US 11,969,462 B2
Personalized vaccine
Kaïdre Bendjama, Illkirch-Graffenstaden (FR); Nathalie Silvestre, Ergersheim (FR); Jean-Baptiste Marchand, Obernai (FR); and Benoît Grellier, Strasbourg (FR)
Assigned to Transgene, Illkirch-Graffenstaden (FR)
Appl. No. 16/625,239
Filed by Transgene, Illkirch-Graffenstaden (FR)
PCT Filed Jun. 21, 2018, PCT No. PCT/EP2018/066668
§ 371(c)(1), (2) Date Dec. 20, 2019,
PCT Pub. No. WO2018/234506, PCT Pub. Date Dec. 27, 2018.
Claims priority of application No. 17305760 (EP), filed on Jun. 21, 2017; and application No. 18305496 (EP), filed on Apr. 23, 2018.
Prior Publication US 2020/0138923 A1, May 7, 2020
Int. Cl. A61K 39/00 (2006.01); C12N 7/00 (2006.01); C12N 15/63 (2006.01); C12Q 1/6886 (2018.01)
CPC A61K 39/0011 (2013.01) [C12N 7/00 (2013.01); C12N 15/63 (2013.01); C12Q 1/6886 (2013.01); A61K 2039/5256 (2013.01); A61K 2039/585 (2013.01); C12N 2710/24134 (2013.01); C12Q 2600/106 (2013.01); C12Q 2600/156 (2013.01)] 18 Claims
 
1. A process for preparing a recombinant poxvirus comprising a heterologous nucleic acid sequence encoding a neopeptide fusion comprising 2 to 15 neopeptides, said process comprising:
(a) identifying a plurality of selected neopeptides, wherein the identification step comprises the following sub-steps i) to v):
i) extracting nucleic acids from a tumor sample and a non-tumor sample;
ii) sequencing corresponding regions from the extracted nucleic acids from the tumor sample and the non-tumor sample;
iii) comparing the nucleic acid sequences obtained from the tumor and non-tumor samples to identify a plurality of tumor specific mutations;
iv) determining the tumor specific mutations that are expressed at the mRNA expression and/or protein translation level in the tumor sample to identify one or more neoantigens, wherein the one or more neoantigens comprise a plurality of potential neopeptides; and
v) identifying and selecting from the plurality of potential neopeptides those that are not present in the proteome of the non-tumor sample to obtain the plurality of selected neopeptides;
(b) generating amino acid sequences for a plurality of potential neopeptide fusions, wherein each potential neopeptide fusion comprises the amino acid sequences of 2 to 15 of the selected neopeptides, optionally comprising intervening linker sequences of 2 to 15 amino acids between one or more of the selected neopeptide sequences, wherein at least 60% of the selected neopeptides in each potential neopeptide fusion comprise a missense or a frameshift mutation;
(c) determining the degree of hydrophobicity of each of said potential neopeptide fusions and selecting a neopeptide fusion that has a negative hydrophobicity score and/or a hydropathy score equal or below 0.1;
(d) generating a nucleic acid fusion sequence for said selected neopeptide fusion; and
(e) generating a recombinant poxvirus by inserting a nucleic acid molecule comprising said nucleic acid fusion sequence into the genome of a parental recombinant poxvirusi wherein the poxvirus is a vaccinia virus.