bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2024.02.12.579937

Urinary Metabolomic Profile is Minimally Impacted by Common Storage Conditions and Additives

Weldon, K. C.·Panitchpakdi, M.·Caraballo-Rodriguez, A. M.·Wolfe, A. J.·Dorrestein, P. C.·Brubaker, L.·Burnett, L.
View original source ↗Export metadata ↓

Abstract

Metabolomics reflects the molecular communications within a biological system. Urine can be obtained non-invasively and is rich in metabolites that are potential biomarkers for human health and disease. The optimal urine storage conditions for metabolomic analysis are unknown. We measured the impact of common storage conditions and the presence of a DNA-stabilizer, AssayAssure(R) (Thermo Scientific), on metabolite content of voided human urine. Urinary metabolite composition was not altered across storage conditions. Although addition of AssayAssure(R) significantly alters metabolic profile by adduct addition, this does not preclude the identification of parent metabolites or overshadow biological differences. These data suggest biobanked urine stored in any of the tested conditions for metabolomic studies may be considered for metabolomic analysis.

Source connections

Explore related subjects

molecular biologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Weldon, K. C., Panitchpakdi, M., Caraballo-Rodriguez, A. M., Wolfe, A. J., Dorrestein, P. C., Brubaker, L., Burnett, L.. 2024-02-14. Urinary Metabolomic Profile is Minimally Impacted by Common Storage Conditions and Additives. https://doi.org/10.1101/2024.02.12.579937

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Integrated Spatial Metabolomics and Proteomics from the Same Tissue Section Using a Conductive ITO-PET Slide

Integrating spatial metabolomics and spatial proteomics on the same tissue section remains challenging because matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) and laser capture microdissection (LCM)-based proteomics impose different requirements on sample slides. Here, we developed and systematically evaluated a conductive indium tin oxide-coated polyethylene terephthalate (ITO-PET) slide that enables sequential MALDI-MSI and LCM-liquid chromatography-mass spectrometry (LCM-LC-MS) analysis of the same tissue section. Using mouse brain tissue as a model, ITO-PET provided MALDI-MSI performance closely comparable to conventional ITO-glass, including spectral concordance (Pearson correlation, R = 0.90), ion detection coverage, metabolite annotation, signal intensity distribution, and preservation of spatial molecular patterns. Following MALDI-MSI, the ITO-PET slide enabled cutting-mode LCM and yielded proteomic signal intensities and numbers of identified protein groups comparable to those obtained with conventional PEN-glass slides. Across different tissue sampling areas, proteomic signal intensity distributions, precursor ion counts, and protein group identifications remained broadly comparable before and after MALDI-MSI, with substantial overlap in identified protein groups. Similar patterns were observed in mouse kidney, lung, spleen, and liver tissues, further supporting the applicability of the workflow across different tissue types. By combining the electrical conductivity required for MALDI-MSI with the mechanical properties required for LCM cutting, the ITO-PET slide addresses a major material incompatibility between the two analytical modalities and enables sequential spatial metabolomic and proteomic analysis from the same tissue section. This workflow provides a practical analytical platform for obtaining complementary molecular information from spatially limited biological specimens.

molecular biology↗
bioRxiv2026

Aβ42-Driven α-synuclein Fibril Polymorphism and Distinct Intracellular Aggregation

The frequent coexistence of -synuclein (-syn) and amyloid-{beta} (A{beta}) aggregates in neurodegenerative diseases suggests that heterotypic interactions between these amyloidogenic proteins may influence disease progression, yet their molecular consequences remain poorly understood. Here, we investigated how distinct aggregation states of A{beta}42, monomers and preformed fibrils (PFFs), modulate -syn fibril formation, structure, and downstream neuronal pathology. Thioflavin T kinetics showed that A{beta}42 monomers delayed -syn fibril formation, whereas A{beta}42 PFFs exhibited a trend toward accelerated aggregation, indicating aggregation state-dependent effects on -syn aggregation. Negative-stain TEM, proteinase K digestion, and solid-state NMR spectroscopy further demonstrated that both A{beta}42 monomers and PFFs altered -syn fibril structure, generating distinct fibril conformations depending on the A{beta}42 concentration and aggregation state. To determine whether these conformational differences influence pathological activity, -syn PFF variants generated in the presence of different concentrations of A{beta}42 monomers or PFFs were applied to dopaminergic neuronal cells. -Syn fibrils formed in the presence of A{beta}42 PFFs showed greater capacity to induce intraneuronal -syn aggregation than -syn PFFs, whereas fibrils formed in the presence of A{beta}42 monomers exhibited similar or reduced seeding capacity relative to -syn PFFs. Together, our findings demonstrate that heterotypic interactions with A{beta}42 reshape -syn aggregation pathways and fibril conformations, generating structurally distinct -syn fibril populations with different neuronal seeding activities. These results provide a molecular framework for understanding how cross-talk between amyloidogenic proteins may contribute to structural and pathological heterogeneity in mixed neurodegenerative diseases.

molecular biology↗
bioRxiv2026

Insulators As Dynamic, Tunable Regulators of Enhancer-Promoter Coordination in Living Drosophila Embryos

The three-dimensional organization of the genome enables enhancers and promoters to interact across vast distances and direct transcription. Yet whether architectural elements, such as insulators, serve as rigid, passive barriers or as dynamic, active organizers of this communication remains unclear. Here, using single-cell, live imaging of a Drosophila transgene in which a single enhancer regulates two equidistant promoters, we confirm that the enhancer engages both promoters simultaneously and show that coordinated bursting is intrinsically more productive than uncoordinated activity. Flanking this system with insulators increases coordinated bursting frequency and transcriptional output, indicating that insulator-mediated looping promotes multi-way enhancer-promoter interaction. Further, bidirectionally-paired, homotypic insulators produce stronger coordination than unidirectional pairs. Inserting an intermediate insulator to generate competing loop configurations, together with two-state promoter modeling, we show that these chromatin loops are highly dynamic. This work reframes insulators as active, tunable regulators that shape the frequency, coordination, and productivity of enhancer-promoter communication.

molecular biology↗