Determination of tgf-beta pathway activity using unique combination of target genes

Abstract

A bioinformatics process which provides an improved means to detect TGF-β cellular signaling pathway in a subject, such as a human, based on the expression levels of one or more unique target gene(s) of the TGF-β 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 TGF-β cellular signaling pathway target genes.

1 . A method of treating a subject suffering from a disease associated with an activated TGF-β cellular signaling pathway comprising:
 a. receiving information regarding the activity level of a TGF-β cellular signaling pathway derived from a sample isolated from the subject, wherein the activity level of the TGF-β cellular signaling pathway is determined by:
 i. calculating an activity level of TGF-β transcription factor element in a sample isolated from the subject, wherein the level of the TGF-β transcription factor element in the sample is calculated by:
 1. receiving data on the expression levels of at least three target genes derived from the sample, wherein the TGF-β transcription factor element controls transcription of the at least three target genes, and wherein the at least three target genes are selected from CDC42EP3, ANGPTL4, ID1, IL11, SERPINE1, JUNB, SKIL, and SMAD7; 
 2. calculating the level of the TGF-β transcription factor element in the sample using a calibrated pathway model, wherein the calibrated pathway model compares the expression levels of the at least three target genes in the sample with expression levels of the at least three target genes in the model which define an activity level of TGF-β transcription factor element; and, 
 
 ii. calculating the activity level of the TGF-β cellular signaling pathway in the sample based on the calculated TGF-β transcription factor element level in the sample; and, 
 
 b. administering to the subject a TGF-β inhibitor if the information regarding the activity level of the TGF-β cellular signaling pathway is indicative of an active TGF-β cellular signaling pathway. 
 
     
     
         2 . The method of  claim 1 , wherein the at least three target genes are ANGPTL4, CDC42EP3, and at least one of ID1, IL11, SERPINE1, JUNB, SKIL, or SMAD7. 
     
     
         3 . The method of  claim 1 , wherein data on the expression levels of the target genes ANGPTL4, CDC42EP3, ID1, SERPINE1, JUNB, SKIL, and SMAD7 is received 
     
     
         4 . The method of  claim 3  wherein data on the expression levels of the additional target genes CDKN1A, CTGF, GADD45B, VEGFA, and SNAI2 is received. 
     
     
         5 . The method of  claim 1 , wherein the calibrated pathway model is a probabilistic model incorporating conditional probabilistic relationships that compare the expression levels of the at least three target genes in the sample with expression levels of the at least three target genes in the model which define a level of TGF-β transcription factor element to determine the activity level of the TGF-β transcription factor element in the sample. 
     
     
         6 . The method of  claim 1 , wherein the calibrated pathway model is a linear model incorporating relationships that compare the expression levels of the at least three target genes in the sample with expression levels of the at least three target genes in the model which define a level of TGF-β transcription factor element to determine the activity level of the TGF-β transcription factor element in the human cancer sample. 
     
     
         7 . The method of  claim 1 , wherein the TGF-β inhibitor is Terameprocol, Fresolimumab, Sotatercept, Galunisertib, SB431542, LY2109761, LDN-193189, SB525334, SB505124, GW788388, LY364947, RepSox, LDN-193189 HCl, K02288, LDN-214117, SD-208, EW-7197, ML347, LDN-212854, DMH1, Pirfenidone, Hesperetin, Trabedersen, Lerdelimumab, Metelimumab, trx-SARA, ID11, Ki26894, or SB-431542. 
     
     
         8 . The method of  claim 1 , wherein the disease is a cancer. 
     
     
         9 . The method of  claim 8 , wherein the cancer is colon, breast, prostate, pancreatic, lung, brain, leukemia, lymphoma, or glioma. 
     
     
         10 . The method of  claim 9 , wherein the cancer is breast cancer. 
     
     
         11 . A kit for measuring expression levels of TGF-β cellular signaling pathway target genes comprising:
 a. a set of polymerase chain reaction primers directed to at least six TGF-β cellular signaling pathway target genes from a sample isolated from a subject; and 
 b. a set of probes directed to the at least six TGF-β cellular signaling pathway target genes;
 wherein the at least six TGF-β cellular signaling pathway target genes are selected from CDC42EP3, ANGPTL4, ID1, SERPINE1, JUNB, SKIL, and SMAD7. 
 
 
     
     
         12 . The kit of  claim 11 , wherein the at least six target genes are ANGPTL4, CDC42EP3, and at least four of ID1, IL11, SERPINE1, JUNB, SKIL, or SMAD7. 
     
     
         13 . The kit of  claim 11 , wherein the target genes are ANGPTL4, CDC42EP3, ID1, SERPINE1, JUNB, SKIL, and SMAD7. 
     
     
         14 . The kit of  claim 13 , wherein the kit includes additional sets of primers and probes directed to target genes CDKN1A, CTGF, GADD45B, VEGFA, and SNAI2. 
     
     
         15 . The kit of  claim 11 , wherein the probes are labeled. 
     
     
         16 . The kit of  claim 14 , wherein the set of probes are SEQ. ID. NOS. 74, 77, 80, 83, 86, 89, 92, 95, 98, 101, 104, and 107. 
     
     
         17 . The kit of  claim 14 , wherein the set of primers are SEQ. ID. NOS. 72 and 73, 75 and 76, 78 and 79, 81 and 82, 84 and 85, 87 and 88, 90 and 91, 93 and 94, 96 and 97, 99 and 100, 102 and 103, and 105 and 106. 
     
     
         18 . The kit of  claim 11 , further comprising a computer program product for determining the activity level of a TGF-β cellular signaling pathway in the subject comprising
 a. a non-transitory computer readable storage medium having computer readable program code embodied therewith, the computer readable program code executable by at least one processor to:
 i. calculate a level of TGF-β transcription factor element in the sample, wherein the level of TGF-β transcription factor element in the sample is associated with TGF-β cellular signaling, and wherein the level of the TGF-β transcription factor element in the sample is calculated by:
 1. receiving data on the expression levels of the at least six target genes derived from the sample; 
 2. calculating the level of the TGF-β transcription factor element in the sample using a calibrated pathway model, wherein the calibrated pathway model compares the expression levels of the at least six target genes in the sample with expression levels of the at least six target genes in the model which define an activity level of the TGF-β transcription factor element; and, 
 
 ii. calculate the activity level of the TGF-β cellular signaling pathway in the sample based on the calculated TGF-β transcription factor element level in the sample.