Aberrant functional connectivity and activity in Parkinson's disease and comorbidity with depression based on radiomic analysis

Identification of Depression Subtypes in Parkinson's Disease Patients via Structural MRI Whole-Brain Radiomics: An Unsupervised Machine Learning Study

OBJECTIVE

Current clinical evaluation may tend to lack precision in detecting depression in Parkinson's disease (DPD). Radiomics features have gradually shown potential as auxiliary diagnostic tools in identifying and distinguishing different subtypes of Parkinson's disease (PD), and a radiomic approach that combines unsupervised machine learning has the potential to identify DPD.

METHODS

Analyze the clinical and imaging data of 272 Parkinson's disease (PD) patients from the PPMI dataset, along with 45 PD patients from the NACC dataset. Extract radiomic features from T1-weighted MRI images and employ principal component analysis (PCA) for dimensionality reduction. Subsequently, apply four unsupervised clustering methods including Gaussian mixture model (GMM), hierarchical clustering, K-means, and partitioning around medoids (PAM) to classify cases in the PPMI dataset into distinct subtypes. Identify high-risk subtypes of DPD on the basis of the time and number of depression progression, and validate these findings using the NACC dataset. The data from the high-risk subtype were divided into a training subtype and a testing subtype in a 7:3 ratio. Multiple logistic regression analysis was conducted on the training subtype data to develop a traditional logistic regression model for the high-risk subtype, which was subsequently compared with a supervised logistic regression model constructed for the entire PPMI cohort. Finally, the performance of both models was evaluated using receiver operating characteristic (ROC) curves. In addition, a decision tree (DT) model was constructed based on independent risk factors of high-risk subtypes and validated using low-risk subtype data. ROC curves were employed to validate this model across training subtype, testing subtype, and low-risk subtype datasets.

RESULTS

The PAM clustering method demonstrates superior performance compared to the other three clustering methods when the number of clusters is 2. High-risk subtypes of DPD can be effectively distinguished in both the PPMI and NACC datasets. A traditional logistic regression model was developed based on rapid-eye-movement behavior disorder, UPDRS I score, UPDRS II score, and ptau in high-risk subgroups. This model exhibits a diagnostic efficacy (AUC = 0.731) that surpasses that of the traditional regression model constructed using the entire PPMI cohort (AUC = 0.674). The prediction model based on high-risk subtypes had AUC values of 0.853 and 0.81 in the training and testing subtypes, sensitivities of 0.765 and 0.786, and specificities of 0.771 and 0.815, respectively. The AUC, sensitivity, and specificity in the nonhigh-risk subtype were 0.859, 0.654, and 0.852, respectively.

CONCLUSION

By identifying MRI structural radiomics and clinical features as potential biomarkers, the radiomic approach and UCA provide new insights into the pathophysiology of DPD to support the clinical diagnosis with high prediction accuracy.

Resting-state functional magnetic resonance imaging and support vector machines for the diagnosis of major depressive disorder in adolescents

BACKGROUND

Research has found that the amygdala plays a significant role in underlying pathology of major depressive disorder (MDD). However, few studies have explored machine learning-assisted diagnostic biomarkers based on amygdala functional connectivity (FC).

AIM

To investigate the analysis of neuroimaging biomarkers as a streamlined approach for the diagnosis of MDD in adolescents.

METHODS

Forty-four adolescents diagnosed with MDD and 43 healthy controls were enrolled in the study. Using resting-state functional magnetic resonance imaging, the FC was compared between the adolescents with MDD and the healthy controls, with the bilateral amygdala serving as the seed point, followed by statistical analysis of the results. The support vector machine (SVM) method was then applied to classify functional connections in various brain regions and to evaluate the neurophysiological characteristics associated with MDD.

RESULTS

Compared to the controls and using the bilateral amygdala as the region of interest, patients with MDD showed significantly lower FC values in the left inferior temporal gyrus, bilateral calcarine, right lingual gyrus, and left superior occipital gyrus. However, there was an increase in the FC value in Vermis-10. The SVM analysis revealed that the reduction in the FC value in the right lingual gyrus could effectively differentiate patients with MDD from healthy controls, achieving a diagnostic accuracy of 83.91%, sensitivity of 79.55%, specificity of 88.37%, and an area under the curve of 67.65%.

CONCLUSION

The results showed that an abnormal FC value in the right lingual gyrus was effective as a neuroimaging biomarker to distinguish patients with MDD from healthy controls.

Causal Forest Machine Learning Analysis of Parkinson's Disease in Resting-State Functional Magnetic Resonance Imaging

In recent years, Artificial Intelligence has been used to assist healthcare professionals in detecting and diagnosing neurodegenerative diseases. In this study, we propose a methodology to analyze functional Magnetic Resonance Imaging signals and perform classification between Parkinson's disease patients and healthy participants using Machine Learning algorithms. In addition, the proposed approach provides insights into the brain regions affected by the disease. The functional Magnetic Resonance Imaging from the PPMI and 1000-FCP datasets were pre-processed to extract time series from 200 brain regions per participant, resulting in 11,600 features. Causal Forest and Wrapper Feature Subset Selection algorithms were used for dimensionality reduction, resulting in a subset of features based on their heterogeneity and association with the disease. We utilized Logistic Regression and XGBoost algorithms to perform PD detection, achieving 97.6% accuracy, 97.5% F1 score, 97.9% precision, and 97.7%recall by analyzing sets with fewer than 300 features in a population including men and women. Finally, Multiple Correspondence Analysis was employed to visualize the relationships between brain regions and each group (women with Parkinson, female controls, men with Parkinson, male controls). Associations between the Unified Parkinson's Disease Rating Scale questionnaire results and affected brain regions in different groups were also obtained to show another use case of the methodology. This work proposes a methodology to (1) classify patients and controls with Machine Learning and Causal Forest algorithm and (2) visualize associations between brain regions and groups, providing high-accuracy classification and enhanced interpretability of the correlation between specific brain regions and the disease across different groups.

Prediction of Early Antidepressant Efficacy in Patients with Major Depressive Disorder Based on Multidimensional Features of rs-fMRI and P11 Gene DNA Methylation: Prédiction de l'efficacité précoce d'un antidépresseur chez des patients souffrant du trouble dépressif majeur d'après les caractéristiques multidimensionnelles de la méthylation de l'ADN du gène P11 et de la IRMf-rs

OBJECTIVE

This study established a machine learning model based on the multidimensional data of resting-state functional activity of the brain and P11 gene DNA methylation to predict the early efficacy of antidepressant treatment in patients with major depressive disorder (MDD).

METHODS

A total of 98 Han Chinese MDD were analysed in this study. Patients were divided into 51 responders and 47 nonresponders according to whether the Hamilton Depression Rating Scale-17 items (HAMD-17) reduction rate was ≥50% after 2 weeks of antidepressant treatment. At baseline, the Illumina HiSeq Platform was used to detect the methylation of 74 CpG sites of the P11 gene in peripheral blood samples. Resting-state functional magnetic resonance imaging (rs-fMRI) scan detected the amplitude of low-frequency fluctuations (ALFF), regional homogeneity (ReHo), and functional connectivity (FC) in 116 brain regions. The least absolute shrinkage and selection operator analysis method was used to perform feature reduction and feature selection. Four typical machine learning methods were used to establish support vector machine (SVM), random forest (RF), Naïve Bayes (NB), and logistic regression (LR) prediction models based on different combinations of functional activity of the brain, P11 gene DNA methylation and clinical/demographic features after screening.

RESULTS

The SVM model based on ALFF, ReHo, FC, P11 methylation, and clinical/demographic features showed the best performance, with 95.92% predictive accuracy and 0.9967 area under the receiver operating characteristic curve, which was better than RF, NB, and LR models.

CONCLUSION

The multidimensional data features combining rs-fMRI, DNA methylation, and clinical/demographic features can predict the early antidepressant efficacy in MDD.

Disrupted topologic efficiency of brain functional connectome in de novo Parkinson's disease with depression

Growing evidence supports that depression in Parkinson's disease (PD) depends on disruptions in specific neural networks rather than regional dysfunction. According to the resting-state functional magnetic resonance imaging data, the study attempted to decipher the alterations in the topological properties of brain networks in de novo depression in PD (DPD). The study also explored the neural network basis for depressive symptoms in PD. We recruited 20 DPD, 37 non-depressed PD and 41 healthy controls (HC). The Graph theory and network-based statistical methods helped analyse the topological properties of brain functional networks and anomalous subnetworks across these groups. The relationship between altered properties and depression severity was also investigated. DPD revealed significantly reduced nodal efficiency in the left superior temporal gyrus. Additionally, DPD decreased five hubs, primarily located in the temporal-occipital cortex, and increased seven hubs, mainly distributed in the limbic cortico-basal ganglia circuit. The betweenness centrality of the left Medio Ventral Occipital Cortex was positively associated with depressive scores in DPD. In contrast to HC, DPD had a multi-connected subnetwork with significantly lower connectivity, primarily distributed in the visual, somatomotor, dorsal attention and default networks. Regional topological disruptions in the temporal-occipital region are critical in the DPD neurological mechanism. It might suggest a potential network biomarker among newly diagnosed DPD patients.

Altered regional homogeneity and homotopic connectivity in Chinese breast cancer survivors with fear of cancer recurrence: A resting-state fMRI study

BACKGROUND

Fear of cancer recurrence (FCR) is one of the most distressing concerns for breast cancer survivors, but the neural mechanism underlying FCR remains unclear.

METHODS

We conducted a cross-sectional study and recruited 62 breast cancer survivors varying in FCR (31 high-FCR individuals and 31 low-FCR individuals) and compared neuroimaging findings. Data from 3 low-FCR subjects were excluded because they did not complete all experiments. All the participants underwent resting-state functional magnetic resonance imaging (rs-fMRI). Regional homogeneity (ReHo) and voxel-mirrored homotopic connectivity (VMHC) were assessed.

RESULTS

Breast cancer survivors with high and low FCR significantly differed in the ReHo of the left caudate nucleus and precuneus as well as in the VMHC of the posterior cerebellar lobe, superior frontal gyrus, orbital frontal gyrus, inferior frontal gyrus, occipital gyrus, inferior parietal lobule and frontal middle gyrus. FCR was negatively correlated with the mean ReHo of the left caudate nucleus (r = -0.501, p < 0.001) and positively correlated with the mean ReHo of the right precuneus (r = 0.505, p < 0.001). In addition, FCR was positively correlated with the mean VMHC of the bilateral superior occipital gyrus (r = 0.438, p < 0.001).

CONCLUSION

These findings suggest that the left caudate nucleus, right precuneus and bilateral superior occipital gyrus are involved in FCR, which may provide preliminary evidence to improve the present understanding of the neural mechanisms of FCR.

The differential diagnosis value of radiomics-based machine learning in Parkinson's disease: a systematic review and meta-analysis

Background

In recent years, radiomics has been increasingly utilized for the differential diagnosis of Parkinson's disease (PD). However, the application of radiomics in PD diagnosis still lacks sufficient evidence-based support. To address this gap, we carried out a systematic review and meta-analysis to evaluate the diagnostic value of radiomics-based machine learning (ML) for PD.

Methods

We systematically searched Embase, Cochrane, PubMed, and Web of Science databases as of November 14, 2022. The radiomics quality assessment scale (RQS) was used to evaluate the quality of the included studies. The outcome measures were the c-index, which reflects the overall accuracy of the model, as well as sensitivity and specificity. During this meta-analysis, we discussed the differential diagnostic value of radiomics-based ML for Parkinson's disease and various atypical parkinsonism syndromes (APS).

Results

Twenty-eight articles with a total of 6,057 participants were included. The mean RQS score for all included articles was 10.64, with a relative score of 29.56%. The pooled c-index, sensitivity, and specificity of radiomics for predicting PD were 0.862 (95% CI: 0.833-0.891), 0.91 (95% CI: 0.86-0.94), and 0.93 (95% CI: 0.87-0.96) in the training set, and 0.871 (95% CI: 0.853-0.890), 0.86 (95% CI: 0.81-0.89), and 0.87 (95% CI: 0.83-0.91) in the validation set, respectively. Additionally, the pooled c-index, sensitivity, and specificity of radiomics for differentiating PD from APS were 0.866 (95% CI: 0.843-0.889), 0.86 (95% CI: 0.84-0.88), and 0.80 (95% CI: 0.75-0.84) in the training set, and 0.879 (95% CI: 0.854-0.903), 0.87 (95% CI: 0.85-0.89), and 0.82 (95% CI: 0.77-0.86) in the validation set, respectively.

Conclusion

Radiomics-based ML can serve as a potential tool for PD diagnosis. Moreover, it has an excellent performance in distinguishing Parkinson's disease from APS. The support vector machine (SVM) model exhibits excellent robustness when the number of samples is relatively abundant. However, due to the diverse implementation process of radiomics, it is expected that more large-scale, multi-class image data can be included to develop radiomics intelligent tools with broader applicability, promoting the application and development of radiomics in the diagnosis and prediction of Parkinson's disease and related fields.

Systematic review registration

https://www.crd.york.ac.uk/PROSPERO/display_record.php?RecordID=383197, identifier ID: CRD42022383197.

Automatic classification of MSA subtypes using Whole-brain gray matter function and Structure-Based radiomics approach

BACKGROUND

This study aims to develop a radiomics method based on the function and structure of whole-brain gray matter to accurately classify multiple system atrophy with predominant Parkinsonism (MSA-P) or predominant cerebellar ataxia (MSA-C).

METHODS

We enrolled 30 MSA-C and 41 MSA-P cases for the internal cohort and 11 MSA-C and 10 MSA-P cases for the external test cohort. We extracted 7,308 features, including gray matter volume (GMV), mean amplitude of low-frequency fluctuation (mALFF), mean regional homogeneity (mReHo), degree of centrality (DC), voxel-mirrored homotopic connectivity (VMHC), and resting-state functional connectivity (RSFC) from 3D-T1 and Rs-fMR data. Feature selection was conducted with t-test and least absolute shrinkage and selection operator (Lasso). Classification was performed using the support vector machine with linear and RBF kernel (SVM-linear/SVM-RBF), random forest and logistic regression. Model performance was assessed via receiver operating characteristic (ROC) curve and compared with DeLong's test.

RESULTS

Feature selection resulted in 12 features, including 1 ALFF, 1 DC and 10 RSFC. All the classifiers showed remarkable classification performance, especially the RF model which exhibited AUC values of 0.91 and 0.80 in the validation and test datasets, respectively. The brain functional activity and connectivity in the cerebellum, orbitofrontal lobe and limbic system were important features to distinguish MSA subtypes with the same disease severity and duration.

CONCLUSION

Radiomics approach has the potential to support clinical diagnostic systems and to achieve high classification accuracy for distinguishing between MSA-C and MSA-P patients at the individual level.

Prognostic impact of examined lymph-node count for patients with esophageal cancer: development and validation prediction model

Esophageal cancer (EC) is a malignant tumor with high mortality. We aimed to find the optimal examined lymph node (ELN) count threshold and develop a model to predict survival of patients after radical esophagectomy. Two cohorts were analyzed: the training cohort which included 734 EC patients from the Chinese registry and the external testing cohort which included 3208 EC patients from the Surveillance, Epidemiology, and End Results (SEER) registry. Cox proportional hazards regression analysis was used to determine the prognostic value of ELNs. The cut-off point of the ELNs count was determined using R-statistical software. The prediction model was developed using random survival forest (RSF) algorithm. Higher ELNs count was significantly associated with better survival in both cohorts (training cohort: HR = 0.98, CI = 0.97-0.99, P < 0.01; testing cohort: HR = 0.98, CI = 0.98-0.99, P < 0.01) and the cut-off point was 18 (training cohort: P < 0.01; testing cohort: P < 0.01). We developed the RSF model with high prediction accuracy (AUC: training cohort: 87.5; testing cohort: 79.3) and low Brier Score (training cohort: 0.122; testing cohort: 0.152). The ELNs count beyond 18 is associated with better overall survival. The RSF model has preferable clinical capability in terms of individual prognosis assessment in patients after radical esophagectomy.

The pathobiological basis of depression in Parkinson disease: challenges and outlooks

Depression, with an estimated prevalence of about 40% is a most common neuropsychiatric disorder in Parkinson disease (PD), with a negative impact on quality of life, cognitive impairment and functional disability, yet the underlying neurobiology is poorly understood. Depression in PD (DPD), one of its most common non-motor symptoms, can precede the onset of motor symptoms but can occur at any stage of the disease. Although its diagnosis is based on standard criteria, due to overlap with other symptoms related to PD or to side effects of treatment, depression is frequently underdiagnosed and undertreated. DPD has been related to a variety of pathogenic mechanisms associated with the underlying neurodegenerative process, in particular dysfunction of neurotransmitter systems (dopaminergic, serotonergic and noradrenergic), as well as to disturbances of cortico-limbic, striato-thalamic-prefrontal, mediotemporal-limbic networks, with disruption in the topological organization of functional mood-related, motor and other essential brain network connections due to alterations in the blood-oxygen-level-dependent (BOLD) fluctuations in multiple brain areas. Other hypothetic mechanisms involve neuroinflammation, neuroimmune dysregulation, stress hormones, neurotrophic, toxic or metabolic factors. The pathophysiology and pathogenesis of DPD are multifactorial and complex, and its interactions with genetic factors, age-related changes, cognitive disposition and other co-morbidities awaits further elucidation.

Machine Learning on Early Diagnosis of Depression

To review the recent progress of machine learning for the early diagnosis of depression (major depressive disorder). The source of data was 32 original studies in the Web of Science. The search terms were "depression" (title) and "random forest" (abstract). The eligibility criteria were the dependent variable of depression, the interventions of machine learning (the decision tree, the naïve Bayesian, the random forest, the support vector machine and/or the artificial neural network), the outcomes of accuracy and/or the area under the receiver operating characteristic curve (AUC) for the early diagnosis of depression, the publication year of 2000 or later, the publication language of English and the publication journal of SCIE/SSCI. Different machine learning methods would be appropriate for different types of data for the early diagnosis of depression, e.g., logistic regression, the random forest, the support vector machine and/or the artificial neural network in the case of numeric data, the random forest in the case of genomic data. Their performance measures reported varied within 60.1-100.0 for accuracy and 64.0-96.0 for the AUC. Machine learning provides an effective, non-invasive decision support system for early diagnosis of depression.

Identifying Depression in Parkinson's Disease by Using Combined Diffusion Tensor Imaging and Support Vector Machine

Objective

To investigate white matter microstructural alterations in Parkinson's disease (PD) patients with depression using the whole-brain diffusion tensor imaging (DTI) method and to explore the DTI–based machine learning model in identifying depressed PD (dPD).

Methods

The DTI data were collected from 37 patients with dPD and 35 patients with non-depressed PD (ndPD), and 25 healthy control (HC) subjects were collected as the reference. An atlas-based analysis method was used to compare fractional anisotropy (FA) and mean diffusivity (MD) among the three groups. A support vector machine (SVM) was trained to examine the probability of discriminating between dPD and ndPD.

Results

As compared with ndPD, dPD group exhibited significantly decreased FA in the bilateral corticospinal tract, right cingulum (cingulate gyrus), left cingulum hippocampus, bilateral inferior longitudinal fasciculus, and bilateral superior longitudinal fasciculus, and increased MD in the right cingulum (cingulate gyrus) and left superior longitudinal fasciculus-temporal part. For discriminating between dPD and ndPD, the SVM model with DTI features exhibited an accuracy of 0.70 in the training set [area under the receiver operating characteristic curve (ROC) was 0.78] and an accuracy of 0.73 in the test set (area under the ROC was 0.71).

Conclusion

Depression in PD is associated with white matter microstructural alterations. The SVM machine learning model based on DTI parameters could be valuable for the individualized diagnosis of dPD.

Aberrant functional connectivity and activity in Parkinson's disease and comorbidity with depression based on radiomic analysis

INTRODUCTION

The current diagnosis of Parkinson's disease (PD) comorbidity with depression (DPD) largely depends on clinical evaluation. However, the modality may tend to lack precision in detecting PD with depression. A radiomic approach that combines functional connectivity and activity with clinical scores has the potential to achieve accurate and differential diagnosis between PD and DPD.

METHODS

In this study, we aimed to employ the radiomic approach to extract large-scale features of functional connectivity and activity for differentiating among DPD, PD with no depression (NDPD), and healthy controls (HC). We extracted 6,557 features of five types from all subjects including clinical characteristics, resting-state functional connectivity (RSFC), amplitude of low-frequency fluctuation (ALFF), regional homogeneity (ReHo), and voxel-mirrored homotopic connectivity (VMHC). Lasso, random forest, and support vector machine (SVM) were implemented for feature selection and dimension reduction based on the training sets, and the prediction performance for different methods in the testing sets was compared.

RESULTS

The results showed that nineteen features were selected for the group of DPD versus HC, 34 features were selected for the group of NDPD versus HC, and 17 features were retained for the group of DPD versus NDPD. In the testing sets, Lasso prediction achieved the accuracies of 0.95, 0.96, and 0.85 for distinguishing between DPD and HC, NDPD and HC, and DPD and NDPD, respectively. Random forest achieved the accuracies of 0.90, 0.82, and 0.90 for distinguishing between DPD and HC, NDPD and HC, and DPD and NDPD, respectively, while SVM yielded the accuracies of 1, 0.86 and 0.65 for distinguishing between DPD and HC, NDPD and HC, and DPD and NDPD, respectively.

CONCLUSIONS

By identifying aberrant functional connectivity and activity as potential biomarkers, the radiomic approach facilitates a deeper understanding and provides new insights into the pathophysiology of DPD to support the clinical diagnosis with high prediction accuracy.