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Bioimpacts. 13(3):191-206. doi: 10.34172/bi.2022.23813

Original Article

Apoptotic effects of human amniotic fluid mesenchymal stem cells conditioned medium on human MCF-7 breast cancer cell line

Roghiyeh Pashaei-Asl 1ORCID logo, Maryam Pashaiasl 2, 3, 4, Esmaeil Ebrahimie 5, Maryam Lale Ataei 2, Maliheh Paknejad 1, *ORCID logo
1Department of Clinical Biochemistry, Faculty of Medicine, Tehran University of Medical Sciences, Tehran, Iran
2Department of Anatomical Sciences, School of Medicine, Tabriz University of Medical Sciences
3Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
4Department of Reproductive Biology, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Tabriz, Iran
5Genomics Research Platform, School of Life Sciences, College of Science, Health and Engineering, La Trobe University, Melbourne, Victoria 3086, Australia
*Corresponding author: Maliheh Paknejad, Email: paknejadma@tums.ac.ir

Abstract

Introduction:

Breast cancer, as the most common malignancy among women, is shown to have a high mortality rate and resistance to chemotherapy. Research has shown the possible inhibitory role of Mesenchymal stem cells in curing cancer. Thus, the present work used human amniotic fluid mesenchymal stem cell-conditioned medium (hAFMSCs-CM) as an apoptotic reagent on the human MCF-7 breast cancer cell line.

Methods:

Conditioned medium (CM) was prepared from hAFMSCs. After treating MCF-7 cells with CM, a number of analytical procedures (MTT, real-time PCR, western blot, and flow cytometry) were recruited to evaluate the cell viability, Bax and Bcl-2 gene expression, P53 protein expression, and apoptosis, respectively. Human fibroblast cells (Hu02) were used as the negative control. In addition, an integrated approach to meta-analysis was performed.

Results:

The MCF-7 cells’ viability was decreased significantly after 24 hours (P < 0.0001) and 72 hours (P < 0.05) of treatment. Compared with the control cells, Bax gene’s mRNA expression increased and Bcl-2’s mRNA expression decreased considerably after treating for 24 hours with 80% hAFMSCs-CM (P = 0.0012, P < 0.0001, respectively); an increasing pattern in P53 protein expression could also be observed. The flow cytometry analysis indicated apoptosis. Results from literature mining and the integrated meta-analysis showed that hAFMSCs-CM is able to activate a molecular network where Bcl2 downregulation stands in harmony with the upregulation of P53, EIF5A, DDB2, and Bax, leading to the activation of apoptosis.

Conclusion:

Our finding demonstrated that hAFMSCs-CM presents apoptotic effect on MCF-7 cells; therefore, the application of hAFMSCs-CM, as a therapeutic reagent, can suppress breast cancer cells’ viabilities and induce apoptosis.

Keywords: MCF-7 cells, hAFMSCs-CM, Bax and Bcl-2 genes, P53, Apoptosis, Meta-analysis

Copyright

© 2023 The Author(s).
This work is published by BioImpacts as an open access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/). Non-commercial uses of the work are permitted, provided the original work is properly cited.


Introduction

Breast cancer remains as the most common lethal cancer among women around the world. 1 Currently, chemotherapy and surgery are the main approaches in the breast cancer clinical cure. However, the toxicity of chemotherapy agents on normal cells and their resistance to drugs have been considered as the main barrier to proceed with chemotherapy. 2,3 Nowadays, other types of treatments such as hormone replacement therapy and complementary therapies are under clinical consideration, among which targeted therapies, gene therapy, and stem cell therapy have gained considerable attention in the breast cancer research field. 4

In the last decade, stem cell treatment has been considered as a new method for discovering potential therapeutic approaches in cancer therapy. 5-10 In this regard, a great deal of researches have underscored the mesenchymal stem cells’ (MSCs) impact and their related factors on cancer cells. 7,11-13 MSCs are defined as regenerative undifferentiated cells capable of being differentiated into various cell types. 14 Recently, several studies have unveiled MSCs’ potential of suppressing tumors by inhibiting tumor cell proliferation and inducing apoptosis in cancer cells. 6,9,10,15,16 It is argued that the human amniotic stem cells (hAECs) anticancer effect is associated with the endogenous production of growth inhibitors which target tumor growth and progression. Some studies showed hAECs express a range of cytotoxic cytokines, such as IFN-γ, TGF-β, TNF-α and TNF-β as apoptotic inducer substances. 17 Additionally, hAECs secrete various interleukins, including IL-3, IL-4, and IL-2, to promote cytotoxicity in NK cells, the targeting of cancer cells, and the inhibition of tumor formation. 18,19

Furthermore, the ability of MSCs to move to primary tumors could be used to deliver anti-cancer factors to the tumor site. 20,21

Human amniotic fluid mesenchymal stem cell-conditioned medium (hAFMSCs-CM), as effective stem cells in treating a number of human diseases, are achieved from pregnant women at the end or the second trimester of pregnancy using amniocentesis. 22,23 Therefore, not only is the generation of such cell lines considerably easier than human embryonic stem cells (hESCs), they are also not subject to hESCs barriers. Some studies have revealed the inhibitory effects of stem cell conditioned medium (CM) on cancer cells. 24,25 CM has many advantages such as easy production, freezing-thawing competence, and packaging. 26

There is sufficient evidence about hAMSCs ability to produce IFN-γ and CXCL10 as key inhibitors of angiogenesis in the literature. 27 IFN-γ has the potential to hinder a tumor growth and enhance the apoptosis. 28,29 The hAMSCs-CM targets the ratio of cells in S and G2/M phase of PBMC cells leading to apoptosis induction. 30 In addition, hAFMSCs express a number of miRNAs (miR-195-3p, miR-19b-1-5p, miR-20a-5p, miR-20b-3p, miR-26a-1-3p, 708-3p, miR-16-1-3p, 3p, miR-15b-3p, 5p, miR-93-3p, miR204) 31-35 that negatively interact with anti-apoptotic targets.

hAFMSCs are known to have anti-cancer effects by inducing P53 (tumor suppresser) and P21 expression as well as reducing cyclin B1 and D1 after five days of co-culturing with human ovarian cancer cell lines. 6 P21 acts as a P53 transcriptional target, inhibiting cell cycle activity in G1/G2 phases. 36 P53 inhibits the proliferation of abnormal cells by adjusting cell cycle checkpoints in most tissues. 36 Various breast cancers mutate P53, resulting in more aggressive forms of the disease. 37

Bcl-2 inhibition by P53, as a transcriptional factor, is crucial for apoptosis induction. As an anti-apoptotic gene with high expression in most breast cancers, Bcl-2 is known as an effective factor in primary breast cancer prognosis. 38,39 Bax is a pro-apoptotic gene within the Bcl-2 family that presents expression in most breast cancers; a low expression of Bax leads to apoptosis resistance in breast cancer. 40

Based on our literature review and meta-analysis, hardly, we could findany study reporting the effect of the cell-free hAFMSCs conditioned medium on MCF-7 cells viability and the apoptosis. Therefore, the present work aims at assessing the apoptosis and meta-analysis of hAFMSCs-CM on breast cancer cell line.


Materials and Methods

hAFMSCs culture

hAFMSCswere prepared in accordance with previous studies. 22 Cells were plated in 25 cm2 cell culture flasks and DMEM-F12 (Dulbecco's Modified Eagle Medium/ Nutrient Mixture F-12) were supplemented with 15% FBS (Fetal Bovine serum), streptomycin (100 μg/mL), penicillin (100 units/mL), and 10 ng/mL of bFGF (basic fibroblast growth factor). The cells were cultured in an incubator with 5% CO2 humidified gas environment at 37°C.

Preparing conditioned medium

The hAFMSCs were cultured in 75 cm2 flasks toprepare the conditioned media. When the cells reached 70% to 80% confluency, they were washed with phosphate buffer saline (PBS) for 3 times and were kept in DMEM-L (Dulbecco's Modified Eagle Medium-Low Glucose), penicillin (100 units/mL), and streptomycin (100 μg/mL) for 48-72 hours at 37°C in a 5% CO2 humidified environment. Afterward, the media were collected from the flasks and centrifuged at 450 g for 10 minutes to acquire the supernatant and discard the pellet. Passing through a 0.22-μm filter, the media were stored at -80˚C (see ).

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Fig. 1. Schematic diagram showing condition medium preparation from hAFMSCs.

MCF-7 and Hu02 cells culture and treatment

MCF-7 (human breast cancer cell line) and Hu02 (human skin fibroblast cell line) cell lines were obtained from IBRC (Iranian Biological Resource Center). The cells were grown in 25 cm2 flasks with ESCs culture medium (DMEM supplemented with 10% FBS, 100 μg/mL of streptomycin, and 100 units/mL of penicillin). Cells were stored in a humid gas environment with 5% CO2 at 37°C. The media were replaced 3 times per week; 80% (v/v) hAFMSCs-CM was used for the treatment.

Cell viability assay

To determine the effect of hAFMSCs-CM, cell viability was evaluated using MTT (3-(4, 5-dimethylthiazol-2- yl)-2, 5-diphenyltetrazolium bromide) (Sigma, Cas# 298-93-1, USA) assay, as explained elsewhere. 6,41 MCF-7 and Hu02 cells were treated with different percentages of hAFMSCs-CM (20%, 40%, & 80%) for 24, 48, and 72 hours, respectively. In order to determine the cell viability, 0.5 mg/mL of MTT reagent was added to each well and incubated for 4 hours. Then, the MTT solution was removed and 100 μL DMSO (Dimethyl sulfoxide) was added to each well of the 96-well plate to solve formazan crystal. ELISA reader (BioTek, USA) was recruited to measure the absorbance at 570 nm. The untreated cells were considered as the control. To calculate the cell viability, the following formula was used:

Cell viability (%) = (Mean optical absorbance of the treated cells/ Mean optical absorbance of the control cells) × 100

RNA extraction and cDNA synthesis

While the control cells were maintained using the normal media and incubated, MCF-7 and Hu02 cells were treated with 80% of hAFMSCs-CM for total RNA extraction.

After 24 hours, total RNA of MCF-7 was extracted using the RiboEx kit (Gene All, Cat No.301-001, Korea) and the complementary DNA (cDNA) was synthesized from the total RNA using BioFACT kit (BioFACT, Cat No.BR441-096, Korea) based on the manufacture's protocols.

Real-time PCR

To characterize the hAFMSCs-CM effects on the pro-apoptotic (Bax) and the anti-apoptotic (Bcl-2) mRNA expression, Real-time PCR was carried out using SYBER Green (BioFACT, Cat. No. DQ385-40h, Korea) in ABI (Applied Biosystems Step One Plus) detection system in compliance with the manufacture's instruction. Table 1 illustrates the sequence of the primers used in this study; GAPDH (housekeeping gene) was considered as the internal control.

Table 1. The primers’ sequence used for the Real Time PCR
Primer Sequences Gene
Forward: 5'- CAAGATCATCAGCAATGCCTCC - 3'
Reverse: 5'- GCCATCACGCCAGTTTCC - 3'
GAPDH
Forward: 5'- GACTCCCCCCGAGAGGTCTT - 3'
Reverse: 5'- ACAGGGCCTTGAGCACCAGTT - 3'
BAX
Forward: 5'- GAGCGTCAACCGGGAGATGTC - 3'
Reverse: 5'- TGCCGGTTCAGGTACTCAGTC - 3'
Bcl-2

Relative gene expression was calculated using 2-∆∆Ct method based on the following formula 42 :

∆∆Ct = ∆Ct (treated) - ∆Ct (untreated) = (Ct, Target gene – Ct GAPDH) (treated) – (Ct Target gene – Ct GAPDH) (untreated)

Western blot analysis

After the hAFMSCs-CM treatment, western blot (WB) analysis was performed to evaluate the amount of P53 protein in MCF-7 and Hu02 cells. While MCF-7 cells were treated with 80% of hAFMSCs-CM, untreated cells were considered as the control. The cells were collected and lysed following a 24-hour incubation, then an electrophoresis was performed when equal amounts of crude protein (50 µg) of sample were loaded in each lane for 10% SDS-PAGE (sodium dodecyl sulfate-polyacrylamide gel). The extracted proteins were transferred to a polyvinylidene fluoride (PVDF) membrane where they were blocked with 2% no-fat milk for 1 hour. Next, they were incubated with mouse anti-P53 (Santa Cruz Biotechnology, sc-126, 1:300) and anti-β- actin (sc-47778, 1:300) at 4°C overnight. Afterward, the membrane was incubated with a probed secondary antibody conjugated to HRP (horseradish peroxidase) (Anti-rabbit 1:1000) for 1 hour. An Enhanced Chemiluminescence detection system was employed for detection. Beta-actin was used for normalization and internal control, and ImageJ software was utilized to analyze the image.

Flow cytometry

Apoptotic cells were exposed to phosphatidylserin in their outer plasma membrane, which were identified by fluorescein isothiocyanate (FITC) labeled Annexin-V/PI (propidium iodide) using flow cytometry. Following a 24 hours treatment of cells with 80% hAFMSCs-CM, MCF-7 and Hu02 cells were harvested by trypsin and washed with PBS. After 8 minutes of centrifugation at 1300 rpm, the cells were re-suspended in 100 µL binding buffer (Invitrogen, Lot #4338210) and were mixed with 2 µL Annexin-V (Invitrogen, Lot #1989095); they were then incubated on ice for 20 minutes in a dark place. The cells’ solution was centrifuged at 1300 rpm for 8 min, after which the supernatant was removed and 100 µL binding buffer was added. The sample solution was combined with 1 µL of PI (Invitrogen, Lot #1957465) and was incubated for 20 minutes in a dark place. Flow Jo (7.6.1) software was used to run the flow cytometry analysis on samples utilizing BD FACS Calibur Flow Cytometry (BD Biosciences, NJ, USA).

Finding a possible molecular network underlying the hAFMSCs-CM function using integrated approach of meta-analysis and literature mining

We conducted a literature-mining-based network analysis and employed an integrated approach of meta-analysis of expression data to ascertain the possible regulatory network underlying hAFMSCs-CM function in breast cancer cells.

As presented in , the following steps were performed:

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Fig. 2. Bioinformatics pipeline employed in this study.

  1. Recruitment of Mutual Ranking (MR) statistics for Co-expression meta-analysis of Bax, Bcl-2, and P53, consulting public transcriptomic data in Gene Expression Omnibus (GEO).

  2. Selection of top 100 co-expressed genes with Bax, Bcl-2, and P53.

  3. Finding shared genes between co-expressed profiles of Bax, Bcl-2, and P53.

  4. Performing Literature-mining based network analysis: Discovery of common targets and regulators with positive interactions with Bax, P53 and apoptosis, and negative interactions with Bcl-2.

Mutual ranking (MR) statistics and Z-transformation of expression data were used for expression data meta-analysis and removal of platform effect, as described elsewhere. 43,44 As compared with the common approach for running the Pearson correlation, MR statistics employs a ranking approach for correlation analysis where it remains unaffected by the experiment. After calculating the rank correlation for each experiment, geometric average of correlation coefficients was ranked in logarithmic manner. 45,46 Correlation rankings were used extensively during the meta-analysis (e.g. Rankprod). 47 The expression data were retrieved from the GEO (NCBI public repository of expression data, https://www.ncbi.nlm.nih.gov/geo/). COXPRESdb v7 tool was performed for analysis. 48 Lower values of MR represent higher level of association where MR value of each gene, including itself, is 0.

Literature mining-based database of Pathway Studio Mammalian (Elsevier) 49,50 was performed, as previously described. 51,52 The database collects data through NLP (Natural Language Processing) algorithm and contains 13 440 356 mined relations from full text published paper and 1 439 833 entities (e.g., proteins/genes, cell process, small molecules, and diseases) (March 2021). The database is enriched with additional inputs from Gene Ontology Consortium for cellular location analysis, MiRbase, and various network construction approaches such as “Common Binding Partner”, “Downstream Target Discovery”, and “Upstream Regulator Discovery”, among others.

Statistical analysis

Each experiment was performed in triplicate. Data were presented as means ± standard error of the mean (SEM). A one-way ANOVA and a t test were conducted to compare the three and the two groups, respectively. Any differences were deemed significant when the P value was smaller than 0.05 (P < 0.05). GraphPad Prism software (La, Jolla, CA) version 8.4.3(686) was utilized to run the statistical analysis.


Results

hAFMSCs-CM effects on MCF-7 cell viability

To investigate the hAFMSCs-CM impact on MCF-7 and Hu02 cell viability, an MTT assay was carried out 3 times (24, 48, and 72 hours) after the treatment. As shown in , hAFMSCs-CM was found to have a cytotoxic effect on MCF-7. Noteworthy, no cytotoxic effects were observed on Hu02 cells. Our data suggest that the cell viability in MCF-7 cells was decreased significantly as a result of CM after the treatments (24, 48, and 72 hours) (see ). With 20% of CM no significant effect on cell viability could be observed; however, in 40% and 80% of CMs (after 24 hours), cell growth was inhibited as compared with the control cells. illustrates the cell viability being declined to 78% (P < 0.0001) when 80% of CM and to 86.99% (P = 0.0027) when 40% of CM were used after the phase 1 of the treatment (24 hours). Upon the completion of the 48-hour and 72-hour incubation (40% CM) phases, the hAFMSCs-CM demonstrated an insignificant effect on the cell viability (P > 0.05). Noteworthy, 80% of the CM was found to have affected the MCF-7 cells considerably (P < 0.05). Although hAFMSCs-CM failed to affect MCF-7’s cell viability, it was found to be capable of promoting the cell viability in Hu02 as normal cells (P = 0.0014, during the 24 hour-treatment).

bi-13-191-g003
Fig. 3. The MCF-7 and Hu02 cell viability was assessed by MTT assay for MCF-7 cells within 24 (A), 48 (B) and 72 (C) hours and for and Hu02 within 24 h (D), 48 h (E) and 72 h (F) treatment with hAFMSCs-CM. After 24 h, a significant decrease in MCF-7 cells viability (P<0.0001) and Hu02 cells viability (P<0.005) was observed. The data are presented as mean ± SEM. Significantly different (** P<0.005, ****P<0.0001).

hAFMSCs-CM effects on Bax and Bcl-2 genes expression and P53 protein expression

Following the hAFMSCs-CM 24-hour treatment, the Bax and Bcl-2 mRNA level expressions were analyzed. The genes’ Ct values were normalized against the GAPDH mRNA level (the housekeeping gene). Notably, as illustrated in , the pro-apoptotic Bax gene’s expression level increased significantly as compared with the control group (P < 0.0001). On the other hand, the anti-apoptotic Bcl-2 gene’s mRNA level decreased considerably when cells were treated with 80% hAFMSCs-CM for 24 hours (P = 0.0012). Nevertheless, as shows, in normal cells (Hu02), the level of the Bax gene declined and Bcl2 increased after the hAFMSCs-CM treatment.

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Fig. 4. Real-time PCR and western blot analysis were used to assess hAFMSCs-CM effect on MCF-7 and Hu02 cells. (A) pro-apoptotic Bax and anti-apoptotic Bcl-2 genes of MCF-7 were treated with 80% hAFMSCs-CM in 24 h. (B) WB analysis and P53 protein quantification were used to evaluate 80% hAFMSCs-CM effect on P53 protein expression compared with the control in MCF-7 cells. (C) Hu02’s Bax and Bcl-2 genes were treated with 80% hAFMSCs-CM within 24 h. (D) WB analysis and P53 protein quantification to evaluate the 80% hAFMSCs-CM effect on P53 protein expression compared with the control in Hu02 cells. P53 protein level was determined by ImageJ analysis. The data are presented as mean ± SEM. (****P<0.0001, ***P<0.005).

illustrates the WB analysis of P53 protein expression, demonstrating a significant (P < 0.0001) increase (about 3.7 fold) after the hAFMSCs-CM treatment, as compared with control (untreated) cells. However, we could not observe meaningful differences in P53 expression in Hu02 cells (P > 0.05) ().

hAFMSCs-CM effects on apoptosis

Apoptosis was measured using a flow cytometry assay via annexin V and PI staining of the cells. As demonstrated in , apoptosis was induced in the female human breast cancer cells by hAFMSCs-CM. The flow cytometry analysis of MCF-7 cells, treated with 80% hAFMSCs-CM for 24 hours, showed early apoptosis (annexin V+ PI-) of nearly 22.7%, whereas the control cells’ apoptotic functions were about 6.2%. Despite insignificant differences among normal cells (P > 0.05), no considerable apoptosis could be observed in Hu02 cells (P > 0.05) ().

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Fig. 5. Apoptotic evaluation using the flow cytometry via annexin V and PI staining. (A) Control MCF-7 cells’ (untreated cells) apoptosis. (B) The effect of 80% hAFMSCs-CM on MCF-7 cells after 24 h -- hAFMSCs-CM induces apoptosis in MCF-7 cells. (C) Quantification of apoptosis in MCF-7 cells. (D) Control Hu02 cells (untreated cells) apoptosis. (E) The effect of 80% hAFMSCs-CM on Hu02 cells after 24 h. hAFMSCs-CM do not affect apoptosis in Hu02 cells. (F) Quantification of apoptosis in Hu02 cells. Fig. 5. represents viable cells (annexin V-PI-) population, early apoptosis (annexin V+ PI-), late apoptosis (annexin V+PI+), and necrotic cells (annexin V-PI Flow cytometry analysis was performed for samples using BD FACS Calibur flow cytometry [BD Biosciences, NJ, USA]). Flow Jo. (7.6.1) software was used to analyze the data.

Meta-analysis based co-expressed genes with Bax, Bcl-2, and P53

Tables 2, 3, and 4 show the genes that were found to be co-expressed with Bax, Bcl-2, and P53 after a meta-analysis. also presents the shared genes found within the meta-analysis derived co-expressed profiles of Bax, Bcl-2, and P53. Notably, Bax and P53 were found to be co-expressed. DDB2 (Damage specific DNA Binding protein 2) is among the top 3 co-expressed genes with Bax that co-expresses with P53. In the same vein, EIF5A (Eukaryotic Translation Initiation Factor 5A) is an important protein that co-expresses with Bax and P53.

Table 2. Meta-analysis-derived co-expressed genes with Bax
Gene Function Entrez Gene ID
0BAXBCL2 associated X: apoptosis regulator581
1FDXRFerredoxin reductase2232
2AP1S1Adaptor related protein complex 1 sigma 1 subunit1174
3DDB2Damage specific DNA binding protein 21643
4RPS27LRibosomal protein S27 like51065
5BBC3BCL2 binding component 327113
6MDM2MDM2 proto-oncogene4193
7ZMAT3Zinc finger matrin-type 364393
8LINC01759Long intergenic non-protein coding RNA 17591.03E+08
9PHLDA3Pleckstrin homology like domain family A member 323612
10PDAP1PDGFA associated protein 111333
11AENApoptosis enhancing nuclease64782
12PFDN6Prefoldin subunit 610471
13TIGARTP53 induced glycolysis regulatory phosphatase57103
14PFN1Profilin 15216
15CDKN1ACyclin dependent kinase inhibitor 1A1026
16PRMT1Protein arginine methyltransferase 13276
17APH1AAph-1 homolog A: gamma-secretase subunit51107
18TRIAP1TP53 regulated inhibitor of apoptosis 151499
19PHPT1Phosphohistidine phosphatase 129085
20ZNF428Zinc finger protein 428126299
21HNRNPUL2Heterogeneous nuclear ribonucleoprotein U like 2221092
22PSENENPresenilin enhancer gamma-secretase subunit55851
23EML2Echinoderm microtubule associated protein like 224139
24EDA2REctodysplasin A2 receptor60401
25ISOC2Isochorismatase domain containing 279763
26MIR34AHGMIR34A host gene1.07E+08
27AP2S1Adaptor related protein complex 2 sigma 1 subunit1175
28ARPC4Actin related protein 2/3 complex subunit 410093
29ARPC1BActin related protein 2/3 complex subunit 1B10095
30RPS19Ribosomal protein S196223
31RFXANKRegulatory factor X associated ankyrin containing protein8625
32GTF2H4General transcription factor IIH subunit 42968
33LAMTOR2Late endosomal/lysosomal adaptor: MAPK and MTOR activator 228956
34THOC6THO complex 679228
35SYMPKSymplekin8189
36TMEM160Transmembrane protein 16054958
37TP53I3Tumor protein p53 inducible protein 39540
38PPP4CProtein phosphatase 4 catalytic subunit5531
39PNKPPolynucleotide kinase 3'-phosphatase11284
40GPX1Glutathione peroxidase 12876
41ITPAInosine triphosphatase3704
42SPATA18Spermatogenesis associated 18132671
43MPDU1Mannose-P-dolichol utilization defect 19526
44EIF5AEukaryotic translation initiation factor 5A1984
45PURPLp53 upregulated regulator of p53 levels643401
46TFPTTCF3 fusion partner29844
47IRF3Interferon regulatory factor 33661
48CHMP4BCharged multivesicular body protein 4B128866
49GDF15Growth differentiation factor 159518
50CYBACytochrome b-245 alpha chain1535
51PGLS6-Phosphogluconolactonase25796
52DLSTDihydrolipoamide S-succinyltransferase1743
53FBXO22F-box protein 2226263
54PIDD1p53-induced death domain protein 155367
55GEMIN7Gem nuclear organelle associated protein 779760
56TNFRSF10BTNF receptor superfamily member 10b8795
57U2AF2U2 small nuclear RNA auxiliary factor 211338
58UBE2MUbiquitin conjugating enzyme E2 M9040
59TMED9Transmembrane p24 trafficking protein 954732
60CTSZCathepsin Z1522
61APOBEC3HApolipoprotein B mRNA editing enzyme catalytic subunit 3H164668
62LAMTOR4Late endosomal/lysosomal adaptor: MAPK and MTOR activator 4389541
63POLHDNA polymerase eta5429
64QTRT1queuine tRNA-ribosyltransferase catalytic subunit 181890
65PTCHD4Patched domain containing 4442213
66HIRAhistone cell cycle regulator7290
67RCC1Regulator of chromosome condensation 11104
68COMMD4COMM domain containing 454939
69TRAPPC1Trafficking protein particle complex 158485
70ARF5ADP ribosylation factor 5381
71BAK1BCL2 antagonist/killer 1578
72RAB35RAB35: member RAS oncogene family11021
73STK16Serine/threonine kinase 168576
74FTLFerritin light chain2512
75PIH1D1PIH1 domain containing 155011
76SHKBP1SH3KBP1 binding protein 192799
77KDELR1KDEL endoplasmic reticulum protein retention receptor 110945
78RANGRFRAN guanine nucleotide release factor29098
79TP53Tumor protein p537157
80PBX2PBX homeobox 25089
81SDHCSuccinate dehydrogenase complex subunit C6391
82MMP14Matrix metallopeptidase 144323
83DPP3dipeptidyl peptidase 310072
84TNFRSF10CTNF receptor superfamily member 10c8794
85PPP1CAProtein phosphatase 1 catalytic subunit alpha5499
86PPP2R1AProtein phosphatase 2 scaffold subunit Aalpha5518
87FUSFUS RNA binding protein2521
88CFL1Cofilin 11072
89TM7SF3Transmembrane 7 superfamily member 351768
90WDR83WD repeat domain 8384292
91FBXL19F-box and leucine rich repeat protein 1954620
92KPTNKaptin: actin binding protein11133
93ALYREFAly/REF export factor10189
94TAX1BP3Tax1 binding protein 330851
95VASPVasodilator stimulated phosphoprotein7408
96MRPS12Mitochondrial ribosomal protein S126183
97LINC02051Long intergenic non-protein coding RNA 20511.08E+08
98SRSF9Serine and arginine rich splicing factor 98683
99TWF2Twinfilin actin binding protein 211344
100DRG2Developmentally regulated GTP binding protein 21819
Table 3. Meta-analysis-derived co-expressed genes with Bcl-2
Gene Function Entrez Gene ID
0BCL2BCL2: apoptosis regulator596
1BACH2BTB domain and CNC homolog 260468
2IKZF1IKAROS family zinc finger 110320
3MDFICMyoD family inhibitor domain containing29969
4ITPKBinositol-trisphosphate 3-kinase B3707
5KIAA1328KIAA132857536
6NFATC1Nuclear factor of activated T cells 14772
7NSD3Nuclear receptor binding SET domain protein 354904
8KDSR3-Ketodihydrosphingosine reductase2531
9LDLRAD4Low density lipoprotein receptor class A domain containing 4753
10NEMP2Nuclear envelope integral membrane protein 21E+08
11ANKRD44Ankyrin repeat domain 4491526
12MYBMYB proto-oncogene: transcription factor4602
13RAPGEF6Rap guanine nucleotide exchange factor 651735
14HNRNPA0Heterogeneous nuclear ribonucleoprotein A010949
15ZXDAZinc finger: X-linked: duplicated A7789
16AFF3AF4/FMR2 family member 33899
17LOC374443C-type lectin domain family 2 member D pseudogene374443
18KIAA1147KIAA114757189
19TNFRSF13BTNF receptor superfamily member 13B23495
20PTGER4Prostaglandin E receptor 45734
21BMI1BMI1 proto-oncogene: polycomb ring finger648
22ITPR1Inositol 1:4:5-trisphosphate receptor type 13708
23LOC100509088Hypothetical LOC1005090881.01E+08
24RHOHRas homolog family member H399
25KCNQ5Potassium voltage-gated channel subfamily Q member 556479
26ESR1Estrogen receptor 12099
27SLC38A1Solute carrier family 38 member 181539
28ELP2Elongator acetyltransferase complex subunit 255250
29GPR174G protein-coupled receptor 17484636
30TAF4BTATA-box binding protein associated factor 4b6875
31RCSD1RCSD domain containing 192241
32SETBP1SET binding protein 126040
33NOP53NOP53 ribosome biogenesis factor29997
34LINC00341Long intergenic non-protein coding RNA 34179686
35LTALymphotoxin alpha4049
36CEP68Centrosomal protein 6823177
37DDHD2DDHD domain containing 223259
38LRCH1Leucine rich repeats and calponin homology domain containing 123143
39ZNF24Zinc finger protein 247572
40TARSL2Threonyl-tRNA synthetase like 2123283
41LRRC8C-DTLRRC8C divergent transcript400761
42PPM1KProtein phosphatase: Mg2+/Mn2+ dependent 1K152926
43SMAD2SMAD family member 24087
44RGS1Regulator of G protein signaling 15996
45FMNL3Formin like 391010
46CD69CD69 molecule969
47C21orf2Chromosome 21 open reading frame 2755
48ZNF407Zinc finger protein 40755628
49GNA13G protein subunit alpha 1310672
50XYLT1xylosyltransferase 164131
51SP4Sp4 transcription factor6671
52RBBP6RB binding protein 6: ubiquitin ligase5930
53LINC00909Long intergenic non-protein coding RNA 909400657
54IRF4Interferon regulatory factor 43662
55WDR7WD repeat domain 723335
56POU6F1POU class 6 homeobox 15463
57PPP3CCProtein phosphatase 3 catalytic subunit gamma5533
58NTRK2Neurotrophic receptor tyrosine kinase 24915
59TSHZ1Teashirt zinc finger homeobox 110194
60PM20D2Peptidase M20 domain containing 2135293
61PRKCEProtein kinase C epsilon5581
62MSI2Musashi RNA binding protein 2124540
63SLC39A6Solute carrier family 39 member 625800
64RSBN1Round spermatid basic protein 154665
65ZBTB32Zinc finger and BTB domain containing 3227033
66EPM2AEPM2A: laforin glucan phosphatase7957
67RFTN1Raftlin: lipid raft linker 123180
68NFATC2Nuclear factor of activated T cells 24773
69N4BP2L1NEDD4 binding protein 2 like 190634
70FOXN3Forkhead box N31112
71LOC107985690Uncharacterized LOC1079856901.08E+08
72ZADH2Zinc binding alcohol dehydrogenase domain containing 2284273
73ARMC5Armadillo repeat containing 579798
74ANKRD33BAnkyrin repeat domain 33B651746
75LEF1Lymphoid enhancer binding factor 151176
76PRDM8PR/SET domain 856978
77STAP1Signal transducing adaptor family member 126228
78JADE2Jade family PHD finger 223338
79MIR155HGMIR155 host gene114614
80RABEP1Rabaptin: RAB GTPase binding effector protein 19135
81P2RY10P2Y receptor family member 1027334
82ARHGEF6Rac/Cdc42 guanine nucleotide exchange factor 69459
83RIC8BRIC8 guanine nucleotide exchange factor B55188
84SYNE3Spectrin repeat containing nuclear envelope family member 3161176
85ABCD2ATP binding cassette subfamily D member 2225
86SPNS3Sphingolipid transporter 3 (putative)201305
87FBXL17F-box and leucine rich repeat protein 1764839
88LNPEPLeucyl and cystinyl aminopeptidase4012
89GRASPGeneral receptor for phosphoinositides 1 associated scaffold protein160622
90LINC00938Long intergenic non-protein coding RNA 938400027
91MAST4Microtubule associated serine/threonine kinase family member 4375449
92RNF157Ring finger protein 157114804
93SOCS2Suppressor of cytokine signaling 28835
94MALT1MALT1 paracaspase10892
95LINC00926Long intergenic non-protein coding RNA 926283663
96CLECL1C-type lectin like 1160365
97CLNKCytokine dependent hematopoietic cell linker116449
98RASGRP1RAS guanyl releasing protein 110125
99FCMRFc fragment of IgM receptor9214
100SDK2Sidekick cell adhesion molecule 254549
Table 4. Meta-analysis-derived co-expressed genes with P53
Gene Function Entrez Gene ID
0TP53Tumor protein p537157
1PFN1Profilin 15216
2BANF1Barrier to autointegration factor 18815
3YWHAETyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein epsilon7531
4CDK4Cyclin dependent kinase 41019
5THOC6THO complex 679228
6RAVER1Ribonucleoprotein: PTB binding 1125950
7ALDH16A1Aldehyde dehydrogenase 16 family member A1126133
8APEX1Apurinic/apyrimidinic endodeoxyribonuclease 1328
9MYBBP1AMYB binding protein 1a10514
10SHMT2Serine hydroxymethyltransferase 26472
11NONONon-POU domain containing octamer binding4841
12TRIM28Tripartite motif containing 2810155
13SMARCC1SWI/SNF related: matrix associated: actin dependent regulator of chromatin subfamily c member 16599
14TRAPPC1Trafficking protein particle complex 158485
15GEMIN4Gem nuclear organelle associated protein 450628
16CASP2Caspase 2835
17SF3B3Splicing factor 3b subunit 323450
18DRG2Developmentally regulated GTP binding protein 21819
19G3BP1G3BP stress granule assembly factor 110146
20BTBD2BTB domain containing 255643
21SF3B4Splicing factor 3b subunit 410262
22PELP1Proline: glutamate and leucine rich protein 127043
23EIF5AEukaryotic translation initiation factor 5A1984
24AAASAladin WD repeat nucleoporin8086
25HNRNPUL1Heterogeneous nuclear ribonucleoprotein U like 111100
26RCC2Regulator of chromosome condensation 255920
27PFASPhosphoribosylformylglycinamidine synthase5198
28CHTF8Chromosome transmission fidelity factor 854921
29DVL2Dishevelled segment polarity protein 21856
30SCAMP4Secretory carrier membrane protein 4113178
31ASB16-AS1ASB16 antisense RNA 1339201
32WDR6WD repeat domain 611180
33MTA2Metastasis associated 1 family member 29219
34CADCarbamoyl-phosphate synthetase 2: aspartate transcarbamylase: and dihydroorotase790
35CHST14Carbohydrate sulfotransferase 14113189
36HNRNPA0Heterogeneous nuclear ribonucleoprotein A010949
37IMPDH2Inosine monophosphate dehydrogenase 23615
38SF3A2Splicing factor 3a subunit 28175
39G6PC3Glucose-6-phosphatase catalytic subunit 392579
40APEX2Apurinic/apyrimidinic endodeoxyribonuclease 227301
41APOBEC3CApolipoprotein B mRNA editing enzyme catalytic subunit 3C27350
42PRPF8Pre-mRNA processing factor 810594
43DDB2Damage specific DNA binding protein 21643
44CTDNEP1CTD nuclear envelope phosphatase 123399
45UCP2Uncoupling protein 27351
46VARSValyl-tRNA synthetase7407
47SETSET nuclear proto-oncogene6418
48PATZ1POZ/BTB and AT hook containing zinc finger 123598
49NOB1NIN1/PSMD8 binding protein 1 homolog28987
50SNRPASmall nuclear ribonucleoprotein polypeptide A6626
51SLC16A13Solute carrier family 16 member 13201232
52MRPS27Mitochondrial ribosomal protein S2723107
53NCOA5Nuclear receptor coactivator 557727
54RPA1Replication protein A16117
55TGIF2TGFB induced factor homeobox 260436
56C17orf49Chromosome 17 open reading frame 49124944
57MAZMYC associated zinc finger protein4150
58DNAAF5Dynein axonemal assembly factor 554919
59GARTPhosphoribosylglycinamide formyltransferase: phosphoribosylglycinamide synthetase: phosphoribosylaminoimidazole synthetase2618
60C19orf54Chromosome 19 open reading frame 54284325
61ATIC5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMP cyclohydrolase471
62PHF23PHD finger protein 2379142
63CBX5Chromobox 523468
64FAM86C1Family with sequence similarity 86 member C155199
65DAXXDeath domain associated protein1616
66ELAVL1ELAV like RNA binding protein 11994
67MTA1Metastasis associated 19112
68MEN1Menin 14221
69TUBBTubulin beta class I203068
70SIGMAR1Sigma non-opioid intracellular receptor 110280
71FAM86B1Family with sequence similarity 86 member B185002
72EIF4A1Eukaryotic translation initiation factor 4A11973
73ALDH1B1Aldehyde dehydrogenase 1 family member B1219
74ELAC2elaC ribonuclease Z 260528
75PTBP1Polypyrimidine tract binding protein 15725
76GLOD4GLyoxalase domain containing 451031
77EXOSC5Exosome component 556915
78ALDH18A1Aldehyde dehydrogenase 18 family member A15832
79RPL22L1RIbosomal protein L22 like 1200916
80RFX5Regulatory factor X55993
81UNGUracil DNA glycosylase7374
82C1QBPComplement C1q binding protein708
83BAXBCL2 associated X: apoptosis regulator581
84EEFSECEukaryotic elongation factor: selenocysteine-tRNA specific60678
85METTL16Methyltransferase like 1679066
86KDELR1KDEL endoplasmic reticulum protein retention receptor 110945
87ZNF286AZinc finger protein 286A57335
88APRTAdenine phosphoribosyltransferase353
89SLC35A4Solute carrier family 35 member A4113829
90ZNF740Zinc finger protein 740283337
91PA2G4Proliferation-associated 2G45036
92PRR3Proline rich 380742
93ZNF362Zinc finger protein 362149076
94VPS35LVPS35 endosomal protein sorting factor like57020
95CHAMP1Chromosome alignment maintaining phosphoprotein 1283489
96SENP3SUMO1/sentrin/SMT3 specific peptidase 326168
97GANABGlucosidase II alpha subunit23193
98UBTFUpstream binding transcription factor: RNA polymerase I7343
99PRKCSHProtein kinase C substrate 80K-H5589
100TSR1TSR1: ribosome maturation factor55720
bi-13-191-g006
Fig. 6. Shared genes between meta-analysis derived co-expressed profiles of Bax, Bcl-2, and P53.

Molecular network underlying hAFMSCs-CM function in MCF-7 cells

illustrates the molecular network underlying the apoptotic function of hAFMSCs-CM in MCF-7 cells. Supplementary data represents the underlying relations, mined sentences through literature mining, and the reference publications. P53 (TP53), EIF5A, DDB2, BcL2, and Bax are hubs in the network where BcL2 downregulation stands in harmony with the upregulation of P53, EIF5A, DDB2, and Bax, leading to apoptosis activation.

bi-13-191-g007
Fig. 7. Molecular network underlying apoptotic function of hAFMSCs function in MCF-7 cells. The positive sign represents the positive/upregulation and the negative sign represents the negative/downregulation interaction.


Discussion

Currently, chemotherapy and surgery are the principal approaches in clinical-base breast cancer treatment. However, the side effects of surgery, the toxicity of chemotherapy agents on normal cells, and drug resistance in cancer cells are undeniable post-treatment problems. 2,3 As a result, other types of breast cancer treatments, such as targeted therapies and gene therapy, have become the focus of recent research. 4 Multiple studies have shown that MSCs can fight cancer, which has led researchers to think about using them as a new treatment. 6,7,11,15,53,54 Nonetheless, the MSCs-CM’s anti-cancer effects, especially hAFMSCs-CM, on breast cancer apoptosis, have not been clearly understood. TROY, TAIL, and Fas Ligand/TNFSF6 were found in the MSCs-CM made from bone marrow. 55

The present work has investigated the apoptotic potential effects of hAFMSCs-CM through cellular and molecular approaches. Our data indicated that MCF-7 cell viability declined as a result of hAFMSCs-CM treatment as compared with control cells. Our findings are consistent with studies that have highlighted the promising aspects of human amniotic-derived MSCs’ effects on cancer inhibition. 6,56

Moreover, we have shown that hAFMSCs-CM induces apoptosis in MCF-7 breast cancer cells due to the increase in Bax gene expression and the decrease in Bcl-2 gene expression. Furthermore, based on the protein analysis and compared with the untreated cells, our data revealed that the level of tumor suppressor protein expression, P53, was enhanced in MCF-7 due to the hAFMSCs-CM treatment (P < 0.0001). There is ample evidence confirming that P53 overexpression in breast cancer downregulates Bcl2 expression, promotes Bax expression, and stimulates Bax function as a result of P53-induced apoptosis. 57-59

Gholizadeh et al stated that hAFMSCs medium could significantly promote p53 expression in the ovarian cancer cell line (P < 0.05). 6 Apoptosis can be caused in breast cancer cells by giving them hAFMSCs-CM, and this could lead to more P53 protein in the cells. Consistently, Kalamegam et al. found that CM from Wharton’s jelly stem cell had inhibitory effects on an ovarian cancer cell line. 12 Similarly, Serhal et al isolated CM from adipose-derived MSCs and assessed its effect on hepatocellular carcinoma cells. They posited that, after the CM treatment, the apoptosis rate increased due to P53 upregulation and retinoblastoma gene expression. They also highlighted the significant decrease in cell proliferation by dint of hTERE downregulation and c-Myc expression. Likewise, the present study found a noticeable decrease in Bcl-2 mRNA level expression and an increase in Bax mRNA level within the treated cells with hAFMSCs-CM in comparison with the untreated cells (P < 0.005). Consistent with our findings, in 2020, Rahmatizadeh et al showed that indirect hAFMSCs co-culturing with human cervical cancer (HeLa) resulted in an increase in the Bax/Bcl-2 ratio and cells’ sensitivity to apoptosis. They also said that the level of p53 mRNA in Hela cells rose a lot after day 5 of co-culture with indirect hAFMSCs, which is when they were mixed with the cells. 60 In 2018, Rodrigues et al reported that P53 is active in human amniotic fluid stem cells. 61 More importantly, we found that P53’s protein level increased after the hAFMSCs-CM treatment. According to our findings, it seems that hAFMSCs-CM could interfere with the apoptosis signal pathway associated with P53, inhibiting Bcl-2 expression. Consistent with this study, Jiao et al. demonstrated that hAMCs decreased tumor size significantly (P < 0.05) in gliomas by increasing Bax expression and reducing Bcl-2 levels. 62 In addition, Qiao and her colleagues reported that MSCs inhibited hepatoma cancer cell lines by downregulating the levels of Bcl-2, c-Myc, Survivin, PCNA, and β-catenin. 9 Conversely, Farahmand et al showed that bone marrow derived stem cell CM has tumorigenic effects on human breast cancer. 63 In this study, we developed a systems biology analysis approach by integrating the meta-analysis of expression data, using rank correlation and Z standardization, and performing literature mining analysis. The employed systems biology approach led us to an apoptotic-promoting gene interaction network, including P53, EIF5A, DDB2, and Bax, activated by hAFMSCs-CM treatment. More research should be conducted to validate this type of treatment.

Research Highlights

What is the current knowledge?

The role of MSCs in clinical application is well researched.

Stem cells such as hAFMSCs have anticancer effects in some tumors.

hAFMSCs-CM ability to downsize tumors should be investigated.

Given that the MSCs is the best among different sources, hAFMSCs-CM could target tumor cells and inhibit their growth rate through expressing apoptotic factors.

What is new here?

The current study focused on apoptotic effect of the cell-free hAFMSCs-CM on the cancer cells, especially the breast cancer.

This study explained the relationship between hAFMSCs-CM and the apoptotic molecules (antitumor).

The meta-analysis study illustrated that an apoptotic-promoting gene interaction network, including P53, EIF5A, DDB2, and Bax, can be activated by hAFMSCs-CM treatment.


Conclusion

The present work revealed that hAFMSCs-CM could promote apoptosis in MCF-7 cells. Our data shown a high level of P53 in MCF-7 cells, but not in normal cells (Hu02). After the treatment, P53 was found competent to downregulate Bcl2 expression and upregulate Bax to induce apoptosis in MCF-7 cells. On the other hand, our data suggest that hAFMSCs-CM has proliferation effects on normal cells but not on p53 expression; thus, we observed a decrease in Bax and an increase in Bcl2 mRNA levels. As per our findings, amniotic fluid-derived stem cells could seemingly target the tumor cells, inhibiting their growth rate by expressing various apoptotic factors. In the end, we suggest that more research be conducted on hAFMSCs’ effects on cancer therapy for stem cell CM.


Acknowledgment

We would like to appreciate Tehran University of Medical Sciences, Tehran, Iran for their financial support and Clinical Research Development Unit of Alzahra Educational, Research and Treatment Center,Tabriz University of Medical Sciences, Tabriz, Iran for their assistance in this research.


Funding

This study was funded by Tehran University of Medical Sciences for a PhD thesis (No. 9611184003).


Ethical Statement

This study was approved by the Ethics Committee of Tehran University of Medical Sciences, Tehran, Iran (ID number IR.TUMS.MEDICINE.REC.1398.690).


Competing Interests

The authors declared no conflict of interest.


Supplementary Materials

Supplementary file 1 contains molecular network relations underlying hAFMSCs function in MCF-7 cells.


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Submitted: 03 May 2021
Revised: 12 Jul 2021
Accepted: 04 Aug 2021
First published online: 30 Mar 2022
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