When to obtain genomic data in acute myeloid leukemia (AML) and which mutations matter

Real-world genomic testing and treatment patterns of newly diagnosed adult acute myeloid leukemia patients within a comprehensive health system

BACKGROUND

We evaluated the frequency of genomic testing and treatment patterns by age category in patients with newly diagnosed (ND) acute myeloid leukemia (AML) treated in both academic- and community-based health systems within a single Midwestern State.

METHODS

Retrospective analysis of data from the Indiana University Health System Enterprise Data Warehouse and two local cancer registries, of 629 patients aged ≥18 years with ND AML during 2011-2018. Primary outcome variables were, proportion of patients with genomic analysis and frequency of mutations. Chemotherapy was categorized as "standard induction" or "other chemotherapy"/targeted therapy, and hypomethylating agents.

RESULTS

Overall, 13% of ND AML patients between 2011 and 2018 had evidence of a genomic sequencing report with a demonstrated increase to 37% since 2016. Genomic testing was more likely performed in patients: aged ≤60 years than >60 years (45% vs. 30%; p = 0.03), treated in academic versus community hospitals (44% vs. 26%; p = 0.01), and in chemotherapy recipients than non-therapy recipients (46% vs. 19%; p < 0.001). Most common mutations were ASXL1, NPM1, and FLT3. Patients ≥75 years had highest proportion (46%) of multiple (≥3) mutations. Overall, 31.2% of patients with AML did not receive any therapy for their disease. This subgroup was older than chemotherapy recipients (mean age: 71.4 vs. 55.7 years, p < 0.001), and was highest (66.2%) in patients ≥75 years.

CONCLUSIONS

Our results highlight the unmet medical need to increase access to genomic testing to afford treatment options, particularly to older AML patients in the real-world setting, in this new era of targeted therapies.

The signature based on seven genomic instability-related genes could predict the prognosis of acute myeloid leukemia patients

BACKGROUND

Acute myeloid leukemia (AML) is the most common acute blood malignancy in adults. The complicated and dynamic genomic instability (GI) is the most prominent feature of AML. Our study aimed to explore the prognostic value of GI-related genes in AML patients.

METHODS

The mRNA data and mutation data were downloaded from the TCGA and GEO databases. Differential expression analyses were completed in limma package. GO and KEGG functional enrichment was conducted using clusterProfiler function of R. Univariate Cox and LASSO Cox regression analyses were performed to screen key genes for Risk score model construction. Nomogram was built with rms package.

RESULTS

We identified 114 DEGs between high TMB patients and low TMB AML patients, which were significantly enriched in 429 GO terms and 13 KEGG pathways. Based on the univariate Cox and LASSO Cox regression analyses, seven optimal genes were finally applied for Risk score model construction, including SELE, LGALS1, ITGAX, TMEM200A, SLC25A21, S100A4 and CRIP1. The Risk score could reliably predict the prognosis of AML patients. Age and Risk score were both independent prognostic indicators for AML, and the Nomogram based on them could also reliably predict the OS of AML patients.

CONCLUSIONS

A prognostic signature based on seven GI-related genes and a predictive Nomogram for AML patients are finally successfully constructed.

Identifying potential germline variants from sequencing hematopoietic malignancies

Next-generation sequencing (NGS) of bone marrow and peripheral blood increasingly guides clinical care in hematological malignancies. NGS data may help to identify single nucleotide variants, insertions/deletions, copy number variations, and translocations at a single time point, and repeated NGS testing allows tracking of dynamic changes in variants during the course of a patient's disease. Tumor cells used for NGS may contain germline, somatic, and clonal hematopoietic DNA alterations, and distinguishing the etiology of a variant may be challenging. We describe an approach using patient history, individual variant characteristics, and sequential NGS assays to identify potential germline variants. Our current criteria for identifying an individual likely to have a deleterious germline variant include a strong family history or multiple cancers in a single patient, diagnosis of a hematopoietic malignancy at a younger age than seen in the general population, variant allele frequency > 0.3 of a deleterious allele in a known germline predisposition gene, and variant persistence identified on clinical NGS panels, despite a change in disease state. Sequential molecular testing of hematopoietic specimens may provide insight into disease pathology, impact patient and family members' care, and potentially identify new cancer-predisposing risk alleles. Ideally, individuals should give consent at the time of NGS testing to receive information about potential germline variants and to allow future contact as research advances.

Identifying potential germline variants from sequencing hematopoietic malignancies

Next-generation sequencing (NGS) of bone marrow and peripheral blood increasingly guides clinical care in hematological malignancies. NGS data may help to identify single nucleotide variants, insertions/deletions, copy number variations, and translocations at a single time point, and repeated NGS testing allows tracking of dynamic changes in variants during the course of a patient's disease. Tumor cells used for NGS may contain germline, somatic, and clonal hematopoietic DNA alterations, and distinguishing the etiology of a variant may be challenging. We describe an approach using patient history, individual variant characteristics, and sequential NGS assays to identify potential germline variants. Our current criteria for identifying an individual likely to have a deleterious germline variant include a strong family history or multiple cancers in a single patient, diagnosis of a hematopoietic malignancy at a younger age than seen in the general population, variant allele frequency > 0.3 of a deleterious allele in a known germline predisposition gene, and variant persistence identified on clinical NGS panels, despite a change in disease state. Sequential molecular testing of hematopoietic specimens may provide insight into disease pathology, impact patient and family members' care, and potentially identify new cancer-predisposing risk alleles. Ideally, individuals should give consent at the time of NGS testing to receive information about potential germline variants and to allow future contact as research advances.

Risk stratification using FLT3 and NPM1 in acute myeloid leukemia patients autografted in first complete remission

FLT3-ITD and NPM1 mutation refine prognostic stratification in acute myeloid leukemia (AML) with intermediate-risk cytogenetics. However, data on their role in patients undergoing autologous stem cell transplantation (Auto-SCT) as post-remission therapy (PRT) are limited. We therefore sought to retrospectively evaluate the role of FLT3-ITD and NPM1 in a cohort of AML patients (n = 405) with intermediate-risk cytogenetics, autografted in first complete remission (CR1). Patients were transplanted between 2000 and 2014 and reported to the European Society for Blood and Marrow Transplantation (EBMT) registry. Leukemia-free survival (LFS) was the primary outcome. Median follow-up was 5.5 years. FLT3-ITD^neg/NPM1^WT was the leading molecular subtype (50%), followed by FLT3-ITD^neg/NPM1^mut (30%). In the univariate analysis, molecular subtype was associated with LFS, overall survival (OS), and relapse incidence (RI) (p < 0.001); 5-year LFS: FLT3-ITD^neg/NPM1^mut 62%, FLT3-ITD^pos/NPM1^mut 38%, FLT3-ITD^neg/NPM1^WT 32%, and FLT3-ITD^pos/NPM1^WT 21%. At 5 years, OS and RI in the FLT3-ITD^neg/NPM1^mut subtype were 74% and 35%, respectively. The corresponding OS and RI in other subtypes were below 48% and over 57%. In a Cox multivariable model, molecular subtype was the strongest predictor of LFS, OS, and relapse. In conclusion, AML patients with intermediate-risk cytogenetics and FLT3-ITD^neg/NPM1^mut experience favorable outcomes when autografted in CR1, suggesting that Auto-SCT is a valid PRT option.

Is There Still a Role for Autologous Stem Cell Transplantation for the Treatment of Acute Myeloid Leukemia?

After intensive induction chemotherapy and complete remission achievement, patients with acute myeloid leukemia (AML) are candidates to receive either high-dose cytarabine-based regimens, or autologous (ASCT) or allogeneic (allo-SCT) hematopoietic stem cell transplantations as consolidation treatment. Pretreatment risk classification represents a determinant key of type and intensity of post-remission therapy. Current evidence indicates that allo-SCT represents the treatment of choice for high and intermediate risk patients if clinically eligible, and its use is favored by increasing availability of unrelated or haploidentical donors. On the contrary, the adoption of ASCT is progressively declining, although numerous studies indicate that in favorable risk AML the relapse rate is lower after ASCT than chemotherapy. In addition, the burden of supportive therapy and hospitalization favors ASCT. In this review, we summarize current indications (if any) to ASCT on the basis of molecular genetics at diagnosis and minimal residual disease evaluation after induction/consolidation phase. Finally, we critically discuss the role of ASCT in older patients with AML and acute promyelocytic leukemia.

Long Non-coding RNAs in Myeloid Malignancies

Acute myeloid leukemia (AML) represents 80% of adult leukemias and 15-20% of childhood leukemias. AML are characterized by the presence of 20% blasts or more in the bone marrow, or defining cytogenetic abnormalities. Laboratory diagnoses of myelodysplastic syndromes (MDS) depend on morphological changes based on dysplasia in peripheral blood and bone marrow, including peripheral blood smears, bone marrow aspirate smears, and bone marrow biopsies. As leukemic cells are not functional, the patient develops anemia, neutropenia, and thrombocytopenia, leading to fatigue, recurrent infections, and hemorrhage. The genetic background and associated mutations in AML blasts determine the clinical course of the disease. Over the last decade, non-coding RNAs transcripts that do not codify for proteins but play a role in regulation of functions have been shown to have multiple applications in the diagnosis, prognosis and therapeutic approach of various types of cancers, including myeloid malignancies. After a comprehensive review of current literature, we found reports of multiple long non-coding RNAs (lncRNAs) that can differentiate between AML types and how their exogenous modulation can dramatically change the behavior of AML cells. These lncRNAs include: H19, LINC00877, RP11-84C10, CRINDE, RP11848P1.3, ZNF667-AS1, AC111000.4-202, SFMBT2, LINC02082-201, MEG3, AC009495.2, PVT1, HOTTIP, SNHG5, and CCAT1. In addition, by performing an analysis on available AML data in The Cancer Genome Atlas (TCGA), we found 10 lncRNAs with significantly differential expression between patients in favorable, intermediate/normal, or poor cytogenetic risk categories. These are: DANCR, PRDM16-DT, SNHG6, OIP5-AS1, SNHG16, JPX, FTX, KCNQ1OT1, TP73-AS1, and GAS5. The identification of a molecular signature based on lncRNAs has the potential for have deep clinical significance, as it could potentially help better define the evolution from low-grade MDS to high-grade MDS to AML, changing the course of therapy. This would allow clinicians to provide a more personalized, patient-tailored therapeutic approach, moving from transfusion-based therapy, as is the case for low-grade MDS, to the introduction of azacytidine-based chemotherapy or allogeneic stem cell transplantation, which is the current treatment for high-grade MDS.