Human CSF pharmacoproteomics establishes in vivo‐relevant BACE1 substrates as pharmacodynamic biomarkers for chronic BACE inhibition in clinical trials
Stefan F Lichtenthaler, Pieter Giesbertz, Ana Graf, Matthew E. Kennedy, Naotaka Horiguchi, Stephan A. Müller- Psychiatry and Mental health
- Cellular and Molecular Neuroscience
- Geriatrics and Gerontology
- Neurology (clinical)
- Developmental Neuroscience
- Health Policy
- Epidemiology
Abstract
Background
BACE1 is a major drug target for Alzheimer’s disease, but several late‐stage clinical trials with BACE‐inhibitors were associated with adverse events, most notably worsening in measures of cognitive function. Inhibition of BACE1‐dependent processing of a set of CNS membrane proteins is possibly responsible for these adverse findings. It is however unknown, which physiological BACE1 substrates are affected in humans at clinically relevant doses of a BACE inhibitor. To identify such substrates, we carried out a quantitative proteomic analysis of cerebrospinal fluid (CSF) from a subset of participants of phase 2 clinical trials with umibecestat or atabecestat or of a phase 3 clinical trial with verubecestat.
Method
Pre‐ and post‐dose CSF samples were quantitatively analyzed by nanoLC‐MS/MS. Selected proteins were further validated by ELISA. Changes in BACE1 substrate abundance were correlated with changes in Ab, sAPPb and with occurence of cognitive worsening.
Result
More than 1,000 CSF proteins were relatively quantified between the BACE inhibitor‐treated groups versus placebo. The cleaved extracellular domains of several BACE1 substrates with established neuronal or synaptic functions displayed a dose‐dependent reduction. This included SEZ6, SEZ6L, CACHD1, CHL1, L1 and the APP family members APLP1 and APLP2. While some substrates, e.g. SEZ6, were reduced to similar degree as Ab and sAPPb, the reduction for other substrates was less than 50%, presumably because they are cleaved by additional proteases other than BACE1. BACE inhibition significantly and dose‐dependently increased CSF abundance of only a single quantified protein, the myelin‐associated glycoprotein. Similar protein changes upon BACE inhibition or BACE1 deletion were seen in CSF of mice and of non‐human primates and indicate that BACE1 substrates are evolutionarily conserved.
Conclusion
BACE inhibitors in clinical trials block cleavage of multiple BACE1 substrates in a dose‐dependent manner. A reduction of the inhibitor dose to less than 50% BACE1 inhibition may be an appropriate strategy to avoid side effects in future clinical trials with BACE inhibitors. Our analysis also demonstrates that proteomics enables pharmacodynamic studies of multiple CSF proteins in single measurements, which are suitable for precision medicine approaches in future clinical trials with BACE inhibitors.