Multiple Subtypes of Alzheimer's Disease Base on Brain Atrophy Pattern

Multimodal subtypes identified in Alzheimer's Disease Neuroimaging Initiative participants by missing-data-enabled subtype and stage inference

Alzheimer's disease is a highly heterogeneous disease in which different biomarkers are dynamic over different windows of the decades-long pathophysiological processes, and potentially have distinct involvement in different subgroups. Subtype and Stage Inference is an unsupervised learning algorithm that disentangles the phenotypic heterogeneity and temporal progression of disease biomarkers, providing disease insight and quantitative estimates of individual subtype and stage. However, a key limitation of Subtype and Stage Inference is that it requires a complete set of biomarkers for each subject, reducing the number of datapoints available for model fitting and limiting applications of Subtype and Stage Inference to modalities that are widely collected, e.g. volumetric biomarkers derived from structural MRI. In this study, we adapted the Subtype and Stage Inference algorithm to handle missing data, enabling the application of Subtype and Stage Inference to multimodal data (magnetic resonance imaging, positron emission tomography, cerebrospinal fluid and cognitive tests) from 789 participants in the Alzheimer's Disease Neuroimaging Initiative. Missing-data Subtype and Stage Inference identified five subtypes having distinct progression patterns, which we describe by the earliest unique abnormality as 'Typical AD with Early Tau', 'Typical AD with Late Tau', 'Cortical', 'Cognitive' and 'Subcortical'. These new multimodal subtypes were differentially associated with age, years of education, Apolipoprotein E (APOE4) status, white matter hyperintensity burden and the rate of conversion from mild cognitive impairment to Alzheimer's disease, with the 'Cognitive' subtype showing the fastest clinical progression, and the 'Subcortical' subtype the slowest. Overall, we demonstrate that missing-data Subtype and Stage Inference reveals a finer landscape of Alzheimer's disease subtypes, each of which are associated with different risk factors. Missing-data Subtype and Stage Inference has broad utility, enabling the prediction of progression in a much wider set of individuals, rather than being restricted to those with complete data.

Delineating the Heterogeneity of Alzheimer's Disease and Mild Cognitive Impairment Using Normative Models of Dynamic Brain Functional Networks

BACKGROUND

Alzheimer's disease (AD), which has been identified as the most common type of dementia, presents considerable heterogeneity in its clinical manifestations. Early intervention at the stage of mild cognitive impairment (MCI) holds potential in AD prevention. However, characterizing the heterogeneity of neurobiological abnormalities and identifying MCI subtypes pose significant challenges.

METHODS

We constructed sex-specific normative age models of dynamic brain functional networks and mapped the deviations of the brain characteristics for individuals from multiple datasets, including 295 patients with AD, 441 patients with MCI, and 1160 normal control participants. Then, based on these individual deviation patterns, subtypes for both AD and MCI were identified using the clustering method, and their similarities and differences were comprehensively assessed.

RESULTS

Individuals with AD and MCI were clustered into 2 subtypes, and these subtypes exhibited significant differences in their intrinsic brain functional phenotypes and spatial atrophy patterns, as well as in disease progression and cognitive decline trajectories. The subtypes with positive deviations in AD and MCI shared similar deviation patterns, as did those with negative deviations. There was a potential transformation of MCI with negative deviation patterns into AD, and participants with MCI had a more severe cognitive decline rate.

CONCLUSIONS

In this study, we quantified neurophysiological heterogeneity by analyzing deviation patterns from the dynamic functional connectome normative model and identified disease subtypes of AD and MCI using a comprehensive resting-state functional magnetic resonance imaging multicenter dataset. The findings provide new insights for developing early prevention and personalized treatment strategies for AD.

Convergent Neuroimaging and Molecular Signatures in Mild Cognitive Impairment and Alzheimer's Disease: A Data-Driven Meta-Analysis with N = 3,118

The current study aimed to evaluate the susceptibility to regional brain atrophy and its biological mechanism in Alzheimer's disease (AD). We conducted data-driven meta-analyses to combine 3,118 structural magnetic resonance images from three datasets to obtain robust atrophy patterns. Then we introduced a set of radiogenomic analyses to investigate the biological basis of the atrophy patterns in AD. Our results showed that the hippocampus and amygdala exhibit the most severe atrophy, followed by the temporal, frontal, and occipital lobes in mild cognitive impairment (MCI) and AD. The extent of atrophy in MCI was less severe than that in AD. A series of biological processes related to the glutamate signaling pathway, cellular stress response, and synapse structure and function were investigated through gene set enrichment analysis. Our study contributes to understanding the manifestations of atrophy and a deeper understanding of the pathophysiological processes that contribute to atrophy, providing new insight for further clinical research on AD.

A review of neuroimaging-based data-driven approach for Alzheimer's disease heterogeneity analysis

Alzheimer's disease (AD) is a complex form of dementia and due to its high phenotypic variability, its diagnosis and monitoring can be quite challenging. Biomarkers play a crucial role in AD diagnosis and monitoring, but interpreting these biomarkers can be problematic due to their spatial and temporal heterogeneity. Therefore, researchers are increasingly turning to imaging-based biomarkers that employ data-driven computational approaches to examine the heterogeneity of AD. In this comprehensive review article, we aim to provide health professionals with a comprehensive view of past applications of data-driven computational approaches in studying AD heterogeneity and planning future research directions. We first define and offer basic insights into different categories of heterogeneity analysis, including spatial heterogeneity, temporal heterogeneity, and spatial-temporal heterogeneity. Then, we scrutinize 22 articles relating to spatial heterogeneity, 14 articles relating to temporal heterogeneity, and five articles relating to spatial-temporal heterogeneity, highlighting the strengths and limitations of these strategies. Furthermore, we discuss the importance of understanding spatial heterogeneity in AD subtypes and their clinical manifestations, biomarkers for abnormal orderings and AD stages, the recent advancements in spatial-temporal heterogeneity analysis for AD, and the emerging role of omics data integration in advancing personalized diagnosis and treatment for AD patients. By emphasizing the significance of understanding AD heterogeneity, we hope to stimulate further research in this field to facilitate the development of personalized interventions for AD patients.

Robustly uncovering the heterogeneity of neurodegenerative disease by using data-driven subtyping in neuroimaging: A review

Neurodegenerative diseases are associated with heterogeneity in genetics, pathology, and clinical manifestation. Understanding this heterogeneity is particularly relevant for clinical prognosis and stratifying patients for disease modifying treatments. Recently, data-driven methods based on neuroimaging have been applied to investigate the subtyping of neurodegenerative disease, helping to disentangle this heterogeneity. We reviewed brain-based subtyping studies in aging and representative neurodegenerative diseases, including Alzheimer's disease, mild cognitive impairment, frontotemporal dementia, and Lewy body dementia, from January 2000 to November 2022. We summarized clustering methods, validation, robustness, reproducibility, and clinical relevance of 71 eligible studies in the present study. We found vast variations in approaches between studies, including ten neuroimaging modalities, 24 cluster algorithms, and 41 methods of cluster number determination. The clinical relevance of subtyping studies was evaluated by summarizing the analysis method of clinical measurements, showing a relatively low clinical utility in the current studies. Finally, we conclude that future studies of heterogeneity in neurodegenerative disease should focus on validation, comparison between subtyping approaches, and prioritise clinical utility.

Knowledge-guided Deep Temporal Clustering for Alzheimer's Disease Subtypes in Completed Clinical Trials

Alzheimer's disease (AD) is a multifaceted neurodegenerative disorder with varied patient progression. We aim to test the hypothesis that AD patients can be categorized into subgroups based on differences in progression. We leveraged data from three randomized clinical trials (RCTs) to develop a knowledge-guided, deep temporal clustering (KG-DTC) framework for AD subtyping. This model combined autoencoders for contextual information capture, k-means clustering for representation formation, and clinical outcome classification for clinical knowledge integration. The derived representations, encompassing demographics, APOE genotype, cognitive assessments, brain volumes, and biomarkers, were clustered using the Gaussian Mixture Model to identify AD subtypes. Our novel KG-DTC framework was developed using placebo data from 2,087 AD patients across three solanezumab clinical trials (EXPEDITION, EXPEDITION2, and EXPEDITION3), achieving high performance in outcome prediction and clustering. The KG-DTC model demonstrated superior clustering structures, especially when combined with k-means clustering loss. External validation with independent clinical trial data showed consistent clustering results, with a 0.33 silhouette score for three clusters. The model's stability was confirmed through a leave-one-out approach, with an average adjusted Rand Index around 0.945. Three distinct AD subtypes were identified, each exhibiting unique patterns of cognitive function, neurodegeneration, and amyloid beta levels. Notably, Subtype 3 (S3) showed rapid cognitive decline across multiple clinical measures (e.g., 0.64 in S1 vs. -1.06 in S2 vs. 15.09 in S3 of average ADAS total change score, p<.001). This innovative approach offers promising insights for understanding variability in treatment outcomes and personalizing AD treatment strategies.

How Many Alzheimer-Perusini's Atypical Forms Do We Still Have to Discover?

Alzheimer-Perusini's (AD) disease represents the most spread dementia around the world and constitutes a serious problem for public health. It was first described by the two physicians from whom it took its name. Nowadays, we have extensively expanded our knowledge about this disease. Starting from a merely clinical and histopathologic description, we have now reached better molecular comprehension. For instance, we passed from an old conceptualization of the disease based on plaques and tangles to a more modern vision of mixed proteinopathy in a one-to-one relationship with an alteration of specific glial and neuronal phenotypes. However, no disease-modifying therapies are yet available. It is likely that the only way to find a few "magic bullets" is to deepen this aspect more and more until we are able to draw up specific molecular profiles for single AD cases. This review reports the most recent classifications of AD atypical variants in order to summarize all the clinical evidence using several discrimina (for example, post mortem neurofibrillary tangle density, cerebral atrophy, or FDG-PET studies). The better defined four atypical forms are posterior cortical atrophy (PCA), logopenic variant of primary progressive aphasia (LvPPA), behavioral/dysexecutive variant and AD with corticobasal degeneration (CBS). Moreover, we discuss the usefulness of such classifications before outlining the molecular-genetic aspects focusing on microglial activity or, more generally, immune system control of neuroinflammation and neurodegeneration.

Cognitive differences across ethnoracial category, socioeconomic status across the Alzheimer's disease spectrum: Can an ability discrepancy score level the playing field?

An ability discrepancy (crystallized minus fluid abilities) might be a personally relevant cognitive marker of risk for Alzheimer's disease (AD) and might help reduce measurement bias often present in traditional measures of cognition. In a large national sample of adults aged 60-104 years (N = 14,257), we investigated whether the intersectionality of group characteristics previously shown to pose a risk for AD including ethnoracial category, socioeconomic status, and sex (a) differed in ability discrepancy compared to traditional neuropsychological tests and (b) moderated the relationship between an ability discrepancy and AD symptom severity. In cognitively normal older adults, results indicated that across each decade, fluid and memory composite scores generally exhibited large group differences with sex, education, and ethnoracial category. In contrast, the ability discrepancy score showed much smaller group differences, thus removing much of the biases inherent in the tests. Women with higher education differed in discrepancy performance from other groups, suggesting a subgroup in which this score might reduce bias to a lesser extent. Importantly, a greater ability discrepancy was associated with greater AD symptom severity across the AD continuum. Subgroup analyses suggest that this relationship holds for all groups except for some subgroups of Hispanic Americans. These findings suggest that an ability discrepancy measure might be a better indicator of baseline cognition than traditional measures that show more egregious measurement bias across diverse groups of people.

A Convolutional Neural Network and Graph Convolutional Network Based Framework for AD Classification

The neuroscience community has developed many convolutional neural networks (CNNs) for the early detection of Alzheimer's disease (AD). Population graphs are thought of as non-linear structures that capture the relationships between individual subjects represented as nodes, which allows for the simultaneous integration of imaging and non-imaging information as well as individual subjects' features. Graph convolutional networks (GCNs) generalize convolution operations to accommodate non-Euclidean data and aid in the mining of topological information from the population graph for a disease classification task. However, few studies have examined how GCNs' input properties affect AD-staging performance. Therefore, we conducted three experiments in this work. Experiment 1 examined how the inclusion of demographic information in the edge-assigning function affects the classification of AD versus cognitive normal (CN). Experiment 2 was designed to examine the effects of adding various neuropsychological tests to the edge-assigning function on the mild cognitive impairment (MCI) classification. Experiment 3 studied the impact of the edge assignment function. The best result was obtained in Experiment 2 on multi-class classification (AD, MCI, and CN). We applied a novel framework for the diagnosis of AD that integrated CNNs and GCNs into a unified network, taking advantage of the excellent feature extraction capabilities of CNNs and population-graph processing capabilities of GCNs. To learn high-level anatomical features, DenseNet was used; a set of population graphs was represented with nodes defined by imaging features and edge weights determined by different combinations of imaging or/and non-imaging information, and the generated graphs were then fed to the GCNs for classification. Both binary classification and multi-class classification showed improved performance, with an accuracy of 91.6% for AD versus CN, 91.2% for AD versus MCI, 96.8% for MCI versus CN, and 89.4% for multi-class classification. The population graph's imaging features and edge-assigning functions can both significantly affect classification accuracy.

Effects of Patchwise Sampling Strategy to Three-Dimensional Convolutional Neural Network-Based Alzheimer's Disease Classification

In recent years, the rapid development of artificial intelligence has promoted the widespread application of convolutional neural networks (CNNs) in neuroimaging analysis. Although three-dimensional (3D) CNNs can utilize the spatial information in 3D volumes, there are still some challenges related to high-dimensional features and potential overfitting issues. To overcome these problems, patch-based CNNs have been used, which are beneficial for model generalization. However, it is unclear how the choice of a patchwise sampling strategy affects the performance of the Alzheimer's Disease (AD) classification. To this end, the present work investigates the impact of a patchwise sampling strategy for 3D CNN based AD classification. A 3D framework cascaded by two-stage subnetworks was used for AD classification. The patch-level subnetworks learned feature representations from local image patches, and the subject-level subnetwork combined discriminative feature representations from all patch-level subnetworks to generate a classification score at the subject level. Experiments were conducted to determine the effect of patch partitioning methods, the effect of patch size, and interactions between patch size and training set size for AD classification. With the same data size and identical network structure, the 3D CNN model trained with 48 × 48 × 48 cubic image patches showed the best performance in AD classification (ACC = 89.6%). The model trained with hippocampus-centered, region of interest (ROI)-based image patches showed suboptimal performance. If the pathological features are concentrated only in some regions affected by the disease, the empirically predefined ROI patches might be the right choice. The better performance of cubic image patches compared with cuboidal image patches is likely related to the pathological distribution of AD. The image patch size and training sample size together have a complex influence on the performance of the classification. The size of the image patches should be determined based on the size of the training sample to compensate for noisy labels and the problem of the curse of dimensionality. The conclusions of the present study can serve as a reference for the researchers who wish to develop a superior 3D patch-based CNN model with an appropriate patch sampling strategy.

Four Distinct Subtypes of Alzheimer's Disease Based on Resting-State Connectivity Biomarkers

BACKGROUND

Alzheimer's disease (AD) is a neurodegenerative disorder with significant heterogeneity. Different AD phenotypes may be associated with specific brain network changes. Uncovering disease heterogeneity by using functional networks could provide insights into precise diagnoses.

METHODS

We investigated the subtypes of AD using nonnegative matrix factorization clustering on the previously identified 216 resting-state functional connectivities that differed between AD and normal control subjects. We conducted the analysis using a discovery dataset (n = 809) and a validated dataset (n = 291). Next, we grouped individuals with mild cognitive impairment according to the model obtained in the AD groups. Finally, the clinical measures and brain structural characteristics were compared among the subtypes to assess their relationship with differences in the functional network.

RESULTS

Individuals with AD were clustered into 4 subtypes reproducibly, which included those with 1) diffuse and mild functional connectivity disruption (subtype 1), 2) predominantly decreased connectivity in the default mode network accompanied by an increase in the prefrontal circuit (subtype 2), 3) predominantly decreased connectivity in the anterior cingulate cortex accompanied by an increase in prefrontal cortex connectivity (subtype 3), and 4) predominantly decreased connectivity in the basal ganglia accompanied by an increase in prefrontal cortex connectivity (subtype 4). In addition to these differences in functional connectivity, differences between the AD subtypes were found in cognition, structural measures, and cognitive decline patterns.

CONCLUSIONS

These comprehensive results offer new insights that may advance precision medicine for AD and facilitate strategies for future clinical trials.

Characterization of Alzheimer’s Disease Subtypes Based on Magnetic Resonance Imaging and Perfusion Single-Photon Emission Computed Tomography

Background: Alzheimer’s disease (AD) is a biologically heterogenous disease. Previous studies have reported the existence of various AD subtypes, and the various clinical features of the subtypes. However, inconsistent results have been obtained. Objective: To clarify the clinical characteristics of the various AD subtypes, by classifying probable AD into subtypes based on magnetic resonance imaging (MRI) and single-photon emission computed tomography (SPECT) findings. Methods: A total of 245 patients with probable AD were classified into the typical AD (TAD) subtype, limbic-predominant (LP) subtype, hippocampal-sparing (HS) subtype, and minimal-change (MC) subtype, based on the presence of medial temporal lobe atrophy on MRI and posterior cerebral hypoperfusion on SPECT. Demographics, including age, sex, body mass index, disease duration, education years, comorbidities, frailty, leisure activity, and neuropsychological findings were compared between the AD subtypes. Results: he frequency of TAD, LP, HS, and MC subtypes was 49%, 20%, 18%, and 13%, respectively. Patients with the LP subtype were older and characterized by fewer major comorbidities, higher frailty, and slower progression of disease. Patients with the HS subtype were younger and characterized by shorter disease duration, lower frailty, and preserved memory, but had prominent constructional dysfunction. Patients of the MC subtype were characterized by shorter disease duration, lower education level, less leisure activity, less impaired memory and orientation, and slower progression. Conclusion: Patients with different AD subtypes differed in their demographic and clinical features. The characterization of patients’ AD subtypes may provide effective support for the diagnosis, treatment, and care of AD patients.

Quantification of Brain β-Amyloid Load in Parkinson's Disease With Mild Cognitive Impairment: A PET/MRI Study

Background

Mild cognitive impairment in Parkinson's disease (PD-MCI) is associated with faster cognitive decline and conversion to dementia. There is uncertainty about the role of β-amyloid (Aβ) co-pathology and its contribution to the variability in PD-MCI profile and cognitive progression.

Objective

To study how presence of Aβ affects clinical and cognitive manifestations as well as regional brain volumes in PD-MCI.

Methods

Twenty-five PD-MCI patients underwent simultaneous PET/3T-MRI with [¹⁸F]flutemetamol and a clinical and neuropsychological examination allowing level II diagnosis. We tested pairwise differences in motor, clinical, and cognitive features with Mann–Whitney U test. We calculated [¹⁸F]flutemetamol (FMM) standardized uptake value ratios (SUVR) in striatal and cortical ROIs, and we performed a univariate linear regression analysis between the affected cognitive domains and the mean SUVR. Finally, we investigated differences in cortical and subcortical brain regional volumes with magnetic resonance imaging (MRI).

Results

There were 8 Aβ+ and 17 Aβ- PD-MCI. They did not differ for age, disease duration, clinical, motor, behavioral, and global cognition scores. PD-MCI-Aβ+ showed worse performance in the overall executive domain (p = 0.037). Subcortical ROIs analysis showed significant Aβ deposition in PD-MCI-Aβ+ patients in the right caudal and rostral middle frontal cortex, in precuneus, in left paracentral and pars triangularis (p < 0.0001), and bilaterally in the putamen (p = 0.038). Cortical regions with higher amyloid load correlated with worse executive performances (p < 0.05). Voxel-based morphometry (VBM) analyses showed no between groups differences.

Conclusions

Presence of cerebral Aβ worsens executive functions, but not motor and global cognitive abilities in PD-MCI, and it is not associated with middle-temporal cortex atrophy. These findings, together with the observation of significant proportion of PD-MCI-Aβ-, suggest that Aβ may not be the main pathogenetic determinant of cognitive deterioration in PD-MCI, but it would rather aggravate deficits in domains vulnerable to Parkinson primary pathology.

A systematic analysis of diagnostic performance for Alzheimer's disease using structural MRI

Background

Alzheimer's disease (AD) is one of the most common neurodegenerative disorders in the elderly. Although numerous structural magnetic resonance imaging (sMRI) studies have reported diagnostic models that could distinguish AD from normal controls (NCs) with 80-95% accuracy, limited efforts have been made regarding the clinically practical computer-aided diagnosis (CAD) system for AD.

Objective

To explore the potential factors that hinder the clinical translation of the AD-related diagnostic models based on sMRI.

Methods

To systematically review the diagnostic models for AD based on sMRI, we identified relevant studies published in the past 15 years on PubMed, Web of Science, Scopus, and Ovid. To evaluate the heterogeneity and publication bias among those studies, we performed subgroup analysis, meta-regression, Begg's test, and Egger's test.

Results

According to our screening criterion, 101 studies were included. Our results demonstrated that high diagnostic accuracy for distinguishing AD from NC was obtained in recently published studies, accompanied by significant heterogeneity. Meta-analysis showed that many factors contributed to the heterogeneity of high diagnostic accuracy of AD using sMRI, which included but was not limited to the following aspects: (i) different datasets; (ii) different machine learning models, e.g. traditional machine learning or deep learning model; (iii) different cross-validation methods, e.g. k-fold cross-validation leads to higher accuracies than leave-one-out cross-validation, but both overestimate the accuracy when compared to validation in independent samples; (iv) different sample sizes; and (v) the publication times. We speculate that these complicated variables might be the adverse factor for developing a clinically applicable system for the early diagnosis of AD.

Conclusions

Our findings proved that previous studies reported promising results for classifying AD from NC with different models using sMRI. However, considering the many factors hindering clinical radiology practice, there would still be a long way to go to improve.

Concordance of Alzheimer’s Disease Subtypes Produced from Different Representative Morphological Measures: A Comparative Study

Background: Gray matter (GM) density and cortical thickness (CT) obtained from structural magnetic resonance imaging are representative GM morphological measures that have been commonly used in Alzheimer’s disease (AD) subtype research. However, how the two measures affect the definition of AD subtypes remains unclear. Methods: A total of 180 AD patients from the ADNI database were used to identify AD subgroups. The subtypes were identified via a data-driven strategy based on the density features and CT features, respectively. Then, the similarity between the two features in AD subtype definition was analyzed. Results: Four distinct subtypes were discovered by both density and CT features: diffuse atrophy AD, minimal atrophy AD (MAD), left temporal dominant atrophy AD (LTAD), and occipital sparing AD. The matched subtypes exhibited relatively high similarity in atrophy patterns and neuropsychological and neuropathological characteristics. They differed only in MAD and LTAD regarding the carrying of apolipoprotein E ε2. Conclusions: The results verified that different representative morphological GM measurement methods could produce similar AD subtypes. Meanwhile, the influences of apolipoprotein E genotype, asymmetric disease progression, and their interactions should be considered and included in the AD subtype definition. This study provides a valuable reference for selecting features in future studies of AD subtypes.

Multi-model and multi-slice ensemble learning architecture based on 2D convolutional neural networks for Alzheimer's disease diagnosis

Alzheimer's Disease (AD) is a chronic neurodegenerative disease without effective medications or supplemental treatments. Thus, predicting AD progression is crucial for clinical practice and medical research. Due to limited neuroimaging data, two-dimensional convolutional neural networks (2D CNNs) have been commonly adopted to differentiate among cognitively normal subjects (CN), people with mild cognitive impairment (MCI), and AD patients. Therefore, this paper proposes an ensemble learning (EL) architecture based on 2D CNNs, using a multi-model and multi-slice ensemble. First, the top 11 coronal slices of grey matter density maps for AD versus CN classifications were selected. Second, the discriminator of a generative adversarial network, VGG16, and ResNet50 were trained with the selected slices, and the majority voting scheme was used to merge the multi-slice decisions of each model. Afterwards, those three classifiers were used to construct an ensemble model. Multi-slice ensemble learning was designed to obtain spatial features, while multi-model integration reduced the prediction error rate. Finally, transfer learning was used in domain adaptation to refine those CNNs, moving them from working solely with AD versus CN classifications to being applicable to other tasks. This ensemble approach achieved accuracy values of 90.36%, 77.19%, and 72.36% when classifying AD versus CN, AD versus MCI, and MCI versus CN, respectively. Compared with other state-of-the-art 2D studies, the proposed approach provides an effective, accurate, automatic diagnosis along the AD continuum. This technique may enhance AD diagnostics when the sample size is limited.