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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.

Finding extracellular vesicle biomarkers for oesophageal cancer early detection

Extracellular vesicles (EVs) are entities secreted by cells that can be involved in cell-to-cell communication. They contain messenger proteins and other molecules, which act like ‘instructions’ to recipient cells.  EVs contain proteins both on their inside and outside.

All cells, including cancer cells, release EVs.  EVs from different cell types have slightly different compositions of proteins, which give them the ‘characteristics’ of their parent cell.

Members of the Goberdhan’s lab have previously shown that EVs released by colorectal cancer cells contain different protein when they are subjected to certain types of stress, such as certain nutrient deficiencies.  These ‘switched’ EVs change recipient cell behaviour, for example, increasing cancer cell growth. Researchers can potentially exploit these differences in EV protein composition to define distinct EV sub-populations: a helpful step towards their use as multi-protein biomarkers.

Dr Jennifer Allen and Ms Karen Billington from the Goberdhan lab are now applying this concept to the early detection of oesophageal cancer. Barrett’s Oesophagus is a pre-cancerous condition whereby oesophageal cells become damaged. Over time the damage can increase and cancer can develop.

Monitoring patients with Barrett’s Oesophagus is in place to try and identify when cancer has developed, however this is done through invasive and costly endoscopy, which may miss cancer in the very early stages. There is a need to identify when Barrett’s Oesophagus has progressed using less-invasive methods that can be used more regularly, so that cancer can be caught earlier.

Jen and Karen are investigating the potential of using EV proteins as biomarkers, which could be identified though simple blood tests. They are using different types of cells – such as normal oesophagus cells, Barrett’s Oesophagus cells and Oesophageal cancer cells – to compare the proteins found on the EVs released by each of these cell types.

The team is working with Dr Elizabeth Bird-Lieberman, a Gastroenterology Consultant at the JR Hospital, to collect blood samples from patients with Barrett’s Oesophagus, to see if EV information could be extracted and tested through simple blood tests – such as that being developed by Prof Jason Davis.

The aim is to identify a handful of proteins via proteomic analysis, that allows them to differentiate EVs from oesophageal cancer cells. If the protein biomarkers associated with the more cancerous cell lines can be detected in patient blood samples, Barrett’s Oesophagus patients could then be routinely tested for specific EV proteins that indicate the presence of parent cancer cells. This simple test could be carried out much more regularly than endoscopy surveillance and would enable earlier detection and treatment of oesophageal cancer in these patients.

Colorectal cancer cell extracellular vesicles. These two vesicles have become deflated and have the characteristic cup-shaped morphology caused by preparation for electron microscopy. Images generated by Dr John Mason (DPAG) and Dr Errin Johnson (EM Facility Manager, Dunn School).

About the study

The Goberdhan lab members are interested in intracellular signalling and cell communication. Their major focus is on how this goes wrong in cancer and other major human diseases. Specifically, they investigate:

  1. The role of amino acid sensing and stress-induced signalling in regulating cellular growth and intercellular communication involving exosomes.
  2. The regulation of exosome formation and heterogeneity by intracellular signalling pathways and membrane trafficking.
  3. The effect of exosome signalling on recipient cell behaviour and cancer progression, particularly in response to microenvironmental stresses applied to exosome-secreting cells.

 

This study is funded by the CRUK Early Detection Primer Award.

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.

 

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.

SCALOP team discover new pancreatic cancer biomarker

The discovery of pancreatic cancer biomarkers (naturally occurring molecules, genes or characteristics which can be used to confirm the presence or predict the outcome of a cancer) is vital in understanding patient outcomes and finding new therapeutic targets. In recent years, improved understanding of the biology of pancreatic cancers has resulted in new combination therapies being developed, including the development of the first successful biomarker-guided therapy in pancreatic cancer known as the POLO trial.

A recent paper from the SCALOP-1 trial team, led by Prof. Somnath Mukherjee, was published in BJC Nature, which has identified proteins that could act as a new biomarker to predict a patient’s outcome from pancreatic cancer. The chemokine protein known as CCL5, found circulating in patient blood, was found in low quantities in patients with better overall pancreatic cancer survival (around 18.5 months, rather than less than a year).

It is already known that CCL5 is involved in tumour invasion, tumour metastasis and the creation of an immune-system-suppressing micro-environment that allows pancreatic cancer to develop quickly. Its identification as a biomarker makes CCL5 a perfect new target for potential drug treatments. For example, blockade therapies that target the CCL5-CCR5 pathway and reduce the presence of CCL5, may produce new opportunities to improve the outcome of other immunotherapies that pancreatic cancer patients are undergoing.

Co-lead of this study, Prof Eric O’Neil from the Department of Oncology, is now investigating combination of CCL5 antagonist drugs with immunotherapy and radiotherapy drugs in animal models, which he hopes will lead to the development of new, more-effective pancreatic treatments in the future.

Next steps for the SCALOP trials

When pancreatic cancer has developed beyond a stage where it is operable, the only option for patients is often chemotherapy or chemoradiotherapy (the combination of chemo and radio therapy). The creation of new combination drugs used in the chemotherapy process has led to some improvement in overall length of patient survival of pancreatic cancer, which remains one of the highest causes of cancer death in the UK, however the use of these drugs is limited by the toxic effect on the body.

Following on from the SCALOP-1 trial, the SCALOP-2 trial, has been run from the University of Oxford, hosted through the Oncology Clinical Trials Office and lead by Prof Somnath Mukherjee. It has completed recruitment earlier in the year and final results are awaited.

Currently in the UK, chemoradiotherapy for locally advanced pancreatic cancer consists of 28 daily treatments of radiotherapy. Although this treatment is effective in controlling local symptoms and slowing down local cancer progression, in most cases it is unable to remove the cancer or shrink it well enough to make it operable. There is a need to find more efficient treatment combinations to improve patient outcomes.

The SCALOP-2 clinical trial compared different ways of combining chemotherapy and chemoradiotherapy to see which combination provides the most benefit to patients who have inoperable pancreatic tumours. This includes testing radiotherapy dose escalation and the use of nelfinavir as a radiosensitizer drug – something that makes tumour cells more sensitive to the effects of radiation therapy. In doing so, it is hoped that researchers can uncover more efficient drug combinations for patients with pancreatic tumours that are inoperable.

Blood and biopsy samples have been collected as a part of SCALOP-2 trial, in order to allow the team to take a more detailed look at proteins, DNA and cells involved in the cancer and how they are affected by treatment. This will tell researchers much more about how a patient’s type of cancer behaves and how it has responded to various treatments, allowing for the discovery of biomarkers just like CCL5 from the SCALOP-1 trial.

More information about the SCALOP-2 trial can be found on the Pancreatic Cancer UK website here.

The search for pancreatic cancer biomarkers

Pancreatic cancer has the lowest survival rate of any cancer in the UK, due in part to the limited ability to diagnose it at an early stage. Earlier detection of pancreatic cancer is a major priority of cancer researchers, in order to identify tumours at an earlier stage when they are more easily treatable.

Identifiable biomarkers (naturally occurring molecules which can be related to the presence of a cancer) is one method that can be used to predict or diagnose pancreatic cancer. Currently, the previously-identified biomarkers available have a limited ability to accurately diagnose pancreatic cancer. There is a need to identify new biomarkers that more accurately predict the presence of pancreatic cancer for improved earlier diagnosis.

Dr Christiana Kartsonaki, a senior scientist at the MRC Population Health Research Unit in the Nuffield Department of Population Health, is leading investigations on the potential of protein biomarkers in blood, using data from the China Kadoorie Biobank. Blood samples from over 500,000 Chinese adults have been collected as part of this data set, allowing researchers to identify circulating proteins in the blood and see which individuals went on to develop pancreatic cancer.

During 9 years of follow-up, 700 individuals from the ~500,000 went on to develop pancreatic cancer. From their blood samples, Dr Christiana Kartsonaki and her colleagues will be able to identify a number of protein biomarkers that are associated with a future risk of pancreatic cancer. This study builds on their previous work on the associations of metabolic and lifestyle factors with risk of pancreatic cancer.

Identification of biomarkers may prove very useful in the establishment of strategies to utilise these proteins in predicting the development of pancreatic cancer and help with its diagnosis.

Results from this research will likely be published next year. Once biomarkers are identified, this work may help researchers understand the role that individual proteins play in the development and progression of pancreatic cancer, and whether they may have therapeutic potential as drug targets in its treatment.

About the study

This study is funded by the Nuffield Department of Population Health, Pancreatic Cancer UK and the CRUK Oxford Centre. It was co-led by Associate Professor Michael Holmes, Professor Zhengming Chen, Dr Yuanjie Pang and Dr Christiana Kartsonaki.

Detecting pancreatic cancer through blood tests

Pancreatic ductal adenocarcinoma (PDAC) makes up 95% of all pancreatic cancer cases and has the lowest survival rate, and early diagnostic methods have yet to be developed. As a result, diagnosis often comes at a later stage when treatment options are limited and prognosis is poor.

Diagnosis at this stage often comes from imaging techniques followed by tissue biopsies, which are not appropriate options to use as standardised, early screening methods. New ways to diagnose PDAC at an earlier stage are needed, without the use of invasive procedures.

Liquid biopsies are becoming a more popular option to fill this demand. Taking a blood sample is minimally invasive, quick, and can tell us a lot of information about a person from their cfDNA (cell free DNA). cfDNA is released from cells and circulates in the blood, containing information about the cell they come from.

Methylation on cfDNA often appears in cancer patients, making it an effective biomarker that can be used to diagnose the presence of cancer with high accuracy and specificity about the cancer (such as location). The concept has many applications, including in the earlier diagnosis of PDAC.

The identification of these biomarkers in blood is often limited to the technology used, with DNA being damaged by the harsh chemicals that are used in the processing. The recent development of TAPS technology at the University of Oxford has helped to overcome this, using a bisulphate-free method, and making it a perfect method for PDAC biomarker identification.

DPhil students Paulina Siejka-Zielinska and Felix Jackson and Postdoctoral Researcher Jingfei Chang from Dr Chunxiao Song’s lab in collaboration with Dr Shivan Sivakumar (consultant medical oncologist) have been investigating TAPS as a method to identify PDAC biomarkers. Using blood samples from PDAC patients and healthy individuals, they are applying TAPS technology to prove that it can be used to accurately detect pancreatic cancer biomarkers in cfDNA.

Preliminary results from this study suggest that cfDNA methylation can be used for the identification of PDAC, as well as being able to accurately distinguish between pancreatic cancer and other pancreatic disorders that effect the DNA, such as pancreatitis.

If this is the case, then the results from this study will make for solid grounds for the application of TAPS in the earlier screening for pancreatic cancer.

About the Song Lab

The Song Lab combine various chemical biology and genome technologies to develop novel tools to analyse the epigenome. The lab apply these tools to two main research areas: the use of epigenetic modifications in circulating cell-free DNA from the blood for non-invasive disease diagnostics including early detection of cancer, and understanding the contribution of epigenetic heterogeneity in cancer development.

Most recently, the TAPS technology developed at the Song Lab has led to the creation of the start up Base Genomics, which has been launched to set a new gold standard in DNA methylation detection using this TAPS technology. Base Genomics will initially focus on developing a blood test for early-stage cancer and minimal residual disease. You can read more about it here.

Leveraging AI and image analysis technology to improve prognostication in colorectal cancer