Abstract: Racial/ethnic disparities in health reflect a combination of genetic and environmental causes, and DNA methylation may be an important mediator. We compared in an exploratory manner the blood DNA methylome of Japanese Americans (JPA) versus European Americans (EUA). Methods Genome-wide buffy coat DNA methylation was profiled among healthy Multiethnic Cohort participant women who were Japanese (JPA; n = 30) or European (EUA; n = 28) Americans aged 60–65. Differentially methylated CpGs by race/ethnicity (DM-CpGs) were identified by linear regression (Bonferroni-corrected P   〈  0.1) and analyzed in relation to corresponding gene expression, a priori selected single nucleotide polymorphisms (SNPs), and blood biomarkers of inflammation and metabolism using Pearson or Spearman correlations (FDR  〈  0.1). Results We identified 174 DM-CpGs with the majority of hypermethylated in JPA compared to EUA (n = 133), often in promoter regions (n = 48). Half (51%) of the genes corresponding to the DM-CpGs were involved in liver function and liver disease, and the methylation in nine genes was significantly correlated with gene expression for DM-CpGs. A total of 156 DM-CpGs were associated with rs7489665 ( SH2B1 ). Methylation of DM-CpGs was correlated with blood levels of the cytokine MIP1B (n = 146). We confirmed some of the DM-CpGs in the TCGA adjacent non-tumor liver tissue of Asians versus EUA. Conclusion We found a number of differentially methylated CpGs in blood DNA between JPA and EUA women with a potential link to liver disease, specific SNPs, and systemic inflammation. These findings may support further research on the role of DNA methylation in mediating some of the higher risk of liver disease among JPA.

Abstract: PURPOSE: To prospectively compare cytogenetics and reverse transcriptase–polymerase chain reaction (RT-PCR) for detection of t(8;21)(q22;q22) and inv(16)(p13q22)/t(16;16)(p13;q22), aberrations characteristic of core-binding factor (CBF) acute myeloid leukemia (AML), in 284 adults newly diagnosed with primary AML. PATIENTS AND METHODS: Cytogenetic analyses were performed at local laboratories, with results reviewed centrally. RT-PCR for AML1/ETO and CBFβ/MYH11 was performed centrally. RESULTS: CBF AML was ultimately identified in 48 patients: 21 had t(8;21) or its variant and AML1/ETO, and 27 had inv(16)/t(16;16), CBFβ/MYH11, or both. Initial cytogenetic and RT-PCR analyses correctly classified 95.7% and 96.1% of patients, respectively (P = .83). Initial cytogenetic results were considered to be false-negative in three AML1/ETO-positive patients with unique variants of t(8;21), and in three CBFβ/MYH11-positive patients with, respectively, an isolated +22; del(16)(q22),+22; and a normal karyotype. The latter three patients were later confirmed to have inv(16)/t(16;16) cytogenetically. Only one of 124 patients reported initially as cytogenetically normal was ultimately RT-PCR–positive. There was no false-positive cytogenetic result. Initial RT-PCR was falsely negative in two patients with inv(16) and falsely positive for AML1/ETO in two and for CBFβ/MYH11 in another two patients. Two patients with del(16)(q22) were found to be CBFβ/MYH11-negative. M4Eo marrow morphology was a good predictor of the presence of inv(16)/t(16;16). CONCLUSION: Patients with t(8;21) or inv(16) can be successfully identified in prospective multi-institutional clinical trials. Both cytogenetics and RT-PCR detect most such patients, although each method has limitations. RT-PCR is required when the cytogenetic study fails; it is also required to determine whether patients with suspected variants of t(8;21), del(16)(q22), or +22 represent CBF AML. RT-PCR should not replace cytogenetics and should not be used as the only diagnostic test for detection of CBF AML because of the possibility of obtaining false-positive or false-negative results.

Abstract: We investigated the relative prognostic significance of cytogenetics in 635 adult acute myeloid leukemia (AML) patients 60 years of age or older treated on front-line protocols. Classification trees and tree-structured survival analysis (TSSA) were used to identify important cytogenetic groups, and their prognostic significance was then assessed in multivariable analysis (MVA). Overall, 48.5% achieved complete remission (CR); 6.6% survived at 5 years. Complex karyotypes with at least 3 abnormalities (complex ≥ 3) and a group including “rare aberrations” predicted lower CR rates (25% and 30%) versus other patients (56%). Compared with complex ≥ 3, the odds of CR were significantly higher for noncomplex karyotypes without rare aberrations on MVA. Cytogenetically, complex ≥ 5 predicted inferior disease-free survival on TSSA, remaining significant on MVA together with white blood cell count (WBC), sex, and age. For survival, complex ≥ 5, rare aberrations, and core-binding factor (CBF) abnormalities were prognostic (P 〈 .001), with 5-year survivals of 0%, 0%, and 19.4%, respectively, and 7.5% for remaining patients. Together with WBC, marrow blasts, sex, and age, the cytogenetic groups remained significant on MVA. In conclusion, pretreatment cytogenetics adds to other prognostic factors in older AML patients. Patients with complex ≥ 5 appear to benefit minimally from current treatment and are better suited for investigational therapy or supportive care. (Blood. 2006;108:63-73)

Abstract: Previous studies have identified broad cytogenetic risk groups in AML, by comparing outcome of pts with different recurring abnormalities, using cytogenetically normal pts as the reference group. Pts with better survival were considered as “favorable”, and those with worse outcome as “unfavorable” risk. To identify prognostic cytogenetic groups for complete remission (CR) and overall survival (OS), without the selection of a reference group, we used classification trees and tree-structured survival analysis (TSSA). We analyzed the outcome of 600 AML pts ≥60 years (yrs), enrolled in the prospective CALGB cytogenetic study 8461 and treated on CALGB front-line AML protocols. Analysis was restricted to cytogenetic aberrations occuring in ≥5 pts. Once prognostic cytogenetic abnormalities for CR and OS were identified, multivariable models were constructed. Median age was 68 (range, 60–86) yrs, and 98% had de novo AML. The most common karyotypes were normal (46%), complex with ≥3 abnormalities (complex ≥3, 19%), and ≥5 abnormalities (complex ≥5, 14%). Core binding factor (CBF) abnormalities, ie, inv(16) and t(8;21), occurred in 5%. Overall, 49.5% of pts achieved CR with only 7% (95%CI: 5%–9%) alive at 5 yrs. Table 1 shows prognostic cytogenetic risk groups identified by classification trees and TSSA for CR and OS, respectively. Table 1: Prognostic Cytogenetic Groups by Tree Analysis CR OS Risk group CR rate Risk group 5-yr OS (95% CI) *P 〈 0.05 compared to CBF; CI, confidence interval Complex≥3 30%* CBF 20 (6–20)% Abnormal, non CBF 46%* 〈 5 abnormalities without CBF or −7 8 (5–10)% Normal 57% Complex≥5 0% CBF 75% −7 0% Table 2 shows the multivariable analyses adjusting for other baseline clinical variables. Only lower % circulating blasts (P=0.0002) and cytogenetic risk groups (P 〈 0.0001) predicted CR. Compared to CBF pts, the odds of CR were significantly lower for pts with complex ≥3 and abnormal, non-CBF karyotypes, whereas the odds of CR for cytogenetically normal pts was not significantly different from CBF pts. For OS, cytogenetic risk groups (P 〈 0.0001), older age (P=0.03), and higher WBC at diagnosis (P=0.02) predicted shorter survival. Compared to CBF pts, the risk of death was significantly higher for those with complex ≥5 karyotype, −7, and 〈 5 abnormalities without CBF or −7. Table 2: Multivariable Analyses CR OS Significant Variables OR (95% CI) Significant Variables HR (95% CI) *CBF is the reference group; OR, odds ratio of achieving CR; HR, hazard ratio of death; CI, confidence interval % circulating blasts 0.90 (0.84–0.95) Age 1.28 (1.09–1.50) Cytogenetics group* WBC 1.03 (1.01–1.04) Complex≥3 0.12 (0.05–0.33) Cytogenetics group* Abnormal, non CBF 0.26 (0.10–0.65) Complex≥5 4.53 (2.80–7.32) Normal 0.44 (0.18–1.09) −7 2.57 (1.39–4.76) 〈 5 abnormalities without CBF or −7 1.62 (1.07–2.46) We conclude that pre-treatment cytogenetics are predictive of CR and OS of older AML pts, particularly identifying pts with complex ≥5 karyotype and −7, who benefit minimally if at all from standard chemotherapy. Such pts may be better suited for investigational therapy or only supportive care.

Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Abstract: Uniparental disomy (UPD) is a way cancer cells duplicate a mutated gene, causing loss of heterozygosity (LOH). Patients with cytogenetically normal acute myeloid leukemia (CN-AML) do not have microscopically detectable chromosome abnormalities, but can harbor UPDs. We examined the prognostic significance of UPDs and frequency of LOH in patients with CN-AML. Experimental Design: We examined the frequency and prognostic significance of UPDs in a set of 425 adult patients with de novo CN-AML who were previously sequenced for 81 genes typically mutated in cancer. Associations of UPDs with outcome were analyzed in the 315 patients with CN-AML younger than 60 years. Results: We detected 127 UPDs in 109 patients. Most UPDs were large and typically encompassed all or most of the affected chromosome arm. The most common UPDs occurred on chromosome arms 13q (7.5% of patients), 6p (2.8%), and 11p (2.8%). Many UPDs significantly cooccurred with mutations in genes they encompassed, including 13q UPD with FLT3-internal tandem duplication (FLT3-ITD; P & lt; 0.001), and 11p UPD with WT1 mutations (P = 0.02). Among patients younger than 60 years, UPD of 11p was associated with longer overall survival (OS) and 13q UPD with shorter disease-free survival (DFS) and OS. In multivariable models that accounted for known prognostic markers, including FLT3-ITD and WT1 mutations, UPD of 13q maintained association with shorter DFS, and UPD of 11p maintained association with longer OS. Conclusions: LOH mediated by UPD is a recurrent feature of CN-AML. Detection of UPDs of 13q and 11p might be useful for genetic risk stratification of patients with CN-AML.

Abstract: As most patients with acute myeloid leukemia (AML) with morphologic complete remission (CR) ultimately relapse, better predictors for outcome are needed. Recently, Cheson et al suggested using cytogenetic remission (CRc) as part of the criteria for CR. To our knowledge, ours is the first relatively large study evaluating the usefulness of CRc attained immediately following induction chemotherapy. Patients and Methods We included AML patients treated on Cancer and Leukemia Group B front-line studies with cytogenetic samples obtained at diagnosis and at the first day of documented CR following induction. Patients with abnormal cytogenetics at diagnosis, and normal cytogenetics at CR (NCR; n = 103) were compared with those with abnormal cytogenetics both at diagnosis and at CR (ACR; n = 15) for overall survival (OS), disease-free survival (DFS), and cumulative incidence of relapse (CIR). Cox proportional hazards models determined the prognostic significance of cytogenetics at CR, adjusting for other covariates. Results Clinical features were similar for both groups, with the exception of favorable cytogenetics [t(8;21), inv(16)/t(16;16), t(15;17)] at diagnosis, which was more frequent (P = .03) in the NCR group. Median follow-up was 3.1 years (range, 1.0 to 11.4 years). ACR patients had significantly shorter OS (P = .006) and DFS (P = .0001), and higher CIR (P = .0001). In multivariable models, the NCR and ACR groups were predictors for OS (P = .03), DFS (P = .02), and CIR (P = .05). The relative risk of relapse or death was 2.1 times higher for ACR patients than for NCR patients (95% CI, 1.1 to 3.9). Conclusion Our data suggest that converting to normal karyotype at the time of first CR is an important prognostic indicator and support the use of CRc as a criterion of CR in AML.

Abstract: An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Abstract: Background: Aberrant expression levels of several miRs have been reported to independently associate with outcome of patients (pts) with CN-AML. In these reports, miR expression was profiled using microarray assays, which interrogate a selected subset of miRs. The advent of next-generation sequencing (NGS) has allowed unbiased measurement of miR expression, but, to our knowledge, NGS has not been used to identify miRs associated with prognosis of AML pts. Here, we analyze small RNA sequencing (smRNA-seq) data from a large cohort of younger adults with CN-AML, for whom outcome data were available, with the goal to identify new prognostic miRs. Methods: We performed smRNA-seq in 281 younger adults (aged 18-59 y) with de novo CN-AML. Cytogenetic analyses were performed in Cancer and Leukemia Group B (CALGB)/Alliance institutional laboratories using standard banding techniques; mutational analyses were done centrally using a targeted DNA sequencing platform. All pts were treated on frontline CALGB/Alliance protocols. Results: We first evaluated which miRs associated with overall survival (OS) in univariable analysis; we detected 9 such miRs. We then used a machine-learning approach, namely random forests, to identify miRs whose concomitant expression could generate an effective outcome predictor in CN-AML. To account for the effect of co-existing prognostic gene mutations, we included the European LeukemiaNet (ELN) risk group status in the random forest analyses. A total of 8 prognostic miRs were identified, 4 of which were also found to be prognostic in univariable analysis (underlined below), thus bringing the total number of unique prognostic miRs to 13: miR-511, miR-1193, miR-155, miR-4517, miR-3681, miR-2355, miR-628, miR-1266, miR-6715a, miR-1180, miR-6715b, miR-132, miR-146b. We used partitioning around medoids to divide our pts into clusters, based on the combined expression levels of the 13 prognostic miRs. Two such clusters were identified: cluster 1 comprised 173 pts and cluster 2 contained 108 pts. Regarding pretreatment and molecular features, pts in cluster 1 had lower percent of bone marrow blasts (P=.04), and had more frequently biallelic CEBPA mutations (P 〈 .001) and less frequently internal tandem duplications of the FLT3 gene (P 〈 .001), RUNX1 (P=.02) and WT1(P=.03) mutations than pts in cluster 2. In outcome analyses, pts in cluster 1 had a higher complete remission rate (CR; 91% vs 73%,P 〈 .001) and a longer disease-free survival (DFS; 5-y rates 52% vs 16%, P 〈 .001) and OS (5-y rates 60% vs 19%,P 〈 .001). In multivariable analysis, cluster 1 status remained significantly associated with higher odds of achieving a CR (P=.001) and longer DFS (P 〈 .001) and OS (P 〈 .001), after adjusting for other covariates. Regarding accuracy of outcome prediction, our composite model had a concordance index of 0.687. When ranked according to importance for prognosis, miR-511 expression was the most significant determinant among the random forest model parameters. To evaluate the reproducibility of our findings, we performed analyses in the publicly available TCGA dataset (Ley et al. NEJM 2013;368:2059). Eighty-eight CN-AML pts with miR expression and survival data were available in the TCGA cohort. As TCGA pts are not classified according to ELN risk groups, we could not directly reproduce the random forest-based cluster analysis. However, a univariable analysis showed that miR-511 and miR-628 expression levels were also prognostic in the TCGA dataset. Next, we evaluated whether the identified prognostic miRs have functional relevance in AML. We focused on miR-511, which was the most important determinant of our outcome predictor and has not been previously studied in AML. Among 6 AML cell lines tested, MV4-11 had the most abundant expression of miR-511. Functional silencing of miR-511 in MV4-11 cells decreased both their viability (as measured by Annexin-PI staining and flow-cytometry, P=.004) and proliferative capacity (as measured by WST1 reagent degradation, P 〈 .001). Conclusion: Unbiased profiling of miRs using smRNA-seq has identified a novel set of 13 miRs with prognostic significance in CN-AML. MiR expression-based cluster status independently associates with clinical outcome of CN-AML pts. Our preliminary in vitro experiments have shown that miR-511, whose association with prognosis was the strongest among the newly identified prognostic miRs, is functionally relevant in AML. Disclosures Uy: Astellas: Consultancy; Pfizer: Consultancy; Curis: Consultancy; GlycoMimetics: Consultancy. Powell:Rafael Pharmaceuticals: Consultancy, Research Funding; Novartis: Consultancy, Speakers Bureau; Jazz Pharmaceuticals: Consultancy, Research Funding, Speakers Bureau; Pfizer: Consultancy, Research Funding; Janssen: Research Funding. Kolitz:Astellas: Research Funding; Boeringer-Ingelheim: Research Funding; Roche: Research Funding. Byrd:Acerta: Research Funding; TG Therapeutics: Other: Travel Expenses, Research Funding, Speakers Bureau; Genentech: Research Funding; Janssen: Consultancy, Other: Travel Expenses, Research Funding, Speakers Bureau; Ohio State University: Patents & Royalties: OSU-2S; Genentech: Research Funding; Novartis: Other: Travel Expenses, Speakers Bureau; BeiGene: Research Funding; TG Therapeutics: Other: Travel Expenses, Research Funding, Speakers Bureau; Novartis: Other: Travel Expenses, Speakers Bureau; Pharmacyclics LLC, an AbbVie Company: Other: Travel Expenses, Research Funding, Speakers Bureau; Acerta: Research Funding; Ohio State University: Patents & Royalties: OSU-2S; Ohio State University: Patents & Royalties: OSU-2S; Gilead: Other: Travel Expenses, Research Funding, Speakers Bureau; Genentech: Research Funding; Acerta: Research Funding; BeiGene: Research Funding; Gilead: Other: Travel Expenses, Research Funding, Speakers Bureau; Janssen: Consultancy, Other: Travel Expenses, Research Funding, Speakers Bureau; Pharmacyclics LLC, an AbbVie Company: Other: Travel Expenses, Research Funding, Speakers Bureau.