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Zheng L, Zhou C, Mao C, Xie C, You J, Cheng W, Liu C, Huang P, Guan X, Guo T, Wu J, Luo Y, Xu X, Zhang B, Zhang M, Wang L, Feng J. Contrastive machine learning reveals Parkinson's disease specific features associated with disease severity and progression. Commun Biol 2024; 7:954. [PMID: 39112797 PMCID: PMC11306336 DOI: 10.1038/s42003-024-06648-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 07/29/2024] [Indexed: 08/10/2024] Open
Abstract
Parkinson's disease (PD) exhibits heterogeneity in terms of symptoms and prognosis, likely due to diverse neuroanatomical alterations. This study employs a contrastive deep learning approach to analyze Magnetic Resonance Imaging (MRI) data from 932 PD patients and 366 controls, aiming to disentangle PD-specific neuroanatomical alterations. The results reveal that these neuroanatomical alterations in PD are correlated with individual differences in dopamine transporter binding deficit, neurodegeneration biomarkers, and clinical severity and progression. The correlation with clinical severity is verified in an external cohort. Notably, certain proteins in the cerebrospinal fluid are strongly associated with PD-specific features, particularly those involved in the immune function. The most notable neuroanatomical alterations are observed in both subcortical and temporal regions. Our findings provide deeper insights into the patterns of brain atrophy in PD and potential underlying molecular mechanisms, paving the way for earlier patient stratification and the development of treatments to slow down neurodegeneration.
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Affiliation(s)
- Liping Zheng
- Institute of Science and Technology for Brain-Inspired Intelligence, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
| | - Cheng Zhou
- Department of Radiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Chengjie Mao
- Department of Neurology and Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Chao Xie
- Institute of Science and Technology for Brain-Inspired Intelligence, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, China
- Zhangjiang Fudan International Innovation Center, Shanghai, China
| | - Jia You
- Institute of Science and Technology for Brain-Inspired Intelligence, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, China
- Zhangjiang Fudan International Innovation Center, Shanghai, China
| | - Wei Cheng
- Institute of Science and Technology for Brain-Inspired Intelligence, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, China
- Zhangjiang Fudan International Innovation Center, Shanghai, China
- Fudan ISTBI-ZJNU Algorithm Centre for Brain-inspired Intelligence, Zhejiang Normal University, Jinhua, China
| | - Chunfeng Liu
- Department of Neurology and Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Peiyu Huang
- Department of Radiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Xiaoujun Guan
- Department of Radiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Tao Guo
- Department of Radiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Jingjing Wu
- Department of Radiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yajun Luo
- Department of Neurology and Clinical Research Center of Neurological Disease, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiaojun Xu
- Department of Radiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Baorong Zhang
- Department of Neurology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Minming Zhang
- Department of Radiology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China.
| | - Linbo Wang
- Institute of Science and Technology for Brain-Inspired Intelligence, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China.
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, China.
- Zhangjiang Fudan International Innovation Center, Shanghai, China.
| | - Jianfeng Feng
- Institute of Science and Technology for Brain-Inspired Intelligence, State Key Laboratory of Medical Neurobiology and MOE Frontiers Center for Brain Science, Fudan University, Shanghai, China.
- Key Laboratory of Computational Neuroscience and Brain-Inspired Intelligence (Fudan University), Ministry of Education, Shanghai, China.
- Zhangjiang Fudan International Innovation Center, Shanghai, China.
- School of Data Science, Fudan University, Shanghai, China.
- Department of Computer Science, University of Warwick, Coventry, UK.
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Gonzalez R, Garitaonandia I, Poustovoitov M, Abramihina T, McEntire C, Culp B, Attwood J, Noskov A, Christiansen-Weber T, Khater M, Mora-Castilla S, To C, Crain A, Sherman G, Semechkin A, Laurent LC, Elsworth JD, Sladek J, Snyder EY, Redmond DE, Kern RA. Neural Stem Cells Derived from Human Parthenogenetic Stem Cells Engraft and Promote Recovery in a Nonhuman Primate Model of Parkinson's Disease. Cell Transplant 2016; 25:1945-1966. [DOI: 10.3727/096368916x691682] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Cell therapy has attracted considerable interest as a promising therapeutic alternative for patients with Parkinson's disease (PD). Clinical studies have shown that grafted fetal neural tissue can achieve considerable biochemical and clinical improvements in PD. However, the source of fetal tissue grafts is limited and ethically controversial. Human parthenogenetic stem cells offer a good alternative because they are derived from unfertilized oocytes without destroying potentially viable human embryos and can be used to generate an unlimited supply of neural cells for transplantation. We have previously reported that human parthenogenetic stem cell-derived neural stem cells (hpNSCs) successfully engraft, survive long term, and increase brain dopamine (DA) levels in rodent and nonhuman primate models of PD. Here we report the results of a 12-month transplantation study of hpNSCs in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-lesioned African green monkeys with moderate to severe clinical parkinsonian symptoms. The hpNSCs manufactured under current good manufacturing practice (cGMP) conditions were injected bilaterally into the striatum and substantia nigra of immunosuppressed monkeys. Transplantation of hpNSCs was safe and well tolerated by the animals with no dyskinesia, tumors, ectopic tissue formation, or other test article-related serious adverse events. We observed that hpNSCs promoted behavioral recovery; increased striatal DA concentration, fiber innervation, and number of dopaminergic neurons; and induced the expression of genes and pathways downregulated in PD compared to vehicle control animals. These results provide further evidence for the clinical translation of hpNSCs and support the approval of the world's first pluripotent stem cell-based phase I/IIa study for the treatment of PD (Clinical Trial Identifier NCT02452723).
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Affiliation(s)
| | | | | | | | | | - Ben Culp
- Axion Research Foundation, Hamden, CT, USA
| | | | | | | | - Marwa Khater
- Department of Reproductive Medicine, University of California San Diego, La Jolla, CA, USA
| | - Sergio Mora-Castilla
- Department of Reproductive Medicine, University of California San Diego, La Jolla, CA, USA
| | - Cuong To
- Department of Reproductive Medicine, University of California San Diego, La Jolla, CA, USA
| | - Andrew Crain
- Stem Cell Research Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Glenn Sherman
- International Stem Cell Corporation, Carlsbad, CA, USA
| | | | - Louise C. Laurent
- Department of Reproductive Medicine, University of California San Diego, La Jolla, CA, USA
| | - John D. Elsworth
- Department of Psychiatry and Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
| | - John Sladek
- Department of Neurology, Pediatrics and Neuroscience, University of Colorado School of Medicine, Aurora, CO, USA
| | - Evan Y. Snyder
- Stem Cell Research Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - D. Eugene Redmond
- Axion Research Foundation, Hamden, CT, USA
- Department of Psychiatry and Neurosurgery, Yale University School of Medicine, New Haven, CT, USA
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Li XY, Teng JJ, Liu Y, Wu YB, Zheng Y, Xie AM. Association of AKT1 gene polymorphisms with sporadic Parkinson's disease in Chinese Han population. Neurosci Lett 2016; 629:38-42. [PMID: 27353512 DOI: 10.1016/j.neulet.2016.06.052] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 05/20/2016] [Accepted: 06/24/2016] [Indexed: 10/21/2022]
Abstract
Genetic variants of AKT1 have been shown to influence brain function of Parkinson's disease (PD) patients, and in this paper our aim is to investigate the association between the three single-nucleotide polymorphisms (rs2498799; rs2494732; rs1130214) and PD in Han Chinese. 413 Han Chinese PD patients and 450 healthy age and gender-matched controls were genotyped using the Polymerase Chain Reaction-Restriction Fragment Length Polymorphism (PCR-RFLP) method. Both the patient and control groups show similar genotype frequencies at the three loci: rs2498799, rs2494732 and rs1130214. We are able to identify a significant difference in the frequencies of genotype (p=0.019) and G allele (OR=0.764, 95% CI=0.587-0.995, p=0.045) both at rs2498799 between the patient and control groups. Furthermore, the association of subjects with GG genotypes versus those with GA+AA genotype remain significant after adjusting for age in the Han Chinese female cohort (OR=0.538, 95%CI=0.345-0.841, p=0.006), which is especially evident in the late-onset cohort (OR=0.521, 95%CI=0.309-0.877, p=0.012). In contrast, allele frequencies at rs2494732 and rs1130214 were similar between patients and controls in all subgroup analyses. These results suggest that polymorphism of AKT1 locus is associated with risk of PD and that the G allele at rs2498799 may decrease the risk of PD in the North-eastern part of Han Chinese female population.
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Affiliation(s)
- Xiao-Yuan Li
- Department of Neurology, Affiliated Hospital of Qingdao University, Qingdao, China; Department of Neurology, Hospital of Integrated Traditional and Western Medicine, Qingdao, China
| | - Ji-Jun Teng
- Department of Neurology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yang Liu
- Department of Neurology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yu-Bin Wu
- Department of Neurology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - Yu Zheng
- Department of Neurology, Affiliated Hospital of Qingdao University, Qingdao, China
| | - An-Mu Xie
- Department of Neurology, Affiliated Hospital of Qingdao University, Qingdao, China.
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Wang Y, Lin L, Xu H, Li T, Zhou Y, Dan H, Jiang L, Liao G, Zhou M, Li L, Zeng X, Li J, Chen Q. Genetic variants in AKT1 gene were associated with risk and survival of OSCC in Chinese Han Population. J Oral Pathol Med 2014; 44:45-50. [PMID: 25060489 DOI: 10.1111/jop.12211] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2014] [Indexed: 02/05/2023]
Abstract
BACKGROUND AKT1 is an important downstream effector of PTEN/PI3K/AKT signal transduction pathway. Aberrant expression and genetic variant of AKT1 gene are suggested to be involved in several types of human cancers, including OSCC. The aim of this study was to investigate the possible association between AKT1 gene polymorphisms and OSCC in Chinese Han Population. METHODS A total of 182 OSCC patients and 207 cancer-free controls were enrolled for this hospital-based study. Five single-nucleotide polymorphisms (SNPs) on AKT1 (rs1130214, rs1130233, rs2494732, rs3730358, rs3803300) were investigated and genotyped by Sequenom Mass ARRAY & iPLEX-MALDI-TOF technology. Chi-square test, SHEsis software, and Kaplan-Meier method were used to evaluate the relationship between selected SNPs and OSCC susceptibility and progression. RESULTS Significant difference of genotype distribution was observed between cases and control group at SNP sites rs1130214 (P = 0.006) and rs3803300 (P = 0.033, P = 0.003 for heterozygote and homozygous mutant, respectively). In the haplotype analysis, haplotype H4 which contained mutant-type allele of rs1130214 and rs3803300 was also related to OSCC risk (OR = 1.974, 95% CI = 1.048-3.718). Moreover, CT genotype of rs3730358 was associated with higher risk of OSCC progression (HR = 2.466, 95% CI = 1.017-5.981). CONCLUSION Our results indicated that rs1130214 and rs3803300 were related to OSCC susceptibility in Chinese Han Population. In addition, rs3730358 might be associated with progression-free survival time of OSCC patients, suggesting that this SNP could be a potential prognosis marker for OSCC.
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Affiliation(s)
- Yun Wang
- State Key Laboratory of Oral Diseases, West China Hospital of Stomatology, Sichuan University, Chengdu, China
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Taheri M, Yousefi K, Naderi M, Hashemi M. Genetic Variation in Akt1 and Risk of Tuberculosis Among Iranian Population. HEALTH SCOPE 2014. [DOI: 10.17795/jhealthscope-16243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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The delivery of tyrosine hydroxylase accelerates the neurorestoration of Macaca Rhesus model of Parkinson's disease provided by Neurturin. Neurosci Lett 2012; 524:10-5. [DOI: 10.1016/j.neulet.2012.06.063] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2012] [Revised: 06/20/2012] [Accepted: 06/24/2012] [Indexed: 11/22/2022]
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Kinases and kinase signaling pathways: potential therapeutic targets in Parkinson's disease. Prog Neurobiol 2012; 98:207-21. [PMID: 22709943 DOI: 10.1016/j.pneurobio.2012.06.003] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2012] [Revised: 05/20/2012] [Accepted: 06/08/2012] [Indexed: 12/24/2022]
Abstract
Complex molecular mechanisms underlying the pathogenesis of Parkinson's disease (PD) are gradually being elucidated. Accumulating genetic evidence implicates dysfunction of kinase activities and phosphorylation pathways in the pathogenesis of PD. Causative and risk gene products associated with PD include protein kinases (such as PINK1, LRRK2 and GAK) and proteins related phosphorylation signaling pathways (such as SNCA, DJ-1). PINK1, LRRK2 and several PD gene products have been associated with mitogen-activated protein (MAP) and protein kinase B (AKT) kinase signaling pathways. C-Jun N-terminal kinase (JNK), extracellular signal-regulated kinases (ERK) and p38, signaling pathways downstream of MAP, are particularly important in PD. JNK and p38 play an integral role in neuronal death. Targeting JNK or p38 signaling may offer an effective therapy for PD. Inhibitors of the ERK signaling pathway, which plays an important role in the development of l-DOPA-induced dyskinesia (LID), have been shown to attenuate this condition in animal models. In this review, we summarize experimental evidence gathered over the last decade on the role of PINK1, LRRK2 and GAK and their related phosphorylation signaling pathways (JNK, ERK, p38 and PI3K/AKT) in PD. It is speculated that improvement or modulation of these signaling pathways will reveal potential therapeutic targets for attenuation of the cardinal symptoms and motor complications in patients with PD in the future.
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