Israeli-led consortium publishes groundbreaking cell-by-cell Atlas of the human body

Scientists unveiled the first draft of the Human Cell Atlas, a groundbreaking comprehensive database of human cells. On November 20, the Human Cell Atlas (HCA) consortium published a collection of more than 40 peer-reviewed papers in Nature and other journals, marking a significant milestone toward understanding the human body in health and disease.

The Human Cell Atlas is an international collaborative consortium launched in 2016 by Israeli biologists Aviv Regev, now at Genentech, and Sarah Teichmann of Cambridge University, along with around 100 other scientists, to map all types of cells in the human body. The project aims to create comprehensive reference maps of all human cells as a basis for understanding human health and for diagnosing, monitoring, and treating disease.

Financial Times, The Economist, Newsweek, and Cell Science were among the publications that covered the publication of the paper collection.

Over the past eight years, the HCA consortium, which now includes more than 3,600 scientists from 102 countries, has been publishing various thematic cellular atlases. The latest publications represent a significant advance toward constructing a 3D atlas of all human cells, contributing to a detailed digital manual of instructions for the organism.

The studies cover an impressive variety of tissues, cell types, and organs, including the brain, immune system, thymus, and endometrium, revealing new biological discoveries important for understanding disease. These papers demonstrate significant advances in mapping individual adult tissues and organs, developing human tissues, and pioneering analytical methods, including those based on artificial intelligence and machine learning.

One of the key advancements is the creation of the most complete intestinal cellular atlas to date. By combining data from 1.6 million cells sampled from nearly 190 people, including both healthy and diseased tissue, researchers have created an intricate map of cells present in the gut, including their type, location, and how they interact with the body. "Spatial and single-cell data provide unique information about how gut cells interact, that can be used to continue piecing together an in-depth understanding of how the human body works," Dr. Amanda Oliver, first author of the study, explained.

This gut atlas uncovered a type of intestinal cell that seems to contribute to inflammation in diseases like ulcerative colitis and Crohn's disease, providing a valuable resource for investigating and treating these conditions. "Intestinal inflammation can cause cells to undergo metaplasia, a shift from one cell type to another," according to Itai Yanai, scientific director of the Applied Bioinformatics Laboratories at NYU Langone Health,

Another significant contribution is the first map of skeleton growth, revealing how the skeleton forms and shedding light on the origins of arthritis. "We're excited to have created the first multi-omic map of the developing human skeleton, something that has vast potential in both understanding how our bones grow and treating conditions that might impact this," Dr. Jan Patrick Pett, co-first author, said,

The HCA has emphasized the need for its information to be as diverse as possible, including efforts to build an Asian Immune Diversity Atlas and ensuring wide human diversity representation. Special care has been taken to reflect human diversity in the data, capturing aspects of genetic, geographic, age, and sex diversity.

"The Human Cell Atlas is a global initiative that is already transforming our understanding of human health,” Professor Sarah Teichmann, founding co-chair of the HCA, stated. “By creating a comprehensive reference map of the healthy human body—a kind of 'Google Maps' for cell biology—it establishes a benchmark for detecting and understanding the changes that underlie health and disease," she added.

The HCA project has received funding from more than a hundred institutions worldwide, including public funders like the European Commission and the US National Institutes of Health, as well as philanthropic organizations such as the Chan Zuckerberg Initiative and Wellcome. Stephen Quake, Head of Science at the Chan Zuckerberg Initiative, said, "The Human Cell Atlas was one of the Chan Zuckerberg Initiative’s first big bets in supporting science, and I’m so pleased to see these landmark papers that share the work with the larger scientific community."

The Human Cell Atlas's mission is to catalog every cell type in the human body, from development to old age. The new resources will be freely accessible to all researchers. The atlas aids scientists in developing medicines and growing organoids, which are miniature versions of organs and tissues used in laboratories to deepen the understanding of their functions and diseases.

Aviv Regev, co-chair of the Human Cell Atlas consortium, emphasized the research's importance for treating diseases, stating, "When things go wrong, they go wrong with our cells first and foremost." She added, "In the next two years, the data from the eighteen subfields will be supplemented, and the first version will be ready. But then there will still be many gaps to fill. The Human Cell Atlas will be expanded and improved for years to come."

Dr. Jeremy Farrar, WHO Chief Scientist, commented, "This landmark collection of papers from the international Human Cell Atlas community underscores the tremendous progress toward mapping every single kind of human cell and how they change as we grow up and age."

The HCA teams have made a strong start, but the project is an ultra-marathon, not a sprint. The first version of the Human Cell Atlas will be published in 2025–26, marking the beginning of a journey toward comprehensive mapping of every cell type in the human body. Over time, scientists believe there will be a second and third version of the atlas.

The Human Cell Atlas will impact every aspect of biology and healthcare, ultimately leading to a new era of precision medicine tailored to individuals based on their unique cellular makeup. As Sarah Teichmann stated, "It establishes a benchmark for detecting and understanding the changes that underlie health and disease."

This article was written in collaboration with generative AI company Alchemiq