Diagnostic biomarkers for detecting, subtyping, and/or assessing progression of multiple sclerosis

Abstract

Disclosed are methods, compositions and kits for detecting Multiple Sclerosis (MS) as well as for distinguishing relapsing-remitting (RRMS) and secondary progressive (SPMS) MS subtypes with high overall accuracy. Autoantibody antigens and biomarkers, for the diagnosis of MS in general, RRMS and SPMS, as well as for the identification of a subject at risk for developing MS, and for the generation of patient-specific MS autoantibody biomarker profiles are also provided.

1 . A method for detecting Multiple Sclerosis (MS) diagnostic autoantibodies in a subject, the method comprising:
 (a) contacting an immunoglobulin-containing biological sample from the subject with a system comprising one or more autoantigens to form a reaction mixture, under conditions that allow for formation in the reaction mixture of an immunocomplex between each autoantigen and its corresponding autoantibody, if its corresponding autoantibody is present in the sample,
 wherein the one or more autoantigens comprise BC099907.1, NM_201998.1, and BC028006.1; and 
   (b) detecting presence or absence of immunocomplexes in the reaction mixture, wherein formation of an immunocomplex between an autoantibody and its corresponding autoantigen indicates presence of the autoantibody in the biological sample.   
     
     
         2 . A method of generating a subject-specific, MS-specific autoantibody profile for a subject, the method comprising:
 (a) contacting an immunoglobulin-containing biological sample from the subject with a system comprising one or more autoantigens to form a reaction mixture, under conditions that allow for formation in the reaction mixture of an immunocomplex between each autoantigen and its corresponding autoantibody, if its corresponding autoantibody is present in the sample,
 wherein the one or more autoantigens comprise BC099907.1, NM_201998.1, and BC028006.1; 
   (b) detecting presence or absence of immunocomplexes in the reaction mixture, wherein formation of an immunocomplex between an autoantibody and its corresponding autoantigen indicates presence of the autoantibody in the sample; and   (c) generating a subject-specific MS-specific autoantibody profile of autoantibodies present in the biological sample.   
     
     
         3 . The method of  claim 1 , wherein the one or more autoantigens further comprise at least one selected from the group consisting of NM_020317.2, NM_001008737.1, NM_004912.3, BC001419.1, NM_002642.1, PV4202, and NM_016011.2. 
     
     
         4 . The method of  claim 1 , wherein the one or more autoantigens further comprise at least one selected from the group consisting of BC001419.1 and NM_016011.2. 
     
     
         5 . The method of  claim 1 , wherein the subject is a human. 
     
     
         6 . The method of  claim 1 , wherein the biological sample is selected from the group consisting of whole blood, plasma, serum, cerebrospinal fluid, saliva, and sputum. 
     
     
         7 . (canceled) 
     
     
         8 . The method of  claim 1 , wherein at least one autoantigen is attached to a solid substrate. 
     
     
         9 . The method of  claim 1 , wherein each one of the autoantigens is attached to a solid substrate and is in the form of an array. 
     
     
         10 . The method of  claim 9 , wherein at least one applies: the array is a microarray; the solid substrate is a nitrocellulose-coated glass slide. 
     
     
         11 . (canceled) 
     
     
         12 . The method of  claim 1 , wherein the immunocomplex is detected using an immunoassay. 
     
     
         13 . The method of  claim 12 , wherein the immunoassay comprises a competition assay, direct immunoassay, indirect immunoassay, immunoprecipitation, immunoblotting, or sandwich immunoassay. 
     
     
         14 . The method of  claim 1 , wherein the subject is advised to be administered a therapeutic agent or receive therapeutic intervention for MS. 
     
     
         15 . The method of  claim 1 , further comprising administering to the subject a therapeutic agent or a therapeutic intervention to treat MS. 
     
     
         16 . A method of subtyping MS in a subject, the method comprising: 
       (a) contacting an immunoglobulin-containing biological sample from the subject with a system comprising a relapsing-remitting MS (RRMS)-specific autoantigen and/or a secondary progressive (SPMS)-specific autoantigen to form a reaction mixture, under conditions that allow for formation in the reaction mixture of an immunocomplex between each autoantigen and its corresponding autoantibody, if its corresponding autoantibody is present in the sample,
 wherein the RRMS-specific autoantigen comprises at least one selected from the group consisting of NM_152729.2, BC024289.1, BC020233.1, BC030813.1, NM_144606.1, and NM_145253.1, and 
 wherein the SPMS-specific autoantigen comprises at least one selected from the group consisting of NP_002497.2, NP_001001547.1, NM_004493.1, NM_018464.2, BC010467.1, NM_005409.3, BC048299.1, NM_022788.2, NP_000556.1, and BC093661 1. 
 
       (b) detecting presence or absence of immunocomplcxes in the reaction mixture, wherein formation of an immunocomplex between an autoantibody and its corresponding autoantigen indicates presence of the autoantibody in the sample; 
       wherein presence of at least one RRMS-specific immunocomplex in the reaction mixture indicates a RRMS subtype, and 
       wherein presence of at least one SPMS-specific immunocomplex in the reaction mixture indicates a SPMS subtype 
     
     
         17 . A method of identifying the pathological progression of MS in a subject in need thereof, the method comprising: 
       (a) contacting an immunoglobulin-containing biological sample from the subject with a system comprising a relapsing-remitting MS (RRMS)-specific autoantigen and/or a secondary progressive (SPMS)-specific autoantigen to form a reaction mixture, under conditions that allow for formation in the reaction mixture of an immunocomplex between each autoantigen and its corresponding autoantibody, if its corresponding autoantibody is present in the sample,
 wherein the RRMS-specific autoantigen comprises at least one selected from the group consisting of NM_152729.2, BC024289.1, BC020233.1, BC030813.1, NM_144606.1, and NM_145253.1, and 
 wherein the SPMS-specific autoantigen comprises at least one selected from the group consisting of NP_002497.2, NP_001001547.1, NM_004493.1, NM_018464.2, BC010467.1, NM_005409.3, BC048299.1, NM_022788.2, NP_000556.1, and BC093661.1; 
 
       (b) detecting presence or absence of immunocomplexes in the reaction mixture, wherein formation of an immunocomplex between an autoantibody and the corresponding autoantigen indicates presence of the autoantibody in the sample; 
       wherein presence of at least one RRMS-specific immunocomplex in the reaction mixture indicates a RRMS subtype, and 
       wherein presence of at least one SPMS-specific immunocomplex in the reaction mixture indicates a SPMS subtype. 
     
     
         18 . A method of identifying a subject at risk of suffering from RRMS, the method comprising: 
       (a) contacting an immunoglobulin-containing biological sample from the subject with a system comprising a relapsing-remitting MS (RRMS)-specific autoantigen, under conditions that allow for formation in the reaction mixture of an immunocomplex between each autoantigen and its corresponding autoantibody, if its corresponding autoantibody is present in the sample, wherein the RRMS-specific autoantigen comprises at least one selected from the group consisting of NM_152729.2, BC024289.1, BC020233.1, BC030813.1, NM_144606.1, and NM_145253.1; 
       (b) detecting presence or absence of immunocomplexes in the reaction mixture, wherein formation of an immunocomplex between an autoantibody and its corresponding autoantigen indicates presence of the autoantibody in the sample; 
       wherein presence of at least one RRMS-specific immunocomplex in the reaction mixture indicates the subject has risk of suffering from or developing RRMS. 
     
     
         19 . A method of identifying a subject at risk of suffering from SPMS, the method comprising: 
       (a) contacting an immunoglobulin-containing biological sample from the subject with a system comprising one or more secondary progressive (SPMS)-spccific autoantigens to form a reaction mixture, under conditions that allow for formation in the reaction mixture of an immunocomplex between each autoantigen and its corresponding autoantibody, if its corresponding autoantibody is present in the sample,
 wherein the one or more SPMS-spccific autoantigens comprise at least one selected from the group consisting of NP_002497.2, NP_001001547.1, NM_004493.1, NM_018464.2, BC010467.1, NM_005409.3, BC048299.1, NM_022788.2, NP_000556.1, and BC093661.1; 
 
       (b) detecting presence or absence of immunocomplexes in the reaction mixture, wherein formation of an immunocomplex between an autoantibody and its corresponding autoantigen indicates presence of the autoantibody in the sample; 
       wherein presence of at least one SPMS-specific immunocomplex in the reaction mixture indicates that the subject has risk of suffering from or developing SPMS. 
     
     
         20 . The method of  claim 16 , wherein the RRMS-specific autoantigen comprises at least one selected from the group consisting of NM_152729.2, BC024289.1, and BC020233.1. 
     
     
         21 . The method of  claim 16 , wherein the RRMS-specific autoantigen further comprises at least one selected from the group consisting of NM_005151.2, NM_004987.3, NM_003141.2, and NP_002167.1. 
     
     
         22 . The method of  claim 16 , wherein the one or more SPMS-specific autoantigens comprise at least one selected from the group consisting of NP_002497.2, NP_001001547.1, NM_004493.1, NM_018464.2, and NP_000556.1. 
     
     
         23 . The method of  claim 16 , wherein the subject is a human. 
     
     
         24 . The method of  claim 16 , wherein the biological sample is selected from the group consisting of whole blood, plasma, serum, cerebrospinal fluid, saliva, and sputum. 
     
     
         25 . (canceled). 
     
     
         26 . The method of  claim 16 , wherein at least one autoantigen is attached to a solid substrate. 
     
     
         27 . The method of  claim 16 , wherein each one of the autoantigens is attached to a solid substrate and is in the form of an array. 
     
     
         28 . The method of  claim 27 , wherein at least one applies: the array is a microarray; the solid substrate is a nitrocellulose-coated glass slide. 
     
     
         29 . (canceled). 
     
     
         30 . The method of  claim 16 , wherein the immunocomplex is detected using an immunoassay. 
     
     
         31 . The method of  claim 30 , wherein the immunoassay comprises a competition assay, direct immunoassay, indirect immunoassay, immunoprecipitation, immunoblotting, or sandwich immunoassay. 
     
     
         32 . The method of  claim 16 , wherein the subject is advised to be administered a therapeutic agent or receive therapeutic intervention for MS. 
     
     
         33 . The method of  claim 16 , further comprising administering to the subject a therapeutic agent or a therapeutic intervention to treat MS. 
     
     
         34 . A kit for detecting MS diagnostic biomarkers, the kit comprising: 
       (a) an array comprising a solid substrate and one or more autoantigens immobilized onto the solid substrate, wherein the one or more autoantigens in the array comprise at least one selected from the first autoantigen group consisting of: BC099907.1, NM_201998.1, BC028006.1, NM_020317.2, NM_003636 1, BC003065.1, NM_001008737.1, XM_003960444.1, BC029796 1, NM_152716.1, XM_379114.1, BC022258.1, BC002733.2, NM_004912.3, BC001419.1, NM_002642.1, PV4202, PV4337, XM_378514.1, XM_086879.4, BC015514.1, NM_005151.2, BC016380.1, BC032451.1, NM_175907.3, BC073782.1, NM_004987.3, BC022362.1, NM_004302, NM_003141.2, NM_005522.3, NM_016011.2, NM_005734.1, NM_004329, NP_002167.1, BC014991.1, NM_004527.2, BC014271.2, XM_378660.1, NM_020467.2, BC033792.1, NM_007255.1, BC017054.1, NM_180699.1, NM_172159.2, NM_199183.1, BC002448.2, NM_005435.2, BC006105.1, and NM_005371.2; 
       (b) assay reagents for detection of immunocomplexes formed by binding of the immobilized autoantigens of (a) to the MS diagnostic autoantibody biomarkers in an immunoglobulin-containing biological sample from a subject; and 
       (c) a package labeling indicating a diagnosis of MS in the subject upon detecting formation of at least one immunocomplex from the first autoantigen group. 
     
     
         35 . The kit of  claim 34 , wherein the one or more autoantigens in the array comprise BC099907.1, NM_201998.1, and BC028006.1. 
     
     
         36 . The kit of  claim 34 , wherein the one or more autoantigens in the array further comprise at least one selected from the group consisting of NM_020317.2, NM_001008737.1, NM_004912.3, BC001419.1, NM_002642.1, PV4202, and NM_016011.2. 
     
     
         37 . The kit of  claim 34 , wherein the one or more autoantigens in the array further comprise at least one selected from the group consisting of BC001419.1 and NM_016011.2. 
     
     
         38 . The kit of  claim 34 , wherein the only autoantigens in the array are the at least one selected from the first autoantigen group. 
     
     
         39 . The kit of  claim 34 , wherein the only autoantigens in the array are BC099907.1, NM_201998.1, and BC028006.1. 
     
     
         40 . The kit of  claim 34 , wherein the only autoantigens in the array are BC099907.1, NM_201998.1, BC028006.1, and at least one selected from the group consisting of NM_020317.2, NM_001008737.1, NM_004912.3, BC001419.1, NM_002642.1, PV4202, and NM_016011.2. 
     
     
         41 . The kit of  claim 34 , wherein the only autoantigens in the array are BC099907.1, NM_201998 1. BC028006.1, and at least one selected from the group consisting of BC001419.1 and NM_016011.2. 
     
     
         42 . The kit of  claim 34 , wherein the package labeling indicates that the subject has about 90% risk of developing MS within the next 1 to 10 years when immunocomplexes are detected for all three of BC099907.1, NM_201998.1, and BC028006.1. 
     
     
         43 . The kit of  claim 34 , wherein at least one applies: the array is an ordered microarray: the solid substrate is a nitrocellulose-coated glass slide. 
     
     
         44 . (canceled) 
     
     
         45 . A kit for detecting MS diagnostic biomarkers, the kit comprising:
 (a) an array comprising a solid substrate and one or more autoantigens immobilized onto the solid substrate, wherein the one or more autoantigens in the array comprise at least one selected from the following groups:
 a RRMS-specific autoantigen group comprising at least one selected from the group consisting of NM_152729.2, BC024289.1, BC020233.1, BC030813.1, NM_144606.1, and NM_145253.1, and 
 a SPMS-specific autoantigen group comprising at least one selected from the group consisting of NP_002497.2, NP_001001547.1, NM_004493.1, NM_018464.2, BC010467.1, NM_005409.3, BC048299.1, NM_022788.2, NP_000556.1, and BC093661.1; 
   (b) assay reagents for detection of immunocomplexes formed by binding of the immobilized autoantigens of (a) to the MS diagnostic autoantibody biomarkers in an immunoglobulin-containing biological sample from a subject; and   (c) a package labeling indicating a diagnosis of RRMS in the subject upon detecting formation of at least one immunocomplex from the RRMS-specific autoantigen group; and/or a diagnosis of SPMS in the subject upon detecting formation of at least one immunocomplex from the SPMS-specific autoantigen group.   
     
     
         46 . The kit of  claim 45 , wherein the RRMS-specific autoantigen comprises at least one selected from the group consisting of NM_152729.2, BC024289.1, and BC020233.1. 
     
     
         47 . The kit of  claim 45 , wherein the RRMS-specific autoantigen further comprises at least one selected from the group consisting of NM_005151.2, NM_004987.3, NM_003141.2, and NP_002167.1. 
     
     
         48 . The kit of  claim 45 , wherein the SPMS-specific autoantigen comprises at least one selected from the group consisting of NP_002497.2, NP_001001547.1, NM_004493.1, NM_018464.2, and NP_000556.1. 
     
     
         49 . The kit of  claim 45 , wherein the only autoantigens in the array are the at least one selected from the RRMS-specific autoantigen group and the SPMS-specific autoantigen group. 
     
     
         50 . The kit of  claim 45 , wherein the only autoantigens in the array are selected from the group consisting of:
 (i) at least one selected from the group consisting of NM_152729.2, BC024289.1, BC020233.1, BC030813.1, NM_144606.1, and NM_145253.1;   (ii) at least one selected from the group consisting of NM_152729.2, BC024289.1, and BC020233.1;   (iii) at least one selected from the group consisting of NM_005151.2, NM_004987.3, NM_003141.2, and NP_002167.1;   (iv) at least one selected from the group consisting of NP_002497.2, NP_001001547.1, NM_004493.1, NM_018464.2, BC010467.1, NM_005409.3, BC048299.1, NM_022788.2, NP_000556.1, and BC093661.1;   (v) at least one selected from the group consisting of NP_002497.2, NP_001001547.1, NM_004493.1, NM_018464.2, and NP_000556.1;   (vi) any combinations of (i)-(v).   
     
     
         51 . The kit of  claim 45 , wherein at least one applies: the array is an ordered microarray; the substrate is a nitrocellulose-coated glass slide. 
     
     
         52 . (canceled)