Differential expression and functional analysis of micro RNAs in <i>Papio</i> <i>anubis</i> induced with endometriosis for early detection of the disease

Irene Mwongeli Waita; Atunga Nyachieo; Daniel Chai; Samson Muuo; Naomi Maina; Daniel Kariuki; Cleophas M. Kyama; Irene Mwongeli Waita; Atunga Nyachieo; Daniel Chai; Samson Muuo; Naomi Maina; Daniel Kariuki; Cleophas M. Kyama

doi:10.3934/molsci.2020015

AIMS Molecular Science

2020, Volume 7, Issue 4: 305-327. doi: 10.3934/molsci.2020015

Previous Article Next Article

Research article

Differential expression and functional analysis of micro RNAs in Papio anubis induced with endometriosis for early detection of the disease

1.
Institute of Basic Sciences, Technology and Innovation, Pan African University, P.O. Box 62000-00200, Nairobi, Kenya
2.
Institute of Primate Research, P.O Box 24481 Karen 00502, Nairobi, Kenya
3.
Kenya Medical Research Institute, P.O Box 54840-00200, Nairobi, Kenya
4.
Department of Biochemistry, College of Health Sciences, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Nairobi, Kenya
5.
Department of Medical Laboratory Sciences, College of Health Sciences, Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Nairobi, Kenya

Received: 07 July 2020 Accepted: 02 September 2020 Published: 10 September 2020

Endometriosis is a common gynecological disorder affecting approximately 10% of women of reproductive age who often experience chronic pelvic pain and infertility. Laparoscopy, which is invasive and expensive, is the gold standard for diagnosis of endometriosis. A simple minimally-invasive test for endometriosis-specific biomarkers which is yet to be realized would offer a timely and accurate diagnosis for the disease thereby allowing early treatment intervention. Although aberrant microRNA expression has been implicated in endometriosis in several studies, conflicting results have been reported. This study hypothesized that the use of an appropriate animal model will provide a unique entry point for the discovery of biomarkers for early diagnosis of endometriosis. The study aimed at identifying miRNAs that are differentially expressed in eutopic endometrium of induced endometriosis in Papio anubis for early detection of endometriosis. Female adult baboons (n = 3) were induced with endometriosis by intraperitoneal inoculation of autologous menstrual endometrium. We sequenced small RNA samples obtained from normal (control) and diseased eutopic endometrium. Quality reads from the sequences were subjected to differential expression analysis to identify dysregulated microRNAs and genes from other non-coding small RNA in the samples using a bioinformatics approach. Through in-silico analysis, gene targets of the dysregulated miRNA and their functions were determined. Our findings show significant high expression of seven microRNAs namely miR-199a-3p, miR-145-5p, miR-214-3p, miR-143-3p, miR-125b-5p, miR-199a-5p and miR-10b-5p. The study also reveals five microRNAs that were significantly down regulated and they include miR-29b-3p, miR-16-5p, miR-342-3p, miR-378a-3p and let-7g-5p. Seventeen genes from non-coding small RNAs were significantly dysregulated. The dysregulated microRNAs and genes play important roles in pathogenesis of endometriosis. Our findings indicate that specific miRNA signatures are associated with endometriosis, and the dysregulated miRNAs could constitute new and informative biomarkers for early diagnosis of endometriosis.
- endometrium,
- miRNAs,
- small RNAs,
- Illumina sequencing,
- endometriosis,
- baboons
Citation: Irene Mwongeli Waita, Atunga Nyachieo, Daniel Chai, Samson Muuo, Naomi Maina, Daniel Kariuki, Cleophas M. Kyama. Differential expression and functional analysis of micro RNAs in Papio anubis induced with endometriosis for early detection of the disease[J]. AIMS Molecular Science, 2020, 7(4): 305-327. doi: 10.3934/molsci.2020015

Related Papers:

Abstract

Endometriosis is a common gynecological disorder affecting approximately 10% of women of reproductive age who often experience chronic pelvic pain and infertility. Laparoscopy, which is invasive and expensive, is the gold standard for diagnosis of endometriosis. A simple minimally-invasive test for endometriosis-specific biomarkers which is yet to be realized would offer a timely and accurate diagnosis for the disease thereby allowing early treatment intervention. Although aberrant microRNA expression has been implicated in endometriosis in several studies, conflicting results have been reported. This study hypothesized that the use of an appropriate animal model will provide a unique entry point for the discovery of biomarkers for early diagnosis of endometriosis. The study aimed at identifying miRNAs that are differentially expressed in eutopic endometrium of induced endometriosis in Papio anubis for early detection of endometriosis. Female adult baboons (n = 3) were induced with endometriosis by intraperitoneal inoculation of autologous menstrual endometrium. We sequenced small RNA samples obtained from normal (control) and diseased eutopic endometrium. Quality reads from the sequences were subjected to differential expression analysis to identify dysregulated microRNAs and genes from other non-coding small RNA in the samples using a bioinformatics approach. Through in-silico analysis, gene targets of the dysregulated miRNA and their functions were determined. Our findings show significant high expression of seven microRNAs namely miR-199a-3p, miR-145-5p, miR-214-3p, miR-143-3p, miR-125b-5p, miR-199a-5p and miR-10b-5p. The study also reveals five microRNAs that were significantly down regulated and they include miR-29b-3p, miR-16-5p, miR-342-3p, miR-378a-3p and let-7g-5p. Seventeen genes from non-coding small RNAs were significantly dysregulated. The dysregulated microRNAs and genes play important roles in pathogenesis of endometriosis. Our findings indicate that specific miRNA signatures are associated with endometriosis, and the dysregulated miRNAs could constitute new and informative biomarkers for early diagnosis of endometriosis.

Abbreviation DE: Differential Expression/Differentially Expressed; DR miRNAs/MTGs: Down Regulated miRNAs/MTGs; EB: Endometrial Tissue Biopsy; GO: Gene Ontology; IPR: Institute of Primate Research; KEGG: Kyoto Encyclopedia of genes and genomes; MiRNA(s): Micro RNA(s); mRNA(s): messenger RNA(s); MTGs: MicroRNA Target Genes; : ; SRA: Sequence Reads Archive; sRNA(s): small RNA(s); UR miRNAs/MTGs: Up Regulated;
Acknowledgments

The study was supported by Pan African University-Institute of Basic sciences, Technology and Innovation (PAUISTI) and a grant from Research, Production and Extension Division (RPE)-JKUAT.

Conflict of interest

The authors declare that they have no competing interests.

References

[1]	Giudice LC, Kao LC (2004) Endometriosis. Lancet 364: 1789-1799. doi: 10.1016/S0140-6736(04)17403-5
[2]	Panir K, Schjenken JE, Robertson SA, et al. (2018) Non-coding RNAs in endometriosis: a narrative review.24: 497-515.
[3]	Tamaresis JS, Irwin JC, Goldfien GA, et al. (2014) Molecular classification of endometriosis and disease stage using high-dimensional genomic data. Endocrinology 155: 4986-4999. doi: 10.1210/en.2014-1490
[4]	Rogers PAW, Adamson GD, Al-Jefout M, et al. (2017) Research Priorities for Endometriosis: Recommendations from a Global Consortium of Investigators in Endometriosis. Reprod Sci 24: 202-226. doi: 10.1177/1933719116654991
[5]	Berkley KJ, Rapkin AJ, Papka RE (2005) The pains of endometriosis. Science 308: 1587-1589. doi: 10.1126/science.1111445
[6]	Nnoaham KE, Hummelshoj L, Webster P, et al. (2011) Impact of endometriosis on quality of life and work productivity: A multicenter study across ten countries. Fertil Steril 96: 366-373.e8. doi: 10.1016/j.fertnstert.2011.05.090
[7]	Simoens S, Dunselman G, Dirksen C, et al. (2012) The burden of endometriosis: Costs and quality of life of women with endometriosis and treated in referral centres. Hum Reprod 27: 1292-1299. doi: 10.1093/humrep/des073
[8]	Nisenblat V, Prentice L, Bossuyt PMM, et al. (2016) Combination of the non-invasive tests for the diagnosis of endometriosis. Cochrane Database Syst Rev 7: CD012281.
[9]	ESHRE (2013) Management of Women with Endometriosis. Guidel Eur Soc Hum Reprod Embryol 1-97.
[10]	Ahn SH, Singh V, Tayade C (2017) Biomarkers in endometriosis: challenges and opportunities. Fertil Steril 107: 523-532. doi: 10.1016/j.fertnstert.2017.01.009
[11]	Bokor A, Kyama CM, Vercruysse L, et al. (2009) Density of small diameter sensory nerve fibres in endometrium: A semi-invasive diagnostic test for minimal to mild endometriosis. Hum Reprod 24: 3025-3032. doi: 10.1093/humrep/dep283
[12]	D'Hooghe TM, Kyama CM, Chai D, et al. (2009) Nonhuman primate models for translational research in endometriosis. Reprod Sci 16: 152-161. doi: 10.1177/1933719108322430
[13]	Kyama CM, Mihalyi A, Chai D, et al. (2007) Baboon model for the study of endometriosis. Women's Heal 3: 637-646. doi: 10.2217/17455057.3.5.637
[14]	Fazleabas AT (2006) A baboon model for inducing endometriosis. Methods Mol Med 121: 95-99.
[15]	Fazleabas AT, Brudney A, Gurates B, et al. (2002) A modified baboon model for endometriosis. Ann N Y Acad Sci 955: 308-317. doi: 10.1111/j.1749-6632.2002.tb02791.x
[16]	Marí-Alexandre J, Sánchez-Izquierdo D, Gilabert-Estellés J, et al. (2016) miRNAs regulation and its role as biomarkers in endometriosis. Int J Mol Sci 17: 1-16. doi: 10.3390/ijms17010093
[17]	Saare M, Rekker K, Laisk-Podar T, et al. (2017) Challenges in endometriosis miRNA studies—From tissue heterogeneity to disease specific miRNAs. Biochim Biophys Acta Mol Basis Dis 1863: 2282-2292. doi: 10.1016/j.bbadis.2017.06.018
[18]	Yovich JL, Rowlands PK, Lingham S, et al. (2020) Pathogenesis of endometriosis: Look no further than John Sampson. Reprod Biomed Online 40: 7-11. doi: 10.1016/j.rbmo.2019.10.007
[19]	Yang Y, Wang Y, Yang J, et al. (2012) Adolescent Endometriosis in China: A Retrospective Analysis of 63 Cases. J Pediatr Adolesc Gynecol 25: 295-299. doi: 10.1016/j.jpag.2012.03.002
[20]	Louise Hull M, Nisenblat V (2013) Tissue and circulating microRNA influence reproductive function in endometrial disease. Reprod Biomed Online 27: 515-529. doi: 10.1016/j.rbmo.2013.07.012
[21]	Valencia-Sanchez MA, Liu J, Hannon GJ, et al. (2006) Control of translation and mRNA degradation by miRNAs and siRNAs. Genes Dev 20: 515-524. doi: 10.1101/gad.1399806
[22]	Ibrahim SA, Hassan H, Götte M (2014) MicroRNA-dependent targeting of the extracellular matrix as a mechanism of regulating cell behavior. Biochim Biophys Acta Gen Subj 1840: 2609-2620. doi: 10.1016/j.bbagen.2014.01.022
[23]	Weber JA, Baxter DH, Zhang S, et al. (2010) The microRNA spectrum in 12 body fluids. Clin Chem 56: 1733-1741. doi: 10.1373/clinchem.2010.147405
[24]	Nothnick WB (2017) MicroRNAs and Endometriosis: Distinguishing Drivers from Passengers in Disease Pathogenesis. Semin Reprod Med 35: 173-180. doi: 10.1055/s-0037-1599089
[25]	Teague EMCO, Van der Hoek KH, Van der Hoek MB, et al. (2009) MicroRNA-regulated pathways associated with endometriosis. Mol Endocrinol 23: 265-275. doi: 10.1210/me.2008-0387
[26]	Santamaria X, Taylor H (2014) MicroRNA and gynecological reproductive diseases. Fertil Steril 101: 1545-1551. doi: 10.1016/j.fertnstert.2014.04.044
[27]	Burney RO, Hamilton AE, Aghajanova L, et al. (2009) MicroRNA expression profiling of eutopic secretory endometrium in women with versus without endometriosis. Mol Hum Reprod 15: 625-631. doi: 10.1093/molehr/gap068
[28]	Datta A, Das P, Dey S, et al. (2019) Genome-wide small RNA sequencing identifies micrornas deregulated in non-small cell lung carcinoma harboring gain-of-function mutant P53. Genes (Basel) 10: 852. doi: 10.3390/genes10110852
[29]	Marí-Alexandre J, Barceló-Molina M, Belmonte-López E, et al. (2018) Micro-RNA profile and proteins in peritoneal fluid from women with endometriosis: their relationship with sterility. Fertil Steril 109: 675-684.e2. doi: 10.1016/j.fertnstert.2017.11.036
[30]	Haikalis ME, Wessels JM, Leyland NA, et al. (2018) MicroRNA expression pattern differs depending on endometriosis lesion type. Biol Reprod 98: 623-633. doi: 10.1093/biolre/ioy019
[31]	Panir K, Schjenken JE, Robertson SA, et al. (2018) Non-coding RNAs in endometriosis: A narrative review. Hum Reprod Update 24: 497-515. doi: 10.1093/humupd/dmy014
[32]	Rekker K, Tasa T, Saare M, et al. (2018) Differentially-expressed mirnas in ectopic stromal cells contribute to endometriosis development: The plausible role of miR-139-5p and miR-375. Int J Mol Sci 19: 1-11. doi: 10.3390/ijms19123789
[33]	Zhao L, Gu C, Ye M, et al. (2018) Integration analysis of microRNA and mRNA paired expression profiling identifies deregulated microRNA-transcription factor-gene regulatory networks in ovarian endometriosis. Reprod Biol Endocrinol 16: 18-22. doi: 10.1186/s12958-018-0335-0
[34]	Yang L, Liu HY (2014) Small RNA molecules in endometriosis: Pathogenesis and therapeutic aspects. Eur J Obstet Gynecol Reprod Biol 183: 83-88. doi: 10.1016/j.ejogrb.2014.10.043
[35]	Vodolazkaia A, Yesilurt BT, Kyama CM, et al. (2016) Vascular endothelial growth factor pathway in endometriosis: Genetic variants and plasma biomarkers. Fertil Steril 105: 988-996. doi: 10.1016/j.fertnstert.2015.12.016
[36]	D'Hooghe TM, Bambra CS, Raeymaekers BM, et al. (1999) Pelvic inflammation induced by diagnostic laparoscopy in baboons. Fertil Steril 72: 1134-1141. doi: 10.1016/S0015-0282(99)00406-9
[37]	D'Hooghe TM, Bambra CS, Raeymaekers BM, et al. (1995) Intrapelvic injection of menstrual endometrium causes endometriosis in baboons (Papio cynocephalus and Papio anubis). Am J Obstet Gynecol 173: 125-134. doi: 10.1016/0002-9378(95)90180-9
[38]	Clontech (2016) Supplement: SMARTer® smRNA-Seq Kit for Illumina®. 1-15.
[39]	Agilent Technologies, Agilent Technologies Agilent DNA 1000 Kit Guide, 2016. Available from: https://www.agilent.com/cs/library/usermanuals/public/G2938-90014_DNA1000Assay_KG.pdf.
[40]	Illumina Inc (2011) Sequencing Library qPCR Quantification Guide. Illumina Tech Manuals 1-27.
[41]	Illumina Inc (2017) Illumina sequencing introduction. Illumina Seq Introd 1-8. Available from: http://www.illumina.com/content/dam/illumina-marketing/documents/products/illumina_sequencing_introduction.pdf.
[42]	Saeidipour B, Bakhshi S (2013) The relationship between organizational culture and knowledge management,& their simultaneous effects on customer relation management. Adv Environ Biol 7: 2803-2809.
[43]	Barturen G, Rueda A, Hamberg M, et al. (2014) sRNAbench: profiling of small RNAs and its sequence variants in single or multi-species high-throughput experiments. Methods Next Gener Seq 1: 21-31.
[44]	Kozomara A, Birgaoanu M, Griffiths-Jones S (2019) MiRBase: From microRNA sequences to function. Nucleic Acids Res 47: D155-D162. doi: 10.1093/nar/gky1141
[45]	Karere GM, Glenn JP, Vandeberg JL, et al. (2010) Identification of baboon microRNAs expressed in liver and lymphocytes. J Biomed Sci 17: 1-8. doi: 10.1186/1423-0127-17-54
[46]	Karere GM, Glenn JP, VandeBerg JL, et al. (2012) Differential microRNA response to a high-cholesterol, high-fat diet in livers of low and high LDL-C baboons. BMC Genomics 13: 320. doi: 10.1186/1471-2164-13-320
[47]	Costa B (2017) sRNA-workflow Documentation. Available from: https://readthedocs.org/projects/srna-workflow/downloads/pdf/master/.
[48]	Agarwal V, Bell GW, Nam JW, et al. (2015) Predicting effective microRNA target sites in mammalian mRNAs. Elife 4: 1-38. doi: 10.7554/eLife.05005
[49]	Georgakilas G, Vlachos IS, Zagganas K, et al. (2016) DIANA-miRGen v3.0: Accurate characterization of microRNA promoters and their regulators. Nucleic Acids Res 44: D190-D195. doi: 10.1093/nar/gkv1254
[50]	Braza-Boïls A, Mari-Alexandre J, Gilabert J, et al. (2014) MicroRNA expression profile in endometriosis: Its relation to angiogenesis and fibrinolytic factors. Hum Reprod 29: 978-988. doi: 10.1093/humrep/deu019
[51]	Laudanski P, Charkiewicz R, Kuzmicki M, et al. (2013) MicroRNAs expression profiling of eutopic proliferative endometrium in women with ovarian endometriosis. Reprod Biol Endocrinol 11: 78. doi: 10.1186/1477-7827-11-78
[52]	Bashti O, Noruzinia M, Garshasbi M, et al. (2018) miR-31 and miR-145 as Potential Non-Invasive Regulatory Biomarkers in Patients with Endometriosis. Cell J 20: 84-89.
[53]	Adammek M, Greve B, Kassens N, et al. (2013) MicroRNA miR-145 inhibits proliferation, invasiveness, and stem cell phenotype of an in vitro endometriosis model by targeting multiple cytoskeletal elements and pluripotency factors. Fertil Steril 99: 1346-1355.e5. doi: 10.1016/j.fertnstert.2012.11.055
[54]	Yang H, Kong W, He L, et al. (2008) MicroRNA expression profiling in human ovarian cancer: miR-214 induces cell survival and cisplatin resistance by targeting PTEN. Cancer Res 68: 425-433. doi: 10.1158/0008-5472.CAN-07-2488
[55]	Obata K, Morland SJ, Watson RH, et al. (1998) Frequent PTEN/MMAC mutations in endometrioid but not serous or mucinous epithelial ovarian tumors. Cancer Res 58: 2095-2097.
[56]	Sanchez G (2013) Las instituciones de ciencia y tecnología en los procesos de aprendizaje de la producción agroalimentaria en Argentina. El Sist argentino innovación Inst Empres y redes El desafío la creación y apropiación Conoc 1-49.
[57]	Welsh P, Doolin O, McConnachie A, et al. (2012) Circulating 25OHD, dietary vitamin D, PTH, and Calcium Associations with Incident Cardiovascular Disease and Mortality: The MIDSPAN Family Study. J Clin Endocrinol Metab 97: 4578-4587. doi: 10.1210/jc.2012-2272
[58]	Wright KR, Mitchell B, Santanam N (2017) Redox regulation of microRNAs in endometriosis-associated pain. Redox Biol 12: 956-966. doi: 10.1016/j.redox.2017.04.037
[59]	Snowdon J, Zhang X, Childs T, et al. (2011) The microRNA-200 family is upregulated in endometrial carcinoma. PLoS One 6: e22828. doi: 10.1371/journal.pone.0022828
[60]	Braza-Boïls A, Salam S, Josep M, et al. (2015) Peritoneal fluid modifies the microRNA expression profile in endometrial and endometriotic cells from women with endometriosis. Hum Reprod 30: 2292-2302. doi: 10.1093/humrep/dev204
[61]	Pateisky P, Pils D, Szabo L, et al. (2018) hsa-miRNA-154-5p expression in plasma of endometriosis patients is a potential diagnostic marker for the disease. Reprod Biomed Online 37: 449-466. doi: 10.1016/j.rbmo.2018.05.007
[62]	Wang L, Huang W, Fang X, et al. (2016) Analysis of Serum microRNA Profile by Solexa Sequencing in Women with Endometriosis. Reprod Sci 23: 1359-1370. doi: 10.1177/1933719116641761
[63]	Hawkins SM, Creighton CJ, Han DY, et al. (2011) Functional microRNA involved in endometriosis. Mol Endocrinol 25: 821-832. doi: 10.1210/me.2010-0371
[64]	Ohlsson Teague EMC, Print CG, Hull ML (2009) The role of microRNAs in endometriosis and associated reproductive conditions. Hum Reprod Update 16: 142-165. doi: 10.1093/humupd/dmp034
[65]	Nap AW (2012) Theories on the Pathogenesis of Endometriosis. Endometr Sci Pract 2014: 42-53. doi: 10.1002/9781444398519.ch5
[66]	Laganà AS, Garzon S, Götte M, et al. (2019) The pathogenesis of endometriosis: Molecular and cell biology insights. Int J Mol Sci 20: 1-42. doi: 10.3390/ijms20225615
[67]	Marquardt RM, Kim TH, Shin JH, et al. (2019) Progesterone and estrogen signaling in the endometrium: What goes wrong in endometriosis? Int J Mol Sci 20: 3822. doi: 10.3390/ijms20153822
[68]	Kashima H, Wu RC, Wang Y, et al. (2015) Laminin C1 expression by uterine carcinoma cells is associated with tumor progression. Gynecol Oncol 139: 338-344. doi: 10.1016/j.ygyno.2015.08.025
[69]	Zheng Y, Khan Z, Zanfagnin V, et al. (2016) Epigenetic Modulation of Collagen 1A1: Therapeutic Implications in Fibrosis and Endometriosis1. Biol Reprod 94: 1-10. doi: 10.1095/biolreprod.115.138115
[70]	Bhagwat SR, Chandrashekar DS, Ruchi K, et al. (2013) Endometrial Receptivity: A Revisit to Functional Genomics Studies on Human Endometrium and Creation of HGEx-ERdb. PLoS One 8: e58419. doi: 10.1371/journal.pone.0058419
[71]	Afshar Y, Hastings J, Roqueiro D, et al. (2013) Changes in Eutopic Endometrial Gene Expression During the Progression of Experimental Endometriosis in the Baboon, Papio Anubis1. Biol Reprod 88: 1-9. doi: 10.1095/biolreprod.112.104497
[72]	Rock JA (1995) The revised American Fertility Society classification of endometriosis: reproducibility of scoring.63: 1108-1110.

Reader Comments

Your name:*

Email:*
© 2020 the Author(s), licensee AIMS Press. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0)