Search bioRxiv⌕ Search

Biology subjects

Weber, M.-A.

Publications and source records attributed to Weber, M.-A..

3 recordsLinked to original sources

Towards Quantitative Imaging Biomarkers of Tumor Dissemination: a Multi-scale Parametric Modeling of Multiple Myeloma

The advent of medical imaging and automatic image analysis is bringing the full quantitative assessment of lesions and tumor burden at every clinical examination within reach. This opens avenues for the development and testing of functional disease models, as well as their use in the clinical practice for personalized medicine. In this paper, we introduce a Bayesian statistical framework, based on mixed-effects models, to quantitatively test and learn functional disease models at different scales, on population longitudinal data. We also derive an effective mathematical model for the crossover between initially detected lesions and tumor dissemination, based on the Iwata-Kawasaki-Shigesada model. We finally propose to leverage this descriptive disease progression model into model-aware biomarkers for personalized risk-assessment, taking all available examinations and relevant covariates into account. As a use case, we study Multiple Myeloma, a disseminated plasma cell cancer, in which proper diagnostics is essential, to differentiate frequent precursor state without end-organ damage from the rapidly developing disease requiring therapy. After learning the best biological models for local lesion growth and global tumor burden evolution on clinical data, and computing corresponding population priors, we use individual model parameters as biomarkers, and can study them systematically for correlation with external covariates, such as sex or location of the lesion. On our cohort of 63 patients with smoldering Multiple Myeloma, we show that they perform substantially better than other radiological criteria, to predict progression into symptomatic Multiple Myeloma. Our study paves the way for modeling disease progression patterns for Multiple Myeloma, but also for other metastatic and disseminated tumor growth processes, and for analyzing large longitudinal image data sets acquired in oncological imaging. It shows the unprecedented potential of model-based biomarkers for better and more personalized treatment decisions and deserves being validated on larger cohorts to establish its role in clinical decision making.

bioinformatics↗

Brain tissue properties and morphometry assessment after chronic complete spinal cord injury

There is much controversy about the potential impact of spinal cord injury (SCI) on brains anatomy and function, which is mirrored in the substantial divergence of findings between animal models and human imaging studies. Given recent advances in quantitative magnetic resonance imaging (MRI) we sought to tackle the unresolved question about the link between the presumed injury associated volume differences and underlying brain tissue property changes in a cohort of chronic complete SCI patients. Using the established computational anatomy methods of voxel-based morphometry (VBM) and voxel-based quantification (VBQ) we performed statistical analyses of grey matter volume and parameter maps indicative for brains myelin, iron and free tissue water content in complete SCI patients (n=14) and healthy individuals (n=14). Our whole-brain analysis showed significant white matter volume loss in the rostral and dorsal part of the spinal cord consistent with Wallerian degeneration of proprioceptive axons in the lemniscal tract in SCI subjects, which correlated with spinal cord atrophy assessed with quantification of the spinal cord cross-sectional area at cervical level. The latter finding suggests that Wallerian degeneration of the lemniscal tract represents a main contributor to the observed spinal cord atrophy, which is highly consistent with preclinical ultrastructural/histological evidence of remote changes in the central nervous system secondary to SCI. Structural changes in the brain representing remote changes in the course of chronic SCI could not be confirmed with conventional VBM or VBQ statistical analysis. Whether and how MRI based brain morphometry and brain tissue property analysis will inform clinical decision making and clinical trial outcomes in spinal cord medicine remains to be determined.

neuroscience↗

Pathway maps enable straightforward yet customized and semi-automated yet insightful analyses of omics data

To explore the molecular processes underlying some biological theme of interest based on public data, gene lists are used herein as input for the construction of annotated pathway maps, employing Cytoscape apps, and then high-throughput (\"omics\") gene expression data are overlaid onto these maps. Seeded with a published set of marker genes of the senescence-associated secretory phenotype and the genes of the cellular senescence KEGG pathway, a gene/protein interaction network and annotated clusters (a \"pathway map\") of cellular senescence are derived. The map can be amended, by adding some application-specific genes, and overlaid with gene expression data describing cellular senescence of fibroblasts and with disease-related gene expression data associated with prostate and pancreatic cancer, and with ischemic stroke, allowing insights into the role of cellular senescence in disease. Some gene expression data are derived from the \"Biomarker Benchmark repository\". The pathway map approach can be followed in principle for any biological theme of interest, fostering much-needed independence from the investigator-biased expert networks usually used for overlaying gene expression data.

genomics↗