<i>GATA3</i> rs3824662A allele in B‐cell acute lymphoblastic leukemia in adults, adolescents and young adults: association with <i>CRLF2</i> rearrangement and poor prognosis
Authors: Paul B. Koller, Hui Zhang, Hagop Kantarjian, Elias Jabbour, Sherry Pierce, Yoshihiro Gocho, Kathryn G. Roberts, Wenjian Yang, Charles G. Mullighan, Jun Yang, Marina Konopleva, Nitin Jain
Journal: American Journal of Hematology (2020)

Outcomes of adult B-cell acute lymphoblastic leukemia (ALL) remains poor, with 5-year disease-free survival (DFS) of only 40%-45%.1 The poor prognosis in adults, in part, has been attributed to increased frequency of high-risk subtypes, such as Philadelphia (Ph)-positive and Ph-like ALL. Note, Ph-like ALL is characterized by a gene expression profile similar to Ph-positive ALL, but without the BCR-ABL1 fusion.2 Ph-like ALL, especially CRLF2+ subtype is associated with inferior DFS and overall survival (OS).3, 4 Thus, Ph-like ALL is significantly over-represented in patients of Hispanic ethnicity and is associated with an inherited GATA3 variants (rs3824662) in children.5 We report here the incidence and clinical outcomes of germline variants of GATA3 in adult and adolescents and young adults (AYAs) patients with B-ALL, with a particular focus on Ph-like ALL. The study population was a total of 178 patients with newly diagnosed B-ALL, who were treated at MD Anderson Cancer Center (MDACC) between 1992-2013 and were initially screened. Of these patients, 139 had evaluable genetic material. Of the 139 patients, 45 were excluded from our analysis as these patients had Ph + ALL. The remaining 94 patients were evaluated for Ph-like ALL and GATA3 germline polymorphism and form the basis of this report. Patient ethnicity was determined from the medical records as indicated by patient self-reporting at the time of the initial visit. All patients received induction chemotherapy at MDACC. Treatment was either HyperCVAD-based or a pediatric regimen that included asparaginase. The study was approved by the institutional research review boards at MDACC and St. Jude Children's Research Hospital. Genomic profiling was done with RNA samples isolated from each patient's tumor cells, and were subjected to gene expression profiling using either U133 Plus 2.0 microarrays (Affymetrix, Santa Clara, CA) or a customized Taqman low-density array (LDA) card to classify Ph-like status as previously described.3 For cases with available germline DNA, the DNA was genotyped for single-nucleotide polymorphisms (SNPs) by using SNP 6.0 microarrays (Affymetrix) or the Infinium Omni 2.5 Exome-8 BeadChip kit (Illumina, San Diego, CA), as previously described4 or Sanger sequencing. These genotypes have been previously described.5 Fluorescence in situ hybridization and flow cytometry were performed to detect CRLF2 rearrangement/overexpression as previously described. The CRLF2+ status includes patients that either had CRLF2 rearrangement by FISH and/or overexpression by flow cytometry.6 Statistical analysis: Baseline characteristics of the three different groups were compared with chi-square test and analysis of variance test. These were used to assess categorical and continuous variables, respectively. The Kaplan-Meier method was used to assess event-free survival (EFS) and OS using the log-rank trend test. The OS was defined as the period from the date of diagnosis to the date of last follow-up or death of any cause. The EFS was defined as the period from beginning of treatment to an event such as relapse, treatment failure, or death from any cause. Patients who underwent allogeneic stem cell transplantation were not censored at the time of transplant. We used univariable analysis and multivariable analysis to identify potential factors at diagnosis that were associated with OS (age, sex, ethnicity, WBC count, hemoglobin, platelet count, Ph-like ALL, CRLF2 status, cytogenetics, GATA3 germline status, and treatment received). For the multivariable analysis, the Cox proportional hazards model was used to determine factors correlated with OS. A P value <.05 (2-tailed) was considered statistically significant. Baseline clinical characteristics are shown in Figure 1A. Median follow up was 113.5 months (5.5-328.4 months). Of the 94 patients, 23 had rs3824662 AA genotype, 45 had AC genotype, and 26 had CC genotype. The frequency of self-reported Hispanic ethnicity was significantly higher in the AA genotype group (83%) than in the AC genotype group (60%) or the CC genotype group (15%); P < .001. Among patients with the AA genotype, 87% had Ph-like ALL; the proportions with Ph-like ALL were 40% of the AC genotype group and 26% of the CC genotype group (P < .001). Within the patients that were of Hispanic ethnicity, there was 1 (25%) patient in the CC genotype, 12 (44%) in the AC genotype group, and 17 (89%) in the AA genotype group who had Ph-like ALL (P = .003) (Table S1). Rates of CRLF2+ in the CC, AC, and AA GATA3 genotype groups were 0%, 29%, and 61%, respectively (P < .001). Specifically, within the patients that were of Hispanic ethnicity, which is where this genotype is more frequent, there were zero patients in the CC genotype, 10 (37%) in the AC genotype group, and 13 (68%) in the AA genotype group who had CRLF2+ ALL (P = .017) (Table S1). The 4-year EFS was 50% for the CC group and 43% for the AC group, whereas it was 17% for the AA group (P = .041 by the log-rank trend test) (Figure 1B). The 4-year OS was 62% for the CC group and 50% for the AC group, whereas it was 26% for the AA group (P = .025 by the log-rank trend test) (Figure 1C). All comparisons reported are comparing the differences between the following three groups: AA vs AC vs CC. The univariate and multivariate analysis for overall survival are reported in Table S2. On univariable analysis, shorter OS was associated with a higher WBC at diagnosis, lower platelets at diagnosis, Ph-like ALL, CRLF2+ status, and the GATA3 AA germline polymorphism. In the multivariable analysis, adjusting for the variables used in the univariable analysis, age (<60 vs ≥60 years), platelet count, and Ph-like ALL were the variables significantly associated with OS: age (hazard ratio [HR], 2.16559 [P = .045]; platelet count HR, 2.898447 [P = .032]; Ph-like ALL HR, 2.548571 [P = .022]). To our knowledge, this is the first report of GATA3 polymorphisms and association with Ph-like ALL in adult patients with B-ALL. We report GATA3 AA genotype is significantly associated with Hispanic ethnicity, Ph-like ALL, and CRLF2+ status within adult patients with Ph-negative ALL. These results are in concurrence with similar results reported in children with Ph-like ALL.2, 5 We have previously reported that, the GATA3 A allele is associated with higher GATA3 mRNA levels than the GATA3 C allele. Additionally, we have previously shown that a gene set enrichment assay of ALL cell lines with ectopic GATA3 overexpression led to a Ph-like gene expression signature compared with vector control cells.5 This is consistent with the GATA3 AA genotype being associated with Ph-like ALL. Thus, we report that among patients with Ph-negative ALL, a GATA3 germline AA polymorphism represents an inherited risk factor for Ph-like ALL and is associated with poor prognosis. Paul Koller: Consulting Fees: Jazz. Hagop Kantarjian: Research Grants: AbbVie, Amgen, Ascentage, BMS, Daiichi-Sankyo, Immunogen, Jazz, Novartis, Pfizer, Sanofi. Honoraria: AbbVie, Actinium (Advisory Board), Adaptive Biotechnologies, Amgen, Apptitude Health, BioAscend, Daiichi-Sankyo, Delta Fly, Janssen Global, Novartis, Oxford Biometical, Pfizer, Takeda. Elias Jabbour: research grants and consultancy fees from Abbvie, Adaptive Biotechnologies, Amgen, BMS, Genentech, Pfizer and Takeda. Charles Mullighan: Research funding: Loxo Oncology, Pfizer, Abbvie. Speaking: Amgen, SAB: Illumina. Marina Konopleva: Grant support and consulting fees from AbbVie, Genentech, F. Hoffmann La-Roche, Stemline Therapeutics, Forty-Seven, consulting fees from Amgen and Kisoji, grant support from Eli Lilly, Cellectis, Calithera, Ablynx, Agios, Ascentage, AstraZeneca, Rafael Pharmaceutical, Sanofi, royalties and stock options from Reata Pharmaceutical Inc., and patent US 7795305 B2 on CDDO-compounds and combination therapies, licensed to Reata Pharmaceutical. Nitin Jain: Research Funding: Pharmacyclics, AbbVie, Genentech, AstraZeneca, BMS, Pfizer, ADC Therapeutics, Incyte, Servier, Cellectis, Verastem, Adaptive Biotechnologies, Precision Biosciences, Fate Therapeutics, Aprea Therapeutics Advisory Board/Honoraria: Pharmacyclics, Janssen, AbbVie, Genentech, AstraZeneca, Verastem, Adaptive Biotechnologies, Servier, Precision Biosciences, TG Therapeutics, Beigene. P.B.K., J.Y., M.K., and N.J. contributed to the conception of the study and wrote the manuscript; P.B.K., H.Z., H.K., E.J., S.P., Y.G., K.G.R., W.Y. C.G.M., J.Y., M.K. and N.J. contributed to the provision of study materials, patient recruitment, acquisition of data, or data analysis and interpretation; and all authors participated in the reviewing of the manuscript and gave final approval to submit for publication. Funding: Defining and Treating Targetable Lesions in AYA Acute Lymphoblastic Leukemia, RP150006, Cancer Prevention & Research Institute of Texas (CPRIT), to MK and NJ. The data that support the findings of this study are available from the corresponding author upon reasonable request. Table S1. Ph-like and CRLF2 status by Hispanic ethnicity Table S2. Univariate and Multivariate Analysis for OS 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.