Assessment and reduction of risk of graft-versus-host disease

Abstract

Methods of assessing and reducing risk of graft versus host disease (GVHD) based on gene expression profiling are described, as well as methods of selecting a suitable transplant donor. Corresponding reagents and kits are also described.

1 . A method of assessing risk, of a candidate human transplant donor, of inducing graft versus host disease (GVHD) in a human transplant recipient, said method comprising:
 (a) comparing a candidate gene expression profile derived from a CD4 +  and/or CD8 +  T cell sample from said candidate human transplant donor to a corresponding reference gene expression profile, wherein said candidate gene expression profile comprises a candidate expression value for a TCIRG1 nucleic acid; wherein said reference gene expression profile comprises a reference expression value for a TCIRG1 nucleic acid, said reference gene expression profile being derived from a comparison of: (i) a GVHD+ expression profile comprising a GVHD+ expression value for a TCIRG1 nucleic acid derived from a CD4 +  and/or CD8 +  T cell sample obtained from a human transplant donor known to have induced GVHD in a human transplant recipient with (ii) a GVHD− expression profile comprising a GVHD− expression value for a TCIRG1 nucleic acid derived from a CD4 +  and/or CD8 +  T cell sample obtained from a human transplant donor known to have not induced GVHD in a human transplant recipient, whereby said reference expression value is determined as being (A) the level of expression midway between said GVHD+ expression value and said GVHD− expression value whereby the midway level separates a GVHD+ class comprising said GVHD+ expression value from a GVHD− class comprising said GVHD− expression value; (B) the level of expression between said GVHD+ expression value and said GVHD− expression value defined as separating expression values into GVHD+ and GVHD− classes on the basis of discriminatory analysis; or (C) both (A) and (B); and   (b) assessing risk of said candidate human transplant donor of inducing GVHD in a human transplant recipient in accordance with said comparing step of said candidate gene expression profile with said reference gene expression profile,   wherein said candidate expression value and said reference expression value are obtained by determining the level of expression of said TCIRG1 nucleic acid.   
     
     
         2 . The method of  claim 1 , wherein said CD4 +  and/or CD8 +  T cell sample is a CD4 +  T cell sample. 
     
     
         3 . The method of  claim 1 , wherein said TCIRG1 nucleic acid comprises the coding sequence of SEQ ID NO: 119. 
     
     
         4 . The method of  claim 1 , wherein said reference expression value is determined as being (A) the level of expression midway between said GVHD+ expression value and said GVHD− expression value. 
     
     
         5 . The method of  claim 1 , wherein a candidate expression value within said GVHD+class is indicative that said candidate human transplant donor has an increased risk of inducing GVHD in a transplant recipient. 
     
     
         6 . The method of  claim 1 , wherein a candidate expression value within said GVHD− class is indicative that said candidate human transplant donor has a reduced risk of inducing GVHD in a transplant recipient. 
     
     
         7 . The method of  claim 1 , wherein the reference gene expression profile is contained within a database. 
     
     
         8 . The method of  claim 1 , wherein said comparing is carried out using a computer algorithm. 
     
     
         9 . The method of  claim 2 , wherein said candidate gene expression profile further comprises a candidate expression value for one or more nucleic acid(s) selected from a CD151 nucleic acid, an EP300 nucleic acid, an FNBP3 nucleic acid, an NMI nucleic acid, a SIL nucleic acid, a SMAD3 nucleic acid, an AKT2 nucleic acid, a FURIN nucleic acid, an ATBFI nucleic acid, a TGIF nucleic acid and a TGFBI nucleic acid, wherein said reference gene expression profile further comprises a reference expression value for said one or more nucleic acid(s), and wherein said candidate expression value and said reference expression value are obtained by determining the level of expression of said one or more nucleic acid(s). 
     
     
         10 . The method of  claim 2 , wherein said candidate gene expression profile further comprises a candidate expression value for one or more nucleic acid(s) selected from a RAN nucleic acid, a FOSB nucleic acid, a MAP2K6 nucleic acid, a SERPINB2 nucleic acid, a TLR4 nucleic acid, a CD3D nucleic acid, a GAB2 nucleic acid, a MAPK81PI nucleic acid, an SMO nucleic acid, a CD151 nucleic acid, an EP300 nucleic acid, an FNBP3 nucleic acid, an IL6R nucleic acid, an NMI nucleic acid, a PDK2 nucleic acid, a PPP1R16B nucleic acid, an SIL nucleic acid, an SNRP70 nucleic acid, an STK38 nucleic acid, a SMAD3 nucleic acid, a PIAS4 nucleic acid, an ADDI nucleic acid, a BAG3 nucleic acid, a VEGF nucleic acid, a YYI nucleic acid, an AKT2 nucleic acid, a FURIN nucleic acid, an ATBFI nucleic acid, a CCNDI nucleic acid, a CHERP nucleic acid, a CSDA nucleic acid, a DOK2 nucleic acid, a FOXJI nucleic acid, an HEXA nucleic acid, a LAMP2 nucleic acid, an MCAM nucleic acid, an NFKB2 nucleic acid, a PTGER4 nucleic acid, a RFXANK nucleic acid, a VIM nucleic acid, a CDC25B nucleic acid, a TGIF nucleic acid and a TGFBI nucleic acid, wherein said reference gene expression profile further comprises a reference expression value for said one or more nucleic acid(s), and wherein said candidate expression value and said reference expression value are obtained by determining the level of expression of said one or more nucleic acid(s). 
     
     
         11 . The method of  claim 10 , wherein said one or more nucleic acid(s) is selected from a SMAD3 nucleic acid, an ATBFI nucleic acid, an AKT2 nucleic acid, a CD151 nucleic acid, an SIL nucleic acid, an FNBP3 nucleic acid, an EP300 nucleic acid, an NMI nucleic acid, a FURIN nucleic acid, a TGIF nucleic acid and a TGFBI nucleic acid. 
     
     
         12 . The method of  claim 11 , wherein said one or more nucleic acid(s) is a SMAD3 nucleic acid. 
     
     
         13 . The method of  claim 1 , wherein said CD4 +  and/or CD8 +  T cell sample is a CD4 +  T cell sample, wherein said candidate gene expression profile further comprises a candidate expression value for one or more nucleic acid(s) selected from a CXCR6 nucleic acid, a SMAD1 nucleic acid, a FAF1 nucleic acid, a BCAP31 nucleic acid, a RANBP2 nucleic acid, an SNRPN nucleic acid, a SOCS5 nucleic acid, an ANXA5 nucleic acid, a CD63 nucleic acid, a CD81 nucleic acid, a CKS2 nucleic acid, a CPE nucleic acid, a MAD nucleic acid, a MYCL1 nucleic acid, a PDCD8 nucleic acid, a RHOA nucleic acid, an SKP2 nucleic acid and a YWHAQ nucleic acid, and wherein said reference gene expression profile further comprises a reference expression value for said one or more nucleic acid(s), and wherein said candidate expression value and said reference expression value are obtained by determining the level of expression of said one or more nucleic acid(s). 
     
     
         14 . The method of  claim 13 , wherein said one or more nucleic acid is selected from a TGIF nucleic acid, an FNBP3 nucleic acid, a TGFBI nucleic acid, an EP300 nucleic acid and a FURIN nucleic acid. 
     
     
         15 . A method of selecting a transplant donor so as to reduce the risk of inducing GVHD in a recipient, said method comprising:
 (a) performing the method of assessing risk of  claim 1 ; and   (b) selecting said donor in accordance with said risk assessment.   
     
     
         16 . A method of selecting a transplant donor so as to reduce the risk of inducing GVHD in a recipient, said method comprising:
 (a) performing the method of assessing risk of  claim 2 ; and   (b) selecting said donor in accordance with said risk assessment.   
     
     
         17 . The method of  claim 15 , wherein said TCIRG1 nucleic acid comprises the coding sequence of SEQ ID NO: 119. 
     
     
         18 . The method of  claim 16 , wherein said candidate gene expression profile further comprises a candidate expression value for one or more nucleic acid(s) selected from a SMAD3 nucleic acid, an ATBFI nucleic acid, an AKT2 nucleic acid, a CD151 nucleic acid, an SIL nucleic acid, an FNBP3 nucleic acid, an EP300 nucleic acid, an NMI nucleic acid, a FURIN nucleic acid, a TGIF nucleic acid and a TGFBI nucleic acid. 
     
     
         19 . The method of  claim 18 , wherein said one or more nucleic acid(s) is a SMAD3 nucleic acid.