Longitudinal profiling of clonal hematopoiesis provides insight into clonal dynamics

Abstract

Background Clonal hematopoiesis of indeterminate potential (CHIP), the age-related expansion of mutant hematopoietic stem cells, confers risk for multiple diseases of aging including hematologic cancer and cardiovascular disease. Whole-exome or genome sequencing can detect CHIP, but due to those assays’ high cost, most population studies have been cross-sectional, sequencing only a single timepoint per individual. Results We developed and validated a cost-effective single molecule molecular inversion probe sequencing (smMIPS) assay for detecting CHIP, targeting the 11 most frequently mutated genes in CHIP along with 4 recurrent mutational hotspots. We sequenced 548 multi-timepoint samples collected from 182 participants in the Women’s Health Initiative cohort, across a median span of 16 years. We detected 178 driver mutations reaching variant allele frequency ≥ 2% in at least one timepoint, many of which were detectable well below this threshold at earlier timepoints. The majority of clonal mutations (52.1%) expanded over time (with a median doubling period of 7.43 years), with the others remaining static or decreasing in size in the absence of any cytotoxic therapy. Conclusions Targeted smMIPS sequencing can sensitively measure clonal dynamics in CHIP. Mutations that reached the conventional threshold for CHIP (2% frequency) tended to continue growing, indicating that after CHIP is acquired, it is generally not lost. The ability to cost-effectively profile CHIP longitudinally will enable future studies to investigate why some CHIP clones expand, and how their dynamics relate to health outcomes at a biobank scale.

Genomic Aging, Clonal Hematopoiesis, and Cardiovascular Disease

“…35 Generally, this is indicative of greater mutational fitness as recently characterized through recent longitudinal studies of CHIP. [118][119][120][121][122] Given the commonality at advanced age, increasingly limited clonal diversity was posited to be a characteristic feature of normal aging. 120 Despite mutations in DNMT3A being more common among individuals with CHIP, DNMT3A clones generally grow slower compared to other driver mutations.…”

Clonal hematopoiesis of indeterminate potential and clonal cytopenias of undetermined significance: 2023 update on clinical associations and management recommendations

“…Clonal hematopoiesis of indeterminate potential (CHIP) is defined by the presence of somatic pathogenic variants in leukemia associated driver oncogenes, present at a variant allele frequency (VAF) of ≥2% (2% threshold was arbitrarily chosen due to the lower limit of detection of most next‐generation sequencing assays), in the absence of cytopenias, cytosis or bone marrow (BM) dysplasia. CH with somatic variants at VAF below 2% are also detectable with higher sensitivity assays such as error corrected and deep targeted sequencing, but longitudinal studies have shown that most of these variants largely remain static or shrink over time, suggesting that majority might not be clinically relevant 16 . When individuals with CH have persistent (≥4 months) cytopenias [defined as the presence of acquired and sustained anemia (hemoglobin <12 g/dL in females and <13 g/dL in males), neutropenia (absolute neutrophil count <1.8 × 10 9 /L), and/or thrombocytopenia (platelets <150 × 10 9 /L), that is not explained by an alternate etiology], a diagnosis of clonal cytopenia of undetermined significance (CCUS) can be made 17 .…”

“…CH mutations are generally detected later in life (age >50 years) but with sensitive assays (error‐corrected sequencing), smaller clones have been detected in younger individuals 30 . Clones less than 2% VAF however, have a less propensity to expand over time, however this is heavily dependent on variant‐specific fitness impact and environment 16 . Specific driver mutations, in particular JAK2 V617F has been predicted to occur in‐utero from phylogenetic reconstruction of clones in myeloproliferative neoplasms 31 .…”

“…CH with somatic variants at VAF below 2% are also detectable with higher sensitivity assays such as error corrected and deep targeted sequencing, but longitudinal studies have shown that most of these variants largely remain static or shrink over time, suggesting that majority might not be clinically relevant. 16 When individuals with CH have persistent (≥4 months) cytopenias [defined as the presence of acquired and sustained anemia (hemoglobin <12 g/dL in females and <13 g/dL in males), neutropenia (absolute neutrophil count <1.8 Â 10 9 /L), and/or thrombocytopenia (platelets <150 Â 10 9 /L), that is not explained by an alternate etiology], a diagnosis of clonal cytopenia of undetermined significance (CCUS) can be made. 17 When individuals with CH and persistent cytopenias also have morphological dysplasia involving ≥10% cells in one or more BM cell lineages, a diagnosis of myelodysplastic syndromes (MDS) is established.…”

“…30 Clones less than 2% VAF however, have a less propensity to expand over time, however this is heavily dependent on variant-specific fitness impact and environment. 16 Specific driver mutations, in particular JAK2 V617F has been predicted to occur in-utero from phylogenetic reconstruction of clones in myeloproliferative neoplasms. 31 Genetic predisposition to CH has been demonstrated with certain loci such as TERT, TCL1A, CD164, SETBP1, KPNA4-TRIM59, TET2, PARP1, ATM, and CHEK2.…”