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This abstract was withdrawn by the authors. Citation Format: Dillon SR, Evans LS, Rickel E, Lewis KE, Swanson R, Levin SD, Wolfson M, Peng SL, Swiderek KM. Withdrawn [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-20-03.

INTRODUCTION Others have described a subset of CD8 T cells (CD8 Treg) with immunosuppressive characteristics in inflammatory disease settings. CD8 Treg activation through canonical T cell receptors results in their oligoclonal expansion and perforin dependent elimination of pathogenic CD4 T cells. We have described the CD8 Treg network in Celiac patients and its potential to eliminate pathogenic CD4 T cells. Here we describe bispecific CD8 Treg modulators that activate CD8 Tregs, resulting in pathogenic CD4 T cell death. METHODS Novel bispecific CD8 Treg modulators were tested for target specificity by Octet and cell binding. The functional impact of CD8 Treg modulators was evaluated using flow and Luminex assays, and in a live cell co-culture system using Celiac patient derived CD8 Tregs and gliadin activated CD4 T cell targets. CD8 Treg modulators with specific molecular formats were then ranked for functional efficacy. RESULTS We tested a panel of bispecific CD8 Treg modulators with monovalent binding affinities in the low nanomolar range that selectively bind the CD8 Treg subset. Within 48 hours of CD8 Treg modulator addition to T cell co-cultures, CD8 Tregs had a rapid increase of cytolytic markers and degranulation in response to CD4 T cell targets. We observed a concomitant increase of activated CD4 T cell death and decrease of pro-inflammatory cytokines. CONCLUSIONS Our results indicate that a targeted approach to engage and activate CD8 Treg reduces pathogenic CD4 T cells. As this newly described CD8 Treg cell network is observed in many autoimmune diseases, we postulate that bispecific CD8 T cell modulators may represent a novel, selective and broadly applicable therapeutic approach for the treatment of human autoimmune diseases.

Acute graft-versus-host disease (aGVHD) remains a major complication of allogeneic hematopoietic cell transplantation (HCT). CD146 and CCR5 are proteins that mark activated T helper 17 (Th17) cells. The Th17 cell phenotype is promoted by the interaction of the receptor ICOS on T cells with ICOS ligand (ICOSL) on dendritic cells (DCs). We performed multiparametric flow cytometry in a cohort of 156 HCT recipients and conducted experiments with aGVHD murine models to understand the role of ICOSL+ DCs. We observed an increased frequency of ICOSL+ plasmacytoid DCs, correlating with CD146+CCR5+ T cell frequencies, in the 64 HCT recipients with gastrointestinal aGVHD. In murine models, donor bone marrow cells from ICOSL-deficient mice compared to those from wild-type mice reduced aGVHD-related mortality. Reduced aGVHD resulted from lower intestinal infiltration of pDCs and pathogenic Th17 cells. We transplanted activated human ICOSL+ pDCs along with human peripheral blood mononuclear cells into immunocompromised mice and observed infiltration of intestinal CD146+CCR5+ T cells. We found that prophylactic administration of a dual human ICOS/CD28 antagonist (ALPN-101) prevented aGVHD in this model better than did the clinically approved belatacept (CTLA-4-Fc), which binds CD80 (B7-1) and CD86 (B7-2) and interferes with the CD28 T cell costimulatory pathway. When started at onset of aGVHD signs, ALPN-101 treatment alleviated symptoms of ongoing aGVHD and improved survival while preserving antitumoral cytotoxicity. Our data identified ICOSL+-pDCs as an aGVHD biomarker and suggest that coinhibition of the ICOSL/ICOS and B7/CD28 axes with one biologic drug may represent a therapeutic opportunity to prevent or treat aGVHD.

Acute graft-versus-host disease (aGVHD) remains a major complication of allogeneic hematopoietic cell transplantation (HCT). CD146 and CCR5 are proteins that mark activated T helper 17 (Th17) cells. The Th17 cell phenotype is promoted by the interaction of the receptor ICOS on T cells with ICOS ligand (ICOSL) on dendritic cells (DCs). We performed multiparametric flow cytometry in a cohort of 156 HCT recipients and conducted experiments with aGVHD murine models to understand the role of ICOSL(+) DCs. We observed an increased frequency of ICOSL(+) plasmacytoid DCs, correlating with CD146(+)CCR5(+) T cell frequencies, in the 64 HCT recipients with gastrointestinal aGVHD. In murine models, donor bone marrow cells from ICOSL-deficient mice compared to those from wild-type mice reduced aGVHD-related mortality. Reduced aGVHD resulted from lower intestinal infiltration of pDCs and pathogenic Th17 cells. We transplanted activated human ICOSL(+) pDCs along with human peripheral blood mono-nuclear cells into immunocompromised mice and observed infiltration of intestinal CD146(+)CCR5(+) T cells. We found that prophylactic administration of a dual human ICOS/CD28 antagonist (ALPN-101) prevented aGVHD in this model better than did the clinically approved belatacept (CTLA-4-Fc), which binds CD80 (B7–1) and CD86 (B7–2) and interferes with the CD28 T cell costimulatory pathway. When started at onset of aGVHD signs, ALPN-101 treatment alleviated symptoms of ongoing aGVHD and improved survival while preserving antitumoral cytotoxicity. Our data identified ICOSL(+)-pDCs as an aGVHD biomarker and suggest that coinhibition of the ICOSL/ICOS and B7/CD28 axes with one biologic drug may represent a therapeutic opportunity to prevent or treat aGVHD.

Background: Despite significant clinical benefit of checkpoint inhibitors (CPI) in some settings, unfortunately, the majority of patients still fail to respond and/or develop resistance. This is likely due to a complex set of factors including, but not limited to, the presence of immunosuppressive myeloid cells and/or T cell exhaustion due to chronic TCR activation in the absence of sufficient costimulation. ALPN-202, a variant CD80 vIgD™-Fc fusion protein that mediates PD-L1-dependent CD28 costimulation and blocks PD-L1 and CTLA-4, was designed to overcome several of these suppressive mechanisms. The objective of these studies was to measure effects of ALPN-202 on the suppression of T cell activation by M2c macrophages and to determine in vivo effects of ALPN-202 on T cell exhaustion in an adoptively transferred human TCR transgenic tumor model. Methods: M2c macrophages differentiated from primary monocytes with M-CSF and IL-10 were cocultured for 72hr with T cells, anti-CD3 and a titration of ALPN-202, anti-PD-1, anti-PD-L1, or anti-CTLA-4 antibodies. Cytokine concentrations in the culture media were measured at 24 and 72 hrs, and T cells and macrophages characterized at 72 hrs by flow cytometry. To measure its anti-tumor activity and effect on T cell exhaustion in vivo, ALPN-202 was evaluated in a humanized model using anti-HPV E6 TCR-transduced human T cells transferred into immunodeficient NSG mice bearing HPV+ SCC152 squamous cell tumors stably expressing PD-L1. Tumor volume was measured twice weekly and on day 38 tumors were harvested, digested, and intratumoral T cells characterized for expression of exhaustion markers. Results: In the in vitro coculture assay, ALPN-202 increased T cell proliferation and production of IL-2, IFNγ, TNFα, GM-CSF, IL-6, and IL-21 significantly more potently than CPI alone. Additionally, the M2c macrophages in the presence of ALPN-202 displayed a dose-dependent elevation of MHC II, CD80, and CD86, indicative of a more pro-inflammatory, M1-like phenotype. In the SCC152 tumor model, ALPN-202 induced a more robust anti-tumor response than CPI while the intratumoral T cells expressed lower levels of exhaustion markers. Conclusions: As a dual checkpoint inhibitor and conditional CD28-costimulator, ALPN-202 induced robust and selective T cell costimulation in vitro which overcame M2c macrophage-mediated suppression more potently than CPI alone. Intriguingly, not only were T cells vigorously activated, but M2c macrophages transitioned to a more M1-like proinflammatory phenotype. In a humanized tumor model, ALPN-202 treatment resulted in potent anti-tumor activity with reduced signs of T cell exhaustion in the TME. The data suggest that by combining CD28 costimulation with CPI, ALPN-202 may provide a more robust and persistent anti-tumor T cell response compared to CPI alone. Citation Format: Mark F. Maurer, Siddarth Chandrasekaran, Katherine Lewis, Sherri Mudri, Kayla Kleist, Fariha Ahmed-Qadri, Chelsea Gudgeon, Steven D. Levin, Stacey R. Dillon, Kristine M. Swiderek, Stanford L. Peng. ALPN-202 combines checkpoint inhibition with conditional T cell costimulation to overcome T cell suppression by M2c macrophages and improve the durability of engineered T cell anti-tumor responses [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr LB-085.

Background:BAFF and APRIL are TNF superfamily members that bind both TACI and BCMA on B cells; BAFF also binds BAFF-R. Together, BAFF and APRIL support B cell development, differentiation, and survival. Their co-neutralization dramatically reduces B cell function, including antibody production, whereas inhibition of either BAFF or APRIL alone mediates relatively modest effects.Objectives:While CTLA-4-based therapeutics that block T cell costimulation provide safe and moderately effective T cell inhibition in many disease settings, and while B cell targeting therapies have demonstrated promising therapeutic potential, we postulate that improved, combined BAFF and APRIL inhibition, either alone or coupled with inhibition of T cell costimulation, will provide more effective and durable relief from severe B cell-related autoimmune diseases like SLE.Methods:We used our directed evolution platform to identify variant domains of the TNF family receptors TACI or BCMA that exhibit enhanced affinity for BAFF and APRIL as compared to their wild-type (WT) counterparts. These variant TACI or BCMA domains (vTD), alone or together with platform-derived CTLA-4 domains (vIgD), were fused to a modified human IgG1 Fc lacking effector function, yielding a panel of immunomodulatory molecules: TACI vTD-Fc, BCMA vTD-Fc, TACI vTD/CTLA-4 vIgD-Fc, & BCMA vTD/CTLA-4 vIgD-Fc. All were evaluated for functional activity: 1)in vitroin primary human B cell & MLR assays and in a Jurkat/NF-kB reporter cell line expressing TACI, and 2)in vivoin standard immunization models, and in the bm12-induced and NZB/NZW spontaneous mouse models of lupus.Results:The novel engineered TACI vTD-Fc or BCMA vTD-Fc fusion proteins significantly inhibited BAFF- and APRIL-mediated signalingin vitroin TACI+Jurkat cells. TACI (or BCMA) vTD/CTLA-4 vIgD-Fc proteins also attenuated T cell activation in primary human lymphocyte assays. When administered to mice, these molecules rapidly and potently reduced key B and T cell subsets, including plasma cells, follicular T helper cells, germinal center cells, & memory T cells. Treatment with TACI vTD-Fc or TACI vTD/CTLA-4 vIgD-Fc proteins also significantly reduced titers of antigen-specific antibodies in immunized mice more so than abatacept or WT TACI-Fc, and potently suppressed anti-dsDNA autoantibodies, blood urea nitrogen levels, proteinuria, and renal immune complex deposition in the bm12 & NZB/W lupus models.Conclusion:Directed evolution of TNFR and IgSF domains has successfully facilitated the development of Fc fusion proteins containing TACI or BCMA vTDs, with or without fusion to CTLA-4 vIgDs. These novel immunomodulators consistently demonstrate potent immunosuppressive activity and efficacyin vitroandin vivo, appearing superior to existing and/or approved immunomodulators like belimumab, abatacept, or atacicept. Such biologics may therefore be attractive candidates for the treatment of serious autoimmune diseases, particularly B cell-related diseases such as SLE, Sjogren’s syndrome, etc.Disclosure of Interests: :Stacey R. Dillon Shareholder of: Shareholder of Alpine Immune Sciences, Inc., Employee of: Employee of Alpine Immune Sciences, Inc., Lawrence S. Evans Shareholder of: Shareholder of Alpine Immune Sciences, Inc., Employee of: Employee of Alpine Immune Sciences, Inc., Mark W. Rixon Shareholder of: Shareholder of Alpine Immune Sciences, Inc., Employee of: Employee of Alpine Immune Sciences, Inc., Joe Kuijper Shareholder of: Shareholder of Alpine Immune Sciences, Inc., Employee of: Employee of Alpine Immune Sciences, Inc., Dan Demonte Shareholder of: Shareholder of Alpine Immune Sciences, Inc., Employee of: Employee of Alpine Immune Sciences, Inc., Katherine E. Lewis Shareholder of: Shareholder of Alpine Immune Sciences, Inc., Employee of: Employee of Alpine Immune Sciences, Inc., Steve Levin Shareholder of: Shareholder of Alpine Immune Sciences, Inc., Employee of: Employee of Alpine Immune Sciences, Inc., Kayla Kleist Shareholder of: Shareholder of Alpine Immune Sciences, Inc., Employee of: Employee of Alpine Immune Sciences, Inc., Sherri Mudri Shareholder of: Shareholder of Alpine Immune Sciences, Inc., Employee of: Employee of Alpine Immune Sciences, Inc., Susan Bort Shareholder of: Shareholder of Alpine Immune Sciences, Inc., Employee of: Employee of Alpine Immune Sciences, Inc., Janhavi Bhandari Shareholder of: Shareholder of Alpine Immune Sciences, Inc., Employee of: Employee of Alpine Immune Sciences, Inc., Fariha Ahmed-Qadri Shareholder of: Shareholder of Alpine Immune Sciences, Inc., Employee of: Employee of Alpine Immune Sciences, Inc., Jing Yang Shareholder of: Alpine Immune Sciences, Inc., Employee of: Alpine Immune Sciences, Inc., Michelle A. Seaberg Shareholder of: Shareholder of Alpine Immune Sciences, Inc., Employee of: Employee of Alpine Immune Sciences, Inc., Rachel Wang Shareholder of: Shareholder of Alpine Immune Sciences, Inc., Employee of: Employee of Alpine Immune Sciences, Inc., Russell Sanderson Shareholder of: Alpine Immune Sciences, Inc., Employee of: Alpine Immune Sciences, Inc., Martin F. Wolfson Shareholder of: Shareholder of Alpine Immune Sciences, Inc., Employee of: Employee of Alpine Immune Sciences, Inc., Jan Hillson Shareholder of: Alpine Immune Sciences, Inc., Employee of: Alpine Immune Sciences, Inc., Stanford L. Peng Shareholder of: Alpine Immune Sciences, Inc., Employee of: CMO and President of Alpine Immune Sciences, Inc., Kristine M. Swiderek Shareholder of: Shareholder of Alpine Immune Sciences, Inc., Employee of: Employee of Alpine Immune Sciences, Inc.

Background ALPN-101 (ICOSL vIgD-Fc) is an Fc fusion protein of a human ICOSL variant immunoglobulin domain (vIgD™) designed to simultaneously inhibit the ICOS and CD28 costimulatory pathways. ICOS and CD28 bind ICOSL and CD80/CD86, respectively, and play critical roles in T cell activation and adaptive immunity. ALPN-101 has demonstrated preliminary efficacy in a model of graft versus host disease (GvHD) (2018 BMT abstract #244). Here we examined its efficacy, exposure, and pharmacodynamics in preparation for upcoming clinical studies. Methods A dose ranging study was conducted with 20, 100, or 500 µg ALPN-101 administered to NSG™ mice engrafted with human PBMC, and compared to belatacept, an approved CTLA-4-Fc protein CD28 pathway inhibitor. Mice were monitored for clinical signs of GvHD, inflammatory cytokines, and phenotype of the transferred cells. Pharmacokinetic analyses were also performed. Results ALPN-101 inhibited T cell activation in the GvHD model with all dose regimens tested (Fig 1). Significantly enhanced survival and reduced disease scores were observed in mice treated with ALPN-101 compared to mice treated with belatacept (i.e. 100% vs. 40% survival at Day 42, respectively; p 80% ICOS+ (Fig 2). Conclusion ALPN-101 is a potent dual ICOS/CD28 T cell antagonist capable–even with a single dose–of inhibiting lethal inflammatory processes with superior efficacy vs continuous CD28 or ICOS single pathway inhibition despite lower PK exposure, likely attributable to superior control of ICOS+ T cells which otherwise escape single pathway blockade. ALPN-101 is thus a promising novel therapeutic candidate for GvHD, and upcoming clinical trials will explore its therapeutic potential in GVHD and other inflammatory diseases.

Unlike HER2-positive breast cancer, there are limited treatment options for patients diagnosed with triple negative and endocrine resistant HER2-negative breast cancer, and as such HER2-negative breast cancer represents a significant unmet medical need. The goal of this work is to use Theraclone’s proprietary I-STAR platform to mine the memory B cell immune repertoire of breast cancer patients for the discovery of therapeutically relevant monoclonal antibodies (mAbs) and targets that may be exploited as candidates for treatment of HER2-negative breast cancer. Matched serum and PBMC samples were collected from breast cancer patients at multiple clinical sites. The selected patient populations included, but were not limited to, patients who were treatment naïve, those who had received immunotherapy or adjuvant chemotherapy, and patients who had an exceptional clinical response to treatment and/or disease. Serum antibody binding to a diverse panel of 5 well characterized breast cancer-derived cell lines of luminal and basal sub-types was determined. Utilizing this approach, patients with a robust serological profile across multiple breast cancer cell lines were identified and prioritized for memory B cell repertoire analysis via the I-STAR platform. Using a high throughput and miniaturized, multiplex flow cytometry assay, the secreted IgG antibodies from over 85,000 individually enriched and expanded B cell clones were screened for binding to the tumor cell line panel and a large number of positive B cell clones were identified. The screening hits can be binned into several unique binding profiles, many of which were confirmed to be shared across multiple patient samples. Deep sequence analysis of the variable regions of the antibodies produced by the B cell clones demonstrated that several of the screening hits were derived from clonally related B cells; the majority of the screening hits represented antibodies derived from unique B cell clones. A representative set of these antibodies was expressed recombinantly for further in vitro characterization. Citation Format: Christy Boozer, Paul Algate, Aurelio Bonavia, Mark Branum, Po-Ying Chan-Hui, Alison Fitch, Brad Greenfield, Claire Sutherland, Kristine Swiderek. Discovery of fully human monoclonal antibodies as therapeutic candidates for the treatment of HER2-negative breast cancer [abstract]. In: Proceedings of the Thirty-Seventh Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2014 Dec 9-13; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2015;75(9 Suppl):Abstract nr P2-16-01.

Background The efficacy of TCN-032, a human monoclonal antibody targeting a conserved epitope on M2e, was explored in experimental human influenza. Methods Healthy volunteers were inoculated with influenza A/Wisconsin/67/2005 (H3N2) and received a single dose of the study drug, TCN-032, or placebo 24 hours later. Subjects were monitored for symptoms, viral shedding, and safety, including cytokine measurements. Oseltamivir was administered 7 days after inoculation. Results Although the primary objective of reducing the proportion of subjects developing any grade ≥2 influenza symptom or pyrexia, was not achieved, TCN-032-treated subjects showed 35% reduction (P = .047) in median total symptom area under the curve (days 1-7) and 2.2 log reduction in median viral load area under the curve (days 2-7) by quantitative polymerase chain reaction (P = .09) compared with placebo-treated subjects. TCN-032 was safe and well tolerated with no additional safety signals after administration of oseltamivir. Serum cytokine levels (interferon γ, tumor necrosis factor α, and interleukin 8 and 10) were similar in both groups. Genotypic and phenotypic analyses showed no difference between virus derived from subjects after TCN-032 treatment and parental strain. Conclusions These data indicate that TCN-032 may provide immediate immunity and therapeutic benefit in influenza A infection, with no apparent emergence of resistant virus. TCN-032 was safe with no evidence of immune exacerbation based on serum cytokine expression. Clinicaltrials.gov registry number. NCT01719874.

SummaryBroadly neutralizing HIV antibodies are much sought after (a) to guide vaccine design, both as templates and as indicators of the authenticity of vaccine candidates, (b) to assist in structural studies, and (c) to serve as potential therapeutics. However, the number of targets on the viral envelope spike for such antibodies has been limited. Here, we describe a set of human monoclonal antibodies that define what is, to the best of our knowledge, a previously undefined target on HIV Env. The antibodies recognize a glycan-dependent epitope on the prefusion conformation of gp41 and unambiguously distinguish cleaved from uncleaved Env trimers, an important property given increasing evidence that cleavage is required for vaccine candidates that seek to mimic the functional HIV envelope spike. The availability of this set of antibodies expands the number of vaccine targets on HIV and provides reagents to characterize the native envelope spike.

Background/Purpose: ALPN-101 is a potent dual inhibitor of the ICOS and CD28 T cell costimulatory pathways designed for therapeutic application in inflammatory diseases. CD28 and ICOS bind CD80/CD86 and ICOS ligand (ICOSL), respectively, and play critical roles in T cell activation and adaptive immunity. ALPN-101 has previously been demonstrated to have potent efficacy - superior to wild type ICOSL-Fc - in models of graft versus host disease (GvHD), a disease reflecting immune-mediated attack of recipient tissue by donor T cells. Here, we examined the efficacy of a single dose of ALPN-101 or repeat dosing with different dose levels in GvHD. We also explored the potential therapeutic benefit of ALPN-101 in another T cell-driven inflammatory disease, hemophagocytic lymphohistiocytosis (HLH), a spectrum of disorders of the immune system characterized by the excessive production of cytokines by activated T cells and macrophages accumulating in organs such as the liver, spleen, bone marrow, and brain, which mediate significant tissue damage. Methods: ALPN-101 was generated using our proprietary variant Ig domain (vIgD™) platform and is an effector-function negative Fc-fusion protein with an engineered variant Ig ICOSL domain capable of binding both ICOS and CD28 with high affinity. ALPN-101 blocks the interaction of these T cell costimulatory molecules with their respective receptors, downregulating T cell activation. The dose ranging GvHD study was executed with ALPN-101 (3x weekly/4 weeks, 20 ug - 500 ug) treatment of NSGTM mice engrafted with human peripheral blood mononuclear cells (PBMC) in comparison to belatacept, a CTLA-4-Fc fusion protein CD28 pathway inhibitor. Mice were monitored daily for clinical signs of GvHD. In a model of primary (inherited) HLH in which perforin-deficient (Prf1(-∕-)) mice are infected with lymphocytic choriomeningitis virus (LCMV), we evaluated both prophylactic (days 0, 3, and 6 post LCMV infection) and delayed (days 3, 5, and 7) treatment with ALPN-101 (400ug/dose). Results: ALPN-101 significantly attenuated T cell activation in the human PBMC-NSG GvHD model at a single 100ug dose and at all multiple doses tested, protecting mice from the effects of xenogeneic T cell activation in vivo. Treated animals exhibited enhanced survival and reduced disease scores compared to control mice treated with saline or belatacept. Flow cytometric analyses of blood collected at 1-2 weeks post cell transfer demonstrated ALPN-101 reduced both the number and activation state of the transferred human CD4+ and CD8+ T cells. In the HLH model, ALPN-101 lessened several of the clinical and laboratory manifestations of HLH, including organomegaly, anemia, CD8+ T cell expansion, and liver inflammation. Conclusion: ALPN-101 is a potent T cell inhibitor capable, even with a single dose, of preventing T cell activation, such as that observed in the huPBMC-NSGTM GvHD and the LCMV-induced HLH models, and thus is a promising novel therapeutic candidate for GvHD and other inflammatory diseases. Preclinical development is underway to support clinical studies of this potentially first-in-class dual ICOS and CD28 inhibitor. Disclosures Dillon: Alpine Immune Sciences: Employment, Equity Ownership. Lewis:Alpine Immune Sciences: Employment, Equity Ownership. Swanson:Alpine Immune Sciences: Employment, Equity Ownership. Evans:Alpine Immune Sciences: Employment, Equity Ownership. Levin:Alpine Immune Sciences: Employment, Equity Ownership. Rixon:Alpine Immune Sciences: Employment, Equity Ownership. Peng:Alpine Immune Sciences: Employment, Equity Ownership. Nichols:Incyte: Research Funding; Alpine Immune Sciences: Research Funding. Swiderek:Alpine Immune Sciences: Employment, Equity Ownership.

It was reported previously that four baby hamster kidney (BHK) proteins with molecular masses of 108, 60, 50, and 42 kDa bind specifically to the 3′-terminal stem-loop of the West Nile virus minus-stand RNA [WNV 3′(−) SL RNA] (P. Y. Shi, W. Li, and M. A. Brinton, J. Virol. 70:6278-6287, 1996). In this study, p42 was purified using an RNA affinity column and identified as TIAR by peptide sequencing. A 42-kDa UV-cross-linked viral RNA-cell protein complex formed in BHK cytoplasmic extracts incubated with the WNV 3′(−) SL RNA was immunoprecipitated by anti-TIAR antibody. Both TIAR and the closely related protein TIA-1 are members of the RNA recognition motif (RRM) family of RNA binding proteins. TIA-1 also binds to the WNV 3′(−) SL RNA. The specificity of these viral RNA-cell protein interactions was demonstrated using recombinant proteins in competition gel mobility shift assays. The binding site for the WNV 3′(−) SL RNA was mapped to RRM2 on both TIAR and TIA-1. However, the dissociation constant ( K d ) for the interaction between TIAR RRM2 and the WNV 3′(−) SL RNA was 1.5 × 10 −8 , while that for TIA-1 RRM2 was 1.12 × 10 −7 . WNV growth was less efficient in murine TIAR knockout cell lines than in control cells. This effect was not observed for two other types of RNA viruses or two types of DNA viruses. Reconstitution of the TIAR knockout cells with TIAR increased the efficiency of WNV growth, but neither the level of TIAR nor WNV replication was as high as in control cells. These data suggest a functional role for TIAR and possibly also for TIA-1 during WNV replication.

Hepatitis A virus (HAV) encodes a single polyprotein which is posttranslationally processed into the functional structural and nonstructural proteins. Only one protease, viral protease 3C, has been implicated in the nine protein scissions. Processing of the capsid protein precursor region generates a unique intermediate, PX (VP1-2A), which accumulates in infected cells and is assumed to serve as precursor to VP1 found in virions, although the details of this reaction have not been determined. Coexpression in transfected cells of a variety of P1 precursor proteins with viral protease 3C demonstrated efficient production of PX, as well as VP0 and VP3; however, no mature VP1 protein was detected. To identify the C-terminal amino acid residue of HAV VP1, we performed peptide sequence analysis by protease-catalyzed [ 18 O]H 2 O incorporation followed by liquid chromatography ion-trap microspray tandem mass spectrometry of HAV VP1 isolated from purified virions. Two different cell culture-adapted isolates of HAV, strains HM175pE and HM175p35, were used for these analyses. VP1 preparations from both virus isolates contained heterogeneous C termini. The predominant C-terminal amino acid in both virus preparations was VP1-Ser274, which is located N terminal to a methionine residue in VP1-2A. In addition, the analysis of HM175pE recovered smaller amounts of amino acids VP1-Glu273 and VP1-Thr272. In the case of HM175p35, which contains valine at amino acid position VP1-273, VP1-Thr272 was found in addition to VP1-Ser274. The data suggest that HAV 3C is not the protease responsible for generation of the VP1 C terminus. We propose the involvement of host cell protease(s) in the production of HAV VP1.

Several autoantibodies related to Type 1 diabetes mellitus and their corresponding autoantigens have been previously identified. While peptide antigens are more widely recognized, lipid antigens like sulfatides and gangliosides are also known epitopes for the diabetic humoral immune response. Islet cell antibodies (ICA) in Type 1 diabetes are heterogeneous immunoglobulins directed against selected antigens in the islets of Langerhans. Moreover, ICA may be the best predictive marker of disease in family members of patients with Type 1 diabetes. The aims of this study were: (1) to purify lipids from porcine pancreas that contain ICA epitopes; (2) to characterize these lipid antigens, and (3) to use the purified lipids in an assay to detect antibodies in patients with Type 1 diabetes. A unique family of 4 lysophospholipids, 1 fully characterized as lysophosphatidylmyoinositol, partially inhibited ICA staining, and therefore, were considered to be candidate antigens for an ICA immunoassay. Using a dot blot immunoassay, we detected antibodies directed against these phospholipids in 28 out of 46 (61%) diabetic sera, while detecting only 1 false positive out of 28 nondiabetic sera (3.6%; p < 0.0001 comparing diabetic vs. nondiabetic serum). Therefore, lysophospholipid immunoassay positivity is present in sera of Type 1 diabetic patients. Furthermore, we detected 15 out of 23 ICA-negative diabetic sera (65.2%), showing that our phospholipid immunoassay does not correlate with ICA positivity.

Gpx2 mRNA, encoding a selenium-dependent glutathione peroxidase (GPX-GI), has been found to be highly expressed in the gastrointestinal tract (GI) mucosal epithelium. In this study, we show that GPX-GI is produced in the mucosal epithelium of the adult rat GI tract and that the activity levels are comparable to that from GPX-1. Post-mitochondrial supernatant GPX activity from the mucosal epithelium of the complete length of the small intestine was partially purified. A sample enriched for putative GPX-GI was fractionated by SDS-polyacrylamide gel electrophoresis. Polypeptides of 21 kDa and 22 kDa were digested with trypsin. After resolving the tryptic peptides by high pressure liquid chromatography (HPLC), the major peaks were analyzed for their amino acid sequence by Microflow-HPLC-Tandem Mass Spectrometry and automated Edman degradation sequencing. Both methods revealed that the 21-kDa sample contained rat GPX-GI determined by the sequence homology with the deduced mouse GPX-GI polypeptide sequence. Rat GPX-1 was also detected in the samples. AntiGPX-GI and antiGPX-1 antibodies were used to determine the distribution of the respective isoenzyme activities along the length of the intestine and with respect to the crypt to villus axis in rats. GPX-GI and GPX-1 activities were uniformly distributed in the middle and lower GI tract and with respect to the crypt to villus axis. GPX-GI activity accounted nearly the same percentage of the total GPX activity as GPX-1 in all of the these compartments. Studies on the distal ileum segment of wildtype and Gpx1 gene knockout mice showed that GPX-GI activity was also at parity with GPX-1 in the mucosal epithelium of this segment.

Microspray tandem mass spectrometry (MS/MS) in combination with database search routines has become a powerful tool for the identification of proteins from femtomole amounts of material following gel electrophoresis and in-gel digestion procedures. However, artifactual modification of susceptible residues can arise during gel electrophoresis, leading to unexpected peptide mass shifts during mass analysis. Consequently, collision-induced dissociation (CID) spectra generated from these derivatized peptides can defy direct interpretation by automated database search routines and remain unidentified. Here, we evaluate the MS/MS spectra of peptides carrying oxidized derivatives of tryptophane and methionine residues, and various modifications of cysteine. We demonstrate that certain of these modifications generate characteristic fragmentation patterns or "fingerprints", during CID analysis, the knowledge of which can facilitate the interpretation of the spectra. We will show that these signature fragment ions are predominantly produced during the CID analysis of singly charged ions although they can be observed in the MS/MS spectra of the doubly charged species as well. In other cases, the CID spectrum lacks a characteristic fingerprint and the modification remains silent. However, CID spectra of related peptides, differing only by their modifications, are similar and all or part of the fragment ion spectra will have shifted by a discreet mass, which facilitates the identification of the modified residue. At the same time, the comparison of related spectra can prevent misinterpretations such as the assignment of a residue mass to the wrong amino acid or a neutral loss fragment ion to a gamma- or b-ion.

Broadly neutralizing HIV antibodies (bnAbs) are typically highly somatically mutated, raising doubts as to whether they can be elicited by vaccination. We used 454 sequencing and designed a novel phylogenetic method to model lineage evolution of the bnAbs PGT121–134 and found a positive correlation between the level of somatic hypermutation (SHM) and the development of neutralization breadth and potency. Strikingly, putative intermediates were characterized that show approximately half the mutation level of PGT121–134 but were still capable of neutralizing roughly 40–80% of PGT121–134 sensitive viruses in a 74-virus panel at median titers between 15- and 3-fold higher than PGT121–134. Such antibodies with lower levels of SHM may be more amenable to elicitation through vaccination while still providing noteworthy coverage. Binding characterization indicated a preference of inferred intermediates for native Env binding over monomeric gp120, suggesting that the PGT121–134 lineage may have been selected for binding to native Env at some point during maturation. Analysis of glycan-dependent neutralization for inferred intermediates identified additional adjacent glycans that comprise the epitope and suggests changes in glycan dependency or recognition over the course of affinity maturation for this lineage. Finally, patterns of neutralization of inferred bnAb intermediates suggest hypotheses as to how SHM may lead to potent and broad HIV neutralization and provide important clues for immunogen design., National Institutes of Health (U.S.) (Bioinformatics and Integrative Genomics Fellowship), National Institutes of Health (U.S.) (Center for Excellence in Genomic Science)

The complete sequence of the FMRFamide precursor cDNA from Helix aspersa is reported here. Since the 5' end of this cDNA is identical to that of the precursor that encodes the heptapeptide analogs of FLRFamide, the two transcripts are probably derived by alternative RNA splicing. A novel pentapeptide, Glp-Phe-Tyr-Arg-Phe-NH2 (pQFYRFamide), predicted from the cDNA sequence, was purified from extracts of H. aspersa ganglia and identified by mass spectroscopy. Partial gene sequences for the FMRFamide precursors of two closely related pulmonate species-Cepaea nemoralis and Polydontes acutangula-were also determined and compared with the cDNA sequence of H. aspersa and a partial gene sequence previously determined from H. pomatia. Not only are the FMRFamide-related sequences and proteolytic processing sites conserved, but the linear arrangement of these landmarks is also retained. Synthetic pQFYRFamide has some effects on the isolated heart and on neuronal potassium currents in H. aspersa that are similar to those of FMRFamide, but it does not activate the neuronal FMRFamide-gated sodium channel.

The structural characterization of proteins and peptides isolated in minute quantities requires the most efficient use of available sample. A mass spectrometer data system was programmed to continuously evaluate incoming liquid chromatography/mass spectrometry data against a user-defined array of information. The resulting conclusions were used to automatically set and modify acquisition parameters in real time to collect collision-induced dissociation spectra for selected ions (tandem mass spectrometry). This approach has provided a mechanism to target specific subsets of masses in a complex mixture and/or to discriminate selectively against masses that are known or not of interest. Masses of contaminants or peptide masses derived from known proteins can be automatically recorded and removed from further consideration for collision-induced dissociation analysis. Once recorded, these "libraries" of masses can be used across multiple analyses. This technique directs the mass spectrometer data system to focus on the analysis of masses significant to the user, even if their signal intensities are well below the intensities of contaminating masses. When combined with a database search program to correlate tandem mass spectra to known protein sequences, the identity of the protein can be established unequivocally by using less than 100 fmol of sample.

The IgG+ memory B cell repertoire of cancer patients demonstrating durable responses to immune checkpoint blockade therapy has been interrogated to identify tumor specific antibodies. Matched serum and PBMC samples have been collected from 10 melanoma patients with durable responses to treatment with ipilimumab. A panel of 7 well characterized melanoma cell lines with a diverse set of oncogenic driver mutations has been employed to assess durable responder patient serum reactivity to cell surface determinants in a live-cell flow cytometry assay. IgG+ memory B cells obtained from several prioritized durable responder melanoma patients have been plated out on 384 well plates at monoclonal density. The memory B cells have been activated in a short term culture system optimized to expand the clonal B cells and induce secretion of IgG. Antibodies secreted from clonally expanded B cells have been screened using live cell high throughput multiplex flow cytometry assays against a panel of melanoma cell lines. A prioritized subset of antibodies, selected on the basis of tumor cell line binding profiles and antibody v-region sequences, has been cloned and expressed as recombinant IgG1. A cell surface target for a prioritized antibody has been identified and the in vitro analysis and characterization of the antibody including functional activity and immunohistochemistry staining on tumor and normal tissues has been carried out in preparation for in vivo testing of efficacy. Citation Format: Mark Branum, Laura Smith, Heather Brett, Paul Algate, Brad Greenfield, William Brown, Kristine M. Swiderek. Derivation and characterization of antibodies from immune checkpoint blockade treated cancer patients. [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 870.

We determined the cysteine connectivity of protegrin PG-2, a leukocyte-derived antimicrobial peptide, by performing sequential enzyme digestions with chymotrypsin and thermolysin, and monitoring each digest by direct liquid chromatography-electrospray mass spectrometric analysis. This approach resolved the disulphide pairing pattern unambiguously with only picomolar amounts of PG-2. The inferred cysteine connectivity was confirmed by traditional amino acid composition analyses using nanomolar amounts of the protegrin. The results suggest that protegrins will assume a tachyplesin-like, disulphide-stabilized anti-parallel beta-sheet configuration in solution.

We purified and characterized an unusual antimicrobial peptide, prophenin-1 (PF-1), from porcine leukocytes. The peptide had a mass of 8,683 and contained 79 residues, including 42 (53.2%) prolines and 15 (19.0%) phenylalanines. Its N-terminal 60 residues consisted of three perfect and three nearly perfect repeats of a decamer, FPPPNFPGPR. Prophenin-1 was encoded on a cathelin-containing precursor and showed substantially more activity against E. coli, a Gram-negative bacterium, than against Listeria monocytogenes, a Gram-positive organism, in vitro.

Most animal studies using passive administration of HIV broadly neutralizing monoclonal antibodies (bnMAbs) have associated protection against high-dose mucosal viral challenge with relatively high serum concentrations of antibody. We recently identified several bnMAbs remarkable for their in vitro potency against HIV. Of these bnMAbs, PGT121 is one of the most broad and potent antibodies isolated to date and shows 10- to 100-fold higher neutralizing activity than previously characterized bnMAbs. To evaluate the protective potency of PGT121 in vivo, we performed a protection study in rhesus macaques. Animals were i.v. administered 5 mg/kg, 1 mg/kg, or 0.2 mg/kg PGT121 24 h before being vaginally challenged with a single high dose of chimeric simian-human immunodeficiency virus (SHIV) SF162P3 . Sterilizing immunity was achieved in all animals administered 5 mg/kg and 1 mg/kg and three of five animals administered 0.2 mg/kg PGT121, with corresponding average antibody serum concentrations of 95 µg/mL, 15 µg/mL, and 1.8 µg/mL, respectively. The results suggest that a protective serum concentration for PGT121 is in the single-digit µg/mL for SHIV SF162P3 , showing that PGT121 can mediate sterilizing immunity at serum concentrations that are significantly lower than those observed in previous studies and that may be achievable through vaccination with the development of a suitable immunogen.

Developments in capillary column liquid chromatography have been driven in part by the need to develop an effective interface between liquid chromatography and mass spectrometry (LC/ MS). Although the cost of commercial columns and pumping systems capable of gradient elution is relatively high, many aspects of the technology are relatively simple to do in house and easily adapted to existing instrumentation. The vacuum environment of the mass spectrometer can accept only a few microliters per minute of solvent flow. This can be accomplished by splitting higher flows or through the use of a novel pumping system that delivers gradients at low flow rates. The interface to the mass spectrometer is most easily accomplished using electrospray ionization. Electrospray has the advantage of producing multiply charged species that permit the analysis of large protein structures on mass spectrometers with limited mass range. Samples eluting from a capillary column are in an ideal form for electrospray mass spectrometry. Concentrations are high and components of interest have been separated from contaminants such as salts that interfere with the electrospray process. Thus, mass spectral analyses can be obtained on samples that are otherwise difficult or impossible to do. The accuracy of electrospray mass spectrometry is sufficient to monitor small changes in the masses of large proteins. This feature is very useful for studying the interactions of proteins with substrates and inhibitors. IC/MS analysis of peptide mixtures resulting from enzyme digestion of large proteins is very useful for rapidly confirming the sequence of recombinant proteins. When combined with automated methods of obtaining fragment ion spectra on individual peptides during an LC/MS run, it is possible to very quickly determine the location of single amino acid changes in mutant proteins.

NAD(P)H:quinone acceptor oxidoreductase (EC 1.6.99.2) (DT-diaphorase) is a FAD-containing reductase that catalyzes a unique 2-electron reduction of quinones. It consists of 2 identical subunits. In this study, it was found that the carboxyl-terminal portion of the 2 subunits can be cleaved by various proteases, whereas the amino-terminal portion cannot. It was also found that proteolytic digestion of the enzyme can be blocked by the prosthetic group FAD, substrates NAD(P)H and menadione, and inhibitors dicoumarol and phenindione. Interestingly, chrysin and Cibacron blue, 2 additional inhibitors, cannot protect the enzyme from proteolytic digestion. The results obtained from this study indicate that the subunit of the quinone reductase has a 2-domain structure, i.e., an amino-terminal compact domain and a carboxyl-terminal flexible domain. A structural model of the quinone reductase is generated based on results obtained from amino-terminal and carboxyl-terminal protein sequence analyses and electrospray mass spectral analyses of hydrolytic products of the enzyme generated by trypsin, chymotrypsin, and Staphylococcus aureus protease. Furthermore, based on the data, it is suggested that the binding of substrates involves an interaction between 2 structural domains.

The living skin equivalent (LSE) is an organotypic co-culture composed of human dermal fibroblasts in a collagen-containing matrix overlaid with human keratinocytes that have formed a stratified epidermis. This model system was used as a dermatotoxicity model in vitro for studying the effects of test samples topically applied to the air-exposed epidermis. Using the colorimetric thiazolyl blue (MTT) conversion assay as a measure of mitochondrial function, the extent of cytotoxicity induced by several well-characterized chemical irritants was evaluated in the LSE. For the seven chemical irritants tested, the concentrations that inhibited MTT conversion by 50% were approximately those threshold concentrations at which irritation was seen in human skin. In addition, nine chemicals that were classified as non-irritating to human skin, including solids and water-insoluble substances, exhibited minimal or no inhibition of MTT conversion when tested at full strength. Time- and dose-dependent release of the pro-inflammatory mediators, prostaglandin E2, prostacyclin and interleukin-1-alpha (IL-1alpha) was seen in LSE exposed to two known chemical irritants, morpholine and hydroxylamine sulphate, but not in LSE exposed to a minimally irritating test sample. The permeability constants (K(p) values) for water, caffeine, hydrocortisone, oestradiol and benzoic acid were determined in the LSE. In all cases the LSE was more permeable than human skin with K(p) values ranging from 0.56 +/- 0.10 x 10(-3) cm/hr for hydrocortisone to 29 +/- 5 x 10(-3) cm/hr for water penetration. The data suggest that organotypic skin cultures can be used as model systems for studying certain aspects of chemically induced dermal irritation. Using rates of water penetration as the most meaningful assessment of barrier competence, the LSE is approximately 30-fold more permeable than human skin. Although incomplete as a percutaneous absorption model, the presence of this partial barrier does influence the responses of cells in the LSE to topically applied chemicals.

Two major glycoproteins, designated PSP-I and PSP-II, were purified from porcine seminal plasma by ammonium sulfate fractionation, CM-cellulose chromatography, gel filtration on Sephadex G-75 (superfine), and reverse phase high performance liquid chromatography. These two proteins exist in several forms differing mainly in the carbohydrate moiety. The complete amino acid sequence of PSP-I has been determined by automated Edman degradation of peptides generated by proteolytic digestion and cyanogen bromide cleavage. The protein is 109 residues long and has a single glycosylation site at the asparagine residue at position 47. In addition, the N-terminal sequence of PSP-II has also been determined. PSP-I is a unique protein; a sequence homology search using the protein data base did not reveal any significant homology with other proteins. PSP-II shares 50% sequence homology with a family of zona pellucida-binding glycoproteins at the N-terminus.

Nitric oxide (NO) conveys a variety of messages between cells, including signals for vasorelaxation, neurotransmission, and cytotoxicity. In some endothelial cells and neurons, a constitutive NO synthase is activated transiently by agonists that elevate intracellular calcium concentrations and promote the binding of calmodulin. In contrast, in macrophages, NO synthase activity appears slowly after exposure of the cells to cytokines and bacterial products, is sustained, and functions independently of calcium and calmodulin. A monospecific antibody was used to clone complementary DNA that encoded two isoforms of NO synthase from immunologically activated mouse macrophages. Liquid chromatography-mass spectrometry was used to confirm most of the amino acid sequence. Macrophage NO synthase differs extensively from cerebellar NO synthase. The macrophage enzyme is immunologically induced at the transcriptional level and closely resembles the enzyme in cytokine-treated tumor cells and inflammatory neutrophils.

Venom of the funnel web spider Agelenopsis aperta inhibits the binding of 125I-omega-conotoxin GVIA (omega-CgTx) to calcium channels in chick brain synaptosomal membranes. Fractionation of the venom by liquid chromatography shows that this inhibitory activity is associated primarily with a diverse class of peptide toxins called omega-agatoxins (omega-Aga). Using binding inhibition as an assay, we purified and identified the novel, 76-amino acid toxin, omega-Aga-IIIA. Inhibition of 125I-omega-CgTx binding to chick synaptosomal membranes by omega-Aga-IIIA and omega-Aga-IIA is correlated with block of potassium-stimulated 45Ca entry into synaptosomes; omega-Aga-IA neither inhibits 125I-omega-CgTx binding nor 45Ca entry under identical conditions. omega-Aga-IIA and omega-Aga-IIIA are 20-30-fold more potent than omega-CgTx as antagonists of synaptosomal calcium channels. However, whereas omega-CgTx completely blocks 45Ca entry into synaptosomes at saturating concentrations, the omega-agatoxins maximally block only 60-70% of 45Ca entry. Pretreatment of synaptosomes with omega-Aga-IIIA occludes block of 45Ca entry by omega-CgTx. The results indicate that, while the omega-agatoxins bind to the entire population of omega-CgTx-sensitive calcium channels in chick synaptosomal membranes, they exert only a partial block of 45Ca flux. Such block could occur via two distinct mechanisms. Toxin binding may alter the kinetics of a homogeneous population of channels, resulting in lower overall conductance upon depolarization. Alternatively, the omega-agatoxins may bind to two distinct channel subtypes, only one of which is blocked as a result of toxin occupation.

DNA clones encoding the glycogen-binding (RG1) subunit of glycogen-associated protein phosphatase were isolated from rabbit skeletal muscle lambda gt11 cDNA libraries. Overlapping clones provided an open reading frame of 3327 nucleotides that predicts a polypeptide of 1109 amino acids with a molecular weight of 124,257. Northern hybridization of rabbit RNA identified a major mRNA transcript of 7.5 kilobases present in skeletal, diaphragm, and cardiac muscle, but not in brain, kidney, liver, and lung. Southern analysis of rabbit genomic DNA digested with various restriction endonucleases gave rise to a single hybridizing fragment, suggesting that a single gene is present. Expression of the complete RG1 subunit coding sequence in Escherichia coli generated a protein of apparent molecular weight on sodium dodecyl sulfate-polyacrylamide gel electrophoresis of approximately 160,000, similar to the size of the polypeptide detected by Western immunoblot in rabbit skeletal muscle extracts. The RG1 subunit shares significant homology with the Saccharomyces cerevisiae GAC1 gene product which is involved in activation of glycogen synthase and glycogen accumulation. The homology with GAC1 substantiates the role of this enzyme in control of glycogen metabolism. Hydropathy analysis of the RG1 subunit amino acid sequence revealed the presence of a hydrophobic region in the COOH terminus, suggesting a potential association with membrane. This result suggests that the same phosphatase regulatory component may be involved in targeting the enzyme both to membranes and to glycogen.

On the base of results obtained by thermal analysis of mineral oils, synthetic ester oils and their mixtures, it should be stated that the synthetic components reduce the volatility and thermooxidation stability of oils without basically influencing the thermal stability.

We had previously demonstrated that a cellular protein specifically interacts with the 3′ end of poliovirus negative-strand RNA. We now report the identity of this protein as heterogeneous nuclear ribonucleoprotein (hnRNP) C1/C2. Formation of an RNP complex with poliovirus RNA was severely impaired by substitution of a lysine, highly conserved among vertebrates, with glutamine in the RNA recognition motif (RRM) of recombinant hnRNP C1, suggesting that the binding is mediated by the RRM in the protein. We have also shown that in a glutathione S -transferase (GST) pull-down assay, GST/hnRNP C1 binds to poliovirus polypeptide 3CD, a precursor to the viral RNA-dependent RNA polymerase, 3D pol , as well as to P2 and P3, precursors to the nonstructural proteins. Truncation of the auxiliary domain in hnRNP C1 (C1ΔC) diminished these protein-protein interactions. When GST/hnRNP C1ΔC was added to in vitro replication reactions, a significant reduction in RNA synthesis was observed in contrast to reactions supplemented with wild-type fusion protein. Indirect functional depletion of hnRNP C from in vitro replication reactions, using poliovirus negative-strand cloverleaf RNA, led to a decrease in RNA synthesis. The addition of GST/hnRNP C1 to the reactions rescued RNA synthesis to near mock-depleted levels. Furthermore, we demonstrated that poliovirus positive-strand and negative-strand RNA present in cytoplasmic extracts prepared from infected HeLa cells coimmunoprecipitated with hnRNP C1/C2. Our findings suggest that hnRNP C1 has a role in positive-strand RNA synthesis in poliovirus-infected cells, possibly at the level of initiation.

The targeting of molecular repertoires to complex systems rather than biochemically pure entities is an accessible approach that can identify proteins of biological interest. We have probed antigens presented by a monolayer of tumor cells for their ability to interact with a pool of aptamers. A glioblastoma-derived cell line, U251, was used as the target for systematic evolution of ligands by exponential enrichment by using a single-stranded DNA library. We isolated specifically interacting oligonucleotides, and biochemical strategies were used to identify the protein target for one of the aptamers. Here we characterize the interaction of the DNA aptamer, GBI-10, with tenascin-C, an extracellular protein found in the tumor matrix. Tenascin-C is believed to be involved in both embryogenesis and oncogenesis pathways. Systematic evolution of ligands by exponential enrichment appears to be a successful strategy for the a priori identification of targets of biological interest within complex systems.

Introduction History and Activities of the ABRF Amino Acid Analysis Protein Sequencing Chemistry and Sample Preparation ABRF Protein Sequence Studies Instrument Technological Improvement/Design over the Course of ABRF Studies Internal Protein Sequencing Peptide Synthesis Carbohydrate Analysis Nucleic Acids ABRF DNA Synthesis Studies ABRF DNA Sequencing Studies Mass Spectrometry Initial Results of the Survey Preliminary Results of the Analysis of ABRF MS1 and MS2 Test Conclusions Surveys of Core Laboratories Laboratory Quality and Compliance Effective Use of Biomolecular Resource Facilities Before Submission of a Request After Receipt of Your Data or Reagents Future of Core Laboratories Paradigm Shift in the Postgenome Era Automation Future Opportunities Acknowledgments Bibliography

VOLTAGE-DEPENDENT calcium channels mediate calcium entry into neurons, which is crucial for many processes in the brain including synaptic transmission, dendritic spiking, gene expression and cell death1–5. Many types of calcium channels exist in mam-malian brains6–19, but high-affinity blockers are available for only two types, L-type channels (targeted by nimodipine and other dihydropyridine channel blockers20–22) and N-type channels (targeted by ω-conotoxin22–26). In a search for new channel blockers, we have identified a peptide toxin from funnel web spider venom, ω-Aga-IVA, which is a potent inhibitor of both calcium entry into rat brain synaptosomes and of 'P-type' calcium channels8 in rat Purkinje neurons. ω-Aga-IVA will facilitate characterization of brain calcium channels resistant to existing channel blockers and may assist in the design of neuroprotective drugs.

The majority of reports indicate that blood platelet membrane fluidity is increased in Alzheimer's disease (AD) patients. The increased membrane fluidity implies that platelet membrane receptors are less exposed to the external environment. To verify this hypothesis we tried to estimate platelet membrane fluidity at its two different depths and receptors' exposure after platelet activation in 12 AD sufferers. Platelet membrane fluidity was measured by the EPR with the use of 2 spin-labelled markers. In AD patients both "near surface" (p0.04) and "deeper depth" (p0.005) fluidity was significantly increased. The exposure of platelet granule membrane protein--P-selectin and membrane glycoprotein receptors: alpha subunit of glycoprotein Ib and beta3 subunit of GP complex IIb/IIIa were measured by flow cytometry with the use of human platelet monoclonal antibodies labelled with fluorescein and ficoerithrin. The exposure of GPIb alpha subunit was significantly decreased both in resting state (p0.0001) and after thrombin activation (p0.005). In thrombin-activated platelets the expression of P-selectin and beta3 subunit of fibrinogen receptor were also significantly decreased (p0.00001 and p0.04, respectively). The authors conclude that both platelet membrane fluidity and receptor exposure might serve as an adjunct marker of in vivo AD diagnosis.

Gpx2 mRNA, encoding a selenium-dependent glutathione peroxidase (GPX-GI), has been found to be highly expressed in the gastrointestinal tract (GI) mucosal epithelium. In this study, we show that GPX-GI is produced in the mucosal epithelium of the adult rat GI tract and that the activity levels are comparable to that from GPX-1. Post-mitochondrial supernatant GPX activity from the mucosal epithelium of the complete length of the small intestine was partially purified. A sample enriched for putative GPX-GI was fractionated by SDS-polyacrylamide gel electrophoresis. Polypeptides of 21 kDa and 22 kDa were digested with trypsin. After resolving the tryptic peptides by high pressure liquid chromatography (HPLC), the major peaks were analyzed for their amino acid sequence by Microflow-HPLC-Tandem Mass Spectrometry and automated Edman degradation sequencing. Both methods revealed that the 21-kDa sample contained rat GPX-GI determined by the sequence homology with the deduced mouse GPX-GI polypeptide sequence. Rat GPX-1 was also detected in the samples. AntiGPX-GI and antiGPX-1 antibodies were used to determine the distribution of the respective isoenzyme activities along the length of the intestine and with respect to the crypt to villus axis in rats. GPX-GI and GPX-1 activities were uniformly distributed in the middle and lower GI tract and with respect to the crypt to villus axis. GPX-GI activity accounted nearly the same percentage of the total GPX activity as GPX-1 in all of the these compartments. Studies on the distal ileum segment of wildtype and Gpx1 gene knockout mice showed that GPX-GI activity was also at parity with GPX-1 in the mucosal epithelium of this segment.

The eukaryotic cytosolic chaperonins are large heterooligomeric complexes with a cylindrical shape, resembling that of the homooligomeric bacterial counterpart, GroEL. In analogy to GroEL, changes in shape of the cytosolic chaperonin have been detected in the presence of MgATP using electron microscopy but, in contrast to the nucleotide-induced conformational changes in GroEL, no details are available about the specific nature of these changes. The present study identifies the structural regions of the cytosolic chaperonin that undergo conformational changes when MgATP binds to the nucleotide binding domains. It is shown that limited proteolysis with trypsin in the absence of MgATP cleaves each of the eight subunits approximately in half, generating two fragments of approximately 30 kDa. Using mass spectrometry (MS) and N-terminal sequence analysis, the cleavage is found to occur in a narrow span of the amino acid sequence, corresponding to the peptide binding regions of GroEL and to the helical protrusion, recently identified in the structure of the substrate binding domain of the archeal group II chaperonin. This proteolytic cleavage is prevented by MgATP but not by ATP in the absence of magnesium, ATP analogs (MgATPyS and MgAMP-PNP) or MgADP. These results suggest that, in analogy to GroEL, binding of MgATP to the nucleotide binding domains of the cytosolic chaperonin induces long range conformational changes in the polypeptide binding domains. It is postulated that despite their different subunit composition and substrate specificity, group I and group II chaperonins may share similar, functionally-important, conformational changes. Additional conformational changes are likely to involve a flexible helix-loop-helix motif, which is characteristic for all group II chaperonins.

In the female mosquito, Aedes aegypti, neurohormones are released from the brain in response to a blood meal and stimulate the ovaries to secrete ecdysteroid hormones, which modulate yolk protein synthesis in the fat body. Neuropeptides with this bioactivity were isolated from head extracts, and partial sequences from these peptides when aligned gave a 31-residue sequence at the amino terminus. Oligonucleotide primers for this sequence were used to amplify with the polymerase chain reaction a genomic DNA product that hybridized to a clone from a head cDNA library. The cDNA encodes a 149-residue preprohormone that is processed into an 86-residue peptide, as indicated by the mass value obtained from the native peptide, with the expected amino-terminal sequence. After modification, the cDNA for the putative neurohormone was expressed in a bacterial system, and the purified peptide had high specific activity in bioassays, thus confirming that it is a steroidogenic gonadotropin, the first to be identified for invertebrates.

Publisher Summary Positive identification of the glycosylation sites during N-terminal sequence analysis could become a real advantage. Usually, glycoamino acids appear as blank cycles during a sequencing run. Further sequence analysis is necessary after deglycosylation of the sample and the identification of oligosaccharide and PTH-Asn derivatives is a time and sample consuming task. The techniques developed for the LF 3600 N-terminal protein sequencer provide a fast and efficient way to positively identify Ser (O-Unked Sac), -Thr (O-Unked Sac) and Asn (N-linked Sac) carbohydrate structures during N-terminal sequence analysis. In addition, different forms of carbohydrate structures at a single amino acid site have different retention times and can be distinguished by further analysis. After fraction collection of individual peaks during the chromatography of a sequencing cycle, the structure of oligosaccharides at a specific site can be further examined with subsequent analyses, such as mass spectral analysis, capillary electrophoresis (CE), or high pH anion exchange chromatography (HPAEC). Adding to the flexibility of the instrument, it can be switched back to the regular mode for high sensitivity protein and peptide sequencing. This chapter describes the use of a modified Beckman LF3600 microsequencing system for the positive identification of glycosylation sites of different protein and peptide samples. The analysis of glycopeptides from carcinoembryonic antigen (CEA) is presented. CEA is a heavily glycosylated membrane bound glycoprotein that has been intensively characterized as an important tumor marker for colonic cancer. An example for a glycoprotein is the starch binding domain (SBD) of enzyme glucoamylase, which is an industrially important exoamylase used for saccharification of liquefied starch from various sources to produce glucose and finally fructose syrups. For both, CEA and SBD, the identification of the glycosylation sites is an important contribution in understanding their functionality.

The 5' noncoding region of poliovirus RNA contains an internal ribosome entry site (IRES) for cap-independent initiation of translation. Utilization of the IRES requires the participation of one or more cellular proteins that mediate events in the translation initiation reaction, but whose biochemical roles have not been defined. In this report, we identify a cellular RNA binding protein isolated from the ribosomal salt wash of uninfected HeLa cells that specifically binds to stem-loop IV, a domain located in the central part of the poliovirus IRES. The protein was isolated by specific RNA affinity chromatography, and 55% of its sequence was determined by automated liquid chromatography-tandem mass spectrometry. The sequence obtained matched that of poly(rC) binding protein 2 (PCBP2), previously identified as an RNA binding protein from human cells. PCBP2, as well as a related protein, PCBP1, was over-expressed in Escherichia coli after cloning the cDNAs into an expression plasmid to produce a histidine-tagged fusion protein. Specific interaction between recombinant PCBP2 and poliovirus stem-loop IV was demonstrated by RNA mobility shift analysis. The closely related PCBP1 showed no stable interaction with the RNA. Stem-loop IV RNA containing a three nucleotide insertion that abrogates translation activity and virus viability was unable to bind PCBP2.

Cleavage of the Gag and Gag-Pol polyprotein precursors is a critical step in proliferation of retroviruses and retroelements. The Ty1 retroelement of Saccharomyces cerevisiae forms virus-like particles (VLPs) made of the Gag protein. Ty1 Gag is not obviously homologous to the Gag proteins of retroviruses. The apparent molecular mass of Gag is reduced from 58 to 54 kDa during particle maturation. Antibodies raised against the C-terminal peptide of Gag react with the 58-kDa polypeptide but not with the 54-kDa one, indicating that Gag is proteolytically processed at the C terminus. A protease cleavage site between positions 401 and 402 of the Gag precursor was defined by carboxy-terminal sequencing of the processed form of Gag. Certain deletion and substitution mutations in the C terminus of the Gag precursor result in particles that are two-thirds the diameter of the wild-type VLPs. While the Ty1 protease is active in these mutants, their transposition rates are decreased 20-fold compared with that of wild-type Ty1. Thus, the Gag C-terminal portion, released in the course of particle maturation, probably plays a significant role in VLP morphogenesis and Ty1 transposition.

Publisher Summary With the introduction of mass spectrometry (MS) into protein chemistry, a new, powerful tool has been implemented to perform different structural analyses on small amounts of samples. The analysis of macromolecules, with electrospray mass spectrometry, in combination with liquid chromatography, within an error of ±0.01%, is a reliable technique for mass determination. Accurate mass determination of a protein, with known primary structure, can indicate possible posttranslational modifications of the protein as well as errors in protein sequence analysis or complementary DNA (cDNA)-derived sequences. The success of a variety of experiments, such as site-directed mutagenesis or covalent modification studies, can be verified quickly without employing large amounts of sample. This chapter explains examples for a variety of structural analyses of low amounts of proteins and peptides, utilizing different mass spectrometric techniques, in combination with micro-HPLC (high-performance liquid chromatography). For demonstration of the different techniques standard proteins as well as “real-life” samples are used. The standard protein used is horse cytochrome c, digested with the endoproteinase Lys-C. This chapter discusses the possible strategies to solve some often encountered structural problems.

We have used mass spectrometry as a structural method to analyze carcinoembryonic antigen (CEA) and other members of the CEA gene family, including engineered anti-CEA antibodies that are use in clinical studies for tumor imaging and therapy. CEA is a highly glycosylated, GPI-anchored, high molecular weight (180 kDa) membrane glycoprotein that is highly expressed in cancers of epithelial cell origin, including colon, lung, breast, and ovary. Since the high level of glycosylation posed serious problems for structural analysis, CEA was deglycosylated with TFMSA, converting all 28- N-glycosylation sites to Asn-GlcNAc derivatives which were easily analyzed by peptide mapping, microsequence analysis, and mass spectrometry. The GPI linkage site was converted to an N-ethanolamine amide which was positively identified by mass spectrometry. Peptide mapping of intact CEA allowed isolation of the majority of the glycopeptides and a mass survey of the structures was performed by SIMS and MS-MS approaches. Structures included high mannose, complex, and polylactosamine. Similar studies were performed on the CEA-related antigen, NCA (non-specific cross reacting antigen or CD66c antigen on granulocytes). The glycosyl units on the N-domain of NCA were shown to contribute to bacterial binding via a lectin site, and when removed by recombinant means, gave a glycoprotein devoid of bacterial binding activity. The glycosylation sites were also identified by peptide mapping and MS or MS-MS analysis. A chimeric anti-CEA antibody used in clinical studies was subjected to peptide mapping and analyzed by LC/ESI-MS, MALDI-TOF, and SIMS, confirming its structure and several posttranslational modifications. A single chain version (sFv) was analyzed by LC/ESI-MS and microsequence analysis, confirming that the correct size protein was expressed and processed by E.coli.