Unveiling the Blueprint: The Formation of Human Bones through Early Skeletal Mapping

Researchers from the Wellcome Sanger Institute and their partners utilized advanced genomic technologies to map out the various cells and pathways implicated in the early stages of skeletal formation. This work is part of the larger Human Cell Atlas¹ (HCA) initiative, providing a resource for studying the potential effects of existing or future drugs on skeletal development during pregnancy.

The research, published today (20 November) in Nature, outlines how cartilage serves as a crucial framework for bone development throughout the skeleton, except for the top of the skull. The team identified all the essential cells responsible for skull development and examined how genetic mutations might lead to premature fusion of soft spots in newborn skulls, potentially limiting brain growth. In the future, these identified cells could serve as targets for diagnosis and treatment of congenital disorders.

Additionally, the team discovered specific genes activated in early bone cells that might correlate with a heightened risk of hip arthritis later in life. They highlighted that other genes linked to early cartilage cells may contribute to an increased risk of knee arthritis, likely due to their function in cartilage repair. Continued research on these cells could pave the way for developing new therapies for these conditions.

Overall, the skeletal atlas developed serves as a publicly accessible resource for enhancing our understanding of bone development and its relation to disorders affecting these tissues in both children and adults.

This publication is part of a larger series of over 40 studies from the HCA, featured in various Nature Portfolio journals, marking a significant advancement in our comprehension of human biology. These interconnected studies have illuminated key aspects of human development, health, and disease, and facilitated the creation of essential analytical tools that contribute to the Human Cell Atlas¹.

In children, skulls undergo complete hardening and fusion between the ages of one and two years. Prior to this, soft spots in the skull exist to accommodate continued brain growth post-birth. However, if these soft spots fuse prematurely, it results in a condition known as craniosynostosis, which can restrict brain expansion.

In the UK, this condition is usually addressed promptly through surgery, but if untreated, it can lead to increased pressure within the skull, which may result in learning challenges, vision issues, and hearing loss². While genetic mutations have been associated with craniosynostosis, identifying the specific human cells affected by these mutations has been challenging until now.

Osteoarthritis (OA) stands as the most prevalent form of arthritis in the UK, leading to painful and stiff joints, such as the hips and knees, over time³. This occurs when the cartilage layer protecting these joints deteriorates or is damaged³. Eventually, major surgery may be required to replace the joint, as adults cannot regenerate new cells to repair the compromised cartilage.

Utilizing state-of-the-art technology⁴, the researchers at the Sanger Institute and their partners mapped skeletal development during the first trimester of pregnancy, from 5 to 11 weeks⁵ post-conception, at both spatial and single-cell levels. This approach allowed for a comprehensive description of all cells, gene networks, and interactions involved in early bone growth, including the arrangement of cells within the swiftly developing tissues.

The single-cell mapping demonstrated that cartilage cells are formed first, providing a structural support for subsequent bone cell growth. The team emphasized that this process takes place throughout the skeleton, excluding the calvarium, or the upper part of the skull. Within the calvarium, they identified new types of early bone cells significant for skull formation. Their investigation led them to explore how genetic mutations linked to craniosynostosis affect these initial bone cells and cause them to fuse prematurely.

Moreover, the researchers found that genetic variations associated with a higher risk of hip OA were involved in the development of early bone cells and their associated regulators, while those impacting knee arthritis risk were tied to cartilage formation.

Using their atlas, the team also examined the effects of specific medications on skeletal development. They created a list of 65 clinically-approved drugs that are currently advised against during pregnancy and pinpointed how these could potentially interfere with skeletal development. Including this information in the atlas underlines the significant impact drugs can have on fetal development, aiding decisions regarding the safety of therapeutics used during pregnancy.

Dr. Ken To, co-first author from the Wellcome Sanger Institute, stated: “Numerous processes work together during the development of the human skeleton and joints. Our research has defined the types of cells and mechanisms necessary for bone formation and skull fusing. By studying these, we can contextualize DNA variants associated with congenital conditions like craniosynostosis, which could help predict how genetic alterations affect the skeleton as it develops. Ultimately, this atlas could enhance our understanding of both youthful and aged skeletal health. Establishing this ‘blueprint’ for bone development also has significant therapeutic implications for generating bone and cartilage cells in laboratory settings.”

Dr. Jan Patrick Pett, co-first author from the Wellcome Sanger Institute, remarked: “We are thrilled to have produced the first multi-omic map of the human developing skeleton, offering extensive potential in understanding bone growth and addressing related conditions. Our multi-dimensional, temporally and spatially resolved atlas facilitated novel computational analyses, creating an integrated perspective on the regulation of developmental processes. Gaining clearer insights into the skeleton’s formation and its influence on conditions such as osteoarthritis may lead to groundbreaking treatments in the future.”

Professor Sarah Teichmann, a co-founder of the Human Cell Atlas and senior author previously at the Wellcome Sanger Institute, now affiliated with the Cambridge Stem Cell Institute at the University of Cambridge, added: “Our unique, freely accessible skeletal atlas provides new insights into cartilage, bone, and joint development during the first trimester, illustrating the involved cells and pathways in unprecedented detail. This atlas merges advanced spatial technologies with genetic analyses and is open for use by researchers globally. Our detailed spatiotemporal atlas contributes to ongoing studies, progressing the entire Human Cell Atlas initiative toward comprehensively understanding human development, health, and disease.”

You can access the freely available human skeletal atlas here:

https://developmental.cellatlas.io/skeleton-development

1. This study is part of the international Human Cell Atlas (HCA) consortium, which aims to develop comprehensive reference maps of all human cells to enhance understanding of human health and improve disease diagnosis, monitoring, and treatment. The HCA is a global collaborative effort involving over 3,500 members from more than 100 countries, dedicated to creating a diverse and accessible atlas that benefits all of humanity. Findings from this initiative are already influencing medical practices, from diagnostics to drug discovery, shaping a new era of precision medicine. You can learn more at https://www.humancellatlas.org
2. Craniosynostosis information can be found on the NHS website: https://www.nhs.uk/conditions/craniosynostosis/
3. Details about Osteoarthritis are available on the NHS website: https://www.nhs.uk/conditions/osteoarthritis/
4. This atlas integrates spatial transcriptomics with single-nuclei transcriptional and epigenetic profiling of 336,000 nucleus droplets. The researchers developed ISS-Patcher, a novel tool for labeling cells in droplet data and associating it with high-resolution sequencing datasets, revealing information on cell types, their locations, and interactions with their surroundings. They also employed a new spatial transcriptomics annotation tool, OrganAxis, to trace the development of cranial bone.
5. The researchers studied human embryonic limb and cranial tissues between 5 to 11 weeks post-conception, sourced from the INSERM biobank in France and the Department of Clinical Neuroscience at the University of Cambridge.
6. The team combined various spatial transcriptomics methods with RNA and DNA sequencing to uncover the gene regulatory networks tied to bone and joint formation, mapping how cell lineages evolve over space and time.