The Growth Kinetics of Clonal Hematopoiesis Inform Risk of Blood Cancer Progression

Abstract

Introduction: Clonal hematopoiesis of indeterminate potential (CHIP) is a frequent consequence of aging associated with increased risk of blood cancers, although overall individual risk is < 1% per annum. Proposed risk factors for blood cancer progression include a variant allele frequency (VAF) > 10%, specific gene mutations or the presence of more than one CHIP clone. However, the relative value of monitoring CHIP clone growth with respect to blood cancer risk is unknown. To address this evidence gap, we measured CHIP at baseline and 3 years later in 11,298 healthy individuals aged ≥70y from the ASPREE randomized clinical trial (www.aspree.org). Methods: A custom, high sensitivity (0.5%) and reproducible amplicon-based targeted sequencing assay was designed to assess CHIP in 19 genes, except for SRSF2, which had poor coverage. CHIP was defined as a VAF ≥ 2% with a minimum of 5 variant reads for previously reported CHIP or 20 for variants not previously reported. The analysis involved measuring CHIP variants in two serial blood samples collected at baseline and year 3 of follow-up for longitudinal analysis. Associations between CHIP and blood cancers were assessed using Cox proportional hazards models. Results: CHIP at baseline was present in 34% of participants who had a corresponding year 3 sample with adequate sequencing depth. Unexpectedly, 1,245/3,110 (40%) CHIP clones present at baseline fell below 2%, while 1,520 new CHIP clones appeared at 3 years. This equated to an incident CHIP rate of 7% per annum. CHIP genes more likely to expand and contract were TP53 and ASXL1 (odds ratio 1.25 and 1.22 respectively). To measure growth characteristics of CHIP clones, we calculated a Fitness Score, FS (Log2(VAF3-year/VAFBaseline) for the 3,110 clones present at baseline. We observed no significant mean fitness advantage for any recurrent CHIP variant other than PPM1D R552* (Figure 1). CHIP variants of DNMT3A (including DNMT3A R882), TET2 and ASXL1 had a statistically significant negative FS. Even variants generally considered most pathogenic (SF3B1 K700E, JAK2 V617F, U2AF1 Q157, TP53 R273) had no significant fitness advantage. Some CHIP clones had a significant growth disadvantage (FS < -1). For example, only 1/28 DNMT3A S393N clones present at baseline remained above 2% and almost half of TP53 variants reduced in size by more than 2-fold at 3 years. We observed 299 blood cancers over a median time of 6.9 years. Individuals with CHIP clones >10% VAF (n= 652) had increased incidence of blood cancers (adjusted hazard ratio, aHR 2.14, confidence interval, CI 1.34-3.42, p=0.002). Genes associated with increased risk for blood cancers were SF3B1/U2AF1 (aHR 3.02, CI 1.63-5.61, p<0.001) and TET2 (n=aHR 1.89, CI 1.18-3.02, p=0.008). Participants with small clones (VAF 2-10%) at baseline or year 3 had no increased risk for blood cancers compared to those without CHIP. To investigate if the growth kinetics of CHIP predicts blood cancer risk, we subdivided CHIP clones into expanding (FS > +1, n= 104), stable (FS -1 to +1, n= 2043) and contracting (FS < -1, n= 963). Baseline VAF of expanding clones were smaller than stable clones: geometric mean 3.9% and 5.0%, respectively (p<0.001). Expanding clones were enriched 2-fold for PPM1D, SF3B1 and JAK2 V617F. Participants with expanding clones (n=99) were more likely to have more than one CHIP variant (50% compared with 39% for stable and 37% for contracting), although 90% of these additional variants were stable or contracting, indicating that the expanding clone was dominant. For similar VAF levels at 3 years, participants with expanding CHIP clones had a higher risk of blood cancer than a stable or contracting one (Figure 2). Conclusions: This is the largest longitudinal study of CHIP variants and associated blood cancer outcomes to date. In contrast to other longitudinal studies, there was little evidence for selective growth advantage of CHIP clones with a VAF ≥ 2%, including those with pathogenic mutations of DNMT3A, SF3B1, U2AF1, TP53 and JAK2. While clone size (VAF > 10%) and gene mutation (SF3B1, U2AF1 and TET2) were associated with increased risk of blood cancer progression, our study cautions clinical intervention of CHIP based upon a single timepoint analysis irrespective of the gene mutation. Instead, we propose monitoring of clone size may be a clinically more useful strategy to inform counselling and patient selection for early intervention studies. Figure 1View largeDownload PPTFigure 1View largeDownload PPT Close modal