Using ‘omics to understand disease progression and monitor the efficacy of gene therapy

Supervisors: Professor Sara Mole, Dr Wendy Heywood, Dr Ahad Rahim

Using ‘omics to understand disease progression and monitor the efficacy of gene therapy for inherited paediatric neurodegenerative diseases

Background:
There are life-limiting inherited neurodegenerative disorders of children that are autosomal recessive lysosomal storage diseases (LSDs, combined incidence ~1:50 000). There is no treatment for most children such as those affected by the neuronal ceroid lipofuscinoses (NCL, Batten disease) and there is a desperate need to develop and follow the effectiveness of novel gene and other therapies. Treatment is needed for the CNS, the eye and some peripheral organs.

Aims/Objectives:
1. To ‘omically profile 2 NCL mouse disease models (CLN5, CLN7), currently held at UCL, that are models for disease that begins in late infancy.
2. To use ‘omics to monitor the efficacy of ongoing gene therapy targeting the brain and periphery for these mouse models.
CLN5 and CLN7 proteins are located in the lysosome matrix and membrane, respectively. Gene therapy is underway for both at UCL – that for CLN5 disease is at an early stage of development and for CLN7 disease is more advanced and revealing some interesting biology.

Methods:
1. Comprehensively profile fluids and tissues from mouse disease models (held at UCL School of Pharmacy) from birth through early disease, to identify proteins whose expression changes, and detect lipids typically altered in LSDs. Use multi-omic technologies (proteomics, metabolomics and lipidomics) and specialised bioinformatics with machine learning to integrate findings for disease prediction and candidate biomarkers to monitor disease status at tissue level and for clinical development. Develop high throughput targeted multiplex assay(s) to measure candidate biomarker proteins and lipids; Use assay(s) to monitor both toxicology and efficacy of gene or other therapies.
2. For each mouse model perform in depth studies to understand and assess the effect of disease on the CNS and peripheral organs, and to do the same for mice being treated by gene therapy from birth and later in the disease. To define the treatment window by integrating these results. Vector backbone being used for CNS gene therapy is AAV9, which has a wide distribution in the brain and spinal cord, targeting both neurons and astrocytes. Vectors currently in use for CLN5 and CLN7 have already shown to be efficacious can be further optimised or adapted using different promoters to drive cell-specific expression as required.

Timeline:
0-12 months: ‘omic discovery
6-18 months: targeted assay development
13 months onwards: organ pathology, efficacy

References:
1. SM kleine Holthaus, S Herranz-Martin, G Massaro, M Aristorena, J Hoke, MP Hughes, R Maswood, O Semenyuk, M Basche, AZ Shah, IP Klaska, AJ Smith, SE Mole, AA Rahim, RR Ali. Neonatal brain-directed gene therapy rescues a mouse model of neurodegenerative CLN6 Batten disease. Hum Mol Genet. 2019; in press.
2. SM kleine Holthaus, J Ribeiro, L Abelleira-Hervas, RA Pearson, Y Duran, A Georgiadis, RD Sampson, M Rizzi, J Hoke, R Maswood, S Azam, UFO Luhmann, AJ Smith, SE Mole, RR Ali. Prevention of Photoreceptor Cell Loss in a Cln6(nclf) Mouse Model of Batten Disease Requires CLN6 Gene Transfer to Bipolar Cells. Mol Ther. 2018; 26(5): 1343-1353.
3. Hughes MP, Smith DA, Morris L, Fletcher C, Colaco A, Huebecker M, Tordo J, Palomar N, Massaro G, Henckaerts E, Waddington SN, Platt FM, Rahim AA. AAV9 intracerebroventricular gene therapy improves lifespan, locomotor function and pathology in a mouse model of Niemann-Pick type C1 disease. Hum Mol Genet. 2018; 27(17):3079-3098.
4. Heywood WE, Hallqvist J, Heslegrave AJ, Zetterberg H, Fenoglio C, Scarpini E, Rohrer JD, Galimberti D, Mills K. CSF pro-orexin and amyloid-β38 expression in Alzheimer's disease and frontotemporal dementia. Neurobiol Aging. 2018; 72:171-176.
5. Heywood WE, Galimberti D, Bliss E, Sirka E, Paterson RW, Magdalinou NK, Carecchio M, Reid E, Heslegrave A, Fenoglio C, Scarpini E, Schott JM, Fox NC, Hardy J, Bahtia K, Heales S, Sebire NJ, Zetterburg H, Mills K. Identification of novel CSF biomarkers for neurodegeneration and their validation by a high-throughput multiplexed targeted proteomic assay. Mol Neurodegener. 2015;10(1):64.