Single cell dynamics on a whole organism scale

PROJECT SUMMARY
The functions of mammalian organs are maintained by the behaviors and dynamics of individual cells. The
ability to systematically map each cell type's temporal dynamics is central to the understanding of many
aspects of biological changes that mammals undergo in development. However, conventional methods are
restricted by inadequate throughput and the limited range of cellular contents that can be measured. While
single-cell genomic techniques have been developed to characterize cell state heterogeneity with high
resolution, nearly all such methods capture only a static snapshot at a single time point, with both temporal and
spatial information lost during cell isolation. Herein, the proposed projects aim to develop novel methodologies
that enable a comprehensive view of single-cell spatiotemporal dynamics across the lifespan of an entire
mammalian organism. Specifically, I will expand on the high-throughput single-cell RNA-seq platform (sci-RNA-
seq), to develop a novel method for concurrently profiling transcriptome, epigenome, and cellular temporal
dynamics (e.g., proliferation, apoptosis) in each of millions of cells. The technique will be employed to
investigate how aging regulates the status of a whole mammalian body by systematically monitoring single cell
state dynamics across a broad range of tissues in young and aged mice. This approach will be powerful
because we can not only visualize in-vivo proliferation and apoptosis behaviors of each cell type but also
dissect its connection with internal transcriptome/epigenome states. In addition to the internal molecular
programs, cell state dynamics are controlled by aspects of tissue architecture such as cell-cell interactions and
extracellular matrix abundance. To profile single cell microenvironment with high throughput and accuracy, we
will develop a novel technique called "microtissue-seq", for co-profiling single-cell molecular contents, cellular
spatial interactions, and extracellular matrix (ECM) proteins across tens of thousands of spatial locations in a
single experiment. We will employ this technique to interrogate how cellular microenvironment regulates
organismal-scale cell state dynamics in different age groups of mice. Overall, the proposed projects will
establish a technical framework for comprehensive profiling single-cell spatiotemporal dynamics at an
unprecedented scale of a whole mammalian organism. By profiling cell-state specific dynamic behaviors
across the lifespan of mice, these technologies and experiments would uniquely enable accurate modeling of
the exquisite program underlying mammalian system maintenance and breakdown with age at single cell
resolution. These multi-pronged approaches also open a new paradigm for understanding the global molecular
programs regulating cell states and dynamics during aging, thereby informing potential pathways to delay the
aging process as well as the rational design of effective therapies to restore tissue homeostasis for patients
with aging-related diseases.

Grant Number: 4DP2HG012522-02
NIH Institute/Center: NIH
Principal Investigator: Junyue Cao