Targeted Screening for Alzheimer's Disease Clinical Trials Using Data-Driven Disease Progression Models.
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ABSTRACT:
SUBMITTER: Oxtoby NP
PROVIDER: S-EPMC9204250 | biostudies-literature | 2022
REPOSITORIES: biostudies-literature
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Targeted Screening for Alzheimer's Disease Clinical Trials Using Data-Driven Disease Progression Models.
Oxtoby Neil P NP Shand Cameron C Cash David M DM Alexander Daniel C DC Barkhof Frederik F
Frontiers in artificial intelligence 20220526
Heterogeneity in Alzheimer's disease progression contributes to the ongoing failure to demonstrate efficacy of putative disease-modifying therapeutics that have been trialed over the past two decades. Any treatment effect present in a subgroup of trial participants (responders) can be diluted by non-responders who ideally should have been screened out of the trial. How to identify (screen-in) the most likely potential responders is an important question that is still without an answer. Here, we ...[more]
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Project description:See Li and Donohue (doi:10.1093/brain/awy089) for a scientific commentary on this article.Dominantly-inherited Alzheimer's disease is widely hoped to hold the key to developing interventions for sporadic late onset Alzheimer's disease. We use emerging techniques in generative data-driven disease progression modelling to characterize dominantly-inherited Alzheimer's disease progression with unprecedented resolution, and without relying upon familial estimates of years until symptom onset. We retrospectively analysed biomarker data from the sixth data freeze of the Dominantly Inherited Alzheimer Network observational study, including measures of amyloid proteins and neurofibrillary tangles in the brain, regional brain volumes and cortical thicknesses, brain glucose hypometabolism, and cognitive performance from the Mini-Mental State Examination (all adjusted for age, years of education, sex, and head size, as appropriate). Data included 338 participants with known mutation status (211 mutation carriers in three subtypes: 163 PSEN1, 17 PSEN2, and 31 APP) and a baseline visit (age 19-66; up to four visits each, 1.1 ± 1.9 years in duration; spanning 30 years before, to 21 years after, parental age of symptom onset). We used an event-based model to estimate sequences of biomarker changes from baseline data across disease subtypes (mutation groups), and a differential equation model to estimate biomarker trajectories from longitudinal data (up to 66 mutation carriers, all subtypes combined). The two models concur that biomarker abnormality proceeds as follows: amyloid deposition in cortical then subcortical regions (∼24 ± 11 years before onset); phosphorylated tau (17 ± 8 years), tau and amyloid-β changes in cerebrospinal fluid; neurodegeneration first in the putamen and nucleus accumbens (up to 6 ± 2 years); then cognitive decline (7 ± 6 years), cerebral hypometabolism (4 ± 4 years), and further regional neurodegeneration. Our models predicted symptom onset more accurately than predictions that used familial estimates: root mean squared error of 1.35 years versus 5.54 years. The models reveal hidden detail on dominantly-inherited Alzheimer's disease progression, as well as providing data-driven systems for fine-grained patient staging and prediction of symptom onset with great potential utility in clinical trials.
| S-EPMC5920320 | biostudies-literature
Project description:BackgroundGiven the complex and progressive nature of Alzheimer's disease (AD), a precision medicine approach for diagnosis and treatment requires the identification of patient subgroups with biomedically distinct and actionable phenotype definitions.MethodsLongitudinal patient-level data for 1160 AD patients receiving placebo or no treatment with a follow-up of up to 18 months were extracted from an integrated clinical trials dataset. We used latent class mixed modelling (LCMM) to identify patient subgroups demonstrating distinct patterns of change over time in disease severity, as measured by the Alzheimer's Disease Assessment Scale-cognitive subscale score. The optimal number of subgroups (classes) was selected by the model which had the lowest Bayesian Information Criterion. Other patient-level variables were used to define these subgroups' distinguishing characteristics and to investigate the interactions between patient characteristics and patterns of disease progression.ResultsThe LCMM resulted in three distinct subgroups of patients, with 10.3% in Class 1, 76.5% in Class 2 and 13.2% in Class 3. While all classes demonstrated some degree of cognitive decline, each demonstrated a different pattern of change in cognitive scores, potentially reflecting different subtypes of AD patients. Class 1 represents rapid decliners with a steep decline in cognition over time, and who tended to be younger and better educated. Class 2 represents slow decliners, while Class 3 represents severely impaired slow decliners: patients with a similar rate of decline to Class 2 but with worse baseline cognitive scores. Class 2 demonstrated a significantly higher proportion of patients with a history of statins use; Class 3 showed lower levels of blood monocytes and serum calcium, and higher blood glucose levels.ConclusionsOur results, 'learned' from clinical data, indicate the existence of at least three subgroups of Alzheimer's patients, each demonstrating a different trajectory of disease progression. This hypothesis-generating approach has detected distinct AD subgroups that may prove to be discrete endophenotypes linked to specific aetiologies. These findings could enable stratification within a clinical trial or study context, which may help identify new targets for intervention and guide better care.
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Project description:Understanding the sequence of biological and clinical events along the course of Alzheimer's disease provides insights into dementia pathophysiology and can help participant selection in clinical trials. Our objective is to train two data-driven computational models for sequencing these events, the Event Based Model (EBM) and discriminative-EBM (DEBM), on the basis of well-characterized research data, then validate the trained models on subjects from clinical cohorts characterized by less-structured data-acquisition protocols. Seven independent data cohorts were considered totalling 2389 cognitively normal (CN), 1424 mild cognitive impairment (MCI) and 743 Alzheimer's disease (AD) patients. The Alzheimer's Disease Neuroimaging Initiative (ADNI) data set was used as training set for the constriction of disease models while a collection of multi-centric data cohorts was used as test set for validation. Cross-sectional information related to clinical, cognitive, imaging and cerebrospinal fluid (CSF) biomarkers was used. Event sequences obtained with EBM and DEBM showed differences in the ordering of single biomarkers but according to both the first biomarkers to become abnormal were those related to CSF, followed by cognitive scores, while structural imaging showed significant volumetric decreases at later stages of the disease progression. Staging of test set subjects based on sequences obtained with both models showed good linear correlation with the Mini Mental State Examination score (R2EBM = 0.866; R2DEBM = 0.906). In discriminant analyses, significant differences (p-value ≤ 0.05) between the staging of subjects from training and test sets were observed in both models. No significant difference between the staging of subjects from the training and test was observed (p-value > 0.05) when considering a subset composed by 562 subjects for which all biomarker families (cognitive, imaging and CSF) are available. Event sequence obtained with DEBM recapitulates the heuristic models in a data-driven fashion and is clinically plausible. We demonstrated inter-cohort transferability of two disease progression models and their robustness in detecting AD phases. This is an important step towards the adoption of data-driven statistical models into clinical domain.
| S-EPMC6675943 | biostudies-literature
Project description:PET is used to measure tau protein accumulation in Alzheimer's disease. Multiple biomarkers have been proposed to track disease progression, most notably the standardized uptake value ratio of PET tracer uptake in a target region of interest relative to a reference region, but literature suggests these region choices are nontrivial. This study presents and evaluates a novel framework, BioDisCVR, designed to facilitate the discovery of useful biomarkers, demonstrated on [18F]AV-1451 tau PET data in multiple cohorts. BioDisCVR enhances signal-to-noise by conducting a data-driven search through the space of possible combinations of regional tau PET signals into a ratio of two composite regions, driven by a user-defined fitness function. This study compares ratio-based biomarkers discovered by the framework with state-of-the-art standardized uptake value ratio biomarkers. Data used is tau PET regional measurements from 198 individuals from the Alzheimer's Disease Neuroimaging Initiative database, used for discovery, and 42 from the Mayo Clinic Alzheimer's Disease Research Center and Mayo Clinic Study of Aging (MCSA), used for external validation. Biomarkers are evaluated by calculating clinical trial sample size estimates for 80% power and 20% effect size. Secondary metrics are a measure of longitudinal consistency (standard deviation of linear mixed-effects model residuals), and separation between cognitive groups (t-statistic of the change over time due to being cognitively impaired). When applied to preclinical (secondary prevention with CU individuals) and clinical (treatment aimed at cognitively impaired individuals) trials on Alzheimer's disease, our data-driven framework BioDisCVR discovered ratio-based tau PET biomarkers vastly superior to previous work, both reducing measurement error and sample size estimates for hypothetical clinical trials. Our analysis suggests remarkable potential for patient benefit (reduced exposure to health risks associated with experimental drugs) and substantial cost savings, through accelerated trials and reduced sample sizes. Our study supports the leveraging of data-driven methods like BioDisCVR for clinical benefit, with the potential to positively impact drug development in Alzheimer's disease and beyond.
| S-EPMC11632366 | biostudies-literature
Project description:Amyloid-β is thought to facilitate the spread of tau throughout the neocortex in Alzheimer's disease, though how this occurs is not well understood. This is because of the spatial discordance between amyloid-β, which accumulates in the neocortex, and tau, which accumulates in the medial temporal lobe during ageing. There is evidence that in some cases amyloid-β-independent tau spreads beyond the medial temporal lobe where it may interact with neocortical amyloid-β. This suggests that there may be multiple distinct spatiotemporal subtypes of Alzheimer's-related protein aggregation, with potentially different demographic and genetic risk profiles. We investigated this hypothesis, applying data-driven disease progression subtyping models to post-mortem neuropathology and in vivo PET-based measures from two large observational studies: the Alzheimer's Disease Neuroimaging Initiative (ADNI) and the Religious Orders Study and Rush Memory and Aging Project (ROSMAP). We consistently identified 'amyloid-first' and 'tau-first' subtypes using cross-sectional information from both studies. In the amyloid-first subtype, extensive neocortical amyloid-β precedes the spread of tau beyond the medial temporal lobe, while in the tau-first subtype, mild tau accumulates in medial temporal and neocortical areas prior to interacting with amyloid-β. As expected, we found a higher prevalence of the amyloid-first subtype among apolipoprotein E (APOE) ε4 allele carriers while the tau-first subtype was more common among APOE ε4 non-carriers. Within tau-first APOE ε4 carriers, we found an increased rate of amyloid-β accumulation (via longitudinal amyloid PET), suggesting that this rare group may belong within the Alzheimer's disease continuum. We also found that tau-first APOE ε4 carriers had several fewer years of education than other groups, suggesting a role for modifiable risk factors in facilitating amyloid-β-independent tau. Tau-first APOE ε4 non-carriers, in contrast, recapitulated many of the features of primary age-related tauopathy. The rate of longitudinal amyloid-β and tau accumulation (both measured via PET) within this group did not differ from normal ageing, supporting the distinction of primary age-related tauopathy from Alzheimer's disease. We also found reduced longitudinal subtype consistency within tau-first APOE ε4 non-carriers, suggesting additional heterogeneity within this group. Our findings support the idea that amyloid-β and tau may begin as independent processes in spatially disconnected regions, with widespread neocortical tau resulting from the local interaction of amyloid-β and tau. The site of this interaction may be subtype-dependent: medial temporal lobe in amyloid-first, neocortex in tau-first. These insights into the dynamics of amyloid-β and tau may inform research and clinical trials that target these pathologies.
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Project description:Clinical trial outcomes for Alzheimer's disease are typically analyzed by using the mixed model for repeated measures (MMRM) or similar models that compare an efficacy scale change from baseline between treatment arms with or without participants' disease stage as a covariate. The MMRM focuses on a single-point fixed follow-up duration regardless of the exposure for each participant. In contrast to these typical models, we have developed a novel semiparametric cognitive disease progression model (DPM) for autosomal dominant Alzheimer's disease based on the Dominantly Inherited Alzheimer Network (DIAN) observational study. This model includes 3 novel features, in which the DPM (1) aligns and compares participants by disease stage, (2) uses a proportional treatment effect similar to the concept of the Cox proportional hazard ratio, and (3) incorporates extended follow-up data from participants with different follow-up durations using all data until last participant visit. We present the DPM model developed by using the DIAN observational study data and demonstrate through simulation that the cognitive DPM used in hypothetical intervention clinical trials produces substantial gains in power compared with the MMRM.
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Project description:ImportanceUndetected biological heterogeneity adversely impacts trials in Alzheimer's disease because rate of cognitive decline - and perhaps response to treatment - differs in subgroups. Recent results show that data-driven approaches can unravel the heterogeneity of Alzheimer's disease progression. The resulting stratification is yet to be leveraged in clinical trials.ObjectiveInvestigate whether image-based data-driven disease progression modelling could identify baseline biological heterogeneity in a clinical trial, and whether these subgroups have prognostic or predictive value.DesignScreening data from the Anti-Amyloid Treatment in Asymptomatic Alzheimer Disease (A4) Study collected between April 2014 and December 2017, and longitudinal data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) observational study downloaded in February 2022 were used.SettingThe A4 Study is an interventional trial involving 67 sites in the US, Canada, Australia, and Japan. ADNI is a multi-center observational study in North America.ParticipantsCognitively unimpaired amyloid-positive participants with a 3-Tesla T1-weighted MRI scan. Amyloid positivity was determined using florbetapir PET imaging (in A4) and CSF Aβ(1-42) (in ADNI).Main outcomes and measuresRegional volumes estimated from MRI scans were used as input to the Subtype and Stage Inference (SuStaIn) algorithm. Outcomes included cognitive test scores and SUVr values from florbetapir and flortaucipir PET.ResultsWe included 1,240 Aβ+ participants (and 407 Aβ- controls) from the A4 Study, and 731 A4-eligible ADNI participants. SuStaIn identified three neurodegeneration subtypes - Typical, Cortical, Subcortical - comprising 523 (42%) individuals. The remainder are designated subtype zero (insufficient atrophy). Baseline PACC scores (A4 primary outcome) were significantly worse in the Cortical subtype (median = -1.27, IQR=[-3.34,0.83]) relative to both subtype zero (median=-0.013, IQR=[-1.85,1.67], P<.0001) and the Subcortical subtype (median=0.03, IQR=[-1.78,1.61], P=.0006). In ADNI, over a four-year period (comparable to A4), greater cognitive decline in the mPACC was observed in both the Typical (-0.23/yr; 95% CI, [-0.41,-0.05]; P=.01) and Cortical (-0.24/yr; [-0.42,-0.06]; P=.009) subtypes, as well as the CDR-SB (Typical: +0.09/yr, [0.06,0.12], P<.0001; and Cortical: +0.07/yr, [0.04,0.10], P<.0001).Conclusions and relevanceIn a large secondary prevention trial, our image-based model detected neurodegenerative heterogeneity predictive of cognitive heterogeneity. We argue that such a model is a valuable tool to be considered in future trial design to control for previously undetected variance.
| S-EPMC9934776 | biostudies-literature
Project description:IntroductionAssessing treatments for Alzheimer's disease (AD) relies on reliable tools for measuring AD progression. In this analysis, we evaluate the sensitivity of clinical progression measures in AD within randomized controlled trials (RCTs) with confirmed positive amyloid (Aβ+) status prior to trial enrollment.MethodsExcluding trials targeting non-cognitive symptoms, we conducted meta-analyses on progression measures from 25 selected RCTs using R version 4.2.0, along with the metafor and emmeans libraries.ResultsThe Functional Activities Questionnaire (FAQ) demonstrated the greatest sensitivity over 12 weeks. Other cognitive measures demonstrated lower sensitivity. The integrated Alzheimer's Disease Rating Scale (iADRS) and Clinical Dementia Rating-Sum of Boxes (CDR-SB) seemed more effective than their individual cognitive components. Neuropsychiatric measures were the least sensitive in measuring progression.DiscussionFunctional measures generally outperformed other measure categories. Purely cognitive domain-based measures were suboptimal for tracking early AD progression. Ideally, future measures should incorporate both cognitive and functional components to enhance sensitivity.HighlightsConcerns remain regarding the limitations of current outcome measures used in AD clinical trials, particularly their sensitivity in the early and preclinical stages of the disease, which hampers their reliability as indicators of AD progression. The Functional Activities Questionnaire (FAQ) demonstrated the most substantial weighted mean change over 12 weeks, followed by the Mini-Mental State Examination (MMSE). Functional measures outperformed other measure categories. Composite scores of integrated Alzheimer's Disease Rating Scale and Clinical Dementia Rating-Sum of Boxes are more sensitive to change than their individual cognitive components, possibly driven by the functional components of the score. Neuropsychiatric measures analyzed in this study appeared to be the least sensitive in measuring progression.
| S-EPMC11667530 | biostudies-literature
Project description:BackgroundResearch using data-driven cluster analysis has proposed five subgroups of diabetes with differences in diabetes progression and risk of complications. We aimed to compare the clinical utility of this subgroup-based approach for predicting patient outcomes with an alternative strategy of developing models for each outcome using simple patient characteristics.MethodsWe identified five clusters in the ADOPT trial (n=4351) using the same data-driven cluster analysis as reported by Ahlqvist and colleagues. Differences between clusters in glycaemic and renal progression were investigated and contrasted with stratification using simple continuous clinical features (age at diagnosis for glycaemic progression and baseline renal function for renal progression). We compared the effectiveness of a strategy of selecting glucose-lowering therapy using clusters with one combining simple clinical features (sex, BMI, age at diagnosis, baseline HbA1c) in an independent trial cohort (RECORD [n=4447]).FindingsClusters identified in trial data were similar to those described in the original study by Ahlqvist and colleagues. Clusters showed differences in glycaemic progression, but a model using age at diagnosis alone explained a similar amount of variation in progression. We found differences in incidence of chronic kidney disease between clusters; however, estimated glomerular filtration rate at baseline was a better predictor of time to chronic kidney disease. Clusters differed in glycaemic response, with a particular benefit for thiazolidinediones in patients in the severe insulin-resistant diabetes cluster and for sulfonylureas in patients in the mild age-related diabetes cluster. However, simple clinical features outperformed clusters to select therapy for individual patients.InterpretationThe proposed data-driven clusters differ in diabetes progression and treatment response, but models that are based on simple continuous clinical features are more useful to stratify patients. This finding suggests that precision medicine in type 2 diabetes is likely to have most clinical utility if it is based on an approach of using specific phenotypic measures to predict specific outcomes, rather than assigning patients to subgroups.FundingUK Medical Research Council.
| S-EPMC6520497 | biostudies-literature