Correlation between methylation level of the SLC19A1 promoter region and methotrexate metabolism in adult acute lymphoblastic leukemia.

Aims: To analyze the methylation level in the promoter region of SLC19A1 in adult acute lymphoblastic leukemia (ALL) patients, and explore the relationship between methotrexate (MTX) drug metabolism and SLC19A1 methylation. Methods: The methylation levels of the SLC19A1 promoter region in 52 adult ALL patients who received high-dose MTX chemotherapy were retrospectively analyzed in combination with clinical indicators and plasma MTX concentration. Results: Methylation levels of 17 CpG units were differently correlated with clinical parameters of ALL patients including gender, age, immunophenotype and Philadelphia chromosome status. Patients with delayed MTX drug excretion had higher methylation levels in the SLC19A1 promoter region. Conclusion: The methylation may affect the MTX plasma level and adverse reactions, which may predict patients at risk of adverse reactions after high-dose MTX therapy.

Effects of genetic polymorphisms on methotrexate levels and toxicity in Chinese patients with acute lymphoblastic leukemia.

Methotrexate (MTX) has an antitumor effect when used for the treatment of acute lymphoblastic leukemia (ALL). This study aims at evaluating the associations between 14 polymorphisms of six genes involved in MTX metabolism with serum MTX concentration and toxicity accompanying high-dose MTX. Polymorphisms in 183 Chinese patients with ALL were analyzed using TaqMan single nucleotide polymorphism genotyping assay. The serum MTX concentration was determined using homogeneous enzyme immunoassay. MTX-related toxicities were also evaluated. Renal toxicity was significantly associated with higher serum MTX concentrations at 24, 48, and 72 hours, and MTX elimination delay (P = 0.001, P < 0.001, P < 0.001, and P < 0.001, respectively), whereas SLCO1B1 rs4149056 was associated with serum MTX concentrations at 48 and 72 hours, and MTX elimination delay in candidate polymorphisms (P = 0.014, P = 0.019, and P = 0.007, respectively). SLC19A1 rs2838958 and rs3788200 were associated with serum MTX concentrations at 24 hours (P = 0.016, P = 0.043, respectively). MTRR rs1801394 was associated with serum MTX concentrations at 72 hours (P = 0.045). Neutropenia was related to SLC19A1 rs4149056 (odds ratio [OR]: 3.172, 95% confidence interval [CI]: 1.310-7.681, P = 0.011). Hepatotoxicity was associated with ABCC2 rs2273697 (OR: 3.494, 95% CI: 1.236-9.873, P = 0.018) and MTRR rs1801394 (OR: 0.231, 95% CI: 0.084-0.632, P = 0.004). Polymorphisms of SLCO1B1, SLC19A1, ABCC2, and MTRR genes help predict higher risk of increased MTX levels or MTX-related toxicities in adult ALL patients.

The clinical characteristics and prognosis in adult Ph negative acute lymphoblastic leukemia with TP53 aberrations.

Very few reports elucidate the prognosis of patients with TP53 aberrations using both measurable residual disease (MRD) and the status of having undergone allogeneic hematopoietic stem cell transplantation (allo-SCT). In this study, aberrations of TP53 were analyzed using next-generation sequencing (NGS) and fluorescence in situ hybridization (FISH) in patients with Philadelphia chromosome-negative (Ph-) ALL enrolled in a prospective single-arm clinical trial at our leukemia center. We analyzed the survival of the patients grouped according to the MRD level at the third month and whether or not received allo-SCT. We found that allo-SCT could improve the OS in patients with TP53 aberrations; Patients having negative MRD at the third month still showed worse 3-year OS and 3-year DFS without undergoing allo-SCT, which is different from previous studies, moreover, the prognostic significance of TP53 deletions was as important as TP53 mutations, the importance of screening both TP53 deletions and mutations in adult Ph- ALL at diagnosis should be emphasized.

Comparison of multi-omics results between patients with acute myeloid leukemia with long-term survival and healthy controls.

Background: Acute myeloid leukemia (AML) is a group of highly heterogeneous diseases, for which approximately 35-40% of patients younger than 60 years old can be cured. However, the multi-omics characteristics and immune cell infiltration (ICI) status of adult long-term survival patients with AML patients compared with healthy controls are still relatively under-explored. Methods: A total of 10 healthy transplant donors (control group) and 11 long-term survival patients with AML with de novo sampling from 2019 to 2020 at the Institute of Hematology in the Hospital of Blood Diseases were enrolled. We simultaneously performed 850 K methylation and bulk RNA-seq on these 21 patients for comparing the differential gene methylation and expression levels between the two groups. The analysis of immune cell gene expression was based on 4 algorithms single sample gene set enrichment analysis (ssGSEA), EPIC, ESTIMATE and immunophenotype score (IPS) on the bulk RNA-seq data. Results: The differential methylation positions (DMPs) of the control group was significantly higher than that of the long-term survival group (P<0.01). The hypomethylated probes for Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment is summarized as follows: the significant pathway was related to NK-cell-mediated cytotoxicity and amino acid metabolism. We also found the Differential expression genes (DEGs) of long-term survival AML were roughly similar, and the DEGs were highly relevant to the cellular amino acid metabolic process pathway by gene set enrichment analysis (GSEA). Based on the further univariate and multivariate Cox survival analyses in GSE37642, genes crosslinked of DEGs and DMPs: LOXL1 and PDZRN4, which characterized as hypomethylated and upregulated, may become an AML prognostic marker (P<0.05). Besides, compared with the long-term-survival AML patients who discontinued chemotherapy after >3 years and the healthy donors, T cell-, natural killer cell-, MHC- and effector cell (EC)-related genes were downregulated; suppressor cells (SC) and checkpoint (CP) cells were significantly upregulated in the long-term-survival AML patients who discontinued chemotherapy after <3 years. Conclusions: In terms of DNA methylation, RNA expression and ICI, AML patients with long-term survival were slightly different than that of healthy people. The profile of long-term AML survivors, especially those who discontinued chemotherapy less than 3 years, still differed from that of healthy people.

Gene Deletions and Prognostic Values in B-Linage Acute Lymphoblastic Leukemia.

Although pediatric-like treatment regimen has remarkably improved the survival rates of adults with acute lymphoblastic leukemia (ALL), the outcome of some adult patients is still poor owing to adverse genetic features. These molecular abnormalities, especially gene deletions, may be considered for the prognosis assessment for adult patients with ALL. In this study, using multiplex ligation-dependent probe amplification (MLPA) method, gene deletions were analyzed in from 211 adult B-ALL patients treated in our center. The data showed that 68.2% (144/211) adult B-ALL patients carried gene deletions, and the frequency is much higher in Ph+B-ALL patients. IKZF1 gene deletion is the most common gene deletion in adult B-ALL, followed by CDKN2A/B deletion. In Ph-B-ALL patients, the overall survival of patients with gene deletions is inferior to that of patients without any gene deletions. More obviously, patients with IKZF1 or CDKN2A/B deletion had a worse prognosis, whereas, allogeneic hematopoietic stem cell transplantation could improve OS in patients with IKZF1 deletion, but not in patients with CDKN2A/B deletion. Moreover, the outcome of Ph-B-ALL patients with double deletion of IKZF1and CDKN2A/B may be much worse than that of patients with IKZF1 or CDKN2A/B alone. Minimal residual disease (MRD) was also analyzed together with gene deletions and demonstrated that gene deletions have a negative impact on survival only in MRD positive Ph-B-ALL patients. In conclusion, gene deletions are closely related with the prognosis of adult Ph-B-ALL patients.

A novel variant translocation (1;9)(p22;q34) resulting in a DEK/NUP214 fusion gene in a patient with acute myeloid leukemia: A case report.

The present case report describes a 46-year-old female patient diagnosed with M4 acute myeloid leukemia (AML), accompanied with a t(1;9)(p22;q34) chromosomal abnormality. Transcriptome sequencing identified a DEK proto-oncogene (DEK)/nucleoporin (NUP)214 fusion gene, which results from the t(6;9)(p23;q34) chromosomal translocation. Polymerase chain reaction analysis and fluorescence in situ hybridization were used to verify the existence of the DEK/NUP214 fusion gene. Few patients with AML with the t(6;9)(p23;q34) chromosomal translocation have been reported to have other chromosomal or karyotype changes. To our knowledge, no AML patient with the DEK/NUP214fusion gene but without the classic t(6;9)(p23;q34) translocations had been reported until now. The prognosis of AML cases with the DEK/NUP214 fusion gene is poor. The rate of complete remission is ~65% (71% in children, 58% in adult patients), while the estimated 5-year survival rate is 28% for children and 9% for adults. The 2008 revision of World Health Organization classification have defined the DEK/NUP214 mutation as a recurrent genetic abnormality of AML. The overall survival of the patient in the current report was ~29 months, and they relapsed twice. To the best of our knowledge, this is the first report of at(1;9)(p22;q34) variant translocation that results in expression of the DEK/NUP214 fusion gene.