Determination of nfkb pathway activity using unique combination of target genes

Abstract

A bioinformatics process which provides an improved means to detect NFkB cellular signaling pathway in a subject, such as a human, based on the expression levels of at least six unique target genes of the NFkB cellular signaling pathway measured in a sample. The invention includes an apparatus comprising a digital processor configured to perform such a method, a non-transitory storage medium storing instructions that are executable by a digital processing device to perform such a method, and a computer program comprising program code means for causing a digital processing device to perform such a method. Kits are also provided for measuring expression levels of unique sets of NFkB cellular signaling pathway target genes.

1 - 20 . (canceled) 
     
     
         21 . A kit for determining an activity level of a NFkB cellular signaling pathway derived from a sample isolated from a subject suffering from a disease associated with an activated NFkB cellular signaling pathway, comprising:
 a set of polymerase chain reaction primers directed to at least six NFkB cellular signaling pathway target genes; and   a set of probes directed to the at least six NFkB cellular signaling pathway target genes;   wherein the at least six NFkB cellular signaling pathway target genes are selected from BCL2L1, BIRC3, CCL2, CCL3, CCL4, CCL5, CCL20, CCL22, CX3CL1, CXCL1, CXCL2, CXCL3, ICAM1, IL1B, IL6, IL8, IRF1, MMP9, NFKB2, NFKBIA, NFKBIE, PTGS2, SELE, STAT5A, TNF, TNFAIP2, TNIP1, TRAF1, and VCAM1.   
     
     
         22 . The kit of  claim 21 , wherein the at least six NFkB cellular signaling pathway target genes are selected from BIRC3, CCL2, CCL5, CCL20, CXCL1, CXCL2, CXCL3, ICAM1, IL6, IL8, IRF1, MMP9, NFKB2, NFKBIA, NFKBIE, TNF, TNFAIP2, TRAF1, and VCAM1. 
     
     
         23 . The kit of  claim 21 , wherein the at least six NFkB cellular signaling pathway target genes comprise at least three target genes selected from CCL2, CCL5, CCL20, CXCL1, CXCL2, CXCL3, ICAM1, IL6, IL8, MMP9, NFKB2, NFKBIA, and TNFAIP2. 
     
     
         24 . The kit of  claim 23 , wherein the at least three target genes are selected from CCL5, CXCL2, ICAM1, IL6, IL8, NFKBIA, and TNFAIP2. 
     
     
         25 . The kit of  claim 21 , wherein the disease is a cancer. 
     
     
         26 . The kit of  claim 25 , wherein the cancer is colon, breast, prostate, pancreatic, lung, brain, leukemia, lymphoma, or glioma. 
     
     
         27 . The kit of  claim 21 , further comprising a calibrated pathway model configured to determine the activity level of the NFkB cellular signaling pathway by:
 receiving data on the expression levels of the at least six NFkB cellular signaling pathway target genes amplified using the set of polymerase chain reaction primers and analyzed by the set of probes;   determining the level of a NFkB transcription factor element in the sample by comparing the received data on the expression levels of the at least six NFkB cellular signaling pathway target genes in the sample with expression levels of the at least six NFkB cellular signaling pathway target genes in the model which define an activity level of NFkB transcription factor element; and   determining the activity level of the NFkB cellular signaling pathway in the sample based on the determined NFkB transcription factor element level in the sample.   
     
     
         28 . The kit of  claim 27 , wherein the calibrated pathway model is a probabilistic model incorporating conditional probabilistic relationships that compare the expression levels of the at least six NFkB cellular signaling pathway target genes in the sample with expression levels of the at least six NFkB cellular signaling pathway target genes in the model which define a level of NFkB transcription factor element to determine the activity level of NFkB transcription factor element in the sample. 
     
     
         29 . The kit of  claim 27 , wherein the calibrated pathway model is a linear model incorporating relationships that compare the expression levels of the at least six NFkB cellular signaling pathway target genes in the sample with expression levels of the at least six NFkB cellular signaling pathway target genes in the model which define a level of NFkB transcription factor element to determine the activity level of NFkB transcription factor element in the sample. 
     
     
         30 . The kit of  claim 21 , wherein the probes are labeled. 
     
     
         31 . A method for determining an activity level of a NFkB cellular signaling pathway derived from a biological sample isolated from a subject suffering from a disease associated with an activated NFkB cellular signaling pathway, comprising:
 receiving a biological sample from the subject;   analyzing, using the kit of  claim 21 , expression levels of at least six NFkB cellular signaling pathway target genes selected from BCL2L1, BIRC3, CCL2, CCL3, CCL4, CCL5, CCL20, CCL22, CX3CL1, CXCL1, CXCL2, CXCL3, ICAM1, IL1B, IL6, IL8, IRF1, MMP9, NFKB2, NFKBIA, NFKBIE, PTGS2, SELE, STAT5A, TNF, TNFAIP2, TNIP1, TRAF1, and VCAM1 by contacting the biological sample with the set of polymerase chain reaction primers directed to the at least six NFkB cellular signaling pathway target genes and the set of probes directed to the at least six NFkB cellular signaling pathway target genes.   
     
     
         32 . The method of  claim 31 , wherein the at least six NFkB cellular signaling pathway target genes comprise at least three target genes selected from CCL2, CCL5, CCL20, CXCL1, CXCL2, CXCL3, ICAM1, IL6, IL8, MMP9, NFKB2, NFKBIA, and TNFAIP2. 
     
     
         33 . The method of  claim 32 , wherein the at least three target genes are selected from CCL5, CXCL2, ICAM1, IL6, IL8, NFKBIA, and TNFAIP2. 
     
     
         34 . The method of  claim 31 , wherein the disease is a cancer. 
     
     
         35 . The method of  claim 34 , wherein the cancer is colon, breast, prostate, pancreatic, lung, brain, leukemia, lymphoma, or glioma. 
     
     
         36 . The method of  claim 31 , wherein analyzing the expression levels of the at least six NFkB cellular signaling pathway target genes comprises a calibrated pathway model configured to determine the activity level of the NFkB cellular signaling pathway by:
 receiving data on the expression levels of the at least six NFkB cellular signaling pathway target genes amplified using the set of polymerase chain reaction primers and analyzed using the set of probes;   determining the level of a NFkB transcription factor element in the sample by comparing the received data on the expression levels of the at least six NFkB cellular signaling pathway target genes in the sample with expression levels of the at least six NFkB cellular signaling pathway target genes in the model which define an activity level of NFkB transcription factor element; and   determining the activity level of the NFkB cellular signaling pathway in the sample based on the determined NFkB transcription factor element level in the sample.   
     
     
         37 . The method of  claim 36 , wherein the calibrated pathway model is a probabilistic model incorporating conditional probabilistic relationships that compare the expression levels of the at least six NFkB cellular signaling pathway target genes in the sample with expression levels of the at least six NFkB cellular signaling pathway target genes in the model which define a level of NFkB transcription factor element to determine the activity level of NFkB transcription factor element in the sample. 
     
     
         38 . The method of  claim 36 , wherein the calibrated pathway model is a linear model incorporating relationships that compare the expression levels of the at least six NFkB cellular signaling pathway target genes in the sample with expression levels of the at least six NFkB cellular signaling pathway target genes in the model which define a level of NFkB transcription factor element to determine the activity level of NFkB transcription factor element in the sample. 
     
     
         39 . The method of  claim 31 , wherein the probes are labeled.