How human cell atlases provide the missing links between genes, diseases and therapies

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A Nature Medicine journal perspective article describes the potential of cell atlases in shaping the future of medicine. Providing the missing link between genes and diseases, single-cell atlases make it possible to develop more precise and specific diagnostic tools by understanding the mechanisms of complex diseases.

Study: Impact of the Human Cell Atlas on medicine. Image Credit: Giovanni Cancemi / ShutterstockStudy: Impact of the Human Cell Atlas on medicine. Image Credit: Giovanni Cancemi / Shutterstock


An in-depth knowledge of cell types, their internal networks, and cell-cell interaction dynamics in health and disease is crucial for understanding disease pathogenesis and discovering novel therapeutics.  

The International Human Cell Atlas (HCA) initiative has significantly contributed to the field of medicine in terms of overcoming the logistics and technical challenges of mapping human cells. Within five years of its establishment, the HCA has provided enormous amounts of highly relevant information on human health.

The community has contributed significantly during the ongoing coronavirus disease 2019 (COVID-19) pandemic in terms of providing early information on the susceptibility of cells to infection and the clinical consequences of infection in the body.

Cell atlas in disease biology

Genetic variations between different cell types decisively contribute to the risk of developing both rare and common complex diseases. Genome-wide association studies (GWAS) and phenome-wide association studies have shown that the genetic factors associated with a disease are often present in non-coding regions, which makes it challenging to connect them to the affected protein-coding gene.  

Using healthy tissue atlases, new disease genes have been identified in cell types uniquely expressed in healthy tissues. For example, cell atlases of the trachea have discovered pulmonary ionocyte, a rare and novel cell type expressing the main causal gene (CFTR) of cystic fibrosis.

Both healthy and disease atlases of specific tissues have made it possible to connect disease genes to specific cell subsets in various inflammatory, autoimmune, respiratory, and neurodegenerative diseases.

In ulcerative colitis, integrating GWAS-derived information with single-cell atlas data has identified major cell types expressing disease-related genes. Besides identifying individual risk genes, cell atlases help interpret gene functions, predict causal processes, and relate genetically distinct diseases with similar morbidities.

Both intrinsic and extrinsic cellular changes play vital roles in disease pathogenesis. Using high-resolution cell atlases, it is now possible to accurately and sensitively distinguish between healthy and disease states.

In Crohn's disease, comparing cellular composition in the affected ileum with the healthy reference atlas has led to the identification of a unique multicellular community of immune and stromal cells, which is predictive of a lack of anti-TNF therapy response.

Single-cell and spatial genomic atlases have contributed significantly to human cancer biology. For example, comparing cancerous and microenvironment cells with healthy cells has made it possible to better understand solid tumors' biological complexity and heterogeneity.  

Atlases mapping cancer cells have also helped discover the mechanisms of neoplastic transformation and drug resistance and identify novel targets for therapeutic interventions.

Cell atlases in disease diagnosis and treatment  

Healthy reference atlases, disease atlases, laboratory techniques, and computational programs have opened up a new path toward developing more advanced diagnostic assays with higher resolution and broader molecular scope.  

The rich and growing human cell atlases currently cover thousands of individuals and millions of cells. Moreover, atlases of peripheral blood mononuclear cells derived from various diseases and immune cells of various tissues are now available. Such a vast reference can be used to develop new diagnostics as well as to better interpret results at the individual level.

Using single-cell profiling of blood immune cells, the blood correlates of anti-PD1 response in tumors have been identified. In histopathology, single-cell and spatial profiling data can be applied together with standard tissue stains to combine genomic and histological analysis.   

Cell atlases can also provide necessary information to determine therapeutic response at the individual level and predict on-target toxicities. A healthy cell atlas is particularly effective in predicting the risk of on-target toxicities for both molecular and cellular treatments. For instance, the neurotoxicity of CD19-targeting chimeric antigen receptor T cells can be predicted by the expression of CD19 in mural cells, vascular smooth muscle cells, and pericytes in the blood–brain barrier.  

Healthy reference atlases and single-cell and spatial genomics have also contributed significantly to the field of molecular drug delivery, regenerative medicine, and cell therapy.

Journal reference:
Dr. Sanchari Sinha Dutta

Written by

Dr. Sanchari Sinha Dutta

Dr. Sanchari Sinha Dutta is a science communicator who believes in spreading the power of science in every corner of the world. She has a Bachelor of Science (B.Sc.) degree and a Master's of Science (M.Sc.) in biology and human physiology. Following her Master's degree, Sanchari went on to study a Ph.D. in human physiology. She has authored more than 10 original research articles, all of which have been published in world renowned international journals.


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