Publications

Empirically establishing drug exposure records directly from untargeted metabolomics data

Haoqi Nina Zhao et al.

bioRxiv [Preprint]. 2024 Oct 26:2024.10.07.617109. doi: 10.1101/2024.10.07.617109.

Despite extensive efforts, extracting information on medication exposure from clinical records remains challenging. To complement this approach, we developed the tandem mass spectrometry (MS/MS) based GNPS Drug Library. This resource integrates MS/MS data for drugs and their metabolites/analogs with controlled vocabularies on exposure sources, pharmacologic classes, therapeutic indications, and mechanisms of action. It enables direct analysis of drug exposure and metabolism from untargeted...

Detection of Tn-antigen in breast and prostate cancer models by VVL-labeled red dye-doped nanoparticles

Alejandra Verhassel et al.

Nanomedicine (Lond). 2024;19(29):2463-2478. doi: 10.1080/17435889.2024.2405454. Epub 2024 Oct 9.

Aim: Fluorescence detection of breast and prostate cancer cells expressing Tn-antigen, a tumor marker, with Vicia villosa lectin (VVL)-labeled nanoparticles.Materials & methods: Breast and prostate cancer cells engineered to express high levels of Tn-antigen and non-engineered controls were incubated with VVL-labeled or unlabeled red dye-doped silica-coated polystyrene nanoparticles. The binding to cells was studied with flow cytometry, confocal microscopy, and electron microscopy.Results: Flow...

Restoring mechanophenotype reverts malignant properties of ECM-enriched vocal fold cancer

Jasmin Kaivola et al.

bioRxiv [Preprint]. 2024 Aug 23:2024.08.22.609159. doi: 10.1101/2024.08.22.609159.

Increased extracellular matrix (ECM) and matrix stiffness promote solid tumor progression. However, mechanotransduction in cancers arising in mechanically active tissues remains underexplored. Here, we report upregulation of multiple ECM components accompanied by tissue stiffening in vocal fold cancer (VFC). We compare non-cancerous (NC) and patient-derived VFC cells - from early (mobile, T1) to advanced-stage (immobile, T3) cancers - revealing an association between VFC progression and...

Concordant inter-laboratory derived concentrations of ceramides in human plasma reference materials via authentic standards

Federico Torta et al.

Nat Commun. 2024 Oct 3;15(1):8562. doi: 10.1038/s41467-024-52087-x.

In this community effort, we compare measurements between 34 laboratories from 19 countries, utilizing mixtures of labelled authentic synthetic standards, to quantify by mass spectrometry four clinically used ceramide species in the NIST (National Institute of Standards and Technology) human blood plasma Standard Reference Material (SRM) 1950, as well as a set of candidate plasma reference materials (RM 8231). Participants either utilized a provided validated method and/or their method of...

The role and regulation of integrins in cell migration and invasion

Megan R Chastney et al.

Nat Rev Mol Cell Biol. 2025 Feb;26(2):147-167. doi: 10.1038/s41580-024-00777-1. Epub 2024 Sep 30.

Integrin receptors are the main molecular link between cells and the extracellular matrix (ECM) as well as mediating cell-cell interactions. Integrin-ECM binding triggers the formation of heterogeneous multi-protein assemblies termed integrin adhesion complexes (IACs) that enable integrins to transform extracellular cues into intracellular signals that affect many cellular processes, especially cell motility. Cell migration is essential for diverse physiological and pathological processes and is...

Profiling steroid hormone landscape of bladder cancer reveals depletion of intratumoural androgens to castration levels: a cross-sectional study

Kimmo Kettunen et al.

EBioMedicine. 2024 Oct;108:105359. doi: 10.1016/j.ebiom.2024.105359. Epub 2024 Sep 28.

BACKGROUND: Bladder cancer is a highly over-represented disease in males. The involvement of sex steroids in bladder carcinogenesis and the utilisation of steroid hormone action as a therapeutic target have been frequently proposed. However, the intratumoural steroid milieu remains unclear.