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Summary: Leukemia stem cells (LSCs) are believed to have more distinct vulnerabilities than the bulk acute myeloid leukemia (AML) cells, but their rarity and the lack of universal markers for their prospective isolation hamper their study. We report that genetically clonal induced pluripotent stem cells (iPSCs) derived from an AML patient and characterized by exceptionally high engraftment potential give rise, upon hematopoietic differentiation, to a phenotypic hierarchy. Through fate-tracking experiments, xenotransplantation, and single-cell transcriptomics, we identify a cell fraction (iLSC) that can be isolated prospectively by means of adherent in vitro growth that resides on the apex of this hierarchy and fulfills the hallmark features of LSCs. Through integrative genomic studies of the iLSC transcriptome and chromatin landscape, we derive an LSC gene signature that predicts patient survival and uncovers a dependency of LSCs, across AML genotypes, on the RUNX1 transcription factor. These findings can empower efforts to therapeutically target AML LSCs.

Human cancers arise through an evolutionary process whereby cells acquire somatic mutations that drive them to outgrow normal cells and create successive clonal populations. “Bottom-up” human cancer evolution models could help illuminate this process, but their creation has faced significant challenges. Here we combined human induced pluripotent stem cell (iPSC) and CRISPR/Cas9 technologies to develop a model of the clonal evolution of acute myeloid leukemia (AML). Through the sequential introduction of 3 disease-causing mutations (ASXL1 C-terminus truncation, SRSF2P95L and NRASG12D), we obtained single, double and triple mutant iPSC lines that, upon hematopoietic differentiation, exhibit progressive dysplasia with increasing number of mutations, capturing distinct premalignant stages, including clonal hematopoiesis, myelodysplastic syndrome, and culminating in a transplantable leukemia. iPSC-derived clonal hematopoietic stem/progenitor cells recapitulate transcriptional and chromatin accessibility signatures of normal and malignant hematopoiesis found in primary human cells. By mapping dynamic changes in transcriptomes and chromatin landscapes, we characterize transcriptional programs driving specific stage transitions and identify vulnerabilities for early therapeutic targeting. Such synthetic “de novo oncogenesis” models can empower the investigation of multiple facets of the malignant transformation of human cells.

The ability to escape apoptosis is a hallmark of cancer-initiating cells and a key factor of resistance to oncolytic therapy. Here, we identify FAM96A as a ubiquitous, evolutionarily conserved apoptosome-activating protein and investigate its potential pro-apoptotic tumor suppressor function in gastrointestinal stromal tumors (GISTs). Interaction between FAM96A and apoptotic peptidase activating factor 1 (APAF1) was identified in yeast two-hybrid screen and further studied by deletion mutants, glutathione-S-transferase pull-down, co-immunoprecipitation and immunofluorescence. Effects of FAM96A overexpression and knock-down on apoptosis sensitivity were examined in cancer cells and zebrafish embryos. Expression of FAM96A in GISTs and histogenetically related cells including interstitial cells of Cajal (ICCs), "fibroblast-like cells" (FLCs) and ICC stem cells (ICC-SCs) was investigated by Northern blotting, reverse transcription-polymerase chain reaction, immunohistochemistry and Western immunoblotting. Tumorigenicity of GIST cells and transformed murine ICC-SCs stably transduced to re-express FAM96A was studied by xeno- and allografting into immunocompromised mice. FAM96A was found to bind APAF1 and to enhance the induction of mitochondrial apoptosis. FAM96A protein or mRNA was dramatically reduced or lost in 106 of 108 GIST samples representing three independent patient cohorts. Whereas ICCs, ICC-SCs and FLCs, the presumed normal counterparts of GIST, were found to robustly express FAM96A protein and mRNA, FAM96A expression was much reduced in tumorigenic ICC-SCs. Re-expression of FAM96A in GIST cells and transformed ICC-SCs increased apoptosis sensitivity and diminished tumorigenicity. Our data suggest FAM96A is a novel pro-apoptotic tumor suppressor that is lost during GIST tumorigenesis.

The transcriptional regulator far upstream binding protein 1 (FUBP1) is essential for fetal and adult hematopoietic stem cell (HSC) self-renewal, and the constitutive absence of FUBP1 activity during early development leads to embryonic lethality in homozygous mutant mice. To investigate the role of FUBP1 in murine embryonic stem cells (ESCs) and in particular during differentiation into hematopoietic lineages, we generatedFubp1knockout (KO) ESC clones using CRISPR/Cas9 technology. Although FUBP1 is expressed in undifferentiated ESCs and during spontaneous differentiation following aggregation into embryoid bodies (EBs), absence of FUBP1 did not affect ESC maintenance. Interestingly, we observed a delayed differentiation of FUBP1-deficient ESCs into the mesoderm germ layer, as indicated by impaired expression of several mesoderm markers includingBrachyuryat an early time point of ESC differentiation upon aggregation to EBs. Coculture experiments with OP9 cells in the presence of erythropoietin revealed a diminished differentiation capacity ofFubp1KO ESCs into the erythroid lineage. Our data showed that FUBP1 is important for the onset of mesoderm differentiation and maturation of hematopoietic progenitor cells into the erythroid lineage, a finding that is supported by the phenotype of FUBP1-deficient mice.

Mouse Double Minute homolog 4 (MDM4) gene up-regulation often occurs in human hepatocellular carcinoma (HCC), but the molecular mechanisms responsible for its induction remain poorly understood. Here we investigated the role of the phosphoinositide-3-kinase/v-akt murine thymoma viral oncogene homolog/mammalian target of rapamycin (PI3K/AKT/mTOR) axis in the regulation of MDM4 levels in HCC. The activity of MDM4 and the PI3K/AKT/mTOR pathway was modulated in human HCC cell lines by way of silencing and overexpression experiments. Expression of main pathway components was analyzed in an AKT mouse model and human HCCs. MDM4 inhibition resulted in growth restraint of HCC cell lines both in vitro and in vivo. Inhibition of the PI3K-AKT and/or mTOR pathways lowered MDM4 protein levels in HCC cells and reactivated p53-dependent transcription. Deubiquitination by ubiquitin-specific protease 2a and AKT-mediated phosphorylation protected MDM4 from proteasomal degradation and increased its protein stability. The eukaryotic elongation factor 1A2 (EEF1A2) was identified as an upstream inducer of PI3K supporting MDM4 stabilization. Also, we detected MDM4 protein up-regulation in an AKT mouse model and a strong correlation between the expression of EEF1A2, activated/phosphorylated AKT, and MDM4 in human HCC (each rho > 0.8, P

Leukemia stem cells (LSCs) are believed to be a prominent source of relapse in acute myeloid leukemia (AML). Human AML LSCs are classically studied via xenotransplantation and defined as cells with (a) self-renewal ability, giving rise to leukemic engraftment that can be maintained over serial transplantation; and (b) ability to give rise to more differentiated progeny that are unable to engraft. LSCs are chemoresistant presumably because they have properties distinct from those of the bulk AML cells. A better understanding of the properties of LSCs can ultimately allow us to develop new therapies specifically targeting these cells to achieve lasting responses or even cures. We recently reported that induced pluripotent stem cells (iPSCs) generated from AML patients (AML-iPSCs) exhibit leukemic features upon hematopoietic differentiation, including extensive proliferation, maintenance of hematopoietic stem cell (HSC) markers, and serial engraftment of a lethal leukemia in immunodeficient mice (Kotini et al. Cell Stem Cell 2017). More recently, we found that the hematopoietic stem/progenitor cells (HSPCs) derived from AML-iPSCs exhibit phenotypic and functional heterogeneity. We first observed the presence of two cell populations with distinct growth characteristics and morphology: a population exhibiting adherent growth (adherent, A) and a population growing in suspension (S). The A cell population contained cells with immature morphology and HSC immunophenotype (CD34+/CD38-/CD90+/CD45RA-/ CD49f+), while the S fraction contained more differentiated cells (CD34-/low/CD38+/CD90-/CD45RA+). Experiments utilizing serial replating, single-cell plating of GFP-labeled cells and mathematical modeling revealed a hierarchical organization, whereby the A cells continuously give rise to the S cell fraction. Time-lapse imaging showed that A cells divide both symmetrically and asymmetrically with the majority (~60%) of cell divisions giving rise to two A cells and less frequently generating either one A and one S (~15%) or two S cells (~15%). Serial transplantation experiments in NSG mice revealed that the engraftment potential was largely contained within the A cell fraction. Cell cycle analysis showed that adherent cells contained a lower S and higher G0/G1 phase fraction than suspension cells. Thus, these AML-iPSC-derived hematopoietic cells exhibit hallmarks of an LSC model, namely phenotypic and functional heterogeneity and hierarchical organization, with the A fraction containing LSCs that serially transplant leukemia and give rise to more differentiated cells (S fraction) without engraftment potential. Transcriptome analyses showed that the A to S transition was predominantly mediated by gene upregulation with only 2 out of 418 differentially expressed genes being downregulated and revealed enrichment for HSC and LSC gene sets in the A fraction. Consistent with a general transcriptional upregulation characterizing the A to S transition, differentially accessible regions by ATAC-seq analysis were found predominantly in intragenic regions and enhancers in A cells, while they mostly localized in gene promoters in S cells. Time-course single cell-RNA-seq analyses and their integration with bulk RNA-seq and ATAC-seq data revealed cell clusters specific to the A cell fraction, which were enriched in HSC, LSC and hESC genes. These integrated analyses revealed candidate genes with a role in maintaining LSC properties. The transcription factor RUNX1 was particularly prominent, with RUNX1 motifs found highly accessible in A compared to S cells. Overexpression of RUNX1 in S cells conferred a more LSC-like immunophenotype. RUNX1 is a key transcriptional regulator of hematopoiesis. It has a well-characterized role during development of the hematopoietic system and is often mutated or translocated in AML. A role of RUNX1 in LSC maintenance was unanticipated in view of its known tumor-suppressor function. In further support for a role for RUNX1 in LSCs, we found RUNX1 expression to significantly correlate with survival in AML patient cohorts. In summary, we developed a new model that enables us to prospectively isolate large numbers of genetically clonal human AML LSCs and perform genome-wide integrative molecular studies, with which we obtained new insights into the biology of AML LSCs. Disclosures No relevant conflicts of interest to declare.

Hepatocellular carcinoma (HCC) is the most common form of liver cancer. It is accounting for one million deaths per year, mostly due to the late time point of diagnosis and especially to the lack of a specified therapy. In more than 90% of HCCs the oncoprotein FUSE Binding Protein 1 (FUBP1) is overexpressed, with neglectable levels in healthy liver tissue. FUBP1 is a single-stranded DNA-binding protein, which was originally discovered as a major upstream regulator of C-MYC gene expression. Additionally, FUBP1 is known to regulate cell cycle inhibitors like p21 and apoptosis regulating proteins like BIK. In a previous study we could show, that the knockdown of FUBP1 sensitizes HCC cell lines for apoptotic stimuli, e.g. mitomycin c treatment, and reduces tumor engraftment and growth in a Hep3B xenograft model. Consequently, FUBP1 inhibition is a very promising starting point of a targeted HCC therapy. In a screening of FDA-approved drugs, using ALPHA-Screen technology, 1,200 substances were tested for their potential to inhibit or prevent the binding of FUBP1 to its target DNA sequence FUSE. We could demonstrate for the first time the effective inhibition of FUBP1 with small molecules: the known Topoisomerase 1 (TOP1) inhibitor camptothecin (CPT) and its clinically used analog 7-ethyl-10-hydroxycamptothecin (SN-38). Both molecules inhibited the interaction between FUBP1 and FUSE in ALPHA-Screen, Surface Plasmone Resonance (SPR) and Microscale Thermopheresis (MST) assays. Furthermore, SN-38 and CPT caused significant increase of the expression levels of FUBP1 target genes (p21, BIK) in hepatocellular carcinoma cell lines as well as in the TOP1-mutated cell line HCT116 G7. Treatment of mice injected subcutaneously with human HCC cell lines (Hep3B or HepG2) or orthotopically with murine Hepa129 cells showed high efficacy of a double treatment including irinotecan, the pro-drug of SN-38, and the apoptosis-inducing agent mitomycin c. Mice treated with either single or double treatment showed significantly prolonged tumor free survival period compared to control groups, with lower rates of tumor remission concerning irinotecan / mitomycin c drug exposure. Most importantly, treatment of 5 patients suffering from intermediate unresectable HCCs with a combinational therapy of irinotecan and mitomycin c delivered via transarterial chemoembolization (TACE) revealed 100% response rate. Two of these patients showed complete tumor remission, with one of them being tumor free for over 1 year untill today, whereas the remaining 3 patients are in stable disease with no major side effects. Along with the in vitro and in vivo experiments, these early clinical results point to a significant breakthrough in HCC-therapy not seen before. Citation Format: Stefanie Hauck, Sabrina Khageh Hosseini, Josephine Wesely, Dieter Steinhilber, Jörg Schulze, Annabelle Vogt, Maria Gonzalez-Carmona, Christian Strassburg, Stefan Zeuzem, Thomas Vogl, Jörg Trojan, Stephan Zangos, Ricardo Biondi, Eugen Proschak, Martin Zörnig. Inhibition of the oncoprotein FUBP1 by SN-38 represents a novel therapeutic option for the treatment of hepatocellular carcinoma. [abstract]. In: Proceedings of the Fourth AACR International Conference on Frontiers in Basic Cancer Research; 2015 Oct 23-26; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2016;76(3 Suppl):Abstract nr B39.