Large collections of genome-wide data can facilitate the characterization of disease states and subtypes, permitting pan-cancer analysis of molecular phenotypes and evaluation of disease context for new therapeutic approaches. We analyzed 9,544 transcriptomes from more than 30 hematologic malignancies, normal blood cell types, and cell lines, and showed that disease types could be stratified in a data-driven manner. We then identified cluster-specific pathway activity, new biomarkers, and in silico drug target prioritization through interrogation of drug target databases. Using known vulnerabilities and available drug screens, we highlighted the importance of integrating molecular phenotype with drug target expression for in silico prediction of drug responsiveness. Our analysis implicated BCL2 expression level as an important indicator of venetoclax responsiveness and provided a rationale for its targeting in specific leukemia subtypes and multiple myeloma, linked several polycomb group proteins that could be targeted by small molecules (SFMBT1, CBX7, and EZH1) with chronic lymphocytic leukemia, and supported CDK6 as a disease-specific target in acute myeloid leukemia. Through integration with proteomics data, we characterized target protein expression for pre-B leukemia immunotherapy candidates, including DPEP1. These molecular data can be explored using our publicly available interactive resource, Hemap, for expediting therapeutic innovations in hematologic malignancies. Significance: This study describes a data resource for researching derailed cellular pathways and candidate drug targets across hematologic malignancies.

Background Tight regulatory loops orchestrate commitment to B cell fate within bone marrow. Genetic lesions in this gene regulatory network underlie the emergence of the most common childhood cancer, acute lymphoblastic leukemia (ALL). The initial genetic hits, including the common translocation that fuses ETV6 and RUNX1 genes, lead to arrested cell differentiation. Here, we aimed to characterize transcription factor activities along the B-lineage differentiation trajectory as a reference to characterize the aberrant cell states present in leukemic bone marrow, and to identify those transcription factors that maintain cancer-specific cell states for more precise therapeutic intervention. Methods We compared normal B-lineage differentiation and in vivo leukemic cell states using single cell RNA-sequencing (scRNA-seq) and several complementary genomics profiles. Based on statistical tools for scRNA-seq, we benchmarked a workflow to resolve transcription factor activities and gene expression distribution changes in healthy bone marrow lymphoid cell states. We compared these to ALL bone marrow at diagnosis and in vivo during chemotherapy, focusing on leukemias carrying the ETV6-RUNX1 fusion. Results We show that lymphoid cell transcription factor activities uncovered from bone marrow scRNA-seq have high correspondence with independent ATAC- and ChIP-seq data. Using this comprehensive reference for regulatory factors coordinating B-lineage differentiation, our analysis of ETV6-RUNX1-positive ALL cases revealed elevated activity of multiple ETS-transcription factors in leukemic cells states, including the leukemia genome-wide association study hit ELK3. The accompanying gene expression changes associated with natural killer cell inactivation and depletion in the leukemic immune microenvironment. Moreover, our results suggest that the abundance of G1 cell cycle state at diagnosis and lack of differentiation-associated regulatory network changes during induction chemotherapy represent features of chemoresistance. To target the leukemic regulatory program and thereby overcome treatment resistance, we show that inhibition of ETS-transcription factors reduced cell viability and resolved pathways contributing to this using scRNA-seq. Conclusions Our data provide a detailed picture of the transcription factor activities characterizing both normal B-lineage differentiation and those acquired in leukemic bone marrow and provide a rational basis for new treatment strategies targeting the immune microenvironment and the active regulatory network in leukemia.

Acute lymphoblastic leukemia is marked by aberrant transcriptional features that alter cell differentiation, self-renewal, and proliferative features. We sought to identify the transcription factors exhibiting altered and subtype-specific expression patterns in BALL and report here that SOX11, a developmental and neuronal transcription factor, is aberrantly expressed in the ETV6-RUNX1 and TCF3-PBX1 subtypes of acute B-cell leukemias. We show that a high expression of SOX11 leads to alterations of gene expression that are typically associated with cell adhesion, migration, and differentiation. A high expression is associated with DNA hypomethylation at the SOX11 locus and a favorable outcome. The results indicate that SOX11 expression marks a group of patients with good outcomes and thereby prompts further study of its use as a biomarker. SOX11 is a transcription factor (TF) encoded by the SOX11 gene located in chromosome 2p25 1. It is a member of the SoxC (sex-determining region Y-related HMG box) group of genes and consists of two functional domains-the N-terminal DNA-binding and the C-terminal transactivation domains 2,3. Other SoxC family members include SOX4 and SOX12. Of these, SOX4 is a crucial TF in B lymphopoiesis and is expressed in the Band T-cell lineages 2,4,5. SOX11 is normally expressed in the developing central nervous system of the embryo, in keratinocytes, and in some other epithelial tissues 1,6-8. It is also expressed in ovarian and breast cancer, in which both tumor suppressor and oncogenic functions have been suggested 9,10. A knockout mouse model revealed the vital role of SOX11 during embryonic development, as SOX11-deficient mice died after birth likely from multiple heart defects, asplenia, and organ hypoplasia in the lungs, stomach, and pancreas 11. SOX11 deletions and mutations are associated with neurodevelopmental disorders 12. Previous studies have shown that SOX11 mRNA and nuclear protein expression is a specific marker for conventional but not indolent mantle cell lymphoma (MCL) 8,13-15. In MCL, SOX11 has been associated with either increased or reduced cell proliferation 16-23 and either good or bad prognosis 24-27. In a cohort of 50 adult acute myeloid leukemia (AML) patients, a high SOX11 expression was associated with FLT/ITD and NPM1 mutations and a shortened disease-free survival 28. There is other evidence linking SOX11 with B-lineage malignancies. Dictor et al. (2009) reported that the nuclear expression of SOX11 was found in eight cases of B-lymphoblastic neoplasias 29. Another study reported the strong nuclear expression of SOX11 in a single B-cell and five T-cell lymphoblastic lymphoma/leukemias 13. Vegliante et al. (2011) demonstrated the increased expression of SOX11 mRNA in ETV6-RUNX1 (E/R) and