as a disease of the genome, an understanding that our recent discoveries suggest should be broadened. Cancer: no longer a disease of the genome, but a disease of the genomes.

References

1. Ju et al. Origins and functional consequences of somatic mitochondrial DNA mutations in human cancer, 2014, eLife

2. Stewart et al. Simultaneous DNA and RNA mapping of somatic mitochondrial mutations across diverse human cancers, 2015, PLoS Genetics

3. Yuan et al. Comprehensive molecular characterization of mitochondrial genomes in human cancers, 2020, Nat. Genet.

4. Gorelick et al. Respiratory complex and tissue lineage drive recurrent mutations in tumour mtDNA. 2021, Nat Metab.

CCBY-NC-SAThis article is reproduced from a Research Feature on Cancer Resesarch UK's Science Blog under a Creative Commons Attribution-NonCommercial-ShareAlike License.

 

Cell Scientist to Watch - Julia Cordero

13th May 2021

Cordero JuliaMáté Pálfy, Features & Reviews Editor at the Journal of Cell Science, caught up with Dr Julia Cordero to find out about her academic journey, from an undergraduate degree in Argentina, to a PhD in the United States, to a postdoc and starting her own group in Glasgow. Click here to read the interview.

Follow the link to read more about Julia's research: Local and Systemic Functions of the Intestine in Health and Disease

A Tale of Two Genomes

27th April 2021

Efforts to elucidate how mutations in a cell's DNA cause cancer have overwhelmingly focused on the DNA within the nucleus, but a new study published Nature Metabolism highlights the exciting potential of also looking at the genome of the cell's energy factories: the mitochondrial genome.

Mitochondria shutterstock 396424405It's known that mitochondrial mutations can be found in cancer cells, but there has been little research into what they do or whether they have any effect on treatment response or how the cancer will progress.

To answer these questions, Dr Payam Gammage at the Beatson Institute collaborated with the Memorial Sloan Kettering Cancer Center in New York to collate and analyse the largest dataset so far of tumour samples that include mitochondrial genome data and the corresponding clinical outcomes of the patients.

By analysing this data from 344 patients with colorectal cancer, the researchers could match groups of mutations to the likelihood of survival. They found that, after controlling for other variables which affect cancer risk like age, the presence of mitochondrial mutations was associated with a 57 to 93% decreased risk of death from colorectal cancer, depending on the type of mitochondrial DNA mutation. The researchers hope that in the future, doctors could use this information to identify patients with more aggressive forms of bowel cancer so they can receive the most effective treatments.

The team also wanted to know how common mitochondrial mutations were in cancer more broadly. By looking at existing data from over 10,000 tumour samples across 23 cancer types to search for recurring mitochondrial mutations, they found that mitochondrial mutations were present in up to 60% of tumours, with 25 out of the 30 most commonly mutated genes across cancers being present in the mitochondrial genome.

These results indicate that mitochondrial mutations could play a role in survival beyond colorectal cancer. Further research is needed to understand the wider implications of mitochondrial mutations in different cancers, and to delve into the biological underpinnings behind it.

Gammage head 2020 067Payam, who co-led the study, said: "This new study shines a light on the impact of mitochondrial DNA mutations in cancer, which have been overlooked for decades. This discovery could have a huge impact on patient care, with potential for changes to suggested treatments and a patient's outlook based upon the mitochondrial DNA status of their cancer. However, further research will be necessary to move these discoveries from the lab to the clinic."

Dr Ed Reznik, co-lead author based at Memorial Sloan Kettering Cancer Center, said: "Using data hiding in plain sight, we have shown that a critical piece of the cell's machinery to make energy is quite often broken in cancers. It now begs the question of how these mutations within mitochondrial DNA might be exploited as drug targets."

Michelle Mitchell, chief executive of Cancer Research UK, said: "This work highlights just how much more there is to discover about the inner workings of cancer, and all those breakthroughs for people with cancer we have yet to unlock. An incredible amount of basic laboratory research like this is being carried out across our Centres and Institutes, which is so important for helping to drive forward these unchartered and pioneering areas of research."

The paper can be read here: Gorelick AN, Kim M, Chatila WK, La K, Hakimi AA, Berger MF, Taylor BS, Gammage PA, Reznik E. Respiratory complex and tissue lineage drive recurrent mutations in tumour mtDNA. Nat Metab. 2021 Apr 8. doi: 10.1038/s42255-021-00378-8

Publication Highlights: April 2021

This month’s publications highlight the collaborative science that the Beatson regularly participates in both in the UK and around the world.

In research published in Nature Metabolism (Respiratory complex and tissue lineage drive recurrent mutations in tumour mtDNA), Payam Gammage, together with colleagues at the Memorial Sloan Kettering Cancer Center in New York, found that mutations in mitochondrial DNA (mtDNA) increased the chances of survival for patients with bowel cancer. The researchers compiled the largest study of tumour samples to date that investigated the mitochondrial genome. Over 20 cancer types were investigated and more than half of the samples showed mutations within mtDNA. Using this information may aid more accurate prognosis and the development of new treatments in the future.

Beatson scientists David Stevenson, Colin Nixon, Douglas Strathdee and Owen Sansom joined a study, led by the CRUK Edinburgh Centre, on treatment resistance in colorectal cancer (CRC) [RAC1B modulates intestinal tumourigenesis via modulation of WNT and EGFR signalling pathways]. As reported in Nature Communications, they frequently detected RAC1B in late stage patient samples and linked its presence to aggressive CRC tumour types. Mechanistically RAC1B is required for the activation of EGFR signalling, and researchers are now translating their in vitro findings into clinical studies of EGFR inhibitors such as cetuximab with anti-RAC1B treatment for enhanced therapeutic success.

In a preprint available on bioRxiv Hing Leung, Arnaud Blomme and colleagues linked the THEM6 protein to drug resistance in advanced prostate cancer (THEM6-mediated lipid remodelling sustains stress resistance in cancer). THEM6 affected the lipid composition of cancer cells, thus altering a cell's stress response, such as that induced by anti-cancer therapy. As the scientists also observed that THEM6 created a 'tumour stimulating' environment in other hormone-dependent cancers, they propose it as a new therapeutic target beyond just prostate cancer.

Together with Karen Blyth, Alexei Vazquez, Dimitris Athineos and Matthias Pietzke, Institute of Cancer scientists investigated the metabolic role of immune-regulated IDO1 that is associated with aggressive pancreatic cancer (Immune-regulated IDO1-dependent tryptophan metabolism is source of one-carbon units for pancreatic cancer and stellate cells). They demonstrated a shift in preference towards tryptophan as a fuel for specialised metabolism that can aid cancer growth. The administration of anti-IOD1 therapy may enhance metabolically-targeted treatment strategies such as serine and glycine restriction but requires further research.

Liver cancer cases have doubled in Scotland

2nd April 2021

liver cancerA new study has shown that the rate of people dying from liver cancer in Scotland has doubled over the past two decades. The study also showed that over the same period Scotland has had the highest number of confirmed deaths from liver cancer per head of population out of any of the four UK nations.

Dr Tom Bird, group leader at the Beatson Institute and Honorary Consultant Hepatologist at Edinburgh Royal Infirmary, co-authored the paper. He said:

'Our analysis of this data is showing that liver cancer has become a much more common type of cancer in the UK.

'Whilst there are signs that survival with liver cancer is improving, it still claims far too many lives each year.'
Dr Tom Bird

Dr Bird continued: 'A major factor driving this long-term rise in cancer cases is fat within the liver related to obesity. We expect the trend to get worse, as the pandemic means that fewer people have come forward with symptoms and people's weights and drinking behaviour have been affected too. I see it every day, with more and more patients coming to me with later stages of the disease.

'But it's important to remember that obesity, and the liver diseases related to it, are both preventable and reversible. That's why we need new public health measures to tackle Scotland's weight problem and reduce the risk of developing cancer in the long-term.'

Professor Linda Bauld, Cancer Research UK's prevention expert, who is based at the University of Edinburgh, said: 'It's shocking that so many people in Scotland are being diagnosed and dying of liver cancer.

'It should worry us all that liver cancer rates have risen over the last few decades in Scotland. Sadly, it is preventable factors like being overweight or obese, smoking and excessive alcohol consumption that increase the risk.

liver cancer 3'When it comes to stemming the tide of disease caused by carrying too much weight, the next Scottish Government has the power to make a difference.

'The pandemic understandably stalled progress on new laws to ban the harmful supermarket junk food multibuy offers which encourage us to stock up on unhealthy items that provide no nutritional value. But it's clear from this study that action is still urgently needed to help us all lead healthier lives.

'This is why the next Scottish Government must bring forward legislation to ban supermarket price promotions on junk food at the earliest opportunity.'
Professor Linda Bauld

'It's vital we see action to help us all keep a healthier weight. The health of future generations depends on it.'

This research has also been covered in a news report on the Cancer Research UK website: Liver cancer rates in the UK are highest amongst men in Scotland

The study can be found here: Burton A, Tataru D, Driver RJ, Bird TG, Huws D, Wallace D, Cross TJS, Rowe IA, Alexander G, Marshall A. Primary liver cancer in the UK: Incidence, incidence-based mortality, and survival by subtype, sex, and nation. JHEP Rep. 2021;3:100232. 

Inhibiting apoptosis is the key function of MCL-1 in breast cancer

1st April 2021

MCL1A study - led by Kirsteen Campbell, Stephen Tait and Karen Blyth and funded by Breast Cancer Now - has shown that a protein called MCL-1 helps breast cancer cells survive and replicate by blocking apoptosis (cell death), and that tumours rely on it to grow more aggressively.

Importantly, a type of drug called BH3 mimetics target MCL-1 and could be used to restart apoptosis in breast cancer. What's more, this finding could have also implications for other cancers including leukaemia, those affecting the lung and glioblastoma.

For more details, see this article published in The Herald.

Reference: Campbell KJ, Mason SM, Winder ML, Willemsen RBE, Cloix C, Lawson H, Rooney N, Dhayade S, Sims AH, Blyth K, Tait SWG. Breast cancer dependence on MCL-1 is due to its canonical anti-apoptotic function. Cell Death Differ. 2021. Online ahead of print.

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