239 research outputs found
Complex-based analysis of dysregulated cellular processes in cancer
Background: Differential expression analysis of (individual) genes is often
used to study their roles in diseases. However, diseases such as cancer are a
result of the combined effect of multiple genes. Gene products such as proteins
seldom act in isolation, but instead constitute stable multi-protein complexes
performing dedicated functions. Therefore, complexes aggregate the effect of
individual genes (proteins) and can be used to gain a better understanding of
cancer mechanisms. Here, we observe that complexes show considerable changes in
their expression, in turn directed by the concerted action of transcription
factors (TFs), across cancer conditions. We seek to gain novel insights into
cancer mechanisms through a systematic analysis of complexes and their
transcriptional regulation.
Results: We integrated large-scale protein-interaction (PPI) and
gene-expression datasets to identify complexes that exhibit significant changes
in their expression across different conditions in cancer. We devised a
log-linear model to relate these changes to the differential regulation of
complexes by TFs. The application of our model on two case studies involving
pancreatic and familial breast tumour conditions revealed: (i) complexes in
core cellular processes, especially those responsible for maintaining genome
stability and cell proliferation (e.g. DNA damage repair and cell cycle) show
considerable changes in expression; (ii) these changes include decrease and
countering increase for different sets of complexes indicative of compensatory
mechanisms coming into play in tumours; and (iii) TFs work in cooperative and
counteractive ways to regulate these mechanisms. Such aberrant complexes and
their regulating TFs play vital roles in the initiation and progression of
cancer.Comment: 22 pages, BMC Systems Biolog
The role of network science in glioblastoma
Network science has long been recognized as a well-established discipline across many biological domains. In the particular case of cancer genomics, network discovery is challenged by the multitude of available high-dimensional heterogeneous views of data. Glioblastoma (GBM) is an example of such a complex and heterogeneous disease that can be tackled by network science. Identifying the architecture of molecular GBM networks is essential to understanding the information flow and better informing drug development and pre-clinical studies. Here, we review network-based strategies that have been used in the study of GBM, along with the available software implementations for reproducibility and further testing on newly coming datasets. Promising results have been obtained from both bulk and single-cell GBM data, placing network discovery at the forefront of developing a molecularly-informed-based personalized medicine.This work was partially supported by national funds through Fundação para a Ciência e a
Tecnologia (FCT) with references CEECINST/00102/2018, CEECIND/00072/2018 and
PD/BDE/143154/2019, UIDB/04516/2020, UIDB/00297/2020, UIDB/50021/2020, UIDB/50022/2020,
UIDB/50026/2020, UIDP/50026/2020, NORTE-01-0145-FEDER-000013, and NORTE-01-0145-FEDER000023 and projects PTDC/CCI-BIO/4180/2020 and DSAIPA/DS/0026/2019. This project has received funding from the European Union’s Horizon 2020 research and innovation program under
Grant Agreement No. 951970 (OLISSIPO project)
Regulatory network analysis of Paneth cell and goblet cell enriched gut organoids using transcriptomics approaches
The epithelial lining of the small intestine consists of multiple cell types, including Paneth cells and goblet cells, that work in cohort to maintain gut health. 3D in vitro cultures of human primary epithelial cells, called organoids, have become a key model to study the functions of Paneth cells and goblet cells in normal and diseased conditions. Advances in these models include the ability to skew differentiation to particular lineages, providing a useful tool to study cell type specific function/dysfunction in the context of the epithelium. Here, we use comprehensive profiling of mRNA, microRNA and long non-coding RNA expression to confirm that Paneth cell and goblet cell enrichment of murine small intestinal organoids (enteroids) establishes a physiologically accurate model. We employ network analysis to infer the regulatory landscape altered by skewing differentiation, and using knowledge of cell type specific markers, we predict key regulators of cell type specific functions: Cebpa, Jun, Nr1d1 and Rxra specific to Paneth cells, Gfi1b and Myc specific for goblet cells and Ets1, Nr3c1 and Vdr shared between them. Links identified between these regulators and cellular phenotypes of inflammatory bowel disease (IBD) suggest that global regulatory rewiring during or after differentiation of Paneth cells and goblet cells could contribute to IBD aetiology. Future application of cell type enriched enteroids combined with the presented computational workflow can be used to disentangle multifactorial mechanisms of these cell types and propose regulators whose pharmacological targeting could be advantageous in treating IBD patients with Crohn's disease or ulcerative colitis
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