Causative agents and diagnostic methods relating to rheumatoid arthritis
Methods, reagents and compositions thereof for predicting RA onset in susceptible individuals, diagnosing RA onset, and/or evaluating efficacy of a therapeutic regimen for treating RA are described herein. Determining the amount of a particular bacterial species comprising SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3 (SEQ ID NO: 1+ bacteria) serves as a biomarker for the above indications.
1. A method for diagnosing and treating new onset rheumatoid arthritis (NORA) in a subject, the method comprising:
a) obtaining a biological sample from the subject;
b) detecting in the biological sample an increased amount of a Prevotella -related species of bacteria relative to that of a biological sample obtained from a control subject, wherein the Prevotella -related species of bacteria comprises SEQ ID NO: 1 or a variant thereof SEQ ID NO: 2 or SEQ ID NO: 3, thereby diagnosing NORA in the subject; and
c) administering a nonsteroidal anti-inflammatory drug (NSAID), a disease-modifying anti-rheumatic drug (DMARD), a steroid, an antibiotic, or an analgesic to the subject diagnosed with NORA.
2. The method of claim 1 , wherein the subject has a familial history of RA and/or exhibits at least one of the seven diagnostic criteria used to diagnose RA selected from the group consisting of morning stiffness in and around joints lasting at least 1 hour before maximal improvement; soft tissue swelling of 3 or more joint areas observed by a physician; swelling of the hand joints; symmetric swelling; rheumatoid nodules; elevated levels of serum rheumatoid factor (RF); and radiographic changes in hand and/or wrist joints.
3. The method of claim 1 , wherein the biological sample is fecal material, biopsies of specific organ tissues, synovial fluid, or synovial fluid biopsies.
4. The method of claim 3 , wherein the specific organ tissues comprise large and small intestinal biopsies.
5. The method of claim 1 , wherein the amount of the Prevotella -related species of bacteria is determined by nucleic acid sequencing.
6. The method of claim 5 , wherein the nucleic acid sequencing is massively parallel 16S rRNA pyrosequencing.
7. The method of claim 5 , wherein the nucleic acid sequencing detects 16S rRNA comprising SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3 and the amount of the 16S rRNA comprising SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3 is indicative of the amount of Prevotella -related species of bacteria in the biological sample.
8. The method of claim 1 , wherein the Prevotella -related species of bacteria is P. copri.
9. The method of claim 1 , wherein the amount of the Prevotella -related species of bacteria is detected using a reagent that specifically binds to the Prevotella -related species of bacteria or a nucleic acid sequence thereof.
10. The method of claim 9 , wherein the reagent is selected from the group consisting of an antibody, an antibody derivative, an antibody fragment, a nucleic acid probe, an oligonucleotide, and an oligonucleotide primer pair specific for Prevotella -related species of bacteria comprising SEQ ID NO: 1, SEQ ID NO: 2, or SEQ ID NO: 3.
11. The method of claim 9 , wherein the reagent is an oligonucleotide primer pair of SEQ ID NO: 4 and SEQ ID NO: 5.
12. The method of claim 9 , wherein detecting of the increased amount of the Prevotella -related species of bacteria includes at least one assay selected from the group consisting of nucleic acid sequencing, PCR amplification, a competitive binding assay, a non-competitive binding assay, a radioimmunoassay, immunohistochemistry, an enzyme-linked immunosorbent assay (ELISA), a sandwich assay, a gel diffusion immunodiffusion assay, an agglutination assay, dot blotting, a fluorescent immunoassay such as fluorescence-activated cell sorting (FACS), a chemiluminescence immunoassay, an immunoPCR immunoassay, a protein A or protein G immunoassay, and an immunoelectrophoresis assay.
13. The method of claim 1 , further comprising processing the biological sample and analyzing the processed biological sample generated thereby to determine the amount of Prevotella -related species in the biological sample.
14. The method of claim 13 , wherein the processing comprises extracting nucleic acids from the biological sample.
15. The method of claim 1 , further comprising obtaining a sample of T cells from the subject to identify T cells specific for the Prevotella -related species of bacteria in the subject.
16. The method of claim 1 , wherein the disease-modifying anti-rheumatic drug (DMARD) is methotrexate.