Selection of Endogenous Control Reference Genes for Studies on Type 1 or Type 2 Endometrial Cancer

Overview

Journal Sci Rep

Specialty Science

Date 2020 May 23

PMID 32439920

Citations 17

Authors

Thangesweran Ayakannu

Anthony H Taylor

Justin C Konje

Affiliations

Soon will be listed here.

Abstract

A panel of 32 candidate reference genes was used to identify the most stable genes for gene normalisation in quantitative RT-PCR studies using endometrial biopsies obtained from women with endometrial cancer (type 1 or type 2) and without cancer (controls). RNA from the biopsies was isolated, examined for purity and quality, and then reverse transcribed into cDNA before being subjected to real-time qRT-PCR analysis in triplicate within the TaqMan gene Expression Assay kit. The most 'stable' endogenous control genes were then identified using the geNorm qbase + 2 and NormFinder software packages. PSMC4, PUM1 and IPO8 were identified as the best reference genes combination for type 1 endometrial cancer (grades 1, 2 and 3), whereas for type 2 endometrial cancer (serous and carcinosarcoma), UBC, MRPL19, PGK1 and PPIA were the best reference genes combination. We conclude that the use of these normaliser combinations should provide accurate interpretation of gene expression at the transcript level in endometrial cancer studies especially for types 1 and 2 cancers.

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References

Krasnov G, Kudryavtseva A, Snezhkina A, Lakunina V, Beniaminov A, Melnikova N . Pan-Cancer Analysis of TCGA Data Revealed Promising Reference Genes for qPCR Normalization. Front Genet. 2019; 10:97. PMC: 6406071. DOI: 10.3389/fgene.2019.00097. View

Amoako A, Gebeh A, Marczylo E, Willets J, Elson J, Marczylo T . Impact of reference gene selection for type 2 cannabinoid receptor gene expression studies in human spermatozoa. Andrologia. 2012; 45(4):278-84. DOI: 10.1111/and.12006. View

Papageorgiou I, Nicholls P, Wang F, Lackmann M, Makanji Y, Salamonsen L . Expression of nodal signalling components in cycling human endometrium and in endometrial cancer. Reprod Biol Endocrinol. 2009; 7:122. PMC: 2774317. DOI: 10.1186/1477-7827-7-122. View

Hoogewijs D, Houthoofd K, Matthijssens F, Vandesompele J, Vanfleteren J . Selection and validation of a set of reliable reference genes for quantitative sod gene expression analysis in C. elegans. BMC Mol Biol. 2008; 9:9. PMC: 2254638. DOI: 10.1186/1471-2199-9-9. View

Huggett J, Dheda K, Bustin S, Zumla A . Real-time RT-PCR normalisation; strategies and considerations. Genes Immun. 2005; 6(4):279-84. DOI: 10.1038/sj.gene.6364190. View

Ayakannu T, Taylor A, Willets J, Brown L, Lambert D, McDonald J . Validation of endogenous control reference genes for normalizing gene expression studies in endometrial carcinoma. Mol Hum Reprod. 2015; 21(9):723-35. DOI: 10.1093/molehr/gav033. View

Pecorelli S . Revised FIGO staging for carcinoma of the vulva, cervix, and endometrium. Int J Gynaecol Obstet. 2009; 105(2):103-4. DOI: 10.1016/j.ijgo.2009.02.012. View

Gebeh A, Marczylo E, Amoako A, Willets J, Konje J . Variation in stability of endogenous reference genes in fallopian tubes and endometrium from healthy and ectopic pregnant women. Int J Mol Sci. 2012; 13(3):2810-2826. PMC: 3317689. DOI: 10.3390/ijms13032810. View

Farias-Eisner G, Su F, Robbins T, Kotlerman J, Reddy S, Farias-Eisner R . Validation of serum biomarkers for detection of early- and late-stage endometrial cancer. Am J Obstet Gynecol. 2009; 202(1):73.e1-5. DOI: 10.1016/j.ajog.2009.07.049. View

10.

Noyes R, Hertig A, Rock J . Reprint of: Dating the Endometrial Biopsy. Fertil Steril. 2019; 112(4 Suppl1):e93-e115. DOI: 10.1016/j.fertnstert.2019.08.079. View

11.

Shaarawy M . Biomarkers of intrinsic angiogenic and anti-angiogenic activity in patients with endometrial hyperplasia and endometrial cancer. Acta Oncol. 2001; 40(4):513-8. DOI: 10.1080/028418601750288253. View

12.

Bustin S . Absolute quantification of mRNA using real-time reverse transcription polymerase chain reaction assays. J Mol Endocrinol. 2000; 25(2):169-93. DOI: 10.1677/jme.0.0250169. View

13.

McDonald M, Bender D . Endometrial Cancer: Obesity, Genetics, and Targeted Agents. Obstet Gynecol Clin North Am. 2019; 46(1):89-105. DOI: 10.1016/j.ogc.2018.09.006. View

14.

Pinto F, Pacheco C, Ferreira D, Moradas-Ferreira P, Tamagnini P . Selection of suitable reference genes for RT-qPCR analyses in cyanobacteria. PLoS One. 2012; 7(4):e34983. PMC: 3319621. DOI: 10.1371/journal.pone.0034983. View

15.

Burns J, Summers B, Wang Y, Melikian A, Berahovich R, Miao Z . A novel chemokine receptor for SDF-1 and I-TAC involved in cell survival, cell adhesion, and tumor development. J Exp Med. 2006; 203(9):2201-13. PMC: 2118398. DOI: 10.1084/jem.20052144. View

16.

Andersen C, Jensen J, Orntoft T . Normalization of real-time quantitative reverse transcription-PCR data: a model-based variance estimation approach to identify genes suited for normalization, applied to bladder and colon cancer data sets. Cancer Res. 2004; 64(15):5245-50. DOI: 10.1158/0008-5472.CAN-04-0496. View

17.

Bustin S, Benes V, Garson J, Hellemans J, Huggett J, Kubista M . The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. Clin Chem. 2009; 55(4):611-22. DOI: 10.1373/clinchem.2008.112797. View

18.

Wong J, Huggins G, Debidda M, Munshi N, De Vivo I . Dichloroacetate induces apoptosis in endometrial cancer cells. Gynecol Oncol. 2008; 109(3):394-402. PMC: 2735772. DOI: 10.1016/j.ygyno.2008.01.038. View

19.

Kashima H, Shiozawa T, Miyamoto T, Suzuki A, Uchikawa J, Kurai M . Autocrine stimulation of IGF1 in estrogen-induced growth of endometrial carcinoma cells: involvement of the mitogen-activated protein kinase pathway followed by up-regulation of cyclin D1 and cyclin E. Endocr Relat Cancer. 2008; 16(1):113-22. DOI: 10.1677/ERC-08-0117. View

20.

Beekman L, Tohver T, Dardari R, Leguillette R . Evaluation of suitable reference genes for gene expression studies in bronchoalveolar lavage cells from horses with inflammatory airway disease. BMC Mol Biol. 2011; 12:5. PMC: 3039571. DOI: 10.1186/1471-2199-12-5. View