Discovery of paradoxical genes: reevaluating the prognostic impact of overexpressed genes in cancer
Oncogenes are typically overexpressed in tumor tissues and often linked to poor prognosis. However, recent advancements in bioinformatics have revealed that many highly expressed genes in tumors are associated with better patient outcomes. These genes, which act as tumor suppressors, are referred to...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2025-01-01
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| Series: | Frontiers in Cell and Developmental Biology |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fcell.2025.1525345/full |
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| author | Dequan Liu Lei Liu Xiangyu Che Guangzhen Wu |
| author_facet | Dequan Liu Lei Liu Xiangyu Che Guangzhen Wu |
| author_sort | Dequan Liu |
| collection | DOAJ |
| description | Oncogenes are typically overexpressed in tumor tissues and often linked to poor prognosis. However, recent advancements in bioinformatics have revealed that many highly expressed genes in tumors are associated with better patient outcomes. These genes, which act as tumor suppressors, are referred to as “paradoxical genes.” Analyzing The Cancer Genome Atlas (TCGA) confirmed the widespread presence of paradoxical genes, and KEGG analysis revealed their role in regulating tumor metabolism. Mechanistically, discrepancies between gene and protein expression-affected by pre- and post-transcriptional modifications-may drive this phenomenon. Mechanisms like upstream open reading frames and alternative splicing contribute to these inconsistencies. Many paradoxical genes modulate the tumor immune microenvironment, exerting tumor-suppressive effects. Further analysis shows that the stage- and tumor-specific expression of these genes, along with their environmental sensitivity, influence their dual roles in various signaling pathways. These findings highlight the importance of paradoxical genes in resisting tumor progression and maintaining cellular homeostasis, offering new avenues for targeted cancer therapy. |
| format | Article |
| id | doaj-art-20931102b68540c9a64f1a972c1d3553 |
| institution | Kabale University |
| issn | 2296-634X |
| language | English |
| publishDate | 2025-01-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Cell and Developmental Biology |
| spelling | doaj-art-20931102b68540c9a64f1a972c1d35532025-01-22T07:14:54ZengFrontiers Media S.A.Frontiers in Cell and Developmental Biology2296-634X2025-01-011310.3389/fcell.2025.15253451525345Discovery of paradoxical genes: reevaluating the prognostic impact of overexpressed genes in cancerDequan LiuLei LiuXiangyu CheGuangzhen WuOncogenes are typically overexpressed in tumor tissues and often linked to poor prognosis. However, recent advancements in bioinformatics have revealed that many highly expressed genes in tumors are associated with better patient outcomes. These genes, which act as tumor suppressors, are referred to as “paradoxical genes.” Analyzing The Cancer Genome Atlas (TCGA) confirmed the widespread presence of paradoxical genes, and KEGG analysis revealed their role in regulating tumor metabolism. Mechanistically, discrepancies between gene and protein expression-affected by pre- and post-transcriptional modifications-may drive this phenomenon. Mechanisms like upstream open reading frames and alternative splicing contribute to these inconsistencies. Many paradoxical genes modulate the tumor immune microenvironment, exerting tumor-suppressive effects. Further analysis shows that the stage- and tumor-specific expression of these genes, along with their environmental sensitivity, influence their dual roles in various signaling pathways. These findings highlight the importance of paradoxical genes in resisting tumor progression and maintaining cellular homeostasis, offering new avenues for targeted cancer therapy.https://www.frontiersin.org/articles/10.3389/fcell.2025.1525345/fullparadoxical genesbioinformaticstumor metabolismdiscordant gene-protein abundancetumor immune microenvironmentsignaling pathway |
| spellingShingle | Dequan Liu Lei Liu Xiangyu Che Guangzhen Wu Discovery of paradoxical genes: reevaluating the prognostic impact of overexpressed genes in cancer Frontiers in Cell and Developmental Biology paradoxical genes bioinformatics tumor metabolism discordant gene-protein abundance tumor immune microenvironment signaling pathway |
| title | Discovery of paradoxical genes: reevaluating the prognostic impact of overexpressed genes in cancer |
| title_full | Discovery of paradoxical genes: reevaluating the prognostic impact of overexpressed genes in cancer |
| title_fullStr | Discovery of paradoxical genes: reevaluating the prognostic impact of overexpressed genes in cancer |
| title_full_unstemmed | Discovery of paradoxical genes: reevaluating the prognostic impact of overexpressed genes in cancer |
| title_short | Discovery of paradoxical genes: reevaluating the prognostic impact of overexpressed genes in cancer |
| title_sort | discovery of paradoxical genes reevaluating the prognostic impact of overexpressed genes in cancer |
| topic | paradoxical genes bioinformatics tumor metabolism discordant gene-protein abundance tumor immune microenvironment signaling pathway |
| url | https://www.frontiersin.org/articles/10.3389/fcell.2025.1525345/full |
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