Compositions and methods for altering complement activation

A method of treating a disease or disorder associated with inappropriate activation of the complement system in a subject in need thereof, the method comprising altering a nucleobase of a complement factor B (CFB) polynucleotide in the subject by administering to the subject one or more guide polynucleotides, or one or more polynucleotides encoding the one or more guide polynucleotides, and a base editor comprising a nucleic acid programmable DNA binding protein (napDNAbp) domain and a deaminase domain, or one or more polynucleotides encoding the base editor, wherein

• (a) said one or more guide polynucleotides targets said base editor to effect an alteration of a nucleobase of the CFB polynucleotide that:
• i. disrupts a splice site in the CFB polynucleotide,
• ii. alters a start codon in the CFB polynucleotide,
• iii. alters a TATA box in the CFB polynucleotide,
• iv. introduces a new stop codon in the CFB polynucleotide, and/or
• v. alters a nucleobase in a codon encoding an amino acid residue within a region of the CFB polypeptide encoded by the CFB polynucleotide selected from the group consisting of:
• serine protease (SP) active site, Mg2+ binding loop, cleavage site, salt bridge, and oxyanion-hole;
• (b) the deaminase domain comprises a TadA variant (TadA*) comprising an amino acid sequence having at least 90% sequence identity to the following TadA*7.10 amino acid sequence:
• MSEVEFSHEYWMRHALTLAKRARDEREVPVGAVLVLNNRVIGEGWNRAIGLHDPTAHAEIMA LRQGGLVMQNYRLIDATLYVTFEPCVMCAGAMIHSRIGRVVFGVRNAKTGAAGSLMDVLHYP GMNHRVEITEGILADECAALLCYFFRMPRQVFNAQKKAQSSTD (SEQ ID NO:
• 1), or a fragment thereof lacking only the N-terminal methionine, wherein the TadA* further comprises a combination of amino acid alterations compared to the TadA*7.10 amino acid sequence selected from the group consisting of:
• i. I76Y, V82T, Y123H, Y147T, and Q154S,
• ii. Y123H, Y147R, and Q154R,
• iii. 176Y, Y133H, Y147R, and Q154R,
• iv. V82S, and Q164R,
• v. I76Y, V82S, Y123H, Y147R, and Q154R, and
• vi. I76Y, V82T, Y123H, Y147R, and Q154;
• (c) the one or more guide polynucleotides comprises a nucleic acid sequence selected from CCUCAGAUGUCUAUGUGUUU (SEQ ID NO:
• 1524), UGCUUACAAUGACUGAGAUCU (SEQ ID NO:
• 1535), UUGCUCCCCAUGGCGUUGGA (SEQ ID NO:
• 3476), CCCCAUGGCGUUGGAAGGCA (SEQ ID NO:
• 3443), and UGCUCCCCAUGGCGUUGGAA (SEQ ID NO:
• 3467) and/or comprising at least 10-23 contiguous nucleotides of a spacer nucleic acid sequence listed in any one of Tables 2A to 2H;
• and/or
• (d) said one or more guide polynucleotides targets said base editor to effect an alteration of a nucleobase in one or more codons encoding an amino acid residue selected from the group consisting of amino acid residue 1, 171, 175, 176, 177, 202, 203, 229, 230, 231, 232, 233, 254, 255, 256, 257, 258, 259, 260, 275, 276, 277, 278, 279, 280, 281, 351, 353, 354, 389, 470, 471, 472, 525, 526, 529, 574, 575, 576, 696, 697, and 699 relative to the following reference sequence:
• Complement factor B amino acid sequence MGSNLSPQLCLMPFILGLLSGGVTTTPWSLAQPQGSCSLEGVEIKGGSFRLLQEGQALEYVC PSGFYPYPVQTRTCRSTGSWSTLKTQDQKTVRKAECRAIHCPRPHDFENGEYWPRSPYYNVS DEISFHCYDGYTLRGSANRTCQVNGRWSGQTAICDNGAGYCSNPGIPIGTRKVGSQYRLEDS VTYHCSRGLTLRGSQRRTCQEGGSWSGTEPSCQDSFMYDTPQEVAEAFLSSLTETIEGVDAE DGHGPGEQQKRKIVLDPSGSMNIYLVLDGSDSIGASNFTGAKKCLVNLIEKVASYGVKPRYG LVTYATYPKIWVKVSEADSSNADWVTKQLNEINYEDHKLKSGTNTKKALQAVYSMMSWPDDV PPEGWNRTRHVIILMTDGLHNMGGDPITVIDEIRDLLYIGKDRKNPREDYLDVYVFGVGPLV NQVNINALASKKDNEQHVFKVKDMENLEDVFYQMIDESQSLSLCGMVWEHRKGTDYHKQPWQ AKISVIRPSKGHESCMGAVVSEYFVLTAAHCFTVDDKEHSIKVSVGGEKRDLEIEVVLFHPN YNINGKKEAGIPEFYDYDVALIKLKNKLKYGQTIRPICLPCTEGTTRALRLPPTTTCQQQKE ELLPAQDIKALFVSEEEKKLTRKEVYIKNGDKKGSCERDAQYAPGYDKVKDISEVVTPRFLC TGGVSPYADPNTCRGDSGGPLIVHKRSRFIQVGVISWGVVDVCKNQKROKQVPAHARDFHIN LFQVLPWLKEKLQDEDLGFL (SEQ ID NO:
• 426), or a corresponding position in another CFB polypeptide sequence;
• thereby altering the nucleobase of the CFB polynucleotide.