An Immunoinformatics Approach in Design of Synthetic Peptide Vaccine Against Influenza Virus.

Peptide-based vaccines are an appealing strategy which involves usage of short synthetic peptides to engineer a highly targeted immune response. These short synthetic peptides contain potential T- and B-cell epitopes. Experimental approaches in identifying these epitopes are time-consuming and expensive; hence immunoinformatics approach came into picture. Immuninformatics approach involves epitope prediction tools, molecular docking, and population coverage analysis in design of desired immunogenic peptides. In order to overcome the antigenic variation of viruses, conserved regions are targeted to find the potential epitopes. The present chapter demonstrates the use of immunoinformatics approach to select potential peptide containing multiple T- (CD8+ and CD4+) and B-cell epitopes from Avian H3N2 M1 Protein. Further, molecular docking (to analyse HLA-peptide interaction) and population coverage analysis have been used to verify the potential of peptide to be presented by polymorphic HLA molecules. In silico approach of epitope prediction has proven to be successful methodology in screening the putative epitopes among numerous possible vaccine targets in a given protein.

Highly conserved hemagglutinin peptides of H1N1 influenza virus elicit immune response.

In the current study, two highly conserved (> 90%) H1N1 hemagglutinin peptides STDTVDTVLEKNVTVTHSVNL (H1) and KVNSVIEKMNTQFTAVGKEF (H2) containing multiple T-cell epitopes have been assessed for their immunogenic potential in vitro, subjecting peripheral blood mononuclear cells from healthy volunteers to repetitive stimulation of chemically synthesised H1 and H2 peptides, and measuring their interferon (IFN)-γ level (ELISA) and proliferation (MTT assay). Further, these peptides were analysed for their binding affinity with 18 different human leukocyte antigen (HLA) class I and II by means of molecular docking. All seven samples tested for H1- and H2-induced IFN-γ secretion were found to have enhanced IFN-γ production. Six (H1) and five (H2) samples have shown proliferative response compared to unstimulated cells. Peptide-induced IFN-γ secretion and proliferation in healthy samples represent the immunogenic potential of these peptides. Further, molecular docking results reveal that the peptides have comparable binding energy to that of native bound peptide for both HLA classes which indicates that these peptides have the capability to be presented by different HLA molecules required for T-cell response. Hence, these conserved immunogenic hemagglutinin peptides are potential candidates for influenza vaccine development.

Immune responses to highly conserved influenza A virus matrix 1 peptides.

Influenza vaccine development is considered to be complicated and challenging. Constantly evolving influenza viruses require continuous global monitoring and reformulation of the vaccine strains. Peptides that are conserved among different strains and subtypes of influenza A virus are strongly considered to be attractive targets for development of cross protective influenza vaccines that stimulate cellular responses. In this study, three highly conserved (>90%) matrix 1 peptides that contain multiple T cell epitopes, ILGFVFTLTVPSERGLQRRRF (PM 1), LIRHENRMVLASTTAKA (PM 2) and LQAYQKRMGVQMQR (PM 3), were assessed for their immunogenic potential in vitro by subjecting peripheral blood mononuclear cells from healthy volunteers to repetitive stimulation with these chemically synthesised peptides and measuring their IFN-γ concentrations, proliferation by ELISA, and 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide assay, respectively. Seven samples were screened for immunogenicity of PM 1 and PM 2, and six for that of PM 3. All six samples had positive responses (IFN-γ secretion) to PM 3 stimulation, as did five and three for PM 2 and PM 1 respectively. In contrast, seven (PM 1 and PM 2) and four (PM 3) samples showed proliferative response as compared with unstimulated cells. The encouraging immunogenic response generated by these highly conserved matrix 1 peptides indicates they are prospective candidates for development of broadly reactive influenza vaccines.

Metadherin peptides containing CD4(+) and CD8(+) T cell epitopes as a therapeutic vaccine candidate against cancer.

The concept of peptide-based vaccines against cancer has made noteworthy progress. Metadherin (MTDH) overexpression and its role in the development of diverse cancers make it an attractive target for cancer immunotherapy. In the current study, six different T cell epitope prediction tools were run to identify MTDH peptides with multiple immunogenic regions. Further, molecular docking was performed to assess HLA-peptide binding interactions. Nine and eleven peptides fragments containing multiple CD8 (+) and CD4 (+) T-cell epitopes, ranging from 9 to 20 amino acids, respectively, were obtained using a consensus immunoinformatics approach. The three peptides that were finally identified as having overlapping CD4 (+) and CD8 (+) T- cell epitopes are ARLREMLSVGLGFLRTELG, FLLGYGWAAACAGAR, YIDDEWSGLNGLSSADP. These peptides were found to not only have multiple T cell epitopes but also to have binding affinity with wide HLA molecules. A molecular docking study revealed that the predicted immunogenic peptides (with single or multiple T cell epitopes) of MTDH have comparable binding energies with naturally bound peptides for both HLA classes I and II. Thus, these peptides have the potential to induce immune responses that could be considered for developing synthetic peptide vaccines against multiple cancers.

Identification of Conserved Peptides Comprising Multiple T Cell Epitopes of Matrix 1 Protein in H1N1 Influenza Virus.

Cell mediated immune response plays a key role in combating viral infection and thus identification of new vaccine targets manifesting T cell mediated response may serve as an ideal approach for influenza vaccine. The present study involves the application of an immunoinformatics-based consensus approach for epitope prediction (three epitope prediction tools each for CD4+ and CD8+ T cell epitopes) and molecular docking to identify peptide sequences containing T cell epitopes using the conserved sequences from all the Matrix 1 protein sequences of H1N1 virus available until April 2015. Three peptides comprising CD4+ and CD8+ T cell epitopes were obtained, which were not exactly reported in earlier studies. Population coverage study of these multi-epitope peptides revealed that they are capable of inducing a potent immune response belonging to individuals from different populations and ethnicity distributed around the globe. Conservation study with other subtypes of influenza virus infecting humans (H2N2, H5N1, H7N9, and H3N2) revealed that these three peptides were conserved (>90%), with 100% identity in most of these strains. Hence, these peptides can impart immunity against H1N1 as well as other subtypes of influenza virus. A molecular docking study of the predicted peptides with class I and II human leukocyte antigen (HLA) molecules has shown that the majority of them have comparable binding energies to that of native peptides. Hence, these peptides from Matrix 1 protein of H1N1 appear to be promising candidates for universal vaccine design.

Folate status and intake of tribal Indian adolescents aged 10 to 17 years.

BACKGROUND: Adequate folate intake and levels are advisable throughout life but are of particular importance during adolescence, a period of rapid growth. However, folate insufficiency in economically deprived Indian adolescents is understudied. OBJECTIVE: This cross-sectional study examined the prevalence of folate deficiency and adequacy of folate intake of 224 tribal Indian adolescents (10 to 17 years of age). The secondary aim was to study the association between anemia status and folate status. METHODS: Radioimmunoassay, multiple-pass 24-hour dietary recall, and HemoCue were used to measure red blood cell (RBC) folate, folate intake, and anemia status, respectively. RESULTS: The geometric mean (95% CI) RBC folate concentration (nmol/L) was 360.2 (329.7 to 393.6), and the mean ± SD folate intake (µg/day) and hemoglobin level (g/L) were 159.9 ± 44.7 and 125.4 ± 13.0, respectively. Almost half of boys and girls aged 10 to 12 and 13 to 15 years and 66.7% of girls aged 16 to 17 years were deficient in RBCfolate (< 340 nmol/L). The mean ± SD folate intake (µg/day) of girls (139.4 ± 34.5) was lower than that of boys (173.8 ± 45.5) (p < .001). With respect to adequacy of folate intake, a greater proportion of girls in the age group of 13-15 years (78.5% vs 38.6%, p < 0.001) and 16-17 years (100.0% vs 76.9%, p = 0.04) had intakes below their Recommended Dietary Allowance (RDA). No association was observed between folate intake and RBC folate deficiency or between anemia status and RBC folate deficiency. CONCLUSIONS: Folate insufficiency was widespread in tribal Indian adolescents. There is an urgent need to develop culturally sensitive strategies for improvement.

Infant and child feeding index reflects feeding practices, nutritional status of urban slum children.

BACKGROUND: Infant and child feeding index (ICFI) an age-specific index, can be used to assess child feeding practices. We used the ICFI to assess feeding practices for urban slum children and the association between ICFI and child nutritional status. METHODS: 446 children aged 6 to 24 months from urban slums of Mumbai, India were studied. We used the 24-hour diet recall to study dietary diversity and a food frequency questionnaire for consumption of food groups during the preceding week. ICFI was computed using five components, namely, breastfeeding, use of bottle, dietary diversity score (DDS), food group frequency score (FGFS) and feeding frequency scores (FFS). Weight, height and Mid-Upper Arm Circumference (MUAC) were measured, and z scores were calculated. Association between ICFI scores and nutritional status was examined. RESULTS: The mean total ICFI score for all was 5.9 ± 1.9. Among the five components, FGFS and FFS differed between children <12 months of age and >12 months and by breast feeding status. In contrast, there were no differences vis-à-vis dietary diversity scores (DDS), breast feeding, and use of bottle. Non-breastfed children had significantly higher DDS scores than did breastfed children. The mean feeding frequency score (FFS) for children <12 months of age was slightly but not significantly lower than scores for children >12 months of age. Mother's age and child's age were significant determinants of ICFI. Multivariate analysis indicated that ICFI was significantly associated with Length-for-Age z scores (LAZ) and BMI-for-Age z scores (BAZ). Sensitivity of ICFI was lower than its specificity. CONCLUSIONS: The results of the present study confirmed that the ICFI can be used to collect information on key components of young child feeding practices and be incorporated into public-health programmes. Further, it could be used to determine the influence of complementary feeding practices on nutritional status of children.

Conserved peptides containing overlapping CD4+ and CD8+ T-cell epitopes in the H1N1 influenza virus: an immunoinformatics approach.

Pandemic threats of the H1N1 influenza virus have drawn attention to developing a universal vaccine against circulating and future strains of this virus. An immunoinformatics study was conducted to identify conserved peptides containing CD4+ and CD8+ T-cell epitopes from all the hemagglutinin (HA) and neuraminidase (NA) protein sequences available until February 2013 to cover the seasonal as well as the pandemic strains of the H1N1 virus. In the present study, six different immunoinformatics prediction programs were used in order to define the epitopes. Five conserved peptides of HA and six of NA protein were obtained that contained overlapping CD4+ and CD8+ T-cell epitopes. These identified peptides have a binding affinity for a large number of major histocompatibility complex (MHC) alleles. WHGSNRPWVSF of NA protein is a new peptide whose T-cell response has not been previously reported. Population coverage studies have shown that these peptide fragments have the capacity to induce a potent immune response among individuals from different populations around the world. Hence, these HA and NA peptides may be considered as interesting candidates for vaccine design.

Extracellular matrix dynamics in hepatocarcinogenesis: a comparative proteomics study of PDGFC transgenic and Pten null mouse models.

We are reporting qualitative and quantitative changes of the extracellular matrix (ECM) and associated receptor proteomes, occurring during the transition from liver fibrosis and steatohepatitis to hepatocellular carcinoma (HCC). We compared two mouse models relevant to human HCC: PDGFC transgenic (Tg) and Pten null mice, models of disease progression from fibrosis and steatohepatitis to HCC. Using mass spectrometry, we identified in the liver of both models proteins for 26 collagen-encoding genes, providing the first evidence of expression at the protein level for 16 collagens. We also identified post-transcriptional protein variants for six collagens and lysine hydroxylation modifications for 14 collagens. Tumor-associated collagen proteomes were similar in both models with increased expression of collagens type IV, VI, VII, X, XIV, XV, XVI, and XVIII. Splice variants for Col4a2, Col6a2, Col6a3 were co-upregulated while only the short form of Col18a1 increased in the tumors. We also identified tumor specific increases of nidogen 1, decorin, perlecan, and of six laminin subunits. The changes in these non-collagenous ECM proteins were similar in both models with the exception of laminin ß3, detected specifically in the Pten null tumors. Pdgfa and Pdgfc mRNA expression was increased in the Pten null liver, a possible mechanism for the similarity in ECM composition observed in the tumors of both models. In contrast and besides the strong up-regulation of integrin α5 protein observed in the liver tumors of both models, the expression of the six other integrins identified was specific to each model, with integrins α2b, α3, α6, and ß1 up-regulated in Pten null tumors and integrins α8 and ß5 up-regulated in the PDGFC Tg tumors. In conclusion, HCC-associated ECM proteins and ECM-integrin networks, common or specific to HCC subtypes, were identified, providing a unique foundation to using ECM composition for HCC classification, diagnosis, prevention, or treatment.

Serum retinol, alpha-tocopherol, and lipid peroxide concentrations in low-income indian pregnant mothers.

Serum alpha-tocopherol, retinol, and malondialdehyde concentrations were measured at 7(th) month of pregnancy in 122 women from low socio-economic background. Maternal anthropometric measurements, 24-hour nutrient intakes, and pregnancy outcome were recorded. One-third (34.3 %) of mothers had low birth weight babies and 10 % delivered preterm. Maternal diets were inadequate in all the nutrients, the most limiting being vitamin A. Three-fourths of mothers had intakes less than 25 % of the Indian recommended daily intake (RDI) of 600 microg retinol equivalents/day. Serum alpha-tocopherol concentrations of 98 % were indicative of deficiency and almost half the mothers had low serum retinol concentrations (< or =10 microg/dL). Mean malondialdehyde level was 7.0 +/- 1.4 nmoles/mL. These values are higher than reports in the literature and were attributable to poor intake of most dietary antioxidants. Malondialdehyde concentrations were negatively correlated with serum alpha-tocopherol. Birth weight was positively correlated with maternal weight and biceps skinfold thickness, macronutrient intakes, serum retinol, and alpha-tocopherol concentrations. Preterm delivery was associated with low anthropometric measurements and low nutrient intakes especially vitamin A. Mothers who delivered preterm had significantly lower malondialdehyde concentrations than those who delivered at term. The role of antioxidant nutrients, especially vitamin A and oxidative stress in relation to fetal growth and pregnancy outcome among mothers from low socioeconomic settings requires attention.