Case Studies

Goal – Identify key regulatory pathways and proteins that mediate damage related to hyper-phosphorylated tau in human brain tissue.

Outcome – Identification of significant targets in multiple key pathways including those related to metabolism, calcium regulation, synaptic processes, protein mis-folding and inflammation.

Collaborators - University of Eastern Finland

Goal – Establish the mechanism of action of two orally available, brain-penetrant small molecule inhibitors of casein kinase 1 delta that improved cognition in a rodent tauopathy model.

Outcome – Confirmation that many tau phosphorylation sites are reduced by drug treatment, as well as significant regulation of pathways demonstrated to involved in phospho-tau dependent disease mechanisms.

Goal – Analyse the context in which melanoma-derived cell lines exploit MEK and PI3K signalling to overcome BRAF V600E resistance.

Outcome – Identification of a number of common effects of combination therapy irrespective of the second target as well as specific effects dependant on targeting either MEK or PI3K.

Collaborators – Moffitt Cancer Centre, Tampa, Florida

Goal – Establish common mechanisms of actions between preclinical mice treated with CK1D inhibitors and post mortem human AD brain tissue.

Outcome – With many pathways, proteins and phosphorylation sites quantified in both datasets several translational biomarkers were identified.

Collaborators University of Eastern Finland

Goal – Profile protein markers of neuroinflammation in AD cerebrospinal fluid.

Outcome – Identification of 41 proteins with at least 60% regulation in AD CSF that were also present in activated microglial cells.

Collaborators – Institute of Neurology, University College London, The Sahlgrenska Academy, University of Gothenburg.

Goal – Characterize plasma clusterin glycosylation associated with increasing brain atrophy. 

Outcome – Eight β64N clusterin glycoforms were associated with hippocampal atrophy in AD. A targeted SRM assay is now in-development.

Collaborators Institute of Psychiatry, Kings College London and University of Oxford

Goal – Identify plasma biomarkers that predict the conversion from mild cognitive impairment to Alzheimer’s disease within 12 months

Outcome – A panel of 10 plasma proteins showed changes in abundance that could predict patients with early conversion to AD with potential application in patient stratification for clinical trial enrolment.

Collaborators Institute of Psychiatry, Kings College London and University of Oxford

Goal – Identify pharmacodynamic biomarkers in AD cerebrospinal fluid.     

Outcome – Common data outputs from SysQuant^® and TMTcalibrator™ enabled the identification of pharmacodynamic biomarker candidates by comparing datasets from human clinical tissue, drug-treated animal tissues and human AD CSF samples.   

Collaborators University of Eastern Finland, Kuopio University Hospital, The Sahlgrenska Academy at the University of Gothenburg, Sahlgrenska University Hospital and Institute of Neurology, University College London

Goal - Expand the utility of CSF in the management of dementia.

Outcome – A targeted mass spectrometry assay for 16 CSF proteins selected from previous discovery experiments and literature review demonstrated excellent diagnostic performance when applied to a cohort of 94 samples (59 AD and 35 non-AD controls).

Collaborators The Sahlgrenska Academy at the University of Gothenburg

Product - Biomarker Discovery & TMT^®SRM

Goal – Produce in-vitro assays for potential skin or lung sensitizers.

Outcome - >200 novel biomarkers identified in discovery, SensiDerm TMT^®SRM 8plex assay developed to validate the top 8 markers. 

Goal – Charecterize tau phosphorylation levels in the TMHT mouse model. 

Outcome – Using the Tau Phosphorylation 6plex and Tau Phosphorylation 7plex assays, levels of phosphorylation at key sites in endogenous mouse tau as well as over-expressed human tau were established. 

Collaborators - QPS

Goal - Identify biomarkers of aspirin resistance in platelet samples.

Outcome – Discovery & qualification of Isoform A of glycoprotein IIIa as a candidate marker of aspirin resistance in platelets.

Collaborators Dept. of Clinical Pharmacology, Kings College London

Goal – To develop a multiplexed assay for the measurement of total expression and regulatory phosphorylation site levels of Estrogen Receptor alpha, Progesterone Receptor beta and HER2 that could be used in classification of Breast tumors.

Outcome – A triple-protein immunoprecipitation

Collaborators Moffitt Cancer Center, Tampa, Florida and Buck Institute for Research on Aging, Novato, California 

Goal Profile signalling pathways driving pancreatic ductal adenocarcinomas

Outcome – Analysis of 32 cases shows pathways controlling how cells interact with each other and the tumor stroma are consistently affected in all patients. However, greater heterogeneity was seen in the activity of several key drug targets highlighting the need for personalised treatments for each patient.

Collaborators King’s College Hospital

Goal – Profile phosphorylated tau and other markers of AD pathology in CSF

Outcome – 87 tau peptides, 11 regulated phosphopeptides. >100 AD pathology related proteins as candidate markers for AD diagnostic and prognosis.

Collaborators The Sahlgrenska Academy at the University of Gothenburg, Sahlgrenska University Hospital and Institute of Neurology, University College London

Goal – Identification of blood biomarkers differentiating between bulbar and limb endophenotypes of ALS.

Outcome - First demonstration of suitability of peripheral blood mononuclear cells as a source of protein to trigger mass spectrometry in TMTcalibrator™. This has generated a list of candidate peptide and protein biomarkers for stratification of ALS patients to guide treatment options.

Collaborators – Dr. Andrea Malaspina, Queen Mary’s University, London, Professor Linda Greensmith, University College London

Goal – Identification of blood biomarkers differentiating between fast and slow progressing forms of bulbar and limb endophenotypes of ALS.

Outcome – We have defined a list of candidate blood biomarkers predicting the subsequent rate of disease progression for stratification of ALS patients at the time of diagnosis. These may aid selection of personalized treatment options.

Collaborators - Dr. Andrea Malaspina, Queen Mary’s University, London, Professor Linda Greensmith, University College London

Goal – Profile Plasma Biomarkers of Cancer

Outcome - 45 serum samples were analyzed in five TMT^®10plex sets with 6,150 peptides (mapping to 616 proteins or 310 protein groups) quantified in all samples. Analytical CV = 9.5%, with biological variability at 22% at the peptide level. 

Goal – PBMC’s are the cellular component of blood and provide a rich source of circulating biomarkers. We performed unbiased, accurate quantitative proteomics to find PBMC-derived biomarkers differentiating bulbar and limb presentations of ALS.

Outcome - We have identified over 200 regulated peptides and 95 proteins in PBMC’s that show regulation between bulbar and limb endophenotypes and/or between fast and slow progressing disease. These are good candidates for further study towards an early stratification test for ALS patients to enable personalized treatment.

Collaborators - Dr. Andrea Malaspina, Queen Mary’s University, London, Professor Linda Greensmith, University College London

Goal – Explore PBMC proteome as a rich source of candidate peripheral biomarkers using TMT® quantification on an Orbitrap Velos Pro.

Outcome – Over 4,000 proteins were quantified including many lower abundance proteins. When compared to the human plasma proteome database around half of plasma proteins were also seen in PBMC’s whereas the PBMC proteome was twice as complex as plasma, confirming their value as a source for peripheral biomarker discovery

Collaborators – Internal project

Goal – Discovery and validation of biomarkers to assess the response to cMet inhibition and functional inactivation

Outcome - 170 novel biomarkers identified in discovery, BioTag TMT^®SRM assay developed to validate the top 28 markers

Collaborators - ProQinase GmBH, Germany & Natural Medical Sciences Institute, University of Tubingen, Germany

Goal – Use SysQuant^® to explore inter-tumoral differences in active cellular processes driving individual liver tumors with a focus on targets of therapy including Sorafenib.

Outcome – Maps of pathway activity showed low level of Raf activity in most tumors suggesting Sorafenib will seldom be an effective treatment. Other kinase targets showed broader activity profiles and represent better targets for HCC treatment.

Collaborators – Professor Nigel Heaton Liver, Renal, Urology, Transplant, Gastro/Gastro Intestinal Surgery Clinical Academic Group

Goal – Identify plasma markers of developmental neurotoxic disorders

Outcome -  >1700 novel biomarker candidates identified in discovery in different species and tissues, TMTcalibrator™ assay developed to monitor the top 136 markers in plasma

Collaborators:

• Entro de Investigacion Principe Felipe, Valencia, Spain
• Institute for Risk Assessment Sciences, University Utrecht, Utrecht, The Netherlands
• Institute for Environmental Studies, VU University, Amsterdam, The Netherlands 
• Department of Environmental Toxicology, Evolutionary Biology Center, Uppsala University, Sweden
• Department of Environmental Medicine, Faculty of Public Health, Slovak Medical University, Slovak republic
• Norwegian Institute of Public Health, Oslo, Norway