NEDD4L intramolecular interactions regulate its auto and substrate NaV1.5 ubiquitination

NEDD4L is a HECT-type E3 ligase that catalyzes the addition of ubiquitin to intracellular substrates such as the cardiac voltage-gated sodium channel, NaV1.5. The intramolecular interactions of NEDD4L regulate its enzymatic activity which is essential for proteostasis. For NaV1.5, this process is critical as alterations in Na+ current is involved in cardiac diseases including arrhythmias and heart failure. In this study, we perform extensive biochemical and functional analyses that implicate the C2 domain and the first WW-linker (1,2-linker) in the autoregulatory mechanism of NEDD4L. Through in vitro and electrophysiological experiments, the NEDD4L 1,2-linker was determined to be important in substrate ubiquitination of NaV1.5. We establish the preferred sites of ubiquitination of NEDD4L to be in the second WW-linker (2,3-linker). Interestingly, NEDD4L ubiquitinates the cytoplasmic linker between the first and second transmembrane domains of the channel (DI-DII) of NaV1.5. Moreover, we design a genetically encoded modulator of Nav1.5 that achieves Na+ current reduction using the NEDD4L HECT domain as cargo of a NaV1.5-binding nanobody. These investigations elucidate the mechanisms regulating the NEDD4 family and furnish a new molecular framework for understanding NaV1.5 ubiquitination.

Valsartan nano-filaments alter mitochondrial energetics and promote faster healing in diabetic rat wounds

Chronic wounds are a common and debilitating condition associated with aging populations that impact more than 6.5 million patients in the United States. We have previously demonstrated the efficacy of daily topical 1% valsartan in treating wounds in diabetic mouse and pig models. Despite these promising results, there remains a need to develop an extended-release formulation that would reduce patient burden by decreasing the frequency of daily applications. Here, we used nanotechnology to self-assemble valsartan amphiphiles into a filamentous structure (val-filaments) that would serve as a scaffold in wound beds and allow for steady, localised and tunable release of valsartan amphiphiles over 24 days. Two topical treatments of this peptide-based hydrogel on full-thickness wounds in Zucker Diabetic Fatty rats resulted in faster rates of wound closure. By day 23, all val-filament treated wounds were completely closed, as compared to one wound closed in the placebo group. Mechanistically, we observed enrichment of proteins involved in cell adhesion and energetics pathways, downregulation of Tgf-β signalling pathway mediators (pSmad2, pSmad3 and Smad4) and increased mitochondrial metabolic pathway intermediates. This study demonstrates the successful synthesis of a sustained-release valsartan filament hydrogel, its impact on mitochondrial energetics and efficacy in treating diabetic wounds.

A cell-free antigen processing system reveals antigenic factors critical for HIV-1 epitope dominance and informs vaccine design

Certain CD4+T cell epitopes have been associated with immune control of HIV-1 replication and the presence of anti-Env neutralizing antibodies. However, it remains unclear what antigen-dependent factors influence the dominance of certain epitopes in HIV-1 proteins. To study HIV-1 epitope dominance, we used a cell-free antigen processing system previously developed by our group that utilizes soluble HLA-DR1*01:01 (DR1), HLA-DM (DM), protein antigen and three cathepsins in a reducing and low pH environment to allow for antigen binding and cleavage. We subjected HIV-1 antigens from Gag, Pol, Env and accessory proteins Vif, Nef, Tat, and Rev to this system. Immunoprecipitation of pMHC-II complexes followed by peptide elution and identification via LC-MS/MS revealed a map of DR1-bound epitopes across the near-full length HIV-1 proteome. Most identified epitopes were DM-resistant, and in some cases, DM narrowed the epitope diversity to one species. Importantly, we identified 28 novel epitopes, including several glycopeptides eluted from DR1. We noted epitope “hot spots” in HIV-1 antigens and striking similarities in epitopes from HIV polyproteins (Gag precursor) versus individual subunits (Gag capsid). Analysis of the location of several epitopes from smaller HIV-1 proteins based on their known crystal structures mapped to regions of low protein stability and higher solvent accessibility. Finally, we found that several epitopes induced memory CD4+T cell responses in persons living with HIV-1. Thus, by using a minimalist in vitro processing system, we can interrogate novel HIV-1 epitopes and understand how DM-resistance and antigen structure influence epitope dominance, which has important implications for vaccine design.

Systemic deletion of Atp7b modifies the hepatocytes' response to copper overload in the mouse models of Wilson disease

Wilson disease (WD) is caused by inactivation of the copper transporter Atp7b and copper overload in tissues. Mice with Atp7b deleted either globally (systemic inactivation) or only in hepatocyte recapitulate various aspects of human disease. However, their phenotypes vary, and neither the common response to copper overload nor factors contributing to variability are well defined. Using metabolic, histologic, and proteome analyses in three Atp7b-deficient mouse strains, we show that global inactivation of Atp7b enhances and specifically modifies the hepatocyte response to Cu overload. The loss of Atp7b only in hepatocytes dysregulates lipid and nucleic acid metabolisms and increases the abundance of respiratory chain components and redox balancing enzymes. In global knockouts, independently of their background, the metabolism of lipid, nucleic acid, and amino acids is inhibited, respiratory chain components are down-regulated, inflammatory response and regulation of chromosomal replication are enhanced. Decrease in glucokinase and lathosterol oxidase and elevation of mucin-13 and S100A10 are observed in all Atp7b mutant strains and reflect the extent of liver injury. The magnitude of proteomic changes in Atp7b-/- animals inversely correlates with the metallothioneins levels rather than liver Cu content. These findings facilitate identification of WD-specific metabolic and proteomic changes for diagnostic and treatment.

Fluid shear stress enhances differentiation of jejunal human enteroids in Intestine-Chip

There is increasing evidence that the study of normal human enteroids duplicates many known aspects of human intestinal physiology. However, this epithelial cell-only model lacks the many nonepithelial intestinal cells present in the gastrointestinal tract and exposure to the mechanical forces to which the intestine is exposed. We tested the hypothesis that physical shear forces produced by luminal and blood flow would provide an intestinal model more closely resembling normal human jejunum. Jejunal enteroid monolayers were studied in the Emulate, Inc. Intestine-Chip under conditions of constant luminal and basolateral flow that was designed to mimic normal intestinal fluid flow, with human umbilical vein endothelial cells (HUVECs) on the basolateral surface and with Wnt3A, R-spondin, and Noggin only on the luminal surface. The jejunal enteroids formed monolayers that remained confluent for 6-8 days, began differentiating at least as early as day 2 post plating, and demonstrated continuing differentiation over the entire time of the study, as shown by quantitative real-time polymerase chain reaction and Western blot analysis. Differentiation impacted villus genes and proteins differently with early expression of regenerating family member 1α (REG1A), early reduction to a low but constant level of expression of Na⁺-K⁺-2Cl^- cotransporter 1 (NKCC1), and increasing expression of sucrase-isomaltase (SI) and downregulated in adenoma (DRA). These results were consistent with continual differentiation, as was shown to occur in mouse villus enterocytes. Compared with differentiated enteroid monolayers grown on Transwell inserts, enteroids exposed to flow were more differentiated but exhibited increased apoptosis and reduced carbohydrate metabolism, as shown by proteomic analysis. This study of human jejunal enteroids-on-chip suggests that luminal and basolateral flow produce a model of continual differentiation over time and NaCl absorption that mimics normal intestine and should provide new insights in intestinal physiology.NEW & NOTEWORTHY This study showed that polarized enteroid models in which there is no basolateral Wnt3a, are differentiated, regardless of the Wnt3a status of the apical media. The study supports the concept that in the human intestine villus differentiation is not an all or none phenomenon, demonstrating that at different days after lack of basolateral Wnt exposure, clusters of genes and proteins exist geographically along the villus with different domains having different functions.

Lack of the MHC class II chaperone H2-O causes susceptibility to autoimmune diseases

DO (HLA-DO, in human; murine H2-O) is a highly conserved nonclassical major histocompatibility complex class II (MHC II) accessory molecule mainly expressed in the thymic medulla and B cells. Previous reports have suggested possible links between DO and autoimmunity, Hepatitis C (HCV) infection, and cancer, but the mechanism of how DO contributes to these diseases remains unclear. Here, using a combination of various in vivo approaches, including peptide elution, mixed lymphocyte reaction, T-cell receptor (TCR) deep sequencing, tetramer-guided naïve CD4 T-cell precursor enumeration, and whole-body imaging, we report that DO affects the repertoire of presented self-peptides by B cells and thymic epithelium. DO induces differential effects on epitope presentation and thymic selection, thereby altering CD4 T-cell precursor frequencies. Our findings were validated in two autoimmune disease models by demonstrating that lack of DO increases autoreactivity and susceptibility to autoimmune disease development.

A combination of cellular, molecular and in vivo approaches reveals that the non-classical MHC class II chaperone DO controls CD4 T cell thymic selection; its absence leads to susceptibility to two murine autoimmune diseases, collagen-induced arthritis and experimental autoimmune encephalomyelitis.

Characterizing the MHC-II immunopeptidome of HIV using a cell-free antigen processing system and peptide:MHC-specific antibodies

The breadth and specificity of CD4+T cell responses in HIV-1 infection are critical determinants of viral load and an individual’s ability to control infection. Most studies of CD4+T cell responses against HIV have relied on indirect evidence from peptide-pulsing analyses. Direct studies of antigen presentation have been hampered by the technical difficulties inherent in isolating peptide:MHC (p:MHC) complexes from HIV-infected cells. This has made it challenging to understand the HIV immunopeptidome, particularly for MHC-II epitopes. Using a cell-free antigen processing system, we have generated a near complete map of potential DR1-restricted HIV-1 epitopes. To confirm that epitopes identified using this system are actually presented by HIV-infected cells, we generated novel reagents termed single-chain diabodies (scDbs), or bispecific antibodies, which contain one Fab fragment against a p:MHC and another against CD3. These antibodies enable the use of CD8+ or CD4+T cells as readouts for antigen presentation. In proof of concept experiments, scDbs directed against immunodominant HIV MHC-I epitopes enhance cytokine production by CD8+ T cells, confirming presentation of these peptides. Preliminary experiments showed similar results with scDbs targeting MHC-II Gag epitopes on dendritic cells overexpressing the relevant peptides. We are now profiling the use of scDbs to detect antigen presentation in HIV-infected macrophages and CD4+T cells, the two target cells of infection. By establishing an immunopeptide map and tools to detect HIV peptide presentation, we can begin to address the kinetics, pathways, and cell types contributing to HIV antigen presentation on MHC-II, which will inform improved vaccine therapies.

Investigating contributions of the accessory molecule HLA-DO to development of autoimmune diseases

Used biochemical and biophysical studies, our laboratory has previously shown that HLA-DO (DO) enhances binding of DM-insensitive peptides, and reduces binding of DM-sensitive peptides to HLA-DR1 molecules. We hypothesized that these properties of DO might be important for ensuring proper presentation of immunodominant epitopes in the thymic medulla, a main DO expressing area; thereby ensuring proper negative selection. To test this hypothesis, we investigated the development of experimental autoimmune encephalomyelitis (EAE) in mice that were H2-O wild type (DO-WT), or knock-out (DO-KO). With this model, we found that DO-KO mice displayed faster disease onset in comparison to DO-WT mice. Accelerated disease onset correlated with increased recovery of MOG specific CD4 cells at all stages of disease in DO-KO mice. More recently, these observations were confirmed with a second autoimmune disease model, collagen induced arthritis (CIA), in transgenic HLA-DR1 expressing mouse. Using in vivo Near Infrared Fluorescence (NIRF) imaging, we found that DR1+DO-KO mice had increased levels of active collagen degradation relative to DR1+DO-WT mice. Diseased DR1+DO-KO mice were also found to have a greater accumulation of CD4 T cells in the affected areas. These observations suggest that DR1+DO-KO mice have larger pools of collagen specific CD4 T cells. Indeed, DR1+DO-KO mice immunized with the immunodominant collagen epitope showed an increased percentage of collagen specific CD4 T cells as compared to DR1+DO-WT mice. As a whole, data from both autoimmune models suggest that loss of DO function leads to an increased peripheral pool of autoreactive CD4 T cells, likely due to faulty negative selection.

Assessing non-classical antigen presentation in HIV-infected CD4+ T cells

CD4+T cells recognize peptides presented by MHC Class II (MHC-II) molecules on B cells, dendritic cells, and macrophages. Interestingly, in humans, activated CD4+ T cells themselves express MHC-II molecules (HLA-DR, -DP, -DQ), but their potential role as antigen processing cells has not been well characterized. Recent promising data in a simian immunodeficiency (SIV) model suggest that antigen presentation by CD4+ T cells may be important in immunity. In these studies, a vaccine incorporating SIV antigens into a cytomegalovirus vector induced MHC-II restricted CD8+ T cells in macaques. Notably, these non-canonical cells were also observed in HIV patients. Clones generated from these MHC-II restricted CD8+ T cells killed autologous HIV-infected CD4+ T cells, suggesting that HIV is processed and presented on MHC-II on CD4+ T cells. To investigate this potentially novel form of antigen presentation, we eluted peptides from HLA-DR on activated CD4+T cells and sequenced them by LC-MS/MS. We show for the first time that human primary CD4+ T cells indeed process and present peptides on HLA-DR. We are currently applying this approach to HIV-infected cells to detect HIV peptides. Given the low sensitivity of untargeted MS for rare viral peptides, we are also generating a library of MHC-II HIV epitopes presented on HLA-DR to help guide more targeted MS analysis. To create this library, we are using a MHC-II cell-free processing system. We have already identified several epitopes from HIV Gag, Pol, Env, Vif, Rev, and Tat, some of which we show elicit memory responses in HIV patients. Our studies reveal a novel role for CD4+ T cells in antigen presentation and show that a cell-free processing system can predict HIV epitopes that may be presented on these cells.

Investigating a role for the MHC class II accessory molecule HLA-DO in autoimmune disease

HLA-DO (DO), H2-O in mice, is a non-classical, non-polymorphic MHC Class II accessory molecule. Expressed primarily in the thymic medulla and B cells little is known about its physiological role in vivo. To gain insight into what role DO might have in CD4 T cell selection, our lab previously used in vitro biochemical assays to show that DO itself enhances the binding of DM insensitive peptides to the HLA-DR1 molecule, while inhibiting the binding of DM sensitive peptides. This led us to hypothesize that in vivo, DO might be important for ensuring proper presentation of immunodominant epitopes in the thymic medulla; thereby ensuring proper negative selection occurs. Lack of DO then could lead to a larger precursor pool of autoreactive CD4+ T cells in the periphery due to faulty negative selection. To test this, we utilized H2-O knock-out (KO) mice and the autoimmune model experimental autoimmune encephalomyelitis (EAE). With this model, we have found that KO mice have a faster onset of disease when compared to C57BL/6 wild-type mice. This increase in onset correlated with the recovery of more MOG specific cells from the CNS of KO mice at all stages of disease. Moreover, naïve mouse data also supports our hypothesis with naïve KO mice having a larger number of MOG specific CD4+ T cells. More recently, we found that KO mice also harbor increased percentages of regulatory T cells (Tregs) in both the naïve and diseased states. Correlating this finding with disease onset, we saw that KO Tregs appear to have impaired upregulating of the inhibitory molecule CTLA-4 in early disease. As a whole, our data suggests that KO mice not only have an increased precursor pool of autoreactive CD4 T cells but might also have impaired Treg function; all leading to faster disease onset.

MHC class II antigen-processing chaperone H2-O shapes CD4 T cell receptor repertoire

HLA-DO (DO) is a MHC class II-encoded, nonpolymorphic heterodimeric protein in humans (known as H2-O in mice). It is expressed only in thymic medulla, B cells and some subsets of dendritic cells. Although DO is found to form a stable complex with HLA—DM, its physical function remains unknown. To solve this mystery, our lab previously proposed a model suggesting that the DO facilitates the binding of DM-resistant peptides and inhibits the binding of DM-sensitive peptides to the HLA-DR1 molecules in vitro. Based on this model, we expected to see lower density of pMHC expression on mTEC cells in thymus of DO-KO mice, leading to faulty negative selection and different CD4 TCR repertoires as compared to DO-WT mice. By developing a “Prime-Restim” strategy based on the principle of mixed lymphocyte reaction, we observed the proliferation of primed DO-WT CD4 T cells in responding to repeated in vitro stimulations by antigen presenting cells from DO-KO mice and vice versa. This strategy led to enrichment of some clonal populations in DO-KO mice reactive to self-peptides presented by B cells from DO-WT mice. To identify the self-antigens these T cell clones recognize, we developed CD4 T cell hybridomas from them and screened their specificities with peptides eluted from B cells of DO-KO and DO-WT mice. We also identified a peptide from an autoimmunity-associated protein that eluted only from DO-KO B cells but not seen from DO-WT B cells. These results demonstrate that in the absence of DO, the peptide repertoire of MHC II in the DO-KO mice is different from the peptide repertoire of MHC II in the DO-WT mice. These findings support the idea that the expression of DO in thymic medulla might lead to better thymic deletion of self-reactive CD4 T cells.

Proteolysis by Granzyme B Enhances Presentation of Autoantigenic Peptidylarginine Deiminase 4 Epitopes in Rheumatoid Arthritis

Proteolysis of autoantigens can alter normal MHC class II antigen processing and has been implicated in the induction of autoimmune diseases. Many autoantigens are substrates for the protease granzyme B (GrB), but the mechanistic significance of this association is unknown. Peptidylarginine deiminase 4 (PAD4) is a frequent target of autoantibodies in patients with rheumatoid arthritis (RA) and a substrate for GrB. RA is strongly associated with specific MHC class II alleles, and elevated levels of GrB and PAD4 are found in the joints of RA patients, suggesting that GrB may alter the presentation of PAD4 by RA-associated class II alleles. In this study, complementary proteomic and immunologic approaches were utilized to define the effects of GrB cleavage on the structure, processing, and immunogenicity of PAD4. Hydrogen-deuterium exchange and a cell-free MHC class II antigen processing system revealed that proteolysis of PAD4 by GrB induced discrete structural changes in PAD4 that promoted enhanced presentation of several immunogenic peptides capable of stimulating PAD4-specific CD4+ T cells from patients with RA. This work demonstrates the existence of PAD4-specific T cells in patients with RA and supports a mechanistic role for GrB in enhancing the presentation of autoantigenic CD4+ T cell epitopes.

Combined Antibody/Lectin Enrichment Identifies Extensive Changes in the O-GlcNAc Sub-proteome upon Oxidative Stress

O-Linked N-acetyl-β-d-glucosamine (O-GlcNAc) is a dynamic post-translational modification that modifies and regulates over 3000 nuclear, cytoplasmic, and mitochondrial proteins. Upon exposure to stress and injury, cells and tissues increase the O-GlcNAc modification, or O-GlcNAcylation, of numerous proteins promoting the cellular stress response and thus survival. The aim of this study was to identify proteins that are differentially O-GlcNAcylated upon acute oxidative stress (H₂O₂) to provide insight into the mechanisms by which O-GlcNAc promotes survival. We achieved this goal by employing Stable Isotope Labeling of Amino Acids in Cell Culture (SILAC) and a novel "G5-lectibody" immunoprecipitation strategy that combines four O-GlcNAc-specific antibodies (CTD110.6, RL2, HGAC39, and HGAC85) and the lectin WGA. Using the G5-lectibody column in combination with basic reversed phase chromatography and C₁₈ RPLC-MS/MS, 990 proteins were identified and quantified. Hundreds of proteins that were identified demonstrated increased (>250) or decreased (>110) association with the G5-lectibody column upon oxidative stress, of which we validated the O-GlcNAcylation status of 24 proteins. Analysis of proteins with altered glycosylation suggests that stress-induced changes in O-GlcNAcylation cluster into pathways known to regulate the cell's response to injury and include protein folding, transcriptional regulation, epigenetics, and proteins involved in RNA biogenesis. Together, these data suggest that stress-induced O-GlcNAcylation regulates numerous and diverse cellular pathways to promote cell and tissue survival.

The hierarchy of two different immunodominant epitopes influences CD4+ T cell responses (APP5P.112)

A cell-free antigen processing system for MHC class II was recently reported that has proved to be effective in identifying physiologically relevant CD4+ T cell epitopes from proteins (Hartman/Kim, et al. Nat Med. 16, pp1333-40 (2010)). This system has also provided insights into the mechanism of epitope selection (Kim, et al. Nat Commun. 5:5369 (2014)). We applied this system to a mixture of two different antigens, H5N1-HA1 and LSA-NRC of malaria to examine if there would be a competition for epitope capture. While each dominant epitope from either protein was identified in the system individually, when both proteins were simultaneously present, HA1 dominant epitope was predominantly selected. The competition between different epitopes was verified in vivo by immunizing HLA-DR1 transgenic mice with a mixture of HA1 and LSA-NRC. A recall T cell proliferation showed that T cells responded only to the HA1 and its dominant epitope. These observations did not change even when DR1 mice were immunized with increasing molar ratio of LSA-NRC to HA1 (1:1, 2:1 or 4:1). However, T cell responded to both antigens if mice were immunized first with LSA-NRC dominant epitope followed by HA1 epitope. These findings show a hierarchy for the selection of dominant epitopes from different proteins during antigen processing. Immunodominance hierarchy among different antigens influences the epitope presentation to the same MHC II, which can be important factor for designing combination vaccines.

Divergent paths for the selection of immunodominant epitopes from distinct antigenic sources

Immunodominant epitopes are few selected epitopes from complex antigens that initiate T cell responses. Here, to provide further insights into this process, we use a reductionist cell-free antigen processing system composed of defined components. We use the system to characterize steps in antigen processing of pathogen-derived proteins or autoantigens and we find distinct paths for peptide processing and selection. Autoantigen-derived immunodominant epitopes are resistant to digestion by cathepsins, whereas pathogen-derived epitopes are sensitive. Sensitivity to cathepsins enforces capture of pathogen-derived epitopes by Major Histocompatibility Complex class II (MHC class II) prior to processing, and resistance to HLA-DM-mediated-dissociation preserves the longevity of those epitopes. We show that immunodominance is established by higher relative abundance of the selected epitopes, which survive cathepsin digestion either by binding to MHC class II and resisting DM-mediated-dissociation, or being chemically resistant to cathepsins degradation. Non-dominant epitopes are sensitive to both DM and cathepsins and are destroyed.

Multiple paths to immunodominance: dominant epitopes are captured by MHC II prior, or post antigen proteolysis, and are enriched by HLA-DM (APP2P.103)

Immunodominance is defined as the responsiveness of T cells to few selected peptide epitopes from complex antigens. To understand the mechanism of epitope selection from antigenic proteins for helper T cells, we used a cell-free antigen processing system composed of five purified proteins: HLA-DR, cathepsins B, H, S, and HLA-DM. We find that immunodominant epitopes are selected differently if derived from self proteins or from pathogens. Sensitivity to cathepsins and resistance to DM-mediated dissociation are equally contributing factors. Self-derived epitopes appear to be less susceptible to cathepsin digestion, whereas pathogen-derived epitopes are sensitive. Cathepsin sensitivity necessitates capture of epitopes by MHC II prior to processing by cathepsins. Resistance to DM-mediated dissociation increases longer epitope survival. We propose that most peptides generated from proteins do not gain immunodominance because they are sensitive to both DM and enzymatic digestions. Thus, immunodominance is established differently for different antigens incorporating functions of DM, cathepsins and MHC II, altogether help to ascertain higher abundance of the immunodominant epitope. Supported by grants from NIAID, R01AI063764 and R21 AI101987 to SS-N.

Cooperative functions of MHC II, HLA-DM, and cathepsins enhance the selection of immunodominant epitopes (P5008)

We developed a minimalist cell-free antigen-processing system for MHC class II that can identify physiologically selected T cell epitopes from antigens. The system utilizes purified proteins: HLA-DR1, cathepsin B, H, S, and HLA-DM. It was designed to mimic the specialized compartment for antigen processing with known defined molecular composition so that it can be a useful tool for elucidating steps involved in antigen processing and understanding the mechanisms of epitope selection. We found that prior digestion of antigens even for a few minutes eliminated the possibility of their immunodominant epitope capture by DR1. However, if those antigens were captured by DR1 first in the presence of DM, dominant epitopes were successfully selected. We observed simultaneously binding of DR1 and DR4 to denatured proteins detected by the biacore method. In another case, pre-digestion of antigen did not destroy the dominant epitope even though it showed sensitivity to DM mediated dissociation. We saw that this epitope got selected because it was less susceptible to enzymatic digestions and it was able to rebind to DR1 even in the presence of DM. Therefore, In general, most peptides generated from proteins do not get a chance to bind MHC II for presentation because they are sensitive to both DM and enzymatic digestions. Selection of immunodominant epitope is the results of collaborative reactions of DR1, DM, and cathepsins by increasing abundance of epitope capture by MHC II.

Huntingtin protein interactions altered by polyglutamine expansion as determined by quantitative proteomic analysis

Huntington disease (HD) is a neurodegenerative disorder caused by an expansion of a polyglutamine repeat within the HD gene product, huntingtin. Huntingtin, a large (347 kDa) protein containing multiple HEAT repeats, acts as a scaffold for protein-protein interactions. Huntingtin-induced toxicity is believed to be mediated by a conformational change in expanded huntingtin, leading to protein misfolding and aggregation, aberrant protein interactions and neuronal cell death. While many non-systematic studies of huntingtin interactions have been reported, they were not designed to identify and quantify the changes in the huntingtin interactome induced by polyglutamine expansion. We used tandem affinity purification and quantitative proteomics to compare and quantify interactions of normal or expanded huntingtin isolated from a striatal cell line. We found that proteins preferentially interacting with expanded huntingtin are enriched for intrinsically disordered proteins, consistent with previously suggested roles of such proteins in neurodegenerative disorders. Our functional analysis indicates that proteins related to energy production, protein trafficking, RNA post-transcriptional modifications and cell death were significantly enriched among preferential interactors of expanded huntingtin. Expanded huntingtin interacted with many mitochondrial proteins, including AIFM1, consistent with a role for mitochondrial dysfunction in HD. Furthermore, expanded huntingtin interacted with the stress granule-associated proteins Caprin-1 and G3BP and redistributed to RNA stress granules under ER-stress conditions. These data demonstrate that a number of key cellular functions and networks may be disrupted by abnormal interactions of expanded huntingtin and highlight proteins and pathways that may be involved in HD cellular pathogenesis and that may serve as therapeutic targets.

Presentation of immunodominant epitopes from mixture of protein antigens is hierarchial (100.21)

Immunodominance is defined as restricted responsiveness of T cells to a few selected epitopes from complex antigens. We have established a reductionist cell-free antigen-processing system for MHC class II that constitutes five purified components: HLA-DR1, HLA-DM, and three cathepsins. This system successfully identified the physiologically selected epitopes from two model antigens. When applied for de novo epitope identification to LSA-NRC of malaria, or HA1-H5N1 (Avian Flu), the system selected epitopes that were confirmed to be immunodominant by their capacity to activate CD4+ T cells in HLA-DR1 positive human volunteers or transgenic mice (Hartman/Kim, et al. Nat Med 16, pp1333-1340 (2010). To evaluate our system to a mixture of the above antigens, the system identified the epitopes from both antigens. We tested the immunogenicity of epitopes and the parent proteins in HLA-DR1 transgenic mice immunized with the mixture of both HA1 and LSA-NRC in a recall T cell proliferation assay. T cells responded only to the HA1 and its immunodominant epitope, while little, if any stimulation against LSA-NRC and its dominant epitope were measured. These observations did not change even when the ratio of LSA-NRC:HA1was 2:1. These findings show a hierarchy for the selection of immunodominant epitopes of different proteins during antigen processing, which can be important in design of combination vaccines.

T cell epitopes derived from autoantigens are selected differently than those from exogenous antigens (130.15)

We have established a novel minimalist cell-free MHC class II antigen-processing system for identifying immunodominant epitopes from protein antigens. The system constitutes HLA-DR1, HLA-DM (DM) and three cathepsins. This system not only identifies the immunogenic epitopes from complex protein antigens, but also provides insight to the mechanism of immunodominance. Understanding of how these immunogenic epitopes are selected certainly provides better strategies for developing effective peptide vaccine designs and therapies against infectious diseases, cancer, autoimmune diseases and allergy. Using our cell-free system, and based on the source of the antigens categorized as exogenous antigens versus autoantigens, we find that both DM and cathepsins are crucial in regulating the selection of immunodominant epitopes. Three types of determinants are generated: first, non-dominant epitopes that are sensitive to both DM mediated dissociation, and cathepsins digestion. These epitopes were eliminated immediately from peptide repertoire. Second, T cell epitopes derived from the exogenous antigen are DM resistant and cathepsin sensitive. Third, T cells epitopes derived from an antoantigen that are sensitive to DM mediated dissociation, but resistant to cathepsin digestion. This shows that generation of immunodominant epitopes is regulated differently depending on the source of proteins antigens.

In vitro enzymatic characterization of near full length EGFR in activated and inhibited states

The epidermal growth factor receptor (EGFR) is a single-pass transmembrane protein with an extracellular ligand-binding region and a cytoplasmic tyrosine kinase. Ligand binding activates the tyrosine kinase, which in turn initiates signaling cascades that influence cell proliferation and differentiation. EGFR activity is essential for normal development of many multicellular organisms, and inappropriate activation of EGFR is associated with multiple human cancers. Several drugs targeting EGFR activity are approved cancer therapies, and new EGFR-targeted therapies are being actively pursued. Much of what is known about EGFR structure and function is derived from studies of soluble receptor fragments. We report here an approach to producing an active, membrane-spanning form of EGFR of suitable purity, homogeneity, and quantity for structural and functional studies. We show that EGFR is capable of direct autophosphorylation of tyrosine 845, which is located on its kinase activation loop, and that the kinase activity of EGFR is approximately 500-fold higher in the presence of EGF vs the inhibitory anti-EGFR antibody cetuximab. The potencies of the small molecule EGFR kinase inhibitors erlotinib and lapatinib for various forms of EGFR were measured, and the therapeutic and mechanistic implications of these results considered.

Organic solvent extraction of proteins and peptides from serum as an effective sample preparation for detection and identification of biomarkers by mass spectrometry

A method to extract peptides and low molecular weight proteins from serum under denaturing conditions using acetonitrile containing 0.1% trifluoroacetic acid has been developed. The extraction procedure precipitates large, abundant proteins to simplify subsequent mass spectral analysis. This sample preparation method provides an efficient way to extract serum peptides, enabling them to be compared and identified using different mass spectrometry approaches. Surface-enhanced laser desorption/ionization-time of flight mass spectrometry analysis of mouse blood serum samples prepared by this method allowed detection of two markers which were significantly reduced in mice with B cell lymphoma tumor. One of these markers has been identified as apolipoprotein A-II.