Interactions between acute myeloid leukemia (AML) and the bone marrow microenvironment (BMME) are critical to leukemia progression and chemoresistance. In the solid tumor microenvironment, altered metabolite levels contribute to cancer progression. We performed a metabolomic analysis of bone marrow serum from patients with AML, revealing increased metabolites compared to age-and sex-matched controls. The most highly elevated metabolite in the AML BMME was lactate. Lactate signaling in solid tumors induces immunosuppressive tumor-associated macrophages and correlates with poor prognosis. This has not yet been studied in the leukemic BMME. Herein, we describe the role of lactate in the polarization of leukemia-associated macrophages (LAMs). Using a murine AML model of blast crisis chronic myelogenous leukemia, we characterize the suppressive phenotype of LAMs through surface markers, transcriptomics, and cytokine profiling. Mice genetically lacking GPR81, the extracellular lactate receptor, were then used to demonstrate GPR81 signaling as a mechanism of both the polarization of LAMs and the direct support of leukemia cells. Furthermore, elevated lactate diminished the function of hematopoietic progenitors and reduced stromal support for normal hematopoiesis. We report microenvironmental lactate as a mechanism of AML-induced immunosuppression and leukemic progression, thus identifying GPR81 signaling as an exciting and novel therapeutic target for treating this devastating disease.

Inflammation-driven tumor implantation, such as port-site metastasis (PSM) following laparoscopic gynecologic surgery and peritoneal seeding during post-surgical recurrence, represents an aggressive clinical problem that remains poorly understood and lacks targeted therapies. To address this, we developed a non-surgical Mesothelium-Inflammation/Injury-Metastasis (MIM) model and investigated the role of the IL-1β/IL1R1/MYD88/IRAK1/4 axis and NLRP3 in epithelial ovarian cancer (EOC) seeding at inflamed or injured sites. This model created by a needle injury recapitulates inflammation-driven peritoneal seeding and mimics PSM and inflammation associated dissemination in peritoneum during recurrence. Seeding was dependent on Il1r1 but not Nlrp3, despite its role in regulating IL-1β production, as Il1ra-/- and Nlrp3-/- mice phenocopied wild-type C57BL/6 mice. Given the limited antitumor efficacy of IL-1β-targeting agents such as Anakinra and Canakinumab, we focused on IRAK4 as a therapeutic target. IRAK4 knockdown significantly prolonged survival, reduced tumor cell adhesion, downregulated E-cadherin and Wnt4, and induced S-phase/mitotic arrest. This led to the development of UR241-2, a small-molecule IRAK4 inhibitor, which was validated through molecular simulations, hotspot analysis, nanoBRET, global kinome profiling, and NF-κβ reporter assays. UR241-2 inhibited NF-κβ nuclear translocation and blocked IL-1β-induced IRAK4 phosphorylation. UR241-2 exhibited favorable drug-like properties, including absence of CYP or hERG inhibition, and acceptable CaCo-2 permeability, plasma protein binding, microsomal stability, and pharmacokinetics. In vivo, UR241-2 reduced SKOV3 xenograft growth, suppressed mesothelial seeding, and increased MHC-II+ macrophages and activated neutrophils in syngeneic high-grade epithelial ovarian HGS3 tumors. RNA-seq revealed enrichment of neutrophil activation signatures and suppression of extracellular matrix (ECM) gene programs. Together, these findings establish a role for the IL-1β/IL1R1/IRAK4 axis in inflammation-driven PSM and peritoneal seeding and ECM regulation in EOC, and demonstrate that IRAK4 inhibition activates antitumor immune responses, providing a therapeutic strategy to block metastatic seeding and improve tumor control.

There is a continued need for identification of novel disease drivers of acute myeloid leukemia (AML) as many patients experience relapse and have poor clinical outcomes. Using genomic analyses of a study dataset of paired diagnosis and relapse specimens (n = 59), we identified recurrent downregulation of CCAAT-enhancer binding protein delta (CEBPD) expression at relapse and inferred CEBPD as one of the key regulators of gene transcription in a subset of relapse patients. Three independent public datasets validated downregulation of CEBPD expression at relapse and predicted it as a candidate tumor suppressor gene in AML. To evaluate CEBPD’s tumor suppressor function, we performed complementary loss- and gain-of-function experiments in human AML cell lines OCI-AML2 and OCI-AML5. Consistent with the prediction, knockdown of CEBPD expression led to activation of MAPK signaling and upregulation of downstream effectors cyclin D1 and TNFα expression with concomitant increase in leukemic growth, while CEBPD overexpression resulted in induction of myeloid differentiation marker CD14 expression in the cell lines. Consistent with prior reports, our integrative genomic analyses and azacytidine treatment experiments further suggest a role for DNA methylation in downregulation of CEBPD expression during AML progression. Collectively, our results provide direct functional evidence for a tumor suppressor function of CEBPD in human cell lines and support prior studies implicating its epigenetic silencing in human AML.

Epithelial ovarian cancer (EOC) cells seed at mesothelial inflammation or injury sites. Lack of animal models recapitulating tumor cells seeding at inflamed sites in EOC hinders mechanistic studies and therapy developments. Here, we developed a non-surgical MIM (Mesothelium Inflammation/Injury Metastasis) model that recapitulates tumor cell seeding at inflamed sites. This model captures temporal changes in tumor immune microenvironment and tumor growth allowing for deeper mechanistic and preclinical therapeutic studies of EOC in-vivo. We show here that HGS-3 high-grade murine serous EOC cells seed at needle-induced injury sites in mesothelium/peritoneal wall, forming tumors both internally and protruding outward. Using MIM model, we found that deletion of IL1R1 in mice reduced EOC cell seeding at mesothelium injury/inflamed site in WT but not IL1ra-deficient mice. Treatment of MiM mice with a novel IRAK4 inhibitor we recently developed (UR241-2) revealed an essential role for IRAK4 signaling downstream IL-1β/IL-1R1 in fostering an anti-tumor inflammatory environment, and reduced tumor burden. We conclude that IRAK4 inhibitors can be more effective than IL-1/IL-1R1 targeting agents to control metastasis and peritoneal tumors, an unmet medical need in EOC recurrence. Downregulation of extracellular matrix (ECM), upregulation of neutrophil activation genes, reduced cell adhesion and migration exhibit how UR241-2 corrects ECM and immune disorders in EOC, making it less conducive to metastasis and tumorigenesis. ### Competing Interest Statement RKS, RGM. LMC and MWB are listed as the inventors on the patents related to UR241-2. Empire Discovery Institute (EDI) had licensed UR241-2 from the University of Rochester for cancer treatment. EDI had no roles in writing this manuscript. EDI and UR Ventures office of University of Rochester have cleared the contents of this manuscript for publication.

Interactions of stem cells with their surrounding microenvironment are known to be essential for both normal development and for sustaining self-renewing adult stem cells, such as the hematopoietic stem cells (HSCs). Since cancers often hijack developmental signals for their progression, it is likely that niche-driven signals that sustain HSCs also influence the growth of leukemias arising from mutations in HSCs and early hematopoietic progenitors, such as acute myeloid leukemia (AML) and blast crisis chronic myeloid leukemia (bcCML). To identify candidate cell surface receptors essential for myeloid leukemia progression, we employed a comprehensive approach integrating our in vivo genome-wide CRISPR screen and our RNA-seq analysis of human LSCs from distinct myeloid leukemia subtypes. Of these, the taurine transporter (TauT), encoded by SLC6A6, was of particular interest since its expression is associated with poor prognosis in acute myeloid leukemia (AML) patients. Our experiments using TauT knockout mice indicate that TauT loss significantly impairs myeloid leukemia progression in vivo. An RNA-Seq analysis of freshly isolated TauT+/+ and TauT-/- leukemia cells identified a striking decrease in glycolysis associated genes in the absence of TauT. Consistent with this, Seahorse analysis showed significantly reduced basal glycolysis and glycolytic capacity in TauT-/- LSCs as compared to TauT+/+ controls. In addition, inhibiting TauT reduced the abundance of key glycolytic metabolites as measured by LC/MS spectrometry. Our experiments showing significant downregulation of mTOR pathway in the absence of TauT indicate that mTOR signaling may regulate glycolysis in leukemia cells. Consistent with a functional role of mTOR downstream of TauT function, our data shows that activating mTOR pathway in TauT-/- cells can rescue expression of glycolysis related genes and leukemic cell growth. Importantly, our experiments inhibiting TauT using shRNAs or small-molecule inhibitors identify a key role of this signal in the growth of patient-derived myeloid leukemia cells. Collectively, our data identify a critical requirement of the taurine-TauT axis in myeloid leukemia progression and indicate that the TauT inhibition may be of therapeutic value in myeloid leukemia. Sonali Sharma, Benjamin J. Rodems, Cameron D. Baker, Christina M. Kaszuba, Edgardo I. Franco, Takashi Ito, Laura M. Calvi, Michael W. Becker, Bradley R. Smith, Paul S. Brookes, Joshua C. Munger, Jane L. Liesveld, Craig T. Jordan, John M. Ashton, Jeevisha Bajaj. Taurine Transporter SLC6A6 promotes myeloid leukemia progression by regulating glycolysis [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 6653.

Relapsed acute myeloid leukemia (relAML) remains a clinical challenge. We have shown that epigenetic heterogeneity may contribute to transcriptional dysregulation and disease progression in AML, but the specific aberrant transcriptional programs have not been identified. We analyzed molecular profiles from patient-matched diagnostic and relapse AML specimens. A subset of differentially expressed genes (DEG) that were disparate in direction of expression change identified 2 patient subtypes. We predicted that transcriptional regulators (TR) might regulate the expression patterns observed. The expression patterns of the top TR predicted for the disparate genes associated with clinical outcomes. The top TR predicted for the disparate DEG and DEG identified in a patient-derived xenograft model of relAML included members of the LIM domain only 2 - LIM domain binding 1 - TAL BHLH TF1, erythroid differentiation factor (LMO2-LDB1-TAL1) multisubunit complex (LTMC). Analysis of DepMap data identified LMO2-dependent cells with a subset highly expressing TAL1, suggesting coordinated regulation. TAL1 copurified in immunoprecipitation for LMO2 and LDB1 followed by tandem mass spectrometry analysis in HEL and K562 cells, and results from chromatin immunoprecipitation experiments suggest significant co-occupancy of TAL1 and LDB1. Loss-of-function experiments targeting LMO2, LDB1, and TAL1 in AML cell lines associated with reduced cell growth, downregulation of cell cycle genes, and a negative association with gene expression patterns observed in relapsed patients with increased TAL1 expression. Our results from primary AML specimens and functional analyses of AML cell lines supports an essential role for the LTMC in AML. Targeting the complex or downstream effectors could provide novel therapeutic considerations for a subset of patients with AML.

Signals from the microenvironment are known to be critical for development, stem cell self-renewal and oncogenic progression. Although some niche-driven signals that promote cancer progression have been identified 1–5 , concerted efforts to map disease-relevant microenvironmental ligands of cancer stem cell receptors have been lacking. Here, we use temporal single-cell RNA-sequencing (scRNA-seq) to identify molecular cues from the bone marrow stromal niche that engage leukaemia stem-enriched cells (LSCs) during oncogenic progression. We integrate these data with our human LSC RNA-seq and in vivo CRISPR screen of LSC dependencies 6 to identify LSC–niche interactions that are essential for leukaemogenesis. These analyses identify the taurine–taurine transporter (TAUT) axis as a critical dependency of aggressive myeloid leukaemias. We find that cysteine dioxygenase type 1 (CDO1)-driven taurine biosynthesis is restricted to osteolineage cells, and increases during myeloid disease progression. Blocking CDO1 expression in osteolineage cells impairs LSC growth and improves survival outcomes. Using TAUT genetic loss-of-function mouse models and patient-derived acute myeloid leukaemia (AML) cells, we show that TAUT inhibition significantly impairs in vivo myeloid leukaemia progression. Consistent with elevated TAUT expression in venetoclax-resistant AML, TAUT inhibition synergizes with venetoclax to block the growth of primary human AML cells. Mechanistically, our multiomic approaches indicate that the loss of taurine uptake inhibits RAG-GTP dependent mTOR activation and downstream glycolysis. Collectively, our work establishes the temporal landscape of stromal signals during leukaemia progression and identifies taurine as a key regulator of myeloid malignancies.

Stromal cells are critical regulators of hematopoietic stem/progenitor cells and skeletal homeostasis. Although precise systems for functional analysis are critical to investigate mechanistically bone and bone marrow (BM)-derived stromal cells, the establishment of reproducible, highly enriched ex vivo methods for stromal cell isolation, culture and evaluation have been challenging, leading to inconsistent data on stromal cell function. In this work, we carefully tested ex vivo culture of murine stromal cells from BM and bone and discovered abundant and persistent contamination of monocytes and macrophages. We succeeded in establishing highly enriched ex vivo culture system for stromal cells by eliminating persistent monocytes and macrophages using selection against the immunological markers F4/80, Ly6C, and CD45. Transcriptional and functional assays of enriched stromal cell culture revealed differential characteristics of stromal cells from different origins, a dormant signature for bone-derived cells and a highly proliferative progenitor-like signature for BM-derived cells. Monocyte and macrophage contamination reduced signatures of immature stromal cells such as expression levels of SOX9 and CD140a as well as the cells' ability to support hematopoietic stem and progenitor cells based on our growth factor-free co-culture system of hematopoietic cells and stromal cells followed by in vivo functional assays. The inhibitory effects of macrophages on stromal cells may be explained by their potent production of inflammatory cytokines such as CXCL2, CCL3, and complement factor (C1q) confirmed by protein immunoassay of culture supernatant, as well as the differential contribution of pre-osteoblasts to the stromal cell population. This study highlights the functional diversity of stromal cells depending on the microenvironment of origin while addressing a critical limitation of murine ex vivo systems. Our robust culture system enables the study of isolated stromal cells function as well as the impact of stromal cells-macrophage crosstalk.

Therapies for acute myeloid leukemia (AML) face formidable challenges due to relapse, often driven by leukemia stem cells (LSCs). Strategies targeting LSCs hold promise for enhancing outcomes, yet paired comparisons of functionally defined LSCs at diagnosis and relapse remain underexplored. We present transcriptome analyses of functionally defined LSC populations at diagnosis and relapse, revealing significant alterations in IL-1 signaling. Interleukin-1 receptor type I (IL1R1) and interleukin-1 receptor accessory protein (IL1RAP) were notably upregulated in leukemia stem and progenitor cells at both diagnosis and relapse. Knockdown of IL1R1 and IL1RAP reduced the clonogenicity and/or engraftment of primary human AML cells. In leukemic MLL-AF9 mice, Il1r1 knockout reduced LSC frequency and extended survival. To target IL-1 signaling at both diagnosis and relapse, we developed UR241-2, a novel interleukin-1 receptor-associated kinase 1 and 4 (IRAK1/4) inhibitor. UR241-2 robustly suppressed IL-1/IRAK1/4 signaling, including NF-κB activation and phosphorylation of p65 and p38, following IL-1 stimulation. UR241-2 selectively inhibited LSC clonogenicity in primary human AML cells at both diagnosis and relapse, while sparing normal hematopoietic stem and progenitor cells. It also reduced AML engraftment in leukemic mice. Our findings highlight the therapeutic potential of UR241-2 in targeting IL-1/IRAK1/4 signaling to eradicate LSCs and improve AML outcomes.

Myelodysplastic syndromes (MDS) are age-related diseases characterized by bone marrow (BM) dysfunction and an increased risk of developing acute leukemia. While there is growing evidence highlighting the crucial role of the BM microenvironment (BMME) in MDS, the specific influence of inflammation on BMME changes, as well as the potential benefits of targeting cytokines therapeutically, remain to be elucidated. We previously found interleukin-1 (IL-1) to be a driver of aging phenotypes of BMME and hematopoietic stem and progenitor cells (HSPCs). In the current study, BM samples from patients with MDS demonstrated upregulated levels of IL-1 family cytokines including IL-18. Utilizing highly purified primary BM-derived mesenchymal stromal cells (MSCs), both interleukin-1b (IL-1b) and IL-18 were found to exert direct effects on MSCs, thus influencing their ability to support HSPCs as well as erythroid progenitors. This confirms the significant involvement of both these IL-1 family cytokines in regulating the BM niche. Furthermore, targeting IL-1 receptor type I (IL-1R1) mitigated these aging phenotypes in elderly mice. We subsequently employed an age-appropriate murine model of MDS by transplanting NUP98-HOXD13 transgenic mice (NHD13Tg) cells into aged wild-type mice. Treatment with inhibitors targeting interleukin-1 receptor-associated kinase 4 (IRAK4) and NLR family pyrin domain containing 3 (NLRP3) reversed the proliferation of dysfunctional MSCs and enhanced their functionality. Additionally, IRAK4 inhibition selectively suppressed MDS clonal cells while sparing non-MDS cells in the BM. These findings suggest that targeting IL-1 signaling holds promise for MDS treatment by addressing the underlying myeloid malignancy and restoring the altered BMME via BM-MSCs.

Interactions between acute myeloid leukemia (AML) and the bone marrow microenvironment (BMME) are critical to leukemia progression and chemoresistance. In the solid tumor microenvironment, altered metabolite levels contribute to cancer progression. We performed a metabolomic analysis of AML patient bone marrow serum, revealing increased metabolites compared to age- and sex-matched controls. The most highly elevated metabolite in the AML BMME was lactate. Lactate signaling in solid tumors induces immunosuppressive tumor-associated macrophages and correlates with poor prognosis. This has not yet been studied in the leukemic BMME. Herein, we describe the role of lactate in the polarization of leukemia-associated macrophages (LAMs). Using a murine AML model of blast crisis chronic myelogenous leukemia (bcCML), we characterize the suppressive phenotype of LAMs by surface markers, transcriptomics, and cytokine profiling. Then, mice genetically lacking GPR81, the extracellular lactate receptor, were used to demonstrate GPR81 signaling as a mechanism of both the polarization of LAMs and the direct support of leukemia cells. Furthermore, elevated lactate diminished the function of hematopoietic progenitors and reduced stromal support for normal hematopoiesis. We report microenvironmental lactate as a mechanism of AML-induced immunosuppression and leukemic progression, thus identifying GPR81 signaling as an exciting and novel therapeutic target for treating this devastating disease.

Acute Myeloid Leukemia (AML) is a life-threatening hematologic malignancy. Despite recent therapeutic advances, rising incidence rates emphasize the urgent need for identification of new targets and therapies. Roles of interleukin receptor-associated kinases IRAK1/4 are emerging in hematologic and solid malignancies. In AML, IRAK4 mRNA is overexpressed at diagnosis, relapses, in residual disease, and in FLT3-ITD-mutant cells, MDS, MPN, and MDS/MPN-negative subtypes. Compared with hematopoietic stem cells, IRAK4 is elevated in t(15;17), inv(16)/t(16;16), and t(11q23)/MLL subtypes, correlating with poor survival. Here, we disclose anti-AML activity of PSP-0119, a novel IRAK4 PROTAC degrader. PSP-0119, inhibited IRAK4 kinase activity, NF-κβ activity, and IL-1β-induced IRAK4 phosphorylation. In-silico docking revealed interactions in CRBN/IRAK4/PSP-0119 ternary complex. PSP-0119 degraded IRAK4 in FLT3-mutant AML cell lines sparing FLT3-wild-type AML cells, FLT3-wild-type patient samples, and normal bone-marrow. Bulk-seq of PSP-0119 treated MOLM-13 cells revealed downregulation of eNOS, a poor AML prognosticator. PSP-0119 suppressed colony formation, cell viability, and MOLM-13 xenograft growth, and synergized with IRAK1 covalent inhibitor JH-X-119-01. PSP-0119 is metabolically stable, retaining 71% of parent compound at 60 minutes in human liver microsomes. In summary, IRAK4 degradation via PSP-0119 as a promising therapeutic strategy for treatment of FLT3-mutant AML.

Allogeneic hematopoietic cell transplantation (HCT) improves outcomes for patients with AML harboring an internal tandem duplication mutation of

Acute myeloid leukemia (AML) is fatal in the majority of adults. Identification of new therapeutic targets and their pharmacologic modulators are needed to improve outcomes. Previous studies had shown that immunization of rabbits with normal peripheral WBCs that had been incubated with fluorodinitrobenzene elicited high titer antibodies that bound to a spectrum of human leukemias. We report that proteomic analyses of immunoaffinity-purified lysates of primary AML cells showed enrichment of scaffolding protein IQGAP1. Immunohistochemistry and gene-expression analyses confirmed IQGAP1 mRNA overexpression in various cytogenetic subtypes of primary human AML compared to normal hematopoietic cells. shRNA knockdown of IQGAP1 blocked proliferation and clonogenicity of human leukemia cell-lines. To develop small molecules targeting IQGAP1 we performed in-silico screening of 212,966 compounds, selected 4 hits targeting the IQGAP1-GRD domain, and conducted SAR of the ‘fittest hit’ to identify UR778Br, a prototypical agent targeting IQGAP1. UR778Br inhibited proliferation, induced apoptosis, resulted in G2/M arrest, and inhibited colony formation by leukemia cell-lines and primary-AML while sparing normal marrow cells. UR778Br exhibited favorable ADME/T profiles and drug-likeness to treat AML. In summary, AML shows response to IQGAP1 inhibition, and UR778Br, identified through in-silico studies, selectively targeted AML cells while sparing normal marrow.

Relapsed acute myeloid leukemia (AML) remains a clinical challenge with patients suffering from poor clinical outcomes. To date, studies have not found specific recurrent somatic events that explain disease relapse in most patients. We have previously shown that epigenetic heterogeneity may contribute to transcriptional dysregulation and disease progression in AML but the specific transcriptional programs that drive disease relapse have not been identified. To characterize the transcriptional landscapes in relapsed AML, we analyzed multi-omics molecular profiles from two cohorts of patient-matched diagnostic and relapse AML specimens (cohorts I: n = 29 and II: n = 30). We identified 5,416 differentially expressed genes (DEGs) between diagnosis and relapse in cohort I. The majority of these DEGs did not associate with DNA methylation changes at their respective promoters. Unsupervised clustering of the DEGs identified two transcriptomic subtypes characterized by a subset of DEGs that were disparate in direction of expression change in the two subtypes. These subtypes were not significantly associated with specific somatic events or evolution patterns between diagnosis and relapse. Similar differential expression patterns and patient clusters were observed in Cohort II. We utilized Binding Analysis for Regulation of Transcription (PMID: 29608647) to computationally predict transcriptional regulators (TRs) that might regulate the disparate gene expression patterns observed. The expression patterns of the top 30 TRs predicted for the disparate genes associated with clinical outcomes in the TCGA and BEAT AML patient cohorts (Advanced Expression Survival Analysis [PMID: 31607216]; p < 0.02). Functional annotation of the top TRs predicted for the disparate genes was notable for transcription factors (TFs) known to regulate hematopoiesis, including members of the LIM domain Only 2 (LMO2) multi-subunit complex (TAL transcription Factor 1 [TAL1], GATA binding protein 1 [GATA1], and LIM domain binding protein 1 [LDB1]). A mouse xenograft model of AML relapse was used to generate gene expression data from the human malignant cells. DEGs were identified between engrafted and post-chemotherapy treated AML cells. BART analysis on the DEGs also identified LMO2/LDB1/LMO2 complex members as potential TRs. The LMO2/LDB1/TAL1 complex is known to function in hematopoiesis and has been shown to have an oncogenic role in T-cell acute lymphoblastic leukemia, where the complex has been shown to enforce a stem cell phenotype in T-cell progenitor cells. However, a functional role for it in relapsed AML has not been defined. We hypothesized that this complex is an oncogenic TR in AML relapse. Analysis of DepMap (https://depmap.org/portal) results in AML cell lines identified LMO2-dependent cells. A subset of these cell lines harbored high expression of TAL1, suggesting coordinated regulation. To confirm interactions between LMO2/LDB1/TAL1 complex members, we performed immunoprecipitation for LMO2 and LDB1 followed by tandem mass spectrometry analysis of binding proteins in HEL and K562 cells. TAL1, Transcription Factor 12, and other known complex members co-purified with LMO2 and LDB1. Loss of function experiments targeting LMO2, TAL1, and LDB1 in these AML cell lines altered gene expression and reduced growth (t-test p < 0.05). Functional analyses of the DEGs identified in the in vitro experiments suggested that loss of function associated with downregulation of cell cycle checkpoints, MYC, and MYC target genes (Normalized enrichment score [NES] < -1.5, q < 0.05). Accordingly, we observed upregulation of cell cycle and MYC gene sets in the patient-matched AML specimens with increased TAL1 expression at relapse (NES > 1.5, q < 0.05). Importantly, overall changes in expression acquired with LMO2 and LDB1 loss of function inversely correlated with DEGs in relapsed patients with higher TAL1 expression (NES < -1.5, q < 0.05). Our data from primary AML specimens and functional analyses in AML cell lines supports an essential role for the LMO2/LDB1/TAL1 complex, especially in AML relapsed disease. The macromolecular protein complex plays a role in the maintenance of hematopoietic stem cells, a role that may be co-opted in AML. Targeting the complex or its downstream effectors could be a novel therapeutic consideration for relapsed AML patients.

Signals from the microenvironment are known to be critical for development, sustaining adult stem cells, and for oncogenic progression. While candidate niche-driven signals that can promote cancer progression have been identified1-6, concerted efforts to comprehensively map microenvironmental ligands for cancer stem cell specific surface receptors have been lacking. Here, we use temporal single cell RNA-sequencing to identify molecular cues from the bone marrow stromal niche that engage leukemia stem cells (LSC) during oncogenic progression. We integrate these data with our RNA-seq analysis of human LSCs from distinct aggressive myeloid cancer subtypes and our CRISPR based in vivo LSC dependency map7 to develop a temporal receptor-ligand interactome essential for disease progression. These analyses identify the taurine transporter (TauT)-taurine axis as a critical dependency of myeloid malignancies. We show that taurine production is restricted to the osteolineage population during cancer initiation and expansion. Inhibiting taurine synthesis in osteolineage cells impairs LSC growth and survival. Our experiments with the TauT genetic loss of function murine model indicate that its loss significantly impairs the progression of aggressive myeloid leukemias in vivo by downregulating glycolysis. Further, TauT inhibition using a small molecule strongly impairs the growth and survival of patient derived myeloid leukemia cells. Finally, we show that TauT inhibition can synergize with the clinically approved oxidative phosphorylation inhibitor venetoclax8, 9 to block the growth of primary human leukemia cells. Given that aggressive myeloid leukemias continue to be refractory to current therapies and have poor prognosis, our work indicates targeting the taurine transporter may be of therapeutic significance. Collectively, our data establishes a temporal landscape of stromal signals during cancer progression and identifies taurine-taurine transporter signaling as an important new regulator of myeloid malignancies.

Patient-derived xenograft (PDX) tumor models are essential for identifying new biomarkers, signaling pathways and novel targets, to better define key factors of therapy response and resistance mechanisms. Therefore, this study aimed at establishing pancreas carcinoma (PC) PDX models with thorough molecular characterization, and the identification of signatures defining responsiveness toward drug treatment. In total, 45 PC-PDXs were generated from 120 patient tumor specimens and the identity of PDX and corresponding patient tumors was validated. The majority of engrafted PDX models represent ductal adenocarcinomas (PDAC). The PDX growth characteristics were assessed, with great variations in doubling times (4 to 32 days). The mutational analyses revealed an individual mutational profile of the PDXs, predominantly showing alterations in the genes encoding KRAS, TP53, FAT1, KMT2D, MUC4, RNF213, ATR, MUC16, GNAS, RANBP2 and CDKN2A. Sensitivity of PDX toward standard of care (SoC) drugs gemcitabine, 5-fluorouracil, oxaliplatin and abraxane, and combinations thereof, revealed PDX models with sensitivity and resistance toward these treatments. We performed correlation analyses of drug sensitivity of these PDX models and their molecular profile to identify signatures for response and resistance. This study strongly supports the importance and value of PDX models for improvement in therapies of PC.