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The next step in personalised cancer medicine

Researchers at the Botnar Research Centre, University of Oxford have developed technology that facilitates standalone long-read Oxford Nanopore sequencing of single cells. This breakthrough technology has the potential to open new avenues within genomics and enable future discoveries to understand the causes of many human diseases.

The work, in part supported by grants from the UKRI (Innovate UK, EPSRC and MRC), results from a collaboration with researchers from the Department of Chemistry at Oxford University, ATDBio, a world leader in complex oligonucleotide chemistry, and pharmaceutical company BristolMyersSquibbs. The study has been published in this week’s issue of Nature Biotechnology.

“The application of accurate long-read single-cell sequencing will have a transformative effect on the wider single-cell sequencing community, as longer and full-length transcriptomic sequencing allows users to capture more information about the transcriptional and functional state of a cell,” says Assistant Professor Adam Cribbs, senior author of the paper and Group Leader in Systems Biology and Next Generation Sequencing Analysis at the Botnar Research Centre. “This means that we move closer to being able to better understand and diagnose diseases such as cancer”.

Single-cell genomics, the ability to examine all information contained in an individual cell, is a rapidly evolving field and is dominated by droplet-based short-read single-cell sequencing applications. In this approach, cells are encapsulated with barcoded RNA-capture microbeads into droplets within an oil emulsion. Each droplet becomes a discrete reaction vessel, associating a different barcode with each cell’s RNA and a unique molecular identifier (UMI) with each RNA transcript.  Once barcoded, RNA from all cells can be pooled and processed conventionally for next generation sequencing.  During sequencing, both the original RNA sequence and the associated barcode and UMI are determined. Key to measuring abundance of each RNA and correctly associating them with their cell of origin is accurate assignment of the UMIs and barcodes.

Long-read sequencing approaches, such as those of Oxford Nanopore Technologies, are currently revolutionising bulk sequencing approaches. “Long-read single-cell technology has the potential to interrogate not only RNA abundance, but also splice variants, structural variation and chimeric transcripts at the single-cell level. Collectively, the ability to determine these features accurately will improve diagnostics and biological understanding. However, Nanopore sequencing can be inaccurate, which hinders the critical steps of barcode and UMI assignment, making its application to single-cell sequencing challenging,” explains Dr Martin Philpott, first author of the paper and Director of the Next-Generation sequencing facility at the Botnar Research Centre.

To overcome these challenges, the team has developed a new approach called single-cell corrected long-read sequencing (scCOLOR-seq) that identifies and corrects errors in the barcode and UMI sequences, permitting standalone cDNA Nanopore sequencing of single cells. “Each mRNA molecule is tagged with a short sequence which identifies it within a certain droplet,” adds Dr Cribbs. “However, Nanopore long-read sequencing is too error prone to reliably sequence these tags, making it difficult to map the mRNA back to its specific cell. What we’ve been able to do is to develop a practical method for building redundancy into the tag, allowing inaccuracies within the sequencing to be pinpointed, and then correct them. The mRNA can then be linked back to an individual cell.”

The research was developed in collaboration with ATDBio, an Oxford/Southampton based company, created by Professor Tom Brown Sr at the Chemistry Department, University of Oxford. Dr Tom Brown Jnr, Chief Scientific Officer of ATDBio, says, “The new scCOLOR-seq method is the first of many innovations resulting from our collaboration with the Botnar Research Centre team. The collaboration has been one of our most interesting and successful, and we are pleased to see our work recognised in Nature Biotechnology. It’s a great example of how we at ATDBio can apply our expert knowledge of nucleic acid chemistry and complex oligonucleotide synthesis to difficult problems in biology and beyond, together with our corporate and academic partners”.

“This study demonstrates an incredible cross-disciplinary team effort to advance single-cell technologies and is the result of strategic investments into these technologies at our department,” adds Professor Udo Oppermann, Director of Laboratory Sciences at the Botnar Research Centre and co-senior author of the paper. “We will continue our collaborative efforts to develop innovative single-cell approaches and – as demonstrated in the paper- apply this to molecular analyses in primary and secondary bone and other haematological cancers. Our intention is to advance these technologies in personalised medicine approaches such as cancer diagnosis allowing rational clinical decision making.”

Two clinical academic research partnerships awarded to Oxford researchers

Dr Karthik Ramasamy and Dr John Jacob are both Oxford clinical researchers that have been awarded a Clinical Academic Research Partnership (CARP) by the MRC. Both have been awarded upwards of £200,000 to fund projects investigating myeloma early detection & brain cancer modelling, respectively. Find out more about the projects being funded with this award below.

Dr Karthik Ramasamy

Earlier diagnosis of the bone marrow cancer myeloma is a high priority for patients since it can both improve survival and allow for better control of symptoms. Every case of myeloma is preceded by a condition called Monoclonal Gammopathy of Undetermined Significance (MGUS) and individuals with MGUS are regularly monitored so that progression to myeloma can be caught early.

While this approach is benefitting some patients, there are two main issues that still need to be overcome to improve earlier myeloma diagnosis:

  1. MGUS is largely symptomless and often undiagnosed, meaning that 80-90% of myeloma patients are diagnosed without first receiving an MGUS diagnosis that would have prompted monitoring for myeloma.
  2. Only 1% of patients with MGUS progress to myeloma every year and the risk of progression is not well defined, placing a large resource burden for monitoring on healthcare providers and creating anxiety for patients.

In this MRC CARP award, Dr Karthik Ramasamy will address both of these challenges. Firstly, working with Professor Kassim Javaid, Professor Daniel Prieto-Alhambra, Dr Constantinos Koshiaris and data from primary care health records, Dr Ramasamy will identify specific clinical signs/symptom clusters associated with MGUS to enable a greater proportion of individuals with MGUS to be diagnosed and monitored. Secondly, additionally collaborating with Dr Ross Sadler, Professor Chris Schofield and Professor James McCullagh, Dr Ramasamy will seek to identify routinely recorded clinical characteristics and additional protein biomarkers that improve prediction of progression from MGUS to myeloma in a cohort of patients undergoing monitoring at Oxford University Hospitals NHS Trust. This latter work is bolstered by a recently awarded CRUK Oxford Centre Development Fund award, which will enable the research team additionally to pilot protein glycosylation analysis in blood samples collected as part of a current study investigating serological markers in plasma cell dyscrasias (BLOOM).

Dr Karthik Ramasamy is Lead Clinician for myeloma and other plasma dyscrasias in Thames Valley Strategic Clinical Network and Divisional Lead of Cancer Research across Thames Valley and South Midlands Research Network.

Learn more about myeloma early detection research in Oxford.

Dr John Jacob

Brain cells that originate in the cerebellum give rise to the most common childhood brain tumour, known as medulloblastoma, which can also affect adults. Although it can be cured, it is often a devastating disease, with common treatment options resulting in an increased risk of adverse side effects such as strokes and seizures.

Like most cancers, the development of new treatment options that improve survival rate and reduce side effects is reliant on researchers establishing models that reflect the human tumours, in order to test the efficacy of new therapeutics before these are tested in patients. Existing models for medulloblastoma have shortcomings making the discovery of new treatment options slow. This is due to:

  1. Growing medulloblastoma cells outside of a patient is hard, due to the change in environmental factors. Growing cells outside the body usually does not accurately reflect the microenvironment that cells are derived from, and so the cells will behave differently and unlike a real tumour. As a result, only a few cell lines from medulloblastoma patients have been successfully grown ex vivo.
  2. Models can be costly, and these include mouse-based models, which pose limitations due to the difference in species
  3. Medullobastoma tumours are genetically different between patients – there is no ‘one size fits all’ model and there is a need to develop more treatment options that target specific genetic subtypes in order to improve survival.

In this CARP award, Dr John Jacob (Nuffield Department of Clinical Neurosciences) aims to investigate a specific genetic subtype of medulloblastoma (known as sonic hedgehog medulloblastoma) – and test if the presence of the tumour microenvironment, which consists of non-cancerous cerebellar tissue, is necessary to better simulate the typical tumour growth conditions.

Working alongside Associate Professor Esther Becker (Nuffield Department of Clinical Neurosciences) and Dr Benjamin Schuster-Boeckler (Big Data Institute & Oxford Ludwig Cancer Institute), the team hope to recreate the in vivo tumour microenvironment more accurately compared to existing models. The Becker group previously established a methodology to grow human cerebellar neurons from human induced pluripotent stem cells (hiPSC). By using hiPSCs to form miniature cerebellar structures, termed cerebellar organoids, the tumour microenvironment can be recreated in a dish.

The team hope to overcome the existing modelling difficulties by growing medulloblastoma cells on these organoids. Dr Jacob, aided by the computational biology expertise of Dr Schuster-Boeckler will then investigate the growth of individual tumour cells, in a more physiological context. The resulting outcomes could mean the development of a new model to test patient-specific therapies on, in order to assess their toxicities and efficacy more accurately.

Dr John Jacob is a consultant neurologist who is interested in better understanding the genetic complexity of cancer and what it means for personalised treatment. Through this award and collaboration, Dr Jacob hopes to improve the success of therapy development and ultimately improve the repertoire of therapies of this cancer.

The Medical Research Council Clinical Academic Research Partnership scheme allows NHS consultants with a PhD or MD to participate in collaborative high-quality research partnerships with established leading biomedical researchers.

 

Eoghan Mullholland awarded colorectal cancer fellowship

As part of UK Pride month, we are spotlighting the work of cancer researcher and University LGBTQ+ Representative Dr Eoghan Mulholland

Artificial intelligence tool for streamlining pathology workflow

Nearly 50,000 cases of prostate cancer are diagnosed each year in the UK. During the diagnostic process, men with suspected prostate cancer undergo a biopsy, which is analysed by pathology services. There are over 60,000 prostate biopsies performed in the UK annually, which represents a high workload for pathology teams. With increasing demand and a shortage of pathologists, tools that could help streamline this workflow would provide significant pathologist time savings and accelerate diagnoses.

To confidently diagnose prostate cancer, pathologists need to identify a number of tissue architecture and cellular cues. All biopsies are stained with Hematoxylin & Eosin (H&E), which allows the pathologist to study the size and shape (morphology) of the cells and tissue. However, in 25-50% cases, H&E staining alone does not provide sufficient evidence for a diagnosis, requiring the additional process of immunohistochemistry (IHC) to study other cellular features.

One bottleneck in the current pathology workflow is the requirement for a pathologist to review the H&E-stained biopsies to determine which require IHC. To address this need, pathologists Dr Richard Colling, Dr Lisa Browning and Professor Clare Verrill (Nuffield Department of Surgical Sciences and Oxford University Hospitals NHS Foundation Trust) teamed up with biomedical image analysts Andrea Chatrian, Professor Jens Rittscher and colleagues (Institute of Biomedical Engineering, Big Data Institute and Ludwig Oxford) to take a multidisciplinary approach.

In their paper in the journal Modern Pathology, the team used prostate biopsies annotated by pathologists at Oxford University Hospitals to train an artificial intelligence (AI) tool to detect tissue regions with ambiguous morphology and decide which cases needed IHC. The tool agreed with the pathologist’s review in 81% of cases on average. By enabling automated request of IHC based on the AI tool results, the pathologist would only need to review the case once all necessary staining had been carried out. This workflow improvement is estimated to save on average 11 minutes of pathologist time for each case, which scales up to 165 pathologist hours for 1000 prostate biopsies needing IHC.

“The NHS spends £27 million on locum and private services to make up for the shortfall in pathology service provision. By using this AI tool to triage prostate biopsies for IHC, pathologists would spend less time reviewing these cases, which would not only lead to financial savings but it would also accelerate prostate cancer diagnoses to inform patients and treating clinicians earlier.” – Professor Clare Verrill, Nuffield Department of Surgical Sciences and Oxford University Hospitals NHS Foundation Trust.

The tool will now be developed and validated further using pathology data from different locations to account for variation in IHC requests between pathologist teams and centres. This future work will continue to take advantage of the PathLAKE Centre of Excellence for digital pathology and artificial intelligence, of which Oxford is a member.

This work was supported by PathLAKE via the Industrial Strategy Challenge Fund, managed and delivered by Innovate UK on behalf of UK Research and Innovation (UKRI), the NIHR Oxford Biomedical Centre, the Engineering and Physical Sciences Research Council (EPSRC), the Medical Research Council (MRC) and the Wellcome Trust.

New study investigates how growth factors in our gut could initiate cancer

The cells that make up our tissues are strictly organised, and various differentiated cell types do different jobs in specific locations. The cell composition of tissues and the way the cells are organised is often different in pre-cancerous conditions, or even severely disrupted when they progress to tumours.

Understanding the molecular signals that cause cell differentiation and prompt the cells to find their location within the tissue, may explain the morphological changes observed in patients with pre-cancerous conditions. Ultimately, the alteration of these signals might be a driving force in tumour development and progression.

A recent paper from the Boccellato Lab at the Ludwig Institute for Cancer Research, University of Oxford, has investigated how the epithelial cell lining of our gastrointestinal tract differentiates based on different growth factors, and how this could ultimately determine how a patient progresses to precancerous conditions that could lead to stomach cancer.

Image: A picture from the published paper showing how normal gastric pits can change shape and functionality if EGF levels are altered, and eventually lead to the pre-cancerous condition Atrophic Gastritis

The team exposed healthy human gut tissue (the mucosoid cultures, patented) to a variety of growth factors, including EGF, BMP and NOGGIN. What they found is that different combinations of these factors help to determine which cells differentiate to form the gastric glands. These glands line the stomach, and contain a variety of different cells that produce digestive enzymes and gastric acid to help to digest our food, or mucus to protect the stomach lining.

For example, exposure to growth factors including EGF and BMP formed the foveolar cells that produce the mucus to line our gut, whereas inhibition of EGF induces the differentiation of cells producing gastric acid and digestive enzymes.

Patient with the pre-cancerous condition called Atrophic Gastritis have a problem with digestion due to the lack of digestive enzymes and gastric acid producing cells. In the biopsies of this pre-cancerous condition, the team have found elevated levels of EGF, which correlated with the lack of those gastric acid producing cells and with a flattened shape of the stomach tissue.

What this study has shown is that specific localisation of growth factors in the tissue microenvironment may be responsible for the differentiation process. So changing the relative quantities or localisation of these growth factors could trigger a change in the epithelium structure and cellular composition over time, potentially leading to cancer.

Building a high-resolution, dynamic map of the growth factors during cancer progression is the next step in this research. The team will also be investigating causes for these growth factor level changes. For example, long-term infection with  Helicobacter pylori bacteria is associated with increased risk of gastric cancer. Investigating how infection alters the growth factor microenvironment is essential to understand the response of the tissue and its potential aberration leading to cancer.

Dr Francesco Boccellato says:

“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.

“This study has allowed us to draw up a new, detailed map of the signalling microenvironment in the healthy human gastric glands, which we can now draw upon in future studies as we investigate how growth factors influence cancer occurrence.”

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.

DeLIVER clinical research study underway as recruitment opens

DeLIVER is a five-year Cancer Research UK-funded research programme led by Professor Ellie Barnes (Nuffield Department of Medicine) that aims to detect liver cancer earlier. Liver cancer is the fastest rising cause of cancer death in the UK, with more than 5,000 deaths per year. To improve survival, it is crucial to diagnose liver cancer earlier, when current treatments are more likely to be successful. However, this is challenging because symptoms are vague and late-presenting, and are frequently masked by co-occurring liver disease, such as cirrhosis.

A major goal of the DeLIVER programme is to learn more about the biology of liver cancer development and to use this information to design more sensitive detection tests. Because many people being tested for liver cancer have the high-risk condition cirrhosis, these tests need to be specific enough to detect liver cancer on top of other changes in the liver caused by cirrhosis. In order to identify the defining characteristics of early liver cancer, researchers need to perform a detailed molecular analysis of tissue from tumours and the background liver in people with liver cancer and cirrhosis and compare this to liver tissue from people with cirrhosis alone.

The DELPHI (Deep Liver Phenotyping and Immunology) study will recruit 100 participants at Oxford University Hospitals NHS Trust. 80 of these recruited participants will have cirrhosis (caused by hepatitis virus B or C, fatty liver disease or alcohol) and 20-30 participants will have liver cancer in addition to cirrhosis. After giving consent, the participants will undergo fine-needle aspiration to collect tissue from the liver. This is a safe technique established in Oxford as one of only a few centres in the UK. Blood samples will also be taken.

Cancer Research UK Clinical Research Fellow Dr Rory Peters is leading the study. He said,

“We are very pleased to have started the recruitment for the DELPHI study. The in-depth analysis of samples from the DELPHI participants will be critical for increasing our understanding of how liver cancer develops and will give insights into how this cancer can be detected earlier.”

The researchers will look at individual cells to understand the cellular make-up of the tumour and surrounding tissue, including infiltrating immune cells, and how this may influence cancer development. By comparing the tissue from participants with and without cancer, they will also look for changes in protein or metabolite levels and alterations in the levels of chemical modification of DNA by methylation using the TAPS assay developed in Oxford by Dr Chunxiao Song. They will investigate whether the changes that they observe from the tissue analysis can also be detected in the blood, which would provide evidence that a blood-based assay could be developed as a less invasive diagnostic test.

Professor Ellie Barnes, Chief Investigator for DeLIVER said,

“The DELPHI study is one of three clinical projects within the DeLIVER programme. Together, these studies will inform us which of our diagnostic technologies perform best at detecting liver cancer at the earliest stages. We hope this work will lead to a step-change in earlier liver cancer diagnosis and improved patient survival.”

 

Read more about the DeLIVER programme in the OxCODE liver cancer early detection research showcase.

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.

New form of gift wrap drives male reproductive success

The transfer of complex mixtures of signals and nutrients between individuals is a key step in several biologically important events in our lives, such as breastfeeding and sexual intercourse. However, we know relatively little about the ways in which the molecular gifts involved are packaged to ensure their successful delivery to the recipient.

By studying such events during mating in the fruit fly, researchers at the University of Oxford have identified a new communication mechanism in which nutrients and signals are combined in fatty droplets that stably store their bioactive cargos in males, until they are transferred to females when they dissipate within minutes. These specialised multi-molecular assemblies called microcarriers, are made by the prostate-like accessory gland of the male and contain a central fatty (lipid) core wrapped with multiple proteins, including a molecule called Sex Peptide. When Sex Peptide is released in the mated female, it stimulates her to produce more progeny and reprogrammes her brain so she rejects other male suitors.

Although Sex Peptide is only produced by a limited group of fruit fly species, lipids and lipid droplets are secreted by many glands, including the human prostate and breast. Preliminary work in flies suggests that one of the genes that is essential for the release of microcarriers from secreting cells also plays a critical role in human glands, including the breast. In fact, this regulatory gene is highly expressed in some breast cancers. This suggests that the mechanisms controlling microcarrier formation may be evolutionarily conserved and that microcarriers may play much broader roles in physiological and pathological cell-cell communication, which have yet to be recognised.

This new cell communication mechanism could have implications for breast cancer and understanding its pathology because the regulatory gene essential for driving reproductive success is also expressed in some breast cancers, so if we can better understand the gene’s mechanism, it might be possible to understand how breast cancer can become pathological.

Please see the full article on the Department of Physiology, Anatomy & Genetics website.

The study was a collaboration between the groups of Professor Clive Wilson and Associate Professor Deborah Goberdhan from the Department of Physiology, Anatomy and Genetics, at The University of Oxford. This work has been supported by funding from the Biotechnology and Biological Sciences Research Council (BBSRC), Cancer Research UK, the Wellcome Trust and the Medical Research Council

Paper to be published in PNAS:

Drosophila Sex Peptide Controls the Assembly of Lipid Microcarriers in Seminal Fluid