Saamin Cheema joined the Mutographs project in January 2021 as a Data Scientist. Here, she reflects on the year she has spent as part of the Mutographs team.

When I first started working with the Mutographs team in January 2021, I had recently completed my Bachelor’s degree in Biochemistry from UCL and was excited about this incredibly exciting and meaningful opportunity. It was the culmination of a journey that started with my A-level project (EPQ) in cancer genetics up to my final year dissertation in bioinformatics.

I work with the analysis team at the Wellcome Sanger Institute to analyse cancer genomes of patients from across the world. Our aim is to discover patterns of mutations (called ‘mutational signatures’) that could be linked to a particular lifestyle or environmental factor involved in cancer development. Prior to starting my role, I was aware of the high-impact nature of the work the Mutographs team is conducting; however, I didn’t realise its sheer scale with thousands of whole genome samples being analysed, nor the depth and breadth of international collaboration involved.

Working through the pandemic

Despite the pandemic and remote working, the Mutographs team have continued their efforts and made significant progress over the past year. Over 3000 samples have now been sequenced and analysed since the Mutographs project started in 2017; we have managed to analyse over 1000 in the past year alone.

With the completion of the Oesophageal Squamous Cell Carcinoma (OSCC) study, the Mutographs team has powered on and is now working on another cancer type, kidney cancer. We have finished collecting the samples and generating the data for the kidney study, and are now at the stage of analysing the mutational signatures with the information gathered on lifestyles and environment.

It has been exciting to analyse this very large dataset of nearly 1000 whole kidney cancer genomes. The team are seeing some promising results with the discovery of new mutational signatures, and we hope to share these findings soon. We have observed that some signatures are enriched in countries with high kidney cancer incidence when compared to countries with low incidence. The team is currently investigating whether this difference can be linked to lifestyle or environmental factors, which could be contributing to the risk of developing kidney cancer.

Returning to the campus

From summer 2021, the Wellcome Sanger Institute where some of the Mutographs team are based, progressively opened its doors with more staff returning to site. I also excitedly moved to Cambridge from my home in the North West of England, and was eager to work with my colleagues in person. After remote working for 8 months, I really appreciated working on site at the beautiful Campus, and benefiting from being part of the scientific community.

Most of the Mutographs team here at Sanger settled into a hybrid work pattern with a mixture of working on site and from home. To assist this new normal of working, Sanger meeting rooms are equipped with technology to allow staff on site to take Zoom meetings together with those working from home. There are also precautions in place to ensure safety for everyone on Campus, including wearing masks and regular PCR testing. This is very much in line with my experience of this research institute which takes its duty of care towards its employees seriously while also ensuring the science can continue.

However, in the last month of 2021, Sanger made the responsible decision to once again advise staff to work mostly from home due to to the rapid spread of the Omicron coronavirus variant in the UK. Fortunately, the Mutographs team has successfully worked from home since March 2020, so we are easily able to continue analysis of data off-site. I am looking forward to when we can return to the vibrant Campus once it is safe again.

Mutographs at the Science Museum

I was really pleased to learn that Mutographs is featured in an exhibition on cancer research, which opened in autumn 2021 in Manchester’s Science and Industry Museum, and will be moving to London’s Science Museum in spring 2022. The exhibition is called Cancer Revolution: Science, Innovation and Hope, and is organised by the Science Museum in partnership with Cancer Research UK.

It takes an honest, uncompromising look at cancer and shares the hopeful side of cancer research. I visited the exhibition in November 2021, and enjoyed seeing how our work in Mutographs fits into the broader world of cancer research. From the impact cancer has on patients and their families to modern day therapies, the exhibition provides an extensive overview of the disease in a new and engaging way. It was interesting to learn about: the importance of studying animal genetics, for example the genes responsible for antler growth in deer are genes related to human cancer; smart and robotic devices developed to increase efficacy of tumour removal surgeries; and new targets for treatments, such as developing drugs to target not only cancer cells directly but the surrounding healthy cells in a tumour which support cancer growth.

The Mutographs project features as a short video in the ‘Seeing and Studying Cancer’ section of the exhibition. Mutographs team members in Cambridge, Lyon and San Diego worked together with the Science Museum to prepare a video sharing our work and aims. It was challenging to film with varying Covid restrictions in place across the different countries, but the teams worked together to create a unified final result.

The Mutographs film as presented at the Cancer Revolution: Science, Innovation and Hope exhibition. The film was produced by the Science Museum and members of the Mutographs team.

Cancer Research UK predict that 1 in 2 people will develop cancer in their lifetime, so there is a necessity for ground breaking research like the Mutographs project. The video shares the project’s ambition to uncover underlying causes of cancer, and generates optimism that this can lead to prevention measures for this disease.

An inspirational year

I have had an inspirational year with Mutographs, settling into a good working rhythm with the team, and cementing my passion for science. I have learnt so much and feel proud to be a part of the project. It is a nurturing environment, and with the team’s guidance and encouragement I have developed my skills and taken on greater responsibilities. Heading into 2022, I look forward to contributing more to the project as we enter the next stages of the kidney study, and begin analysis on more cancer types, starting with head and neck cancers.

The header image is of the entrance to the Science and Industry Museum in Manchester, taken in November 2021. Image credit: Saamin Cheema. 

In this blog, Mutographs patient advocates Maggie and Mimi share their involvement in the research, their own experiences of cancer, and their journey around the globe. As told to Louise Walker, Public Engagement and Involvement Coordinator for Mutographs and edited by Alison Cranage, Wellcome Sanger Institute.  

Signatures, fingerprints, ‘tell-tale signs’ are all terms that have been used to describe patterns of changes, or mutations, in a cell’s DNA that can lead to cancer. It was in 2013 that Sanger Institute scientists coined the term ‘mutational signatures’ to describe these patterns of mutations, each with a specific cause. Ultraviolet (UV) light leaves distinctive changes in a cell’s DNA, while tobacco smoke leaves a different arrangement of mutations. These complex patterns, made visible through genomic sequencing the 6 billion letters of a cell’s DNA, serve as a fossil record. They can give scientists clues to what has happened in a cell’s history, and what caused it to become cancerous.

Researchers have discovered around 50 different mutational signatures to date, but the cause for only half of them. The Mutographs team aims to uncover more. The potential impact is huge – if we can find causes of cancer, previously hidden, we may be able to avoid them.

Maggie Blanks and Mimi McCord were asked to be involved in the project by the scientific team during the preparation of the funding application. They now sit on the steering group and take part in meetings and conferences about the work, bringing the patient perspective to this complex project. They have visited partner sites and organisations in Kenya and the Czech Republic and more recently Iran, though this one had to happen virtually. They describe their role as bringing a ‘human level’ to the research.

“Cancer research starts with the patient and ends with the patient. All this has been done for the patient’s benefit. The human element in this is very real and very vital. And I think that’s what Maggie and I are able to bring.” – Mimi 

We spoke to them about their experiences and involvement in the project so far.

Oesophageal Cancer

Two types of oesophageal cancer are being studied by the Mutographs team – oesophageal adenocarcinoma and oesophageal squamous cell carcinoma (OSCC). These cancers are of interest partly because of their unusual global distribution.

In the UK, about 9,200 people a year are diagnosed with oesophageal cancer, with Oesophageal adenocarcinoma being the most common type (source) .

Mimi shared her own experiences of the disease.

“My late husband was diagnosed with oesophageal adenocarcinoma following difficulty in swallowing. He was 47 and had no previous health issues at all. He had persistent heartburn, which he was self-medicating with Rennies. I would cheerfully buy them, completely unknowing that these were masking a symptom. Anyway, difficulty in swallowing sent him to his doctor. An endoscopy showed that not only was it oesophageal adenocarcinoma, but it was advanced and he had metastatic disease pretty much throughout his body, and he died nine weeks later.

“I knew nothing about oesophageal cancer. I knew the gullet, food pipe, etc, but nothing else. But his death was completely preventable. So as a result of that I founded what was the McCord Oesophageal Cancer Fund and is now Heartburn Cancer UK. I remain a very passionate advocate in raising awareness of the link between heartburn, Barrett’s oesophagus [where cells of the oesophagus change shape], and oesophageal adenocarcinoma.”

Rates of oesophageal cancer vary hugely across the globe. Some countries, including Iran and Kenya, have a high incidence of the squamous cell version of disease with 20 to 30 people per 100,000 affected. In other countries, like the UK, Japan and Brazil, the rate is less than 6 per 100,000. Within countries there are ‘hot zones’ where it is more common in some regions than others. These differences can’t be explained by known lifestyle or environmental factors.

The Mutographs team have studied the genome sequences and accompanying health and lifestyle data from 500 people with oesophageal squamous cell carcinoma (OSCC). Donors are from eight countries with varying disease rates. The results of this study were published in October 2021 in the scientific journal Nature Genetics.

The Mutographs team includes expertise in epidemiology and mutational signature analysis to work out what might be responsible for the cancer in any given location. OSCC has never been studied at this scale before, comparing genomic and lifestyle datasets from across continents.

Maggie and Mimi bring patient expertise to the team. Maggie, who set up the Pancreatic Cancer Research Fund after her husband Alan died from pancreatic cancer, summarised ways that patient advocates can contribute to research projects:

“On a broad level, we explore ways the patient experience or viewpoint can be incorporated into the research, and explore and support ways patients can be involved actively in the research design process. We consider and recommend ways that information and outcomes can be shared with patients and the public. In more detail, perhaps that would mean things like exploring the room for patient involvement in the methodology that’s used in the project. So for example, questionnaire design, or other materials design, making these patient-centred and relevant.”

Cancer across the globe

Another element to their role has been to visit partner sites in Kenya, the Czech Republic and Iran to find out more about the context of cancer treatment and healthcare in those areas, and to identify ways to effectively convey any findings that come from the Mutographs study.

As well as varying cancer incidence rates, attitudes and treatments for cancer are very different in different parts of the world. Maggie and Mimi discussed their visits to Kenya and the Czech Republic – both trips were in person, before the pandemic.

Mimi said: “Travelling, particularly to Kenya, for me, has been the most interesting part. Seeing a completely different culture, a completely different way of dealing with cancer. There is a huge stigma attached to cancer there. Seeing the facilities made me realise here we have a privileged life in many ways.”

“And then, in contrast, the Czech Republic visit and seeing how they deal with cancer, which was more similar to here in the UK. What was different there was the incorporation of patient advocates within the government health system, which we don’t have, and I think it’s something that would be a useful tool for us.”

“Being able to see how the different countries deal with cancer, the politics behind it, the politics within it, and how it is dealt with as a whole is important for me.”

For Maggie, seeing cancer in different cultures led her to think about the role that patients can play in research that spans the globe.

“When we’re thinking about patient and public involvement [PPI] in a place, country or region, we need to consider how cancer is viewed in that scenario.  In the region of Kenya that we visited, cancer was associated with stigma and with secrecy. So the question for me was – how does PPI apply here? How do you go about involving patients, and how do you disseminate the results of research in that sort of scenario.”

Maggie and Mimi visited Iran, virtually, in 2020. Iran is of particular interest to the Mutographs team because while OSCC rates are low in the capital of Tehran, they are high in other areas of the country – particularly the Golestan Provence in the North East.

They met researchers in Golestan who have been working to try and understand why OSCC rates are so high. Over 50,000 people have taken part in studies over recent years, and Maggie and Mimi asked how the researchers had engaged with communities so well. The team highlighted working with trusted local community leaders and healthcare workers as a key factor in their success. Participants were also able to benefit from free diagnostic procedures, plus the study itself created jobs.

“It was really good to hear how passionate the study team was about helping communities that have been so badly affected by OSCC. The team in Iran has really shown the benefits of engaging patients early on in the research process,” said Mimi.

The risk factors for OSCC are still only partially understood. There is some evidence that drinking alcohol, smoking, drinking scalding hot liquids – like tea – and opium consumption may have a role to play.

Next steps

Despite the profound global differences in rates of OSCC, the teams’ analysis of mutational signatures did not identify a known or new mutational process that could be responsible for the disparities³. Their results were published in October 2021 in the scientific journal Nature Genetics.

Instead, their results show that the overall mutational profile of OSCC is extremely consistent around the world. They also highlighted that mutations in the APOBEC protein in cells are likely to be involved.

The Mutographs team are continuing their work into a  range of cancers including bowel, pancreatic and kidney. Like the two forms of oesophageal cancer, each of these has a varied global distribution – and the team hope to use the power of mutational signatures to uncover why. The search for hidden causes of cancer continues.

Maggie and Mimi will continue to support the team and keep bringing the ‘human level’ to the project. More virtual trips are planned for the future and they are also working with the Mutographs team and their collaborators to find ways to further embed patient involvement in studies like this.

Dr Sarah Moody is a postdoctoral researcher at the Wellcome Sanger Institute working in the Mutographs team. She reflected on Maggie and Mimi’s role and PPI in the project.

“Having Maggie and Mimi on the Mutographs team really helps to remind us of the people behind the samples. It’s easy to forget that the data on our computer screens is from people who have not only donated their tissue but also spent the extra time and effort to provide the additional information on their lifestyles which is essential to our project. Keeping that connection to the patients and helping to understand cancer and cancer research from their point of view, wherever they are in the world, is important and helps to remind us why we do this work.”

Find out more

• Cancer research at the Sanger Institute
• Cancer Grand Challenges website: Mutographs

The Mutographs team has added an unexpected piece to the complex puzzle surrounding the development of oesophageal squamous cell carcinoma (OSCC): no mutational signature exists to explain the profound difference in incidence rates across the world. The findings, published in Nature Genetics, unearth many new avenues for exploration. Here, Mutographs postdoctoral researcher Sarah Moody discusses the surprising findings and where they could take the team next.

Oesophageal cancer affected about 6.3 people per 100,000 worldwide in 2020 and was the 11th most common cancer type that year (source: IARC Globocan). Of these cases, most were a type called oesophageal squamous cell carcinoma (OSCC), which affects many people in areas of Iran, China and East African countries such as Kenya, Tanzania and Malawi. It is not nearly as common in other parts of the world such as Brazil, Japan and the UK.

The reason why the numbers of people affected varies so much between all these places is a bit of a mystery, but it has been speculated that there could be a particular lifestyle or environmental factor that is linked to the increased number of cases.

Surprising answers to important questions

To investigate this, we recruited patients from each of the eight countries mentioned above, who provided us with samples of their tumour and answered a detailed questionnaire about the risk factors for OSCC, including tobacco, alcohol and drinking extremely hot beverages, among others.

In the tumour DNA, we looked for differences in the pattern of mutations, known as mutational signatures. While we don’t yet know the cause of all the known mutational signatures, we do know that some are caused by lifestyle and environment factors such as smoking and exposure to UV light from the sun (read more here). It is also likely that there are yet undiscovered mutational signatures and investigating them is a core aim of the Cancer Grand Challenges Mutographs programme.

When we embarked on this study, we were looking for a mutational signature which was only present or increased in areas where OSCC is common. If we could link such a signature to a particular cancer risk factor, we could not only explain the difference in the number of cases across the world, but also potentially identify ways to prevent it.

But what we found was that the mutational signatures present in OSCC samples were extremely similar, regardless of where in the world the cancer occurred.

This result took us by surprise, given the differences in lifestyles and environments of the patients involved in the study. However, these results do tie in with those coming from other teams in the Mutographs Cancer Grand Challenges programme. Our colleagues Allan Balmain and David Adams and their teams have shown that in mice, some compounds known to cause cancer in people do not generate a mutational signature. This means that these compounds do not act by causing mutations in DNA – they must, instead, act in some other way that leads to cancer.

Understanding how these compounds lead to cancer is a vital question, and researchers across Mutographs are planning to explore this further.

APOBEC – an avenue for further exploration?

Although we did not find a mutational signature that could explain why OSCC is more common in certain places, we still made some interesting findings about the cancer itself.

Most importantly, we found evidence of two particular mutational signatures in around 90% of OSCC cases, which is a far higher number than most other cancer types.

These two signatures are called SBS2 and SBS13 in the reference set of mutational signatures housed in COSMIC (read more about COSMIC in my colleague Ellie’s blog here) and are associated with the activity of the APOBEC family of proteins.

APOBEC proteins normally act to protect against viral infections, and some of them do this by causing mutations in the virus genome. Previous research has shown that APOBEC can also cause mutations in some human cancers, but we don’t yet understand the reason why this happens.

The presence of SBS2 and SBS13 in almost all cases of OSCC suggests that these signatures are very important in the development of this particular form of cancer. Despite this, we found no link between any known OSCC risk factor and the number of mutations caused by APOBEC.

So, many questions remain: Why is the APOBEC signature so common in OSCC? What causes APOBEC to start targeting human DNA? Could this process be prevented?

Many questions remain, and we leave behind some important clues

As is often the case in science, we set off asking one question but ended up with many new ones.

The reasons behind the unusual distribution of oesophageal cancer cases remains, for now, a mystery.

We leave behind some important clues, and the largest set of whole genome sequencing data for OSCC currently available. This dataset is available to all scientists, and it is our hope that our findings will go on to inform further research, which will hopefully answer some of these questions.

Read the paper in Nature Genetics.

When most people hear the term “genetic disease,” they think of inherited conditions that a person is born with. However, cancer is also driven by changes to genes called mutations that happen throughout a person’s life. Our increasing understanding of this process is changing cancer treatment. 

Scientists have thought that cancer is linked to changes in the DNA since the late 19th century, when the German pathologist David von Hansemann noticed that the abnormal division of cancer cells under the microscope led to errors in the number of chromosomes. But it was only in 1982 that the first naturally-occurring mutation linked to human cancer was discovered. This mutation, changing a single DNA letter in the HRAS gene, paved the way for the identification of many more mutations that transform normal genes into drivers of tumour development. As more genes and mutations linked to cancer were discovered, scientists needed a way to collect and share this information. They needed to build a catalogue of genetic changes in cancer. 

What is COSMIC? 

COSMIC, the Catalogue Of Somatic Mutations In Cancer, is a comprehensive resource used by scientists to record and investigate the genetic mutations found in cancer. Launched in 2004, the database originally covered only four genes, HRAS, KRAS, NRAS and BRAF. These genes are all in the same molecular “pathway”, which regulates when a cell divides. A mutation in one of these genes can lead to errors in this process, leaving a cell dividing uncontrollably and causing the growth of a tumour.

Recent leaps forward in large-scale genetic sequencing of tumours has led to the discovery of hundreds of genes linked to cancer. COSMIC has had to grow in size to match the huge amount of data being generated – it has now catalogued over 70 million mutations from dozens of different cancer types. 

Currently, the COSMIC team is part of the Wellcome Sanger Institute, based at the  Wellcome Genome Campus, curating a range of different types of information about mutations in cancer. These include the Cancer Gene Census, an expertly curated list of the most important genes involved in driving cancer, and COSMIC-3D, a platform for understanding how mutations affect the 3D structure of the proteins produced by genes linked to cancer. These resources are used by scientists worldwide for projects relating to cancer biology and drug discovery, with over 5,000 page views every day.

How does COSMIC support the Mutographs project?

 As well as recording the specific mutations seen in tumours, COSMIC also curates a list of patterns of mutation called “mutational signatures”. DNA mutations can be caused by a range of different things, from errors in cell division to damage from external forces like ultraviolet light from the sun. Looking for these signatures in patients’ tumours can help scientists to identify the causes of cancer. One example of this is the story of aristolochic acid, a chemical found in a number of traditional medicines. This substance was already known to be linked to kidney problems, but the discovery of its specific mutational signature in patients with liver cancer in Asia led scientists to link the use of some kinds of herbal remedies to this disease. Discoveries like this can aid public health initiatives to help people limit their exposure to dangerous substances, reducing their cancer risk. The Mutographs project uses COSMIC’s list of mutational signatures to help identify the possible causes of patients’ cancers, and how this varies in different parts of the world.

From mutations to medicines

Keeping track of the mutations that cause cancer helps the development of targeted cancer treatments. For example, the discovery that melanoma skin cancer is often driven by a mutation in the BRAF gene led to the development of drugs that can specifically target this mutation, dramatically improving outcomes for some cancer patients. The benefit of COSMIC’s catalogue of mutations in cancer is that it can also be used to work out which other cancer types an existing treatment might work for. The same BRAF mutation has been found in some colon cancer patients, so scientists are now researching how the targeted drugs used in melanoma might also be added to colon cancer treatment regimens to make them more effective.

One of the newest COSMIC projects is Actionability, which aims to track the availability of drugs that target specific mutations in cancer and monitor clinical trials investigating these new treatments. At the moment, full information has been collected for 39 genes, with a further 161 having some human clinical study data. This resource will support research into targeted cancer treatments, with the ultimate aim of using our increasing knowledge of genetic changes in cancer to improve patient treatment using therapies personalised to the unique set of mutations in their tumour.

As more and more data is generated, COSMIC continues to grow and gather important information. This information will be of huge value to the Mutographs team, who will continue to use COSMIC resources in their search for finding preventable causes of cancer. Very soon, COSMIC will be launching more exciting products that will help provide further answers to some of the key questions in global cancer research.

M’s story

To find out more about how cancer care works in Iran, we were lucky enough to be able to have a video call with a cancer patient, M. Reza Roshandel was again present to help us with our questions and to make M feel more comfortable. Her son-in-law was also on the call so we could gain a family perspective.

M is a 69 year old breast cancer survivor from the city of Kordkuy, about 40 km from Gorgan in the Golestan province. She was diagnosed three years ago and had to travel to Gorgan for her treatment, which included a radical mastectomy (removal of the whole breast) and chemotherapy. She finished her treatment a year ago and is in remission, although still has regular check-ups.

Family first

One of the most striking things we found about talking to M was how little she was worried for herself. She has four daughters and one son who were all grown up and married at the time of her diagnosis. Her first thought was how her diagnosis would affect them. She didn’t want her children to worry about her or be stressed about having to care for her. Fortunately for M, her children were supportive and organised a rota between them so they could help take care of her.

However, she did not want to talk about her cancer with her family, and has discouraged her daughters from trying to find out more with the philosophy of ‘the less you know, the better’. We found out from M and Reza that in rural areas especially, cancer can still carry an element of stigma, and people don’t really like talking about it. However, M did have a supportive community of other people affected by cancer to help her through her treatment.

M’s trust in her medical team was extremely strong. She didn’t feel the need to find out more information about cancer or her treatment because she felt that the medical team had given her all the information she needed. While she did have some challenges, particularly side effects from the chemotherapy, she said that there was nothing they could have done to treat her better.

Helping research

While M didn’t have any samples directly collected for Mutographs, she did donate tissue to the Golestan Cancer Biobank. Tissue and other biological samples that are stored here are available to researchers at Iranian and international universities and hospitals who would like to further investigate cancer. M was very happy to donate tissue because helping her community is very important for her. The surgeon had fully explained to her why they wanted to take the sample and so she felt well informed. When we asked her if she was curious about what happened to the sample or any research that had been done using her tissue, she said no.

Treatment over comfort

One element of our conversation that stood out to us was that in Iran, the medical teams don’t always prioritise patient comfort and support. They are more focused on treating the disease itself. Patients need a referral to access painkillers. Care to help to make them more comfortable is also rare, especially in rural areas. Reza was however very eager to point out though that the attitudes are changing and some people, particularly in large cities, are starting to pioneer a more supportive approach.

Helping the community and making changes

We are very grateful that M let us into her home (even if we were there as pictures on a laptop screen!), and it was fascinating to find out more about the medical system in Iran and M’s experiences. Her feelings of duty towards her family and her community were very strong, and this was a big motivator for her to donate samples to research.

We were very encouraged to hear that attitudes towards talking about cancer are changing for the better and that there is an increasing focus on making patients comfortable. Hopefully as time goes on, cancer patients and their families in Iran can experience more support for their mental health and there will be more focus on comfort as well as treating the disease.

We are never ones to shy away from an opportunity though, and we realised that needing to stay at home has its advantages, even when doing trips abroad. Using virtual platforms, we were able to chat to people and ‘visit’ places that previously hadn’t been very accessible for us. The opportunity arose to have conversations with study coordinators for the Mutographs project in Iran, so of course we jumped at the chance.

We were able to have four virtual ‘visits’ to the Iranian team in total – one to the team in Tehran, one to the study coordinator based in the Golestan province, one to the biobank collecting samples in Golestan and one to the home of a cancer patient.

Over the next two blogposts, we’ll be bringing you our highlights from these trips.

Studying oesophageal cancer in Iran

Iran has long been a source of curiosity to cancer researchers and doctors, in particular because of the rates of oesophageal squamous cell carcinoma (OSCC). The rate of this cancer is relatively low in the Iranian capital city, Tehran. But if you travel to the Golestan province in the north east of the country, you’ll find much higher rates. The reasons behind this aren’t fully known and this is one of the questions that the Mutographs team hopes to investigate. Previous evidence from epidemiological studies has indicated that drinking very hot tea, a custom in Iran, could be linked to OSCC. The Mutographs team are looking for genetic signals from mutational signatures that might help to shed some more light on this potential cause.

Golestan province

Iran is home to about 83 million people. The country is ethnically diverse and its inhabitants have many different backgrounds, communities and cultures. The Golestan province is in north east Iran and has a population of around 1.8 million. The capital city in this province is called Gorgan, which is located about 40 km from the coast of the Caspian Sea. It also has gorgeous mountainous views that our host Gholamreza Roshandel showed us from his office. The province is near the border with Turkmenistan and a large number of people in this province are of Turkmen ancestry, especially in the city of Gonbad, where the highest rates of OSCC are reported. Some communities in the province retain a unique identity expressed through their language and culture.

Investigating cancer

One of the most fascinating parts of our visit was finding out about the research that has already been undertaken to understand why OSCC is so high in this region. The Mutographs study coordinator in Golestan, Gholamreza Roshandel (known as Reza), took us through the history.

A leading gastroenterologist, Reza Malekzadeh, set up two studies focused on gastroesophageal cancer in Northern Iran. One was a ‘case-control’ study, where people with and without cancer are directly compared. The other was a ‘cohort’ study, which follows a large number of people who don’t have cancer over a long period of time to see if there are any factors seen in people that go on to develop symptoms of cancer. These collaborative studies were set up between teams in Iran, IARC, and the National Cancer Institute (NCI) in the US. Starting in 2003, Dr Malekzadeh and his team have created a community of people from the region who are willing to donate biological samples such as tissue and blood and fill in questionnaires about their lifestyle. Some of the people are cancer patients but others don’t have signs of the disease. The participants benefit from diagnostic facilities provided free of charge by trained local doctors and gastroenterologists from Tehran.

These studies have focused solely on the Golestan province, particularly around the city of Gonbad and surrounding rural areas as they have the highest rates of OSCC. The two study designs together have recruited over 51,000 participants. The evidence from the studies pointed to drinking very hot tea and consuming opium as potential reasons behind developing OSCC.

In addition to the above-mentioned studies, a recent cancer research project has been started in 2016 by the Golestan Cancer Biobank (GoCB) at the Golestan University of Medical Sciences. The main aim of the GoCB is to collect and preserve biological samples and risk factor data from cancer patients throughout the Golestan province, and to provide these samples and data to local, national or international research projects.

The study team have been providing samples and questionnaire information to the Mutographs study so we can explore the genetic evidence.

The benefits of engaging the community

The two studies that were originally set up in the Golestan province have been hugely successful. Many of the 50,000 people recruited to the larger study (the Golestan Cohort Study) are still actively followed up by the team and happy to take part today, which is a great outcome.

Reza Roshandel explained to us how the team have managed to engage with the community so well. The region is home to many different cultures with their own customs and some speak a different language. The study leaders were careful from the very beginning to engage with these communities on their own terms, with the help of trusted local leaders who spoke the same language. By doing this, they gained the acceptance of the community, who were also eager to help as they knew many people who had been affected by cancer.

A particularly effective method was to use the local health workers, known as Behvarz. These are local members of the community who have been trained to help with healthcare needs. They work from local ‘health houses’ based in the villages. They deal with basic medical issues and will refer patients to a specialist where needed. In addition to local doctors, the Behvarz were able to identify and refer anyone who would like to take part in the studies.

There were also benefits for the participants. Anyone enrolled in the study who developed symptoms of gastro-oesophageal cancer was referred to the specialist Atrak clinic. Here, they received diagnostic procedures such as an endoscopy for free. Iranians usually pay for healthcare through a health insurance scheme. The public insurance, provided by the government, covers about 70% of the costs, so being able to have the diagnostic procedures for free is a huge bonus.

Another reason that the studies were so successful is that they created jobs and opportunities for these rural regions. The local doctors were sent to Tehran to train in techniques for detecting upper GI disorders, with the directive that they had to return to their local community to practice. Local people, often women of Turkmen ancestry, were trained to help with the study at the health houses.

Keeping people informed

Making use of these community connections was also important when it came to feeding back the results of the study. The study team provided pamphlets and information to be kept in the health houses to inform people how they can reduce their risk of cancer. Some people, particularly in rural regions, are illiterate, so the study team also produced media and videos and relied on family members who could read to help spread the word.

Learning lessons

It was really good to hear how passionate Reza and his team were about helping these communities that have been so badly affected by OSCC. The team in Iran have really shown the benefits of engaging patients early on in the research process and this is something we hope that research teams doing this type of field work will consider when designing studies like these.

The computational work was much less affected, though again adapting to extend IT resources to home was required. Some changes did have consequences on overall productivity though. For example, having children at home for such a long time gave a precious opportunity to have more quality time with them, which inevitably crept into working time.

The Mutographs work flow was greatly affected because access to samples fully depends on direct contact with vulnerable patients and local regulations have been changing all the time. But international partners and the team at IARC have made exceptional efforts to get things going. With this collaborative effort, all the hurdles, from a patient agreeing to participate, to treatment being provided, samples being collected, sent, recovered, processed, analysed, DNA extracted and sent, retrieved processed and analysed, were overcome. The end result has been a great move forward for the project, culminating in a number of manuscripts including a major piece of work being submitted on the 15^th of December.

There were achievements in the interaction with patients as well. Once the despair of not being able to realise the planned visits of centres around the UK receded, the new approaches were embraced to continue this work online. So it was that virtual visits were organised to meet researchers, medical and healthcare staff as well as patients in countries that this year seemed more out of reach than ever. The work, communication and exchange with our partners continued, strengthening the relationships and increasing our knowledge. These visits now leave the horizon open for the future to reach further and gather a wider view and understanding of the context of cancer around the world. This is a positive outcome to take away from this very strange year.

We have adapted to the difficulties this year threw at us and we have learned important lessons and now as we and the world slowly get back on our feet, we hope for a better year 2021.

Behnoush Abedi-Ardekani (MD) a scientist and pathologist at IARC takes us through the meticulous analysis of Mutographs tissue samples to determine their suitability for sequencing and further analysis at the Wellcome Sanger Institute, UK.

What is pathology and why it is part of Mutographs?

Pathology is a medical specialty which means “studying lesions”. Every disease in our body is caused by the accumulation of toxic factors that eventually affect the integrity and functionality of our cells and their genomic content, leading to symptoms and signs. Clinical symptoms appear when pathological structural and cellular changes have already been established in our body. The ultimate aim of all physicians is the correct diagnosis of disease and appropriate planning for patient management. The pathologists’ aim is the same, with a deeper level of analysis: “studying and interpreting cellular changes at microscopic level”. The pathologist adds this level of information to clinical and radiological data to provide a final diagnosis. The discovery of the microscope in the 19^th century led to a revolutionary change to the field of pathology from studying gross pathologies to cellular levels. Today, impressive advances in technology and whole genome sequencing, have shifted the understanding of diseases to the genomic level. Equally, modern pathology is not limited to analysis of cellular and morphological features, but greatly expanded to the analysis, interpretation and integration of these features with molecular data. Molecular pathology is a new era of practice in the field.

Cancer is a chronic disease and pathology has a crucial role in diagnosis, morphological and molecular typing, and guidance of the therapeutic approaches and patient management. The principal role of pathology is the same in both diagnosis and research. While genomic analysis lies at the base of the Mutographs project, pathology is the fundamental part of the process that serves to evaluate the cancer tissues and to confirm their characteristics and suitability for the study.

Pathology workflow of Mutographs samples at IARC

Mutographs aims to analyse the genomic data of 5000 cancers, from five cancer types. Around 40 collaborating centers distributed in five continents are recruiting patients and collecting their biological material, including a piece of cancer tissue. The collected tissues are preserved frozen, stored in local centers and shipped to IARC in appropriate and regular timetables for microscopic examination and extraction of genomic content (DNA) of eligible ones.  In a medical set up, we don’t freeze tissues for the purpose of diagnosis, but research needs go further than microscopy alone and we know that the genomic content of cells is better preserved when frozen. As a result, the Mutographs’ tissue samples must be examined frozen, which is much more challenging for the pathologist than the routine practice of analysing fixed tissues.

Let’s follow the journey of Mutographs’s biological material, specifically the cancer tissues, through their processing and evaluation at IARC:

When the biological material arrives at IARC, it is transferred to deep-freezing storage.

Then the tissues are gradually taken to the pathology lab, where they are prepared for analysis. The frozen tissues are sectioned by cryostat: a sharp blade in a cold chamber at -30°C. The ultrathin sections 3μm thick are placed on labelled glass slides. The remaining tissue is kept in a frozen block and are stored back in the freezer.

In order to visualise the details of the ultrathin sections of tissue on the slides, they need to be stained. The routine and first level staining for all tissues is called H&E and consists of Hematoxylin and Eosin that create a contrast between cellular components. Hematoxylin stains the nuclei blue and Eosin stains tha cytoplasm of the cells and the extracellular matrix of tissues pink. The intensity of the colours, the ratio between them and their distribution in the tissue provides valuable information, vital for pathologists to provide a diagnosis.

The high quality images are then analysed in fine detail by a team of pathologists with specific expertise. The Mutographs pathology workflow is led by Bahnoush Abedi-Ardekani. She oversees the entire process and provides microscopic reports of the tissues in collaboration with a team of eight external pathologists: six gastrointestinal pathologists and two nephropathologists. Each cancer tissue sample is examined and reported by one pathologist and a randomly selected 20% of samples are independently examined and reported by two experts. Every pathologist has the option of consulting for a second opinion through the web-based pathology report platform. Any disagreement between the analyses is resolved by seeking a third report or a re-examination and discussion session.

The samples with a confirmed morphological type with at least 50% viable cells are selected and a list is sent to the biobank.

Finally, those samples containing at least 800 ng of DNA are kept and the DNA shipped to the Wellcome Sanger Institute in the UK for whole genome sequencing and analysis. Pathology examination and genomics complement each other to drive forward cancer research.

The International Agency for Research on Cancer (IARC), is an intergovernmental institution located in Lyon, France, that forms part of the World Health Organisation. Its role is to coordinate and conduct research into the aetiology of cancer as well as to collect and publish surveillance data on cancer prevalence around the world. For this, it collaborates with research centres, university hospitals or clinical hospitals with associated research units all over the world to collect tumour samples.

Sandra Perdomo, a scientist at IARC, describes the workflow that the samples included in the Mutographs study follow:

In the collaborating centres around the world, cases are identified and a biopsy is taken to confirm diagnosis. The patient is then invited to participate, consent is signed and samples consisting of a blood sample and the remaining tissue of the biopsy are stored. In the cases when surgery is the primary treatment, a piece of the surgical resection is also kept. Information about the patient such as age, gender, habits and risk exposure such as alcohol, tobacco, diet, occupational, etc; as well as clinical data is collected and entered in a centralised online database at IARC. The samples are sent to IARC to be added to its large biobank containing almost 7 million biological samples.

Once at IARC, the samples are inventoried and their corresponding information is curated, verified and stored in the database. The tissue samples and processed and slides are prepared in the histopathology lab. These are reviewed by four pathologists to confirm the tumour type and tissue characteristics. The quality of the tissue is assessed to make sure it contains at least 50% tumour cells and is adequate for sequencing. The suitable tissues are sent to the lab for DNA extraction along with the blood sample from the same patient. The DNA quantity and quality are checked and shipped to the Sanger Institute for sequencing together with core data exclusively concerning the sample, without any specific reference to the patient to preserve privacy.

The Mutographs’ project manager at the Sanger Institute, Laura Humphreys follows on the journey of the samples once they arrive in the UK: At the Sanger Institute the DNA samples undergo further quality control checks and enter the high throughput DNA sequencing pipeline – this requires input from many individuals, teams and also robots and results in high quality sequence data which is then passed on to the Mutographs scientists for detailed analysis. The samples are all given a new unique reference number at Sanger which can be linked to the clinical data, but not to the patient. Ultimately the data from patients’ samples will be presented to the scientific community through publications and conference presentations. We also hope to provide a research update directly to the collaborating medical centres and patients or family members in the final stages of the project.

Over the past months as SARS-Cov2 spread across the world, IARC teams all working remotely, have been following closely the situation in all contributing centres, nearly all of which are health research facilities. In many institutes, much non-essential work was curtailed and patient recruitment slowed down.

The IARC scientist Estelle Chanudet talks about how centres around the world have coped with the local restrictions to continue the work enabling the collection of samples for research:

At the Ontario Institute for Cancer Research, Canada, Mutographs collaborators began working remotely in mid-March and technical work, such as fine laser cutting of tumour pieces to capture the tumour cells, was on hold. Dr Wilson reported that a small number of lab staff received approval to return to work on June 1^st, 2020, with physical distancing measures in place.

South Africa went into lockdown on March 26^th, and although this has been eased somewhat since June 1^st, Universities are still closed. Dr Parker reported that the University of Cape Town is looking at a phased return of staff and students, weary of the peaking of covid-19 cases. Hospital procedures are limited to only essential surgeries since the Western cape has almost 70% of the Covid-19 incidence and deaths. The Hospital Ethics Committee has ruled that no samples may be collected for research purposes during the lockdown in order to minimise “non-essential” activities and traffic through the hospital.

Across the world, hospitals have been putting in place protocols to ensure patient and health personal safety during recruitment. Collaborating centres in Poland continued recruitment collecting samples whenever possible to avoid close contact of health personnel with patients.

In Argentina, the team led by Dr Vaccaro at the Hospital Italiano de Buenos Aires adapted the Mutographs protocol in order to minimize the risks of contagion while safeguarding the original ethical and legal principles. As such, the enrolment stage of patient identification, initial interview, information about the protocol, signature of informed consent, lifestyle questionnaires and clinical information was conducted exclusively via telephone or video calls and documents were provided electronically. All patients were also tested for Covid-19 before surgery.

Despite Iran being badly hit by SARS-Cov2, teams in the Digestive Diseases Research Institute in Teheran, Iran, led by Professor Malekzadeh, continued their critical clinical work, also liaising with other Mutographs collaborators across the country.

Similarly, other participating institutions like the National Cancer Institute in Lithuania and Charles University in Prague, Czech Republic, slowly continued recruitment during the epidemic as for many patients critical surgery was necessary and already scheduled.

Other centers like Barretos Cancer hospital and Porto Alegre Hospital in Brazil as well as the International Organization for Cancer Prevention and Research (IOCPR) in Serbia had to stop recruitment for many weeks. Staff were sent back to work remotely and in some collaborators in the project were reassigned to work on Covid-19 specific projects or general clinical assistance.

The situation across all continents continues to be closely monitored thanks to regular feedback from committed collaborators, despite the crisis context. Together with the continuous work completed before the crisis and the re-direction towards data analysis, these efforts continue to drive research forward in hope for a better future for cancer patients and for all of us.

So we packed our bags, or computers rather, and went home to set up work stations in the best way possible. Perhaps not at the same time, but ultimately all of the Mutographs teams around the world ended up at home with computers and wifi connections. Halh Al-Serori Kings College London, UK:  “I usually don’t work from home, so at the beginning it was a bit challenging to pause lab work and cut off much of the casual social interactions which usually happen at work. But the biggest challenge was to learn to put work away at the end of the day, recharge, and start the next day with a fresh mind. It is a learning process and as science becomes more virtual through webinars, online meetings and workshops, the connection within the scientific community grows stronger even helping to navigate students to successful graduation.”

Mishu Islam, University of California San Diego, USA: “The first few days of lock-down were not easy. Gradually, I accommodated the new norm of life and now the days are quite normal for me. I made two workplaces at my home so that I do not feel bored.  Now my only complaint is I cannot see the faces of my dear labmates except for the zoom meetings.”

Sergey Senkin, IARC, France: “a polaroid photo of me in my lockdown setup from earlier this year. Since lockdown was relaxed I have been able to retrieve a monitor from work, so now it looks slightly more professional!”

Thus, we settled to do everything we could from home. It soon became evident that the amount of data to be analysed, curated and written into articles was rather overwhelmingly abundant.

Phoebe He, University of California San Diego, USA: “It’s hard to believe it’s been 3 months since I last saw everyone in the lab in person! Fortunately with the nature of our work being computational I still manage to meet everyone regularly through zoom meetings while keeping a busy working schedule and enjoying the convenience and comfort of working from home.”

Sarah Moody, Sanger, UK: “Moving to remote working has been a challenge, but luckily, we have rallied together as a team and adapted. We have been using video conferencing to stay in touch, on which my cat Cara makes frequent appearances either asleep in the background or invading my desk!  We continue to make good progress on the project, and are hoping to submit the first paper soon. We will update on our findings on the blog as well, so watch this space!”

Not just the research was affected, but our work to engage with the public and specially with patients, was drastically cut short to the dismay of our patient advocates. Mimi McCord, Heartburn Cancer, UK: “our planned visits within the Mutographs project are on hold as the restrictions to face to face interactions and support affect us all. None of us has a choice at the moment but we hope we will be able to resume our work as Patient Advocates later in the year.”

As soon as we got to grips with all these tasks and also the planning and preparation for an eventual re-start of lab work, some of us were confronted with the fact that we are not alone. All of a sudden we had the children at home, having to occupy them, home school them and guide them through their own coping with the impact of the lock down. Alas, we share our time as best we can to provide support and educate, which is a task of variable complexity, very dependent of the age and character of the children… they rule the world, our world for sure…

Jill Kucab, Kings College London, UK: “Much of our work requires us to be in the lab, studying cellular models. While being separated from the lab is frustrating, this is actually a great opportunity to think about our data, design new experiments or strategies and catch up on the scientific literature. Additionally, the lockdown coincided with the completion of Master’s student projects, so there have been thesis revisions to tend to. I have also had the added challenge/pleasure of home schooling my kids (2 and 5) since the end of March, when schools and nurseries shut. The experience of working from home while also managing a daily education/entertainment plan for small children has forced me to be extremely flexible and focused (even when the kids aren’t!).”

Burcak Otlu, University of California San Diego, USA: “Covid-19 has definitely changed our lives. After March 13 2020, we started working from home. We talked and shared our work on zoom meetings and emailed each other more than before. Finally, we managed to progress in research with this new remote working setting. Being at home made us do more house errands and home schooling kids was the other challenge we faced. Eventually, we got over it and our daughter graduated with a virtual ceremony from elementary school!!!”

It has been a time of reflection too, when we have had the time to look around ourselves and appreciate nature that little bit more closely.

Erik Bergstrom, University of California San Diego, USA: “Working from home with a lack of in-person interactions definitely took time to adjust to, but having a view of the Pacific Ocean throughout the workday is definitely not something to complain about.”

David Phillips, Kings College London, UK: “I am one of the lucky ones with a garden view; there is plenty of activity in it…”

Remarkably, in many ways we are closer and more in touch in this time of distancing than ever before. Laura Humphreys, Sanger, UK: “We are adapting and working more flexibly, with increased tolerance and appreciation of each other’s personal circumstances, which will only be positive for the project as well as for us as an international team and as individuals”. And so the science continues and lockdown reinforces what we already knew – that collaboration and sharing of data and ideas are essential.