Mai, Ming

Abstract Leukemia stem cells (LSCs) are linked to relapse in acute myeloid leukemia (AML). The LSC17 gene expression score robustly captures LSC stemness properties in AML and can be used to predict survival outcomes and response to therapy, enabling risk-adapted, upfront treatment approaches. The LSC17 score was developed and validated in a research setting. To enable widespread use of the LSC17 score in clinical decision making, we established a laboratory-developed test (LDT) for the LSC17 score that can be deployed broadly in clinical molecular diagnostic laboratories. We extensively validated the LSC17 LDT in a College of American Pathologists/Clinical Laboratory Improvements Act (CAP/CLIA)-certified laboratory, determining specimen requirements, a synthetic control, and performance parameters for the assay. Importantly, we correlated values from the LSC17 LDT to clinical outcome in a reference cohort of patients with AML, establishing a median assay value that can be used for clinical risk stratification of individual patients with newly diagnosed AML. The assay was established in a second independent CAP/CLIA-certified laboratory, and its technical performance was validated using an independent cohort of patient samples, demonstrating that the LSC17 LDT can be readily implemented in other settings. This study enables the clinical use of the LSC17 score for upfront risk-adapted management of patients with AML.

Abstract Objectives Pure erythroid leukemia (PEL) is exceptionally rare in the pediatric setting. Four pediatric PEL cases with t(1;16)(p31;q24) NFIA-CBFA2T3 were reported previously. We present a case of an infant with PEL presenting with erythroblastic sarcoma and harboring a novel t(1;8)(p31.3;q21.3) NFIA-RUNX1T1 fusion detected by RNA sequencing and conventional karyotype. Methods Bone marrow (BM) and abdominal mass biopsies from the patient were evaluated with extensive immunohistochemical, flow cytometric, cytogenetic, and molecular studies. Results The patient was a female infant who presented between 2 and 5 months of age with cytopenias and an enlarging abdominal mass. Blasts in the BM and abdominal mass expressed CD71 and CD117 with focal expression of CD43, E-cadherin, epithelial membrane antigen, and hemoglobin A. They were negative for additional myeloid, lymphoid, and nonhematolymphoid markers. These findings were most consistent with PEL and erythroblastic sarcoma. RNA sequencing revealed the novel NFIA-RUNX1T1 fusion. Conclusions Along with the previously reported PELs with NFIA-CBFA2T3 fusions, we describe a subset of PELs that occur in children, that frequently display extramedullary disease, and that harbor rearrangements of NFIA with core binding factor genes. We hypothesize that, together, these cases represent a rare but distinct clinicopathologic group of pediatric PELs with recurrent genetic abnormality.

Abstract Introduction: The BCR-ABL1 genomic fusion event in chronic myelogenous and B-lymphoblastic leukemias (CML, ALL) commonly produces the major chimeric transcript variants e13 (or e14)-a2 or e1-a2, which are translated respectively to p210 and p190 bcr-abl1 oncoproteins. However, substantial transcript heterogeneity is present including alternative splice forms in a given leukemia, as well as rare alternative chimeric transcript types. Relatively little is known regarding the molecular response of alternative transcript variants of BCR-ABL1 during tyrosine kinase inhibition (TKI) therapy, in part because of the lack of effective disease burden monitoring methods. We present an approach to detection of the various BCR-ABL1 mRNA types using a multiplex quantitative RT-PCR (QRT-PCR) methodology. This technique enables diagnosis and molecular tracking of unusual BCR-ABL1 variants and can improve our understanding of how these uncommon leukemias behave in response to TKI therapies. Furthermore, the method is more generally applicable for simultaneous QRT-PCR detection and measurement of different mRNA species. Methods: Patient samples for diagnostic evaluation were obtained and total RNA extraction was performed using the Qiagen RNeasy Mini Kit (Qiagen USA, Valencia, CA). Reverse transcription was done using Multiscribe Reverse Transcriptase (Life Technologies, Grand Island, NY). Eleven fluorescent primer and probe mixes were designed (e1a2-FAM, e6a2-Cyc 5, e13a2-FAM, e14a2-FAM, e19a2-Cyc 5, e1a3-FAM, e12a3-Cyc 5, e13a3-FAM, e14a3-FAM, e19a3-Cyc 5, and Gusb reference control-HEX). 10 uL reactions were performed (95 C X 10 min, 45 cycles of 95 C X 10 sec and 60 C X 30 sec) using four multiplex wells per sample. Double strand oligonucleotides (oligos) for each target type were synthesized (IDT, Coralville IA) and diluted in a range of 106, 105, 104, 103, 100, 10, 1 and 0.1 copies/uL. Results of the new multiplex QRT-PCR assay were compared against our standard method of qualitative multiplex RT-PCR and fluorescent probe hybridization. Results: Results for the target BCR-ABL1 oligo controls are summarized in the table. The data show a wide dynamic range of detection with reproducible copy number detection at very low level. All PCR targets had excellent correlation coefficients (R2) and good to excellent PCR efficiency. Specificity was excellent, except for some cross-reactivity of A3 templates. This minor interference did not detract from assay performance or interpretation. Thirty-two patient samples were evaluated using the multiplex QRT-PCR assay and the current lab method. For 13 known BCR-ABL1 negative and 19 positive patient samples, concordance/accuracy and specificity were 100%. Furthermore, relative quantification of transcript abundance was obtained by the multiplex QRT-PCR approach, enabling distinction between diagnostic and post-treatment mRNA levels. Alternative splicing events producing additional transcripts (e1-a2) were resolved in the same specimen and always quantified well below the primary transcript level. Table 1.Transcript TypeDynamic Range(log)Sensitivity(copies/uL)Specificity(%)R2Efficiencye1-a2 (p190)6101000.971.74e6-a2 (p195)711000.951.76e13-a2/ e14-a2 (p210)61010011.99e19-a2 (p230)610E19A3 also detected0.991.89e1-a3 (p190)6101000.981.90e13-a3/ e14-a3 (p210)610E12A3 also detected11.99e12-a3410001000.991.78e19-a3 (p230)61010011.95 Conclusions: We demonstrate a powerful and relatively simple method for concurrent detection and quantitative measurement of multiple common and unusual alternative BCR-ABL1 mRNA transcripts. The results of this study provide a basis for more detailed monitoring of molecular disease levels during TKI therapy in leukemic patients with rare BCR-ABL1 types, and in turn, potentially enhance the ability to more optimally individualize clinical management for these patients. The platform is flexible and novel BCR-ABL1 transcript types can also be incorporated relatively easily. A similar strategy is applicable to the detection of chimeric mRNA species in other types of leukemias. Our approach can also be used to evaluate targeted RNA expression profiles of other prognostic or theranostic tumor markers in individual patients. Disclosures No relevant conflicts of interest to declare.

Chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL) is a low-grade B-cell neoplasm and ∼2% to 9% patients develop an aggressive lymphoma, most commonly diffuse large B-cell lymphoma (Richter transformation, DLBCL-RT). Programmed death-1 (PD-1) pathway plays a crucial role in tumor host immunity evasion and its blockade has emerged as an effective anti-cancer immunotherapy. PD-L1 and PD-1 expression has shown predictive value in anti-PD cancer immunotherapy; however, it has not been well documented in CLL/SLL and DLBCL-RT. We evaluated PD-1 and PD-L1 expression by immunohistochemistry in 39 CLL/SLL, 15 DLBCL-RT, and 26 other DLBCL. In CLL/SLL, neoplastic B-cell PD-1 expression was weak and restricted to prolymphocytes/paraimmunoblasts within proliferation centers (PCs) and accentuated PCs of all sizes. Neoplastic B-cell PD-1 expression was highly prevalent and demonstrated increased intensity in DLBCL-RT, but in contrast was only rarely seen in other DLBCL (12/15 vs. 1/26; P<0.0001). An excellent correlation (90% concordance) was observed between neoplastic B-cell PD-1 immunohistochemistry positivity and molecularly defined CLL/SLL clonal relatedness in DLBCL-RT. PD-L1 expression was observed on the neoplastic B cells in rare DLBCL-RT and other DLBCL cases (1/15 vs. 1/26; P>0.05) as well as background histiocytes and dendritic cells. Overall survival of DLBCL-RT was significantly inferior to that of the other DLBCL (median, 16.9 vs. 106.1 mo; P=0.002). Our findings suggest a biological continuum from prolymphocytes/paraimmunoblasts in CLL/SLL PCs to the neoplastic B-cells in DLBCL-RT. The characteristic PD-1 expression in DLBCL-RT makes it a potential surrogate marker for determining clonal relatedness to CLL/SLL, which may have important prognostic and therapeutic implications.