A Precision Medicine Framework Using Artificial Intelligence for the Identification and Confirmation of Genomic Biomarkers of Response to an Alzheimer's Disease Therapy: Analysis of the Blarcamesine (ANAVEX2-73) Phase 2a Clinical Study

Harald Hampel 1, Coralie Williams 2, Adrien Etcheto 2, Federico Goodsaid 3, Frédéric Parmentier 2, Jean Sallantin 4, Walter E Kaufmann 5 6, Christopher U Missling 5, Mohammad Afshar 2

Affiliations

PMID: 32318621
PMCID: PMC7167374
DOI: 10.1002/trc2.12013

Abstract

Introduction: The search for drugs to treat Alzheimer's disease (AD) has failed to yield effective therapies. Here we report the first genome-wide search for biomarkers associated with therapeutic response in AD. Blarcamesine (ANAVEX2-73), a selective sigma-1 receptor (SIGMAR1) agonist, was studied in a 57-week Phase 2a trial (NCT02244541). The study was extended for a further 208 weeks (NCT02756858) after meeting its primary safety endpoint.

Methods: Safety, clinical features, pharmacokinetic, and efficacy, measured by changes in the Mini-Mental State Examination (MMSE) and the Alzheimer's Disease Cooperative Study-Activities of Daily Living scale (ADCS-ADL), were recorded. Whole exome and transcriptome sequences were obtained for 21 patients. The relationship between all available patient data and efficacy outcome measures was analyzed with unsupervised formal concept analysis (FCA), integrated in the Knowledge Extraction and Management (KEM) environment.

Results: Biomarkers with a significant impact on clinical outcomes were identified at week 57: mean plasma concentration of blarcamesine (slope MMSE:P < .041), genomic variants SIGMAR1 p.Gln2Pro (ΔMMSE:P < .039; ΔADCS-ADL:P < .063) and COMT p.Leu146fs (ΔMMSE:P < .039; ΔADCS-ADL:P < .063), and baseline MMSE score (slope MMSE:P < .015). Their combined impact on drug response was confirmed at week 148 with linear mixed effect models.

Discussion: Confirmatory Phase 2b/3 clinical studies of these patient selection markers are ongoing. This FCA/KEM analysis is a template for the identification of patient selection markers in early therapeutic development for neurologic disorders.

Keywords: Alzheimer's disease; association rules; biomarker; genomic analysis; knowledge extraction management; machine learning; mixed effect models; precision medicine; unsupervised analysis.

Conflict of interest statement

Harald Hampel is an employee of Eisai Inc. and serves as Senior Associate Editor for the Journal Alzheimer's & Dementia; during the past three years he had received lecture fees from Servier, Biogen and Roche, research grants from Pfizer, Avid, and MSD Avenir (paid to the institution), travel funding from Eisai, Functional Neuromodulation, Axovant, Eli Lilly and company, Takeda and Zinfandel, GE‐Healthcare and Oryzon Genomics, consultancy fees from Qynapse, Jung Diagnostics, Cytox Ltd., Axovant, Anavex, Takeda and Zinfandel, GE Healthcare, Oryzon Genomics, and Functional Neuromodulation, and participated in scientific advisory boards of Functional Neuromodulation, Axovant, Eisai, Eli Lilly and company, Cytox Ltd., GE Healthcare, Takeda and Zinfandel, Oryzon Genomics and Roche Diagnostics. He is co‐inventor in the following patents as a scientific expert and has received no royalties: In Vitro Multiparameter Determination Method for The Diagnosis and Early Diagnosis of Neurodegenerative Disorders Patent Number: 8916388. In Vitro Procedure for Diagnosis and Early Diagnosis of Neurodegenerative Diseases Patent Number: 8298784. Neurodegenerative Markers for Psychiatric Conditions Publication Number: 20120196300. In Vitro Multiparameter Determination Method for The Diagnosis and Early Diagnosis of Neurodegenerative Disorders Publication Number: 20100062463. In Vitro Method for The Diagnosis and Early Diagnosis of Neurodegenerative Disorders Publication Number: 20100035286. In Vitro Procedure for Diagnosis and Early Diagnosis of Neurodegenerative Diseases Publication Number: 20090263822. In Vitro Method for The Diagnosis of Neurodegenerative Diseases Patent Number: 7547553. CSF Diagnostic in Vitro Method for Diagnosis of Dementias and Neuroinflammatory Diseases Publication Number: 20080206797. In Vitro Method for The Diagnosis of Neurodegenerative Diseases Publication Number: 20080199966. Neurodegenerative Markers for Psychiatric Conditions Publication Number: 20080131921. Coralie Williams, Adrien Etcheto, and Frédéric Parmentier are employed by Ariana Pharmaceuticals. Mohammad Afshar is employed by and a shareholder of Ariana Pharmaceuticals. Federico Goodsaid is employed by and a shareholder of Regulatory Pathfinders. Walter E. Kaufmann is employed by Anavex Life Sciences Corp. Christopher U. Missling is employed by and a shareholder of Anavex Life Sciences Corp.