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Mazziotta C, Badiale G, Cervellera CF, Morciano G, Di Mauro G, Touzé A, Pinton P, Tognon M, Martini F, Rotondo JC. All-trans retinoic acid exhibits anti-proliferative and differentiating activity in Merkel cell carcinoma cells via retinoid pathway modulation. J Eur Acad Dermatol Venereol 2024; 38:1419-1431. [PMID: 38450801 DOI: 10.1111/jdv.19933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 01/22/2024] [Indexed: 03/08/2024]
Abstract
BACKGROUND The limited therapies available for treating Merkel cell carcinoma (MCC), a highly aggressive skin neoplasm, still pose clinical challenges, and novel treatments are required. Targeting retinoid signalling with retinoids, such as all-trans retinoic acid (ATRA), is a promising and clinically useful antitumor approach. ATRA drives tumour cell differentiation by modulating retinoid signalling, leading to anti-proliferative and pro-apoptotic effects. Although retinoid signalling is dysregulated in MCC, ATRA activity in this tumour is unknown. This study aimed to evaluate the impact of ATRA on the pathological phenotype of MCC cells. METHODS The effect of ATRA was tested in various Merkel cell polyomavirus-positive and polyomavirus-negative MCC cell lines in terms of cell proliferation, viability, migration and clonogenic abilities. In addition, cell cycle, apoptosis/cell death and the retinoid gene signature were evaluated upon ATRA treatments. RESULTS ATRA efficiently impaired MCC cell proliferation and viability in MCC cells. A strong effect in reducing cell migration and clonogenicity was determined in ATRA-treated cells. Moreover, ATRA resulted as strongly effective in arresting cell cycle and inducing apoptosis/cell death in all tested MCC cells. Enrichment analyses indicated that ATRA was effective in modulating the retinoid gene signature in MCC cells to promote cell differentiation pathways, which led to anti-proliferative and pro-apoptotic/cell death effects. CONCLUSIONS These results underline the potential of retinoid-based therapy for MCC management and might open the way to novel experimental approaches with other retinoids and/or combinatorial treatments.
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Affiliation(s)
- Chiara Mazziotta
- Department of Medical Sciences, University of Ferrara, Ferrara, Italy
- Center for Studies on Gender Medicine-Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Giada Badiale
- Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | | | | | - Giulia Di Mauro
- Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Antoine Touzé
- Biologie des infections à Polyomavirus team, UMR INRA ISP 1282, University of Tours, Tours, France
| | - Paolo Pinton
- Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Mauro Tognon
- Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Fernanda Martini
- Department of Medical Sciences, University of Ferrara, Ferrara, Italy
- Center for Studies on Gender Medicine-Department of Medical Sciences, University of Ferrara, Ferrara, Italy
- Laboratory for Technologies of Advanced Therapies (LTTA), University of Ferrara, Ferrara, Italy
| | - John Charles Rotondo
- Department of Medical Sciences, University of Ferrara, Ferrara, Italy
- Center for Studies on Gender Medicine-Department of Medical Sciences, University of Ferrara, Ferrara, Italy
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Tognon M, Martini F, Rotondo JC, Fiume G. Editorial: Recent advances in diagnosis, prognosis, and therapy of oncogenic virus-driven tumors. Front Oncol 2024; 14:1402877. [PMID: 38660129 PMCID: PMC11040595 DOI: 10.3389/fonc.2024.1402877] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Accepted: 03/28/2024] [Indexed: 04/26/2024] Open
Affiliation(s)
- Mauro Tognon
- Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | - Fernanda Martini
- Department of Medical Sciences, University of Ferrara, Ferrara, Italy
| | | | - Giuseppe Fiume
- Department of Experimental and Clinical Medicine, University of Catanzaro "Magna Graecia", Catanzaro, Italy
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3
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Mahajan A, Hong J, Krukovets I, Shin J, Tkachenko S, Espinosa-Diez C, Owens GK, Cherepanova OA. Integrative analysis of the lncRNA-miRNA-mRNA interactions in smooth muscle cell phenotypic transitions. Front Genet 2024; 15:1356558. [PMID: 38660676 PMCID: PMC11039880 DOI: 10.3389/fgene.2024.1356558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 03/25/2024] [Indexed: 04/26/2024] Open
Abstract
Objectives: We previously found that the pluripotency factor OCT4 is reactivated in smooth muscle cells (SMC) in human and mouse atherosclerotic plaques and plays an atheroprotective role. Loss of OCT4 in SMC in vitro was associated with decreases in SMC migration. However, molecular mechanisms responsible for atheroprotective SMC-OCT4-dependent effects remain unknown. Methods: Since studies in embryonic stem cells demonstrated that OCT4 regulates long non-coding RNAs (lncRNAs) and microRNAs (miRNAs), making them candidates for OCT4 effect mediators, we applied an in vitro approach to investigate the interactions between OCT4-regulated lncRNAs, mRNAs, and miRNAs in SMC. We used OCT4 deficient mouse aortic SMC (MASMC) treated with the pro-atherogenic oxidized phospholipid POVPC, which, as we previously demonstrated, suppresses SMC contractile markers and induces SMC migration. Differential expression of lncRNAs, mRNAs, and miRNAs was obtained by lncRNA/mRNA expression array and small-RNA microarray. Long non-coding RNA to mRNA associations were predicted based on their genomic proximity and association with vascular diseases. Given a recently discovered crosstalk between miRNA and lncRNA, we also investigated the association of miRNAs with upregulated/downregulated lncRNA-mRNA pairs. Results: POVPC treatment in SMC resulted in upregulating genes related to the axon guidance and focal adhesion pathways. Knockdown of Oct4 resulted in differential regulation of pathways associated with phagocytosis. Importantly, these results were consistent with our data showing that OCT4 deficiency attenuated POVPC-induced SMC migration and led to increased phagocytosis. Next, we identified several up- or downregulated lncRNA associated with upregulation of the specific mRNA unique for the OCT4 deficient SMC, including upregulation of ENSMUST00000140952-Hoxb5/6 and ENSMUST00000155531-Zfp652 along with downregulation of ENSMUST00000173605-Parp9 and, ENSMUST00000137236-Zmym1. Finally, we found that many of the downregulated miRNAs were associated with cell migration, including miR-196a-1 and miR-10a, targets of upregulated ENSMUST00000140952, and miR-155 and miR-122, targets of upregulated ENSMUST00000155531. Oppositely, the upregulated miRNAs were anti-migratory and pro-phagocytic, such as miR-10a/b and miR-15a/b, targets of downregulated ENSMUST00000173605, and miR-146a/b and miR-15b targets of ENSMUST00000137236. Conclusion: Our integrative analyses of the lncRNA-miRNA-mRNA interactions in SMC indicated novel potential OCT4-dependent mechanisms that may play a role in SMC phenotypic transitions.
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Affiliation(s)
- Aatish Mahajan
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Junyoung Hong
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Irene Krukovets
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Junchul Shin
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
| | - Svyatoslav Tkachenko
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH, United States
| | - Cristina Espinosa-Diez
- Center for Molecular Medicine and Genetics, Wayne State University, Detroit, MI, United States
| | - Gary K. Owens
- Robert M. Berne Cardiovascular Research Center, University of Virginia, Charlottesville, VA, United States
| | - Olga A. Cherepanova
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, United States
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4
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Ashby HE, Jones GN, Leedhanachoke O, Jen P, Helphenstine N, Al Akhrass F. Merkel Cell Carcinoma Masquerading Clinically as a Cyst in a Young Patient. Int Med Case Rep J 2024; 17:289-293. [PMID: 38596400 PMCID: PMC11001544 DOI: 10.2147/imcrj.s449543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 03/21/2024] [Indexed: 04/11/2024] Open
Abstract
Merkel cell carcinoma (MCC) is an extremely rare and aggressive tumor. Here we report an unusual MCC that manifested as an abruptly enlarging, painful skin lesion over the right antecubital fossa and masqueraded as an epidermal cyst in a 42-year-old male. The lesion was surgically excised and subjected to histopathologic and immunohistochemical examinations. The subsequent analysis allowed for the diagnosis of MCC. Clinicians should always be cognizant of MCC, which can be easily misdiagnosed. Early diagnosis and appropriate treatment are keys to improving the survival rates of MCC patients.
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Affiliation(s)
| | - Grayson N Jones
- Department of Pathology, Pikeville Medical Center, Pikeville, KY, USA
| | - Oon Leedhanachoke
- Department of General Surgery, Pikeville Medical Center, Pikeville, KY, USA
| | - Phillip Jen
- Department of BioMedical Science, University of Pikeville, Pikeville, KY, USA
| | - Noah Helphenstine
- Department of BioMedical Science, University of Pikeville, Pikeville, KY, USA
| | - Fadi Al Akhrass
- Department of Infectious Diseases, Pikeville Medical Center, Pikeville, KY, USA
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Wagner C, Urquiza-Garcia U, Zurbriggen MD, Beyer HM. GMOCU: Digital Documentation, Management, and Biological Risk Assessment of Genetic Parts. Adv Biol (Weinh) 2024; 8:e2300529. [PMID: 38263723 DOI: 10.1002/adbi.202300529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 01/02/2024] [Indexed: 01/25/2024]
Abstract
The continuous evolution of molecular biology and gene synthesis methods paired with an ever-increasing potential of synthetic biology approaches and genome engineering toolkits enables the rapid design of genetic bioparts and genetically modified organisms. Although various software solutions assist with specific design tasks and challenges, lab internal documentation and ensuring compliance with governmental regulations on biosafety assessment of the generated organisms remain the responsibility of individual academic researchers. This results in inconsistent and redundant documentation regimes and a significant time and labor burden. GMOCU (GMO documentation) is a standardized semi-automatic user-oriented software approach -written in Python and freely available- that unifies lab internal data documentation on genetic parts and genetically modified organisms (GMOs). It automatizes biological risk evaluations and maintains a shared up-to-date inventory of bioparts for team-wide data navigation and sharing. GMOCU further enables data export into customizable formats suitable for scientific publications, official biosafety documents, and the research community.
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Affiliation(s)
- Christoph Wagner
- Institute of Synthetic Biology, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
| | - Uriel Urquiza-Garcia
- Institute of Synthetic Biology, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
- CEPLAS-Cluster of Excellence on Plant Sciences, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
| | - Matias D Zurbriggen
- Institute of Synthetic Biology, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
- CEPLAS-Cluster of Excellence on Plant Sciences, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
| | - Hannes M Beyer
- Institute of Synthetic Biology, Heinrich-Heine-University Düsseldorf, Universitätsstrasse 1, D-40225, Düsseldorf, Germany
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Wang X, Mijiti W, Jia Q, Yi Z, Ma J, Zhou Z, Xie Z. Exploration of altered miRNA expression and function in MSC-derived extracellular vesicles in response to hydatid antigen stimulation. Front Microbiol 2024; 15:1381012. [PMID: 38601938 PMCID: PMC11004373 DOI: 10.3389/fmicb.2024.1381012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 03/14/2024] [Indexed: 04/12/2024] Open
Abstract
Background Hydatid disease is caused by Echinococcus parasites and can affect various tissues and organs in the body. The disease is characterized by the presence of hydatid cysts, which contain specific antigens that interact with the host's immune system. Mesenchymal stem cells (MSCs) are pluripotent stem cells that can regulate immunity through the secretion of extracellular vesicles (EVs) containing microRNAs (miRNAs). Methods In this study, hydatid antigens were isolated from sheep livers and mice peritoneal cavities. MSCs derived from mouse bone marrow were treated with different hydatid antigens, and EVs were isolated and characterized from the conditioned medium of MSCs. Small RNA library construction, miRNA target prediction, and differential expression analysis were conducted to identify differentially expressed miRNAs. Functional enrichment and network construction were performed to explore the biological functions of the target genes. Real-time PCR and Western blotting were used for miRNA and gene expression verification, while ELISA assays quantified TNF, IL-1, IL-6, IL-4, and IL-10 levels in cell supernatants. Results The study successfully isolated hydatid antigens and characterized MSC-derived EVs, demonstrating the impact of antigen concentration on MSC viability. Key differentially expressed miRNAs, such as miR-146a and miR-9-5p, were identified, with functional analyses revealing significant pathways like Endocytosis and MAPK signaling associated with these miRNAs' target genes. The miRNA-HUB gene regulatory network identified crucial miRNAs and HUB genes, such as Traf1 and Tnf, indicating roles in immune modulation and osteogenic differentiation. Protein-protein interaction (PPI) network analysis highlighted central HUB genes like Akt1 and Bcl2. ALP activity assays confirmed the influence of antigens on osteogenic differentiation, with reduced ALP activity observed. Expression analysis validated altered miRNA and chemokine expression post-antigen stimulation, with ELISA analysis showing a significant reduction in CXCL1 expression in response to antigen exposure. Conclusion This study provides insights into the role of MSC-derived EVs in regulating parasite immunity. The findings suggest that hydatid antigens can modulate the expression of miRNAs in MSC-derived EVs, leading to changes in chemokine expression and osteogenic capacity. These findings contribute to a better understanding of the immunomodulatory mechanisms involved in hydatid disease and provide potential therapeutic targets for the development of new treatment strategies.
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Affiliation(s)
- Xin Wang
- Department of Orthopedics and Trauma, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, Xinjiang, China
| | - Wubulikasimu Mijiti
- Department of Orthopedics and Trauma, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, Xinjiang, China
| | - Qiyu Jia
- Department of Orthopedics and Trauma, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, Xinjiang, China
| | - Zhifei Yi
- Department of Orthopedics and Trauma, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, Xinjiang, China
| | - Junchao Ma
- Department of Orthopedics and Trauma, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, Xinjiang, China
| | - Ziyu Zhou
- Department of Orthopedics and Trauma, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, Xinjiang, China
| | - Zengru Xie
- Department of Orthopedics and Trauma, The First Affiliated Hospital of Xinjiang Medical University, Ürümqi, Xinjiang, China
- Key Laboratory of High Incidence Disease Research in Xingjiang (Xinjiang Medical University), Ministry of Education, Ürümqi, Xinjiang, China
- Xinjiang Clinical Research Center for Orthopedics, Xinjiang Medical University, Ürümqi, Xinjiang, China
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7
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Siqueira SM, Campos-do-Carmo G, da Silva PRG, Small IÁ, De Melo AC. The prognostic role of PD-L1 expression and the presence of polyomavirus in Merkel cell carcinoma cases. Infect Agent Cancer 2024; 19:1. [PMID: 38178185 PMCID: PMC10768145 DOI: 10.1186/s13027-023-00564-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 12/20/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND Merkel cell carcinoma (MCC) comprises a rare malignant primary skin tumor presenting neuroendocrine differentiation. Recently, agents blocking the programmed cell death protein 1 and programmed cell death protein ligand 1 pathway (PD-1/PD-L1) have demonstrated objective and durable tumor regressions in patients presenting advanced MCC. This study aimed to describe the sociodemographic, clinical, and histopathological characteristics of MCC patients, also assessing the prevalence of PD-L1 expression and Merkel cell Polyomavirus (MCPyV), as well as their prognostic roles. METHODS Data from patients diagnosed with MCC between 1996 and 2019 at a reference cancer center in Rio de Janeiro, southeastern Brazil, were evaluated in a retrospective study. Tumor samples were tested for MCPyV and PD-L1 employing immunohistochemistry. Survival analyses were carried out employing the Kaplan-Meier method and curves were compared using the log-rank test. A multiple semiparametric Cox model was used. Values p < 0.05 were considered significant. RESULTS A total of 65 patients were included in the study, with a mean age at diagnosis of 72 (standard deviation 13.9). A total of 56.9% (37/65) of the patients were male, 86.2% (56/65) were white, and 56.9% (37/64) were illiterate or with incomplete elementary school. MCPyV immunohistochemistry was positive in 29 cases (44.6%) and PD-L1 positivity was ≥ 1% in 42 cases (64.6%). Significant associations between MCPyV and PD-L1 expression ≥ 1% (p = 0.003) and PD-L1 expression ≥ 5% (p = 0.005) were noted. Concerning the multivariate analysis, only education level and advanced MCC stage indicated statistically significant worse progression-free survival. Regarding overall survival (OS), being male, education level and advanced stage comprised risk factors. The estimated OS at 60 months for stages I to III was of 48.9% and for stage IV, 8.9%. CONCLUSIONS This is the first large Brazilian cohort to assess the prevalence of MCPyV in MCC tumors, as well as PD-L1 expression and their associations. No correlations were noted between MCPyV infection or PD-L1 expression and survival rates.
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Affiliation(s)
- Stella Meireles Siqueira
- Division of Clinical Research and Technological Development, Brazilian National Cancer Institute, Rio de Janeiro, Brazil.
| | | | | | - Isabele Ávila Small
- Division of Clinical Research and Technological Development, Brazilian National Cancer Institute, Rio de Janeiro, Brazil
| | - Andreia Cristina De Melo
- Division of Clinical Research and Technological Development, Brazilian National Cancer Institute, Rio de Janeiro, Brazil
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Li S, Li T, Shi YQ, Xu BJ, Deng YY, Sun XG. Identification of Hub genes with prognostic values in colorectal cancer by integrated bioinformatics analysis. Cancer Biomark 2024; 40:27-45. [PMID: 38393891 PMCID: PMC11191499 DOI: 10.3233/cbm-230113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 12/10/2023] [Indexed: 02/25/2024]
Abstract
BACKGROUND Our study aimed to investigate the Hub genes and their prognostic value in colorectal cancer (CRC) via bioinformatics analysis. METHODS The data set of colorectal cancer was downloaded from the GEO database (GSE21510, GSE110224 and GSE74602) for differential expression analysis using the GEO2R tool. Hub genes were screened by protein-protein interaction (PPI) comprehensive analysis. GEPIA was used to verify the expression of Hub genes and evaluate its prognostic value. The protein expression of Hub gene in CRC was analyzed using the Human Protein Atlas database. The cBioPortal was used to analyze the type and frequency of Hub gene mutations, and the effects of mutation on the patients' prognosis. The TIMER database was used to study the correlation between Hub genes and immune infiltration in CRC. Gene set enrichment analysis (GSEA) was used to explore the biological function and signal pathway of the Hub genes and corresponding co-expressed genes. RESULTS We identified 346 differentially expressed genes (DEGs), including 117 upregulated and 229 downregulated. Four Hub genes (AURKA, CCNB1, EXO1 and CCNA2) were selected by survival analysis and differential expression validation. The protein and mRNA expression levels of AURKA, CCNB1, EXO1 and CCNA2 were higher in CRC tissues than in adjacent tissues. There were varying degrees of immune cell infiltration and gene mutation of Hub genes, especially B cells and CD8+ T cells. The results of GSEA showed that Hub genes and their co-expressed genes mainly participated in chromosome segregation, DNA replication, translational elongation and cell cycle. CONCLUSION Overexpression of AURKA, CCNB1, CCNA2 and EXO1 had a better prognosis for CRC and this effect was correlation with gene mutation and infiltration of immune cells.
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Affiliation(s)
- Shan Li
- Precision Preventive Medicine Laboratory of Basic Medical School, Jiujiang University, Jiujiang, Jiangxi, China
| | - Ting Li
- Department of Pathology, Affiliated Hospital of Jiujiang University, Jiujiang, Jiangxi, China
| | - Yan-Qing Shi
- Department of Pathology, Affiliated Hospital of Jiujiang University, Jiujiang, Jiangxi, China
| | - Bin-Jie Xu
- Precision Preventive Medicine Laboratory of Basic Medical School, Jiujiang University, Jiujiang, Jiangxi, China
| | - Yu-Yong Deng
- Precision Preventive Medicine Laboratory of Basic Medical School, Jiujiang University, Jiujiang, Jiangxi, China
| | - Xu-Guang Sun
- Art School, Jiujiang University, Jiujiang, Jiangxi, China
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Fan Y, Shi C, Huang N, Fang F, Tian L, Wang J. Recurrent Implantation Failure: Bioinformatic Discovery of Biomarkers and Identification of Metabolic Subtypes. Int J Mol Sci 2023; 24:13488. [PMID: 37686293 PMCID: PMC10487894 DOI: 10.3390/ijms241713488] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/02/2023] [Accepted: 08/14/2023] [Indexed: 09/10/2023] Open
Abstract
Recurrent implantation failure (RIF) is a challenging scenario from different standpoints. This study aimed to investigate its correlation with the endometrial metabolic characteristics. Transcriptomics data of 70 RIF and 99 normal endometrium tissues were retrieved from the Gene Expression Omnibus database. Common differentially expressed metabolism-related genes were extracted and various enrichment analyses were applied. Then, RIF was classified using a consensus clustering approach. Three machine learning methods were employed for screening key genes, and they were validated through the RT-qPCR experiment in the endometrium of 10 RIF and 10 healthy individuals. Receiver operator characteristic (ROC) curves were generated and validated by 20 RIF and 20 healthy individuals from Peking University People's Hospital. We uncovered 109 RIF-related metabolic genes and proposed a novel two-subtype RIF classification according to their metabolic features. Eight characteristic genes (SRD5A1, POLR3E, PPA2, PAPSS1, PRUNE, CA12, PDE6D, and RBKS) were identified, and the area under curve (AUC) was 0.902 and the external validated AUC was 0.867. Higher immune cell infiltration levels were found in RIF patients and a metabolism-related regulatory network was constructed. Our work has explored the metabolic and immune characteristics of RIF, which paves a new road to future investigation of the related pathogenic mechanisms.
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Affiliation(s)
- Yuan Fan
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, Beijing 100044, China; (Y.F.); (C.S.); (N.H.); (F.F.)
- Reproductive Medical Center, Peking University People’s Hospital, Beijing 100044, China
| | - Cheng Shi
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, Beijing 100044, China; (Y.F.); (C.S.); (N.H.); (F.F.)
- Reproductive Medical Center, Peking University People’s Hospital, Beijing 100044, China
| | - Nannan Huang
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, Beijing 100044, China; (Y.F.); (C.S.); (N.H.); (F.F.)
- Reproductive Medical Center, Peking University People’s Hospital, Beijing 100044, China
| | - Fang Fang
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, Beijing 100044, China; (Y.F.); (C.S.); (N.H.); (F.F.)
- Reproductive Medical Center, Peking University People’s Hospital, Beijing 100044, China
| | - Li Tian
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, Beijing 100044, China; (Y.F.); (C.S.); (N.H.); (F.F.)
- Reproductive Medical Center, Peking University People’s Hospital, Beijing 100044, China
| | - Jianliu Wang
- Department of Obstetrics and Gynecology, Peking University People’s Hospital, Beijing 100044, China; (Y.F.); (C.S.); (N.H.); (F.F.)
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