HRP20211419T1 - Predviđanje epitopa t-stanica korisnih za cijepljenje - Google Patents
Predviđanje epitopa t-stanica korisnih za cijepljenje Download PDFInfo
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- HRP20211419T1 HRP20211419T1 HRP20211419TT HRP20211419T HRP20211419T1 HR P20211419 T1 HRP20211419 T1 HR P20211419T1 HR P20211419T T HRP20211419T T HR P20211419TT HR P20211419 T HRP20211419 T HR P20211419T HR P20211419 T1 HRP20211419 T1 HR P20211419T1
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- 238000002255 vaccination Methods 0.000 title claims 5
- 230000004048 modification Effects 0.000 claims 44
- 238000012986 modification Methods 0.000 claims 44
- 108091005573 modified proteins Proteins 0.000 claims 18
- 102000035118 modified proteins Human genes 0.000 claims 18
- 102000004169 proteins and genes Human genes 0.000 claims 17
- 108090000623 proteins and genes Proteins 0.000 claims 17
- 238000000034 method Methods 0.000 claims 16
- 108091005601 modified peptides Proteins 0.000 claims 11
- 230000035772 mutation Effects 0.000 claims 10
- 239000012634 fragment Substances 0.000 claims 8
- 150000001413 amino acids Chemical class 0.000 claims 7
- 102000043131 MHC class II family Human genes 0.000 claims 6
- 108091054438 MHC class II family Proteins 0.000 claims 6
- 230000002163 immunogen Effects 0.000 claims 6
- 108090000765 processed proteins & peptides Proteins 0.000 claims 5
- 102000018713 Histocompatibility Antigens Class II Human genes 0.000 claims 4
- 108010027412 Histocompatibility Antigens Class II Proteins 0.000 claims 4
- 206010028980 Neoplasm Diseases 0.000 claims 4
- 108700026244 Open Reading Frames Proteins 0.000 claims 2
- 201000011510 cancer Diseases 0.000 claims 2
- 206010069754 Acquired gene mutation Diseases 0.000 claims 1
- 238000012163 sequencing technique Methods 0.000 claims 1
- 230000037439 somatic mutation Effects 0.000 claims 1
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- G—PHYSICS
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- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
- G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
- G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
- G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
- G01N33/6878—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids in eptitope analysis
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- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
- G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
- G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
- G01N33/5005—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells
- G01N33/5008—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics
- G01N33/5044—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving human or animal cells for testing or evaluating the effect of chemical or biological compounds, e.g. drugs, cosmetics involving specific cell types
- G01N33/5047—Cells of the immune system
- G01N33/505—Cells of the immune system involving T-cells
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- 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
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- A—HUMAN NECESSITIES
- A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
- A61P—SPECIFIC THERAPEUTIC ACTIVITY OF CHEMICAL COMPOUNDS OR MEDICINAL PREPARATIONS
- A61P35/00—Antineoplastic agents
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- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
- G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
- G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
- G01N33/68—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing involving proteins, peptides or amino acids
- G01N33/6803—General methods of protein analysis not limited to specific proteins or families of proteins
- G01N33/6845—Methods of identifying protein-protein interactions in protein mixtures
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- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
- G16B20/20—Allele or variant detection, e.g. single nucleotide polymorphism [SNP] detection
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- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B20/00—ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
- G16B20/30—Detection of binding sites or motifs
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- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B25/00—ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
- G16B25/10—Gene or protein expression profiling; Expression-ratio estimation or normalisation
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- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16B—BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- G16B5/00—ICT specially adapted for modelling or simulations in systems biology, e.g. gene-regulatory networks, protein interaction networks or metabolic networks
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- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N2333/00—Assays involving biological materials from specific organisms or of a specific nature
- G01N2333/435—Assays involving biological materials from specific organisms or of a specific nature from animals; from humans
- G01N2333/705—Assays involving receptors, cell surface antigens or cell surface determinants
- G01N2333/70503—Immunoglobulin superfamily, e.g. VCAMs, PECAM, LFA-3
- G01N2333/70539—MHC-molecules, e.g. HLA-molecules
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- G—PHYSICS
- G01—MEASURING; TESTING
- G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
- G01N2500/00—Screening for compounds of potential therapeutic value
- G01N2500/04—Screening involving studying the effect of compounds C directly on molecule A (e.g. C are potential ligands for a receptor A, or potential substrates for an enzyme A)
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- Molecular Biology (AREA)
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- Hematology (AREA)
- Urology & Nephrology (AREA)
- General Health & Medical Sciences (AREA)
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- Bioinformatics & Computational Biology (AREA)
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- Proteomics, Peptides & Aminoacids (AREA)
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- Animal Behavior & Ethology (AREA)
- Pharmacology & Pharmacy (AREA)
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- Tropical Medicine & Parasitology (AREA)
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- Mycology (AREA)
- Oncology (AREA)
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Claims (12)
1. Postupak za predviđanje jedne ili više imunogenih modifikacija aminokiselina koje su korisne za cijepljenje, naznačen time, što se modifikacije javljaju u proteinu koji sadrži neoantigen povezan sa tumorom pacijenta, gdje postupak obuhvaća korake:
a) utvrđivanja rezultata vezanja modificiranog peptida koji predstavlja fragment modificiranog proteina za jednu ili više molekula MHC klase II kod navedenog pacijenta,
b) utvrđivanja rezultata ekspresije ili zastupljenosti modificiranog proteina, pri čemu utvrđivanje rezultata ekspresije ili zastupljenosti modificiranog proteina obuhvaća utvrđivanje nivoa ekspresije proteina sa kojim je modifikacija povezana i određivanje učestalosti modificiranog proteina u okviru proteina sa kojim je modifikacija povezana, pri čemu se učestalost modificiranog proteina u okviru proteina sa kojim je modifikacija povezana određuje utvrđivanjem učestalosti alelne varijante, i
c) predviđanja jedne ili više imunogenih modifikacija aminokiselina,
gdje rezultat vezanja navedenog peptida za navedenu molekulu MHC klase II odražava vjerojatnost vezanja navedenog peptida za navedenu molekulu MHC klase II,
gdje učestalost alelne varijante predstavlja zbroj detektiranih sekvenci, u konkretnim očitavanjima, koja obuhvaćaju mjesto mutacije i nose mutaciju, podijeljen zbrojem svih detektiranih sekvenci, u konkretnim očitavanjima, koja obuhvaćaju mjesto mutacije,
pri čemu se, za utvrđivanje rezultata ekspresije ili zastupljenosti modificiranog proteina, rezultat nivoa ekspresije proteina sa kojim je modifikacija povezana množi rezultatom učestalosti modificiranog proteina u okviru proteina sa kojim je modifikacija povezana,
gdje se predviđanje imunogenih modifikacija aminokiselina odnosi na predviđanje da li će peptid koji sadrži takve modifikacije aminokiselina biti imunogen, i stoga koristan kao epitop u cijepljenju.
2. Postupak za izbor i/ili rangiranje imunogenih modifikacija aminokiselina koje su korisne za cijepljenje, naznačen time, što se modifikacije javljaju u proteinu koji sadrži neoantigen povezan sa tumorom pacijenta, gdje postupak obuhvaća korake:
a) utvrđivanja rezultata vezanja modificiranog peptida koji je fragment modificiranog proteina za jedan ili više molekula MHC klase II navedenog pacijenta,
i
b) utvrđivanja rezultata ekspresije ili zastupljenosti modificiranog proteina, pri čemu utvrđivanje rezultata ekspresije ili zastupljenosti modificiranog proteina obuhvaća utvrđivanje nivoa ekspresije proteina sa kojim je modifikacija povezana i određivanje učestalosti modificiranog proteina u okviru proteina sa kojim je modifikacija povezana, pri čemu se učestalost modificiranog proteina u okviru proteina sa kojim je modifikacija povezana određuje utvrđivanjem učestalosti alelne varijante,
pri čemu postupak obuhvaća izvođenje koraka a) i b) na dvije ili više različitih modifikacija, i gdje postupak dalje obuhvaća korak:
c) odabira i/ili rangiranja imunogenih modifikacija aminokiselina korisnih za cijepljenje,
gdje rezultat vezanja navedenog peptida za navedenu molekulu MHC klase II odražava vjerojatnost vezanja navedenog peptida za navedenu molekulu MHC klase II,
gdje učestalost alelne varijante predstavlja zbroj detektiranih sekvenci, u konkretnim očitavanjima, koja obuhvaćaju mjesto mutacije i nose mutaciju, podijeljen zbrojem svih detektiranih sekvenci, u konkretnim očitavanjima, koja obuhvaćaju mjesto mutacije,
pri čemu se, za utvrđivanje rezultata ekspresije ili zastupljenosti modificiranog proteina, rezultat nivoa ekspresije proteina sa kojim je modifikacija povezana množi rezultatom učestalosti modificiranog proteina u okviru proteina sa kojim je modifikacija povezana.
3. Postupak prema patentnom zahtjevu 2, koji obuhvaća usporedbu rezultata navedene dvije ili više različitih modifikacija, pri čemu se, poželjno, rezultati navedene dvije ili više različitih modifikacija uspoređuju rangiranjem različitih modifikacija prema njihovim rezultatima vezanja za MHC klase II.
4. Postupak prema bilo kojem od patentnih zahtjeva 1 do 3, koji obuhvaća izvođenje koraka a) na dva ili više različitih modificiranih peptida, pri čemu navedena dva ili više različitih modificiranih peptida sadrže istu modifikaciju/modifikacije.
5. Postupak prema patentnom zahtjevu 4, naznačen time, što
dva ili više različitih modificiranih peptida koji sadrže istu modifikaciju/modifikacije sadrže različite fragmente modificiranog proteina, pri čemu navedeni različiti fragmenti sadrže istu modifikaciju/modifikacije prisutne u proteinu, i/ili
dva ili više različitih modificiranih peptida koji sadrže istu modifikaciju/modifikacije sadrže različite potencijalne fragmente vezanja MHC klase II modificiranog proteina, gdje navedeni fragmenti sadrže istu modifikaciju/modifikacije prisutne u proteinu, i/ili
dva ili više različitih modificiranih peptida koji sadrže istu modifikaciju/modifikacije razlikuju se po dužini i/ili položaju modifikacije/modifikacija.
6. Postupak prema patentnim zahtjevima 4 ili 5, koji dalje obuhvaća odabir modificiranog/ modificiranih peptida od dva ili više različitih modificiranih peptida koji sadrže istu modifikaciju/modifikacije koji imaju vjerojatnost ili imaju najveću vjerojatnost za vezanje za jednu ili više molekula MHC klase II.
7. Postupak prema bilo kojem od patentnih zahtjeva 4 do 6, naznačen time, što se najbolji rezultat vezanja za jednu ili više molekula MHC klase II dva ili više različitih modificiranih peptida koji sadrže istu modifikaciju/modifikacije dodjeljuje modifikaciji/modifikacijama.
8. Postupak prema bilo kojem od patentnih zahtjeva 1 do 7, naznačen time, što se navedeno određivanje nivoa ekspresije proteina sa kojim je modifikacija povezana i/ili određivanje učestalosti modificiranog proteina u okviru proteina sa kojim je modifikacija povezana obavlja na nivou RNK.
9. Postupak prema bilo kojem od patentnih zahtjeva 1 do 8, naznačen time, što modificirani peptid sadrži fragment modificiranog proteina, pri čemu navedeni fragment sadrži modifikaciju prisutnu u proteinu.
10. Postupak prema bilo kojem od patentnih zahtjeva 1 do 9, koji dalje obuhvaća identifikaciju nesinonimnih mutacija u jednom ili više područja koji kodiraju proteine.
11. Postupak prema bilo kojem od patentnih zahtjeva 1 do 10, naznačen time, što se modifikacije aminokiselina identificiraju djelomičnim ili potpunim sekvenciranjem genoma ili transkriptoma jedne ili više stanica, kao što su jedna ili više stanica raka i izborno jedna ili više ne-kancerogenih stanica i identificiranjem mutacija u jednom ili više područja koji kodiraju proteine.
12. Postupak prema patentnom zahtjevu 10 ili 11, naznačen time, što su navedene mutacije somatske mutacije i/ili mutacije raka.
Applications Claiming Priority (3)
| Application Number | Priority Date | Filing Date | Title |
|---|---|---|---|
| PCT/EP2015/053021 WO2016128060A1 (en) | 2015-02-12 | 2015-02-12 | Predicting t cell epitopes useful for vaccination |
| PCT/EP2016/052684 WO2016128376A1 (en) | 2015-02-12 | 2016-02-09 | Predicting t cell epitopes useful for vaccination |
| EP16704567.3A EP3256853B1 (en) | 2015-02-12 | 2016-02-09 | Predicting t cell epitopes useful for vaccination |
Publications (1)
| Publication Number | Publication Date |
|---|---|
| HRP20211419T1 true HRP20211419T1 (hr) | 2021-12-10 |
Family
ID=52469061
Family Applications (1)
| Application Number | Title | Priority Date | Filing Date |
|---|---|---|---|
| HRP20211419TT HRP20211419T1 (hr) | 2015-02-12 | 2021-09-08 | Predviđanje epitopa t-stanica korisnih za cijepljenje |
Country Status (22)
| Country | Link |
|---|---|
| US (2) | US11156617B2 (hr) |
| EP (2) | EP3256853B1 (hr) |
| JP (2) | JP6882178B2 (hr) |
| KR (3) | KR102359213B1 (hr) |
| CN (2) | CN107430132B (hr) |
| AU (2) | AU2016217965B2 (hr) |
| BR (1) | BR112017017293A2 (hr) |
| CA (1) | CA2982971A1 (hr) |
| CY (1) | CY1124558T1 (hr) |
| DK (1) | DK3256853T3 (hr) |
| ES (1) | ES2888430T3 (hr) |
| HK (1) | HK1246852A1 (hr) |
| HR (1) | HRP20211419T1 (hr) |
| HU (1) | HUE056658T2 (hr) |
| IL (1) | IL253627B (hr) |
| LT (1) | LT3256853T (hr) |
| MX (3) | MX2017010332A (hr) |
| PL (1) | PL3256853T3 (hr) |
| PT (1) | PT3256853T (hr) |
| RS (1) | RS62416B1 (hr) |
| SI (1) | SI3256853T1 (hr) |
| WO (2) | WO2016128060A1 (hr) |
Families Citing this family (35)
| Publication number | Priority date | Publication date | Assignee | Title |
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| WO2015048744A2 (en) | 2013-09-30 | 2015-04-02 | Moderna Therapeutics, Inc. | Polynucleotides encoding immune modulating polypeptides |
| LT3134131T (lt) | 2014-04-23 | 2022-02-10 | Modernatx, Inc. | Nukleorūgšties vakcinos |
| WO2016128060A1 (en) | 2015-02-12 | 2016-08-18 | Biontech Ag | Predicting t cell epitopes useful for vaccination |
| EP3328394A4 (en) * | 2015-07-30 | 2019-03-13 | ModernaTX, Inc. | PEPTIDE CONCATEMERIC EPITAOPE RNA |
| US20170199961A1 (en) | 2015-12-16 | 2017-07-13 | Gritstone Oncology, Inc. | Neoantigen Identification, Manufacture, and Use |
| CN108495649A (zh) | 2016-01-08 | 2018-09-04 | 瓦西博迪公司 | 治疗性抗癌新表位疫苗 |
| US20170224796A1 (en) | 2016-02-05 | 2017-08-10 | Xeme Biopharma Inc. | Therapeutic Cancer Vaccine Containing Tumor-Associated Neoantigens and Immunostimulants in a Delivery System |
| CN108700566A (zh) | 2016-02-19 | 2018-10-23 | 河谷控股Ip有限责任公司 | 免疫原性调节的方法 |
| KR101925040B1 (ko) * | 2016-11-11 | 2018-12-04 | 한국과학기술정보연구원 | Mhc와 펩타이드 사이의 결합 친화성 예측 방법 및 장치 |
| RU2022106357A (ru) * | 2017-02-01 | 2022-03-24 | МОДЕРНАТиЭкс, ИНК. | Противораковые рнк-вакцины |
| KR102565256B1 (ko) | 2017-02-12 | 2023-08-08 | 바이오엔테크 유에스 인크. | Hla 기반 방법 및 조성물, 및 이들의 용도 |
| TWI672503B (zh) * | 2017-03-31 | 2019-09-21 | 行動基因生技股份有限公司 | 致免疫性之癌症特異抗原決定位的排名系統 |
| US11905525B2 (en) | 2017-04-05 | 2024-02-20 | Modernatx, Inc. | Reduction of elimination of immune responses to non-intravenous, e.g., subcutaneously administered therapeutic proteins |
| WO2018224166A1 (en) * | 2017-06-09 | 2018-12-13 | Biontech Rna Pharmaceuticals Gmbh | Methods for predicting the usefulness of disease specific amino acid modifications for immunotherapy |
| EP3694532A4 (en) | 2017-10-10 | 2021-07-14 | Gritstone Oncology, Inc. | IDENTIFICATION OF NEOANTIGENS BY MEANS OF HOT SPOTS |
| WO2019090343A1 (en) * | 2017-11-06 | 2019-05-09 | Memorial Sloan Kettering Cancer Center | Heat-inactivated vaccinia virus as a vaccine immune adjuvant |
| CN111630602A (zh) | 2017-11-22 | 2020-09-04 | 磨石肿瘤生物技术公司 | 减少新抗原的接合表位呈递 |
| WO2019147921A1 (en) | 2018-01-26 | 2019-08-01 | Nantcell, Inc. | Rapid verification of virus particle production for a personalized vaccine |
| EP3743102A1 (en) | 2018-01-26 | 2020-12-02 | Nantcell, Inc. | Compositions and methods for combination cancer vaccine and immunologic adjuvant therapy |
| CN108491689B (zh) * | 2018-02-01 | 2019-07-09 | 杭州纽安津生物科技有限公司 | 基于转录组的肿瘤新抗原鉴定方法 |
| CA3111903A1 (en) * | 2018-09-27 | 2020-04-02 | Vaccibody As | Method for selecting neoepitopes |
| US20210379170A1 (en) * | 2018-11-15 | 2021-12-09 | Nouscom Ag | Selection of cancer mutations for generation of a personalized cancer vaccine |
| US20200224206A1 (en) * | 2018-12-05 | 2020-07-16 | Linearx, Inc. | Amplicon Expression Vector Vaccines |
| CN113474840A (zh) * | 2018-12-21 | 2021-10-01 | 百欧恩泰美国公司 | 用于预测hla ii类特异性表位及表征cd4+ t细胞的方法和系统 |
| CN111621564B (zh) * | 2019-02-28 | 2022-03-25 | 武汉大学 | 一种鉴定有效肿瘤新抗原的方法 |
| WO2020221783A1 (en) * | 2019-04-29 | 2020-11-05 | Vaccibody As | Methods for pre-selection of neoepitopes |
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