survey of human brain transcriptome diversity at the single cell level

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 112; no. 23; pp. 7285 - 7290
• Main Authors: Darmanis, Spyros, Sloan, Steven A., Zhang, Ye, Enge, Martin, Caneda, Christine, Shuer, Lawrence M., Gephart, Melanie G. Hayden, Barres, Ben A., Quake, Stephen R.
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences 09.06.2015; National Acad Sciences
• Subjects: Adult; adults; Biological Sciences; Brain; Brain - cytology; Brain - embryology; Brain - metabolism; Cells; HLA Antigens - immunology; Human subjects; Humans; major histocompatibility complex; Neurons; Neurons - cytology; Neurons - immunology; Ribonucleic acid; RNA; Sequence Analysis, RNA; Single-Cell Analysis; surveys; Transcriptome; transcriptomics; human brain; single cells; RNAseq; neurons; interneurons
• ISSN: 0027-8424; 1091-6490; 1091-6490
• DOI: 10.1073/pnas.1507125112

Significance The brain comprises an immense number of cells and cellular connections. We describe the first, to our knowledge, single cell whole transcriptome analysis of human adult cortical samples. We have established an experimental and analytical framework with which the complexity of the human brain can be dissected on the single cell level. Using this approach, we were able to identify all major cell types of the brain and characterize subtypes of neuronal cells. We observed changes in neurons from early developmental to late differentiated stages in the adult. We found a subset of adult neurons which express major histocompatibility complex class I genes and thus are not immune privileged. The human brain is a tissue of vast complexity in terms of the cell types it comprises. Conventional approaches to classifying cell types in the human brain at single cell resolution have been limited to exploring relatively few markers and therefore have provided a limited molecular characterization of any given cell type. We used single cell RNA sequencing on 466 cells to capture the cellular complexity of the adult and fetal human brain at a whole transcriptome level. Healthy adult temporal lobe tissue was obtained during surgical procedures where otherwise normal tissue was removed to gain access to deeper hippocampal pathology in patients with medical refractory seizures. We were able to classify individual cells into all of the major neuronal, glial, and vascular cell types in the brain. We were able to divide neurons into individual communities and show that these communities preserve the categorization of interneuron subtypes that is typically observed with the use of classic interneuron markers. We then used single cell RNA sequencing on fetal human cortical neurons to identify genes that are differentially expressed between fetal and adult neurons and those genes that display an expression gradient that reflects the transition between replicating and quiescent fetal neuronal populations. Finally, we observed the expression of major histocompatibility complex type I genes in a subset of adult neurons, but not fetal neurons. The work presented here demonstrates the applicability of single cell RNA sequencing on the study of the adult human brain and constitutes a first step toward a comprehensive cellular atlas of the human brain.