Clonal evolution and treatment outcomes in hematopoietic neoplasms arising in patients with germline <i>RUNX1</i> mutations
Authors: Curtis Lachowiez, Sarah Bannon, Sanam Loghavi, Feng Wang, Rashmi Kanagal‐Shamanna, Rohtesh Mehta, Naval Daver, Gautam Borthakur, Naveen Pemmaraju, Farhad Ravandi, Keyur P. Patel, Guillermo Garcia‐Manero, Koichi Takahashi, Hagop Kantarjian, Kapil Bhalla, Courtney D. DiNardo
Journal: American Journal of Hematology (2020)

To the Editor: The runt-related transcription factor 1 (RUNX1) gene encodes a myeloid transcription factor essential for normal hematopoietic development and myeloid differentiation.1 Familial platelet disorder with a propensity to myeloid malignancies (FPD/MM) is a rare autosomal dominant cancer predisposition syndrome. It is associated with inherited germline RUNX1 mutations identified in up to 30% of patients with a family history of myelodysplastic syndrome (MDS) and/or acute myeloid leukemia (AML), and is associated with a 30%-40% lifetime risk of developing MDS, AML, or T-cell acute lymphoblastic leukemia (ALL), often at young age (approximately 30-40 years).2 Clonal evolution is frequent in patients with germline RUNX1 mutations, occurring in most patients by age 50.2 Hematologic malignancies (HM) developing in patients with germline RUNX1 mutations often arise in the context of additional somatic mutations in the alternative RUNX1 allele, or genes frequently mutated in myeloid malignancies and active signaling pathways.3 An increased understanding of the clinical and molecular characteristics both at diagnosis and during treatment of an associated HM may improve clinical decision-making in patients with this rare entity. Individuals with a diagnosis of a germline RUNX1 mutation evaluated at The University of Texas M.D. Anderson Cancer Center were included in this IRB-approved retrospective cohort review. Further details regarding data collection and statistical analysis can be found within the data supplement, Appendix S1. Twelve patients from seven unrelated families with germline RUNX1 mutations were included. Patient demographics, historical findings, RUNX1 variants, and representative pedigrees of two affected families are described in the data supplement, Appendix S1. Abnormal bone marrow morphology was present in 80% of patients without HM at diagnosis, including hypocellularity (40%) and dysmegakaryopoeisis (80%). The fifth patient developed trilineage dyspoesis on repeat bone marrow examination 7 months after their initial evaluation. Figure S3 in Appendix S1 demonstrates the progressive morphological findings on sequential bone marrow examination in one patient from presentation to the development of dysmegakaryopoeisis in the form of small, hypolobated megakaryocytes, a common morphological finding in patients with germline RUNX1 mutations.4 Morphological, cytogenetic, and molecular findings at diagnosis and follow up are shown in Figure 1. Diploid cytogenetics were seen in all patients without HM at initial evaluation. A gene fusion was identified on molecular testing (EBF1-PDGFRB) in the patient with B-ALL, without aberrant T-cell markers on immunophenotyping. Abnormal karyotypes were identified in both MDS patients (del(11q) and del(5q)). Two patients with AML had diploid karyotypes while the other two had karyotypes associated with adverse prognostic risk: 49,XX,+X,+1,del(1)(p13p32)x2,+8 [6]/47,XX,+21 [1]/46,XX[13] and del(7), respectively. Molecular and cytogenetic analysis identified clonality in 10 (83%) patients at a median age of 42 years. Mutations in CBL, DNTM3A, and BCOR were identified in patients without progression to HM. Clonal kinetics in these patients remained relatively stable on serial molecular evaluation, suggesting certain mutations are not sufficient for leukemogenic transformation.3 The BCOR and CBL mutations have been described in germline RUNX1 patients with HM,3 though as observed in our cohort, often in the context of acquired co-mutations. Patients with HM harbored mutations in BCOR, RUNX1 (c.334_339del, c.485G > A), and genes affecting signaling (KRAS, and KIT), tumor suppressors (PHF6, WT1, and TP53), cellular metabolism (IDH1), and chromatin-spliceosome machinery (EED, SRSF2, and SF3B1). Both patients with somatic mutations in RUNX1 developed HM, suggesting biallelic RUNX1 aberrations are sufficient for malignant transformation. Patient outcomes are shown in Table S4 in Appendix S1. Seven patients developed HM (ALL: 1, AML: 2, sAML: 2, MDS: 2) at a median age of 46 years. 83% of patients receiving induction chemotherapy achieved a CR, though most (80%) did not have full platelet count recovery, likely related to their germline RUNX1 mutation. The estimated median overall survival (OS) in patients diagnosed with any HM (MDS, ALL, AML) was 5.9 years (range: 4 months-NR). Three AML patients received intensive anthracycline-based chemotherapy. The fourth received the triplet of cladribine, low dose cytarabine, and venetoclax alternating with azacitidine and venetoclax (NCT # NCT03586609). All four patients achieved a CR, and three underwent consolidative alloHSCT-three with myeloablative, one with reduced intensity, and one with unknown conditioning. Two patients relapsed a median of 1.3 years following HSCT and received intensive salvage therapy with mitoxantrone, etoposide, and cytarabine (MEC) or idarubicin+ cytarabine (IA), followed by a second allo-HSCT in one patient. All three AML patients undergoing HSCT are now deceased (cause of death was secondary to progressive disease, disseminated adenovirus infection, and unknown, respectively), a median of 2.9 years following initial HSCT. The AML patient receiving lower-intensity therapy remains in a MRD-negative CR. Median OS in AML patients was 4.5 years, comparable to outcomes in patients with somatic RUNX1 mutations treated with intensive chemotherapy.5 The patient with ALL underwent intensive induction with a pediatric (AALL1131; NCT02883049) based regimen with incorporation of dasatinib given the TKI sensitivity of the EBF1-PDGFRB fusion6 and ultimately achieved a MRD-negative CR following consolidation. Given the observed increased risk of relapse in patients with Ph-like ALL and persistent MRD detection following induction, the patient is currently transitioning to allo-HSCT. Both MDS patients underwent myeloablative MUD allo-HSCT, and remain alive in remission without significant complications after a median follow up of 3.6 years since diagnosis. After a median follow up time of 3.5 years, the median OS was not reached in patients undergoing surveillance. All six patients continue active surveillance with routine bloodwork and clinical examinations in addition to annual bone marrow biopsy and aspiration. The diagnosis and management of FDP/MM continues to represent a clinical challenge regarding both diagnosis and management. This is highlighted by the 15% of cases in this study that were identified incidentally during workup of cytopenias or HM, with the identification of a RUNX1 mutation on somatic NGS leading to a germline evaluation. Additionally, three related patients had a large deletion of exons 1-6 of the RUNX1 gene. These large deletions, along with intronic and splice site mutations frequently go undetected on NGS panels that lack coverage of the entire RUNX1 gene, thus a negative somatic NGS panel does not rule out an underlying FPD/AML. In such cases, sequencing of the entire gene and deletion/duplication analysis associated with the suspected disorder should be performed. Determining the risk of malignant transformation remains particularly difficult. A combination of clinical, pathological, and molecular features coupled with close clinical surveillance is necessary to accurately identify and intervene in patients at risk of progressing to a HM.4 The complexities of management are highlighted by the five patients who continue on surveillance with dysplasia or hypocellularity on bone marrow examination, with or without associated clonal hematopoiesis, without overt progression to malignancy after a median follow up of 3.5 years. While mutations in epigenetic genes appear to be associated with a more indolent clinical course, certain somatic mutations such as those in active signaling pathways or bi-allelic RUNX1 mutations may identify patients at high risk for progression to a HM. Treatment outcomes in patients with germline RUNX1 mutations and HM are infrequently reported. Patients with HM in our series had a myeloid predominance (86%, n = 6), and presented at a younger age (median age 46 years) compared to patients with somatic mutations in RUNX1.5 Standard induction therapy resulted in a CR rate of 83% without apparent or untoward toxicity, and a median OS of 5.9 years. As anticipated on longitudinal molecular evaluation, clinical remissions correlated with resolution of acquired somatic clones, while the persistence or emergence of somatic clones was associated with relapse or persistent disease. Five patients underwent allo-HSCT. Patients with MDS appeared to particularly benefit from HSCT, without development of any significant transplantation-associated complications, and a median OS that had not been reached after a median follow up of 3.6 years. This data suggests HSCT is effective in patients with germline RUNX1 mutations developing AML or MDS, however must be interpreted in the context of the small sample size and retrospective nature of this analysis. In conclusion, we confirm early clonal evolution with the development of pre-leukemic and subsequent leukemic clones is common in patients with germline RUNX1 mutations. Furthermore, this data highlights the promise of surveillance and future potential for early intervention prior to development of an overt hematologic malignancy in this at-risk population. In patients with an established malignancy, we provide evidence of the efficacy of both standard induction and low intensity therapies in conjunction with HSCT for the treatment of malignancies associated with germline RUNX1 mutations. The authors declare no potential conflict of interest. Data will be available on request of the corresponding author. Appendix S1. Supporting Information. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.