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Single-cell Protein-Transcriptome Atlas of Haematopoiesis across the Human Lifespan



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Quiroga Londoño, Mariana 


The haematopoietic system is responsible for the continuous production of stem and progenitor cells, which divide and mature to produce a wide variety of specialised circulating blood cells. Proper regulation of lineage decisions is key to ensure the right balance between the generation of differentiated cells and the maintenance of the haematopoietic stem cell compartment. A dysregulation in this balance can lead to blood-related diseases. Throughout an individual's life, human haematopoiesis demonstrates significant variations, likely in response to changing demands and physiological needs. Moreover, age-related alterations in the blood system are believed to impede its functionality. Both transcriptomic and proteomic regulation play crucial roles in maintaining the haematopoietic balance. Interestingly, many classical haematopoietic populations showcase heterogeneity in both expression and function. Studying genes and cell surface proteins at the single-cell level using a combination of scRNA-seq and index sorting has proven valuable for inferring individual cellular states and identifying subpopulations for further research. Nevertheless, traditional methods that measure both transcripts and proteins from single cells via index sorting/FACS often have scale limitations. Typically, they can provide data on only a limited number of genes and proteins when used in parallel. These constraints make it difficult to capture the full complexity of cellular states and do not enable tissue scale analysis. We take advantage of the method Cellular Indexing of Transcriptomes and Epitopes by Sequencing (CITE-seq), which enables the simultaneous combination of highly multiplexed cell surface protein marker detection with unbiased transcriptome profiling for thousands of single cells, allowing more detailed characterisation of cellular phenotypes than transcriptome measurements alone.

To investigate age-related changes, cells can be gathered from tissues representing various stages of human development. By taking advantage of a custom panel of 198 oligo conjugated antibodies, we successfully profiled over 250,000 cells collected from tissues representing prenatal development (including yolk sac, embryonic and fetal liver, and bone marrow), newborn (cord blood), paediatric (bone marrow), as well as adult (bone marrow and spleen).

Our prenatal and neonatal analysis revealed unique surface protein profiles and differentiation biases already present in the prenatal tissues. In the analysis of CD34+ cells, the yolk sac had a pronounced presence of eosinophil, basophil, and mast cell progenitors compared to other tissues. Distinct differences in cell proportions for myeloid groups like megakaryocyte progenitors, myeloid-erythroid progenitors, and common lymphoid progenitors were observed between yolk sac and the other examined tissues. The paediatric exploration suggested a preference for lymphoid differentiation in the earlier stages of childhood. Furthermore, we noted a higher expression of the dendritic cell marker HLA-DR in older children, providing insight into potential maturation of certain immune cell populations as children age. In our analysis of extramedullary haematopoiesis, we observed differential surface protein expression in medullary and extramedullary haematopoietic stem cell and multipotent progenitors. We emphasised, for example, the prevalence of lineage-priming/activation markers in the spleen compared to the bone marrow, and the notable expression of lymphoid markers in the spleen. Most of these analyses rely on the transcriptomic landscape and use the protein for validation and further exploration. However, I developed a bioinformatic pipeline to enable integrated analysis of samples from numerous individuals and tissues across the different developmental stages, and our latest unreported findings for differential abundance analysis indicated an initial lymphoid-skewed tendency emerging from fetal bone marrow, intensifying during the paediatric phase, and gradually diminishing as one approaches adulthood. Preliminary data also revealed the presence of a distinct haematopoietic stem cell population exclusive to the fetal stages. This extensive atlas serves as a valuable resource and reference to understand blood-related diseases, shedding light on the stage and tissue-specific characteristics of human haematopoiesis.





Göttgens, Berthold


Adult bone marrow, CITE-seq, Cord blood, Extramedullary haematopoiesis, Fetal haematopoiesis, Haematopoiesis, Haematopoietic stem and progenitor cells, Human, Human Cell Atlas, Paediatric bone marrow, Proteomics, Single-cell multi-omics, Transcriptomics


Doctor of Philosophy (PhD)

Awarding Institution

University of Cambridge
Aging Biology Foundation MRC Human Cell Atlas Wellcome Trust La Caixa Foundation Cancer Research UK Sir Henry Dale (Wellcome/Royal Society) BBSRC Newnham College Wellcome MRC - Cambridge Stem Cell Institute
Is supplemented by: