Consequences of mutant TET2 on clonality and subclonal hierarchy

Abstract

Somatic mutations in TET2 are common in myelodysplastic syndromes (MDS), myeloproliferative, and overlap syndromes. TET2 mutant (TET2^MT) clones are also found in asymptomatic elderly individuals, a condition referred to as clonal hematopoiesis of indeterminate potential (CHIP). In various entities of TET2^MT neoplasia, we examined the phenotype in relation to the strata of TET2 hits within the clonal hierarchy. Using deep sequencing, 1781 mutations were found in 1205 of 4930 patients; 40% of mutant cases were biallelic. Hierarchical analysis revealed that of TET2^MT cases >40% were ancestral, e.g., representing 8% of MDS. Higher (earlier) TET2 lesion rank within the clonal hierarchy (greater clonal burden) was associated with impaired survival. Moreover, MDS driven by ancestral TET2^MT is likely derived from TET2^MT CHIP with a penetrance of ~1%. Following ancestral TET2 mutations, individual disease course is determined by secondary hits. Using multidimensional analyses, we demonstrate how hits following the TET2 founder defect induces phenotypic shifts toward dysplasia, myeloproliferation, or progression to AML. In summary, TET2^MT CHIP-derived MDS is a subclass of MDS that is distinct from de novo disease.

Fig. 1

Topology and demographics of TET2 mutations in myeloid neoplasms. a Schematic drawing of TET2 gene showing location, distribution, types of mutations, and age-related increases in the number of mutations. For details of mutation and disease subtypes, see Supplementary Fig. 1. b Distribution of number and type of TET2^MT across the spectrum TET2^MT. c The frequencies of single and multiple mutations in each disease subtype and the distribution of mutant VAF by MDS subtype

Fig. 2

Clonal architecture of TET2 mutants. a Co-occurring mutations in TET2^MT patients. b Frequency of somatic mutations co-occurring with TET2^MT. c The average number of mutations of patients without a TET2^MT, a single TET2^MT, or double TET2^MT. d Mutational profiles of TET2^MT (solid bars) and TET2^WT (hashed bars) within disease subtype

Fig. 3

Clonal hierarchy of TET2 mutations. a Cross-sectional analysis of patient samples to identify clonal hierarchy of TET2 (second sphere to the left top row represents a patient with three TET2 mutations, including an ancestral and two different subclonal hits). b Distribution of TET2^MT patients based on the position of TET2^MT within the clonal hierarchy, and the frequency of other mutations throughout the clonal hierarchy. c The average number of mutations of MDS, MPN, and AML patients with ancestral hits of various genes. d Meta-analysis to show the frequency of TET2^MT CHIP and CHIP-related MDS. Values above arrows are reverse direction multipliers of percentages of individuals

Fig. 4

Secondary hits of TET2 mutants. a Associations between disease phenotypes and mutation rates are quantified by the odds ratios, MDS (X) vs. MPN (Y), and high risk vs. low risk (Z). Mutations showing significant enrichment in comparison to patients with only a TET2^MT (shown in smaller gray ball) are indicated by color according to OR 95% CI limits. Red color indicates separation of CI in all directions, blue indicates separation in two of the three directions, green indicates separation in a single direction, black indicates no separation. The sizes of the spheres are proportional to the frequency of the mutation in our cohort. The largest white ball is the total cohort of all ancestral TET2^MT carriers combined. Tables shown provide odds ratio point estimates for each associated plot. b. Associations between phenotypes and mutation rates are quantified by odds ratios, leukopenia (X), anemia (Y), and thrombocytopenia (Z). c. Associations between phenotypes and mutation rates are quantified by odds ratios, myeloid dysplasia (X), erythroid dysplasia (Y), and megakaryoctye dysplasia (Z). Definitions for classification of dysplasia types and cytopenias are provided in Supplementary Table 2