Transcriptome sequencing and miRNA-mRNA network construction in exosome of macrophage M2 in stomach adenocarcinoma
Abstract Background Stomach adenocarcinoma (STAD) is the most common histological type of gastric cancer (GC). Macrophages are an essential part of the tumor microenvironment. We attempted to search for potential molecular markers associated with macrophages, which might be helpful for STAD diagnosi...
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| Format: | Article |
| Language: | English |
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BMC
2023-06-01
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| Series: | World Journal of Surgical Oncology |
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| Online Access: | https://doi.org/10.1186/s12957-023-03070-1 |
| _version_ | 1797789681036820480 |
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| author | Dun Pan Zhipeng Li Xin Lin Liangqing Li |
| author_facet | Dun Pan Zhipeng Li Xin Lin Liangqing Li |
| author_sort | Dun Pan |
| collection | DOAJ |
| description | Abstract Background Stomach adenocarcinoma (STAD) is the most common histological type of gastric cancer (GC). Macrophages are an essential part of the tumor microenvironment. We attempted to search for potential molecular markers associated with macrophages, which might be helpful for STAD diagnosis and treatment. Methods Firstly, exosome in macrophages was extracted for RNA sequencing to identify differentially expressed microRNAs (miRNAs) (DEmiRNAs). Then, DEmiRNAs and differentially expressed mRNAs (DEmRNAs) were screened in the Cancer Genome Atlas (TCGA) database. The miRNAs related to macrophage M2 polarization were obtained by intersecting the DEmiRNAs obtained from the sequencing data and TCGA data. Using the Pearson correlation coefficient method, the mRNAs significantly related to macrophage M2 were screened out, followed by construction of the macrophage M2-miRNA-mRNA network. Subsequently, real-time-polymerase chain reaction (RT-PCR) and online datasets were applied to validate the expression of DEmiRNAs and DEmRNAs. Results A total of 6 DEmiRNAs were identified in RNA sequencing; 59 DEmiRNAs and 1838 DEmRNAs were identified in TCGA database. Among which, a common miRNA (hsa-miR-133a-3p) associated with the M2 polarization of macrophages was identified. Fifteen common mRNAs were obtained between DEmRNAs and mRNAs targeted by DEmiRNAs. Eventually, a core macrophage M2-1 down-regulated miRNA-7 and up-regulated mRNAs network was constructed, including hsa-miR-133a-3p, SLC39A1, TTYH3, HAVCR2, TPM3, XPO1, POU2F1, and MMP14. The expression of miRNA and mRNAs was in line with the validation results of RT-PCR and online datasets. Conclusion In this study, the screening of biomarkers in exosome of macrophage M2 may contribute to the prognosis of STAD patients. |
| first_indexed | 2024-03-13T01:54:08Z |
| format | Article |
| id | doaj.art-0de95b509e2043a18403009d66f5add3 |
| institution | Directory Open Access Journal |
| issn | 1477-7819 |
| language | English |
| last_indexed | 2024-03-13T01:54:08Z |
| publishDate | 2023-06-01 |
| publisher | BMC |
| record_format | Article |
| series | World Journal of Surgical Oncology |
| spelling | doaj.art-0de95b509e2043a18403009d66f5add32023-07-02T11:17:45ZengBMCWorld Journal of Surgical Oncology1477-78192023-06-0121111710.1186/s12957-023-03070-1Transcriptome sequencing and miRNA-mRNA network construction in exosome of macrophage M2 in stomach adenocarcinomaDun Pan0Zhipeng Li1Xin Lin2Liangqing Li3Department of Gastrointestinal Surgery, the First Affiliated Hospital, Fujian Medical UniversityDepartment of Gastrointestinal Surgery, the First Affiliated Hospital, Fujian Medical UniversityDepartment of Gastrointestinal Surgery, the First Affiliated Hospital, Fujian Medical UniversityDepartment of Gastrointestinal Surgery, the First Affiliated Hospital, Fujian Medical UniversityAbstract Background Stomach adenocarcinoma (STAD) is the most common histological type of gastric cancer (GC). Macrophages are an essential part of the tumor microenvironment. We attempted to search for potential molecular markers associated with macrophages, which might be helpful for STAD diagnosis and treatment. Methods Firstly, exosome in macrophages was extracted for RNA sequencing to identify differentially expressed microRNAs (miRNAs) (DEmiRNAs). Then, DEmiRNAs and differentially expressed mRNAs (DEmRNAs) were screened in the Cancer Genome Atlas (TCGA) database. The miRNAs related to macrophage M2 polarization were obtained by intersecting the DEmiRNAs obtained from the sequencing data and TCGA data. Using the Pearson correlation coefficient method, the mRNAs significantly related to macrophage M2 were screened out, followed by construction of the macrophage M2-miRNA-mRNA network. Subsequently, real-time-polymerase chain reaction (RT-PCR) and online datasets were applied to validate the expression of DEmiRNAs and DEmRNAs. Results A total of 6 DEmiRNAs were identified in RNA sequencing; 59 DEmiRNAs and 1838 DEmRNAs were identified in TCGA database. Among which, a common miRNA (hsa-miR-133a-3p) associated with the M2 polarization of macrophages was identified. Fifteen common mRNAs were obtained between DEmRNAs and mRNAs targeted by DEmiRNAs. Eventually, a core macrophage M2-1 down-regulated miRNA-7 and up-regulated mRNAs network was constructed, including hsa-miR-133a-3p, SLC39A1, TTYH3, HAVCR2, TPM3, XPO1, POU2F1, and MMP14. The expression of miRNA and mRNAs was in line with the validation results of RT-PCR and online datasets. Conclusion In this study, the screening of biomarkers in exosome of macrophage M2 may contribute to the prognosis of STAD patients.https://doi.org/10.1186/s12957-023-03070-1Stomach adenocarcinomaExosomeMacrophage M2RNA sequencingmiRNAmRNA |
| spellingShingle | Dun Pan Zhipeng Li Xin Lin Liangqing Li Transcriptome sequencing and miRNA-mRNA network construction in exosome of macrophage M2 in stomach adenocarcinoma World Journal of Surgical Oncology Stomach adenocarcinoma Exosome Macrophage M2 RNA sequencing miRNA mRNA |
| title | Transcriptome sequencing and miRNA-mRNA network construction in exosome of macrophage M2 in stomach adenocarcinoma |
| title_full | Transcriptome sequencing and miRNA-mRNA network construction in exosome of macrophage M2 in stomach adenocarcinoma |
| title_fullStr | Transcriptome sequencing and miRNA-mRNA network construction in exosome of macrophage M2 in stomach adenocarcinoma |
| title_full_unstemmed | Transcriptome sequencing and miRNA-mRNA network construction in exosome of macrophage M2 in stomach adenocarcinoma |
| title_short | Transcriptome sequencing and miRNA-mRNA network construction in exosome of macrophage M2 in stomach adenocarcinoma |
| title_sort | transcriptome sequencing and mirna mrna network construction in exosome of macrophage m2 in stomach adenocarcinoma |
| topic | Stomach adenocarcinoma Exosome Macrophage M2 RNA sequencing miRNA mRNA |
| url | https://doi.org/10.1186/s12957-023-03070-1 |
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