Transcriptomic analyses of patient peripheral blood with hemoglobin depletion reveal glioblastoma biomarkers
Abstract Peripheral blood is gaining prominence as a noninvasive alternative to tissue biopsy to develop biomarkers for glioblastoma (GBM); however, widely utilized blood-based biomarkers in clinical settings have not yet been identified due to the lack of a robust detection approach. Here, we descr...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2023-01-01
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| Series: | npj Genomic Medicine |
| Online Access: | https://doi.org/10.1038/s41525-022-00348-3 |
| _version_ | 1811175734157246464 |
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| author | Dan Qi Yiqun Geng Jacob Cardenas Jinghua Gu S. Stephen Yi Jason H. Huang Ekokobe Fonkem Erxi Wu |
| author_facet | Dan Qi Yiqun Geng Jacob Cardenas Jinghua Gu S. Stephen Yi Jason H. Huang Ekokobe Fonkem Erxi Wu |
| author_sort | Dan Qi |
| collection | DOAJ |
| description | Abstract Peripheral blood is gaining prominence as a noninvasive alternative to tissue biopsy to develop biomarkers for glioblastoma (GBM); however, widely utilized blood-based biomarkers in clinical settings have not yet been identified due to the lack of a robust detection approach. Here, we describe the application of globin reduction in RNA sequencing of whole blood (i.e., WBGR) and perform transcriptomic analysis to identify GBM-associated transcriptomic changes. By using WBGR, we improved the detection sensitivity of informatic reads and identified differential gene expression in GBM blood. By analyzing tumor tissues, we identified transcriptomic traits of GBM blood. Further functional enrichment analyses retained the most changed genes in GBM. Subsequent validation elicited a 10-gene panel covering mRNA, long noncoding RNA, and microRNA (i.e., GBM-Dx panel) that has translational potential to aid in the early detection or clinical management of GBM. Here, we report an integrated approach, WBGR, with comprehensive analytic capacity for blood-based marker identification. |
| first_indexed | 2024-04-10T19:41:42Z |
| format | Article |
| id | doaj.art-2c57a57891044956bca3ec4bc011a2a7 |
| institution | Directory Open Access Journal |
| issn | 2056-7944 |
| language | English |
| last_indexed | 2024-04-10T19:41:42Z |
| publishDate | 2023-01-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | npj Genomic Medicine |
| spelling | doaj.art-2c57a57891044956bca3ec4bc011a2a72023-01-29T12:18:04ZengNature Portfolionpj Genomic Medicine2056-79442023-01-018111310.1038/s41525-022-00348-3Transcriptomic analyses of patient peripheral blood with hemoglobin depletion reveal glioblastoma biomarkersDan Qi0Yiqun Geng1Jacob Cardenas2Jinghua Gu3S. Stephen Yi4Jason H. Huang5Ekokobe Fonkem6Erxi Wu7Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White HealthDepartment of Neurosurgery and Neuroscience Institute, Baylor Scott & White HealthBaylor Scott & White Research InstituteBaylor Scott & White Research InstituteInstitute for Cellular and Molecular Biology (ICMB), College of Natural Sciences, The University of Texas at AustinDepartment of Neurosurgery and Neuroscience Institute, Baylor Scott & White HealthDepartment of Neurosurgery and Neuroscience Institute, Baylor Scott & White HealthDepartment of Neurosurgery and Neuroscience Institute, Baylor Scott & White HealthAbstract Peripheral blood is gaining prominence as a noninvasive alternative to tissue biopsy to develop biomarkers for glioblastoma (GBM); however, widely utilized blood-based biomarkers in clinical settings have not yet been identified due to the lack of a robust detection approach. Here, we describe the application of globin reduction in RNA sequencing of whole blood (i.e., WBGR) and perform transcriptomic analysis to identify GBM-associated transcriptomic changes. By using WBGR, we improved the detection sensitivity of informatic reads and identified differential gene expression in GBM blood. By analyzing tumor tissues, we identified transcriptomic traits of GBM blood. Further functional enrichment analyses retained the most changed genes in GBM. Subsequent validation elicited a 10-gene panel covering mRNA, long noncoding RNA, and microRNA (i.e., GBM-Dx panel) that has translational potential to aid in the early detection or clinical management of GBM. Here, we report an integrated approach, WBGR, with comprehensive analytic capacity for blood-based marker identification.https://doi.org/10.1038/s41525-022-00348-3 |
| spellingShingle | Dan Qi Yiqun Geng Jacob Cardenas Jinghua Gu S. Stephen Yi Jason H. Huang Ekokobe Fonkem Erxi Wu Transcriptomic analyses of patient peripheral blood with hemoglobin depletion reveal glioblastoma biomarkers npj Genomic Medicine |
| title | Transcriptomic analyses of patient peripheral blood with hemoglobin depletion reveal glioblastoma biomarkers |
| title_full | Transcriptomic analyses of patient peripheral blood with hemoglobin depletion reveal glioblastoma biomarkers |
| title_fullStr | Transcriptomic analyses of patient peripheral blood with hemoglobin depletion reveal glioblastoma biomarkers |
| title_full_unstemmed | Transcriptomic analyses of patient peripheral blood with hemoglobin depletion reveal glioblastoma biomarkers |
| title_short | Transcriptomic analyses of patient peripheral blood with hemoglobin depletion reveal glioblastoma biomarkers |
| title_sort | transcriptomic analyses of patient peripheral blood with hemoglobin depletion reveal glioblastoma biomarkers |
| url | https://doi.org/10.1038/s41525-022-00348-3 |
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