FR3 Brugia malayi list of putative T cell epitopes

Below is a list of putative T cell epitopes identified using the iVax Immunoinformatics Toolkit, by screening over 11,000 proteins belonging to the genome-derived B. malayi protein sequences (EpiVax, Providence, Rhode Island), in collaboration with Dr. Anne De Groot at the University of Rhode Island.  All putative epitope sequences can be synthesized and it is recommended, if choosing to have peptides synthesized commercially or within respective institutions, to have peptides synthesized with >85% purity.

“EpiMatrix takes overlapping 9-mer frames derived from the conserved target protein sequences and scores them for potential binding affinity against a panel of Class I or Class II HLA alleles; each frame-by-allele assessment that scores highly and is predicted to bind is a putative T cell epitope. ClustiMer takes EpiMatrix output and identifies clusters of 9-mers that contain large numbers of putative T cell epitopes. BlastiMer automates the process of submitting the previously identified sequences to BLAST to determine if any share similarities with the human genome; any such similar sequences would be likely to be tolerated or to elicit an unwanted autoimmune response.” [EpiVax, Inc.]. For more information on the software and/or interest in purchasing the private web-based immunogenicity screening services, please visit the following website: http://www.epivax.com/vaccine-design-redesign/ivax-web-based-vaccine-design/ .

Additonal notes: Higher Epivax scores (for overall proteins) and Cluster scores (~25mers within proteins), for individual peptides, indicate higher predicted immunogenicity for the likelihood of binding to class II MHC (class II HLA). The predicted confidence of binding across all eight alleles ranged from 90% to 99%. Alleles represented within the software predictions are as follows: DRB1*0101, DRB1*0301, DRB1*0401, DRB1*0701, DRB1*0801, DRB1*1101, DRB1*1301, and DRB1*1501. Membrane topology prediction software, Phobius, was used to determine putative signal sequences (http://phobius.sbc.su.se/). Filarial conservation analyses was done by using the BLAST function within the BROAD Institute’s Filarial Worms Database ( http://www.broadinstitute.org/annotation/genome/filarial_worms/MultiHome.html ). For more information on the genome-derived putative T cell epitopes, please contact the FR3 Molecular Resources Division.: genome@smith.edu or Melissa Torres mtorres3@smith.edu.

Protein of Interest: thioredoxin peroxidase-2 (Tpx2)

Peptide designation: BmP1

 

 Ac-LGQFKGKYVVLLFYPLDFTFV-amide

  • Cluster length: 21 AAs
  • Cluster Score: 21.41
  • Gene ID: GI-2851423-SP-Q17172-2-TDX_2
  • EpiVax score for overall protein antigenicity: -27.61
  • Sequence conservation with Wuchereria bancrofti and Loa loa thioredoxin peroxidases (WUBG_01631.1 and LOAG_01338.1)
Protein of Interest: JUV-P120, excretory/secretory protein

Peptide designation: BmP2

 

 Ac-QQNLQKQQSMFEKLLKSNRILLQN-amide

  • Cluster Length: 24 AAs
  • Cluster Score: 53.3
  • Protein of Interest: JUV-P120, excretory/secretory protein
  • GenBank Locus Tag: Bm1_29765
  • Gene ID: GI-170585244-REF-XP_001897395-1
  • EpiVax score for overall protein antigenicity: 95.2
  • Phobius-predicted signal sequence AAs 1-22
  • No conservation with other filarial proteins
Protein of Interest: JUV-P120, excretory/secretory protein

Peptide designation: BmP3

 

 Ac-CENKLQLLHKLHSTLQQLQKQQQFLN-amide

  • Cluster Length: 24 AAs
  • Cluster Score: 53.3
  • GenBank Locus Tag: Bm1_18010
  • Gene ID: GI-170579968-REF-XP_001895060-1
  • EpiVax score for overall protein antigenicity: 77.17
  • Phobius-predicted signal sequence AAs 1-19
  • No conservation with other filarial proteins
Protein of Interest: Galectin

Peptide designation: BmP5

 

 Ac-EYAFQIFINSERYATYAH-amide

  • Cluster Length: 18 AAs
  • Cluster Score: 19.52
  • GenBank Locus Tag: Bm1_24940
  • Gene ID: GI-170583137-ref-XP_001896448-1
  • EpiVax score for overall protein antigenicity: 19.52
  • Sequence conservation with Wuchereria bancrofti hypothetical protein (WUBG_10133.1) and Loa loa beta-galactoside-binding lectin (LOAG_01794.1)
Protein of Interest: Hypothetical protein, 57.5 kDa in VMA7-RPS25A intergenic region

Peptide designation: BmP6

 

 Ac-LPLYTNNYFLSSSSIICHYH-amide

  • Cluster Length: 20 AAs
  • Cluster Score: 36.25
  • GenBank Locus Tag: Bm1_22830
  • Gene ID: GI-170582199-REF-XP_001896022-1
  • EpiVax score for overall protein antigenicity: 392.44 (*Very high scoring)
  • Phobius-predicted signal sequence AAs 1-19
  • No conservation with other filarial proteins
Protein of Interest: Hypothetical protein, 57.5 kDa in VMA7-RPS25A intergenic region

Peptide designation: BmP7

 

 Ac-YLYYHHHYHHQLPLLSSLPINLP-amide

  • Cluster Length: 23 AAs
  • Cluster Score: 38.36
  • GenBank Locus Tag: Bm1_22830
  • Gene ID: GI-170582199-REF-XP_001896022-1
  • EpiVax score for overall protein antigenicity: 392.44 (*Very high scoring)
  • Phobius-predicted signal sequence AAs 1-19
  • No conservation with other filarial proteins
Protein of Interest: Hypothetical protein

Peptide designation: BmP8

 Ac-MEDIMHQINRLKRATKS-amide

  • Cluster Length: 17 AAs
  • Cluster Score: 24.92
  • GenBank Locus Tag: Bm1_45480
  • Gene ID: GI-170591602-REF-XP_001900559-1
  • EpiVax score for overall protein antigenicity: 236.75 (*Very high scoring)
  • Phobius-predicted signal sequence AAs 1-25
  • No conservation with other filarial proteins
Protein of Interest: Hypothetical protein

Peptide designation: BmP9

 

 Ac-DEKWRPNEPYKLSQALITITI-amide

  • Cluster Length: 21 AAs)
  • Cluster Score: 23.65
  • GenBank Locus Tag: Bm1_20570
  • Gene ID: GI-170581175-REF-XP_001895568-1
  • EpiVax score for overall protein antigenicity: 223.31 (*Very high scoring)
  • Phobius-predicted signal sequence AAs 1-20
  • No conservation with other filarial proteins
Protein of Interest: Hypothetical protein

Peptide designation: BmP10

 

 Ac-SSRLQMLYRNILELTKRVRLMVSRV-amide

  • Cluster Length: 25 AAs
  • Cluster Score: 42.43
  • GenBank Locus Tag: Bm1_06120
  • Gene ID: GI-170574167-REF-XP_001892693-1
  • EpiVax score for overall protein antigenicity: 244.33 (*Very high scoring)
  • Sequence conservation with Wuchereria bancrofti hypothetical protein (WUBG_02193.1)
Protein of Interest: Krox-like protein

Peptide designation: BmP11

 

 Ac-VSAVLRSNVVLRSNATLWSNAA-amide

  • Cluster length: 22 AAs
  • Cluster Score: 50.68
  • GenBank Locus Tag: Bm1_14700
  • Gene ID: GI-170578429-REF-XP_001894406-1
  • EpiVax score for overall protein antigenicity: 262 (*Very high scoring)
  • No conservation with other filarial proteins
Protein of Interest: Krox-like protein

Peptide designation: BmP12

 

 Ac-DATLRSNVVLRSNATLWSNAT-amide

  • Cluster Length: 21 AAs
  • Cluster Score: 40.61
  • GenBank Locus Tag: Bm1_14700
  • Gene ID: GI-170578429-REF-XP_001894406-1
  • EpiVax score for overall protein antigenicity: 262 (*Very high scoring)
  • No conservation with other filarial proteins
Protein of Interest: UDP-glucoronosyl and UDP-glucosyl transferase family protein

Peptide designation: BmP13

 

 Ac-TDKMTYLQRLKNLIITILTTKLLDNH-amide

  • Cluster Length: 26 AAs
  • Cluster Score: 40.61
  • GenBank Locus Tag: Bm1_13480
  • Gene ID: GI-170577851-REF-XP_001894161-1
  • EpiVax score for overall protein antigenicity: 69.1
  • No conservation with other filarial proteins
Protein of Interest: Leucine Rich Repeat family

Peptide designation: BmP14

 

 Ac-KYNEIKQLMNMQLTNLSSLTILSLTGN-amide

  • Cluster Length: 27 AAs
  • Cluster Score: 49.84
  • GenBank Locus Tag: Bm1_40135
  • Gene ID: GI-170589441-REF-XP_001899482-1
  • EpiVax score for overall protein antigenicity: 60.85
  • Phobius-predicted signal sequence AAs 1-19
  • No conservation with other filarial proteins
Protein of Interest: Leucine Rich Repeat family

Peptide designation: BmP15

 

 Ac-TDSLVGMRALRVLSLRCNNIGDIE-amide

  • Cluster Length: 23 AAs
  • Cluster Score: 45.58
  • GenBank Locus Tag: Bm1_40135
  • Gene ID: GI-170589441-REF-XP_001899482-1
  • EpiVax score for overall protein antigenicity: 60.85
  • Phobius-predicted signal sequence AAs 1-19
  • Sequence conservation with Wuchereria bancrofti leucine rich repeat family protein (WUBG_07350.1) and Loa loa hypothetical protein (LOAG_06354.1)
Protein of Interest: Hypothetical protein

Peptide designation: BmP16

 

 Ac-LKYVKVNRSRAIGVHLVSALPKILIRSE-amide

  • Cluster Length: 28 AAs
  • Cluster Score: 56.15
  • GenBank Locus Tag: Bm1_40225
  • Gene ID: GI-170589481-ref-XP_001899502-1
  • EpiVax score for overall protein antigenicity: 56.51
  • Sequence conservation with Wuchereria bancrofti hypothetical protein (WUBG_04072.1) and Loa loa hypothetical protein (LOAG_1800.1)
Protein of Interest: Hypothetical protein

Peptide designation: BmP17

 

 Ac-LATYVGVIRRKVFLHFLKVLSKASEQQN-amide

  • Cluster Length: 28 AAs
  • Cluster Score: 69.02
  • GenBank Locus Tag: Bm1_40225
  • Gene ID: GI-170589481-ref-XP_001899502-1
  • EpiVax score for overall protein antigenicity: 56.51
  • Sequence conservation with Wuchereria bancrofti hypothetical protein (WUBG_04072.1) and Loa loa hypothetical protein (LOAG_1800.1)
Protein of Interest: Hypothetical protein

Peptide designation: BmP18

 

 Ac-MITLAESYIQIWRLNTSKTREQRAG-amide

  • Cluster Length: 25 AAs
  • Cluster Score: 49.59
  • GenBank Locus Tag: Bm1_04265
  • Gene ID: GI-170573075-REF-XP_001892341-1
  • EpiVax score for overall protein antigenicity: 131.85 (*high scoring)
  • Sequence conservation with Wuchereria bancrofti U4/U6.U5 tri-snRNP-associated protein (WUBG_02375.1) and Loa loa ubiquitin specific peptidase (LOAG_04171.1)
Protein of Interest: Putative oxidoreductase

Peptide designation: BmP19

 

 Ac-KSGLLTVEKNLRLLANKKISLNIE-amide

  • Cluster Length: 24 AAs
  • Cluster Score: 67.31
  • GenBank Locus Tag: Bm1_41060
  • Gene ID: GI-170589824-REF-XP_001899673-1
  • EpiVax score for overall protein antigenicity: -0.61
  • Sequence conservation with Wuchereria bancrofti hypothetical protein (WUBG_10631.1)