Effects of distinct drugs on gene transcription in an osteosarcoma cell line

Zhou,Hui; Cui,Xiaofeng; Yuan,Hongping; Zhang,Boyin; Meng,Chunyang; Zhao,Dongxu

doi:10.3892/ol.2017.6767

Effects of distinct drugs on gene transcription in an osteosarcoma cell line

Authors:
- Hui Zhou
- Xiaofeng Cui
- Hongping Yuan
- Boyin Zhang
- Chunyang Meng
- Dongxu Zhao
View Affiliations

Affiliations: Department of Anesthesia, China‑Japan Union Hospital, Jilin University, Changchun, Jilin 130033, P.R. China, Department of Gastrointestinal Colorectal and Anal Surgery, China‑Japan Union Hospital, Jilin University, Changchun, Jilin 130033, P.R. China, Department of Nephrology, The Fourth Hospital of Jilin University, Changchun, Jilin 130011, P.R. China, Department of Orthopedics, China‑Japan Union Hospital, Jilin University, Changchun, Jilin 130033, P.R. China
Published online on: August 18, 2017 https://doi.org/10.3892/ol.2017.6767
Pages: 4694-4700
Copyright: © Zhou et al. This is an open access article distributed under the terms of Creative Commons Attribution License.

Metrics: Total Views: 0 (Spandidos Publications: | PMC Statistics: )

Metrics: Total PDF Downloads: 0 (Spandidos Publications: | PMC Statistics: )

Cited By (CrossRef): 0 citations Loading Articles...

Abstract

Osteosarcoma (OS) is a common cancerous bone tumor which has a detrimental impact on the lives of patients and their families. The present study aimed at investigating the underlying molecular mechanism of various drug treatments pertaining to OS, including dimethyl sulfoxide (DMSO), doxorubicin (DXP), Nutlin‑3, actinomycin D (ActD) and etoposide (Eto). Microarray and p53 chromatin immunoprecipitation combined with sequencing (ChIP‑seq) datasets of the OS cell line U2OS treated with distinct drugs were acquired from the Gene Expression Omnibus and differentially-expressed genes (DEGs) were screened for alignment analysis. The p53‑binding target genes were identified and ChIP‑seq and microarray gene expression data were combined to identify directly and indirectly targeted genes. A regulatory network of p53 was constructed with the acquired data. Finally, the Database for Annotation, Visualization and Integrated Discovery was interrogated for annotation of target genes. A total of 212 p53‑binding peaks were obtained in the untreated group, whereas thousands of peaks were obtained in the treated groups. In total, ~1,000 target genes were identified in each of DXP, DMSO, Eto and ActD treatment groups, whereas the Nutlin‑3 treatment group identified an increased number, with 5,458 target genes obtained. Several common DEGs including MDM2, TP53I3, RRM2B, FAS and SESN1 were targeted by all the drugs with the exception of DMSO. p53 regulated various genes including EHF, HOXA10 and BHLHE40 in the Nutlin‑3 treatment group, whereas p53 regulated EHF, RFX3, TRAF40 and TCF7L2 in the DXR treatment group. The results of the present study indicate that p53 was able to directly regulate target genes including MDM2, TP53I3 and RRM2B or indirectly regulate numerous further genes through several hub genes including EHF and RFX through various drug treatments in U2OS cells. Furthermore, p53 regulated distinct molecular processes in various drug treatments.

View Figures

View References

1	Burke ME, Albritton K and Marina N: Challenges in the recruitment of adolescents and young adults to cancer clinical trials. Cancer. 110:2385–2393. 2007. View Article : Google Scholar : PubMed/NCBI
2	Luetke A, Meyers PA, Lewis I and Juergens H: Osteosarcoma treatment-where do we stand? A state of the art review. Cancer Treat Rev. 40:523–532. 2014. View Article : Google Scholar : PubMed/NCBI
3	Kere J: Neuropeptide S receptor 1: An asthma susceptibility geneAllergy Frontiers: Future Perspectives. Springer; pp. 191–205. 2010, View Article : Google Scholar
4	Ahmed H, Salama A, Salem SE and Bahnassy AA: A case of synchronous double primary breast carcinoma and osteosarcoma: Mismatch repair genes mutations as a possible cause for multiple early onset malignant tumors. Am J Case Rep. 13:218–223. 2012. View Article : Google Scholar : PubMed/NCBI
5	Vogelstein B, Lane D and Levine AJ: Surfing the p53 network. Nature. 408:307–310. 2000. View Article : Google Scholar : PubMed/NCBI
6	Mulligan LM, Matlashewski GJ, Scrable HJ and Cavenee WK: Mechanisms of p53 loss in human sarcomas. Proc Natl Acad Sci USA. 87:5863–5867. 1990. View Article : Google Scholar : PubMed/NCBI
7	Toguchida J, Yamaguchi T, Dayton SH, Beauchamp RL, Herrera GE, Ishizaki K, Yamamuro T, Meyers PA, Little JB, Sasaki MS, et al: Prevalence and spectrum of germline mutations of the p53 gene among patients with sarcoma. N Engl J Med. 326:1301–1308. 1992. View Article : Google Scholar : PubMed/NCBI
8	Luo Y, Deng Z and Chen J: Pivotal regulatory network and genes in osteosarcoma. Arch Med Sci. 9:569–575. 2013. View Article : Google Scholar : PubMed/NCBI
9	Sobell HM: Actinomycin and DNA transcription. Proc Natl Acad Sci USA. 82:5328–5331. 1985. View Article : Google Scholar : PubMed/NCBI
10	Fornari FA, Randolph JK, Yalowich JC, Ritke MK and Gewirtz DA: Interference by doxorubicin with DNA unwinding in MCF-7 breast tumor cells. Mol Pharmacol. 45:649–656. 1994.PubMed/NCBI
11	Hande KR: Etoposide: Four decades of development of a topoisomerase II inhibitor. Eur J Cancer. 34:1514–1521. 1998. View Article : Google Scholar : PubMed/NCBI
12	Shinohara T and Uesugi M: In-vivo activation of the p53 pathway by small-molecule antagonists of MDM2. Tanpakushitsu Kakusan Koso. 52 (13 Suppl):S1816–S1817. 2007.
13	Miyachi M, Kakazu N, Yagyu S, Katsumi Y, Tsubai-Shimizu S, Kikuchi K, Tsuchiya K, Iehara T and Hosoi H: Restoration of p53 pathway by nutlin-3 induces cell cycle arrest and apoptosis in human rhabdomyosarcoma cells. Clin Cancer Res. 15:4077–4084. 2009. View Article : Google Scholar : PubMed/NCBI
14	Ling YH, el-Naggar AK, Priebe W and Perez-Soler R: Cell cycle-dependent cytotoxicity, G2/M phase arrest, and disruption of p34cdc2/cyclin B1 activity induced by doxorubicin in synchronized P388 cells. Mol Pharmacol. 49:832–841. 1996.PubMed/NCBI
15	Xu H and Krystal GW: Actinomycin D decreases Mcl-1 expression and acts synergistically with ABT-737 against small cell lung cancer cell lines. Clin Cancer Res. 16:4392–4400. 2010. View Article : Google Scholar : PubMed/NCBI
16	Hsiao M, Low J, Dorn E, Ku D, Pattengale P, Yeargin J and Haas M: Gain-of-function mutations of the p53 gene induce lymphohematopoietic metastatic potential and tissue invasiveness. Am J Pathol. 145:7021994.PubMed/NCBI
17	Menendez D, Nguyen TA, Freudenberg JM, Mathew VJ, Anderson CW, Jothi R and Resnick MA: Diverse stresses dramatically alter genome-wide p53-binding and transactivation landscape in human cancer cells. Nucleic Acids Res. 41:7286–7301. 2013. View Article : Google Scholar : PubMed/NCBI
18	Smeenk L, van Heeringen SJ, Koeppel M, Gilbert B, Janssen-Megens E, Stunnenberg HG and Lohrum M: Role of p53 serine 46 in p53 target gene regulation. PLoS One. 6:e175742011. View Article : Google Scholar : PubMed/NCBI
19	Gautier L, Cope L, Bolstad BM and Irizarry RA: affy-analysis of Affymetrix GeneChip data at the probe level. Bioinformatics. 20:307–315. 2004. View Article : Google Scholar : PubMed/NCBI
20	Langmead B and Salzberg SL: Fast gapped-read alignment with Bowtie 2. Nat Methods. 9:357–359. 2012. View Article : Google Scholar : PubMed/NCBI
21	Zhang Y, Liu T, Meyer CA, Eeckhoute J, Johnson DS, Bernstein BE, Nusbaum C, Myers RM, Brown M, Li W and Liu XS: Model-based analysis of ChIP-Seq (MACS). Genome Biol. 9:R1372008. View Article : Google Scholar : PubMed/NCBI
22	Ji H, Jiang H, Ma W, Johnson DS, Myers RM and Wong WH: An integrated software system for analyzing ChIP-chip and ChIP-seq data. Nat Biotechnol. 26:1293–1300. 2008. View Article : Google Scholar : PubMed/NCBI
23	Huang DW, Sherman BT, Tan Q, Kir J, Liu D, Bryant D, Guo Y, Stephens R, Baseler MW, Lane HC and Lempicki RA: DAVID bioinformatics resources: Expanded annotation database and novel algorithms to better extract biology from large gene lists. Nucleic Acids Res. 35:W169–W175. 2007. View Article : Google Scholar : PubMed/NCBI
24	Shimizu S, Kanaseki T, Mizushima N, Mizuta T, Arakawa-Kobayashi S, Thompson CB and Tsujimoto Y: Role of Bcl-2 family proteins in a non-apoptotic programmed cell death dependent on autophagy genes. Nat Cell Biol. 6:1221–1228. 2004. View Article : Google Scholar : PubMed/NCBI
25	Kim Y, Starostina NG and Kipreos ET: The CRL4Cdt2 ubiquitin ligase targets the degradation of p21Cip1 to control replication licensing. Genes Dev. 22:2507–2519. 2008. View Article : Google Scholar : PubMed/NCBI
26	Dujardin F, Binh MB, Bouvier C, Gomez-Brouchet A, Larousserie F, Muret Ad, Louis-Brennetot C, Aurias A, Coindre JM, Guillou L, et al: MDM2 and CDK4 immunohistochemistry is a valuable tool in the differential diagnosis of low-grade osteosarcomas and other primary fibro-osseous lesions of the bone. Mod Pathol. 24:624–637. 2011. View Article : Google Scholar : PubMed/NCBI
27	Lukin DJ, Carvajal LA, Liu WJ, Resnick-Silverman L and Manfredi JJ: p53 promotes cell survival due to the reversibility of its cell cycle checkpoints. Mol Cancer Res. 13:16–28. 2015. View Article : Google Scholar : PubMed/NCBI
28	Lee YS, Oh JH, Yoon S, Kwon MS, Song CW, Kim KH, Cho MJ, Mollah ML, Je YJ, Kim YD, et al: Differential gene expression profiles of radioresistant non-small-cell lung cancer cell lines established by fractionated irradiation: Tumor protein p53-inducible protein 3 confers sensitivity to ionizing radiation. Int J Radiat Oncol Biol Phys. 77:858–866. 2010. View Article : Google Scholar : PubMed/NCBI
29	Voltan R, Secchiero P, Corallini F and Zauli G: Selective induction of TP53I3/p53-inducible gene 3 (PIG3) in myeloid leukemic cells, but not in normal cells, by Nutlin-3. Mol Carcinog. 53:498–504. 2014. View Article : Google Scholar : PubMed/NCBI
30	Qin X, Zhang S, Li B, Liu XD, He XP, Shang ZF, Xu QZ, Zhao ZQ, Ye QN and Zhao PK: p53-dependent upregulation of PIG3 transcription by γ-ray irradiation and its interaction with KAP1 in responding to DNA damage. Chin Sci Bull. 56:3162–3171. 2011. View Article : Google Scholar
31	Bourdon A, Minai L, Serre V, Jais JP, Sarzi E, Aubert S, Chrétien D, de Lonlay P, Paquis-Flucklinger V, Arakawa H, et al: Mutation of RRM2B, encoding p53-controlled ribonucleotide reductase (p53R2), causes severe mitochondrial DNA depletion. Nat Genet. 39:776–780. 2007. View Article : Google Scholar : PubMed/NCBI
32	Kimura T, Takeda S, Sagiya Y, Gotoh M, Nakamura Y and Arakawa H: Impaired function of p53R2 in Rrm2b-null mice causes severe renal failure through attenuation of dNTP pools. Nat Genet. 34:440–445. 2003. View Article : Google Scholar : PubMed/NCBI
33	Kas K, Finger E, Grall F, Gu X, Akbarali Y, Boltax J, Weiss A, Oettgen P, Kapeller R and Libermann TA: ESE-3, a novel member of an epithelium-specific ets transcription factor subfamily, demonstrates different target gene specificity from ESE-1. J Biol Chem. 275:2986–2998. 2000. View Article : Google Scholar : PubMed/NCBI
34	Tugores A, Le J, Sorokina I, Snijders AJ, Duyao M, Reddy PS, Carlee L, Ronshaugen M, Mushegian A, Watanaskul T, et al: The epithelium-specific ETS protein EHF/ESE-3 is a context-dependent transcriptional repressor downstream of MAPK signaling cascades. J Biol Chem. 276:20397–20406. 2001. View Article : Google Scholar : PubMed/NCBI
35	Jolma A, Kivioja T, Toivonen J, Cheng L, Wei G, Enge M, Taipale M, Vaquerizas JM, Yan J, Sillanpää MJ, et al: Multiplexed massively parallel SELEX for characterization of human transcription factor binding specificities. Genome Res. 20:861–873. 2010. View Article : Google Scholar : PubMed/NCBI
36	Maijgren S, Sur I, Nilsson M and Toftgård R: Involvement of RFX proteins in transcriptional activation from a Ras-responsive enhancer element. Arch Dermatol Res. 295:482–489. 2004. View Article : Google Scholar : PubMed/NCBI
37	Sengupta P, Xu Y, Wang L, Widom R and Smith BD: Collagen alpha1(I) gene (COL1A1) is repressed by RFX family. J Biol Chem. 280:21004–21014. 2005. View Article : Google Scholar : PubMed/NCBI
38	Badis G, Berger MF, Philippakis AA, Talukder S, Gehrke AR, Jaeger SA, Chan ET, Metzler G, Vedenko A, Chen X, et al: Diversity and complexity in DNA recognition by transcription factors. Science. 324:1720–1723. 2009. View Article : Google Scholar : PubMed/NCBI