scholarly journals Innate responses to gene knockouts impact overlapping gene networks and vary with respect to resistance to viral infection

2018 ◽  
Vol 115 (14) ◽  
pp. E3230-E3237 ◽  
Author(s):  
Yonghong Liu ◽  
Yuanyuan Liu ◽  
Jiaming Wu ◽  
Bernard Roizman ◽  
Grace Guoying Zhou
Keyword(s):  
Cell Lines ◽  
Gene Networks ◽  
Single Gene ◽  
Parental Cell ◽  
Parental Cell Line ◽  
Gene Encoding ◽  
Overlapping Gene ◽  
Gene Knockouts ◽  
Cluster 2 ◽  
Hsv 1

Analyses of the levels of mRNAs encoding IFIT1, IFI16, RIG-1, MDA5, CXCL10, LGP2, PUM1, LSD1, STING, and IFNβ in cell lines from which the gene encoding LGP2, LSD1, PML, HDAC4, IFI16, PUM1, STING, MDA5, IRF3, or HDAC 1 had been knocked out, as well as the ability of these cell lines to support the replication of HSV-1, revealed the following: (i) Cell lines lacking the gene encoding LGP2, PML, or HDAC4 (cluster 1) exhibited increased levels of expression of partially overlapping gene networks. Concurrently, these cell lines produced from 5 fold to 12 fold lower yields of HSV-1 than the parental cells. (ii) Cell lines lacking the genes encoding STING, LSD1, MDA5, IRF3, or HDAC 1 (cluster 2) exhibited decreased levels of mRNAs of partially overlapping gene networks. Concurrently, these cell lines produced virus yields that did not differ from those produced by the parental cell line. The genes up-regulated in cell lines forming cluster 1, overlapped in part with genes down-regulated in cluster 2. The key conclusions are that gene knockouts and subsequent selection for growth causes changes in expression of multiple genes, and hence the phenotype of the cell lines cannot be ascribed to a single gene; the patterns of gene expression may be shared by multiple knockouts; and the enhanced immunity to viral replication by cluster 1 knockout cell lines but not by cluster 2 cell lines suggests that in parental cells, the expression of innate resistance to infection is specifically repressed.

The Cisplatin, 5-fluorouracil, Irinotecan, and Gemcitabine Treatment in Resistant 2D and 3D Model Triple Negative Breast Cancer Cell Line: ABCG2 Expression Data

2021 ◽  
Vol 21 ◽  
Author(s):  
Fatma Kubra Ata ◽  
Serap Yalcin
Keyword(s):  
Breast Cancer ◽  
Cell Culture ◽  
Cell Line ◽  
Cell Lines ◽  
Expression Profile ◽  
Three Dimensional ◽  
Parental Cell ◽  
Parental Cell Line ◽  
Xtt Assay ◽  
Gene And Protein Expression

Background: Chemotherapeutics have been commonly used in cancer treatment. Objective: In this study, the effects of Cisplatin, 5-fluorouracil, Irinotecan, and Gemcitabine have been evaluated on two-dimensional (2D) (sensitive and resistance) cell lines and three dimensional (3D) spheroid structure of MDA-MB-231. The 2D cell culture lacks a natural tissue-like structural so, using 3D cell culture has an important role in the development of effective drug testing models. Furthermore, we analyzed the ATP Binding Cassette Subfamily G Member 2 (ABCG2) gene and protein expression profile in this study. We aimed to establish a 3D breast cancer model that can mimic the in vivo 3D breast cancer microenvironment. Methods: The 3D spheroid structures were multiplied (globally) using the three-dimensional hanging drop method. The cultures of the parental cell line MDA-MB-231 served as the controls. After adding the drugs in different amounts we observed a clear and well-differentiated spheroid formation for 24 h. The viability and proliferation capacity of 2D (sensitive and resistant) cell lines and 3D spheroid cell treatment were assessed by the XTT assay. Results: Cisplatin, Irinotecan, 5-Fu, and Gemcitabine-resistant MDA-MB-231 cells were observed to begin to disintegrate in a three-dimensional clustered structure at 24 hours. Additionally, RT-PCR and protein assay showed overexpression of ABCG2 when compared to the parental cell line. Moreover, MDA-MB-231 cells grown in 3D showed decreased sensitivity to chemotherapeutics treatment. Conclusion: More resistance to chemotherapeutics and altered gene expression profile was shown in 3D cell cultures when compared with the 2D cells. These results might play an important role to evaluate the efficacy of anticancer drugs, explore mechanisms of MDR in the 3D spheroid forms.

scholarly journals cis Expression of DC-SIGN Allows for More Efficient Entry of Human and Simian Immunodeficiency Viruses via CD4 and a Coreceptor

2001 ◽  
Vol 75 (24) ◽  
pp. 12028-12038 ◽  
Author(s):  
Benhur Lee ◽  
George Leslie ◽  
Elizabeth Soilleux ◽  
Una O'Doherty ◽  
Sarah Baik ◽  
...  
Keyword(s):  
Cell Lines ◽  
Viral Entry ◽  
Parental Cell ◽  
Jurkat Cells ◽  
Target Cells ◽  
Parental Cell Line ◽  
Dependent Manner ◽  
Immunodeficiency Virus ◽  
T Cell Lines

ABSTRACT DC-SIGN is a C-type lectin expressed on dendritic cells and restricted macrophage populations in vivo that binds gp120 and acts intrans to enable efficient infection of T cells by human immunodeficiency virus type 1 (HIV-1). We report here that DC-SIGN, when expressed in cis with CD4 and coreceptors, allowed more efficient infection by both HIV and simian immunodeficiency virus (SIV) strains, although the extent varied from 2- to 40-fold, depending on the virus strain. Expression of DC-SIGN on target cells did not alleviate the requirement for CD4 or coreceptor for viral entry. Stable expression of DC-SIGN on multiple lymphoid lines enabled more efficient entry and replication of R5X4 and X4 viruses. Thus, 10- and 100-fold less 89.6 (R5/X4) and NL4–3 (X4), respectively, were required to achieve productive replication in DC-SIGN-transduced Jurkat cells when compared to the parental cell line. In addition, DC-SIGN expression on T-cell lines that express very low levels of CCR5 enabled entry and replication of R5 viruses in a CCR5-dependent manner, a property not exhibited by the parental cell lines. Therefore, DC-SIGN expression can boost virus infection in cis and can expand viral tropism without affecting coreceptor preference. In addition, coexpression of DC-SIGN enabled some viruses to use alternate coreceptors like STRL33 to infect cells, whereas in its absence, infection was not observed. Immunohistochemical and confocal microscopy data indicated that DC-SIGN was coexpressed and colocalized with CD4 and CCR5 on alveolar macrophages, underscoring the physiological significance of these cis enhancement effects.

A Novel Microarray Gene Expression Analysis of Murine AML Cell Lines Provides Clues to the Development of Drug Resistance to Ara-C

Blood ◽  
2008 ◽  
Vol 112 (11) ◽  
pp. 5017-5017
Author(s):  
Susan K Rathe ◽  
David Largaespada
Keyword(s):  
Gene Expression ◽  
Cell Line ◽  
Cell Lines ◽  
Ribosomal Subunit ◽  
Nuclear Factor Κb ◽  
Parental Cell ◽  
Parental Cell Line ◽  
Drug Resistant ◽  
Microarray Gene Expression ◽  
Expression Microarrays

Abstract Acute myeloid leukemia (AML) has the ability to evade cell death in the presence of chemotherapeutic cocktails containing cytosine arabinoside (Ara-C). This lab previously developed two highly resistant murine AML cell lines, B117H and B140H, by introducing increasing concentrations of Ara-C to their parental cell lines, B117P and B140P, respectively. B117H and B140H can tolerate Ara-C concentrations ~1000X that of their drug sensitive parental cell lines. mRNA from all four cell lines were used in gene expression microarrays for the purpose of comparing Ara-C drug resistant murine AML cell lines with their Ara-C drug sensitive parental lines. A novel algorithm was developed to evaluate the changes in gene expression between the drug resistant and drug sensitive cells. The algorithm differed from more conventional algorithms in two key ways. First, the detection data was normalized by using ribosomal subunit 9 (Rsp9) as the normalization gene, and secondly it calculated fold change by comparing the minimum value of one population to the maximum value of the other population. The output of this algorithm was a list of genes with significant gene expression changes. These genes were next submitted to the Ingenuity Pathway Analysis (IPA) process. IPA implicated nuclear factor-κB (NFκB) in the Ara-C resistance process. Cell growth assays confirmed that the Ara-C drug resistant B117H cell line was significantly more sensitive to NFκB inhibition than its Ara-C sensitive parental cell line. This leads us to believe that the selection of Ara-C resistance may also concomitantly make some AML cells highly sensitive to killing by NFκB inhibition. This theory is being tested further through the use of drug combination assays, to determine if a synergistic or antagonistic relationship exists between Ara-C and various drugs that affect the NFκB pathway.

scholarly journals Activation of the erythropoietin receptor by the Friend spleen focus- forming virus gp55 glycoprotein induces constitutive protein tyrosine phosphorylation

Blood ◽  
1992 ◽  
Vol 80 (12) ◽  
pp. 3070-3078 ◽  
Author(s):  
MO Showers ◽  
JF Moreau ◽  
D Linnekin ◽  
B Druker ◽  
AD D'Andrea
Keyword(s):  
Growth Factor ◽  
Tyrosine Kinase ◽  
Tyrosine Phosphorylation ◽  
Cell Lines ◽  
Kinase Activity ◽  
Parental Cell ◽  
Erythropoietin Receptor ◽  
Parental Cell Line ◽  
Tyrosine Kinase Activity ◽  
Murine Cell

The erythropoietin receptor (EPO-R) can be activated to signal cell growth by binding either EPO or gp55, the Friend spleen focus-forming virus (SFFV) glycoprotein. EPO binding induces tyrosine kinase activity and rapid tyrosine phosphorylation of several cellular substrates. To test for gp55-induced tyrosine kinase activity, we performed immunoblots on two murine cell lines that stably express EPO-R and gp55. Stimulation of the parental cell line, Ba/F3, with murine interleukin-3 (IL-3) resulted in rapid, dose-dependent tyrosine phosphorylation of a 97-Kd substrate. Stimulation with IL-3 or EPO of the Ba/F3 cells expressing the recombinant EPO-R (Ba/F3-EPO-R) resulted in tyrosine phosphorylation of the same p97 substrate. These latter cells, when transformed to growth factor-independence by the Friend gp55 glycoprotein, exhibited constitutive tyrosine phosphorylation of the 97-Kd substrate. Other growth factor-independent Ba/F3 subclones, transformed with either the oncoprotein, v-abl, or with a constitutively activated EPO-R, also had constitutive phosphorylation of a 97-Kd substrate. In CTLL-2-EPO-R cells, a T-lymphocyte line stably transfected with the EPO-R, the 97-Kd substrate was tyrosine- phosphorylated in response to IL-2 or EPO. The 97-Kd protein was constitutively phosphorylated in CTLL-2-EPO-R-gp55 cells. In conclusion, a 97-Kd protein found in two murine cell lines is tyrosine-phosphorylated in response to multiple growth factors and viral oncoproteins, and appears to be a central phosphoprotein in signal transduction.

scholarly journals Cytogenetic Evolution of Human Ovarian Cell Lines Associated with Chemoresistance and Loss of Tumorigenicity

2003 ◽  
Vol 25 (3) ◽  
pp. 115-122 ◽  
Author(s):  
Stéphanie Struski ◽  
Martine Doco‐Fenzy ◽  
Michael Koehler ◽  
Ilse Chudoba ◽  
Francis Levy ◽  
...  
Keyword(s):  
Cell Line ◽  
Cell Lines ◽  
Chromosomal Abnormalities ◽  
Parental Cell ◽  
Comparative Genomic ◽  
Parental Cell Line ◽  
Multicolor Fish ◽  
Ovarian Cell ◽  
Genomic Changes ◽  
Ovarian Cell Lines

In order to identify genomic changes associated with a resistant phenotype acquisition, we used comparative genomic hybridization (CGH) to compare a human ovarian cell line, Igrov1, and four derived subcell lines, resistant to vincristine and presenting a reversion of malignant properties. Multicolor FISH (Multiplex‐FISH and Spectral Karyotype) and conventional FISH are also used to elucidate the karyotype of parental cell line. The drug‐resistant subcell lines displayed many chromosomal abnormalities suggesting the implication of different pathways leading to a multidrug resistance phenotype. However, these cell lines shared two common rearrangements: an unbalanced translocation der(8)t(8;13)(p22;q?) and a deletion of the 11p. These chromosomal imbalances could reflected the acquisition of the chemoresistance (der(8)) or the loss of tumorigenicity properties (del(11p)). Colour figure can be viewed onhttp://www.esacp.org/acp/2003/25‐3/struski.htm.

scholarly journals Certain changes in ornithine decarboxylase gene methylation accompany gene amplification

1991 ◽  
Vol 279 (2) ◽  
pp. 435-440 ◽  
Author(s):  
J Wahlfors
Keyword(s):  
Cell Line ◽  
Cell Lines ◽  
Gene Amplification ◽  
Ornithine Decarboxylase ◽  
Myeloma Cell ◽  
Parental Cell ◽  
Resistant Cell ◽  
Methylation Pattern ◽  
Parental Cell Line ◽  
Flanking Region

The ornithine decarboxylase (ODC; EC 4.1.1.17) gene in parental, dexamethasone-resistant and 2-difluoromethylornithine (DFMO)-resistant human IgG-myeloma-cell lines was studied with the aid of methylation-sensitive restriction endonucleases and probes recognizing different parts of the gene. In all cell lines the promoter region of the ODC gene appeared to be heavily methylated, whereas the first long intron was unmethylated. Methylation analyses of several clones from the parental cell line revealed that these cells are heterogeneous with respect to the methylation status of the ODC gene, whereas all clones from DFMO-resistant cell lines displayed the same methylation pattern. Two of the parental clones represented a hypomethylated type very close to that exclusively found among the DFMO-resistant clones with ODC gene amplification. This typical methylation pattern was due to decreased methylation of a few CCGG sequences in the 3′-flanking region of the gene. It is possible that this kind of hypomethylation favours the initiation of the gene-amplification process in certain individual cells. This hypothesis was supported by the finding that no hypomethylation was present in the ODC gene of another human myeloma cell line that had acquired resistance to DFMO without gene amplification. In a dexamethasone-resistant cell line that overproduced ODC mRNA at normal gene dosage there were some minor differences between the methylation pattern of the ODC gene of different clones, but no such hypomethylation could be found in clones from the parental cell line. In dexamethasone-resistant cells the ODC gene was hypomethylated around the two HpaII sites and three CfoI sites in the coding region and also, as well as in cells with amplified ODC sequences, in the 3′-flanking region of the gene. Some hypomethylation in the distant 5′-flanking region was also observed.

scholarly journals Targeting of Deregulated Wnt/β-Catenin Signaling by PRI-724 and LGK974 Inhibitors in Germ Cell Tumor Cell Lines

2021 ◽  
Vol 22 (8) ◽  
pp. 4263
Author(s):  
Silvia Schmidtova ◽  
Katarina Kalavska ◽  
Veronika Liskova ◽  
Jana Plava ◽  
Svetlana Miklikova ◽  
...  
Keyword(s):  
Germ Cell ◽  
Cell Line ◽  
Cell Lines ◽  
Treatment Options ◽  
Germ Cell Tumors ◽  
Parental Cell ◽  
Parental Cell Line ◽  
Testicular Germ Cell ◽  
Apoptotic Effect ◽  
Pathway Inhibition

The majority of patients with testicular germ cell tumors (GCTs) can be cured with cisplatin-based chemotherapy. However, for a subset of patients present with cisplatin-refractory disease, which confers a poor prognosis, the treatment options are limited. Novel therapies are therefore urgently needed to improve outcomes in this challenging patient population. It has previously been shown that Wnt/β-catenin signaling is active in GCTs suggesting that its inhibitors LGK974 and PRI-724 may show promise in the management of cisplatin-refractory GCTs. We herein investigated whether LGK-974 and PRI-724 provide a treatment effect in cisplatin-resistant GCT cell lines. Taking a genoproteomic approach and utilizing xenograft models we found the increased level of β-catenin in 2 of 4 cisplatin-resistant (CisR) cell lines (TCam-2 CisR and NCCIT CisR) and the decreased level of β-catenin and cyclin D1 in cisplatin-resistant NTERA-2 CisR cell line. While the effect of treatment with LGK974 was limited or none, the NTERA-2 CisR exhibited the increased sensitivity to PRI-724 in comparison with parental cell line. Furthermore, the pro-apoptotic effect of PRI-724 was documented in all cell lines. Our data strongly suggests that a Wnt/β-catenin signaling is altered in cisplatin-resistant GCT cell lines and the inhibition with PRI-724 is effective in NTERA-2 CisR cells. Further evaluation of Wnt/β-catenin pathway inhibition in GCTs is therefore warranted.

scholarly journals Activation of the erythropoietin receptor by the Friend spleen focus- forming virus gp55 glycoprotein induces constitutive protein tyrosine phosphorylation

Blood ◽  
1992 ◽  
Vol 80 (12) ◽  
pp. 3070-3078 ◽  
Author(s):  
MO Showers ◽  
JF Moreau ◽  
D Linnekin ◽  
B Druker ◽  
AD D'Andrea
Keyword(s):  
Growth Factor ◽  
Tyrosine Kinase ◽  
Tyrosine Phosphorylation ◽  
Cell Lines ◽  
Kinase Activity ◽  
Parental Cell ◽  
Erythropoietin Receptor ◽  
Parental Cell Line ◽  
Tyrosine Kinase Activity ◽  
Murine Cell

Abstract The erythropoietin receptor (EPO-R) can be activated to signal cell growth by binding either EPO or gp55, the Friend spleen focus-forming virus (SFFV) glycoprotein. EPO binding induces tyrosine kinase activity and rapid tyrosine phosphorylation of several cellular substrates. To test for gp55-induced tyrosine kinase activity, we performed immunoblots on two murine cell lines that stably express EPO-R and gp55. Stimulation of the parental cell line, Ba/F3, with murine interleukin-3 (IL-3) resulted in rapid, dose-dependent tyrosine phosphorylation of a 97-Kd substrate. Stimulation with IL-3 or EPO of the Ba/F3 cells expressing the recombinant EPO-R (Ba/F3-EPO-R) resulted in tyrosine phosphorylation of the same p97 substrate. These latter cells, when transformed to growth factor-independence by the Friend gp55 glycoprotein, exhibited constitutive tyrosine phosphorylation of the 97-Kd substrate. Other growth factor-independent Ba/F3 subclones, transformed with either the oncoprotein, v-abl, or with a constitutively activated EPO-R, also had constitutive phosphorylation of a 97-Kd substrate. In CTLL-2-EPO-R cells, a T-lymphocyte line stably transfected with the EPO-R, the 97-Kd substrate was tyrosine- phosphorylated in response to IL-2 or EPO. The 97-Kd protein was constitutively phosphorylated in CTLL-2-EPO-R-gp55 cells. In conclusion, a 97-Kd protein found in two murine cell lines is tyrosine-phosphorylated in response to multiple growth factors and viral oncoproteins, and appears to be a central phosphoprotein in signal transduction.

scholarly journals Integration of Time-Series Transcriptomic Data with Genome-Scale CHO Metabolic Models for mAb Engineering

Processes ◽  
2020 ◽  
Vol 8 (3) ◽  
pp. 331 ◽  
Author(s):  
Zhuangrong Huang ◽  
Seongkyu Yoon
Keyword(s):  
Cell Lines ◽  
Chinese Hamster ◽  
Parental Cell ◽  
Process Conditions ◽  
Parental Cell Line ◽  
Specific Cell ◽  
Scale Models ◽  
Metabolic Models ◽  
Genome Scale ◽  
The Impact

Chinese hamster ovary (CHO) cells are the most commonly used cell lines in biopharmaceutical manufacturing. Genome-scale metabolic models have become a valuable tool to study cellular metabolism. Despite the presence of reference global genome-scale CHO model, context-specific metabolic models may still be required for specific cell lines (for example, CHO-K1, CHO-S, and CHO-DG44), and for specific process conditions. Many integration algorithms have been available to reconstruct specific genome-scale models. These methods are mainly based on integrating omics data (i.e., transcriptomics, proteomics, and metabolomics) into reference genome-scale models. In the present study, we aimed to investigate the impact of time points of transcriptomics integration on the genome-scale CHO model by assessing the prediction of growth rates with each reconstructed model. We also evaluated the feasibility of applying extracted models to different cell lines (generated from the same parental cell line). Our findings illustrate that gene expression at various stages of culture slightly impacts the reconstructed models. However, the prediction capability is robust enough on cell growth prediction not only across different growth phases but also in expansion to other cell lines.

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