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LncRNAs expression signatures of colon cancer

ABSTRACT: LncRNAs have been recently implicated as having oncogenic and tumor suppressor roles.To further investigate the function of lncRNA in colon cancer, we have employed lncRNA microarray to identify lncRNA with the potential to involve the metastasis of colon cancer. Human peripheral blood from healthy donors was irradiated ex vivo, and a 74-gene consensus signature was identified that distinguished between four radiation doses (0.5, 2, 5 and 8 Gy) and control samples. The same set of genes separated samples by exposure level at both six and 24 hours after treatment, with overlap evident only at the highest two doses (5 and 8 Gy). Expression of five genes (CDKN1A, FDXR, SESN1, BBC3 and PHPT1) from this signature was quantified in the same RNA samples by real-time PCR, confirming low variability between donors as well as the predicted radiation response pattern. The experimental samples are divided into three groups(normalM-cM-^@M-^Aprimary tumor and metastatic tumor) to compare lncRNA expression profiling of those

ORGANISM(S): Homo sapiens

SUBMITTER: shi debing

PROVIDER: E-GEOD-52413 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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lncRNAs expression signatures of colon cancer

Project description:LncRNAs have been recently implicated as having oncogenic and tumor suppressor roles.To further investigate the function of lncRNA in colon cancer, we have employed lncRNA microarray to identify lncRNA with the potential to involve the metastasis of colon cancer. Human peripheral blood from healthy donors was irradiated ex vivo, and a 74-gene consensus signature was identified that distinguished between four radiation doses (0.5, 2, 5 and 8 Gy) and control samples. The same set of genes separated samples by exposure level at both six and 24 hours after treatment, with overlap evident only at the highest two doses (5 and 8 Gy). Expression of five genes (CDKN1A, FDXR, SESN1, BBC3 and PHPT1) from this signature was quantified in the same RNA samples by real-time PCR, confirming low variability between donors as well as the predicted radiation response pattern.

2013-11-16 | GSE52413 | GEO

Transcription profiling of human peripheral blood to development gene expression signatures for practical radiation biodosimetry

Project description:To further development of our gene expression approach to biodosimetry, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish radiation dose across an exposure range relevant for medical decision-making in a radiological emergency. Human peripheral blood from healthy donors was irradiated ex vivo, and a 74-gene consensus signature was identified that distinguished between four radiation doses (0.5, 2, 5 and 8 Gy) and control samples. The same set of genes separated samples by exposure level at both six and 24 hours after treatment, with overlap evident only at the highest two doses (5 and 8 Gy). Expression of five genes (CDKN1A, FDXR, SESN1, BBC3 and PHPT1) from this signature was quantified in the same RNA samples by real-time PCR, confirming low variability between donors as well as the predicted radiation response pattern. Experiment Overall Design: Radiation induced gene expression in human blood was measured at 6 and 24 hours after exposure to doses of 0, 0.5, 2, 5 and 8 Gy g-rays. Five independent experiments were performed at each time (6 or 24 hours) using different donors for each experiment

2008-10-18 | E-GEOD-8917 | biostudies-arrayexpress

Development of gene expression for stress in heat- and shake-induced injury in the rat jejunum

Project description:To further development of our gene expression approach to biodosimetry, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish radiation dose across an exposure range relevant for medical decision-making in a radiological emergency. Human peripheral blood from healthy donors was irradiated ex vivo, and a 74-gene consensus signature was identified that distinguished between four radiation doses (0.5, 2, 5 and 8 Gy) and control samples. The same set of genes separated samples by exposure level at both six and 24 hours after treatment, with overlap evident only at the highest two doses (5 and 8 Gy). Expression of five genes (CDKN1A, FDXR, SESN1, BBC3 and PHPT1) from this signature was quantified in the same RNA samples by real-time PCR, confirming low variability between donors as well as the predicted radiation response pattern. Heat and shake stress induced gene expression in rat jejunum was measured with or without 3 days stressed (Control and S3d groups) The conditions of the treatment for rats were as follows: 35M-BM-0C with a vibration of 0.1 M-CM-^W g for 3 daysM-oM-<M-^L 2 h/day in a temperature shake. each group had 3 sample replications, and each sample were mixed by 3 rats total RNA

2014-09-18 | E-GEOD-61498 | biostudies-arrayexpress

Development of gene expression signatures for ASC activated by LL-37

Project description:To further development of our gene expression approach to ASC-mediated regeneration, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish radiation dose across an exposure range relevant for medical decision-making in a radiological emergency. Human peripheral blood from healthy donors was irradiated ex vivo, and a 74-gene consensus signature was identified that distinguished between four radiation doses (0.5, 2, 5 and 8 Gy) and control samples. The same set of genes separated samples by exposure level at both six and 24 hours after treatment, with overlap evident only at the highest two doses (5 and 8 Gy). Expression of five genes (CDKN1A, FDXR, SESN1, BBC3 and PHPT1) from this signature was quantified in the same RNA samples by real-time PCR, confirming low variability between donors as well as the predicted radiation response pattern.

2015-12-30 | GSE76392 | GEO

Development of gene expression for stress in heat- and shake-induced injury in the rat jejunum

2014-09-18 | GSE61498 | GEO

Development of gene expression signatures for practical radiation biodosimetry

Project description:To further development of our gene expression approach to biodosimetry, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to distinguish radiation dose across an exposure range relevant for medical decision-making in a radiological emergency. Human peripheral blood from healthy donors was irradiated ex vivo, and a 74-gene consensus signature was identified that distinguished between four radiation doses (0.5, 2, 5 and 8 Gy) and control samples. The same set of genes separated samples by exposure level at both six and 24 hours after treatment, with overlap evident only at the highest two doses (5 and 8 Gy). Expression of five genes (CDKN1A, FDXR, SESN1, BBC3 and PHPT1) from this signature was quantified in the same RNA samples by real-time PCR, confirming low variability between donors as well as the predicted radiation response pattern. Keywords: Dose Response, stress response, radiation response, biodosimetry

2008-07-01 | GSE8917 | GEO

Profiling mRNA, miRNA and lncRNA expression changes in endothelial cells in response to increasing doses of ionizing radiation [RNA-seq]

Project description:RNA seq for lncRNA and mRNA differential expression analysis, and small RNA seq for miRNA differential expression analysis were performed in primary human aotic endothelial cells treated with increasing doses of radiation (1 Gy, 2 Gy, 4 Gy, 8 Gy and 10 Gy). Total RNA was collected 24 h and 72 h after radiation. Comparisons were made with unirradiated cells plated for 24 h and 72 h repsectively.

2022-05-07 | GSE202119 | GEO

Gene expression profiles of TIE2 expressing Monocytes (TEMs)

Project description:To identify the gene expressing profiles of TIE2 expressing Monocytes(TEMs), we have employed the Agilent lncRNA Gene Expression 4Ã180K(Design ID:042818) microarray. Human peripheral blood mononuclear cells (PBMCs) in venous blood from healthy donors were isolated by Lymphoprep (Axis-Shield, Norway). Human monocytes in PBMCs, identified as cells that expressed CD14, were enriched by positive immunomagnetic selection using anti-CD14 MicroBeads (Miltenyi, Germany). TEMs (TIE2+CD14+) and TIE2-Monocytes (Tie2-CD14+) were then isolated by FACS-sorting (Aria II, BD Biosciences) using FITC-conjugated anti-CD14 (BD Biosciences, USA) and APC-conjugated anti-TIE2 (R&D System, USA) antibodies.Three TEMs samples together with their paried TIE2-Monocytes were detected.Expressions of sixteen genes (CDKN1A, FDXR, SESN1, BBC3 and PHPT1) from this signature was quantified in the same RNA samples by real-time PCR, confirming low variability between donors as well as the predicted radiation response pattern. The gene expressions of three independent paried TEMs and TIE2- Monocytes samples from different donors were measured.

2017-05-17 | E-GEOD-57783 | biostudies-arrayexpress

Deficient radiation transcription response in COVID-19 patients

Project description:The ongoing SARS-CoV-2 pandemic has resulted in over 6.3 million deaths and 560 million COVID-19 cases worldwide. Clinical management of hospitalised patients is complex due to the heterogeneous course of COVID-19. Low-dose radiotherapy (LD-RT) is known to dampen localised chronic inflammation, and has been suggested to be used to reduce lung inflammation in COVID-19 patients. However, it is unknown whether SARS-CoV-2 alters the radiation response and associated radiation exposure related risk. We generated gene expression profiles from circulating leukocytes of hospitalised COVID-19 patients and healthy donors. The p53 signalling pathway was found to be dysregulated, with mRNA levels of p53, ATM and CHK2 being lower in COVID-19 patients. Several key p53 target genes involved in cell cycle arrest, apoptosis and p53 feedback inhibition were up-regulated in COVID-19 patients, while other p53 target genes were downregulated. This dysregulation has functional consequences as the transcription of p53-dependant genes (CCNG1, GADD45A, DDB2, SESN1, FDXR, APOBEC) was reduced 24 h after X-ray exposure ex-vivo to both low (100 mGy) or high (2 Gy) doses. In conclusion, SARS-CoV-2 infection affects a DNA damage response that may modify radiation-induced health risks in exposed COVID-19 patients.

2023-02-01 | GSE223885 | GEO

AM_GeneExpressionAfterIonisingRadiation

Project description:Abstract Purpose: There is a recognised need to develop new methods of high throughput, rapid and minimally invasive individual dose assessment for radiation exposure. The aim of this work is to establish a panel of highly radiation responsive genes suitable for biological dosimetry and to explore inter-individual variation in response to ionising radiation exposure.Materials and method: Analysis of gene expression in response to radiation was carried out using three independent techniques (microarray, Multiplex Quantitative RT-PCR and nCounter Analysis System) in human lymphocytes in culture and circulating blood exposed ex vivo from the same donors. Results: Variations in transcriptional response to exposure to ionising radiation analysed by microarray allowed the identification of genes which can be validated and measured accurately as biomarkers of radiation exposure using other techniques. We have identified genes which are consistently up-regulated following exposure at different time points to either 2 or 4 Gy of X-rays, for all individuals in blood and cultured lymphocytes. Most down-regulated genes including cyclins, centromeric and mitotic checkpoints proteins, particularly those associated with chromosome instability and cancer can only be detected in dividing cells. Conclusions: The data provides evidence that there are a number of genes which seem suitable for biological dosimetry, like SESN1, GADD45A, CDKN1A, CCNG1, FDXR, BBC3 and MDM2. ÊThese biomarkers could potentially be used for triage after large-scale radiological incidents. Variations in transcriptional response accurately measured by MQRT-PCRæ may allow the identification of biomarkers of radiation sensitivity and individual susceptibility and therefore being useful in radiation oncology.

2011-10-20 | E-TABM-1083 | biostudies-arrayexpress

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