Systematic functional dissection of germline noncoding risk variants impacting clonal hematopoiesis.

Area of Science:

• Hematology
• Genetics
• Cancer Biology

Background:

• Clonal hematopoiesis of indeterminate potential (CHIP) is a precursor to myeloid malignancies.
• Mechanisms of CHIP predisposition and progression are poorly understood.
• Genome-wide association studies (GWAS) linked non-coding loci to CHIP risk.

Purpose of the Study:

• Investigate if CHIP risk variants in non-coding loci modulate enhancer elements in hematopoietic stem cells (HSCs).
• Identify functional non-coding variants associated with CHIP risk.

Main Methods:

• Screened 1,374 non-coding variants from 51 CHIP-associated loci using Massively Parallel Reporter Assays (MPRA) in MUTZ-3 cells.
• Utilized a lentiviral MPRA library of ~73,000 constructs in CD34+ MUTZ-3 cells.
• Employed targeted genome editing to validate enhancer activity and gene expression changes.

Main Results:

• Identified 87 variants from 32 GWAS loci with regulatory activity.
• Demonstrated enhancer activity for 3 variants affecting NKD2, FLT3, and MSI2 transcription.
• Showed that increased MSI2 levels, driven by a CHIP risk allele, enhance clonal expansion of TET2-deficient hematopoietic stem and progenitor cells.

Conclusions:

• Non-coding genetic variants associated with CHIP can function as enhancers in HSCs.
• These variants provide a mechanistic link between genetic predisposition and the expansion of CHIP clones.
• Findings offer insights into leukemia prevention strategies by targeting CHIP.