WO2012159643A1 - Vaccins individualisés pour le cancer - Google Patents

Vaccins individualisés pour le cancer Download PDF

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Publication number
WO2012159643A1
WO2012159643A1 PCT/EP2011/002576 EP2011002576W WO2012159643A1 WO 2012159643 A1 WO2012159643 A1 WO 2012159643A1 EP 2011002576 W EP2011002576 W EP 2011002576W WO 2012159643 A1 WO2012159643 A1 WO 2012159643A1
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WO
WIPO (PCT)
Prior art keywords
cancer
cells
vaccine
tumor
antigen
Prior art date
Application number
PCT/EP2011/002576
Other languages
English (en)
Inventor
Ugur Sahin
Sebastian Kreiter
Mustafa DIKEN
Jan DIEKMANN
Michael Koslowski
Cedrik Britten
John Castle
Martin LÖWER
Bernhard RENARD
Tana Omokoko
Johannes Hendrikus DE GRAAF
Original Assignee
Biontech Ag
Tron - Translationale Onkologie An Der Universitätsmedizin Der Johannes Gutenberg-Universität Mainz Gemeinnützige Gmbh
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Application filed by Biontech Ag, Tron - Translationale Onkologie An Der Universitätsmedizin Der Johannes Gutenberg-Universität Mainz Gemeinnützige Gmbh filed Critical Biontech Ag
Priority to PCT/EP2011/002576 priority Critical patent/WO2012159643A1/fr
Priority to ES21168360T priority patent/ES2946072T3/es
Priority to HRP20230443TT priority patent/HRP20230443T1/hr
Priority to HUE18199105A priority patent/HUE057608T2/hu
Priority to AU2012261237A priority patent/AU2012261237B2/en
Priority to ES18199105T priority patent/ES2897656T3/es
Priority to SI201231660T priority patent/SI2714071T1/sl
Priority to PL21168360.2T priority patent/PL3892295T3/pl
Priority to HUE12723117A priority patent/HUE046152T2/hu
Priority to PT181991050T priority patent/PT3473267T/pt
Priority to SG2013070727A priority patent/SG193553A1/en
Priority to EP18199105.0A priority patent/EP3473267B1/fr
Priority to CA2836494A priority patent/CA2836494C/fr
Priority to BR112013029834A priority patent/BR112013029834A8/pt
Priority to PT12723117T priority patent/PT2714071T/pt
Priority to HUE21168360A priority patent/HUE062102T2/hu
Priority to RU2013157150A priority patent/RU2670745C9/ru
Priority to MEP-2019-237A priority patent/ME03498B/fr
Priority to SI201232029T priority patent/SI3892295T1/sl
Priority to MX2013013659A priority patent/MX360823B/es
Priority to EP12723117.3A priority patent/EP2714071B1/fr
Priority to DK21168360.2T priority patent/DK3892295T3/da
Priority to JP2014511773A priority patent/JP6444171B2/ja
Priority to PT211683602T priority patent/PT3892295T/pt
Priority to NZ730355A priority patent/NZ730355A/en
Priority to LTEP12723117.3T priority patent/LT2714071T/lt
Priority to US14/119,348 priority patent/US10738355B2/en
Priority to EP23169466.2A priority patent/EP4223311A1/fr
Priority to NZ718326A priority patent/NZ718326B2/en
Priority to ES12723117T priority patent/ES2746233T3/es
Priority to DK18199105.0T priority patent/DK3473267T3/da
Priority to FIEP21168360.2T priority patent/FI3892295T3/fi
Priority to NZ617217A priority patent/NZ617217B2/en
Priority to SI201231954T priority patent/SI3473267T1/sl
Priority to RS20211268A priority patent/RS62497B1/sr
Priority to LTEP18199105.0T priority patent/LT3473267T/lt
Priority to RSP20191210 priority patent/RS59369B1/sr
Priority to PL18199105T priority patent/PL3473267T3/pl
Priority to CN201280029551.XA priority patent/CN103608033B/zh
Priority to EP21168360.2A priority patent/EP3892295B1/fr
Priority to LTEP21168360.2T priority patent/LT3892295T/lt
Priority to PL12723117T priority patent/PL2714071T3/pl
Priority to DK12723117.3T priority patent/DK2714071T3/da
Priority to PCT/EP2012/002209 priority patent/WO2012159754A2/fr
Priority to NZ742420A priority patent/NZ742420A/en
Priority to SG10201911616QA priority patent/SG10201911616QA/en
Priority to CN201610330937.4A priority patent/CN105999250B/zh
Priority to CN202010087649.7A priority patent/CN111286537A/zh
Priority to RS20230380A priority patent/RS64230B1/sr
Priority to HRP20211595TT priority patent/HRP20211595T1/hr
Publication of WO2012159643A1 publication Critical patent/WO2012159643A1/fr
Priority to ZA2013/06944A priority patent/ZA201306944B/en
Priority to MX2020011767A priority patent/MX2020011767A/es
Priority to JP2016172519A priority patent/JP6456888B2/ja
Priority to AU2017213515A priority patent/AU2017213515B2/en
Priority to JP2018237242A priority patent/JP2019050831A/ja
Priority to HRP20191535 priority patent/HRP20191535T1/hr
Priority to AU2019229434A priority patent/AU2019229434B2/en
Priority to CY20191100986T priority patent/CY1122110T1/el
Priority to JP2020089657A priority patent/JP7297715B2/ja
Priority to US16/920,286 priority patent/US11248264B2/en
Priority to CY20211100945T priority patent/CY1124685T1/el
Priority to US17/576,170 priority patent/US20220282322A1/en
Priority to AU2022201275A priority patent/AU2022201275A1/en
Priority to JP2023045776A priority patent/JP2023083289A/ja
Priority to CY20231100248T priority patent/CY1126128T1/el

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Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6876—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
    • C12Q1/6883—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material
    • C12Q1/6886—Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes for diseases caused by alterations of genetic material for cancer
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/0005—Vertebrate antigens
    • A61K39/0011—Cancer antigens
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K2039/80—Vaccine for a specifically defined cancer
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q2600/00—Oligonucleotides characterized by their use
    • C12Q2600/156—Polymorphic or mutational markers

Definitions

  • the present invention relates to the provision of vaccines which are specific for a patient's tumor and are potentially useful for immunotherapy of the primary tumor as well as tumor metastases.
  • Cancer is a primary cause of mortality, accounting for 1 in 4 of all deaths.
  • the treatment of cancer has traditionally been based on the law of averages - what works best for the largest number of patients. However, owing to the molecular heterogeneity in cancer, often less than 25% of treated individuals profit from the approved therapies.
  • Individualized medicine based on tailored treatment of patients is regarded as a potential solution to low efficacies and high costs for innovation in drug development.
  • T cells play a central role in cell-mediated immunity in humans and animals.
  • the recognition and binding of a particular antigen is mediated by the T cell receptors (TCRs) expressed on the surface of T cells.
  • TCR T cell receptor
  • the T cell receptor (TCR) of a T cell is able to interact with immunogenic peptides (epitopes) bound to major histocompatibility complex (MHC) molecules and presented on the surface of target cells.
  • MHC major histocompatibility complex
  • TAA pathogen- and tumor-associated antigens
  • Cells presenting immunogenic peptides (epitopes) derived from these antigens can be specifically targeted by either active or passive immunization strategies. Active immunization may tend to induce and expand antigen specific T cells in the patient, which are able to specifically recognize and kill diseased cells.
  • Different antigen formats can be used for tumor vaccination including whole cancer cells, proteins, peptides or immunizing vectors such as RNA, DNA or viral vectors that can be applied either directly in vivo or in vitro by pulsing of DCs following transfer into the patient.
  • Cancers may arise from the accumulation of genomic mutations and epigenetic changes, of which a fraction may have a causative role.
  • human cancers carry on average 100-120 non-synonymous mutations, of which many are targetable by vaccines. More than 95% of mutations in a tumor are unique and patient specific (Weide et al. 2008: J. Immunother. 31, 180-188).
  • the number of protein changing somatic mutations, which may result in tumor specific T cell epitopes, is in the range of 30 to 400. It has been predicted in silico that there are 40 to 60 HLA class I restricted epitopes per patient derived from tumor specific somatic mutations (Azuma et al. 1993: Nature 366, 76-79). Moreover, de novo immunogenic HLA class II restricted epitopes likely also result from tumor-associated mutations, however their number is still unknown.
  • non-synonymous mutations are causally involved in neoplastic transformation, crucial for maintaining the oncogenic phenotype (driver mutations) and may represent a potential "Achilles' heel" of cancer cells.
  • non-synonymous mutations are not subject to central immune tolerance, they can be ideal candidates for individual cancer vaccine development. Mutations found in the primary tumor may also be present in metastases.
  • metastatic tumors of a patient acquire additional genetic mutations during individual tumor evolution which are often clinically relevant (Suzuki et al. 2007: Mol Oncol 1 (2), 172- 180; Campbell et al. 2010: Nature 467 (7319), 1109-1113).
  • the molecular characteristics of many metastases deviate significantly from those of primary tumors.
  • the technical problem underlying the present invention is to provide a highly effective individualized cancer vaccine.
  • the present invention is based on the identification of patient specific cancer mutations and targeting a patient's individual cancer mutation "signature".
  • the present invention which involves a genome, preferably exome, or transcriptome sequencing based individualized immunotherapy approach aims at immunotherapeutically targeting multiple individual mutations in cancer.
  • Sequencing using Next Generation Sequencing (NGS) allows a fast and cost effective identification of patient specific cancer mutations.
  • NGS Next Generation Sequencing
  • MHC major histocompatibility complex
  • neo-epitopes identified according to the present application are provided in a patient in the form of a polypeptide comprising said neo- epitopes and following appropriate processing and presentation by MHC molecules the neo- epitopes are displayed to the patient's immune system for stimulation of appropriate T cells.
  • such polypeptide is provided in the patient by administering RNA encoding the polypeptide.
  • RNA encoding the polypeptide is provided in the patient by administering RNA encoding the polypeptide.
  • IVTT-RNA in vitro transcribed RNA
  • RNA may be translated in transfected cells and the expressed protein following processing presented on the MHC molecules on the surface of the cells to elicit an immune response.
  • RNA does not need to enter the nucleus in order to be expressed and moreover cannot integrate into the host genome, thereby eliminating the risk of oncogenesis. Transfection rates attainable with RNA are relatively high. Furthermore, the amounts of protein achieved correspond to those in physiological expression.
  • the present invention relates to efficient methods for providing individualized recombinant cancer vaccines inducing an efficient and specific immune response in a cancer patient and potentially targeting the primary tumor as well as tumor metastases.
  • the cancer vaccines provided according to the invention when administered to a patent provide a collection of MHC presented epitopes specific for the patient's tumor suitable for stimulating, priming and/or expanding T cells directed against cells expressing antigens from which the MHC presented epitopes are derived.
  • the vaccines described herein are preferably capable of inducing or promoting a cellular response, preferably cytotoxic T cell activity, against a cancer disease characterized by presentation of one or more cancer expressed antigens with class I MHC. Since a vaccine provided according to the present invention will target cancer specific mutations it will be specific for the patient's tumor.
  • the present invention relates to a method for providing an individualized cancer vaccine comprising the steps:
  • the method of the invention comprises the following steps: i) providing a tumor specimen from a cancer patient and a non-tumorigenous specimen which preferably is derived from the cancer patient;
  • step (iii) designing a polypeptide comprising epitopes incorporating the sequence differences determined in step (ii);
  • step (iv) providing the polypeptide designed in step (iii) or a nucleic acid, preferably RNA, encoding said polypeptide; and v) providing a vaccine comprising the polypeptide or nucleic acid provided in step (iv).
  • a tumor specimen relates to any sample such as a bodily sample derived from a patient containing or being expected of containing tumor or cancer cells.
  • the bodily sample may be any tissue sample such as blood, a tissue sample obtained from the primary tumor or from tumor metastases or any other sample containing tumor or cancer cells.
  • a bodily sample is blood and cancer specific somatic mutations or sequence differences are determined in one or more circulating tumor cells (CTCs) contained in the blood.
  • a tumor specimen relates to one or more isolated tumor or cancer cells such as circulating tumor cells (CTCs) or a sample containing one or more isolated tumor or cancer cells such as circulating tumor cells (CTCs).
  • a non-tumorigenous specimen relates to any sample such as a bodily sample derived from a patient or another individual which preferably is of the same species as the patient, preferably a healthy individual not containing or not being expected of containing tumor or cancer cells.
  • the bodily sample may be any tissue sample such as blood or a sample from a non- tumorigenous tissue.
  • the term "cancer mutation signature" may refer to all cancer mutations present in one or more cancer cells of a patient or it may refer to only a portion of the cancer mutations present in one or more cancer cells of a patient. Accordingly, the present invention may involve the identification of all cancer specific mutations present in one or more cancer cells of a patient or it may involve the identification of only a portion of the cancer specific mutations present in one or more cancer cells of a patient. Generally, the method of the invention provides for the identification of a number of mutations which provides a sufficient number of neo-epitopes to be included into a vaccine.
  • a "cancer mutation” relates to a sequence difference between the nucleic acid contained in a cancer cell and the nucleic acid contained in a normal cell.
  • the mutations identified in the methods according to the present invention are non- synonymous mutations, preferably non-synonymous mutations of proteins expressed in a tumor or cancer cell.
  • cancer specific somatic mutations or sequence differences are determined in the genome, preferably the entire genome, of a tumor specimen.
  • the method of the invention may comprise identifying the cancer mutation signature of the genome, preferably the entire genome of one or more cancer cells.
  • the step of identifying cancer specific somatic mutations in a tumor specimen of a cancer patient comprises identifying the genome-wide cancer mutation profile.
  • cancer specific somatic mutations or sequence differences are determined in the exome, preferably the entire exome, of a tumor specimen.
  • the method of the invention may comprise identifying the cancer mutation signature of the exome, preferably the entire exome of one or more cancer cells.
  • the step of identifying cancer specific somatic mutations in a tumor specimen of a cancer patient comprises identifying the exome-wide cancer mutation profile.
  • cancer specific somatic mutations or sequence differences are determined in the transcriptome, preferably the entire transcriptome, of a tumor specimen.
  • the method of the invention may comprise identifying the cancer mutation signature of the transcriptome, preferably the entire transcriptome of one or more cancer cells.
  • the step of identifying cancer specific somatic mutations in a tumor specimen of a cancer patient comprises identifying the transcriptome-wide cancer mutation profile.
  • the step of identifying cancer specific somatic mutations or identifying sequence differences comprises single cell sequencing of one or more, preferably 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1, 12, 13, 14, 15, 16, 17, 18, 19, 20 or even more cancer cells.
  • the method of the invention may comprise identifying a cancer mutation signature of said one or more cancer cells.
  • the cancer cells are circulating tumor cells. The cancer cells such as the circulating tumor cells may be isolated prior to single cell sequencing.
  • the step of identifying cancer specific somatic mutations or identifying sequence differences involves using next generation sequencing ( ⁇ GS).
  • the step of identifying cancer specific somatic mutations or identifying sequence differences comprises sequencing genomic DNA and/or RNA of the tumor specimen.
  • sequence information obtained from the tumor specimen is preferably compared with a reference such as sequence information obtained from sequencing nucleic acid such as DNA or RNA of normal noncancerous cells such as germline cells which may either be obtained from the patient or a different individual.
  • normal genomic germline DNA is obtained from peripheral blood mononuclear cells (PBMCs)
  • a vaccine provided according to the methods of the present invention relates to a vaccine which when administered to a patent preferably provides a collection of MHC presented epitopes, such as 2 or more, 5 or more, 10 or more, 15 or more, 20 or more, 25 or more, 30 or more and preferably up to 60, up to 55, up to 50, up to 45, up to 40, up to 35 or up to 30 MHC presented epitopes, incorporating sequence changes based on the identified mutations or sequence differences.
  • MHC presented epitopes incorporating sequence changes based on the identified mutations or sequence differences are also termed "neo-epi topes" herein.
  • T cells targeting the epitopes when bound to MHC preferably results in T cells targeting the epitopes when bound to MHC and thus, the patient's tumor, preferably the primary tumor as well as tumor metastases, expressing antigens from which the MHC presented epitopes are derived and presenting the same epitopes on the surface of the tumor cells.
  • the method of the invention may comprise the arbitrary inclusion of a sufficient number of neo-epitopes (preferably in the form of an encoding nucleic acid) into a vaccine or it may comprise the further step of determining the usability of the identified mutations in epitopes for cancer vaccination.
  • further steps can involve one or more of the following: (i) assessing whether the sequence changes are located in known or predicted MHC presented epitopes, (ii) in vitro and/or in silico testing whether the sequence changes are located in MHC presented epitopes, e.g.
  • flanking sequences each may comprise 3 or more, 5 or more, 10 or more, 15 or more, 20 or more and preferably up to 50, up to 45, up to 40, up to 35 or up to 30 amino acids and may flank the epitope sequence N-terminally and/or C-terminally.
  • the method of the invention comprises a manual or computer-based analytical process in which the identified mutations are analyzed and selected for their usability in the respective vaccine to be provided.
  • said analytical process is a computational algorithm- based process.
  • said analytical process comprises one or more, preferably all of the following steps: identifying expressed, protein modifying mutations, e.g. by analyzing transcripts;
  • identifying mutations which are potentially immunogenic i.e. by comparing the data obtained with available datasets of confirmed immunogenic epitopes, e.g. those contained in public immune epitope databases such as i.e. the IMMUNE EPITOPE DATABASE AND ANALYSIS RESOURCE at http://www.immunoepitope.org
  • the step of identifying mutations which are potentially immunogenic may comprise determining and/or ranking epitopes according to a prediction of their MHC-binding capacity, preferably MHC class-I binding capacity.
  • the epitopes can be selected and/or ranked by using further parameters such as protein impact, associated gene expression, sequence uniqueness, predicted presentation likelihood, and association with oncogenes.
  • the collection of mutation based neo-epitopes identified according to the invention and provided by a vaccine of the invention is preferably present in the form of a polypeptide comprising said neo-epitopes polyepitopic polypeptide) or a nucleic acid, in particular RNA, encoding said polypeptide.
  • the neo-epitopes may be present in the polypeptide in the form of a vaccine sequence, i.e. present in their natural sequence context, e.g. flanked by amino acid sequences also flanking said epitopes in the naturally occurring protein.
  • flanking sequences each may comprise 5 or more, 10 or more, 15 or more, 20 or more and preferably up to 50, up to 45, up to 40, up to 35 or up to 30 amino acids and may flank the epitope sequence N-terminally and/or C-terminally.
  • a vaccine sequence may comprise 20 or more, 25 or more, 30 or more, 35 or more, 40 or more and preferably up to 50, up to 45, up to 40, up to 35 or up to 30 amino acids.
  • the neo-epitopes and/or vaccine sequences are lined up in the polypeptide head-to-tail.
  • the neo-epitopes and/or vaccine sequences are spaced by linkers, in particular neutral linkers.
  • linker according to the invention relates to a peptide added between two peptide domains such as epitopes or vaccine sequences to connect said peptide domains.
  • linker sequence There is no particular limitation regarding the linker sequence. However, it is preferred that the linker sequence reduces steric hindrance between the two peptide domains, is well translated, and supports or allows processing of the epitopes. Furthermore, the linker should have no or only little immunogenic sequence elements.
  • Linkers preferably should not create non-endogenous neo-epitopes like those generated from the junction suture between adjacent neo-epitopes, which might generate unwanted immune reactions. Therefore, the polyepitopic vaccine should preferably contain linker sequences which are able to reduce the number of unwanted MHC binding junction epitopes. Hoyt et al. (EMBO J. 25(8), 1720-9, 2006) and Zhang et al. (J. Biol.
  • the linker each may comprise 3 or more, 6 or more, 9 or more, 10 or more, 15 or more, 20 or more and preferably up to 50, up to 45, up to 40, up to 35 or up to 30 amino acids.
  • the linker is enriched in glycine and/or serine amino acids.
  • the linker comprises the amino acid sequence (GGS) a (GSS) b (GGG) c (SSG) d (GSG)e wherein a, b, c, d and e is independently a number selected from 0, 1 , 2, 3, 4, 5, 6, 7, 8, 9, 10, 1 1, 12, 13, 14, 15, 16, 17, 18, 19, or 20 and wherein a + b + c + d + e are different from 0 and preferably are 2 or more. 3 or more, 4 or more or 5 or more.
  • the linker comprises a sequence as described herein including the linker sequences described in the examples such as the sequence GGSGGGGSG.
  • a polyepitopic polypeptide according to the present invention is administered to a patient in the form of a nucleic acid, preferably RNA such as in vitro transcribed or synthetic RNA, which may be expressed in cells of a patient such as antigen presenting cells to produce the polypeptide.
  • RNA such as in vitro transcribed or synthetic RNA
  • the polypeptide according to the invention is processed to produce the neo-epitopes identified according to the invention.
  • Administration of a vaccine provided according to the invention may provide MHC class Il-presented epitopes that are capable of eliciting a CD4+ helper T cell response against cells expressing antigens from which the MHC presented epitopes are derived.
  • a vaccine provided according to the invention may provide MHC class I-presented epitopes that are capable of eliciting a CD8+ T cell response against cells expressing antigens from which the MHC presented epitopes are derived.
  • a vaccine provided according to the invention is useful for polyepitopic stimulation of cytotoxic and/or helper T cell responses.
  • the present invention provides a vaccine which is obtainable by the method according to the invention.
  • the present invention relates to a vaccine comprising a recombinant polypeptide comprising mutation based neo-epitopes, said neo- epitopes resulting from cancer specific somatic mutations in a tumor specimen of a cancer patient, or a nucleic acid encoding said polypeptide.
  • Preferred embodiments of such vaccine are as described above in the context of the method of the invention.
  • a vaccine provided according to the invention may comprise a pharmaceutically acceptable carrier and may optionally comprise one or more adjuvants, stabilizers etc.
  • the vaccine may in the form of a therapeutic or prophylactic vaccine.
  • Another aspect relates to a method for inducing an immune response in a patient, comprising administering to the patient a vaccine provided according to the invention.
  • Another aspect relates to a method of treating a cancer patient comprising the steps:
  • Another aspect relates to a method of treating a cancer patient comprising administering the vaccine according to the invention to the patient.
  • the invention provides the vaccines described herein for use in the methods of treatment described herein, in particular for use in treating or preventing cancer.
  • the treatments of cancer described herein can be combined with surgical resection and/or radiation and/or traditional chemotherapy.
  • RNA comprises a poly(A)-tail consisting of 120 nucleotides and in another preferred embodiment the RNA molecule comprises a 5 '-cap analog
  • the RNA comprises the poly(A)- tail consisting of 120 nucleotides and the 5 '-cap analog.
  • the terms used herein are defined as described in "A multilingual glossary of biotechnological terms: (IUPAC Recommendations)", H.G.W. Leuenberger, B. Nagel, and H. Kolbl, Eds., (1995) Helvetica Chimica Acta, CH-4010 Basel, Switzerland..
  • the vaccine provided according to the invention is a recombinant vaccine.
  • recombinant in the context of the present invention means "made through genetic engineering".
  • a "recombinant entity” such as a recombinant polypeptide in the context of the present invention is not occurring naturally, and preferably is a result of a combination of entities such as amino acid or nucleic acid sequences which are not combined in nature.
  • a recombinant polypeptide in the context of the present invention may contain several amino acid sequences such as neo-epitopes or vaccine sequences derived from different proteins or different portions of the same protein fused together, e.g., by peptide bonds or appropriate linkers.
  • naturally occurring refers to the fact that an object can be found in nature.
  • a peptide or nucleic acid that is present in an organism (including viruses) and can be isolated from a source in nature and which has not been intentionally modified by man in the laboratory is naturally occurring.
  • the term “vaccine” relates to a pharmaceutical preparation (pharmaceutical composition) or product that upon administration induces an immune response, in particular a cellular immune response, which recognizes and attacks a pathogen or a diseased cell such as a cancer cell.
  • a vaccine may be used for the prevention or treatment of a disease.
  • individualized cancer vaccine concerns a particular cancer patient and means that a cancer vaccine is adapted to the needs or special circumstances of an individual cancer patient.
  • immune response refers to an integrated bodily response to an antigen and preferably refers to a cellular immune response or a cellular as well as a humoral immune response. The immune response may be protective/preventive/prophylactic and/or therapeutic.
  • inducing an immune response may mean that there was no immune response against a particular antigen before induction, but it may also mean that there was a certain level of immune response against a particular antigen before induction and after induction said immune response is enhanced.
  • inducing an immune response also includes “enhancing an immune response”.
  • an immune response against a tumor expressed antigen may be induced in a patient having a cancer disease or in a subject being at risk of developing a cancer disease. Inducing an immune response in this case may mean that the disease condition of the subject is ameliorated, that the subject does not develop metastases, or that the subject being at risk of developing a cancer disease does not develop a cancer disease.
  • a “cellular immune response”, a “cellular response”, a “cellular response against an antigen” or a similar term is meant to include a cellular response directed to cells characterized by presentation of an antigen with class I or class II MHC.
  • the cellular response relates to cells called T cells or T-lymphocytes which act as either "helpers” or “killers”.
  • the helper T cells also termed CD4 + T cells
  • the helper T cells play a central role by regulating the immune response and the killer cells (also termed cytotoxic T cells, cytolytic T cells, CD8 + T cells or CTLs) kill diseased cells such as cancer cells, preventing the production of more diseased cells.
  • the present invention involves the stimulation of an anti-tumor CTL response against tumor cells expressing one or more tumor expressed antigens and preferably presenting such tumor expressed antigens with class I MHC.
  • an “antigen” covers any substance that will elicit an immune response.
  • an “antigen” relates to any substance, preferably a peptide or protein, that reacts specifically with antibodies or T-lymphocytes (T cells).
  • the term "antigen” comprises any molecule which comprises at least one epitope.
  • an antigen in the context of the present invention is a molecule which, optionally after processing, induces an immune reaction, which is preferably specific for the antigen (including cells expressing the antigen).
  • any suitable antigen may be used, which is a candidate for an immune reaction, wherein the immune reaction is preferably a cellular immune reaction.
  • the antigen is preferably presented by a cell, preferably by an antigen presenting cell which includes a diseased cell, in particular a cancer cell, in the context of MHC molecules, which results in an immune reaction against the antigen.
  • An antigen is preferably a product which corresponds to or is derived from a naturally occurring antigen. Such naturally occurring antigens include tumor antigens.
  • the antigen is a tumor antigen, i.e., a part of a tumor cell such as a protein or peptide expressed in a tumor cell which may be derived from the cytoplasm, the cell surface or the cell nucleus, in particular those which primarily occur intracellularly or as surface antigens of tumor cells.
  • tumor antigens include the carcinoembryonal antigen, a 1 -fetoprotein, isoferritin, and fetal sulphoglycoprotein, a2-H-ferroprotein and ⁇ - fetoprotein.
  • a tumor antigen preferably comprises any antigen which is expressed in and optionally characteristic with respect to type and/or expression level for tumors or cancers as well as for tumor or cancer cells.
  • tumor antigen or “tumor-associated antigen” relates to proteins that are under normal conditions specifically expressed in a limited number of tissues and/or organs or in specific developmental stages, for example, the tumor antigen may be under normal conditions specifically expressed in stomach tissue, preferably in the gastric mucosa, in reproductive organs, e.g., in testis, in trophoblastic tissue, e.g., in placenta, or in germ line cells, and are expressed or aberrantly expressed in one or more tumor or cancer tissues.
  • the tumor antigens in the context of the present invention include, for example, differentiation antigens, preferably cell type specific differentiation antigens, i.e., proteins that are under normal conditions specifically expressed in a certain cell type at a certain differentiation stage, cancer/testis antigens, i.e., proteins that are under normal conditions specifically expressed in testis and sometimes in placenta, and germ line specific antigens.
  • differentiation antigens preferably cell type specific differentiation antigens, i.e., proteins that are under normal conditions specifically expressed in a certain cell type at a certain differentiation stage
  • cancer/testis antigens i.e., proteins that are under normal conditions specifically expressed in testis and sometimes in placenta
  • germ line specific antigens i.e., proteins that are under normal conditions specifically expressed in testis and sometimes in placenta
  • the tumor antigen or the aberrant expression of the tumor antigen identifies cancer cells.
  • the tumor antigen that is expressed by a cancer cell in a subject is preferably a self-protein in said subject.
  • the tumor antigen in the context of the present invention is expressed under normal conditions specifically in a tissue or organ that is non- essential, i.e., tissues or organs which when damaged by the immune system do not lead to death of the subject, or in organs or structures of the body which are not or only hardly accessible by the immune system.
  • tumor antigen tumor antigen
  • tumor expressed antigen tumor expressed antigen
  • cancer antigen cancer expressed antigen
  • immunogenicity relates to the relative effectivity of an antigen to induce an immune reaction.
  • an "antigen peptide" preferably relates to a portion or fragment of an antigen which is capable of stimulating an immune response, preferably a cellular response against the antigen or cells characterized by expression of the antigen and preferably by presentation of the antigen such as diseased cells, in particular cancer cells.
  • an antigen peptide is capable of stimulating a cellular response against a cell characterized by presentation of an antigen with class I MHC and preferably is capable of stimulating an antigen -responsive CTL.
  • the antigen peptides according to the invention are MHC class I and/or class II presented peptides or can be processed to produce MHC class I and/or class II presented peptides.
  • the antigen peptides comprise an amino acid sequence substantially corresponding to the amino acid sequence of a fragment of an antigen.
  • said fragment of an antigen is an MHC class I and/or class II presented peptide.
  • an antigen peptide according to the invention comprises an amino acid sequence substantially corresponding to the amino acid sequence of such fragment and is processed to produce such fragment, i.e., an MHC class I and/or class II presented peptide derived from an antigen.
  • a peptide If a peptide is to be presented directly, i.e., without processing, in particular without cleavage, it has a length which is suitable for binding to an MHC molecule, in particular a class I MHC molecule, and preferably is 7-20 amino acids in length, more preferably 7-12 amino acids in length, more preferably 8-1 1 amino acids in length, in particular 9 or 10 amino acids in length.
  • a peptide is part of a larger entity comprising additional sequences, e.g. of a vaccine sequence or polypeptide, and is to be presented following processing, in particular following cleavage
  • the peptide produced by processing has a length which is suitable for binding to an MHC molecule, in particular a class I MHC molecule, and preferably is 7-20 amino acids in length, more preferably 7-12 amino acids in length, more preferably 8-1 1 amino acids in length, in particular 9 or 10 amino acids in length.
  • the sequence of the peptide which is to be presented following processing is derived from the amino acid sequence of an antigen, i.e., its sequence substantially corresponds and is preferably completely identical to a fragment of an antigen.
  • an antigen peptide or vaccine sequence in one embodiment comprises a sequence of 7-20 amino acids in length, more preferably 7-12 amino acids in length, more preferably 8-1 1 amino acids in length, in particular 9 or 10 amino acids in length which substantially corresponds and is preferably completely identical to a fragment of an antigen and following processing of the antigen peptide or vaccine sequence makes up the presented peptide.
  • such peptide produced by processing comprises the identified sequence change.
  • an antigen peptide or epitope may be present in a vaccine as a part of a larger entity such as a vaccine sequence and/or a polypeptide comprising more than one antigen peptide or epitope.
  • the presented antigen peptide or epitope is produced following suitable processing.
  • Peptides having amino acid sequences substantially corresponding to a sequence of a peptide which is presented by the class I MHC may differ at one or more residues that are not essential for TCR recognition of the peptide as presented by the class I MHC, or for peptide binding to MHC. Such substantially corresponding peptides are also capable of stimulating an antigen-responsive CTL and may be considered immunologically equivalent.
  • Peptides having amino acid sequences differing from a presented peptide at residues that do not affect TCR recognition but improve the stability of binding to MHC may improve the immunogenicity of the antigen peptide, and may be referred to herein as "optimized peptide".
  • an antigen peptide when presented by MHC should be recognizable by a T cell receptor.
  • the antigen peptide if recognized by a T cell receptor is able to induce in the presence of appropriate co-stimulator ⁇ ' signals, clonal expansion of the T cell carrying the T cell receptor specifically recognizing the antigen peptide.
  • antigen peptides in particular if presented in the context of MHC molecules, are capable of stimulating an immune response, preferably a cellular response against the antigen from which they are derived or cells characterized by expression of the antigen and preferably characterized by presentation of the antigen.
  • an antigen peptide is capable of stimulating a cellular response against a cell characterized by presentation of the antigen with class I MHC and preferably is capable of stimulating an antigen-responsive CTL.
  • Such cell preferably is a target cell.
  • Antigen processing refers to the degradation of a polypeptide or antigen into procession products, which are fragments of said polypeptide or antigen (e.g., the degradation of a polypeptide into peptides) and the association of one or more of these fragments (e.g., via binding) with MHC molecules for presentation by cells, preferably antigen presenting cells, to specific T cells.
  • Antigen presenting cells are cells which present peptide fragments of protein antigens in association with MHC molecules on their cell surface. Some APCs may activate antigen specific T cells.
  • Professional antigen-presenting cells are very efficient at internalizing antigen, either by phagocytosis or by receptor-mediated endocytosis, and then displaying a fragment of the antigen, bound to a class II MHC molecule, on their membrane.
  • the T cell recognizes and interacts with the antigen-class II MHC molecule complex on the membrane of the antigen- presenting cell.
  • An additional co-stimulatory signal is then produced by the antigen- presenting cell, leading to activation of the T cell.
  • the expression of co-stimulatory molecules is a defining feature of professional antigen-presenting cells.
  • dendritic cells which have the broadest range of antigen presentation, and are probably the most important antigen-presenting cells, macrophages, B-cells, and certain activated epithelial cells.
  • DCs Dendritic cells
  • Dendritic cells are conveniently categorized as “immature” and “mature” cells, which can be used as a simple way to discriminate between two well characterized phenotypes. However, this nomenclature should not be construed to exclude all possible intermediate stages of differentiation.
  • Immature dendritic cells are characterized as antigen presenting cells with a high capacity for antigen uptake and processing, which correlates with the high expression of Fey receptor and mannose receptor.
  • the mature phenotype is typically characterized by a lower expression of these markers, but a high expression of cell surface molecules responsible for T cell activation such as class I and class II MHC, adhesion molecules (e. g. CD54 and CD1 1) and costimulatory molecules (e. g., CD40, CD80, CD86 and 4-1 BB).
  • Dendritic cell maturation is referred to as the status of dendritic cell activation at which such antigen-presenting dendritic cells lead to T cell priming, while presentation by immature dendritic cells results in tolerance.
  • Dendritic cell maturation is chiefly caused by biomolecules with microbial features detected by innate receptors (bacterial DNA, viral RNA, endotoxin, etc.), pro-inflammatory cytokines (TNF, IL-1, IFNs), ligation of CD40 on the dendritic cell surface by CD40L, and substances released from cells undergoing stressful cell death.
  • the dendritic cells can be derived by culturing bone marrow cells in vitro with cytokines, such as granulocyte-macrophage colony-stimulating factor (GM-CSF) and tumor necrosis factor alpha.
  • GM-CSF granulocyte-macrophage colony-stimulating factor
  • Non-professional antigen-presenting cells do not constitutively express the MHC class II proteins required for interaction with naive T cells; these are expressed only upon stimulation of the non-professional antigen-presenting cells by certain cytokines such as IFNy.
  • Antigen presenting cells can be loaded with MHC class I presented peptides by transducing the cells with nucleic acid, preferably RNA, encoding a peptide or polypeptide comprising the peptide to be presented, e.g. a nucleic acid encoding the antigen.
  • a pharmaceutical composition of the invention comprising a gene delivery vehicle that targets a dendritic or other antigen presenting cell may be administered to a patient, resulting in transfection that occurs in vivo.
  • In vivo transfection of dendritic cells may generally be performed using any methods known in the art, such as those described in WO 97/24447, or the gene gun approach described by Mahvi et al., Immunology and cell Biology 75: 456-460, 1997.
  • the term "antigen presenting cell” also includes target cells.
  • Target cell shall mean a cell which is a target for an immune response such as a cellular immune response.
  • Target cells include cells that present an antigen or an antigen epitope, i.e. a peptide fragment derived from an antigen, and include any undesirable cell such as a cancer cell.
  • the target cell is a cell expressing an antigen as described herein and preferably presenting said antigen with class I MHC.
  • epitope refers to an antigenic determinant in a molecule such as an antigen, i.e., to a part in or fragment of the molecule that is recognized by the immune system, for example, that is recognized by a T cell, in particular when presented in the context of MHC molecules.
  • An epitope of a protein such as a tumor antigen preferably comprises a continuous or discontinuous portion of said protein and is preferably between 5 and 100, preferably between 5 and 50, more preferably between 8 and 30, most preferably between 10 and 25 amino acids in length, for example, the epitope may be preferably 9, 10, 1 1, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21 , 22, 23, 24, or 25 amino acids in length. It is particularly preferred that the epitope in the context of the present invention is a T cell epitope.
  • an epitope may bind to MHC molecules such as MHC molecules on the surface of a cell and thus, may be a "MHC binding peptide” or "antigen peptide".
  • MHC binding peptide relates to a peptide which binds to an MHC class I and/or an MHC class II molecule.
  • the binding peptides are typically 8-10 amino acids long although longer or shorter peptides may be effective.
  • the binding peptides are typically 10-25 amino acids long and are in particular 13-18 amino acids long, whereas longer and shorter peptides may be effective.
  • epitope preferably a cell expressing or comprising and preferably presenting the antigen.
  • the terms relate to an immunogenic portion of an antigen.
  • it is a portion of an antigen that is recognized (i.e., specifically bound) by a T cell receptor, in particular if presented in the context of MHC molecules.
  • Preferred such immunogenic portions bind to an MHC class I or class II molecule.
  • an immunogenic portion is said to "bind to" an MHC class I or class II molecule if such binding is detectable using any assay known in the art.
  • neo-epitope refers to an epitope that is not present in a reference such as a normal non-cancerous or germline cell but is found in cancer cells. This includes, in particular, situations wherein in a normal non-cancerous or germline cell a corresponding epitope is found, however, due to one or more mutations in a cancer cell the sequence of the epitope is changed so as to result in the neo-epitope.
  • portion refers to a fraction. With respect to a particular structure such as an amino acid sequence or protein the term “portion” thereof may designate a continuous or a discontinuous fraction of said structure.
  • a portion of an amino acid sequence comprises at least 1%, at least 5%, at least 10%, at least 20%, at least 30%, preferably at least 40%, preferably at least 50%, more preferably at least 60%, more preferably at least 70%, even more preferably at least 80%, and most preferably at least 90% of the amino acids of said amino acid sequence.
  • said discontinuous fraction is composed of 2, 3, 4, 5, 6, 7, 8, or more parts of a structure, each part being a continuous element of the structure.
  • a discontinuous fraction of an amino acid sequence may be composed of 2, 3, 4, 5, 6, 7, 8, or more, preferably not more than 4 parts of said amino acid sequence, wherein each part preferably comprises at least 5 continuous amino acids, at least 10 continuous amino acids, preferably at least 20 continuous amino acids, preferably at least 30 continuous amino acids of the amino acid sequence.
  • part and fragment are used interchangeably herein and refer to a continuous element.
  • a part of a structure such as an amino acid sequence or protein refers to a continuous element of said structure.
  • a portion, a part or a fragment of a structure preferably comprises one or more functional properties of said structure.
  • a portion, a part or a fragment of an epitope, peptide or protein is preferably immunologically equivalent to the epitope, peptide or protein it is derived from.
  • a "part" of a structure such as an amino acid sequence preferably comprises, preferably consists of at least 10%, at least 20%, at least 30%, at least 40%, at least 50%, at least 60%, at least 70%, at least 80%, at least 85%, at least 90%, at least 92%, at least 94%, at least 96%, at least 98%, at least 99% of the entire structure or amino acid sequence.
  • immunoreactive cell in the context of the present invention relates to a cell which exerts effector functions during an immune reaction.
  • An “immunoreactive cell” preferably is capable of binding an antigen or a cell characterized by presentation of an antigen or an antigen peptide derived from an antigen and mediating an immune response.
  • such cells secrete cytokines and/or chemokines, secrete antibodies, recognize cancerous cells, and optionally eliminate such cells.
  • immunoreactive cells comprise T cells (cytotoxic T cells, helper T cells, tumor infiltrating T cells), B cells, natural killer cells, neutrophils, macrophages, and dendritic cells.
  • T cells cytotoxic T cells, helper T cells, tumor infiltrating T cells
  • B cells natural killer cells
  • neutrophils neutrophils, macrophages, and dendritic cells.
  • immunoreactive cells are T cells, preferably CD4 + and/or CD8 + T cells.
  • an "immunoreactive cell” recognizes an antigen or an antigen peptide derived from an antigen with some degree of specificity, in particular if presented in the context of MHC molecules such as on the surface of antigen presenting cells or diseased cells such as cancer cells.
  • said recognition enables the cell that recognizes an antigen or an antigen peptide derived from said antigen to be responsive or reactive.
  • the cell is a helper T cell (CD4 + T cell) bearing receptors that recognize an antigen or an antigen peptide derived from an antigen in the context of MHC class II molecules such responsiveness or reactivity may involve the release of cytokines and/or the activation of CD8 + lymphocytes (CTLs) and/or B-cells.
  • CTLs CD8 + lymphocytes
  • the cell is a CTL such responsiveness or reactivity may involve the elimination of cells presented in the context of MHC class I molecules, i.e., cells characterized by presentation of an antigen with class I MHC, for example, via apoptosis or perforin-mediated cell lysis.
  • CTL responsiveness may include sustained calcium flux, cell division, production of cytokines such as IFN- ⁇ and TNF-a. up- regulation of activation markers such as CD44 and CD69, and specific cytolytic killing of antigen expressing target cells. CTL responsiveness may also be determined using an artificial reporter that accurately indicates CTL responsiveness. Such CTL that recognizes an antigen or an antigen peptide derived from an antigen and are responsive or reactive are also termed "antigen-responsive CTL" herein. If the cell is a B cell such responsiveness may involve the release of immunoglobulins.
  • T cell and "T lymphocyte” are used interchangeably herein and include T helper cells (CD4+ T cells) and cytotoxic T cells (CTLs, CD8+ T cells) which comprise cytolytic T cells.
  • T helper cells CD4+ T cells
  • CTLs cytotoxic T cells
  • T cells belong to a group of white blood cells known as lymphocytes, and play a central role in cell-mediated immunity. They can be distinguished from other lymphocyte types, such as B cells and natural killer cells by the presence of a special receptor on their cell surface called T cell receptor (TCR).
  • TCR T cell receptor
  • the thymus is the principal organ responsible for the maturation of T cells.
  • T helper cells assist other white blood cells in immunologic processes, including maturation of B cells into plasma cells and activation of cytotoxic T cells and macrophages, among other functions. These cells are also known as CD4+ T cells because they express the CD4 protein on their surface. Helper T cells become activated when they are presented with peptide antigens by MHC class II molecules that are expressed on the surface of antigen presenting cells (APCs). Once activated, they divide rapidly and secrete small proteins called cytokines that regulate or assist in the active immune response.
  • APCs antigen presenting cells
  • Cytotoxic T cells destroy virally infected cells and tumor cells, and are also implicated in transplant rejection. These cells are also known as CD8+ T cells since they express the CDS glycoprotein at their surface. These cells recognize their targets by binding to antigen associated with MHC class I, which is present on the surface of nearly every cell of the body.
  • T cells have a T cell receptor (TCR) existing as a complex of several proteins.
  • the actual T cell receptor is composed of two separate peptide chains, which are produced from the independent T cell receptor alpha and beta (TCRa and TCRP) genes and are called a- and ⁇ -TCR chains, ⁇ T cells (gamma delta T cells) represent a small subset of T cells that possess a distinct T cell receptor (TCR) on their surface.
  • TCRa and TCRP T cell receptor alpha and beta
  • ⁇ T cells gamma delta T cells
  • TCR gamma delta T cells
  • the first signal in activation of T cells is provided by binding of the T cell receptor to a short peptide presented by the major histocompatibility complex (MHC) on another cell.
  • MHC major histocompatibility complex
  • the partner cell is usually a professional antigen presenting cell (APC), usually a dendritic cell in the case of naive responses, although B cells and macrophages can be important APCs.
  • APC professional antigen presenting cell
  • the peptides presented to CD8+ T cells by MHC class I molecules are typically 8-10 amino acids in length; the peptides presented to CD4+ T cells by MHC class II molecules are typically longer, as the ends of the binding cleft of the MHC class II molecule are open.
  • a T cell receptor is capable of binding to a predetermined target if it has a significant affinity for said predetermined target and binds to said predetermined target in standard assays.
  • "Affinity” or "binding affinity” is often measured by equilibrium dissociation constant (KD).
  • KD equilibrium dissociation constant
  • a T cell receptor is preferably capable of binding specifically to a predetermined target.
  • a T cell receptor is specific for a predetermined target if it is capable of binding to said predetermined target while it is not (substantially) capable of binding to other targets, i.e. has no significant affinity for other targets and does not significantly bind to other targets in standard assays.
  • Cytotoxic T lymphocytes may be generated in vivo by incorporation of an antigen or an antigen peptide into antigen-presenting cells in vivo.
  • the antigen or antigen peptide may be represented as protein, as DNA (e.g. within a vector) or as RNA.
  • the antigen may be processed to produce a peptide partner for the MHC molecule, while a fragment thereof may be presented without the need for further processing. The latter is the case in particular, if these can bind to MHC molecules.
  • administration to a patient by intradermal injection is possible. However, injection may also be carried out intranodally into a lymph node (Maloy et al. (2001), Proc Natl Acad Sci USA 95:3299-303).
  • the resulting cells present the complex of interest and are recognized by autologous cytotoxic T lymphocytes which then propagate.
  • Specific activation of CD4+ or CD8+ T cells may be detected in a variety of ways. Methods for detecting specific T cell activation include detecting the proliferation of T cells, the production of cytokines (e.g., lymphokines), or the generation of cytolytic activity.
  • cytokines e.g., lymphokines
  • MHC major histocompatibility complex
  • MHC proteins or molecules are important for signaling between lymphocytes and antigen presenting cells or diseased cells in immune reactions, wherein the MHC proteins or molecules bind peptides and present them for recognition by T cell receptors.
  • the proteins encoded by the MHC are expressed on the surface of cells, and display both self antigens (peptide fragments from the cell itself) and non-self antigens (e.g., fragments of invading microorganisms) to a T cell.
  • MHC region is divided into three subgroups, class I, class II, and class III.
  • MHC class I proteins contain an ot-chain and p2-microglobulin (not part of the MHC encoded by chromosome 15). They present antigen fragments to cytotoxic T cells.
  • MHC class II proteins contain a- and ⁇ - chains and they present antigen fragments to T-helper cells.
  • MHC class III region encodes for other immune components, such as complement components and some that encode cytokines.
  • HLA genes in the MHC region that encode antigen-presenting proteins on the cell surface are referred to as human leukocyte antigen (HLA) genes.
  • MHC is often used to refer to HLA gene products.
  • HLA genes include the nine so-called classical MHC genes: HLA-A, HLA-B, HLA-C, HLA-DPA1, HLA-DPB 1 , HLA-DQA1, HLA-DQB1, HLA-DRA, and HLA-DRB 1.
  • an MHC molecule is an HLA molecule.
  • cell characterized by presentation of an antigen or “cell presenting an antigen” or similar expressions is meant a cell such as a diseased cell, e.g. a cancer cell, or an antigen presenting cell presenting the antigen it expresses or a fragment derived from said antigen, e.g. by processing of the antigen, in the context of MHC molecules, in particular MHC Class I molecules.
  • disease characterized by presentation of an antigen denotes a disease involving cells characterized by presentation of an antigen, in particular with class I MHC. Presentation of an antigen by a cell may be effected by transfecting the cell with a nucleic acid such as RNA encoding the antigen.
  • fragment of an antigen which is presented or similar expressions is meant that the fragment can be presented by MHC class I or class II, preferably MHC class I, e.g. when added directly to antigen presenting cells.
  • the fragment is a fragment which is naturally presented by cells expressing an antigen.
  • immunologically equivalent means that the immunologically equivalent molecule such as the immunologically equivalent amino acid sequence exhibits the same or essentially the same immunological properties and/or exerts the same or essentially the same immunological effects, e.g., with respect to the type of the immunological effect such as induction of a humoral and/or cellular immune response, the strength and/or duration of the induced immune reaction, or the specificity of the induced immune reaction.
  • immunologically equivalent is preferably used with respect to the immunological effects or properties of a peptide used for immunization.
  • an amino acid sequence is immunologically equivalent to a reference amino acid sequence if said amino acid sequence when exposed to the immune system of a subject induces an immune reaction having a specificity of reacting with the reference amino acid sequence.
  • immune effector functions in the context of the present invention includes any functions mediated by components of the immune system that result, for example, in the killing of tumor cells, or in the inhibition of tumor growth and/or inhibition of tumor development, including inhibition of tumor dissemination and metastasis.
  • the immune effector functions in the context of the present invention are T cell mediated effector functions.
  • Such functions comprise in the case of a helper T cell (CD4 + T cell) the recognition of an antigen or an antigen peptide derived from an antigen in the context of MHC class II molecules by T cell receptors, the release of cytokines and/or the activation of CD8 ⁇ lymphocytes (CTLs) and/or B-cells, and in the case of CTL the recognition of an antigen or an antigen peptide derived from an antigen in the context of MHC class I molecules by T cell receptors, the elimination of cells presented in the context of MHC class I molecules, i.e., cells characterized by presentation of an antigen with class I MHC, for example, via apoptosis or perforin-mediated cell lysis, production of cytokines such as IFN- ⁇ and TNF- ⁇ , and specific cytolytic killing of antigen expressing target cells.
  • a helper T cell CD4 + T cell
  • CTLs CD8 ⁇ lymphocytes
  • CTL CD8 ⁇ lymphocytes
  • the term “genome” relates to the total amount of genetic information in the chromosomes of an organism.
  • the term “exome” refers to the coding regions of a genome.
  • the term “transcriptome” relates to the set of all RNA molecules.
  • a nucleic acid is according to the invention preferably deoxyribonucleic acid (DNA) or ribonucleic acid (RNA), more preferably RNA, most preferably in vitro transcribed RNA ( ⁇ RNA) or synthetic RNA.
  • Nucleic acids include according to the invention genomic DNA, cDNA, mRNA, recombinantly produced and chemically synthesized molecules.
  • a nucleic acid may be present as a single-stranded or double- stranded and linear or covalently circularly closed molecule.
  • a nucleic acid can, according to the invention, be isolated.
  • isolated nucleic acid means, according to the invention, that the nucleic acid (i) was amplified in vitro, for example via polymerase chain reaction (PCR), (ii) was produced recombinantly by cloning, (iii) was purified, for example, by cleavage and separation by gel electrophoresis, or (iv) was synthesized, for example, by chemical synthesis.
  • a nucleic can be employed for introduction into, i.e. transfection of, cells, in particular, in the form of RNA which can be prepared by in vitro transcription from a DNA template.
  • the RNA can moreover be modified before application by stabilizing sequences, capping, and polyadenylation.
  • mutation refers to a change of or difference in the nucleic acid sequence (nucleotide substitution, addition or deletion) compared to a reference.
  • a “somatic mutation” can occur in any of the cells of the body except the germ cells (sperm and egg) and therefore are not passed on to children. These alterations can (but do not always) cause cancer or other diseases.
  • a mutation is a non-synonymous mutation.
  • non-synonymous mutation refers to a mutation, preferably a nucleotide substitution, which does result in an amino acid change such as an amino acid substitution in the translation product.
  • cancer mutation signature refers to a set of mutations which are present in cancer cells when compared to non-cancerous reference cells.
  • a “reference” may be used to correlate and compare the results obtained in the methods of the invention from a tumor specimen.
  • the "reference” may be obtained on the basis of one or more normal specimens, in particular specimens which are not affected by a cancer disease, either obtained from a patient or one or more different individuals, preferably healthy individuals, in particular individuals of the same species.
  • a “reference” can be determined empirically by testing a sufficiently large number of normal specimens.
  • next Generation Sequencing or “NGS” in the context of the present invention mean all novel high throughput sequencing technologies which, in contrast to the "conventional” sequencing methodology known as Sanger chemistry, read nucleic acid templates randomly in parallel along the entire genome by breaking the entire genome into small pieces.
  • NGS technologies are able to deliver nucleic acid sequence information of a whole genome, exome, transcriptome (all transcribed sequences of a genome) or methylome (all methylated sequences of a genome) in very short time periods, e.g. within 1-2 weeks, preferably within 1-7 days or most preferably within less than 24 hours and allow, in principle, single cell sequencing approaches.
  • Multiple NGS platforms which are commercially available or which are mentioned in the literature can be used in the context of the present invention e.g. those described in detail in Zhang et al. 2011: The impact of next- generation sequencing on genomics. J. Genet Genomics 38 (3), 95-109; or in Voelkerding et al. 2009: Next generation sequencing: From basic research to diagnostics. Clinical chemistry 55, 641-658.
  • NGS technologies/platforms are examples of such NGS technologies/platforms.
  • Sequencing-by-ligation approaches e.g. implemented in the SOLidTM platform of Applied Biosystems (now Life Technologies Corporation, Carlsbad, California).
  • SOLidTM platform of Applied Biosystems
  • a pool of all possible oligonucleotides of a fixed length are labeled according to the sequenced position.
  • Oligonucleotides are annealed and ligated; the preferential ligation by DNA ligase for matching sequences results in a signal informative of the nucleotide at that position.
  • the DNA is amplified by emulsion PCR. The resulting bead, each containing only copies of the same DNA molecule, are deposited on a glass slide.
  • he PolonatorTM G.007 platform of Dover Systems also employs a sequencing-by-ligation approach by using a randomly arrayed, bead -based, emulsion PCR to amplify DNA fragments for parallel sequencing.
  • Single-molecule sequencing technologies such as e.g. implemented in the PacBio RS system of Pacific Biosciences (Menlo Park, California) or in the HeliScopeTM platform of Helicos Biosciences (Cambridge, Massachusetts).
  • the distinct characteristic of this technology is its ability to sequence single DNA or RNA molecules without amplification, defined as Single-Molecule Real Time (SMRT) DNA sequencing.
  • SMRT Single-Molecule Real Time
  • HeliScope uses a highly sensitive fluorescence detection system to directly detect each nucleotide as it is synthesized.
  • FRET fluorescence resonance energy transfer
  • Other fluorescence-based single-molecule techniques are from U.S. Genomics (GeneEngineTM) and Genovoxx (AnyGeneTM).
  • Nano-technologies for single-molecule sequencing in which various nano structures are used which are e.g. arranged on a chip to monitor the movement of a polymerase molecule on a single strand during replication.
  • approaches based on nano-technologies are the GridONTM platform of Oxford Nanopore Technologies (Oxford, UK), the hybridization-assisted nano-pore sequencing (HANSTM) platforms developed by Nabsys (Providence, Rhode Island), and the proprietary ligase-based DNA sequencing platform with DNA nanoball (DNB) technology called combinatorial probe-anchor ligation (cPALTM).
  • Electron microscopy based technologies for single-molecule sequencing e.g. those developed by LightSpeed Genomics (Sunnyvale, California) and Halcyon Molecular (Redwood City, California)
  • Ion semiconductor sequencing which is based on the detection of hydrogen ions that are released during the polymerisation of DNA.
  • Ion Torrent Systems San Francisco, California
  • Each well holds a different DNA template.
  • Beneath the wells is an ion-sensitive layer and beneath that a proprietary Ion sensor.
  • DNA and RNA preparations serve as starting material for NGS.
  • Such nucleic acids can be easily obtained from samples such as biological material, e.g. from fresh, flash- frozen or formalin-fixed paraffin embedded tumor tissues (FFPE) or from freshly isolated cells or from CTCs which are present in the peripheral blood of patients.
  • FFPE paraffin embedded tumor tissues
  • Normal non-mutated genomic DNA or RNA can be extracted from normal, somatic tissue, however germline cells are preferred in the context of the present invention.
  • Germline DNA or RNA is extracted from peripheral blood mononuclear cells (PBMCs) in patients with non-hematological malignancies.
  • PBMCs peripheral blood mononuclear cells
  • nucleic acids extracted from FFPE tissues or freshly isolated single cells are highly fragmented, they are suitable for NGS applications.
  • RNA relates to a molecule which comprises at least one ribonucleotide residue and preferably being entirely or substantially composed of ribonucleotide residues.
  • bonucleotide relates to a nucleotide with a hydroxyl group at the 2'-position of a ⁇ -D-ribofuranosyl group.
  • RNA comprises double-stranded RNA, single-stranded RNA, isolated RNA such as partially or completely purified RNA, essentially pure RNA, synthetic RNA, and recombinantly generated RNA such as modified RNA which differs from naturally occurring RNA by addition, deletion, substitution and/or alteration of one or more nucleotides. Such alterations can include addition of non-nucleotide material, such as to the end(s) of a RNA or internally, for example at one or more nucleotides of the RNA. Nucleotides in RNA molecules can also comprise non-standard nucleotides, such as non-naturally occurring nucleotides or chemically synthesized nucleotides or deoxynucleotides. These altered RNAs can be referred to as analogs or analogs of naturally- occurring RNA.
  • RNA includes and preferably relates to "mRNA".
  • mRNA means "messenger- RNA” and relates to a "transcript” which is generated by using a DNA template and encodes a peptide or polypeptide.
  • an mRNA comprises a 5'-UTR, a protein coding region, and a 3'-UTR.
  • mRNA only possesses limited half-life in cells and in vitro.
  • mRNA may be generated by in vitro transcription from a DNA template.
  • the in vitro transcription methodology is known to the skilled person. For example, there is a variety of in vitro transcription kits commercially available.
  • RNA may be stabilized and its translation increased by one or more modifications having a stabilizing effects and/or increasing translation efficiency of RNA.
  • modifications are described, for example, in PCT/EP2006/009448 incorporated herein by reference.
  • it may be modified within the coding region, i.e. the sequence encoding the expressed peptide or protein, preferably without altering the sequence of the expressed peptide or protein, so as to increase the GC-content to increase mRNA stability and to perform a codon optimization and, thus, enhance translation in cells.
  • modification in the context of the RNA used in the present invention includes any modification of an RNA which is not naturally present in said RNA.
  • the RNA used according to the invention does not have uncapped 5 '-triphosphates. Removal of such uncapped 5 '-triphosphates can be achieved by treating RNA with a phosphatase.
  • RNA according to the invention may have modified ribonucleotides in order to increase its stability and/or decrease cytotoxicity.
  • 5 -m ethyl cyti dine is substituted partially or completely, preferably completely, for cytidine.
  • pseudouridine is substituted partially or completely, preferably completely, for uridine.
  • the term "modification” relates to providing an RNA with a 5 '-cap or 5 ; - cap analog.
  • the term “5'-cap” refers to a cap structure found on the 5'-end of an mRNA molecule and generally consists of a guanosine nucleotide connected to the mRNA via an unusual 5' to 5' triphosphate linkage. In one embodiment, this guanosine is methylated at the 7-position.
  • the term “conventional 5'-cap” refers to a naturally occurring RNA 5'-cap, preferably to the 7-methylguanosine cap (m 7 G).
  • 5'-cap includes a 5'-cap analog that resembles the RNA cap structure and is modified to possess the ability to stabilize RNA and/or enhance translation of RNA if attached thereto, preferably in vivo and/or in a cell.
  • the 5' end of the RNA includes a Cap structure having the following general formula:
  • Ri and R 2 are independently hydroxy or methoxy and W, X “ and Y “ are independently oxygen, sulfur, selenium, or BH 3 .
  • Ri and R 2 are hydroxy and W “ , X “ and Y “ are oxygen.
  • one of Rj and R 2 preferably Ri is hydroxy and the other is methoxy and W " , X “ and Y " are oxygen.
  • Rj and R 2 are hydroxy and one of W " , X “ and Y “ , preferably X " is sulfur, selenium, or BH 3 , preferably sulfur, while the other are oxygen.
  • one of Ri and R 2 preferably R 2 is hydroxy and the other is methoxy and one of W “ , X “ and Y “ , preferably X " is sulfur, selenium, or BH 3 , preferably sulfur while the other are oxygen.
  • the nucleotide on the right hand side is connected to the RNA chain through its 3' group.
  • the Cap structure having the above structure wherein Rj is methoxy, R 2 is hydroxy, X " is sulfur and W " and Y " are oxygen exists in two diastereoisomeric forms (Rp and Sp).
  • Rp and Sp diastereoisomeric forms
  • RNA with a 5'-cap or 5'-cap analog may be achieved by in vitro transcription of a DNA template in presence of said 5 '-cap or 5 '-cap analog, wherein said 5 '-cap is co- transcriptionally incorporated into the generated RNA strand, or the RNA may be generated, for example, by in vitro transcription, and the 5 '-cap may be attached to the RNA post- transcriptionally using capping enzymes, for example, capping enzymes of vaccinia virus.
  • RNA may comprise further modifications.
  • a further modification of the RNA used in the present invention may be an extension or truncation of the naturally occurring poly(A) tail or an alteration of the 5'- or 3 '-untranslated regions (UTR) such as introduction of a UTR which is not related to the coding region of said RNA, for example, the exchange of the existing 3'-UTR with or the insertion of one or more, preferably two copies of a 3'-UTR derived from a globin gene, such as alpha2-globin, alpha 1-globin, beta-globin, preferably beta-globin, more preferably human beta-globin.
  • UTR 5'- or 3 '-untranslated regions
  • RNA having an unmasked poly-A sequence is translated more efficiently than RNA having a masked poly-A sequence.
  • poly(A) tail or "poly-A sequence” relates to a sequence of adenyl (A) residues which typically is located on the 3 '-end of a RNA molecule and "unmasked poly-A sequence” means that the poly-A sequence at the 3' end of an RNA molecule ends with an A of the poly-A sequence and is not followed by nucleotides other than A located at the 3' end, i.e. downstream, of the poly-A sequence.
  • a long poly-A sequence of about 120 base pairs results in an optimal transcript stability and translation efficiency of RNA.
  • the RNA used according to the present invention may be modified so as to be present in conjunction with a poly-A sequence, preferably having a length of 10 to 500, more preferably 30 to 300, even more preferably 65 to 200 and especially 100 to 150 adenosine residues.
  • the poly-A sequence has a length of approximately 120 adenosine residues.
  • the poly-A sequence can be unmasked.
  • incorporation of a 3 '-non translated region (UTR) into the 3 '-non translated region of an RNA molecule can result in an enhancement in translation efficiency.
  • a synergistic effect may be achieved by incorporating two or more of such 3 '-non translated regions.
  • the 3 '-non translated regions may be autologous or heterologous to the RNA into which they are introduced.
  • the 3 '-non translated region is derived from the human ⁇ -globin gene.
  • a combination of the above described modifications i.e. incorporation of a poly-A sequence, unmasking of a poly-A sequence and incorporation of one or more 3 '-non translated regions, has a synergistic influence on the stability of RNA and increase in translation efficiency.
  • RNA relates to the "half-life" of RNA.
  • "Half-life” relates to the period of time which is needed to eliminate half of the activity, amount, or number of molecules.
  • the half-life of an RNA is indicative for the stability of said RNA.
  • the half-life of RNA may influence the "duration of expression" of the RNA. It can be expected that RNA having a long half-life will be expressed for an extended time period.
  • RNA if according to the present invention it is desired to decrease stability and/or translation efficiency of RNA, it is possible to modify RNA so as to interfere with the function of elements as described above increasing the stability and/or translation efficiency of RNA.
  • expression is used according to the invention in its most general meaning and comprises the production of RNA and/or peptides or polypeptides, e.g. by transcription and/or translation.
  • expression or “translation” relates in particular to the production of peptides or polypeptides. It also comprises partial expression of nucleic acids. Moreover, expression can be transient or stable.
  • the term expression also includes an "aberrant expression” or "abnormal expression”.
  • "Aberrant expression” or “abnormal expression” means according to the invention that expression is altered, preferably increased, compared to a reference, e.g. a state in a subject not having a disease associated with aberrant or abnormal expression of a certain protein, e.g., a tumor antigen.
  • An increase in expression refers to an increase by at least 10%, in particular at least 20%, at least 50% or at least 100%), or more. In one embodiment, expression is only found in a diseased tissue, while expression in a healthy tissue is repressed.
  • a tumor antigen specifically expressed in gastric mucosa means that said protein is primarily expressed in gastric mucosa and is not expressed in other tissues or is not expressed to a significant extent in other tissue or organ types.
  • a protein that is exclusively expressed in cells of the gastric mucosa and to a significantly lesser extent in any other tissue, such as testis is specifically expressed in cells of the gastric mucosa.
  • a tumor antigen may also be specifically expressed under normal conditions in more than one tissue type or organ, such as in 2 or 3 tissue types or organs, but preferably in not more than 3 different tissue or organ types. In this case, the tumor antigen is then specifically expressed in these organs. For example, if a tumor antigen is expressed under normal conditions preferably to an approximately equal extent in lung and stomach, said tumor antigen is specifically expressed in lung and stomach.
  • transcription relates to a process, wherein the genetic code in a DNA sequence is transcribed into RNA. Subsequently, the R A may be translated into protein.
  • transcription comprises "in vitro transcription", wherein the term “in vitro transcription” relates to a process wherein RNA, in particular mRNA, is in vitro synthesized in a cell-free system, preferably using appropriate cell extracts.
  • cloning vectors are applied for the generation of transcripts. These cloning vectors are generally designated as transcription vectors and are according to the present invention encompassed by the term "vector".
  • the RNA used in the present invention preferably is in vitro transcribed RNA (rVT-RNA) and may be obtained by in vitro transcription of an appropriate DNA template.
  • the promoter for controlling transcription can be any promoter for any RNA polymerase.
  • RNA polymerases are the T7, T3, and SP6 RNA polymerases.
  • the in vitro transcription according to the invention is controlled by a T7 or SP6 promoter.
  • a DNA template for in vitro transcription may be obtained by cloning of a nucleic acid, in particular cDNA, and introducing it into an appropriate vector for in vitro transcription.
  • the cDNA may be obtained by reverse transcription of RNA.
  • translation relates to the process in the ribosomes of a cell by which a strand of messenger RNA directs the assembly of a sequence of amino acids to make a peptide or polypeptide.
  • Expression control sequences or regulatory sequences which according to the invention may be linked functionally with a nucleic acid, can be homologous or heterologous with respect to the nucleic acid.
  • a coding sequence and a regulatory sequence are linked together "functionally” if they are bound together covalently, so that the transcription or translation of the coding sequence is under the control or under the influence of the regulatory sequence. If the coding sequence is to be translated into a functional protein, with functional linkage of a regulatory sequence with the coding sequence, induction of the regulatory sequence leads to a transcription of the coding sequence, without causing a reading frame shift in the coding sequence or inability of the coding sequence to be translated into the desired protein or peptide.
  • control sequence comprises, according to the invention, promoters, ribosome-binding sequences and other control elements, which control the transcription of a nucleic acid or the translation of the derived RNA.
  • the regulatory sequences can be controlled.
  • the precise structure of regulatory sequences can vary depending on the species or depending on the cell type, but generally comprises 5'-untranscribed and 5'- and 3 '-untranslated sequences, which are involved in the initiation of transcription or translation, such as TATA-box, capping- sequence, CAAT-sequence and the like.
  • S'-untranscribed regulatory sequences comprise a promoter region that includes a promoter sequence for transcriptional control of the functionally bound gene.
  • Regulatory sequences can also comprise enhancer sequences or upstream activator sequences.
  • the RNA to be expressed in a cell is introduced into said cell.
  • the RNA that is to be introduced into a cell is obtained by in vitro transcription of an appropriate DNA template.
  • RNA capable of expressing and “RNA encoding” are used interchangeably herein and with respect to a particular peptide or polypeptide mean that the RNA, if present in the appropriate environment, preferably within a cell, can be expressed to produce said peptide or polypeptide.
  • RNA according to the invention is able to interact with the cellular translation machinery to provide the peptide or polypeptide it is capable of expressing.
  • nucleic acids in particular exogenous or heterologous nucleic acids, in particular RNA into a cell.
  • the cell can form part of an organ, a tissue and/or an organism.
  • administration of a nucleic acid is either achieved as naked nucleic acid or in combination with an administration reagent.
  • administration of nucleic acids is in the form of naked nucleic acids.
  • the RNA is administered in combination with stabilizing substances such as RNase inhibitors.
  • the present invention also envisions the repeated introduction of nucleic acids into cells to allow sustained expression for extended time periods.
  • Cells can be transfected with any carriers with which RNA can be associated, e.g. by forming complexes with the RNA or forming vesicles in which the RNA is enclosed or encapsulated, resulting in increased stability of the RNA compared to naked RNA.
  • Carriers useful according to the invention include, for example, lipid-containing carriers such as cationic lipids, liposomes, in particular cationic liposomes, and micelles, and nanoparticles.
  • Cationic lipids may form complexes with negatively charged nucleic acids. Any cationic lipid may be used according to the invention.
  • RNA which encodes a peptide or polypeptide into a cell, in particular into a cell present in vivo, results in expression of said peptide or polypeptide in the cell.
  • the targeting of the nucleic acids to particular cells is preferred.
  • a carrier which is applied for the administration of the nucleic acid to a cell for example, a retrovirus or a liposome
  • a molecule such as an antibody which is specific for a surface membrane protein on the target cell or a ligand for a receptor on the target cell may be incorporated into the nucleic acid carrier or may be bound thereto.
  • proteins which bind to a surface membrane protein which is associated with endocytosis may be incorporated into the liposome formulation in order to enable targeting and/or uptake.
  • proteins encompass capsid proteins of fragments thereof which are specific for a particular cell type, antibodies against proteins which are internalized, proteins which target an intracellular location etc.
  • peptide refers to substances comprising two or more, preferably 3 or more, preferably 4 or more, preferably 6 or more, preferably 8 or more, preferably 10 or more, preferably 13 or more, preferably 16 more, preferably 21 or more and up to preferably 8, 10, 20, 30, 40 or 50, in particular 100 amino acids joined covalently by peptide bonds.
  • polypeptide or protein refers to large peptides, preferably to peptides with more than 100 amino acid residues, but in general the terms “peptide”, “polypeptide” and “protein” are synonyms and are used interchangeably herein.
  • sequence change with respect to peptides or proteins relates to amino acid insertion variants, amino acid addition variants, amino acid deletion variants and amino acid substitution variants, preferably amino acid substitution variants. All these sequence changes according to the invention may potentially create new epitopes.
  • Amino acid insertion variants comprise insertions of single or two or more amino acids in a particular amino acid sequence.
  • Amino acid addition variants comprise amino- and/or carboxy-terminal fusions of one or more amino acids, such as 1, 2, 3, 4 or 5, or more amino acids.
  • Amino acid deletion variants are characterized by the removal of one or more amino acids from the sequence, such as by removal of 1, 2, 3, 4 or 5, or more amino acids.
  • Amino acid substitution variants are characterized by at least one residue in the sequence being removed and another residue being inserted in its place.
  • derived means according to the invention that a particular entity, in particular a particular sequence, is present in the object from which it is derived, in particular an organism or molecule.
  • derived in particular means that the relevant amino acid sequence is derived from an amino acid sequence in which it is present.
  • cell or "host cell” preferably is an intact cell, i.e. a cell with an intact membrane that has not released its normal intracellular components such as enzymes, organelles, or genetic material.
  • An intact cell preferably is a viable cell, i.e. a living cell capable of carrying out its normal metabolic functions.
  • cell includes according to the invention prokaryotic cells (e.g., E. coli) or eukaryotic cells (e.g., dendritic cells, B cells, CHO cells, COS cells, 562 cells, HEK293 cells, HELA cells, yeast cells, and insect cells).
  • the exogenous nucleic acid may be found inside the cell (i) freely dispersed as such, (ii) incorporated in a recombinant vector, or (iii) integrated into the host cell genome or mitochondrial DNA.
  • Mammalian cells are particularly preferred, such as cells from humans, mice, hamsters, pigs, goats, and primates.
  • the cells may be derived from a large number of tissue types and include primary cells and cell lines. Specific examples include keratinocytes, peripheral blood leukocytes, bone marrow stem cells, and embryonic stem cells.
  • the cell is an antigen-presenting cell, in particular a dendritic cell, a monocyte, or macrophage.
  • a cell which comprises a nucleic acid molecule preferably expresses the peptide or polypeptide encoded by the nucleic acid.
  • clonal expansion refers to a process wherein a specific entity is multiplied.
  • the term is preferably used in the context of an immunological response in which lymphocytes are stimulated by an antigen, proliferate, and the specific lymphocyte recognizing said antigen is amplified.
  • clonal expansion leads to differentiation of the lymphocytes.
  • reducing or “inhibiting” relate to the ability to cause an overall decrease, preferably of 5% or greater, 10% or greater, 20% or greater, more preferably of 50% or greater, and most preferably of 75% or greater, in the level.
  • inhibitor or similar phrases includes a complete or essentially complete inhibition, i.e. a reduction to zero or essentially to zero.
  • Terms such as “increasing”, “enhancing”, “promoting” or “prolonging” preferably relate to an increase, enhancement, promotion or prolongation by about at least 10%, preferably at least 20%, preferably at least 30%, preferably at least 40%, preferably at least 50%, preferably at least 80%, preferably at least 100%, preferably at least 200% and in particular at least 300%. These terms may also relate to an increase, enhancement, promotion or prolongation from zero or a non-measurable or non-detectable level to a level of more than zero or a level which is measurable or detectable.
  • the agents, compositions and methods described herein can be used to treat a subject with a disease, e.g., a disease characterized by the presence of diseased cells expressing an antigen and presenting an antigen peptide.
  • a disease e.g., a disease characterized by the presence of diseased cells expressing an antigen and presenting an antigen peptide.
  • Particularly preferred diseases are cancer diseases.
  • the agents, compositions and methods described herein may also be used for immunization or vaccination to prevent a disease described herein.
  • the term "disease” refers to any pathological state, including cancer diseases, in particular those forms of cancer diseases described herein.
  • normal refers to the healthy state or the conditions in a healthy subject or tissue, i.e., non-pathological conditions, wherein “healthy” preferably means non-cancerous.
  • Disease involving cells expressing an antigen means according to the invention that expression of the antigen in cells of a diseased tissue or organ is detected. Expression in cells of a diseased tissue or organ may be increased compared to the state in a healthy tissue or organ. An increase refers to an increase by at least 10%, in particular at least 20%, at least 50%, at least 100%, at least 200%, at least 500%, at least 1000%, at least 10000% or even more. In one embodiment, expression is only found in a diseased tissue, while expression in a healthy tissue is repressed. According to the invention, diseases involving or being associated with cells expressing an antigen include cancer diseases.
  • Cancer (medical term: malignant neoplasm) is a class of diseases in which a group of cells display uncontrolled growth (division beyond the normal limits), invasion (intrusion on and destruction of adjacent tissues), and sometimes metastasis (spread to other locations in the body via lymph or blood). These three malignant properties of cancers differentiate them from benign tumors, which are self-limited, and do not invade or metastasize. Most cancers form a tumor but some, like leukemia, do not.
  • Malignant tumor is essentially synonymous with cancer. Malignancy, malignant neoplasm, and malignant tumor are essentially synonymous with cancer.
  • tumor refers to an abnormal growth of cells (called neoplastic cells, tumorigenous cells or tumor cells) preferably forming a swelling or lesion.
  • tumor cell an abnormal cell that grows by a rapid, uncontrolled cellular proliferation and continues to grow after the stimuli that initiated the new growth cease. Tumors show partial or complete lack of structural organization and functional coordination with the normal tissue, and usually form a distinct mass of tissue, which may be either benign, pre-malignant or malignant.
  • a benign tumor is a tumor that lacks all three of the malignant properties of a cancer. Thus, by definition, a benign tumor does not grow in an unlimited, aggressive manner, does not invade surrounding tissues, and does not spread to non-adjacent tissues (metastasize).
  • Neoplasm is an abnormal mass of tissue as a result of neoplasia.
  • Neoplasia new growth in Greek
  • the growth of the cells exceeds, and is uncoordinated with that of the normal tissues around it. The growth persists in the same excessive manner even after cessation of the stimuli. It usually causes a lump or tumor.
  • Neoplasms may be benign, pre-malignant or malignant.
  • “Growth of a tumor” or “tumor growth” relates to the tendency of a tumor to increase its size and/or to the tendency of tumor cells to proliferate.
  • cancer and “cancer disease” are used interchangeably with the terms “tumor” and “tumor disease”.
  • Cancers are classified by the type of cell that resembles the tumor and, therefore, the tissue presumed to be the origin of the tumor. These are the histology and the location, respectively.
  • cancer comprises leukemias, seminomas, melanomas, teratomas, lymphomas, neuroblastomas, gliomas, rectal cancer, endometrial cancer, kidney cancer, adrenal cancer, thyroid cancer, blood cancer, skin cancer, cancer of the brain, cervical cancer, intestinal cancer, liver cancer, colon cancer, stomach cancer, intestine cancer, head and neck cancer, gastrointestinal cancer, lymph node cancer, esophagus cancer, colorectal cancer, pancreas cancer, ear, nose and throat (ENT) cancer, breast cancer, prostate cancer, cancer of the uterus, ovarian cancer and lung cancer and the metastases thereof.
  • ENT ear, nose and throat
  • cancer according to the invention also comprises cancer metastases and relapse of cancer.
  • the main types of lung cancer are small cell lung carcinoma (SCLC) and non-small cell lung carcinoma (NSCLC).
  • SCLC small cell lung carcinoma
  • NSCLC non-small cell lung carcinoma
  • Adenocarcinomas account for approximately 10% of lung cancers. This cancer usually is seen peripherally in the lungs, as opposed to small cell lung cancer and squamous cell lung cancer, which both tend to be more centrally located.
  • Skin cancer is a malignant growth on the skin.
  • the most common skin cancers are basal cell cancer, squamous cell cancer, and melanoma.
  • Malignant melanoma is a serious type of skin cancer. It is due to uncontrolled growth of pigment cells, called melanocytes.
  • a "carcinoma” is a malignant tumor derived from epithelial cells. This group represents the most common cancers, including the common forms of breast, prostate, lung and colon cancer.
  • Bronchiolar carcinoma is a carcinoma of the lung, thought to be derived from epithelium of terminal bronchioles, in which the neoplastic tissue extends along the alveolar walls and grows in small masses within the alveoli. Mucin may be demonstrated in some of the cells and in the material in the alveoli, which also includes denuded cells.
  • Adenocarcinoma is a cancer that originates in glandular tissue. This tissue is also part of a larger tissue category known as epithelial tissue. Epithelial tissue includes skin, glands and a variety of other tissue that lines the cavities and organs of the body. Epithelium is derived embryologically from ectoderm, endoderm and mesoderm. To be classified as adenocarcinoma, the cells do not necessarily need to be part of a gland, as long as they have secretory properties. This form of carcinoma can occur in some higher mammals, including humans. Well differentiated adenocarcinomas tend to resemble the glandular tissue that they are derived from, while poorly differentiated may not.
  • Adenocarcinomas can arise in many tissues of the body due to the ubiquitous nature of glands within the body. While each gland may not be secreting the same substance, as long as there is an exocrine function to the cell, it is considered glandular and its malignant form is therefore named adenocarcinoma. Malignant adenocarcinomas invade other tissues and often metastasize given enough time to do so. Ovarian adenocarcinoma is the most common type of ovarian carcinoma. It includes the serous and mucinous adenocarcinomas, the clear cell adenocarcinoma and the endometrioid adenocarcinoma.
  • Renal cell carcinoma also known as renal cell cancer or renal cell adenocarcinoma is a kidney cancer that originates in the lining of the proximal convoluted tubule, the very small tubes in the kidney that filter the blood and remove waste products. Renal cell carcinoma is by far the most common type of kidney cancer in adults and the most lethal of all the genitorurinary tumors. Distinct subtypes of renal cell carcinoma are clear cell renal cell carcinoma and papillary renal cell carcinoma. Clear cell renal cell carcinoma is the most common form of renal cell carcinoma. When seen under a microscope, the cells that make up clear cell renal cell carcinoma appear very pale or clear. Papillary renal cell carcinoma is the second most common subtype. These cancers form little finger-like projections (called papillae) in some, if not most, of the tumors.
  • papillae finger-like projections
  • Lymphoma and leukemia are malignancies derived from hematopoietic (blood-forming) cells.
  • Blastic tumor or blastoma is a tumor (usually malignant) which resembles an immature or embryonic tissue. Many of these tumors are most common in children.
  • metastasis is meant the spread of cancer cells from its original site to another part of the body.
  • the formation of metastasis is a very complex process and depends on detachment of malignant cells from the primary tumor, invasion of the extracellular matrix, penetration of the endothelial basement membranes to enter the body cavity and vessels, and then, after being transported by the blood, infiltration of target organs.
  • a new tumor i.e. a secondary tumor or metastatic tumor
  • Tumor metastasis often occurs even after the removal of the primary tumor because tumor cells or components may remain and develop metastatic potential.
  • the term "metastasis” according to the invention relates to "distant metastasis" which relates to a metastasis which is remote from the primary tumor and the regional lymph node system.
  • the cells of a secondary or metastatic tumor are like those in the original tumor. This means, for example, that, if ovarian cancer metastasizes to the liver, the secondary tumor is made up of abnormal ovarian cells, not of abnormal liver cells. The tumor in the liver is then called metastatic ovarian cancer, not liver cancer.
  • metastasis can occur in the following ways: by direct contact or extension, it can invade nearby tissue or organs located near or around the ovary, such as the fallopian tubes, uterus, bladder, rectum, etc.; by seeding or shedding into the abdominal cavity, which is the most common way ovarian cancer spreads. Cancer cells break off the surface of the ovarian mass and "drop" to other structures in the abdomen such as the liver, stomach, colon or diaphragm; by breaking loose from the ovarian mass, invading the lymphatic vessels and then traveling to other areas of the body or distant organs such as the lung or liver; by breaking loose from the ovarian mass, invading the blood system and traveling to other areas of the body or distant organs.
  • metastatic ovarian cancer includes cancer in the fallopian tubes, cancer in organs of the abdomen such as cancer in the bowel, cancer in the uterus, cancer in the bladder, cancer in the rectum, cancer in the liver, cancer in the stomach, cancer in the colon, cancer in the diaphragm, cancer in the lungs, cancer in the lining of the abdomen or pelvis (peritoneum), and cancer in the brain.
  • metastatic lung cancer refers to cancer that has spread from the lungs to distant and/or several sites in the body and includes cancer in the liver, cancer in the adrenal glands, cancer in the bones, and cancer in the brain.
  • CTCs circulating tumor cells
  • circulating tumor cells relates to cells that have detached from a primary tumor or tumor metastases and circulate in the bloodstream. CTCs may constitute seeds for subsequent growth of additional tumors (metastasis) in different tissues. Circulating tumor cells are found in frequencies in the order of 1-10 CTC per mL of whole blood in patients with metastatic disease.
  • Research methods have been developed to isolate CTC. Several research methods have been described in the art to isolate CTCs, e.g. techniques which use of the fact that epithelial cells commonly express the cell adhesion protein EpCAM, which is absent in normal blood cells.
  • Immunomagnetic bead-based capture involves treating blood specimens with antibody to EpCAM that has been conjugated with magnetic particles, followed by separation of tagged cells in a magnetic field. Isolated cells are then stained with antibody to another epithelial marker, cytokeratin. as well as a common leukocyte marker CD45, so as to distinguish rare CTCs from contaminating white blood cells. This robust and semi-automated approach identifies CTCs with an average yield of approximately 1 CTC/mL and a purity of 0.1% (Allard et al, 2004: Clin Cancer Res 10, 6897-6904).
  • a second method for isolating CTCs uses a microfluidic-based CTC capture device which involves flowing whole blood through a chamber embedded with 80,000 microposts that have been rendered functional by coating with antibody to EpCAM. CTCs are then stained with secondary antibodies against either cytokeratin or tissue specific markers, such as PSA in prostate cancer or HER2 in breast cancer and are visualized by automated scanning of microposts in multiple planes along three dimensional coordinates. CTC-chips are able to identifying cytokerating-positive circulating tumor cells in patients with a median yield of 50 cells/ml and purity ranging from 1-80% (Nagrath et a!., 2007: Nature 450, 1235- 1239).
  • CTC Circulating Tumor Cell
  • Veridex, LLC Raritan, NJ
  • FDA U.S. Food and Drug Administration
  • a relapse or recurrence occurs when a person is affected again by a condition that affected them in the past. For example, if a patient has suffered from a tumor disease, has received a successful treatment of said disease and again develops said disease said newly developed disease may be considered as relapse or recurrence.
  • a relapse or recurrence of a tumor disease may but does not necessarily occur at the site of the original tumor disease. Thus, for example, if a patient has suffered from ovarian tumor and has received a successful treatment a relapse or recurrence may be the occurrence of an ovarian tumor or the occurrence of a tumor at a site different to ovary.
  • a relapse or recurrence of a tumor also includes situations wherein a tumor occurs at a site different to the site of the original tumor as well as at the site of the original tumor.
  • the original tumor for which the patient has received a treatment is a primary tumor and the tumor at a site different to the site of the original tumor is a secondary or metastatic tumor.
  • treat is meant to administer a compound or composition as described herein to a subject in order to prevent or eliminate a disease, including reducing the size of a tumor or the number of tumors in a subject; arrest or slow a disease in a subject; inhibit or slow the development of a new disease in a subject; decrease the frequency or severity of symptoms and/or recurrences in a subject who currently has or who previously has had a disease; and/or prolong, i.e. increase the lifespan of the subject.
  • treatment of a disease includes curing, shortening the duration, ameliorating, preventing, slowing down or inhibiting progression or worsening, or preventing or delaying the onset of a disease or the symptoms thereof.
  • being at risk is meant a subject, i.e. a patient, that is identified as having a higher than normal chance of developing a disease, in particular cancer, compared to the general population.
  • a subject who has had, or who currently has, a disease, in particular cancer is a subject who has an increased risk for developing a disease, as such a subject may continue to develop a disease.
  • Subjects who currently have, or who have had, a cancer also have an increased risk for cancer metastases.
  • immunotherapy relates to a treatment involving activation of a specific immune reaction.
  • terms such as “protect”, “prevent”, “prophylactic”, “preventive”, or “protective” relate to the prevention or treatment or both of the occurrence and/or the propagation of a disease in a subject and, in particular, to minimizing the chance that a subject will develop a disease or to delaying the development of a disease.
  • a person at risk for a tumor would be a candidate for therapy to prevent a tumor.
  • a prophylactic administration of an immunotherapy for example, a prophylactic administration of the composition of the invention, preferably protects the recipient from the development of a disease.
  • a therapeutic administration of an immunotherapy for example, a therapeutic administration of the composition of the invention, may lead to the inhibition of the progress/growth of the disease. This comprises the deceleration of the progress/growth of the disease, in particular a disruption of the progression of the disease, which preferably leads to elimination of the disease.
  • Immunotherapy may be performed using any of a variety of techniques, in which agents provided herein function to remove diseased cells from a patient. Such removal may take place as a result of enhancing or inducing an immune response in a patient specific for an antigen or a cell expressing an antigen.
  • immunotherapy may be active immunotherapy, in which treatment relies on the in vivo stimulation of the endogenous host immune system to react against diseased cells with the administration of immune response-modifying agents (such as polypeptides and nucleic acids as provided herein).
  • immune response-modifying agents such as polypeptides and nucleic acids as provided herein.
  • the agents and compositions provided herein may be used alone or in combination with conventional therapeutic regimens such as surgery, irradiation, chemotherapy and/or bone marrow transplantation (autologous, syngeneic, allogeneic or unrelated).
  • immunotherapy or “vaccination” describes the process of treating a subject with the purpose of inducing an immune response for therapeutic or prophylactic reasons.
  • in vivo relates to the situation in a subject.
  • subject means “subject”, “individual”, “organism” or “patient” are used interchangeably and relate to vertebrates, preferably mammals.
  • mammals in the context of the present invention are humans, non-human primates, domesticated animals such as dogs, cats, sheep, cattle, goats, pigs, horses etc., laboratory animals such as mice, rats, rabbits, guinea pigs, etc. as well as animals in captivity such as animals of zoos.
  • animal as used herein also includes humans.
  • subject may also include a patient, i.e., an animal, preferably a human having a disease, preferably a disease as described herein.
  • autologous transplant refers to a transplant of tissue or organs derived from the same subject. Such procedures are advantageous because they overcome the immunological barrier which otherwise results in rejection.
  • heterologous is used to describe something consisting of multiple different elements. As an example, the transfer of one individual's bone marrow into a different individual constitutes a heterologous transplant.
  • a heterologous gene is a gene derived from a source other than the subject.
  • compositions for an immunization or a vaccination preferably one or more agents as described herein are administered together with one or more adjuvants for inducing an immune response or for increasing an immune response.
  • adjuvant relates to compounds which prolongs or enhances or accelerates an immune response.
  • the composition of the present invention preferably exerts its effect without addition of adjuvants.
  • the composition of the present application may contain any known adjuvant.
  • Adjuvants comprise a heterogeneous group of compounds such as oil emulsions (e.g.. Freund s adjuvants), mineral compounds (such as alum), bacterial products (such as Bordetella pertussis toxin), liposomes, and immune-stimulating complexes.
  • adjuvants examples include monophosphoryl- lipid-A (MPL SmithKline Beecham). Saponins such as QS21 (SmithKline Beecham), DQS21 (SmithKline Beecham; WO 96/33739), QS7, QS17, QS18, and QS-L1 (So et al., 1997, Mol.
  • cytokines in a vaccination, owing to their regulatory properties on lymphocytes.
  • cytokines comprise, for example, interleukin-12 (IL-12) which was shown to increase the protective actions of vaccines (cf. Science 268: 1432- 1434, 1995), GM-CSF and IL-18.
  • Said compounds comprise co-stimulating molecules provided in the form of proteins or nucleic acids such as B7-1 and B7-2 (CD80 and CD86, respectively).
  • a "tumor specimen” is a sample such as a bodily sample containing tumor or cancer cells such as circulating tumor cells (CTC), in particular a tissue sample, including body fluids, and/or a cellular sample.
  • a "non- tumorigenous specimen” is a sample such as a bodily sample not containing rumor or cancer cells such as circulating tumor cells (CTC), in particular a tissue sample, including body fluids, and/or a cellular sample.Such bodily samples may be obtained in the conventional manner such as by tissue biopsy, including punch biopsy, and by taking blood, bronchial aspirate, sputum, urine, feces or other body fluids.
  • the term “sample” also includes processed samples such as fractions or isolates of biological samples, e.g. nucleic acid or cell isolates.
  • the therapeutically active agents, vaccines and compositions described herein may be administered via any conventional route, including by injection or infusion.
  • the administration may be carried out, for example, orally, intravenously, intraperitoneally, intramuscularly, subcutaneously or transdermally.
  • administration is carried out intranodally such as by injection into a lymph node.
  • Other forms of administration envision the in vitro transfection of antigen presenting cells such as dendritic cells with nucleic acids described herein followed by administration of the antigen presenting cells.
  • an "effective amount” refers to the amount which achieves a desired reaction or a desired effect alone or together with further doses.
  • the desired reaction preferably relates to inhibition of the course of the disease. This comprises slowing down the progress of the disease and, in particular, interrupting or reversing the progress of the disease.
  • the desired reaction in a treatment of a disease or of a condition may also be delay of the onset or a prevention of the onset of said disease or said condition.
  • an effective amount of an agent described herein will depend on the condition to be treated, the severeness of the disease, the individual parameters of the patient, including age, physiological condition, size and weight, the duration of treatment, the type of an accompanying therapy (if present), the specific route of administration and similar factors. Accordingly, the doses administered of the agents described herein may depend on various of such parameters. In the case that a reaction in a patient is insufficient with an initial dose, higher doses (or effectively higher doses achieved by a different, more localized route of administration) may be used.
  • compositions of the invention are preferably sterile and contain an effective amount of the therapeutically active substance to generate the desired reaction or the desired effect.
  • compositions of the invention are generally administered in pharmaceutically compatible amounts and in pharmaceutically compatible preparation.
  • pharmaceutically compatible refers to a nontoxic material which does not interact with the action of the active component of the pharmaceutical composition. Preparations of this kind may usually contain salts, buffer substances, preservatives, carriers, supplementing immunity-enhancing substances such as adjuvants, e.g. CpG oligonucleotides, cytokines, chemokines, saponin, GM-CSF and/or R A and, where appropriate, other therapeutically active compounds.
  • the salts should be pharmaceutically compatible. However, salts which are not pharmaceutically compatible may used for preparing pharmaceutically compatible salts and are included in the invention.
  • Pharmacologically and pharmaceutically compatible salts of this kind comprise in a non-limiting way those prepared from the following acids: hydrochloric, hydrobromic, sulfuric, nitric, phosphoric, maleic, acetic, salicylic, citric, formic, malo ic, succinic acids, and the like.
  • Pharmaceutically compatible salts may also be prepared as alkali metal salts or alkaline earth metal salts, such as sodium salts, potassium salts or calcium salts.
  • a pharmaceutical composition of the invention may comprise a pharmaceutically compatible carrier.
  • carrier refers to an organic or inorganic component, of a natural or synthetic nature, in which the active component is combined in order to facilitate application.
  • pharmaceutically compatible carrier includes one or more compatible solid or liquid fillers, diluents or encapsulating substances, which are suitable for administration to a patient.
  • the components of the pharmaceutical composition of the invention are usually such that no interaction occurs which substantially impairs the desired pharmaceutical efficacy.
  • compositions of the invention may contain suitable buffer substances such as acetic acid in a salt, citric acid in a salt, boric acid in a salt and phosphoric acid in a salt.
  • compositions may, where appropriate, also contain suitable preservatives such as benzalkonium chloride, chlorobutanol, paraben and thimerosal.
  • compositions are usually provided in a uniform dosage form and may be prepared in a manner known per se.
  • Pharmaceutical compositions of the invention may be in the form of capsules, tablets, lozenges, solutions, suspensions, syrups, elixirs or in the form of an emulsion, for example.
  • compositions suitable for parenteral administration usually comprise a sterile aqueous or nonaqueous preparation of the active compound, which is preferably isotonic to the blood of the recipient.
  • suitable carriers and solvents are Ringer solution and isotonic sodium chloride solution.
  • sterile, fixed oils are used as solution or suspension medium.
  • the sequence In the wild type cells, the sequence is T/T. In the tumor cells, the sequence is a mix of T/G.
  • mice were immunized twice (dO, d7) with mutated peptide sequences (100 g + 50 ⁇ g PolyI:C; s.c). At day 12 mice were sacrificed and the spleen cells harvested. IFNy ELISpot was performed using 5xl0 5 spleen cells /well as effectors and 5x10 4 bone marrow dendritic cells loaded with peptides (2 g/ml for 2h at 37°C and 5% C0 2 ) as target cells.
  • the effector spleen cells were tested against the mutated peptide, the wild type peptide and a control peptide (vesiculostomatitis virus nucleoprotein, VSV-NP, aa 52 - 59). Shown is the mean measured spot number from which the background spots against VSV-NP were subtracted for every mouse (empty circles: mice immunized with wildtype peptide; filled boxes: mice immunized with mutated peptides). Data are shown for each mouse and mean ⁇ SEM is depicted.
  • VSV-NP vesiculostomatitis virus nucleoprotein
  • B16F10 cells (7,5 x 10 )were inoculated subcutaneously on dO. Mice were vaccinated with peptide 30 (Jerini Peptide Technologies (Berlin); 100 g peptide + 50 ⁇ g PolyI:C s.c. (Invivogen)) on day -4, day +2, day +9. The control group received only Poly I:C (50 ⁇ g s.c.). Tumor growth was monitored until day + 16 *, p ⁇ 0,05 in Log-rank (Mantel-Cox) test.
  • A Examples of enhanced protein expression ⁇ left eGFP, right Luciferase) with RNA optimized for stability and translational efficiency
  • B Example of polyepitopic expansion of antigen-specific CD8 + and CD4 + T cells with RNA optimized for effective antigen routing (s. Reference Kreiter, Konrad, Sester et al, Cancer Immunol. Immunother. 56: 1577-1587, 2007).
  • T C
  • the vaccine vehicle integrates functional elements for increased expression and optimized immunogenicity. Up to 30 mutated epitopes that are spaced by linkers can be integrated per molecule in their natural sequence context.
  • RNA polyepitope construct (A) Schematic diagram of a RNA polyepitope construct. Cap : cap analogon; 5 'UTR : 5 'untranslated region; L : linker; Seq. 1 : RNA sequence coding for peptide containing mutated aa; 3 'UTR : 3 'untranslated seuquence; poly-A : poly-A tail.
  • B Sequence of the RNA constructs coding for 2 aa sequences including a mutated aa from B16F10. The start- and stop-codon as well as the signal peptide and the MITD sequence are not part of the schematic drawing which is symbolized by "..
  • A-C Data for IFNy ELISpot using 5 x 10 5 spleen cells per well as effectors and 5 x 10 4 BMDC as target cells.
  • the BMDC were loaded with peptide (2 ⁇ for 2h at 37°C and 5% C0 2 ) or transfected with RNA (20 ⁇ g) by electroporation.
  • the control RNA was eGFP (left panel) or a RNA construct coding for 2 unrelated peptides containing mutated aa separated by a linker. Data are shown as mean ⁇ SEM.
  • A Data for mutation peptide 30, wild type peptide 30 and RNA coding for mutation 30 and 31 are shown.
  • the RNA vaccine can be constructed with (top) or without linkers (bottom) between mutation-encoding peptides.
  • Good epitopes include those that include the somatic mutation ("*") and bind to MHC molecules.
  • Bad epitopes include epitopes that bind to MHC molecules but contain either parts of two peptides (bottom) or parts of peptide and linker sequences (top).
  • CTC circulating tumor cells
  • the molecular analysis of drug-resistant CTCs may provide a further insight into resistance mechanisms (e.g. mutations in specific signaling pathways or loss of target expression) in individual patients.
  • An additional possibility from the profiling and genetic characterization of CTCs is the identification of novel cancer targets for the development of new targeted therapies. This new diagnostic strategy is referred to as "Liquid Tumor Biopsy.” As this profiling could be quickly and repetitively done, requiring only patient blood and no surgery, this would provide a "real time" view of the tumor state.
  • Mutations from tumor cells We demonstrate our ability to identify mutations using B16 melanoma cells, exome capture to extract protein coding regions, next-generation sequencing using our HiSeq 2000, followed by bioinformatics analysis using our "iCAM" software pipeline ( Figure 1). We identify 2448 non- synonymous mutations and selected 50 for confirmation. We were able to confirm all 50 somatic mutations.
  • CTCs circulating tumor cells
  • samples included 5-10mm tail samples from C57BL/6 mice (“Black6”) and highly aggressive B16F10 murine melanoma cells (“B16”), which are originally derived from Black6 mice.
  • Circulating tumor cells were created using fluorescent labeled B16 melanoma cells.
  • B16 cells were resuspended in PBS and an equal volume of freshly prepared CFSE-Solution (5 ⁇ in PBS) was added to the cells. The sample was gentle mixed by vortex followed by incubation for 10 min at room temperature. To stop the labeling reaction, the equal amount of PBS containing 20% FSC was added to the sample and mixed gently by vortex. Following 20 min incubation at room temperature, the cells were washed twice using PBS. Finally, the cells were resuspended in PBS and injected intravenously (i.v.) in mice. After 3 minutes the mice were sacrificed and blood collected.
  • CFSE-Solution 5 ⁇ in PBS
  • Erythrocytes from the blood samples were lysed by adding 1,5 ml fresh prepared PharmLyse Solution (Beckton Dickinson) per 100 ⁇ blood. After one washing step, 7-AAD was added to the sample and incubated for 5 min at room temperature. The incubation was followed by two washing steps and the sample was resuspended in 500 ⁇ PBS.
  • the CFSE labeled circulating B16 cells were sorted with an Aria I cells-sorter (BD). Single cells were sorted on 96-well-v-bottem plated prepared with 50 ⁇ /well RLT buffer (Quiagen). After finishing the sorting the plates were stored at -80°C until the Nucleic acid extraction and sample preparation started.
  • Aria I cells-sorter BD
  • Single cells were sorted on 96-well-v-bottem plated prepared with 50 ⁇ /well RLT buffer (Quiagen). After finishing the sorting the plates were stored at -80°C until the Nucleic acid extraction and sample preparation started.
  • Nucleic acid extraction and sample preparation nucleic acids from B16 cells (DNA and RNA) and Black6 tail tissue (DNA) were extracted using Qiagen DNeasy Blood and Tissue kit (DNA) and Qiagen R easy Micro kit (RNA). For individual sorted CTCs, RNA was extracted and a SMART-based cDNA synthesis and unspecific amplification performed. RNA from sorted CTC cells was extracted with the RNeasy Micro Kit (Qiagen, Hilden, Germany) according to the instructions of the supplier.
  • First strand cDNA synthesized according to the manufacturer's instructions was subjected to 35 cycles of amplification with 5 U PfuUltra Hotstart High- Fidelity DNA Polymerase (Stratagene, La Jolla, CA) and 0.48 ⁇ primer TS-PCR primer in the presence of 200 ⁇ dNTP (cycling conditions: 2 min at 95 °C for, 30 s at 94 °C, 30 s at 65 °C, 1 min at 72 °C for, final extension of 6 min at 72 °C).
  • Successful amplification of the CTC genes was controlled with specific primers to monitor actin and GAPDH.
  • DNA sequencing Exome capture for DNA resequencing was performed using the Agilent Sure-Select solution-based capture assay [Gnirke A et al: Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol 2009, 27:182-189], in this case designed to capture all mouse protein coding regions.
  • 3 ug purified genomic DNA was fragmented to 150-200 bp's using a Covaris S2 ultrasound device.
  • gDNA fragments were end repaired using T4 DNA polymerase, Klenow DNA polymerase and 5' phosphorylated using T4 polynucleotide kinase.
  • Blunt ended gDNA fragments were 3' adenylated using Klenow fragment (3' to 5' exo minus).
  • 3' single T- overhang Illumina paired end adapters were ligated to the gDNA fragments using a 10: 1 molar ratio of adapter to genomic DNA insert using T4 DNA ligase.
  • Adapter ligated gDNA fragments were enriched pre capture and flow cell specific sequences were added using Illumina PE PCR primers 1.0 and 2.0 and Herculase II polymerase (Agilent) using 4 PCR cycles. 500 ng of adapter ligated, PCR enriched gDNA fragments were hybridized to Agilent's SureSelect biotinylated mouse whole exome RNA library baits for 24 hrs at 65 °C. Hybridized gDNA/RNA bait complexes where removed using streptavidin coated magnetic beads.
  • gDNA/RNA bait complexes were washed and the RNA baits cleaved off during elution in SureSelect elution buffer leaving the captured adapter ligated, PCR enriched gDNA fragments.
  • gDNA fragments were PCR amplified post capture using Herculase II DNA polymerase (Agilent) and SureSelect GA PCR Primers for 10 cycles.
  • Exome enriched gDNA libraries were clustered on the cBot using Truseq SR cluster kit v2.5 using 7 p and 50 bps were sequenced on the Illumina HiSeq2000 using Truseq SBS kit-HS 50 bp.
  • RNA sequencing Barcoded mRNA-seq cDNA libraries were prepared from 5 ug of total RNA using a modified version of the Illumina mRNA-seq protocol. mRNA was isolated using Seramag Oligo(dT) magnetic beads (Thermo Scientific). Isolated mRNA was fragmented using divalent cations and heat resulting in fragments ranging from 160-220 bp. Fragmented mRNA was converted to cDNA using random primers and SuperScriptll (Invitrogen) followed by second strand synthesis using DNA polymerase I and RNaseH.
  • cDNA was end repaired using T4 DNA polymerase, Klenow DNA polymerase and 5' phosphorylated using T4 polynucleotide kinase. Blunt ended cDNA fragments were 3' adenylated using Klenow fragment (3' to 5' exo minus). 3' single T- overhang Illumina multiplex specific adapters were ligated using a 10: 1 molar ratio of adapter to cDNA insert using T4 DNA ligase. cDNA libraries were purified and size selected at 200-220 bp using the E-Gel 2% SizeSelect gel (Invitrogen).
  • CTCs For the RNA-Seq profiling of CTCs, a modified version of this protocol was used in which 500-700 ng SMART amplified cDNA was used, paired end adapters were ligated and PCR enrichment was done using Illumina PE PCR primers 1.0 and 2.0.
  • RNA-Seq transcriptome analysis sequence reads were aligned to the reference genomic sequence [Mouse Genome Sequencing Consortium. Initial sequencing and comparative analysis of the mouse genome. Nature, 420, 520-562 (2002)] using bowtie (version 0.12.5) [Langmead B. et al. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10.R25] using parameters "-v2 -best" for genome alignments and default parameters for transcript alignments.
  • the alignment coordinates were compared to the exon coordinates of the RefSeq transcripts [Pruitt KD. et al. NCBI Reference Sequence (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res. 2005 Jan 1 ;33(Database issue) :D 501-4] and for each transcript the counts of overlapping alignments were recorded. Sequence reads not alignable to the genomic sequence were aligned to a database of all possible exon-exon junction sequences of the RefSeq transcripts.
  • the counts of reads aligning to the splice junctions were aggregated with the respective transcript counts obtained in the previous step and normalized to RPKM (number of reads which map per kilobase of exon model per million mapped reads [Mortazavi, A. et al. (2008). Mapping and quantifying mammalian transcriptomes by rna-seq. Nat Methods, 5(7):621-628]) for each transcript. Both gene expression and exon expression values were calculated based on the normalized number of reads overlapping each gene or exon, respectively.
  • CTCs As per the bulk tumor iCAM process, 50 nt, single end, reads from the Illumina HiSeq 2000 were aligned using bwa (version 0.5.8c) [5]) using default options to the reference mouse genome assembly mm9. As CTC NGS reads were derived from the R A-Seq assay, reads were also aligned to transcriptome sequences, including exon- exon junctions, using bowtie (above). Using all alignments, the nucleotide sequences from the reads were compared to both the reference genome and the bulk-tumor derived B16 mutations. Identified mutations were evaluated both using perl scripts and manually using the software program samtools and the IGV (Integrated Genome Viewer) to image the results.
  • bwa version 0.5.8c
  • mutant discover ⁇ ' is the identification of somatic mutations in tumor cells, from sample to NGS data to a list of mutations.
  • somatic mutations in the B16 samples, we identified 2448 somatic mutations using exome resequencing. Mutation prioritization
  • iCAM individual cancer mutation detection pipeline
  • Somatic mutation identification Mutations are identified using three different algorithms, for both the B16 and Black6 samples (Mutation discover ⁇ ', above).
  • the first iCAM step is to combine the output lists from each algorithm to generate a high- confidence list of somatic mutations.
  • GATK and samtools report variants in one sample relative to a reference genome.
  • SomaticSniper automatically reports potential somatic variations from tumor and normal data pairs. We further filtered results through the intersection of the results obtained from replicates.
  • the final step for each somatic mutation is to assign a confidence value (p-value) for each mutation based on coverage depth, SNP quality, consensus quality and mapping quality.
  • Mutation impact the impact of the filtered, consensus, somatic mutations is determined by a script within the iCaM mutation pipeline.
  • the transcript sequence is translated with and without the mutation to determine if there is a change in amino acid sequence.
  • Mutation expression the iCAM pipeline selects somatic mutations that are found in genes and exons that are expressed in tumor cells. Expression levels are determined through NGS RNA- Seq of tumor cells (above). The number of reads that overlap a gene and an exon indicates expression levels. These counts are normalized to RPKM (Reads Per Kilobase of exon model per Million mapped reads, [Mortazavi A. et ah Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008 Jul;5(7):621-8. Epub 2008 May 30]) and those expressed above 10 RPKM are selected.
  • RPKM Reads Per Kilobase of exon model per Million mapped reads
  • MHC binding to determine the likelihood that an epitope containing the mutated peptide is binds to an MHC molecule, the iCAM pipeline runs a modified version of the MHC prediction software from the Immune Epitope Database (http://www.iedb.org/). The local installation includes modifications to optimize data flow through the algorithm. For the B16 and Black6 data, the prediction was run using all available black6 MHC class I alleles and all epitopes for the respective peptide lengths. Mutations are selected which fall in an epitope ranked in the 95th percentile of the prediction score distribution of the IEDB training data (http.V/mhcbmdingpredictions. immuneepitope.org/dataset.html), considering all MHC alleles and all potential epitopes overlapping the mutation.
  • Mutation selection criteria somatic mutations are selected by the following criteria: a) have unique sequence content, b) identified by all three programs, c) high mutation confidence, d) non-synonymous protein change, e) high transcript expression, f) and favorable MHC class I binding prediction.
  • the output of this process is a list of somatic mutations, prioritized based on likely immunogenicity.
  • somatic mutations there are 2448 somatic mutations. 1247 of these mutations are found in gene transcripts. Of these, 734 cause non-synonymous protein changes. Of these, 149 are in genes expressed in the tumor cells. Of these, 102 of these expressed, non-synonymous mutations are predicted to be presented on MHC molecules. These 102 likely immunogenic mutations are then passed to mutation confirmation (below).
  • Somatic mutations from DNA exome-resequencing were confirmed by either of two methods, resequencing of the mutated region and RNA-Seq analysis.
  • a genomic region containing the mutation was amplified by standard PCR from 50 ng of both the tumor DNA and the normal control DNA.
  • the size of the amplified products was in the range of 150 to 400 nt.
  • the specificity of the reaction was controlled by loading the PCR product on the Qiaxel device (Qiagen).
  • PCR products were purified using the minElute PCR purification kit (Qiagen).
  • Specific PCR products were sequenced using the standard Sanger sequencing method (Eurofins), followed by electropherogram analysis.
  • RNA-Seq RNA-Seq
  • Table 1 List of genes containing the 50 validated mutations
  • Genes containing the 50 identified and confirmed somatic mutations with annotation regarding gene symbol, gene name, and predicted localization and function.
  • immunoglobulin domain Ig
  • short basic domain secreted
  • mice were immunized twice (dO, d7) subcutaneously with 100 ⁇ g peptide (+ 50 ⁇ g Polyl.C as adjuvant) comprising either the mutated or the wild type aa sequence (see Table 2). All peptides had a length of 27 aa with the mutated/wild type aa at the central position. At day 12 mice were sacrificed and the spleen cells were harvested.
  • IFNy ELISpot was performed using 5xl0 5 spleen cells/well as effectors and 5xl0 4 bone marrow dendritic cells loaded with peptides (2 ⁇ g/ml) as target cells.
  • the effector spleen cells were tested against the mutated peptide, the wild type peptide and a control peptide (vesiculostomatitis virus nucleoprotein, VSV-NP).
  • the data prove that the identified and prioritized mutations can be utilized to induce tumor specific T-cell immunity after being utilized as peptide vaccine in antigen naive mice.
  • Table 2 Listing of mutated sequences that induced a T-cell reactivity specific for the mutated versus the wild type peptide. The amino acid exchange is marked underlined.
  • Validated mutations from protein-coding regions of a patient constitute the pool from which candidates can be selected for assembly of the poly-neo-epitope vaccine template to be used as precursor for GMP manufacturing of the RNA vaccine.
  • Suitable vector cassettes as vaccine backbone has been already described (Holtkamp, S. et al., Blood, 108: 4009-4017, 2006; Kreiter, S. et al., Cancer Immunol. Immunother., 56: 1577-1587, 2007; Kreiter, S. et al., J.Immunol., 180: 309-318, 2008).
  • the preferred vector cassettes are modified in their coding and untranslated regions (UTR) and ensure maximized translation of the encoded protein for extended periods (Holtkamp, S. et al., Blood, 108: 4009-4017, 2006; Kuhn, A. N. et al., Gene Ther., 17: 961 -971 , 2010).
  • the vector backbone contains antigen routing modules for the simultaneous expansion of cytotoxic as well as helper T-cells (Kreiter, S. et al., Cancer Immunol. Immunother., 56: 1577-1587, 2007; Kreiter, S. et al., J. Immunol., 180: 309-318, 2008; Kreiter, S. et al., Cancer Research, in press: 2010 ( Figure 5).
  • RNA vaccine can be used to present multiple MHC class I and class II epitopes simultaneously.
  • the rVAC poly-neo-epitope RNA vaccine sequences are built from stretches of up to 30 amino acids that include the mutation in the center. These sequences are connected head-to- tail via short linkers to form a poly-neo-epitope vaccine coding for up to 30 or more selected mutations and their flanking regions. These patient-specific individually tailored inserts are codon-optimized and cloned into the RNA backbone described above. Quality control of such constructs includes in vitro transcription and expression in cells for validation of functional transcription and translation. Analysis of translation will be performed with antibodies against the c-terminal targeting domain.
  • RNA poly-neo epitope concept is based on a long in vitro transcribed mRNA which consists of sequentially arranged sequences coding for the mutated peptides connected by linker sequences (see Fig. 6).
  • the coding sequences are chosen from the non synonymous mutations and are always built up of the codon for the mutated amino acid flanked by regions of 30 to 75 base-pairs from the original sequence context.
  • the linker sequence codes for amino acids that are preferentially not processed by the cellular antigen processing machinery.
  • In vitro transcription constructs are based on the pSTl-A120 vector containing a T7 promotor, a tandem beta-globin 3' UTR sequence and a 120-bp poly(A) tail, which have been shown to increase the stability and translational efficiency of the RNA thereby enhancing the T-cell stimulatory capacity of the encoded antigen (Holtkamp S. et al., Blood 2006; PMID: 16940422).
  • an MHC class I signal peptide fragment and the transmembrane and cytosolic domains including the stop-codon (MHC class I trafficking signal or MITD) flanking a poly-linker sequence for cloning the epitopes were inserted (Kreiter S. et al., J. Immunol., 180: 309-318, 2008). The latter have been shown to increase the antigen presentation, thereby enhancing the expansion of antigen-specific CD8+ and CD4+ T cells and improving effector functions.
  • biepitopic vectors were used, i.e. encoding one polypeptide containing two mutated epitopes. Codon optimized sequences coding for (i) a mutated epitope of 20 to 50 amino acids, (ii) a glycine/serine-rich linker, (iii) a second mutated epitope of 20 to 50 amino acids, and (iv) an additional glycine/serine-rich linker - flanked by suitable recognition sites for restriction endonucleases to be cloned into the pSTl -based construct as described above - were designed and synthesized by a commercial provider (Geneart, Regensburg, Germany). After verification of the sequence, these were cloned into the pSTl - based vector backbone to obtain constructs as depicted in Figure 6.
  • the pSTl -A120-based plasmids as described above were linearized with a class lis restriction endonuclease.
  • the linearized plasmid DNAs were purified by phenol chloroform extraction and ethanol precipitation.
  • Linearized vector DNAs were quantified spectrophotometrically and subjected to in vitro transcription essentially as described by Pokrovskaya and Gurevich (1994, Anal. Biochem. 220: 420-423).
  • a cap analog has been added to the transcription reaction to obtain R As with the correspondingly modified 5'-cap structures.
  • GTP was present at 1.5 raM
  • the cap-analog was present at 6.0 mM. All other NTPs were present at 7.5 mM.
  • RNAs were purified from these reactions using the MEGAclear Kit (Ambion, Austin/TX, USA) as per manufacturer's protocol. RNA concentration and quality were assessed by spectrophotometry and analysis on a 2100 Bioanalyzer (Agilent, Santa Clara, CA, USA).
  • T-cells from peptide vaccinated mice were used as effector cells.
  • T-cells induced by peptide vaccination as described above are capable of recognizing the target cells (bone marrow dendritic cells, BMDC) either pulsed with peptide (2 ⁇ g/ml for 2h at 37°C and 5% C0 2 ) or transfected with RNA (20 ⁇ g produced as described above) by electroporation.
  • BMDC bone marrow dendritic cells
  • RNA encoded poly-neo epitope including glycine / serine rich linker can be translated and processed in antigen presenting cells leading to presentation of the correct epitope that is recognized by the antigen specific T- cells.
  • Example 6 Poly-neo-epitope vaccine design - The relevance of the linker
  • the poly-neo-epitope RNA construct contains a backbone construct into which multiple somatic mutation-encoding peptides connected with a linker peptide sequence are placed.
  • one embodiment of the RNA poly-neo-epitope vaccine contains linkers designed to increase MHC Class I and II presentation of antigenic peptides and decrease presentation of deleterious epitopes.
  • Linker the linker sequence was designed to connect multiple mutation-containing peptides. The linker should enable creation and presentation of the mutation epitope while hinder creation of deleterious epitopes, such as those created at the junction suture between adjacent peptides or between linker sequence and endogenous peptides.
  • junction epitopes may not only compete with the intended epitopes to be presented on the cell surface, decreasing vaccine efficacy, but could generate an unwanted auto-immune reaction.
  • linker sequence to a) avoid creating "junction” peptides that bind to MHC molecules, b) avoid proteasomal processing to create “junction” peptides, c) be efficiently translated and processed by the proteasome.
  • Table 5 shows the results of several different linkers, different linker lengths, and the use of no linker and five linkers.
  • the number of MHC-binding junction peptides ranges from 2 to 91 for the 9 aa and 10 aa epitope predictions (top and middle).
  • the size of the linker influences the number of junction peptides (bottom).
  • the fewest 9 aa epitopes are predicted for the 7 aa linker sequence GGSGGGG.
  • Linker 1 and Linker 2 used in the RNA poly-neo epitope vaccine constructs tested experimentally also had a favorably low number of predicted junctional neoepitopes. This holds true for predictions of 9-mers and 10-mers.
  • sequence of the linker is critically important for the creation of bad MHC binding epitopes.
  • length of the linker sequence impacts the number of bad MHC binding epitopes. We find that sequences that are G-rich hinder the creation of MHC-binding ligands.
  • Table 5 Impact of Linker Part. The predicted number of bad epitopes, defined as MHC Class I binding epitopes that contain junction sequences, for each peptide linker. Here, 9 amino acid epitopes are considered. Top: the number of 9 aa junction epitopes for no linker and 5 diverse linkers. Middle: the number of 10 aa junction epitopes for no linker and 5 diverse linkers. Lower: the number of 99 aa junction epitopes for similar linkers of different lengths. Glycine-rich linkers have the fewest junction epitopes. Linker sequence # junction epitopes (9aa)
  • the linker should allow the mutation-containing peptides to be efficiently translated and processed by the proteasome.
  • Amino acids glycine and serine are flexible [Schlessinger A and Rost B., Proteins. 2005 Oct 1 ;61 (1): 1 15-26]; including them in a linker results in a more flexible protein.
  • the linker should be glycine rich to hinder the creation of MHC binding bad epitopes; should hinder the ability of the proteasome to process linker peptides, which can be accomplished through inclusion of glycine; and should be flexible to increase access to mutation containing peptides, which can be accomplished through the combination of glycine and serine amino acids. Therefore, in one embodiment of the vaccine construct of the invention, the sequences GGSGGGGSGG and GGSGGGSGGS are preferably included as linker sequences.
  • Example 7 RNA poly-neo epitope vaccine
  • RNA poly-neo epitope vaccine constructs are based on the pSTl-A120 vector containing a T7 promotor, a tandem beta-globin 3' UTR sequence and a 120-bp poly(A) tail, which have been shown to increase the stability and translational efficiency of the RNA thereby enhancing the T-cell stimulatory capacity of the encoded antigen ((Holtkamp S. et al., Blood 2006; PMID: 16940422).
  • MHC class I signal peptide fragment and the transmembrane and cytosolic domains including the stop-codon (MHC class I trafficking signal or MITD) flanking a poly-linker sequence for cloning the epitopes were inserted (Kreiter S. et al., J. Immunol., 180: 309-318, 2008). The latter have been shown to increase the antigen presentation, thereby enhancing the expansion of antigen-specific CD8+ and CD4+ T cells and improving effector functions.
  • RNA poly-neo epitope constructs for the 50 identified and validated mutations of B16F10 3 RNA constructs were generated.
  • the construct consists of codon optimized sequences coding for (i) a mutated epitope of 25 amino acids, (ii) a glycine/serine-rich linker, (iii) repetitions of mutated epitope sequence followed by a glycine/serine-rich linker.
  • the chain of mutated epitope containing sequences and linkers is flanked by suitable recognition sites for restriction endonucl eases to be cloned into the pSTl -based construct as described above.
  • the vaccine constructs were designed and synthesized by GENEART. After verification of the sequence, these were cloned into the pSTl -based vector backbone to obtain the RNA poly-neo epitope vaccine constructs.
  • RNA vaccines a master plasmid template will be generated by gene synthesis and cloning
  • Plasmids will be used for clinical grade RNA production, quality control and release of the RNA vaccine.
  • the RNA vaccine can be used as a naked vaccine in formulation buffer or encapsulated into nanoparticles or liposomes for direct injection into e.g. lymph nodes, s.c., i.v., i.m..
  • the RNA vaccine can be used for in vitro transfection e.g of dendritic cells for adoptive transfer.

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Abstract

La présente invention concerne la fourniture de vaccins qui sont spécifiques pour une tumeur de patient et sont potentiellement utiles pour une immunothérapie de la tumeur primaire ainsi que des métastases de tumeur. Dans un aspect, la présente invention concerne un procédé pour produire un vaccin anticancéreux individualisé comprenant les étapes suivantes : (a) identification de mutations somatiques spécifiques au cancer dans un spécimen de tumeur d'un patient cancéreux pour produire une signature de mutation cancéreuse du patient; et (b) production d'un vaccin comprenant la signature de mutation cancéreuse obtenue dans l'étape (a). Dans un autre aspect, la présente invention concerne des vaccins qui peuvent être obtenus par ledit procédé.
PCT/EP2011/002576 2011-05-24 2011-05-24 Vaccins individualisés pour le cancer WO2012159643A1 (fr)

Priority Applications (65)

Application Number Priority Date Filing Date Title
PCT/EP2011/002576 WO2012159643A1 (fr) 2011-05-24 2011-05-24 Vaccins individualisés pour le cancer
ES21168360T ES2946072T3 (es) 2011-05-24 2012-05-23 Vacunas individualizadas para el cáncer
HRP20230443TT HRP20230443T1 (hr) 2011-05-24 2012-05-23 Individualizirana cjepiva protiv raka
HUE18199105A HUE057608T2 (hu) 2011-05-24 2012-05-23 Individualizált vakcinák a rák ellen
AU2012261237A AU2012261237B2 (en) 2011-05-24 2012-05-23 Individualized vaccines for cancer
ES18199105T ES2897656T3 (es) 2011-05-24 2012-05-23 Vacunas individualizadas para el cáncer
SI201231660T SI2714071T1 (sl) 2011-05-24 2012-05-23 Individualizirana cepiva proti raku
PL21168360.2T PL3892295T3 (pl) 2011-05-24 2012-05-23 Zindywidualizowane szczepionki przeciwnowotworowe
HUE12723117A HUE046152T2 (hu) 2011-05-24 2012-05-23 Rák elleni egyedi vakcinák
PT181991050T PT3473267T (pt) 2011-05-24 2012-05-23 Vacinas individualizadas para o cancro
SG2013070727A SG193553A1 (en) 2011-05-24 2012-05-23 Individualized vaccines for cancer
EP18199105.0A EP3473267B1 (fr) 2011-05-24 2012-05-23 Vaccins individualisés pour le cancer
CA2836494A CA2836494C (fr) 2011-05-24 2012-05-23 Vaccins individualises pour le cancer
BR112013029834A BR112013029834A8 (pt) 2011-05-24 2012-05-23 vacinas individualizadas para câncer
PT12723117T PT2714071T (pt) 2011-05-24 2012-05-23 Vacinas individualizadas para o cancro
HUE21168360A HUE062102T2 (hu) 2011-05-24 2012-05-23 Individualizált vakcinák a rák ellen
RU2013157150A RU2670745C9 (ru) 2011-05-24 2012-05-23 Индивидуализированные противоопухолевые вакцины
MEP-2019-237A ME03498B (fr) 2011-05-24 2012-05-23 Vaccins individualisés pour le cancer
SI201232029T SI3892295T1 (sl) 2011-05-24 2012-05-23 Individualizirana cepiva proti raku
MX2013013659A MX360823B (es) 2011-05-24 2012-05-23 Vacunas individualizadas para el cancer.
EP12723117.3A EP2714071B1 (fr) 2011-05-24 2012-05-23 Vaccins individualisés pour le cancer
DK21168360.2T DK3892295T3 (da) 2011-05-24 2012-05-23 Individualiserede vacciner mod cancer
JP2014511773A JP6444171B2 (ja) 2011-05-24 2012-05-23 癌の個別化ワクチン
PT211683602T PT3892295T (pt) 2011-05-24 2012-05-23 Vacinas individualizadas para o cancro
NZ730355A NZ730355A (en) 2011-05-24 2012-05-23 Individualized vaccines for cancer
LTEP12723117.3T LT2714071T (lt) 2011-05-24 2012-05-23 Individualizuotos vakcinos nuo vėžio
US14/119,348 US10738355B2 (en) 2011-05-24 2012-05-23 Individualized vaccines for cancer
EP23169466.2A EP4223311A1 (fr) 2011-05-24 2012-05-23 Vaccins individualisés pour le cancer
NZ718326A NZ718326B2 (en) 2011-05-24 2012-05-23 Individualized vaccines for cancer
ES12723117T ES2746233T3 (es) 2011-05-24 2012-05-23 Vacunas individualizadas para el cáncer
DK18199105.0T DK3473267T3 (da) 2011-05-24 2012-05-23 Individualiserede vacciner mod cancer
FIEP21168360.2T FI3892295T3 (fi) 2011-05-24 2012-05-23 Yksilöityjä rokotteita syöpää varten
NZ617217A NZ617217B2 (en) 2011-05-24 2012-05-23 Individualized vaccines for cancer
SI201231954T SI3473267T1 (sl) 2011-05-24 2012-05-23 Individualizirana cepiva za rak
RS20211268A RS62497B1 (sr) 2011-05-24 2012-05-23 Individualizovane vakcine protiv kancera
LTEP18199105.0T LT3473267T (lt) 2011-05-24 2012-05-23 Individualizuotos vakcinos nuo vėžio
RSP20191210 RS59369B1 (sr) 2011-05-24 2012-05-23 Individualizovane vakcine protiv kancera
PL18199105T PL3473267T3 (pl) 2011-05-24 2012-05-23 Zindywidualizowane szczepionki przeciwnowotworowe
CN201280029551.XA CN103608033B (zh) 2011-05-24 2012-05-23 用于癌症的个体化疫苗
EP21168360.2A EP3892295B1 (fr) 2011-05-24 2012-05-23 Vaccins individualisés pour le cancer
LTEP21168360.2T LT3892295T (lt) 2011-05-24 2012-05-23 Individualizuotos vakcinos nuo vėžio
PL12723117T PL2714071T3 (pl) 2011-05-24 2012-05-23 Zindywidualizowane szczepionki przeciwrakowe
DK12723117.3T DK2714071T3 (da) 2011-05-24 2012-05-23 Individualiserede vacciner mod cancer
PCT/EP2012/002209 WO2012159754A2 (fr) 2011-05-24 2012-05-23 Vaccins individualisés pour le cancer
NZ742420A NZ742420A (en) 2011-05-24 2012-05-23 Individualized vaccines for cancer
SG10201911616QA SG10201911616QA (en) 2011-05-24 2012-05-23 Individualized vaccines for cancer
CN201610330937.4A CN105999250B (zh) 2011-05-24 2012-05-23 用于癌症的个体化疫苗
CN202010087649.7A CN111286537A (zh) 2011-05-24 2012-05-23 用于癌症的个体化疫苗
RS20230380A RS64230B1 (sr) 2011-05-24 2012-05-23 Individualizovane vakcine protiv kancera
HRP20211595TT HRP20211595T1 (hr) 2011-05-24 2012-05-23 Individualizirana cjepiva protiv raka
ZA2013/06944A ZA201306944B (en) 2011-05-24 2013-09-16 Individualized vaccines for cancer
MX2020011767A MX2020011767A (es) 2011-05-24 2013-11-22 Vacunas individualizadas para el cancer.
JP2016172519A JP6456888B2 (ja) 2011-05-24 2016-09-05 癌の個別化ワクチン
AU2017213515A AU2017213515B2 (en) 2011-05-24 2017-08-10 Individualized vaccines for cancer
JP2018237242A JP2019050831A (ja) 2011-05-24 2018-12-19 癌の個別化ワクチン
HRP20191535 HRP20191535T1 (hr) 2011-05-24 2019-08-27 Individualizirana cjepiva protiv raka
AU2019229434A AU2019229434B2 (en) 2011-05-24 2019-09-13 Individualized vaccines for cancer
CY20191100986T CY1122110T1 (el) 2011-05-24 2019-09-18 Εξατομικευμενα εμβολια για τον καρκινο
JP2020089657A JP7297715B2 (ja) 2011-05-24 2020-05-22 癌の個別化ワクチン
US16/920,286 US11248264B2 (en) 2011-05-24 2020-07-02 Individualized vaccines for cancer
CY20211100945T CY1124685T1 (el) 2011-05-24 2021-11-02 Εξατομικευμενα εμβολια για τον καρκινο
US17/576,170 US20220282322A1 (en) 2011-05-24 2022-01-14 Individualized vaccines for cancer
AU2022201275A AU2022201275A1 (en) 2011-05-24 2022-02-24 Individualized vaccines for cancer
JP2023045776A JP2023083289A (ja) 2011-05-24 2023-03-22 癌の個別化ワクチン
CY20231100248T CY1126128T1 (el) 2011-05-24 2023-05-25 Εξατομικευμενα εμβολια για τον καρκινο

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