Human Protein Sequences Research Articles

In silico analyses of human collagen protein function prediction

Collagen is the extracellular matrix protein in the several connective tissues in the human body. It is an important component for mediating cell-cell interactions and pathological conditions in human body. In this study we perform the analysis of physiochemical properties and investigate the functional characteristics of human collagen proteins. Also investigate the functional protein groups by the statistical analysis. The collagen protein family consisting 28 members in human which are involving in the complex structure of protein. The protein function, protein sequence properties, domain composition, phylogenetic and protein-protein interaction (PPI) networks analysis of human collagen alpha-1 protein sequences are implemented by the online bioinformatics tools which are currently available. Based on the PCA analysis amino acid composition, features of collagen protein sequences are divided into two supreme influential functional groups such as collagen 12, 14, 20 formed one group and the rest of others formed another group. The protein-protein interaction network study using STRING showed that top interacting score of functional group proteins 0.952, 0.939 and 0.929. The most common functional domain of collagen proteins are VWC, C4, LamG, VWA, KU, C1Q, TSPN and FN3. Physicochemical, functional and phylogenetic classification can give extensive information of protein’s structure and function. The depiction of alpha-1 chains of collagen protein family in human collagen 12, 14 and 20 as a prospective protein cluster. These three proteins are possess, low glycine and proline, very high aliphatic index and a close evolutionary relation in the human skin.J. bio-sci. 24: 55-65, 2016

Abstract 3580: Enhancing adoptive cell therapies through exogenous regulation

Abstract Adoptive cell therapy with chimeric antigen receptor (CAR) modified T cells has demonstrated remarkable clinical efficacy in the treatment of certain B cell malignancies and more recently in multiple myeloma. However, in solid tumors, CAR-T therapy has been far less successful, likely due to the lack of robust CAR-T cell expansion, the immunosuppressive microenvironment, and clonal heterogeneity within these tumors. The trafficking of CAR-T cells to tumor sites provides an opportunity for selective delivery of cargo that can enhance CAR-T cell activity at the site of the tumor. Interleukin-12 (IL12) and membrane tethered interleukin-15 (mbIL15) have previously been shown to enhance CAR-T activity, yet the unregulated expression of either compromises safety and/or efficacy. The Obsidian Therapeutics platform equips engineered immune cells with new functionalities whose activity can be regulated via the administration of FDA-approved small-molecule drugs, putting dosing control back in the hands of the treating physician. We utilize small, fully human protein sequences called destabilizing domains (DDs) that confer reversible destabilization to a fused target protein. In the absence of ligand the fusion protein is degraded, whereas the presence of small molecule ligand restores expression and functionality. Furthermore, stabilization is titratable with small molecule ligand dose, providing finely tuned control over target protein expression and function. We have applied our technology to create DD-IL12 and DD-mbIL15 “cassettes” that provide exogenous regulation of cytokine activity when transduced into CAR-Ts for enhanced cellular function. We describe here the successful implementation of the DD technology in engineered primary human T cells and show small-molecule ligand controlled regulation of DD-IL12 and DD-mbIL15 protein expression in vivo in mouse models. These data demonstrate the feasibility of exogenous control over protein expression in primary human T cells for the development of next-generation CAR-T cell products with enhanced efficacy and more favorable safety profiles. Citation Format: Celeste Richardson, Kutlu Elpek, Michelle Ols, Tariq Kassum, Steve Shamah. Enhancing adoptive cell therapies through exogenous regulation [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3580.

Kinase Substrate Profiling Using a Proteome-wide Serine-Oriented Human Peptide Library

The human proteome encodes >500 protein kinases and hundreds of thousands of potential phosphorylation sites. However, the identification of kinase-substrate pairs remains an active area of research because the relationships between individual kinases and these phosphorylation sites remain largely unknown. Many techniques have been established to discover kinase substrates but are often technically challenging to perform. Moreover, these methods frequently rely on substrate reagent pools that do not reflect human protein sequences or are biased by human cell line protein expression profiles. Here, we describe a new approach called SERIOHL-KILR (serine-oriented human library-kinase library reactions) to profile kinase substrate specificity and to identify candidate substrates for serine kinases. Using a purified library of >100000 serine-oriented human peptides expressed heterologously in Escherichia coli, we perform in vitro kinase reactions to identify phosphorylated human peptide sequences by liquid chromatography and tandem mass spectrometry. We compare our results for protein kinase A to those of a well-established positional scanning peptide library method, certifying that SERIOHL-KILR can identify the same predominant motif elements as traditional techniques. We then interrogate a small panel of cancer-associated PKCβ mutants using our profiling protocol and observe a shift in substrate specificity likely attributable to the loss of key polar contacts between the kinase and its substrates. Overall, we demonstrate that SERIOHL-KILR can rapidly identify candidate kinase substrates that can be directly mapped to human sequences for pathway analysis. Because this technique can be adapted for various kinase studies, we believe that SERIOHL-KILR will have many new victims in the future.

Is the activity of CGRP and Adrenomedullin regulated by RAMP (−2) and (−3) in Trypanosomatidae? An in-silico approach

The Calcitonin-Like Receptor (CLR) belongs to the classical seven-transmembrane segment molecules coupled to heterotrimeric G proteins. Its pharmacology depends on the simultaneous expression of the so-called Receptor Activity Modifier Proteins (RAMP-) −1, −2 and −3. RAMP-associated proteins modulate glycosylation and cellular traffic of CLR, therefore determining its pharmacodynamics. In higher eukaryotes, the complex formed by CLR and RAMP-1 is more akin to bind Calcitonin Gene-Related Peptide (CGRP), whereas those formed by CLR and RAMP-2 or RAMP-3, bind preferentially Adrenomedullin (AM). In lower eukaryotes, RAMPs, or any homologous protein, have not been identified until now. Herein we demonstrated a negative chemotactic response elicited by CGRP (10−9 and 10−8 M) and AM (10−9 to 10−5 M). Whether or not this response is receptor mediated should be verified, as well as the expression of a 24 kDa band in Leishmania, recognized by western blot analysis by the use of (human-)-RAMP-2 antibodies as detection probes. Queries with human RAMP-2 and RAMP-3 protein sequences in blastp against Leishmania (Viannia) braziliensis predicted proteome, allowed us to detect two sequence alignments in the parasite: A RAMP-2-aligned sequence corresponding to Leishmania folylpolyglutamate synthase (FPGS), and a RAMP-3 aligned protein, a hypothetical Leishmania protein with yet unknown function. The presence of homologous of these proteins was described in-silico in other members of the Trypanosomatidae. These preliminary and not yet complete data suggest the feasibility that both CGRP and Adrenomedullin activities may be regulated by homologs of RAMP- (−2) and (−3) in these parasites.

Predicting the effects of the single nucleotide polymorphism A122V on CXC chemokine receptor type 1 of Bos taurus (Artiodactyla: Bovidae) cattle by in silico analyses

Este estudo objetivou predizer bioquimicamente as estruturas primárias e secundárias da proteína receptora de quimiocina CXCR1 bovina não polimórfica e polimórfica carreando o polimorfismo A122V por análises in silico. Duas sequências da proteína CXCR1 de bovino Bos taurus foram selecionadas a partir da base de dados de sequências de proteínas UniProtKB/Swiss-Prot: a) uma sequência não polimórfica (A7KWG0), contendo o aminoácido alanina (A) na posição 122, e b) uma sequência polimórfica, apresentando o aminoácido valina (V) na mesma posição. As estruturas primárias e secundárias da proteína foram preditas empregando os programas ProtParam e Chou & Fasman Protein Secondary Structure Prediction CFSSP. Diferenças nos parâmetros físicos e químicos não foram previstas a partir da estrutura primária de ambas as proteínas analisadas. A presença de um domínio helicoidal, situado nas posições 100 e 150, foi exclusivamente encontrada na proteína CXCR1 não polimórfica. Resíduos de aminoácidos de propriedades bioquímicas variáveis foram detectados na posição 122 na proteína CXCR1 dos ruminantes e humana, sugerindo que esse peptídeo é altamente polimórfico em vertebrados. Os resultados aqui descritos predizem diferenças no padrão da estrutura secundária da proteína CXCR1 bovina não polimórfica e polimórfica A122V empregando ferramentas de Bioinformática.

Overexpression of DYRK1A, a Down Syndrome Candidate gene, Impairs Primordial Germ Cells Maintenance and Migration in zebrafish

DYRK1A, located on chromosome 21, is a major candidate gene of Down syndrome (DS, trisomy21), and its overexpression is associated with abnormal phenotype of Down syndrome patients. The defects of gonads and germ cells in Down Syndrome suggest that overexpression of DYRK1A has potential effect on primordial germ cells (PGCs) development. Human and zebrafish DYRK1A protein sequence possess 75.6% similarity and same function domains, suggesting the evolutional conservation. Here, we used zebrafish model to detect the definite role of excessive expression of DYRK1A in PGCs development during embryogenesis. We injected DYRK1A mRNA into embryos and detected the PGCs marker gene vasa and nanos1. Results showed depletion in numbers and disordering migration of PGCs in human or zebrafish DYRK1A overexpressed zebrafish embryos. Quantitative proteome analysis indicated that embryonic proteins were significantly altered in DYRK1A overexpressed embryos. Of note, ca15b and piwil1, two identified critical factors for PGCs development, showed ectopic expression induced by overexpressed DYRK1A. In brief, we demonstrate that overexpression of DYRK1A, a candidate gene of Down’s syndrome, impairs PGCs development during early embryogenesis by altering key factors in embryos. Importantly, our work may provide a conceivable mechanism for the gonads and germ cells defects of Down syndrome patients.

Effect of enrofloxacin on the proteome of earthworms

The environmental and human health risks of veterinary drugs are becoming public health issues. Enrofloxacin (EF) is an extensively used animal-specific antibacterial agent that leaves drug residues in the environment. This study investigated the proteomic response of the earthworm Eisenia fetida to EF exposure. Earthworms were exposed to EF in soil at 1–500mg·kg−1, and samples were collected at intervals during a 28 day period. The extracted proteins were separated by two dimensional electrophoresis to detect differentially expressed proteins (DEPs) in EF-exposed earthworms. In total, 35 unique DEPs were found. These proteins were subjected to MALDI-TOF/TOF-MS analysis and identified through comparison of their mass spectra with those in protein databases. The DEPs were grouped on the basis of their function, into metabolism, stress-related, transport, transcription, and predicted/hypothetical protein categories. Knowledge of proteins that are induced or repressed by EF in earthworms could provide insight into mechanisms of sub-clinical physiological effects of xenobiotic residues in the environment, and may also help understand synergy between pollutants. As several DEPs in E. fetida showed similarity to human protein sequences, E. fetida has potential as an indicator species to assess the environmental and biological risks of drug residues.

Tau-peptide fragments and their copper(II) complexes: Effects on Amyloid-β aggregation

Abstract Recent studies suggest that the interaction of Aβ and Tau may be significant in the pathogenesis of Alzheimer’s diseases (AD). In addition, the potential influence of copper on Tau-related pathology in AD has not been previously addresseded and the interaction between Tau protein, Aβ and copper has even more recently been associated with AD. While the copper(II) interaction with the Aβ peptide has exhaustively been studied, the few studies carried out on copper(II) complexes with peptide fragments from Tau protein have been focused on the pseudo-repeats of Tau protein in the microtubule-binding region. No data have been reported about the metal complexes with peptides derived from the N-terminal portion of Tau protein, outside the microtubule-binding domain, despite increased levels of peptide fragments from this region have been detected in the Cerebrospinal fluid (CSF) of AD patients. Here we examine the interaction of two peptides fragments, encompassing the 1–25 or 26–44 residues of the human Tau protein sequence, with Aβ as well as the Cu2+-binding features of these two naturally occurring peptides. The CD experiments showed that copper(II) differently affects the peptide conformation of the two ligands and provided also insight into the donor atoms involved in metal coordination. Stoichiometry of copper(II) complexes was obtained by means of High resolution ESI-MS. Finally, the influence of the studied peptide on Aβ’s fibrillogenesis, either in the presence or absence of Cu2+, was investigated by means of Th-T fluorescence coupled with turbidimetric measurements. The observed different effect on the in vitro Aβ’s aggregation, was correlated with the affinity of copper(II) with the two peptide ligands. The overall results indicate that copper(II) can bind these peptides using the histidine residue or amino group as anchoring sites and that copper(II) binding may have a possible involvement in AD.

Abstract 4540: MiVax: an innovative cancer neoantigen prediction system

Abstract T cell epitopes bearing tumor-specific mutations discovered using next generation sequencing stimulate T cell-mediated processes that lead to tumor regression. Although neoantigen prediction using computational methods rapidly identifies epitope candidates in the mutanome, a large proportion prove to be non-immunogenic. Innovative computational tools validated for infectious disease can be applied to enhance design of personalized cancer immunotherapies by classification of predicted epitopes according to potential for mounting a tumor-specific response. We developed the JanusMatrix algorithm that parses query sequences into MHC-facing and T cell receptor (TCR)-facing sequences and screens sequence databases to identify MHC ligands that share TCR faces with host-related proteins. A database of human protein sequences is available to identify tumor-specific epitopes that may reduce anti-tumor activity by sequences that activate regulatory T cells (Tregs) trained in the thymus on self-antigens. Similarly, tumor-specific epitope candidates are screened using databases composed of human commensal- or pathogen-derived sequences to identify epitopes that, respectively, may detrimentally or beneficially cross-react with T cells raised over the course of an individual’s immune history. We conducted retrospective analyses of cancer vaccine efficacy studies performed in mice [Kreiter et al. 2015 Nature 520, 692-696] showing that mutanome-directed vaccines effective at preventing tumor growth contained higher numbers of class I and II MHC neo-epitopes and had lower potential to cross-react with other murine proteins, as identified by the MiVax platform. Likewise, an evaluation of mutanomes derived from non-small cell lung cancer patients [Rizvi et al. 2014 Science 348, 124-128] revealed that improved clinical outcomes were observed in patients with mutanomes enriched in class I MHC neo-epitopes with TCR faces distinct from other self-epitopes. While retrospective in nature, the suite of tools used for these analyses have been extensively validated in prospective vaccine studies for infectious disease. Removal of Treg epitopes identified by JanusMatrix has led to the development of a novel H7N9 influenza vaccine scheduled for Phase I clinical trial. These results highlight the benefits of using in silico tools for the selection of high-value neoantigen candidates and how they can improve the design and efficacy of cancer vaccines. Neoantigens with low Treg activation potential may then be used to support development of personalized therapies including vaccination and in vitro expansion of tumor infiltrating lymphocytes for adoptive cell transfer. Citation Format: Lenny Moise, Guilhem Richard, Frances Terry, William Martin, Ann De Groot. MiVax: an innovative cancer neoantigen prediction system [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 4540. doi:10.1158/1538-7445.AM2017-4540

Serological profiling of the EBV immune response in Chronic Fatigue Syndrome using a peptide microarray.

BackgroundEpstein-Barr-Virus (EBV) plays an important role as trigger or cofactor for various autoimmune diseases. In a subset of patients with Chronic Fatigue Syndrome (CFS) disease starts with infectious mononucleosis as late primary EBV-infection, whereby altered levels of EBV-specific antibodies can be observed in another subset of patients.MethodsWe performed a comprehensive mapping of the IgG response against EBV comparing 50 healthy controls with 92 CFS patients using a microarray platform. Patients with multiple sclerosis (MS), systemic lupus erythematosus (SLE) and cancer-related fatigue served as controls. 3054 overlapping peptides were synthesised as 15-mers from 14 different EBV proteins. Array data was validated by ELISA for selected peptides. Prevalence of EBV serotypes was determined by qPCR from throat washing samples.ResultsEBV type 1 infections were found in patients and controls. EBV seroarray profiles between healthy controls and CFS were less divergent than that observed for MS or SLE. We found significantly enhanced IgG responses to several EBNA-6 peptides containing a repeat sequence in CFS patients compared to controls. EBNA-6 peptide IgG responses correlated well with EBNA-6 protein responses. The EBNA-6 repeat region showed sequence homologies to various human proteins.ConclusionPatients with CFS had a quite similar EBV IgG antibody response pattern as healthy controls. Enhanced IgG reactivity against an EBNA-6 repeat sequence and against EBNA-6 protein is found in CFS patients. Homologous sequences of various human proteins with this EBNA-6 repeat sequence might be potential targets for antigenic mimicry.

The neXtProt peptide uniqueness checker: a tool for the proteomics community

SummaryThe neXtProt peptide uniqueness checker allows scientists to define which peptides can be used to validate the existence of human proteins, i.e. map uniquely versus multiply to human protein sequences taking into account isobaric substitutions, alternative splicing and single amino acid variants.Availability and implementationThe pepx program is available at https://github.com/calipho-sib/pepx and can be launched from the command line or through a cgi web interface. Indexing requires a sequence file in FASTA format. The peptide uniqueness checker tool is freely available on the web at https://www.nextprot.org/tools/peptide-uniqueness-checker and from the neXtProt API at https://api.nextprot.org/.

A genetic variant of the sperm-specific SLO3 K+ channel has altered pH and Ca2+ sensitivities

To fertilize an oocyte, sperm must first undergo capacitation in which the sperm plasma membrane becomes hyperpolarized via activation of potassium (K+) channels and resultant K+ efflux. Sperm-specific SLO3 K+ channels are responsible for these membrane potential changes critical for fertilization in mouse sperm, and they are only sensitive to pH i However, in human sperm, the major K+ conductance is both Ca2+- and pH i -sensitive. It has been debated whether Ca2+-sensitive SLO1 channels substitute for human SLO3 (hSLO3) in human sperm or whether human SLO3 channels have acquired Ca2+ sensitivity. Here we show that hSLO3 is rapidly evolving and reveal a natural structural variant with enhanced apparent Ca2+ and pH sensitivities. This variant allele (C382R) alters an amino acid side chain at a principal interface between the intramembrane-gated pore and the cytoplasmic gating ring of the channel. Because the gating ring contains sensors to intracellular factors such as pH and Ca2+, the effectiveness of transduction between the gating ring and the pore domain appears to be enhanced. Our results suggest that sperm-specific genes can evolve rapidly and that natural genetic variation may have led to a SLO3 variant that differs from wild type in both pH and intracellular Ca2+ sensitivities. Whether this physiological variation confers differences in fertility among males remains to be established.

Review Studies of GJB2 Gene in Patients with Hearing Impairment in Pakistan

Deafness is inherited as one of the most frequent type of neurosensory disorder. The specific physiologic mechanisms of the different types of hearing loss are still unknown. Recent studies have listed numerous causative agents for hearing loss. Genetic factors contribute to a greater extent in hearing disability. GJB2 gene is one of the most promising candidates. 35delG is the most common mutation which accounts for about 50% of all GJB2 gene mutation. After collection of data and isolation of blood, extraction of DNA was performed for each sample. Direct sequencing of GJB2 gene was performed. Primary sequencing data of the representative sample concluded that GJB2 gene is not mutated in the studied family. There are other candidates for hearing disability; further investigations are needed for assessment of other members of the selected family or other genes that are responsible for hearing loss. Human GJB2 protein was compared with that of mouse and rabbit. The data from multiple alignment shows that there is only alteration at nine different points of rabbit compared to human GJB2 protein while this variation is sixteen times when we compared human GJB2 protein sequence with that of mouse.

Expression profile of rrbp1 genes during embryonic development and in adult tissues of Xenopus laevis

Recent studies suggest that ribosome-binding protein 1 (RRBP1) is involved in multiple diseases such as tumorigenesis and cardiomyopathies. However, its function during embryonic development remains largely unknown. We searched Xenopus laevis database with human RRBP1 protein sequence and identified two cDNA sequences encoding Xenopus orthologs of RRBP1 including rrbp1a (NM_001089623) and rrbp1b (NM_001092468). Both genes were firstly detected at blastula stage 8 with weak signals in animal hemisphere by whole mount in situ hybridization. Evident expression of rrbp1 was mainly detected in cement gland and notochord at neurula and tailbud stages. Heart expression of rrbp1 was detected at stage 36. RT-PCR results indicated that very weak expression of rrbp1a was firstly detected in oocytes, followed by increasing expression until stage 39. Differently, very weak expression of rrbp1b was firstly observed at stage 2, and then maintained at a lower level to stage 17 followed by an intense expression from stages 19–39. Moreover, both expression profiles were also different in adult tissues. This study reports Xenopus rrbp1 expression during early embryonic development and in adult tissues. Our study will facilitate the functional analysis of Rrbp1 family during embryonic development.

Ser422 phosphorylation blocks human Tau cleavage by caspase-3: Biochemical implications to Alzheimer’s Disease

Proteolytic truncation of microtubule associated human (h) Tau protein by caspase-3 at the carboxy (C) terminus has been linked to the pathogenesis of Alzheimer’s Disease (AD). This cleavage likely occurs between Asp421↓Ser422 leading to the formation of 421-mer truncated Tau protein which has been found to be present as aggregate in high level after phosphorylation in mortal AD brain tissue compared to normal. At least 50 phosphorylation sites involving Ser, Thr and Tyr residues have been identified or proposed in hTau and a selected number of them have been implicated in hTau aggregation following latter’s proteolytic truncation. Interestingly, it is further noted that Ser422 residue present in the P1′ position of hTau caspase-3 cleavage region is a potential phosphorylation site. So we became interested to examine in vitro the effect of phospho-Ser422 residue on hTau cleavage by caspase-3 which is a crucial upstream event associated with hTau self-assembly leading to AD pathogenesis. The goal of this project is to study in vitro the caspase-3 cleavage site of hTau protein and to examine the kinetics of this cleavage following Ser422 phosphorylation and treatment with caspase-3 inhibitors. This is achieved by designing peptides from the sequence of hTau protein containing the proposed caspase-3 cleavage region. Peptides were designed from 441-mer major human Tau protein sequence that encompasses the proposed caspase-3 cleavage site [Asp421↓Ser422]. Corresponding phospho-, dextro-Ser422 and dextro-Asp421 analogs were also designed. Peptides were synthesized by solid phase chemistry, purified and fully characterized by mass spectrometry. These were then incubated with recombinant caspase-3 enzyme under identical condition for digestion and analyzed for cleavage by mass spectrometry and RP-HPLC chromatograms. Our results indicated that while the control peptide is efficiently cleaved by caspase-3 at Asp421↓Ser422 site producing the expected N- and C-terminal fragment peptides, the corresponding phospho-Ser422 peptide remained completely resistant to the cleavage. Substitution of Asp421 by its dextro isoform also blocks peptide cleavage by caspase-3. However substitution of Ser422 by its dextro isoform in the peptide did not affect the cleavage significantly. The above results were further confirmed by caspase-3 digestion experiment in the presence of varying amounts of caspase-3 inhibitor (Ac-DQVD-aldehyde) which was found to block this cleavage in a highly effective manner. Our results highlighted the crucial significance of Ser422 phosphorylation and suggest that the kinase associated with this Ser-phosphorylation may protect Tau from aggregation. Thus specific promoters/activators of this kinase may find useful therapeutic benefits in arresting Tau truncation by caspase-3 and the progression of AD. In addition our data demonstrated that Tau-peptides where Ser422 or Asp421 are substituted by their respective dextro isomers, exhibit different cleavage kinetics by caspase-3 and this may have important implications in therapeutic intervention of Tau aggregation and associated AD.

Abstract A018: High-value T cell epitope selection for mutanome-directed cancer immunotherapy using an innovative cancer neo-epitope classification system

Abstract T cell epitopes bearing tumor-specific mutations discovered using whole-exomic and transcriptomic sequencing of tumor-normal pairs stimulate T cell-mediated processes that lead to tumor regression. Although neo-epitope prediction using computational methods rapidly identifies epitope candidates in the mutanome, a large proportion of neo-epitopes prove to be non-immunogenic. Innovative computational tools validated for infectious disease targets can be applied to enhance design of personalized cancer immunotherapies by classification of predicted epitopes by potential for mounting a tumor-specific response. Tumor-specific epitopes with potential to stimulate naïve T cells and epitopes that may cross-react with antigen-experienced T cells raised in infection are valuable targets. Epitopes with potential to activate regulatory T cells trained on self and commensal antigens are counter-indicated. We developed the JanusMatrix algorithm that parses query sequences into MHC-facing and T cell receptor (TCR)-facing sequences and screens sequence databases to identify MHC ligands that share TCR faces with host-related proteins. A database of human protein sequences is available to identify tumor-specific epitopes that may reduce anti-tumor activity by sequences that activate regulatory T cells (Tregs) trained in the thymus on self-antigens. Similarly, tumor-specific epitope candidates are screened using databases composed of antigens derived from human commensals or pathogens to identify epitopes that, respectively, may detrimentally or beneficially cross-react with T cells raised over the course of an individual's immune history. Neo-epitope candidates are ranked according to MHC binding potential, TCR face homology. We conducted retrospective analyses of cancer vaccine efficacy studies performed in mice [Kreiter et al. 2015 Nature 520, 692–696] showing that mutanome-directed vaccines effective at preventing tumor growth contained higher numbers of class I and II MHC neo-epitopes, as identified by EpiVax's iVAX platform, and had lower potential to cross-react with other murine proteins. An evaluation of mutanomes derived from non-small cell lung cancer patients [Rizvi et al. 2014 Science 348, 124-128] confirmed these findings. Improved clinical outcomes were observed in patients with mutanomes enriched in class I MHC neo-epitopes with TCR faces distinct from other human-derived epitopes. These results highlight the benefits of using in silico prediction tools for the selection of neo-epitopes and how they can improve the design and efficacy of future cancer vaccines. While retrospective in nature, the suite of tools used for these analyses have been extensively validated in prospective vaccine studies for infectious disease. Removal of Treg epitopes, identified by JanusMatrix, has led to the development of more immunogenic vaccine antigens. EpiVax's H7N9 influenza Treg epitope-depleted vaccine is scheduled for Phase I clinical trial. Direct application of JanusMatrix to the neo-epitope-driven cancer vaccine discovery and design pipeline will focus candidate selection on higher-value sequences than what conventional T cell epitope mapping algorithms generate. Neo-epitopes with low Treg activation potential may then be used to support development of personalized therapies including vaccination and in vitro expansion of tumor infiltrating lymphocytes for adoptive cell transfer. Citation Format: Lenny Moise, Guilhem Richard, Frances Terry, William Martin, Anne De Groot. High-value T cell epitope selection for mutanome-directed cancer immunotherapy using an innovative cancer neo-epitope classification system [abstract]. In: Proceedings of the Second CRI-CIMT-EATI-AACR International Cancer Immunotherapy Conference: Translating Science into Survival; 2016 Sept 25-28; New York, NY. Philadelphia (PA): AACR; Cancer Immunol Res 2016;4(11 Suppl):Abstract nr A018.

Tiered Human Integrated Sequence Search Databases for Shotgun Proteomics.

The results of analysis of shotgun proteomics mass spectrometry data can be greatly affected by the selection of the reference protein sequence database against which the spectra are matched. For many species there are multiple sources from which somewhat different sequence sets can be obtained. This can lead to confusion about which database is best in which circumstances-a problem especially acute in human sample analysis. All sequence databases are genome-based, with sequences for the predicted gene and their protein translation products compiled. Our goal is to create a set of primary sequence databases that comprise the union of sequences from many of the different available sources and make the result easily available to the community. We have compiled a set of four sequence databases of varying sizes, from a small database consisting of only the ∼20,000 primary isoforms plus contaminants to a very large database that includes almost all nonredundant protein sequences from several sources. This set of tiered, increasingly complete human protein sequence databases suitable for mass spectrometry proteomics sequence database searching is called the Tiered Human Integrated Search Proteome set. In order to evaluate the utility of these databases, we have analyzed two different data sets, one from the HeLa cell line and the other from normal human liver tissue, with each of the four tiers of database complexity. The result is that approximately 0.8%, 1.1%, and 1.5% additional peptides can be identified for Tiers 2, 3, and 4, respectively, as compared with the Tier 1 database, at substantially increasing computational cost. This increase in computational cost may be worth bearing if the identification of sequence variants or the discovery of sequences that are not present in the reviewed knowledge base entries is an important goal of the study. We find that it is useful to search a data set against a simpler database, and then check the uniqueness of the discovered peptides against a more complex database. We have set up an automated system that downloads all the source databases on the first of each month and automatically generates a new set of search databases and makes them available for download at http://www.peptideatlas.org/thisp/ .

Enabling N-to-C Ser/Thr Ligation for Convergent Protein Synthesis via Combining Chemical Ligation Approaches.

In this article, Ser/Thr ligation(on/off) has been realized to enable N-to-C successive peptide ligations using a salicylaldehyde semicarbazone (SAL(off)) group by in situ activation with pyruvic acid of the peptide SAL(off) ester into the peptide salicylaldehyde (SAL(on)) ester. In addition, a peptide with a C-terminal thioester and N-terminal Ser or Thr as the middle peptide segment can undergo one-pot Ser/Thr ligation and native chemical ligation in the N-to-C direction. The utility of this combined ligation strategy in the N-to-C direction has been showcased through the convergent assembly of a human cytokine protein sequence, GlcNAcylated interleukin-25.

Preparation and Characterization of a Polyclonal Antibody against Human Actin Filament-Associated Protein-120 kD.

Actin filament-associated protein-120kD (AFAP-120) is an alternatively spliced isoform of actin filament-associated protein-110kD (AFAP-110) and contains an additional neuronal insert (NINS) fragment in addition to identical domains to the AFAP-110. Unlike AFAP-110 widely expressed in tissues, AFAP-120 is specifically expressed in the nervous system and plays a role in organizing dynamic actin structures during neuronal differentiation. However, anti-AFAP-120 antibody is still commercially unavailable, and this may hinder the function research for AFAP-120. In this study, we simultaneously used the ABCpred online server and the BepiPred 1.0 server to predict B-cell epitopes in the exclusive NINS sequence of human AFAP-120 protein, and found that a 16aa-peptide sequence was the consensus epitope predicted by both tools. This peptide was chemically synthesized and used as an immunogen to develop polyclonal antibody against AFAP-120 (anti-AFAP-120). The sensitivity and specificity of anti-AFAP-120 were analyzed with immunoblotting, immunoprecipitation, and immunofluorescence assays. Our results indicated that anti-AFAP-120 could react with over-expressed and endogenous human AFAP-120 protein under denatured condition, but not with human AFAP-110 protein. Moreover, native human AFAP-120 protein could also be recognized by the anti-AFAP-120 antibody. These results suggested that the prepared anit-AFAP-120 antibody would be a useful tool for studying the biochemical and biological functions of AFAP-120.

Membrane-Spanning Sequences in Endoplasmic Reticulum Proteins Promote Phospholipid Flip-Flop

The mechanism whereby phospholipids rapidly flip-flop in the endoplasmic reticulum (ER) membrane remains unknown. We previously demonstrated that the presence of a hydrophilic residue in the center of the model transmembrane peptide sequence effectively promoted phospholipid flip-flop and that hydrophilic residues composed 4.5% of the central regions of the membrane-spanning sequences of human ER membrane proteins predicted by SOSUI software. We hypothesized that ER proteins with hydrophilic residues might play a critical role in promoting flip-flop. Here, we evaluated the flip rate of fluorescently labeled lipids in vesicles containing each of the 11 synthetic peptides of membrane-spanning sequences, using a dithionite-quenching assay. Although the flippase activities of nine peptides were unexpectedly low, the peptides based on the EDEM1 and SPAST proteins showed enhanced flippase activity with three different fluorescently labeled lipids. The substitution of hydrophobic Ala with His or Arg in the central region of the EDEM1 or SPAST peptides, respectively, attenuated their ability to flip phospholipids. Interestingly, substituting Ala with Arg or His at a location outside of the central region of EDEM1 or SPAST, respectively, also affected the enhancement of flip-flop. These results indicated that both Arg and His are important for the ability of these two peptides to increase the flip rates. The EDEM1 peptide exhibited high activity at significantly low peptide concentrations, suggesting that the same side positioning of Arg and His in α-helix structure is critical for the flip-flop promotion and that the EDEM1 protein is a candidate flippase in the ER.