Pharmacogenetic Method for Prediction of the Efficacy of Methotrexate Monotherapy in Recent-Onset Arthritis

Abstract

Pharmacogenetic methods for determining a predicting responsiveness to antifolate therapy for subjects that present with recent-onset undifferentiated arthritis. The methods are based on the determination of a set of clinical parameter values and determining a predicted responsiveness to antifolate therapy by correlating the parameter values with predefined responsiveness values associated with ranges of parameter values. Parameters values that are decisive for responsiveness to antifolate therapy may include polymorphisms in the methylenetetrahydrofolate dehydrogenase (MTHFD1) gene as well as in three genes involved in the adenosine release pathway, the presence or absence of Rheumatoid factors, gender, pre- or postmenopausal status and/or smoking status.

What is claimed is: 
     
         1 . A method for determining clinical responsiveness to antifolate therapy in a subject afflicted with, or at risk of developing, arthritis comprising detecting the presence of a polymorphism in the methylenetetrahydrofolate dehydrogenase (MTHFD1) gene, wherein the presence of the polymorphism is indicative of clinical responsiveness to the antifolate therapy. 
     
     
         2 . The method according to  claim 1 , wherein the polymorphism is a polymorphism that results in an amino acid change with respect to the amino acid sequence of SEQ ID NO: 1. 
     
     
         3 . The method according to  claim 1 , wherein the polymorphism is the single nucleotide polymorphism 1958G>A. 
     
     
         4 . The method according to  claim 1 , wherein the presence of the MTHFD1 1958 G-allele carrier is indicative of clinical responsiveness to the antifolate therapy. 
     
     
         5 . The method according to  claim 1 , further comprising detecting the presence of a polymorphism in at least one gene selected from the group consisting of adenosine monophosphate deaminase (AMPD1), aminoimidazole carboxamide ribonucleotide transformylase (ATIC), and inosine triphosphate pyrophosphatase (ITPA), wherein the presence of the polymorphism is indicative of clinical responsiveness to the antifolate therapy. 
     
     
         6 . The method according to  claim 5 , wherein the method comprises detecting the presence of a polymorphism in each of the genes encoding methylenetetrahydrofolate dehydrogenase (MTHFD1) gene, adenosine monophosphate deaminase (AMPD1), aminoimidazole carboxamide ribonucleotide transformylase (ATIC), and inosine triphosphate pyrophosphatase (ITPA) wherein the presence of a polymorphism in at least one of these four genes is indicative of clinical responsiveness to the antifolate therapy. 
     
     
         7 . The method according to  claim 5 , wherein:
 a) the polymorphism in the adenosine monophosphate deaminase (AMPD1) gene is a polymorphism that results in an amino acid change with respect to the amino acid sequence of SEQ ID NO: 2;   b) the polymorphism in the aminoimidazole carboxamide ribonucleotide transformylase (ATIC) gene is a polymorphism that results in an amino acid change with respect to the amino acid sequence of SEQ ID NO: 3; and,   c) the polymorphism in the inosine triphosphate pyrophosphatase (ITPA) gene is a polymorphism that results in an amino acid change with respect to the amino acid sequence of SEQ ID NO: 4.   
     
     
         8 . The method according to  claim 5 , wherein the polymorphism is a single nucleotide polymorphism. 
     
     
         9 . The method according to  claim 5 , wherein:
 a) the single nucleotide polymorphism in the adenosine monophosphate deaminase (AMPD1) gene is 34C>T;   b) the single nucleotide polymorphism in the aminoimidazole carboxamide ribonucleotide transformylase (ATIC) gene is 347 C>G; and   c) the single nucleotide polymorphism in the inosine triphosphate pyrophosphatase (ITPA) gene is 94 C>A.   
     
     
         10 . The method according to  claim 5 , wherein the presence of at least one genotype selected from MTHFD1 1958 G-allele carrier, AMPD1 34 T-allele carrier, ITPA 94 CC genotype, and ATIC 347 CC genotype is indicative of clinical responsiveness to the antifolate therapy. 
     
     
         11 . The method according to  claim 1 , wherein the polymorphism is detected by microarray analysis, DNA sequencing or allele specific PCR techniques. 
     
     
         12 . The method according to  claim 1 , wherein the method further comprises the step of: a) determining the clinical responsiveness to the antifolate therapy by correlating the presence of the polymorphism with a predefined responsiveness value associated with each particular polymorphism. 
     
     
         13 . The method according to  claim 12 , wherein a responsiveness score is calculated as the sum of the responsiveness values for each polymorphism. 
     
     
         14 . The method according to  claim 12 , wherein the method further comprises the step of:
 b) determining a set of clinical parameter values comprising at least one of:
 i) the gender of the subject and optionally the pre- or postmenopausal status of a female subject; 
 ii) DAS at baseline, wherein DAS is disease activity score as defined by the European League Against Rheumatism; 
 iii) the presence or absence of Rheumatoid factor; and, 
 iv) smoking status; and, 
   c) determining the clinical responsiveness to the antifolate therapy by correlating the values determined in steps a) and b) with a predefined responsiveness value associated with each particular polymorphism and parameter value.   
     
     
         15 . The method according to  claim 14 , wherein a responsiveness score is calculated as the sum of the responsiveness values for each polymorphism and for each parameter value. 
     
     
         16 . The method according to  claim 15 , wherein the responsiveness values assigned to the respective polymorphisms and parameter values are defined as between 50% and 150% of the values in a)-i):
 a) 0 for male gender; 1 for female gender;   b) 0 for DAS at baseline <3.8;
 2.8 for DAS at baseline >3.8, but <5.1; 
 3.4 for DAS at baseline >5.1; 
   c) 0 for Rheumatoid factor negative and non-smoker;
 0.8 for Rheumatoid factor negative and smoker; 
 0.75 for Rheumatoid factor positive and non-smoker; 
 2.2 for Rheumatoid factor positive and smoker; 
   d) 0.98 for MTHFD1 1958 AA genotype;   e) 1.2 for AMPD1 34 CC genotype;   f) 1.7 for ITPA A-allele carrier;   h) 1.1 for ATIC 347 G-allele carrier; and,   i) 0 for other genotypes;   
       and whereby the maximum responsiveness score is 11.5. 
     
     
         17 . The method according to  claim 16 , wherein the responsiveness values assigned to the respective polymorphisms and parameter values are:
 a) 0 for male gender; 1 for female gender;   b) 0 for DAS at baseline <3.8;
 3 for DAS at baseline >3.8, but <5.1; 
 3.5 for DAS at baseline >5.1; 
   c) 0 for Rheumatoid factor negative and non-smoker;
 1 for Rheumatoid factor negative and smoker; 
 1 for Rheumatoid factor positive and non-smoker; 
 2 for Rheumatoid factor positive and smoker; 
   d) 1 for MTHFD1 1958 AA genotype;   e) 1 for AMPD1 34 CC genotype;   f) 2 for ITPA A-allele carrier;   h) 1 for ATIC 347 G-allele carrier; and,   i) 0 for other genotypes.   
     
     
         18 . The method according to  claim 16 , wherein a responsiveness score of a subject of 6 or more indicates that the subject is not responsive to antifolate therapy. 
     
     
         19 . The method according to  claim 18 , wherein a responsiveness score of a subject of more than 3.5 but less than 6 indicates that the subject has an intermediate responsiveness to antifolate therapy. 
     
     
         20 . The method according to  claim 1 , wherein the individual is an individual with recent onset undifferentiated arthritis. 
     
     
         21 . The method according to  claim 1 , wherein said antifolate is methotrexate. 
     
     
         22 . A kit comprising at least one oligonucleotide capable of hybridizing to, or adjacent to, a polymorphic site in a DNA sequence present in the methylenetetrahydrofolate dehydrogenase (MTHFD1) gene. 
     
     
         23 . The kit according to  claim 22 , wherein the polymorphism is the single nucleotide polymorphism 1958G>A. 
     
     
         24 . The kit according to  claim 22 , wherein the kit further comprises an oligonucleotide capable of hybridizing to, or adjacent to, a polymorphic site in a DNA sequence present in one or more genes selected from the group consisting of adenosine monophosphate deaminase (AMPD1), aminoimidazole carboxamide ribonucleotide transformylase (A TIC), inosine triphosphate pyrophosphatase (ITPA). 
     
     
         25 . The kit according to  claim 24 , wherein the polymorphism one or more of
 a) the 34C>T single nucleotide polymorphism in the adenosine monophosphate deaminase (AMPD1) gene;   b) the 347 C>G single nucleotide polymorphism in the aminoimidazole carboxamide ribonucleotide transformylase (ATIC) gene; and,   c) the 94 A>C single nucleotide polymorphism in the inosine triphosphate pyrophosphatase (ITPA) gene.   
     
     
         26 . The kit according to  claim 22 , wherein the oligonucleotides are provided on a solid carrier. 
     
     
         27 . A method for determining a predicted clinical responsiveness to antifolate therapy in a subject afflicted with, or at risk of developing, arthritis, comprising the steps of:
 a) receiving at a computer one or more of the polymorphisms as defined in  claim 1 ;   b) receiving at a computer one or more of clinical parameter values for the individual comprising:
 i) the gender of the subject and optionally the pre- or postmenopausal status of a female subject; 
 ii) DAS at baseline, wherein DAS is disease activity score as defined by the European League Against Rheumatism; 
 iii) the presence or absence of Rheumatoid factor; and, 
 iv) smoking status; and, 
   c) correlating each of the polymorphisms and parameter values and with a responsiveness value associated with each particular parameter value.   
     
     
         28 . A computer comprising a processor and memory, the processor being arranged to read from said memory and write into said memory, the memory comprising data and instructions arranged to provide said processor with the capacity to perform a method of determining a predicted responsiveness of a subject to antifolate therapy, wherein the method comprises the steps of:
 a) determining for the subject one or more of the polymorphisms as defined in  claim 1 ;   b) determining for the subject one or more of clinical parameter values for the individual comprising:
 i) the gender of the subject and optionally the pre- or postmenopausal status of a female subject; 
 ii) DAS at baseline, wherein DAS is disease activity score as defined by the European League Against Rheumatism; 
 iii) the presence or absence of Rheumatoid factor; and, 
 smoking status; and, 
   c) determining the predicted responsiveness of a subject to antifolate therapy by correlating the parameter values determined in steps a) and b) with a predefined responsiveness value associated with each particular parameter value.   
     
     
         29 . The computer according to  claim 28 , wherein the computer has an input connected to a sample analyzer for receiving analysis data signals of a biological sample, and wherein the processor is arranged for determining from said analysis data signals: i) one or more of the polymorphisms as defined in any one of  claim 1 ; and, ii) the presence or absence of Rheumatoid factor. 
     
     
         30 . The computer according to  claim 28 , wherein the processor is arranged for calculating a responsiveness score as the sum of the responsiveness values for each parameter value. 
     
     
         31 . A sample analyzer comprising a computer in accordance with  claim 28 . 
     
     
         32 . A computer program product comprising data and instructions and arranged to be loaded in a memory of a computer, the data and instructions being arranged to provide said computer with the capacity to perform a method of determining a predicted responsiveness of a subject to antifolate therapy, wherein the method comprises the steps of:
 a) determining for the subject one or more of the polymorphisms as defined in  claim 1 ;   b) determining for the subject one or more of clinical parameter values for the individual comprising:
 i) the gender of the subject and optionally the pre- or postmenopausal status of a female subject; 
 ii) DAS at baseline, wherein DAS is disease activity score as defined by the European League Against Rheumatism; 
 iii) the presence or absence of Rheumatoid factor; and, 
 iv) smoking status; and, 
   c) determining the predicted responsiveness of a subject to antifolate therapy by correlating the parameter values determined in steps a) and b) with a predefined responsiveness value associated with each particular parameter value.   
     
     
         33 . A data carrier provided with a computer program product as claimed in  claim 32 . 
     
     
         34 . A method for determining a predicted responsiveness of a subject to antifolate therapy, the method comprising:
 a) receiving characteristics of a subject, the characteristics comprising at least two of: a polymorphism as defined in  claim 1 , and an indicator of a presence or absence of Rheumatoid factor in a blood sample from the subject;   b) assigning a responsiveness value to each of the characteristics; and   c) determining a predicted responsiveness of the subject to antifolate therapy, the predicted responsiveness being determined based at least partly on the determined responsiveness values.   
     
     
         35 . A method according to  claim 34 , wherein at least some of the characteristics are received from a blood sample analyzer. 
     
     
         36 . The method according to  claim 34 , wherein the subject is a subject with recent onset undifferentiated arthritis. 
     
     
         37 . The method according to  claim 34 , wherein the received characteristics include indicators of least one of: i) the gender of the subject and optionally the pre- or postmenopausal status of a female subject; ii) DAS at baseline, wherein DAS is disease activity score as defined by the European League Against Rheumatism; and, iii) smoking status. 
     
     
         38 . The method according to  claim 37 , wherein at least some of the characteristics are entered into a user interface that communicates the characteristics via one or more networks. 
     
     
         39 . The method according to  claim 34 , further comprising transmitting the predicted responsiveness via email. 
     
     
         40 . The method according to  claim 34 , further comprising transmitting the predicted responsiveness to a server that is accessible to authorized users. 
     
     
         41 . The method according to  claim 40 , wherein authorized users comprise at least one of the subject and a healthcare provider for the subject. 
     
     
         42 . The method according to  claim 34 , wherein assigning comprises accessing data in a computer memory associating responsiveness values with characteristics. 
     
     
         43 . The method according to  claim 34 , wherein the determined predicted responsiveness is expressed as a percentage chance that the subject responds to antifolate therapy. 
     
     
         44 . A system for determining a predicted responsiveness of an subject to antifolate therapy, the system comprising:
 a) means for receiving characteristics of a subject, the characteristics comprising at least two of: a polymorphisms as defined in  claim 1 , and an indicator of a presence or absence of Rheumatoid factor in a blood sample from the subject;   b) means for assigning a responsiveness value to each of the characteristics; and,   c) means for determining a predicted responsiveness of the subject to antifolate therapy, the predicted responsiveness being determined based at least partly on the determined responsiveness values.   
     
     
         45 . A system for determining a predicted responsiveness of an subject to antifolate therapy, the system comprising:
 a) a blood sample analyzer configured to analyze a blood sample provided by the individual and determine at least two of: a polymorphisms as defined in  claim 1 , and an indicator of a presence or absence of Rheumatoid factor in a blood sample from the subject; and,   b) a computing device configured to assign a responsiveness value to each of the indicators determined by the blood sample analyzer, wherein the computing device accesses data stored in a memory associating ranges of values for each of the indicators with respective responsiveness values, the computing device further configured to determine a predicted responsiveness of the subject to antifolate therapy based at least partly on the assigned responsiveness values.   
     
     
         46 . The system according to  claim 45 , wherein the blood sample analyzer is located remote from the computing device. 
     
     
         47 . The system according to  claim 45 , wherein the indicators are transmitted to the computing device via a network communication link. 
     
     
         48 . The system according to  claim 45 , wherein the blood sample analyzer is located proximate the computing device. 
     
     
         49 . The system according to  claim 45 , wherein the computing device is further configured to transmit one or more electronic messages indicating the determined predicted responsiveness. 
     
     
         50 . The system according to  claim 45 , wherein the computing device receives the indicators via a web interface in data communication with the computing device. 
     
     
         51 . The system of  claim 45 , wherein the computing device is further configured to assign a risk value to indicators indicating at least one of: i) the gender of the subject and optionally the pre- or postmenopausal status of a female subject; DAS at baseline, wherein DAS is disease activity score as defined by the European League Against Rheumatism; and, iii) smoking status.