Finding neoepitopes in mouse models of personalized cancer immunotherapy

Background

Cancer immunotherapy uses one’s own immune system to fight cancerous cells. As immune system is hard-wired to distinguish self and non-self, cancer immunotherapy is predicted to target cancerous cells specifically, therefore is less toxic than chemotherapy and radiation therapy, two major treatments for cancer. Cancer immunologists have spent decades to search for the specific targets in cancerous cells.

Methods

Due to the recent advances in high throughput sequencing and bioinformatics, evidence has merged that the neoantigens in cancerous cells are probably the cancer-specific targets that lead to the destruction of cancer.We will review the transplantable murine tumor models for cancer immunotherapy and the bioinformatics tools used to navigate mouse genome to identify tumor-rejecting neoantigens.

Results

Several groups have independently identified point mutations that can be recognized by T cells of host immune system. It is consistent with the note that the formation of peptide-MHC I-TCR complex is critical to activate T cells. Both anchor residue and TCR-facing residue mutations have been reported. While TCR-facing residue mutations may directly activate specific T cells, anchor residue mutations improve the binding of peptides to MHC I molecules, which increases the presentation of peptides and the T cell activation indirectly.

Conclusions

Our work indicates that the affinity of neoepitopes for MHC I is not a predictor for anti-tumor immune responses in mice. Instead differential agretopic index (DAI), the numerical difference of epitope-MHC I affinities between the mutated and un-mutated sequences is a significant predictor. A similar bioinformatics pipeline has been developed to generate personalized vaccines to treat human ovarian cancer in a Phase I clinical trial.

     

Enhancing the Thermostability of Serratia plymuthica Sucrose Isomerase Using B-Factor-Directed Mutagenesis

The sucrose isomerase of Serratia plymuthica AS9 (AS9 PalI) was expressed in Escherichia coli BL21(DE3) and characterized. The half-life of AS9 PalI was 20 min at 45°C, indicating that it was unstable. In order to improve its thermostability, six amino acid residues with higher B-factors were selected as targets for site-directed mutagenesis, and six mutants (E175N, K576D, K174D, G176D, S575D and N577K) were designed using the RosettaDesign server. The E175N and K576D mutants exhibited improved thermostability in preliminary experiments, so the double mutant E175N/K576D was constructed. These three mutants (E175N, K576D, E175N/K576D) were characterized in detail. The results indicate that the three mutants exhibit a slightly increased optimal temperature (35°C), compared with that of the wild-type enzyme (30°C). The mutants also share an identical pH optimum of 6.0, which is similar to that of the wild-type enzyme. The half-lives of the E175N, K576D and E175N/K576D mutants were 2.30, 1.78 and 7.65 times greater than that of the wild-type enzyme at 45°C, respectively. Kinetic studies showed that the K_m values for the E175N, K576D and E175N/K576D mutants decreased by 6.6%, 2.0% and 11.0%, respectively, and their k_cat/K_m values increased by 38.2%, 4.2% and 19.4%, respectively, compared with those of the wild-type enzyme. After optimizing the conditions for isomaltulose production at 45°C, we found that the E175N, K576D and E175N/K576D mutants displayed slightly improved isomaltulose yields, compared with the wild-type enzyme. Therefore, the mutants produced in this study would be more suitable for industrial biosynthesis of isomaltulose.     

茶梅体细胞胚胎发生和植株的再生

在山茶属植物中,我们曾报道过金花茶和云南山茶组织培养形成胚状体和再生植株。茶梅(Camellia sasanqua)也是山茶属的一种重要的观赏植物,其植株矮小,花色鲜艳且具香味,除供观花外,还可做成不同造型的盆景供观赏,在园艺上也可用作茶花嫁接的砧木。茶梅组织培养通过体细胞胚状体产生植株,至今尚未见报道。现把部份实验结果报道如下。     

Purification and characterization of a novel monomeric glutathione peroxidase from rat liver

A novel glutathione peroxidase, which is active toward hydroperoxides of phospholipid in the presence of a detergent, has been purified to homogeneity from a rat liver postmicrosomal supernatant fraction by ammonium sulfate fractionation and three different column chromatographies. From a DE52 column, glutathione peroxidase active toward phosphatidylcholine dilinoleoyl hydroperoxides was eluted in one major and two minor peaks. The enzyme in the major peak was found to be separated from the "classic" glutathione peroxidase and glutathione S-transferases and further purified by Sephacryl S-200 and Mono Q column chromatographies. The purified enzyme was found to be homogeneous on polyacrylamide gel electrophoresis under nondenaturing conditions as well as that in the presence of sodium dodecyl sulfate. The molecular weight of the enzyme as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis was 22,000, and that by gel filtration was comparable, indicating that the enzyme protein is a single polypeptide. The purified enzyme was found to catalyze the reduction of phosphatidylcholine dilinoleoyl hydroperoxides to the corresponding hydroxy derivatives. The isoelectric point of the enzyme was found at pH 6.2, and the optimum pH for the enzyme activity was 8.0. The enzyme was active toward cumene hydroperoxide, H2O2, and 1-monolinolein hydroperoxides in the absence of a detergent. The enzyme activity toward phospholipid hydroperoxides was minute in the absence of a detergent but was remarkably enhanced by the addition of a detergent. From these results, the presently purified enzyme is obviously different from the classic glutathione peroxidase and also from phospholipid hydroperoxide glutathione peroxidase purified from pig heart (Ursini, F., Maiorino, M., and Gregolin, C. (1985) Biochim. Biophys. Acta 839, 62-70), though considerably similar to the latter.     

A bombesin-like peptide from skin of Sanguirana varians

Bombesin-like peptides (BLPs) are a family of neuro-endocrinic peptides that mediates a variety of biological activities. A BLP named bombesin-SV from the skin secretions of the frog, Sanguirana varians, was purified and characterized. Its amino acid sequence is pEMIFGAPMWALGHLM-NH2 determined by Edman degradation and mass spectrometry. The cDNA encoding bombesin-SV precursor was cloned from skin cDNA library of S. varians. The precursor is composed of 67 amino acid residues including a copy of mature bombesin-SV. Two predicted enzymatic processing sites (-Lys-Arg-) are flanked at the mature bombesin-SV sequence. In the in vitro myotropic contraction experiment, the synthesized bombesin-SV displayed the stimulating effect toward rat stomach strips, suggesting that bombesin-SV acts as agonist as most other BLPs do.     

A genome scan for quantitative trait loci affecting three ear traits in a White Duroc × Chinese Erhualian resource population

Chinese Erhualian pigs have larger and floppier ears compared with White Duroc pigs (small, half- or fully-pricked ears). To identify quantitative trait loci (QTL) for ear weight and area as well as erectness, a genome-wide scan with 194 microsatellites was performed in a White Duroc × Chinese Erhualian resource population (>1000 F₂ animals). Twenty-three genome-wide significant QTL and 12 suggestive QTL were identified. All QTL for ear erectness and size detected in two previous studies, bar two on SSC6 and 9, were confirmed here. The 1% genome-wide significant QTL at 70 cM on SSC5 and at 58 cM on SSC7 have profound and pleiotropic effects on the three ear traits, with Erhualian alleles increasing weight and area but decreasing erectness. Notably, the 95% confidence interval of the QTL for weight and area on SSC7 spanned only 3 cM. New QTL reaching 1% genome-wide significance were found on SSC8 (at 37 cM) for all three ear traits, on SSC4 and 16 for weight and area, and on SSCX for area. Unexpectedly, Erhualian alleles at these loci were associated with lighter and smaller or erect ear. Some new suggestive QTL were also found on other chromosome regions. Almost all the QTL for weight and area had essentially additive effects, while the QTL for erectness on SSC2, 5 and 7 showed not only additive effects but also partial dominance effects of Erhualian alleles. The two most significant QTL on SSC7 and SSC5 could be promising targets for fine mapping and identification of the causative mutations.     

A New PAMPA Model Proposed on the Basis of a Synthetic Phospholipid Membrane

The purpose of this work was to investigate the synthetic phospholipid dependence of permeability measured by parallel artificial membrane permeability assay (PAMPA) method. Three phospholipids with hydrophobic groups of different lengths and phosphorylcholine as the hydrophilic group were concisely synthesized. Ten model drug molecules were selected because of their distinct human fraction absorbed (%FA) values and various pK_a characteristics. In vitro drug permeation experiments were designed to determine the effect of the incubation time (4–20 h), pH gradient (4.6–9.32) and carbon chain length (8, 10, 12) on the drug permeability through the synthetic phospholipid membrane in the PAMPA system. The results showed that intensive and significant synthetic phospholipids dependence of permeability influenced by the length of lipid’s hydrophobic carbon chain. The effective permeability constant (P_e) of each drug increased rapidly with time, then decreased slightly after reaching the maximum; the pH gradient changed the drug permeability according to the pH-partition hypothesis for drugs with diverse pK_a values; and longer hydrophobic chains in the synthetic phospholipid membrane improved the drug permeability, as observed for all test drugs at almost all incubation time points. This newly proposed PAMPA model considered the synthetic phospholipid membrane and showed good P_e-%FA correlation for the passive transport of drugs, making it a helpful supplementary method for PAMPA systems.     

The addition of Co2+ enhances the catalytic efficiency and thermostability of recombinant glucose isomerase from Thermobifida fusca

Glucose isomerase is an important industrial enzyme that catalyzes the reversible isomerization of glucose to fructose. In this study, the effect of cobalt ions (Co²⁺) on the catalytic efficiency and thermostability of recombinant glucose isomerase from Thermobifida fusca was analyzed. The activity of glucose isomerase from engineered Escherichia coli supplemented with 1 mM Co²⁺ (C-GI) reached 41 U/ml, 2.1-fold higher than enzyme prepared from E. coli without additive (GI). The purified C-GI also exhibited an increased specific activity (23.8 U/mg compared to 12.1 U/mg for GI) and a greater thermostability (half-life of 17 h at 75 °C, 11.3-fold higher than GI (1.5 h)). The optimal temperature for C-GI shifted from 80 °C to 85 °C and demonstrated higher activity over pH 7.0–9.0. The k_cat/K_m value of C-GI (89.3 M^?1 s^?1) for the isomerization of glucose to fructose was nearly 1.75-fold higher than that of GI. In addition, the engineered cells were immobilized with the method of flocculation-cross linking. The immobilized cells supplemented with 1 mM Co²⁺ (C-IGI) had a better operational performance than cells without additives (IGI); at the end of 6 cycles, the conversion rate of C-IGI was still 43.1%, meeting the conversion rate requirement.     

The effects of climate warming on the migratory status of early summer populations of Mythimna separata (Walker) moths: A case‐study of enhanced corn damage in central‐northern China, 1980–2016

Mythimna separata (Walker) moths captured in light traps were monitored in Luohe, central‐northern China, from 1980 to 2016. Annual average temperature recorded an increase of 0.298°C/10 years in this region in the period. Our results indicate that a rising April and May average temperature and earlier occurrences of days recording the highest day temperature (30°C) caused an advanced peak and increasing proportion of high ovarian development levels of first‐generation females in earlier summers. Results using Johnson's formulation of “oogenesis‐flight syndrome” indicate that increasing sexual maturity proportion has resulted in more emigrant individuals in the local first‐generation moth becoming residents, and then increased individuals rapidly in the local second‐generation moth since 2006. Consequences of this action have a boom in corn damage since 2007 in this region. Advanced peak dates of the first and second‐generation moth revealed the same response to increasing average monthly temperatures in the monitoring period. Increasing temperatures, the average May temperature exceeds or equal to 22°C, during the early 2000's may represent a physiological threshold for M. separata development. Our results suggest that climate warming may impact M. separata migratory status and cause a problem of crop production in this region.