ALBERT

Description: Cell surface major histocompatibility complex (MHC) I molecules are associated with self peptides that are collectively referred to as the self MHC I immunopeptidome (sMII). Despite the tremendous importance of the sMII, very little is known on its genesis and molecular composition. On the other hand, it is well established that the signalling pathway involving mammalian target of rapamycin (mTOR) plays an essential role in the regulation of processes such as ribosome biogenesis and protein translation which are critical for cell growth, proliferation and differentiation. In this work, we studied the influence of mTOR on the sMII for two major reasons: the tremendous importance of this pathway in oncogenic processes its role in the control of protein synthesis, which is at the origin of the generation of the sMII. To achieve this goal, we developed a novel high-throughput mass spectrometry approach that yields an accurate definition of the nature and relative abundance of unlabeled peptides presented by MHC I molecules. Starting from EL4 thymoma peptide extracts, more than 200 MHC I-associated peptides were sequenced with high confidence level across more than 5500 peptide clusters reproductibly identified through replicate injections (n = 3). Comparison of the sMII of EL4 thymomas before and after rapamycin stimulation revealed that 13% of the MHC I-associated peptides were significant overexpressed (fold change ≥ 2, p-value ≤ 0.05) after mTOR inhibition. Out of the 27 MHC I peptide candidates showing differential expression, 60% of peptide source proteins were linked to cell development and/or proliferation including ITFIFKSL and NAIKNHWNSTM assigned to FK506 binding protein 12 (mTOR) and myeloblastosis oncogene (c-myb) proteins, respectively. These results indicate that cell signalling events have a major impact on the composition of the sMII that can be monitored by analyses of high-throughput MS-based quantitative profiles. Figure 1: Relative Quantification of Differentially Expressed MHC I peptides. Volcano Plot representation illustrates MHC I peptides reproductibly detected across replicate injections (n=3). Peptides over-expressed on EL4 cells after rapamycin stimulation are highlighted in blue. Figure 1:. Relative Quantification of Differentially Expressed MHC I peptides. Volcano Plot representation illustrates MHC I peptides reproductibly detected across replicate injections (n=3). Peptides over-expressed on EL4 cells after rapamycin stimulation are highlighted in blue.

Description: Abstract 1156 Poster Board I-178 Introduction cGVHD is the main cause of impaired quality of life, morbidity and mortality in patients surviving after allogeneic transplantation. To date, no validated biomarkers for diagnosis and follow-up of cGVHD have been established. Among proposed pathophysiological mechanisms, one involves increased turnover of extracellular matrix components as a result of immune-mediated tissue destruction. We hypothesized that analysis of urinary excretion of degradation peptides from collagen (hydroxylysylpyridinoline [HP] and lysylpyridinoline [LP]) and elastin (desmosine [DES]) using high-sensitivity nano-flow liquid chromatography tandem mass spectrometry (nanoLC-MS/MS) might lead to identification of potential biomarkers in patients with cGVHD. Patients and Methods We elected to compare 3 groups: 16 allogeneic transplant recipients with newly diagnosed or relapsing cGVHD before initiation of systemic immunosuppressive therapy (group A), 13 pts with lymphoma who underwent autologous transplantation, in order to measure the impact of high-dose chemotherapy (group B) and 10 healthy volunteers (group C). Clinical characterization of cGVHD was performed according to NIH criteria. Pts already on glucocorticoids and those with bloodstream infection or proteinuria were excluded. Morning urine samples were collected in fasting subjects, then processed and frozen at -80°C until analysis by nanoLC-MS/MS. Samples were purified using mixed-mode strong cation exchange cartridges, derivatized using propionic anhydride and analyzed with nanoLC-MS/MS. Results Pts with cGVHD (group A) were collected at a median of 229 (107-2966) days post transplant; 8 pts had de novo cGVHD, 8 presented with obvious clinical flare-up and 3 had previously suffered from acute GVHD. cGVHD was mild in 1 (6%), moderate in 8 (50%) and severe in 7 (44%) pts. Affected organs included mouth in 12 pts, skin in 11, liver in 11, eyes in 5, GI tract in 5, joints/fascia in 2, genital tract in 1 and lungs in 1. Thrombocytopenia was present in 4 (25%) pts and eosinophilia in 7 (44%). All transplants had been performed for hematological malignancies, using myeloablative (7 pts) or reduced-intensity conditioning (9 pts). Donors were HLA-identical siblings (13 pts), 10/10 (2 pts) or 9/10 (1 pt) unrelated volunteers. Stem cell source was peripheral blood in all but one pts. Pts from group B were collected at a median of 123 (90-377) days post transplant. As shown in enclosed figure, urinary concentrations of DES and HP in group A and B were similar, but both groups showed a marked increase in levels of these compounds compared to group C (p

Description: The polycomb group protein Bmi-1 is a well known determinant of hematopoietic stem cell function. Bmi-1-/- mice display severe hematopoietic defects, including progressive loss of hematopoietic cells from the bone marrow. Bmi-1 is dispensable for hematopoietic stem cell specification, but essential for their maintenance, an effect attributable to its ability to promote HSC self-renewal. The mechanism by which Bmi-1 regulates this process is not completely understood. Bmi-1 has been shown to repress the INK4A/ARF locus encoding the cell cycle inhibitors p16ink4a and p19arf , to interact with the E4F1 protein and to regulate the DNA damage response pathway, however experimental manipulation of these proteins/pathways only partially rescues the hematopoietic defects of the Bmi-1-/-mice. It thus appears that the mechanism by which Bmi-1 regulates HSC self-renewal remains to be determined. Towards this goal, we purified Bmi-1 containing protein complexes from cellular extracts and identified Bmi-1 interaction partners by mass spectrometry. We observed that the protein Ubap2l, which has never been shown to associate with Bmi-1 and for which no link with polycomb group protein function has been described, was consistently found in Bmi-1-containing protein complexes. Immunoprecipitation experiments revealed that Ubap2l indirectly associates with Bmi-1 via an interaction with the polycomb group protein Rnf2. We then evaluated the possibility that Ubap2l might be involved in the regulation of HSC activity. We observed that Ubap2l transcripts are more abundant in primitive HSC populations compared to total BM. CFC assays performed with BM cells infected with Ubap2l shRNAs revealed that Ubap2l knockdown causes a modest and progressive loss of progenitor activity when cells are kept in culture, with multipotent and bipotent progenitors being substantially more affected than unipotent progenitors. We transplanted these cells in mice and observed a gradual decrease in the percentage of donor derived cells expressing Ubap2l shRNAs in the peripheral blood of the recipient mice, with the most striking effect observed 16 weeks post-transplantation in the BM. Bmi-1 has been shown to regulate the proliferative capacity of both progenitor and stem cells, and its deletion in BM cells is known to dramatically reduce the reconstitution activity of these cells at early time points following transplantation. In contrast, Ubap2l appears to preferentially regulate LTR-HSC activity. We tested the effects of Ubap2l silencing on leukemic cells in vivo and observed that a reduction of Ubap2l levels in these cells had an important impact on their ability to reconstitute recipient mice, suggesting that Ubap2l also plays a role in leukemic stem cell activity. We determined if the mechanism by which Ubap2l regulates HSC activity is related to Bmi-1 function by simultaneously introducing Bmi-1 cDNA and Ubap2l shRNAs in BM cells and found that Bmi-1 is able to rescue the long-term reconstitution defect caused by Ubap2l downregulation in these cells. We observed that Ubap2l silencing does not significantly affect the expression of the known Bmi-1 targets p16ink4a and p19arf, implying that Ubap2l regulates HSC activity via a Bmi-1-dependent mechanism that does not involve repression of the INK4A/ARF locus. One explanation for the two Bmi-1 dependent mechanisms at play in the regulation of HSC activity could be that Bmi-1 is part of two separate protein complexes, each regulating different aspects of hematopoietic cell function. To test this hypothesis, we fractionated cellular extracts and were indeed able to resolve two distinct Bmi-1 containing protein complexes, distinguishable by the presence of Ubap2l. Based on the results we obtained, we propose a model in which two different Bmi-1 containing protein complexes regulate hematopoietic stem cell function. An Ubap2l-independent complex, which is most likely involved in the repression of the INK4A/ARF locus, and could be responsible for the effects of Bmi-1 on multipotent progenitors and STR-HSCs, and an Ubap2l-dependent complex, which operates via a yet to be defined mechanism unrelated to p16Ink4a and p19Arf, and would account for the effects of Bmi-1 on LTR-HSC activity. These results position Ubap2l as a key regulator of LTR-HSC activity and unveil a novel protein complex mediating the effects of Bmi-1 on LTR-HSCs. Disclosures: No relevant conflicts of interest to declare.

Description: Key Points Quantitative proteomics identifies BRG as the main ATPase of BAF complexes expressed in leukemia. BRG is essential for the proliferation of leukemic cells.

Description: Abstract 1587 Although important efforts have been invested in the discovery of genes that regulate normal or leukemic hematopoietic stem cells (HSC) self-renewal, the number of validated candidates remains low, due largely to the unavailability of functionally pure stem cell populations. Moreover, it is often difficult to identify the normal counterpart cell from which leukemia originated, further complicating studies based on comparative gene expression. In this study, we used a series of recently characterized Hoxa9 + Meis1 acute myeloid leukemias (AML) derived from fetal liver (FL) cells (Wilhelm BT et al., submitted). These leukemias are remarkably similar in several aspects including their L-HSC frequency (between ∼1 in 100 to 350) except for one leukemia (FLA2) in which 70% of the cells show repopulation ability (i.e., L-HSC). We reasoned that comparative mRNA profiling of FLA2 to the phenotypically similar FLB1 (0.3% L-HSC) might identify genes uniquely associated with L-HSC self-renewal. We observed a 2–3-fold upregulation of Gpx3 in FLA2, which was confirmed by qRT-PCR. In accordance with this, all 14 of the tested Gpx3 promoter region CpG sequences were methylated in FLB1 and hypomethylated in FLA2 cells. The higher expression of GPx3 in FLA2 was confirmed at the protein level and reflected in elevated glutathione peroxidase activity in comparison to FLB1. Importantly, we also observed in FLA2 a relative reduction in reactive oxygen species (ROS) level (DCFDA) and a concomitant decrease in p38 MAPK activation (western blot and mass spectrometry). The correlation of Gpx3 levels with L-HSC frequency could be reflective of their functional dependence on this enzyme. FLA2 cells being difficult to manipulate ex vivo, to address this we utilized retroviruses encoding shRNAs and a GFP reporter to explore the in vivo function of FLA2 cells with downregulated Gpx3. The decrease in percentage of GFP+ donor cells when leukemia became apparent (∼19 days) from that of populations initially transplanted, was 4-fold higher following Gpx3 knockdown in comparison to shLuciferase transduction. Moreover, those shGpx3 infected FLA2 remaining at day 19 displayed a 3-fold decrease in GFP mean fluorescence intensity relative to their control counterparts. These results show that GFPhigh cells were selectively depleted, and suggest that Gpx3 is critical for the competitiveness of L-HSCs. Because redox metabolism has been implicated in HSC self-renewal, we also analyzed its expression and function in normal HSC to gain further insight into the role of GPx3 in stem cell activity. Interestingly, compared to FL-HSCs, isolated 3 and 4 week bone marrow (BM), HSCs exhibited a 39- and 6-fold decrease in Gpx3 expression, respectively. A correlation of Gpx3 levels with enhanced self-renewal was also observed in vitro as overexpression of several nuclear determinants of HSC expansion such as Hoxb4, NA10HD, Klf10 and Prdm16 promoted Gpx3 expression by 3.2 to 19.2-fold. We next infected BM cells enriched for HSCs with retroviruses carrying shRNAs to Gpx3. shRNA targeting of Gpx3 dramatically inhibited hematopoietic reconstitution. Transplantations of sublethally irradiated recipients indicated that Gpx3 knockdown significantly impaired both early and late donor-derived hematopoiesis. These results suggest that GPx3 is critical for repopulation mediated by both short and long-term repopulating cells. In reciprocal gain-of-function experiments, Lin-CD150+CD48- cells engineered to overexpress Gpx3, showed a marked competitive advantage over controls when transplanted following a 7-day ex vivo culture step. Insertional mutagenesis was ruled out as proviral integration analyses of six recipients confirmed polyclonal hematopoiesis. Moreover, some mice were in part reconstituted by the same clones, indicating that self-renewal occurred in vitro prior to transplantation. Phenotypic analysis of late-transplant hematopoietic tissues showed that Gpx3-transduced cells contributed to lymphoid and myeloid repopulation, confirming their multipotentiality. Together, these results indicate that Gpx3 enhances HSC expansion ex vivo possibly through modulation of self-renewal activity. In conclusion, a unique model of primary L-HSC was exploited to identify Gpx3 as a critical determinant for the competitiveness of L-HSCs and complementary experiments demonstrated a key role for this gene in normal HSC self-renewal. Disclosures: No relevant conflicts of interest to declare.

Description: Key Points UBAP2L interacts with BMI1 as part of a novel Polycomb subcomplex. UBAP2L regulates HSC activity via a mechanism unrelated to the repression of the Ink4a/Arf locus.

Description: BACKGROUND: 60% to 70% of Acute Myeloid Leukemia (AML) patients enter complete remission after induction regimen, but the majority relapse within 3 years due to the outgrowth of therapy resistant Leukemia Stem Cells (LSCs). Identification of novel treatment strategies effective against these cells thus represents an outstanding medical need. We developed a cell culture method, which transiently maintains LSC activity ex vivo (Pabst et al., Nature Methods, 2014) and enables chemical interrogation of cell types relevant for the progression of the disease. Overall, HSCs and LSCs share numerous biological traits, making specific LSC eradication challenging. However, striking differences in energy metabolism between normal and leukemic stem cells have recently been suggested. While HSCs appear to rely primarily on anaerobic glycolysis for energy production, LSCs seem to depend on mitochondrial oxidative phosphorylation for their survival. Targeting mitochondrial respiration could therefore represent an effective approach for the specific eradication of LSCs. AIM: We aimed to identify novel therapeutic targets for AMLs with poor treatment outcome. The study relied on the Leucegene approach that integrates results generated by RNA sequencing analysis of primary human AML specimens, detailed clinical and cytogenetic annotations provided by the Quebec leukemia cell bank and ex vivo responses of primary AML samples to various chemical compounds. Our study specifically focused on specimens originating from patients with poor (overall survival 〈 3 years) and good (overall survival ≥ 3 years) response to standard chemotherapy, and did not include cases of Acute Promyelocytic Leukemia (APL). RESULTS: We identified Mubritinib, previously described as an ERBB2 inhibitor, as a novel anti-leukemic agent, which selectively inhibits the viability of leukemic cells from therapy-resistant AML patients, but does not affect normal CD34+ cord blood cells. Exposure to Mubritinib triggered apoptotic cell death in a subset of AML samples with high mitochondrial function-related gene expression, high relapse rates, and short overall survival. Sensitivity to Mubritinib also strongly associated with the intermediate cytogenetic risk category, normal karyotype (NK), and NPM1, FLT3 (ITD) and DNMT3A mutations. Conversely, resistance to Mubritinib associated with favorable cytogenetic risk AMLs, Core Binging Factor (CBF) leukemias and KIT mutations. Mubritinib has been developed as an ERBB2 kinase inhibitor. Intriguingly, we found that ERBB2 is not expressed in Mubritinib-sensitive AML specimens, suggesting that the anti-leukemic activity of this compound is likely not mediated by ERBB2 inhibition. Using a combination of functional genomics and biochemical analyses, we demonstrated that Mubritinib directly inhibits the mitochondrial Electron Transport Chain (ETC) complex I, which leads to a decrease in oxidative phosphorylation activity and to induction of oxidative stress. The impact of Mubritinib on AML progression was explored using a syngeneic mouse model (MLL-AF9 tdTomato-positive leukemia). Recipients of MLL-AF9 cells treated with Mubritinib exhibited a 19-fold decrease in the number of tdTomato-positive cells in the bone marrow and a 42-fold decrease in the spleens compared to control mice. Short-term treatment also led to a 37% increase in the median overall survival of Mubritinib exposed recipients compared to vehicle treated mice. Importantly, and in agreement with our observation that Mubritinib treatment does not impede proliferation of normal hematopoietic CD34+ cells in vitro, Mubritinib treatment had no impact on the number of non-transduced (tdTomato negative) nucleated bone marrow cells of recipients. CONCLUSIONS: We uncovered the clinical, mutational, and transcriptional landscape of mitochondrial vulnerability in AML and identified Mubritinib as a novel ETC complex I inhibitor with therapeutic potential for approximately 30% of AML cases currently lacking effective treatment options. As Mubritinib completed a phase I clinical trial in the context of ERBB2-positive solid tumors, our work suggests an opportunity to re-purpose Mubritinib's usage for this genetically distinct subgroup of poor outcome AML patients. Disclosures No relevant conflicts of interest to declare.

Description: MHC I–associated peptides (MIPs) play an essential role in normal homeostasis and diverse pathologic conditions. MIPs derive mainly from defective ribosomal products (DRiPs), a subset of nascent proteins that fail to achieve a proper conformation and the physical nature of which remains elusive. In the present study, we used high-throughput proteomic and transcriptomic methods to unravel the structure and biogenesis of MIPs presented by HLA-A and HLA-B molecules on human EBV-infected B lymphocytes from 4 patients. We found that although HLA-different subjects present distinctive MIPs derived from different proteins, these MIPs originate from proteins that are functionally interconnected and implicated in similar biologic pathways. Secondly, the MIP repertoire of human B cells showed no bias toward conserved versus polymorphic genomic sequences, were derived preferentially from abundant transcripts, and conveyed to the cell surface a cell-type–specific signature. Finally, we discovered that MIPs derive preferentially from transcripts bearing miRNA response elements. Furthermore, whereas MIPs of HLA-disparate subjects are coded by different sets of transcripts, these transcripts are regulated by mostly similar miRNAs. Our data support an emerging model in which the generation of MIPs by a transcript depends on its abundance and DRiP rate, which is regulated to a large extent by miRNAs.

Description: Background: Cell surface MHC I molecules are associated with self peptides that are collectively referred to as the self MHC I immunopeptidome (sMII). The sMII plays vital roles: it shapes the repertoire of developing thymocytes, transmits survival signals to mature CD8 T cells, amplifies responses against intracellular pathogens, allows immunosurveillance of neoplastic cells, and influences mating preferences in mice. Despite the tremendous importance of the sMII, very little is known on its genesis and molecular composition. Methodology/Principal Findings: We developed a novel high-throughput mass spectrometry approach that yields an accurate definition of the nature and relative abundance of unlabeled peptides presented by MHC I molecules. Two major points emerged from a comprehensive analysis of the sMII of primary mouse thymocytes: the sMII is enriched in peptides derived from highly abundant transcripts; and the sMII conceals a tissue-specific signature that emanates from about 17% of genes represented in the sMII. We found that about 25% of MHC I-associated peptides were differentially expressed on normal versus neoplastic thymocytes. Remarkably, about half of those peptides derived from molecules implicated in neoplastic transformation. Integration of peptidomic and transcriptomic data unveiled that, in most cases, overexpression of MHC I peptides on cancer cells entailed posttranscriptional mechanisms. Finally, mice immunized against peptides overexpressed by 10 to ≥ 85 fold on cancer cells generated specific cytotoxic T-cell responses against malignant cells endogenously expressing the target epitope. Conclusion: High-throughput analysis and sequencing of MHC I-associated peptides yields unique insights into the genesis of the sMII in normal and neoplastic cells, and can be used to discover peptide targets for cancer immunotherapy. Furthermore, global portrayal of the sMII offers a novel perspective into how neoplastic transformation affects protein metabolism. Figure 1. Relative Quantification of Differentially Expressed MHC I peptides and Source mRNAs from Thymocytes and EL4 Cells
 (A) Volcano Plot representation illustrate MHC I peptides reproducibly detected across biological replicates (n = 3). Peptides over- and underexpressed on EL4 cells relative to thymocytes (p-values≤0.05; fold change ≥ 2.5) were highlighted in blue and red, respectively. MS-MS spectra of circled peptides are shown in B and C.
 B) Scatter plot shows the correlation between relative expression of mRNA and that of MHC I peptide. Expression ratios for source mRNA (x axis) and MHC I peptide (y axis) between EL4 cells and thymocytes were plotted on a log 2 scale for 47 pairs. A Spearman correlation coefficient was calculated from the linear regression. MHC I peptides overexpressed in EL4 cells or normal thymocytes are highlighted in blue and red, respectively; peptides that were not differentially expressed are in grey. Dashed box includes peptides whose overexpression on EL4 cells did not correlated with increased mRNA levels of their source protein. Figure 1. Relative Quantification of Differentially Expressed MHC I peptides and Source mRNAs from Thymocytes and EL4 Cells
 (A) Volcano Plot representation illustrate MHC I peptides reproducibly detected across biological replicates (n = 3). Peptides over- and underexpressed on EL4 cells relative to thymocytes (p-values≤0.05; fold change ≥ 2.5) were highlighted in blue and red, respectively. MS-MS spectra of circled peptides are shown in B and C.
 B) Scatter plot shows the correlation between relative expression of mRNA and that of MHC I peptide. Expression ratios for source mRNA (x axis) and MHC I peptide (y axis) between EL4 cells and thymocytes were plotted on a log 2 scale for 47 pairs. A Spearman correlation coefficient was calculated from the linear regression. MHC I peptides overexpressed in EL4 cells or normal thymocytes are highlighted in blue and red, respectively; peptides that were not differentially expressed are in grey. Dashed box includes peptides whose overexpression on EL4 cells did not correlated with increased mRNA levels of their source protein.

Description: As highly proliferative erythroid progenitors commit to terminal differentiation, they also progressively undergo growth arrest. To determine the mechanisms underlying the appropriate timing of erythroid gene expression and those associated with growth cessation, we analyzed the dynamical composition of the multiprotein complex nucleated by the bHLH transcription factor SCL, a crucial regulator of erythropoiesis that absolutely requires interaction with other factors to activate transcription. In progenitor cells, the SCL complex marks a subset of erythroid specific genes (alpha-globin, P4.2, glycophorin A) that are transcribed later in differentiating cells, conducting cells toward terminal maturation. To unravel the regulation of transcription by SCL, we used tagging/proteomics approaches in two differentiation-inducible erythroid cell lines, coupled with binding assays to immobilized DNA templates and chromatin immunoprecipitation. Our analyses reveal that the core complex comprised of known proteins (SCL, GATA-1, LMO2, Ldb1 and E2A) and two additional E protein family members, HEB and E2-2, did not change with differentiation. Strikingly, this complex recruits HDAC1-2 in undifferentiated cells which were exchanged with TRRAP, a chromatin remodelling factor, upon differentiation, suggesting an epigenetic regulation of erythroid differentiation mediated by the core SCL complex. Finally, we identified the corepressor ETO2 targeted via this complex through direct interaction with E2A/HEB. In vivo, ETO2 represses the transcription of SCL target genes both in transient assays and in chromatin. During erythroid differentiation, ETO2 remains associated with the SCL complex bound to erythroid promoters. However, the stoichiometry of ETO2 and SCL/HEB changes as SCL and HEB levels increase with erythroid differentiation, both in nuclear extracts and on DNA. To determine the functional consequence of this imbalance in activator to co-repressor ratio, we delivered ETO2 siRNA in primary hematopoietic cells and found an accelerated onset of SCL target genes on induction of erythroid differentiation, and conversely, these genes were decreased following ectopic ETO2 expression. Strikingly, inhibition of ETO2 expression in erythroid progenitors arrests cell proliferation, indicating that ETO2 is required for their expansion. We therefore analyzed gene expression in purified erythroid progenitors and differentiating erythroid cells (E1-E5) and found an inverse correlation between the mRNA levels of ETO2 and cyclin-dependent kinase inhibitors. Moreover, ETO2 siRNA treatment of primary erythroid progenitors results in increased p21 CDKI and Gfi1b expression, as assessed by real-time PCR. Finally, we show by chromatin immunoprecipitation that Gfi-1b, p21 and p27, are direct targets of the SCL- ETO2 complex. We therefore conclude that ETO2 regulates the erythroid lineage fate by repressing SCL marked erythroid genes in undifferentiated cells, and by controlling the expansion of erythroid progenitors. Our study elucidates the dual function of ETO2 in the erythroid lineage and sheds light on epigenetic mechanisms coordinating red blood cell proliferation and differentiation.