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The global Human Cell Atlas (HCA) consortium has announced significant progress in its efforts to map human cells in health and disease. A new collection of over 40 peer-reviewed studies, published in Nature and other Nature Portfolio journals, highlights developments in single-cell and spatial genomics, artificial intelligence (AI) tools, and biomedical discoveries that are expanding our understanding of the human body.
Large-Scale Cellular Datasets and Methods
The HCA is a collaborative international initiative aiming to build comprehensive reference maps of all human cells. These datasets, which integrate genetic, geographic, age, and sex diversity, provide a foundation for understanding cellular behavior in health and disease. To date, the HCA has profiled over 100 million cells from more than 10,000 individuals. The ultimate goal is to develop a continuously updated atlas incorporating billions of cells across tissues and organs.
The studies in this new collection showcase three key aspects of the HCA’s mission: mapping adult and developing tissues, and advancing computational methods for analyzing cellular data. Researchers have developed and utilized innovative single-cell and spatial genomics techniques, as well as AI algorithms, to generate detailed insights into tissue structure and function.
According to Aviv Regev of Genentech, a founding co-chair of the HCA, "This is a pivotal moment for the HCA community as we move towards achieving the first draft of the Human Cell Atlas. This collection of studies showcases the major advances from biology to AI achieved since the publication of the HCA White Paper in 2017."
Exploring Tissue-Specific Discoveries
Several studies provide detailed atlases of individual tissues, revealing new biological insights with implications for disease research. For instance, a study on the human gut identified a specific cell type potentially linked to gut inflammation, offering a helpful resource for understanding and treating conditions such as ulcerative colitis and Crohn’s disease (Oliver et al.).
Other contributions focus on developmental biology, including the first atlas of human skeletal development. This study uncovers how the skeleton forms and identifies cells involved in skeletal conditions, providing a foundation for studying arthritis and other bone-related diseases (To et al.). Similarly, a multiomic atlas of the first-trimester placenta maps genetic programs underlying placental development, shedding light on its role in embryo nutrition and protection (Shu et al.).
These atlases are advancing our knowledge of tissue formation as well as serving as blueprints for therapeutic development. "This new level of insight into the specific genes, mechanisms, and cell types within tissues is laying the groundwork for more precise diagnostics, innovative drug discovery, and advanced regenerative medicine approaches," said Sarah Teichmann of the Cambridge Stem Cell Institute, another founding co-chair of the HCA.
Advancing Equity in Genomic Science
The HCA has emphasized diversity and equity in its work, promoting the inclusion of underrepresented populations in genomic research. Studies such as the Asian Immune Diversity Atlas and analyses of COVID-19 samples from Malawi highlight the power of global scientific collaboration. Partha Majumder, co-chair of the HCA Equity Working Group, emphasized, "A key priority for HCA is to ensure a representation of the vast range of human diversity—genetic, cultural, and geographical."
In addition to promoting inclusivity, the consortium has developed ethical guidelines to address challenges in genomic research. These principles aim to provide a framework for responsible and equitable science, making them accessible to researchers worldwide (Kirby et al.).
AI Tools Driving Cellular Classification
AI is playing a big role in interpreting the massive datasets generated by the HCA. One example is SCimilarity (Heimberg et al.), an AI tool designed to compare single-cell datasets and identify similar cell types across different tissues, akin to reverse image search. Other studies, such as those by Ergan et al. and Fischer et al., tackle cell annotation challenges, classifying cells into hierarchical groups based on their properties.
Building Toward the First Draft Atlas
The collaborative efforts of over 3,600 HCA members from more than 100 countries are culminating in the assembly of the first draft Human Cell Atlas. This evolving resource will remain freely accessible, enabling ongoing research to better understand human biology and improve disease diagnostics and treatments. Jeremy Farrar, Chief Scientist of the World Health Organization, remarked, "This landmark collection underscores the tremendous progress toward mapping every single kind of human cell and how they change as we grow up and age."
The HCA’s work continues to serve as a foundation for advancing cell biology, providing tools and knowledge that are already informing new approaches to biomedical research.
The full collection of publications can be viewed here.