E1 enzyme mutants and uses thereof

An isolated E1 enzyme variant polypeptide selected from the group consisting of:

• a) a UBA3 variant polypeptide comprising a variant of the amino acid sequence of SEQ ID NO:2, wherein the variant has a mutation of the amino acid selected from the group consisting of amino acid residue 171, 201, 204, 205, 209, 211, 228, 229, 249, 305, 311, 314 and 324;
• b) a UBA3 variant polypeptide comprising a fragment of a variant of the amino acid sequence of SEQ ID NO:2, wherein the fragment comprises at least 15 contiguous amino acids of SEQ ID NO:
• 2, and wherein the fragment has a mutation of the amino acid selected from the group consisting of amino acid residue 171, 201, 204, 205, 209, 211, 228, 229, 249, 305, 311, 314 and 324;
• c) a polypeptide comprising an amino acid sequence selected from the group consisting of:
• an SAE2 variant of SEQ ID NO:27 with a mutation at residue 121, a UBA1 variant of SEQ ID NO:28 with a mutation at residue 548, a UBA1 variant of SEQ ID NO:29, with a mutation at residue 580, a UBA4 variant of SEQ ID NO:30 with a mutation at residue 185, a UBA5 variant of SEQ ID NO:31 with a mutation at residue 187, a UBA6 variant of SEQ ID NO:32 with a mutation at residue 573, a UBA7 variant of SEQ ID NO:33 with a mutation at residue 544, an ATG7 variant of SEQ ID NO:34 with a mutation at residue 480, a moeb variant of SEQ ID NO:35 with a mutation at residue 134 and a thif variant of SEQ ID NO:36 with a mutation at residue 131;
• and
• d) a polypeptide comprising a fragment of the variant E1 enzyme in c), wherein the fragment comprises at least 15 contiguous amino acids of the E1 enzyme comprising the mutated amino acid;
• wherein the E1 enzyme variant has a decreased sensitivity to an E1 enzyme inhibitor.

A method for determining whether a test cell has a drug-resistant phenotype, the method comprising:

• a) measuring the expression or activity of an E1 enzyme variant sequence in the test cell;
• b) comparing the expression or activity of the E1 enzyme variant sequence measured in step a) to the expression or activity of the E1 enzyme sequence in a control cell not having a drug-resistant phenotype;
• and
• c) determining that the test cell has a drug resistant phenotype if the expression or activity of the E1 enzyme variant sequence in the test cell differs compared to the expression or activity of the E1 enzyme variant sequence in the control cell,
• wherein the drug is an E1 enzyme inhibitor.

A method for treating a subject with a drug therapy comprising an E1 enzyme inhibitor, the method comprising:

• a. obtaining from the subject a pre-administration biological sample and a post-administration biological sample;
• b. measuring the expression level of a E1 enzyme variant sequence in the two samples;
• and
• c. providing the drug therapy when the expression level of the E1 enzyme variant sequence indicates that the patient will benefit from the treatment.