Developing Gender-Specific Gene Expression Biodosimetry Using a Panel of Radiation-Responsive Genes for Determining Radiation Dose in Human Peripheral Blood

Li, Shuang; Lü, Xue; Jiao, Feng; Tian, Mei; Wang, Jun; Chen, Hu; Chen, Deqing; Liu, Qingjie

doi:10.1667/rr15355.1

Cited by 37 publications

(26 citation statements)

References 47 publications

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“…A recent bioinformatics study showed that HO-related DEGs are mainly associated with oxidative phosphorylation in a mouse burn/tenotomy-induced HO model (34), but in humans, this has not been confirmed. An interesting study showed that RPS27L is significantly upregulated after irradiation in human peripheral blood (53). Another study showed that RPS27L is a physiological regulator of p53 that suppresses genomic instability and tumorigenesis (54).…”

Section: Discussionmentioning

confidence: 99%

Identification of the Biomarkers and Pathological Process of Heterotopic Ossification: Weighted Gene Co-Expression Network Analysis

et al. 2020

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Heterotopic ossification (HO) is the formation of abnormal mature lamellar bone in extra-skeletal sites, including soft tissues and joints, which result in high rates of disability. The understanding of the mechanism of HO is insufficient. The aim of this study was to explore biomarkers and pathological processes in HO+ samples. The gene expression profile GSE94683 was downloaded from the Gene Expression Omnibus database. Sixteen samples from nine HO- and seven HO+ subjects were analyzed. After data preprocessing, 3,529 genes were obtained for weighted gene co-expression network analysis. Highly correlated genes were divided into 13 modules. Finally, the cyan and purple modules were selected for further study. Gene ontology functional annotation and Kyoto Encyclopedia of Genes and Genomes pathway enrichment indicated that the cyan module was enriched in a variety of components, including protein binding, membrane, nucleoplasm, cytosol, poly(A) RNA binding, biosynthesis of antibiotics, carbon metabolism, endocytosis, citrate cycle, and metabolic pathways. In addition, the purple module was enriched in cytosol, mitochondrion, protein binding, structural constituent of ribosome, rRNA processing, oxidative phosphorylation, ribosome, and non-alcoholic fatty liver disease. Finally, 10 hub genes in the cyan module [actin related protein 3 (ACTR3), ADP ribosylation factor 4 (ARF4), progesterone receptor membrane component 1 (PGRMC1), ribosomal protein S23 (RPS23), mannose-6-phosphate receptor (M6PR), WD repeat domain 12 (WDR12), synaptosome associated protein 23 (SNAP23), actin related protein 2 (ACTR2), siah E3 ubiquitin protein ligase 1 (SIAH1), and glomulin (GLMN)] and 2 hub genes in the purple module [proteasome 20S subunit alpha 3 (PSMA3) and ribosomal protein S27 like (RPS27L)] were identified. Hub genes were validated through quantitative real-time polymerase chain reaction. In summary, 12 hub genes were identified in two modules that were associated with HO. These hub genes could provide new biomarkers, therapeutic ideas, and targets in HO.

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Section: Discussionmentioning

confidence: 99%

Identification of the Biomarkers and Pathological Process of Heterotopic Ossification: Weighted Gene Co-Expression Network Analysis

et al. 2020

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“…In order to observe the variation of whole blood RNA and leukocyte RNA in response to different preservation durations in this study, six target genes were selected to represent different cellular regulatory pathways as described in the literature (Micke et al, 2006;Wang et al, 2015). These selected genes are known to be induced or repressed by ex vivo blood handling and can be the biomarkers of blood mRNA for monitoring changes in blood specimens after collection and preservation (Jin et al, 2013;Li et al, 2019;Malentacchi et al, 2016). Previous research has shown that pre-analytical factors can affect very sensitive analytical procedures of RNA, such as RT-qPCR (Nussbaumer, Gharehbaghi-Schnell & Korschineck, 2006).…”

Section: Discussionmentioning

confidence: 99%

Effects of preservation duration at 4 °C on the quality of RNA in rabbit blood specimens

Song

Zhou

2020

PeerJ

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A prolonged preservation duration of blood specimens at 4 °C may occur due to the distance from collection points to storage facilities in many biobanks, especially for multicenter studies. This could lead to RNA degradation, affecting downstream analyses. However, effects of preservation durations at 4 °C on RNA quality in blood specimens need to be studied. We collected rabbit blood using EDTA tubes and stored them at 4 °C for different preservation durations. Then, we examined the quality of RNA from whole blood and leukocytes isolated from rabbit blood. Our results show that the purity of whole blood RNA and leukocyte RNA does not indicate significant change after rabbit blood is stored at 4 °C for different preservation durations (from 1 h to 7 days). The integrity of leukocyte RNA indicates the same result as above, but the integrity of whole blood RNA is significantly decreased after rabbit blood is stored at 4 °C for over 3 days. Moreover, expression of SMAD7, MKI67, FOS, TGFβ1 and HIF1α of whole blood RNA and leukocyte RNA remains basically stable, but PCNA expression of whole blood RNA or leukocyte RNA is significantly decreased after rabbit blood is stored at 4 °C for over 24 h or 7 days. Therefore, these results suggest that high-quality RNA is obtained from the fresher blood specimens and if blood specimens are stored for over 3 days at 4 °C, the quality of leukocyte RNA is more stable and of better quality than that of whole blood RNA.

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“…In order to observe the variation of whole blood RNA and leukocyte RNA in response to different preservation durations in this study, six target genes were selected to represent different cellular regulatory pathways as described in the literature (Micke et al 2006;Wang et al 2015). These selected genes are known to be induced or repressed by ex vivo blood handling, and can be the biomarkers of blood mRNA for monitoring changes in blood specimens after collection and preservation (Jin et al 2013;Li et al 2019;Malentacchi et al 2016). Previous research has shown that pre-analytical factors can affect very sensitive analytical procedures of RNA, such as RT-qPCR (Nussbaumer et al 2006).…”

Section: Discussionmentioning

confidence: 99%

Peer Review #3 of "Effects of preservation duration at 4 °C on the quality of RNA in rabbit blood specimens (v0.1)"

2020

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A prolonged preservation duration of blood specimens at 4 ℃ may occur due to the distance from collection points to storage facilities in many biobanks, especially for multicenter studies. This could lead to RNA degradation, affecting downstream analyses.However, effects of preservation durations at 4 ℃ on RNA quality in blood specimens need to be studied. We collected rabbit blood using EDTA tubes and stored them at 4 ℃ for different preservation durations. Then, we examined the quality of RNA from whole blood and leukocytes isolated from rabbit blood. Our results show that the purity of whole blood RNA and leukocyte RNA does not indicate significant change after rabbit blood is stored at 4 ℃ for different preservation durations (from 1 hour to 7 days). The integrity of leukocyte RNA indicates the same result as above, but the integrity of whole blood RNA is significantly decreased after rabbit blood is stored at 4 ℃ for over 3 days. Moreover, expression of SMAD7, MKI67, FOS, TGFβ1 and HIF1α of whole blood RNA and leukocyte RNA remains basically stable, but PCNA expression of whole blood RNA or leukocyte RNA is significantly decreased after rabbit blood is stored at 4 ℃ for over 24 hours or 7 days.Therefore, these results suggest that high-quality RNA is obtained from the fresher blood specimens, and if blood specimens are stored for over 3 days at 4 ℃, the quality of leukocyte RNA is more stable and of better quality than that of whole blood RNA.

show abstract

Developing Gender-Specific Gene Expression Biodosimetry Using a Panel of Radiation-Responsive Genes for Determining Radiation Dose in Human Peripheral Blood

Cited by 37 publications

References 47 publications

Identification of the Biomarkers and Pathological Process of Heterotopic Ossification: Weighted Gene Co-Expression Network Analysis

Identification of the Biomarkers and Pathological Process of Heterotopic Ossification: Weighted Gene Co-Expression Network Analysis

Effects of preservation duration at 4 °C on the quality of RNA in rabbit blood specimens

Peer Review #3 of "Effects of preservation duration at 4 °C on the quality of RNA in rabbit blood specimens (v0.1)"

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