Cambridge Institute for Medical Research

Cambridge, United Kingdom

Cambridge Institute for Medical Research

Cambridge, United Kingdom
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Calero-Nieto F.J.,University of Leeds | Calero-Nieto F.J.,Cambridge Institute for Medical Research | Bert A.G.,Center for Cancer Biology | Cockerill P.N.,University of Leeds
Epigenetics and Chromatin | Year: 2010

Background. Silencing of transgenes in mice is a common phenomenon typically associated with short multi-copy transgenes. We have investigated the regulation of the highly inducible human granulocyte-macrophage colony-stimulating-factor gene (Csf2) in transgenic mice. Results. In the absence of any previous history of transcriptional activation, this transgene was expressed in T lineage cells at the correct inducible level in all lines of mice tested. In contrast, the transgene was silenced in a specific subset of lines in T cells that had encountered a previous episode of activation. Transgene silencing appeared to be both transcription-dependent and mediated by epigenetic mechanisms. Silencing was accompanied by loss of DNase I hypersensitive sites and inability to recruit RNA polymerase II upon stimulation. This pattern of silencing was reflected by increased methylation and decreased acetylation of histone H3 K9 in the transgene. We found that silenced lines were specifically associated with a single pair of tail-to-tail inverted repeated copies of the transgene embedded within a multi-copy array. Conclusions. Our study suggests that epigenetic transgene silencing can result from convergent transcription of inverted repeats which can lead to silencing of an entire multi-copy transgene array. This mechanism may account for a significant proportion of the reported cases of transgene inactivation in mice. © 2010 Calero-Nieto et al; licensee BioMed Central Ltd.


News Article | November 17, 2016
Site: www.eurekalert.org

A team of Cambridge researchers led by scientists at the Babraham Institute have discovered the hidden connections in our genomes that contribute to common diseases. Using a pioneering technique developed at the Babraham Institute, the results are beginning to make biological sense of the mountains of genetic data linking very small changes in our DNA sequence to our risk of disease. Discovering these missing links will inform the design of new drugs and future treatments for a range of diseases, including rheumatoid arthritis and other types of autoimmune disease. Comparing the genome sequences of hundreds of thousands of patients and healthy volunteers has revealed single-letter changes found more frequently in the DNA sequences of individuals with specific diseases. In most cases, the disease-linked changes occur in the large swaths of DNA located between genes, often referred to as junk DNA. The fact that the changes are not in or near genes has made it challenging to understand how they could cause disease. Now, as reported in the leading journal Cell, the Promoter Capture Hi-C technique is being used to fill in the missing pieces by charting interactions between genes and sequences far away on the DNA thread. The Promoter Capture Hi-C technique works by identifying parts of the genome that physically contact and regulate genes. The long thread of DNA is highly folded inside cells, allowing regions very far apart on the thread to contact each other directly. Dr Peter Fraser, Head of the BBSRC-funded Nuclear Dynamics research programme at the Babraham Institute which coordinated the study and a senior author on the paper, explained: "By identifying which parts of the genome connect with which genes we have discovered hundreds of thousands of regions that are necessary to switch genes on and off. Small changes to the DNA sequence of these distal regulatory regions can interfere with the normal control of genes, leading to a greater chance of developing a specific disease. The power of this approach is that it allows us to make biological sense of very tiny changes in the genome that have big impacts on health." By mapping the regions of the genome that interact with genes in 17 different blood cell types the researchers were able to create an "atlas" of contacts between genes and the remote regions that regulate them in each cell type. They then matched this information to known changes in DNA at these regions that are linked to specific diseases. This allowed them to uncover which genes are affected by these DNA changes, pointing to their roles in disease. The different blood cell types were obtained from blood samples donated by healthy volunteers of the NIHR Cambridge BioResource or by culture of blood stem cells in the laboratory of Dr Mattia Frontini, leader of the blood cell epigenome team at the University of Cambridge's Department of Haematology. Professor John Todd, Director of the JDRF/Wellcome Trust Diabetes and Inflammation Laboratory and founder and former principal investigator of the Cambridge BioResource said: "These results are a giant leap in understanding the inherited and cellular origins of common diseases and in how the human genome works." The team found thousands of new genes linked to specific diseases, including autoimmune diseases such as rheumatoid arthritis, type 1 diabetes and Crohn's disease that are currently incurable and notoriously difficult to treat or prevent. This knowledge could enable new drugs to be designed targeting those genes, or repurposing of already existing drugs to treat these conditions. Dr Mikhail Spivakov, group leader in the Nuclear Dynamics research programme at the Babraham Institute and a senior author on the paper, said: "Mapping the genome's regulatory interactions establishes the missing link between a genetic change at one part of the genome with the gene it ultimately affects. While the results currently look promising, it will take many more years of work and rigorous testing before new treatments become available as a result of this fundamental research". As a large multi-partner study, this research was collaboratively undertaken by the Babraham Institute, the JDRF/Wellcome Trust Diabetes and Inflammation Laboratory in the Cambridge Institute for Medical Research and the Departments of Medicine and Haematology at the University of Cambridge, the EMBL-European Bioinformatics Institute, the NHS Blood and Transplant organisation and the MRC Biostatistics Unit. The research was funded by a grant from the Medical Research Council whereas the researchers and organisations involved are supported by several funders including the UK's Biotechnology and Biological Sciences Research Council, the British Heart Foundation, the Juvenile Diabetes Research Foundation (JDRF) and the Wellcome Trust in addition to funding from the European Commission (multiple sources).


News Article | October 31, 2016
Site: www.sciencedaily.com

For the nearly 400,000 individuals around the world with hemophilia A and hemophilia B -- rare blood disorders that impair a person's ability to form clots to stop bleeding -- relief may someday come from a treatment with similarities to another blood disorder, known as factor V Leiden. In a study published online today in Blood, the Journal of the American Society of Hematology (ASH), researchers report that they have developed a new therapy that gives the clotting process more time to produce thrombin, an enzyme needed for clotting. They suggest this treatment could someday help all patients with hemophilia, including those who develop antibodies against standard therapy. Hemophilia is caused by a deficiency in certain clotting factors, factor VIII for hemophila A and factor IX for hemophilia B. Standard treatment for hemophilia is administration of the missing factor. However, this requires every-other-day intravenous injections, is under-effective, and in some cases results in the development of antibodies that reject the factor, so researchers tried a new approach based on observations relating to a common mutation associated with excessive clotting, factor V Leiden. "We know that patients who have severe hemophilia and also have mutations that increase clotting, such as factor V Leiden, experience less-severe bleeding," said study co-author Trevor Baglin, MD, of Cambridge University's Addenbrooke's Hospital. Dr. Baglin and colleagues pursued a novel strategy to reduce the activity of an enzyme -- activated protein C (APC) -- that promotes bleeding. In patients with factor V Leiden, defects in the anticoagulant APC mechanism lead to an overactive production of thrombin, an enzyme that is needed to form a clot. The team, led by Professor James A. Huntington, PhD, exploited this insight by developing a direct inhibitor of APC. Researchers modified serine protease inhibitors, known as serpins, to make them specific and efficient inhibitors of APC. "We hypothesized that if we targeted the protein C pathway we could prolong thrombin production," said Dr. Huntington, of the Cambridge Institute for Medical Research at the University of Cambridge. "We engineered a serpin so that it could selectively prevent APC from shutting down thrombin production before the formation of a stable clot." To test their theory, the team administered the serpin to mice with hemophilia B and clipped their tails. In this model, the blood loss decreased as the dose increased, with the highest dose reducing bleeding to the level of the healthy mice. Further injury models underscored that the serpin helped the majority of the mice form stable clots, with higher doses resulting in quicker clot formation. The serpin was also able to accelerate clot formation when added to blood samples from hemophilia A patients. "It is our understanding that because we are targeting a general anti-clotting process, our serpin could effectively treat patients with either hemophilia A or B, including those who develop inhibitors to more traditional therapy," stated Dr. Huntington. He went on to add, "Additionally, we have focused on engineering the serpin to be both subcutaneously delivered and long-acting. This will free patients from the cumbersome thrice-weekly infusions that are necessary under many contemporary therapy regimens." Explaining the roadmap for this therapy's further development, Dr. Baglin noted, "Within three years, we hope to be conducting our first-in-man trials of a subcutaneously-administered form of our serpin. It is important to remember that the majority of people in the world with hemophilia have no access to therapy. A stable, subcutaneous, long-acting, effective hemostatic agent could bring treatment to a great deal many more hemophilia sufferers."


News Article | October 27, 2016
Site: www.eurekalert.org

(WASHINGTON, October 27, 2016) -- For the nearly 400,000 individuals around the world with hemophilia A and hemophilia B -- rare blood disorders that impair a person's ability to form clots to stop bleeding -- relief may someday come from a treatment with similarities to another blood disorder, known as factor V Leiden. In a study published online today in Blood, the Journal of the American Society of Hematology (ASH), researchers report that they have developed a new therapy that gives the clotting process more time to produce thrombin, an enzyme needed for clotting. They suggest this treatment could someday help all patients with hemophilia, including those who develop antibodies against standard therapy. Hemophilia is caused by a deficiency in certain clotting factors, factor VIII for hemophila A and factor IX for hemophilia B. Standard treatment for hemophilia is administration of the missing factor. However, this requires every-other-day intravenous injections, is under-effective, and in some cases results in the development of antibodies that reject the factor, so researchers tried a new approach based on observations relating to a common mutation associated with excessive clotting, factor V Leiden. "We know that patients who have severe hemophilia and also have mutations that increase clotting, such as factor V Leiden, experience less-severe bleeding," said study co-author Trevor Baglin, MD, of Cambridge University's Addenbrooke's Hospital. Dr. Baglin and colleagues pursued a novel strategy to reduce the activity of an enzyme -- activated protein C (APC) -- that promotes bleeding. In patients with factor V Leiden, defects in the anticoagulant APC mechanism lead to an overactive production of thrombin, an enzyme that is needed to form a clot. The team, led by Professor James A. Huntington, PhD, exploited this insight by developing a direct inhibitor of APC. Researchers modified serine protease inhibitors, known as serpins, to make them specific and efficient inhibitors of APC. "We hypothesized that if we targeted the protein C pathway we could prolong thrombin production," said Dr. Huntington, of the Cambridge Institute for Medical Research at the University of Cambridge. "We engineered a serpin so that it could selectively prevent APC from shutting down thrombin production before the formation of a stable clot." To test their theory, the team administered the serpin to mice with hemophilia B and clipped their tails. In this model, the blood loss decreased as the dose increased, with the highest dose reducing bleeding to the level of the healthy mice. Further injury models underscored that the serpin helped the majority of the mice form stable clots, with higher doses resulting in quicker clot formation. The serpin was also able to accelerate clot formation when added to blood samples from hemophilia A patients. "It is our understanding that because we are targeting a general anti-clotting process, our serpin could effectively treat patients with either hemophilia A or B, including those who develop inhibitors to more traditional therapy," stated Dr. Huntington. He went on to add, "Additionally, we have focused on engineering the serpin to be both subcutaneously delivered and long-acting. This will free patients from the cumbersome thrice-weekly infusions that are necessary under many contemporary therapy regimens." Explaining the roadmap for this therapy's further development, Dr. Baglin noted, "Within three years, we hope to be conducting our first-in-man trials of a subcutaneously-administered form of our serpin. It is important to remember that the majority of people in the world with hemophilia have no access to therapy. A stable, subcutaneous, long-acting, effective hemostatic agent could bring treatment to a great deal many more hemophilia sufferers." This study forms part of a patent application by authors, and the serpin is being developed into a therapeutic by a start-up company, ApcinteX, with funding from Medicxi. Blood, the most cited peer-reviewed publication in the field of hematology, is available weekly in print and online. Blood is the official journal of the American Society of Hematology (ASH), the world's largest professional society concerned with the causes and treatment of blood disorders. ASH's mission is to further the understanding, diagnosis, treatment, and prevention of disorders affecting blood, bone marrow, and the immunologic, hemostatic, and vascular systems by promoting research, clinical care, education, training, and advocacy in hematology. blood® is a registered trademark of the American Society of Hematology.


Chen K.-F.,Downing Site | Possidente B.,Skidmore College | Lomas D.A.,University College London | Crowther D.C.,Downing Site | Crowther D.C.,Cambridge Institute for Medical Research
DMM Disease Models and Mechanisms | Year: 2014

Circadian behavioural deficits, including sleep irregularity and restlessness in the evening, are a distressing early feature of Alzheimer's disease (AD). We have investigated these phenomena by studying the circadian behaviour of transgenic Drosophila expressing the amyloid beta peptide (Aβ). We find that Aβ expression results in an age-related loss of circadian behavioural rhythms despite ongoing normal molecular oscillations in the central clock neurons. Even in the absence of any behavioural correlate, the synchronised activity of the central clock remains protective, prolonging lifespan, in Aβ flies just as it does in control flies. Confocal microscopy and bioluminescence measurements point to processes downstream of the molecular clock as the main site of Aβ toxicity. In addition, there seems to be significant non-cell-autonomous Aβ toxicity resulting in morphological and probably functional signalling deficits in central clock neurons.


Gribble F.M.,Cambridge Institute for Medical Research
Proceedings of the Nutrition Society | Year: 2012

Hormones from the gastrointestinal (GI) tract are released following food ingestion and trigger a range of physiological responses including the coordination of appetite and glucose homoeostasis. The aim of this review is to discuss the pathways by which food ingestion triggers secretion of cholecystokinin (CCK), glucose-dependent insulinotropic polypeptide (GIP) and glucagon-like peptide-1 (GLP-1) and the altered patterns of gut hormone release observed following gastric bypass surgery. Our understanding of how ingested nutrients trigger secretion of these gut hormones has increased dramatically, as a result of physiological studies in human subjects and animal models and in vitro studies on cell lines and primary intestinal cultures. Specialised enteroendocrine cells located within the gut epithelium are capable of directly detecting a range of nutrient stimuli through a range of receptors and transporters. It is concluded that the arrival of nutrients at the apical surface of enteroendocrine cells is a major stimulus for gut hormone release, thereby coupling these endocrine signals to the arrival of absorbed nutrients in the bloodstream. © The Author 2012.


Maxwell P.H.,Cambridge Institute for Medical Research | Eckardt K.-U.,Friedrich - Alexander - University, Erlangen - Nuremberg
Nature Reviews Nephrology | Year: 2016

Small-molecule stabilizers of hypoxia inducible factor (HIF) are being developed for the treatment of renal anaemia. These molecules inhibit prolyl hydroxylase domain-containing (PHD) enzymes, resulting in HIF activation and increased production of erythropoietin. Currently, renal anaemia is treated with recombinant human erythropoietin or related analogues, referred to as conventional erythropoiesis stimulating agents (ESAs). Advantages of PHD enzyme inhibitors over conventional ESAs include their oral administration and their simpler-and potentially cheaper-production. Importantly, inhibition of PHD enzymes is likely to have a range of consequences other than increasing levels of erythropoietin, and these effects could be beneficial-for instance by reducing the need for parenteral iron-but might in some instances be harmful. Several companies are currently testing PHD enzyme inhibitors in patients with renal anaemia and have reported clear evidence of efficacy without serious safety concerns. A central question that current studies are beginning to address is whether using PHD enzyme inhibitors will influence hard end points, including mortality and the rate of cardiovascular events. In terms of approaches to therapy, the exquisite specificity of conventional ESAs is a striking contrast to the pleiotropic effects of activating HIF. Excitingly, PHD inhibitors could also be useful for conditions besides renal anaemia, such as protection from ischaemic injury. © 2016 Macmillan Publishers Limited.


Read R.J.,Cambridge Institute for Medical Research | Adams P.D.,Lawrence Berkeley National Laboratory | McCoy A.J.,Cambridge Institute for Medical Research
Acta Crystallographica Section D: Biological Crystallography | Year: 2013

In the case of translational noncrystallographic symmetry (tNCS), two or more copies of a component in the asymmetric unit of the crystal are present in a similar orientation. This causes systematic modulations of the reflection intensities in the diffraction pattern, leading to problems with structure determination and refinement methods that assume, either implicitly or explicitly, that the distribution of intensities is a function only of resolution. To characterize the statistical effects of tNCS accurately, it is necessary to determine the translation relating the copies, any small rotational differences in their orientations, and the size of random coordinate differences caused by conformational differences. An algorithm to estimate these parameters and refine their values against a likelihood function is presented, and it is shown that by accounting for the statistical effects of tNCS it is possible to unmask the competing statistical effects of twinning and tNCS and to more robustly assess the crystal for the presence of twinning.


Vicinanza M.,Cambridge Institute for Medical Research | Korolchuk V.I.,Cambridge Institute for Medical Research | Korolchuk V.I.,Northumbria University | Ashkenazi A.,Cambridge Institute for Medical Research | And 4 more authors.
Molecular Cell | Year: 2015

Phosphatidylinositol 3-phosphate (PI(3)P), the product of class III PI3K VPS34, recruits specific autophagic effectors, like WIPI2, during the initial steps of autophagosome biogenesis and thereby regulates canonical autophagy. However, mammalian cells can produce autophagosomes through enigmatic noncanonical VPS34-independent pathways. Here we show that PI(5)P can regulate autophagy via PI(3)P effectors and thereby identify a mechanistic explanation for forms of noncanonical autophagy. PI(5)P synthesis by the phosphatidylinositol 5-kinase PIKfyve was required for autophagosome biogenesis, and it increased levels of PI(5)P, stimulated autophagy, and reduced the levels of autophagic substrates. Inactivation of VPS34 impaired recruitment of WIPI2 and DFCP1 to autophagic precursors, reduced ATG5-ATG12 conjugation, and compromised autophagosome formation. However, these phenotypes were rescued by PI(5)P in VPS34-inactivated cells. These findings provide a mechanistic framework for alternative VPS34-independent autophagy-initiating pathways, like glucose starvation, and unravel a cytoplasmic function for PI(5)P, which previously has been linked predominantly to nuclear roles. © 2015 The Authors.


Vinuesa C.G.,Australian National University | Linterman M.A.,Cambridge Institute for Medical Research | Goodnow C.C.,Australian National University | Randall K.L.,Australian National University
Immunological Reviews | Year: 2010

Germinal centers (GCs) are specialized microenvironments formed after infection where activated B cells can mutate their B-cell receptors to undergo affinity maturation. A stringent process of selection allows high affinity, non-self-reactive B cells to become long-lived memory B cells and plasma cells. While the precise mechanism of selection is still poorly understood, the last decade has advanced our understanding of the role of T cells and follicular dendritic cells (FDCs) in GC B-cell formation and selection. T cells and non-T-cell-derived CD40 ligands on FDCs are essential for T-dependent (TD) and T-independent GC formation, respectively. TD-GC formation requires Bcl-6-expressing T cells capable of signaling through SAP, which promotes formation of stable T:B conjugates. By contrast, differentiation of B blasts along the extrafollicular pathway is less dependent on SAP. T-follicular helper (Tfh) cell-derived CD40L, interleukin-21, and interleukin-4 play important roles in GC B-cell proliferation, survival, and affinity maturation. A role for FDC-derived integrin signals has also emerged: GC B cells capable of forming an immune synapse with FDCs have a survival advantage. This emerges as a powerful mechanism to ensure death of B cells that bind self-reactive antigen, which would not normally be presented on FDCs. © 2010 John Wiley & Sons AS.

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