1
|
Seifallahi M, Galvin JE, Ghoraani B. Detection of mild cognitive impairment using various types of gait tests and machine learning. Front Neurol 2024; 15:1354092. [PMID: 39055321 PMCID: PMC11269186 DOI: 10.3389/fneur.2024.1354092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Accepted: 06/27/2024] [Indexed: 07/27/2024] Open
Abstract
Introduction Alzheimer's disease and related disorders (ADRD) progressively impair cognitive function, prompting the need for early detection to mitigate its impact. Mild Cognitive Impairment (MCI) may signal an early cognitive decline due to ADRD. Thus, developing an accessible, non-invasive method for detecting MCI is vital for initiating early interventions to prevent severe cognitive deterioration. Methods This study explores the utility of analyzing gait patterns, a fundamental aspect of human motor behavior, on straight and oval paths for diagnosing MCI. Using a Kinect v.2 camera, we recorded the movements of 25 body joints from 25 individuals with MCI and 30 healthy older adults (HC). Signal processing, descriptive statistical analysis, and machine learning techniques were employed to analyze the skeletal gait data in both walking conditions. Results and discussion The study demonstrated that both straight and oval walking patterns provide valuable insights for MCI detection, with a notable increase in identifiable gait features in the more complex oval walking test. The Random Forest model excelled among various algorithms, achieving an 85.50% accuracy and an 83.9% F-score in detecting MCI during oval walking tests. This research introduces a cost-effective, Kinect-based method that integrates gait analysis-a key behavioral pattern-with machine learning, offering a practical tool for MCI screening in both clinical and home environments.
Collapse
Affiliation(s)
- Mahmoud Seifallahi
- Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL, United States
| | - James E. Galvin
- Comprehensive Center for Brain Health, Department of Neurology, University of Miami, Boca Raton, FL, United States
| | - Behnaz Ghoraani
- Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, FL, United States
| |
Collapse
|
2
|
Takemoto Y, Ito D, Komori S, Kishimoto Y, Yamada S, Hashizume A, Katsuno M, Nakatochi M. Comparing preprocessing strategies for 3D-Gene microarray data of extracellular vesicle-derived miRNAs. BMC Bioinformatics 2024; 25:221. [PMID: 38902629 PMCID: PMC11188187 DOI: 10.1186/s12859-024-05840-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 06/12/2024] [Indexed: 06/22/2024] Open
Abstract
BACKGROUND Extracellular vesicle-derived (EV)-miRNAs have potential to serve as biomarkers for the diagnosis of various diseases. miRNA microarrays are widely used to quantify circulating EV-miRNA levels, and the preprocessing of miRNA microarray data is critical for analytical accuracy and reliability. Thus, although microarray data have been used in various studies, the effects of preprocessing have not been studied for Toray's 3D-Gene chip, a widely used measurement method. We aimed to evaluate batch effect, missing value imputation accuracy, and the influence of preprocessing on measured values in 18 different preprocessing pipelines for EV-miRNA microarray data from two cohorts with amyotrophic lateral sclerosis using 3D-Gene technology. RESULTS Eighteen different pipelines with different types and orders of missing value completion and normalization were used to preprocess the 3D-Gene microarray EV-miRNA data. Notable results were suppressed in the batch effects in all pipelines using the batch effect correction method ComBat. Furthermore, pipelines utilizing missForest for missing value imputation showed high agreement with measured values. In contrast, imputation using constant values for missing data exhibited low agreement. CONCLUSIONS This study highlights the importance of selecting the appropriate preprocessing strategy for EV-miRNA microarray data when using 3D-Gene technology. These findings emphasize the importance of validating preprocessing approaches, particularly in the context of batch effect correction and missing value imputation, for reliably analyzing data in biomarker discovery and disease research.
Collapse
Affiliation(s)
- Yuto Takemoto
- Public Health Informatics Unit, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, 1-1-20 Daiko-Minami, Higashi-Ku, Nagoya, 461-8673, Japan
| | - Daisuke Ito
- Department of Neurology, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Shota Komori
- Department of Neurology, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Yoshiyuki Kishimoto
- Department of Neurology, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Shinichiro Yamada
- Department of Neurology, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Atsushi Hashizume
- Department of Neurology, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
- Department of Clinical Research Education, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Masahisa Katsuno
- Department of Neurology, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
- Department of Clinical Research Education, Nagoya University Graduate School of Medicine, 65 Tsurumai-Cho, Showa-Ku, Nagoya, 466-8550, Japan
| | - Masahiro Nakatochi
- Public Health Informatics Unit, Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, 1-1-20 Daiko-Minami, Higashi-Ku, Nagoya, 461-8673, Japan.
| |
Collapse
|
3
|
Ma L, Tan ECK, Bush AI, Masters CL, Goudey B, Jin L, Pan Y, Group AR. Elucidating the Link Between Anxiety/Depression and Alzheimer's Dementia in the Australian Imaging Biomarkers and Lifestyle (AIBL) Study. J Epidemiol Glob Health 2024:10.1007/s44197-024-00266-w. [PMID: 38896210 DOI: 10.1007/s44197-024-00266-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 06/10/2024] [Indexed: 06/21/2024] Open
Abstract
BACKGROUND The associations between mood disorders (anxiety and depression) and mild cognitive impairment (MCI) or Alzheimer's dementia (AD) remain unclear. METHODS Data from the Australian Imaging, Biomarker & Lifestyle (AIBL) study were subjected to logistic regression to determine both cross-sectional and longitudinal associations between anxiety/depression and MCI/AD. Effect modification by selected covariates was analysed using the likelihood ratio test. RESULTS Cross-sectional analysis was performed to explore the association between anxiety/depression and MCI/AD among 2,209 participants with a mean [SD] age of 72.3 [7.4] years, of whom 55.4% were female. After adjusting for confounding variables, we found a significant increase in the odds of AD among participants with two mood disorders (anxiety: OR 1.65 [95% CI 1.04-2.60]; depression: OR 1.73 [1.12-2.69]). Longitudinal analysis was conducted to explore the target associations among 1,379 participants with a mean age of 71.2 [6.6] years, of whom 56.3% were female. During a mean follow-up of 5.0 [4.2] years, 163 participants who developed MCI/AD (refer to as PRO) were identified. Only anxiety was associated with higher odds of PRO after adjusting for covariates (OR 1.56 [1.03-2.39]). However, after additional adjustment for depression, the association became insignificant. Additionally, age, sex, and marital status were identified as effect modifiers for the target associations. CONCLUSION Our study provides supportive evidence that anxiety and depression impact on the evolution of MCI/AD, which provides valuable epidemiological insights that can inform clinical practice, guiding clinicians in offering targeted dementia prevention and surveillance programs to the at-risk populations.
Collapse
Affiliation(s)
- Liwei Ma
- The Florey Institute of Neuroscience and Mental Health, Melbourne, Australia, Victoria, 3052
- Florey Department of Neuroscience and Mental Health, The University of Melbourne, Melbourne, Victoria, 3052, Australia
| | - Edwin C K Tan
- Faculty of Medicine and Health, The University of Sydney School of Pharmacy, The University of Sydney, Camperdown, New South Wales, 2050, Australia
| | - Ashley I Bush
- The Florey Institute of Neuroscience and Mental Health, Melbourne, Australia, Victoria, 3052
- Florey Department of Neuroscience and Mental Health, The University of Melbourne, Melbourne, Victoria, 3052, Australia
| | - Colin L Masters
- The Florey Institute of Neuroscience and Mental Health, Melbourne, Australia, Victoria, 3052
| | - Benjamin Goudey
- Florey Department of Neuroscience and Mental Health, The University of Melbourne, Melbourne, Victoria, 3052, Australia
| | - Liang Jin
- The Florey Institute of Neuroscience and Mental Health, Melbourne, Australia, Victoria, 3052.
- Florey Department of Neuroscience and Mental Health, The University of Melbourne, Melbourne, Victoria, 3052, Australia.
| | - Yijun Pan
- The Florey Institute of Neuroscience and Mental Health, Melbourne, Australia, Victoria, 3052.
- Florey Department of Neuroscience and Mental Health, The University of Melbourne, Melbourne, Victoria, 3052, Australia.
- Department of Organ Anatomy, Graduate School of Medicine, Tohoku University, Sendai, 980-8575, Miyagi, Japan.
| | - Aibl Research Group
- The Florey Institute of Neuroscience and Mental Health, Melbourne, Australia, Victoria, 3052
| |
Collapse
|
4
|
Krothapalli M, Buddendorff L, Yadav H, Schilaty ND, Jain S. From Gut Microbiota to Brain Waves: The Potential of the Microbiome and EEG as Biomarkers for Cognitive Impairment. Int J Mol Sci 2024; 25:6678. [PMID: 38928383 PMCID: PMC11203453 DOI: 10.3390/ijms25126678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Revised: 06/09/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
Alzheimer's disease (AD) is a prevalent neurodegenerative disorder and a leading cause of dementia. Aging is a significant risk factor for AD, emphasizing the importance of early detection since symptoms cannot be reversed once the advanced stage is reached. Currently, there is no established method for early AD diagnosis. However, emerging evidence suggests that the microbiome has an impact on cognitive function. The gut microbiome and the brain communicate bidirectionally through the gut-brain axis, with systemic inflammation identified as a key connection that may contribute to AD. Gut dysbiosis is more prevalent in individuals with AD compared to their cognitively healthy counterparts, leading to increased gut permeability and subsequent systemic inflammation, potentially causing neuroinflammation. Detecting brain activity traditionally involves invasive and expensive methods, but electroencephalography (EEG) poses as a non-invasive alternative. EEG measures brain activity and multiple studies indicate distinct patterns in individuals with AD. Furthermore, EEG patterns in individuals with mild cognitive impairment differ from those in the advanced stage of AD, suggesting its potential as a method for early indication of AD. This review aims to consolidate existing knowledge on the microbiome and EEG as potential biomarkers for early-stage AD, highlighting the current state of research and suggesting avenues for further investigation.
Collapse
Affiliation(s)
- Mahathi Krothapalli
- USF Center for Microbiome Research, Microbiomes Institute, University of South Florida, Tampa, FL 33612, USA; (M.K.); (L.B.); (H.Y.)
- Department of Neurosurgery and Brain Repair, University of South Florida, Tampa, FL 33612, USA;
| | - Lauren Buddendorff
- USF Center for Microbiome Research, Microbiomes Institute, University of South Florida, Tampa, FL 33612, USA; (M.K.); (L.B.); (H.Y.)
- Department of Neurosurgery and Brain Repair, University of South Florida, Tampa, FL 33612, USA;
| | - Hariom Yadav
- USF Center for Microbiome Research, Microbiomes Institute, University of South Florida, Tampa, FL 33612, USA; (M.K.); (L.B.); (H.Y.)
- Department of Neurosurgery and Brain Repair, University of South Florida, Tampa, FL 33612, USA;
| | - Nathan D. Schilaty
- Department of Neurosurgery and Brain Repair, University of South Florida, Tampa, FL 33612, USA;
- Center for Neuromusculoskeletal Research, University of South Florida, Tampa, FL 33612, USA
| | - Shalini Jain
- USF Center for Microbiome Research, Microbiomes Institute, University of South Florida, Tampa, FL 33612, USA; (M.K.); (L.B.); (H.Y.)
- Department of Neurosurgery and Brain Repair, University of South Florida, Tampa, FL 33612, USA;
| |
Collapse
|
5
|
Keller G, Corvalan N, Carello MA, Arruabarrena MM, Martínez-Canyazo C, De Los Santos L, Spehrs J, Vila-Castelar C, Allegri RF, Quiroz YT, Crivelli L. Performance on the Latin American version of the Face-Name Associative Memory Exam (LAS-FNAME) distinguishes individuals with Mild Cognitive Impairment from age-matched controls in a sample from Argentina. APPLIED NEUROPSYCHOLOGY. ADULT 2024:1-9. [PMID: 38447166 DOI: 10.1080/23279095.2024.2323627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
INTRODUCTION The Latin American Spanish version of the Face-Name Associative Memory Exam (LAS-FNAME) has shown promise in identifying cognitive changes in those at risk for Alzheimer's disease (AD). However, its applicability for Mild Cognitive Impairment (MCI) detection in the Latin American population remains unexplored. This study aims to analyze the psychometric properties in terms of validity and reliability and diagnostic performance of the LAS-FNAME for the detection of memory disorders in patients with amnestic MCI (aMCI). MATERIALS AND METHODS The study included 31 participants with aMCI, diagnosed by a neurologist according to Petersen's criteria, and 19 healthy controls. Inclusion criteria for the aMCI group were to be 60 years of age or older, report cognitive complaints, have a memory test score (Craft Story 21) below a -1.5 z-score and have preserved functioning in activities of daily living. Participants completed LAS-FNAME and a comprehensive neuropsychological assessment. RESULTS LAS-FNAME showed the ability to discriminate against healthy controls from patients with aMCI (AUC= 75) in comparison with a gold-standard memory test (AUC = 69.1). LAS-FNAME also showed evidence of concurrent and divergent validity with a standard memory test (RAVLT) (r = 0.58, p < .001) and with an attention task (Digit Span) (r = -0.37, p = .06). Finally, the reliability index was very high (α = 0.88). DISCUSSION LAS-FNAME effectively distinguished aMCI patients from healthy controls, suggesting its potential for detecting early cognitive changes in Alzheimer's prodromal stages among Spanish speakers.
Collapse
Affiliation(s)
- G Keller
- Department of Cognitive Neurology, Neuropsychology and Neuropsychiatry, FLENI, Buenos Aires, Argentina
| | - N Corvalan
- Department of Cognitive Neurology, Neuropsychology and Neuropsychiatry, FLENI, Buenos Aires, Argentina
| | - M A Carello
- Department of Cognitive Neurology, Neuropsychology and Neuropsychiatry, FLENI, Buenos Aires, Argentina
| | - M M Arruabarrena
- Department of Cognitive Neurology, Neuropsychology and Neuropsychiatry, FLENI, Buenos Aires, Argentina
| | - C Martínez-Canyazo
- Department of Cognitive Neurology, Neuropsychology and Neuropsychiatry, FLENI, Buenos Aires, Argentina
| | - L De Los Santos
- Department of Cognitive Neurology, Neuropsychology and Neuropsychiatry, FLENI, Buenos Aires, Argentina
| | - J Spehrs
- Department of Cognitive Neurology, Neuropsychology and Neuropsychiatry, FLENI, Buenos Aires, Argentina
| | - C Vila-Castelar
- Department of Psychiatry, Multicultural Assessment & Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - R F Allegri
- Department of Cognitive Neurology, Neuropsychology and Neuropsychiatry, FLENI, Buenos Aires, Argentina
- Buenos Aires Argentina, Institute of Neuroscience (INEU) - FLENI-CONICET, Buenos Aires, Argentina
| | - Y T Quiroz
- Department of Psychiatry, Multicultural Assessment & Research Center, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - L Crivelli
- Department of Cognitive Neurology, Neuropsychology and Neuropsychiatry, FLENI, Buenos Aires, Argentina
- Buenos Aires Argentina, Institute of Neuroscience (INEU) - FLENI-CONICET, Buenos Aires, Argentina
| |
Collapse
|
6
|
Jung M, Jung JS, Pfeifer J, Hartmann C, Ehrhardt T, Abid CL, Kintzel J, Puls A, Navarrete Santos A, Hollemann T, Riemann D, Rujescu D. Neuronal Stem Cells from Late-Onset Alzheimer Patients Show Altered Regulation of Sirtuin 1 Depending on Apolipoprotein E Indicating Disturbed Stem Cell Plasticity. Mol Neurobiol 2024; 61:1562-1579. [PMID: 37728850 PMCID: PMC10896791 DOI: 10.1007/s12035-023-03633-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 08/31/2023] [Indexed: 09/21/2023]
Abstract
Late-onset Alzheimer's disease (AD) is a complex multifactorial disease. The greatest known risk factor for late-onset AD is the E4 allele of the apolipoprotein E (APOE), while increasing age is the greatest known non-genetic risk factor. The cell type-specific functions of neural stem cells (NSCs), in particular their stem cell plasticity, remain poorly explored in the context of AD pathology. Here, we describe a new model that employs late-onset AD patient-derived induced pluripotent stem cells (iPSCs) to generate NSCs and to examine the role played by APOE4 in the expression of aging markers such as sirtuin 1 (SIRT1) in comparison to healthy subjects carrying APOE3. The effect of aging was investigated by using iPSC-derived NSCs from old age subjects as healthy matched controls. Transcript and protein analysis revealed that genes were expressed differently in NSCs from late-onset AD patients, e.g., exhibiting reduced autophagy-related protein 7 (ATG7), phosphatase and tensin homolog (PTEN), and fibroblast growth factor 2 (FGF2). Since SIRT1 expression differed between APOE3 and APOE4 NSCs, the suppression of APOE function in NSCs also repressed the expression of SIRT1. However, the forced expression of APOE3 by plasmids did not recover differently expressed genes. The altered aging markers indicate decreased plasticity of NSCs. Our study provides a suitable in vitro model to investigate changes in human NSCs associated with aging, APOE4, and late-onset AD.
Collapse
Affiliation(s)
- Matthias Jung
- Institute of Physiological Chemistry (IPC), Faculty of Medicine, Martin Luther University Halle-Wittenberg, Hollystrasse 1, 06114, Halle (Saale), Germany.
| | - Juliane-Susanne Jung
- Institute of Anatomy and Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, Grosse Steinstrasse 52, 06118, Halle (Saale), Germany
| | - Jenny Pfeifer
- Institute of Physiological Chemistry (IPC), Faculty of Medicine, Martin Luther University Halle-Wittenberg, Hollystrasse 1, 06114, Halle (Saale), Germany
| | - Carla Hartmann
- Institute of Physiological Chemistry (IPC), Faculty of Medicine, Martin Luther University Halle-Wittenberg, Hollystrasse 1, 06114, Halle (Saale), Germany
| | - Toni Ehrhardt
- Institute of Physiological Chemistry (IPC), Faculty of Medicine, Martin Luther University Halle-Wittenberg, Hollystrasse 1, 06114, Halle (Saale), Germany
| | - Chaudhry Luqman Abid
- Institute of Physiological Chemistry (IPC), Faculty of Medicine, Martin Luther University Halle-Wittenberg, Hollystrasse 1, 06114, Halle (Saale), Germany
| | - Jenny Kintzel
- Institute of Physiological Chemistry (IPC), Faculty of Medicine, Martin Luther University Halle-Wittenberg, Hollystrasse 1, 06114, Halle (Saale), Germany
| | - Anne Puls
- Institute of Physiological Chemistry (IPC), Faculty of Medicine, Martin Luther University Halle-Wittenberg, Hollystrasse 1, 06114, Halle (Saale), Germany
| | - Anne Navarrete Santos
- Institute of Anatomy and Cell Biology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, Grosse Steinstrasse 52, 06118, Halle (Saale), Germany
| | - Thomas Hollemann
- Institute of Physiological Chemistry (IPC), Faculty of Medicine, Martin Luther University Halle-Wittenberg, Hollystrasse 1, 06114, Halle (Saale), Germany
| | - Dagmar Riemann
- Department Medical Immunology, Faculty of Medicine, Martin Luther University Halle-Wittenberg, Magdeburger Strasse 2, 06112, Halle (Saale), Germany
| | - Dan Rujescu
- Department of Psychiatry and Psychotherapy, Division of General Psychiatry, Medical University of Vienna, Währinger Gürtel 18-20, 1090, Vienna, Austria
| |
Collapse
|
7
|
Ma L, Low YLC, Zhuo Y, Chu C, Wang Y, Fowler CJ, Tan ECK, Masters CL, Jin L, Pan Y. Exploring the association between cancer and cognitive impairment in the Australian Imaging Biomarkers and Lifestyle (AIBL) study. Sci Rep 2024; 14:4364. [PMID: 38388558 PMCID: PMC10884016 DOI: 10.1038/s41598-024-54875-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 02/17/2024] [Indexed: 02/24/2024] Open
Abstract
An inverse association between cancer and Alzheimer's disease (AD) has been demonstrated; however, the association between cancer and mild cognitive impairment (MCI), and the association between cancer and cognitive decline are yet to be clarified. The AIBL dataset was used to address these knowledge gaps. The crude and adjusted odds ratios for MCI/AD and cognitive decline were compared between participants with/without cancer (referred to as C+ and C- participants). A 37% reduction in odds for AD was observed in C+ participants compared to C- participants after adjusting for all confounders. The overall risk for MCI and AD in C+ participants was reduced by 27% and 31%, respectively. The odds of cognitive decline from MCI to AD was reduced by 59% in C+ participants after adjusting for all confounders. The risk of cognitive decline from MCI to AD was halved in C+ participants. The estimated mean change in Clinical Dementia Rating-Sum of boxes (CDR-SOB) score per year was 0.23 units/year higher in C- participants than in C+ participants. Overall, an inverse association between cancer and MCI/AD was observed in AIBL, which is in line with previous reports. Importantly, an inverse association between cancer and cognitive decline has also been identified.
Collapse
Affiliation(s)
- Liwei Ma
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Yi Ling Clare Low
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Yuanhao Zhuo
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Chenyin Chu
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Yihan Wang
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Christopher J Fowler
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Edwin C K Tan
- The University of Sydney School of Pharmacy, Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, 2006, Australia
| | - Colin L Masters
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, 3010, Australia
| | - Liang Jin
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.
| | - Yijun Pan
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, 3010, Australia.
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, 3052, Australia.
- Department of Organ Anatomy, Graduate School of Medicine, Tohoku University, Sendai, Miyagi, 980-8575, Japan.
| |
Collapse
|
8
|
Zhang Z, Liu X, Zhang S, Song Z, Lu K, Yang W. A review and analysis of key biomarkers in Alzheimer's disease. Front Neurosci 2024; 18:1358998. [PMID: 38445255 PMCID: PMC10912539 DOI: 10.3389/fnins.2024.1358998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 02/02/2024] [Indexed: 03/07/2024] Open
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative disorder that affects over 50 million elderly individuals worldwide. Although the pathogenesis of AD is not fully understood, based on current research, researchers are able to identify potential biomarker genes and proteins that may serve as effective targets against AD. This article aims to present a comprehensive overview of recent advances in AD biomarker identification, with highlights on the use of various algorithms, the exploration of relevant biological processes, and the investigation of shared biomarkers with co-occurring diseases. Additionally, this article includes a statistical analysis of key genes reported in the research literature, and identifies the intersection with AD-related gene sets from databases such as AlzGen, GeneCard, and DisGeNet. For these gene sets, besides enrichment analysis, protein-protein interaction (PPI) networks utilized to identify central genes among the overlapping genes. Enrichment analysis, protein interaction network analysis, and tissue-specific connectedness analysis based on GTEx database performed on multiple groups of overlapping genes. Our work has laid the foundation for a better understanding of the molecular mechanisms of AD and more accurate identification of key AD markers.
Collapse
Affiliation(s)
- Zhihao Zhang
- School of Computer Science and Technology, Xinjiang University, Ürümqi, China
- College of Medical Engineering and Technology, Xinjiang Medical University, Ürümqi, China
| | - Xiangtao Liu
- College of Medical Engineering and Technology, Xinjiang Medical University, Ürümqi, China
| | - Suixia Zhang
- College of Medical Engineering and Technology, Xinjiang Medical University, Ürümqi, China
- College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou, China
- State Key Laboratory of Pathogenesis, Prevention, Treatment of Central Asian High Incidence Diseases, First Affiliated Hospital of Xinjiang Medical University, Ürümqi, China
| | - Zhixin Song
- College of Medical Engineering and Technology, Xinjiang Medical University, Ürümqi, China
| | - Ke Lu
- School of Computer Science and Technology, Xinjiang University, Ürümqi, China
| | - Wenzhong Yang
- School of Computer Science and Technology, Xinjiang University, Ürümqi, China
| |
Collapse
|
9
|
Cho SB. Comorbidity Genes of Alzheimer's Disease and Type 2 Diabetes Associated with Memory and Cognitive Function. Int J Mol Sci 2024; 25:2211. [PMID: 38396891 PMCID: PMC10889845 DOI: 10.3390/ijms25042211] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/02/2024] [Accepted: 02/10/2024] [Indexed: 02/25/2024] Open
Abstract
Alzheimer's disease (AD) and type 2 diabetes mellitus (T2DM) are comorbidities that result from the sharing of common genes. The molecular background of comorbidities can provide clues for the development of treatment and management strategies. Here, the common genes involved in the development of the two diseases and in memory and cognitive function are reviewed. Network clustering based on protein-protein interaction network identified tightly connected gene clusters that have an impact on memory and cognition among the comorbidity genes of AD and T2DM. Genes with functional implications were intensively reviewed and relevant evidence summarized. Gene information will be useful in the discovery of biomarkers and the identification of tentative therapeutic targets for AD and T2DM.
Collapse
Affiliation(s)
- Seong Beom Cho
- Department of Biomedical Informatics, College of Medicine, Gachon University, 38-13, Dokgeom-ro 3 Street, Namdon-gu, Incheon 21565, Republic of Korea
| |
Collapse
|
10
|
Han Y, Zeng X, Hua L, Quan X, Chen Y, Zhou M, Chuang Y, Li Y, Wang S, Shen X, Wei L, Yuan Z, Zhao Y. The fusion of multi-omics profile and multimodal EEG data contributes to the personalized diagnostic strategy for neurocognitive disorders. MICROBIOME 2024; 12:12. [PMID: 38243335 PMCID: PMC10797890 DOI: 10.1186/s40168-023-01717-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 11/07/2023] [Indexed: 01/21/2024]
Abstract
BACKGROUND The increasing prevalence of neurocognitive disorders (NCDs) in the aging population worldwide has become a significant concern due to subjectivity of evaluations and the lack of precise diagnostic methods and specific indicators. Developing personalized diagnostic strategies for NCDs has therefore become a priority. RESULTS Multimodal electroencephalography (EEG) data of a matched cohort of normal aging (NA) and NCDs seniors were recorded, and their faecal samples and urine exosomes were collected to identify multi-omics signatures and metabolic pathways in NCDs by integrating metagenomics, proteomics, and metabolomics analysis. Additionally, experimental verification of multi-omics signatures was carried out in aged mice using faecal microbiota transplantation (FMT). We found that NCDs seniors had low EEG power spectral density and identified specific microbiota, including Ruminococcus gnavus, Enterocloster bolteae, Lachnoclostridium sp. YL 32, and metabolites, including L-tryptophan, L-glutamic acid, gamma-aminobutyric acid (GABA), and fatty acid esters of hydroxy fatty acids (FAHFAs), as well as disturbed biosynthesis of aromatic amino acids and TCA cycle dysfunction, validated in aged mice. Finally, we employed a support vector machine (SVM) algorithm to construct a machine learning model to classify NA and NCDs groups based on the fusion of EEG data and multi-omics profiles and the model demonstrated 92.69% accuracy in classifying NA and NCDs groups. CONCLUSIONS Our study highlights the potential of multi-omics profiling and EEG data fusion in personalized diagnosis of NCDs, with the potential to improve diagnostic precision and provide insights into the underlying mechanisms of NCDs. Video Abstract.
Collapse
Affiliation(s)
- Yan Han
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, 999078, Macau SAR, China
| | - Xinglin Zeng
- Centre for Cognitive and Brain Sciences, University of Macau, Avenida da Universidade, Taipa, 999078, Macau SAR, China
| | - Lin Hua
- Centre for Cognitive and Brain Sciences, University of Macau, Avenida da Universidade, Taipa, 999078, Macau SAR, China
| | - Xingping Quan
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, 999078, Macau SAR, China
| | - Ying Chen
- School of Health Economics and Management, Nanjing University of Chinese Medicine, Nanjing, 210023, Jiangsu, China
| | - Manfei Zhou
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, 999078, Macau SAR, China
| | | | - Yang Li
- Department of Gastrointestinal Surgery, Second Clinical Medical College of Jinan University, Shenzhen People's Hospital, Shenzhen, 518020, China
| | - Shengpeng Wang
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, 999078, Macau SAR, China
| | - Xu Shen
- Jiangsu Key Laboratory of Drug Target and Drug for Degenerative Diseases, Nanjing University of Chinese Medicine, Nanjing, 210023, China
| | - Lai Wei
- School of Pharmaceutical Science, Southern Medical University, Guangzhou, 510515, China
| | - Zhen Yuan
- Centre for Cognitive and Brain Sciences, University of Macau, Avenida da Universidade, Taipa, 999078, Macau SAR, China.
| | - Yonghua Zhao
- State Key Laboratory of Quality Research in Chinese Medicine, Institute of Chinese Medical Sciences, University of Macau, Avenida da Universidade, Taipa, 999078, Macau SAR, China.
- Department of Pharmaceutical Sciences, Faculty of Health Sciences, University of Macau, Taipa, Macau SAR 999078, China.
| |
Collapse
|
11
|
Zhang Y, Li Y, Song S, Li Z, Lu M, Shan G. Predicting Conversion Time from Mild Cognitive Impairment to Dementia with Interval-Censored Models. J Alzheimers Dis 2024; 101:147-157. [PMID: 39121117 DOI: 10.3233/jad-240285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/11/2024]
Abstract
Background Mild cognitive impairment (MCI) patients are at a high risk of developing Alzheimer's disease and related dementias (ADRD) at an estimated annual rate above 10%. It is clinically and practically important to accurately predict MCI-to-dementia conversion time. Objective It is clinically and practically important to accurately predict MCI-to-dementia conversion time by using easily available clinical data. Methods The dementia diagnosis often falls between two clinical visits, and such survival outcome is known as interval-censored data. We utilized the semi-parametric model and the random forest model for interval-censored data in conjunction with a variable selection approach to select important measures for predicting the conversion time from MCI to dementia. Two large AD cohort data sets were used to build, validate, and test the predictive model. Results We found that the semi-parametric model can improve the prediction of the conversion time for patients with MCI-to-dementia conversion, and it also has good predictive performance for all patients. Conclusions Interval-censored data should be analyzed by using the models that were developed for interval- censored data to improve the model performance.
Collapse
Affiliation(s)
- Yahui Zhang
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
| | - Yulin Li
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
| | - Shangchen Song
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
| | - Zhigang Li
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
| | - Minggen Lu
- School of Community Health Sciences, University of Nevada, Reno, NV, USA
| | - Guogen Shan
- Department of Biostatistics, University of Florida, Gainesville, FL, USA
| |
Collapse
|
12
|
Jin LW, Di Lucente J, Ruiz Mendiola U, Suthprasertporn N, Tomilov A, Cortopassi G, Kim K, Ramsey JJ, Maezawa I. The ketone body β-hydroxybutyrate shifts microglial metabolism and suppresses amyloid-β oligomer-induced inflammation in human microglia. FASEB J 2023; 37:e23261. [PMID: 37878335 DOI: 10.1096/fj.202301254r] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Revised: 09/15/2023] [Accepted: 10/03/2023] [Indexed: 10/26/2023]
Abstract
Fatty acids are metabolized by β-oxidation within the "mitochondrial ketogenic pathway" (MKP) to generate β-hydroxybutyrate (BHB), a ketone body. BHB can be generated by most cells but largely by hepatocytes following exercise, fasting, or ketogenic diet consumption. BHB has been shown to modulate systemic and brain inflammation; however, its direct effects on microglia have been little studied. We investigated the impact of BHB on Aβ oligomer (AβO)-stimulated human iPS-derived microglia (hiMG), a model relevant to the pathogenesis of Alzheimer's disease (AD). HiMG responded to AβO with proinflammatory activation, which was mitigated by BHB at physiological concentrations of 0.1-2 mM. AβO stimulated glycolytic transcripts, suppressed genes in the β-oxidation pathway, and induced over-expression of AD-relevant p46Shc, an endogenous inhibitor of thiolase, actions that are expected to suppress MKP. AβO also triggered mitochondrial Ca2+ increase, mitochondrial reactive oxygen species production, and activation of the mitochondrial permeability transition pore. BHB potently ameliorated all the above mitochondrial changes and rectified the MKP, resulting in reduced inflammasome activation and recovery of the phagocytotic function impaired by AβO. These results indicate that microglia MKP can be induced to modulate microglia immunometabolism, and that BHB can remedy "keto-deficiency" resulting from MKP suppression and shift microglia away from proinflammatory mitochondrial metabolism. These effects of BHB may contribute to the beneficial effects of ketogenic diet intervention in aged mice and in human subjects with mild AD.
Collapse
Affiliation(s)
- Lee-Way Jin
- Department of Pathology and Laboratory Medicine and Medical Investigation of Neurodevelopmental Disorders, University of California Davis Medical Center, Sacramento, California, USA
- Medical Investigation of Neurodevelopmental Disorders Institute, University of California Davis Medical Center, Sacramento, California, USA
- Alzheimer's Disease Research Center, University of California Davis Medical Center, Sacramento, California, USA
| | - Jacopo Di Lucente
- Department of Pathology and Laboratory Medicine and Medical Investigation of Neurodevelopmental Disorders, University of California Davis Medical Center, Sacramento, California, USA
| | - Ulises Ruiz Mendiola
- Department of Pathology and Laboratory Medicine and Medical Investigation of Neurodevelopmental Disorders, University of California Davis Medical Center, Sacramento, California, USA
| | - Nopparat Suthprasertporn
- Department of Pathology and Laboratory Medicine and Medical Investigation of Neurodevelopmental Disorders, University of California Davis Medical Center, Sacramento, California, USA
| | - Alexey Tomilov
- Department of Molecular Biosciences, University of California, Davis, Davis, California, USA
| | - Gino Cortopassi
- Department of Molecular Biosciences, University of California, Davis, Davis, California, USA
| | - Kyoungmi Kim
- Medical Investigation of Neurodevelopmental Disorders Institute, University of California Davis Medical Center, Sacramento, California, USA
- Department of Public Health Sciences, University of California, Davis, Davis, California, USA
| | - Jon J Ramsey
- Department of Molecular Biosciences, University of California, Davis, Davis, California, USA
| | - Izumi Maezawa
- Department of Pathology and Laboratory Medicine and Medical Investigation of Neurodevelopmental Disorders, University of California Davis Medical Center, Sacramento, California, USA
- Medical Investigation of Neurodevelopmental Disorders Institute, University of California Davis Medical Center, Sacramento, California, USA
- Alzheimer's Disease Research Center, University of California Davis Medical Center, Sacramento, California, USA
| |
Collapse
|
13
|
Yu Z, Shi Z, Dan T, Dere M, Kim M, Li Q, Wu G. Uncovering Diverse Mechanistic Spreading Pathways in Disease Progression of Alzheimer's Disease. J Alzheimers Dis Rep 2023; 7:855-872. [PMID: 37662609 PMCID: PMC10473126 DOI: 10.3233/adr-230081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 07/24/2023] [Indexed: 09/05/2023] Open
Abstract
Background The AT[N] research framework focuses on three major biomarkers in Alzheimer's disease (AD): amyloid-β deposition (A), pathologic tau (T), and neurodegeneration [N]. Objective We hypothesize that the diverse mechanisms such as A⟶T and A⟶[N] pathways from one brain region to others, may underlie the wide variation in clinical symptoms. We aim to uncover the causal-like effect of regional AT[N] biomarkers on cognitive decline as well as the interaction with non-modifiable risk factors such as age and APOE4. Methods We apply multi-variate statistical inference to uncover all possible mechanistic spreading pathways through which the aggregation of an upstream biomarker (e.g., increased amyloid level) in a particular brain region indirectly impacts cognitive decline, via the cascade build-up of a downstream biomarker (e.g., reduced metabolism level) in another brain region. Furthermore, we investigate the survival time for each identified region-to-region pathological pathway toward the AD onset. Results We have identified a collection of critical brain regions on which the amyloid burdens exert an indirect effect on the decline in memory and executive function (EF) domain, being mediated by the reduction of metabolism level at other brain regions. APOE4 status has been found not only involved in many A⟶N mechanistic pathways but also significantly contributes to the risk of developing AD. Conclusion Our major findings include 1) the region-to-region A⟶N⟶MEM and A⟶N⟶MEM pathways exhibit distinct spatial patterns; 2) APOE4 is significantly associated with both direct and indirect effects on the cognitive decline while sex difference has not been identified in the mediation analysis.
Collapse
Affiliation(s)
- Zhentao Yu
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
| | - Zhuoyu Shi
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA
| | - Tingting Dan
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA
| | - Mustafa Dere
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA
| | - Minjeong Kim
- Department of Computer Science, University of North Carolina, Greensboro, NC, USA
| | - Quefeng Li
- Department of Biostatistics, University of North Carolina, Chapel Hill, NC, USA
| | - Guorong Wu
- Department of Psychiatry, University of North Carolina, Chapel Hill, NC, USA
- Department of Computer Science, University of North Carolina, Chapel Hill, NC, USA
- Department of Statistics and Operations Research, University of North Carolina, Chapel Hill, NC, USA
- UNC Neuroscience Center, University of North Carolina, Chapel Hill, NC, USA
- Carolina Institute of Developmental Disabilities, University of North Carolina, Chapel Hill, NC, USA
| | | |
Collapse
|
14
|
Mao C, Xu J, Rasmussen L, Li Y, Adekkanattu P, Pacheco J, Bonakdarpour B, Vassar R, Shen L, Jiang G, Wang F, Pathak J, Luo Y. AD-BERT: Using pre-trained language model to predict the progression from mild cognitive impairment to Alzheimer's disease. J Biomed Inform 2023; 144:104442. [PMID: 37429512 PMCID: PMC11131134 DOI: 10.1016/j.jbi.2023.104442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 06/13/2023] [Accepted: 07/07/2023] [Indexed: 07/12/2023]
Abstract
OBJECTIVE We develop a deep learning framework based on the pre-trained Bidirectional Encoder Representations from Transformers (BERT) model using unstructured clinical notes from electronic health records (EHRs) to predict the risk of disease progression from Mild Cognitive Impairment (MCI) to Alzheimer's Disease (AD). METHODS We identified 3657 patients diagnosed with MCI together with their progress notes from Northwestern Medicine Enterprise Data Warehouse (NMEDW) between 2000 and 2020. The progress notes no later than the first MCI diagnosis were used for the prediction. We first preprocessed the notes by deidentification, cleaning and splitting into sections, and then pre-trained a BERT model for AD (named AD-BERT) based on the publicly available Bio+Clinical BERT on the preprocessed notes. All sections of a patient were embedded into a vector representation by AD-BERT and then combined by global MaxPooling and a fully connected network to compute the probability of MCI-to-AD progression. For validation, we conducted a similar set of experiments on 2563 MCI patients identified at Weill Cornell Medicine (WCM) during the same timeframe. RESULTS Compared with the 7 baseline models, the AD-BERT model achieved the best performance on both datasets, with Area Under receiver operating characteristic Curve (AUC) of 0.849 and F1 score of 0.440 on NMEDW dataset, and AUC of 0.883 and F1 score of 0.680 on WCM dataset. CONCLUSION The use of EHRs for AD-related research is promising, and AD-BERT shows superior predictive performance in modeling MCI-to-AD progression prediction. Our study demonstrates the utility of pre-trained language models and clinical notes in predicting MCI-to-AD progression, which could have important implications for improving early detection and intervention for AD.
Collapse
Affiliation(s)
- Chengsheng Mao
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Jie Xu
- Department of Health Outcomes and Biomedical Informatics, University of Florida, Gainesville, FL, United States; Weill Cornell Medicine, New York, NY, United States
| | - Luke Rasmussen
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Yikuan Li
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | | | - Jennifer Pacheco
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Borna Bonakdarpour
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Robert Vassar
- Department of Neurology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Li Shen
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, United States
| | | | - Fei Wang
- Weill Cornell Medicine, New York, NY, United States
| | | | - Yuan Luo
- Department of Preventive Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States.
| |
Collapse
|
15
|
Tran T, Finlayson M, Nalder E, Trothen T, Donnelly C. Occupational Therapist-Led Mindfulness Training Program for Older Adults Living with Early Cognitive Decline in Primary Care: A Pilot Randomized Controlled Trial. J Alzheimers Dis Rep 2023; 7:775-790. [PMID: 37662611 PMCID: PMC10473152 DOI: 10.3233/adr-230006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/25/2023] [Indexed: 09/05/2023] Open
Abstract
Background Community-dwelling older adults with early cognitive deficits experience less efficiency in performing everyday life tasks, resulting in decreased satisfaction and other adverse psychological outcomes. Mindfulness training has been linked to cognitive and psychological improvements and, most recently, has been identified as a potential intervention supporting performance of everyday life activities. Objective This study aimed to evaluate whether mindfulness practice can improve perceived performance and satisfaction with everyday life activity and secondary psychological outcomes. Methods This study is a pilot randomized controlled trial (RCT) in an interprofessional primary care team practice in Toronto, Ontario, Canada. The participants were 27 older adults aged 60 years of age or older living with early cognitive deficits. Participants were randomized into an 8-Week mindfulness training program (n = 14) group or a Wait-List Control (WLC; n = 13) group compared at baseline, post-intervention and 4-weeks follow-up. MANOVAs with post-hoc independent t-tests were used to compare between groups at different time points. Results There was a significant improvement in anxiety for the intervention group compared to the WLC group at post-intervention; Time-2 (mean difference = 3.90; CI = 0.04-7.75; p = 0.04) with large effect size (d = 0.80). Conclusion Mindfulness training significantly improved anxiety scores for patients with early cognitive deficits post-intervention. Further work is required to test the sustainability of reduced anxiety over time, but this study demonstrated that MBSR is a promising primary care intervention for those living with early cognitive deficits. This study warrants the pursuit of a future study in exploring how long the reduced anxiety effects would be sustained.
Collapse
Affiliation(s)
- Todd Tran
- Queen’s University, Faculty of Health Sciences, School of Rehabilitation Therapy, Aging & Health, Kingston, ON, Canada
- Clinical Site: Women’s College Hospital, Toronto, ON, Canada
- University of Toronto, Temerty Faculty of Medicine, Department of Occupational Science & Occupational Therapy, Toronto, ON, Canada
| | - Marcia Finlayson
- Queen’s University, Faculty of Health Sciences, School of Rehabilitation Therapy, Aging & Health, Kingston, ON, Canada
| | - Emily Nalder
- University of Toronto, Temerty Faculty of Medicine, Department of Occupational Science & Occupational Therapy, Toronto, ON, Canada
| | - Tracy Trothen
- Queen’s University, Faculty of Health Sciences, School of Rehabilitation Therapy, Aging & Health, Kingston, ON, Canada
- Queen’s University, jointly appointed to the School of Rehabilitation Therapy and School of Religion (Theological Hall), Kingston, ON, Canada
| | - Catherine Donnelly
- Queen’s University, Faculty of Health Sciences, School of Rehabilitation Therapy, Aging & Health, Kingston, ON, Canada
| |
Collapse
|
16
|
Van der Auwera S, Garvert L, Ameling S, Völzke H, Nauck M, Völker U, Grabe HJ. The interplay between micro RNAs and genetic liability to Alzheimer's Disease on memory trajectories in the general population. Psychiatry Res 2023; 323:115141. [PMID: 36905902 DOI: 10.1016/j.psychres.2023.115141] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 02/20/2023] [Accepted: 02/28/2023] [Indexed: 03/13/2023]
Abstract
Deficits in cognitive function and memory are common early symptoms of neurodegenerative disorders, such as Alzheimer's Disease (AD). Several studies have discussed micro RNAs (miRNAs) as potential epigenetic early detection biomarkers. In a longitudinal general population sample (n = 548) from the Study of Health in Pomerania, we analyzed the associations between 167 baseline miRNA levels and changes in verbal memory scores with a mean follow-up time of 7.4 years. We additionally assessed the impact of an individual's genetic liability for AD on verbal memory scores in n = 2,334 subjects and a possible interactions between epigenetic and genetic markers. Results revealed two miRNAs associated with changes in immediate verbal memory over time. In interaction analyses between miRNAs and a polygenic risk score for AD, five miRNAs showed a significant interaction effect on changes in verbal memory. All of these miRNAs have previously been identified in the context of AD, neurodegeneration or cognition. Our study provides candidate miRNAs for a decline in verbal memory as an early symptom of neurodegeneration and AD. Further experimental studies are needed to verify the diagnostic value of these miRNA markers in the prodromal stage of AD.
Collapse
Affiliation(s)
- Sandra Van der Auwera
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany; German Center for Neurodegenerative Diseases DZNE, Site Rostock/Greifswald, Greifswald, Germany.
| | - Linda Garvert
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany
| | - Sabine Ameling
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany; German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, Greifswald, Germany
| | - Henry Völzke
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, Greifswald, Germany; Institute for Community Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Matthias Nauck
- German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, Greifswald, Germany; Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald, Germany
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, Greifswald, Germany; German Centre for Cardiovascular Research (DZHK), Partner Site Greifswald, Greifswald, Germany
| | - Hans J Grabe
- Department of Psychiatry and Psychotherapy, University Medicine Greifswald, Greifswald, Germany; German Center for Neurodegenerative Diseases DZNE, Site Rostock/Greifswald, Greifswald, Germany
| |
Collapse
|
17
|
A new EEG determinism analysis method based on multiscale dispersion recurrence plot. Biomed Signal Process Control 2023. [DOI: 10.1016/j.bspc.2022.104301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
|
18
|
Salem H, Suchting R, Gonzales MM, Seshadri S, Teixeira AL. Apathy as a Predictor of Conversion from Mild Cognitive Impairment to Alzheimer's Disease: A Texas Alzheimer's Research and Care Consortium (TARCC) Cohort-Based Analysis. J Alzheimers Dis 2023; 92:129-139. [PMID: 36710674 DOI: 10.3233/jad-220826] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
BACKGROUND Apathy is among the neuropsychiatric symptoms frequently observed in people with cognitive impairment. It has been postulated to be a potential predictor of conversion from mild cognitive impairment (MCI) to Alzheimer's disease (AD). OBJECTIVE To detect conversion rates from MCI to AD, and to determine the effect of apathy on the progression to AD in patients with MCI enrolled in the Texas Alzheimer's Research and Care Consortium (TARCC) cohort. METHODS Apathy was determined by a positive response to the respective item in the Neuropsychiatric Inventory -Questionnaire (NPI-Q) completed by family members or caregivers. The final dataset included 2,897 observations from 1,092 individuals with MCI at the baseline. Kaplan-Meier survival curves were estimated to provide indices of the probability of conversion to AD over time across all individuals as well as between those with and without apathy. Cox proportional hazards regression measured the hazard associated with apathy and several other predictors of interest. RESULTS Over a period of 8.21 years, 17.3% of individuals had conversion from MCI to AD (n = 190 of 1,092 total individuals) across observations. The median time-to-conversion across all participants was 6.41 years. Comparing individuals with apathy (n = 158) versus without apathy (n = 934), 36.1% and 14.2% had conversion to AD, respectively. The median time-to-conversion was 3.79 years for individuals with apathy and 6.83 years for individuals without apathy. Cox proportional hazards regression found significant effects of several predictors, including apathy, on time-to-conversion. Age and cognitive performance were found to moderate the relationship between apathy and time-to-conversion. CONCLUSIONS Apathy is associated with progression from MCI to AD, suggesting that it might improve risk prediction and aid targeted intervention delivery.
Collapse
Affiliation(s)
- Haitham Salem
- Department of Psychiatry and Behavioral Sciences, University of Texas Health Science Center, Houston, TX, USA
- Department of Psychiatry and Human Behavior, Warren Alpert Medical School, Brown University, Providence, RI, USA
| | - Robert Suchting
- Department of Psychiatry and Behavioral Sciences, University of Texas Health Science Center, Houston, TX, USA
| | - Mitzi M Gonzales
- Biggs Institute, University of Texas Health Science Center, San Antonio, TX, USA
| | - Sudha Seshadri
- Biggs Institute, University of Texas Health Science Center, San Antonio, TX, USA
| | - Antonio L Teixeira
- Department of Psychiatry and Behavioral Sciences, University of Texas Health Science Center, Houston, TX, USA
| |
Collapse
|
19
|
Clark C, Rabl M, Dayon L, Popp J. The promise of multi-omics approaches to discover biological alterations with clinical relevance in Alzheimer's disease. Front Aging Neurosci 2022; 14:1065904. [PMID: 36570537 PMCID: PMC9768448 DOI: 10.3389/fnagi.2022.1065904] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 11/21/2022] [Indexed: 12/12/2022] Open
Abstract
Beyond the core features of Alzheimer's disease (AD) pathology, i.e. amyloid pathology, tau-related neurodegeneration and microglia response, multiple other molecular alterations and pathway dysregulations have been observed in AD. Their inter-individual variations, complex interactions and relevance for clinical manifestation and disease progression remain poorly understood, however. Heterogeneity at both pathophysiological and clinical levels complicates diagnosis, prognosis, treatment and drug design and testing. High-throughput "omics" comprise unbiased and untargeted data-driven methods which allow the exploration of a wide spectrum of disease-related changes at different endophenotype levels without focussing a priori on specific molecular pathways or molecules. Crucially, new methodological and statistical advances now allow for the integrative analysis of data resulting from multiple and different omics methods. These multi-omics approaches offer the unique advantage of providing a more comprehensive characterisation of the AD endophenotype and to capture molecular signatures and interactions spanning various biological levels. These new insights can then help decipher disease mechanisms more deeply. In this review, we describe the different multi-omics tools and approaches currently available and how they have been applied in AD research so far. We discuss how multi-omics can be used to explore molecular alterations related to core features of the AD pathologies and how they interact with comorbid pathological alterations. We further discuss whether the identified pathophysiological changes are relevant for the clinical manifestation of AD, in terms of both cognitive impairment and neuropsychiatric symptoms, and for clinical disease progression over time. Finally, we address the opportunities for multi-omics approaches to help discover novel biomarkers for diagnosis and monitoring of relevant pathophysiological processes, along with personalised intervention strategies in AD.
Collapse
Affiliation(s)
- Christopher Clark
- Department of Psychiatry, Psychotherapy and Psychosomatics, University of Zürich, Zürich, Switzerland,Geriatric Psychiatry, University Hospital of Psychiatry Zürich, Zürich, Switzerland,*Correspondence: Christopher Clark,
| | - Miriam Rabl
- Geriatric Psychiatry, University Hospital of Psychiatry Zürich, Zürich, Switzerland,University of Lausanne, Lausanne, Switzerland
| | - Loïc Dayon
- Nestlé Institute of Food Safety and Analytical Sciences, Nestlé Research, Lausanne, Switzerland,Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Julius Popp
- Department of Psychiatry, Psychotherapy and Psychosomatics, University of Zürich, Zürich, Switzerland,Geriatric Psychiatry, University Hospital of Psychiatry Zürich, Zürich, Switzerland,Old Age Psychiatry, Department of Psychiatry, Lausanne University Hospital, Lausanne, Switzerland
| |
Collapse
|
20
|
Zhang Q, Yang P, Pang X, Guo W, Sun Y, Wei Y, Pang C. Preliminary exploration of the co-regulation of Alzheimer's disease pathogenic genes by microRNAs and transcription factors. Front Aging Neurosci 2022; 14:1069606. [PMID: 36561136 PMCID: PMC9764863 DOI: 10.3389/fnagi.2022.1069606] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 11/15/2022] [Indexed: 12/12/2022] Open
Abstract
Background Alzheimer's disease (AD) is the most common form of age-related neurodegenerative disease. Unfortunately, due to the complexity of pathological types and clinical heterogeneity of AD, there is a lack of satisfactory treatment for AD. Previous studies have shown that microRNAs and transcription factors can modulate genes associated with AD, but the underlying pathophysiology remains unclear. Methods The datasets GSE1297 and GSE5281 were downloaded from the gene expression omnibus (GEO) database and analyzed to obtain the differentially expressed genes (DEGs) through the "R" language "limma" package. The GSE1297 dataset was analyzed by weighted correlation network analysis (WGCNA), and the key gene modules were selected. Next, gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathway enrichment analysis for the key gene modules were performed. Then, the protein-protein interaction (PPI) network was constructed and the hub genes were identified using the STRING database and Cytoscape software. Finally, for the GSE150693 dataset, the "R" package "survivation" was used to integrate the data of survival time, AD transformation status and 35 characteristics, and the key microRNAs (miRNAs) were selected by Cox method. We also performed regression analysis using least absolute shrinkage and selection operator (Lasso)-Cox to construct and validate prognostic features associated with the four key genes using different databases. We also tried to find drugs targeting key genes through DrugBank database. Results GO and KEGG enrichment analysis showed that DEGs were mainly enriched in pathways regulating chemical synaptic transmission, glutamatergic synapses and Huntington's disease. In addition, 10 hub genes were selected from the PPI network by using the algorithm Between Centrality. Then, four core genes (TBP, CDK7, GRM5, and GRIA1) were selected by correlation with clinical information, and the established model had very good prognosis in different databases. Finally, hsa-miR-425-5p and hsa-miR-186-5p were determined by COX regression, AD transformation status and aberrant miRNAs. Conclusion In conclusion, we tried to construct a network in which miRNAs and transcription factors jointly regulate pathogenic genes, and described the process that abnormal miRNAs and abnormal transcription factors TBP and CDK7 jointly regulate the transcription of AD central genes GRM5 and GRIA1. The insights gained from this study offer the potential AD biomarkers, which may be of assistance to the diagnose and therapy of AD.
Collapse
Affiliation(s)
- Qi Zhang
- School of Computer Science, Sichuan Normal University, Chengdu, China
| | - Ping Yang
- School of Computer Science, Sichuan Normal University, Chengdu, China
| | - Xinping Pang
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Wenbo Guo
- School of Computer Science, Sichuan Normal University, Chengdu, China
| | - Yue Sun
- School of Computer Science, Sichuan Normal University, Chengdu, China
| | - Yanyu Wei
- National Key Laboratory of Science and Technology on Vacuum Electronics, School of Electronic Science and Engineering, University of Electronic Science and Technology of China, Chengdu, China
| | - Chaoyang Pang
- School of Computer Science, Sichuan Normal University, Chengdu, China
| |
Collapse
|
21
|
Zhang Q, Chen B, Yang P, Wu J, Pang X, Pang C. Bioinformatics-based study reveals that AP2M1 is regulated by the circRNA-miRNA-mRNA interaction network and affects Alzheimer's disease. Front Genet 2022; 13:1049786. [PMID: 36468008 PMCID: PMC9716081 DOI: 10.3389/fgene.2022.1049786] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 10/31/2022] [Indexed: 09/30/2023] Open
Abstract
Alzheimer's disease (AD) is a progressive neurological disease that worsens with time. The hallmark illnesses include extracellular senile plaques caused by β-amyloid protein deposition, neurofibrillary tangles caused by tau protein hyperphosphorylation, and neuronal loss accompanying glial cell hyperplasia. Noncoding RNAs are substantially implicated in related pathophysiology, according to mounting data. However, the function of these ncRNAs is mainly unclear. Circular RNAs (circRNAs) include many miRNA-binding sites (miRNA response elements, MREs), which operate as miRNA sponges or competing endogenous RNAs (ceRNAs). The purpose of this study was to look at the role of circular RNAs (circRNAs) and microRNAs (miRNAs) in Alzheimer's disease (AD) as possible biomarkers. The Gene Expression Omnibus (GEO) database was used to obtain an expression profile of Alzheimer's disease patients (GSE5281, GSE122603, GSE97760, GSE150693, GSE1297, and GSE161435). Through preliminary data deletion, 163 genes with significant differences, 156 miRNAs with significant differences, and 153 circRNAs with significant differences were identified. Then, 10 key genes, led by MAPT and AP2M1, were identified by the mediation center algorithm, 34 miRNAs with obvious prognosis were identified by the cox regression model, and 16 key circRNAs were selected by the database. To develop competitive endogenous RNA (ceRNA) networks, hub circRNAs and mRNAs were used. Finally, GO analysis and clinical data verification of key genes were carried out. We discovered that a down-regulated circRNA (has_circ_002048) caused the increased expression of numerous miRNAs, which further inhibited the expression of a critical mRNA (AP2M1), leading to Alzheimer's disease pathology. The findings of this work contribute to a better understanding of the circRNA-miRNA-mRNA regulating processes in Alzheimer's disease. Furthermore, the ncRNAs found here might become novel biomarkers and potential targets for the development of Alzheimer's drugs.
Collapse
Affiliation(s)
- Qi Zhang
- School of Computer Science, Sichuan Normal University, Chengdu, China
| | - Bishuang Chen
- School of Computer Science, Sichuan Normal University, Chengdu, China
| | - Ping Yang
- School of Computer Science, Sichuan Normal University, Chengdu, China
| | - Jipan Wu
- School of Computer Science, Sichuan Normal University, Chengdu, China
| | - Xinping Pang
- West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Chaoyang Pang
- School of Computer Science, Sichuan Normal University, Chengdu, China
| |
Collapse
|
22
|
Identification of potential blood biomarkers for early diagnosis of Alzheimer’s disease through immune landscape analysis. NPJ AGING 2022; 8:15. [PMCID: PMC9636153 DOI: 10.1038/s41514-022-00096-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 10/12/2022] [Indexed: 11/06/2022]
Abstract
AbstractMild cognitive impairment (MCI) is a clinical precursor of Alzheimer’s disease (AD). Recent genetic studies have reported on associations between AD risk genes and immunity. Here, we obtained samples and data from 317 AD, 432 MCI, and 107 cognitively normal (CN) subjects and investigated immune-cell type composition and immune clonal diversity of T-cell receptor (TRA, TRB, TRG, and TRD) and B-cell receptor (IGH, IGK, and IGL) repertoires through bulk RNA sequencing. We found the proportions of plasma cells, γδ T cells, neutrophils, and B cells were significantly different and the diversities of IGH, IGK, and TRA were significantly small with AD progression. We then identified a differentially expressed gene, WDR37, in terms of risk of MCI-to-AD conversion. Our prognosis prediction model using the potential blood-based biomarkers for early AD diagnosis, which combined two immune repertoires (IGK and TRA), WDR37, and clinical information, successfully classified MCI patients into two groups, low and high, in terms of risk of MCI-to-AD conversion (log-rank test P = 2.57e-3). It achieved a concordance index of 0.694 in a discovery cohort and of 0.643 in an independent validation cohort. We believe that further investigation, using larger sample sizes, will lead to practical clinical use in the near future.
Collapse
|
23
|
Wang E, Lemos Duarte M, Rothman LE, Cai D, Zhang B. Non-coding RNAs in Alzheimer's disease: perspectives from omics studies. Hum Mol Genet 2022; 31:R54-R61. [PMID: 35994042 PMCID: PMC9585665 DOI: 10.1093/hmg/ddac202] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 08/16/2022] [Accepted: 08/17/2022] [Indexed: 11/13/2022] Open
Abstract
Neurodegenerative diseases such as Alzheimer's disease (AD) are characterized by the progressive loss of neurons in the brain and the spinal cord. The pathophysiology of AD is multifactorial with heterogeneous molecular manifestations. The lack of efficacious therapies for AD reinforces the importance of exploring in depth multifaceted disease mechanisms. Recent progresses on AD have generated a large amount of RNA-sequencing data at both bulk and single cell levels and revealed thousands of genes with expression changes in AD. However, the upstream regulators of such gene expression changes are largely unknown. Non-coding RNAs (ncRNAs) represent the majority of the human transcriptome, and regulatory ncRNAs have been found to play an important role in regulating gene expression. A single miRNA usually targets a number of mRNAs and thus such ncRNAs are particular important for understanding disease mechanisms and developing novel therapeutics. This review aims to summarize the recent findings on the roles of ncRNAs in AD from ncRNA-omics studies with a focus on ncRNA signatures, interactions between ncRNAs and mRNAs, and ncRNA-regulated pathways in AD. We also review the potential of specific ncRNAs to serve as biomarkers and therapeutic targets for AD. In the end, we point out future directions for studying ncRNAs in AD.
Collapse
Affiliation(s)
- Erming Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Mariana Lemos Duarte
- Department of Neurology, Alzheimer’s Disease Research Center and Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Research & Development, James J. Peters VA Medical Center, Bronx, NY 10468, USA
| | - Lauren E Rothman
- Department of Neurology, Alzheimer’s Disease Research Center and Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Research & Development, James J. Peters VA Medical Center, Bronx, NY 10468, USA
| | - Dongming Cai
- Department of Neurology, Alzheimer’s Disease Research Center and Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Research & Development, James J. Peters VA Medical Center, Bronx, NY 10468, USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Icahn Institute of Genomics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| |
Collapse
|
24
|
Li L, Yu X, Sheng C, Jiang X, Zhang Q, Han Y, Jiang J. A review of brain imaging biomarker genomics in Alzheimer’s disease: implementation and perspectives. Transl Neurodegener 2022; 11:42. [PMID: 36109823 PMCID: PMC9476275 DOI: 10.1186/s40035-022-00315-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2022] [Accepted: 08/24/2022] [Indexed: 11/25/2022] Open
Abstract
Alzheimer’s disease (AD) is a progressive neurodegenerative disease with phenotypic changes closely associated with both genetic variants and imaging pathology. Brain imaging biomarker genomics has been developed in recent years to reveal potential AD pathological mechanisms and provide early diagnoses. This technique integrates multimodal imaging phenotypes with genetic data in a noninvasive and high-throughput manner. In this review, we summarize the basic analytical framework of brain imaging biomarker genomics and elucidate two main implementation scenarios of this technique in AD studies: (1) exploring novel biomarkers and seeking mutual interpretability and (2) providing a diagnosis and prognosis for AD with combined use of machine learning methods and brain imaging biomarker genomics. Importantly, we highlight the necessity of brain imaging biomarker genomics, discuss the strengths and limitations of current methods, and propose directions for development of this research field.
Collapse
|
25
|
Wang KR, McGeachie MJ. DisiMiR: Predicting Pathogenic miRNAs Using Network Influence and miRNA Conservation. Noncoding RNA 2022; 8:ncrna8040045. [PMID: 35893228 PMCID: PMC9326518 DOI: 10.3390/ncrna8040045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Revised: 06/17/2022] [Accepted: 06/21/2022] [Indexed: 11/16/2022] Open
Abstract
MiRNAs have been shown to play a powerful regulatory role in the progression of serious diseases, including cancer, Alzheimer's, and others, raising the possibility of new miRNA-based therapies for these conditions. Current experimental methods, such as differential expression analysis, can discover disease-associated miRNAs, yet many of these miRNAs play no functional role in disease progression. Interventional experiments used to discover disease causal miRNAs can be time consuming and costly. We present DisiMiR: a novel computational method that predicts pathogenic miRNAs by inferring biological characteristics of pathogenicity, including network influence and evolutionary conservation. DisiMiR separates disease causal miRNAs from merely disease-associated miRNAs, and was accurate in four diseases: breast cancer (0.826 AUC), Alzheimer's (0.794 AUC), gastric cancer (0.853 AUC), and hepatocellular cancer (0.957 AUC). Additionally, DisiMiR can generate hypotheses effectively: 78.4% of its false positives that are mentioned in the literature have been confirmed to be causal through recently published research. In this work, we show that DisiMiR is a powerful tool that can be used to efficiently and flexibly to predict pathogenic miRNAs in an expression dataset, for the further elucidation of disease mechanisms, and the potential identification of novel drug targets.
Collapse
Affiliation(s)
| | - Michael J. McGeachie
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA 02115, USA;
| |
Collapse
|
26
|
Lin RH, Wang CC, Tung CW. A Machine Learning Classifier for Predicting Stable MCI Patients Using Gene Biomarkers. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:ijerph19084839. [PMID: 35457705 PMCID: PMC9025386 DOI: 10.3390/ijerph19084839] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 12/14/2022]
Abstract
Alzheimer’s disease (AD) is a neurodegenerative disorder with an insidious onset and irreversible condition. Patients with mild cognitive impairment (MCI) are at high risk of converting to AD. Early diagnosis of unstable MCI patients is therefore vital for slowing the progression to AD. However, current diagnostic methods are either highly invasive or expensive, preventing their wide applications. Developing low-invasive and cost-efficient screening methods is desirable as the first-tier approach for identifying unstable MCI patients or excluding stable MCI patients. This study developed feature selection and machine learning algorithms to identify blood-sample gene biomarkers for predicting stable MCI patients. Two datasets obtained from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) database were utilized to conclude 29 genes biomarkers (31 probes) for predicting stable MCI patients. A random forest-based classifier performed well with area under the receiver operating characteristic curve (AUC) values of 0.841 and 0.775 for cross-validation and test datasets, respectively. For patients with a prediction score greater than 0.9, an excellent concordance of 97% was obtained, showing the usefulness of the proposed method for identifying stable MCI patients. In the context of precision medicine, the proposed prediction model is expected to be useful for identifying stable MCI patients and providing medical doctors and patients with new first-tier diagnosis options.
Collapse
Affiliation(s)
- Run-Hsin Lin
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli County 35053, Taiwan;
- Graduate Institute of Data Science, College of Management, Taipei Medical University, Taipei 10675, Taiwan
| | - Chia-Chi Wang
- Department and Graduate Institute of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, Taipei 10617, Taiwan;
| | - Chun-Wei Tung
- Institute of Biotechnology and Pharmaceutical Research, National Health Research Institutes, Miaoli County 35053, Taiwan;
- Graduate Institute of Data Science, College of Management, Taipei Medical University, Taipei 10675, Taiwan
- Correspondence: ; Tel.: +88-6-3724-6166 (ext. 35771); Fax: +88-6-3758-6456
| |
Collapse
|
27
|
Chen Y, Qian X, Zhang Y, Su W, Huang Y, Wang X, Chen X, Zhao E, Han L, Ma Y. Prediction Models for Conversion From Mild Cognitive Impairment to Alzheimer’s Disease: A Systematic Review and Meta-Analysis. Front Aging Neurosci 2022; 14:840386. [PMID: 35493941 PMCID: PMC9049273 DOI: 10.3389/fnagi.2022.840386] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 02/02/2022] [Indexed: 11/13/2022] Open
Abstract
Background and PurposeAlzheimer’s disease (AD) is a devastating neurodegenerative disorder with no cure, and available treatments are only able to postpone the progression of the disease. Mild cognitive impairment (MCI) is considered to be a transitional stage preceding AD. Therefore, prediction models for conversion from MCI to AD are desperately required. These will allow early treatment of patients with MCI before they develop AD. This study performed a systematic review and meta-analysis to summarize the reported risk prediction models and identify the most prevalent factors for conversion from MCI to AD.MethodsWe systematically reviewed the studies from the databases of PubMed, CINAHL Plus, Web of Science, Embase, and Cochrane Library, which were searched through September 2021. Two reviewers independently identified eligible articles and extracted the data. We used the Critical Appraisal and Data Extraction for Systematic Reviews of Prediction Modeling Studies (CHARMS) checklist for the risk of bias assessment.ResultsIn total, 18 articles describing the prediction models for conversion from MCI to AD were identified. The dementia conversion rate of elderly patients with MCI ranged from 14.49 to 87%. Models in 12 studies were developed using the data from the Alzheimer’s Disease Neuroimaging Initiative (ADNI). C-index/area under the receiver operating characteristic curve (AUC) of development models were 0.67–0.98, and the validation models were 0.62–0.96. MRI, apolipoprotein E genotype 4 (APOE4), older age, Mini-Mental State Examination (MMSE) score, and Alzheimer’s Disease Assessment Scale cognitive (ADAS-cog) score were the most common and strongest predictors included in the models.ConclusionIn this systematic review, many prediction models have been developed and have good predictive performance, but the lack of external validation of models limited the extensive application in the general population. In clinical practice, it is recommended that medical professionals adopt a comprehensive forecasting method rather than a single predictive factor to screen patients with a high risk of MCI. Future research should pay attention to the improvement, calibration, and validation of existing models while considering new variables, new methods, and differences in risk profiles across populations.
Collapse
Affiliation(s)
- Yanru Chen
- Evidence-Based Nursing, School of Nursing, Lanzhou University, Lanzhou, China
| | - Xiaoling Qian
- Department of Neurology, Second Hospital of Lanzhou University, Lanzhou, China
| | - Yuanyuan Zhang
- Evidence-Based Nursing, School of Nursing, Lanzhou University, Lanzhou, China
| | - Wenli Su
- Evidence-Based Nursing, School of Nursing, Lanzhou University, Lanzhou, China
| | - Yanan Huang
- Evidence-Based Nursing, School of Nursing, Lanzhou University, Lanzhou, China
| | - Xinyu Wang
- Evidence-Based Nursing, School of Nursing, Lanzhou University, Lanzhou, China
| | - Xiaoli Chen
- Evidence-Based Nursing, School of Nursing, Lanzhou University, Lanzhou, China
| | - Enhan Zhao
- Evidence-Based Nursing, School of Nursing, Lanzhou University, Lanzhou, China
| | - Lin Han
- Evidence-Based Nursing, School of Nursing, Lanzhou University, Lanzhou, China
- Department of Nursing, Gansu Provincial Hospital, Lanzhou, China
- *Correspondence: Yuxia Ma,
| | - Yuxia Ma
- Evidence-Based Nursing, School of Nursing, Lanzhou University, Lanzhou, China
- First School of Clinical Medicine, Lanzhou University, Lanzhou, China
- *Correspondence: Yuxia Ma,
| |
Collapse
|
28
|
Wang M, Song WM, Ming C, Wang Q, Zhou X, Xu P, Krek A, Yoon Y, Ho L, Orr ME, Yuan GC, Zhang B. Guidelines for bioinformatics of single-cell sequencing data analysis in Alzheimer's disease: review, recommendation, implementation and application. Mol Neurodegener 2022; 17:17. [PMID: 35236372 PMCID: PMC8889402 DOI: 10.1186/s13024-022-00517-z] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 01/18/2022] [Indexed: 12/13/2022] Open
Abstract
Alzheimer's disease (AD) is the most common form of dementia, characterized by progressive cognitive impairment and neurodegeneration. Extensive clinical and genomic studies have revealed biomarkers, risk factors, pathways, and targets of AD in the past decade. However, the exact molecular basis of AD development and progression remains elusive. The emerging single-cell sequencing technology can potentially provide cell-level insights into the disease. Here we systematically review the state-of-the-art bioinformatics approaches to analyze single-cell sequencing data and their applications to AD in 14 major directions, including 1) quality control and normalization, 2) dimension reduction and feature extraction, 3) cell clustering analysis, 4) cell type inference and annotation, 5) differential expression, 6) trajectory inference, 7) copy number variation analysis, 8) integration of single-cell multi-omics, 9) epigenomic analysis, 10) gene network inference, 11) prioritization of cell subpopulations, 12) integrative analysis of human and mouse sc-RNA-seq data, 13) spatial transcriptomics, and 14) comparison of single cell AD mouse model studies and single cell human AD studies. We also address challenges in using human postmortem and mouse tissues and outline future developments in single cell sequencing data analysis. Importantly, we have implemented our recommended workflow for each major analytic direction and applied them to a large single nucleus RNA-sequencing (snRNA-seq) dataset in AD. Key analytic results are reported while the scripts and the data are shared with the research community through GitHub. In summary, this comprehensive review provides insights into various approaches to analyze single cell sequencing data and offers specific guidelines for study design and a variety of analytic directions. The review and the accompanied software tools will serve as a valuable resource for studying cellular and molecular mechanisms of AD, other diseases, or biological systems at the single cell level.
Collapse
Affiliation(s)
- Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Won-min Song
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Chen Ming
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Qian Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Xianxiao Zhou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Peng Xu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Azra Krek
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
| | - Yonejung Yoon
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Lap Ho
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| | - Miranda E. Orr
- Department of Internal Medicine, Section of Gerontology and Geriatric Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina USA
- Sticht Center for Healthy Aging and Alzheimer’s Prevention, Wake Forest School of Medicine, Winston-Salem, North Carolina USA
| | - Guo-Cheng Yuan
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, New York, NY 10029 USA
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Icahn Institute of Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1470 Madison Avenue, Room S8-111, New York, NY 10029 USA
| |
Collapse
|
29
|
Ogonowski N, Salcidua S, Leon T, Chamorro-Veloso N, Valls C, Avalos C, Bisquertt A, Rentería ME, Orellana P, Duran-Aniotz C. Systematic Review: microRNAs as Potential Biomarkers in Mild Cognitive Impairment Diagnosis. Front Aging Neurosci 2022; 13:807764. [PMID: 35095478 PMCID: PMC8790149 DOI: 10.3389/fnagi.2021.807764] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/15/2021] [Indexed: 12/14/2022] Open
Abstract
The rate of progression from Mild Cognitive Impairment (MCI) to Alzheimer's disease (AD) is estimated at >10% per year, reaching up to 80-90% after 6 years. MCI is considered an indicator of early-stage AD. In this context, the diagnostic screening of MCI is crucial for detecting individuals at high risk of AD before they progress and manifest further severe symptoms. Typically, MCI has been determined using neuropsychological assessment tools such as the Montreal Cognitive Assessment (MoCA) or Mini-Mental Status Examination (MMSE). Unfortunately, other diagnostic methods are not available or are unable to identify MCI in its early stages. Therefore, identifying new biomarkers for MCI diagnosis and prognosis is a significant challenge. In this framework, miRNAs in serum, plasma, and other body fluids have emerged as a promising source of biomarkers for MCI and AD-related cognitive impairments. Interestingly, miRNAs can regulate several signaling pathways via multiple and diverse targets in response to pathophysiological stimuli. This systematic review aims to describe the current state of the art regarding AD-related target genes modulated by differentially expressed miRNAs in peripheral fluids samples in MCI subjects to identify potential miRNA biomarkers in the early stages of AD. We found 30 articles that described five miRNA expression profiles from peripheral fluid in MCI subjects, showing possible candidates for miRNA biomarkers that may be followed up as fluid biomarkers or therapeutic targets of early-stage AD. However, additional research is needed to validate these miRNAs and characterize the precise neuropathological mechanisms.
Collapse
Affiliation(s)
- Natalia Ogonowski
- Latin American Institute for Brain Health (BrainLat), Universidad Adolfo Ibanez, Santiago, Chile
- Cognitive Neuroscience Center (CNC), National Scientific and Technical Research Council (CONICET), Universidad de San Andrés, Buenos Aires, Argentina
| | - Stefanny Salcidua
- Latin American Institute for Brain Health (BrainLat), Universidad Adolfo Ibanez, Santiago, Chile
- Faculty of Engineering and Sciences, Universidad Adolfo Ibanez, Santiago, Chile
| | - Tomas Leon
- Global Brain Health Institute, Trinity College, Dublin, Ireland
- Memory and Neuropsychiatric Clinic (CMYN) Neurology Department, Hospital del Salvador, Faculty of Medicine, University of Chile, Santiago, Chile
| | | | | | - Constanza Avalos
- Latin American Institute for Brain Health (BrainLat), Universidad Adolfo Ibanez, Santiago, Chile
| | | | - Miguel E. Rentería
- Department of Genetics and Computational Biology, Queensland Institute of Medical Research (QIMR) Berghofer Medical Research Institute, Brisbane, QLD, Australia
| | - Paulina Orellana
- Latin American Institute for Brain Health (BrainLat), Universidad Adolfo Ibanez, Santiago, Chile
- Center for Social and Cognitive Neuroscience (CSCN), School of Psychology, Universidad Adolfo Ibanez, Santiago, Chile
| | - Claudia Duran-Aniotz
- Latin American Institute for Brain Health (BrainLat), Universidad Adolfo Ibanez, Santiago, Chile
- Center for Social and Cognitive Neuroscience (CSCN), School of Psychology, Universidad Adolfo Ibanez, Santiago, Chile
| |
Collapse
|
30
|
Peña-Bautista C, Álvarez-Sánchez L, Cañada-Martínez AJ, Baquero M, Cháfer-Pericás C. Epigenomics and Lipidomics Integration in Alzheimer Disease: Pathways Involved in Early Stages. Biomedicines 2021; 9:1812. [PMID: 34944628 PMCID: PMC8698767 DOI: 10.3390/biomedicines9121812] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 11/23/2021] [Accepted: 11/29/2021] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Alzheimer Disease (AD) is the most prevalent dementia. However, the physiopathological mechanisms involved in its development are unclear. In this sense, a multi-omics approach could provide some progress. METHODS Epigenomic and lipidomic analysis were carried out in plasma samples from patients with mild cognitive impairment (MCI) due to AD (n = 22), and healthy controls (n = 5). Then, omics integration between microRNAs (miRNAs) and lipids was performed by Sparse Partial Least Squares (s-PLS) regression and target genes for the selected miRNAs were identified. RESULTS 25 miRNAs and 25 lipids with higher loadings in the sPLS regression were selected. Lipids from phosphatidylethanolamines (PE), lysophosphatidylcholines (LPC), ceramides, phosphatidylcholines (PC), triglycerides (TG) and several long chain fatty acids families were identified as differentially expressed in AD. Among them, several fatty acids showed strong positive correlations with miRNAs studied. In fact, these miRNAs regulated genes implied in fatty acids metabolism, as elongation of very long-chain fatty acids (ELOVL), and fatty acid desaturases (FADs). CONCLUSIONS The lipidomic-epigenomic integration showed that several lipids and miRNAs were differentially expressed in AD, being the fatty acids mechanisms potentially involved in the disease development. However, further work about targeted analysis should be carried out in a larger cohort, in order to validate these preliminary results and study the proposed pathways in detail.
Collapse
Affiliation(s)
- Carmen Peña-Bautista
- Alzheimer’s Disease Research Group, Health Research Institute La Fe, 46026 Valencia, Spain; (C.P.-B.); (L.Á.-S.); (M.B.)
| | - Lourdes Álvarez-Sánchez
- Alzheimer’s Disease Research Group, Health Research Institute La Fe, 46026 Valencia, Spain; (C.P.-B.); (L.Á.-S.); (M.B.)
- Division of Neurology, University and Polytechnic Hospital La Fe, 46026 Valencia, Spain
| | | | - Miguel Baquero
- Alzheimer’s Disease Research Group, Health Research Institute La Fe, 46026 Valencia, Spain; (C.P.-B.); (L.Á.-S.); (M.B.)
- Division of Neurology, University and Polytechnic Hospital La Fe, 46026 Valencia, Spain
| | - Consuelo Cháfer-Pericás
- Alzheimer’s Disease Research Group, Health Research Institute La Fe, 46026 Valencia, Spain; (C.P.-B.); (L.Á.-S.); (M.B.)
| |
Collapse
|
31
|
Akiyama S, Higaki S, Ochiya T, Ozaki K, Niida S, Shigemizu D. JAMIR-eQTL: Japanese genome-wide identification of microRNA expression quantitative trait loci across dementia types. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2021; 2021:6420097. [PMID: 34730175 PMCID: PMC8570227 DOI: 10.1093/database/baab072] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 09/17/2021] [Accepted: 10/23/2021] [Indexed: 12/14/2022]
Abstract
MicroRNAs (miRNAs) are small non-coding RNAs shown to regulate gene expression by binding to complementary transcripts. Genetic variants, including single-nucleotide polymorphisms and short insertions/deletions, contribute to traits and diseases by influencing miRNA expression. However, the association between genetic variation and miRNA expression remains to be elucidated. Here, by using genotype data and miRNA expression data from 3448 Japanese serum samples, we developed a computational pipeline to systematically identify genome-wide miRNA expression quantitative trait loci (miR-eQTLs). Not only did we identify a total of 2487 cis-miR-eQTLs and 3 155 773 trans-miR-eQTLs at a false discovery rate of <0.05 in six dementia types (Alzheimer's disease, dementia with Lewy bodies, vascular dementia, frontotemporal lobar degeneration, normal-pressure hydrocephalus and mild cognitive impairment) and all samples, including those from patients with other types of dementia, but also we examined the commonality and specificity of miR-eQTLs among dementia types. To enable data searching and downloading of these cis- and trans-eQTLs, we developed a user-friendly database named JAMIR-eQTL, publicly available at https://www.jamir-eqtl.org/. This is the first miR-eQTL database designed for dementia types. Our integrative and comprehensive resource will contribute to understanding the genetic basis of miRNA expression as well as to the discovery of deleterious mutations, particularly in dementia studies. Database URL: https://www.jamir-eqtl.org/.
Collapse
Affiliation(s)
- Shintaro Akiyama
- Medical Genome Center, Research Institute, National Center for Geriatrics and Gerontology, Aichi 474-8511, Japan
| | - Sayuri Higaki
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Aichi 460-0001, Japan
| | - Takahiro Ochiya
- Institute of Medical Science, Tokyo Medical University, Tokyo 160-8402, Japan
| | - Kouichi Ozaki
- Medical Genome Center, Research Institute, National Center for Geriatrics and Gerontology, Aichi 474-8511, Japan.,Center for Integrative Medical Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Shumpei Niida
- Medical Genome Center, Research Institute, National Center for Geriatrics and Gerontology, Aichi 474-8511, Japan
| | - Daichi Shigemizu
- Medical Genome Center, Research Institute, National Center for Geriatrics and Gerontology, Aichi 474-8511, Japan.,Center for Integrative Medical Sciences, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Medical Research Institute, Tokyo Medical and Dental University (TMDU), Tokyo 113-8510, Japan
| |
Collapse
|
32
|
Bloch L, Friedrich CM. Data analysis with Shapley values for automatic subject selection in Alzheimer's disease data sets using interpretable machine learning. Alzheimers Res Ther 2021; 13:155. [PMID: 34526114 PMCID: PMC8444618 DOI: 10.1186/s13195-021-00879-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 07/21/2021] [Indexed: 12/22/2022]
Abstract
BACKGROUND For the recruitment and monitoring of subjects for therapy studies, it is important to predict whether mild cognitive impaired (MCI) subjects will prospectively develop Alzheimer's disease (AD). Machine learning (ML) is suitable to improve early AD prediction. The etiology of AD is heterogeneous, which leads to high variability in disease patterns. Further variability originates from multicentric study designs, varying acquisition protocols, and errors in the preprocessing of magnetic resonance imaging (MRI) scans. The high variability makes the differentiation between signal and noise difficult and may lead to overfitting. This article examines whether an automatic and fair data valuation method based on Shapley values can identify the most informative subjects to improve ML classification. METHODS An ML workflow was developed and trained for a subset of the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort. The validation was executed for an independent ADNI test set and for the Australian Imaging, Biomarker and Lifestyle Flagship Study of Ageing (AIBL) cohort. The workflow included volumetric MRI feature extraction, feature selection, sample selection using Data Shapley, random forest (RF), and eXtreme Gradient Boosting (XGBoost) for model training as well as Kernel SHapley Additive exPlanations (SHAP) values for model interpretation. RESULTS The RF models, which excluded 134 of the 467 training subjects based on their RF Data Shapley values, outperformed the base models that reached a mean accuracy of 62.64% by 5.76% (3.61 percentage points) for the independent ADNI test set. The XGBoost base models reached a mean accuracy of 60.00% for the AIBL data set. The exclusion of those 133 subjects with the smallest RF Data Shapley values could improve the classification accuracy by 2.98% (1.79 percentage points). The cutoff values were calculated using an independent validation set. CONCLUSION The Data Shapley method was able to improve the mean accuracies for the test sets. The most informative subjects were associated with the number of ApolipoproteinE ε4 (ApoE ε4) alleles, cognitive test results, and volumetric MRI measurements.
Collapse
Affiliation(s)
- Louise Bloch
- Department of Computer Science, University of Applied Sciences and Arts Dortmund, Dortmund, 44227 Germany
- Institute for Medical Informatics, Biometry and Epidemiology (IMIBE), University Hospital Essen, Essen, 45122 Germany
| | - Christoph M. Friedrich
- Department of Computer Science, University of Applied Sciences and Arts Dortmund, Dortmund, 44227 Germany
- Institute for Medical Informatics, Biometry and Epidemiology (IMIBE), University Hospital Essen, Essen, 45122 Germany
| | - for the Alzheimer’s Disease Neuroimaging Initiative
- Department of Computer Science, University of Applied Sciences and Arts Dortmund, Dortmund, 44227 Germany
- Institute for Medical Informatics, Biometry and Epidemiology (IMIBE), University Hospital Essen, Essen, 45122 Germany
| |
Collapse
|
33
|
Lin F, Zhang H, Bao J, Li L. Identification of Potential Diagnostic miRNAs Biomarkers for Alzheimer Disease Based on Weighted Gene Coexpression Network Analysis. World Neurosurg 2021; 153:e315-e328. [PMID: 34224891 DOI: 10.1016/j.wneu.2021.06.118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 11/24/2022]
Abstract
BACKGROUND Alzheimer disease (AD) is an age-related neurodegenerative disease that accounts for nearly three fourths of dementia cases. Searching for potential biomarkers will help clinicians in the early diagnosis and treatment of AD. METHODS Firstly, we downloaded detailed AD data from the Gene Expression Omnibus (GEO) database for identification of differentially expressed microribonucleic acids (DEmiRNAs) and differentially expressed messenger ribonucleic acids (DEmRNAs). Secondly, functional enrichment analysis was used to identify the biological functions of DEmRNAs. Thirdly, weighted gene coexpression network analysis was used to identify important modules and hub miRNAs. In addition, the miRNA-mRNA regulatory network was constructed. Fourthly, the GSE120584 dataset was used for electronic expression verification and diagnostic analysis. Finally, real-time polymerase chain reaction in vitro verification was performed. RESULTS We obtained 1005 DEmiRNAs and 97 DEmRNAs, respectively. Functional enrichment found that DEmRNAs was enriched in the N-glycan biosynthesis pathway, which was associated with AD. In the weighted gene coexpression network analysis, we found that the brown module was the optimal module. Moreover, 11 hub miRNAs were identified. A total of 216 negatively regulated miRNA-mRNA regulation effects are involved. Hub miRNAs were found to have potential diagnostic value in the receiver operating characteristic analysis. CONCLUSION Eleven hub miRNAs were identified, and DEmRNAs was found to be significantly enriched in the N-glycan biosynthesis pathway, which contributes to the early diagnosis and treatment of AD.
Collapse
Affiliation(s)
- Feng Lin
- Department of Neurology, The Second People's Hospital of Liaocheng City, The Second Hospital of Liaocheng Affiliated to Shandong First Medical University, Linqing City, China
| | - Haiqi Zhang
- Department of Neurology, The Second People's Hospital of Liaocheng City, The Second Hospital of Liaocheng Affiliated to Shandong First Medical University, Linqing City, China
| | - Jinglei Bao
- Department of Neurology, The Second People's Hospital of Liaocheng City, The Second Hospital of Liaocheng Affiliated to Shandong First Medical University, Linqing City, China.
| | - Long Li
- Department of Neurosurgery, Xuanwu Hospital, Capital Medical University, Beijing, China
| |
Collapse
|
34
|
Veenstra TD. Omics in Systems Biology: Current Progress and Future Outlook. Proteomics 2021; 21:e2000235. [PMID: 33320441 DOI: 10.1002/pmic.202000235] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/25/2020] [Indexed: 12/16/2022]
Abstract
Biological research has undergone tremendous changes over the past three decades. Research used to almost exclusively focus on a single aspect of a single molecule per experiment. Modern technologies have enabled thousands of molecules to be simultaneously analyzed and the way that these molecules influence each other to be discerned. The change is so dramatic that it has given rise to a whole new descriptive suffix (i.e., omics) to describe these fields of study. While genomics was arguably the initial driver of this new trend, it quickly spread to other biological entities resulting in the creation of transcriptomics, proteomics, metabolomics, etc. The development of these "big four omics" created a wave of other omic fields, such as epigenomics, glycomics, lipidomics, microbiomics, and even foodomics; all with the purpose of comprehensively studying all the molecular entities or processes within their respective domain. The large number of omic fields that are invented even led to the term "panomics" as a way to classify them all under one category. Ultimately, all of these omic fields are setting the foundation for developing systems biology; in which the focus will be on determining the complex interactions that occur within biological systems.
Collapse
|