Age-related mutations associated with clonal hematopoietic expansion and malignancies

Abstract

Several genetic alterations characteristic of leukemia and lymphoma have been detected in the blood of individuals without apparent hematological malignancies. The Cancer Genome Atlas (TCGA) provides a unique resource for comprehensive discovery of mutations and genes in blood that may contribute to the clonal expansion of hematopoietic stem/progenitor cells. Here, we analyzed blood-derived sequence data from 2,728 individuals from TCGA and discovered 77 blood-specific mutations in cancer-associated genes, the majority being associated with advanced age. Remarkably, 83% of these mutations were from 19 leukemia and/or lymphoma-associated genes, and nine were recurrently mutated (DNMT3A, TET2, JAK2, ASXL1, TP53, GNAS, PPM1D, BCORL1 and SF3B1). We identified 14 additional mutations in a very small fraction of blood cells, possibly representing the earliest stages of clonal expansion in hematopoietic stem cells. Comparison of these findings to mutations in hematological malignancies identified several recurrently mutated genes that may be disease initiators. Our analyses show that the blood cells of more than 2% of individuals (5-6% of people older than 70 years) contain mutations that may represent premalignant events that cause clonal hematopoietic expansion.

Figure 1. Blood-specific mutations identified in 58 out of 2,728 TCGA cases from 11 cancer types

(a) Rose chart illustrating the distribution of blood-specific nonsynonymous mutations in 31 genes. The variant allele fractions (VAF) of the 77 mutations are indicated in the center. (b) Rose chart illustrating the age distribution of samples with blood-specific mutations. Higher frequencies of blood-specific mutations are found in older age groups (60s, 70s, and 80s) versus younger ones (40s and 50s). The cancer type distribution is shown in the center. (c) Distribution of blood-specific mutations in DNMT3A, TET2, JAK2, ASXL1, SF3B1, and GNAS in different age groups. Total includes all blood-specific mutations in 556 cancer associated genes identified in each age group.

Figure 2. Blood-specific mutations and their association with age

(a) Box plot showing positive correlation between blood-specific mutations in leukemia/lymphoma genes and age. Age information is not available for one of the 58 cases with blood specific mutations. (b) The wide spectrum and lower average variant allele fractions in blood-specific mutations, compared to the ~50% VAF for germline variants identified in the same samples.

Figure 3. Low VAF blood-specific, hotspot mutations identified in the TCGA and WHISP cohorts using a readcount based approach

Blood-specific mutations identified by the variant detection pipeline are in blue. An additional 14 blood-specific events (13 shown in green) with VAFs between 2% and 10% were identified in the TCGA samples and their positive associations with older ages were confirmed. 13 hotspot variants were identified in WHISP samples (n = 557) and seven (in green) have variant allele fractions ranging from 2% to ~10%. One JAK2 V617F identified in a TCGA sample was not shown due to a VAF higher than 50%. (a) DNMT3A R882C, (b) DNMT3A R882H, (c) GNAS R202H, (d) JAK2 V617F, and (e) SF3B1 K700E.

Figure 4. Comparison of mutation frequencies in blood samples from 58 TCGA cases with mutations in cancer-associated genes in 151 MPN, 150 MDS, 160 CLL, and 200 AML cases

(a) Mutation frequencies of major genes involved in hematological malignancies. (b) The average number of non-synonymous mutations found in TCGA blood normal cases, MPN, MDS, and AML patients across 556 cancer associated genes.

Figure 5. Clonal expansion model

The distinct roles of a set of genes including DNMT3A, ASXL1, TET2, GNAS, JAK2, PPM1D, IDH1, NRAS, NPM1, and FLT3 in the initiation of hematopoietic clonal expansion.