Abstract
Acute lymphoblastic leukemia (ALL) represents 20% of adult leukemias. Recent technologic advances have enabled detailed characterization of the genetic basis of leukemogenesis in ALL, including somatic structural DNA rearrangements and sequence mutations that disrupt lymphoid development, signaling, tumor suppression, and epigenetic modification. These studies also showed differences in the molecular profiles of pediatric vs adult ALL. However, adults with ALL, especially older adults (≥40 years), were underrepresented in these large series. Clinical outcomes of older adults with ALL are inferior to younger patients (<40 years) and the molecular basis for these differences is not completely understood.
Hematopoietic stem cells accumulate DNA mutations with aging, and age-related clonal hematopoiesis (ARCH) has been linked to increased incidence of myeloid malignancies. The prevalence of ARCH increases logarithmically as the population ages, but its role in lymphoid leukemogenesis has not been fully established. We hypothesize that ARCH is a common precursor lesion for the development of ALL in older adults, and patients with ARCH-associated ALL have different clinical outcomes compared to patients whose disease do not harbor these mutations.
We retrospectively studied adults with ALL treated at the University of Chicago and Moffitt Cancer Center between July 2014 and April 2021. Genetic profiling of tumor samples was performed by using Miseq Illumina next-generation sequencing (NGS) platform with a comprehensive sequencing panel covering commonly mutated myeloid and lymphoid genes. We classified pathogenicity using American College of Medical Genetics and Genomics guidelines.
In total, 345 patients were studied: 286 (83%) had B-ALL, 49 (14%) had T-ALL and 10 (3%) had early T-precursor (ETP)-ALL. Overall, median age at diagnosis was 47 years (range, 18-88 years), and 211 (61%) were ≥40 years at diagnosis; 154 (45%) were women. Cytogenetic groups were as follows: 24% had Ph+ ALL, 13% had Ph-like ALL, and 3% had ALL with KMT2A rearrangement. The most frequent mutation in our adult ALL cohort was the loss of CDKN2A gene (32%), followed by mutations in TP53 (17%), IKZF1 (16%), NOTCH1 (9%), NRAS (9%), and JAK2 (6%) genes. Mutations involving the recurrently mutated genes in ARCH were seen in 110 of 345 patients (32%) with the following order of frequency: TP53 (17%), DNMT3A (5%), TET2 (4%), RUNX1 (3.5%), ASXL1 (3%), IDH1/2 (2%), BCORL1 (2%), EZH2 (1%), CUX1 (1%), and U2AF1 (1%) (Figure 1A). ARCH-associated mutations were more common in older adults (≥40 years) compared to young adults (41% vs 17%, p< 0.0001). Variant allelic frequencies (VAFs) for the ARCH-associated mutations were higher than the mutations involving signaling pathways, which suggests the ancestral nature of the former and secondary nature of the latter (Figure 1B). We further observed clonal dynamics in patients with serial diagnosis, remission and relapse samples available for sequencing. Founder ARCH clones re-emerged at the time of relapse (patient 92 and 100), and were also detectable at the time of complete remission with persistent measurable residual disease (patient 100) (Figure 1C). The overall survival (OS) for patients with ARCH-associated ALL was shorter than patients without ARCH, but the difference did not reach statistical significance (median OS, 39 months vs 84 months, p= 0.16) (Figure 1D).
Our results indicate that ARCH is commonly identified as an ancestral event in older adults with ALL, with TP53 mutations being the most prevalent. Unlike patients with AML and TP53 mutations, patients with ALL and ARCH-associated mutations had comparable clinical outcomes to patients without ARCH. This may reflect the frequent use of antibody-based therapies (i.e. blinatumomab and inotuzumab) at diagnosis (on a clinical trial basis) or relapse in the two centers where these patients were treated. Collectively, these data suggest that ARCH may constitute a fertile soil for acute lymphoblastic leukemogenesis and further studies are warranted to interrogate the dynamic interplay between myeloid and lymphoid compartments of these patients.
Figure 1 Figure 1.
Disclosures
Stock: Pfizer: Consultancy, Honoraria, Research Funding; amgen: Honoraria; agios: Honoraria; jazz: Honoraria; kura: Honoraria; kite: Honoraria; morphosys: Honoraria; servier: Honoraria; syndax: Consultancy, Honoraria; Pluristeem: Consultancy, Honoraria. Shah: BeiGene: Consultancy, Honoraria; Incyte: Research Funding; Acrotech/Spectrum: Honoraria; Novartis: Consultancy, Other: Expenses; Pfizer: Consultancy, Other: Expenses; Amgen: Consultancy; Servier Genetics: Other; Jazz Pharmaceuticals: Research Funding; Precision Biosciences: Consultancy; Pharmacyclics/Janssen: Honoraria, Other: Expenses; Kite, a Gilead Company: Consultancy, Honoraria, Other: Expenses, Research Funding; Adaptive Biotechnologies: Consultancy; Bristol-Myers Squibb/Celgene: Consultancy, Other: Expenses.
Detection of a novel, primate-specific ‘kill switch’ tumor suppression mechanism that may fundamentally control cancer risk in humans: an unexpected twist in the basic biology of TP53
