Keywords
Endometriosis, MiRNA, Extracellular vesicle
Endometriosis is an inflammatory disorder that affects 10–15% of women of reproductive age and is
characterized by the presence of endometrial tissue outside the uterus1. The symptoms are heterogeneous, with
the most common including pelvic pain, dysmenorrhea, and infertility 2. Often, Nonspecific symptoms may
lead to misinterpretation, resulting in delays in diagnosis 3. Visualization of ovarian endometriotic cysts and
deep endometriotic lesions can be performed using ultrasonography and MRI; however, these methods are
unable to identify peritoneal endometriosis or endometriosis-associated adhesions 4. The American Society for
Reproductive Medicine (ASRM) classification system categorizes endometriosis into four stages based on the
1Department of Genetics, Faculty of Basic Sciences and New Biological Technologies, University of Science and
Culture, ACECR, Tehran, Iran. 2Department of Genetics, Reproductive Biomedicine Research Center, Royan
Institute for Reproductive Biomedicine, ACECR, Tehran, Iran. 3Department of Endocrinology and Female Infertility,
Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, ACECR, Tehran,
Iran. 4Department of Stem Cells and Developmental Biology, Cell Science Research Center, Royan Institute for
Stem Cell Biology and Technology, ACECR, Tehran, Iran. 5Department of Basic and Population Based Studies
in NCD, Reproductive Epidemiology Research Center, Royan Institute, ACECR, Tehran, Iran. 6Department of
Obstetrics and Gynecology, Arash Women’s Hospital, Tehran University of Medical Sciences, Tehran, Iran. email:
[email protected];
[email protected]
OPEN
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number of lesions and the degree of infiltration. More advanced stages of endometriosis (III-IV) can lead to
complications such as pelvic pain, which may lead to a hysterectomy. Moreover, Pearce et al. demonstrated
that malignant transformation of ovarian endometrioma into ovarian cancer, particularly the clear cell and
endometrioid subtypes5.
The gold standard diagnosis of endometriosis is performed by laparoscopy with direct visualization. This
procedure is invasive, costly, and in endometrioma cases through the excision of ovaries can lead to subfertility
or infertility in women since is associated with diminished ovarian reserve 6. Therefore, the need for a non-
invasive, biomarker-based approach is evident 7. To the best of our knowledge, reliable diagnostic biomarkers
are still unavailable.
Extracellular vesicles (EVs) refer to a diverse population of vesicles that vary in size and biogenesis
mechanism, which are released into the extracellular space by various cell types 8. Exosomes and microvesicles
are two main subtypes of EVs that can transfer signals to recipient cells, establishing a new communication
mechanism between cells, which they are considered as a novel communication paradigm9. mRNA and miRNA
derived from EVs are functional and can exchange genetic material among cells 10. Recently, there has been
increasing interest in utilizing the content of EVs—especially miRNA—as a diagnostic biomarker 11.
miRNAs are small non-coding RNA molecules, typically ranging from 20 to 24 nucleotides in length. It is
estimated that approximately 30% of transcriptomes are regulated by miRNAs 12,13. A miRNA can be found
bound to proteins, such as Argonaute proteins, sorted in EVs, or circulating freely in plasma/ serum. miRNAs
play vital functional roles in cells, such as differentiation, neoplastic transformation, regeneration, and cell
replication14. Several studies have demonstrated that the dysregulation of miRNAs is involved in endometriosis
and may develop lesion implantation, angiogenesis, proliferation, adhesion, and increased levels of cytokines,
such as migration inhibitory factor (MIF) 15. In a study conducted by Caroline Frisendahl et al., it was shown
that the downregulation of miR-193 and miR-374 promotes cell migration and may serve as therapeutic targets
for this condition16. Research has also evaluated the expression of miRNAs in the serum, plasma17and ectopic /
eutopic tissues of endometriosis patients18.
Based on current knowledge, a consensus biomarker for the diagnosis of endometriosis has not yet been
identified. However, studies have demonstrated that the number of EVs elevates in the early stages of the
disease19. The spread and stability of EVs, make them an ideal biomarker14.
Consequently, we have chosen to measure the expression levels of candidate miRNAs found in plasma-
derived EVs. This decision is based on the belief that these miRNAs could serve as non-invasive diagnostic
biomarkers for endometriosis, representing a promising avenue for exploration.
Results
Results of effect sized analysis
Cohen’s d values for the significantly dysregulated miRNAs ranged from 0.61 to 0.92 indicating moderate to
large effect sizes. Despite the limited sample size, these effect sizes suggest meaningful biological differences
between the endometriosis and control groups (Supplementary Table S1).
Selection of MiRNAs and prediction of targets
Using bioinformatics tools, we evaluated potential targets and signaling pathways of microRNAs in the 60
selected articles. The analysis of the results ultimately yielded a list of 15 miRNAs (Table 1).
MiRTarBase database, enrichment, and pathway analysis
miR-148a, miR-451a, miR-154, miR-23b, and miR-100 were selected as candidate microRNAs for further
investigation due to their potential involvement in the development of endometriosis. The selection criteria were
based on the target genes regulated by these microRNAs and their established significance in the pathogenesis
of endometriosis.
miR-451a
No pathogenic single nucleotide polymorphisms (SNPs)of miR-451a were identified. The five signaling pathways
in which miR-451a received the highest scores were analyzed using Enrichr software (Supplementary Table S2).
miR-148a
The miR-148a molecule is an intergenic microRNA. The signaling pathways associated with this miRNA suggest
a potential link to cancer. To date, no pathogenic SNPs have been reported for this miRNA (Supplementary
Table S3).
miR-23b
miR-23b is located in intron 3 of the AOPEP (aminopeptidase O) gene on chromosome 9q, and no pathogenic
SNPs associated with this miRNA have been reported (Supplementary Table S4).
miR-100
miR-100 is a secretory microRNA that is studied in various fluids, tissues, and EVs27,33. It is an intergenic RNA
located on chromosome 11q (Supplementary Table S5).
miR-154
miR-154 is an intergenic microRNA, and no SNPs have been reported for it. Bioinformatics analysis indicates
that miR-154 is involved in the Hippo signaling pathway (Supplementary Table S6).
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Final list of MiRNAs selection
The dysregulation of miR-451a in plasma, serum, and endometriotic tissue has been investigated. miR-451a
plays a role in regulating the expression of the MIF cytokine. miR-23b and miR-23a are downregulated in
both ectopic and eutopic endometrium when compared to normal endometrium 18. Microarray analysis
has demonstrated that miR-100-5p is expressed differentially in ectopic tissue compared to eutopic tissue 27.
Furthermore, bioinformatics analysis has identified COX-2 as the target of miR-100.
Bioinformatics analyses have demonstrated that miR-154 plays a role in the Hippo signaling pathway.
In addition, miR-154, in conjunction with other microRNAs such as miR-196b-5p, may serve as a potential
diagnostic biomarker for endometriosis30. Research indicates that miR-148a regulates the expression of DNMT1
and HLA-G mRNA34 (Table 2). In the first step, studies conducted without any time limitations up to April 2023
were reviewed. Subsequently, five miRNAs were selected for the laboratory phase using bioinformatics analysis.
STRING model
Protein-protein interaction networks were analyzed using the STRING database (Fig. 1).
The expression level of Circulating and EV- associated candidate MiRNAs
After successfully passing the normality test, the data were analyzed using a parametric test. The data were
normalized with miR-16. Our findings indicated that miR-451, miR-23b, miR-148a, and miR-100 were
significantly downregulated in the endometriosis group compared to the control group. Surprisingly, miR-154
was not detected in either group (Fig. 2).
miRNA name Reasons for selection of miRNAs
miR-451a Targeting of MIF
miR-23b-3p Targeting of SF-1, STAR
And Cyp19A1
miR-100-5p Targeting of COX2
miR-154-5p Involved in the Hippo signaling pathway
miR-148a-3p Targeting of HLA-G, DNMT1
Table 2. Candidate MiRNAs based on their targets. In the first step, the studies conducted in 2007–2023 were
reviewed, then using bioinformatics analysis 5 miRNAs were selected for the laboratory phase.
miRNA name Up/Down regulation (controversy) Reasons for selection Some of references
miR-451a Up (5)*
Down (2) Targeting of MIF 16,19
miR-196a-5p Up (1) Targeting of PGR 20
miR-503-5p Up (1)
Down (1)
Targeting of SMAD2
Location of host gene
21
miR-29c-3p Up (4)
Down (1)
Targeting of C-JUN and MMP2
Detection by NGS study and highlight it
22
miR-196b-5p Up (1)
Down (4)
Targeting of TGFBR2
Exonic miR
Involved in estrogen signaling
23
miR-200a-3p Up (1)
Down (5) Targeting of TGFB and SMAD 24
miR-200b-3p Down (5) Targeting of TGFB 24
miR-23a Down (1) Targeting of SF-1 and STAR
And Cyp19A1
18
miR-23b Down (2) Targeting of SF-1 and STAR
And Cyp19A1
18,25
miR-126-3p Up (2)
Down (4) Targeting of CXCL12 26
miR-100-5p Up (6) Targeting of COX2 27,28
miR-199a Up (2)
Down (3) Targeting of TGFB2 and TGFR1 27,29
miR-154-5p Down (1) Involved in hippo signaling pathway 30
miR-214-3p Down (1) Use of it in fibrosis therapy of endometriosis 31
miR-148a Up (3)
Down (2) Targeting of Hela-G 32
Table 1. The list of candidate mirnas. *These numbers refer to count of articles that evaluation intended
miRNAs.
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qRT-PCR efficiency results
Amplification efficiency determined via Lin Reg PCR indicated a range between 1.91 and 1.92 for all candidate
miRAN, except for miR-154, which indicate an efficiency of 1.0. This result supports the specificity and reliability
of the qRT-PCR reactions, while indicating a lack of detectable expression for miR-154 in both case and control
group (Supplementary Table S7).
Discussion
The aim of this study was to investigate whether the expression levels of plasma derived circulating and EV-
associated candidate miRNAs changes and the end can serve as a potential biomarker for the disease. EV-miRNAs
have higher stability, specificity and sensitivity compared other type biomarkers such as circulating cell- free
DNA, making them potentially more effective for early disease detection and monitoring. The packaging of EVs
is purposeful and they are tissue specific allowing for targeted diagnosis and monitoring. In additional they can
more accurate and reliable than traditional biomarker like proteins35–37.
Fig. 1. STRING model. The protein- protein interaction acquired via SRING database.
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In the first step, we identified candidate miRNAs based on previous literature. Subsequently, through
bioinformatics analysis, we performed a final selection of miRNAs. The expression levels of these miRNAs
had been evaluated in serum, plasma, and tissue in previous studies 17,18,30. The expression levels of individual
microRNAs exhibit considerable variability across studies, attributable to multiple confounding factors,
including: sample size, sample type (serum, plasma, tissue, or extracellular vesicles), menstrual cycle phase
of subjects, experimental techniques used and sampling conditions. To minimize inter-individual variability,
we collected all samples in the morning and restricted sampling to early proliferative phase (menstrual cycle
days 3–5). Notably, the expression profile of EV-associated microRNAs diverges from cellular or tissue-derived
patterns. This discrepancy arises from two biologically significant mechanisms: active sorting and cellular
clearance.
Fig. 2. Relative expression of miRNAs in plasma. Plasma EVs derived candidate miRNAs were evaluated
with the RT-PCR from women with endometriosis (n = 13) and control group (n = 11). Data represent the
mean ± SEM, and the miRNAs expression is normalized to the miR-16 expression. *P < 0.05.
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miRNAs can regulate the expression levels of messenger RNAs (mRNAs) and play an essential role in both
normal and abnormal biological processes. In addition to cellular miRNAs, they can secrete from different
cell types via EVs 38. EVs transport and also transduce miRNAs into target cells, even distant via the blood
circulation. EVs- derived miRNA changes the expression levels and functions of recipient cells 39. Therefore,
investigating plasma-derived miRNAs will aid for endometriosis progression, therapy, and the identification of
novel diagnostic biomarker. We chose candidate miRNAs based on their targets and signaling pathway, which
play an important role in endometriosis.
The macrophage migration inhibitory factor (MIF) is one of the targets of miR-451a. Endometriotic cells
secrete the MIF cytokine and has mitogenic properties that promote the growth of these cells. MIF can stimulate
the secretion of factors associated with cell proliferation and angiogenesis. Elevated levels of MIF have been
shown in endometriotic tissues and peritoneal fluid of patients with endometriosis 40. The expression level of
miR-451a is inversely related to the extent of lesions 17. Also, the miR-451a serves as a reproducible diagnostic
serum biomarker1. Our findings indicate that miR-451a is downregulated in EV-derived plasma, which may
influence the progression of the disease.
The steroidogenic factor-1 (SF-1) regulates through miR-23a and miR-23b. SF-1 and other estrogenic
enzymes regulate estrogen formation that has a significant role in endometriosis. An increase in the expression
level of SF-1 is associated with a reduction in the expression levels of miR-23a and miR-23b in endometrial
tissue. The upregulation of SF-1 leads to an increase in the expression of steroidogenic acute regulatory protein
(stAR) and cytochrome P450 aromatase (CYP19A1), both of which are essential components of the estrogen
synthesis pathway18. Also, our study indicates that the expression level of miR-23b reduce in EV-plasma derived
can lead to the dysregulation of target genes and contribute to the progression of endometriosis.
Bioinformatics analysis has demonstrated that COX-2 is a validated target of miR-100. COX-2 is expressed
during proliferation, differentiation, and inflammation, which are prominent indexes of endometriosis. COX-2
has a significant role in pain associated with endometriosis41. Despite the downregulation of miR-100 in ectopic
versus eutopic endometrium38,22 our study indicates that the expression level of EV-derived plasma miR-100
decreases in the endometriosis group.
The expression level of miR-154 is not affected by the menstrual cycle. It can be considered, either alone
or in combination with hsa-miR-196b-5p, hsa-miR-378a-3p, and hsa-miR-33a-5p, as a non-invasive potential
diagnostic biomarker30. In addition, miR-154 is involved in the Hippo signaling pathway which has crucial
roles in both normal and abnormal functions of endometrial cells in endometriosis. This pathway regulates cell
proliferation, apoptosis and epithelial mesenchymal transition (EMT) process. Therefore, dysregulation of Hippo
signaling pathway can develop endometriosis42. We could not detect miR-154 in the EVs derived from plasma
of our participants, including both the case and control groups. We performed amplification efficiency analysis
with LinReg PCR software. While all other miRNAs showed amplification above 1.91, miR-154 exhibited an
efficiency of 1.0 consistence with the true absence of miR- 154. This finding indicates that the lack of detectable
expression of miR-154 in circulating and EV- associated RNA derived from plasma of case and control groups
in this study is probably due to inter- individual or population specific variability, differences in RNA isolation
Methods
or sample processing and technical limitation.
Hypoxia is a hallmark of endometriosis that leads to altered methylation of the promoters of several genes
involved in the development of endometriosis. The miR-148a/AUF complex suppresses the function of DNMT1
mRNA, resulting in hypomethylation 34. HLA-G can protect the fetus from maternal immune surveillance
and rejection. Finding has shown that serum levels of HLA-G are higher in women with endometriosis
compared to a control group, that indicatea the runaway power of ectopic endometrial tissue of the immune
system34. Additionally, miR-148a is an element of the G protein-coupled estrogen receptor (GPER)/miR-148a/
HLA-G signaling pathway in ovarian endometriosis. The expression level of miR-148a is reduced in both the
endometrium and endometriosis-associated ovarian cancer32. Furthermore, miR-148a can affect the expression
of BCL-2 and the activity of caspase-3/9, making it a potential candidate for treatment of endometriosis32.
We showed that the expression levels of miR-451a, miR-23b, miR-148 and miR-100 significantly decrease
in plasma derived EV of endometriosis patients. We propose that plasma-derived EV-miRNAs could serve as a
potential diagnostic biomarker for endometriosis. However, further studies with a larger case and control groups
are suggested to validate these findings.
Materials and methods
Eligibility criteria and search strategy
At the first, we reviewed all published studies in the PubMed database, without any time limitations, up to April
2023. The search terms applied were (“MicroRNAs“[Mesh]) OR (“microRNA “[Title/Abstract]) OR (“miR“[Title/
Abstract]) AND (“endometriosis“[Title]) OR (“endometriosis“[Title/Abstract]) OR (“Endometriosis“[Mesh]).
We assessed studies involving patients with endometriosis that examined miRNAs in relation to their role in
disease development or their potential as diagnostic biomarkers. The study population consisted of women with
endometriosis at any stage, diagnosed through laparoscopy and/or Doppler sonography (Fig. 3).
Study selection
All obtained references were independently screened on the keywords in title/abstract or Mesh terms. Five
miRNAs were selected for our next in vitro phase using bioinformatics analysis. Finally, the expression level
of candidate miRNAs were evaluated in the plasma derived EV in the case (n = 13) and control group (n = 11).
Bioinformatics analysis
By utilizing the miRTarBase database ( https://mirtarbase.cuhk.edu.cn), the validated targets of miRNAs were
acquired. Followed by the identification of associated miRNA pathway using the lists of uploaded genes in the
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Fig. 3. Flow diagram of inclusion and exclusion steps and search strategy. This flow diagram illustrates the
systematic process of applying inclusion and exclusion criteria during the research, as well as the search
strategy used to identify relevant studies.
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Enrichr software ( https://maayanlab.cloud/Enrichr/). Ultimately, five miRNAs were selected for the invitro
phase.
Criteria for MiRNAs selection
Two criteria for selection of miRANs is considered. First, the role of miRNA in progrresion of endometriosis
or intredused it as a potentially diagnostic biomarker based on previous litreture. Second, specific targets or
pathway miRNAs in roled in endometriosis based on bioinformatics analysis.
STRING model
The validated targets of candidate miRNAs were acquired from the miRTarBase database based on reports
with more consensus assay including q-PCR, micro array and NGS. After removing repetitive targets among
five miRNAs the overlapping targets between miRTarBase and TargetScan ( https://www.targetscan.org) were
identified. Then protein- protein interaction achieved by the STRING (https://string-db.org/) database.
Patients and control groups
Twenty-four women aged 20–37 years old with normal body mass index (BMI) were enrolled in this study
between June and august 2019 at the Royan Institute (Tehran, Iran). The study was approved by the Research
Ethics Committee of the Royan Institute (Code No.: IR.ACECR.ROYAN.REC.1398.144), and written informed
consent was obtained from all participants.
The presence of the disease was confirmed either by the laparoscopy and histopathological examinations
(n = five) or doppler sonography( n n = eight). All cases who selected by laparoscopy suffered of an ovarian
endometrioma at stages III–IV according to the Revised American Fertility Society Classification System
(ARMS).
The control group was composed of 11 normal ovulatory women without endometriosis who were infertile
due to male factors. The absence of the endometrioma cysts was confirmed with the doppler sonography.
Women with a history of an irregular menstruation, cancers, inflammatory and autoimmune disease, fibroma,
and adenoma were excluded from the study.
At the sampling time, all women were on days two-five of the menstrual cycle phase. No subjects had taken
any hormonal treatments at least three months ago. All of the samples were collected in the morning.
Effect sized analysis
To show that sample size cannot affect the validity of the results, Cohen’s d was calculated to estimate effect size,
using conventional thresholds (α = 0.05, two tail).
Plasma isolation
Peripheral blood samples (6 ml) were collected into a tube containing citrate as the anticoagulant agent. Whole
blood was centrifuged at 2500 g at room temperature for 15 min. The plasma was transferred into a new
microtube, and then centrifuge procedure was repeated. Platelet-free plasma (PFP) was isolated by a high-speed
centrifugation at 13,000 g for 5 min. Finally, the PFPs were aliquoted and stored at −80 °C until use.
RNA extraction of plasma and EV isolation
Total RNA including circulating and EV- associated RNA was extracted from 2 ml of plasma. we used the
Plasma/Serum Circulating and Exosomal RNA Purification Mini Kit (Cat. No. 51000, Norgen Biotek). Briefly
2 ml of plasma was mixed with lysis buffer A to disrupt EV membranes. And release their RNA contents. Ethanol
was then added, and the lysate was passed through spin column to bind RNA. After several washing steps, RNA
was eluted in 50 ml of elution solution A and sorted at −80 °C until further analysis. This kit designed to extract
total RNA from plasma/ serum including both circulating and EV-associated RNA. The kit lyses extracellular
vesicles during the extraction process, allowing access to vesicle-contained RNA without requiring physical EV
isolation (e.g., ultracentrifugation or NTA).
Quantitative reverse transcription PCR assay
Immediately after extracting RNA, cDNA was synthesized using reverse transcription (RT) enzyme (Takara,
USA) following the manufacturer’s protocol. Stem-loop primers were used for more specifics. Primers were
designed based on miRNA sequences obtained from the miRbase ( https://mirbase.org/) database as follows
(Supplementary Table S8). The prepared master mix contained 10ng RNA, 4 ml enzyme buffer, 1 ml RT enzyme,
and 1 ml stem loop master primer. The expression level of the candidate miRNAs was measured by the RT-PCR
SYBR Green. Then, the expression levels of miRNAs were normalized with the expression level of hsa-miR-16.
Assessment of PCR efficiency
LinReg PCR software was used to calculate the efficiency of each qRT-PCR reaction. This software analysis row
fluorescence data, adjust the base line automatically, and identifies the exponential phase (Window of linearity)
for each sample. Then it uses linear regression to estimate the slope of that phase, which is used to determine the
reaction efficiency for each sample.
Statistical analysis
The expression level of plasma derived EVs candidate miRNAs were assessed between the normal and
endometriosis group. All data was analyzed for normal distribution. After successfully passing the normality
parametric test, the SPSS software was used. A P value < 0.05 was considered as statistically significant.
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Data availability
The archived datasets analyzed in support of the conclusions of this article will be made available upon request
by the first or corresponding authors.
Received: 13 April 2025; Accepted: 30 June 2025
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Acknowledgements
This study was financially sponsored by the genetic department of Royan Institute Tehran, Iran. The authors
dedicate this article to the memory of Dr. Saeid Kazemi Ashtiani, the late founder of Royan Institute.
Author contributions
SAS, PA, FSh, AM, MT, MSh, Contributed to conception and design; SAS, Contributed to all experimental work,
data and statistical analysis, and interpretation of data; PA, MT, Were responsible for overall supervision; MH,
AM Cooperated in the sampling section; MH, ZCh, Was responsible for patients assessment and diagnosis,
also for patient recruitment to study; SAS Collected the samples; AGh, Calculated the number of samples; ZCh
Cooperated with some experimental tests; FSh helped in design of E.V , approval tests and supervision of man-
uscript in EV isolation part; AGh analyzed the row data; MSh, AGh, RA helped with interpretation of results;
SAS, ZCh Drafted the initial manuscript and wrote the manuscript; PA, MT, AM Contributed to revise and edit
the manuscript; All authors read and approved the final manuscript.
Funding
No funds, grants, or other support was received except full financial support from the genetic department of
Royan Institute Tehran, Iran. Institutional Review Board Statement: The study was conducted in accordance
with the Declaration of Helsinki, and approved by the Research Ethics Committee of the Royan Institute (Code
No.: IR.ACECR.ROYAN.REC.1398.144).
Declarations
Competing interests
The authors declare no competing interests.
Informed consent
Informed consent was obtained from all subjects involved in the study.
Additional information
Supplementary Information The online version contains supplementary material available at h t t p s : / / d o i . o r g / 1
0 . 1 0 3 8 / s 4 1 5 9 8 - 0 2 5 - 0 9 6 6 0 - 1 .
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