Single-cell genomics technologies, especially single-cell RNA sequencing (scRNA-seq), are revolutionizing biological and clinical research. We are expanding these methods by developing single-cell ‘multiomics’ assays, which simultaneously probe multiple different molecular features in single cells. These methods will allow us to identify and characterize cell types and states at a finer resolution than enabled by previously developed technologies, and improve our understanding of how different regulatory features work together in a concerted fashion to coordinate cellular activity. Multiomics methods could also be used to link relationships between data from separate studies that measured different features, making them a kind of ‘Rosetta Stone’ for genomics research.

We recently developed single-cell Nucleosome Occupancy and Methylation sequencing (scNOMe-seq), an assay which simultaneously measures chromatin accessibility and DNA methylation. Our current projects expand on this work by seeking to incorporate quantification of protein and RNA levels into the single-cell assay as well. We envision that such multiomics methods will allow researchers to examine regulatory processes in healthy and diseased tissues with unprecedented detail.

The Human Cell Atlas, an international consortium of scientists, aims to “create comprehensive reference maps of all human cells […] as a basis for both understanding human health and diagnosing, monitoring, and treating disease.” This ambitious collaboration was enabled by recent technological advances, particularly those in the field of single-cell genomics. We are part of two Human Cell Atlas projects that aim to generate cellular draft atlases of the human heart and the gut, respectively.

The heart is a complex organ whose function relies on the coordinated interplay of heterogenous cell populations with specialized functions. However, the precise composition of the cardiac cell populations and their respective roles are incompletely understood. Single-cell genomics technologies provide us with the means to identify all cell types within the human heart, to discern key differences between these populations, and to understand the varying roles they play in the pathogenesis of cardiovascular disease. In collaboration with Oni Basu, we previously benchmarked single-cell and single-nuclei RNA-seq technologies. We are now part of an international group of researchers applying these technologies to generate a cellular atlas of the human heart. Our efforts will include characterizing cell states and types in the heart, and identifying expression networks. Importantly, we will integrate transcriptomic and epigenetic assays with spatial approaches to obtain a cellular atlas of the heart in three dimensions. This work is funded by the Chan Zuckerberg Initiative.

Crohn’s disease (CD) is a debilitating chronic inflammatory bowel disorder that can present at different locations throughout the entire gastrointestinal (GI) tract. Despite intensive research whose findings suggest that CD arises from a combination of genetic, environmental, and microbial factors, the cellular and molecular mechanisms leading to CD remain obscure. The clinical heterogeneity of CD and the cellular complexity of the gut have made it difficult to identify cellular and molecular drivers of the disease, and represent significant roadblocks for CD-related research. We collaborate with the labs of Oni Basu, Gene Chang, and Matthew Stephens to address some of these challenges. Together, we aim to create a human gut cell atlas of the ileum and proximal colon in CD patients and healthy controls in order to identify cell-type-, disease-, and stage-specific markers of CD, and to gain insights into the molecular mechanisms of disease etiology. To that end, we are applying single-cell genomics strategies to characterize primary patient samples and ex vivo organoid models. This work is funded by the Helmsley Charitable Trust.

We are part of a number of different collaborations that span institution and discipline. These interdisciplinary partnerships allow us to apply single-cell technologies in different contexts and to pursue novel questions in model systems.

Cardiac development is an intricately regulated process. Together with Ivan Moskowitz and his group, we are studying how specific signaling pathways help to control cardiac differentiation across time and space in mice. This question is particularly well suited for the application of single-cell technologies because the early stages of cardiac development occur in close proximity to other developing organs. Using single-cell RNA-seq allows us to ‘dissect’ the embryo by identifying both cardiac and non-cardiac cell populations, and to track changes in cell population and transcription during development.