A Roadmap for the Human Oral and Craniofacial Cell Atlas

Abstract

Oral and craniofacial tissues are uniquely adapted for continuous and intricate functioning, including breathing, feeding, and communication. To achieve these vital processes, this complex is supported by incredible tissue diversity, variously composed of epithelia, vessels, cartilage, bone, teeth, ligaments, and muscles, as well as mesenchymal, adipose, and peripheral nervous tissue. Recent single cell and spatial multiomics assays-specifically, genomics, epigenomics, transcriptomics, proteomics, and metabolomics-have annotated known and new cell types and cell states in human tissues and animal models, but these concepts remain limitedly explored in the human postnatal oral and craniofacial complex. Here, we highlight the collaborative and coordinated efforts of the newly established Oral and Craniofacial Bionetwork as part of the Human Cell Atlas, which aims to leverage single cell and spatial multiomics approaches to first understand the cellular and molecular makeup of human oral and craniofacial tissues in health and to then address common and rare diseases. These powerful assays have already revealed the cell types that support oral tissues, and they will unravel cell types and molecular networks utilized across development, maintenance, and aging as well as those affected in diseases of the craniofacial complex. This level of integration and cell annotation with partner laboratories across the globe will be critical for understanding how multiple variables, such as age, sex, race, and ancestry, influence these oral and craniofacial niches. Here, we 1) highlight these recent collaborative efforts to employ new single cell and spatial approaches to resolve our collective biology at a higher resolution in health and disease, 2) discuss the vision behind the Oral and Craniofacial Bionetwork, 3) outline the stakeholders who contribute to and will benefit from this network, and 4) outline directions for creating the first Human Oral and Craniofacial Cell Atlas.

Keywords: Human Cell Atlas; bone; craniofacial; multiomics; musculoskeletal; oral mucosa; palate; periodontium; saliva; single cell genomics; spatial biology; tongue.

Figure 1.

Collaboration opportunity across initiatives, networks, groups, and consortia. The Human Cell Atlas Oral and Craniofacial Bionetwork (HCA-OCBN; established 2020) is a collection of aligned investigators with the goal of mapping healthy human tissues of the oral and craniofacial complex. This network is using single cell and spatial multiomics to achieve these goals. (A) Since the Human Genome Project was completed in 2003, there have been several initiatives established that can benefit human oral and craniofacial research. There is enormous potential for fruitful collaboration between OCBN and initiatives such as FaceBase (established 2009), CZI Biohub (2016; Chan Zuckerberg Initiative), and HubMAP (2020; Human Biomolecular Atlas Program). Some of these groups are already collaborating with the OCBN (blue lines). (B) Collaboration within the OCBN can be as focused as sharing tissues and fluid samples or supporting computational analysis. As of May 2022, projects are growing monthly across new OCBN teams. Map generated from https://app.datawrapper.de/. AMP, Accelerating Medicines Partnership Program; ENCODE, Encyclopedia of DNA Elements; GTEx, Genotype-Tissue Expression project; HTAN, Human Tumor Atlas Network; ImmGen, Immunological Genome Project; sc-EQT, single-cell eQTLGen Consortium; TCGA, The Cancer Genome Atlas.

Figure 2.

A blueprint for the Human Oral and Craniofacial Cell Atlas. Oral and craniofacial tissue niches are incredibly diverse, including periodontium, tooth, palate, buccal mucosa, tongue, tonsils, salivary glands, and fluid from the saliva—these do not account for microniches that are unaccounted for among these tissue spaces. Each niche is supported by some combination of epithelia, cartilage, bone, ligaments, muscles, adipose tissue, blood and lymphatic vessels, and nerves, and these tissues are harmoniously integrated into the vital functions of communication, feeding, breathing, defense, sensing, and early digestion. The Human Oral and Craniofacial Cell Atlas, supported by the Oral and Craniofacial Bionetwork (OCBN), aims to create comprehensive and integrated cell atlases to understand the common and unique cell types that support these niches in health and to uncover which cell types and networks are affected in disease. We will do this using single cell and spatial multiomic approaches (transcriptome, epigenomic, proteomic), and we will incorporate additional omics technologies as assays are refined and available. Thus far, most work from the OCBN and others has focused on single cell transcriptomic (scRNAseq) and epigenomic (ATACseq) approaches from healthy adults, including nearly all major tissue niches and saliva. Work is currently being done with the OCBN for collecting, integrating, visualizing, sharing, and applying the knowledge gained from these early studies. The number of studies developed so far and the total number of cells profiled are depicted under each tissue. Tissue illustrations inspired by Huang et al. (2021). Credit: Heather McDonald, BioSerendipity, LLC.

Figure 3.

Applied spatial multiomics for coordinated and integrated analyses. Coordinated efforts across the Human Cell Atlas are working toward building a consensus of the necessary metadata (clinical and biological) to generate a common coordinate framework for the human body. Future work including these additional layers of data will highlight the diversity of cell types and states across humans considering age, sex, race, ethnicity, ancestry, and oral and systemic health history, as well as the specific niche, tissue orientation, and health status of that niche (healthy, inflamed) at the time of sample collection. There is an immense need to interrogate a higher number of molecular dimensions or human tissues—genome, transcriptome, epigenetic modifications, proteome, T cell receptor and B cell receptor repertoires (TCR/BCR), and metabolome of the collected sample itself—as no single “omics” technology can fully define the complexity of molecular mechanisms, but taken together, these integrated data have the potential to provide a more comprehensive landscape of basic biological processes and human disease. Multimodal sequencing has the capacity to move the field from descriptive “snapshots” toward a mechanistic understanding of gene regulatory networks and, importantly, to refine sources of cellular heterogeneity as already applied to the immune system. The use of multimodal single cell and spatial multiomics is therefore revolutionizing our understanding of cellular biology; however, relying on the dissociation of cells from their natural tissue environment limits our ability to understand the role of intrinsic and extrinsic factors that underpin cellular communication and organ function. Spatial multiomic approaches, which include information on the location of cells, will still need to be integrated with these single cell multiomic maps.

Figure 4.

The vision for a globally representative Human Oral and Craniofacial Cell Atlas. To accomplish the goals of the OCBN, we will require the development of inter- and intrainstitute partnerships to connect oral health care teams (namely but not exclusively: oral pathology, oral surgeons and periodontists, endodontics, oral medicine, oral radiology, and general dentists) with medical care teams (namely but not exclusively: ear/nose/throat, dermatology, gastroenterology, pulmonology, allergists, endocrinologists, pediatricians, neurologists, pathologists, clinical genetics, oncologists, radiologists as well as internal and emergency medicine providers). This collaborative approach will allow us to lead the burgeoning field of integrated precision oral health through the application of innovative investigative approaches (single cell, spatially mapped genomics, epigenomics, transcriptomics, and proteomics as well as other “omics” approaches such as metabolomics and microbiomics). Furthermore, defining oral and craniofacial tissue mucosal niches across the life span and building on those reference data will provide unparalleled opportunities to interrogate the mechanisms of common and rare oral and craniofacial diseases across the life span. We will be working collaboratively with other research centers, investigator networks, and related consortia to make data and samples available to the broader research community to address common and rare health concerns globally; to develop scalable representative disease and therapeutic models; and to further integrate, analyze, and discover actionable targets through artificial intelligence/machine learning technologies. In total, our network should have a positive impact on precision medicine for all patients. Credit: Heather McDonald, BioSerendipity, LLC.