OpenLB
Open Library of Bioscience
Advanced Search
International journal of biological sciences
2016;12 (4): 427-45.

MiRNA Transcriptome Profiling of Spheroid-Enriched Cells with Cancer Stem Cell Properties in Human Breast MCF-7 Cell Line.

Lily Boo, Wan Yong Ho, Norlaily Mohd Ali, Swee Keong Yeap, Huynh Ky, Kok Gan Chan, Wai Fong Yin, Dilan Amila Satharasinghe, Woan Charn Liew, Sheau Wei Tan, Han Kiat Ong, Soon Keng Cheong
Author Information
  1. Lily Boo: 1. Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, 43000 Cheras, Malaysia;
  2. Wan Yong Ho: 2. Faculty of Medicine and Health Sciences, University of Nottingham (Malaysia Campus), 43500 Semenyih, Malaysia;
  3. Norlaily Mohd Ali: 1. Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, 43000 Cheras, Malaysia;
  4. Swee Keong Yeap: 3. Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Malaysia.
  5. Huynh Ky: 4. Department of Agriculture Genetics and Breeding, College of Agriculture and Applied Biology, Cantho University, 84071, Vietnam.
  6. Kok Gan Chan: 5. Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia.
  7. Wai Fong Yin: 5. Division of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, Kuala Lumpur, Malaysia.
  8. Dilan Amila Satharasinghe: 3. Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Malaysia.; 6. Faculty of Veterinary Medicine and Animal Science, University of Peradeniya, 20400, Sri Lanka.
  9. Woan Charn Liew: 3. Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Malaysia.
  10. Sheau Wei Tan: 3. Institute of Bioscience, Universiti Putra Malaysia, 43400 Serdang, Malaysia.
  11. Han Kiat Ong: 1. Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, 43000 Cheras, Malaysia;
  12. Soon Keng Cheong: 1. Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, 43000 Cheras, Malaysia;; 7. Cryocord Sdn Bhd, Persiaran Cyberpoint Selatan, 63000 Cyberjaya, Malaysia.
PMID: 27019627 DOI: 10.7150/ijbs.12777

Abstract

Breast cancer is the second leading cause of cancer-related mortality worldwide as most patients often suffer cancer relapse. The reason is often attributed to the presence of cancer stem cells (CSCs). Recent studies revealed that dysregulation of microRNA (miRNA) are closely linked to breast cancer recurrence and metastasis. However, no specific study has comprehensively characterised the CSC characteristic and miRNA transcriptome in spheroid-enriched breast cells. This study described the generation of spheroid MCF-7 cell in serum-free condition and the comprehensive characterisation for their CSC properties. Subsequently, miRNA expression differences between the spheroid-enriched CSC cells and their parental cells were evaluated using next generation sequencing (NGS). Our results showed that the MCF-7 spheroid cells were enriched with CSCs properties, indicated by the ability to self-renew, increased expression of CSCs markers, and increased resistance to chemotherapeutic drugs. Additionally, spheroid-enriched CSCs possessed greater cell proliferation, migration, invasion, and wound healing ability. A total of 134 significantly (p<0.05) differentially expressed miRNAs were identified between spheroids and parental cells using miRNA-NGS. MiRNA-NGS analysis revealed 25 up-regulated and 109 down-regulated miRNAs which includes some miRNAs previously reported in the regulation of breast CSCs. A number of miRNAs (miR-4492, miR-4532, miR-381, miR-4508, miR-4448, miR-1296, and miR-365a) which have not been previously reported in breast cancer were found to show potential association with breast cancer chemoresistance and self-renewal capability. The gene ontology (GO) analysis showed that the predicted genes were enriched in the regulation of metabolic processes, gene expression, DNA binding, and hormone receptor binding. The corresponding pathway analyses inferred from the GO results were closely related to the function of signalling pathway, self-renewability, chemoresistance, tumorigenesis, cytoskeletal proteins, and metastasis in breast cancer. Based on these results, we proposed that certain miRNAs identified in this study could be used as new potential biomarkers for breast cancer stem cell diagnosis and targeted therapy.

Keywords

MCF-7 breast cancer cancer stem cells miRNA transcriptome next generation sequencing spheroid culture.

References

Oncogene. 2000 Jun 29;19(28):3138-45 [PMID: 10918568]
Nature. 2001 Nov 1;414(6859):105-11 [PMID: 11689955]
Clin Cancer Res. 2003 Jan;9(1 Pt 2):447S-54S [PMID: 12538499]
Proc Natl Acad Sci U S A. 2003 Apr 1;100(7):3983-8 [PMID: 12629218]
Crit Rev Oncol Hematol. 2003 May;46(2):165-86 [PMID: 12711360]
Cell Cycle. 2004 Apr;3(4):414-5 [PMID: 15004528]
Dev Cell. 2004 Apr;6(4):483-95 [PMID: 15068789]
Breast Cancer Res Treat. 2004 Jun;85(3):281-91 [PMID: 15111767]
Oncogene. 2004 Sep 20;23(43):7274-82 [PMID: 15378087]
Mol Cancer Ther. 2004 Oct;3(10):1335-42 [PMID: 15486201]
Cancer Res. 2005 Aug 15;65(16):7065-70 [PMID: 16103053]
Cancer Res. 2005 Dec 1;65(23):10946-51 [PMID: 16322242]
Mol Interv. 2006 Jun;6(3):140-8 [PMID: 16809475]
Dev Biol. 2007 Feb 1;302(1):1-12 [PMID: 16989803]
Nat Methods. 2006 Oct;3(10):801-6 [PMID: 16990812]
Breast Cancer Res. 2006;8(5):R59 [PMID: 17062128]
Stem Cell Rev. 2005;1(2):131-8 [PMID: 17142847]
Oncogene. 2007 May 14;26(22):3279-90 [PMID: 17496922]
Cancer Res. 2007 Jul 1;67(13):6130-5 [PMID: 17616669]
Int J Oncol. 2007 Dec;31(6):1403-13 [PMID: 17982667]
Virchows Arch. 2008 Jan;452(1):1-10 [PMID: 18040713]
Cell. 2007 Dec 14;131(6):1109-23 [PMID: 18083101]
Cell Stem Cell. 2007 Nov;1(5):555-67 [PMID: 18371393]
J Clin Invest. 2008 Jun;118(6):2111-20 [PMID: 18497886]
Breast Cancer Res. 2008;10(3):R52 [PMID: 18541018]
J Cell Mol Med. 2009 Aug;13(8B):2236-52 [PMID: 18681906]
Cell Cycle. 2008 Sep 1;7(17):2643-6 [PMID: 18719391]
Oncogene. 2009 Jan 22;28(3):461-8 [PMID: 18978815]
Nucleic Acids Res. 2009 Jan;37(1):1-13 [PMID: 19033363]
Nat Protoc. 2009;4(1):44-57 [PMID: 19131956]
Int J Cancer. 2009 May 1;124(9):2060-70 [PMID: 19132753]
BMC Mol Biol. 2009 Feb 22;10:12 [PMID: 19232136]
PLoS One. 2009;4(4):e5311 [PMID: 19390579]
Cell Death Differ. 2010 Feb;17(2):209-14 [PMID: 19461655]
BMC Med Genomics. 2009 Jun 09;2:35 [PMID: 19508715]
J Cell Mol Med. 2010 Jun;14(6B):1693-706 [PMID: 19538464]
Lab Invest. 2010 Feb;90(2):234-44 [PMID: 20010854]
Proc Natl Acad Sci U S A. 2010 Jan 12;107(2):610-5 [PMID: 20080726]
J Biotechnol. 2010 Jul 1;148(1):3-15 [PMID: 20097238]
Cancer Res. 2010 Apr 1;70(7):2809-18 [PMID: 20332239]
J Invest Dermatol. 2010 Jul;130(7):1877-86 [PMID: 20376064]
Endocrinology. 2010 Jun;151(6):2462-73 [PMID: 20382698]
Clin Cancer Res. 2010 May 1;16(9):2580-90 [PMID: 20388854]
Biochem Pharmacol. 2010 Aug 15;80(4):423-30 [PMID: 20394737]
Cancer Res. 2010 Jun 1;70(11):4624-33 [PMID: 20484027]
Oncogene. 2010 Jul 22;29(29):4194-204 [PMID: 20498642]
J Biomol Screen. 2010 Aug;15(7):820-9 [PMID: 20639504]
Discov Med. 2005 Jun;5(27):278-82 [PMID: 20704888]
Urol Oncol. 2012 May-Jun;30(3):314-8 [PMID: 20843707]
J Natl Cancer Inst. 2010 Nov 3;102(21):1637-52 [PMID: 20935265]
Cancer Genomics Proteomics. 2010 Sep-Oct;7(5):261-77 [PMID: 20952761]
Breast Cancer Res. 2010;12(5):210 [PMID: 21067538]
Oncogene. 2011 Apr 21;30(16):1880-91 [PMID: 21170085]
Breast Cancer Res. 2011 Jan 10;13(1):R2 [PMID: 21219636]
Biochem Biophys Res Commun. 2011 Apr 1;407(1):28-33 [PMID: 21342656]
Int J Cancer. 2010 Dec 15;127(12):2893-917 [PMID: 21351269]
Cancer Epidemiol Biomarkers Prev. 2011 May;20(5):733-9 [PMID: 21357727]
Cancer Res. 2011 Apr 15;71(8):2926-37 [PMID: 21393507]
Cell Stem Cell. 2011 May 6;8(5):486-98 [PMID: 21549325]
BMC Gastroenterol. 2011 Jun 14;11:71 [PMID: 21669008]
Sci Signal. 2011 Jun 14;4(177):ra41 [PMID: 21673316]
J Clin Pathol. 2011 Nov;64(11):937-46 [PMID: 21680574]
J Mammary Gland Biol Neoplasia. 2011 Sep;16(3):257-70 [PMID: 21818544]
Breast Cancer Res. 2011 Aug 12;13(4):215 [PMID: 21884641]
Genome Med. 2011 Aug 31;3(8):56 [PMID: 21888691]
Cancer Res. 2011 Sep 15;71(18):5950-4 [PMID: 21917736]
Methods Mol Biol. 2012;826:163-75 [PMID: 22167648]
Oncogene. 2012 Oct 18;31(42):4509-16 [PMID: 22179828]
BMC Cancer. 2012 Jan 28;12:48 [PMID: 22284662]
Cell Struct Funct. 2012;37(1):27-38 [PMID: 22307404]
Breast Cancer Res. 2012 Feb 21;14(1):R34 [PMID: 22353773]
PLoS One. 2012;7(2):e31864 [PMID: 22359637]
EMBO J. 2012 Apr 4;31(7):1752-63 [PMID: 22373578]
BMC Biol. 2012 Mar 22;10:29 [PMID: 22439642]
Nat Methods. 2012 Mar 25;9(5):509-16 [PMID: 22447133]
Br J Cancer. 2012 Apr 24;106(9):1512-9 [PMID: 22472879]
Arch Dermatol Res. 2013 Jan;305(1):35-47 [PMID: 22740085]
J Cell Sci. 2012 Jul 1;125(Pt 13):3015-24 [PMID: 22797912]
Nat Methods. 2012 Jul;9(7):671-5 [PMID: 22930834]
PLoS One. 2012;7(9):e44398 [PMID: 22970209]
PLoS One. 2012;7(9):e44640 [PMID: 22970274]
J Transl Med. 2012 Sep 19;10 Suppl 1:S6 [PMID: 23046710]
Nature. 2012 Nov 15;491(7424):399-405 [PMID: 23103869]
Sensors (Basel). 2012;12(9):12347-60 [PMID: 23112716]
Stem Cell Res Ther. 2012 Oct 31;3(5):41 [PMID: 23114057]
PLoS One. 2012;7(11):e49605 [PMID: 23185379]
Int J Oncol. 2013 Feb;42(2):453-9 [PMID: 23229446]
Cancer Res. 2013 May 1;73(9):2884-96 [PMID: 23338610]
Curr Opin Cell Biol. 2013 Apr;25(2):254-64 [PMID: 23347562]
Anal Biochem. 2013 Jun 1;437(1):17-9 [PMID: 23435308]
Carcinogenesis. 2013 Jul;34(7):1653-9 [PMID: 23514750]
BMC Cancer. 2013 May 02;13:221 [PMID: 23638973]
Cancer Cell Int. 2013 Jun 24;13(1):62 [PMID: 23799994]
PLoS One. 2013 Jun 24;8(6):e66809 [PMID: 23826142]
Int J Mol Sci. 2013 Jul 15;14(7):14712-23 [PMID: 23860207]
Braz J Med Biol Res. 2013 Jul;46(7):634-42 [PMID: 23903680]
Eur J Cancer. 2013 Nov;49(17):3598-608 [PMID: 23968733]
Cell. 2013 Sep 26;155(1):135-47 [PMID: 24074866]
PLoS One. 2013 Nov 25;8(11):e80266 [PMID: 24282530]
PLoS One. 2013 Nov 26;8(11):e82062 [PMID: 24303078]
J Cancer Sci Ther. 2012 Jul 26;4(7):214-222 [PMID: 24319544]
Carcinogenesis. 2014 May;35(5):1110-20 [PMID: 24374827]
PLoS One. 2014 Jan 07;9(1):e84941 [PMID: 24409314]
Front Genet. 2014 Jan 03;4:295 [PMID: 24427168]
Science. 1988 Apr 8;240(4849):177-84 [PMID: 2451290]
Front Endocrinol (Lausanne). 2014 Feb 04;5:10 [PMID: 24550888]
Oncotarget. 2014 Mar 15;5(5):1174-84 [PMID: 24632568]
PLoS One. 2014 Mar 17;9(3):e92248 [PMID: 24638075]
PLoS One. 2014 Apr 16;9(4):e95240 [PMID: 24740415]
Oncogenesis. 2014 May 26;3:e104 [PMID: 24861464]
Front Genet. 2014 May 27;5:149 [PMID: 24904649]
Cancer Gene Ther. 2014 Jul;21(7):290-6 [PMID: 24924200]
Clin Cancer Res. 2014 Sep 1;20(17):4636-46 [PMID: 24963047]
PLoS One. 2014 Aug 08;9(8):e102602 [PMID: 25105419]
Biomed Res Int. 2014;2014:187105 [PMID: 25126546]
PLoS One. 2014 Aug 19;9(8):e104510 [PMID: 25136862]
PLoS One. 2014 Sep 12;9(9):e106314 [PMID: 25215888]
Biomed Pharmacother. 2014 Oct;68(8):935-42 [PMID: 25451164]
Neoplasia. 2015 Jan;17(1):1-15 [PMID: 25622895]
Oncol Rep. 2015 Apr;33(4):1837-43 [PMID: 25634491]
J Cancer. 2015 Jul 28;6(9):901-12 [PMID: 26284142]
J Immunol Methods. 1983 Dec 16;65(1-2):55-63 [PMID: 6606682]

MeSH Term

Breast Neoplasms
Gene Expression Profiling
Gene Expression Regulation, Neoplastic
High-Throughput Nucleotide Sequencing
Humans
MCF-7 Cells
MicroRNAs
Neoplastic Stem Cells

Chemicals

MicroRNAs
Journal Article Research Support, Non-U.S. Gov't

Word Cloud

Similar Articles

Cited By