Assessment of the PI3K cellular signaling pathway activity using mathematical modelling of target gene expression

1. A method for correcting abnormal activity of a PI3K cellular signaling pathway in a subject, the method comprising:

physically measuring expression levels of three or more target genes of the PI3K cellular signaling pathway derived from a sample extracted from the subject, wherein the genes comprise three or more of AGRP, BCL2L11, BCL6, BNIP3, BTG1, CAT, CAV1, CCND1, CCND2, CCNG2, CDKN1A, CDKN1B, ESR1, FASLG, FBXO32, GADD45A, INSR, MXI1, NOS3, PCK1, POMC, PPARGC1A, PRDX3, RBL2, SOD2 and TNFSF10; and

determining, by processor circuitry, activity of the PI3K cellular signaling pathway in the tissue and/or cells and/or the body fluid of the subject based on the expression levels of the three or more target genes of the PI3K cellular signaling pathway measured in the extracted sample of the tissue and/or the cells and/or the body fluid of the subject,

wherein the determining comprises:

determining a level of a FOXO transcription factor (TF) element in the extracted sample of the tissue and/or the cells and/or the body fluid of the subject based on the expression levels of the three or more target genes of the PI3K cellular signaling pathway, the FOXO TF element controlling transcription of the three or more target genes of the PI3K cellular signaling pathway; and

determining the activity of the PI3K cellular signaling pathway in the tissue and/or the cells and/or the body fluid of the subject based on the level of the FOXO TF element in the extracted sample of the tissue and/or the cells and/or the body fluid of the subject;

determining that the PI3K cellular signaling pathway is operating abnormally in the subject based on the determined activity of the PI3K cellular signaling pathway;

selecting, based on the determined abnormal operation of the PI3K cellular signaling pathway, a specific treatment configured to remedy the determined abnormal operation of the PI3K cellular signaling pathway; and

administering, in response to the determined abnormal operation of the PI3K cellular signaling pathway and the selection of a specific treatment configured to remedy said determined abnormal operation, the selected specific treatment, wherein the determined abnormal operation of the PI3K cellular signaling pathway is overactive and the selected specific treatment inhibits or deregulates the activity of the PI3K cellular signaling pathway.

2. The method of claim 1 , wherein the determining is further based on expression levels of at least one target gene of the PI3K cellular signaling pathway measured in the extracted sample of the tissue and/or the cells and/or the body fluid of the subject selected from the group consisting of: ATP8A1, C10orf10, CBLB, DDB1, DYRK2, ERBB3, EREG, EXT1, FGFR2, IGF 1R, IGFBP1, IGFBP3, LGMN, PPM1D, SEMA3C, SEPP1, SESN1, SLC5A3, SMAD4 and TLE4.

3. The method of claim 1 , wherein the determining is further based on expression levels of at least one target gene of the PI3K cellular signaling pathway measured in the extracted sample of the tissue and/or the cells and/or the body fluid of the subject selected from the group consisting of: ATG14, BIRCS, IGFBP1, KLF2, KLF4, MYOD1, PDK4, RAG1, RAG2, SESN1, SIRT1, STK11 and TXNIP.

4. The method of claim 1 , wherein the method is further used in at least one of the following forms of medical intervention:

diagnosis based on the determined activity of the PI3K cellular signaling pathway in the tissue and/or the cells and/or the body fluid of the subject;

prognosis based on the determined activity of the PI3K cellular signaling pathway in the tissue and/or the cells and/or the body fluid of the subject;

drug prescription based on the determined activity of the PI3K cellular signaling pathway in the tissue and/or the cells and/or the body fluid of the subject;

prediction of drug efficacy based on the determined activity of the PS3K cellular signaling pathway in the tissue and/or the cells and/or the body fluid of the subject;

prediction of adverse effects based on the determined activity of the PI3K cellular signaling pathway in the tissue and/or the cells and/or the body fluid of the subject;

monitoring of drug efficacy;

drug development;

assay development;

pathway research;

cancer staging;

enrollment of the subject in a clinical trial based on the determined activity of the PI3K cellular signaling pathway in the tissue and/or the cells and/or the body fluid of the subject;

selection of subsequent test to be performed; and

selection of companion diagnostics tests.

5. The method of claim 1 , wherein the set of target genes of the PI3K cellular signaling pathway includes at least nine target genes selected from the group comprising: AGRP, BCL2L11, BCL6, BNIP3, BTG1, CAT, CAV1, CCND1, CCND2, CCNG2, CDKN1A, CDKN1B, ESR1, FASLG, FBXO32, GADD45A, INSR, MXIL NOS3, PCK1, POMC, PPARGC1A, PRDX3, RBL2, SOD2 and TNFSF10.

6. The method of claim 5 , wherein the set of target genes of the PI3K cellular signaling pathway further includes at least one target gene selected from the group consisting of: ATP8A1, C10orf10, CBLB, DDB1, DYRK2, ERBB3, EREG, EXT1, FGFR2, IGF1R, IGFBP1, IGFBP3, LGMN, PPM1D, SEMA3C, SEPP1, SESN1, SLC5A3, SMAD4 and TLE4.

7. The method of claim 5 , wherein the set of target genes of the PI3K cellular signaling pathway further includes at least one target gene selected from the group consisting of: ATG14, BIRC5, IGFBP1, KLF2, KLF4, MYOD1, PDK4, RAG1, RAG2, SESN1, SIRT1, STK11 and TXNIP.

8. The method of claim 1 , further comprising:

providing, based on the determined abnormal operation of the PI3K cellular signaling pathway, a recommendation for medical intervention configured to remedy the determined abnormal operation of the PI3K cellular signaling pathway.

9. The method of claim 1 , further comprising determining that a tumor afflicting the subject is at least partially driven by deregulation of the PI3K cellular signaling pathway.

10. The method of claim 8 , wherein the medical intervention comprises prescribing an inhibitor of the PI3K cellular signaling pathway to the subject.

11. The method of claim 1 , wherein the obtaining of the expression levels of the three or more target genes includes measuring the expression levels of the three or more target genes.

12. The method of claim 1 , wherein the target genes are mRNA direct target genes, and wherein the method further comprises:

constructing a network between the expression levels of the three or more mRNA direct target genes and the activity of the cellular signaling pathway, and

training the network by:

determining the level of the FOXO TF element in the extracted sample of the tissue and/or the cells and/or the body fluid of the subject, the FOXO TF element controlling transcription of the three or more mRNA direct target genes of the PI3K cellular signaling pathway;

determining the activity of the PI3K cellular signaling pathway in the tissue and/or cells and/or the body fluid of the subject; and

measuring the nodes representing corresponding probe set nodes of the corresponding three or more mRNA direct target genes.

13. The method of claim 1 , wherein selecting a specific treatment configured to remedy the determined abnormal operation of the PI3K cellular signaling pathway comprises recommending or selecting a drug that downregulates the activity of the PI3K cellular signaling pathway.