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Mendonça V, Soares-Lima SC, Moreira MAM. Exploring cross-tissue DNA methylation patterns: blood-brain CpGs as potential neurodegenerative disease biomarkers. Commun Biol 2024; 7:904. [PMID: 39060467 PMCID: PMC11282059 DOI: 10.1038/s42003-024-06591-x] [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: 11/02/2023] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
The difficulty of obtaining samples from certain human tissues has led to efforts to find accessible sources to analyze molecular markers derived from DNA. In this study, we look for DNA methylation patterns in blood samples and its association with the brain methylation pattern in neurodegenerative disorders. Using data from methylation databases, we selected 18,293 CpGs presenting correlated methylation levels between blood and brain (bb-CpGs) and compare their methylation level between blood samples from patients with neurodegenerative diseases (Alzheimer's disease, Parkinson's disease, Multiple Sclerosis, and X Fragile Syndrome) and healthy controls. Sixty-four bb-CpGs presented significant distinct methylation levels in patients, being: nine for Alzheimer's disease, nine for Parkinson's disease, 28 for Multiple Sclerosis, and 18 for Fragile X Syndrome. Similar differences in methylation pattern for the nine Alzheimer's bb-CpGs was also observed when comparing brain tissue from patients vs. controls. The genomic regions of some of these 64 bb-CpGs are placed close to or inside genes previously associated with the respective condition. Our findings support the rationale of using blood DNA as a surrogate of brain tissue to analyze changes in CpG methylation level in patients with neurodegenerative diseases, opening the possibility for characterizing new biomarkers.
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Affiliation(s)
- Vanessa Mendonça
- Genetic Graduation Program, Genetics Deparment, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Tumoral Genetics and Virology Program, Instituto Nacional de Cancer, Rio de Janeiro, Brazil
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2
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He W, Zhang S, Qi Z, Liu W. Unveiling the potential of estrogen: Exploring its role in neuropsychiatric disorders and exercise intervention. Pharmacol Res 2024; 204:107201. [PMID: 38704108 DOI: 10.1016/j.phrs.2024.107201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 04/01/2024] [Accepted: 04/28/2024] [Indexed: 05/06/2024]
Abstract
Neuropsychiatric disorders shorten human life spans through multiple ways and become major threats to human health. Exercise can regulate the estrogen signaling, which may be involved in depression, Alzheimer's disease (AD) and Parkinson's disease (PD), and other neuropsychiatric disorders as well in their sex differences. In nervous system, estrogen is an important regulator of cell development, synaptic development, and brain connectivity. Therefore, this review aimed to investigate the potential of estrogen system in the exercise intervention of neuropsychiatric disorders to better understand the exercise in neuropsychiatric disorders and its sex specific. Exercise can exert a protective effect in neuropsychiatric disorders through regulating the expression of estrogen and estrogen receptors, which are involved in neuroprotection, neurodevelopment, and neuronal glucose homeostasis. These processes are mediated by the downstream factors of estrogen signaling, including N-myc downstream regulatory gene 2 (Ndrg2), serotonin (5-HT), delta like canonical Notch ligand 1 (DLL1), NOD-like receptor thermal protein domain associated protein 3 (NLRP3), etc. In addition, exercise can act on the estrogen response element (ERE) fragment in the genes of estrogenic downstream factors like β-amyloid precursor protein cleavase 1 (BACE1). However, there are few studies on the relationship between exercise, the estrogen signaling pathway, and neuropsychiatric disorders. Hence, we review how the estrogen signaling mediates the mechanism of exercise intervention in neuropsychiatric disorders. We aim to provide a theoretical perspective for neuropsychiatric disorders affecting female health and provide theoretical support for the design of exercise prescriptions.
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Affiliation(s)
- Wenke He
- Key Laboratory of Adolescent Health Assessment and Exercise Intervention of Ministry of Education, East China Normal University, Shanghai 200241, China; College of Physical Education and Health, East China Normal University, Shanghai 200241,China
| | - Sen Zhang
- Key Laboratory of Adolescent Health Assessment and Exercise Intervention of Ministry of Education, East China Normal University, Shanghai 200241, China; College of Physical Education and Health, East China Normal University, Shanghai 200241,China
| | - Zhengtang Qi
- Key Laboratory of Adolescent Health Assessment and Exercise Intervention of Ministry of Education, East China Normal University, Shanghai 200241, China; College of Physical Education and Health, East China Normal University, Shanghai 200241,China.
| | - Weina Liu
- Key Laboratory of Adolescent Health Assessment and Exercise Intervention of Ministry of Education, East China Normal University, Shanghai 200241, China; College of Physical Education and Health, East China Normal University, Shanghai 200241,China.
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3
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Do AN, Ali M, Timsina J, Wang L, Western D, Liu M, Sanford J, Rosende-Roca M, Boada M, Puerta R, Wilson T, Ruiz A, Pastor P, Wyss-Coray T, Cruchaga C, Sung YJ. CSF proteomic profiling with amyloid/tau positivity identifies distinctive sex-different alteration of multiple proteins involved in Alzheimer's disease. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.15.24304164. [PMID: 38559166 PMCID: PMC10980123 DOI: 10.1101/2024.03.15.24304164] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
In Alzheimer's disease (AD), the most common cause of dementia, females have higher prevalence and faster progression, but sex-specific molecular findings in AD are limited. Here, we comprehensively examined and validated 7,006 aptamers targeting 6,162 proteins in cerebral spinal fluid (CSF) from 2,077 amyloid/tau positive cases and controls to identify sex-specific proteomic signatures of AD. In discovery (N=1,766), we identified 330 male-specific and 121 female-specific proteomic alternations in CSF (FDR <0.05). These sex-specific proteins strongly predicted amyloid/tau positivity (AUC=0.98 in males; 0.99 in females), significantly higher than those with age, sex, and APOE-ε4 (AUC=0.85). The identified sex-specific proteins were well validated (r≥0.5) in the Stanford study (N=108) and Emory study (N=148). Biological follow-up of these proteins led to sex differences in cell-type specificity, pathways, interaction networks, and drug targets. Male-specific proteins, enriched in astrocytes and oligodendrocytes, were involved in postsynaptic and axon-genesis. The male network exhibited direct connections among 152 proteins and highlighted PTEN, NOTCH1, FYN, and MAPK8 as hubs. Drug target suggested melatonin (used for sleep-wake cycle regulation), nabumetone (used for pain), daunorubicin, and verteporfin for treating AD males. In contrast, female-specific proteins, enriched in neurons, were involved in phosphoserine residue binding including cytokine activities. The female network exhibits strong connections among 51 proteins and highlighted JUN and 14-3-3 proteins (YWHAG and YWHAZ) as hubs. Drug target suggested biperiden (for muscle control of Parkinson's disease), nimodipine (for cerebral vasospasm), quinostatin and ethaverine for treating AD females. Together, our findings provide mechanistic understanding of sex differences for AD risk and insights into clinically translatable interventions.
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Affiliation(s)
- Anh N Do
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
| | - Muhammad Ali
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Jigyasha Timsina
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Lihua Wang
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Daniel Western
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Menghan Liu
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Jessie Sanford
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
| | - Matitee Rosende-Roca
- Research Center and Memory clinic Fundació ACE. Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Merce Boada
- Research Center and Memory clinic Fundació ACE. Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Raquel Puerta
- Research Center and Memory clinic Fundació ACE. Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Ted Wilson
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Agustin Ruiz
- Research Center and Memory clinic Fundació ACE. Institut Català de Neurociències Aplicades, Universitat Internacional de Catalunya, Barcelona, Spain
| | - Pau Pastor
- Memory Disorders Unit, Department of Neurology, University Hospital Mutua Terrassa, Terrassa, Spain
| | - Tony Wyss-Coray
- Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA
| | - Carlos Cruchaga
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
- Hope Center for Neurologic Diseases, Washington University in St. Louis, St. Louis, MO, USA
| | - Yun Ju Sung
- Division of Biostatistics, Washington University School of Medicine, St. Louis, MO, USA
- NeuroGenomics and Informatics Center, Washington University School of Medicine, St. Louis, MO, USA
- Department of Psychiatry, Washington University School of Medicine, St. Louis, MO, USA
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Bayram E, Reho P, Litvan I, Ding J, Gibbs JR, Dalgard CL, Traynor BJ, Scholz SW, Chia R. Genetic analysis of the X chromosome in people with Lewy body dementia nominates new risk loci. NPJ Parkinsons Dis 2024; 10:39. [PMID: 38378815 PMCID: PMC10879525 DOI: 10.1038/s41531-024-00649-7] [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: 09/25/2023] [Accepted: 02/01/2024] [Indexed: 02/22/2024] Open
Abstract
Sex influences the prevalence and symptoms of Lewy body dementia (LBD). However, genome-wide association studies typically focus on autosomal variants and exclude sex-specific risk factors. We addressed this gap by performing an X chromosome-wide association study using whole-genome sequence data from 2591 LBD cases and 4391 controls. We identified a significant risk locus within intron 1 of MAP3K15 (rs141773145, odds ratio = 2.42, 95% confidence interval = 1.65-3.56, p-value = 7.0 × 10-6) in female LBD cases conditioned for APOE ε4 dosage. The locus includes an enhancer region that regulates MAP3K15 expression in ganglionic eminence cells derived from primary cultured neurospheres. Rare variant burden testing showed differential enrichment of missense mutations in TEX13A in female LBD cases, that did not reach significance (p-value = 1.34 × 10-4). These findings support the sex-specific effects of genetic factors and a potential role of Alzheimer's-related risk for females with LBD.
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Affiliation(s)
- Ece Bayram
- Department of Neurosciences, Parkinson and Other Movement Disorders Center, University of California San Diego, La Jolla, CA, USA
| | - Paolo Reho
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
| | - Irene Litvan
- Department of Neurosciences, Parkinson and Other Movement Disorders Center, University of California San Diego, La Jolla, CA, USA
| | - Jinhui Ding
- Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - J Raphael Gibbs
- Computational Biology Group, Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD, USA
| | - Clifton L Dalgard
- Department of Anatomy, Physiology & Genetics, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
- The American Genome Center, Uniformed Services University of the Health Sciences, Bethesda, MD, USA
| | - Bryan J Traynor
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
- Neuromuscular Diseases Research Section, National Institute on Aging, Bethesda, MD, USA
- Therapeutics Development Laboratory, National Center for Advancing Translational Sciences, Rockville, MD, USA
| | - Sonja W Scholz
- Neurodegenerative Diseases Research Unit, National Institute of Neurological Disorders and Stroke, Bethesda, MD, USA
- Department of Neurology, Johns Hopkins University Medical Center, Baltimore, MD, USA
| | - Ruth Chia
- Neuromuscular Diseases Research Section, National Institute on Aging, Bethesda, MD, USA.
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5
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Reed EG, Keller-Norrell PR. Minding the Gap: Exploring Neuroinflammatory and Microglial Sex Differences in Alzheimer's Disease. Int J Mol Sci 2023; 24:17377. [PMID: 38139206 PMCID: PMC10743742 DOI: 10.3390/ijms242417377] [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: 11/20/2023] [Revised: 12/04/2023] [Accepted: 12/09/2023] [Indexed: 12/24/2023] Open
Abstract
Research into Alzheimer's Disease (AD) describes a link between AD and the resident immune cells of the brain, the microglia. Further, this suspected link is thought to have underlying sex effects, although the mechanisms of these effects are only just beginning to be understood. Many of these insights are the result of policies put in place by funding agencies such as the National Institutes of Health (NIH) to consider sex as a biological variable (SABV) and the move towards precision medicine due to continued lackluster therapeutic options. The purpose of this review is to provide an updated assessment of the current research that summarizes sex differences and the research pertaining to microglia and their varied responses in AD.
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Affiliation(s)
- Erin G. Reed
- Department of Pharmaceutical Sciences, Northeast Ohio Medical University, Rootstown, OH 44242, USA
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6
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Kim SJ, Bae YJ, Park YH, Jang H, Kim JP, Seo SW, Seong JK, Kim GH. Sex differences in the structural rich-club connectivity in patients with Alzheimer's disease. Front Aging Neurosci 2023; 15:1209027. [PMID: 37771522 PMCID: PMC10525353 DOI: 10.3389/fnagi.2023.1209027] [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: 04/20/2023] [Accepted: 08/24/2023] [Indexed: 09/30/2023] Open
Abstract
Background and objectives Alzheimer's disease (AD) is more prevalent in women than in men; however, there is a discrepancy in research on sex differences in AD. The human brain is a large-scale network with hub regions forming a central core, the rich-club, which is vital to cognitive functions. However, it is unknown whether alterations in the rich-clubs in AD differ between men and women. We aimed to investigate sex differences in the rich-club organization in the brains of patients with AD. Methods In total, 260 cognitively unimpaired individuals with negative amyloid positron emission tomography (PET) scans, 281 with prodromal AD (mild cognitive impairment due to AD) and 285 with AD dementia who confirmed with positive amyloid PET scans participated in the study. We obtained high-resolution T1-weighted and diffusion tensor images and performed network analysis. Results We observed sex differences in the rich-club and feeder connections in patients with AD, suggesting lower structural connectivity strength in women than in men. We observed a significant group-by-sex interaction in the feeder connections, particularly in the thalamus. In addition, the connectivity strength of the thalamus in the feeder connections was significantly correlated with general cognitive function in only men with prodromal AD and women with AD dementia. Conclusion Our findings provide important evidence for sex-specific alterations in the structural brain network related to AD.
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Affiliation(s)
- Soo-Jong Kim
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Neuroscience Center, Samsung Medical Center, Seoul, Republic of Korea
- Department of Intelligent Precision Healthcare Convergence, Sungkyunkwan University, Suwon, Republic of Korea
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea
| | - Youn Jung Bae
- School of Biomedical Engineering, Korea University, Seoul, Republic of Korea
| | - Yu Hyun Park
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Neuroscience Center, Samsung Medical Center, Seoul, Republic of Korea
- Department of Intelligent Precision Healthcare Convergence, Sungkyunkwan University, Suwon, Republic of Korea
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea
| | - Hyemin Jang
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Neuroscience Center, Samsung Medical Center, Seoul, Republic of Korea
| | - Jun Pyo Kim
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Neuroscience Center, Samsung Medical Center, Seoul, Republic of Korea
| | - Sang Won Seo
- Department of Neurology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea
- Department of Intelligent Precision Healthcare Convergence, Sungkyunkwan University, Suwon, Republic of Korea
- Department of Health Sciences and Technology, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea
- Alzheimer’s Disease Convergence Research Center, Samsung Medical Center, Seoul, Republic of Korea
- Department of Digital Health, SAIHST, Sungkyunkwan University, Seoul, Republic of Korea
| | - Joon-Kyung Seong
- School of Biomedical Engineering, Korea University, Seoul, Republic of Korea
- Department of Artificial Intelligence, Korea University, Seoul, Republic of Korea
| | - Geon Ha Kim
- Department of Neurology, Ewha Womans University College of Medicine, Seoul, Republic of Korea
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Garces A, Martinez B, De La Garza R, Roy D, Vallee KA, Fields JA, Moore DJ, Rodrigo H, Roy U. Differential expression of interferon-induced protein with tetratricopeptide repeats 3 (IFIT3) in Alzheimer's disease and HIV-1 associated neurocognitive disorders. Sci Rep 2023; 13:3276. [PMID: 36841839 PMCID: PMC9968324 DOI: 10.1038/s41598-022-27276-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 12/29/2022] [Indexed: 02/27/2023] Open
Abstract
The United Nations projects that one in every six people will be over the age of 65 by the year 2050. With a rapidly aging population, the risk of Alzheimer's disease (AD) becomes a major concern. AD is a multifactorial disease that involves neurodegeneration in the brain with mild dementia and deficits in memory and other cognitive domains. Additionally, it has been established that individuals with Human Immunodeficiency Virus-1 (HIV-1) experience a 5 to 10-year accelerated aging and an increased risk of developing HIV-associated neurocognitive disorders (HAND). Despite a significant amount of clinical evidence pointing towards a potential overlap between neuropathogenic processes in HAND and AD, the underlying epigenetic link between these two diseases is mostly unknown. This study is focused on identifying differentially expressed genes observed in both AD and HAND using linear regression models and a more robust significance analysis of microarray. The results established that the dysregulated type 1 and 2 interferon pathways observed in both AD and HAND contribute to the similar pathologies of these diseases within the brain. The current study identifies the important roles of interferon pathways in AD and HAND, a relationship that may be useful for earlier detection in the future.
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Affiliation(s)
- Armando Garces
- Department of Health and Biomedical Sciences, University of Texas Rio Grande Valley, One West University Blvd, Brownsville, TX, 78520, USA
| | - Bryan Martinez
- Department of Health and Biomedical Sciences, University of Texas Rio Grande Valley, One West University Blvd, Brownsville, TX, 78520, USA
| | - Roberto De La Garza
- Department of Health and Biomedical Sciences, University of Texas Rio Grande Valley, One West University Blvd, Brownsville, TX, 78520, USA
| | - Deepa Roy
- Department of Health and Biomedical Sciences, University of Texas Rio Grande Valley, One West University Blvd, Brownsville, TX, 78520, USA
| | - Kaylie-Anna Vallee
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Jerel Adam Fields
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - David J Moore
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Hansapani Rodrigo
- School of Mathematical and Statistical Sciences, University of Texas Rio Grande Valley (UTRGV), Edinburg, TX, USA.
| | - Upal Roy
- Department of Health and Biomedical Sciences, University of Texas Rio Grande Valley, One West University Blvd, Brownsville, TX, 78520, USA.
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Zeng M, Feng A, Zhao C, Zhang B, Guo P, Liu M, Zhang Q, Zhang Y, Fan R, Lyu J, Zheng X. Adenosine ameliorated Aβ 25-35-induced brain injury through the inhibition of apoptosis and oxidative stress via an ERα pathway. Brain Res 2022; 1788:147944. [PMID: 35568086 DOI: 10.1016/j.brainres.2022.147944] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 05/04/2022] [Accepted: 05/08/2022] [Indexed: 12/15/2022]
Abstract
Previous studies have shown that adenosine has estrogen-like activity mediated by estrogen receptor α (ERɑ). This study aimed to examine the effects of adenosine on Aβ25-35-induced brain injury and the underlying mechanisms involved. Adenosine (Ade, 20 mg/kg, i.g.) was administered for four weeks, followed by the induction of Alzheimer's disease (AD) by Aβ25-35 (200 µM, 3 µL/20 g, i.c.v.). Furthermore, a specific ERα blocker (MPP, 0.3 mg/kg, i.p.) was administered 30 min before the treatments of adenosine to evaluate whether the observed effects elicited by adenosine were mediated via ERα. In addition, the learning and memory ability, neuronal damage, and the levels of amyloid β-protein (Aβ), phosphorylated Tau Protein (p-Tau), apoptosis, oxidative stress, immune cells, and ERα were examined. The antagonistic effect of MPP (1 µM) against adenosine (5 µM) in Aβ25-35 (20 µM, 24 h)-induced N9 and PC-12 cells was also investigated. Adenosine improved learning and memory ability, reduced neuronal damage, downregulated Aβ42/Aβ40, p-Tau, apoptosis, and oxidative stress, transformed immune cells, and increased the expression of ERα following Aβ25-35 challenge. MPP could block these effects. Moreover, MPP also blocked the effects of adenosine on the levels of apoptosis and reactive oxygen species (ROS) in Aβ25-35-induced N9 and PC-12 cells. Adenosine ameliorated Aβ25-35-induced brain injury by inhibiting apoptosis and oxidative stress, possibly via an ERα pathway.
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Affiliation(s)
- Mengnan Zeng
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China; The Engineering and Technology Center for Chinese Medicine Development of Henan Province, Zhengzhou, China
| | - Aozi Feng
- Department of Clinical Research, the First Affiliated Hospital of Jinan University, Guangzhou, China
| | - Chenxin Zhao
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
| | - Beibei Zhang
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China; The Engineering and Technology Center for Chinese Medicine Development of Henan Province, Zhengzhou, China
| | - Pengli Guo
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China; The Engineering and Technology Center for Chinese Medicine Development of Henan Province, Zhengzhou, China
| | - Meng Liu
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China; The Engineering and Technology Center for Chinese Medicine Development of Henan Province, Zhengzhou, China
| | - Qinqin Zhang
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China; The Engineering and Technology Center for Chinese Medicine Development of Henan Province, Zhengzhou, China
| | - Yuhan Zhang
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China; The Engineering and Technology Center for Chinese Medicine Development of Henan Province, Zhengzhou, China
| | - Ruyi Fan
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China
| | - Jun Lyu
- Department of Clinical Research, the First Affiliated Hospital of Jinan University, Guangzhou, China.
| | - Xiaoke Zheng
- College of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, China; The Engineering and Technology Center for Chinese Medicine Development of Henan Province, Zhengzhou, China.
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Guo L, Zhong MB, Zhang L, Zhang B, Cai D. Sex Differences in Alzheimer's Disease: Insights From the Multiomics Landscape. Biol Psychiatry 2022; 91:61-71. [PMID: 33896621 PMCID: PMC8996342 DOI: 10.1016/j.biopsych.2021.02.968] [Citation(s) in RCA: 70] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Revised: 02/22/2021] [Accepted: 02/22/2021] [Indexed: 01/03/2023]
Abstract
Alzheimer's disease (AD) has complex etiologies, and the impact of sex on AD varies over the course of disease development. The literature provides some evidence of sex-specific contributions to AD. However, molecular mechanisms of sex-biased differences in AD remain elusive. Multiomics data in tandem with systems biology approaches offer a new avenue to dissect sex-stratified molecular mechanisms of AD and to develop sex-specific diagnostic and therapeutic strategies for AD. Single-cell transcriptomic datasets and cell deconvolution of bulk tissue transcriptomic data provide additional insights into brain cell type-specific impact on sex-biased differences in AD. In this review, we summarize the impact of sex chromosomes and sex hormones on AD, the impact of sex-biased differences during AD development, and the interplay between sex and a major AD genetic risk factor, the APOE ε4 genotype, through the multiomics landscape. Several sex-biased molecular pathways such as neuroinflammation and bioenergetic metabolism have been identified. The importance of sex chromosome and sex hormones, as well as the associated pathways in AD pathogenesis, is further strengthened by findings from omics studies. Future research efforts should integrate the multiomics data from different brain regions and different cell types using systems biology approaches, and leverage the knowledge into a holistic examination of sex differences in AD. Advances in systems biology technologies and increasingly available large-scale multiomics datasets will facilitate future studies dissecting such complex signaling mechanisms to better understand AD pathogenesis in both sexes, with the ultimate goals of developing efficacious sex- and APOE-stratified preventive and therapeutic interventions for AD.
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Affiliation(s)
- Lei Guo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Margaret B Zhong
- Department of Neuroscience, Barnard College of Columbia University, New York, New York
| | - Larry Zhang
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York; Research and Development Service, James J. Peters VA Medical Center, Bronx, New York
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, New York.
| | - Dongming Cai
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, New York; Alzheimer Disease Research Center, Icahn School of Medicine at Mount Sinai, New York, New York; Ronald M. Loeb Center for Alzheimer's Disease, Icahn School of Medicine at Mount Sinai, New York, New York; Research and Development Service, James J. Peters VA Medical Center, Bronx, New York.
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10
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Martins J, Czamara D, Sauer S, Rex-Haffner M, Dittrich K, Dörr P, de Punder K, Overfeld J, Knop A, Dammering F, Entringer S, Winter SM, Buss C, Heim C, Binder EB. Childhood adversity correlates with stable changes in DNA methylation trajectories in children and converges with epigenetic signatures of prenatal stress. Neurobiol Stress 2021; 15:100336. [PMID: 34095363 PMCID: PMC8163992 DOI: 10.1016/j.ynstr.2021.100336] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2021] [Revised: 04/01/2021] [Accepted: 05/01/2021] [Indexed: 12/12/2022] Open
Abstract
Childhood maltreatment (CM) is an established major risk factor for a number of negative health outcomes later in life. While epigenetic mechanisms, such as DNA methylation (DNAm), have been proposed as a means of embedding this environmental risk factor, little is known about its timing and trajectory, especially in very young children. It is also not clear whether additional environmental adversities, often experienced by these children, converge on similar DNAm changes. Here, we calculated a cumulative adversity score, which additionally to CM includes socioeconomic status (SES), other life events, parental psychopathology and epigenetic biomarkers of prenatal smoking and alcohol consumption. We investigated the effects of CM alone as well as the adversity score on longitudinal DNAm trajectories in the Berlin Longitudinal Child Study. This is a cohort of 173 children aged 3-5 years at baseline of whom 86 were exposed to CM. These children were followed-up for 2 years with extensive psychometric and biological assessments as well as saliva collection at 5 time points providing genome-wide DNAm levels. Overall, only a few DNAm patterns were stable over this timeframe, but less than 10 DNAm regions showed significant changes. At baseline, neither CM nor the adversity score associated with DNAm changes. However, in 6 differentially methylated regions (DMRs), CM and the adversity score significantly moderated DNAm trajectories over time. A number of these DMRs have previously been associated with adverse prenatal exposures. In our study, children exposed to CM also presented with epigenetic signatures indicative of increased prenatal exposure to tobacco and alcohol, as compared to non-CM exposed children. These epigenetic signatures of prenatal exposure strongly correlate with DNAm regions associated with CM and the adversity score. Finally, weighted correlation network analysis revealed a module of CpGs exclusively associated with CM. While our study identifies DNAm loci specifically associated with CM, especially within long non-coding RNAs, the majority of associations were found with the adversity score with convergent association with indicators of adverse prenatal exposures. This study highlights the importance of mapping not only of the epigenome but also the exposome and extending the observational timeframe to well before birth.
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Affiliation(s)
- Jade Martins
- Dept. of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Darina Czamara
- Dept. of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Susann Sauer
- Dept. of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Monika Rex-Haffner
- Dept. of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
| | - Katja Dittrich
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Campus Virchow, Department of Child and Adolescent Psychiatry, Augustenburger Platz 1, D-13353 Berlin, Germany
| | - Peggy Dörr
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Campus Virchow, Department of Child and Adolescent Psychiatry, Augustenburger Platz 1, D-13353 Berlin, Germany
| | - Karin de Punder
- Natura Foundation, Research and Development, Numansdrop, 3281, NC, Netherlands
| | - Judith Overfeld
- Charité − Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Institute of Medical Psychology, Campus Charité Mitte, Luisenstraße 57, 10117 Berlin, Germany
| | - Andrea Knop
- Charité − Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Institute of Medical Psychology, Campus Charité Mitte, Luisenstraße 57, 10117 Berlin, Germany
| | - Felix Dammering
- Charité − Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Institute of Medical Psychology, Campus Charité Mitte, Luisenstraße 57, 10117 Berlin, Germany
| | - Sonja Entringer
- Charité − Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Institute of Medical Psychology, Campus Charité Mitte, Luisenstraße 57, 10117 Berlin, Germany
- University of California, Irvine, Development, Health, and Disease Research Program, Orange, CA, USA
| | - Sibylle M. Winter
- Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Campus Virchow, Department of Child and Adolescent Psychiatry, Augustenburger Platz 1, D-13353 Berlin, Germany
| | - Claudia Buss
- Charité − Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Institute of Medical Psychology, Campus Charité Mitte, Luisenstraße 57, 10117 Berlin, Germany
- University of California, Irvine, Development, Health, and Disease Research Program, Orange, CA, USA
| | - Christine Heim
- Charité − Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, Institute of Medical Psychology, Campus Charité Mitte, Luisenstraße 57, 10117 Berlin, Germany
- Dept. of Biobehavioral Health, College of Health & Human Development, The Pennsylvania State University, University Park, PA, USA
| | - Elisabeth B. Binder
- Dept. of Translational Research in Psychiatry, Max Planck Institute of Psychiatry, Munich, Germany
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, 30329, USA
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11
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Branch CL, Semenov GA, Wagner DN, Sonnenberg BR, Pitera AM, Bridge ES, Taylor SA, Pravosudov VV. The genetic basis of spatial cognitive variation in a food-caching bird. Curr Biol 2021; 32:210-219.e4. [PMID: 34735793 DOI: 10.1016/j.cub.2021.10.036] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/15/2021] [Accepted: 10/14/2021] [Indexed: 01/02/2023]
Abstract
Spatial cognition is used by most organisms to navigate their environment. Some species rely particularly heavily on specialized spatial cognition to survive, suggesting that a heritable component of cognition may be under natural selection. This idea remains largely untested outside of humans, perhaps because cognition in general is known to be strongly affected by learning and experience.1-4 We investigated the genetic basis of individual variation in spatial cognition used by non-migratory food-caching birds to recover food stores and survive harsh montane winters. Comparing the genomes of wild, free-living birds ranging from best to worst in their performance on a spatial cognitive task revealed significant associations with genes involved in neuron growth and development and hippocampal function. These results identify candidate genes associated with differences in spatial cognition and provide a critical link connecting individual variation in spatial cognition with natural selection.
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Affiliation(s)
- Carrie L Branch
- Cornell Lab of Ornithology, Cornell University, Ithaca, NY 14850, USA.
| | - Georgy A Semenov
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
| | - Dominique N Wagner
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
| | - Benjamin R Sonnenberg
- Ecology, Evolution, and Conservation Biology Graduate Program, University of Nevada, Reno, NV 89557, USA
| | - Angela M Pitera
- Ecology, Evolution, and Conservation Biology Graduate Program, University of Nevada, Reno, NV 89557, USA
| | - Eli S Bridge
- Ecology and Evolutionary Biology, University of Oklahoma, Norman, OK 73019, USA
| | - Scott A Taylor
- Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
| | - Vladimir V Pravosudov
- Ecology, Evolution, and Conservation Biology Graduate Program, University of Nevada, Reno, NV 89557, USA.
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12
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Smith RG, Pishva E, Shireby G, Smith AR, Roubroeks JAY, Hannon E, Wheildon G, Mastroeni D, Gasparoni G, Riemenschneider M, Giese A, Sharp AJ, Schalkwyk L, Haroutunian V, Viechtbauer W, van den Hove DLA, Weedon M, Brokaw D, Francis PT, Thomas AJ, Love S, Morgan K, Walter J, Coleman PD, Bennett DA, De Jager PL, Mill J, Lunnon K. A meta-analysis of epigenome-wide association studies in Alzheimer's disease highlights novel differentially methylated loci across cortex. Nat Commun 2021; 12:3517. [PMID: 34112773 PMCID: PMC8192929 DOI: 10.1038/s41467-021-23243-4] [Citation(s) in RCA: 61] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Accepted: 04/16/2021] [Indexed: 01/01/2023] Open
Abstract
Epigenome-wide association studies of Alzheimer's disease have highlighted neuropathology-associated DNA methylation differences, although existing studies have been limited in sample size and utilized different brain regions. Here, we combine data from six DNA methylomic studies of Alzheimer's disease (N = 1453 unique individuals) to identify differential methylation associated with Braak stage in different brain regions and across cortex. We identify 236 CpGs in the prefrontal cortex, 95 CpGs in the temporal gyrus and ten CpGs in the entorhinal cortex at Bonferroni significance, with none in the cerebellum. Our cross-cortex meta-analysis (N = 1408 donors) identifies 220 CpGs associated with neuropathology, annotated to 121 genes, of which 84 genes have not been previously reported at this significance threshold. We have replicated our findings using two further DNA methylomic datasets consisting of a further >600 unique donors. The meta-analysis summary statistics are available in our online data resource ( www.epigenomicslab.com/ad-meta-analysis/ ).
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Affiliation(s)
- Rebecca G Smith
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Ehsan Pishva
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, The Netherlands
| | - Gemma Shireby
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Adam R Smith
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Janou A Y Roubroeks
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, The Netherlands
| | - Eilis Hannon
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Gregory Wheildon
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Diego Mastroeni
- Banner ASU Neurodegenerative Research Center, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Gilles Gasparoni
- Department of Genetics, University of Saarland (UdS), Saarbruecken, Germany
| | - Matthias Riemenschneider
- Department of Psychiatry and Psychotherapy, Saarland University Hospital (UKS), Homburg, Germany
| | - Armin Giese
- Center for Neuropathology and Prion Research, Ludwig-Maximilians-University (LMU), Munich, Germany
| | - Andrew J Sharp
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Vahram Haroutunian
- Department of Psychiatry, The Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Department of Neuroscience, The Icahn School of Medicine at Mount Sinai, New York, NY, USA
- JJ Peters VA Medical Center, Bronx, NY, USA
| | - Wolfgang Viechtbauer
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, The Netherlands
| | - Daniel L A van den Hove
- Department of Psychiatry and Neuropsychology, School for Mental Health and Neuroscience (MHeNS), Maastricht University, Maastricht, The Netherlands
- Laboratory of Translational Neuroscience, Department of Psychiatry, Psychosomatics and Psychotherapy, University of Wuerzburg, Würzburg, Germany
| | - Michael Weedon
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Danielle Brokaw
- Banner ASU Neurodegenerative Research Center, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - Paul T Francis
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Alan J Thomas
- Institute of Neuroscience, Newcastle University, Newcastle Upon Tyne, UK
| | - Seth Love
- Dementia Research Group, Institute of Clinical Neurosciences, School of Clinical Sciences, University of Bristol, Bristol, UK
| | - Kevin Morgan
- Human Genetics Group, University of Nottingham, Nottingham, UK
| | - Jörn Walter
- Department of Genetics, University of Saarland (UdS), Saarbruecken, Germany
| | - Paul D Coleman
- Banner ASU Neurodegenerative Research Center, Biodesign Institute, Arizona State University, Tempe, AZ, USA
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, IL, USA
| | - Philip L De Jager
- Center for Translational and Computational Neuroimmunology, Department of Neurology and Taub Institute, Columbia University Medical Center, New York, NY, USA
- The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Jonathan Mill
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK
| | - Katie Lunnon
- University of Exeter Medical School, College of Medicine and Health, University of Exeter, Exeter, UK.
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13
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Qorri B, Tsay M, Agrawal A, Au R, Gracie J. Using machine intelligence to uncover Alzheimer’s disease progression heterogeneity. EXPLORATION OF MEDICINE 2020. [DOI: 10.37349/emed.2020.00026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Aim: Research suggests that Alzheimer’s disease (AD) is heterogeneous with numerous subtypes. Through a proprietary interactive ML system, several underlying biological mechanisms associated with AD pathology were uncovered. This paper is an introduction to emerging analytic efforts that can more precisely elucidate the heterogeneity of AD.
Methods: A public AD data set (GSE84422) consisting of transcriptomic data of postmortem brain samples from healthy controls (n = 121) and AD (n = 380) subjects was analyzed. Data were processed by an artificial intelligence platform designed to discover potential drug repurposing candidates, followed by an interactive augmented intelligence program.
Results: Using perspective analytics, six perspective classes were identified: Class I is defined by TUBB1, ASB4, and PDE5A; Class II by NRG2 and ZNF3; Class III by IGF1, ASB4, and GTSE1; Class IV is defined by cDNA FLJ39269, ITGA1, and CPM; Class V is defined by PDE5A, PSEN1, and NDUFS8; and Class VI is defined by DCAF17, cDNA FLJ75819, and SLC33A1. It is hypothesized that these classes represent biological mechanisms that may act alone or in any combination to manifest an Alzheimer’s pathology.
Conclusions: Using a limited transcriptomic public database, six different classes that drive AD were uncovered, supporting the premise that AD is a heterogeneously complex disorder. The perspective classes highlighted genetic pathways associated with vasculogenesis, cellular signaling and differentiation, metabolic function, mitochondrial function, nitric oxide, and metal ion metabolism. The interplay among these genetic factors reveals a more profound underlying complexity of AD that may be responsible for the confluence of several biological factors. These results are not exhaustive; instead, they demonstrate that even within a relatively small study sample, next-generation machine intelligence can uncover multiple genetically driven subtypes. The models and the underlying hypotheses generated using novel analytic methods may translate into potential treatment pathways.
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Affiliation(s)
- Bessi Qorri
- Department of Biomedical and Molecular Sciences, Queen’s University, Kingston, ON K7L 3N6, Canada
| | - Mike Tsay
- NetraMark Corp, Toronto, ON M4E 1G8, Canada
| | | | - Rhoda Au
- Department of Anatomy & Neurobiology, Neurology and Epidemiology, Boston University Schools of Medicine and Public Health, Boston, MA 02218, USA
| | - Joseph Gracie
- NetraMark Corp, Toronto, ON M4E 1G8, Canada 5Department of Pathology and Molecular Medicine, Queen’s University, Kingston, ON K7L 3N6, Canada
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14
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Lv L, Zhang D, Hua P, Yang S. The glial-specific hypermethylated 3' untranslated region of histone deacetylase 1 may modulates several signal pathways in Alzheimer's disease. Life Sci 2020; 265:118760. [PMID: 33212149 DOI: 10.1016/j.lfs.2020.118760] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 11/10/2020] [Accepted: 11/10/2020] [Indexed: 12/17/2022]
Abstract
AIMS Epigenetic regulation plays an important role in the progression of Alzheimer's disease (AD). Here, we identified differential methylation probes (DMP) and investigated their potential mechanistic roles in AD. MAIN METHODS DMPs were identified via bioinformatic analysis of GSE66351, which was made up with 106 AD samples and 84 control samples derived from three separate brain regions. Differentially expressed genes (DEGs) were analyzed based on GSE5281 comprising 45 control samples and 58 AD samples. Gene ontology (GO), gene set enrichment analysis (GSEA), and protein-protein interaction (PPI) were used to identify pathways and hub genes. KEY FINDINGS We found 9007 DMPs in Occipital Cortex glia, 1527 in OC neurons, 100 in Temporal Cortex, and 194 in Frontal Cortex. 74 DEGs were identified in Primary Visual Cortex, 67 of which were downregulated while seven upregulated. 482 were upregulated and 697 downregulated in medial temporal gyrus. In superior frontal gyrus, 687 were upregulated and 85 downregulated. GO and PPI revealed that pathways involving epithelial-cell differentiation, cellular responses to lipids, transcription corepressor activities, apoptotic and organ growth were modulated by histone deacetylase 1 (HDAC1) and associated with AD. Additionally, GSEA illustrated that the transforming growth factor beta signaling pathway was significantly enriched in some brain regions and HDAC1 played an important role in this pathway. SIGNIFICANCE We found the glial-specific 3'UTR of HDAC1 was hypermethylated and HDAC1 was overexpressed in AD patients. Moreover, we also speculate that HDAC1 triggered signaling pathways linked to many different biological processes and functions via the regulation of histone deacetylation.
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Affiliation(s)
- Lei Lv
- Department of Cardio-Vascular Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China
| | - Dingwen Zhang
- Department of General Surgery, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510030, China
| | - Ping Hua
- Department of Cardio-Vascular Surgery, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.
| | - Songran Yang
- Biobank and Bioinformatics Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou 510120, China.
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15
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Soleimani Zakeri NS, Pashazadeh S, MotieGhader H. Gene biomarker discovery at different stages of Alzheimer using gene co-expression network approach. Sci Rep 2020; 10:12210. [PMID: 32699331 PMCID: PMC7376049 DOI: 10.1038/s41598-020-69249-8] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 07/08/2020] [Indexed: 12/24/2022] Open
Abstract
Alzheimer's disease (AD) is a chronic neurodegenerative disorder. It is the most common type of dementia that has remained as an incurable disease in the world, which destroys the brain cells irreversibly. In this study, a systems biology approach was adopted to discover novel micro-RNA and gene-based biomarkers of the diagnosis of Alzheimer's disease. The gene expression data from three AD stages (Normal, Mild Cognitive Impairment, and Alzheimer) were used to reconstruct co-expression networks. After preprocessing and normalization, Weighted Gene Co-Expression Network Analysis (WGCNA) was used on a total of 329 samples, including 145 samples of Alzheimer stage, 80 samples of Mild Cognitive Impairment (MCI) stage, and 104 samples of the Normal stage. Next, three gene-miRNA bipartite networks were reconstructed by comparing the changes in module groups. Then, the functional enrichment analyses of extracted genes of three bipartite networks and miRNAs were done, respectively. Finally, a detailed analysis of the authentic studies was performed to discuss the obtained biomarkers. The outcomes addressed proposed novel genes, including MBOAT1, ARMC7, RABL2B, HNRNPUL1, LAMTOR1, PLAGL2, CREBRF, LCOR, and MRI1and novel miRNAs comprising miR-615-3p, miR-4722-5p, miR-4768-3p, miR-1827, miR-940 and miR-30b-3p which were related to AD. These biomarkers were proposed to be related to AD for the first time and should be examined in future clinical studies.
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Affiliation(s)
| | - Saeid Pashazadeh
- Faculty of Electrical and Computer Engineering, University of Tabriz, Tabriz, Iran.
| | - Habib MotieGhader
- Department of Computer Engineering, Gowgan Educational Center, Tabriz Branch, Islamic Azad University, Tabriz, Iran
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16
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Geng Z, Wu X, Wang L, Zhou S, Tian Y, Wang K, Wei L. Reduced delayed reward selection by Alzheimer’s disease and mild cognitive impairment patients during intertemporal decision-making. J Clin Exp Neuropsychol 2020; 42:298-306. [PMID: 31914851 DOI: 10.1080/13803395.2020.1711873] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Zhi Geng
- Department of Neurology, the First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Province Key Laboratory of Cognition and Neuropsychiatric Disorders, Hefei, China
| | - Xingqi Wu
- Department of Neurology, the First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Province Key Laboratory of Cognition and Neuropsychiatric Disorders, Hefei, China
| | - Lu Wang
- Department of Neurology, the First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Province Key Laboratory of Cognition and Neuropsychiatric Disorders, Hefei, China
| | - Shanshan Zhou
- Department of Neurology, the First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Province Key Laboratory of Cognition and Neuropsychiatric Disorders, Hefei, China
- Collaborative Innovation Centre of Neuropsychiatric Disorders and Mental Health, Hefei, China
| | - Yanghua Tian
- Department of Neurology, the First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Province Key Laboratory of Cognition and Neuropsychiatric Disorders, Hefei, China
- Collaborative Innovation Centre of Neuropsychiatric Disorders and Mental Health, Hefei, China
| | - Kai Wang
- Department of Neurology, the First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Province Key Laboratory of Cognition and Neuropsychiatric Disorders, Hefei, China
- Collaborative Innovation Centre of Neuropsychiatric Disorders and Mental Health, Hefei, China
| | - Ling Wei
- Department of Neurology, the First Affiliated Hospital of Anhui Medical University, Hefei, China
- Anhui Province Key Laboratory of Cognition and Neuropsychiatric Disorders, Hefei, China
- Collaborative Innovation Centre of Neuropsychiatric Disorders and Mental Health, Hefei, China
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17
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Sun Y, Lin J, Zhang L. The application of weighted gene co-expression network analysis in identifying key modules and hub genes associated with disease status in Alzheimer's disease. ANNALS OF TRANSLATIONAL MEDICINE 2019; 7:800. [PMID: 32042816 DOI: 10.21037/atm.2019.12.59] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Background Alzheimer's disease (AD) is the most common neurodegenerative condition that affects more than 15 million individuals globally. However, a predictive molecular biomarker to distinguish the different stages of AD patients is still lacking. Methods A weighted gene co-expression network analysis (WGCNA) was employed to systematically identify the co-expressed gene modules and hub genes connected with AD development based on a microarray dataset (GSE1297) from the Gene Expression Omnibus (GEO) database. An independent validation cohort, GSE28146, was utilized to assess the diagnostic efficiency for distinguishing the different stages of AD. Quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) and western blotting analysis were applied to examine the mRNA and protein level of GRIK1, respectively, in AD mice established with the expression of mutant amyloid precursor protein and wild type mice. The morphology of neurons was investigated using phalloidin staining. Results We identified 16 co-expressed genes modules, with the pink module showing significant association with all three disease statuses [neurofibrillary tangle (NFT), BRAAK, and mini-mental state examination (MMSE)]. Enrichment analysis specified that these modules were enriched in phosphatidylinositol 3-kinase (PI3K) signaling and ion transmembrane transport. The validation cohort GSE28146 confirmed that six hub genes in the pink module could distinguish severe and non-severe AD patients [area under the curve (AUC) >0.7]. These hub genes might act as a biomarker and help to differentiate diverse pathological stages for AD patients. Finally, one of the hubs, GRIK1, was validated by an animal AD model. The mRNA and protein level of GRIK1 in the AD hippocampus was increased compared with the control group (NC) hippocampus. Phalloidin staining showed that dendritic length of the GRIK1 pCDNA3.1 group was shorter than that of the NC group. Conclusions In summary, we systematically recognized co-expressed gene modules and genes related to AD stages, which gave insight into the fundamental mechanisms of AD progression and revealed some probable targets for the treatment of AD.
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Affiliation(s)
- Yan Sun
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin 150000, China
| | - Jinghan Lin
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin 150000, China
| | - Liming Zhang
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin 150000, China
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18
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Burger A, Kotze MJ, Stein DJ, Janse van Rensburg S, Howells FM. The relationship between measurement of in vivo brain glutamate and markers of iron metabolism: A proton magnetic resonance spectroscopy study in healthy adults. Eur J Neurosci 2019; 51:984-990. [PMID: 31585485 DOI: 10.1111/ejn.14583] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2019] [Accepted: 09/18/2019] [Indexed: 01/10/2023]
Abstract
Fundamental human studies which address associations between glutamate and iron metabolism are needed. Basic research reports associations between glutamate and iron metabolism. Human studies report sex differences in iron metabolism and glutamate concentrations, which suggest that these relationships may differ by sex. We hypothesised associations would be apparent between in vivo glutamate and peripheral markers of iron metabolism, and these associations would differ by sex. To test this, we recruited 40 healthy adults (20 men, 20 women) and measured (a) standard clinical biomarker concentrations for iron metabolism and (b) an in vivo proxy for glutamate concentration, glutamate with glutamine in relation to total creatine containing metabolites using proton magnetic resonance spectroscopy studies with a two-dimensional chemical shift imaging slice, with voxels located in bilateral dorsolateral prefrontal cortices, anterior cingulate cortices and frontal white matter. Only the female group reported significant associations between peripheral markers of iron metabolism and Glx:tCr concentration: (a) right dorsolateral prefrontal cortex Glx:tCr associated positively with serum transferrin (r = .60, p = .006) and negatively with transferrin saturation (r = -.62, p = .004) and (b) right frontal white matter Glx:tCr associated negatively with iron concentration (r = -.59, p = .008) and transferrin saturation (r = -.65, p = .002). Our results support associations between iron metabolism and our proxy for in vivo glutamate concentration (Glx:tCr). These associations were limited to women, suggesting a stronger regulatory control between iron and glutamate metabolism. These associations support additional fundamental research into the molecular mechanisms of this regulatory control.
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Affiliation(s)
- Antoinette Burger
- Department of Psychiatry and Mental Health, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Neuroscience Institute, University of Cape Town, Cape Town, South Africa
| | - Maritha J Kotze
- Division of Chemical Pathology, Department of Pathology, Stellenbosch University, Cape Town, South Africa
| | - Dan J Stein
- Department of Psychiatry and Mental Health, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Neuroscience Institute, University of Cape Town, Cape Town, South Africa.,SU/UCT MRC Unit on Risk and Resilience in Mental Disorders, Department of Psychiatry and Mental Health, University of Cape Town, Cape Town, South Africa
| | - Susan Janse van Rensburg
- Division of Chemical Pathology, Department of Pathology, Stellenbosch University, Cape Town, South Africa
| | - Fleur M Howells
- Department of Psychiatry and Mental Health, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa.,Neuroscience Institute, University of Cape Town, Cape Town, South Africa
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Toro CA, Zhang L, Cao J, Cai D. Sex differences in Alzheimer's disease: Understanding the molecular impact. Brain Res 2019; 1719:194-207. [PMID: 31129153 DOI: 10.1016/j.brainres.2019.05.031] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 04/10/2019] [Accepted: 05/22/2019] [Indexed: 12/14/2022]
Abstract
Alzheimer's disease (AD) is a common neurodegenerative disorder that presents with cognitive impairment and behavioral disturbance. Approximately 5.5 million people in the United States live with AD, most of whom are over the age of 65 with two-thirds being woman. There have been major advancements over the last decade or so in the understanding of AD neuropathological changes and genetic involvement. However, studies of sex impact in AD have not been adequately integrated into the investigation of disease development and progression. It becomes indispensable to acknowledge in both basic science and clinical research studies the importance of understanding sex-specific differences in AD pathophysiology and pathogenesis, which could guide future effort in the discovery of novel targets for AD. Here, we review the latest and most relevant literature on this topic, highlighting the importance of understanding sex dimorphism from a molecular perspective and its association to clinical trial design and development in AD research field.
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Affiliation(s)
- Carlos A Toro
- National Center for the Medical Consequences of Spinal Cord Injury, James J Peters VA Medical Center, Bronx, NY 10468, United States; Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States.
| | - Larry Zhang
- Research and Development, James J Peters VA Medical Center, Bronx, NY 10468, United States; Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States
| | - Jiqing Cao
- Research and Development, James J Peters VA Medical Center, Bronx, NY 10468, United States; Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States.
| | - Dongming Cai
- Research and Development, James J Peters VA Medical Center, Bronx, NY 10468, United States; Neurology Section, James J Peters VA Medical Center, Bronx, NY 10468, United States; Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY 10029, United States.
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Sun LL, Yang SL, Sun H, Li WD, Duan SR. Molecular differences in Alzheimer's disease between male and female patients determined by integrative network analysis. J Cell Mol Med 2018; 23:47-58. [PMID: 30394676 PMCID: PMC6307813 DOI: 10.1111/jcmm.13852] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Revised: 06/28/2018] [Accepted: 07/20/2018] [Indexed: 12/17/2022] Open
Abstract
Alzheimer's disease (AD) is a complex neurodegenerative disease and the most common cause of dementia among the elderly. There has been increasing recognition of sex differences in AD prevalence, clinical manifestation, disease course and prognosis. However, there have been few studies on the molecular mechanism underlying these differences. To address this issue, we carried out global gene expression and integrative network analyses based on expression profiles (GSE84422) across 17 cortical regions of 125 individuals with AD. There were few genes that were differentially expressed across the 17 regions between the two sexes, with only four (encoding glutamate metabotropic receptor 2, oestrogen‐related receptor beta, kinesin family member 26B, and aspartoacylase) that were differentially expressed in three regions. A pan‐cortical brain region co‐expression network analysis identified pathways and genes (eg, glycogen synthase kinase 3β) that were significantly associated with clinical characteristics of AD (such as neurofibrillary score) in males only. Similarity analyses between region‐specific networks indicated that male patients exhibited greater variability, especially in the superior parietal lobule, dorsolateral prefrontal cortex and occipital visual cortex. A network module analysis revealed an association between clinical traits and crosstalk of sex‐specific modules. An examination of temporal and spatial patterns of sex differences in AD showed that molecular networks were more conserved in females than in males in different cortical regions and at different AD stages. These findings provide insight into critical molecular pathways governing sex differences in AD pathology.
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Affiliation(s)
- Lin-Lin Sun
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Song-Lin Yang
- Department of Critical Care Medicine, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Hui Sun
- Pharmaceutical Experiment Teaching Center, College of Pharmacy, Harbin Medical University, Harbin, China
| | - Wei-Da Li
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
| | - Shu-Rong Duan
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, China
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