HRP20192342T1 - Postupci i kompozicije za određivanje rezistencije na terapiju posredovanu androgenim receptorom - Google Patents

Postupci i kompozicije za određivanje rezistencije na terapiju posredovanu androgenim receptorom Download PDF

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HRP20192342T1
HRP20192342T1 HRP20192342TT HRP20192342T HRP20192342T1 HR P20192342 T1 HRP20192342 T1 HR P20192342T1 HR P20192342T T HRP20192342T T HR P20192342TT HR P20192342 T HRP20192342 T HR P20192342T HR P20192342 T1 HRP20192342 T1 HR P20192342T1
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Croatia
Prior art keywords
amino acid
polypeptide
nucleic acid
modified
optionally
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HRP20192342TT
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James David Joseph
Jeffrey H. Hager
John Lee Sensintaffar
Nhin LU
Jing Qian
Nicholas D. Smith
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Aragon Pharmaceuticals, Inc.
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Publication of HRP20192342T1 publication Critical patent/HRP20192342T1/hr

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Claims (56)

1. Postupak za utvrđivanje je li subjekt pokazuje ili će pokazati slabiji odgovor na terapiju s antagonistom androgenog receptora (AR) prve ili druge generacije, koji obuhvaća: (a) ispitivanje uzorka koji sadrži molekulu nukleinske kiseline koja kodira AR polipeptid iz subjekta, da bi se utvrdilo je li kodirani AR polipeptid modificiran na poziciji aminokiseline koja odgovara poziciji aminokiseline 876 u aminokiselinskoj sekvenciji navedenoj u SEQ ID NO: 1; i (b) karakterizaciju subjekta kao rezistentnog ili onog koji će postati rezistentan na terapiju s AR antagonistom prve ili druge generacije ukoliko subjekt posjeduje modifikaciju.
2. Postupak prema patentnom zahtjevu 1, pri čemu je subjektu primijenjen AR antagonist prve ili druge generacije za liječenje karcinoma, opcionalno gdje karcinom predstavlja karcinom prostate.
3. Postupak izbora subjekta za terapiju AR antagonistom treće generacije, koji obuhvaća: (a) ispitivanje uzorka koji sadrži molekulu nukleinske kiseline koja kodira AR polipeptid iz subjekta, da bi se utvrdilo je li kodirani AR polipeptid modificiran na poziciji aminokiseline koja odgovara poziciji aminokiseline 876 u aminokiselinskoj sekvenciiji navedenoj u SEQ ID NO: 1; i (b) karakterizaciju subjekta kao kandidata za terapiju s AR antagonistom treće generacije ukoliko subjekt posjeduje modifikaciju.
4. Postupak prema bilo kojem od patentnih zahtjeva 1-3, pri čemu modifikacija obuhvaća supstituciju ili deleciju aminokiseline na poziciji aminokiseline 876 u AR polipeptidu.
5. Postupak prema patentnom zahtjevu 4, pri čemu je modifikacija supstitucija fenilalanina s aminokiselinom izabranom između leucina, izoleucina, valina, alanina, glicina, metionina, serina, treonina, cisteina, triptofana, lizina, arginina, histidina, prolina, tirozina, asparagina, glutamina, asparaginske kiseline i glutaminske kiseline na poziciji aminokiseline 876 AR polipeptida, opcionalno pri čemu je modifikacija supstitucija fenilalanina s aminokiselinom izabranom između glicina, alanina, valina, leucina i izoleucina na poziciji aminokiseline 876 AR polipeptida, opcionalno pri čemu je modifikacija supstitucija fenilalanina s leucinom na poziciji aminokiseline 876 AR polipeptida.
6. Postupak prema bilo kojem od patentnih zahtjeva 1-4, pri čemu modifikacija obuhvaća deleciju nukleinske kiseline koja kodira aminokiselinu na poziciji 876 AR polipeptida.
7. Postupak prema bilo kojem od patentnih zahtjeva 1-6, pri čemu nukleinska kiselina koja kodira modificiran AR polipeptid sadrži (i) mutaciju timina (t) u citozin (c) na poziciji u nukleinskoj kiselini koja odgovara poziciji 2626 nukleinske kiseline u sekvenciji nukleotida koja je navedena u SEQ ID NO: 18; (ii) mutaciju citozina (c) u adenin (a) na poziciji u nukleinskoj kiselini koja odgovara poziciji 2628 nukleinske kiseline u sekvenciji nukleotida koja je navedena u SEQ ID NO: 18; ili (ii) mutaciju citozina (c) u gvanin (g) na poziciji u nukleinskoj kiselini koja odgovara poziciji 2628 nukleinske kiseline u sekvenciji nukleotida koja je navedena u SEQ ID NO: 18.
8. Postupak prema patentnom zahtjevu 7, pri čemu nukleinska kiselina kodira leucin na aminokiselinskoj poziciji 876 AR polipeptida.
9. Postupak prema bilo kojem od patentnih zahtjeva 1-8, pri čemu je molekula nukleinske kiseline RNK ili DNK, opcionalno gdje je DNK genomska DNK.
10. Postupak prema bilo kojem od patentnih zahtjeva 1-8, pri čemu postupak dalje obuhvaća izoliranje mRNK iz uzorka RNK.
11. Postupak prema bilo kojem od patentnih zahtjeva 1-10, gdje ispitivanje obuhvaća povećanje nukleinske kiseline koja kodira aminokiselinu na poziciji 876 AR polipeptida, opcionalno gdje se povećanje odvija lančanom reakcijom polimeraze (PCR-om), opcionalno gdje PCR povećanje podrazumijeva upotrebu para oligonukleotidnih početnica koje okružuju regiju koja kodira aminokiselinu na poziciji 876 AR polipeptida.
12. Postupak prema bilo kojem od patentnih zahtjeva 1-11, pri čemu postupak obuhvaća sekvenciranje povećane nukleinske kiseline.
13. Postupak prema bilo kojem od patentnih zahtjeva 1-12, gdje ispitivanje obuhvaća dovođenje u vezu nukleinske kiseline s probom specifičnom za sekvenciju nukleinske kiseline, pri čemu se proba specifična za sekvenciju nukleinske kiseline: (a) veže za nukleinsku kiselinu koja kodira modificirani receptor koji je modificiran na poziciji aminokiseline 876; i (b) ne veže se za nukleinsku kiselinu koja kodira receptor divljeg tipa koji sadrži fenilalanin na aminokiselinskoj poziciji 876.
14. Postupak prema bilo kojem od patentnih zahtjeva 1-13, pri čemu je uzorak iz uzorka tumorskih stanica iz subjekta.
15. Postupak prema bilo kojem od patentnih zahtjeva 1-14, pri čemu je uzorak iz uzorka biopsije tumora, uzorka krvi, uzorka seruma, uzorka limfe ili aspirata koštane srži.
16. Postupak prema patentnom zahtjevu 14 ili 15, pri čemu uzorak sadrži cirkulirajuće tumorske stanice (CTC) ili diseminirane tumorske stanice (DTC).
17. Postupak prema bilo kojem od patentnih zahtjeva 1-16, pri čemu AR antagonista prve ili druge generacije inhibira AR polipeptid divlјeg tipa kompetitivnim antagonizmom, opcionalno pri čemu je AR antagonista druge generacije izabran između ARN-509, enzalutamida (MDV3100) i RD162.
18. Postupak prema bilo kojem od patentnih zahtjeva 1-17, pri čemu je subjekt sa oboljenjem ili poremećajem izabranim između karcinoma, upalnog poremećaja ili proliferativnog poremećaja, opcionalno pri čemu subjekt ima karcinom, opcionalno gdje karcinom predstavlja karcinom prostate, karcinom dojke, karcinom mokraćnog mjehura ili hepatocelularni karcinom, opcionalno gdje karcinom predstavlja karcinom prostate, opcionalno pri čemu je subjekt sa karcinomom prostate koji je rezistentan na kastraciju.
19. Postupak prema bilo kojem od patentnih zahtjeva 1-18, pri čemu je subjekt sa solidnim tumorom.
20. Postupak prema bilo kojem od patentnih zahtjeva 1-19, pri čemu je subjekt liječen AR antagonistom prve ili druge generacije prije uzimanja uzorka, opcionalno gdje uzorak predstavlja uzorak dobiven u tjedan dana, 2 tjedna, 3 tjedna, 1 mjesec, 2 mjeseca, 3 mjeseca, 4 mjeseca, 5 mjeseci, 6 mjeseci, 7 mjeseci, 8 mjeseci, 9 mjeseci, 10 mjeseci, 11 mjeseci, 12 mjeseci, 14 mjeseci, 16 mjeseci, 18 mjeseci, 20 mjeseci, 22 mjeseca ili 24 mjeseca nakon prve primjene AR antagonista prve ili druge generacije, opcionalno pri čemu je uzorak dobiven 1, 2, 3, 4, 5, 6, 7, 8, 9 ili 10 puta tijekom trajanja tretmana s AR antagonistom prve ili druge generacije.
21. Postupak prema bilo kojem od patentnih zahtjeva 1-20, pri čemu subjekt odgovara na tretman AR antagonistom prve ili druge generacije kad se on prvi put primjeni.
22. Postupak praćenja spojeva koji antagoniziraju modificiran AR, koji obuhvaća: (a) ekspresiju modificiranoga AR u stanici, pri čemu je modificirani AR modificiran na poziciji aminokiseline koja odgovara poziciji aminokiseline 876 u aminokiselinskoj sekvenciji navedenoj u SEQ ID NO: 1; (b) dovođenje stanice u vezu sa spojem koji se ispituje; i (c) utvrđivanje nivoa aktivnosti AR u stanici, pri čemu smanjenje aktivnosti ukazuje da spoj antagonizira modificirani AR receptor.
23. Postupak prema patentnom zahtjevu 22, pri čemu ispitivani spoj pokazuje potpunu antagonističku aktivnost u odnosu na modificirani AR receptor.
24. Postupak prema patentnom zahtjevu 22 ili 23, pri čemu ispitivani spoj ne pokazuje agonističku aktivnost u odnosu na modificiran AR receptor.
25. Postupak prema bilo kojem od patentnih zahtjeva 22-24, pri čemu je modifikacija supstitucija ili delecija aminokiseline na poziciji 876 AR polipeptida.
26. Postupak prema patentnom zahtjevu 23, pri čemu je modifikacija supstitucija fenilalanina sa aminokiselinom izabranom između leucina, izoleucina, valina, alanina, glicina, metionina, serina, treonina, cisteina, triptofana, lizina, arginina, histidina, prolina, tirozina, asparagina, glutamina, asparaginske kiseline i glutaminske kiseline na poziciji aminokiseline 876 AR polipeptida, opcionalno gdje je modifikacija supstitucija fenilalanina s aminokiselinom izabranom između glicina, alanina, valina, leucina i izoleucina na poziciji aminokiseline 876 AR polipeptida, opcionalno gdje je modifikacija supstitucija fenilalanina s leucinom na poziciji aminokiseline 876 AR polipeptida.
27. Postupak prema bilo kojem od patentnih zahtjeva 22-26, gdje je stanica deficitarna u ekspresiji AR divlјeg tipa, izražava nizak nivo AR divljeg tipa ili izražava modificiran AR receptor.
28. Postupak prema bilo kojem od patentnih zahtjeva 22-27, gdje je stanica izabrana između HeLa, CV1, COS7, HepG2, HEK-293, DU145, PC3, TSY-PR1, LNCaP, CWR, VCaP i LAPC4.
29. Postupak prema bilo kojem od patentnih zahtjeva 22-28, gdje stanica sadrži gen reportera koji je operativno povezan s promotorom koji odgovara na androgene, opcionalno gdje se aktivnost određuje analizom ekspresije gena reportera.
30. Postupak prema patentnom zahtjevu 29, gdje promotor sadrži element odgovora na androgene, opcionalno gdje je element odgovora na androgene 4xARE ili element probazina.
31. Postupak prema bilo kojem od patentnih zahtjeva 22-30, gdje promotor predstavlja promotor probazina, antigena specifičnog za prostatu, MMTV LTR, FASN, STEAP4, TMPRSS2, ORM1 ili NKX3.1 promotor.
32. Postupak prema bilo kojem od patentnih zahtjeva 22-31, gdje gen reporter kodira protein izabran između luciferaze, fluorescentnog proteina, bioluminescentnog proteina ili enzima.
33. Izolirani AR polipeptid, ili njegova varijanta s AR aktivnošću, koji sadrži modifikaciju na poziciji aminokiseline koja odgovara poziciji aminokiseline 876 u aminokiselinskoj sekvenciji navedenoj u SEQ ID NO: 1, pri čemu modifikacija rezultira rezistencijom modificiranog AR polipeptida ili varijante na AR antagonistu.
34. Izolirani AR polipeptid prema patentnom zahtjevu 33, pri čemu modifikacija obuhvaća supstituciju aminokiseline na poziciji 876 u usporedbi sa AR divljeg tipa koji je naveden u SEQ ID NO: 1, opcionalno gdje je supstitucija F876L.
35. Izolirani AR polipeptid prema patentnom zahtjevu 34 koji je sa sekvencijom aminokiselina koja je navedena u SEQ ID NO: 5.
36. Izolirani AR polipeptid prema patentnom zahtjevu 33, pri čemu modifikacija obuhvaća deleciju aminokiseline na poziciji 876.
37. Izolirani AR polipeptid prema bilo kojem od patentnih zahtjeva 33-36, pri čemu polipeptid sadrži supstituciju aminokiseline na poziciji 876 u usporedbi s AR divljeg tipa koji je naveden u SEQ ID NO: 1 i jednu ili više dodatnih supstitucija aminokiselina, opcionalno pri čemu supstitucija aminokiseline na poziciji 876 je F876L.
38. Izolirani AR polipeptid prema patentnom zahtjevu 37, pri čemu je jedna ili više dodatnih supstitucija aminokiselina izabrana između jedne ili više supstitucija aminokiselina povezanih s karcinom prostate koji je rezistentan na kastraciju, opcionalno pri čemu je jedna ili više dodatnih supstitucija aminokiselina izabrana između T877A, W741C, W741L, W741R, L701H i H874Y.
39. Izolirani AR polipeptid prema bilo kojem od patentnih zahtjeva 33-38, pri čemu polipeptid sadrži sekvenciju aminokiselina navedenu u SEQ ID NO: 5 ili varijantu koja je najmanje ili najmanje oko 60%, 70%, 75%, 80%, 85%, 90%, 95%, 96%, 97%, 98%, 99% ili više identična polipeptidu čija je sekvencija navedena u SEQ ID NO: 5, gdje aminokiselina na poziciji 876 nije fenilalanin.
40. Izolirani AR polipeptid prema bilo kojem od patentnih zahtjeva 33-39 koji je rekombinantan protein.
41. Izolirana molekula nukleinske kiseline koja kodira modificirani AR polipeptid prema bilo kojem od patentnih zahtjeva 33-40.
42. Izolirana nukleinska kiselina prema patentnom zahtjevu 41, pri čemu je nukleinska kiselina molekula DNK ili RNK.
43. Izolirana nukleinska kiselina prema patentnom zahtjevu 41, pri čemu je nukleinska kiselina molekula cDNK.
44. Izolirana nukleinska kiselina prema patentnom zahtjevu 41 ili patentnom zahtjevu 42, pri čemu nukleinska kiselina sadrži sekvenciju nukleinskih kiselina navedenu u SEQ ID NO: 19 ili varijantu koja je najmanje ili najmanje 90%, 95%, 96%, 97% 98%, 99% ili više identična sa sekvencijom nukleinskih kiselina koja je navedena u SEQ ID NO: 19, gdje kodon nukleinske kiseline koji kodira aminokiselinu na poziciji 876 ne kodira fenilalanin, opcionalno gdje molekula nukleinske kiseline kodira leucin na poziciji 876 AR polipeptida.
45. Vektor, koji sadrži molekulu nukleinske kiseline prema bilo kojem od patentnih zahtjeva 41-44, opcionalno pri čemu je vektor virusni ili plazmidni vektor.
46. Vektor prema patentnom zahtjevu 45, gdje je nukleinska kiselina operativno povezana s promotorom, opcionalno gdje je promotor konstitutivni ili inducibilni promotor.
47. Stanica domaćin, koja sadrži vektor prema bilo kojem od patentnih zahtjeva 45-46.
48. Stanica domaćin prema patentnom zahtjevu 47, pri čemu je stanica prokariotska stanica ili eukariotska stanica, opcionalno pri čemu je stanica stanica sisavaca, bakterijska stanica, stanica kvasca, stanica insekta, biljna stanica ili stanica vodozemaca.
49. Mutirani AR polipeptid kojeg izražava stanica domaćin prema bilo kojem od patentnih zahtjeva 47-48.
50. Mikročip koji sadrži modificirani AR polipeptid prema bilo kojem od patentnih zahtjeva 33-40 ili nukleinsku kiselinu prema bilo kojem od patentnih zahtjeva 41-44.
51. Mikročip prema patentnom zahtjevu 50, pri čemu modificiran AR polipeptid sadrži supstituciju aminokiseline koja je tipa F876L ili nukleinsku kiselinu koja kodira modificirani AR polipeptid sa supstitucijom aminokiseline koja je F876L.
52. Komplet koji sadrži jedan ili više reagensa za otkrivanje nukleinske kiseline koja kodira modificirani AR polipeptid koji sadrži modifikaciju na poziciji aminokiseline 876 ili modificiranoga AR polipeptida koji sadrži modifikaciju na poziciji aminokiseline 876, opcionalno gdje modificirani AR polipeptid sadrži aminokiselinsku supstituciju koja je F876L i dalјe sadrži oligonukleotidnu početnicu koja se (a) veže za nukleinsku kiselinu koja kodira modificirani AR koji je modificiran na poziciji aminokiseline 876; i (b) ne veže se za nukleinsku kiselinu koja kodira AR divljeg tipa koji je sa fenilalaninom kao aminokiselinom na poziciji 876.
53. Komplet prema patentnom zahtjevu 52, koji sadrži mikročip koji sadrži (a) modificirani AR polipeptid sa modifikacijom koja je F876S ili njegov dio koji sadrži modifikaciju koja je F876S; ili (b) molekula nukleinske kiseline koja kodira mutirani AR polipeptid koji sa modifikacijom koja je F876S, ili njegov dio koji sadrži modifikaciju koja je F876S.
54. Sistem za otkrivanje modificiranoga AR koji je rezistentan na inhibiciju s AR antagonistom prve ili druge generacije kod subjekta, koji sadrži: (a) uzorak koji sadrži molekulu nukleinske kiseline koja kodira AR polipeptid iz subjekta; i (b) (i) genski ekspresijski čip koji sadrži nukleinsku kiselinu koja kodira mutirani AR polipeptid ili njegov dio koji je modificiran na poziciji aminokiseline koja odgovara poziciji aminokiseline 876 u aminokiselinskoj sekvenciji navedenoj u SEQ ID NO: 1, opcionalno pri čemu se genski ekspresijski čip nalazi na mikročipu, ili (b) (ii) probu specifičnu za sekvenciju nukleinske kiseline, pri čemu se proba specifična za sekvenciju nukleinske kiseline: (i) veže za nukleinsku kiselinu koja kodira modificirani AR koji je modificiran na poziciji aminokiseline 876; i (ii) ne veže za nukleinsku kiselinu koja kodira AR divljeg tipa koji sadrži fenilalanin na aminokiselinskoj poziciji 876, ili (b) (iii) par oligonukleotidnih početnica koje okružuju regiju nukleinske kiseline koja kodira aminokiselinu 876 AR polipeptida.
55. Izolirano antitijelo koje se veže za modificiran AR polipeptid prema bilo kojem od patentnih zahtjeva 33-40, pri čemu se antitijelo ne veže ili se veže s nižim afinitetom za AR polipeptid divljeg tipa koji je sa sekvencijom aminokiselina koja je navedena u SEQ ID NO: 1.
56. Antitijelo prema patentnom zahtjevu 55, pri čemu modificiran AR polipeptid sadrži aminokiselinsku supstituciju koja je F876L.
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