Replication-dependent histone pre-mRNA misprocessing and innate immune sensing
Lead Research Organisation:
University of Edinburgh
Department Name: MRC Human Genetics Unit
Abstract
Viruses are tiny organisms that are everywhere. In order to make more copies of themselves viruses infect the cells of other organisms, including humans. Being able to fight off viruses is absolutely necessary for our survival; simply put, if a person cannot do so, they will die.
How do our cells realise that they are being infected by a virus? It turns out that the way we do this is by sensing the presence of viral genetic material (referred to as DNA and RNA) as the virus enters the cell. Much as a dog might bark to wake up the owner when a burglar breaks into a house, our cells 'raise the alarm' when they sense viral DNA and RNA by producing a very powerful chemical called interferon. Interferon acts as a kind of cellular disinfectant and is very good at killing virus. However, like a disinfectant, too much interferon can be dangerous, so that it is important that interferon is used carefully, and only when needed.
Aicardi-Goutières syndrome (AGS) is the name of a severe disease that can affect children. Over the last 30 years, we have learned that AGS is associated with very high levels of interferon. As explained above, we know that interferon is normally only produced when we are infected with a virus. However, in AGS, there is no viral infection. The question arises then, why are levels of interferon so high in AGS? The answer to this question is explained in general terms by the fact that our own cells are full of our own DNA and RNA, which also has the potential to trigger the production of interferon. Because of this, safety mechanisms exist to minimise the risk that we might misinterpret our own DNA and RNA as virus. These mechanisms include dedicated 'waste-disposal' systems for getting rid of (old) self DNA and RNA, keeping self DNA and RNA separate from the alarm systems that sense viruses, and the marking of self DNA and RNA with a stamp saying 'self'. In brief, a person with AGS has an inherited problem with one of these mechanisms, so that the cells in a person with AGS confuse their own DNA or RNA with that coming from a virus. Very recently, we have identified a new cause of AGS, which is the subject of this grant application.
Almost all cells in our body have a special compartment called the nucleus, the place in the cell where our genetic material (composed of DNA) is stored. This DNA is arranged in tiny thread-like structures called chromosomes. Chromosomes are coated by other chemicals, in particular a material called histone. We have discovered that some people with AGS are not able to make the correct amount of histone, and that this triggers the production of interferon. This is very interesting, because how the cell ensures that the genetic material in the nucleus does not trigger an interferon response is not properly understood. We intend to study the detailed mechanism of the disease in this new type of AGS. In doing so, our work should not only be of potential benefit to people with the devastating disease AGS, it will also shed light on a fundamental aspect of how human cells stay healthy.
How do our cells realise that they are being infected by a virus? It turns out that the way we do this is by sensing the presence of viral genetic material (referred to as DNA and RNA) as the virus enters the cell. Much as a dog might bark to wake up the owner when a burglar breaks into a house, our cells 'raise the alarm' when they sense viral DNA and RNA by producing a very powerful chemical called interferon. Interferon acts as a kind of cellular disinfectant and is very good at killing virus. However, like a disinfectant, too much interferon can be dangerous, so that it is important that interferon is used carefully, and only when needed.
Aicardi-Goutières syndrome (AGS) is the name of a severe disease that can affect children. Over the last 30 years, we have learned that AGS is associated with very high levels of interferon. As explained above, we know that interferon is normally only produced when we are infected with a virus. However, in AGS, there is no viral infection. The question arises then, why are levels of interferon so high in AGS? The answer to this question is explained in general terms by the fact that our own cells are full of our own DNA and RNA, which also has the potential to trigger the production of interferon. Because of this, safety mechanisms exist to minimise the risk that we might misinterpret our own DNA and RNA as virus. These mechanisms include dedicated 'waste-disposal' systems for getting rid of (old) self DNA and RNA, keeping self DNA and RNA separate from the alarm systems that sense viruses, and the marking of self DNA and RNA with a stamp saying 'self'. In brief, a person with AGS has an inherited problem with one of these mechanisms, so that the cells in a person with AGS confuse their own DNA or RNA with that coming from a virus. Very recently, we have identified a new cause of AGS, which is the subject of this grant application.
Almost all cells in our body have a special compartment called the nucleus, the place in the cell where our genetic material (composed of DNA) is stored. This DNA is arranged in tiny thread-like structures called chromosomes. Chromosomes are coated by other chemicals, in particular a material called histone. We have discovered that some people with AGS are not able to make the correct amount of histone, and that this triggers the production of interferon. This is very interesting, because how the cell ensures that the genetic material in the nucleus does not trigger an interferon response is not properly understood. We intend to study the detailed mechanism of the disease in this new type of AGS. In doing so, our work should not only be of potential benefit to people with the devastating disease AGS, it will also shed light on a fundamental aspect of how human cells stay healthy.
Technical Summary
Most antiviral responses are initiated by innate immune receptors that detect viral nucleic acid. Since the basic molecular structure of DNA and RNA is conserved across species, the existence of such receptors implies the necessity for mechanisms to avoid the sensing of self nucleic acids as non-self. The monogenic type I interferonopathies, disorders associated with enhanced type I interferon signalling where such signalling is considered central to pathogenesis, emphasize the fundamental importance of nucleic acid signalling in the induction of type I interferon, and highlight the risks to human health of nucleic acid sensing as an antiviral strategy.
One way to avoid a situation of type I interferon-mediated autoinflammation is to physically separate self nucleic acids from viral nucleic acid sensors. Thus, it was previously considered that the double stranded (ds) DNA sensor cyclic GMP-AMP synthase, cGAS, was exclusively confined to the cytosol. However, in a surprising recent finding, it has been shown that cGAS can be found within the nucleus, begging the question as to how genomic DNA does not trigger a potent type I interferon response. The present study builds on an observation that we have made, suggesting that chronic type I interferon activation can occur due to a disturbance of histone protein stoichiometry, and consequent abnormalities in chromatin state. As a corollary of this, we suggest that histones play an essential role in rendering nuclear DNA non-immunogenic.
The overall goal of our proposal is to understand how a disturbance of chromatin histone composition leads to engagement of the type I interferon signalling machinery. To do this, we will take advantage of a unique patient resource, acquired over almost two decades. Additionally, we will derive a series of cellular tools that we can use to interrogate this question.
One way to avoid a situation of type I interferon-mediated autoinflammation is to physically separate self nucleic acids from viral nucleic acid sensors. Thus, it was previously considered that the double stranded (ds) DNA sensor cyclic GMP-AMP synthase, cGAS, was exclusively confined to the cytosol. However, in a surprising recent finding, it has been shown that cGAS can be found within the nucleus, begging the question as to how genomic DNA does not trigger a potent type I interferon response. The present study builds on an observation that we have made, suggesting that chronic type I interferon activation can occur due to a disturbance of histone protein stoichiometry, and consequent abnormalities in chromatin state. As a corollary of this, we suggest that histones play an essential role in rendering nuclear DNA non-immunogenic.
The overall goal of our proposal is to understand how a disturbance of chromatin histone composition leads to engagement of the type I interferon signalling machinery. To do this, we will take advantage of a unique patient resource, acquired over almost two decades. Additionally, we will derive a series of cellular tools that we can use to interrogate this question.
Planned Impact
Beyond the academic beneficiaries listed, we highlight the following as areas in which important impacts from our research are likely to accrue:
This project will tackle a fundamental issue in biology; that is, the discrimination of self from non-self relating to endogenous nucleic acids and innate immune signalling. This is a rapidly developing field of high clinical, academic and industrial interest. For example, beyond the study of rare disease, a role for innate immune sensing and type I interferon induction is now widely appreciated in cancer and neuroinflammation.
By providing insights into how chromatin is maintained as immunologically inert, our study will provide fundamental biological data. More generally, the study will develop expertise in the MRC IGMM, and the UK more broadly, in this rapidly developing field, which has both basic-science interest and clear translational potential (as one example, witness the work of the PI in considering treatments of interferon driven disease: N Engl J Med. 2018 Dec 6;379(23):2275-7). During the course of this study we will develop new data, and new methods of analysis for the interrogation of questions pertinent to this research area, which will likely have applicability to other fields e.g. cancer and cellular senescence.
The group most likely to directly benefit from our work are patients with Aicardi-Goutières syndrome and their families. The identification of the genetic basis of a rare disease immediately allows for diagnostic/confirmatory testing in suspected cases, as well as carrier and prenatal diagnostic testing for individuals and couples. The availability of a genetic test can obviate the need for other more invasive, expensive, and time-consuming investigations, thus reducing morbidity and delays in diagnosis. Furthermore, the importance of the molecular definition of the associated 1 in 4 risk of recurrence, and the provision of a choice about prenatal testing for at-risk couples in this situation, must not be underestimated. These aspects of our work represent true translational medicine - changes which can be incorporated into routine medical provision in the UK, indeed - worldwide, in the near term. Thus, other groups with interest in our work will include molecular diagnostic service providers, neurologists and specialists in autoinflammation. A precise genetic diagnosis will help to define a cohort of patients for future clinical outcome and intervention studies, so that in the longer term we hope that our work will provide the foundation for novel therapeutic development.
The University of Edinburgh expects medical and basic science students to undertake research projects as part of their degreee. This proposal will therefore allow the PI to host and train undergraduate and masters students, and thereby further develop expertise in this area within the UK scientific community. Finally, the current application will underpin the development of the named post-doc, Dr Carolina Uggenti, as a career scientist, involving her not just in experimental procedures but also in project management, and the preparation of results for publication and dissemination.
This project will tackle a fundamental issue in biology; that is, the discrimination of self from non-self relating to endogenous nucleic acids and innate immune signalling. This is a rapidly developing field of high clinical, academic and industrial interest. For example, beyond the study of rare disease, a role for innate immune sensing and type I interferon induction is now widely appreciated in cancer and neuroinflammation.
By providing insights into how chromatin is maintained as immunologically inert, our study will provide fundamental biological data. More generally, the study will develop expertise in the MRC IGMM, and the UK more broadly, in this rapidly developing field, which has both basic-science interest and clear translational potential (as one example, witness the work of the PI in considering treatments of interferon driven disease: N Engl J Med. 2018 Dec 6;379(23):2275-7). During the course of this study we will develop new data, and new methods of analysis for the interrogation of questions pertinent to this research area, which will likely have applicability to other fields e.g. cancer and cellular senescence.
The group most likely to directly benefit from our work are patients with Aicardi-Goutières syndrome and their families. The identification of the genetic basis of a rare disease immediately allows for diagnostic/confirmatory testing in suspected cases, as well as carrier and prenatal diagnostic testing for individuals and couples. The availability of a genetic test can obviate the need for other more invasive, expensive, and time-consuming investigations, thus reducing morbidity and delays in diagnosis. Furthermore, the importance of the molecular definition of the associated 1 in 4 risk of recurrence, and the provision of a choice about prenatal testing for at-risk couples in this situation, must not be underestimated. These aspects of our work represent true translational medicine - changes which can be incorporated into routine medical provision in the UK, indeed - worldwide, in the near term. Thus, other groups with interest in our work will include molecular diagnostic service providers, neurologists and specialists in autoinflammation. A precise genetic diagnosis will help to define a cohort of patients for future clinical outcome and intervention studies, so that in the longer term we hope that our work will provide the foundation for novel therapeutic development.
The University of Edinburgh expects medical and basic science students to undertake research projects as part of their degreee. This proposal will therefore allow the PI to host and train undergraduate and masters students, and thereby further develop expertise in this area within the UK scientific community. Finally, the current application will underpin the development of the named post-doc, Dr Carolina Uggenti, as a career scientist, involving her not just in experimental procedures but also in project management, and the preparation of results for publication and dissemination.
Organisations
People |
ORCID iD |
| Yanick Crow (Principal Investigator) | |
| Carolina Uggenti (Researcher) |