scholarly journals CELLector: Genomics Guided Selection of Cancer in vitro Models

2018 ◽  
Author(s):  
Hanna Najgebauer ◽  
Mi Yang ◽  
Hayley E Francies ◽  
Clare Pacini ◽  
Euan A Stronach ◽  
...  
Keyword(s):  
Cell Lines ◽  
Cancer Cell ◽  
Cancer Cell Line ◽  
R Package ◽  
Cancer Cell Lines ◽  
In Vitro Models ◽  
Computational Method ◽  
R Shiny ◽  
Selection Of

The selection of appropriate cancer models is a key prerequisite for maximising translational potential and clinical relevance of in vitro oncology studies. We developed CELLector: a computational method (implemented in an open source R Shiny application and R package) allowing researchers to select the most relevant cancer cell lines in a patient-genomic guided fashion. CELLector leverages tumour genomics data to identify recurrent sub-types with associated genomic signatures. It then evaluates these signatures in cancer cell lines to rank them and prioritise their selection. This enables users to choose appropriate models for inclusion/exclusion in retrospective analyses and future studies. Moreover, this allows bridging data from cancer cell line screens to precisely defined sub-cohorts of primary tumours. Here, we demonstrate usefulness and applicability of our method through example use cases, showing how it can be used to prioritise the development of new in vitro models and to effectively unveil patient-derived multivariate prognostic and therapeutic markers.

Design, Synthesis, Molecular Docking, and Anticancer Evaluation of Pyrazole Linked Pyrazoline Derivatives with Carbothioamide Tail as EGFR Kinase Inhibitors

2020 ◽  
Vol 21 (1) ◽  
pp. 42-60
Author(s):  
Farah Nawaz ◽  
Ozair Alam ◽  
Ahmad Perwez ◽  
Moshahid A. Rizvi ◽  
Mohd. Javed Naim ◽  
...  
Keyword(s):  
Molecular Docking ◽  
Cell Line ◽  
Cell Lines ◽  
Cancer Cell ◽  
Cancer Cell Line ◽  
Cancer Cell Lines ◽  
Kinase Assay ◽  
Cervix Uteri ◽  
Egfr Kinase

Background: The Epidermal Growth Factor Receptor (known as EGFR) induces cell differentiation and proliferation upon activation through the binding of its ligands. Since EGFR is thought to be involved in the development of cancer, the identification of new target inhibitors is the most viable approach, which recently gained momentum as a potential anticancer therapy. Objective: To assess various pyrazole linked pyrazoline derivatives with carbothioamide for EGFR kinase inhibitory as well as anti-proliferative activity against human cancer cell lines viz. A549 (non-small cell lung tumor), MCF-7 (breast cancer cell line), SiHa (cancerous tissues of the cervix uteri), and HCT-116 (colon cancer cell line). Methods: In vitro EGFR kinase assay, in vitro MTT assay, Lactate dehydrogenase release, nuclear staining (DAPI), and flow cytometry cell analysis. Results: Compounds 6h and 6j inhibited EGFR kinase at concentrations of 1.66μM and 1.9μM, respectively. Furthermore, compounds 6h and 6j showed the most potent anti-proliferative results against the A549 KRAS mutation cell line (IC50 = 9.3 & 10.2μM). Through DAPI staining and phase contrast microscopy, it was established that compounds 6h and 6j also induced apoptotic activity in A549 cells. This activity was further confirmed by FACS using Annexin-V-FITC and Propidium Iodide (PI) labeling. Molecular docking studies performed on 6h and 6j suggested that the compounds can bind to the hinge region of ATP binding site of EGFR tyrosine kinase in a similar pose as that of the standard drug gefitinib. Conclusion: The potential anticancer activity of compounds 6h and 6j was confirmed and need further exploration in cancer cell lines of different tissue origin and signaling pathways, as well as in animal models of cancer development.

In vitro chemotherapeutic and antiangiogenic properties of cardenolides from Acokanthera oblongifolia (Hochst.) Codd

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Maha M. Soltan ◽  
Howaida I. Abd-Alla ◽  
Amal Z. Hassan ◽  
Atef G. Hanna
Keyword(s):  
Cell Lines ◽  
Cancer Cell ◽  
Cancer Cell Line ◽  
Cancer Cell Lines ◽  
Enzyme Inactivation ◽  
Enzyme Linked Immunosorbent Assay ◽  
Anticancer Properties ◽  
Mechanistic Investigation ◽  
G2m Phase

Abstract Acovenoside A and acobioside A were isolated from Acokanthera oblongifolia. Their anticancer properties were explored regarding, antiproliferative and antiangiogenic activities. The study included screening phase against six cancer cell lines followed by mechanistic investigation against HepG2 cancer cell line. The sulforhodamine-B (SRB) was used to determine their growth inhibitory power. In the other hand, flow cytometry techniques were recorded the cell death type and cell cycle analysis. The clonogenic (colony formation) and wound healing assays, enzyme-linked immunosorbent assay (ELISA) and molecular docking, were performed to evaluate the antiangiogenesis capability. Both compounds were strongly, inhibited four cancer cell lines at GI50 less than 100 nM. The in vitro mechanistic investigation against HepG2 resulted in cell accumulations at G2M phase and induction of apoptosis upon treating cells separately, with 400 nM Acov-A and 200 nM Acob-A. Interestingly, the same concentrations were able to activate caspase-3 by 7.2 and 4.8-fold, respectively. Suppressing the clonogenic capacity of HepG2 cells (20 and 40 nM) and inhibiting the migration of the colon Caco-2 cancer cells were provoke the results of vascular endothelial growth factor receptor2 (VEGFR2) kinase enzyme inactivation. The docked study was highly supportive, to the antiangiogenic approach of both cardenolides. The isolated cardenolides could orchestrate pivotal events in fighting cancer.

scholarly journals Comparing cancer cell lines and tumor samples by genomic profiles

2015 ◽  
Author(s):  
Rileen Sinha ◽  
Nikolaus Schultz ◽  
Chris Sander
Keyword(s):  
Cell Lines ◽  
Cancer Cell ◽  
Cancer Cell Line ◽  
Cancer Cell Lines ◽  
Response To Therapy ◽  
Computational Method ◽  
The Cancer Genome Atlas ◽  
Cancer Genome Atlas ◽  
Cancer Types ◽  
Tumor Material

Cancer cell lines are often used in laboratory experiments as models of tumors, although they can have substantially different genetic and epigenetic profiles compared to tumors. We have developed a general computational method, TumorComparer, to systematically quantify similarities and differences between tumor material when detailed genetic and molecular profiles are available. The comparisons can be flexibly tailored to a particular biological question by placing a higher weight on functional alterations of interest (weighted similarity). In a first pan-cancer application, we have compared 260 cell lines from the Cancer Cell Line Encyclopaedia (CCLE) and 1914 tumors of six different cancer types from The Cancer Genome Atlas (TCGA), using weights to emphasize genomic alterations that frequently recur in tumors. We report the potential suitability of particular cell lines as tumor models and identify apparently unsuitable outlier cell lines, some of which are in wide use, for each of the six cancer types. In future, this weighted similarity method may be generalized for use in a clinical setting to compare patient profiles consisting of genomic patterns combined with clinical attributes, such as diagnosis, treatment and response to therapy.

Guide for Selection of Relevant Cell Lines During the Evaluation of new Anti-Cancer Compounds

2018 ◽  
Vol 18 (8) ◽  
pp. 1072-1081
Author(s):  
Angel J. Ruiz-Moreno ◽  
Patricia Torres-Barrera ◽  
Mireya Velázquez-Paniagua ◽  
Alexander Dömling ◽  
Marco A. Velasco-Velázquez
Keyword(s):  
Cell Line ◽  
Cell Lines ◽  
Cancer Cell ◽  
Cancer Cell Line ◽  
Cancer Cell Lines ◽  
Activity Analysis ◽  
Anti Cancer ◽  
Line Selection ◽  
Cell Line Selection ◽  
Selection Of

Background: Human cancer cell lines are valuable models for anti-cancer drug development. Although all cancer cells share common biological features, each cancer cell line has unique genotypic/ phenotypic characteristics that affect drug response. Thus, the information obtained with a specific cancer cell line cannot be easily extrapolated to other cancer cells. Consequently, cell line selection during experimental design is critical for providing proper and clinically relevant structure-activity analysis. Methods: Herein, we critically review the use of cancer cell lines as tools for activity analysis by comparing two different scenarios: i) the use of multiple cancer cell lines, with the NCI-60 Program as the most representative example; and, ii) the selection of a single cell line with specific biological characteristics that match the rationale of compound design. Results: Considering that most laboratories evaluate the activity of new compounds using few cell lines, we provide a systematic strategy for selection based on the expression levels and genetic status of the target and the effectiveness of target inhibition or silencing. We exemplify the use of public databases for data retrieval and analysis as well as the critical comparison of such information with published results. Conclusion: This approach refines cell line selection, avoiding the perpetuation of published poor selection and enhancing the relevance of the results.

scholarly journals Design, Synthesis and Anticancer activity of novel Triazole substituted Quinazoline Hybrids

2020 ◽  
Vol 11 (3) ◽  
pp. 3569-3579
Author(s):  
Paduri Karunakar ◽  
Swetha Gujjewar ◽  
Somesh Sharma ◽  
Srinivasu Pothukanuri ◽  
Krubakaran Muthusamy ◽  
...  
Keyword(s):  
Anticancer Activity ◽  
Cell Lines ◽  
Cancer Cell ◽  
Biological Activities ◽  
Cancer Cell Line ◽  
Cancer Cell Lines ◽  
Breast Cancer Cell Lines ◽  
Liver Carcinoma ◽  
Synthetic Approach

Quinazolines and 1,2,4-triazoles are important class of nitrogen containing heterocyclic compounds having immense biological importance. From the literature review, pharmacokinetic properties of a drug can be modified or enhanced by building a triazole moiety into a compound like quinazoline. Therefore, the study of new hybrid systems which combines triazole system with quinazoline is still seemed warranted. In the present study, a sequence of novel 1,2,4-triazole derivatives containing quinazolinyl moiety were designed, synthesized and screened for their in vitro anticancer activity. Thirteen new hybrids are synthesized from readily accessible 5-bromoanthranilic acid. All the hybrid compounds were well explicated by IR, 1H, 13C NMR, and mass spectral data. Out of 13, some of the compounds manifested moderate to good antiproliferative activity against two cancer cell lines (HepG2 and MCF7). Remarkably, compounds 8A, 16H and 16K displayed potent activity (14- 49 µM) on both HepG2 (liver carcinoma) and MCF-7 (breast cancer) cell lines whereas compounds 8B, 8F, 16L, and 15 displayed substantial activity against HepG2 cancer cell line (34-65 µM). Synthetic approach described here is very simple and can be used for the syntheses of related compounds library which is useful for the exploration of further biological activities and is currently underway in our laboratory

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