PhD Studentship: Understanding the transcriptional response to low-dose interleukin-2 in the blood

The PhD project is associated with the Horizon 2020 funded project MIROCALS (http://www.mirocals.eu/en/), a clinical trial of low-dose interleukin-2 (IL2) in patients with amyotrophic lateral sclerosis (https://clinicaltrials.gov/ct2/show/NCT03039673). As part of the trial, longitudinal biosamples are being collected to analyse the response of the patients to the drug.

At the University of Sheffield, within SITraN (http://sitran.org/), we are leading the Transcriptomics workpackage, of which the main objective is to establish the changes in transcriptomic profiles in response to both riluzole and IL-2 treatment. In addition, we also want to establish the gene expression profiles associated with emerging biomarkers of ALS, and those profiles associated with responders and non-responders to IL2. Measurements to quantify the levels of biomarkers and establish which patients are responders are being completed by our collaborators in other workpackages and will feed into our analyses.

Blood samples are being taken throughout the treatment period and patients will be followed up for 18 months. Patients are already being recruited to the study and the blood and CSF samples from across trial sites France and the UK will be sent to Sheffield for processing and transcriptional analysis. A total of 216 patients will be recruited to the double-blind, randomized and placebo-controlled study.

Following blood collection, samples are being processed to collect the white blood cells on LeukoLock filters and preserve the RNA in RNAlater. RNA will be extracted using the LeukoLock Total RNA Isolation System, the quantity and quality of the RNA assayed, before the RNA is biotinylated and applied to the Clariom D arrays (Affymetrix). These arrays will allow us to distinguish not only differential expression of genes but also detect alternatively spliced exons, using the Transcriptome Analysis Console (TAC) (Affymetrix). Weighted gene co-expression network analysis will be used to identify genes behaving similarly following treatment and DAVID and Webgestalt online software will be used to identify significantly enriched biological pathways. Gene and splicing changes will be validated through reverse transcriptase PCR (RT-PCR) and quantitative PCR (q-PCR) on a sub group of patients.]

Finally, functional studies to determine whether the effect of IL2 in blood is replicated in neuronal and glial cells will be conducted using individual and co-cultures, to establish the key biological pathways that are neuroprotective through IL2 treatment.

The student will be joining the research group led by Dr Janine Kirby (https://www.sheffield.ac.uk/neuroscience/staff/kirby) which focuses on the genetics of ALS, using transcriptomics to establish diagnostic and prognostic biomarkers for ALS and also has a broader focus on how genomic medicine can be applied to facilitate personalised medicine in the future. For any enquiries about this post, or to discuss the project informally, please email j.kirby@sheffield.ac.uk .

Funding Notes

The Faculty Scholarships for Medicine, Dentistry & Health cover fees and stipend at Home/EU level. Overseas students may apply but will need to fund the fee differential between Home and Overseas rate from another source.