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Yang C, Zheng C, Zhuang Y, Xu S, Li J, Hu C. Synaptic Vesicle-Related Proteins and Ubiquilin 2 in Cortical Synaptosomes Mediate Cognitive Impairment in Vascular Dementia Rats. Mol Neurobiol 2024:10.1007/s12035-024-04327-w. [PMID: 38990251 DOI: 10.1007/s12035-024-04327-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: 03/27/2024] [Accepted: 06/21/2024] [Indexed: 07/12/2024]
Abstract
Synaptic dysfunction is considered the best neuropathological correlate of cognitive decline in vascular dementia (VaD). However, the alterations of synaptic proteins at the synaptosomal level in VaD remain unclear. In this study, a VaD model was established in male rats using bilateral common carotid artery occlusion (2VO). We performed a novel object recognition task to evaluate cognitive impairment. Immunohistochemistry was used to assess the expression of neuron-specific nuclear binding protein (NeuN). Brain synaptosomes were isolated and subjected to label-free proteomic analysis to quantify and identify the synaptic features of differentially expressed proteins (DEPs). Synaptic and hub protein expression was detected in synaptosomes using western blotting. We found that male rats with VaD presented impaired memory and decreased NeuN protein expression in the cortex. Synaptosome proteomic analysis revealed 604 DEPs, with 493 and 111 markedly downregulated and upregulated proteins, respectively. KEGG analysis and SynGO annotation revealed that the synaptic vesicle (SV) cycle may be a key signaling pathway in VaD. Hub protein analysis of the main nodes in the protein network identified UBQLN2 and SV-related proteins, including CLTC, SNAP91, AP2S1, CLTA, VAMP2, EPN1, UBQLN2, AP2B1, AP2A2, and AP2M1. Western blotting showed that the levels of SV2A, CLTC, AP2S1, and VAMP2 decreased in the synaptosomes of 2VO rats, while UBQLN2 expression significantly increased. Our results suggest that the disruption in the presynaptic SV cycle is a key event in male rats with VaD, which could be characterized by the aberrant SV2A expression. SV-related proteins and UBQLN2 may be essential in synaptopathy. Thus, targeting the specific molecular markers in synaptosomes may be critical for the development of mechanism-directed therapies against VaD.
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Affiliation(s)
- Cuicui Yang
- Department of Clinical Trial Center, Beijing Tiantan Hospital, Capital Medical University, No.119 South Fourth Ring West Road, Beijing, 100070, China.
- Department of Pharmacy, Xuanwu Hospital of Capital Medical University, Beijing, 100053, China.
| | - Cengceng Zheng
- Department of Pharmacy, Xuanwu Hospital of Capital Medical University, Beijing, 100053, China
| | - Yuming Zhuang
- School of Traditional Chinese Medicine, Capital Medical University, Beijing, 100069, China
| | - Shuhong Xu
- Department of Clinical Trial Center, Beijing Tiantan Hospital, Capital Medical University, No.119 South Fourth Ring West Road, Beijing, 100070, China
| | - Jian Li
- Department of Clinical Trial Center, Beijing Tiantan Hospital, Capital Medical University, No.119 South Fourth Ring West Road, Beijing, 100070, China
| | - Chaoying Hu
- Phase I Clinical Trial Unit, Beijing Ditan Hospital of Capital Medical University, No. 8 East Jingshun Road, Beijing, 100015, China.
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Shi CL, Han XL, Chen JC, Pan QF, Gao YC, Guo PY, Min XL, Gao YJ. Single-nucleus transcriptome unveils the role of ferroptosis in ischemic stroke. Heliyon 2024; 10:e32727. [PMID: 38994078 PMCID: PMC11237950 DOI: 10.1016/j.heliyon.2024.e32727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Revised: 06/06/2024] [Accepted: 06/07/2024] [Indexed: 07/13/2024] Open
Abstract
Multiple cell death pathways are involved in neuronal death in ischemic stroke (IS). However, the role of different cell death pathways in different cell types has not been elucidated. By analyzing three single-nucleus RNA sequencing (snRNA-seq) data of IS, we first found that a variety of programmed cell death (PCD) -related genes were significantly changed in different cell types. Based on machine learning and virtual gene knockout, we found that ferroptosis related genes, ferritin heavy chain 1 (Fth1) and ferritin light chain (Ftl1), play a key role in IS. Ftl1 and Fth1 can promote microglia activation, as well as the production of inflammatory factors and chemokines. Cell communication analysis showed that activated microglia could enhance chemotactic peripheral leukocyte infiltration, such as macrophages and neutrophils, through Spp1-Cd44 and App-Cd74 signaling, thereby aggravating brain tissue damage. Furthermore, real-time quantitative polymerase chain reaction (RT-qPCR) showed that P2ry12 and Mef2c were significantly decreased in oxygen-glucose deprivation (OGD) group, while Ftl1, Fth1, Apoe, Ctsb, Cd44 and Cd74 were significantly increased in OGD group. Collectively, our findings suggested targeted therapy against microglia Ftl1 and Fth1 might improve the state of microglia, reduce the infiltration of peripheral immune cells and tissue inflammation, and then improve the ischemic brain injury in mouse.
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Affiliation(s)
- Cheng-Long Shi
- Department of Neurosurgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650032, China
| | - Xiu-Li Han
- Department of Stomatology, Kunming Children's Hospital, Kunming, 650100, China
| | - Jing-Ce Chen
- Department of Orthopedics, The First People's Hospital of Yunnan Province, Kunming, 650100, China
| | - Qian-Fan Pan
- Department of Neurosurgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650032, China
| | - Yong-Chao Gao
- Department of Neurosurgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650032, China
| | - Peng-Yan Guo
- Department of Neurosurgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650032, China
| | - Xiao-Li Min
- Department of Neurosurgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650032, China
| | - Yong-Jun Gao
- Department of Neurosurgery, The Second Affiliated Hospital of Kunming Medical University, Kunming, 650032, China
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Zhong Z, Sun MM, He M, Huang HP, Hu GY, Ma SQ, Zheng HZ, Li MY, Yao L, Cong DY, Wang HF. Proteomics and its application in the research of acupuncture: An updated review. Heliyon 2024; 10:e33233. [PMID: 39022010 PMCID: PMC11253069 DOI: 10.1016/j.heliyon.2024.e33233] [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: 07/14/2023] [Revised: 12/06/2023] [Accepted: 06/17/2024] [Indexed: 07/20/2024] Open
Abstract
As a complementary and alternative therapy, acupuncture is widely used in the prevention and treatment of various diseases. However, the understanding of the mechanism of acupuncture effects is still limited due to the lack of systematic biological validation. Notably, proteomics technologies in the field of acupuncture are rapidly evolving, and these advances are greatly contributing to the research of acupuncture. In this study, we review the progress of proteomics research in analyzing the molecular mechanisms of acupuncture for neurological disorders, pain, circulatory disorders, digestive disorders, and other diseases, with an in-depth discussion around acupoint prescription and acupuncture manipulation modalities. The study found that proteomics has great potential in understanding the mechanisms of acupuncture. This study will help explore the mechanisms of acupuncture from a proteomic perspective and provide information to support future clinical decisions.
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Affiliation(s)
- Zhen Zhong
- Changchun University of Chinese Medicine, No.1035 Boshuo Road, Jingyue National High Tech Industrial Development Zone, 130117, Changchun, China
| | - Meng-Meng Sun
- Changchun University of Chinese Medicine, No.1035 Boshuo Road, Jingyue National High Tech Industrial Development Zone, 130117, Changchun, China
| | - Min He
- Changchun University of Chinese Medicine, No.1035 Boshuo Road, Jingyue National High Tech Industrial Development Zone, 130117, Changchun, China
| | - Hai-Peng Huang
- Changchun University of Chinese Medicine, No.1035 Boshuo Road, Jingyue National High Tech Industrial Development Zone, 130117, Changchun, China
| | - Guan-Yu Hu
- The Third Affiliated Hospital of Southern Medical University, No.183, West of Zhongshan Avenue, Tianhe District, Guangzhou, 510630, Guangdong Province, China
| | - Shi-Qi Ma
- Changchun University of Chinese Medicine, No.1035 Boshuo Road, Jingyue National High Tech Industrial Development Zone, 130117, Changchun, China
| | - Hai-Zhu Zheng
- Changchun University of Chinese Medicine, No.1035 Boshuo Road, Jingyue National High Tech Industrial Development Zone, 130117, Changchun, China
| | - Meng-Yuan Li
- Changchun University of Chinese Medicine, No.1035 Boshuo Road, Jingyue National High Tech Industrial Development Zone, 130117, Changchun, China
| | - Lin Yao
- Changchun University of Chinese Medicine, No.1035 Boshuo Road, Jingyue National High Tech Industrial Development Zone, 130117, Changchun, China
| | - De-Yu Cong
- Department of Tuina, Traditional Chinese Medicine Hospital of Jilin Province, 130000, Changchun, China
| | - Hong-Feng Wang
- Changchun University of Chinese Medicine, No.1035 Boshuo Road, Jingyue National High Tech Industrial Development Zone, 130117, Changchun, China
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4
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Toader C, Dobrin N, Brehar FM, Popa C, Covache-Busuioc RA, Glavan LA, Costin HP, Bratu BG, Corlatescu AD, Popa AA, Ciurea AV. From Recognition to Remedy: The Significance of Biomarkers in Neurodegenerative Disease Pathology. Int J Mol Sci 2023; 24:16119. [PMID: 38003309 PMCID: PMC10671641 DOI: 10.3390/ijms242216119] [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] [Received: 10/10/2023] [Revised: 10/28/2023] [Accepted: 11/06/2023] [Indexed: 11/26/2023] Open
Abstract
With the inexorable aging of the global populace, neurodegenerative diseases (NDs) like Alzheimer's disease (AD), Parkinson's disease (PD), and amyotrophic lateral sclerosis (ALS) pose escalating challenges, which are underscored by their socioeconomic repercussions. A pivotal aspect in addressing these challenges lies in the elucidation and application of biomarkers for timely diagnosis, vigilant monitoring, and effective treatment modalities. This review delineates the quintessence of biomarkers in the realm of NDs, elucidating various classifications and their indispensable roles. Particularly, the quest for novel biomarkers in AD, transcending traditional markers in PD, and the frontier of biomarker research in ALS are scrutinized. Emergent susceptibility and trait markers herald a new era of personalized medicine, promising enhanced treatment initiation especially in cases of SOD1-ALS. The discourse extends to diagnostic and state markers, revolutionizing early detection and monitoring, alongside progression markers that unveil the trajectory of NDs, propelling forward the potential for tailored interventions. The synergy between burgeoning technologies and innovative techniques like -omics, histologic assessments, and imaging is spotlighted, underscoring their pivotal roles in biomarker discovery. Reflecting on the progress hitherto, the review underscores the exigent need for multidisciplinary collaborations to surmount the challenges ahead, accelerate biomarker discovery, and herald a new epoch of understanding and managing NDs. Through a panoramic lens, this article endeavors to provide a comprehensive insight into the burgeoning field of biomarkers in NDs, spotlighting the promise they hold in transforming the diagnostic landscape, enhancing disease management, and illuminating the pathway toward efficacious therapeutic interventions.
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Affiliation(s)
- Corneliu Toader
- Department of Neurosurgery, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (C.T.); (L.A.G.); (H.P.C.); (B.-G.B.); (A.D.C.); (A.V.C.)
- Department of Vascular Neurosurgery, National Institute of Neurology and Neurovascular Diseases, 077160 Bucharest, Romania
| | - Nicolaie Dobrin
- Department of Neurosurgery, Clinical Emergency Hospital “Prof. Dr. Nicolae Oblu”, 700309 Iasi, Romania
| | - Felix-Mircea Brehar
- Department of Neurosurgery, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (C.T.); (L.A.G.); (H.P.C.); (B.-G.B.); (A.D.C.); (A.V.C.)
- Department of Neurosurgery, Clinical Emergency Hospital “Bagdasar-Arseni”, 041915 Bucharest, Romania
| | - Constantin Popa
- Department of Neurology, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania
- Department of Neurology, National Institute of Neurology and Neurovascular Diseases, 077160 Bucharest, Romania
- Medical Science Section, Romanian Academy, 060021 Bucharest, Romania
| | - Razvan-Adrian Covache-Busuioc
- Department of Neurosurgery, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (C.T.); (L.A.G.); (H.P.C.); (B.-G.B.); (A.D.C.); (A.V.C.)
| | - Luca Andrei Glavan
- Department of Neurosurgery, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (C.T.); (L.A.G.); (H.P.C.); (B.-G.B.); (A.D.C.); (A.V.C.)
| | - Horia Petre Costin
- Department of Neurosurgery, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (C.T.); (L.A.G.); (H.P.C.); (B.-G.B.); (A.D.C.); (A.V.C.)
| | - Bogdan-Gabriel Bratu
- Department of Neurosurgery, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (C.T.); (L.A.G.); (H.P.C.); (B.-G.B.); (A.D.C.); (A.V.C.)
| | - Antonio Daniel Corlatescu
- Department of Neurosurgery, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (C.T.); (L.A.G.); (H.P.C.); (B.-G.B.); (A.D.C.); (A.V.C.)
| | - Andrei Adrian Popa
- Department of Neurosurgery, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (C.T.); (L.A.G.); (H.P.C.); (B.-G.B.); (A.D.C.); (A.V.C.)
| | - Alexandru Vlad Ciurea
- Department of Neurosurgery, “Carol Davila” University of Medicine and Pharmacy, 020021 Bucharest, Romania; (C.T.); (L.A.G.); (H.P.C.); (B.-G.B.); (A.D.C.); (A.V.C.)
- Medical Science Section, Romanian Academy, 060021 Bucharest, Romania
- Neurosurgery Department, Sanador Clinical Hospital, 010991 Bucharest, Romania
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Rajeev V, Chai YL, Poh L, Selvaraji S, Fann DY, Jo DG, De Silva TM, Drummond GR, Sobey CG, Arumugam TV, Chen CP, Lai MKP. Chronic cerebral hypoperfusion: a critical feature in unravelling the etiology of vascular cognitive impairment. Acta Neuropathol Commun 2023; 11:93. [PMID: 37309012 DOI: 10.1186/s40478-023-01590-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 05/25/2023] [Indexed: 06/14/2023] Open
Abstract
Vascular cognitive impairment (VCI) describes a wide spectrum of cognitive deficits related to cerebrovascular diseases. Although the loss of blood flow to cortical regions critically involved in cognitive processes must feature as the main driver of VCI, the underlying mechanisms and interactions with related disease processes remain to be fully elucidated. Recent clinical studies of cerebral blood flow measurements have supported the role of chronic cerebral hypoperfusion (CCH) as a major driver of the vascular pathology and clinical manifestations of VCI. Here we review the pathophysiological mechanisms as well as neuropathological changes of CCH. Potential interventional strategies for VCI are also reviewed. A deeper understanding of how CCH can lead to accumulation of VCI-associated pathology could potentially pave the way for early detection and development of disease-modifying therapies, thus allowing preventive interventions instead of symptomatic treatments.
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Affiliation(s)
- Vismitha Rajeev
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Memory Aging and Cognition Centre, National University Health System, Singapore, Singapore
| | - Yuek Ling Chai
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Memory Aging and Cognition Centre, National University Health System, Singapore, Singapore
| | - Luting Poh
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Memory Aging and Cognition Centre, National University Health System, Singapore, Singapore
| | - Sharmelee Selvaraji
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Memory Aging and Cognition Centre, National University Health System, Singapore, Singapore
- Integrative Sciences and Engineering Programme, NUS Graduate School, National University of Singapore, Singapore, Singapore
| | - David Y Fann
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Dong-Gyu Jo
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
| | - T Michael De Silva
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, Victoria, Australia
| | - Grant R Drummond
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, Victoria, Australia
| | - Christopher G Sobey
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, Victoria, Australia
| | - Thiruma V Arumugam
- School of Pharmacy, Sungkyunkwan University, Suwon, Republic of Korea
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, Victoria, Australia
| | - Christopher P Chen
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- Memory Aging and Cognition Centre, National University Health System, Singapore, Singapore
- NUS Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Mitchell K P Lai
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
- Memory Aging and Cognition Centre, National University Health System, Singapore, Singapore.
- NUS Healthy Longevity Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.
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6
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Philbert SA, Xu J, Church SJ, Unwin RD, Roncaroli F, Cooper GJS. Pan-cerebral sodium elevations in vascular dementia: Evidence for disturbed brain-sodium homeostasis. Front Aging Neurosci 2022; 14:926463. [PMID: 35923550 PMCID: PMC9340791 DOI: 10.3389/fnagi.2022.926463] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/28/2022] [Indexed: 01/31/2023] Open
Abstract
Vascular dementia (VaD) is the second most common cause of cognitive impairment amongst the elderly. However, there are no known disease-modifying therapies for VaD, probably due to incomplete understanding of the molecular basis of the disease. Despite the complex etiology of neurodegenerative conditions, a growing body of research now suggests the potential involvement of metal dyshomeostasis in the pathogenesis of several of the age-related dementias. However, by comparison, there remains little research investigating brain metal levels in VaD. In order to shed light on the possible involvement of metal dyshomeostasis in VaD, we employed inductively coupled plasma-mass spectrometry to quantify the levels of essential metals in post-mortem VaD brain tissue (n = 10) and age-/sex-matched controls (n = 10) from seven brain regions. We found novel evidence for elevated wet-weight cerebral sodium levels in VaD brain tissue in six out of the seven regions analyzed. Decreased cerebral-potassium levels as well as increased Na/K ratios (consistent with high tissue sodium and low potassium levels) were also observed in several brain regions. These data suggest that reduced Na+/K+-exchanging ATPase (EC 7.2.2.13) activity could contribute to the contrasting changes in sodium and potassium measured here.
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Affiliation(s)
- Sasha A. Philbert
- Division of Cardiovascular Sciences, Centre for Advanced Discovery and Experimental Therapeutics, Faculty of Biology, Medicine and Health, School of Medical Sciences, The University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
- *Correspondence: Sasha A. Philbert,
| | - Jingshu Xu
- Division of Cardiovascular Sciences, Centre for Advanced Discovery and Experimental Therapeutics, Faculty of Biology, Medicine and Health, School of Medical Sciences, The University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Stephanie J. Church
- Division of Cardiovascular Sciences, Centre for Advanced Discovery and Experimental Therapeutics, Faculty of Biology, Medicine and Health, School of Medical Sciences, The University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Richard D. Unwin
- Division of Cardiovascular Sciences, Centre for Advanced Discovery and Experimental Therapeutics, Faculty of Biology, Medicine and Health, School of Medical Sciences, The University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
- Division of Cancer Sciences, Stoller Biomarker Discovery Centre, Faculty of Biology, Medicine and Health, School of Medical Sciences, The University of Manchester, Manchester, United Kingdom
| | - Federico Roncaroli
- Division of Neuroscience and Experimental Psychology, Geoffrey Jefferson Brain Research Centre, Faculty of Biology, Medicine and Health, School of Biological Sciences, The University of Manchester, Manchester, United Kingdom
| | - Garth J. S. Cooper
- Division of Cardiovascular Sciences, Centre for Advanced Discovery and Experimental Therapeutics, Faculty of Biology, Medicine and Health, School of Medical Sciences, The University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
- Faculty of Science, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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7
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Philbert SA, Xu J, Scholefield M, Church SJ, Unwin RD, Cooper GJS. Contrasting Sodium and Potassium Perturbations in the Hippocampus Indicate Potential Na+/K+-ATPase Dysfunction in Vascular Dementia. Front Aging Neurosci 2022; 14:822787. [PMID: 35153731 PMCID: PMC8832097 DOI: 10.3389/fnagi.2022.822787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 01/04/2022] [Indexed: 12/14/2022] Open
Abstract
Vascular dementia (VaD) is thought to be the second most common cause of age-related dementia amongst the elderly. However, at present, there are no available disease-modifying therapies for VaD, probably due to insufficient understanding about the molecular basis of the disease. While the notion of metal dyshomeostasis in various age-related dementias has gained considerable attention in recent years, there remains little comparable investigation in VaD. To address this evident gap, we employed inductively coupled-plasma mass spectrometry to measure the concentrations of nine essential metals in both dry- and wet-weight hippocampal post-mortem tissue from cases with VaD (n = 10) and age-/sex-matched controls (n = 10). We also applied principal component analysis to compare the metallomic pattern of VaD in the hippocampus with our previous hippocampal metal datasets for Alzheimer’s disease, Huntington’s disease, Parkinson’s disease, and type-2 diabetes, which had been measured using the same methodology. We found substantive novel evidence for elevated hippocampal Na levels and Na/K ratios in both wet- and dry-weight analyses, whereas decreased K levels were present only in wet tissue. Multivariate analysis revealed no distinguishable hippocampal differences in metal-evoked patterns between these dementia-causing diseases in this study. Contrasting levels of Na and K in hippocampal VaD tissue may suggest dysfunction of the Na+/K+-exchanging ATPase (EC 7.2.2.13), possibly stemming from deficient metabolic energy (ATP) generation. These findings therefore highlight the potential diagnostic importance of cerebral sodium measurement in VaD patients.
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Affiliation(s)
- Sasha A. Philbert
- Centre for Advanced Discovery and Experimental Therapeutics, Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
- *Correspondence: Sasha A. Philbert,
| | - Jingshu Xu
- Centre for Advanced Discovery and Experimental Therapeutics, Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Melissa Scholefield
- Centre for Advanced Discovery and Experimental Therapeutics, Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Stephanie J. Church
- Centre for Advanced Discovery and Experimental Therapeutics, Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
| | - Richard D. Unwin
- Centre for Advanced Discovery and Experimental Therapeutics, Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
- Faculty of Science, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Garth J. S. Cooper
- Centre for Advanced Discovery and Experimental Therapeutics, Division of Cardiovascular Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, United Kingdom
- Stoller Biomarker Discovery Centre, Division of Cancer Sciences, School of Medical Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, United Kingdom
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8
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Proteomic Analysis of Perihematoma Tissue from Patients with Intracerebral Hemorrhage Using iTRAQ-Based Quantitative Proteomics. Neuromolecular Med 2021; 23:395-403. [PMID: 33389597 DOI: 10.1007/s12017-020-08637-9] [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: 04/29/2020] [Accepted: 11/24/2020] [Indexed: 11/27/2022]
Abstract
Intracerebral hemorrhage is a complicated disorder with limited proven prognostic and therapeutic targets and elusive mechanisms. With proteomic methods, we aimed to explore the global protein expression profile of perihematomal tissue from ICH patients and identify potential pathophysiological pathways and protein markers. Using iTRAQ-labeling quantitative proteomics technology, four ICH brain sample and four non-ICH brain samples were analyzed. Among the 3740 quantifiable proteins, 884 were dysregulated in the patients compared to those in the controls (p < 0.05). After bioinformatics analysis, the differentially expressed proteins were found to be mostly involved in hemostatic processes, nutrient metabolism signaling pathways, and antioxidation pathways. Moreover, fibronectin 1 was revealed to be at the center of the protein-protein interaction networks. In summary, the potential pathways and brain protein markers that could potentially be used to predict the prognosis of ICH were obtained from the altered proteomic profile of perihematomal tissue. Thus, these data may yield novel insights into the mechanisms of ICH-induced secondary brain injury.
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9
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Liu D, Yang S, Kavdia K, Sifford JM, Wu Z, Xie B, Wang Z, Pagala VR, Wang H, Yu K, Dey KK, High AA, Serrano GE, Beach TG, Peng J. Deep Profiling of Microgram-Scale Proteome by Tandem Mass Tag Mass Spectrometry. J Proteome Res 2020; 20:337-345. [PMID: 33175545 DOI: 10.1021/acs.jproteome.0c00426] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Tandem mass tag (TMT)-based mass spectrometry (MS) enables deep proteomic profiling of more than 10,000 proteins in complex biological samples but requires up to 100 μg protein in starting materials during a standard analysis. Here, we present a streamlined protocol to quantify more than 9000 proteins with 0.5 μg protein per sample by 16-plex TMT coupled with two-dimensional liquid chromatography and tandem mass spectrometry (LC/LC-MS/MS). In this protocol, we optimized multiple conditions to reduce sample loss, including processing each sample in a single tube to minimize surface adsorption, increasing digestion enzymes to shorten proteolysis and function as carriers, eliminating a desalting step between digestion and TMT labeling, and developing miniaturized basic pH LC for prefractionation. By profiling 16 identical human brain tissue samples of Alzheimer's disease (AD), vascular dementia (VaD), and non-dementia controls, we directly compared this new microgram-scale protocol to the standard-scale protocol, quantifying 9116 and 10,869 proteins, respectively. Importantly, bioinformatics analysis indicated that the microgram-scale protocol had adequate sensitivity and reproducibility to detect differentially expressed proteins in disease-related pathways. Thus, this newly developed protocol is of general application for deep proteomics analysis of biological and clinical samples at sub-microgram levels.
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Affiliation(s)
- Danting Liu
- Departments of Structural Biology and Developmental Neurobiology, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Shu Yang
- Departments of Structural Biology and Developmental Neurobiology, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Kanisha Kavdia
- Center for Proteomics and Metabolomics, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Jeffrey M Sifford
- Departments of Structural Biology and Developmental Neurobiology, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Zhiping Wu
- Departments of Structural Biology and Developmental Neurobiology, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Boer Xie
- Center for Proteomics and Metabolomics, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Zhen Wang
- Departments of Structural Biology and Developmental Neurobiology, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Vishwajeeth R Pagala
- Center for Proteomics and Metabolomics, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Hong Wang
- Center for Proteomics and Metabolomics, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Kaiwen Yu
- Departments of Structural Biology and Developmental Neurobiology, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Kaushik Kumar Dey
- Departments of Structural Biology and Developmental Neurobiology, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Anthony A High
- Center for Proteomics and Metabolomics, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Geidy E Serrano
- Banner Sun Health Research Institute, Sun City, Arizona 85351, United States
| | - Thomas G Beach
- Banner Sun Health Research Institute, Sun City, Arizona 85351, United States
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Center for Proteomics and Metabolomics, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
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10
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Abstract
Introduction: Protein thiols are susceptible to oxidation in health and disease. Redox proteomics methods facilitate the identification, quantification, and rationalization of oxidation processes including those involving protein thiols. These residues are crucial to understanding redox homeostasis underpinning normal cell functioning and regulation as well as novel biomarkers of pathology and promising novel drug targets.Areas covered: This article reviews redox proteomic approaches to study of protein thiols in some important human pathologies and assesses the clinical potential of individual Cys residues as novel biomarkers for disease detection and as targets for novel treatments.Expert commentary: Although protein thiols are not as routinely used as redox biomarkers as some other lesions such as carbonylation, there has been growing recent interest in their potential. Driven largely by developments in high-resolution mass spectrometry it is possible now to identify proteins that are redox modified at thiol groups or that interact with regulatory oxidoreductases. Thiols that are specifically susceptible to modification by reactive oxygen species can be routinely identified now and quantitative MS can be used to quantify the proportion of a protein that is redox modified.
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Affiliation(s)
- David Sheehan
- Department of Chemistry, Khalifa University, Abu Dhabi, United Arab Emirates.,School of Biochemistry and Cell Biology, University College Cork, Cork, Ireland
| | - Brian McDonagh
- Department of Physiology, School of Medicine, National University of Ireland, Galway, Ireland
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11
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Phosphoproteomic and Kinomic Signature of Clinically Aggressive Grade I (1.5) Meningiomas Reveals RB1 Signaling as a Novel Mediator and Biomarker. Clin Cancer Res 2019; 26:193-205. [DOI: 10.1158/1078-0432.ccr-18-0641] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 06/17/2018] [Accepted: 10/10/2019] [Indexed: 11/16/2022]
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12
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Abulizi N, Quin C, Brown K, Chan YK, Gill SK, Gibson DL. Gut Mucosal Proteins and Bacteriome Are Shaped by the Saturation Index of Dietary Lipids. Nutrients 2019; 11:nu11020418. [PMID: 30781503 PMCID: PMC6412740 DOI: 10.3390/nu11020418] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 02/01/2019] [Accepted: 02/13/2019] [Indexed: 02/07/2023] Open
Abstract
The dynamics of the tripartite relationship between the host, gut bacteria and diet in the gut is relatively unknown. An imbalance between harmful and protective gut bacteria, termed dysbiosis, has been linked to many diseases and has most often been attributed to high-fat dietary intake. However, we recently clarified that the type of fat, not calories, were important in the development of murine colitis. To further understand the host-microbe dynamic in response to dietary lipids, we fed mice isocaloric high-fat diets containing either milk fat, corn oil or olive oil and performed 16S rRNA gene sequencing of the colon microbiome and mass spectrometry-based relative quantification of the colonic metaproteome. The corn oil diet, rich in omega-6 polyunsaturated fatty acids, increased the potential for pathobiont survival and invasion in an inflamed, oxidized and damaged gut while saturated fatty acids promoted compensatory inflammatory responses involved in tissue healing. We conclude that various lipids uniquely alter the host-microbe interaction in the gut. While high-fat consumption has a distinct impact on the gut microbiota, the type of fatty acids alters the relative microbial abundances and predicted functions. These results support that the type of fat are key to understanding the biological effects of high-fat diets on gut health.
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Affiliation(s)
- Nijiati Abulizi
- Department of Biology, IKBSAS, University of British Columbia, Okanagan campus, Kelowna V1V 1V7, Canada.
| | - Candice Quin
- Department of Biology, IKBSAS, University of British Columbia, Okanagan campus, Kelowna V1V 1V7, Canada.
| | - Kirsty Brown
- Department of Biology, IKBSAS, University of British Columbia, Okanagan campus, Kelowna V1V 1V7, Canada.
| | - Yee Kwan Chan
- Department of Biology, IKBSAS, University of British Columbia, Okanagan campus, Kelowna V1V 1V7, Canada.
| | - Sandeep K Gill
- Department of Biology, IKBSAS, University of British Columbia, Okanagan campus, Kelowna V1V 1V7, Canada.
| | - Deanna L Gibson
- Department of Biology, IKBSAS, University of British Columbia, Okanagan campus, Kelowna V1V 1V7, Canada.
- Department of Medicine, Faculty of Medicine, University of British Columbia, Vancouver V6T 1Z3, Canada.
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13
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Wang K, Chen Z, Long L, Tao Y, Wu Q, Xiang M, Liang Y, Xie X, Jiang Y, Xiao Z, Yan Y, Qiu S, Yi B. iTRAQ-based quantitative proteomic analysis of differentially expressed proteins in chemoresistant nasopharyngeal carcinoma. Cancer Biol Ther 2018; 19:809-824. [PMID: 30067426 DOI: 10.1080/15384047.2018.1472192] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Nasopharyngeal carcinoma (NPC) is a highly prevalent disease in Southeast Asia. The disease is typically diagnosed in the later stages, and chemotherapy resistance often causes treatment failure. To investigate the underlying mechanisms of drug resistance, we searched for chemoresistant-associated proteins in NPC and drug-resistant NPC cell lines using isobaric tags for relative and absolute quantitation combined with nano liquid chromatography-tandem mass spectrometry. The chemoresistant NPC cell lines CNE1DDP and CNE2DDP were resistant to 1 mg/L cisplatin, had resistant indexes of 4.58 and 2.63, respectively, and clearly grew more slowly than the NPC cell lines CNE1 and CNE2. Using three technical replicates, we identified 690 nonredundant proteins, 56 of which were differentially expressed in both groups of cell lines (CNE1 vs. CNE1DDP and CNE2 vs. CNE2DDP). Gene Ontology, KEGG pathway, and miRNA analyses and protein-protein interactions of differentially expressed proteins showed that proteins TRIM29, HSPB1, CLIC1, ANXA1, and STMN1, among others, may play a role in the mechanisms of chemoresistance in clinical therapy. The chemotherapy-resistant proteomic profiles obtained may allow the identification of novel biomarkers for early detection of chemoresistance in NPC and other cancers.
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Affiliation(s)
- Kun Wang
- a Department of Clinical Laboratory , Xiangya Hospital, Central South University , Changsha , Hunan Province , China
| | - Zhen Chen
- a Department of Clinical Laboratory , Xiangya Hospital, Central South University , Changsha , Hunan Province , China
| | - Lu Long
- a Department of Clinical Laboratory , Xiangya Hospital, Central South University , Changsha , Hunan Province , China
| | - Ya Tao
- a Department of Clinical Laboratory , Xiangya Hospital, Central South University , Changsha , Hunan Province , China
| | - Qiong Wu
- a Department of Clinical Laboratory , Xiangya Hospital, Central South University , Changsha , Hunan Province , China
| | - Manlin Xiang
- a Department of Clinical Laboratory , Xiangya Hospital, Central South University , Changsha , Hunan Province , China
| | - Yunlai Liang
- a Department of Clinical Laboratory , Xiangya Hospital, Central South University , Changsha , Hunan Province , China
| | - Xulin Xie
- a Department of Clinical Laboratory , Xiangya Hospital, Central South University , Changsha , Hunan Province , China
| | - Yuan Jiang
- a Department of Clinical Laboratory , Xiangya Hospital, Central South University , Changsha , Hunan Province , China.,b Department of Clinical Laboratory , Hunan Cancer Hospital , Changsha , Hunan Province , China
| | - Zhiqiang Xiao
- c The Higher Educational Key Laboratory for Cancer Proteomics and Translational Medicine of Hunan Province , Xiangya Hospital, Central South University , Changsha , Hunan Province , China
| | - Yahui Yan
- d Department of pathology , Xiangya Hospital, Central South University , Changsha , Hunan Province , China
| | - Shiyang Qiu
- a Department of Clinical Laboratory , Xiangya Hospital, Central South University , Changsha , Hunan Province , China
| | - Bin Yi
- a Department of Clinical Laboratory , Xiangya Hospital, Central South University , Changsha , Hunan Province , China
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14
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Jylhä A, Nättinen J, Aapola U, Mikhailova A, Nykter M, Zhou L, Beuerman R, Uusitalo H. Comparison of iTRAQ and SWATH in a clinical study with multiple time points. Clin Proteomics 2018; 15:24. [PMID: 30069167 PMCID: PMC6065059 DOI: 10.1186/s12014-018-9201-5] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 07/23/2018] [Indexed: 12/21/2022] Open
Abstract
Background Advances in mass spectrometry have accelerated biomarker discovery in many areas of medicine. The purpose of this study was to compare two mass spectrometry (MS) methods, isobaric tags for relative and absolute quantitation (iTRAQ) and sequential window acquisition of all theoretical fragment ion spectra (SWATH), for analytical efficiency in biomarker discovery when there are multiple methodological constraints such as limited sample size and several time points for each patient to be analyzed. Methods A total of 140 tear samples were collected from 28 glaucoma patients at 5 time points in a glaucoma drug switch study. Samples were analyzed with iTRAQ and SWATH methods using NanoLC-MSTOF mass spectrometry. Results We discovered that even though iTRAQ is faster than SWATH with respect to analysis time per sample, it loses in sensitivity, reliability and robustness. While SWATH analysis yielded complete data of 456 proteins in all samples, with iTRAQ we were able to quantify 477 proteins in total but on average only 125 proteins were quantified in a sample. 283 proteins were common in the datasets produced by the two methods. Repeatability of the methods was assessed by calculating percent relative standard deviation (% RSD) between replicate MS analyses: SWATH was more repeatable (56% of proteins < 20% RSD), compared to iTRAQ (43% of proteins < 20% RSD). Despite the overall benefits of SWATH, both methods showed less than 1 log fold change difference in the expression of 74% common proteins. In addition, comparison to MS/MS peptide results using 8 isotopically labeled peptide standards, SWATH and iTRAQ showed similar results in terms of accuracy. Moreover, both methods detected similar trends in a longitudinal analysis of protein expression of two known tear biomarkers. Conclusions Overall, we conclude that SWATH should be preferred for biomarker discovery studies when analyzing limited volumes of clinical samples collected at multiple time points. Trial Registeration The study was approved by the Ethics Committee at Tampere University Hospital and was registered in EU clinical trials register (EudraCT Number: 2010-021039-14).
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Affiliation(s)
- Antti Jylhä
- 1Department of Ophthalmology, SILK, The Centre for Proteomics and Personalized Medicine (PPM), Faculty of Medicine and Life Sciences, University of Tampere, Arvo Ylpön katu 34, ARVO, PL 100, 33014 Tampere, Finland.,2BioMediTech, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Janika Nättinen
- 1Department of Ophthalmology, SILK, The Centre for Proteomics and Personalized Medicine (PPM), Faculty of Medicine and Life Sciences, University of Tampere, Arvo Ylpön katu 34, ARVO, PL 100, 33014 Tampere, Finland.,2BioMediTech, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Ulla Aapola
- 1Department of Ophthalmology, SILK, The Centre for Proteomics and Personalized Medicine (PPM), Faculty of Medicine and Life Sciences, University of Tampere, Arvo Ylpön katu 34, ARVO, PL 100, 33014 Tampere, Finland.,2BioMediTech, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Alexandra Mikhailova
- 1Department of Ophthalmology, SILK, The Centre for Proteomics and Personalized Medicine (PPM), Faculty of Medicine and Life Sciences, University of Tampere, Arvo Ylpön katu 34, ARVO, PL 100, 33014 Tampere, Finland.,2BioMediTech, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Matti Nykter
- 2BioMediTech, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Lei Zhou
- 3Singapore Eye Research Institute, Singapore, Singapore.,4Duke-NUS SRP NBD, Singapore, Singapore.,5Department of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore.,6Ophthalmology and Visual Sciences Academic Clinical Research Program, Duke-NUS Medical School, Singapore, Singapore
| | - Roger Beuerman
- 1Department of Ophthalmology, SILK, The Centre for Proteomics and Personalized Medicine (PPM), Faculty of Medicine and Life Sciences, University of Tampere, Arvo Ylpön katu 34, ARVO, PL 100, 33014 Tampere, Finland.,3Singapore Eye Research Institute, Singapore, Singapore.,4Duke-NUS SRP NBD, Singapore, Singapore
| | - Hannu Uusitalo
- 1Department of Ophthalmology, SILK, The Centre for Proteomics and Personalized Medicine (PPM), Faculty of Medicine and Life Sciences, University of Tampere, Arvo Ylpön katu 34, ARVO, PL 100, 33014 Tampere, Finland.,2BioMediTech, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland.,7Tays Eye Center, Tampere University Hospital, Tampere, Finland
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15
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Parada CA, Osbun J, Kaur S, Yakkioui Y, Shi M, Pan C, Busald T, Karasozen Y, Gonzalez-Cuyar LF, Rostomily R, Zhang J, Ferreira M. Kinome and phosphoproteome of high-grade meningiomas reveal AKAP12 as a central regulator of aggressiveness and its possible role in progression. Sci Rep 2018; 8:2098. [PMID: 29391485 PMCID: PMC5794791 DOI: 10.1038/s41598-018-19308-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Accepted: 12/29/2017] [Indexed: 01/05/2023] Open
Abstract
There is a need to better understand meningioma oncogenesis for biomarker discovery and development of targeted therapies. Histological or genetic criteria do not accurately predict aggressiveness. Post-translational studies in meningioma progression are lacking. In the present work, we introduce a combination of mass spectrometry-based phosphoproteomics and peptide array kinomics to profile atypical and anaplastic (high-grade) meningiomas. In the discovery set of fresh-frozen tissue specimens (14), the A-kinase anchor protein 12 (AKAP12) protein was found downregulated across the grades. AKAP12 knockdown in benign meningioma cells SF4433 increases proliferation, cell cycle, migration, invasion, and confers an anaplastic profile. Differentially regulated pathways were characteristic of high-grade meningiomas. Low AKAP12 expression in a larger cohort of patients (75) characterized tumor invasiveness, recurrence, and progression, indicating its potential as a prognostic biomarker. These results demonstrate AKAP12 as a central regulator of meningioma aggressiveness with a possible role in progression.
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Affiliation(s)
- Carolina Angelica Parada
- Departments of Neurosurgery/University of Washington School of Medicine, University of Washington Medical Center, Seattle/WA, 98195, USA
| | - Joshua Osbun
- Departments of Neurosurgery/University of Washington School of Medicine, University of Washington Medical Center, Seattle/WA, 98195, USA
| | - Sumanpreet Kaur
- Departments of Neurosurgery/University of Washington School of Medicine, University of Washington Medical Center, Seattle/WA, 98195, USA
| | - Youssef Yakkioui
- Departments of Neurosurgery/University of Washington School of Medicine, University of Washington Medical Center, Seattle/WA, 98195, USA
| | - Min Shi
- Department of Pathology/University of Washington School of Medicine, Harborview Medical Center, Seattle/WA, 98104, USA
| | - Catherine Pan
- Department of Pathology/University of Washington School of Medicine, Harborview Medical Center, Seattle/WA, 98104, USA
| | - Tina Busald
- Departments of Neurosurgery/University of Washington School of Medicine, University of Washington Medical Center, Seattle/WA, 98195, USA
| | - Yigit Karasozen
- Departments of Neurosurgery/University of Washington School of Medicine, University of Washington Medical Center, Seattle/WA, 98195, USA
| | - Luis Francisco Gonzalez-Cuyar
- Department of Pathology/University of Washington School of Medicine, Harborview Medical Center, Seattle/WA, 98104, USA
| | - Robert Rostomily
- Departments of Neurosurgery/University of Washington School of Medicine, University of Washington Medical Center, Seattle/WA, 98195, USA
| | - Jing Zhang
- Department of Pathology/University of Washington School of Medicine, Harborview Medical Center, Seattle/WA, 98104, USA
| | - Manuel Ferreira
- Departments of Neurosurgery/University of Washington School of Medicine, University of Washington Medical Center, Seattle/WA, 98195, USA.
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16
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Garranzo-Asensio M, San Segundo-Acosta P, Martínez-Useros J, Montero-Calle A, Fernández-Aceñero MJ, Häggmark-Månberg A, Pelaez-Garcia A, Villalba M, Rabano A, Nilsson P, Barderas R. Identification of prefrontal cortex protein alterations in Alzheimer's disease. Oncotarget 2018. [PMID: 29541381 PMCID: PMC5834268 DOI: 10.18632/oncotarget.24303] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Alzheimer’s disease (AD) is the most common form of dementia in developed countries. A better understanding of the events taking place at the molecular level would help to identify novel protein alterations, which might be used in diagnosis or for treatment development. In this study, we have performed the high-throughput analysis of 706 molecules mostly implicated in cell-cell communication and cell signaling processes by using two antibody microarray platforms. We screened three AD pathological groups -each one containing four pooled samples- from Braak stages IV, V and VI, and three control groups from two healthy subjects, five frontotemporal and two vascular dementia patients onto Panorama and L-Series antibody microarrays to identify AD-specific alterations not common to other dementias. Forty altered proteins between control and AD groups were detected, and validated by i) meta-analysis of mRNA alterations, ii) WB, and iii) FISH and IHC using an AD-specific tissue microarray containing 44 samples from AD patients at different Braak stages, and frontotemporal and vascular dementia patients and healthy individuals as controls. We identified altered proteins in AD not common to other dementias like the E3 ubiquitin-protein ligase TOPORS, Layilin and MICB, and validated the association to AD of the previously controverted proteins DDIT3 and the E3 ubiquitin-protein ligase XIAP. These altered proteins constitute interesting targets for further immunological analyses using sera, plasma and CSF to identify AD blood- or cerebrospinal fluid-biomarkers and to perform functional analysis to determine their specific role in AD, and their usefulness as potential therapeutic targets of intervention.
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Affiliation(s)
- Maria Garranzo-Asensio
- Biochemistry and Molecular Biology Department I, Chemistry Faculty, Complutense University of Madrid, Madrid, Spain
| | - Pablo San Segundo-Acosta
- Biochemistry and Molecular Biology Department I, Chemistry Faculty, Complutense University of Madrid, Madrid, Spain
| | - Javier Martínez-Useros
- Translational Oncology Division, OncoHealth Institute, Fundacion Jimenez Diaz University Hospital, Madrid, Spain
| | - Ana Montero-Calle
- Biochemistry and Molecular Biology Department I, Chemistry Faculty, Complutense University of Madrid, Madrid, Spain
| | - María Jesús Fernández-Aceñero
- Servicio de Anatomía Patológica Hospital Clínico San Carlos, Instituto de Investigación Sanitaria del Hospital Clínico San Carlos (IdISSC), Departamento de Anatomía Patològica, Facultad de Medicina, Complutense University of Madrid, Madrid, Spain
| | - Anna Häggmark-Månberg
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Stockholm, Sweden
| | | | - Mayte Villalba
- Biochemistry and Molecular Biology Department I, Chemistry Faculty, Complutense University of Madrid, Madrid, Spain
| | - Alberto Rabano
- Alzheimer Disease Research Unit, CIEN Foundation, Queen Sofia Foundation Alzheimer Center, Madrid, Spain
| | - Peter Nilsson
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Rodrigo Barderas
- Biochemistry and Molecular Biology Department I, Chemistry Faculty, Complutense University of Madrid, Madrid, Spain.,UFIEC, National Institute of Health Carlos III, Majadahonda, Madrid, Spain
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17
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Datta A, Chai YL, Tan JM, Lee JH, Francis PT, Chen CP, Sze SK, Lai MKP. An iTRAQ-based proteomic analysis reveals dysregulation of neocortical synaptopodin in Lewy body dementias. Mol Brain 2017; 10:36. [PMID: 28800743 PMCID: PMC5553757 DOI: 10.1186/s13041-017-0316-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 07/21/2017] [Indexed: 02/08/2023] Open
Abstract
Lewy body dementias are the second most common cause of neurodegenerative dementia in the elderly after Alzheimer's disease (AD). The two clinical subgroups of Lewy body dementias, namely, dementia with Lewy bodies (DLB) and Parkinson's disease dementia (PDD), are differentiated by the chronology of cognitive symptoms relative to parkinsonism. At present, there remains a debate on whether DLB and PDD are separate disease entities, or fall within the same spectrum of Lewy body dementias. In this study, we compared the detergent-soluble proteome via an 8-plex isobaric tag for relative and absolute quantitation (iTRAQ) analysis of pooled lysates from the prefrontal cortex (BA9) of DLB (n = 19) and PDD (n = 21) patients matched a priori for amyloid (total Aβ42) burden, semi-quantitative scores for Lewy bodies and neurofibrillary tangles together with age-matched control (n = 21) subjects. A total of 1914 proteins were confidently identified by iTRAQ (false discovery rate = 0%). None of the proteins showed a significant yet opposite regulation in between DLB and PDD when compared to aged controls in the proteomic data set as well as following immunoblot analysis of the pooled and individual lysates involving all 61 subjects. The postsynaptic protein, synaptopodin (SYNPO) was significantly down-regulated in both DLB and PDD subgroups, suggesting a defective synaptic transmission in the demented patients. In conclusion, the largely similar proteome of DLB and PDD matched for amyloid burden suggests that variations in concomitant AD-related pathology, abnormal post-translational modifications or protein-protein interactions, defective intracellular trafficking or misfolding of proteins could play a part in driving the clinically observed differences between these two subgroups of Lewy body dementias. This further indicates that amyloid-targeting therapeutic strategies may show different efficacies in DLB versus PDD.
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Affiliation(s)
- Arnab Datta
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Unit 09-01, Centre for Translational Medicine (MD6), 14 Medical Drive, Kent Ridge, Singapore 117599, Singapore. .,Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, Building 10 Room 6N318, Bethesda, MD 20814, USA.
| | - Yuek Ling Chai
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Unit 09-01, Centre for Translational Medicine (MD6), 14 Medical Drive, Kent Ridge, Singapore 117599, Singapore
| | - Jing Min Tan
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Unit 09-01, Centre for Translational Medicine (MD6), 14 Medical Drive, Kent Ridge, Singapore 117599, Singapore
| | - Jasinda H Lee
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Unit 09-01, Centre for Translational Medicine (MD6), 14 Medical Drive, Kent Ridge, Singapore 117599, Singapore
| | - Paul T Francis
- Wolfson Centre for Age-related Diseases, King's College London, Guy's Campus, St Thomas Street, London SE1 1UL, UK
| | - Christopher P Chen
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Unit 09-01, Centre for Translational Medicine (MD6), 14 Medical Drive, Kent Ridge, Singapore 117599, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Mitchell K P Lai
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Unit 09-01, Centre for Translational Medicine (MD6), 14 Medical Drive, Kent Ridge, Singapore 117599, Singapore. .,Wolfson Centre for Age-related Diseases, King's College London, Guy's Campus, St Thomas Street, London SE1 1UL, UK.
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18
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Adav SS, Sze SK. Insight of brain degenerative protein modifications in the pathology of neurodegeneration and dementia by proteomic profiling. Mol Brain 2016; 9:92. [PMID: 27809929 PMCID: PMC5094070 DOI: 10.1186/s13041-016-0272-9] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/16/2016] [Indexed: 02/06/2023] Open
Abstract
Dementia is a syndrome associated with a wide range of clinical features including progressive cognitive decline and patient inability to self-care. Due to rapidly increasing prevalence in aging society, dementia now confers a major economic, social, and healthcare burden throughout the world, and has therefore been identified as a public health priority by the World Health Organization. Previous studies have established dementia as a 'proteinopathy' caused by detrimental changes in brain protein structure and function that promote misfolding, aggregation, and deposition as insoluble amyloid plaques. Despite clear evidence that pathological cognitive decline is associated with degenerative protein modifications (DPMs) arising from spontaneous chemical modifications to amino acid side chains, the molecular mechanisms that promote brain DPMs formation remain poorly understood. However, the technical challenges associated with DPM analysis have recently become tractable due to powerful new proteomic techniques that facilitate detailed analysis of brain tissue damage over time. Recent studies have identified that neurodegenerative diseases are associated with the dysregulation of critical repair enzymes, as well as the misfolding, aggregation and accumulation of modified brain proteins. Future studies will further elucidate the mechanisms underlying dementia pathogenesis via the quantitative profiling of the human brain proteome and associated DPMs in distinct phases and subtypes of disease. This review summarizes recent developments in quantitative proteomic technologies, describes how these techniques have been applied to the study of dementia-linked changes in brain protein structure and function, and briefly outlines how these findings might be translated into novel clinical applications for dementia patients. In this review, only spontaneous protein modifications such as deamidation, oxidation, nitration glycation and carbamylation are reviewed and discussed.
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Affiliation(s)
- Sunil S. Adav
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore
| | - Siu Kwan Sze
- Division of Structural Biology and Biochemistry, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore
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19
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Sethi S, Chourasia D, Parhar IS. Approaches for targeted proteomics and its potential applications in neuroscience. J Biosci 2016; 40:607-27. [PMID: 26333406 DOI: 10.1007/s12038-015-9537-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
An extensive guide on practicable and significant quantitative proteomic approaches in neuroscience research is important not only because of the existing overwhelming limitations but also for gaining valuable understanding into brain function and deciphering proteomics from the workbench to the bedside. Early methodologies to understand the functioning of biological systems are now improving with high-throughput technologies, which allow analysis of various samples concurrently, or of thousand of analytes in a particular sample. Quantitative proteomic approaches include both gel-based and non-gel-based methods that can be further divided into different labelling approaches. This review will emphasize the role of existing technologies, their advantages and disadvantages, as well as their applications in neuroscience. This review will also discuss advanced approaches for targeted proteomics using isotope-coded affinity tag (ICAT) coupled with laser capture microdissection (LCM) followed by liquid chromatography tandem mass spectrometric (LC-MS/MS) analysis. This technology can further be extended to single cell proteomics in other areas of biological sciences and can be combined with other 'omics' approaches to reveal the mechanism of a cellular alterations. This approach may lead to further investigation in basic biology, disease analysis and surveillance, as well as drug discovery. Although numerous challenges still exist, we are confident that this approach will increase the understanding of pathological mechanisms involved in neuroendocrinology, neuropsychiatric and neurodegenerative disorders by delivering protein biomarker signatures for brain dysfunction.
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Affiliation(s)
- Sumit Sethi
- Brain Research Institute, Jeffrey Cheah School of Medicine and Health Sciences, MONASH University, Selangor Darul Ehsan, Malaysia,
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Gallart-Palau X, Lee BST, Adav SS, Qian J, Serra A, Park JE, Lai MKP, Chen CP, Kalaria RN, Sze SK. Gender differences in white matter pathology and mitochondrial dysfunction in Alzheimer's disease with cerebrovascular disease. Mol Brain 2016; 9:27. [PMID: 26983404 PMCID: PMC4794845 DOI: 10.1186/s13041-016-0205-7] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 02/22/2016] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Dementia risk in women is higher than in men, but the molecular neuropathology of this gender difference remains poorly defined. In this study, we used unbiased, discovery-driven quantitative proteomics to assess the molecular basis of gender influences on risk of Alzheimer's disease with cerebrovascular disease (AD + CVD). RESULTS We detected modulation of several redox proteins in the temporal lobe of AD + CVD subjects, and we observed sex-specific alterations in the white matter (WM) and mitochondria proteomes of female patients. Functional proteomic analysis of AD + CVD brain tissues revealed increased citrullination of arginine and deamidation of glutamine residues of myelin basic protein (MBP) in female which impaired degradation of degenerated MBP and resulted in accumulation of non-functional MBP in WM. Female patients also displayed down-regulation of ATP sub-units and cytochromes, suggesting increased severity of mitochondria impairment in women. CONCLUSIONS Our study demonstrates that gender-linked modulation of white matter and mitochondria proteomes influences neuropathology of the temporal lobe in AD + CVD.
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Affiliation(s)
- Xavier Gallart-Palau
- />Division of Chemical Biology & BioTechnology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore
| | - Benjamin S. T. Lee
- />Division of Chemical Biology & BioTechnology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore
| | - Sunil S. Adav
- />Division of Chemical Biology & BioTechnology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore
| | - Jingru Qian
- />Division of Chemical Biology & BioTechnology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore
| | - Aida Serra
- />Division of Chemical Biology & BioTechnology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore
| | - Jung Eun Park
- />Division of Chemical Biology & BioTechnology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore
| | - Mitchell K. P. Lai
- />Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Christopher P. Chen
- />Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
- />Memory, Aging and Cognition Centre, National University Health System, Singapore, Singapore
| | - Raj N. Kalaria
- />Institute for Ageing and Health, NIHR Biomedical Research Building, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne, NE4 5PL UK
| | - Siu Kwan Sze
- />Division of Chemical Biology & BioTechnology, School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore, 637551 Singapore
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Revollo J, Petibone DM, McKinzie P, Knox B, Morris SM, Ning B, Dobrovolsky VN. Whole genome and normalized mRNA sequencing reveal genetic status of TK6, WTK1, and NH32 human B-lymphoblastoid cell lines. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2015; 795:60-9. [PMID: 26774668 DOI: 10.1016/j.mrgentox.2015.11.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 11/12/2015] [Accepted: 11/14/2015] [Indexed: 01/05/2023]
Abstract
Closely related TK6, WTK1, and NH32 human B-lymphoblastoid cell lines differ in their p53 functional status. These lines are used frequently in genotoxicity studies and in studies aimed at understanding the role of p53 in DNA repair. Despite their routine use, little is known about the genetic status of these cells. To provide insight into their genetic composition, we sequenced and analyzed the entire genome of TK6 cells, as well as the normalized transcriptomes of TK6, WTK1, and NH32 cells. Whole genome sequencing (WGS) identified 21,561 genes and 5.17×10(6) small variants. Within the small variants, 50.54% were naturally occurring single nucleotide polymorphisms (SNPs) and 49.46% were mutations. The mutations were comprised of 92.97% single base-pair substitutions and 7.03% insertions or deletions (indels). The number of predicted genes, SNPs, and small mutations are similar to frequencies observed in the human population in general. Normalized mRNA-seq analysis identified the expression of transcripts bearing SNPs or mutations for TK6, WTK1, and NH32 as 2.88%, 2.04%, and 1.71%, respectively, and several of the variant transcripts identified appear to have important implications in genetic toxicology. These include a single base deletion mutation in the ferritin heavy chain gene (FTH1) resulting in a frame shift and protein truncation in TK6 that impairs iron metabolism. SNPs in the thiopurine S-methyltransferase (TPMT) gene (TPMT*3A SNP), and in the xenobiotic metabolizing enzyme, NADPH quinine oxidoreductase 1 (NQO1) gene (NQO1*2 SNP), are both associated with decreased enzyme activity. The clinically relevant TPMT*3A and NQO1*2 SNPs can make these cell lines useful in pharmacogenetic studies aimed at improving or tailoring drug treatment regimens that minimize toxicity and enhance efficacy.
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Affiliation(s)
- Javier Revollo
- Division of Genetic and Molecular Toxicology, FDA/NCTR, Jefferson, AR 72079, United States
| | - Dayton M Petibone
- Division of Genetic and Molecular Toxicology, FDA/NCTR, Jefferson, AR 72079, United States.
| | - Page McKinzie
- Division of Genetic and Molecular Toxicology, FDA/NCTR, Jefferson, AR 72079, United States
| | - Bridgett Knox
- Division of Systems Biology, FDA/NCTR, Jefferson, AR 72079, United States
| | - Suzanne M Morris
- Division of Genetic and Molecular Toxicology, FDA/NCTR, Jefferson, AR 72079, United States
| | - Baitang Ning
- Division of Systems Biology, FDA/NCTR, Jefferson, AR 72079, United States
| | - Vasily N Dobrovolsky
- Division of Genetic and Molecular Toxicology, FDA/NCTR, Jefferson, AR 72079, United States
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Wang C, Zhao J, Xu R, Zhao J, Duan S. Identification of pivotal markers in vascular dementia based on proteomics data. Dement Geriatr Cogn Disord 2015; 39:312-20. [PMID: 25823411 DOI: 10.1159/000375296] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 01/10/2015] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVE The aim of this study was to analyze protein expression profiles of vascular dementia (VaD) subjects for investigating the underlying therapeutic markers. METHODS Protein expression profile data were acquired from a quantitative clinical proteomic study, including 10 nondemented elderly controls and 10 age-matched VaD subjects. Differentially expressed proteins (DEPs) were identified between VaD subjects and controls, followed by function prediction using DAVID (Database for Annotation, Visualization, and Integrated Discovery). Then, a protein-protein interaction (PPI) network was constructed by comparing it with the STRING (Search Tool for the Retrieval of Interacting Genes) database, and the pathway crosstalk analysis was conducted based on overlapping PPI network and enriched pathways. Furthermore, the subpathway was screened and analyzed by the iSubpathwayMiner package in R. RESULTS A total of 144 DEPs were screened from VaD subjects and the controls. They were significantly enriched in many pathways. High-degree proteins were detected in the PPI network, such as ATP5B (ATP synthase subunit β). Furthermore, 'metabolic pathways' and 'Alzheimer's disease' were the significant pathways screened in the crosstalk analysis. At last, upregulated proteins were enriched in 2 subpathways of 1 pathway, while downregulated proteins were enriched in 162 subpathways of 36 pathways. CONCLUSION By analyzing the differential expressions of proteins, the potential underlying therapeutic markers and mechanism of VaD might be elucidated.
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Affiliation(s)
- Chunyan Wang
- Department of Neurology, The First Affiliated Hospital of Harbin Medical University, Harbin, PR China
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Datta A, Sze SK. Data for iTRAQ profiling of micro-vesicular plasma specimens: In search of potential prognostic circulatory biomarkers for Lacunar infarction. Data Brief 2015; 4:510-7. [PMID: 26966714 PMCID: PMC4783520 DOI: 10.1016/j.dib.2015.07.021] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 07/07/2015] [Accepted: 07/07/2015] [Indexed: 01/11/2023] Open
Abstract
To discover potential prognostic biomarkers of Lacunar infarction (LACI), here we present quantitative proteomics data of plasma microvesicle-enriched fraction derived by comparative isobaric profiling of three groups of prospectively followed-up LACI patients (LACI – no adverse outcome, LACI –recurrent vascular event and LACI – cognitive decline) and a demographically matched control group. We confidently (unused prot score >3, FDR=1.1%) identified 183 proteins, 43 out of which were significantly regulated (p-value<0.05) in at least one of the three LACI groups in comparison to control group. Bioinformatics analysis and data mining revealed upregulation of brain-specific proteins including myelin basic protein, proteins of coagulation cascade (e.g., fibrinogen alpha chain, fibrinogen beta chain) and focal adhesion (e.g., integrin alpha-IIb, talin-1, and filamin-A) while albumin was downregulated in both groups of patients with adverse outcome. The data of this study are also in line with our previously published article entitled “Discovery of prognostic biomarker candidates of Lacunar infarction by quantitative proteomics of microvesicles enriched plasma” by Datta et al. (2014). The raw data had been deposited to the ProteomeXchange consortium with identifier PXD000748.
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Affiliation(s)
- Arnab Datta
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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Brea D, Agulla J, Staes A, Gevaert K, Campos F, Sobrino T, Blanco M, Dávalos A, Castillo J, Ramos-Cabrer P. Study of Protein Expression in Peri-Infarct Tissue after Cerebral Ischemia. Sci Rep 2015; 5:12030. [PMID: 26153530 PMCID: PMC4495553 DOI: 10.1038/srep12030] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Accepted: 06/11/2015] [Indexed: 11/26/2022] Open
Abstract
In this work, we report our study of protein expression in rat peri-infarct tissue, 48 h after the induction of permanent focal cerebral ischemia. Two proteomic approaches, gel electrophoresis with mass spectrometry and combined fractional diagonal chromatography (COFRADIC), were performed using tissue samples from the periphery of the induced cerebral ischemic lesions, using tissue from the contra-lateral hemisphere as a control. Several protein spots (3408) were identified by gel electrophoresis, and 11 showed significant differences in expression between peri-infarct and contra-lateral tissues (at least 3-fold, p < 0.05). Using COFRADIC, 5412 proteins were identified, with 72 showing a difference in expression. Apart from blood-related proteins (such as serum albumin), both techniques showed that the 70 kDa family of heat shock proteins were highly expressed in the peri-infarct tissue. Further studies by 1D and 2D western blotting and immunohistochemistry revealed that only one member of this family (the inducible form, HSP72 or HSP70i) is specifically expressed by the peri-infarct tissue, while the majority of this family (the constitutive form, HSC70 or HSP70c) is expressed in the whole brain. Our data support that HSP72 is a suitable biomarker of peri-infarct tissue in the ischemic brain.
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Affiliation(s)
- David Brea
- 1] Neurology Department, Neurovascular Area, Clinical Neurosciences Research Laboratory, University Clinical Hospital, Health Research Institute of Santiago de Compostela (IDIS), University of Santiago de Compostela, Spain [2] Cellular and Molecular Neurobiology Research Group and Grup de Recerça en Neurociencies del IGTP, Department of Neurosciences, Fundació Institut d'Investigació en Ciències de la Salut Germans Trias I Pujol-Universitat Autónoma de Barcelona, Badalona, Spain
| | - Jesús Agulla
- 1] Neurology Department, Neurovascular Area, Clinical Neurosciences Research Laboratory, University Clinical Hospital, Health Research Institute of Santiago de Compostela (IDIS), University of Santiago de Compostela, Spain [2] Research Unit, University Hospital of Salamanca and Institute of Health Sciences of Castilla and Leon, Salamanca, Spain
| | - An Staes
- 1] Department of Medical Protein Research, VIB, Ghent, Belgium [2] Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Kris Gevaert
- 1] Department of Medical Protein Research, VIB, Ghent, Belgium [2] Department of Biochemistry, Ghent University, Ghent, Belgium
| | - Francisco Campos
- Neurology Department, Neurovascular Area, Clinical Neurosciences Research Laboratory, University Clinical Hospital, Health Research Institute of Santiago de Compostela (IDIS), University of Santiago de Compostela, Spain
| | - Tomás Sobrino
- Neurology Department, Neurovascular Area, Clinical Neurosciences Research Laboratory, University Clinical Hospital, Health Research Institute of Santiago de Compostela (IDIS), University of Santiago de Compostela, Spain
| | - Miguel Blanco
- Neurology Department, Neurovascular Area, Clinical Neurosciences Research Laboratory, University Clinical Hospital, Health Research Institute of Santiago de Compostela (IDIS), University of Santiago de Compostela, Spain
| | - Antoni Dávalos
- Cellular and Molecular Neurobiology Research Group and Grup de Recerça en Neurociencies del IGTP, Department of Neurosciences, Fundació Institut d'Investigació en Ciències de la Salut Germans Trias I Pujol-Universitat Autónoma de Barcelona, Badalona, Spain
| | - José Castillo
- Neurology Department, Neurovascular Area, Clinical Neurosciences Research Laboratory, University Clinical Hospital, Health Research Institute of Santiago de Compostela (IDIS), University of Santiago de Compostela, Spain
| | - Pedro Ramos-Cabrer
- Neurology Department, Neurovascular Area, Clinical Neurosciences Research Laboratory, University Clinical Hospital, Health Research Institute of Santiago de Compostela (IDIS), University of Santiago de Compostela, Spain
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Beyer K. Highlights from the latest articles in biomarkers in medicine. Biomark Med 2015. [DOI: 10.2217/bmm.14.93] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Uncovering Neurodegenerative Protein Modifications via Proteomic Profiling. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2015; 121:87-116. [DOI: 10.1016/bs.irn.2015.06.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Gallart-Palau X, Serra A, Qian J, Chen CP, Kalaria RN, Sze SK. Temporal lobe proteins implicated in synaptic failure exhibit differential expression and deamidation in vascular dementia. Neurochem Int 2014; 80:87-98. [PMID: 25497727 DOI: 10.1016/j.neuint.2014.12.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Revised: 11/26/2014] [Accepted: 12/02/2014] [Indexed: 12/20/2022]
Abstract
Progressive synaptic failure precedes the loss of neurons and decline in cognitive function in neurodegenerative disorders, but the specific proteins and posttranslational modifications that promote synaptic failure in vascular dementia (VaD) remain largely unknown. We therefore used an isobaric tag for relative and absolute proteomic quantitation (iTRAQ) to profile the synapse-associated proteome of post-mortem human cortex from vascular dementia patients and age-matched controls. Brain tissue from VaD patients exhibited significant down-regulation of critical synaptic proteins including clathrin (0.29; p < 1.0⋅10(-3)) and GDI1 (0.51; p = 3.0⋅10(-3)), whereas SNAP25 (1.6; p = 5.5⋅10(-3)), bassoon (1.4; p = 1.3⋅10(-3)), excitatory amino acid transporter 2 (2.6; p = 9.2⋅10(-3)) and Ca(2+)/calmodulin dependent kinase II (1.6; p = 3.0⋅10(-2)) were substantially up-regulated. Our analyses further revealed divergent patterns of protein modification in the dementia patient samples, including a specific deamidation of synapsin1 predicted to compromise protein structure. Our results reveal potential molecular targets for intervention in synaptic failure and prevention of cognitive decline in VaD.
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Affiliation(s)
| | - Aida Serra
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Jingru Qian
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Christopher P Chen
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore; Memory, Aging and Cognition Centre, National University Health System, Singapore
| | - Raj N Kalaria
- Institute for Ageing and Health, NIHR Biomedical Research Building, Newcastle University, Campus for Ageing and Vitality, Newcastle upon Tyne NE4 5PL, United Kingdom
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, Singapore.
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Zhang Y, Kang Y, Zhou Q, Zhou J, Wang H, Jin H, Liu X, Ma D, Li X. Quantitative proteomic analysis of serum from pregnant women carrying a fetus with conotruncal heart defect using isobaric tags for relative and absolute quantitation (iTRAQ) labeling. PLoS One 2014; 9:e111645. [PMID: 25393621 PMCID: PMC4230941 DOI: 10.1371/journal.pone.0111645] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2014] [Accepted: 10/03/2014] [Indexed: 12/13/2022] Open
Abstract
Objective To identify differentially expressed proteins from serum of pregnant women carrying a conotruncal heart defects (CTD) fetus, using proteomic analysis. Methods The study was conducted using a nested case-control design. The 5473 maternal serum samples were collected at 14–18 weeks of gestation. The serum from 9 pregnant women carrying a CTD fetus, 10 with another CHD (ACHD) fetus, and 11 with a normal fetus were selected from the above samples, and analyzed by using isobaric tags for relative and absolute quantitation (iTRAQ) coupled with two-dimensional liquid chromatography-tandem mass spectrometry(2D LC-MS/MS). The differentially expressed proteins identified by iTRAQ were further validated with Western blot. Results A total of 105 unique proteins present in the three groups were identified, and relative expression data were obtained for 92 of them with high confidence by employing the iTRAQ-based experiments. The downregulation of gelsolin in maternal serum of fetus with CTD was further verified by Western blot. Conclusions The identification of differentially expressed protein gelsolin in the serum of the pregnant women carrying a CTD fetus by using proteomic technology may be able to serve as a foundation to further explore the biomarker for detection of CTD fetus from the maternal serum.
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Affiliation(s)
- Ying Zhang
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Yuan Kang
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Qiongjie Zhou
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Jizi Zhou
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
| | - Huijun Wang
- Children's Hospital, Fudan University, Shanghai, China
| | - Hong Jin
- Department of Chemistry, Fudan University, Shanghai, China
- Institute of Biomedicine, Fudan University, Shanghai, China
| | - Xiaohui Liu
- Department of Chemistry, Fudan University, Shanghai, China
| | - Duan Ma
- Key Laboratory of Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
- * E-mail: (XL); (DM)
| | - Xiaotian Li
- Obstetrics and Gynecology Hospital, Fudan University, Shanghai, China
- Key Laboratory of Molecular Medicine, Ministry of Education, Department of Biochemistry and Molecular Biology, Institute of Biomedical Sciences, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Key Laboratory of Female Reproductive Endocrine Related Diseases, Shanghai, China
- * E-mail: (XL); (DM)
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Datta A, Chen CP, Sze SK. Discovery of prognostic biomarker candidates of lacunar infarction by quantitative proteomics of microvesicles enriched plasma. PLoS One 2014; 9:e94663. [PMID: 24752076 PMCID: PMC3994162 DOI: 10.1371/journal.pone.0094663] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 03/18/2014] [Indexed: 11/25/2022] Open
Abstract
Background Lacunar infarction (LACI) is a subtype of acute ischemic stroke affecting around 25% of all ischemic stroke cases. Despite having an excellent recovery during acute phase, certain LACI patients have poor mid- to long-term prognosis due to the recurrence of vascular events or a decline in cognitive functions. Hence, blood-based biomarkers could be complementary prognostic and research tools. Methods and Finding Plasma was collected from forty five patients following a non-disabling LACI along with seventeen matched control subjects. The LACI patients were monitored prospectively for up to five years for the occurrence of adverse outcomes and grouped accordingly (i.e., LACI-no adverse outcome, LACI-recurrent vascular event, and LACI-cognitive decline without any recurrence of vascular events). Microvesicles-enriched fractions isolated from the pooled plasma of four groups were profiled by an iTRAQ-guided discovery approach to quantify the differential proteome. The data have been deposited to the ProteomeXchange with identifier PXD000748. Bioinformatics analysis and data mining revealed up-regulation of brain-specific proteins including myelin basic protein, proteins of coagulation cascade (e.g., fibrinogen alpha chain, fibrinogen beta chain) and focal adhesion (e.g., integrin alpha-IIb, talin-1, and filamin-A) while albumin was down-regulated in both groups of patients with adverse outcome. Conclusion This data set may offer important insight into the mechanisms of poor prognosis and provide candidate prognostic biomarkers for validation on larger cohort of individual LACI patients.
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Affiliation(s)
- Arnab Datta
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Christopher P. Chen
- Memory, Aging and Cognition Centre, National University Health System, Singapore, Singapore
- Department of Pharmacology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
- * E-mail:
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