Proteomic Maps of Human Gastrointestinal Stromal Tumor Subgroups*

Liu, Yu; Li, Zhigui; Xu, Zhiqiang; Jin, Xiuxiu; Gong, Yanqiu; Xia, Xuyang; Yao, Yuqin; Xu, Zhaofen; Zhou, Yong; Xu, Hong‐Xi; Li, Shuangqing; Peng, Yong; Wu, Xiaoting; Dai, Lunzhi

doi:10.1074/mcp.ra119.001361

Cited by 12 publications

(11 citation statements)

References 55 publications

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“…Relative quantification of identified proteins was determined according to the weighted ratios of the uniquely identified peptides that belonged to a specific protein. Parameters for protein identification and quantification were as previously reported 40 , except the false discovery rate (FDR) was ≤ 1%. A paired t test was performed to determine statistical significance between the DUGL and AGL.…”

Section: Methodsmentioning

confidence: 99%

Proteomics provides insights into the inhibition of Chinese hamster V79 cell proliferation in the deep underground environment

Liu

Gao

et al. 2020

Sci Rep

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As resources in the shallow depths of the earth exhausted, people will spend extended periods of time in the deep underground space. However, little is known about the deep underground environment affecting the health of organisms. Hence, we established both deep underground laboratory (DUGL) and above ground laboratory (AGL) to investigate the effect of environmental factors on organisms. Six environmental parameters were monitored in the DUGL and AGL. Growth curves were recorded and tandem mass tag (TMT) proteomics analysis were performed to explore the proliferative ability and differentially abundant proteins (DAPs) in V79 cells (a cell line widely used in biological study in DUGLs) cultured in the DUGL and AGL. Parallel Reaction Monitoring was conducted to verify the TMT results. γ ray dose rate showed the most detectable difference between the two laboratories, whereby γ ray dose rate was significantly lower in the DUGL compared to the AGL. V79 cell proliferation was slower in the DUGL. Quantitative proteomics detected 980 DAPs (absolute fold change ≥ 1.2, p < 0.05) between V79 cells cultured in the DUGL and AGL. Of these, 576 proteins were up-regulated and 404 proteins were down-regulated in V79 cells cultured in the DUGL. KEGG pathway analysis revealed that seven pathways (e.g. ribosome, RNA transport and oxidative phosphorylation) were significantly enriched. These data suggest that proliferation of V79 cells was inhibited in the DUGL, likely because cells were exposed to reduced background radiation. The apparent changes in the proteome profile may have induced cellular changes that delayed proliferation but enhanced survival, rendering V79 cells adaptable to the changing environment.

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Section: Methodsmentioning

confidence: 99%

Proteomics provides insights into the inhibition of Chinese hamster V79 cell proliferation in the deep underground environment

Liu

Gao

et al. 2020

Sci Rep

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“…Therefore, it is important to identify novel therapeutic targets for GISTs. In 2019, Liu et al reported proteomics maps of human GISTs and indicated that patients with high PTPN1 expression had low risk of developing metastasis [ 22 ]. However, the global alteration of protein post-translational modifications in GISTs has been yet unknown.…”

Section: Discussionmentioning

confidence: 99%

Quantitative proteomic analysis of aberrant expressed lysine acetylation in gastrointestinal stromal tumors

et al. 2021

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Background Gastrointestinal stromal tumor (GIST) is a common digestive tract tumor with high rate of metastasis and recurrence. Currently, we understand the genome, transcriptome and proteome in GIST. However, posttranscriptional modification features in GIST remain unclear. In the present study, we aimed to construct a complete profile of acetylome in GIST. Methods Five common protein modifications, including acetylation, succinylation, crotonylation, 2-hydroxyisobutyrylation, and malonylation were tested among GIST subgroups and significantly differentially- expressed lysine acetylation was found. The acetylated peptides labeled with Tandem Mass Tag (TMT)under high sensitive mass spectrometry, and some proteins with acetylation sites were identified. Subsequently, these proteins and peptides were classified into high/moderate (H/M) risk and low (L) risk groups according to the modified NIH classification standard. Furthermore, cell components, molecular function, biological processes, KEGG pathways and protein interaction networks were analyzed. Results A total of 2904 acetylation sites from 1319 proteins were identified, of which quantitative information of 2548 sites from 1169 proteins was obtained. Finally, the differentially-expressed lysine acetylation sites were assessed and we found that 42 acetylated sites of 38 proteins were upregulated in the H/M risk group compared with the L risk group, while 48 acetylated sites of 44 proteins were downregulated, of which Ki67 K1063Ac and FCHSD2 K24Ac were the two acetylated proteins that were most changed. Conclusions Our novel findings provide further understanding of acetylome in GIST and might demonstrate the possibility in the acetylation targeted diagnosis and therapy of GIST.

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“…Relative quantification of identified proteins was determined according to the weighted ratios of the uniquely identified peptides that belonged to a specific protein. Parameters for protein identification and quantification were as previously reported [14], except the false discovery rate (FDR) was ≤ 1%. A paired t test was performed to determine statistical significance between the DUGL and AGL.…”

Section: Protein Identification and Quantificationmentioning

confidence: 99%

Proteomics provides insights into the inhibition of Chinese hamster V79 cell proliferation in the deep underground environment

Liu

et al. 2020

Preprint

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Background: To characterize the environment of deep underground laboratory (DUGL) with a rock cover of 1470m and observe the effect of the DUGL environment on the growth and metabolism of Chinese hamster V79 cells. Results: Six environmental parameters in the DUGL and an above ground laboratory (AGL; control) were monitored. Compared to the AGL, O2 concentration was not significantly different, total γ ray dose rate was significantly lower (p=0.005), and relative humidity (p<0.001), air pressure (p<0.001), and concentration of CO2 and radon gas (p<0.001) were significantly higher in the DUGL. The growth curves of cultured V79 cells showed cell proliferation was slower in the DUGL. Tandem mass tag (TMT) proteomics analysis was performed to identify differentially abundant proteins (DAPs) in V79 cells cultured in the DUGL and AGL. Parallel Reaction Monitoring (PRM) was conducted to verify TMT results. TMT detected 980 DAPs, defined as proteins with a ≥1.2-absolute fold change in relative abundance (p <0.05) between V79 cells cultured in the DUGL and AGL. Of these, 576 proteins were up-regulated and 404 proteins were down-regulated in V79 cells cultured in the DUGL. GO term enrichment analysis of up-regulated proteins revealed enrichment of proteins involved in translation, ribosome, proton-transporting ATP synthase activity, oxygen binding, and oxygen transporter activity et al. GO term enrichment analysis of downregulated proteins demonstrated enrichment of proteins involved in the endoplasmic reticulum lumenand respiratory chain. KEGG pathway analysis revealed that ribosome (p<0.001), base excision repair (p<0.001), RNA transport (p=0.009), Huntington's disease (p=0.023), and oxidative phosphorylation (OXPPL) (p=0.035) pathways were significantly enriched. Conclusion: Proliferation of V79 cells was inhibited in the DUGL, likely because cells were exposed to reduced cosmic ray muons flux. There were apparent changes in the proteome profile of the V79 cells cultured in the DUGL, which affected proteins related to the ribosome, RNA transport, translation, energy metabolism, and DNA repair.These proteins may have induced cellular changes that delayed proliferation but enhanced survival, making the V79 cells adaptable to the changing environment. Our findings provide insight into the cellular stress response that is triggered in the absence of normal levels of radiation.

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Proteomic Maps of Human Gastrointestinal Stromal Tumor Subgroups*

Cited by 12 publications

References 55 publications

Proteomics provides insights into the inhibition of Chinese hamster V79 cell proliferation in the deep underground environment

Proteomics provides insights into the inhibition of Chinese hamster V79 cell proliferation in the deep underground environment

Quantitative proteomic analysis of aberrant expressed lysine acetylation in gastrointestinal stromal tumors

Proteomics provides insights into the inhibition of Chinese hamster V79 cell proliferation in the deep underground environment

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