Whole blood transcriptome refers to the genome-wide expression of all genes from cells contained in the blood. The transcriptomic analysis of whole blood has the potential to revolutionize non-invasive diagnostic identification of diseases as it provides a comprehensive gene expression profile of an organism’s physiological state.
In this article, we discuss what the whole blood transcriptome is, and the novel transcriptomic technologies bringing blood gene expression studies to the forefront of medical diagnostics and molecular research.
What is whole blood?
Whole blood is comprised of erythrocytes (red blood cells), leukocytes (white blood cells), and platelets. Each cell type is generated during hematopoiesis after the asymmetric division of hematopoietic stem cells in the bone marrow.
Mature erythrocytes lack a nucleus and are relatively transcriptionally inactive compared to nucleated cells (Doss et al., 2015). In contrast, leukocytes are primarily immune cells. They comprise numerous different cell types with distinct transcriptional profiles but complementary immunological roles.
Blood is the pipeline of the body and can also contain other non-blood cells, small vesicles and molecular signals. It provides insight into the physiological state of a system and can serve as a reporter for both systemic disease and localized tissue-specific changes.
The whole blood transcriptome
The abundance of different cell types and the diversity of transcriptional states in whole blood makes it a rich source of easily accessible gene expression data for analysis of physiological or pathological conditions, even in inaccessible tissues (Basu et al., 2021).
The whole blood transcriptome is highly dynamic in nature and responds rapidly to environmental perturbations such as disease, infection or injury. Studies use the whole blood transcriptome to provide a snapshot of the levels of mRNA present at defined time points.
Transcriptomic studies that use bulk RNA-seq methods often reflect both the overall level of gene expression but also indicate the abundance of different cell types in whole blood. For example, upon infection with COVID-19 the whole blood transcriptome has an increase of inflammatory immune response genes relating to neutrophils and macrophages (Jackson et al., 2022).
Novel techniques for whole blood transcriptome analyses
Single-cell RNA-seq and RNA-seq on sorted blood cell populations provide comprehensive gene expression datasets for specific cell types contained in the blood but these cell isolation technologies remain prohibitively expensive and variable (Uhlen et al., 2019).
In contrast, extraction of whole blood is routine in multicenter diagnostics. This makes it attractive for large studies due to the low cost and reduced variability of sample preparation compared to sorted cell populations.
Novel ultra-high-throughput bulk RNA-seq approaches, such as Bulk RNA Barcoding and Sequencing (MERCURIUS™ BRB-seq), are optimized for whole blood transcriptome studies (Alpern et al., 2019). When combined with standard whole blood extraction, researchers can perform larger-scale cohort studies at a lower cost than ever before.
MERCURIUS™ BRB-seq kits are optimized for whole blood because they include a human globin blocker reagent. This is important because RNA extracted from whole blood samples contains high levels of hemoglobin RNAs from the red blood cell component (Mastrokolias et al., 2012; Mele et al., 2015). These high abundance hemoglobin transcripts occupy sequencing space and interfere with sensitive measurements of the rest of the blood transcriptome (Harrington et al., 2020).
The human globin blocker reagent comprises specific oligonucleotides that anneal to highly abundant human globin gene transcripts (HBB, HBA1, and HBA2). It prevents their reverse transcription and inclusion in the final sequencing library and ensures sequencing reads are used for more relevant genes in a study.
- Alpern, D., Gardeux, V., Russeil, J., Mangeat, B., Meireles-Filho, A.C., Breysse, R., Hacker, D. and Deplancke, B., 2019. BRB-seq: ultra-affordable high-throughput transcriptomics enabled by bulk RNA barcoding and sequencing. Genome biology, 20(1), pp.1-15.
- Basu, M., Wang, K., Ruppin, E. and Hannenhalli, S., 2021. Predicting tissue-specific gene expression from whole blood transcriptome. Science Advances, 7(14), p.eabd6991.
- Doss, J.F., Corcoran, D.L., Jima, D.D., Telen, M.J., Dave, S.S. and Chi, J.T., 2015. A comprehensive joint analysis of the long and short RNA transcriptomes of human erythrocytes. BMC genomics, 16(1), pp.1-16.
- Harrington, C.A., Fei, S.S., Minnier, J., Carbone, L., Searles, R., Davis, B.A., Ogle, K., Planck, S.R., Rosenbaum, J.T. and Choi, D., 2020. RNA-Seq of human whole blood: Evaluation of globin RNA depletion on Ribo-Zero library method. Scientific reports, 10(1), pp.1-12.
- Jackson, H., Rivero Calle, I., Broderick, C., Habgood-Coote, D., d’Souza, G., Nichols, S., Vito, O., Gómez-Rial, J., Rivero-Velasco, C., Rodríguez-Núñez, N. and Barbeito-Castiñeiras, G., 2022. Characterisation of the blood RNA host response underpinning severity in COVID-19 patients. Scientific reports, 12(1), pp.1-14.
- Mastrokolias, A., den Dunnen, J.T., van Ommen, G.B., t Hoen, P.A. and van Roon-Mom, W., 2012. Increased sensitivity of next generation sequencing-based expression profiling after globin reduction in human blood RNA. Bmc Genomics, 13(1), pp.1-9.
- Melé, M., Ferreira, P.G., Reverter, F., DeLuca, D.S., Monlong, J., Sammeth, M., Young, T.R., Goldmann, J.M., Pervouchine, D.D., Sullivan, T.J. and Johnson, R., 2015. The human transcriptome across tissues and individuals. Science, 348(6235), pp.660-665.
- Uhlen, M., Karlsson, M.J., Zhong, W., Tebani, A., Pou, C., Mikes, J., Lakshmikanth, T., Forsström, B., Edfors, F., Odeberg, J. and Mardinoglu, A., 2019. A genome-wide transcriptomic analysis of protein-coding genes in human blood cells. Science, 366(6472), p.eaax9198.