Biology subjects

Kreis, J.

Publications and source records attributed to Kreis, J..

4 recordsLinked to original sources

bioRxiv2023

Stromal signals dominate gene expression signature scores that aim to describe cancer-intrinsic stemness or mesenchymality characteristics

PurposeEpithelial-to-mesenchymal transition (EMT) in cancer cells confers migratory ability, a crucial aspect of tumor metastasis that frequently leads to death. In multiple studies, authors proposed gene expression signatures for EMT, stemness, and mesenchymality (EMT-related) characteristics of tumors based on bulk tumor expression profiling. However, recent studies have suggested that non-cancerous cells in the tumor micro- or macroenvironment heavily influence individual signature profiles. Experimental DesignWe analyzed scores of 11 published and frequently referenced gene expression signatures in bulk, single cell, and pseudo bulk expression data across multiple cancer types. ResultsOur study strengthens and extends the influence of non-cancerous cells on signatures that were proposed to describe EMT-related (EMT, mesenchymal, or stemness) characteristics in various cancer types. The cell type composition, especially the amount of tumor cells, of a tumor sample frequently dominates EMT-related signature scores. Additionally, our analyses revealed that stromal cells, most often fibroblasts, are the main drivers of the EMT-related signature scores. ConclusionsWe call attention to the risk of false conclusions about tumor properties when interpreting EMT-related signatures, especially in a clinical setting: high patient scores of EMT-related signatures or calls of "stemness subtypes" often result from low tumor cell content in tumor biopsies rather than cancer cell-specific stemness or mesenchymality/EMT characteristics.

bioinformatics↗

bioRxiv2020

Rab7 mediates Wnt-dependent mesoderm patterning and gastrulation in Xenopus

Early embryogenesis requires tightly controlled temporal and spatial activity of growth factors. Modulation is achieved at multiple levels, from cellular transcription to tissue-scale propagation, concerning activation, maintenance, or termination of signaling. Intracellularly, the endolysosomal system emerged as important factor for such regulations. Endocytosis and early endosomes mainly orchestrate activation and transduction of signals, while late endosomes are thought to mediate lysosome-based termination. Only few reports attributed activating roles to late endosomes, mainly for Wnt pathway activation. In Xenopus, few is known about developmental roles of endosomal regulators, or their function for signaling, especially true for late endosomes. Therefore, we chose to analyze a hypothesized positive role of Rab7 in this context, a small GTPase mainly known for its role as a late endosomal regulator. We analyzed if Rab7 participates in early activation of growth factor signaling, focusing on Wnt signaling. We found rab7 expressed very localized throughout development, and inhibition resulted in strong gastrulation defects. Concomitantly, Rab7 was strictly required for both, exogenous activation and endogenous Wnt-mediated patterning of the mesoderm. Summary StatementThe late endosomal regulator Rab7 is required for gastrulation movements and axis elongation in Xenopus by positively regulating Wnt signaling-mediated mesoderm patterning.

developmental biology↗

bioRxiv2019

Feature selection strategies for drug sensitivity prediction

Drug sensitivity prediction constitutes one of the main challenges in personalized medicine. The major difficulty of this problem stems from the fact that the sensitivity of cancer cells to treatment depends on an unknown subset of a large number of biological features. Although feature selection is the key to interpretable results and identification of potential biomarkers, a comprehensive assessment of feature selection methods for drug sensitivity prediction has so far not been performed. We propose feature selection approaches driven by prior knowledge of drug targets, target pathways, and gene expression signatures. We asses these methodologies on Genomics of Drug Sensitivity in Cancer (GDSC) dataset, a panel of around 1000 cell lines screened against multiple anticancer compounds. We compare our results with a baseline model utilizing genome-wide gene expression features and common data-driven feature selection techniques. Together, 2484 unique models were evaluated, providing a comprehensive study of feature selection strategies for the drug response prediction problem. For 23 drugs, the models achieve better predictive performance when the features are selected according to prior knowledge of drug targets and pathways. The best correlation of observed and predicted response using the test set is achieved for Linifanib (r=0.75). Extending the drug-dependent features with gene expression signatures yields models that are most predictive of drug response for 60 drugs, with the best performing example of Dabrafenib. Examples of how pre-selection of features benefits the model interpretability are given for Dabrafenib, Linifanib and Quizartinib. Based on GDSC drug data, we find that feature selection driven by prior knowledge tends to yield better results for drugs targeting specific genes and pathways, while models with the genome-wide features perform better for drugs affecting general mechanisms such as metabolism and DNA replication. For a significant group of the compounds, even a very small number of features based on simple drug properties is often highly predictive of drug sensitivity, can explain the mechanism of drug action and be used as guidelines for their prescription. In general, choosing appropriate feature selection strategies has the potential to develop interpretable models that are indicative for therapy design.

bioinformatics↗

bioRxiv2018

A dual function of FGF signaling in Xenopus left-right axis formation

Organ left-right (LR) asymmetry is a conserved vertebrate feature, which is regulated by left-sided activation of Nodal signaling. Nodal asymmetry is established by a leftward fluid-flow generated at the ciliated LR organizer (LRO). While the role of fibroblast growth factor (FGF) signaling pathways during mesoderm development are conserved, diverging results from different model organisms suggested a non-conserved function in LR asymmetry. Here, we demonstrate that FGF is required during gastrulation in a dual function at consecutive stages of Xenopus embryonic development. In the early gastrula, FGF is necessary for LRO precursor induction, acting in parallel to FGF-mediated mesoderm induction. During late gastrulation, the FGF/Ca2+-branch is required for specification of the flow sensing lateral LRO cells, a function related to FGF-mediated mesoderm morphogenesis. This second function in addition requires input from the calcium channel Polycystin-2. Thus, analogous to mesoderm development, FGF activity is required in a dual role for laterality specification, namely for generating and sensing of leftward flow. Moreover, our data show that FGF functions in LR asymmetric development are conserved across vertebrate species, from fish to mammals.

developmental biology↗