Abstract 3005: Whole-genome sequencing identified novel non-coding mutations causal of oncogene activation in T-cell acute lymphoblastic leukemia

There is growing evidence that non-coding sequences in human genome often function as transcriptional regulatory elements of protein-coding genes. In fact, germline polymorphisms and somatically acquired mutations within regulatory DNA can profoundly alter chromatin structure and modify gene transcription, directly contributing to tumorigenesis. However, there is a paucity of unbiased genome-wide characterization of somatic non-coding mutations in cancer. Using T-cell acute lymphoblastic leukemia (T-ALL) as a model disease, we herein report a systematic interrogation of driver non-coding genomic alterations by paired whole-genome and transcriptome sequencing of 31 children with T-ALL. To identify non-coding mutations with potential regulatory impact in a genome-wide fashion, our analytical pipeline consisted of 3 approaches: 1) the “hotspot analysis” for recurring mutations at the nearby positions, 2) the “regional recurrence analysis” for predefined regulatory regions with significant enrichment of non-coding mutations, 3) the “transcriptional factor analysis” for mutations that potentially result in gain/loss of transcription factor binding sites and alter expression of adjacent genes. Remarkably, T-ALL oncogenes LMO1 and TAL1 emerged as loci with the most significant recurring non-coding mutations. At the LMO1 locus, 3 patients (9.7%) showed an identical single-nucleotide mutation proximal to the transcription start site of the long isoform of LMO1. This recurring mutation resulted in the gain of a canonical Myb binding site (AACGG) and ~120-fold increase in LMO1 transcription compared to patients with wildtype genotype. TAL1 overexpression was observed in 15 patients, of whom 11 had intrachromosomal rearrangement (STIL-TAL1 fusion). The remaining 4 patients had somatic insertion that created a MYB-mediated super enhancer, consistent with recent reports. LMO1 enhancer mutation was further confirmed in an independent validation cohort (N=26), in which we additionally identified a novel intrachromosomal rearrangement between MED17 and LMO1 resulting in transcriptional activation of the latter. In a panel of T-ALL cell lines, LMO1 enhancer mutation was again associated with dramatic overexpression of LMO1, an active enhancer histone mark (H3K27ac), Dnase hypersensitivity, and allele-specific binding of MYB. Interestingly, we also observed robust binding of TAL1, CREBBP, RUNX1, ETS1, ELF1 and RNA Polymerase II at this site. Reporter gene assay confirmed the MYB-mediated transcription activation effects of this LMO1 enhancer mutation in vitro. In this genome-wide investigation of non-coding mutations in T-ALL, we identified novel enhancer mutations with drastic effects on oncogene activation. Our findings expand the understanding of how genomic alterations in regulatory DNA contribute to cancer pathogenesis.

Citation Format: Maoxiang Qian, Shaoyan Hu, Hui Zhang, Yu Guo, Jin Yang, Xujie Zhao, Lin Wan, Jun Lu, Jian Pan, Meimei Chang, Shirley K. Kham, Yong Cheng, Chunliang Li, Allen E. Yeoh, Anders Skanderup, Jun J. Yang. Whole-genome sequencing identified novel non-coding mutations causal of oncogene activation in T-cell acute lymphoblastic leukemia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3005. doi:10.1158/1538-7445.AM2017-3005

Clinical utility of microarray-based gene expression profiling in the diagnosis and subclassification of leukemia: report from the International Microarray Innovations in Leukemia Study Group

PURPOSE

The Microarray Innovations in Leukemia study assessed the clinical utility of gene expression profiling as a single test to subtype leukemias into conventional categories of myeloid and lymphoid malignancies.

METHODS

The investigation was performed in 11 laboratories across three continents and included 3,334 patients. An exploratory retrospective stage I study was designed for biomarker discovery and generated whole-genome expression profiles from 2,143 patients with leukemias and myelodysplastic syndromes. The gene expression profiling-based diagnostic accuracy was further validated in a prospective second study stage of an independent cohort of 1,191 patients.

RESULTS

On the basis of 2,096 samples, the stage I study achieved 92.2% classification accuracy for all 18 distinct classes investigated (median specificity of 99.7%). In a second cohort of 1,152 prospectively collected patients, a classification scheme reached 95.6% median sensitivity and 99.8% median specificity for 14 standard subtypes of acute leukemia (eight acute lymphoblastic leukemia and six acute myeloid leukemia classes, n = 693). In 29 (57%) of 51 discrepant cases, the microarray results had outperformed routine diagnostic methods.

CONCLUSION

Gene expression profiling is a robust technology for the diagnosis of hematologic malignancies with high accuracy. It may complement current diagnostic algorithms and could offer a reliable platform for patients who lack access to today's state-of-the-art diagnostic work-up. Our comprehensive gene expression data set will be submitted to the public domain to foster research focusing on the molecular understanding of leukemias.

An international standardization programme towards the application of gene expression profiling in routine leukaemia diagnostics: the Microarray Innovations in LEukemia study prephase

Gene expression profiling has the potential to enhance current methods for the diagnosis of haematological malignancies. Here, we present data on 204 analyses from an international standardization programme that was conducted in 11 laboratories as a prephase to the Microarray Innovations in LEukemia (MILE) study. Each laboratory prepared two cell line samples, together with three replicate leukaemia patient lysates in two distinct stages: (i) a 5-d course of protocol training, and (ii) independent proficiency testing. Unsupervised, supervised, and r² correlation analyses demonstrated that microarray analysis can be performed with remarkably high intra-laboratory reproducibility and with comparable quality and reliability.

Rapid detection of prognostically important childhood acute lymphoblastic leukemia chimeric transcripts using multiplex SYBR green real-time reverse transcription PCR

Childhood acute lymphoblastic leukaemia (ALL) is a heterogenous disease in which oncogene fusion transcripts are known to influence the biological behaviour of the different ALL subtypes. Screening for prognostically important transcripts is an important diagnostic step in treatment stratification and prognostication of affected patients. We describe a SYBR-Green real-time multiplex PCR assay to screen for transcripts TEL-AML1, E2A-PBX1, MLL-AF4, and the two breakpoints of BCR-ABL (p190 and p210). Validation of the assay was based on conventional karyotyping results. This new assay provides a rapid, sensitive, and accurate detection method for prognostically important transcripts in childhood ALL.

A molecular epidemiologic study of thalassemia using newborns' cord blood in a multiracial Asian population in Singapore: results and recommendations for a population screening program

DNA technology provides a new avenue to perform neonatal screening tests for single-gene diseases in populations of high frequency. Thalassemia is one of the high-frequency single-gene disorders affecting Singapore and many countries in the malaria belt. The authors explored the feasibility of using PCR-based diagnostic screening on 1,116 unselected sequential cord blood samples for neonatal screening. The cord blood samples were screened for the most common reported alpha- and beta-thalassemia mutations in each ethnic group (Chinese, Malays, and Indians) in a multiracial population. The carrier frequency for alpha-thalassemia mutations was about 6.4% in the Chinese (alpha deletions = 3.9%, alpha deletions = 2.5%), 4.8% in Malays, and 5.2% in Indians. Only alpha deletions were observed in the Chinese. The carrier frequency for beta-thalassemia mutations was 2.7% in the Chinese, 6.3% in Malays, and 0.7% in Indians. Extrapolating to the population distribution of Singapore, the authors found a higher overall expected carrier frequency for alpha- and beta-thalassemia mutations of 9% compared with a previous population study of 6% by phenotype. The highly accurate results make this molecular epidemiologic screening an ideal method to screen for and prevent severe thalassemia in high-risk populations.

Alterations of the AML1 transcription factor in human leukemia

The identification of clonal chromosomal translocations in human leukemias provided one of the first insights into the underlying pathogenesis of this clinically heterogeneous disease. Over the last decade a large number of these chromosomal rearrangements have been molecularly cloned and the involved genes identified. A surprising finding that has emerged from this work is that many of these chromosomal alterations target the genes encoding the AML1/CBFbeta transcription factor complex, a critical regulator of normal hematopoiesis. In this review, we summarize our present understanding of the mechanisms through which alterations of AML1/CBFbeta contribute to leukemogenesis.

Pre-existing antidepressant medication and the outcome of group cognitive-behavioural therapy

OBJECTIVE

This study aimed to investigate the impact of pre-existing medication on the outcome of group cognitive-behavioural therapy (CBT) in the treatment of patients with depression.

METHOD

Of the 71 patients diagnosed with major depression who participated in group CBT, 25 were on medication (CBT-M) and 46 were unmedicated (CBT). The patients received 12 sessions of group CBT over a 3-month period. The dependent measures used were the Beck Depression Inventory, Zung Self-Rating Depression Scale, Automatic Thoughts Questionnaire, Hopelessness Scale, Dysfunctional Attitude Scale, Daily Activity Rating Scale and Daily Mood Rating Scale.

RESULTS

Both the CBT and CBT-M groups showed statistically significant improvement in depression scores and cognitive process measures. However, the rate of improvement for both groups on these measures did not differ.

CONCLUSION

The study indicated that pre-existing antidepressant medication did not enhance or detract from the positive treatment outcome of depressed patients receiving a group CBT treatment.

Autologous bone marrow transplantation in a child with acute promyelocytic leukemia in second remission

Acute myeloid leukemia (AML) comprises 15%-20% of childhood acute leukemia cases. The long-term disease free survival (DFS) in childhood AML is poor with standard chemotherapy alone. Early intensive chemotherapy is generally regarded to be necessary for achieving high complete remission (CR) rates. Recent experience has shown that incorporation of early intensification with high-dose melphalan conditioning and autologous bone marrow transplantation (BMT) during the first remission significantly improves long-term DFS in children with AML. In this article, we report the use of autologous BMT for treatment of a three-and-half year old child with acute promyelocytic leukemia (APL or M3) in second remission. The patient was conditioned with high-dose melphalan of 180 mg/kg prior to bone marrow reinfusion. A total of 4.0 x 10(7)/kg mononuclear cells and 1.07 x 10(5)/kg granulomonocytic colony forming units (CFU-GM) were infused. Haematopoietic stem cells were enriched by almost 20-fold after the separation and cryopreservation procedures. Haematological recovery was achieved four-and-a-half weeks post-BMT. She has remained in complete remission 18 months after transplantation. Our experience in this patient indicates that this procedure can be used in second remission and it may provide a better alternative for the management of childhood AML in Singapore.

An evaluation of minimal residual disease in childhood acute lymphoblastic leukaemia

Evaluation of minimal residual disease (MRD) in acute lymphoblastic leukaemia (ALL) is important for disease prognostication and early relapse detection. In this study, the rearranged third complementarity-determining-region (CDR-III) of immunoglobulin heavy chain (IgH) was used as a surrogate tumour marker for MRD evaluation. DNA obtained from marrows at diagnosis was amplified by the polymerase chain reaction (PCR) using a pair of consensus primers. After 2 rounds of DNA amplification and polyacrylamide gel separation, the nucleotide sequences of 87.5% (21/24) consecutive children with B-lineage ALL were obtained by automated sequencing. There were between 1-4 rearrangements per patient. Although the J5 and J6 joining regions were preferentially used, the rearranged sequences were unique for all 25 sequences obtained. Oligoprobes to the DNJ region were constructed and quantitation in 7 patients showed a detection sensitivity of 1 leukaemic cell in 10(4) to 10(5) normal cells compared to 3 in 100 using conventional morphological criteria. Serial bone marrow showed progressive decrease in the quantity of leukaemic cells, and no leukaemic sequences were detected during cessation of therapy in 4/7 patients. One patient with detectable MRD, absconded treatment and eventually relapsed. These results are consistent with the need to eliminate the leukaemic clones below MRD detection levels before the end of therapy at 2 years. In conclusion, this study describes a novel, simplified and sensitive method of MRD detection in childhood leukaemia.