scholarly journals Hub genes in a pan-cancer co-expression network show potential for predicting drug responses

F1000Research ◽  
2019 ◽  
Vol 7 ◽  
pp. 1906
Author(s):  
Francisco Azuaje ◽  
Tony Kaoma ◽  
Céline Jeanty ◽  
Petr V. Nazarov ◽  
Arnaud Muller ◽  
...  
Keyword(s):  
Cell Lines ◽  
Drug Sensitivity ◽  
Topological Analysis ◽  
Molecular Networks ◽  
Model Organisms ◽  
Hub Genes ◽  
Diverse Range ◽  
Drug Responses ◽  
Using Data

Background: The topological analysis of networks extracted from different types of “omics” data is a useful strategy for characterizing biologically meaningful properties of the complex systems underlying these networks. In particular, the biological significance of highly connected genes in diverse molecular networks has been previously determined using data from several model organisms and phenotypes. Despite such insights, the predictive potential of candidate hubs in gene co-expression networks in the specific context of cancer-related drug experiments remains to be deeply investigated. The examination of such associations may offer opportunities for the accurate prediction of anticancer drug responses.  Methods: Here, we address this problem by: a) analyzing a co-expression network obtained from thousands of cancer cell lines, b) detecting significant network hubs, and c) assessing their capacity to predict drug sensitivity using data from thousands of drug experiments. We investigated the prediction capability of those genes using a multiple linear regression model, independent datasets, comparisons with other models and our own in vitro experiments. Results: These analyses led to the identification of 47 hub genes, which are implicated in a diverse range of cancer-relevant processes and pathways. Overall, encouraging agreements between predicted and observed drug sensitivities were observed in public datasets, as well as in our in vitro validations for four glioblastoma cell lines and four drugs. To facilitate further research, we share our hub-based drug sensitivity prediction model as an online tool. Conclusions: Our research shows that co-expression network hubs are biologically interesting and exhibit potential for predicting drug responses in vitro. These findings motivate further investigations about the relevance and application of our unbiased discovery approach in pre-clinical, translationally-oriented research.

scholarly journals Hub genes in a pan-cancer co-expression network show potential for predicting drug responses

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 1906 ◽  
Author(s):  
Francisco Azuaje ◽  
Tony Kaoma ◽  
Céline Jeanty ◽  
Petr V. Nazarov ◽  
Arnaud Muller ◽  
...  
Keyword(s):  
Cell Lines ◽  
Drug Sensitivity ◽  
Topological Analysis ◽  
Molecular Networks ◽  
Model Organisms ◽  
Hub Genes ◽  
Diverse Range ◽  
Drug Responses ◽  
Using Data

Background: The topological analysis of networks extracted from different types of “omics” data is a useful strategy for characterizing biologically meaningful properties of the complex systems underlying these networks. In particular, the biological significance of highly connected genes in diverse molecular networks has been previously determined using data from several model organisms and phenotypes. Despite such insights, the predictive potential of candidate hubs in gene co-expression networks in the specific context of cancer-related drug experiments remains to be deeply investigated. The examination of such associations may offer opportunities for the accurate prediction of anticancer drug responses.  Methods: Here, we address this problem by: a) analyzing a co-expression network obtained from thousands of cancer cell lines, b) detecting significant network hubs, and c) assessing their capacity to predict drug sensitivity using data from thousands of drug experiments. We investigated the prediction capability of those genes using a multiple linear regression model, independent datasets, comparisons with other models and our own in vitro experiments. Results: These analyses led to the identification of 47 hub genes, which are implicated in a diverse range of cancer-relevant processes and pathways. Overall, encouraging agreements between predicted and observed drug sensitivities were observed in public datasets, as well as in our in vitro validations for four glioblastoma cell lines and four drugs. To facilitate further research, we share our hub-based drug sensitivity prediction model as an online tool. Conclusions: Our research shows that co-expression network hubs are biologically interesting and exhibit potential for predicting drug responses in vitro. These findings motivate further investigations about the relevance and application of our unbiased discovery approach in pre-clinical, translationally-oriented research.

scholarly journals Consistency of in vitro drug sensitivities within pharmacological classes

2021 ◽  
Vol 15 (1) ◽  
pp. 12
Author(s):  
Casey Hon ◽  
Sisira Nair ◽  
Petr Smirnov ◽  
Hossein Sharifi-Noghabi ◽  
Nikta Feizi ◽  
...  
Keyword(s):  
Cell Lines ◽  
Drug Sensitivity ◽  
Cancer Therapeutics ◽  
The Other ◽  
Comparative Analyses ◽  
Potential Sources ◽  
The Common ◽  
Pharmacogenomic Studies

Multiple comparative analyses between the common drugs and cell lines of the Genomics of Drug Sensitivity in Cancer (GDSC) and the Cancer Therapeutics Response Portal (CTRP) have previously shown low consistency between the in vitro phenotypic measures of a drug in one study with the other. While several potential sources of inconsistency have been tested, the similar targets of tested compounds has yet to be tested as a contributing factor of discrepancy. This analysis includes two methods of reclassifying drugs into classes based on their targets to identify the truer set of consistent cell lines, showing an increased correlation between the two pharmacogenomic studies.

scholarly journals Functional human genes typically exhibit epigenetic conservation

PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0253250
Author(s):  
Daniel Rud ◽  
Paul Marjoram ◽  
Kimberly Siegmund ◽  
Darryl Shibata
Keyword(s):  
Cell Lines ◽  
Drug Sensitivity ◽  
Single Gene ◽  
Functional Genes ◽  
Human Tissues ◽  
Gene Conservation ◽  
Individual Culture ◽  
Human Genes

Recent DepMap CRISPR-Cas9 single gene disruptions have identified genes more essential to proliferation in tissue culture. It would be valuable to translate these finding with measurements more practical for human tissues. Here we show that DepMap essential genes and other literature curated functional genes exhibit cell-specific preferential epigenetic conservation when DNA methylation measurements are compared between replicate cell lines and between intestinal crypts from the same individual. Culture experiments indicate that epigenetic drift accumulates through time with smaller differences in more functional genes. In NCI-60 cell lines, greater targeted gene conservation correlated with greater drug sensitivity. These studies indicate that two measurements separated in time allow normal or neoplastic cells to signal through conservation which human genes are more essential to their survival in vitro or in vivo.

Characterization of two new high-grade B-cell lymphoma cell lines with MYC and BCL2 rearrangements that are suitable for in vitro drug sensitivity studies

2018 ◽  
Vol 60 (4) ◽  
pp. 1043-1052
Author(s):  
Marie-Sophie Dheur ◽  
Hélène A. Poirel ◽  
Geneviève Ameye ◽  
Gaëlle Tilman ◽  
Pascale Saussoy ◽  
...  
Keyword(s):  
B Cell ◽  
Cell Lines ◽  
Drug Sensitivity ◽  
Cell Lymphoma ◽  
B Cell Lymphoma ◽  
Lymphoma Cell ◽  
High Grade ◽  
Sensitivity Studies

Connecting gene expression subtypes of colorectal cancer (CRC) with cell lines and drug resistance.

2013 ◽  
Vol 31 (15_suppl) ◽  
pp. e14544-e14544
Author(s):  
Eva Budinska ◽  
Jenny Wilding ◽  
Vlad Calin Popovici ◽  
Edoardo Missiaglia ◽  
Arnaud Roth ◽  
...  
Keyword(s):  
Gene Expression ◽  
Cell Line ◽  
Clinical Significance ◽  
Cell Lines ◽  
Drug Response ◽  
Drug Sensitivity ◽  
Expression Profiles ◽  
Enrichment Analysis ◽  
Gene Set Enrichment Analysis

e14544 Background: We identified CRC gene expression subtypes (ASCO 2012, #3511), which associate with established parameters of outcome as well as relevant biological motifs. We now substantiate their biological and potentially clinical significance by linking them with cell line data and drug sensitivity, primarily attempting to identify models for the poor prognosis subtypes Mesenchymal and CIMP-H like (characterized by EMT/stroma and immune-associated gene modules, respectively). Methods: We analyzed gene expression profiles of 35 publicly available cell lines with sensitivity data for 82 drug compounds, and our 94 cell lines with data on sensitivity for 7 compounds and colony morphology. As in vitro, stromal and immune-associated genes loose their relevance, we trained a new classifier based on genes expressed in both systems, which identifies the subtypes in both tissue and cell cultures. Cell line subtypes were validated by comparing their enrichment for molecular markers with that of our CRC subtypes. Drug sensitivity was assessed by linking original subtypes with 92 drug response signatures (MsigDB) via gene set enrichment analysis, and by screening drug sensitivity of cell line panels against our subtypes (Kruskal-Wallis test). Results: Of the cell lines 70% could be assigned to a subtype with a probability as high as 0.95. The cell line subtypes were significantly associated with their KRAS, BRAF and MSI status and corresponded to our CRC subtypes. Interestingly, the cell lines which in matrigel created a network of undifferentiated cells were assigned to the Mesenchymal subtype. Drug response studies revealed potential sensitivity of subtypes to multiple compounds, in addition to what could be predicted based on their mutational profile (e.g. sensitivity of the CIMP-H subtype to Dasatinib, p<0.01). Conclusions: Our data support the biological and potentially clinical significance of the CRC subtypes in their association with cell line models, including results of drug sensitivity analysis. Our subtypes might not only have prognostic value but might also be predictive for response to drugs. Subtyping cell lines further substantiates their significance as relevant model for functional studies.

scholarly journals Synthesis of Chromene 4 Aldehyde and 6-Phenyl-6h-Chromeno [4,3-B] Quinoline Derivatives as Anticancer and Apoptosis Inducing Agents

2021 ◽  
Vol 9 (10) ◽  
pp. 1764-1772
Author(s):  
Rizuana Sultana
Keyword(s):  
Cell Lines ◽  
Morphological Changes ◽  
Quinoline Derivatives ◽  
Significant Extent ◽  
Diverse Range ◽  
Synthetic Strategy ◽  
Induced Apoptosis ◽  
Apoptosis Inducing Agents ◽  
Mcf 7

Abstract: A series of novel chromene 3-aldehyde and quinoline derivatives have been synthesized using diversely substituted nitroarenes in the presence of In, dil. HCl, H2O (reductive amination) and evaluated for in vitro cytotoxic activity in three different cancer cell lines (MDA-MB-453, MCF-7, A549 and PC3). The synthetic strategy utilized to access these hybrids is operationally simple and works with great substrate scope. Interestingly, compound 6i was induced apoptosis to a significant extent in MDA-MB-453 cell lines. And these selected compounds 6i was led to morphological changes after treatment with MDA-MB-453 cell lines and found clear destabilization of mitochondrial membrane potential behind the observed anticancer activity. This strategy is operationally simple and works with a diverse range of substrates and warrants future investigations for further anticancer drug development.

Effects of mycoplasma contamination on phenotypic expression of mitochondrial mutants in human cells

1981 ◽  
Vol 1 (4) ◽  
pp. 321-329
Author(s):  
C J Doersen ◽  
E J Stanbridge
Keyword(s):  
Protein Synthesis ◽  
Infected Cell ◽  
Cell Lines ◽  
Resistant Strain ◽  
Drug Sensitivity ◽  
Mitochondrial Protein ◽  
Phenotypic Expression ◽  
Mitochondrial Protein Synthesis ◽  
Protein Synthesis Inhibitors

HeLa cells sensitive to the mitochondrial protein synthesis inhibitors erythromycin (ERY) and chloramphenicol (CAP) and HeLa variants resistant to the effects of these drugs were purposefully infected with drug-sensitive and -resistant mycoplasma strains. Mycoplasma hyorhinis and the ERY-resistant strain of Mycoplasma orale, MO-ERYr, did not influence the growth of HeLa and ERY-resistant ERY2301 cells in the presence or absence of ERY. M. hyorhinis also did not affect the growth of HeLa and CAP-resistant Cap-2 cells in the presence or absence of CAP. However, both HeLa and Cap-2 cells infected with the CAP-resistant strain of M. hyorhinis, MH-CAPr, were more sensitive to the cytotoxic effect of CAP. This may be due to the glucose dependence of the cells, which was compromised by the increased utilization of glucose by MH-CAPr in these infected cell cultures. In vitro protein synthesis by isolated mitochondria was significantly altered by mycoplasma infection of the various cell lines. A substantial number of mycoplasmas copurified with the mitochondria, resulting in up to a sevenfold increase in the incorporation of [3H]leucine into the trichloroacetic acid-insoluble material. More importantly, the apparent drug sensitivity or resistance of mitochondrial preparations from mycoplasma-infected cells reflected the drug sensitivity or resistance of the contaminating mycoplasmas. These results illustrate the hazards in interpreting mitochondrial protein synthesis data derived from mycoplasma-infected cell lines, particularly putative mitochondrially encoded mutants resistant to inhibitors of mitochondrial protein synthesis.

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