Scientists announce progress toward ambitious atlas of human cells

By Will Dunham

Scientists unveiled on Wednesday the first blueprint of human skeletal development as they make progress toward the goal of completing a biological atlas of every cell type in the body to better understand human health and diagnose and treat disease.

The work is part of the ongoing Human Cell Atlas project that was begun in 2016 and involves researchers around the world. The human body comprises roughly 37 trillion cells, with each cell type having a unique function.

The researchers aim to have a first draft of the atlas done in the next year or two. Aviv Regev, founding co-chair of the project and currently executive vice president and head of research and early development at U.S. biotech company Genentech, said the work is important on two levels.

"First of all, it's our basic human curiosity. We want to know what we're made of. I think humans have always wanted to know what they're made of. And, in fact, biologists have been mapping cells since the 1600s for that reason," Regev said.

"The second and very pragmatic reason is that this is essential for us in order to understand and treat disease. Cells are the basic unit of life, and when things go wrong, they go wrong with our cells, first and foremost," Regev said.

The researchers mapped skeletal development in the first trimester of pregnancy, allowing them to describe all the cells, gene networks and interactions involved with bone growth during the early stages of human development.

They showed how cartilage acts as a scaffold for bone development across the skeleton, apart from the top of the skull. They mapped all the cells critical for skull formation and examined how genetic mutations may cause soft spots in a newborn baby's skull to fuse too early, constraining the developing brain's growth.

Knowledge of these cells, the researchers said, potentially could be used as diagnostic and therapeutic targets for identifying and treating congenital conditions. They also found that certain genes activated in early bone cells might be associated with an increased risk of developing hip arthritis in adulthood.

The researchers presented the gastrointestinal tract atlas, spanning from the tissues of the mouth down to the esophagus, stomach, intestines and colon. They identified a gut cell type that may be involved in inflammation, potentially insightful for conditions such as Crohn's disease and ulcerative colitis.

And they offered an atlas of the developing human thymus, an organ that trains immune cells to protect against infections and cancer.

The findings were published in Nature and affiliated Nature Portfolio journals.

"While the primary focus has been on mapping the cells of the healthy human body, the project has already contributed valuable insights into diseases such as cancer, COVID-19, cystic fibrosis and diseases affecting the heart, lung and gut, among others," said Alexandra-Chloe Villani of Massachusetts General Hospital and the Broad Institute of MIT and Harvard, a member of the project's organizing committee.

The research employs new data and analytical tools, some based on artificial intelligence and machine learning.

The Human Cell Atlas data allows researchers "to train foundation models, like a 'ChatGPT for cells,' which help us annotate new cells or search for a new cell within the tens of millions of profiles," said Sarah Teichmann of the Cambridge Stem Cell Institute, the project's founding co-chair.

"These help us make unexpected connections, for example between cells seen in fibrotic lung diseases and in tumors in the pancreas," Teichmann said.

Understanding human anatomical complexity at the cellular level has been a challenge.

"Fundamentally, these studies tell us how tissues, organs and humans are built," said Muzlifah Haniffa of Wellcome Sanger Institute and Newcastle University, a member of the project's organizing committee.

"Understanding human development is critical to understand developmental disorders, childhood disorders that have a prenatal onset, as well as diseases that also affect adults, as developmental pathways can re-emerge in later life disease. Practical applications include new diagnostic, clinical management and therapeutic strategies for the clinic," Haniffa added.