Publications

Structural Repetition Detector: multi-scale quantitative mapping of molecular complexes through microscopy

Afonso Mendes et al.

Res Sq [Preprint]. 2024 Oct 15:rs.3.rs-5182329. doi: 10.21203/rs.3.rs-5182329/v1.

From molecules to organelles, cells exhibit recurring structural motifs across multiple scales. Understanding these structures provides insights into their functional roles. While superresolution microscopy can visualise such patterns, manual detection in large datasets is challenging and biased. We present the Structural Repetition Detector (SReD), an unsupervised computational framework that identifies repetitive biological structures by exploiting local texture repetition. SReD formulates...

Imaging cell architecture and dynamics

Lucy Collinson et al.

J Cell Sci. 2024 Oct 15;137(20):jcs263575. doi: 10.1242/jcs.263575. Epub 2024 Oct 30.

No abstract

Multiparameter imaging reveals clinically relevant cancer cell-stroma interaction dynamics in head and neck cancer

Karolina Punovuori et al.

Cell. 2024 Dec 12;187(25):7267-7284.e20. doi: 10.1016/j.cell.2024.09.046. Epub 2024 Oct 28.

Epithelial tumors are characterized by abundant inter- and intra-tumor heterogeneity, which complicates diagnostics and treatment. The contribution of cancer-stroma interactions to this heterogeneity is poorly understood. Here, we report a paradigm to quantify phenotypic diversity in head and neck squamous cell carcinoma (HNSCC) with single-cell resolution. By combining cell-state markers with morphological features, we identify phenotypic signatures that correlate with clinical features,...

Encapsulated mitochondria to reprogram the metabolism of M2-type macrophages for anti-tumor therapy

Yonghui Wang et al.

Nanoscale. 2024 Nov 21;16(45):20925-20939. doi: 10.1039/d4nr02471k.

M2-type macrophages (M2Φ) play a pro-tumorigenic role and are closely associated with tumor development, where metabolic dysregulation exacerbates the immunosuppressive tumor microenvironment and fosters tumor growth. Mitochondria serve as the regulatory center of cellular metabolism, yet effective methods to modulate M2Φ mitochondria within the tumor microenvironment remain lacking. In this study, we developed a technique utilizing the bio-encapsulation of mitochondria in Zeolitic Imidazolate...

Glutaraldehyde-enhanced autofluorescence as a general tool for 3D morphological imaging

Miika Niemeläinen et al.

Biol Open. 2024 Nov 15;13(11):bio060428. doi: 10.1242/bio.060428. Epub 2024 Nov 11.

Routine histochemical techniques are capable of producing vast amount of information from diverse sample types, but these techniques are limited in their ability to generate 3D information. Autofluorescence imaging can be used to analyse samples in 3D but it suffers from weak/low signal intensities. Here, we describe a simple chemical treatment with glutaraldehyde to enhance autofluorescence for 3D fluorescence imaging and to generate detailed morphological images on whole-mount samples. This...

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...