ALBERT

Description: Chromosomal translocations involving 11q23, resulting in rearrangements of the mixed lineage leukemia gene (MLL, re-named KMT2A) are frequent events in childhood leukemia. MLL is highly promiscuous, with approximately 80 fusions now characterized. Although fluorescence in situ hybridization (FISH) has high specificity for detecting MLL-rearrangements (MLL-r), sensitivity is limited and the translocation partner gene (TPG) cannot always be identified. In contrast, long-distance inverse-PCR (LDI-PCR) permits sequence-specific characterization of MLL breakpoints and the resultant fusion gene, which can then be used for monitoring minimal residual disease (MRD). A limitation of LDI-PCR is the relatively large input of DNA (≈ 1μg) required, with a blast cell percentage of 〉 20-30% to achieve sufficient sensitivity. Next-generation sequencing (NGS) approaches such as RNAseq and whole-genome sequencing (WGS) have the potential to identify multiple gene fusions, however their ability to detect the full spectrum of MLL fusions is limited by coverage, read depth and thereby cost. Such limitations can potentially be overcome with targeted sequencing panels, although their performance against "gold standard" assays, such as LDI-PCR, is unknown. We therefore aimed to assess the ability of a novel, targeted NGS approach for characterizing patient-specific MLLgene rearrangements from low inputs of RNA. The Archer™ FusionPlex™ Heme and Myeloid panels utilize anchored multiplex PCR-based enrichment (AMP-E) to rapidly enrich a number of targets, including MLL, creating libraries for NGS. The NGS libraries are generated using rapid workflows and are compatible with nucleic acid inputs of ≈ 20-200ng. Briefly, double stranded cDNA is generated from patient RNA and subjected to end repair, adenylation and ligation with unique, half-functional adaptors. Following two rounds of nested PCR with primers attached to common sequencing adaptors, the resulting target amplicons become functional and ready for clonal amplification and sequencing. Using AMP-E, we tested 23 paediatric MLL-r samples (15 ALL, 8 AML) that had previously been analyzed by LDI-PCR and were known to harbor 8 different MLL fusions, including MLL-AFF1 (n = 8), -MLLT3 (5), -MLLT10 (3), -ELL (2), -DCP1A (1), -MLLT1 (1), - AFF3 (1), and -TNRC18 (1). A patient sample known to express BCR-ABL1 was used as a positive control and a cytogenetically normal AML sample in remission was used as a negative control in each panel. The median blast count for samples analyzed was 86.1% (range 25%-97%). On average, 100ng of RNA was used per sample, with RIN values ranging from 2.7 to 9.1. Libraries generated using either the Archer™ FusionPlex™ Heme or Myeloid kit were sequenced to sufficient read depths by Illumina MiSeq® and NextSeq®, respectively. Bioinformatic analyses were performed with the Archer™ Analysis 4.1 software. Results were then compared with fusions identified by LDI-PCR. There was high concordance between AMP-E and LDI-PCR, with all MLL fusion genes identified by LDI-PCR also detected by AMP-E. Of note, an ALL sample with t(11;19), unable to be characterized by LDI-PCR, was identified by AMP-E to express MLL-MLLT1. The control BCR-ABL1 fusion was identified in every run and there were no false-negative results. Furthermore, AMP-E identified multiple MLL-fusion transcripts in 56.5% of patients. Analysis of paired diagnosis-relapse samples from an AML patient with MLL-MLLT3demonstrated that the two discrete transcripts present at diagnosis persisted at relapse, with emergence of a third transcript. In summary, detection of MLL gene fusions in acute leukemia using AMP-E is both sensitive and specific. The low RNA requirement, rapid workflow, compatibility with Illumina MiSeq® and cloud-based proprietary analysis software, together with the array of additional fusions and mutations detected by the Archer™ panels, show promise for translation into clinical diagnostic settings. The persistence of discrete transcript isoforms at relapse also highlights the potential for AMP-E to identify multiple, patient-specific MLL fusion transcripts which may have utility in refining prognostication, MRD monitoring and informing future functional studies of MLL-driven leukemogenesis. Disclosures No relevant conflicts of interest to declare.

Description: Cytogenetically normal acute myeloid leukaemia (CN-AML) accounts for approximately 25%-30% of paediatric AML cases and carries a high risk of relapse. Minimal residual disease (MRD) is an essential factor in predicting relapse in acute leukaemia but is difficult to track for many CN-AML patients, due to the lack of a distinct and stable molecular marker. Consequently, new biomarkers are urgently required for MRD monitoring of the disease. Splicing variants, products of another hallmark of human cancers, aberrant splicing, have been shown informative in predicting responses to cancer treatment. Therefore, we characterized splicing events according to different cytogenetic features by targeted RNA-seq and interrogated the use of splicing variants in MRD monitoring of CN-AML. A total of 29 AML samples, collected from 18 de novo paediatric AML patients (median age 5.66 years, range 0.67 - 16.38 years) were analysed for this study. Among the 29 samples, 52% harboured a chromosome translocation, 21% were cytogenetically normal, and 28% showed a complex karyotype (defined as having 3 or more cytogenetic features). 100ng of total RNA, extracted from peripheral blood or bone marrow were subjected to library preparation using the Archer™ FusionPlex™ Heme and Myeloid panels, then sequenced using Illumina MiSeq® or NextSeq®. Novel splicing events and genetic mutations were identified by the Archer Dx analysis software in conjunction with normalisations against the library size and probe numbers. Splicing variants were validated using splicing junction-specific probe assays. Our results revealed 3249 novel splicing events in 29 AML samples. These events were classified into 4 major types (65% intron retention, 10% exon skipping, 8% exon out of order and 8% intra-exon gap), and 9 minor events that were combinations of the major types (9%). The number of splicing events per sample was not associated with the disease status or the presence of the mutations in the spliceosome encoding gene, SF3B1 or U2AF1. Instead, splicing variants were associated with cytogenetic features. Of note, an intron 13 retention of the KMT2A (MLL) gene was identified in all CN-AML samples, and was consistently expressed approximately 100 times higher in the CN-AML compared to other AML cases or remission samples. To assess whether KMT2A intron 13 retention could be a potential molecular MRD marker to monitor CN-AML, we measured its expression in samples from 5 independent CN-AML patients who had available samples for 3 time-points of disease progression. Our results demonstrated, with 95% detection power, that KMT2A intron 13 retention was differentially expressed at different time points (Figure 1). Moreover, the expression level of this splicing variant correlated with disease progression in every patient examined. In conclusion, these data suggest that intron 13 retention of KMT2A may be a novel molecular marker for MRD monitoring in CN-AML. Disclosures No relevant conflicts of interest to declare.

Description: Rearrangements of the mixed lineage leukemia gene (MLL, re-named KMT2A) result in aggressive leukemia. Current risk stratification of MLL-rearranged (MLL-r) leukemia is directed by the fusion partner gene and, increasingly, by minimal residual disease (MRD) assessment after induction therapy. The clinical significance of quantifying fusion transcript levels in leukemia patients is firmly established in chronic myeloid leukemia and acute promyelocytic leukemia but is less well studied in MLL-r patients. Real-time quantitative PCR (RQ-PCR) is the standardized assay for molecular MRD monitoring in patients with MLL-rearranged leukemia. However, this method is less precise when few leukemic cells are present, thus limiting its application for highly sensitive MRD monitoring. Droplet digital PCR (ddPCR) allows for absolute quantification of fusion transcripts when multiple copies of fusion transcripts are present per cell. Therefore, we aimed to evaluate whether determining MLL fusion transcript levels by ddPCR could improve the sensitivity of MRD monitoring in MLL-r leukemia. A total of 44 diagnostic and follow-up samples obtained from paediatric MLL-r leukemia patients (26 ALL, 18 AML) were subjected to targeted next-generation sequencing to obtain patient-specific fusion sequences. MLL fusion transcripts were quantified by ddPCR in a total of 17 samples obtained from 4 paediatric AML patients with MLL fusions involving MLLT3 (n = 3) and MLLT10 (n = 1). Fusion-specific probe assays were designed from each of the patient specific fusion sequences for MRD assessment by ddPCR. To determine the detection limit of this method in quantifying MLL fusion transcripts, two MLL-r AML cell lines (MV4-11 and THP-1), and one MLL-wt cell line (Kasumi-1) were used. MLL fusion transcript level of detection of ddPCR was determined by serially diluting MLL-r cDNA into MLL-wt cDNA (Kasumi-1). Using 20ng of MLL-r cDNA in 200ng diluent as the highest concentration, a 10-fold dilution series was performed to make concentrations ranging from 10−2 to 10−7. Each ddPCR reaction mixture contained 11ul of cDNA mix as template with 1X Supermix no dUTP (Bio-Rad), 500 nM of both F/R primers and 250 nM of 5'-FAM labelled probe (IDT). Droplets were generated using a QX200 Droplet Generator (Bio-Rad). A general thermal cycler protocol with annealing at 61°C for 1 minute was performed and positive fluorescence droplets were read using QX200 Droplet Reader (Bio-Rad). MRD of patient samples, derived from ddPCR, was then compared to MRD derived from DNA-based RQ-PCR, following the guidelines established by the EuroMRD group. Our ddPCR method showed high reliability and sensitivity, with the detection limit determined to be 10-5 for a cell line with low MLL fusion transcript expression (THP-1), and 10-6 for a cell line with high MLL fusion transcript expression (MV4-11). Comparison of results obtained by RQ- PCR and ddPCR in a total of 17 diagnostic and follow-up samples from 4 AML patients showed excellent/good concordance between methods for 13 samples with moderate MRD levels. The 4 samples with low levels of MRD (10-4 to 10-5) below the quantitative range as defined by EuroMRD for RQ-PCR were all detectable by ddPCR, highlighting that ddPCR could provide robust and highly sensitive MRD assays compared to the standardized RQ-PCR assays. In conclusion, ddPCR is a promising technique that can reproducibly and reliably quantify MLL-r transcripts for MRD monitoring of MLL-r leukemia. Highly sensitive and robust molecular MRD monitoring by ddPCR holds promise for improving response-based therapeutic stratification and prediction of molecular relapse before overt hematological relapse. Disclosures No relevant conflicts of interest to declare.

Description: Follicular Lymphoma (FL) is the most common indolent Non-Hodgkin Lymphoma. Despite generally favorable survival outcomes, 20% of FL patients experience 'Progression of Disease within 24 months' (POD24) and subsequently have poor long-term overall survival (OS) (Casulo, JCO 2015). Unfortunately, POD24 has limited clinical value because it cannot guide up-front clinical decisions. Accurate pre-therapy prognosticators are vital for clinical trial design and are also increasingly being mandated by funding agencies for stratification of patients to emerging front-line treatments. The new 'state-of-the-art' prognosticators 'm7-FLIPI' and POD24-PI' (Pastore, Lancet Oncol 2015; Jurinovic, Blood 2016) supplement clinical parameters with genetic mutational status. However, their applicability to population based cohorts including early-stage and asymptomatic patients remains unknown. Furthermore, there is significant heterogeneity of outcome within these prognostic groupings. The established biological and prognostic importance of the tumor microenvironment (TME) in FL suggests that prognosis would be enhanced by incorporating information on host immunity (Scott, Nat Rev Can 2014). Forty-five pre-treatment FL biopsies were categorized into 'hot' or 'cold' immune nodes by multiplex immunofluorescent imaging and respectively characterized by concordant high or low expression of multiple immune effector and checkpoint-associated proteins. (Fig 1A). Consistent with these findings, gene expression using the Nanostring platform showed that immune effectors (CD4/CD8/TNFa/CD137/CD56) positively correlated with immune checkpoints (PD-1/PD-L1/PD-L2/TIM3/LAG3/CD163/CD68) indicative of an adaptive immune response. Additionally, high-throughput unbiased TCRb sequencing showed the intratumoral TCR repertoire was more clonal in 'hot' compared to 'cold' FL samples (p=0.024), indicative of a skewed T-cell immune response (Fig 1B). We then applied these findings to an independent population-based cohort of 175 cases of FL from the rituximab era with long-term follow-up (median ~7 years), including advanced (n=137) and localized cases (n=38). The aims were to: a) identify new targetable immune parameters of prognostic importance in the rituximab-era; and b) compare and contrast these with published prognostic tools: FLIPI, FLIPI-2, m7-FLIPI, POD24-PI and 'immune survival score' ('ISS', Dave, NEJM 2004). OS was not only inferior in those experiencing POD24 (HR 4.88, p2-fold increase in 5-year patient health costs. Hence, POD24, as well as FFS and TT2T were therefore chosen as the primary outcome measures. M7 mutation frequencies were similar to those previously published (Pastore, Lancet Oncol 2015). However, the prognostic utility of the m7-FLIPI could not be demonstrated, whereas the FLIPI, FLIPI-2, and POD24-PI retained their prognostic value. The POD24-PI was most predictive of FFS (p