Expression Levels in Various Cell Lines of Natural Antisense Transcripts

SummaryWe have worked out an efficient and time saving procedure for the expression of recombinant human prothrombin. The glycoprotein was expressed in the vaccinia virus expression system in several mammalian cell lines. The kidney cell lines Vero and BHK and the human cell line Hela were found to efficiently secrete prothrombin. Expression levels of 3–4 µg of factor II per 106 cells per day corresponding to 18–23 mU per 106 cells per day were achieved. Since the expression levels obtained with the vaccinia virus/Vero cell system were comparable to those obtained in amplified transformed CHO cells it provides an alternative system for the efficient expression of human prothrombin and may allow to further elucidate structure-function relationships of (pro)thrombin and its various effectors.

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The expression of the GATA6 gene in oral carcinoma cell lines

World Journal of Surgical Oncology ◽

10.1186/s12957-021-02245-y ◽

2021 ◽

Vol 19 (1) ◽

Author(s):

Cheng-Lin Xu ◽

Wei-Qun Guan ◽

Xue-Ying Wang

Keyword(s):

Cell Lines ◽

Carcinoma Cell ◽

Carcinoma Cells ◽

Expression Levels ◽

Carcinoma Cell Lines ◽

Human Tongue ◽

Adenoid Cystic ◽

Significant Difference ◽

Oral Epithelial ◽

Gata6 Gene

Abstract Background This study aimed to investigate the expression level of the GATA6 gene in different oral cancer cells. Methods In this study, we sub-cultured normal oral epithelial cell lines HOK, human tongue squamous cell carcinoma cell lines CAL-27 and SCC-4, and human salivary gland adenoid cystic carcinoma cell lines SACC-LM and SACC-83. Subsequently, we used reverse transcription-polymerase chain reaction RT-PCR and Western blot methods to detect the mRNA and the protein expressions of GATA6 in normal oral epithelial cells, human tongue squamous cell carcinoma cells, and human salivary gland adenoid cystic carcinoma cells. Results The results of this study showed that the mRNA expression levels of GATA6 in CAL-27, SCC-4, and SACC-LM cells were significantly increased when compared with the HOK cells. However, the mRNA expression level of GATA6 in the SACC-83 cells had no significant difference compared with the HOK cells. The protein expression levels of GATA6 in the SCC-4 and SACC-LM cells were, however, significantly increased whereas the protein expression levels of GATA6 in the CAL-27 and SACC-83 cells had no significant difference when compared with the HOK cells. Conclusion The GATA6 gene may be related to the occurrence and progression of certain oral cancers.

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Phytochemical Analysis, Antioxidant and Anticancer Potential of Sideritis niveotomentosa: Endemic Wild Species of Turkey

Molecules ◽

10.3390/molecules26092420 ◽

2021 ◽

Vol 26 (9) ◽

pp. 2420

Author(s):

Ela Nur Şimşek Şimşek Sezer ◽

Tuna Uysal

Keyword(s):

Cell Lines ◽

Phenolic Content ◽

Radical Scavenging ◽

Total Phenolic ◽

Phytochemical Analysis ◽

Expression Levels ◽

Phenolic Contents ◽

Scavenging Effect ◽

Methanolic Extracts ◽

Total Antioxidant

Sideritis niveotomentosa Hub. -Mor. is a local endemic species belonging to the Lamiaceae family. In this study, GC/MS analysis, total antioxidant capacity and anticancer effects of different extracts obtained from S. niveotomentosa were investigated comparatively. Total phenolic contents of extracts were determined by the Folin–Ciocalteu method, total flavonoid contents by aluminum chloride method, and also the free radical scavenging activities of the extracts by DPPH (2,2-diphenyl-1-picryl-hydrazyl-hydrate) assay. The cytotoxic effect of the extracts was studied via MTT (3-(4,5-Dimethylthiazol-2-yl)-2,5-Diphenyltetrazolium Bromide) assay on DLD1, HL60 and ARH77 cell lines. Pro-apoptotic gene expression levels were also tested in the most sensitive cell line ARH77 by Real-Time PCR. The expression levels of 4 pro-apoptotic genes, APAF, BAX, CASP3, and HRK were found to be upregulated in ARH77 cells that were treated extracts. Results showed that methanolic extracts contain more phenolic content than acetone extracts, consistent with DPPH results. As a result, Sideritis niveotomentosa extracts, especially methanolic extracts, are rich in phenolic content and have a strong radical scavenging effect. In addition, the extracts showed selective effects on cell lines. This study is pioneering in terms of future studies, and the findings provide hope for future experimentation.

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Natural Antisense Transcripts at the Interface between Host Genome and Mobile Genetic Elements

Frontiers in Microbiology ◽

10.3389/fmicb.2017.02292 ◽

2017 ◽

Vol 8 ◽

Cited By ~ 14

Author(s):

Hany S. Zinad ◽

Inas Natasya ◽

Andreas Werner

Keyword(s):

Mobile Genetic Elements ◽

Host Genome ◽

Antisense Transcripts ◽

Natural Antisense Transcripts ◽

Genetic Elements

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A strategy to obtain recombinant cell lines with high expression levels. Lentiviral vector-mediated transgenesis

BMC Proceedings ◽

10.1186/1753-6561-5-s8-p7 ◽

2011 ◽

Vol 5 (S8) ◽

Cited By ~ 12

Author(s):

Claudio Prieto ◽

Diego Fontana ◽

Marina Etcheverrigaray ◽

Ricardo Kratje

Keyword(s):

Cell Lines ◽

Lentiviral Vector ◽

High Expression ◽

Expression Levels ◽

Recombinant Cell

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Detection of tumor-derived extracellular vesicles in plasma from patients with solid cancer

BMC Cancer ◽

10.1186/s12885-021-08007-z ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Silvia R. Vitale ◽

Jean A. Helmijr ◽

Marjolein Gerritsen ◽

Hicret Coban ◽

Lisanne F. van Dessel ◽

...

Keyword(s):

Cell Lines ◽

Extracellular Vesicles ◽

Digital Pcr ◽

Circulating Tumor Dna ◽

Solid Cancer ◽

Expression Levels ◽

Healthy Donors ◽

Spin Column ◽

High Concordance ◽

Tumor Dna

Abstract Background Extracellular vesicles (EVs) are actively secreted by cells into body fluids and contain nucleic acids of the cells they originate from. The goal of this study was to detect circulating tumor-derived EVs (ctEVs) by mutant mRNA transcripts (EV-RNA) in plasma of patients with solid cancers and compare the occurrence of ctEVs with circulating tumor DNA (ctDNA) in cell-free DNA (cfDNA). Methods For this purpose, blood from 20 patients and 15 healthy blood donors (HBDs) was collected in different preservation tubes (EDTA, BCT, CellSave) and processed into plasma within 24 h from venipuncture. EVs were isolated with the ExoEasy protocol from this plasma and from conditioned medium of 6 cancer cell lines and characterized according to MISEV2018-guidelines. RNA from EVs was isolated with the ExoRNeasy protocol and evaluated for transcript expression levels of 96 genes by RT-qPCR and genotyped by digital PCR. Results Our workflow applied on cell lines revealed a high concordance between cellular mRNA and EV-RNA in expression levels as well as variant allele frequencies for PIK3CA, KRAS and BRAF. Plasma CD9-positive EV and GAPDH EV-RNA levels were significantly different between the preservation tubes. The workflow detected only ctEVs with mutant transcripts in plasma of patients with high amounts (> 20%) of circulating tumor DNA (ctDNA). Expression profiling showed that the EVs from patients resemble healthy donors more than tumor cell lines supporting that most EVs are derived from healthy tissue. Conclusions We provide a workflow for ctEV detection by spin column-based generic isolation of EVs and PCR-based measurement of gene expression and mutant transcripts in EV-RNA derived from cancer patients’ blood plasma. This workflow, however, detected tumor-specific mutations in blood less often in EV-RNA than in cfDNA.

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Natural antisense transcripts as therapeutic targets

Drug Discovery Today Therapeutic Strategies ◽

10.1016/j.ddstr.2013.03.001 ◽

2013 ◽

Vol 10 (3) ◽

pp. e119-e125 ◽

Cited By ~ 5

Author(s):

Paul Halley ◽

Olga Khorkova ◽

Claes Wahlestedt

Keyword(s):

Therapeutic Targets ◽

Antisense Transcripts ◽

Natural Antisense Transcripts

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Synaptotagmin 13 Is Highly Expressed in Estrogen Receptor-Positive Breast Cancer

Current Oncology ◽

10.3390/curroncol28050346 ◽

2021 ◽

Vol 28 (5) ◽

pp. 4080-4092

Author(s):

Takahiro Ichikawa ◽

Masahiro Shibata ◽

Takahiro Inaishi ◽

Ikumi Soeda ◽

Mitsuro Kanda ◽

...

Keyword(s):

Breast Cancer ◽

Estrogen Receptor ◽

Mrna Expression ◽

Cell Lines ◽

Mrna Levels ◽

Pcr Array ◽

Array Analysis ◽

Expression Levels ◽

Er Positive ◽

Mrna Expression Levels

Background: Accumulating evidence indicates tumor-promoting roles of synaptotagmin 13 (SYT13) in several cancers; however, no studies have investigated its expression in breast cancer (BC). This study aimed to clarify the significance of SYT13 in BC. Methods: SYT13 mRNA expression levels were evaluated in BC cell lines. Polymerase chain reaction (PCR) array analysis was conducted to determine the correlation between expression levels of SYT13 and other tumor-associated genes. Then, the association of SYT13 expression levels in the clinical BC specimens with patients’ clinicopathological factors was evaluated. These findings were subsequently validated using The Cancer Genome Atlas (TCGA) database. Results: Among 13 BC cell lines, estrogen receptor (ER)-positive cells showed higher SYT13 mRNA levels than ER-negative cells. PCR array analysis revealed positive correlations between SYT13 and several oncogenes predominantly expressed in ER-positive BC, such as estrogen receptor 1, AKT serine/threonine kinase 1, and cyclin-dependent kinases 4. In 165 patients, ER-positive specimens exhibited higher SYT13 mRNA expression levels than ER-negative specimens. The TCGA database analysis confirmed that patients with ER-positive BC expressed higher SYT13 levels than ER-negative patients. Conclusion: This study suggests that SYT13 is highly expressed in ER-positive BC cells and clinical specimens, and there is a positive association of SYT13 with the ER signaling pathways.

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Identification of long noncoding natural antisense transcripts (lncNATs) correlated with drought stress response in wild rice (Oryza nivara)

10.21203/rs.3.rs-280217/v1 ◽

2021 ◽

Author(s):

Yong-Chao Xu ◽

Jie Zhang ◽

Dong-Yan Zhang ◽

Ying-Hui Nan ◽

Song Ge ◽

...

Keyword(s):

Drought Stress ◽

Stress Response ◽

Wild Rice ◽

Oryza Rufipogon ◽

Cultivated Rice ◽

Antisense Transcripts ◽

High Genetic Diversity ◽

Natural Antisense Transcripts ◽

Form Complex ◽

Oryza Nivara

Abstract Background Wild rice, including Oryza nivara and Oryza rufipogon, which are considered as the ancestors of Asian cultivated rice (Oryza sativa L.), possess high genetic diversity and serve as a crucial resource for breeding novel cultivars of cultivated rice. Although many rice domestication related traits, such as seed shattering and plant architecture, have been intensively studied at the phenotypic and genomic levels, further investigation is needed to understand the molecular basis of phenotypic differences between cultivated and wild rice. Drought stress is one of the most severe abiotic stresses affecting rice growth and production. Adaptation to drought stress involves a cascade of genes and regulatory factors that form complex networks. Long noncoding natural antisense transcripts (lncNATs), a class of long noncoding RNAs (lncRNAs), regulate the corresponding sense transcripts and play an important role in plant growth and development. However, the contribution of lncNATs to drought stress response in wild rice remains largely unknown. Results Here, we conducted strand-specific RNA sequencing (ssRNA-seq) analysis of Nipponbare (O. sativa ssp. japonica) and two O. nivara accessions (BJ89 and BJ278) to determine the role of lncNATs in drought stress response in wild rice. A total of 1,246 lncRNAs were identified, including 1,091 coding–noncoding NAT pairs, of which 50 were expressed only in Nipponbare, and 77 were expressed only in BJ89 and/or BJ278. Of the 1,091 coding–noncoding NAT pairs, 240 were differentially expressed between control and drought stress conditions. Among these 240 NAT pairs, 12 were detected only in Nipponbare, and 187 were detected uniquely in O. nivara. Furthermore, 10 of the 240 coding–noncoding NAT pairs were correlated with genes previously demonstrated to be involved in stress response; among these, nine pairs were uniquely found in O. nivara, and one pair was shared between O. nivara and Nipponbare. Conclusion We identified lncNATs associated with drought stress response in cultivated rice and O. nivara. These results will improve our understanding of the function of lncNATs in drought tolerance and accelerate rice breeding.

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