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CLC number: R592

On-line Access: 2020-04-07

Received: 2020-06-05

Revision Accepted: 2020-03-11

Crosschecked: 2020-03-11

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Journal of Zhejiang University SCIENCE B 2020 Vol.21 No.4 P.291-304


Comparative transcriptomic analysis of vascular endothelial cells after hypoxia/re-oxygenation induction based on microarray technology

Author(s):  Jia Xu, Jiu-Kun Jiang, Xiao-Lin Li, Xiao-Peng Yu, Ying-Ge Xu, Yuan-Qiang Lu

Affiliation(s):  Department of Emergency Medicine, the First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou 310003, China; more

Corresponding email(s):   luyuanqiang@zju.edu.cn

Key Words:  Human umbilical vein endothelial cells (HUVECs), Hypoxia, Re-oxygenation, Microarray, Pleckstrin homology-like domain family A member 1 (PHLDA1), Long non-coding RNA (lncRNA)

Jia Xu, Jiu-Kun Jiang, Xiao-Lin Li, Xiao-Peng Yu, Ying-Ge Xu, Yuan-Qiang Lu. Comparative transcriptomic analysis of vascular endothelial cells after hypoxia/re-oxygenation induction based on microarray technology[J]. Journal of Zhejiang University Science B, 2020, 21(4): 291-304.

@article{title="Comparative transcriptomic analysis of vascular endothelial cells after hypoxia/re-oxygenation induction based on microarray technology",
author="Jia Xu, Jiu-Kun Jiang, Xiao-Lin Li, Xiao-Peng Yu, Ying-Ge Xu, Yuan-Qiang Lu",
journal="Journal of Zhejiang University Science B",
publisher="Zhejiang University Press & Springer",

%0 Journal Article
%T Comparative transcriptomic analysis of vascular endothelial cells after hypoxia/re-oxygenation induction based on microarray technology
%A Jia Xu
%A Jiu-Kun Jiang
%A Xiao-Lin Li
%A Xiao-Peng Yu
%A Ying-Ge Xu
%A Yuan-Qiang Lu
%J Journal of Zhejiang University SCIENCE B
%V 21
%N 4
%P 291-304
%@ 1673-1581
%D 2020
%I Zhejiang University Press & Springer
%DOI 10.1631/jzus.B2000043

T1 - Comparative transcriptomic analysis of vascular endothelial cells after hypoxia/re-oxygenation induction based on microarray technology
A1 - Jia Xu
A1 - Jiu-Kun Jiang
A1 - Xiao-Lin Li
A1 - Xiao-Peng Yu
A1 - Ying-Ge Xu
A1 - Yuan-Qiang Lu
J0 - Journal of Zhejiang University Science B
VL - 21
IS - 4
SP - 291
EP - 304
%@ 1673-1581
Y1 - 2020
PB - Zhejiang University Press & Springer
ER -
DOI - 10.1631/jzus.B2000043

Objective: To provide comprehensive data to understand mechanisms of vascular endothelial cell (VEC) response to hypoxia/re-oxygenation. Methods: human umbilical vein endothelial cells (HUVECs) were employed to construct hypoxia/re-oxygenation-induced VEC transcriptome profiling. Cells incubated under 5% O2, 5% CO2, and 90% N2 for 3 h followed by 95% air and 5% CO2 for 1 h were used in the hypoxia/re-oxygenation group. Those incubated only under 95% air and 5% CO2 were used in the normoxia control group. Results: By using a well-established microarray chip consisting of 58 339 probes, the study identified 372 differentially expressed genes. While part of the genes are known to be VEC hypoxia/re-oxygenation-related, serving as a good control, a large number of genes related to VEC hypoxia/re-oxygenation were identified for the first time. Through bioinformatic analysis of these genes, we identified that multiple pathways were involved in the reaction. Subsequently, we applied real-time polymerase chain reaction (PCR) and western blot techniques to validate the microarray data. It was found that the expression of apoptosis-related proteins, like pleckstrin homology-like domain family A member 1 (PHLDA1), was also consistently up-regulated in the hypoxia/re-oxygenation group. STRING analysis found that significantly differentially expressed genes SLC38A3, SLC5A5, Lnc-SLC36A4-1, and Lnc-PLEKHJ1-1 may have physical or/and functional protein–protein interactions with PHLDA1. Conclusions: The data from this study have built a foundation to develop many hypotheses to further explore the hypoxia/re-oxygenation mechanisms, an area with great clinical significance for multiple diseases.


方法:采用缺氧孵育3 h后复氧1 h的HUVEC为缺氧/复氧组,同时常氧孵育的HUVEC为常氧对照组.应用含58 339条探针的全转录组芯片检测每组三个样本.对差异表达基因进行生信分析和功能验证.


Darkslateblue:Affiliate; Royal Blue:Author; Turquoise:Article


[1]Atkeson A, Yeh SY, Malhotra A, et al., 2009. Endothelial function in obstructive sleep apnea. Prog Cardiovasc Dis, 51(5):351-362.

[2]Bader AM, Klose K, Bieback K, et al., 2015. Hypoxic preconditioning increases survival and pro-angiogenic capacity of human cord blood mesenchymal stromal cells in vitro. PLoS ONE, 10(9):e0138477.

[3]Baldea I, Teacoe I, Olteanu DE, et al., 2018. Effects of different hypoxia degrees on endothelial cell cultures—time course study. Mech Ageing Dev, 172:45-50.

[4]Basile DP, Friedrich JL, Spahic J, et al., 2011. Impaired endothelial proliferation and mesenchymal transition contribute to vascular rarefaction following acute kidney injury. Am J Physiol Renal Physiol, 300(3):F721-F733.

[5]Carden DL, Granger DN, 2000. Pathophysiology of ischaemia-reperfusion injury. J Pathol, 190(3):255-266.

[6]E S, Costa MC, Kurc S, et al., 2018. The circulating non-coding RNA landscape for biomarker research: lessons and prospects from cardiovascular diseases. Acta Pharmacol Sin, 39(7):1085-1099.

[7]Eltzschig HK, Collard CD, 2004. Vascular ischaemia and reperfusion injury. Br Med Bull, 70(1):71-86.

[8]Fearon AE, Carter EP, Clayton NS, et al., 2018. PHLDA1 mediates drug resistance in receptor tyrosine kinase-driven cancer. Cell Rep, 22(9):2469-2481.

[9]Ferrucci M, Biagioni F, Ryskalin L, et al., 2018. Ambiguous effects of autophagy activation following hypoperfusion/ ischemia. Int J Mol Sci, 19(9):2756.

[10]Filippi I, Saltarella I, Aldinucci C, et al., 2018. Different adaptive responses to hypoxia in normal and multiple myeloma endothelial cells. Cell Physiol Biochem, 46(1):203-212.

[11]Fu PF, Zheng X, Fan X, et al., 2019. Role of cytoplasmic lncRNAs in regulating cancer signaling pathways. J Zhejiang Univ-Sci B (Biomed & Biotechnol), 20(1):1-8.

[12]Gudenas BL, Wang J, Kuang SZ, et al., 2019. Genomic data mining for functional annotation of human long noncoding RNAs. J Zhejiang Univ-Sci B (Biomed & Biotechnol), 20(6):476-487.

[13]Guo YX, Jia PY, Chen YQ, et al., 2020. PHLDA1 is a new therapeutic target of oxidative stress and ischemia reperfusion-induced myocardial injury. Life Sci, 245:117347.

[14]Haybar H, Shokuhian M, Bagheri M, et al., 2019. Involvement of circulating inflammatory factors in prognosis and risk of cardiovascular disease. J Mol Cell Cardiol, 132:110-119.

[15]Jiang JK, Fang W, Hong LJ, et al., 2017. Distribution and differentiation of myeloid-derived suppressor cells after fluid resuscitation in mice with hemorrhagic shock. J Zhejiang Univ-Sci B (Biomed & Biotechnol), 18(1):48-58.

[16]Johnson EO, Chang KH, de Pablo Y, et al., 2011. PHLDA1 is a crucial negative regulator and effector of Aurora A kinase in breast cancer. J Cell Sci, 124(16):2711-2722.

[17]Li F, Lee KE, Simon MC, 2018. Detection of hypoxia and HIF in paraffin-embedded tumor tissues. In: Huang LE (Ed.), Hypoxia: Methods and Protocols. Humana Press, New York, p.277-282.

[18]Li WY, Zhao YL, Fu P, 2018. Hypoxia induced factor in chronic kidney disease: friend or foe? Front Med (Lausanne), 4:259.

[19]Liao JK, Zulueta JJ, Yu FS, et al., 1995. Regulation of bovine endothelial constitutive nitric oxide synthase by oxygen. J Clin Invest, 96(6):2661-2666.

[20]Lim To WK, Kumar P, Marshall JM, 2015. Hypoxia is an effective stimulus for vesicular release of ATP from human umbilical vein endothelial cells. Placenta, 36(7):759-766.

[21]Mansoori Z, Ghaedi H, Sadatamini M, et al., 2018. Downregulation of long non-coding RNAs LINC00523 and LINC00994 in type 2 diabetes in an Iranian cohort. Mol Biol Rep, 45(5):1227-1233.

[22]McQuillan LP, Leung GK, Marsden PA, et al., 1994. Hypoxia inhibits expression of eNOS via transcriptional and posttranscriptional mechanisms. Am J Physiol, 267(5):H1921-H1927.

[23]Mineo M, Ricklefs F, Rooj AK, et al., 2016. The long non-coding RNA HIF1A-AS2 facilitates the maintenance of mesenchymal glioblastoma stem-like cells in hypoxic niches. Cell Rep, 15(11):2500-2509.

[24]Moad AIH, Muhammad TST, Oon CE, et al., 2013. Rapamycin induces apoptosis when autophagy is inhibited in T-47D mammary cells and both processes are regulated by Phlda1. Cell Biochem Biophys, 66(3):567-587.

[25]Nagai MA, 2016. Pleckstrin homology-like domain, family A, member 1 (PHLDA1) and cancer (Review). Biomed Rep, 4(3):275-281.

[26]Nallamshetty S, Chan SY, Loscalzo J, 2013. Hypoxia: a master regulator of microRNA biogenesis and activity. Free Radic Biol Med, 64:20-30.

[27]Niu QF, Li DL, Yang Y, et al., 2019. Establishment of human vascular endothelial hypoxia/reoxygeneration injury cell model. China J Oral Maxillofac Surg, 17(4):295-299 (in Chinese).


[29]Pan H, Wang BH, Li ZB, et al., 2019. Mitochondrial superoxide anions induced by exogenous oxidative stress determine tumor cell fate: an individual cell-based study. J Zhejiang Univ-Sci B (Biomed & Biotechnol), 20(4):310-321.

[30]Pan J, Zhu JY, Kee HS, et al., 2015. A review of compression, ventilation, defibrillation, drug treatment, and targeted temperature management in cardiopulmonary resuscitation. Chin Med J (Engl), 128(4):550-554.

[31]Salvadori M, Rosso G, Bertoni E, 2015. Update on ischemia-reperfusion injury in kidney transplantation: pathogenesis and treatment. World J Transplant, 5(2):52-67.

[32]Sellheyer K, Nelson P, 2011. Follicular stem cell marker PHLDA1 (TDAG51) is superior to cytokeratin-20 in differentiating between trichoepithelioma and basal cell carcinoma in small biopsy specimens. J Cutan Pathol, 38(7):542-550.

[33]Shay JES, Celeste Simon M, 2012. Hypoxia-inducible factors: crosstalk between inflammation and metabolism. Semin Cell Dev Biol, 23(4):389-394.

[34]Sun Y, George J, Rocha S, 2015. Dose-dependent effects of allopurinol on human foreskin fibroblast cells and human umbilical vein endothelial cells under hypoxia. PLoS ONE, 10(4):e0123649.

[35]Tang X, Lin CP, Guo DQ, et al., 2016. CLOCK promotes endothelial damage by inducing autophagy through reactive oxygen species. Oxid Med Cell Longev, 2016:9591482.

[36]Taylor MA, Das BC, Ray SK, 2018. Targeting autophagy for combating chemoresistance and radioresistance in glioblastoma. Apoptosis, 23(11-12):563-575.

[37]Urbanek T, Kuczmik W, Basta-Kaim A, et al., 2014. Rapamycin induces of protective autophagy in vascular endothelial cells exposed to oxygen-glucose deprivation. Brain Res, 1553:1-11.

[38]Wang JC, Li XX, Sun X, et al., 2018. Activation of AMPK by simvastatin inhibited breast tumor angiogenesis via impeding HIF-1α-induced pro-angiogenic factor. Cancer Sci, 109(5):1627-1637.

[39]Wu JB, Lei Z, Yu JG, 2015. Hypoxia induces autophagy in human vascular endothelial cells in a hypoxia-inducible factor 1-dependent manner. Mol Med Rep, 11(4):2677-2682.

[40]Xie XJ, Yang YM, Jiang JK, et al., 2017. Association between the vascular endothelial growth factor single nucleotide polymorphisms and diabetic retinopathy risk: a meta-analysis. J Diabetes, 9(8):738-753.

[41]Zampetaki A, Albrecht A, Steinhofel K, 2018. Long non-coding RNA structure and function: is there a link? Front Physiol, 9:1201.

[42]Zhang Q, Fang W, Ma L, et al., 2018. VEGF levels in plasma in relation to metabolic control, inflammation, and microvascular complications in type-2 diabetes: a cohort study. Medicine (Baltimore), 97(14):e0415.

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