Compositions and methods for treating hepatitis b virus infection
AssigneesBeam Therapeutics Inc., Institut National De La Sante Et De La Recherche Medicale (Inserm)
InventorsElena SMEKALOVA, LUIS BARRERA, Fabien ZOULIM,, Maria Guadalupe MARTINEZ,, Barbara TESTONI
Life of this patent
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Abstract
The invention features compositions and methods for introducing mutations into the hepatitis B virus (HBV) genome.
Claims23
A method of editing a nucleobase of a hepatitis B virus (HBV) genome, the method comprising contacting the HBV genome with one or more guide RNAs and a base editor comprising a polynucleotide programmable DNA binding domain and an adenosine deaminase, wherein said guide RNA targets said base editor to effect an alteration of the nucleobase of the HBV genome, and wherein said one or more guide RNAs comprise a nucleotide sequence, from 5′ to 3′, or a 1, 2, 3, 4, or 5 nucleotide 5′ and/or 3′ truncation fragment thereof, selected from one or more of ACAAGAAUCCUCACAAUACC (SEQ ID NO:
- (SEQ ID NO:
- 405)
- ACAAGAAUCCUCACAAUACC,
- (SEQ ID NO:
- 406)
- UCGCUGGAUGUGUCUGCGGC,
- (SEQ ID NO:
- 407)
- CACCUGUAUUCCCAUCCCAU,
- (SEQ ID NO:
- 408)
- GGGGCCAAGUCUGUACAGCA,
- (SEQ ID NO:
- 409)
- GCUGACGCAACCCCCACUGG,
- (SEQ ID NO:
- 410)
- GGAGCUACUGUGGAGUUACU,
- (SEQ ID NO:
- 411)
- UUCUUCUAGGGGACCUGCCU,
- (SEQ ID NO:
- 412)
- GAGGACAAACGGGCAACAUA,
- (SEQ ID NO:
- 413)
- UUGUCAACAAGAAAAACCCC,
- (SEQ ID NO:
- 414)
- CCCAAGGUCUUACAUAAGAG,
- (SEQ ID NO:
- 415)
- CCGGGCAACGGGGUAAAGGU,
- (SEQ ID NO:
- 416)
- ACACAGAAAGGCCUUGUAAG,
- (SEQ ID NO:
- 10834)
- GAAAGCCCAAGAUGAUGGGA,
- and
- (SEQ ID NO:
- 417)
- CACGCACGCGCUGAUGGCCC.
A method of editing a nucleobase of a hepatitis B virus (HBV) genome, the method comprising:
- (i) contacting a cell comprising an HBV genome with one or more guide RNAs and a base editor comprising a polynucleotide programmable DNA binding domain and an adenosine deaminase or cytidine deaminase, wherein said guide RNA targets said base editor to effect an alteration of the nucleobase of the HBV genome, thereby editing a nucleobase in the HBV genome;
- and
- (ii) contacting the cell with an antiretroviral drug, wherein contacting the cell with the antiretroviral drug is associated with an increase in base editing efficiency relative to a reference cell not contacted with the antiretroviral drug.
A method reducing HBsAg produced from integrated HBV DNA, the method comprising contacting a cell comprising an HBV genome with one or more guide RNAs and a base editor comprising a polynucleotide programmable DNA binding domain and an adenosine deaminase or cytidine deaminase, wherein said guide RNA targets said base editor to effect an alteration of the nucleobase of the HBV genome, thereby reducing HBsAg production from an integrated HBV DNA.
A method of editing a nucleobase of a hepatitis B virus (HBV) genome, the method comprising contacting a cell comprising an HBV genome with an mRNA encoding a base editor comprising a polynucleotide programmable DNA binding domain and an adenosine deaminase or cytidine deaminase, and one or more guide RNAs comprising the sequences GAAAGCCCAGGAUGAUGGGA (SEQ ID NO:
- 657) and CCAUGCCCCAAAGCCACCCA (SEQ ID NO:
- 662), wherein said one or more guide RNAs target said base editor to effect an alteration of the nucleobase of the HBV genome, thereby editing a nucleobase in the HBV genome.
A method of treating hepatitis B virus (HBV) infection in a subject comprising administering to a subject in need thereof a fusion protein, protein complex, or polynucleotide encoding said fusion protein or protein complex, said fusion protein or protein complex comprising a polynucleotide programmable DNA binding domain and a base editor domain that is an adenosine deaminase domain, and one or more guide RNAs that target the base editor domain to effect an A·T to G·C alteration of a nucleobase of the HBV genome, wherein said one or more guide RNAs comprise a nucleotide sequence, from 5′ to 3′, or a 1, 2, 3, 4, or 5 nucleotide 5′ and/or 3′ truncation fragment thereof, selected from one or more of
- (SEQ ID NO:
- 405)
- ACAAGAAUCCUCACAAUACC,
- (SEQ ID NO:
- 406)
- UCGCUGGAUGUGUCUGCGGC,
- (SEQ ID NO:
- 407)
- CACCUGUAUUCCCAUCCCAU,
- (SEQ ID NO:
- 408)
- GGGGCCAAGUCUGUACAGCA,
- (SEQ ID NO:
- 409)
- GCUGACGCAACCCCCACUGG,
- (SEQ ID NO:
- 410)
- GGAGCUACUGUGGAGUUACU,
- (SEQ ID NO:
- 411)
- UUCUUCUAGGGGACCUGCCU,
- (SEQ ID NO:
- 412)
- GAGGACAAACGGGCAACAUA,
- (SEQ ID NO:
- 413)
- UUGUCAACAAGAAAAACCCC,
- (SEQ ID NO:
- 414)
- CCCAAGGUCUUACAUAAGAG,
- (SEQ ID NO:
- 415)
- CCGGGCAACGGGGUAAAGGU,
- (SEQ ID NO:
- 416)
- ACACAGAAAGGCCUUGUAAG,
- and
- (SEQ ID NO:
- 417)
- CACGCACGCGCUGAUGGCCC.
A method of treating a hepatitis B virus (HBV) infection in a subject, comprising administering to a subject in need thereof with one or more guide RNAs and a base editor comprising a polynucleotide programmable DNA binding domain and an adenosine deaminase or cytidine deaminase, wherein said one or more guide RNAs comprise the sequences GAAAGCCCAGGAUGAUGGGA (SEQ ID NO:
- 657) and CCAUGCCCCAAAGCCACCCA (SEQ ID NO:
- 662) that target said base editor to effect an alteration of the nucleobase of the HBV genome, thereby editing a nucleobase in the HBV genome.
A composition comprising a base editor(s) bound to a guide RNA(s), wherein said guide RNA(s) comprises a nucleotide sequence, from 5′ to 3′, or a 1, 2, 3, 4, or 5 nucleotide 5′ and/or 3′ truncation fragment thereof, selected from one or more of
- (SEQ ID NO:
- 405)
- ACAAGAAUCCUCACAAUACC,
- (SEQ ID NO:
- 406)
- UCGCUGGAUGUGUCUGCGGC,
- (SEQ ID NO:
- 407)
- CACCUGUAUUCCCAUCCCAU,
- (SEQ ID NO:
- 408)
- GGGGCCAAGUCUGUACAGCA,
- (SEQ ID NO:
- 409)
- GCUGACGCAACCCCCACUGG,
- (SEQ ID NO:
- 410)
- GGAGCUACUGUGGAGUUACU,
- (SEQ ID NO:
- 411)
- UUCUUCUAGGGGACCUGCCU,
- (SEQ ID NO:
- 412)
- GAGGACAAACGGGCAACAUA,
- (SEQ ID NO:
- 413)
- UUGUCAACAAGAAAAACCCC,
- (SEQ ID NO:
- 414)
- CCCAAGGUCUUACAUAAGAG,
- (SEQ ID NO:
- 415)
- CCGGGCAACGGGGUAAAGGU,
- (SEQ ID NO:
- 416)
- ACACAGAAAGGCCUUGUAAG,
- and
- (SEQ ID NO:
- 417)
- CACGCACGCGCUGAUGGCCC.
A pharmaceutical composition for the treatment of HBV infection comprising:
- (i) a base editor, or a nucleic acid encoding the base editor, and one or more guide RNAs (gRNA) comprising a nucleic acid sequence complementary to an HBV gene in a pharmaceutically acceptable excipient, wherein said one or more guide RNAs comprise a nucleotide sequence, from 5′ to 3′, or a 1, 2, 3, 4, or 5 nucleotide 5′ and/or 3′ truncation fragment thereof, selected from one or more of ACAAGAAUCCUCACAAUACC (SEQ ID NO:
- 405), UCGCUGGAUGUGUCUGCGGC (SEQ ID NO:406), CACCUGUAUUCCCAUCCCAU (SEQ ID NO:
- 407), GGGGCCAAGUCUGUACAGCA (SEQ ID NO:
- 408), GCUGACGCAACCCCCACUGG (SEQ ID NO:
- 409), GGAGCUACUGUGGAGUUACU (SEQ ID NO:
- 410), UUCUUCUAGGGGACCUGCCU (SEQ ID NO:
- 411), GAGGACAAACGGGCAACAUA (SEQ ID NO:
- 412), UUGUCAACAAGAAAAACCCC (SEQ ID NO:
- 413), CCCAAGGUCUUACAUAAGAG (SEQ ID NO:
- 414), CCGGGCAACGGGGUAAAGGU (SEQ ID NO:
- 415), ACACAGAAAGGCCUUGUAAG (SEQ ID NO:
- 416), and CACGCACGCGCUGAUGGCCC (SEQ ID NO:
- 417).
A guide RNA comprise a nucleotide sequence, from 5′ to 3′, or a 1, 2, 3, 4, or 5 nucleotide 5′ and/or 3′ truncation fragment thereof, selected from one or more of
- (SEQ ID NO:
- 405)
- ACAAGAAUCCUCACAAUACC,
- (SEQ ID NO:
- 406)
- UCGCUGGAUGUGUCUGCGGC,
- (SEQ ID NO:
- 407)
- CACCUGUAUUCCCAUCCCAU,
- (SEQ ID NO:
- 408)
- GGGGCCAAGUCUGUACAGCA,
- (SEQ ID NO:
- 409)
- GCUGACGCAACCCCCACUGG,
- (SEQ ID NO:
- 410)
- GGAGCUACUGUGGAGUUACU,
- (SEQ ID NO:
- 411)
- UUCUUCUAGGGGACCUGCCU,
- (SEQ ID NO:
- 412)
- GAGGACAAACGGGCAACAUA,
- (SEQ ID NO:
- 413)
- UUGUCAACAAGAAAAACCCC,
- (SEQ ID NO:
- 414)
- CCCAAGGUCUUACAUAAGAG,
- (SEQ ID NO:
- 415)
- CCGGGCAACGGGGUAAAGGU,
- (SEQ ID NO:
- 416)
- ACACAGAAAGGCCUUGUAAG,
- and
- (SEQ ID NO:
- 417)
- CACGCACGCGCUGAUGGCCC.
Dependencies are inferred from the claim text.