Identification and validation of core genes in tumor-educated platelets for human gastrointestinal tumor diagnosis using network-based transcriptomic analysis
Gastrointestinal (GI) tumors have increasing incidence worldwide with their underlying mechanisms still not being fully understood. The use of tumor-educated platelets (TEPs) in liquid biopsy is a newly-emerged blood-based cancer diagnostic method. Herein, we aimed to investigate the genomic changes...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Taylor & Francis Group
2023-12-01
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| Series: | Platelets |
| Subjects: | |
| Online Access: | http://dx.doi.org/10.1080/09537104.2023.2212071 |
| _version_ | 1797684052747091968 |
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| author | Yuhong Jiang Jun He Xiaobo Wang Chao Liu Weihan Zhou Dekun Liu Zhushu Guo Kuijie Liu |
| author_facet | Yuhong Jiang Jun He Xiaobo Wang Chao Liu Weihan Zhou Dekun Liu Zhushu Guo Kuijie Liu |
| author_sort | Yuhong Jiang |
| collection | DOAJ |
| description | Gastrointestinal (GI) tumors have increasing incidence worldwide with their underlying mechanisms still not being fully understood. The use of tumor-educated platelets (TEPs) in liquid biopsy is a newly-emerged blood-based cancer diagnostic method. Herein, we aimed to investigate the genomic changes of TEPs in GI tumor development and their potential functions using network-based meta-analysis combined with bioinformatic methods. We used a total of three eligible RNA-seq datasets, which were integrated using multiple meta-analysis methods on the NetworkAnalyst website, and identified 775 DEGs (differentially expressed genes; 51 up-regulated and 724 down-regulated genes) in GI tumor relative to healthy control (HC) samples. These TEP DEGs were mostly enriched in bone marrow-derived cell types and associated with gene ontology (GO) of “carcinoma” and could affect pathways of “Integrated Cancer Pathway” and “Generic transcription pathway” respectively for highly and lowly expressed DEGs. Combined network-based meta-analysis and protein–protein interaction (PPI) analysis identified cyclin dependent kinase 1 (CDK1) and heat shock protein family A (Hsp70) member 5 (HSPA5) to be the hub genes with the highest degree centrality (DC), being up-regulated and down-regulated in TEPs, respectively. GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) results showed that the hub genes were primarily related to cell cycle and division, nucleobase-containing compound and carbohydrate transport, and endoplasmic reticulum unfolded protein response. Additionally, the nomogram model suggested that the two-gene signature owns extraordinary predictive power for GI tumor diagnosis. Further, the two-gene signature was demonstrated to have potential value for metastatic GI tumor diagnosis. The expression levels of CDK1 and HSPA5 in clinical platelet samples were verified to be consistent with the results from bioinformatic analysis. This study identified a two-gene signature encompassing CDK1 and HSPA5 that can be used as a biomarker for GI tumor diagnosis and maybe even cancer-associated thrombosis (CAT)-related prognosis. |
| first_indexed | 2024-03-12T00:24:52Z |
| format | Article |
| id | doaj.art-22715b3c9de643c2b79d026b96c12b5a |
| institution | Directory Open Access Journal |
| issn | 0953-7104 1369-1635 |
| language | English |
| last_indexed | 2024-03-12T00:24:52Z |
| publishDate | 2023-12-01 |
| publisher | Taylor & Francis Group |
| record_format | Article |
| series | Platelets |
| spelling | doaj.art-22715b3c9de643c2b79d026b96c12b5a2023-09-15T10:38:12ZengTaylor & Francis GroupPlatelets0953-71041369-16352023-12-0134110.1080/09537104.2023.22120712212071Identification and validation of core genes in tumor-educated platelets for human gastrointestinal tumor diagnosis using network-based transcriptomic analysisYuhong Jiang0Jun He1Xiaobo Wang2Chao Liu3Weihan Zhou4Dekun Liu5Zhushu Guo6Kuijie Liu7The Second Xiangya Hospital of Central South UniversityThe Second Xiangya Hospital of Central South UniversityThe Second Xiangya Hospital of Central South UniversityThe Second Xiangya Hospital of Central South UniversityThe Second Xiangya Hospital of Central South UniversityThe Second Xiangya Hospital of Central South UniversityThe Second Xiangya Hospital of Central South UniversityThe Second Xiangya Hospital of Central South UniversityGastrointestinal (GI) tumors have increasing incidence worldwide with their underlying mechanisms still not being fully understood. The use of tumor-educated platelets (TEPs) in liquid biopsy is a newly-emerged blood-based cancer diagnostic method. Herein, we aimed to investigate the genomic changes of TEPs in GI tumor development and their potential functions using network-based meta-analysis combined with bioinformatic methods. We used a total of three eligible RNA-seq datasets, which were integrated using multiple meta-analysis methods on the NetworkAnalyst website, and identified 775 DEGs (differentially expressed genes; 51 up-regulated and 724 down-regulated genes) in GI tumor relative to healthy control (HC) samples. These TEP DEGs were mostly enriched in bone marrow-derived cell types and associated with gene ontology (GO) of “carcinoma” and could affect pathways of “Integrated Cancer Pathway” and “Generic transcription pathway” respectively for highly and lowly expressed DEGs. Combined network-based meta-analysis and protein–protein interaction (PPI) analysis identified cyclin dependent kinase 1 (CDK1) and heat shock protein family A (Hsp70) member 5 (HSPA5) to be the hub genes with the highest degree centrality (DC), being up-regulated and down-regulated in TEPs, respectively. GO and Kyoto Encyclopedia of Genes and Genomes (KEGG) results showed that the hub genes were primarily related to cell cycle and division, nucleobase-containing compound and carbohydrate transport, and endoplasmic reticulum unfolded protein response. Additionally, the nomogram model suggested that the two-gene signature owns extraordinary predictive power for GI tumor diagnosis. Further, the two-gene signature was demonstrated to have potential value for metastatic GI tumor diagnosis. The expression levels of CDK1 and HSPA5 in clinical platelet samples were verified to be consistent with the results from bioinformatic analysis. This study identified a two-gene signature encompassing CDK1 and HSPA5 that can be used as a biomarker for GI tumor diagnosis and maybe even cancer-associated thrombosis (CAT)-related prognosis.http://dx.doi.org/10.1080/09537104.2023.2212071diagnosisgastrointestinal tumorgene expression omnibustranscriptomic analysistumor-educated platelets |
| spellingShingle | Yuhong Jiang Jun He Xiaobo Wang Chao Liu Weihan Zhou Dekun Liu Zhushu Guo Kuijie Liu Identification and validation of core genes in tumor-educated platelets for human gastrointestinal tumor diagnosis using network-based transcriptomic analysis Platelets diagnosis gastrointestinal tumor gene expression omnibus transcriptomic analysis tumor-educated platelets |
| title | Identification and validation of core genes in tumor-educated platelets for human gastrointestinal tumor diagnosis using network-based transcriptomic analysis |
| title_full | Identification and validation of core genes in tumor-educated platelets for human gastrointestinal tumor diagnosis using network-based transcriptomic analysis |
| title_fullStr | Identification and validation of core genes in tumor-educated platelets for human gastrointestinal tumor diagnosis using network-based transcriptomic analysis |
| title_full_unstemmed | Identification and validation of core genes in tumor-educated platelets for human gastrointestinal tumor diagnosis using network-based transcriptomic analysis |
| title_short | Identification and validation of core genes in tumor-educated platelets for human gastrointestinal tumor diagnosis using network-based transcriptomic analysis |
| title_sort | identification and validation of core genes in tumor educated platelets for human gastrointestinal tumor diagnosis using network based transcriptomic analysis |
| topic | diagnosis gastrointestinal tumor gene expression omnibus transcriptomic analysis tumor-educated platelets |
| url | http://dx.doi.org/10.1080/09537104.2023.2212071 |
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