Human and Non-Human Primate Brain Atlases and Tools

The recording of this webinar is now available: https://youtu.be/RJFVDqcaRZI

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The incredible complexity of the human brain poses enormous challenges in understanding how the brain underlies our thoughts and behaviors, and what goes wrong in disease. Furthermore, the inaccessibility of the human brain necessitates the use of closely related model organisms to understand many aspects of brain structure and function that cannot be studied in human. New highly scalable technologies for studying individual cells on the basis of the genes they use are rapidly accelerating the field to create complete maps of the types of cells that make up the brain. These methods also allow mapping of homologous cell types across species to understand what can be studied in model organisms and what is unique about the human brain.

This webinar will present results from the BRAIN Initiative Cell Census Network (biccn.org) recently published in Science that describes the first draft of a brain-wide cell atlas of the adult human brain. Based on a single cell RNA sequencing (single cell transcriptomics), this effort describes the exceptional diversity of brain cell types and their distribution across the brain, identifying over 3000 cell types. These cell atlasing efforts have entered the next phase through the BRAIN Initiative Cell Atlas Network (BICAN) focused on human and closely related non-human primate model organisms. These new efforts use a combination of single cell transcriptomics, epigenomics and spatial transcriptomics to identify all cell types and map their spatial organization both in local tissue microarchitecture and the larger-scale microarchitecture of the brain.

Finally, these cell atlases are created to be foundational community resources in the spirit of the Human Genome Project. Effective open access tools are essential to realize the potential of these resources to standardize and accelerate efforts across the field to understand brain function and disease. Tools to visualize these data and for users to map their own data against will be described.

There will be time for Q&A with the presenters at the end of the presentations.

Read more about the HMBA Atlas, including links to papers and datasets: https://www.biccn.org/science/human-and-nhp-cell-atlas 

Research presented in this webinar has been supported by the BRAIN Initiative Cell Atlas Network (BICAN) of the National Institutes of Health under award number UM1MH130981.

Speakers:

Ed Lein - Senior Investigator at the Allen Institute for Brain Science: Introduction

Kimberly Siletti - Assistant Professor at the University Medical Center Utrecht 

Bio:  Kimberly Siletti is an Assistant Professor at the University Medical Center Utrecht in the Netherlands. Her group focuses on the molecular mechanisms that generate cellular diversity in the brain. She completed her PhD in 2017 at The Rockefeller University with Jim Hudspeth, studying cell development in the inner ear. She followed this work as a postdoctoral researcher in Sten Linnarsson’s group at the Karolinska Institute in Sweden, where she used single-cell methods to survey both the developing mouse and adult human brains.

Title of talk: Transcriptomic cell-type diversity across the human brain 

• This talk will discuss the first census of transcriptomic cell-type diversity across the entire human brain. A collaboration with the Allen Institute for Brain Science, these efforts profiled nuclei from approximately 100 dissections across the forebrain, midbrain, and hindbrain in three donors. The talk will discuss the study design and main observations, including the extensive regional diversity identified across all cell types. 
• Read “Transcriptomic diversity of cell types across the adult human brain” here: https://doi.org/10.1126/science.add7046

Rebecca Hodge - Assistant Investigator at the Allen Institute for Brain science

Bio: Rebecca Hodge is an Assistant Investigator at the Allen Institute for Brain science working on large-scale projects to generate comprehensive, brain wide atlases of cellular diversity in human and non-human primate brains using multiomic and spatial transcriptomic methods. She is also a member of the Seattle Alzheimer’s Disease Cell Atlas consortium (SEA-AD) where she helps to lead efforts to generate a high-resolution multimodal cellular atlas of Alzheimer’s Disease. Prior to joining the Allen Institute, she completed postdoctoral research at the University of Washington and the Center for Integrative Brain Research at Seattle Children’s Research Institute and her PhD at the University of British Columbia.

Title of talk: Building comprehensive cellular atlases of human and non-human primate brains using single cell genomics

• Efforts to characterize the cellular diversity of the brain using single cell transcriptomics have revealed an enormous diversity of cell types in the mouse and human brain. This talk will discuss our efforts to extend this work to generate a comprehensive census of cell types across all regions of brain in both human and non-human primate model species using transcriptomics and epigenomics. It will also discuss how comparisons of cell types across humans and model animal species enable us to understand species-specific and conserved features of cell types in the brain.
• Read "Comparative transcriptomics reveals human-specific cortical features" here: https://www.science.org/doi/10.1126/science.ade9516 
• Read:  Interindividual variation in human cortical cell type abundance and expression" here:  https://www.science.org/doi/10.1126/science.adf2359
• Read "Transcriptomic cytoarchitecture reveals principles of human neocortex organization" here:  https://www.science.org/doi/10.1126/science.adf6812 

Stephanie Seeman - Scientist at the Allen Institute for Brain Science

Bio: Stephanie Seeman is a Scientist at the Allen Institute for Brain Science working on building comprehensive spatial atlases of cell types in the human and non-human primate brain. Stephanie has also worked on projects to explore not only how different cell types in the brain are spatially arranged but how they communicate with each other to sense the world around us. Prior to joining the Allen Institute, Stephanie completed her PhD at the University of Washington.

Title of talk: Building a Spatial Atlas of Human and Non-Human Primate Brain

• Cell types are often defined by their transcriptomic signature in a way that removes them from the physical context of the brain in which they reside. Spatial transcriptomics allows us to measure the gene expression signature of cells in thin sections of brain tissue so that we can understand how cell types are spatially arranged and interact. This talk will discuss our efforts to build spatial atlases of the human and non-human primate brain.
• Read "Comparative transcriptomics reveals human-specific cortical features" here: https://www.science.org/doi/10.1126/science.ade9516 
• Read "Transcriptomic cytoarchitecture reveals principles of human neocortex organization" here:  https://www.science.org/doi/10.1126/science.adf6812 

Elysha Fiabane - Product Manager at the Allen Institute for Brain Science 

Bio: Elysha Fiabane is a Product Manager on the Data and Technology team at the Allen Institute for Brain Science. Her primary focus is on continuously improving the data visualization and analysis tools like Cell Types Knowledge Explorer, ABC Atlas and MapMyCells which are publicly available to neuroscientists. Previously Elysha held product leadership positions in health technology companies like athenahealth and Pear Therapeutics. Elysha holds a BA in Linguistics and Sociology from Boston College.

Title of talk: Web Tools for Visualizing and Analyzing Human and Mammalian Brain Atlases

• Cell Types Knowledge Explorer https://knowledge.brain-map.org/celltypes
• ABC Atlas https://portal.brain-map.org/atlases-and-data/bkp/abc-atlas
• MapMyCells http://knowledge.brain-map.org/mapmycells/process/

Moderator: 

Jimena Garcia - Program Manager, Inclusive Research at Allen Institute