Spatial genomics: Tracking biomolecules across space and time

Biology works through precise control of macromolecules in space and time. In every cell, thousands of genes are expressed as RNA and proteins. To profile DNA, RNA, and proteins in situ, new spatial genomics experiments [1] are exploding in popularity due to their high resolution and large scale. These techniques have the capacity to profile thousands of genes across millions of cells in a single experiment. At Arcadia, we are eager to use spatial genomics as a discovery platform in a range of new species. These datasets will not only give us a detailed look at how cells and tissues are organized, but we can also integrate spatial genomics methods into larger experiments involving live imaging, genetic manipulation, or diverse cell populations.

Goal

In this project, we aim to adapt pre-existing spatial genomics platforms to work in our hands, to build upon them, and ultimately apply them across research areas.

Major milestones

We’ve mapped out several milestones on the path toward establishing spatial as a powerful, go-to spatial genomics technique at Arcadia:

1. Use commercial or novel approaches to profile gene expression with subcellular resolution. We’ve chosen Chlamydomonas reinhardtii undergoing ciliary assembly.

2. Combine imaging with in situ barcode assignment to decode genetic perturbations, sometimes called pooled optical screening.

3. Analyze genotype and phenotype of pooled, barcoded cell lines in situ.

4. Use spatial genomics to profile a variety of molecules in diverse tissues. We want to be able to profile brain tissue, non-human embryos, and targeted organs. After starting with the genome and transcriptome, we want to explore tracking all sorts of interesting biomolecules, including DNA, RNA, protein, glycans, and small molecules.

Progress

We are starting this project by establishing spatial genomics protocols in Arcadia’s new laboratory. This page organizes our ongoing efforts to build and apply commercial and home-built spatial genomics rig(s). To start, we are investigating sequential hybridization approaches like those used in SeqFISH, MERFISH, and the commercial solution offered by Vizgen. We chose this approach for its subcellular resolution and broad applicability.

Our first subject of study is the process of ciliary assembly in the marine algae Chlamydomonas reinhardtii. The goal is to map gene expression in space and time while the algae regenerate their cilia. The cells must coordinate dozens of macromolecules to grow a functional organelle, and with spatial genomics, we can gain new insights by studying this process spatially in many cells at once. Using a small panel of genes, we will develop procedures for multiplexed single molecule FISH in Chlamydomonas, including probe design, fixation, ciliary imaging, and of course, fluorescent hybridization, imaging, and analysis.

Our first spatial genomics experiments

We are currently working on things like fixation, sample mounting, and cyclic imaging that are required to produce MERFISH data.

Our first step was to design probes for our initial organism of interest, C. reinhardtii. See our pub for a Colab-based pipeline to generate MERFISH probes in any organism:

Discontinuing this project

We stopped pursuing the effort in which we’d planned to apply spatial genomics tools. With no immediate need for spatial genomics, we decided to ice this project. We may return to it if we eventually have a greater need for this type of technology.