Long-term longitudinal analysis of 4,187 participants reveals insights into determinants of clonal hematopoiesis

Abstract

Clonal hematopoiesis of indeterminate potential (CHIP) is linked to diverse aging-related diseases, including hematologic malignancy and atherosclerotic cardiovascular disease (ASCVD). While CHIP is common among older adults, the underlying factors driving its development are largely unknown. To address this, we performed whole-exome sequencing on 8,374 blood DNA samples collected from 4,187 Atherosclerosis Risk in Communities Study (ARIC) participants over a median follow-up of 21 years. During this period, 735 participants developed incident CHIP. Splicing factor genes (SF3B1, SRSF2, U2AF1, and ZRSR2) and TET2 CHIP grow significantly faster than DNMT3A non-R882 clones. We find that age at baseline and sex significantly influence the incidence of CHIP, while ASCVD and other traditional ASCVD risk factors do not exhibit such associations. Additionally, baseline synonymous passenger mutations are strongly associated with CHIP status and are predictive of new CHIP clone acquisition and clonal growth over extended follow-up, providing valuable insights into clonal dynamics of aging hematopoietic stem and progenitor cells. This study also reveals associations between germline genetic variants and incident CHIP. Our comprehensive longitudinal assessment yields insights into cell-intrinsic and -extrinsic factors contributing to the development and progression of CHIP clones in older adults.

Fig. 1. CHIP in ARIC Study visits.

Distributions of clonal hematopoiesis of indeterminate potential (CHIP) at baseline (a–d) and follow-up (e–h) visits. CHIP prevalence increases with age, reaching approximately 30% when individuals reach 80 years (a, e). Error bands in (a, e) show a 95% confidence interval around the fitted logistic regression line. Most individuals with CHIP typically carry a single clone (b, f). In the earlier decades of life (under 70 years), many individuals carry mutations in DNMT3A or other less commonly mutated CHIP genes (c, g). However, individuals aged 70 and older show a higher incidence of CHIP involving genes such as TET2, ASXL1, and splicing factors (c, g), and the size of these clones tends to be relatively larger in later years (d, h). Box plots display median (center line), 25th and 75th percentiles (box edges), and whiskers extend to ±1.5 * interquartile range. VAF variant allele fraction.

Fig. 2. Longitudinal dynamics of 352 trackable CHIP clones (VAF ≥ 2%) detected at baseline and follow-up visits.

Here, 233 clones are growing, 33 are shrinking, and 86 are static. CHIP clonal hematopoiesis of indeterminate potential; VAF variant allele fraction.

Fig. 3. Distribution of incident clonal hematopoiesis indeterminate potential (CHIP) among older adults.

a The vast majority (over 83%) of individuals with incident CHIP carry a single clone, b with approximately 37% of the clones exhibiting an expanded state (VAF > = 10%). b DNMT3A and TET2 show higher proportions of smaller incident clones (VAF between 2% and 10%), while ASXL1, JAK2, U2AF1, and ZRSR2 display expanded clones. c The median clone size exceeds 10% for ASXL1, SF3B1, U2AF1, and ZRSR2 CHIP. Box plots display median (center line), 25th and 75th percentiles (box edges), and whiskers extend to ±1.5 * interquartile range. d Like CHIP prevalence (Fig. 1), CHIP incidence increases with age. Error bands show a 95% confidence interval around the fitted logistic regression line. VAF variant allele fraction.

Fig. 4. Association of clinical cardiovascular risk factors with incident clonal hematopoiesis of indeterminate potential (CHIP).

Forest plot showing odds ratio (OR) with a 95% confidence interval (CI) from multivariable logistic regression analyses examining the association between incident overall CHIP (N = 3614; 709 cases and 2905 controls), incident DNMT3A CHIP (N = 3614; 302 cases and 3312 controls,) and incident TET2 CHIP (N = 3614; 160 cases and 3454 controls), and baseline cardiovascular risk factors. Uncorrected P-values are from two-sided Z-tests. The adjusted model accounted for age, sex, race, body mass index (BMI), high-density lipoprotein cholesterol (HDL-C), non-HDL-C, cholesterol medication usage, smoking history, hypertension, atherosclerotic cardiovascular disease (ASCVD, including coronary heart disease and/or ischemic stroke), type 2 diabetes (T2D), and batch effects. Inverse rank normalization was performed before the analysis to account for potential variations in BMI, HDL-C, and non-HDL-C distribution. The results indicate that age is independently and significantly associated with a higher incidence of CHIP. Additionally, nominal non-significant associations are observed for male sex, European American, BMI, and history of ASCVD with incident CHIP categories. ***P < 0.0025 (0.05/20); **P < 0.01; *P < 0.05.

Fig. 5. Genetic determinants of incident CHIP.

Association of prevalent clonal hematopoiesis of indeterminate potential (CHIP) with incident CHIP: a, b polygenic risk score (PRS) and c germline variants analysis. a Distribution of PRS in ARIC AA and EA participants. b Ancestry-stratified PRS was calculated using 21 independent variants (P < 5E−8; Supplementary Data 5) from Kessler et al.. Logistic regression was performed, adjusting for age, sex, smoking status, top five principal components of ancestry, and batch effect. Data are presented as odds ratio (OR) with a 95% confidence interval (CI) and uncorrected P-value from a two-sided Z-test. The results show a strong association between prevalent CHIP PRS and incident CHIP. c Forest plot of odds ratio with 95% CI from inverse variant-weighted fixed-effect meta-analyses of single-variant associations for incident overall CHIP, incident DNMT3A CHIP, and incident TET2 CHIP in ARIC AA (n = 637) and ARIC EA (n = 2378) participants. Uncorrected P-values are from two-sided Z-tests. Single-variant association adjusted for age, age², sex, top ten principal components of ancestry, and batch effect, followed by multi-ancestry meta-analysis, was conducted to investigate the association of genome-wide significant (P < 5E−8) prevalent CHIP-associated variants and incident CHIP at a significant level of P < 0.05. This figure presents the lead variant(s) from each locus, and the full list is available in Supplementary Data 6–8. Several germline variants previously associated with prevalent CHIP were found to be associated with incident CHIP, indicating a shared genetic basis between prevalent and incident CHIP. ARIC AA the Atherosclerosis Risk in Communities Study African American; ARIC EA European American; EA effect allele; EAF effect allele frequency; SNV single nucleotide variant.

Fig. 6. Association of passenger counts with CHIP.

Association of synonymous passenger mutation counts with a presence of CHIP, b number of CHIP clones, and c growth of CHIP clones. Forest plot of odds ratio (OR) with a 95% confidence interval (CI) showing the effects of (inverse rank normalized) synonymous passenger counts on CHIP-related outcomes (listed below in a–c)—models accounted for age at baseline, age², self-reported sex, self-reported race, body mass index (BMI), high-density lipoprotein cholesterol (HDL-C), non-HDL-C, cholesterol medication usage, smoking history, hypertension, atherosclerotic cardiovascular disease (ASCVD, including coronary heart disease and/or ischemic stroke), type 2 diabetes (T2D), and batch effects (including ARIC baseline visit and visit center). Uncorrected P-values are from two-sided Z-tests. a Model 1: four separate multivariable logistic regression analyses were performed for outcomes (i) no CHIP (n = 2905) vs. presence of CHIP at either visit (n = 1147), (ii) no CHIP at baseline (n = 3614) vs. CHIP detected at baseline (i.e. prevalent CHIP, n = 438), (iii) no CHIP at follow-up visit (n = 3043) vs. CHIP detected at the follow-up visit (n = 1009), and (iv) no CHIP (n = 2905) vs. incident CHIP (n = 709). b Model 2: multivariable multinomial logistic regression was performed for the number of CHIP clones as outcomes, i.e., no CHIP clone (n = 2905) vs. one clone (n = 877), 2 clones (n = 206), 3 clones (n = 43), or ≥4 clones (n = 21). c Multivariable logistic regression was performed for no CHIP clone (or no change in clone size, dVAF = 0; n = 2909) vs. growing CHIP clone (i.e. dVAF > 0; n = 936). BMI, HDL-C, and non-HDL-C values were inverse rank normalized. CHIP: clonal hematopoiesis of indeterminate potential; dVAF = VAF_follow-up − VAF_baseline.