Global Proteomic Profiling Research Articles

1763-P: Acarbose Protects from Central and Peripheral Metabolic Imbalance Induced by Exposure to Benzene

Benzene is a well-known human carcinogen that is one of the major components of air pollution. Few epidemiological studies suggested an association between adverse health effects of benzene at low doses and the development of insulin resistance. Regardless, a detailed analysis of the metabolic effects of benzene exposure and its target tissues has rarely been done. We assessed the effects of chronic and acute exposure to benzene at 50 ppm in inhalation chambers in mice. We show that exposure to benzene for 4 weeks (5h/day), induced hyperglycemia and hyperinsulinemia, associated with impairment in gluconeogenesis and lipid metabolism in males. Females were completely resistant to the negative metabolic consequences of benzene exposure. Moreover, chronic benzene exposure promoted hypothalamic gliosis, ER stress, and elevation of inflammatory genes in male mice. In support, a global proteome profile has identified inflammatory and ER stress pathways in the hypothalamus of the benzene exposed animals suggesting their role in a benzene-induced metabolic imbalance. In support, benzene exposure triggered alterations in neuron-glia interactions by modulating neuronal sensing under hyperglycemic conditions within hypothalamic glucose-sensing VMH neurons. Mechanistically, acute benzene exposure activated hypothalamic ER stress and neuroinflammatory responses, while pharmacological inhibition of IRE1α-XBP1 pathway alleviated glial inflammatory cytokines production suggesting that this may be the primary mechanism by which benzene causes changes in metabolic status. A diabetes drug, Acarbose that extends animals’ life span in a sex-specific manner, and protected against benzene induced metabolic imbalance, ER stress, and neuroinflammatory responses. Acarbose imitates the slowing of dietary carbohydrate digestion, suggesting that choosing a diet with a low glycemic index might be a potential strategy for reducing the effect of benzene exposure even at lower levels. Disclosure L. Kniess Debarba: None. A. Mulka: None. P.I. Fakhoury: None. O. Didyuk: None. A.A. Awada: None. J. Lima: None. L. Koshko: None. U. Klueh: Research Support; Self; Abbott. Other Relationship; Self; Cell and Molecular Tissue Engineering, LLC. M. Sadagurski: None. Funding American Diabetes Association (1-18-JDF-063 to M.S.)

Comparative proteomics analysis of patients with quick development and slow development Chronic Obstructive Pulmonary Disease (COPD)

BackgroundThe development of Chronic Obstructive Pulmonary Disease (COPD) has been assessed and divided into slow development (SD), normal development (ND) and quick development (QD). Little is known about the plasma proteome characters among these three phenotypes. MethodsWe performed a comparative proteomic analysis in the plasma of normal control (NC), SD, ND and QD phenotype COPD patients using isobaric tags for relative and absolute quantitation (iTRAQ) technique. ResultsA total of 683 proteins were successfully identified in the plasma samples, of which 394 were considered as high-quality proteins (95% confidential peptides ≥ 2). Further, a total of 25, 19 and 27 different abundant proteins (DAPs) were identified in SD, ND and QD groups, respectively. Gene ontology (GO) classification analysis of all DAPs showed that immune system process (GO:0002376) were the most significant. The pathway enrichment analysis showed that innate immune response (GO:0045087), receptor-mediated endocytosis (GO:0006898) and proteolysis (GO:0006508) were the branch-end terms. Notably, the 15 QD special DAPs were considered as potential markers for identify patient might have quick development COPD, and thus provided more aggressive treatment strategy for these patients. ConclusionThis work provides an insight into global plasma proteome profiles among the SD, ND and QD phenotypes of COPD patients. The most significant GO terms that the DAPs enriched in were immune system related terms. In addition, the 15 QD specific DPAs provided candidates of potential markers to predict the development types of COPD patients.

Targeting Cellular Metabolism in Acute Myeloid Leukemia and The Role of Patient Heterogeneity.

Acute myeloid leukemia (AML) is an aggressive blood cancer resulting in accumulation of immature, dysfunctional blood cells in the bone marrow. Changes in cell metabolism are features of many cancers, including AML and this may be exploited as a therapeutic target. In this study we investigated the in vitro antileukemic effects of seven metabolic inhibitors that target different metabolic pathways. The metabolic inhibitors were tested on AML cells derived from 81 patients using proliferation and viability assays; we also compared global gene expression and proteomic profiles for various patient subsets. Metformin, 2DG, 6AN, BPTES and ST1326 had strong antiproliferative and proapoptotic effects for most patients, whereas lonidamine and AZD3965 had an effect only for a minority. Antiproliferative effects on AML cells were additive when combined with the chemotherapeutic agent AraC. Using unsupervised hierarchical clustering, we identified a strong antiproliferative effect on AML cells after treatment with metabolic inhibitors for a subset of 29 patients. Gene expression and proteomic studies suggested that this subset was characterized by altered metabolic and transcriptional regulation. In addition, the Bcl-2 inhibitor venetoclax, in combination with 2DG or 6AN, increased the antiproliferative effects of these metabolic inhibitors on AML cells. Therapeutic targeting of cellular metabolism may have potential in AML, but the optimal strategy will likely differ between patients.

Comprehensive Map of the Artemisia annua Proteome and Quantification of Differential Protein Expression in Chemotypes Producing High versus Low Content of Artemisinin

Artemisia annua is well known for biosynthesizing the antimalarial drug artemisinin. Here, a global proteomic profiling of A. annua is conducted with identification of a total of 13403 proteins based on the genome sequence annotation database. Furthermore, a spectral library is generated to perform quantitative proteomic analysis using data independent acquisition mass spectrometry. Specifically, proteins between two chemotypes that produce high (HAP) and low (LAP) artemisinin content, respectively, are comprehensively quantified and compared. 182 proteins are identified with abundance significantly different between these two chemotypes means after the statistic use the p-value and fold change it is found 182 proteins can reach the demand conditions which represent the expression are significantly different between the high artemisnin content plants (HAPs) and the low artemisnin content plants (LAPs). Data are available via ProteomeXchange with identifier PXD015547. Overall, this current study globally identifies the proteome of A. annua and quantitatively compares the targeted sub-proteomes between the two cultivars of HAP and LAP, providing systematic information on metabolic pathways of A. annua.

Thermal Proteome Profiling Identifies Oxidative-Dependent Inhibition of the Transcription of Major Oncogenes as a New Therapeutic Mechanism for Select Anticancer Compounds.

Identification of the molecular mechanism of action (MoA) of bioactive compounds is a crucial step for drug development but remains a challenging task despite recent advances in technology. In this study, we applied multidimensional proteomics, sensitivity correlation analysis, and transcriptomics to identify a common MoA for the anticancer compounds RITA, aminoflavone (AF), and oncrasin-1 (Onc-1). Global thermal proteome profiling revealed that the three compounds target mRNA processing and transcription, thereby attacking a cancer vulnerability, transcriptional addiction. This led to the preferential loss of expression of oncogenes involved in PDGF, EGFR, VEGF, insulin/IGF/MAPKK, FGF, Hedgehog, TGFβ, and PI3K signaling pathways. Increased reactive oxygen species level in cancer cells was a prerequisite for targeting the mRNA transcription machinery, thus conferring cancer selectivity to these compounds. Furthermore, DNA repair factors involved in homologous recombination were among the most prominently repressed proteins. In cancer patient samples, RITA, AF, and Onc-1 sensitized to poly(ADP-ribose) polymerase inhibitors both in vitro and ex vivo These findings might pave a way for new synthetic lethal combination therapies.Significance: These findings highlight agents that target transcriptional addiction in cancer cells and suggest combination treatments that target RNA processing and DNA repair pathways simultaneously as effective cancer therapies.

Toxicokinetics of Brominated Azo Dyes in the Early Life Stages of Zebrafish (Danio rerio) Is Prone to Aromatic Substituent Changes.

Brominated azo dyes (BADs) have been identified as predominant indoor brominated pollutants in daycare dust; thus, their potential health risk to children is of concern. However, the toxicities of BADs remain elusive. In this study, the toxicokinetics of two predominant BADs, Disperse Blue 373 (DB373) and Disperse Violet 93 (DV93), and their suspect metabolite 2-bromo-4,6-dinitroaniline (BDNA) was investigated in embryos of zebrafish (Danio rerio). The bioconcentration factor of DV93 at 120 hpf is 6.2-fold lower than that of DB373. The nontarget analysis revealed distinct metabolism routes between DB373 and DV93 by reducing nitro groups to nitroso (DB373) or amine (DV93), despite their similar structures. NAD(P)H quinone oxidoreductase 1 (NQO1) and pyruvate dehydrogenase were predicted as the enzymes responsible for the reduction of DB373 and DV93 by correlating time courses of the metabolites and enzyme development. Further in vitro recombinant enzyme and in vivo inhibition results validated NQO1 as the enzyme specifically reducing DB373, but not DV93. Global proteome profiling revealed that the expression levels of proteins from the "apoptosis-induced DNA fragmentation" pathway were significantly upregulated by all three BADs, supporting the bioactivation of BADs to mutagenic aromatic amines. This study discovered the bioactivation of BADs via distinct eukaryotic enzymes, implying their potential health risks.

Prolyl 4-hydroxylase alpha 1 protein expression risk-stratifies early stage colorectal cancer.

Colorectal cancer (CRC) is one of the most prevalent and lethal malignancies. Especially for early stage CRC, prognostic molecular markers are needed to guide therapy. In this study, we first extracted total proteomes from matched pairs of fresh cancer and benign mucosal tissues from 22 CRC patients. Global proteomic profiling with Fourier transform liquid chromatography-mass spectrometry sequencing and label free quantitation uncovered that P4HA1 (prolyl 4-hydroxylase alpha 1) was overexpressed in CRC relative to benign colonic mucosa. We then investigated expression by immunohistochemical staining with P4HA1-specific antibodies using CRC tissue microarrays. Independent validation cohorts of 599 cases of early stage CRC and 91 cases of late stage CRC were examined. Multivariate and univariate survival analyses revealed that high expression of P4HA1 protein was an independent poor prognostic marker for patients with early stage CRC, especially of the microsatellite stable subtype. Our study provides strong support for P4HA1 as a predictive protein marker for precision diagnostics, therapeutic decision-making, and drug development for early stage colorectal cancer and demonstrates the utility of proteomic profiling to identify novel protein biomarkers.

Comparative Proteomic Analysis of Serum from Pigs Experimentally Infected with Trichinella spiralis, Trichinella britovi, and Trichinella pseudospiralis.

Although the available proteomic studies have made it possible to identify and characterize Trichinella stage-specific proteins reacting with infected host-specific antibodies, the vast majority of these studies do not provide any information about changes in the global proteomic serum profile of Trichinella-infested individuals. In view of the above, the present study aimed to examine the protein expression profile of serum obtained at 13 and 60 days postinfection (d.p.i.) from three groups of pigs experimentally infected with Trichinella spiralis, Trichinella britovi, and Trichinella pseudospiralis and from uninfected, control pigs by two-dimensional gel electrophoresis (2-DE) followed by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. The comparative proteomic analysis of the T. spiralis group vs. the control group revealed 5 differently expressed spots at both 13 and 60 d.p.i. Experimental infection with T. britovi induced significant expression changes in 3 protein spots at 13 d.p.i. and in 6 protein spots at 60 d.p.i. in comparison with the control group. Paired analyses between the group infected with T. pseudospiralis and the uninfected control group revealed 6 differently changed spots at 13 d.p.i. and 2 differently changed spots at 60 d.p.i. Among these 27 spots, 15 were successfully identified. Depending on the Trichinella species triggering the infection and the time point of serum collection, they were IgM heavy-chain constant region, antithrombin III-precursor, immunoglobulin gamma-chain, clusterin, homeobox protein Mohawk, apolipoprotein E precursor, serum amyloid P-component precursor, Ig lambda chains, complement C3 isoform X1, and apolipoprotein A-I. Our results demonstrate that various Trichinella species and different phases of the invasion produce a distinct, characteristic proteomic pattern in the serum of experimentally infected pigs.

Marizomib suppresses triple-negative breast cancer via proteasome and oxidative phosphorylation inhibition.

Purpose: Lacking effective targeted therapies, triple-negative breast cancer (TNBCs) is highly aggressive and metastatic disease, and remains clinically challenging breast cancer subtype to treat. Despite the survival dependency on the proteasome pathway genes, FDA-approved proteasome inhibitors induced minimal clinical response in breast cancer patients due to weak proteasome inhibition. Hence, developing effective targeted therapy using potent proteasome inhibitor is required.Methods: We evaluated anti-cancer activity of a potent proteasome inhibitor, marizomib, in vitro using breast cancer lines and in vivo using 4T1.2 murine syngeneic model, MDA-MB-231 xenografts, and patient-derived tumor xenografts. Global proteome profiling, western blots, and RT-qPCR were used to investigate the mechanism of action for marizomib. Effect of marizomib on lung and brain metastasis was evaluated using syngeneic 4T1BR4 murine TNBC model in vivo.Results: We show that marizomib inhibits multiple proteasome catalytic activities and induces a better anti-tumor response in TNBC cell lines and patient-derived xenografts alone and in combination with the standard-of-care chemotherapy. Mechanistically, we show that marizomib is a dual inhibitor of proteasome and oxidative phosphorylation (OXPHOS) in TNBCs. Marizomib reduces lung and brain metastases by reducing the number of circulating tumor cells and the expression of genes involved in the epithelial-to-mesenchymal transition. We demonstrate that marizomib-induced OXPHOS inhibition upregulates glycolysis to meet the energetic demands of TNBC cells and combined inhibition of glycolysis with marizomib leads to a synergistic anti-cancer activity.Conclusions: Our data provide a strong rationale for a clinical evaluation of marizomib in primary and metastatic TNBC patients.

S-Palmitoylation as a Functional Regulator of Proteins Associated with Cisplatin Resistance in Bladder Cancer.

Protein S-palmitoylation is a powerful post-translational modification that regulates protein trafficking, localization, turnover, and signal transduction. Palmitoylation controls several important cellular processes, and, if dysregulated, can lead to cancer, cardiovascular disease, and neurological disorders. The role of protein palmitoylation in mediating resistance to systemic cisplatin-based chemotherapies in cancer is currently unknown. This is of particular interest because cisplatin is currently the gold standard of treatment for bladder cancer (BC), and there are no feasible options after resistance is acquired. Using unbiased global proteomic profiling of purified S-palmitoylated peptides combined with intensive bioinformatics analyses, we identified 506 candidate palmitoylated proteins significantly enriched in cisplatin-resistant BC cells. One of these proteins included PD-L1, which is highly palmitoylated in resistant cells. Pharmacological inhibition of fatty acid synthase (FASN) suppressed PD-L1 palmitoylation and expression, which suggests the potential use of FASN-PD-L1-targeted therapeutic strategies in BC patients. Taken together, these results highlight the role of protein palmitoylation in mediating BC chemoresistance.

The Amniotic Fluid Proteome Differs Significantly between Donor and Recipient Fetuses in Pregnancies Complicated by Twin-to-Twin Transfusion Syndrome.

BackgroundTwin-to-twin transfusion syndrome (TTTS) is a serious complication of monochorionic twin pregnancies. It results from disproportionate blood supply to each fetus caused by abnormal vascular anastomosis within the placenta. Amniotic fluid (AF) is an indicator reflecting the various conditions of the fetus, and an imbalance in AF volume is essential for the antenatal diagnosis of TTTS by ultrasound. In this study, two different mass spectrometry quantitative approaches were performed to identify differentially expressed proteins (DEPs) within matched pairs of AF samples.MethodsWe characterized the AF proteome in pooled AF samples collected from donor and recipient twin pairs (n = 5 each) with TTTS by a global proteomics profiling approach and then preformed the statistical analysis to determine the DEPs between the two groups. Next, we carried out a targeted proteomic approach (multiple reaction monitoring) with DEPs to achieve high-confident TTTS-associated AF proteins.ResultsA total of 103 AF proteins that were significantly altered in their abundances between donor and recipient fetuses. The majority of upregulated proteins identified in the recipient twins (including carbonic anhydrase 1, fibrinogen alpha chain, aminopeptidase N, alpha-fetoprotein, fibrinogen gamma chain, and basement membrane-specific heparan sulfate proteoglycan core protein) have been associated with cardiac or dermatologic disease, which is often seen in recipient twins as a result of volume overload. In contrast, proteins significantly upregulated in AF collected from donor twins (including IgGFc-binding protein, apolipoprotein C-I, complement C1q subcomponent subunit B, apolipoprotein C-III, apolipoprotein A-II, decorin, alpha-2-macroglobulin, apolipoprotein A-I, and fibronectin) were those previously shown to be associated with inflammation, ischemic cardiovascular complications or renal disease.ConclusionIn this study, we identified proteomic biomarkers in AF collected from donor and recipient twins in pregnancies complicated by TTTS that appear to reflect underlying functional and pathophysiological challenges faced by each of the fetuses.

Discovery of a First-in-Class Mitogen-Activated Protein Kinase Kinase 1/2 Degrader.

MEK1 and MEK2 (also known as MAP2K1 and MAP2K2) are the "gatekeepers" of the ERK signaling output with redundant roles in controlling ERK activity. Numerous inhibitors targeting MEK1/2 have been developed including three FDA-approved drugs. However, acquired resistance to MEK1/2 inhibitors has been observed in patients, and new therapeutic strategies are needed to overcome the resistance. Here, we report a first-in-class degrader of MEK1/2, MS432 (23), which potently and selectively degraded MEK1 and MEK2 in a VHL E3 ligase- and proteasome-dependent manner and suppressed ERK phosphorylation in cells. It inhibited colorectal cancer and melanoma cell proliferation much more effectively than its negative control MS432N (24), and its effect was phenocopied by MEK1/2 knockdown. Compound 23 was highly selective for MEK1/2 in global proteomic profiling studies. It was also bioavailable in mice and can be used for in vivo efficacy studies. We provide two well-characterized chemical tools to the biomedical community.

ITRAQ-Based Quantitative Proteomic Comparison of 2D and 3D Adipocyte Cell Models Co-cultured with Macrophages Using Online 2D-nanoLC-ESI-MS/MS

The demand for novel three-dimensional (3D) cell culture models of adipose tissue has been increasing, and proteomic investigations are important for determining the underlying causes of obesity, type II diabetes, and metabolic disorders. In this study, we performed global quantitative proteomic profiling of three 3D-cultured 3T3-L1 cells (preadipocytes, adipocytes and co-cultured adipocytes with macrophages) and their 2D-cultured counterparts using 2D-nanoLC-ESI-MS/MS with iTRAQ labelling. A total of 2,885 shared proteins from six types of adipose cells were identified and quantified in four replicates. Among them, 48 proteins involved in carbohydrate metabolism (e.g., PDHα, MDH1/2, FH) and the mitochondrial fatty acid beta oxidation pathway (e.g., VLCAD, ACADM, ECHDC1, ALDH6A1) were relatively up-regulated in the 3D co-culture model compared to those in 2D and 3D mono-cultured cells. Conversely, 12 proteins implicated in cellular component organisation (e.g., ANXA1, ANXA2) and the cell cycle (e.g., MCM family proteins) were down-regulated. These quantitative assessments showed that the 3D co-culture system of adipocytes and macrophages led to the development of insulin resistance, thereby providing a promising in vitro obesity model that is more equivalent to the in vivo conditions with respect to the mechanisms underpinning metabolic syndromes and the effect of new medical treatments for metabolic disorders.

Loss of Phospholipase C Gamma 1 (PLCG1) Impairs AML1-ETO Induced Leukemia Stem Cell Self-Renewal

Chromosomal translocations found in acute myeloid leukemia (AML) can generate oncogenic fusions with aberrant epigenetic and transcriptional functions. However, direct therapeutic targeting of leukemia fusion proteins has not been accomplished so far. Although high remission rates can be induced in patients diagnosed with AML1-ETO/t(8;21)-positive AML only half of them achieve long-term disease-free survival (Papaemmanuiel et al., NEJM, 2016). In the other half of these patients, the disease maintaining leukemia stem cell (LSC) clone is not eliminated by chemotherapy. A functional characteristic of LSCs is unlimited self-renewal capacity and several signaling pathways have been identified that maintain stem cell self-renewal. Targeting the oncogene induced self-renewal capacity of LSCs has great potential to eliminate the malignant clone and prevent relapse. To identify oncogenic cellular functions with relevance for LSC self-renewal, we performed global proteome profiling in murine AML1-ETO9a (AE) compared to MLL-AF9 (MA9) driven LSCs. Gene set enrichment analyses revealed a significant enrichment of calcium-dependent cellular functions and Phospholipase C (PLC)-signaling in AE LSCs. These data could be confirmed in sorted CD34+ blasts from AE-positive AML when compared to non-AE-AML. All PLC family members are regulators of Ca2+ homeostasis. However, when analyzing published AML gene expression datasets we found exclusively PLCG1 to be highly expressed in t(8;21) AML. Conditional activation of AE in embryonic stem cells resulted in induction of PLCG1 expression and PLCG1 was identified as a direct target of the AE fusion by ChIP-sequencing in AE-positive Kasumi-1 cells.Here, PLCG1 depletion resulted in reduced Ca2+ release, impaired proliferation and reduced colony formation in vitro. In a xenograft model, inactivation of PLCG1 resulted not only in delayed disease development (median survival shNT vs. shPLCG1: 135 days vs. not reached, p=0.02) but also in reduction of disease penetrance by 87%. Consistent with these results, transcriptome analysis revealed strong induction of gene sets related to myeloid differentiation and down-regulation of gene sets linked to proliferation, stemness and c-Myc targets. To confirm the functional role of PLCG1-signaling in AE-driven LSCs, we generated a new conditional knockout mouse model for Plcg1 and induced leukemia using the oncogenes AE and KRAS-G12D (AE/K). Genetic inactivation of Plcg1in vivo after engraftment of leukemic cells resulted in significant reduction of LSC numbers (p=0.04) and a reduction of disease penetrance by 67% in primary recipients. Isolated LSCs revealed induction of differentiation, loss of cell cycle activity and failed to re-establish disease in secondary recipients (Plcg1+/+ vs. Plcg1-/-: median survival 12 days vs. not reached; p=0.0001). In contrast, genetic deletion of Plcg1 appeared to be dispensable for normal murine HSC function during primary and secondary transplantation. Primary human t(8;21) AML cells (derived from 4 different donors) showed impaired colony forming capacity following PLCG1 inactivation in vitro irrespective of co-occurring mutations while colony formation of human CD34+ BM cells was not affected to a major extent. As Ca2+ signaling appeared deregulated in t(8;21) AML, we aimed to investigate the effects of pharmacologic Ca2+ inhibition as a tractable target downstream of PLCG1. To assess specifically for LSC function, we treated primary recipient mice with established AE/K-driven leukemia with the clinically approved calcineurin inhibitor ciclosporin (CsA), a compound that blocks intracellular Ca2+ release. CsA-treated animals showed reduction in total leukemic burden (spleen weight diluent vs. CsA, p=0.01) and LSC numbers (p=0.02). This resulted in increased survival of secondary recipient hosts (diluent vs. CsA: median 15 vs. 29 days, p=0.0002). These effects could not be observed for other oncogenes (e.g. MA9), confirming its specificity for AE-induced disease. Consistently, CsA treated primary human t(8;21)-positive AML blasts failed to form colonies in methylcellulose. In summary, our findings identified PLCG1-dependent Ca2+ signaling as a critical pathway for t(8;21) LSC maintenance and self-renewal. Most importantly, as PLCG1 is dispensable for maintenance of normal HSPCs, PLCG1 could serve as a novel therapeutic target in t(8;21) AML. Disclosures Döhner: Daiichi: Honoraria; Jazz: Honoraria; Novartis: Honoraria; Celgene: Honoraria; Janssen: Honoraria; CTI Biopharma: Consultancy, Honoraria. Bullinger:Novartis: Honoraria; Menarini: Honoraria; Jazz Pharmaceuticals: Honoraria; Abbvie: Honoraria; Astellas: Honoraria; Amgen: Honoraria; Seattle Genetics: Honoraria; Sanofi: Honoraria; Janssen: Honoraria; Hexal: Honoraria; Gilead: Honoraria; Daiichi Sankyo: Honoraria; Celgene: Honoraria; Bristol-Myers Squibb: Honoraria; Bayer: Other: Financing of scientific research; Pfizer: Honoraria.

Selective Dependency of MLL-Rearranged Leukemia on Immunoproteasome Function

Several cellular pathways control the fine balance between self-renewal and differentiation to maintain leukemia-initiating cell (LIC) function. To identify cellular dependencies with relevance for oncogenic fusion proteins, we performed global proteome profiling. Acute myeloid leukemia (AML) was induced by retroviral expression of either MLL-AF9 (MA9) or AML1-ETO9a (AE) in murine hematopoietic stem and progenitor cells (HSPCs) (Lineage-Sca1+Kit+, LSK) which were subsequently transplanted into irradiated syngeneic recipients. After onset of leukemia, LIC-enriched (GFP+ Kithigh) cells isolated from 4 different primary recipients (per oncogene) were analyzed by in-depth quantitative proteomic analysis using high-resolution mass spectrometry (MS). More than 3,000 proteins were quantified with 868 proteins being differentially expressed between MA9 and AE LIC-enriched populations. In MLL-rearranged (MLLr) cells, gene set enrichment analysis (GSEA) revealed significant enrichment of cellular functions related to protein degradation and proteasome function. As this enrichment is present in MLLr-leukemia but not AE-driven LICs, may indicate an oncogene specific vulnerability. Expression of proteasome subunits is highly heterogeneous between different cell types and therefore may also be influenced by the underlying differentiation stage or oncogenic fusion. In published AML gene-expression datasets, immunoproteasome (IP) subunits PSMB8/LMP7 (p=0.0003***), PSMB9/LMP2 (p=0.0007***) and PSMB10/MECL1 (p<0.0001****) showed significantly higher expression in MLLr compared to non-MLLr-AML. IP is a proteasomal variant constitutively expressed in cells of hematopoietic origin, induced under stimulation with pro-inflammatory cytokines and relevant for mediating stress-responses during inflammation and infection. To assess for functional dependency of MLLr cells on IP subunits we performed an in vitro CRISPR/Cas9 dropout screen in MLLr MOLM-13 cells. Genetic inactivation of PSMB8/LMP7 resulted in outcompetition with 3/5 sgRNAs, while there was less dependency detectable for the other subunits. Specificity of this finding was confirmed in 5 different cell lines (4 MLLr; 1 non-MLLr) by RNAi using 2 shRNAs against PSMB8/LMP7 versus non-targeting control. To confirm these findings in primary cells, we used a previously published conventional LMP7 knockout mouse model (Fehling et al., Science, 1994). LSK cells sorted from the bone marrow (BM) of LMP7 knockout and wildtype mice were retrovirally transformed with either MA9, MLL-ENL (ME) or NUP98-HOXA9 (as non-MLLr control) to assess for disease development by serial plating in methylcellulose. Only in MA9 or ME transformed cells LMP7-deficiency limited re-plating capacity to 2-4 rounds. When we injected 2,5x 104 MA9-infected LSK cells into sublethally irradiated recipient mice, recipients of MA9-LMP7-/- cells (n=12) and MA9-LMP7+/+ (n=12) showed development of AML. However, recipients of MA9-LMP7-/- cells had a significant delay in AML development (median survival 63.0 days for LMP7+/+ versus 92.5 days for LMP7 -/- animals, p=0.0387*). Besides the significant delay in AML development, disease penetrance was reduced by 50%, indicating that deficiency for LMP7 impairs development of MA9 driven AML. In contrast, immunophenotypic abundance of HSPCs in LMP7-/- versus LMP7+/+ animals revealed comparable numbers in all relevant subpopulations. Competitive transplantation of LMP7-/- BM into recipient hosts showed no competitive disadvantage or lack of self-renewal capacity compared to LMP7+/+ controls. Pharmacologic inhibition of IP function using the specific LMP7-inhibitor PR-957 (ONX-0914) resulted in significant delay of disease development in secondary recipient hosts. To assess its effect on LIC frequency we performed limiting dilution assays of MA9 leukemic cells in sublethally irradiated recipient mice. PR-957 treatment reduced LIC frequency compared to DMSO control (1/57410 vs. 1/4450). Pharmacologic inhibition of PSMB8/LMP7 in human MLLr leukemia cell lines induced cellular differentiation. Likewise, cell cycle and metabolism appeared affected, functions which could be confirmed by global transcriptome analysis. Taken together, our studies uncover a selective dependency of MLLr-leukemia on IP function and identify PSMB8/LMP7 as a tractable target. Disclosures Heidel: Celgene: Consultancy; Novartis: Consultancy, Research Funding; CTI: Consultancy.

Assessment of the Utility of the Oral Fluid and Plasma Proteomes for Hydrocodone Exposure.

Non-medical use and abuse of prescription opioids is a growing problem in both the civilian and military communities, with minimal technologies for detecting hydrocodone use. This study explored the proteomic changes that occur in the oral fluid and blood plasma following controlled hydrocodone administration in 20 subjects. The global proteomic profile was determined for samples taken at four time points per subject: pre-exposure and 4, 6, or 168hours post-exposure. The oral fluid samples analyzed herein provided greater differentiation between baseline and response time points than was observed with blood plasma, at least partially due to significant person-to-person relative variability in the plasma proteome. A total of 399 proteins were identified from oral fluid samples, and the abundance of 118 of those proteins was determined to be significantly different upon metabolism of hydrocodone (4 and 6hour time points) as compared to baseline levels in the oral fluid (pre-dose and 168hours). We present an assessment of the oral fluid and plasma proteome following hydrocodone administration, which demonstrates the potential of oral fluid as a noninvasive sample that may reveal features of hydrocodone in opioid use, and with additional study, may be useful for other opioids and in settings of misuse.

Proteomic analysis of thioproline misincorporation in Escherichia coli

Recently it was discovered that thioproline, an unnatural analog of proline, can arise in vivo from the reaction of cysteine and formaldehyde in cells under oxidative stress. Sequence-specific bioincorporation of thioproline into proteins was studied via shotgun proteomics of Escherichia coli (E. coli) cells. In a strain auxotrophic for proline, thioproline was found widely incorporated in lieu of proline when the cells were incubated with thioproline. In total 1428 proteins and 235 distinct thioproline-containing peptides were identified. Label-free relative quantitation revealed 102 differentially expressed proteins (82 up-regulated and 20 down-regulated) in the thioproline-treated group (with thioproline in the medium) relative to the control group (with proline in the culture medium). Pathway enrichment analysis of the differentially expressed proteins showed that amino acid biosynthesis and protein synthesis has been most affected by thioproline exposure, as expected. Phenotypically, the thioproline-treated group was found to exhibit slower cell growth and stronger antioxidant capacity relative to the control. SignificanceThioproline is a secondary metabolite of formaldehyde and a structural analog of proline. It is also known to exhibit a wide variety of pharmaceutical properties, but its exact biochemical role in the cell has not been elucidated. In this paper, we studied thioproline misincorporation (in lieu of proline) events during protein synthesis in E. coli. Global proteome profiling revealed that thioproline is extensively misincorporated throughout the proteome in E. coli cells exposed to thioproline, and pathways related to amino acid and protein biosynthesis are up-regulated. In addition, we demonstrated that pretreatment with thioproline appeared to increase E. coli cells' capacity to tolerate oxidative stress. Our findings suggest a novel explanation of thioproline's known antioxidative properties. This is, to our knowledge, the first ever study of thioproline misincorporation at the proteome level in any organism.

Integrative Tumor Profiling Following a Ketogenic Diet Offers a Window into the Interplay between Metabolic Vulnerabilities and Radiation Sensitization in Glioblastoma.

Glioblastoma (GBM) continues to be an invariably fatal malignancy with limited treatment options. Although considerable progress has been made in understanding molecular alterations in these tumors, this level of knowledge has not translated to clinical improvements. Metabolic reprogramming represents a hallmark of cancer and may serve as a therapeutic target. A ketogenic diet (KD) is a clinical strategy designed to target tumor metabolism and represents an active area of research. Although both preclinical and clinical data demonstrating efficacy has been mixed, a recent report suggests an unprecedented potential of a KD to enhance radiation response (RT) in an orthotopic model using an established mouse GBM cell line. In this study, we sought to validate these findings by determining the capacity of a KD to enhance RT in an aggressive, patient-derived GBM stem cell model and perform an integrative analysis on tissue to both define metabolic changes related to a KD and provide a mechanistic framework of activity. Immune deficient mice (nu/nu) were injected orthotopically with patient derived mesenchymal GBM tumor stem cells and randomized to four treatment arms (n=8/arm). Mice were fed ad libitum standard diet (SD) or KD (Bio-Serve; 1:4) alone or in combination with hypofractionated RT (hfRT; 6 Gy x 3). LC/GC-MS will be used to perform global metabolomic and proteomic profiling of tumor, serum, and normal brain of treated mice. Blood glucose and ketones were measured using the Abbott Precision Xtra meter kit. A KD demonstrated improved survival in GBM tumor bearing mice when compared to SD (mOS 22d vs. 17d; p=0.001) and equivalent survival when compared to SD mice treated with hfRT (mOS 24d; p= 0.57). The combination of KD and hfRT led to marked improvement in overall survival (mOS not reached; p<0.001). Although studies remain ongoing, at Day 29, 7/8 mice treated with KD+hfRT remained alive, while all 8 mice treated with SD+hfRT required euthanization due to neurologic progression. Surprisingly, alterations in blood ketone levels or glucose were not observed in mice treated with a KD. Global metabolomic and proteomic profiling of tumor, serum, and normal brain are ongoing. The anti-tumor activity and potent radiation sensitization of a KD was validated in an aggressive patient-derived GBM model. Ongoing integrative profiling of tumor and serum in mice treated with a KD will be presented to provide a previously undescribed insight into mechanisms of anti-tumor activity. As a KD is challenging to implement clinically, these mechanistic-based studies will provide a unique opportunity to learn how metabolism may be therapeutically exploited to provide a framework for the identification of novel mechanisms of radiation sensitization.

Global plasma protein profiling reveals DCM characteristic protein signatures

To identify potential biomarkers supporting better phenotyping and to improve understanding of the pathophysiology of dilated cardiomyopathy (DCM), this study comparatively analyzed plasma protein profiles of DCM patients and individuals with low normal and normal left ventricular ejection fraction (LVEF) by mass spectrometry.After plasma depletion using a MARS Hu-6 column, global proteome profiling was performed using a LTQ-Orbitrap Velos mass spectrometer. To compare and confirm results, two different discovery sets of samples were investigated. Differentially abundant proteins are involved in lipid metabolism, coagulation, and acute phase response. Serum paraoxonase 1 (PON1), cystatin C, lysozyme C, apolipoprotein A-II, and apolipoprotein M were validated by targeted protein analysis in a third independent patient cohort. Additionally, PON1 levels were also determined by an ELISA. These data highlight PON1 as a potential marker for differentiating DCM patients not only from patients with normal LVEF, but also from heart failure patients with preserved ejection fraction.The results highlight lipid metabolism and inflammation as the major pathways being altered in DCM patients in comparison to patients presenting with suspicious myocarditis to the hospital. SignificanceSeveral studies focused on the identification of heart failure (HF) associated protein signatures in blood plasma, but only few that are largely based on only small sample series considered specific HF pathologies. Therefore, we performed a comparative global blood plasma protein profiling of a larger sample of individuals with reduced left ventricular ejection fraction (LVEF) classified as dilated cardiomyopathy patients and individuals with normal LVEF but presenting with suspicious myocarditis. DCM patients displayed altered levels of proteins involved in lipid metabolism, coagulation, and acute phase response. The most reliable candidates, such as serum paraoxonase 1 (PON1), cystatin C, lysozyme C, apolipoprotein A-II, and apolipoprotein M were validated by targeted protein analysis in an independent patient cohort. PON1 levels were also determined by an ELISA. These data highlight PON1 as a potential marker for differentiating DCM patients not only from patients with normal LVEF, but also from heart failure patients with preserved ejection fraction.

Global proteomic profiling of the uniquely human CHRFAM7A gene in transgenic mouse brain

The uniquely human α7-nAChR gene (CHRFAM7A) is evolved from the fusion of two partially duplicated genes, FAM7 and α7-nAChR gene (CHRNA7), and is inserted on same chromosome 15, 5′ end of the CHRNA7 gene. Transcription of CHRFAM7A gene produces a 1256-bp open reading frame encoding dup-α7-nAChR, where a 27-aminoacid residues from FAM7 replaced the 146-aminoacid residues of the N-terminal extracellular ligand binding domain of α7-nAChR. In vitro, dup-α7-nAChR has been shown to form hetero-pentamer with α7-nAChR and dominant-negatively regulates the channel functions of α7-nAChR. However, the contribution of CHRFAM7A gene to the biology of α7-nAChR in the brain in vivo remains largely a matter of conjecture. CHRFAM7A transgenic mouse was created and differentially expressed proteins were profiled from the whole brain using iTRAQ-2D-LC-MS/MS proteomic technology. Proteins with a fold change of ≥1.2 or ≤0.83 and p < 0.05 were considered to be significant. Bioinformatics analysis showed that over-expression of the CHRFAM7A gene significantly modulated the proteins commonly involved in the signaling pathways of α7-nAChR-mediated neuropsychiatric disorders including Parkinson's disease, Alzheimer's disease, Huntington's disease, and alcoholism, suggesting that the CHRFAM7A gene contributes to the pathogenesis of neuropsychiatric disorders mostly likely through fine-tuning the functions of α7-nAChR in the brain.