Doctoral Training Partnerships: a range of postgraduate training is funded by the Research Councils. For information on current funding routes, see the common terminology at https://www.ukri.org/apply-for-funding/how-we-fund-studentships/. Training grants may be to one organisation or to a consortia of research organisations. This portal will show the lead organisation only.

Immunotherapy toxicity is mediated by the activity of T lymphocyte clones that are driven by specific antigenic targets. In this project the student will use mouse and human samples to identify candidate T cell antigens that drive these maladaptive immune responses. These results will determine how changes in transcription caused by immunotherapy can change the display of antigen, and the potential this has for triggering tissue-damaging T cell responses.

Mammalian mitochondria contain several copies of their own genome (mtDNA) which encodes 13 essential subunits of the oxidative phosphorylation (OXPHOS) system. Pathogenic variants in the mitochondrial genome can result in mitochondrial diseases, which are a major group of inherited conditions affecting ~1 in 8,000 humans. These disorders are currently incurable and effectively untreatable, with heterogeneous penetrance, presentation and prognosis. This project aims at addressing the lack of effective treatment for these disorders. We will exploit a recently developed mouse models that recapitulate common molecular features of mtDNA disease. These models will be treated with programmable nuclease (mtZFNs and mitoTALENs) and mitochondrial base editors (DdCBE and TALED) to induce specific reduction of mutant mtDNA in germline. We will follow a reversion of mitochondrial dysfunction phenotypes using single-cell genomics, proteomics and dedicated methods assessing mitochondrial function. The results obtained within this project will constitute proof of principle that mtDNA mutation correction using genome modification tools could provide a therapeutic route for mitochondrial diseases of diverse genetic origin.

Individuals with Intellectual Disability of known genetic origin show differences in behavioural characteristics depending on the membership of their gene variant to a group with convergent cellular mechanisms, referred to as a Gene Functional Network (GFN). However, the relationships between GFNs and brain organisation are yet to be explored. I propose using network analyses to examine whether genetic cause, classified by GFN membership, is associated with differences in organisational principles of behaviour, brain function and brain structure. Two GFNs will be examined: those that are direct and indirect modifiers of synaptic physiology, and those that are chromatin structure modifiers.

It is now clear that much of the complexity afforded by our biological machinery is at the level of protein variation rather than due to a high number of distinct genes. The divergences among highly related, but chemically different, protein molecules arise from allelic DNA variation, alternative splicing and chemical modification of the proteins once they have been synthesised. This generates a vast array of protein variants each having subtle but specific cellular roles. Each has differences in mass and can therefore be studied by using a mass spectrometer giving further insight into disease mechanisms. Mass spectrometers measure the mass of charged molecules (ions) such as proteins and peptides. From these mass measurements, both the identity of proteins present and their amount can be calculated. This has applications across virtually all aspects of human cell biology and physiology in health and disease. In addition to knowing which proteins are present in their samples, researchers also want to know how abundant they are and how their abundance changes in response to stress, drug treatment or disease state. Also, they often want to know how proteins are regulated via chemical modifications to specific amino acid residues in their sequence (post translational modifications or PTM's) and how these change upon perturbation. The increasing sensitivity and resolution of modern mass spectrometry instrumentation is now allowing an unprecedented characterisation of proteins within complex biological samples. The CRUK Cambridge Institute Proteomics Facility (CIPF) is a well-established internationally recognized proteomic facility offering access to proteomics expertise and infrastructure primarily to the Cambridge biomedical community but also nationally and internationally. CIPF uses mass spectrometry as its major tool to interrogate the proteome and in this application seeks funds to extend its capabilities through the purchase of a state-of-the-art instrument, the Orbitrap Eclipse Tribrid Mass Spectrometer with an associated uHPLC. The Eclipse is much more sensitive than CIPF's current instruments. It processes samples more quickly and hence will increase the capacity of CIPF and reduce sample turnaround significantly. This instrument excels at quantitative measurements using isobaric tagging methods. Its extended mass range opens the way to analyse protein isoform (proteoforms) and its ion mobility function helps distinguish biomolecules with similar masses but subtly different behaviors. Together this instrument will allow proteomic analysis of the most challenging low-abundance or highly complex biological samples, identify more proteins and their PTM's and quantify their levels more accurately. The cohort of co-applicants in this proposal are world class scientists from diverse parts of the Cambridge biomedical research community and their research includes stem cell research; epigenetics; infectious diseases; mitochondrial biology, critical care (acute respiratory disease) and cancer biology. To help them achieve their research aims they require more advanced workflows to gain greater depth of information and with a higher degree of confidence. Increasingly requests are received for analysis from samples where cell numbers are limited and/or where the more elaborate analysis of ultra-low abundant peptides is required. The acquisition of the Eclipse importantly will provide added sensitivity and functionalities that will be transformational to the MRC-funded research detailed here, our current user base and the wider Cambridge biomedical community.