ABSTRACT
Current strategies to treat pediatric acute lymphoblastic leukemia rely on risk stratification algorithms using categorical data. We investigated whether using continuous variables assigned different weights would improve risk stratification. We developed and validated a multivariable Cox model for relapse-free survival (RFS) using information from 21199 patients. We constructed risk groups by identifying cutoffs of the COG Prognostic Index (PICOG) that maximized discrimination of the predictive model. Patients with higher PICOG have higher predicted relapse risk. The PICOG reliably discriminates patients with low vs. high relapse risk. For those with moderate relapse risk using current COG risk classification, the PICOG identifies subgroups with varying 5-year RFS. Among current COG standard-risk average patients, PICOG identifies low and intermediate risk groups with 96% and 90% RFS, respectively. Similarly, amongst current COG high-risk patients, PICOG identifies four groups ranging from 96% to 66% RFS, providing additional discrimination for future treatment stratification. When coupled with traditional algorithms, the novel PICOG can more accurately risk stratify patients, identifying groups with better outcomes who may benefit from less intensive therapy, and those who have high relapse risk needing innovative approaches for cure.
Subject(s)
Burkitt Lymphoma , Precursor B-Cell Lymphoblastic Leukemia-Lymphoma , Precursor Cell Lymphoblastic Leukemia-Lymphoma , Child , Humans , Young Adult , Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/diagnosis , Precursor B-Cell Lymphoblastic Leukemia-Lymphoma/therapy , Prognosis , Precursor Cell Lymphoblastic Leukemia-Lymphoma/diagnosis , Precursor Cell Lymphoblastic Leukemia-Lymphoma/therapy , Recurrence , Risk Assessment , Disease-Free SurvivalABSTRACT
Recurrent chromosomal abnormalities and gene mutations detected at the time of diagnosis of acute myeloid leukemia (AML) are associated with particular disease features, treatment response and survival of AML patients, and are used to denote specific disease entities in the World Health Organization classification of myeloid neoplasms and acute leukemia. However, large studies that integrate cytogenetic and comprehensive mutational information are scarce. We created a comprehensive oncoprint of mutations associated with recurrent cytogenetic findings by combining the information on mutational patterns of 80 cancer- and leukemia-associated genes with cytogenetic findings in 1603 adult patients with de novo AML. We show unique differences in the mutational profiles among major cytogenetic subsets, identify novel associations between recurrent cytogenetic abnormalities and both specific gene mutations and gene functional groups, and reveal differences in cytogenetic and mutational features between patients younger than 60 years and those aged 60 years or older. The identified associations between cytogenetic and molecular genetic data may help guide mutation testing in AML, and result in more focused application of targeted therapy in patients with de novo AML.
Subject(s)
Chromosome Aberrations , Gene Ontology , Genes, Neoplasm , Leukemia, Myeloid, Acute/genetics , Mutation , Adult , Age Factors , Aged , DNA Mutational Analysis , DNA, Neoplasm/genetics , Female , Humans , Karyotyping , Male , Middle AgedABSTRACT
Core-binding factor acute myeloid leukemia (CBF-AML) is defined by the presence of either t(8;21)(q22;q22)/RUNX1-RUNX1T1 or inv(16)(p13.1q22)/t(16;16)(p13.1;q22)/CBFB-MYH11. The resulting fusion genes require a 'second hit' to initiate leukemogenesis. Mutation assessment of 177 adults with CBF-AML, including 68 with t(8;21) and 109 with inv(16)/t(16;16), identified not only mutations well known in CBF-AML but also mutations in the CCND1 and CCND2 genes, which represent novel frequent molecular alterations in AML with t(8;21). Altogether, CCND1 (n=2) and CCND2 (n=8) mutations were detected in 10 (15%) patients with t(8;21) in our cohort. A single CCND2 mutation was also found in 1 (0.9%) patient with inv(16). In contrast, CCND1 and CCND2 mutations were detected in only 11 (0.77%) of 1426 non-CBF-AML patients. All CCND2 mutations cluster around the highly conserved amino-acid residue threonine 280 (Thr280). We show that Thr280Ala-mutated CCND2 leads to increased phosphorylation of the retinoblastoma protein, thereby causing significant cell cycle changes and increased proliferation of AML cell lines. The identification of CCND1 and CCND2 mutations as frequent mutational events in t(8;21) AML may provide further justification for cell cycle-directed therapy in this disease.
Subject(s)
Chromosomes, Human, Pair 21 , Chromosomes, Human, Pair 8 , Cyclin D1/genetics , Cyclin D2/genetics , Leukemia, Myeloid, Acute/genetics , Mutation , Translocation, Genetic , Adolescent , Adult , Aged , Biomarkers, Tumor/genetics , Female , Follow-Up Studies , Humans , Leukemia, Myeloid, Acute/pathology , Male , Middle Aged , Neoplasm Staging , Prognosis , Survival Rate , Young AdultSubject(s)
Chromosomes, Human, Pair 11 , DNA (Cytosine-5-)-Methyltransferases/genetics , Histone-Lysine N-Methyltransferase/genetics , Isocitrate Dehydrogenase/genetics , Leukemia, Myeloid, Acute/genetics , Mutation , Myeloid-Lymphoid Leukemia Protein/genetics , Splicing Factor U2AF/genetics , Trisomy , fms-Like Tyrosine Kinase 3/genetics , Adult , Aged , Aged, 80 and over , DNA Methyltransferase 3A , Female , Humans , Male , Middle AgedSubject(s)
Cell Lineage , Drug Resistance, Neoplasm/genetics , Histone-Lysine N-Methyltransferase/genetics , Homeodomain Proteins/genetics , Myeloid-Lymphoid Leukemia Protein/genetics , Neoplasm Recurrence, Local/genetics , Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/genetics , Adolescent , Adult , Child , Child, Preschool , Disease-Free Survival , Female , Gene Rearrangement , Humans , Male , Neoplasm Recurrence, Local/mortality , Precursor T-Cell Lymphoblastic Leukemia-Lymphoma/mortality , Prognosis , Retrospective StudiesSubject(s)
Leukemia/genetics , Oncogene Proteins, Fusion/genetics , Transcriptome/genetics , Adult , Aged , Aged, 80 and over , Chromosomes, Human, Pair 11/genetics , Chromosomes, Human, Pair 19/genetics , DNA Mutational Analysis , Female , Humans , Male , MicroRNAs/analysis , MicroRNAs/genetics , Middle Aged , Myeloid-Lymphoid Leukemia Protein/genetics , Neoplasm Proteins/genetics , Nuclear Proteins/genetics , Transcription Factors/genetics , Translocation, Genetic , Young AdultABSTRACT
DNMT3B encodes a DNA methyltransferase implicated in aberrant epigenetic changes contributing to leukemogenesis. We tested whether DNMT3B expression, measured by NanoString nCounter assay, associates with outcome, gene and microRNA expression and DNA methylation profiles in 210 older (⩾60 years) adults with primary, cytogenetically normal acute myeloid leukemia (CN-AML). Patients were dichotomized into high versus low expressers using median cut. Outcomes were assessed in the context of known CN-AML prognosticators. Gene and microRNA expression, and DNA methylation profiles were analyzed using microarrays and MethylCap-sequencing, respectively. High DNMT3B expressers had fewer complete remissions (CR; P=0.002) and shorter disease-free (DFS; P=0.02) and overall (OS; P<0.001) survival. In multivariable analyses, high DNMT3B expression remained an independent predictor of lower CR rates (P=0.04) and shorter DFS (P=0.04) and OS (P=0.001). High DNMT3B expression associated with a gene expression profile comprising 363 genes involved in differentiation, proliferation and survival pathways, but with only four differentially expressed microRNAs (miR-133b, miR-148a, miR-122, miR-409-3p) and no differential DNA methylation regions. We conclude that high DNMT3B expression independently associates with adverse outcome in older CN-AML patients. Gene expression analyses suggest that DNMT3B is involved in the modulation of several genes, although the regulatory mechanisms remain to be investigated to devise therapeutic approaches specific for these patients.
Subject(s)
DNA (Cytosine-5-)-Methyltransferases/genetics , Gene Expression Regulation, Leukemic , Leukemia, Myeloid, Acute/diagnosis , Leukemia, Myeloid, Acute/genetics , MicroRNAs/genetics , Age Factors , Aged , Aged, 80 and over , Cytarabine/therapeutic use , DNA Methylation , Daunorubicin/therapeutic use , Female , Gene Expression Profiling , Humans , Induction Chemotherapy , Karyotyping , Leukemia, Myeloid, Acute/drug therapy , Leukemia, Myeloid, Acute/mortality , Male , Microarray Analysis , Middle Aged , Prognosis , Survival Analysis , DNA Methyltransferase 3BSubject(s)
Philadelphia Chromosome , Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics , Adolescent , Bone Marrow Transplantation , Child , Humans , Neoplasm, Residual , Precursor Cell Lymphoblastic Leukemia-Lymphoma/mortality , Precursor Cell Lymphoblastic Leukemia-Lymphoma/therapy , Risk FactorsABSTRACT
Intrachromosomal amplification of chromosome 21 (iAMP21) defines a distinct cytogenetic subgroup of childhood B-cell precursor acute lymphoblastic leukaemia (BCP-ALL). To date, fluorescence in situ hybridisation (FISH), with probes specific for the RUNX1 gene, provides the only reliable detection method (five or more RUNX1 signals per cell). Patients with iAMP21 are older (median age 9 years) with a low white cell count. Previously, we demonstrated a high relapse risk when these patients were treated as standard risk. Recent studies have shown improved outcome on intensive therapy. In view of these treatment implications, accurate identification is essential. Here we have studied the cytogenetics and outcome of 530 iAMP21 patients that highlighted the association of specific secondary chromosomal and genetic changes with iAMP21 to assist in diagnosis, including the gain of chromosome X, loss or deletion of chromosome 7, ETV6 and RB1 deletions. These iAMP21 patients when treated as high risk showed the same improved outcome as those in trial-based studies regardless of the backbone chemotherapy regimen given. This study reinforces the importance of intensified treatment to reduce the risk of relapse in iAMP21 patients. This now well-defined patient subgroup should be recognised by World Health Organisation (WHO) as a distinct entity of BCP-ALL.
Subject(s)
Chromosomes, Human, Pair 21 , Cytogenetic Analysis , Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics , Adolescent , Adult , Child , Child, Preschool , Core Binding Factor Alpha 2 Subunit/genetics , Female , Humans , In Situ Hybridization, Fluorescence , Male , Precursor Cell Lymphoblastic Leukemia-Lymphoma/therapy , Treatment Outcome , Young AdultSubject(s)
Myeloid-Lymphoid Leukemia Protein/genetics , Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics , Translocation, Genetic , Histone-Lysine N-Methyltransferase , Humans , Infant , Precursor Cell Lymphoblastic Leukemia-Lymphoma/diagnosis , Precursor Cell Lymphoblastic Leukemia-Lymphoma/drug therapy , Prognosis , Treatment OutcomeABSTRACT
Acute myeloid leukemia (AML) is hypothesized to be sustained by self-renewing leukemia stem cells (LSCs). Recently, gene expression signatures (GES) from functionally defined AML LSC populations were reported, and expression of a 'core enriched' (CE) GES, representing 44 genes activated in LCSs, conferred shorter survival in cytogenetically normal (CN) AML. The prognostic impact of the CE GES in the context of other molecular markers, including gene mutations and microRNA (miR) expression alterations, is unknown and its clinical utility is unclear. We studied associations of the CE GES with known molecular prognosticators, miR expression profiles, and outcomes in 364 well-characterized CN-AML patients. A high CE score (CE(high)) associated with FLT3-internal tandem duplication, WT1 and RUNX1 mutations, wild-type CEBPA and TET2, and high ERG, BAALC and miR-155 expression. CE(high) patients had a lower complete remission (CR) rate (P=0.003) and shorter disease-free (DFS, P<0.001) and overall survival (OS, P<0.001) than CE(low) patients. These associations persisted in multivariable analyses adjusting for other prognosticators (CR, P=0.02; DFS, P<0.001; and OS, P<0.001). CE(high) status was accompanied by a characteristic miR expression signature. Fifteen miRs were upregulated in both younger and older CE(high) patients, including miRs relevant for stem cell function. Our results support the clinical relevance of LSCs and improve risk stratification in AML.
Subject(s)
Biomarkers, Tumor/genetics , Leukemia, Myeloid, Acute/genetics , MicroRNAs/genetics , Stem Cells/metabolism , Transcriptome , Adolescent , Adult , Aged , Aged, 80 and over , Cytogenetic Analysis , Female , Humans , Leukemia, Myeloid, Acute/mortality , Leukemia, Myeloid, Acute/therapy , Male , Middle Aged , Oligonucleotide Array Sequence Analysis , Prognosis , Remission Induction , Stem Cells/pathology , Survival Rate , Young AdultABSTRACT
Phase-diverse Fresnel coherent diffractive imaging has been shown to reveal the structure and composition of biological specimens with high sensitivity at nanoscale resolution. However, the method has yet to be applied using X-ray illumination with energy in the so-called 'water-window' that lies between the carbon and oxygen K edges. In this range, differences in the strength of the X-ray interaction for protein based biological materials and water is increased. Here we demonstrate a proof-of-principle application of FCDI at an X-ray energy within the water-window to a dehydrated cellular sample composed of red blood cells infected with the trophozoite stage of the malaria parasite, Plasmodium falciparum. Comparison of the results to both optical and electron microscopy shows that the correlative imaging methods that include water-window FCDI will find utility in studying cellular architecture.
Subject(s)
Erythrocytes/parasitology , Erythrocytes/ultrastructure , Image Enhancement/methods , Malaria, Falciparum/pathology , Malaria/pathology , Refractometry/methods , X-Ray Diffraction/methods , Malaria/diagnostic imaging , Malaria/parasitology , Malaria, Falciparum/diagnostic imaging , Malaria, Falciparum/parasitology , Microscopy, Phase-Contrast/methods , Radiography , Reproducibility of Results , Sensitivity and SpecificitySubject(s)
Biomarkers, Tumor/genetics , Leukemia, Myeloid, Acute/genetics , MicroRNAs/genetics , Myeloid-Lymphoid Leukemia Protein/genetics , Tandem Repeat Sequences/genetics , Adult , Aged , Cohort Studies , Cytogenetic Analysis , Female , Histone-Lysine N-Methyltransferase , Humans , Leukemia, Myeloid, Acute/mortality , Male , Middle Aged , Prognosis , Survival Rate , TrisomyABSTRACT
Patients with Down syndrome (DS) and acute lymphoblastic leukemia (ALL) have distinct clinical and biological features. Whereas most DS-ALL cases lack the sentinel cytogenetic lesions that guide risk assignment in childhood ALL, JAK2 mutations and CRLF2 overexpression are highly enriched. To further characterize the unique biology of DS-ALL, we performed genome-wide profiling of 58 DS-ALL and 68 non-DS (NDS) ALL cases by DNA copy number, loss of heterozygosity, gene expression and methylation analyses. We report a novel deletion within the 6p22 histone gene cluster as significantly more frequent in DS-ALL, occurring in 11 DS (22%) and only 2 NDS cases (3.1%) (Fisher's exact P=0.002). Homozygous deletions yielded significantly lower histone expression levels, and were associated with higher methylation levels, distinct spatial localization of methylated promoters and enrichment of highly methylated genes for specific pathways and transcription factor-binding motifs. Gene expression profiling demonstrated heterogeneity of DS-ALL cases overall, with supervised analysis defining a 45-transcript signature associated with CRLF2 overexpression. Further characterization of pathways associated with histone deletions may identify opportunities for novel targeted interventions.
Subject(s)
DNA Methylation , Down Syndrome/genetics , Gene Deletion , Gene Expression Profiling , Histones/genetics , Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics , Base Sequence , DNA Primers , Down Syndrome/complications , Humans , Mutation , Precursor Cell Lymphoblastic Leukemia-Lymphoma/complications , Real-Time Polymerase Chain ReactionSubject(s)
Down Syndrome/genetics , Janus Kinase 1/genetics , Janus Kinase 2/genetics , Janus Kinase 3/genetics , Leukemia, Myeloid/genetics , Mutation , Precursor Cell Lymphoblastic Leukemia-Lymphoma/genetics , Adolescent , Child , Child, Preschool , Down Syndrome/blood , Down Syndrome/mortality , Female , Humans , Leukemia, Myeloid/blood , Leukemia, Myeloid/mortality , Leukocyte Count , Male , Precursor Cell Lymphoblastic Leukemia-Lymphoma/blood , Precursor Cell Lymphoblastic Leukemia-Lymphoma/mortality , PrognosisABSTRACT
An optical diagnostic system is designed and constructed for imaging a free mercury jet interacting with a high intensity proton beam in a pulsed high-field solenoid magnet. The optical imaging system employs a backilluminated, laser shadow photography technique. Object illumination and image capture are transmitted through radiation-hard multimode optical fibers and flexible coherent imaging fibers. A retroreflected illumination design allows the entire passive imaging system to fit inside the bore of the solenoid magnet. A sequence of synchronized short laser light pulses are used to freeze the transient events, and the images are recorded by several high speed charge coupled devices. Quantitative and qualitative data analysis using image processing based on probability approach is described. The characteristics of free mercury jet as a high power target for beam-jet interaction at various levels of the magnetic induction field is reported in this paper.