Oral colostrum priming shortens hospitalization without changing the immunomicrobial milieu

OBJECTIVE

Oral colostrum priming (OCP) after birth in preterm infants is associated with improved weight gain and modification of the oral immunomicrobial environment. We hypothesized that OCP would modify salivary immune peptides and the oral microbiota in preterm infants.

STUDY DESIGN

We conducted a prospective, randomized clinical trial to determine the effects of OCP on salivary immune peptide representation in preterm infants (<32 weeks completed gestation at birth). Saliva samples were collected before and after OCP. Salivary immune peptide representation was determined via mass spectroscopy. Oral microbiota representation was determined via sequencing of the 16S rRNA gene.

RESULTS

Neonates who received OCP (n=48) had a 16-day reduction in the median length of hospitalization as compared with infants who did not receive OCP (n=51). No differences in salivary immune peptide sequence representation before OCP between groups were found. Longitudinal changes in peptides were detected (lysozyme C, immunoglobulin A, lactoferrin) but were limited to a single peptide difference (α-defensin 1) between primed and unprimed infants after OCP. We found no difference in microbial diversity between treatment groups at any time point, but diversity decreased significantly over time in both groups. OCP treatment marginally modified oral taxa with a decline in abundance of Streptococci in the OCP group at 30 days of life.

CONCLUSIONS

OCP had neither an effect on the salivary peptides we examined nor on overall oral bacterial diversity and composition. Infants who received OCP had a reduced length of hospitalization and warrants further investigation.

In vivo mapping of a dynamic ribonucleoprotein granule interactome in early Drosophila embryos

Macromolecular complexes and organelles play crucial roles within cells, but their native architectures are often unknown. Here, we use an evolutionarily conserved germline organelle, the germ granule, as a paradigm. In Drosophila embryos, we map one of its interactomes using a novel in vivo crosslinking approach that employs two interacting granule proteins and determines their common neighbor molecules. We identified an in vivo granule assembly of Tudor, Aubergine, motor and metabolic proteins, and RNA helicases, and provide evidence for direct interactions within this assembly using purified components. Our study indicates that germ granules contain efficient biochemical reactors involved in post‐transcriptional gene regulation.

Spatially Directed Proteomics of the Human Lens Outer Cortex Reveals an Intermediate Filament Switch Associated With the Remodeling Zone

PURPOSE

To quantify protein changes in the morphologically distinct remodeling zone (RZ) and adjacent regions of the human lens outer cortex using spatially directed quantitative proteomics.

METHODS

Lightly fixed human lens sections were deparaffinized and membranes labeled with fluorescent wheat germ agglutinin (WGA-TRITC). Morphology directed laser capture microdissection (LCM) was used to isolate tissue from four distinct regions of human lens outer cortex: differentiating zone (DF), RZ, transition zone (TZ), and inner cortex (IC). Liquid chromatography-tandem mass spectrometry (LC-MS/MS) of the plasma membrane fraction from three lenses (21-, 22-, and 27-year) revealed changes in major cytoskeletal proteins including vimentin, filensin, and phakinin. Peptides from proteins of interest were quantified using multiple reaction monitoring (MRM) mass spectrometry and isotopically-labeled internal peptide standards.

RESULTS

Results revealed an intermediate filament switch from vimentin to beaded filament proteins filensin and phakinin that occurred at the RZ. Several other cytoskeletal proteins showed significant changes between regions, while most crystallins remained unchanged. Targeted proteomics provided accurate, absolute quantification of these proteins and confirmed vimentin, periplakin, and periaxin decrease from the DF to the IC, while filensin, phakinin, and brain acid soluble protein 1 (BASP1) increase significantly at the RZ.

CONCLUSIONS

Mass spectrometry-compatible fixation and morphology directed laser capture enabled proteomic analysis of narrow regions in the human lens outer cortex. Results reveal dramatic cytoskeletal protein changes associated with the RZ, suggesting that one role of these proteins is in membrane deformation and/or the establishment of ball and socket joints in the human RZ.

Abstract 3050: Proteotoxic isolevuglandins are a central feature of radiation-induced pulmonary injury

The development of radiation induced lung injury (RiPI) is a major barrier that limits the dose that can be administered for controlling locally advanced lung cancer. Although progress has been made toward identifying the pathophysiological events responsible for RiPI, there is still a substantial gap in knowledge. It is well established that oxidative stress is central to the progression of RiPR. In addition, reoccurring cellular injury appears to be a critical event for promotion of radiation-induced fibrosis. Yet, the exact mechanism by which reactive oxygen species (ROS) promotes injury and the nature of the reoccurring injury remain to be fully elucidated. Isolevuglandins are generated by free radical peroxidation of phospholipid-esterified arachidonic acid. Isoketalation, defined as covalent adduction of isolevuglandins to the ϵ-amino group of protein lysine residues, is emerging as a novel mechanism by which ROS contributes to the genesis of some diseases. Although isoketalation promotes proteotoxicity and cytotoxicity that can contribute to disease progression, there is currently a lack of knowledge concerning its role in RiPI, the identity of susceptible proteins or whether the process can be genetically regulated. We used a multifaceted approach that included wild type, Nrf2 and p47 null mice, confocal microscopy, and LC-MS/MS analysis of affinity purified proteins to address these questions. Mass spectrometry and gene ontology analysis identified several potential protein targets involved in cytoskeletal regulation, Wnt signaling, integrin signaling, chemokine and cytokine signaling and histone biology. Genetic evidence linking oxidant challenge to protein adduction was provided from the mouse knockout studies where it was shown that Nrf2 expression suppressed, while NADPH oxidase activity promoted isoketalation. We found that when isoketalation exceeded a critical level, cells underwent apoptosis. We identified the cell types in mouse lung that are susceptible to adduction. In a C57BL/6j murine model of radiation induced pulmonary injury we found that ionizing radiation increased the level of adduction concomitant with the development of a chronic apoptotic phenotype. We used human idiopathic pulmonary fibrotic (IPF) tissue as a surrogate for radiation-induced pulmonary fibrotic tissue, which is very hard to obtain. Human IPF and radiation-induced lung injury share a common phenotype that includes slow/chronic development and a prominent ROS component. We found an abundance of adducted protein in human IPF compared to control lung tissue, identified collagen 1α1 as one of the highly adducted proteins and show that adduction impairs collagen degradation by MMP1. In summary, these data support the hypothesis that radiation-induced oxidant stress promotes pulmonary injury, in part, by a hitherto, unrecognized mechanism: isoketalation. Supported in part by NIH/NHLBI Grant RO1HL112286.

Citation Format: Stacy Mont, Sean S. Davies, L Jackson Roberts, Raymond L. Mernaugh, W Hayes McDonald, Brahm H. Segal, Jonathan A. Kropski, Timothy S. Blackwell, Konjeti R. Sekhar, James J. Galligan, Lawrence J. Marnett, Michael L. Freeman. Proteotoxic isolevuglandins are a central feature of radiation-induced pulmonary injury. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3050.

Accumulation of isolevuglandin-modified protein in normal and fibrotic lung

Protein lysine modification by γ-ketoaldehyde isomers derived from arachidonic acid, termed isolevuglandins (IsoLGs), is emerging as a mechanistic link between pathogenic reactive oxygen species and disease progression. However, the questions of whether covalent modification of proteins by IsoLGs are subject to genetic regulation and the identity of IsoLG-modified proteins remain unclear. Herein we show that Nrf2 and Nox2 are key regulators of IsoLG modification in pulmonary tissue and report on the identity of proteins analyzed by LC-MS following immunoaffinity purification of IsoLG-modified proteins. Gene ontology analysis revealed that proteins in numerous cellular pathways are susceptible to IsoLG modification. Although cells tolerate basal levels of modification, exceeding them induces apoptosis. We found prominent modification in a murine model of radiation-induced pulmonary fibrosis and in idiopathic pulmonary fibrosis, two diseases considered to be promoted by gene-regulated oxidant stress. Based on these results we hypothesize that IsoLG modification is a hitherto unrecognized sequelae that contributes to radiation-induced pulmonary injury and IPF.

Binding of the Covalent Flavin Assembly Factor to the Flavoprotein Subunit of Complex II

Escherichia coli harbors two highly conserved homologs of the essential mitochondrial respiratory complex II (succinate:ubiquinone oxidoreductase). Aerobically the bacterium synthesizes succinate:quinone reductase as part of its respiratory chain, whereas under microaerophilic conditions, the quinol:fumarate reductase can be utilized. All complex II enzymes harbor a covalently bound FAD co-factor that is essential for their ability to oxidize succinate. In eukaryotes and many bacteria, assembly of the covalent flavin linkage is facilitated by a small protein assembly factor, termed SdhE in E. coli. How SdhE assists with formation of the covalent flavin bond and how it binds the flavoprotein subunit of complex II remain unknown. Using photo-cross-linking, we report the interaction site between the flavoprotein of complex II and the SdhE assembly factor. These data indicate that SdhE binds to the flavoprotein between two independently folded domains and that this binding mode likely influences the interdomain orientation. In so doing, SdhE likely orients amino acid residues near the dicarboxylate and FAD binding site, which facilitates formation of the covalent flavin linkage. These studies identify how the conserved SdhE assembly factor and its homologs participate in complex II maturation.

Supporting data for analysis of the Helicobacter pylori exoproteome

The goal of this research was to analyze the composition of the Helicobacter pylori exoproteome at multiple phases of bacterial growth (Snider et al., 2015) [1]. H. pylori was grown in a serum-free medium and at serial time points, aliquots were centrifuged and fractionated to yield culture supernatant, a soluble cellular fraction, and a membrane fraction. Samples were analyzed by single dimensional LC-MS/MS analyses and multidimensional protein identification technology (MudPIT). Here we present data showing the numbers of assigned spectra and proportional abundance of individual proteins in each of the samples analyzed, along with a calculation of the level of enrichment of individual proteins in the supernatant compared to the soluble cellular fraction.

Alteration of the Helicobacter pylori membrane proteome in response to changes in environmental salt concentration

PURPOSE

Helicobacter pylori infection and a high dietary salt intake are each risk factors for the development of gastric cancer. We hypothesize that changes in environmental salt concentrations lead to alterations in the H. pylori membrane proteome.

EXPERIMENTAL DESIGN

Label-free and iTRAQ methods were used to identify H. pylori proteins that change in abundance in response to alterations in environmental salt concentrations. In addition, we biotinylated intact bacteria that were grown under high- or low-salt conditions, and thereby analyzed salt-induced changes in the abundance of surface-exposed proteins.

RESULTS

Proteins with increased abundance in response to high salt conditions included CagA, the outer membrane protein HopQ, and fibronectin domain-containing protein HP0746. Proteins with increased abundance in response to low salt conditions included VacA, two VacA-like proteins (ImaA and FaaA), outer-membrane iron transporter FecA3, and several proteins involved in flagellar activity. Consistent with the proteomic data, bacteria grown in high salt conditions exhibited decreased motility compared to bacteria grown in lower salt conditions.

CONCLUSION AND CLINICAL RELEVANCE

Alterations in the H. pylori membrane proteome in response to high salt conditions may contribute to the increased risk of gastric cancer associated with a high salt diet.

P-REX1 creates a positive feedback loop to activate growth factor receptor, PI3K/AKT and MEK/ERK signaling in breast cancer

Phosphatidylinositol 3-kinase (PI3K) promotes cancer cell survival, migration, growth and proliferation by generating phosphatidylinositol 3,4,5-trisphosphate (PIP3) in the inner leaflet of the plasma membrane. PIP3 recruits pleckstrin homology domain-containing proteins to the membrane to activate oncogenic signaling cascades. Anticancer therapeutics targeting the PI3K/AKT/mTOR (mammalian target of rapamycin) pathway are in clinical development. In a mass spectrometric screen to identify PIP3-regulated proteins in breast cancer cells, levels of the Rac activator PIP3-dependent Rac exchange factor-1 (P-REX1) increased in response to PI3K inhibition, and decreased upon loss of the PI3K antagonist phosphatase and tensin homolog (PTEN). P-REX1 mRNA and protein levels were positively correlated with ER expression, and inversely correlated with PI3K pathway activation in breast tumors as assessed by gene expression and phosphoproteomic analyses. P-REX1 increased activation of Rac1, PI3K/AKT and MEK/ERK signaling in a PTEN-independent manner, and promoted cell and tumor viability. Loss of P-REX1 or inhibition of Rac suppressed PI3K/AKT and MEK/ERK, and decreased viability. P-REX1 also promoted insulin-like growth factor-1 receptor activation, suggesting that P-REX1 provides positive feedback to activators upstream of PI3K. In support of a model where PIP3-driven P-REX1 promotes both PI3K/AKT and MEK/ERK signaling, high levels of P-REX1 mRNA (but not phospho-AKT or a transcriptomic signature of PI3K activation) were predictive of sensitivity to PI3K inhibitors among breast cancer cell lines. P-REX1 expression was highest in estrogen receptor-positive breast tumors compared with many other cancer subtypes, suggesting that neutralizing the P-REX1/Rac axis may provide a novel therapeutic approach to selectively abrogate oncogenic signaling in breast cancer cells.

Iron Toxicity in the Retina Requires Alu RNA and the NLRP3 Inflammasome

Excess iron induces tissue damage and is implicated in age-related macular degeneration (AMD). Iron toxicity is widely attributed to hydroxyl radical formation through Fenton's reaction. We report that excess iron, but not other Fenton catalytic metals, induces activation of the NLRP3 inflammasome, a pathway also implicated in AMD. Additionally, iron-induced degeneration of the retinal pigmented epithelium (RPE) is suppressed in mice lacking inflammasome components caspase-1/11 or Nlrp3 or by inhibition of caspase-1. Iron overload increases abundance of RNAs transcribed from short interspersed nuclear elements (SINEs): Alu RNAs and the rodent equivalent B1 and B2 RNAs, which are inflammasome agonists. Targeting Alu or B2 RNA prevents iron-induced inflammasome activation and RPE degeneration. Iron-induced SINE RNA accumulation is due to suppression of DICER1 via sequestration of the co-factor poly(C)-binding protein 2 (PCBP2). These findings reveal an unexpected mechanism of iron toxicity, with implications for AMD and neurodegenerative diseases associated with excess iron.

Shotgun proteomics: identification of unique protein profiles of apoptotic bodies from biliary epithelial cells

Shotgun proteomics is a powerful analytic method to characterize complex protein mixtures in combination with multidimensional liquid chromatography-tandem mass spectrometry (LC-MS/MS). We used this platform for proteomic characterization of apoptotic bodies in an effort to define the complex protein mixtures found in primary cultures of human intrahepatic biliary epithelial cells (HiBEC), human renal proximal tubular epithelial cells, human bronchial epithelial cells, isolated intrahepatic biliary epithelial cells from explanted primary biliary cirrhosis (PBC), and control liver using a total of 24 individual samples. Further, as additional controls and for purposes of comparison, proteomic signatures were also obtained from intact cells and apoptotic bodies. The data obtained from LC-MS/MS, combined with database searches and protein assembly algorithms, allowed us to address significant differences in protein spectral counts and identify unique pathways that may be a component of the induction of the signature inflammatory cytokine response against BECs, including the Notch signaling pathway, interleukin (IL)8, IL6, CXCR2, and integrin signaling. Indeed, there are 11 proteins that localize specifically to apoptotic bodies of HiBEC and eight proteins that were specifically absent in HiBEC apoptotic bodies.

CONCLUSION

Proteomic analysis of BECs from PBC liver compared to normal liver are significantly different, suggesting that an immunological attack affects the repertoire of proteins expressed and that such cells should be thought of as living in an environment undergoing continuous selection secondary to an innate and adaptive immune response, reflecting an almost "Darwinian" bias.

Short forms of Ste20-related proline/alanine-rich kinase (SPAK) in the kidney are created by aspartyl aminopeptidase (Dnpep)-mediated proteolytic cleavage

The Ste20-related kinase SPAK regulates sodium, potassium, and chloride transport in a variety of tissues. Recently, SPAK fragments, which lack the catalytic domain and are inhibitory to Na(+) transporters, have been detected in kidney. It has been hypothesized that the fragments originate from alternative translation start sites, but their precise origin is unknown. Here, we demonstrate that kidney lysate possesses proteolytic cleavage activity toward SPAK. Ion exchange and size exclusion chromatography combined with mass spectrometry identified the protease as aspartyl aminopeptidase. The presence of the protease was verified in the active fractions, and recombinant aspartyl aminopeptidase recapitulated the cleavage pattern observed with kidney lysate. Identification of the sites of cleavage by mass spectrometry allowed us to test the function of the smaller fragments and demonstrate their inhibitory action toward the Na(+)-K(+)-2Cl(-) cotransporter, NKCC2.

Abstract 434: LDL Apheresis Significantly Alters HDL Cargo and Function in Familial Hypercholesterolemia Subjects

In addition to cholesterol, HDL transports a wide-variety of cargo including vitamins, nucleic acids, and a diverse set of proteins. Outside of the reverse cholesterol transport pathway, HDL has alternative functions that contribute to its anti-atherogenicity, including anti-inflammatory, anti-oxidant, and signaling capacities. Recently, we found that HDL transports and delivers functional microRNAs to recipient cells, which likely confers HDL’s ability to suppress adhesion molecule expression in endothelial cells. As such, changes to HDL’s cargo impact many of these alternative functions, and thus its protective capacity. HDL dysfunction has been identified among patients with familial hypercholesterolemia (FH), an inherited disease due to mutations in the LDL receptor and associated with severe elevations in LDL-cholesterol (LDL-C) levels, which may necessitate LDL apheresis (LA) in management. Here we demonstrate that LA significantly alters HDL’s miRNA and protein signatures. We believe that these changes may have profound consequences on HDL’s protective capacity. Using density-gradient ultracentrifugation, we found 31 proteins to be significantly altered on HDL after LA, as determined by shotgun proteomics and multidimensional protein identification technology analysis. For example, vitamin D-binding protein (1.74-fold) was increased, while lipopolysaccharide-binding protein (-1.92-fold), platelet-activating factor acetylhydrolase (-2.06), and apolipoprotein A-V (-2.4-fold) were found to be decreased. Gene ontology and KEGG enrichment analysis demonstrated roles of these proteins in response to stress, coagulation, hemostasis, and vesicle-mediated transport. Fast-protein liquid chromatography was used to further purify HDL for miRNA profiling using TaqMan OpenArrays, and we found 8 HDL-miRNAs to be significantly altered -- 3 down (miR-302b -13.9-fold, miR-224 -1.8, miR-572 -2.4-fold) and 5 up (miR-7 9.8-fold, miR-208b 16.2-fold, miR-34a-3p 3-fold, miR-627 2.4-fold, miR-1183 4.8-fold). Both miR-302b and miR-224 decreased; these are miRNAs previously reported to suppress proliferation through targeting AKT2 and apoptosis, respectively. As such, these changes likely alter HDL’s function in FH subjects.

Sepp1(UF) forms are N-terminal selenoprotein P truncations that have peroxidase activity when coupled with thioredoxin reductase-1

Mouse selenoprotein P (Sepp1) consists of an N-terminal domain (residues 1-239) that contains one selenocysteine (U) as residue 40 in a proposed redox-active motif (-UYLC-) and a C-terminal domain (residues 240-361) that contains nine selenocysteines. Sepp1 transports selenium from the liver to other tissues by receptor-mediated endocytosis. It also reduces oxidative stress in vivo by an unknown mechanism. A previously uncharacterized plasma form of Sepp1 is filtered in the glomerulus and taken up by renal proximal convoluted tubule (PCT) cells via megalin-mediated endocytosis. We purified Sepp1 forms from the urine of megalin(-/-) mice using a monoclonal antibody to the N-terminal domain. Mass spectrometry revealed that the purified urinary Sepp1 consisted of N-terminal fragments terminating at 11 sites between residues 183 and 208. They were therefore designated Sepp1(UF). Because the N-terminal domain of Sepp1 has a thioredoxin fold, Sepp1(UF) were compared with full-length Sepp1, Sepp1(Δ240-361), and Sepp1(U40S) as a substrate of thioredoxin reductase-1 (TrxR1). All forms of Sepp1 except Sepp1(U40S), which contains serine in place of the selenocysteine, were TrxR1 substrates, catalyzing NADPH oxidation when coupled with H2O2 or tert-butylhydroperoxide as the terminal electron acceptor. These results are compatible with proteolytic cleavage freeing Sepp1(UF) from full-length Sepp1, the form that has the role of selenium transport, allowing Sepp1(UF) to function by itself as a peroxidase. Ultimately, plasma Sepp1(UF) and small selenium-containing proteins are filtered by the glomerulus and taken up by PCT cells via megalin-mediated endocytosis, preventing loss of selenium in the urine and providing selenium for the synthesis of glutathione peroxidase-3.

A unique covalent bond in basement membrane is a primordial innovation for tissue evolution

Basement membrane, a specialized ECM that underlies polarized epithelium of eumetazoans, provides signaling cues that regulate cell behavior and function in tissue genesis and homeostasis. A collagen IV scaffold, a major component, is essential for tissues and dysfunctional in several diseases. Studies of bovine and Drosophila tissues reveal that the scaffold is stabilized by sulfilimine chemical bonds (S = N) that covalently cross-link methionine and hydroxylysine residues at the interface of adjoining triple helical protomers. Peroxidasin, a heme peroxidase embedded in the basement membrane, produces hypohalous acid intermediates that oxidize methionine, forming the sulfilimine cross-link. We explored whether the sulfilimine cross-link is a fundamental requirement in the genesis and evolution of epithelial tissues by determining its occurrence and evolutionary origin in Eumetazoa and its essentiality in zebrafish development; 31 species, spanning 11 major phyla, were investigated for the occurrence of the sulfilimine cross-link by electrophoresis, MS, and multiple sequence alignment of de novo transcriptome and available genomic data for collagen IV and peroxidasin. The results show that the cross-link is conserved throughout Eumetazoa and arose at the divergence of Porifera and Cnidaria over 500 Mya. Also, peroxidasin, the enzyme that forms the bond, is evolutionarily conserved throughout Metazoa. Morpholino knockdown of peroxidasin in zebrafish revealed that the cross-link is essential for organogenesis. Collectively, our findings establish that the triad-a collagen IV scaffold with sulfilimine cross-links, peroxidasin, and hypohalous acids-is a primordial innovation of the ECM essential for organogenesis and tissue evolution.

Abstract PD1-9: P-REX1 employs a positive feedback loop to activate growth factor receptor/PI3K signaling

A mass spectrometry-based proteomic screen in ER+ breast cancer cells revealed that levels of P-REX1 are decreased upon PTEN loss, and increased upon PI3K inhibition. P-REX1 integrates signaling inputs from receptor tyrosine kinases (RTKs)/PI3K (via the PI3K phospholipid product PIP3) and G protein-coupled receptors (via Gbg subunits) to drive guanine exchange factor (GEF) activity on Rac1. RNAi knockdown of PREX1 and overexpression of exogenous PREX1 in ER+ breast cancer cells respectively decreased and increased activation of insulin-like growth factor receptor-1 (IGF-1R)/insulin receptor (InsR), PI3K/AKT/SGK3, and MEK/Erk under steady-state and growth factor (IGF-1, Heregulin)-stimulated conditions. While the P-REX1 homologue P-REX2a was previously shown to inhibit PTEN phosphatase activity to activate the PI3K/AKT pathway, we did not detect an effect of P-REX1 on PTEN activity. PREX1 knockdown suppressed PI3K/AKT signaling in PTEN-null breast cancer cells; therefore, P-REX1 and P-REX2a may not be functionally redundant. Knockdown and overexpression of PREX1 respectively increased and decreased doxorubicin-induced apoptosis in ER+ breast cancer cells, linking PREX1 with a pro-survival phenotype. Inhibition of signaling nodes downstream of PI3K (AKT, mTOR) derepresses feedback to activate RTKs and PI3K; knockdown of PREX1 abrogated the PI3K activation induced by inhibition of mTORC1/mTORC2. Structural analysis of P-REX1 revealed that the DH domain (which binds Gβγ and is required for GEF activity) is dispensable for P-REX1 effects on PI3K signaling, while the PH domain [which binds PIP3 and PI(3,4)P2] is required. These data place P-REX1 in a positive feedback loop, whereby PI3K generates PIP3 and PI(3,4)P2, and P-REX1 binds these phospholipids at the plasma membrane. In turn, P-REX1 promotes RTK activation, and RTKs activate PI3K/AKT and MEK/Erk signaling.

Gene expression profiling of diverse types of solid tumors (n = 2,009) and cancer cell lines (n = 807) revealed that PREX1 mRNA is most abundant in ER+ breast tumors compared to other subtypes. Reverse-phase protein array (RPPA) analysis of lysates from 712 breast tumors showed that P-REX1 levels are inversely correlated with markers of PI3K/AKT/mTOR pathway activation. Further, P-REX1 levels are higher in ER+ tumors than ER- tumors. In another series of 1,293 carcinomas, PREX1 was genetically amplified or mutated in 6.2% of cases, and in 5% of breast cancers. We then tested whether PREX1 lesions co-exist with other PI3K pathway-activating lesions. Among genes encoding proteins implicated in RTK/PI3K signaling and phosphatidylinositol metabolism, we found a significant enrichment for PREX1 mutation/amplification in 54/79 (68%) genes across 1,523 carcinomas. We tested the effects of 7 PREX1 mutants found in breast tumors on PI3K signaling in vitro. A G344R mutation in the PREX1 PH domain conferred increased affinity for PIP3 and PI(3,4)P2, and increased the levels of phospho-AKT. These findings suggest that P-REX1 is an ER+ breast tumor-specific oncogene, and PREX1 mutations increase its oncogenic effects in breast cancer. We propose that neutralizing P-REX1 function is a novel therapeutic approach to selectively abrogate oncogenic signaling in ER+ breast cancers while sparing normal tissues.

Citation Information: Cancer Res 2013;73(24 Suppl): Abstract nr PD1-9.

Proteome informatics research group (iPRG)_2012: a study on detecting modified peptides in a complex mixture

The proteome informatics research group of the Association of Biomolecular Resource Facilities conducted a study to assess the community's ability to detect and characterize peptides bearing a range of biologically occurring post-translational modifications when present in a complex peptide background. A data set derived from a mixture of synthetic peptides with biologically occurring modifications combined with a yeast whole cell lysate as background was distributed to a large group of researchers and their results were collectively analyzed. The results from the twenty-four participants, who represented a broad spectrum of experience levels with this type of data analysis, produced several important observations. First, there is significantly more variability in the ability to assess whether a results is significant than there is to determine the correct answer. Second, labile post-translational modifications, particularly tyrosine sulfation, present a challenge for most researchers. Finally, for modification site localization there are many tools being employed, but researchers are currently unsure of the reliability of the results these programs are producing.

Abstract PR05: P-REX1 creates a positive feedback loop to activate growth factor receptor/PI3K signaling

A mass spectrometry-based proteomic screen in ER+ breast cancer cells revealed that levels of P-REX1 are decreased upon loss of PTEN, and increased upon inhibition of PI3K. P-REX1 is a cytoplasmic protein that integrates signaling inputs from receptor tyrosine kinases (RTKs)/PI3K (via the PI3K phospholipid product PIP3) and G protein-coupled receptors (via Gβγ subunits) to drive guanine exchange factor (GEF) activity on Rac1, promoting cytoskeletal remodeling and cell migration. RNAi-mediated knockdown of PREX1 and overexpression of exogenous PREX1 in ER+ breast cancer cells, respectively, decreased and increased activation of insulin-like growth factor receptor-1 (IGF-1R)/insulin receptor (InsR), PI3K/AKT/SGK3, and MEK/Erk under steady-state and growth factor (IGF-1, Heregulin)-stimulated conditions. While the P-REX1 homologue P-REX2a was previously shown to inhibit PTEN phosphatase activity to activate the PI3K/AKT pathway, we did not detect an effect of P-REX1 on PTEN activity. PREX1 knockdown suppressed PI3K/AKT signaling in PTEN-null breast cancer cells; therefore, P-REX1 and P-REX2a may not be functionally redundant. Inhibition of signaling nodes downstream of PI3K (AKT, mTOR) derepresses feedback to activate RTKs and PI3K; knockdown of PREX1 abrogated the PI3K activation induced by inhibition of mTORC1/mTORC2. Structural analysis of P-REX1 revealed that the DH domain (which binds Gβγ and is required for GEF activity) is dispensable for P-REX1 effects on PI3K signaling, while the PH domain [which binds PIP3 and PI(3,4)P2] is required. These data place P-REX1 in a positive feedback loop, whereby PI3K generates PIP3 and PI(3,4)P2, P-REX1 binds these phospholipids at the plasma membrane, P-REX1 promotes RTK activation, and RTKs activate PI3K/AKT and MEK/Erk signaling.

Gene expression profiling of diverse types of solid tumors (n = 2,009) and cancer cell lines (n = 807) revealed that PREX1 mRNA is most abundant in ER+ breast tumors compared to other subtypes. Reverse-phase protein array (RPPA) analysis of lysates from 712 breast tumors revealed that P-REX1 levels are inversely correlated with markers of PI3K/AKT/mTOR pathway activation. Furthermore, P-REX1 levels are higher in ER+ tumors than ER- tumors. In another series of 1,293 carcinomas, PREX1 was amplified or mutated in 6.2% of cases, and in 5% of breast cancers. Finally, we tested whether PREX1 lesions co-exist with other PI3K pathway-activating lesions. Among genes encoding proteins implicated in RTK/PI3K signaling and phosphatidylinositol metabolism, we found a significant enrichment for PREX1 mutation/amplification in 54/79 (68%) genes across 1,523 carcinomas. We tested the effects of 7 PREX1 mutants found in breast tumors on PI3K signaling in vitro. A G344R mutation in the PREX1 PH domain conferred increased affinity for PIP3 and PI(3,4)P2, and increased levels of phospho-AKT. These findings suggest that P-REX1 is an ER+ breast tumor-specific oncogene, and PREX1 mutations increase its oncogenic effects in breast cancer. We propose that neutralizing P-REX1 function is a novel therapeutic approach to selectively abrogate oncogenic signaling in ER+ breast cancers while sparing normal tissues.

This abstract is also presented as Poster A060.

Citation Format: Lloye M. Dillon, Jennifer R. Bean, Wei Yang, Justin M. Balko, W. Hayes McDonald, David B. Friedman, Ana M. Gonzalez-Angulo, Gordon B. Mills, Carlos L. Arteaga, Todd W. Miller. P-REX1 creates a positive feedback loop to activate growth factor receptor/PI3K signaling. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Breast Cancer Research: Genetics, Biology, and Clinical Applications; Oct 3-6, 2013; San Diego, CA. Philadelphia (PA): AACR; Mol Cancer Res 2013;11(10 Suppl):Abstract nr PR05.

Identification of proteins at active, stalled, and collapsed replication forks using isolation of proteins on nascent DNA (iPOND) coupled with mass spectrometry

Both DNA and chromatin need to be duplicated during each cell division cycle. Replication happens in the context of defects in the DNA template and other forms of replication stress that present challenges to both genetic and epigenetic inheritance. The replication machinery is highly regulated by replication stress responses to accomplish this goal. To identify important replication and stress response proteins, we combined isolation of proteins on nascent DNA (iPOND) with quantitative mass spectrometry. We identified 290 proteins enriched on newly replicated DNA at active, stalled, and collapsed replication forks. Approximately 16% of these proteins are known replication or DNA damage response proteins. Genetic analysis indicates that several of the newly identified proteins are needed to facilitate DNA replication, especially under stressed conditions. Our data provide a useful resource for investigators studying DNA replication and the replication stress response and validate the use of iPOND combined with mass spectrometry as a discovery tool.

Abstract LB-37: P-REX1 is a novel PTEN-interacting protein that activates PI3K signaling in breast cancer

The mechanism(s) underlying regulation of the tumor suppressor phosphatase PTEN, which negatively regulates phosphatidylinositol 3-kinase (PI3K) signaling, remains unclear. The PI3K/AKT pathway regulates cancer cell growth, survival, and metabolism. Since PTEN is expressed and PI3K is hyperactivated in the majority of breast cancers, we hypothesized that PTEN is inhibited by protein interactions, thus derepressing PI3K signaling. A proteomic screen to identify novel PTEN-binding proteins in breast cancer cells revealed interaction with P-REX1, a known Rac guanine exchange factor (GEF). A separate proteomic experiment to identify PTEN/PI3K-regulated proteins showed that P-REX1 levels are decreased upon loss of PTEN and increased upon inhibition of PI3K. PTEN/P-REX1 interaction and the effects of pharmacological PI3K pathway inhibitors on P-REX1 levels were validated by immunoprecipitation/immunoblot analyses. In reverse-phase protein array analysis of lysates from 597 primary human breast tumors, levels of P-REX1 protein were positively correlated with PTEN protein, and inversely correlated with phospho-AKT-T308 (both p&lt;0.005). Comparing diverse types of carcinomas (n=2,009 from International Genomics Consortium's expO) and cancer cell lines (n=807 from Cancer Cell Line Encyclopedia), PREX1 mRNA levels were highest in ER+ and HER2+ breast cancer. In another series of 1,293 epithelial tumors (from The Cancer Genome Atlas), PREX1 is amplified or mutated in 6.2% of cases, and in 5% of breast cancers. Since multiple genomic lesions that can activate the PI3K pathway are known to co-exist in cancer cells, we tested whether PREX1 lesions co-exist with other PI3K pathway-activating lesions. Among genes encoding proteins implicated in growth factor receptor/PI3K/PTEN signaling and phosphatidylinositol metabolism, we found a significant enrichment for PREX1 mutation/amplification in 54/79 (68%) genes across 1,523 carcinomas. Overexpression and RNAi knockdown experiments revealed that P-REX1 increases steady-state and insulin-like growth factor-1 (IGF-1)-induced PI3K-dependent AKT phosphorylation in ER+ breast cancer cells. Studies are underway to identify the mechanistic role of P-REX1 in PI3K/PTEN signaling, and to determine whether P-REX1 directly inhibits PTEN. Our findings suggest that 1) P-REX1 is an activator of the PI3K/AKT pathway, 2) expression and mutation patterns implicate PREX1 in PI3K activation, and 3) neutralizing P-REX1 effects on PTEN/PI3K may be a novel therapeutic approach to selectively abrogate PI3K signaling in ER+ and HER2+ breast cancers while sparing normal tissues.

Citation Format: Lloye M. Dillon, Jennifer R. Bean, Justin M. Balko, W. Hayes McDonald, David B. Friedman, Ana M. Gonzalez-Angulo, Gordon B. Mills, Carlos L. Arteaga, Todd W. Miller. P-REX1 is a novel PTEN-interacting protein that activates PI3K signaling in breast cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr LB-37. doi:10.1158/1538-7445.AM2013-LB-37

Electrophilic adduction of ubiquitin activating enzyme E1 by N,N-diethyldithiocarbamate inhibits ubiquitin activation and is accompanied by striatal injury in the rat

Previous studies have shown ubiquitin activating enzyme E1 to be sensitive to adduction through both Michael addition and SN(2) chemistry in vitro. E1 presents a biologically important putative protein target for adduction due to its role in initiating ubiquitin based protein processing and the involvement of impaired ubiquitin protein processing in two types of familial Parkinson's disease. We tested whether E1 is susceptible to xenobiotic-mediated electrophilic adduction in vivo and explored the potential contribution of E1 adduction to neurodegenerative events in an animal model. N,N-Diethyldithiocarbamate (DEDC) was administered to rats using a protocol that produces covalent cysteine modifications in vivo, and brain E1 protein adducts were characterized and mapped using shotgun LC-MS/MS. E1 activity, global and specific protein expression, and protein carbonyls were used to characterize cellular responses and injury in whole brain and dorsal striatal samples. The data demonstrate that DEDC treatment produced S-(ethylaminocarbonyl) adducts on Cys234 and Cys179 residues of E1 and decreased the levels of activated E1 and total ubiquitinated proteins. Proteomic analysis of whole brain samples identified expression changes for proteins involved in myelin structure, antioxidant response, and catechol metabolism, systems often disrupted in neurodegenerative disease. Our studies also delineated localized injury within the striatum as indicated by decreased levels of tyrosine hydroxylase, elevated protein carbonyl content, increased antioxidant enzyme and α-synuclein expression, and enhanced phosphorylation of tau and tyrosine hydroxylase. These data are consistent with E1 having similar susceptibility to adduction in vivo as previously reported in vitro and support further investigation into environmental agent adduction of E1 as a potential contributing factor to neurodegenerative disease. Additionally, this study supports the predictive value of in vitro screens for identifying sensitive protein targets that can be used to guide subsequent in vivo experiments.

Dnt1 acts as a mitotic inhibitor of the spindle checkpoint protein dma1 in fission yeast

The interaction between Dma1 and Dnt1 in fission yeast is characterized. The results show that, similar to its homologue Chfr in higher eukaryotes, Dma1 in fission yeast can also affect factors required for microtubule nucleation and spindle formation at early mitosis.

The Schizosaccharomyces pombe checkpoint protein Dma1 couples mitotic progression with cytokinesis and is important in delaying mitotic exit and cytokinesis when kinetochores are not properly attached to the mitotic spindle. Dma1 is a ubiquitin ligase and potential functional relative of the human tumor suppressor Chfr. Dma1 delays mitotic exit and cytokinesis by ubiquitinating a scaffold protein (Sid4) of the septation initiation network, which, in turn, antagonizes the ability of the Polo-like kinase Plo1 to promote cell division. Here we identify Dnt1 as a Dma1-binding protein. Several lines of evidence indicate that Dnt1 inhibits Dma1 function during metaphase. First, Dnt1 interacts preferentially with Dma1 during metaphase. Second, Dma1 ubiquitin ligase activity and Sid4 ubiquitination are elevated in dnt1∆ cells. Third, the enhanced mitotic defects in dnt1Δ plo1 double mutants are partially rescued by deletion of dma1⁺, suggesting that the defects in dnt1∆ plo1 double mutants are attributable to excess Dma1 activity. Taken together, these data show that Dnt1 acts to restrain Dma1 activity in early mitosis to allow normal mitotic progression.

The evolutionary imprint of domestication on genome variation and function of the filamentous fungus Aspergillus oryzae

The domestication of animals, plants, and microbes fundamentally transformed the lifestyle and demography of the human species [1]. Although the genetic and functional underpinnings of animal and plant domestication are well understood, little is known about microbe domestication [2-6]. Here, we systematically examined genome-wide sequence and functional variation between the domesticated fungus Aspergillus oryzae, whose saccharification abilities humans have harnessed for thousands of years to produce sake, soy sauce, and miso from starch-rich grains, and its wild relative A. flavus, a potentially toxigenic plant and animal pathogen [7]. We discovered dramatic changes in the sequence variation and abundance profiles of genes and wholesale primary and secondary metabolic pathways between domesticated and wild relative isolates during growth on rice. Our data suggest that, through selection by humans, an atoxigenic lineage of A. flavus gradually evolved into a "cell factory" for enzymes and metabolites involved in the saccharification process. These results suggest that whereas animal and plant domestication was largely driven by Neolithic "genetic tinkering" of developmental pathways, microbe domestication was driven by extensive remodeling of metabolism.

Long isoform mouse selenoprotein P (Sepp1) supplies rat myoblast L8 cells with selenium via endocytosis mediated by heparin binding properties and apolipoprotein E receptor-2 (ApoER2)

In vivo studies have shown that selenium is supplied to testis and brain by apoER2-mediated endocytosis of Sepp1. Although cultured cell lines have been shown to utilize selenium from Sepp1 added to the medium, the mechanism of uptake and utilization has not been characterized. Rat L8 myoblast cells were studied. They took up mouse Sepp1 from the medium and used its selenium to increase their glutathione peroxidase (Gpx) activity. L8 cells did not utilize selenium from Gpx3, the other plasma selenoprotein. Neither did they utilize it from Sepp1(Δ240-361), the isoform of Sepp1 that lacks the selenium-rich C-terminal domain. To identify Sepp1 receptors, a solubilized membrane fraction was passed over a Sepp1 column. The receptors apoER2 and Lrp1 were identified in the eluate by mass spectrometry. siRNA experiments showed that knockdown of apoER2, but not of Lrp1, inhibited (75)Se uptake from (75)Se-labeled Sepp1. The addition of protamine to the medium or treatment of the cells with chlorate also inhibited (75)Se uptake. Blockage of lysosome acidification did not inhibit uptake of Sepp1 but did prevent its digestion and thereby utilization of its selenium. These results indicate that L8 cells take up Sepp1 by an apoER2-mediated mechanism requiring binding to heparin sulfate proteoglycans. The presence of at least part of the selenium-rich C-terminal domain of Sepp1 is required for uptake. RT-PCR showed that mouse tissues express apoER2 in varying amounts. It is postulated that apoER2-mediated uptake of long isoform Sepp1 is responsible for selenium distribution to tissues throughout the body.