̽��ֱ�� of Cambridge - NHS Blood and Transplant (NHSBT)

‘Programmable molecular scissors’ could help fight COVID-19 infection

cjb250 — Wed, 16 Nov 2022 10:00:18 +0000

Enzymes are naturally occurring biological catalysts, which enable the chemical transformations required for our bodies to function – from translating the genetic code into proteins, right through to digesting food. Although most enzymes are proteins, some of these crucial reactions are catalysed by RNA, a chemical cousin of DNA, which can fold into enzymes known as ribozymes. Some classes of ribozyme are able to target specific sequences in other RNA molecules and cut them precisely.

In 2014, Dr Alex Taylor and colleagues discovered that artificial genetic material known as XNA – in other words, synthetic chemical alternatives to RNA and DNA not found in nature – could be used to create the world’s first fully-artificial enzymes, which Taylor named XNAzymes.

At the beginning, XNAzymes were inefficient, requiring unrealistic laboratory conditions to function. Earlier this year, however, his lab reported a new generation of XNAzymes, engineered to be much more stable and efficient under conditions inside cells. These artificial enzymes can cut long, complex RNA molecules and are so precise that if the target sequence differs by just a single nucleotide (the basic structural unit of RNA), they will recognise not to cut it. This means they can be programmed to attack mutated RNAs involved in cancer or other diseases, leaving normal RNA molecules well alone.

Now, in research published today in Nature Communications, Taylor and his team at the Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), ̽��ֱ�� of Cambridge, report how they have used this technology to successfully ‘kill’ live SARS-CoV-2 virus.

Taylor, a Sir Henry Dale Fellow and Affiliated Researcher at St John’s College, Cambridge, said: “Put simply, XNAzymes are molecular scissors which recognise a particular sequence in the RNA, then chop it up. As soon as scientists published the RNA sequence of SARS-CoV-2, we started scanning through looking for sequences for our XNAzymes to attack.”

While these artificial enzymes can be programmed to recognise specific RNA sequences, the catalytic core of the XNAzyme – the machinery that operates the ‘scissors’ – does not change. This means that creating new XNAzymes can be done in far less time than it normally takes to develop antiviral drugs.

As Taylor explained: “It’s like having a pair of scissors where the overall design remains the same, but you can change the blades or handles depending on the material you want to cut. ̽��ֱ��power of this approach is that, even working by myself in the lab at the start of the pandemic, I was able to generate and screen a handful of these XNAzymes in a matter of days.”

Taylor then teamed up with Dr Nicholas Matheson to show that his XNAzymes were active against live SARS-CoV-2 virus, taking advantage of CITIID’s state-of-the-art Containment Level 3 Laboratory – the largest academic facility for studying high risk biological agents like SARS-CoV-2 in the country.

“It's really encouraging that for the first time – and this has been a big goal of the field – we actually have them working as enzymes inside cells, and inhibiting replication of live virus,” said Dr Pehuén Pereyra Gerber, who performed the experiments on SARS-CoV-2 in Matheson’s lab.

“What we’ve shown is proof of principle, and it’s still early days,” added Matheson, “It’s worth remembering, however, that the amazingly successful Pfizer and Moderna COVID-19 vaccines are themselves based on synthetic RNA molecules – so it’s a really exciting and rapidly developing field, with enormous potential.”

Taylor checked the target viral sequences against databases of human RNAs to ensure they were not present in our own RNA. Because the XNAzymes are highly specific, this should in theory prevent some of the ‘off-target’ side-effects that similar, less accurate molecular therapeutics may cause, such as liver toxicity.

SARS-CoV-2 has the ability to evolve and change its genetic code, leading to new variants against which vaccines are less effective. To get around this problem, Taylor not only targeted regions of the viral RNA that mutate less frequently, but he also designed three of the XNAzymes to self-assemble into a ‘nanostructure’ that cuts different parts of the virus genome.

“We’re targeting multiple sequences, so for the virus to evade the therapy it would have to mutate at several sites at once,” he said. “In principle, you could combine lots of these XNAzymes together into a cocktail. But even if a new variant does appear that is capable of getting round this, because we already have the catalytic core, we can rapidly make new enzymes to keep ahead of it.”

XNAzymes could potentially be administered as drugs to protect people exposed to COVID-19, to prevent the virus taking hold, or to treat patients with infection, helping rid the body of the virus. This sort of approach might be particularly important for patients who, because of a weakened immune system, struggle to clear the virus on their own.

̽��ֱ��next step for Taylor and his team is to make XNAzymes that are even more specific and robust – “bulletproof,” he says – allowing them to remain in the body for longer, and work as even more effective catalysts, in smaller doses.

̽��ֱ��research was funded by the Wellcome Trust, the Royal Society, the Medical Research Council, NHS Blood and Transplant, and Addenbrooke’s Charitable Trust.

Reference
Pereyra Gerber, P, Donde, MJ, Matheson, NJ and Taylor, AI. XNAzymes targeting the SARS-CoV-2 genome inhibit viral infection. Nature Communications (2022). DOI: 10.1038/s41467-022-34339-w

Cambridge scientists have used synthetic biology to create artificial enzymes programmed to target the genetic code of SARS-CoV-2 and destroy the virus, an approach that could be used to develop a new generation of antiviral drugs.

XNAzymes are molecular scissors which recognise a particular sequence in the RNA, then chop it up

Alex Taylor

Jordan Siemens (Getty Images)

A 3d animation of the COVID-19 Virus or Coronavirus being broken apart

̽��ֱ��text in this work is licensed under a Creative Commons Attribution 4.0 International License. Images, including our videos, are Copyright © ̽��ֱ�� of Cambridge and licensors/contributors as identified. All rights reserved. We make our image and video content available in a number of ways – as here, on our main website under its Terms and conditions, and on a range of channels including social media that permit your use and sharing of our content under their respective Terms.

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First ever clinical trial of lab-grown red blood cell transfusion

cjb250 — Mon, 07 Nov 2022 00:05:46 +0000

̽��ֱ��manufactured blood cells were grown from stem cells from donors. ̽��ֱ��red cells were then transfused into volunteers in the RESTORE randomised controlled clinical trial.

This is the first time in the world that red blood cells that have been grown in a laboratory have been given to another person as part of a trial into blood transfusion.

If proved safe and effective, manufactured blood cells could in time revolutionise treatments for people with blood disorders such as sickle cell and rare blood types. It can be difficult to find enough well-matched donated blood for some people with these disorders.

Chief Investigator Professor Cedric Ghevaert, Professor in Transfusion Medicine and Consultant Haematologist at the ̽��ֱ�� of Cambridge and NHS Blood and Transplant, said: “We hope our lab grown red blood cells will last longer than those that come from blood donors. If our trial, the first such in the world, is successful, it will mean that patients who currently require regular long-term blood transfusions will need fewer transfusions in future, helping transform their care.”

̽��ֱ��RESTORE trial is a joint research initiative by NHS Blood and Transplant and the ̽��ֱ�� of Bristol, working with the ̽��ֱ�� of Cambridge, Guy’s and St Thomas’ NHS Foundation Trust, NIHR Cambridge Clinical Research Facility, and Cambridge ̽��ֱ�� Hospitals NHS Foundation Trust. It is part-funded by a National Institute for Health and Care Research (NIHR) grant.

Professor Ashley Toye, Professor of Cell Biology at the ̽��ֱ�� of Bristol and Director of the NIHR Blood and Transplant Unit in red cell products, said: “This challenging and exciting trial is a huge stepping stone for manufacturing blood from stem cells. This is the first-time lab grown blood from an allogeneic donor has been transfused and we are excited to see how well the cells perform at the end of the clinical trial.”

̽��ֱ��trial is studying the lifespan of the lab grown cells compared with infusions of standard red blood cells from the same donor. ̽��ֱ��lab-grown blood cells are all fresh, so the trial team expect them to perform better than a similar transfusion of standard donated red cells, which contains cells of varying ages.

Additionally, if manufactured cells last longer in the body, patients who regularly need blood may not need transfusions as often. That would reduce iron overload from frequent blood transfusions, which can lead to serious complications.

̽��ֱ��trial is the first step towards making lab grown red blood cells available as a future clinical product. For the foreseeable future, manufactured cells could only be used for a very small number of patients with very complex transfusions needs. NHSBT continues to rely on the generosity of donors.

Co-Chief Investigator Dr Rebecca Cardigan, Head of Component Development NHS Blood and Transplant and Affiliated Lecturer at the ̽��ֱ�� of Cambridge, said: “It’s really fantastic that we are now able to grow enough red cells to medical grade to allow this trial to commence. We are really looking forward to seeing the results and whether they perform better than standard red cells.”

Two people have so far been transfused with the lab grown red cells. They were closely monitored and no untoward side effects were reported. They are well and healthy. ̽��ֱ��identities of participants infused so far are not currently being released, to help keep the trial ‘blinded’.

̽��ֱ��amount of lab grown cells being infused varies but is around 5-10mls - about one to two teaspoons.

Donors were recruited from NHSBT’s blood donor base. They donated blood to the trial and stem cells were separated out from their blood. These stem cells were then grown to produce red blood cells in a laboratory at NHS Blood and Transplant’s Advanced Therapies Unit in Bristol. ̽��ֱ��recipients of the blood were recruited from healthy members of the NIHR BioResource.

A minimum of 10 participants will receive two mini transfusions at least four months apart, one of standard donated red cells and one of lab grown red cells, to find out if the young red blood cells made in the laboratory last longer than cells made in the body.

Further trials are needed before clinical use, but this research marks a significant step in using lab grown red blood cells to improve treatment for patients with rare blood types or people with complex transfusion needs.

John James OBE, Chief Executive of the Sickle Cell Society, said: “This research offers real hope for those difficult to transfuse sickle cell patients who have developed antibodies against most donor blood types. However, we should remember that the NHS still needs 250 blood donations every day to treat people with sickle cell and the figure is rising. ̽��ֱ��need for normal blood donations to provide the vast majority of blood transfusions will remain. We strongly encourage people with African and Caribbean heritage to keep registering as blood donors and start giving blood regularly.”

Dr Farrukh Shah, Medical Director of Transfusion for NHS Blood and Transplant, said: “Patients who need regular or intermittent blood transfusions may result develop antibodies against minor blood groups which makes it harder to find donor blood which can be transfused without the risk of a potentially life-threatening reaction. This world leading research lays the groundwork for the manufacture of red blood cells that can safely be used to transfuse people with disorders like sickle cell. ̽��ֱ��need for normal blood donations to provide the vast majority of blood will remain. But the potential for this work to benefit hard to transfuse patients is very significant.”

Adapted from a press release from NHS Blood and Transplant

Cambridge researchers are taking part in the world’s first clinical trial of red blood cells that have been grown in a laboratory for transfusion into another person.

If our trial is successful, it will mean that patients who currently require regular long-term blood transfusions will need fewer transfusions in future, helping transform their care

Cedric Ghevaert

First ever clinical trial of lab-grown red blood cell transfusion

NHS Blood and Transplant

Cell culture flasks in the incubator during manufacture of red blood cells

Yes

Remdesivir likely to be highly effective antiviral against SARS-CoV-2 for some patients

cjb250 — Mon, 14 Dec 2020 10:00:18 +0000

̽��ֱ��response to the COVID-19 pandemic has been hampered by the lack of effective antiviral drugs against SARS-CoV-2, the coronavirus that causes the disease. Scientists had pinned hope on the drug remdesivir, originally developed to treat hepatitis C and subsequently tested against Ebola. However, results from large clinical trials have been inconclusive, and in early October the World Health Organization (WHO) announced that the drug did not significantly reduce mortality rates. ̽��ֱ��question is more complicated, however, and a clinical team have now used a different approach to determine the effects of the drug on COVID-19 in a closely monitored patient.

Dr James Thaventhiran from the MRC Toxicology Unit at the ̽��ֱ�� of Cambridge said: “There have been different studies supporting or questioning remdesivir’s effectiveness, but some of those conducted during the first wave of infection may not be optimal for assessing its antiviral properties.

“Mortality is due to a combination of factors, likely including unchecked viral replication and, importantly, the response of the immune system. A clinical trial that looks only at remdesivir’s impact on mortality will have difficulty distinguishing between these two factors. This limits our ability to ask the simple question: how good is remdesivir as an antiviral?”

To answer this question, a team led by scientists at the ̽��ֱ�� of Cambridge and Barts Health NHS Trust examined the case of a 31 year old man with XLA, a rare genetic condition that affects the body's ability to produce antibodies and hence fight infection.

̽��ֱ��patient’s illness began with fever, cough, nausea and vomiting, and on day 19 he tested positive for SARS-CoV-2. His symptoms persisted and on day 30 he was admitted to hospital, where he was given supplemental oxygen due to breathing difficulties.

Unusually, his fever and inflammation of the lungs persisted for longer than 30 days, but without causing severe breathing problems or spreading to other organs. ̽��ֱ��researchers say this may have been due to his inability to produce antibodies – although antibodies fight infection, they can also cause damage to the body and even lead to severe disease.

At first, the patient was treated with hydroxychloroquine and azithromycin, which had little effect, and the treatments were stopped on day 34. ̽��ֱ��patient then commenced a ten-day course of remdesivir. Within 36 hours, his fever and shortness of breath had improved and his nausea and vomiting ceased. Rising oxygen saturation allowed him to be taken off supplemental oxygen.

This dramatic clinical response was accompanied by a progressive decrease in levels of C-reactive protein (CRP), a substance produced by the liver in response to inflammation. At the same time, doctors saw an increase in the number of his immune cells known as lymphocytes, and chest scans showed that his lung inflammation was clearing. ̽��ֱ��patient was discharged on day 43.

A week after discharge, the patient’s fever, shortness of breath and nausea returned. He was readmitted to hospital on day 54 and given supplemental oxygen. He again tested positive for SARS-CoV-2, was found to have lung inflammation, and his CRP levels had increased and his lymphocyte count fallen.

On day 61, the patient began treatment with a further ten-day course of remdesivir. Once again, his symptoms improved rapidly, his fever dropped and he was taken off supplemental oxygen. His CRP and lymphocyte count normalised. Following additional treatment with convalescent plasma on days 69 and 70, he was discharged three days later and is no longer symptomatic.

̽��ֱ��team found that the patient’s virus levels fell progressively during his first course of remdesivir, corresponding with the improvement in his symptoms. His virus levels increased again, as did his symptoms, when the first course of the treatment ceased, but the effect of the second course of remdesivir was even more rapid and complete. By day 64, he was no longer testing positive for the coronavirus.

̽��ֱ��patient’s inability to clear his infection without antiviral medication is very likely to be due to his lack of antibodies, say the researchers. However, there are other immune cells that contribute to fighting infection, including those known as CD8+ T cells. ̽��ֱ��team observed that the patient was able to produce CD8+ T cells that responded to the ‘spike protein’ on the surface of the virus – spike proteins give the virus its characteristic crown profile (hence the name coronavirus). While insufficient to clear the infection spontaneously, this likely contributed to the clearance of virus during the second course of remdesivir.

Dr Nicholas Matheson from the Cambridge Institute of Therapeutic Immunology and Infectious Disease (CITIID) at the ̽��ֱ�� of Cambridge added: “Our patient’s unusual condition gave us a rare insight into the effectiveness of remdesivir as a treatment for coronavirus infection. ̽��ֱ��dramatic response to the drug – on repeated challenge – suggests that it can be a highly effective treatment, at least for some patients.”

̽��ֱ��team further suspect that remdesivir is likely to be most beneficial when administered early in infection, before the virus is able to trigger a potentially catastrophic immune response. They say that the course of their patient’s disease also underscores the important – but often conflicting – roles that antibodies play in protecting us from infection.

“ ̽��ֱ��fact that our patient was unable to fight off the disease without treatment suggests that antibodies contribute to the control of SARS-CoV-2,” explained Dr Matthew Buckland from the Department of Clinical Immunology, Barts Health, London. “But this lack of antibodies may also have prevented his COVID-19 from becoming life-threatening, because he had no antibodies to trigger a damaging immune response.

“All of this suggests that treatments will need to be tailored for individual patients, depending on their underlying condition – for example, whether it is the virus that is causing the symptoms, or the immune response. ̽��ֱ��extended viral monitoring in our study was clinically necessary because in April 2020 we didn’t know if this drug would be effective. Adopting this approach more widely could further clarify how best to use remdesivir for clinical benefit.”

̽��ֱ��research was supported by the Medical Research Council, the NIHR Bioresource, NHS Blood and Transplant, Wellcome and the European Union’s Horizon 2020 programme.

Reference
Buckland, MS et al. Successful treatment of COVID-19 with remdesivir in the absence of humoral immunity, a case report. Nat Comms; 14 Dec 2020; DOI: 10.1038/s41467-020-19761-2

̽��ֱ��drug remdesivir is likely to be a highly effective antiviral against SARS-CoV-2, according to a new study by a team of UK scientists. Writing in Nature Communications, the researchers describe giving the drug to a patient with COVID-19 and a rare immune disorder, and observing a dramatic improvement in his symptoms and the disappearance of the virus.

Our patient’s unusual condition gave us a rare insight into the effectiveness of remdesivir as a treatment for coronavirus infection

Nicholas Matheson

NIH Image Gallery

Creative rendition of SARS-COV-2 virus particles

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Scientists create ‘genetic atlas’ of proteins in human blood

cjb250 — Wed, 06 Jun 2018 17:00:44 +0000

̽��ֱ��study, published today in the journal Nature, characterised the genetic underpinnings of the human plasma ‘proteome’, identifying nearly 2,000 genetic associations with almost 1,500 proteins. Previously, there was only a small fraction of this knowledge, mainly because researchers could measure only a few blood proteins simultaneously in a robust manner.

̽��ֱ��researchers used a new technology (“SOMAscan”) developed by a company, SomaLogic, to measure 3,600 proteins in the blood of 3,300 people. They then analysed the DNA of these individuals to see which regions of their genomes were associated with protein levels, yielding a four-fold increase on previous knowledge.

“Compared to genes, proteins have been relatively understudied in human blood, even though they are the ‘effectors’ of human biology, are disrupted in many diseases, and are the targets of most medicines,” says Dr Adam Butterworth from the Department of Public Health and Primary Care at the ̽��ֱ�� of Cambridge, a senior author of the study. “Novel technologies are now allowing us to start addressing this gap in our knowledge.”

One of the uses for this genetic map is to identify particular biological pathways that cause disease, exemplified in the paper by pinpointing specific pathways that lead to Crohn’s disease and eczema.

“Thanks to the genomics revolution over the past decade, we’ve been good at finding statistical associations between the genome and disease, but the difficulty has been then identifying the disease-causing genes and pathways,” says Dr James Peters, one of the study’s principal authors. “Now, by combining our database with what we know about associations between genetic variants and disease, we are able to say a lot more about the biology of disease.”

In some cases, the researchers identified multiple genetic variants influencing levels of a protein. By combining these variants into a ‘score’ for that protein, they were able to identify new associations between proteins and disease. For example, MMP12, a protein previously associated with lung disease was found to be also related to heart disease – however, whereas higher levels of MMP12 are associated with lower risk of lung disease, the opposite is true in heart disease and stroke; this could be important as drugs developed to target this protein for treating lung disease patients could inadvertently increase the risk of heart disease.

MSD scientists were instrumental in highlighting how the proteomic genetic data could be used for drug discovery. For example, in addition to highlighting potential side-effects, findings of the study can further aid drug development through novel insights on protein targets of new and existing drugs. By linking drugs, proteins, genetic variation and diseases, the team has suggested existing drugs that could potentially also be used to treat a different disease, and increased confidence that certain drugs currently in development might be successful in clinical trials.

̽��ֱ��researchers are making all of their results openly available for the global community to use.

“Our database is really just a starting point,” says first author Benjamin Sun, also from the Department of Public Health and Primary Care. “We’ve given some examples in this study of how it might be used, but now it’s over to the research community to begin using it and finding new applications.”

Caroline Fox MD, Vice President and Head of Genetics and Pharmacogenomics at MSD, adds: “We are so pleased to participate in this collaboration, as it is a great example of how a public private partnership can be leveraged for research use in the broader scientific community.”

̽��ֱ��research was funded by MSD*, National Institute for Health Research, NHS Blood and Transplant, British Heart Foundation, Medical Research Council, UK Research and Innovation, and SomaLogic.

Professor Metin Avkiran, Associate Medical Director at the British Heart Foundation, said: “Although our DNA provides our individual blueprint, it is the variations in the structure, function and amount of the proteins encoded by our genes which determine our susceptibility to disease and our response to medicines. This study provides exciting new insight into how proteins in the blood are controlled by our genetic make-up and opens up opportunities for developing new treatments for heart and circulatory disease.”

* MSD (trademark of Merck & Co., Inc., Kenilworth, NJ USA)

Reference
Sun, BB et al. Genomic atlas of the human plasma proteome. Nature; 7 June 2018; DOI: 10.1038/s41586-018-0175-2

An international team of researchers led by scientists at the ̽��ֱ�� of Cambridge and MSD has created the first detailed genetic map of human proteins, the key building blocks of biology. These discoveries promise to enhance our understanding of a wide range of diseases and aid development of new drugs.

Compared to genes, proteins have been relatively understudied in human blood, even though they are the ‘effectors’ of human biology, are disrupted in many diseases, and are the targets of most medicines

Adam Butterworth

qimono

Red blood cells

Researcher Profile: Benjamin Sun

“My work involves analysing big 'omic' data,” says Benjamin Sun, a clinical medical student on the MB-PhD programme at Cambridge. By this, he means data from genomic and proteomic studies, for example – terabytes of ‘big data’ that require the use of supercomputer clusters to analyse.

“My aim is to understand how variation in the human genome affects protein levels in blood, which I hope will allow us to better understand processes behind diseases and help inform drug targeting.”

Benjamin did pre-clinical training at Cambridge before intercalating – taking time out of his medical training to study a PhD, funded by an MRC-Sackler Scholarship, at the Department of Public Health and Primary Care.

“Having completed my PhD, I am currently spending the final two years of my programme at the Clinical School to complete my medical degree. My aim is to become an academic clinician like many of the inspiring figures here at the Cambridge. Balancing clinical work with research can sometimes be tough but definitely highly rewarding.”

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