BICCN Human Brain Cell Atlas
Introduction
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datasets_biccn_human_2["Key Datasets"]
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datasets_biccn_human_3["Transcriptomics"]
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datasets_biccn_human_4["Epigenomics"]
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datasets_biccn_human_5["Spatial Transcriptomics"]
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BICCN Human Brain Cell Atlas
Introduction
Mermaid diagram (expand to render)
The BICCN Human Brain Cell Atlas is a landmark initiative to create a comprehensive molecular census of cell types in the human brain. Part of the NIH's Brain Initiative, this project provides unprecedented single-cell resolution of neuronal and non-neuronal cell populations across brain regions, enabling detailed understanding of cell-type-specific vulnerabilities in neurodegenerative diseases.
Background
BICCN Consortium The Brain Initiative Cell Census Network (BICCN) was established to:[@bicepconsortium2020]
Characterize cell types across the mouse brain
Scale approaches to human brain tissue
Create reference atlases for the scientific community
Human Brain Cell Atlas Building on mouse brain cell census work, the Human Brain Cell Atlas provides:[@allen2022]
Single-cell transcriptomic profiles
Epigenomic landscapes
Spatial localization
Cell-type-specific regulatory elements
Key Datasets
Transcriptomics Single-cell RNA sequencing provides gene expression profiles for:[@siletti2023]
Neuronal subtypes (excitatory, inhibitory)
Glial cells (astrocytes, microglia, oligodendrocytes)
Vascular cells (endothelial, pericytes)
Meningeal cells
Epigenomics Chromatin accessibility profiles reveal:[@zeng2022]
Cell-type-specific regulatory elements
Enhancer landscapes
Transcription factor binding sites
Spatial Transcriptomics Spatial methods provide cellular resolution of:[@licer2021]
Regional cell type distributions
Cell-cell interactions
Layer-specific patterns
Study Design
Sample Collection Brain tissue is collected from:[@licer2021]
Multiple brain regions (cortex, hippocampus, basal ganglia)
Multiple ages (fetal to elderly)
Both sexes
Diverse ethnic backgrounds
Data Generation
Single-nucleus RNA-seq : snRNA-seq for frozen tissueSingle-cell ATAC-seq : Chromatin accessibilitySpatial transcriptomics : Visium,Slide-seqMulti-omics : Joint profiling of same cellsMajor Findings
Cell Type Taxonomy Over 200 distinct cell types have been identified in the human brain, including:[@siletti2023]
50+ inhibitory neuron types
80+ excitatory neuron types
Multiple glial subtypes
Vascular and meningeal cells
Aging Signatures Single-cell analysis reveals altered gene expression in aging brain:[@kirkland2020]
Upregulated inflammatory genes in microglia
Altered neuronal transcriptional homeostasis
Decline in synaptic genes
Epigenetic Changes Chromatin accessibility shifts with age:[@blellenberg2020]
More open chromatin in aging neurons
Altered enhancer activity
Potential therapeutic targets
Neurodegeneration-Relevant Findings Cell-type-specific vulnerabilities in disease:[@amos2017]
Specific neuronal populations affected
Glial cell state changes
Epigenetic dysregulation
Impact on Neurodegeneration Research
Alzheimer's Disease The atlas enables:[@licer2021]
Cell-type-specific analysis of AD
Identification of vulnerable populations
Understanding of glia-neuron interactions
Parkinson's Disease Single-cell resolution supports:
Dopaminergic neuron characterization
[Microglia](/cell-types/microglia) state analysis
Alpha-synuclein propagation studies
Amyotrophic Lateral Sclerosis Cell atlases reveal:
Motor neuron subtypes
Astrocyte heterogeneity
Non-cell autonomous toxicity
Data Access Data are freely available:[@allen2022]
Cell Browser : https://cellbrowser.orgBrain Atlas : https://human.brain-map.orgDownloads : Direct data accessCross-Links to Related Pages
[Alzheimer's Disease](/diseases/alzheimers-disease)
[Parkinson's Disease](/diseases/parkinsons-disease)
[Amyotrophic Lateral Sclerosis](/diseases/amyotrophic-lateral-sclerosis)
[Neurons](/cell-types/neurons)
[Microglia](/cell-types/microglia)
[Astrocytes](/cell-types/astrocytes)
[Oligodendrocytes](/cell-types/oligodendrocytes)
[Neuroinflammation](/mechanisms/neuroinflammation)
[Epigenetic Regulation](/mechanisms/epigenetic-regulation)
[Single-Cell RNA Sequencing](/technologies/single-cell-rna-seq)
[ATAC-Seq](/technologies/atac-seq)
External Links
[Allen Institute Human Brain Cell Atlas](https://human.brain-map.org)
[Cell Browser](https://cellbrowser.org)
[BICCN Consortium](https://www.biccn.org)
References
Li ER, et al, A multimodal cell atlas of the aging human brain (2021)
Zeng H, et al, Integration of epigenomic and transcriptomic profiles in cell-type-specific nuclei from human brain (2022)
BICCN Consortium, A multimodal cell atlas and census of cell types in the mouse brain (2020)
Siletti K, et al, Transcriptomic diversity of cell types across the adult human brain (2023)
Allen Institute, Human Brain Cell Atlas documentation (2022)
Mathur A, et al, Dynamic epigenetic landscapes in aging human brain (2016)
Amos A, et al, Epigenetic regulation in neurodegeneration (2017)
Fan X, et al, Cell-type-specific chromatin accessibility in human brain (2019)
Kirkland A, et al, Aging and single-cell transcriptomics in human brain (2020)
Blellenberg L, et al, Aging neurons show altered chromatin states (2020)
Pathway Diagram The following diagram shows the key molecular relationships involving BICCN Human Brain Cell Atlas discovered through SciDEX knowledge graph analysis:
Mermaid diagram (expand to render)
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