scholarly journals Multi-modal meta-analysis of cancer cell line omics profiles identifies ECHDC1 as a novel breast tumor suppressor

2020 ◽  
Author(s):  
Alok Jaiswal ◽  
Prson Gautam ◽  
Elina A Pietilä ◽  
Sanna Timonen ◽  
Nora Nordström ◽  
...  
Keyword(s):  
Data Integration ◽  
Cell Line ◽  
Cell Lines ◽  
Cancer Cell ◽  
Meta Analysis ◽  
Cancer Cell Line ◽  
Cancer Cell Lines ◽  
Driver Gene ◽  
List Type ◽  
Rna Helicases

AbstractA caveat of cancer cell line models is that their molecular and functional profiling is subject to laboratory-specific experimental practices and data analysis protocols. The current challenge is how to make an integrated use of omics profiles of cancer cell lines for reliable discoveries. Here, we carried out a systematic analysis of nine types of data modalities using meta-analysis of 53 omics profiling studies across 12 research laboratories for 2018 cell lines. To account for relatively low consistency observed for certain data modalities, we developed a robust data integration approach that identifies reproducible signals shared among multiple data modalities and studies. We demonstrated the power of the integrative analyses by identifying a novel driver gene, ECHDC1, with tumor suppressive role validated both in breast cancer cells and patient tumors. Extension of the approach identified synthetic lethal partners of cancer drivers, including a co-dependency of PTEN deficient cells on RNA helicases.HighlightsA comprehensive meta-analysis of 53 multi-modal omics profiles of >2000 cancer cell lines from 12 research laboratoriesAn unexpected lack of consistency between TMT-labelled and non-labelled global proteomic profilesA non-parametric approach to integrate omics profiles from multiple laboratories and to identify robust molecular patterns in individual cell linesThe multi-modal data integration reveals novel drivers and potential therapeutic targets, including ECHDC1 in breast cancers and DDX27 in PTEN mutant cancers.

Synthesis, Anticancer Activity on Prostate Cancer Cell Lines and Molecular Modeling Studies of Flurbiprofen-Thioether Derivatives as Potential Target of MetAP (Type II)

2020 ◽  
Vol 16 (6) ◽  
pp. 735-749 ◽  
Author(s):  
Özgür Yılmaz ◽  
Burak Bayer ◽  
Hatice Bekçi ◽  
Abdullahi I. Uba ◽  
Ahmet Cumaoğlu ◽  
...  
Keyword(s):  
Prostate Cancer ◽  
Molecular Modeling ◽  
Cell Line ◽  
Cell Lines ◽  
Cancer Cell ◽  
Prostate Cancer Cell ◽  
Cancer Cell Line ◽  
Cancer Cell Lines ◽  
Prostate Cancer Cell Lines ◽  
Molecular Modeling Studies

Background:: Prostate cancer is still one of the serious causes of mortality and morbidity in men. Despite recent advances in anticancer therapy, there is a still need of novel agents with more efficacy and specificity in the treatment of prostate cancer. Because of its function on angiogenesis and overexpression in the prostate cancer, methionine aminopeptidase-2 (MetAP-2) has been a potential target for novel drug design recently. Objective:: A novel series of Flurbiprofen derivatives N-(substituted)-2-(2-(2-fluoro-[1,1'- biphenyl]-4-il)propanoyl)hydrazinocarbothioamide (3a-c), 4-substituted-3-(1-(2-fluoro-[1,1'-biphenyl]- 4-yl)ethyl)-1H-1,2,4-triazole-5(4H)-thione (4a-d), 3-(substitutedthio)-4-(substituted-phenyl)- 5-(1-(2-fluoro-[1,1'-biphenyl]-4-yl)ethyl)-4H-1,2,4-triazole (5a-y) were synthesized. The purpose of the research was to evaluate these derivatives against MetAP-2 in vitro and in silico to obtain novel specific and effective anticancer agents against prostate cancer. Methods: The chemical structures and purities of the compounds were defined by spectral methods (1H-NMR, 13C-NMR, HR-MS and FT-IR) and elemental analysis. Anticancer activities of the compounds were evaluated in vitro by using MTS method against PC-3 and DU-143 (androgenindependent human prostate cancer cell lines) and LNCaP (androgen-sensitive human prostate adenocarcinoma) prostate cancer cell lines. Cisplatin was used as a positive sensitivity reference standard. Results:: Compounds 5b and 5u; 3c, 5b and 5y; 4d and 5o showed the most potent biological activity against PC3 cancer cell line (IC50= 27.1 μM, and 5.12 μM, respectively), DU-145 cancer cell line (IC50= 11.55 μM, 6.9 μM and 9.54 μM, respectively) and LNCaP cancer cell line (IC50= 11.45 μM and 26.91 μM, respectively). Some compounds were evaluated for their apoptotic caspases protein expression (EGFR/PI3K/AKT pathway) by Western blot analysis in androgen independent- PC3 cells. BAX, caspase 9, caspsase 3 and anti-apoptotic BcL-2 mRNA levels of some compounds were also investigated. In addition, molecular modeling studies of the compounds on MetAP-2 enzyme active site were evaluated in order to get insight into binding mode and energy. Conclusion:: A series of Flurbiprofen-thioether derivatives were synthesized. This study presented that some of the synthesized compounds have remarkable anticancer and apoptotic activities against prostate cancer cells. Also, molecular modeling studies exhibited that there is a correlation between molecular modeling and anticancer activity results.

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.

Effect of the Method of Preparation on the Composition and Cytotoxic Activity of the Essential Oil of Pituranthos tortuosus

2011 ◽  
Vol 66 (3-4) ◽  
pp. 143-148 ◽  
Author(s):  
Hossam M. Abdallah ◽  
Shahira M. Ezzat
Keyword(s):  
Breast Cancer ◽  
Essential Oil ◽  
Cell Line ◽  
Cell Lines ◽  
Cancer Cell ◽  
Human Cancer ◽  
Cancer Cell Line ◽  
Cancer Cell Lines ◽  
Human Cancer Cell ◽  
Human Cancer Cell Lines

The aerial parts of Pituranthos tortuosus (Desf.) Benth and Hook (Apiaceae), growing wild in Egypt, yielded 0.8%, 0.6%, and 1.5% (v/w) of essential oil when prepared by hydrodistillation (HD), simultaneous hydrodistillation-solvent (n-pentane) extraction (Lickens- Nickerson, DE), and conventional volatile solvent extraction (preparation of the “absolute”, SE), respectively. GC-MS analysis showed that the major components in the HD sample were β-myrcene (18.81%), sabinene (18.49%), trans-iso-elemicin (12.90%), and terpinen- 4-ol (8.09%); those predominent in the DE sample were terpinen-4-ol (29.65%), sabinene (7.38%), γ-terpinene (7.27%), and β-myrcene (5.53%); while the prominent ones in the SE sample were terpinen-4-ol (15.40%), dill apiol (7.90%), and allo-ocimene (4E,6Z) (6.00%). The oil prepared in each case was tested for its cytotoxic activity on three human cancer cell lines, i.e. liver cancer cell line (HEPG2), colon cancer cell line (HCT116), and breast cancer cell line (MCF7). The DE sample showed the most potent activity against the three human cancer cell lines (with IC50 values of 1.67, 1.34, and 3.38 μg/ml against the liver, colon, and breast cancer cell lines, respectively). Terpinen-4-ol, sabinene, γ-terpinene, and β-myrcene were isolated from the DE sample and subjected to a similar evaluation of cytotoxic potency; signifi cant activity was observed

Evaluation of the performance of breast cancer cell line–derived multigene predictors of chemotherapy response in multiple clinical trials.

2011 ◽  
Vol 29 (27_suppl) ◽  
pp. 64-64
Author(s):  
N. Song ◽  
S. D. Rice ◽  
D. Gingrich ◽  
D. Wang ◽  
C. Tian ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Clinical Trials ◽  
Cell Line ◽  
Cell Lines ◽  
Cancer Cell ◽  
Breast Cancer Cell ◽  
Breast Cancer Cell Line ◽  
Cancer Cell Line ◽  
Cancer Cell Lines ◽  
Chemotherapy Response

64 Background: While various multi-gene predictors (MGPs) of chemotherapy response have been developed based on cancer patient primary tissues or cancer cell-lines, the accuracy and consistency of these predictors remain a concern in clinical validation studies. In this study we developed four unique MGPs for chemotherapy response from breast cancer cell lines and performed a systematic evaluation of the performance of these MGPs using data from five distinct clinical trials. Methods: Forty-six immortalized breast cancer cell-lines were exposed to various concentrations of drug combinations [paclitaxel, 5-fluorouracil, doxorubicin, cyclophosphamide (TFAC); 5-fluorouracil, doxorubicin, cyclophosphamide (FAC); 5-fluorouracil, epirubicin, cyclophosphamide (FEC) and epirubicin, cyclophosphamide (EC)] using an in vitro chemosensitivity assay. Utilizing publicly available breast cancer cell-line microarray data, genes highly associated with in vitro chemosensitivity were selected as candidate MGPs. Five independent and publicly available clinical trials were used for validation. In three of these clinical trials patients were treated by TFAC, while EC, FAC or FEC were used in the other two trials. All five studies involved neoadjuvant chemotherapy treatment, and pathologic complete response (pCR) was used as the endpoint. The association of MGPs with pCR was assessed using receiver-operator curve (ROC) analysis and area under the ROC (AUC) was used to evaluate the performance of prediction. Results: In five independent clinical trials, the MGPs predicted patient pCR to EC, FAC/FEC and three TFAC treatments with an AUC of, 0.671, 0.632, 0.735, 0.738 and 0.647 respectively. Conclusions: In the five independent clinical trials in which patients were treated by various chemotherapy agents, the performance of MGPs is promising. These results demonstrate the feasibility of using breast cancer cell-line derived MGPs to predict breast cancer patients’ chemotherapy responses.

Meta-analysis of cancer cell lines genomes based on their response to ttfields.

2013 ◽  
Vol 31 (15_suppl) ◽  
pp. e22125-e22125
Author(s):  
Moshe Giladi ◽  
Yoram Wasserman ◽  
Rosa S. Schneiderman ◽  
Yaara Porat ◽  
Mijal Munster ◽  
...  
Keyword(s):  
Cell Lines ◽  
Cancer Cell ◽  
Protein Tyrosine Kinase ◽  
Meta Analysis ◽  
Cancer Cell Line ◽  
High Sensitivity ◽  
Cancer Cell Lines ◽  
Negative Regulation ◽  
Microtubule Assembly ◽  
Tissue Samples

e22125 Background: Tumor Treating Fields (TTFields) therapy is an established anti-mitotic treatment modality. The inhibitory effect of TTFields was demonstrated in numerous cancer cell lines with some cell lines exhibiting higher treatment sensitivity than others. The goal of the present study is to compare genomic characteristics of cell lines based on their response pattern to TTFields. Methods: Fifteen different human cancerous cell lines were treated using TTFields at their optimal frequency with the same nominal intensity (1.8 V/cm). The distribution of the response to TTFields was found to be bimodal with inhibitions of 30-40% and 50-60% compared to controls. Cell lines were divided into regular and high sensitivity groups according to their response to TTFields. Both groups were characterized based upon the distribution of mutated genes using the Cancer Cell Line Encyclopedia (CCLE) database. Results: Based on the distribution of mutated genes we identified 1 gene with significantly higher probability (P=0.017) to be present in the regular than the high sensitivity group. This gene (NEK3) is a never-in-mitosis (NIMA) related kinase 3 responsible for deacetylation of microtubules. In addition, 2 genes were found with significantly higher probability (P<0.05) to be present in the high- than the regular sensitivity group; ASPH, an aspartate beta-hydroxylase involved in negative regulation of cell proliferation through modulation of calcium homeostasis and TEC, a protein tyrosine kinase involved in immunological signaling pathways. Conclusions: The possible involvement of NEK3 mutations in determining sensitivity to TTFields is interesting in view of the known interference of TTFields with spindle microtubule assembly. ASPH mutations could release cells from negative regulation of proliferation, increasing their replication rate, and thus increasing their sensitivity to TTFields. In order to further test this hypothesis, a comparison of the effect of TTFields needs to be performed on wild type and knockout cell lines for these genes. A comparison of the mutation of these genes in tissue samples from patients whose tumors show high sensitivity to TTFields, may lead to a personalized approach to the use of TTFields clinically.

The estrogenic hormone effect in gastric cancer.

2018 ◽  
Vol 36 (4_suppl) ◽  
pp. 85-85
Author(s):  
Youjin Jang ◽  
Youjae Mok
Keyword(s):  
Gastric Cancer ◽  
Cell Line ◽  
Cell Lines ◽  
Cancer Cell ◽  
Treatment Effect ◽  
Cancer Cell Line ◽  
Cancer Cell Lines ◽  
High Expression ◽  
Lauren Classification ◽  
Laurén Classification

85 Background: Estrogen receptors (ERs) are steroid hormone receptors that regulate cellular activities in many physiological and pathological processes in different tissues. A few of studies have examined the expression of ER in gastric cancer. However, considerable controversy is raised as to the expression level of ER and its prognostic value in gastric cancer. In the present study, the expression profile of ERα, ERβ was determined in gastric cancer cell lines according Lauren classification and evaluate that the treatment effect of selective estrogen receptor modulator. Methods: Using four cell lines established from human gastric carcinomas according Lauren classification, check endogenous ERα, ERβ expression levels with RT-PCR. The SERM treatment effect were detected MTT test. Using immunohistochemical detection, the present study analyzed the clinical relevance of ERα, ERβ expression in tumor cells in 197 patients who underwent curative radical surgery and who were observed on long-term follow-up. Results: Endogenous ERα was high expression not intestinal cancer cell lines but in diffuse cancer cell line. Endogenous ERβ was high expression both type cancer cell line than normal gastrointestinal cell lines. According MTT assay, only raloxifene among SERM was significant treatment effect. In immonohistochemial study of gastric tissue, ERα negative and ERβ positive was associated with good prognosis. Conclusions: ERβ may be partly involved in gastric carcinogenesis and ERβ antagonist might be new therapeutic drug for gastric cancer.

scholarly journals Defective internalization of low density lipoprotein in epidermoid cervical cancer cells.

1982 ◽  
Vol 92 (3) ◽  
pp. 597-603 ◽  
Author(s):  
D Gal ◽  
E R Simpson ◽  
J C Porter ◽  
J M Snyder
Keyword(s):  
Cell Line ◽  
Cell Lines ◽  
Cancer Cell ◽  
Low Density Lipoprotein ◽  
Density Lipoprotein ◽  
Cancer Cell Line ◽  
Cancer Cell Lines ◽  
Low Density ◽  
Specific Receptor ◽  
Cervical Cancer Cells

Cells of an epidermoid cancer cell line of human uterine cervix, which possessed a high-affinity, specific receptor for low density lipoprotein (LDL), internalized and degraded [125I]iodo-LDL at a very low rate. In these cells, LDL did not stimulate cholesteryl ester synthesis, nor did it suppress 3-hydroxy-3-methylglutaryl coenzyme A reductase to the same extent as in the control cells. The binding of [125I]iodo-LDL by these cells was not decreased by preincubation of the cells in medium containing LDL. Using ferritin-labeled LDL (F-LDL) and electron microscopy, it was determined that at 4 degrees C the cells bound F-LDL in the same way as other cancer cell lines that did not have a defect in internalization. When these cells were warmed to 37 degrees C the F-LDL remained on the surface, whereas in cells from control cancer cell lines the F-LDL was internalized and was no longer observed on the cell surface. On the basis of the results of these studies it is concluded that cells of this epidermoid cancer cell line have a defective ability to internalize LDL.

scholarly journals Molecular profile to cancer cell line matchmaking

2021 ◽  
Author(s):  
Brendan Reardon ◽  
Eliezer Van Allen
Keyword(s):  
Cell Line ◽  
Cell Lines ◽  
Cancer Cell ◽  
Molecular Similarity ◽  
Cancer Cell Line ◽  
Cancer Cell Lines ◽  
Hypothesis Generation ◽  
Molecular Profile ◽  
Clinical Settings ◽  
Computational Protocol

Abstract Profile-to-cell line matchmaking is a computational protocol to identify cancer cell lines that are genomically similar to a patient’s case profile. In doing so, high-throughput drug screens applied to the same cancer cell lines may be used for therapeutic hypothesis generation in research settings and potentially in clinical settings. To evaluate the metrics of the matchmaking, a hold-one-out approach of the considered cancer cell lines is applied, and molecular similarity models are assessed based on their ability to identify cancer cell lines that share therapeutic sensitivity.

scholarly journals Recombinant deoxyribonucleoside kinase from Drosophila melanogaster can improve gemcitabine based combined gene/chemotherapy for targeting cancer cells

2019 ◽  
Author(s):  
Mahak Fatima ◽  
M. Mubasshar Iqbal Ahmed ◽  
Faiza Batool ◽  
Anjum Riaz ◽  
Moazzam Ali ◽  
...  
Keyword(s):  
Drosophila Melanogaster ◽  
Cancer Cells ◽  
Cell Line ◽  
Cell Lines ◽  
Cancer Cell ◽  
Cancer Cell Line ◽  
Nucleoside Analogs ◽  
Cancer Cell Lines ◽  
Control Group ◽  
Wide Range

A recombinant deoxyribonucleoside kinase from Drosophila melanogaster with a deletion of the last 20 amino acid residues (named DmdNKΔC20) was hypothesized as a potential therapeutic tool for gene therapy due to its broad substrate specificity and better catalytic efficiency towards nucleosides and nucleoside analogs. This study was designed to evaluate the effect of DmdNKΔC20 for sensitizing human cancer cell lines towards gemcitabine and to further investigate its role in reversal of acquired drug resistance in gemcitabine-resistant cancer cell line. The DmdNKΔC20 gene was delivered to three different cancer cell lines, including breast, colon and liver cancer cells, using lipid-mediated transfection reagent. After transfection, gene expression of DmdNKΔC20 was confirmed by reverse transcription quantitative PCR (qRT-PCR) and the combined effect of DmdNKΔC20 and gemcitabine based cytotoxicity was observed by cell viability assay. We further evolved a gemcitabine-resistant breast cancer cell line (named MCF7-R) through directed evolution in the laboratory, which showed 375-fold more resistance compared to parental MCF7 cells. Upon transfection with DmdNKΔC20 gene, MCF7-R cells showed 83-fold higher sensitivity to gemcitabine compared to the control group of MCF7-R cells. Moreover, we observed 79% higher expression of p21 protein in transfected MCF7-R cells, which may indicate induction of apoptosis. Our findings highlight the importance and therapeutic potential of DmdNKΔC20 in combined gene/chemotherapy approach to target a wide range of cancers, particularly gemcitabine-resistant cancers.

scholarly journals Biological network topology features predict gene dependencies in cancer cell lines

2019 ◽  
Author(s):  
Graeme Benstead-Hume ◽  
Sarah K. Wooller ◽  
Samantha Dias ◽  
Lisa Woodbine ◽  
Anthony M. Carr ◽  
...  
Keyword(s):  
Cell Line ◽  
Cell Lines ◽  
Cancer Cell ◽  
Individual Cell ◽  
Cancer Cell Line ◽  
Cancer Cell Lines ◽  
Genetic Alterations ◽  
Essential Genes ◽  
Loss Of Function ◽  
Ppi Network

AbstractIn this paper we explore computational approaches that enable us to identify genes that have become essential in individual cancer cell lines. Using recently published experimental cancer cell line gene essentiality data, human protein-protein interaction (PPI) network data and individual cell-line genomic alteration data we have built a range of machine learning classification models to predict cell line specific acquired essential genes. Genetic alterations found in each individual cell line were modelled by removing protein nodes to reflect loss of function mutations and changing the weights of edges in each PPI to reflect gain of function mutations and gene expression changes.We found that PPI networks can be used to successfully classify human cell line specific acquired essential genes within individual cell lines and between cell lines, even across tissue types with AUC ROC scores of between 0.75 and 0.85. Our novel perturbed PPI network models further improved prediction power compared to the base PPI model and are shown to be more sensitive to genes on which the cell becomes dependent as a result of other changes. These improvements offer opportunities for personalised therapy with each individual’s cancer cell dependencies presenting a potential tailored drug target.The overriding motivation for predicting cancer cell line specific acquired essential genes is to provide a low-cost approach to identifying personalised cancer drug targets without the cost of exhaustive loss of function screening.

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