Studying the Parkinson's disease metabolome and exposome in biological samples through different analytical and cheminformatics approaches: a pilot study.

Parkinson's disease (PD) is the second most prevalent neurodegenerative disease, with an increasing incidence in recent years due to the aging population. Genetic mutations alone only explain <10% of PD cases, while environmental factors, including small molecules, may play a significant role in PD. In the present work, 22 plasma (11 PD, 11 control) and 19 feces samples (10 PD, 9 control) were analyzed by non-target high-resolution mass spectrometry (NT-HRMS) coupled to two liquid chromatography (LC) methods (reversed-phase (RP) and hydrophilic interaction liquid chromatography (HILIC)). A cheminformatics workflow was optimized using open software (MS-DIAL and patRoon) and open databases (all public MSP-formatted spectral libraries for MS-DIAL, PubChemLite for Exposomics, and the LITMINEDNEURO list for patRoon). Furthermore, five disease-specific databases and three suspect lists (on PD and related disorders) were developed, using PubChem functionality to identifying relevant unknown chemicals. The results showed that non-target screening with the larger databases generally provided better results compared with smaller suspect lists. However, two suspect screening approaches with patRoon were also good options to study specific chemicals in PD. The combination of chromatographic methods (RP and HILIC) as well as two ionization modes (positive and negative) enhanced the coverage of chemicals in the biological samples. While most metabolomics studies in PD have focused on blood and cerebrospinal fluid, we found a higher number of relevant features in feces, such as alanine betaine or nicotinamide, which can be directly metabolized by gut microbiota. This highlights the potential role of gut dysbiosis in PD development.

How can data visualization support interdisciplinary research? LuxTIME: studying historical exposomics in Belval.

The Luxembourg Time Machine (LuxTIME) is an interdisciplinary project that studies the historical exposome during the industrialization of the Minett region, located in the south of Luxembourg. Exposome research encompasses all external and internal non-genetic factors influencing the health of the population, such as air pollution, green spaces, noise, work conditions, physical activity, and diet. Due to the wide scope of the interdisciplinary project, the historical study of the exposome in Belval involved the collection of quantitative and qualitative data from the National Archive of Luxembourg, various local archives (e.g., the communes of Esch-sur-Alzette and Sanem), the National Library, the Library of National Statistics STATEC, the National Geoportal of Luxembourg, scientific data from other research centers, and information from newspapers and journals digitized in eluxemburgensia. The data collection and the resulting inventory were performed to create a proof of concept to critically test the potential of a multi-layered research design for the study of the historical exposome in Belval. The guiding navigation tool throughout the project was data visualization. It has facilitated the exploration of the data collected (or just the data) and the metadata. It has also been a valuable tool for mapping knowledge and defining the scope of the project. Furthermore, different data visualization techniques have helped us to reflect on the process of knowledge sharing, to understand how the relevance of certain topics changed throughout the project and why, and to learn about the publication process in different journals and the experience of the participants. Data visualization is used not only as a means to an end but also to embrace the idea of sandcastles using a speculative and process-oriented approach to advance knowledge within all research fields involved. LuxTIME has proven to be an ideal case study to explore the possibilities offered by different data visualization concepts and techniques resulting in a data visualization toolbox that could be evaluated and extended in other interdisciplinary projects.