Newcastle University Single Cell Functional Genomics Unit (NUSCU)

Lead Research Organisation: Newcastle University
Department Name: Institute of Genetic Medicine

Abstract

Newcastle University (NU) has a well-established track record studying the molecular basis of rare disease underpinned by unique cohorts of patients with defined phenotypes and biobanked tissue, built through 21 Nationally Commissioned NHS clinical services, which we lead in partnership with the Newcastle upon Tyne Hospitals (NUTH) NHS Foundation Trust. Our work on rare mitochondrial, neuromuscular & musculoskeletal diseases, rare childhood cancers, rare immune deficiencies, and novel cell therapies is renowned internationally, with each receiving substantial centre, fellowship, and programme level support from the MRC, NIHR, Wellcome Trust, European Union, Arthritis Research UK (ARUK), Leukaemia and Lymphoma Research (LLR), and Cancer Research UK (CRUK); >£100M combined since 2008.

Over the last two years, each area has independently converged on single cell functional genomics and proteomic approaches to advance our understanding of pathogenesis and thus explain why patients with the same disorder develop different clinical phenotypes, and respond to treatments in different ways. We aim to bring together expertise and infrastructure focused on the genomic, epigenomic, transcriptomic and proteomic characterisation of single cells by forming the Newcastle University Single Cell Functional Genomics Unit (NUSCU).

The Unit will be academically led, have a dedicated bioinformatics team and hardware, and interface nationally through the newly established Northern Single Cell Consortium and CyTOF-UK users group. NUSCU will be managed by a dedicated facilities manager funded by NU leading in in-house technical team, building on a successful business model which will lead to self-sustainability within 3-years.

Technical Summary

Foundations for the Newcastle University Single Cell Functional Genomics Unit are already in place, incl >£1M investment in 2012-13 in 18-colour fluorescent cell sorting (FACSAria Fusion), analysis (LSRFortessa), image flow cytometry (Image Stream), quantitative multiplex RNA analysis (Nanostring), and >£75K/yr on personnel and maintenance. Although this enables the isolation of cell types and a limited number of functional analyses, the comprehensive analysis of the whole genome, transcriptome, epigenome and a substantial component of the cell proteome is not currently possible in the North East of England. We seek to enable the work described above, through: (i) isolation of single cells from tissue section and suspension for whole genome sequencing and gene expression studies; (ii) in-house whole-genome DNA and RNA sequencing and linked epigenetic analysis; (iii) high throughput single-cell proteomics; (iv) a dedicated bioinformatic infrastructure. It is critical to establish this equipment on-site, as the research proposed will use patient tissue or fragile stem cell populations/cell lines which cannot be transported.

We request
Cell and sub-cellular trapping from solid tissues by laser micro dissection with optical tweezers (Zeuss PALM CombiSystem)
Single-cell targeted gene expression analysis, global transcriptome analysis, mRNA sequencing, and genome amplification for whole-genome sequencing (Fluidigm C1 & BioMark system)
Whole genome and transcriptome next-generation sequencing and linked epigenetic analysis (Illumina HiSeq 2500, linked sample preparation equipment, robotics and qPCR validation of RNAseq data)
High throughput single cell proteomics with mass spectrometry based cytometry (Cytometry by Time Of Flight, CyTOF)
Dedicated computational and bioinformatic infrastructure, enabling data processing and storage using newly developed algorithms (5 high-performance computer nodes @1TB/32core), which will complement our existing computing infrast

Planned Impact

The main beneficiaries of the creation of cutting-edge technologies will be the UK economy; the NHS and patients.

Effects on the Economy
The Higher education sector has long been seen to be important for the national economy and the University research base seen as vital to fostering innovation. The importance of higher education in the local economy is now being attested with universities recognized as a vital source of economic activity in a region. Reports, published (3 April 2014) by Universities UK, reveal the different levels of international revenue, job creation and off-campus expenditure for institutions in each region of England. The five HEIs of the north-east generated £1.1bn in revenue in 2011-12. Through knock-on effects they generated an additional £1.5 billion in other industries throughout the UK, with the majority (£1.1 billion) in the region. International revenue was £244 million. The Universities themselves provided 14,661 full-time jobs and generated 15,261 full-time equivalent jobs outside the universities, with most (11,493) based in the region. The embedding of these cutting-edge technologies within the academic and clinical infrastructure of the North East will enable further academic-industry collaboration.

Increasingly Universities are working collaboratively in consortia of partnerships. The Newcastle University Single Cell Functional Genomics Unit (NUSCU) will work with a great many partners: NHS Trusts, the Academic Health Sciences Network, the life sciences industry and pharmaceutical companies, patient groups and the public to deliver innovation and patient benefit.

Effects on healthcare
The new single cell technology will enable breakthroughs in many areas of health research and will have impact in many forms. It will influence Government legislation, healthcare practice and health policy, for instance the move for legislative change in enabling new procedures to prevent the transmission of mitochondrial disease. Validatof the use of single cell-omics in human embryos, will pave the way to its wider application in the development of less invasive procedures for detecting genetic mutations and chromosomal anomalies in human oocytes and embryos. It will also underpin advances in our understanding of basic human developmental biology, providing new measures against which to test existing and novel assisted reproductive technologies. It will be an essential part of the translational research pathway; where we can understand the pathogenesis, we can identify targets for therapy that will ultimately enable personalised or stratified medicine - the right treatment for the right patient at the right time. This will be more efficient for the NHS as well as beneficial for the patient.