The centre occasionally has positions for doctoral research (MD and PhD). If you are interested, please e-mail the Head of Centre with a copy of your CV. Students should have at least an upper second class degree.
UCL student projects: The centre can host a number of students for final year projects. If you are interested, please e-mail the relevant Principle Investigator for an informal discussion.
Development and application of proteomic methods for cancer biomarker discovery
Supervisors: Dr John Timms and Professor Justin Hsuan
The project will develop and apply proteomic methods for the discovery of serum biomarkers for early detection of ovarian and neuroendocrine cancers. Novel strategies incorporating immunodepletion, multi-dimensional protein/peptide separations, mass tagging and mass spectrometry will be applied to unique sets of sera from women prior to cancer diagnosis. The project brings together proteomics expertise on UCL’s Bloomsbury and Royal Free campuses, provides access to state-of-the art instrumentation and builds on previous research in this area.
This project forms part of our combined research efforts in cancer detection, diagnosis and prognosis. The work aims to develop and apply novel proteomic methods for the identification of biomarkers in serum that can be used for the early detection of cancer. Early detection is crucial to reducing morbidity and mortality since early stage disease can be more effectively treated. The project will focus on the application of novel proteomic profiling technologies for improved coverage of low-abundance serum proteins and peptides with biomarker potential.
Novel proteomic strategies will be developed that incorporate immunoaffinity depletion with multi-dimensional protein and peptide separations linked to quantitative mass tagging and state-of-the-art liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis. Optimised and complimentary methods will then be used to compare the protein profiles of unique discovery sets of sera from women recruited to the UK Collaborative Trial of Ovarian Cancer Screening (UKCTOCS) which pre-date diagnosis of ovarian and neuroendocrine cancers and sera from diagnosed cancer cases and controls. By identifying differences between pre-diagnosis samples, cases and matched healthy controls and time-dependent changes occurring during disease progression, the focus will be on the earliest disease-specific changes in proteins in the bloodstream. Selected candidates from this and our on-going profiling work in ovarian and neuroendocrine cancers will be further tested in UKCTOCS validation sets using immune-based and newly developed MS-based assays. It is hoped that this research will lead to the translation of early biomarkers of disease for the development of blood tests for screening and diagnosis that will ultimately save lives.
Intelligent Design of Tissue Scaffolds for Regenerative Medicine
This project brings together leading expertise in regenerative medicine, proteomics, and systems bioinformatics to help improve the efficacy of a pioneering clinical programme in cartilage tissue transplantation. It forms part of an integrated programme at UCL and is a logical next step in a long-term, NHS- and UCL-backed programme to deliver a new generation of hollow-organ therapies into clinical practice.
Interdisciplinary Clinical and Biomedical Science
The need for partial laryngeal replacement: Conventional solutions to advanced structural disorders of the larynx (voice box) and trachea (windpipe) leave much to be desired. Adults with these problems require frequent hospitalisation. Of the 2000 persons per annum with laryngeal cancer in the UK (NCASP. DAHNO: 4th head and neck cancer audit report. DoH, 2009), 800 undergo local resection leaving permanent defects in the vocal cords and hoarseness. The 500 most advanced cases have their larynx removed completely. The remainder undergo chemo-radiotherapy which achieves good cure rates, but has high morbidity and 5% mortality, and can leave a permanently functionless larynx. If a regenerative solution existed which provided anatomical restoration of the larynx, the results of resection would be improved (e.g. by replacing vocal cord with vocal cord instead of scar), some laryngectomies would be avoided, and the threshold for selecting chemo-radiotherapy over surgery would be raised, thus avoiding the toxic side-effects of this combination. The availability of tissue engineered partial laryngeal implants would also transform the treatment of the 400 patients with advanced trauma to the larynx, where undesirable long-term tracheostomy is the only option for many presently.
Laryngeal allo- (i.e. donor) transplantation may offer an option for some in the future, but requires immunosuppression with associated morbidity and mortality. The larynx is however an ideal subject for tissue engineering: there is defined clinical need, cells used have limited need for an immediate blood supply, and partial laryngeal/tracheal or total tracheal reconstructions have relatively simple functional requirements: conduction of air, mucus and sound.
Clinical experience with tracheal regeneration: Our team includes the leaders of the group which implanted the first autologous (i.e. originating from the recipient) stem-cell based airway replacement (Lancet, 2008). We used a 4.5cm decellularised human tracheal scaffold, repopulated with autologous epithelial cells and stem-cell derived chondrocytes. At two years, the patient is well and active with normal lung function. Four further patients have received similar implants. This success demonstrates that such constructs have therapeutic potential, but as these were urgent, compassionate use applications (that is, desperate need and no good conventional treatment), the method was applied before some desirable preclinical work had been completed. One important piece of work is to understand the contribution of the scaffold material to the integration and eventual functional success of the implanted cells.
Biologic and synthetic scaffolds: The donor scaffolds we have used in these patients and in the laboratory work which led up to it are stripped of cells. This removes those parts which would normally cause it to reject if transplanted directly without immunosuppression (the ‘major histocompatibility antigens’), and was thought to remove all biologically active molecules, leaving behind only structural proteins such as collagen and elastin. These ‘biologic’ scaffolds are then re-seeded with the patient’s own cells to produce the finished organ ‘construct’ for transplantation. However, pilot work by our group has shown that this is not the case: advanced quantitative mass spectrometry employed to comprehensively define a scaffold proteome revealed over 2,800 peptide sequences and 150 extracellular proteins with high confidence. These proteins have a wide range of known and suspected functions of potential relevance to the integration and function of the re-cellularised, implanted graft. Functions include stem cell migration, division, differentiation and blood vessel formation (angiogenesis). This discovery may well explain why biologic scaffolds like these seem to perform much better than synthetic ones in animal and human studies.
Whilst decellularised scaffolds are clearly excellent for the clinical applications we explore, it is highly desirable, in the longer term, to be able to manufacture synthetic scaffolds to perform the same job. This would avoid the need for retrieval from transplant donors, increase the immediacy and pool (creating an ‘off-the-shelf’ alternative) and avoid ethical, storage and infection issues. To achieve similar performance to biologic scaffolds, we propose that a better understanding of the effects of the various residual proteins in decellularised tissues will lead to a choice of such proteins for ‘decorating’ synthetic materials, thus producing a new generation of ‘intelligent scaffolds’ for regenerative medicine purposes. The result would be a much more clinically accessible, cheaper and effective product for patients with airway and other disorders.
Interdisciplinary Computer and Biomedical Science
This project will take advantage of extensive database information to annotate and build the scaffold interactome in silico. A novel specialist relational database will be developed to integrate the proteomics data from scaffolds with a range of other sources of information, and to build an integrated resource that can be mined for patterns and relationships between proteins conferring different scaffold functions.
Model building: In more detail, the identifiers of proteins detected in different scaffolds will first be entered into this database. Information about the large-scale structure of protein-protein interactions will then be integrated using resources such as BioGrid; revealing how these proteins interact and also how they interact with key structural proteins such as collagen within the cartilage. Protein complex data from resources such as CORUM will add finer-detailed information. Inclusion of “missing-links”, whether protein or other molecular types identified from molecular interaction databases, will be assessed via re-interrogation of proteomic data with altered filtering and target assessment, and using biochemical validation in the laboratory. When experimental interaction data is unavailable, putative protein-protein interactions will be investigated using ab initio tools such as meta-PPISP. Moving to even finer detail, assignment of structural domains within the PDB will allow atomic-level protein-protein interfaces to be established. When structural information is limited, protein domain architecture can be characterized via motifs and profiles using resources such as InterPro, or predicted using ab initio methods such as DomPred.
Functional annotation: The overall functional characterization of the proteins in terms of GO classes will also be integrated into the model. Such annotation may simply be copied from UniProt when the proteins are well-characterized, or alternatively established by homology using BLAST. In cases where well-characterized homologues do not exist, ab initio functional prediction will be carried out using tools such as FFPred. All of this supporting data will be managed within the relational database so that features of the dataset can be easily queried and analyzed using network visualization packages such as CytoScape and data-mining tools such as Weka.
Future developments: In addition to defining the role of each protein within the scaffold, this model will underpin future structural comparisons between scaffolds obtained from different anatomical sites and prepared using different procedures, incorporate quantitative information on molecular abundance, identify structural components lost during decellularisation and which could advantageously be reconstituted, and inform the intelligent design of synthetic scaffolds.