Transcriptomic analyses of patient peripheral blood with hemoglobin depletion reveal glioblastoma biomarkers

Dan Qi; Yiqun Geng; Jacob Cardenas; Jinghua Gu; S Stephen Yi; Jason H Huang; Ekokobe Fonkem; Erxi Wu

doi:10.1038/s41525-022-00348-3

Transcriptomic analyses of patient peripheral blood with hemoglobin depletion reveal glioblastoma biomarkers

NPJ Genom Med. 2023 Jan 25;8(1):2. doi: 10.1038/s41525-022-00348-3.

Authors

Dan Qi^#¹, Yiqun Geng^#^{1

2}, Jacob Cardenas³, Jinghua Gu³, S Stephen Yi^{4

5

6

7}, Jason H Huang^{8

9}, Ekokobe Fonkem^{10

11}, Erxi Wu^{12

13

14

15}

Affiliations

¹ Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX, 76508, USA.
² Laboratory of Molecular Pathology, Shantou University Medical College, 515041, Shantou, China.
³ Baylor Scott & White Research Institute, Dallas, TX, 75204, USA.
⁴ Institute for Cellular and Molecular Biology (ICMB), College of Natural Sciences, The University of Texas at Austin, Austin, TX, 78712, USA.
⁵ Oden Institute for Computational Engineering and Sciences (ICES), The University of Texas at Austin, Austin, TX, 78712, USA.
⁶ Department of Biomedical Engineering, Cockrell School of Engineering, The University of Texas at Austin, Austin, TX, 78712, USA.
⁷ Department of Oncology, LIVESTRONG Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, 78712, USA.
⁸ Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX, 76508, USA. [email protected].
⁹ Texas A & M University School of Medicine, Temple, TX, 76508, USA. [email protected].
¹⁰ Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX, 76508, USA. [email protected].
¹¹ Texas A & M University School of Medicine, Temple, TX, 76508, USA. [email protected].
¹² Department of Neurosurgery and Neuroscience Institute, Baylor Scott & White Health, Temple, TX, 76508, USA. [email protected].
¹³ Department of Oncology, LIVESTRONG Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, 78712, USA. [email protected].
¹⁴ Texas A & M University School of Medicine, Temple, TX, 76508, USA. [email protected].
¹⁵ Texas A & M University School of Pharmacy, College Station, TX, 77843, USA. [email protected].

^# Contributed equally.

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.

Grants and funding

R35 GM133658/GM/NIGMS NIH HHS/United States