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New clinical prediction tools for myeloma

Myeloma is a cancer of the bone marrow that caused 117,077 deaths worldwide in 2020 (International Agency for Research on Cancer). Earlier diagnosis improves the rate of survival but unfortunately, delays in myeloma diagnosis are common and result in poorer patient outcomes.

One of the reasons for the diagnostic delay is that myeloma symptoms are non-specific and relatively common in people without cancer. For example, back pain is associated with myeloma yet there are many other non-myeloma causes of this symptom. Additional measures are therefore needed to highlight the possibility of myeloma in patients where GPs do not originally suspect this disease.

GPs frequently order simple laboratory tests, such as the full blood count, to investigate patients presenting with non-specific symptoms. Previous work by Dr Constantinos Koshiaris, Dr Jason Oke, Dr Brian Nicholson and colleagues from Oxford’s Nuffield Department of Primary Care Health Sciences and the University of Exeter identified certain abnormalities in blood test results that indicate a higher risk of myeloma, such as low haemoglobin which can be observed up to 2 years before a myeloma diagnosis.

In this paper published recently in the British Journal of General Practice, the Oxford researchers have developed new clinical prediction models for myeloma that incorporate both symptoms and blood test results. Using the Clinical Practice Research Datalink (GOLD version), a primary care database containing electronic health records for more than 11 million patients in the UK, the team identified the most common symptoms and full blood count results recorded for patients with myeloma. The most predictive of these were included in the models they developed and the new tools were validated against a set of test data. Decisions made using their prediction models resulted in fewer false positives and more true positives when compared to single tests or symptoms alone.

By identifying patients at highest risk of myeloma in primary care, these new prediction rules have the potential to reduce diagnostic delays by a substantial amount. Further research is now needed to understand more about the feasibility and implementation of this tool in the primary care setting and the impact it will have on the diagnostic pathway and patient outcomes.

Early Detection Award for research into the clinical application of single cell genomics

Myelodysplastic syndromes (MDS) are a group of blood cancers in which the bone marrow fails to make normal levels of blood cells. MDS can be broadly classified into two major groups: high-risk MDS, in which patients progress to acute myeloid leukaemia with a very poor survival rate; and low-risk MDS, in which the disease is less aggressive but patients still suffer from a huge burden of symptoms, often the result of anaemia.

There are a number of exciting new targeted treatment options for low-risk MDS. However, these do not work in all patients and, particularly given the high economic cost of newer treatments, current biomarkers are not sufficiently predictive of treatment response. There is a need to more precisely categorise MDS to predict the disease trajectory and the response to therapy so that the most effective treatment can be given to each patient.

Large investments in sequencing technology in clinical laboratory services are enabling precision medicine in certain cancers and revolutionising patient care. Dr Onima Chowdhury, MRC Clinical Academic Research Fellow and Consultant Haematologist (MRC Weatherall Institute of Molecular Medicine and Oxford University Hospitals) is working with Professor Adam Mead, Dr Supat Thongjuea and Dr Lynn Quek at the MRC WIMM to explore the use of single-cell genomics in the clinical diagnosis and management of MDS. Funded by a Cancer Research UK Early Detection and Diagnosis Primer Award, the team will seek to develop a simple, clinically applicable processing and analysis pipeline, as well as identifying biomarkers that correlate and can perhaps supersede current diagnostic modalities.

Long-term, the team hope that this approach will be able to improve outcomes of patients through improved diagnosis, risk prediction and targeted treatment in MDS and other haematological malignancies.

New funding for early diagnosis research using platelets

It is known that the earlier a cancer is detected, the more likely a cancer patient is to have better outcomes. One of the challenges for achieving early detection is to develop a minimally invasive test to detect the signs of early cancer in the body.

Because blood tests are simple to carry out in the clinic, a lot of effort has been focused on detecting molecules released from cancer cells in blood samples – so-called ‘liquid biopsies’. However, the majority of techniques that are used currently have a low sensitivity for early-stage cancers, due to low levels of cancer cell-derived molecules being present in blood plasma.

Dr Bethan Psaila, Cancer Research UK (CRUK) Advanced Clinician Scientist, Group Leader at the Medical Research Council Weatherall Institute of Molecular Medicine (MRC WIMM) and principal investigator at the Radcliffe Department of Medicine at Oxford University, is pioneering an approach that might be able to enrich for cancer-derived molecules in the blood. Working with Professor Chris Gregory (University of Edinburgh), Professor Paul Rees (University of Swansea) and Dr Henkjan Gersen (University of Bristol), Beth is leading a multi-disciplinary team that brings together cancer cell biologists, and imaging and engineering expertise to explore the use of platelets for early cancer diagnosis.

Platelets perfuse tumours and take up cancer cell-derived biomolecules. Isolating platelets from the blood and analysing their contents will hopefully be a more sensitive method for detecting cancer-specific molecules in the blood.

In this newly funded project, the team will use state-of-the-art pre-clinical models as well as samples from patients with colorectal cancer, pancreatic cancer and oesophageal cancer as exemplar cancers to assess the utility of ‘tumour-educated’ platelets (TEPs) for early cancer diagnosis. They will use detailed imaging and biomechanical techniques to assess whether TEPs can be reliably distinguished from platelets in healthy people or those with non-malignant disorders.

This multi-institutional project is funded by a Cancer Research UK Early Detection and Diagnosis Project Award and builds on a successful CRUK Innovation Award the team received after a workshop on liquid biopsy technologies in 2018. The ~£650,000 award will run for four years and will support two DPhil studentships, a postdoctoral research scientist and a research assistant.

Drinking alcohol regularly increases cancer risk in Chinese populations

A new study demonstrates that reducing alcohol consumption in China could be an important cancer prevention strategy. Full story on the NDPH website.

For Western populations, there is a well-established association between regular alcohol consumption and a greater risk of various types of cancer. However, it was unknown whether these increased risks were the same for Eastern populations, which have very different drinking patterns and alcohol tolerance. Cancer rates are rising rapidly in China, and this may be partly due to more frequent alcohol consumption as citizens become more affluent. A new study led by NDPH on the large China Kadoorie Biobank has investigated this, with the findings published today in the International Journal of Cancer.

The study assessed over half a million adults recruited across ten diverse regions in China between 2004 and 2008. Each participant was questioned about their drinking habits, then followed up for a median period of 10 years. By the end of the study, almost 27,000 individuals had developed cancer (13,342 men, 13,619 women).

About a third of the men in the study drank regularly (at least once every week). Compared with those who abstained from alcohol, regular drinkers had a 26% higher risk for cancers previously associated with alcohol (ie, mouth/throat, oesophagus, colon-rectum and liver) and a 7% higher risk for all types of cancer. The risks were greater in those who drank daily or drank outside of meals.

For most of the cancers investigated, there was a clear dose-response relationship. Each 280 g/week higher alcohol intake was associated with an increased risk of 98% for oesophageal cancer; 74% for mouth/throat cancer; 52% for liver cancer and 19% for colon-rectum cancer. The study also found that each 280 g/week higher alcohol intake increased the risk of lung cancer (25%) and gallbladder cancer (60%), even though these cancers had not previously been clearly linked with alcohol.

In East Asia, many people cannot metabolise alcohol effectively due to an inherited deficiency in the enzyme aldehyde dehydrogenase 2. This causes the carcinogenic compound acetaldehyde to accumulate, which can lead to facial flushing. In this study, those who experienced flushing after drinking had stronger associations between alcohol intake and cancer risk, particularly for oesophageal and lung cancer. This suggests that the risk of developing cancer is greater for those with low alcohol tolerability.

The associations remained strong when the researchers controlled for potential confounding variables including age, region, education, income, body mass index, physical activity, and fresh fruit intake. The association between alcohol and lung cancer was similar for regular smokers and those who had never smoked regularly. Nevertheless, large-scale genetic studies are needed to determine if the associations between alcohol and cancer are likely to be causal.

Very few women in the study drank alcohol regularly, hence the study was unable to assess whether the association between alcohol and cancer risk was the same for women.

Lead author Dr Pek Kei Im said: ‘Our study has clearly shown that among Chinese men, alcohol consumption is associated with increased risks of several types of cancer, including some that were less clearly established to be alcohol-related previously. This suggests that lowering population levels of alcohol consumption is an important strategy for cancer prevention in China.’

Detecting for multiple cancers in one simple test

Biomarkers – or biological markers – are used in many areas of health and disease as measures of a biological or clinical state. In the context of cancer, identifying biomarkers of early stage cancer is crucial for being able to detect disease earlier and improving the outcomes of patients with cancer. However, biomarkers alone are not sufficient for earlier detection. We also need to develop cost-effective, non-invasive, simple-to-use technologies that can be used in the clinic to detect these biomarkers with high sensitivity, specificity and accuracy.

Professor Jason Davis in the Department of Chemistry at the University of Oxford is working on just that. Professor Davis’ research has focused on developing portable, handheld diagnostic tests that use a range of electroanalytical methods for biomarker detection. This includes recent work on using novel electrochemical impedance-based sensing technology to detect C-reactive protein, a marker of inflammation in the body.

These methods are advantageous for use in diagnostics since they generate results in a few minutes and are more sensitive than other commonly used techniques such as ELISA (enzyme-linked immunosorbent assay). They also do not require the sample to be processed before testing, meaning that a single drop of blood can be analysed directly, without needing further reagents or equipment. Multiple different biomarkers can be analysed simultaneously, potentially allowing multi-cancer blood tests in the future.

To further develop this technology into a clinically implementable assay, five years ago, Osler Diagnostics was spun out of Professor Davis’ lab. The ultimate aim is that this assay could be applied in GP surgeries to test for disease in asymptomatic individuals.

Professor Davis is currently looking at clinical applications within cardiac, cancer and neurological diseases and welcomes interest from researchers who would like to contribute their biomarker ideas and clinical problems.

About the researchers

The Davis Group runs an interdisciplinary research programme within the Department of Chemistry that develops and applies methods for the fabrication of advanced functional interfaces, and are actively engaged in the development of molecular detection, diagnostic, theranostic, and imaging methodologies.

Understanding how cancer arises from infected tissue

Whilst rates in the UK are relatively low, stomach cancer is still the third highest cause of cancer mortalities worldwide. The largest risk factor for stomach cancer is a chronic infection of the H. pylori bacteria. The contributions of other factors like diets high in salt, smoked foods, smoking and obesity are also important.

H. pylori can be found in the gut, and some strains cause gastritis & stomach ulcers. Long term colonisation can result in persistent cellular and tissue damage. Over time, the damaged gut lining can lose its structure and eventually become so undefined that the patient develops atrophic gastritis – a precancerous condition that could eventually lead to cancer.

A to F shows the increasing change of structure to existing gastric epithelium, as a result of prolonged H. pylori infections. (A) The normal gastric epithelium is organised in invaginations called glands. (B) A remarkable increase in size is observed in the inflamed stomach after H.pylori infection, a condition called chronic gastritis. (C) Atrophic gastritis, a precancerous condition with a higher chance of leading to cancer: the glandular structure is lost. (D) The emergence of a new type of gland with different features: a condition known as intestinal metaplasia to cancer. (E-F) The progression from dysplasia to cancer. Credit: Correa & Piazuelo, 2013

 

Understanding how persistent infection can result in increased risk of cancer is the focus of Dr Francesco Boccellato, Ludwig Institute, and his lab. Improving the knowledge of underlying mechanisms in early cancer biology may help us to understand how cancers originate in various parts of the body, and thus giving doctors more insight to detect cancer earlier in patients with precancerous conditions.

Francesco’s most recent project is investigating the role of growth factors in the determination of gut epithelial cells. The cellular lining of the gut, known as the epithelium, is where most stomach cancers originate. The epithelium is made up of a variety of different types of cells, responsible for different things such as mucus secretion, production of gastric acid and digestive enzymes.

Cross section of the stomach lining showing a gastric gland with different cell types that make up the epithelium. What causes stem cells to differentiate into these different cells is the focus of the Boccellato lab. Credit: Boccellato lab

The team are investigating what it is that activates stem cells to differentiate into different epithelial cells, in the hope of identifying new ways that the cells can become cancerous.

It is Francesco’s hypothesis that the specific localisation of growth factors in the tissue microenvironment may be responsible for the differentiation process. If this is the case, then it may be that a change in the relative quantities or localisation of these growth factors triggers a change in the epithelium structure and cellular composition over time.

The team are investigating this through in vitro models known as mucosoid cultures – growing human epithelial cells outside of the body and exposing them to different conditions to see how the cells regenerate and differentiate. Mucosoids are an innovative stem cell based cultivation system developed by the Boccellato lab, which enables an exceptional long term regeneration and maintenance of epithelial cells. The cells form a polarised monolayer producing mucus on the top side similar to the epithelium in a patient.

Top: example of a mucosoid with cells (the plasma membrane is labelled in green) producing protective mucins (MUC5AC) labelled in red (the yellow is where the two labels overlap creating the mucus layer). Bottom: example of a mucosoid with cells (the plasma membrane is labelled in red and the nuclei in blue) showing one cells producing Pepsinogen (in green) the precursor of pepsin, the main digestive enzyme. Source: Boccellato et al., GUT 2019

The results of Francesco’s investigation into the role of growth factors in determining gut cell differentiation and progression into atrophic gastritis are expected in Spring 2021. It is hoped that by better understanding the role of growth factors underlying the epithelial structures in pre-cancerous conditions, we can detect when cancers may appear and thus treat them earlier. Further studies will elucidate the role of bacterial infections (like H.pylori) in this process of re-shaping the tissue.

The H. pylori-cancer relationship is a great model for understanding other infection-based cancers. Colon cancer, gallbladder cancer, cervical cancer, stomach cancer and lymphoma are all examples of cancers that can be caused by bacterial infection. By better understanding how gut tissues work and progress to pre-cancerous conditions, we can apply this to other cancer models to see if the same is true.

A final line of investigation by the team will be into how H. pylori bacteria access gut cells to cause damage. The epithelium is usually protected by a mucus barrier, on which our natural and harmless microflora grow. Healthy gut bacteria cannot perforate this mucus barrier to reach epithelial cells, but H. pylori appears to be able to. Francesco is investigating what makes this possible, so that we may be able to develop drugs that prevent H. pylori infections from reaching the epithelium and causing damage.

About the Boccellato lab

The Boccellato lab is investigating oncogenic pathogens and how they contribute to cancer. Patients infected with those pathogens have a higher chance of developing cancer, but the malignancy arises many years after the initial infection event. Cancer may develop as a result of a long battle between the pathogen that persists, hides and damages the tissue, and the host that attacks the pathogen and continuously repairs the damage caused by the infection.

The team use innovative tissue culture systems of human primary cells to re-build the infection niche in vitro and to understand the long term effect of infection on epithelial cells.  

References

Boccellato F.  GUT. 2019 Mar;68(3):400-413. doi: 10.1136/gutjnl-2017-314540. Epub 2018 Feb 21.

Sepe LP, Hartl., mBio. 2020 Sep 22;11(5):e01911-20.doi: 10.1128/mBio.01911-20.

Boccellato F, Meyer F. Cell Host Microbe. 2015 Jun 10;17(6):728-30.doi: 10.1016/j.chom.2015.05.016.

Piazuelo MB, Correa P. Gastric cáncer: Overview. Colomb Med (Cali). 2013;44(3):192-201. Published 2013 Sep 30.

 

Detecting myeloma earlier

Several research projects are underway in Oxford focusing on different points in the clinical care pathway to improve myeloma early detection.

Following the cancer metabolomic breadcrumb trail

By analysing the metabolic molecules that tumour cells leave behind, Dr James Larkin is investigating the applications of metabolomics in the early detection of many cancers.

New sequencing methods for distinguishing DNA modifications

Chemical modifications made to the DNA base cytosine play an important role in the regulation of gene expression across the genome. Cytosine can be chemically modified in four ways, with 5-methylcytosine (5mC) being the most common. Demethylation of 5mC by the TET family of enzymes results in the stable intermediates 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC) and 5-carboxycytosine (5caC). From what has been discovered so far, these modifications appear to have distinct functions. For example, 5mC is associated with repressed regions of the genome whereas 5hmC is present in active ones. However, to study these modifications further, robust sequencing methods are needed that can detect each of these four modifications specifically.

The traditional gold standard method for detecting DNA methylation is bisulphite sequencing. However, this relies on a harsh chemical treatment that degrades most of the DNA sample and is an indirect detection method, which decreases sequencing quality. Recently, a bisulphite-free method called TAPS has been developed by Ludwig Oxford’s Song lab, which has the advantage of preserving more of the DNA, increasing sensitivity, and directly detecting modified cytosines for improved DNA sequencing quality.

Despite its advantages, TAPS cannot distinguish between the different types of cytosine modifications. Other methods already exist that can do so but these use subtraction, for example, measuring 5mC and subtracting this signal from a combined measure of 5mC and 5hmC to obtain 5hmC levels. In addition to the disadvantages of using bisulphite and/or indirect detection strategies, these subtraction methods also need higher sequencing depths and generate very noisy data that can be difficult to interpret. New subtraction-free methods are therefore needed to specifically, directly and sensitively detect these four cytosine modifications in the genome.

In this paper published in Nature Communications, Dr Yibin Liu from Dr Chunxiao Song’s lab (Ludwig Oxford) and Dr Zhiyuan Hu from Professor Ahmed Ahmed’s lab (Weatherall Institute of Molecular Medicine and Nuffield Department of Women’s and Reproductive Health, University of Oxford) have developed a suite of TAPS-related whole genome sequencing methods for specifically detecting 5mC, 5hmC, 5fC and 5caC. They have named these TAPSβ (for 5mC), chemical-assisted pyridine borane sequencing (CAPS; for 5hmC), pyridine borane sequencing (PS; for 5caC and 5fC) and pyridine borane sequencing for 5caC (PS-c; for 5caC).

With these new methods, the research community is now armed to tackle more of the questions about the distinct and important functions of cytosine modifications in the genome and how their distribution is altered in diseases such as in cancer.

Bowel cancer patients going undiagnosed due to COVID distruption

A new study led by the University of Oxford has found that since the first coronavirus lockdown the number of people diagnosed with bowel cancer in England has fallen sharply, with a deficit persisting up to October 2020.

Between April and October 2020, over 3,500 fewer patients than expected were diagnosed with bowel cancer in England. Since bowel cancer is more likely to be curable if it is detected at an early stage, these results suggest that many patients, whose diagnosis has yet to be made, may die unnecessarily. The results are published today in The Lancet Gastroenterology & Hepatology.

The research was carried out by a team of clinicians and academic researchers from across the UK, including from the University of Leeds and the University of Newcastle.

For this study, the researchers assessed the patterns of referral for bowel cancer investigation, diagnosis and treatment within the English NHS from 1 January 2019 to 31 October 2020.

The results showed that, compared with an average month in 2019, during April 2020 at the peak of the first wave of coronavirus:

  • the monthly number of referrals by GPs to hospital clinics for investigation of possible bowel cancer reduced by 63% (from 36,274 to 13,440);
  • the number of colonoscopies performed fell by 92% (from 46,441 to 3,484); and
  • the monthly number of people with confirmed bowel cancer referred for treatment fell by 22% (from 2,781 to 2,158), and the number of operations performed fell by 31% from (2,003 to 1,378).

This is the first study to assess the impact of the COVID-19 pandemic on the diagnosis and management of bowel cancer across England.

Full story available on the Nuffield Department of Population Health website.