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3.杨欣 3.4区EN 多囊卵巢综合征合并无胰岛素抵抗子宫内膜的蛋白质组学和生物信息学分析 组学研究-Pcos 如何开展与筛选标准。
3.杨欣 3.4区EN 多囊卵巢综合征合并无胰岛素抵抗子宫内膜的蛋白质组学和生物信息学分析 组学研究-Pcos 如何开展与筛选标准。
Xin Yang, Wang Xiaoping, Ding Nan, Zhang Jian, Li Xiaofeng, Yuan Liwei,
Mengni Zhao & Fang Wang
To cite this article: Xin Yang, Wang Xiaoping, Ding Nan, Zhang Jian, Li Xiaofeng, Yuan
Liwei, Mengni Zhao & Fang Wang (2023): Proteomic and bioinformatic analysis of human
endometrium from polycystic ovarian syndrome with and without insulin resistance,
Gynecological Endocrinology, DOI: 10.1080/09513590.2023.2173948
Research Article
CONTACT Fang Wang ery_fwang@lzu.edu.cn Reproductive Medicine Center, Second Hospital of Lanzhou University, Lanzhou 730000, China.
†
Xin Yang and Xiaoping Wang contributed equally to this research.
Supplemental data for this article can be accessed online at https://doi.org/10.1080/09513590.2023.2173948.
© 2023 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group
This is an Open Access article distributed under the terms of the Creative Commons Attribution-NonCommercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits
unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
2 X. YANG ET AL.
was considered to be IR [10]). The Rotterdam criteria met the DAVID and the results were visualized with the software package
following 2–3 items: (1) Oligo- and/or anovulation; (2) Clinical ggplot2 in R. A p value < .05 was considered significant, and
and/or biochemical signs of hyperandrogenism; (3) Polycystic enriched GO terms or pathways were sorted by p values.
ovaries. At the same time, women were excluded from the study The tool Venn calculator can generate counts and detailed
if they had any of the following conditions: hypothyroidism, elements for each non-empty intersection for datasets with an
hyperprolactinemia, adrenal disease, hypertension, diabetes, hor- arbitrary number of groups. We plot the Venn diagram using
mone medication and the drugs affecting glucose metabolism PCOS vs. control, PCOS-IR vs. PCOS-non-IR differential pro-
in the last 3 months, pregnancy, and lactation. The control group teins, and then perform PCA with the ggprepel package R.
(n = 7) included women with successful pregnancies due to male Lasso regression analysis was performed to screen the key
factors and a routine ultrasound scan revealed normal ovarian proteins affecting the pregnancy outcomes in PCOS patients by
morphology and they had regular menstrual cycles. Demographic R (http://www.R-project.org) and Empower Stats (http://www.
characteristics and clinical biochemical parameters of the par- empowerstats.com, X&Y Solutions, Inc., Boston, MA). Key pro-
ticipants were collected. Demographic characteristics include age teins were found from raw data and differences in expression
and BMI recorded from outpatient medical records. Clinical levels between groups were analyzed.
biochemical indexes included basal testosterone (T), basal lutein-
izing hormone (LH), and basal follicle-stimulating hormone
(FSH), fasting blood glucose (FBG), fasting insulin (FINS), cho- Statistical analysis
lesterol (CHO), triglyceride (TG), high-density lipoprotein cho-
Normally distributed continuous data are presented as the
lesterol (HDL-C), low-density lipoprotein cholesterol (LDL-C),
means ± SE and were compared using the Student’s t test, while
and thyroid stimulating hormone (TSH), which were measured
non-parametric data were presented as the median (interquartile
at 2 to 5 days of menstruation by the Laboratory of Lanzhou
range) and were compared using the Mann–Whitney U test,
University Second Hospital. We then followed up on the preg-
categorical variables using the chi-square test or Fisher exact
nancy outcomes after the patient’s hospital visit, including live
test when appropriate. A two-sided p value < .05 was considered
births and miscarriages prior to 24 weeks. We recorded the time
statistically significant for all tests.
of endometrial collection and the time of the last menstrual
period of pregnancy, in months, and calculated the interval
between the time of endometrial collection and the time of final
Results
pregnancy. Informal permission was signed by all participants
prior to sample collection. The study was approved by the local Subject clinical characteristics
ethics committee of Lanzhou University Second Hospital. All
subjects gave informed consent prior to participation (Ethical Clinical and biochemical parameters for all subjects used in the
Approval Number: 2017 A-057). proteomic analysis are presented in Table 1. BMI, LH, T, FBG,
The endometrial samples were obtained using a pipelle endo- FINS, HOMA-IR, TG, and the interval between the time of
metrial aspirator at the time of hysteroscopy when the endometrium endometrial collection and the time of final pregnancy were
was in the proliferative phase (histological examination ensured statistically different among the three groups, and HDL-C and
that samples were taken during the proliferative phase) and during live birth rates were much lower in the PCOS-IR group than
the month in which the blood samples were obtained, then rinsed in the PCOS-non-IR group and the control group (p < .05). There
the surface with phosphate-buffered saline (PBS) to clean the excess were no statistical differences in age, FSH, CHO, LDL-C, and
blood and stored at –80 °C for proteomic techniques used. TSH between the three groups (p > .05).
Sample preparation and fractionation, data dependent acqui-
sition (DDA) mass spectrometry assay, mass spectrometry data
analysis, and database search were completed by Shanghai Table 1. Baseline clinical and biochemical parameters in PCOS-IR, PCOS-non-IR,
and control groups.
Applied Protein Technology (Supplementary document 1 provides
detailed procedures). PCOS-non-IR PCOS-IR
Control (n = 7) (n = 12) (n = 21) p value
Age (year) 27.00 ± 2.94 26.83 ± 2.533 25.24 ± 3.45 .246
BMI (kg/m2) 21.39 ± 2.81 20.80 ± 2.42 26.10 ± 3.00 <.001
Bioinformatic analysis FSH (mIU/mL) 5.67 ± 0.83 6.78 ± 0.96 6.42 ± 1.82 .295
LH (mIU/mL) 5.34 ± 0.63 10.93 ± 5.37 10.45 ± 5.33 .045
The data were normalized using the Limma package of the R T (ng/dL) 24.69 ± 11.36 38.8 ± 10.60 46.93 ± 17.65 .006
language. Differentially expressed proteins (DEPs) between PCOS FBG (mmol/L) 4.54 ± 0.41 4.94 ± 0.55 5.10 ± 0.59 .001
and control, PCOS-IR and PCOS-non-IR were identified as that FINS (mIU/mL) 8.97 ± 3.90 8.76 ± 11.77 24.68 ± 11.77 <.001
HOMA-IR 1.80 ± 0.80 1.94 ± 0.52 5.90 ± 2.94 <.001
with |log2 fold change (log2 FC) |>1 as the cutoff value. Proteins CHO (mmol/L) 3.65 ± 0.81 3.86 ± 0.75 4.17 ± 0.74 .279
with p < .05 calculated by the Bayes test were included in the TG (mmol/L) 0.99 ± 0.43 1.03 ± 0.63 1.85 ± 0.95 .013
DEPs list. The DEPs analysis was performed in R 4.1.0. The HDL-C (mmol/L) 1.45 ± 0.43 1.47 ± 0.24 1.14 ± 0.25 .007
ggpubr package was used to map volcanoes to visually show the LDL-C (mmol/L) 2.22 ± 0.52 2.44 ± 0.56 2.82 ± 0.71 .110
TSH (μIU/mL) 3.44 ± 2.22 2.61 ± 1.03 3.12 ± 1.51 .501
expression of differential proteins between PCOS and control, IP (mouth) 5.29 ± 1.60 8.42 ± 4.38 9.05 ± 2.69 .033
PCOS-IR and PCOS-non-IR. Live birth rate 7/7 (100.00%) 10/12 (83.33%) 10/21 (47.62%) .014
Gene ontology (GO) is an important method and tool to BMI: body mass index; FSH: follicle-stimulating hormone; LH: luteinizing hor-
annotate genes and their products, which is beneficial to the mone; T: testosterone; FBG: fasting blood glucose; FINS: fasting insulin;
integration and utilization of biological data. The annotated, HOMA-IR: homeostasis model assessment of insulin resistance; CHO: choles-
visualized Database DAVID is an online data synthesis tool that terol; TG: triglyceride; HDL-C: high-density lipoprotein cholesterol; LDL-C:
low-density lipoprotein cholesterol; TSH: thyroid stimulating hormone; IP:
lays the foundation for successful high-throughput gene function interval between the time of endometrial collection and the time of final
analysis. The GO and KEGG of the DEPs between PCOS and pregnancy.
control, PCOS-IR and PCOS-non-IR, were enriched using p < .05 was considered statistically significant.
Gynecological Endocrinology 3
Figure 1. Sample expression correction box diagram and volcano diagram. A: Protein expression before normalization. B: Protein expression after sample normal-
ization. The red sample represents the PCOS-non-IR group, the green sample represents the PCOS-IR group and the blue sample represents the control group. C:
PCOS vs. Control. D: PCOS-IR vs. PCOS-non-IR. (Red dots represent up-regulated differential proteins, green dots represent down-regulated proteins, and no sig-
nificantly changed genes are marked as gray dots).
Data processing and screening of differential genes was enriched in the extracellular exosome, membrane, cytosol,
blood microparticles, nucleoplasm, focal adhesions, and perinu-
The original dataset is normalized and presented as boxplots before clear regions of the cytoplasm (Figure 3B). The MF were enriched
and after normalization (Figure 1A,B). All samples had 5331 proteins in protein binding, RNA binding, long-chain fatty acid transporter
identified, 275 proteins were differentially expressed in the PCOS activity, electron carrier activity, GTP binding, and ATPase activity
vs. control group and 215 proteins were differentially expressed in (Figure 3C). The KEGG were enriched for salmonella infection,
the PCOS-IR group vs. PCOS-non-IR group, differences have been prion disease, oxidative phosphorylation, Parkinson’s disease, and
indicated in the volcano diagram (Figure 1C,D). metabolic pathways (Figure 3D).
GO and KEGG enrichment of DEPs in endometrial tissues Identification of key proteins in endometrial tissues
between different groups between different groups
All DEPs were uploaded to the DAVID online tool for analysis We visually displayed the intersection of differential proteins between
of GO and KEGG pathway enrichment. Then, the R language PCOS vs. control and PCOs-IR vs. PCOs-non-IR groups using Venn
ggplot2 package is used for visual processing. The DEPs were diagrams and found 25 proteins with significant differences between
classified into three groups including biological process (BP), the groups (ACTR1A, ZC3H15, C1QC, NPIPB5, EMC4, TSC22D2,
cellular component (CC), and molecular function (MF). DDX1, BRI3BP, CKB, PRDX2, CNN3, ABRAXAS2, CYBA, MCM7,
In the PCOS vs. control group, DEPs of BP were enriched TMEM167A, GLT8D1, MUC5B, ATRX, TTPAL, HM13, KRT9,
in cellular protein metabolic processes, platelet degranulation, TAGLN2, USP5, TUBA4A, and ORM1) (Figure 4A). We performed
post-translational protein modification, extracellular matrix orga- PCA using 25 PCOS vs. control, PCOS-IR vs. PCOS-non-IR dif-
nization, translational initiation, and cellular response to oxida- ferential proteins and found that the differential proteins were clearly
tive stress (Figure 2A). CCs were enriched in extracellular distinguished between PCOS-IR, PCOS-non-IR, and control (Figure
exosomes, blood microparticles, endoplasmic reticulum, extra- 4B). Then using the LASSO regression model, we screened out five
cellular spaces, spectrin-associated cytoskeletons, and focal adhe- DEPs, which ACTR1A, TSC22D2, CKB, ABRAXAS2, and TAGLN2
sions (Figure 2B). The MF were enriched in RNA binding, were associated with live birth of patients with PCOS (Figure 4C,D).
structural constituent of the cytoskeleton, protein binding, spec- Then using the LASSO regression model, we screened five DEPs,
trin binding, extracellular matrix structural constituent, collagen ACTR1A, TSC22D2, CKB, ABRAXAS22, and TAGLN2, for associ-
binding, and actin binding (Figure 2C). KEGG were enriched ation with live birth in patients with PCOS (Figure 4E).
in coronavirus disease – COVID-19, complement and coagulation
cascades, DNA replication, ferroelectricity, ECM-receptor inter-
action, and carbon metabolism (Figure 2D). The expression of key proteins between PCOS-IR, PCOS-
In the PCOS-IR vs. PCOS-non-IR group, the DEPs of BP were non-IR, and control groups
enriched in platelet degranulation, neutrophil degranulation, viral
processes, very long-chain fatty acid catabolic processes, golgi to The expression levels of the key proteins were extracted from the
plasma membrane transport, protein localization to the plasma raw data, the protein expression was transformed by LOG2 so
membrane, and intracellular protein transport (Figure 3A). CC that the data followed a normal distribution, and the differences
4 X. YANG ET AL.
Figure 2. PCOS vs. Control: GO and KEGG enrichment of differentially expressed proteins (DEPs). (A) biological process, (B) cellular component, (C) molecular
function, and (D) KEGG pathway analysis.
Figure 3. PCOS-IR vs. PCOS-non-IR: GO and KEGG enrichment of differentially expressed proteins (DEPs). (A) biological process, (B) cellular component, (C) molecular
function, and (D) KEGG pathway analysis.
Gynecological Endocrinology 5
Figure 4. A: Venn diagrams to visually display the intersection of differential proteins between PCOS vs. control and PCOs-IR vs. PCOs-non-IR groups. B: PCA between
the PCOS-IR, PCOS-non-IR and control groups. The red sample represents the PCOS-non-IR group, the green sample represents the PCOS-IR group and the blue
sample represents the control group. C and D: The LASSO regression model for live birth of PCOS-IR patients. E: ROC of different factors on pregnancy outcome.
Figure 5. Analysis of key proteins expression: (A, B, E) ACTR1A and CKB were higher in PCOS-IR group, while TSC22D2 was lower in PCOS-IR group (p < .05). (C
and D) ABRAXAS2 was higher in all PCOS groups and TAGLN2 was low in all PCOS groups (p < .05), but there was no difference between the PCOS-IR and
PCOS-non-IR groups (p > .05). Pearson correlation analysis between key proteins and HOMA-IR: (F and G) ACTR1A and CKB was significantly positively correlated
with HOMA-IR. (H, I, and J) there was no significant correlation between TAGLN2, ABRAXAS2 and TSC22D2 with HOMA-IR.
between the groups were analyzed. We find that ACTR1A and and PCOS-non-IR groups (p > .05) (Figure 5D,C). Pearson cor-
CKB are higher in the PCOS-IR group, while TSC22D2 is lower relation analysis shows that ACTR1A and CKB are significantly
in the PCOS-IR group (p < .05) (Figure 5A,B,E). ABRAXAS2 was positively correlated with HOMA-IR and negatively correlated
higher in all PCOS groups and TAGLN2 was lower in all PCOS with HOMA-IR, while TAGLN2, TSC22D2, and ABRAXAS2 are
groups (p < .05), but there was no difference between the PCOS-IR not correlated with HOMA-IR (Figure 5F–J).
6 X. YANG ET AL.
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