Mapping and modeling the spatiotemporal proteome architecture of human cells

Emma Lundberg, PhD
Associate Professor of Bioengineering and of Pathology
Friday, September 20, 2024
11:00am - 12:00pm
James H. Clark Center, Room S360, 3rd floor next to the Coffee Shop
Zoom link
Abstract:
Biological systems are functionally defined by the nature, amount, and spatial location of their proteins. We have generated an image-based map of the subcellular distribution of the human proteome and showed that there is great complexity to the subcellular organization of the cell giving rise to potential pleiotropic effects. As much as half of all proteins localize to multiple compartments and around 20% of the human proteome shows temporal variability. Our temporal mapping results show that cell cycle progression explains less than half of all temporal protein variability and that most cycling proteins are regulated post-translationally, rather than by transcriptomic cycling. This work is critically dependent on computational image analysis, and I will discuss machine learning approaches for embedding spatial subcellular patterns, and how such embeddings as well as generative AI can be used to build multi-scale models of cell architecture. In summary, I will demonstrate the importance of spatial proteomics data for improved single-cell biology and present how the freely available Human Protein Atlas database (www.proteinatlas.org) can be used as a resource for life science.
Short Biography: Dr. Lundberg is Associate Professor of Bioengineering and Pathology at Stanford University, and Director of the Cell Atlas, of the Human Protein Atlas (www.proteinatlas.org), In the interface between bioimaging, proteomics and artificial intelligence her research aims to define the spatiotemporal organization of the human proteome at a cellular and subcellular level, with the goal to build integrated models of human cells to understand how variations in protein expression patterns contribute to cellular function and disease.
Dr. Lundberg is an advocate for open science and have a strong interest in science communication, both to scientific audiences and the general public through innovative media. She has been the secretary general of the Human Proteome Organization, and held advisory roles for many open access databases and cell mapping efforts such as the Human Cell Atlas consortium, UniProt db, Reactome db, Human Proteome Project, Chan-Zuckerberg initiative, EMBL-EBI Bioimaging Ecosystem Steering Group and Pharma Companies. As a token of her scientific and leadership skills, Dr. Lundberg has been received many awards including the Göran Gustafsson Award, Royal Microscopy Society Scientific Achievement Award, Anne Heidenthal prize and two listings as top 10 under 40; future leaders in biopharma and omics. Dr. Lundberg is determined to develop large-scale integrative spatial proteomics studies and shaping the next era of biology and pathology