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Human Lifetime Physiology Reveals an Engraftment-Enhancing Gene Expression Program

Year: 2025

Type: article

Abstract: Graft failure and poor graft function due to insufficient engraftment have high rates of mortality in blood and marrow transplant (BMT) patients. Although some aspects of the principles governing human hematopoietic engraftment are known, the field lacks a holistic understanding of the biologic mechanisms dictating this process. This knowledge gap limits the ability to design rational approaches for preventing or mitigating graft failure and poor graft function as a complication of BMT. Furthermore, the need for improved understanding of engraftment biology is not only relevant in the allogeneic setting, but also the autologous setting, as illustrated by markedly delayed engraftment in the first patient treated on a recent clinical trial of CRISPR-mediated gene correction in sickle cell disease. To address this knowledge gap, we sought to identify the molecular properties that distinguish actively engrafting hematopoietic stem and progenitor cells (HSCPs) from those that are not actively repopulating the bone marrow. Given feasibility issues in collecting donor cells that are actively engrafting in patients, we reasoned that relevant physiology occurs during mid-gestation, when human HSCs are actively migrating out of the fetal liver to engraft the newly formed bone marrow. We collected 58,041 CD34+ HSPCs from 26 independent human donors spanning first trimester, mid-gestation, and every decade of postnatal life through age 77. We performed single cell RNA-sequencing (scRNA-seq) and applied a novel bioinformatic approach, consensus non-negative matrix factorization, to de novo identify 35 distinct gene expression programs (GEPs) used to varying degrees at different phases of human life. One such GEP had peak utilization during mid-gestation, and none postnatally. This GEP is defined by heat shock proteins, AP-1 transcription factors, zinc finger protein mRNA stability factors, and surface markers previously associated with lymphocyte activation. We hypothesized that this GEP would be associated with higher efficiency engraftment given it's specific utilization during the phase of life when bone marrow engraftment first occurs, and thus tested this hypothesis in mouse xenograft transplantation assays. Upon FACS isolation of mid-gestation HSPCs with high or low utilization of this GEP, HSPCs with high utilization engrafted more efficiently than their low utilization counterparts in limiting dilution transplant assays in NSG mice, and also gave rise to multi-potent engraftment with higher frequency. Thus, we have leveraged naturally occurring human physiology to identify a GEP conferring efficient engraftment properties upon human HSPCs. The genes contributing to this program provide insight into the molecular drivers of bone marrow engraftment and represent candidate targets for intervention and augmentation to prevent engraftment failure.

Source: Transplantation and Cellular Therapy

DOI: 10.1016/j.jtct.2025.01.468

Authors: Parker Cote, Michael Kuoch, Jennifer Whangbo, Grant Rowe, Hojun Li

Institutions: University of California San Diego, Massachusetts Institute of Technology, Dana-Farber Cancer Institute, Boston Children's Hospital, Rady Children's Hospital-San Diego

Language: English

Topic: Hematopoietic Stem Cell Transplantation

Subfield: Hematology

Field: Medicine

Domain: Health Sciences

SDG: Good health and well-being

Open Access status: hybrid

Estimated APC paid: $3,650