Integrated network analysis identifying potential novel drug candidates and targets for Parkinson's disease

Quan, Pusheng; Wang, Kai; Shi, Yan; Wen, Shirong; Wei, Chengqun; Zhang, Xinyu; Cao, Jingwei; Yao, Lifen

doi:10.1038/s41598-021-92701-2

Cited by 11 publications

(6 citation statements)

References 46 publications

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“…In addition to investigating individual variant effects with colocalization and epistasis, visualizing biological networks can help with understanding complex molecular relationships and interactions. In PD research, genetic and gene expression data has been used in community network analysis to nominate pathways and genes for drug target and functional prioritization 19 , 20 .…”

Section: Methodsmentioning

confidence: 99%

The IPDGC/GP2 Hackathon - an open science event for training in data science, genomics, and collaboration using Parkinson’s disease data

Leonard

Murtadha²,

Martínez-Carrasco³

et al. 2023

npj Parkinsons Dis.

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Open science and collaboration are necessary to facilitate the advancement of Parkinson’s disease (PD) research. Hackathons are collaborative events that bring together people with different skill sets and backgrounds to generate resources and creative solutions to problems. These events can be used as training and networking opportunities, thus we coordinated a virtual 3-day hackathon event, during which 49 early-career scientists from 12 countries built tools and pipelines with a focus on PD. Resources were created with the goal of helping scientists accelerate their own research by having access to the necessary code and tools. Each team was allocated one of nine different projects, each with a different goal. These included developing post-genome-wide association studies (GWAS) analysis pipelines, downstream analysis of genetic variation pipelines, and various visualization tools. Hackathons are a valuable approach to inspire creative thinking, supplement training in data science, and foster collaborative scientific relationships, which are foundational practices for early-career researchers. The resources generated can be used to accelerate research on the genetics of PD.

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Section: Methodsmentioning

confidence: 99%

The IPDGC/GP2 Hackathon - an open science event for training in data science, genomics, and collaboration using Parkinson’s disease data

Leonard

Murtadha²,

Martínez-Carrasco³

et al. 2023

npj Parkinsons Dis.

View full text Add to dashboard Cite

show abstract

Section: Project Summaries (Containing Both Methods and Results)mentioning

confidence: 99%

The IPDGC/GP2 Hackathon - an open science event for training in data science, genomics, and collaboration using Parkinson’s disease data

Leonard

Murtadha

Martínez-Carrasco

et al. 2022

Preprint

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BackgroundOpen science and collaboration are necessary to facilitate the advancement of Parkinson’s disease (PD) research. Hackathons are collaborative events that bring together people with different skill sets and backgrounds to generate resources and creative solutions to problems. These events can be used as training and networking opportunities.ObjectiveTo coordinate a virtual hackathon to develop novel PD research tools.Methods49 early career scientists from 12 countries collaborated in a virtual 3-day hackathon event in May 2021, during which they built tools and pipelines with a focus on PD. Resources were created with the goal of helping scientists accelerate their own research by having access to the necessary code and tools.ResultsEach team was allocated one of nine different projects, each with a different goal. These included developing post-genome-wide association studies (GWAS) analysis pipelines, downstream analysis of genetic variation pipelines, and various visualization tools.ConclusionHackathons are a valuable approach to inspire creative thinking, supplement training in data science, and foster collaborative scientific relationships, which are foundational practices for early career researchers. The resources generated can be used to accelerate research on the genetics of PD.

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“…1B and C). We screened the ratios between the three catalytic subunit mRNA considering the possible difference of these ratios in PD 20 . The ratio between PSMB10 and PSMB8 (PSMB10/8) best represented the alteration in the levels of these IP mRNA between the PD and HC groups.…”

Section: Transcript Regulation Of Ip In Pdmentioning

confidence: 99%

Alteration of immunoproteasome mRNA in PBMCs of patients with Parkinson’s disease

Kim

Nguyen

et al. 2022

Preprint

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Background Immunoproteasome, a part of ubiquitin–proteasome system, is involved in protein degradation and immune response. However, the relationship between immunoproteasome and Parkinson’s disease (PD) was not evaluated clearly. We hypothesized that the shift of immunoproteasome attributes to PD due to its role in immune system and protein homeostasis. Objective To determine whether immunoproteasome mRNA in peripheral blood mononuclear cells is expressed differently between patients with PD and healthy controls and to test its value as a biomarker of PD Methods Blood samples were collected from 19 healthy controls and 40 patients with PD of comparable ages. Peripheral blood mononuclear cells were isolated and used to measure by RT-qPCR the mRNA levels of three catalytic subunits of immunoproteasome, namely, PSMB8, PSMB9, and PSMB10. Results The levels PSMB9 and PSMB10 mRNA were not different between the PD group and healthy control group, whereas the PSMB8 mRNA in PD group significantly increased. The ratio of PSMB10 and PSMB8 (PSMB10/8) best reflected significant difference between the PD group and healthy control group (p = 0.002). This ratio can discriminate all PD, mild PD (Hoehn and Yahr ≤ 2.5), and drug-naive PD from healthy controls. We found correlation between the PSMB10/8 ratio with the UPDRS total and Part III score in the mild PD subgroup and drug-naive PD subgroups Conclusion The expression of PSMB8 mRNA increased in PD, and the PSMB10/8 ratio can differentiate Parkinson’s disease from healthy controls.

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Integrated network analysis identifying potential novel drug candidates and targets for Parkinson's disease

Cited by 11 publications

References 46 publications

The IPDGC/GP2 Hackathon - an open science event for training in data science, genomics, and collaboration using Parkinson’s disease data

The IPDGC/GP2 Hackathon - an open science event for training in data science, genomics, and collaboration using Parkinson’s disease data

The IPDGC/GP2 Hackathon - an open science event for training in data science, genomics, and collaboration using Parkinson’s disease data

Alteration of immunoproteasome mRNA in PBMCs of patients with Parkinson’s disease

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