A5084687928- Cancer, Stress, Anesthesia, and Immune Response
- Chemokine receptors and signaling
- Cancer Cells and Metastasis
- Cancer, Hypoxia, and Metabolism
- Cancer Research and Treatments
- Peptidase Inhibition and Analysis
- Hedgehog Signaling Pathway Studies
- Nanoplatforms for cancer theranostics
- Inflammatory mediators and NSAID effects
- Bioinformatics and Genomic Networks
- Forest Management and Policy
- RNA and protein synthesis mechanisms
- Computational Drug Discovery Methods
- Economic and Environmental Valuation
- Genomics and Chromatin Dynamics
- Angiogenesis and VEGF in Cancer
- Cancer-related Molecular Pathways
- Estrogen and related hormone effects
- Advanced Proteomics Techniques and Applications
- MicroRNA in disease regulation
- CRISPR and Genetic Engineering
- DNA Repair Mechanisms
- Tannin, Tannase and Anticancer Activities
- Genomics and Phylogenetic Studies
- RNA modifications and cancer
Université de Lorraine
2023-2024
Université de Strasbourg
2023-2024
Bureau d'Economie Théorique et Appliquée
2023-2024
Universitat de Lleida
2023
Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement
2023
University of Eastern Finland
2023
Karolinska Institutet
2008-2023
Centre National de la Recherche Scientifique
2023
AgroParisTech
2023
Science for Life Laboratory
2012-2020
The InParanoid project gathers proteomes of completely sequenced eukaryotic species plus Escherichia coli and calculates pairwise ortholog relationships among them. new release 7.0 the database has grown by an order magnitude over previous version now includes 100 their collective 1.3 million proteins organized into 42.7 groups. algorithm itself been revised is both more specific sensitive. Based on results from our recent benchmarking low-complexity filters in homology assignment, a...
In the growing field of genomics, multiple alignment programs are confronted with ever increasing amounts data. To address this issue we have dramatically improved running time and memory requirement Kalign, while maintaining its high accuracy. Kalign version 2 also supports nucleotide alignment, a newly introduced extension allows for external sequence annotation to be included into procedure. We demonstrate that Kalign2 is exceptionally fast memory-efficient, permitting accurate very large...
Abstract Cancer-associated fibroblasts (CAF) stimulate tumor growth and metastasis. Signals supporting CAF function are thus emerging as candidate therapeutic targets in the microenvironment. The chemokine CXCL14 is a potent inducer of protumorigenic functions. This study aimed at learning how protumoral functions CXCL14-expressing maintained. We found that nitric oxide synthase NOS1 upregulated stimulated with CXCL14. Induction Nos1 was associated oxidative stress occurred together...
Abstract A role for Hedgehog (Hh) signalling in the development of colorectal cancer (CRC) has been proposed. In CRC and other solid tumours, Hh ligands are upregulated; however, a specific antagonist provided no benefit clinical trial. Here we use reporter mice to show that downstream activity is unexpectedly diminished mouse model colitis-associated colon cancer, restricted stroma. Functionally, stroma-specific activation markedly reduces tumour load blocks progression advanced neoplasms,...
Abstract Purpose: Fibroblasts expressing the orphan chemokine CXCL14 have been previously shown to associate with poor breast cancer prognosis and promote growth. This study explores mechanism underlying survival associations of stromal CXCL14. Experimental Design: Tumor cell epithelial-to-mesenchymal transition (EMT), invasion, metastasis were studied in vitro vivo models together fibroblasts overexpressing An approach for receptor identification included loss-of-function studies followed...
FunCoup (http://FunCoup.sbc.su.se) is a database that maintains and visualizes global gene/protein networks of functional coupling have been constructed by Bayesian integration diverse high-throughput data. achieves high coverage orthology-based data sources from different model organisms platforms. We here present release 2.0 in which the updated methodology has refined. It contains new type Genetic Interaction, three species: chicken, dog zebra fish. As extensively transfers information...
The HMGA2 protein has experimentally been linked to EMT and cancer stemness. Recent studies imply that tumour-stroma interactions regulate these features thereby contribute tumour aggressiveness.We analysed 253 cases of pancreatic ductal adenocarcinoma (PDAC) 155 ampullary (AAC) for expression by IHC. data were correlated with stroma abundance supplemented experimental studies.HMGA2 acts as an independent prognostic marker associated a significantly shorter overall survival in both types....
Motivation Analyzing groups of functionally coupled genes or proteins in the context global interaction networks has become an important aspect bioinformatic investigations. Assessing statistical significance crosstalk enrichment between within can be a valuable tool for functional annotation experimental gene sets. Results Here we present CrossTalkZ, method and software to assess pairs protein large biological networks. We demonstrate that standard z-score is generally appropriate unbiased...
To identify new regulators of homologous recombination repair, we carried out a genome-wide short-interfering RNA screen combined with ionizing irradiation using RAD51 foci formation as readout. All candidates were confirmed by independent RNAs and validated in secondary assays like repair activity RPA formation. Network analysis the top modifiers identified gene clusters involved well components ribosome, proteasome spliceosome, which are known to be required for effective DNA repair. We...
Abstract Cancer‐associated fibroblasts (CAFs) regulate tumour growth, metastasis and response to treatment. Recent studies indicate the existence of functionally distinct CAF subsets. Suggested mechanisms whereby CAFs can impact on treatment include paracrine signalling affecting cancer cell drug sensitivity effects uptake. PDGFRβ is an important regulator fibroblasts. Experimental have linked PDGFRβ‐positive also reduced This study has investigated potential role in adjuvant tamoxifen...
Inhibition of WEE1 kinase by AZD1775 has shown promising results in clinical cancer trials, but markers predicting response are lacking. Here we analysed a panel human breast (BC) cell lines global proteome/transcriptome profiling and identified two groups basal-like BC (BLBCs): ‘PTEN low’ BLBCs were highly sensitive to failed recover following removal AZD1775, while high’ recovered. induced phosphorylation DNA-PK, protecting cells from replication-associated DNA damage promoting cellular...
microRNA (miRNA) dysregulation is a common feature of cancer cells, but the complex roles miRNAs in are not fully elucidated. Here, we used functional genomics to identify oncogenic non-small cell lung and evaluate their impact on response epidermal growth factor (EGFR)-targeting therapy. Our data demonstrate that with an AAGUGC motif seed sequence increase both proliferation sensitivity EGFR inhibitors. Global transcriptomics, proteomics target prediction resulted identification several...
// Fuad Bahram 1, 2, 5, * , Per Hydbring 6, Susanna Tronnersjö 7, Siti Mariam Zakaria 1 Oliver Frings 3 Sara Fahlén 8 Helén Nilsson 9 Jacob Goodwin Natalie von der Lehr 10 Yingtao Su 11 Bernhard Lüscher 4 Alina Castell Lars-Gunnar Larsson Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden 2 Plant Forest Genetics, Swedish University Agricultural Sciences, Uppsala, Oncology-Pathology, Science for Life Laboratory, Institute...
Network analysis is an important tool for functional annotation of genes and proteins. A common approach to discern structure in a global network infer clusters, or modules, assume coherence within each module, which may represent complex pathway. It however not trivial define optimal modules. Although many methods have been proposed, it unclear perform best general. seems that most produce far from results but different ways. MGclus new algorithm designed detect modules with strongly...
Increased expression of GLI1, the main Hedgehog signalling pathway effector, is related to unfavourable prognosis and progressive disease certain breast cancer subtypes. We used conditional transgenic mice induced overexpress GLI1 in mammary epithelium either alone or combination with deletion one Trp53 allele address role elevated tumour initiation progression. Induced facilitates gland formation this was further increased upon heterozygous . The GLI1‐induced primary tumours were different...
Gene expression analysis is often used to investigate the molecular and functional underpinnings of a phenotype. However, differential individual genes limited in that it does not consider how interact with each other networks. To address this shortcoming we propose number network-based analyses give additional insights into studied process. These were applied dataset sex-specific gene chicken gonad brain at different developmental stages. We first constructed global interaction network....