WO2022122889A1 - Methods and compositions for detecting the activation of mtor pathway - Google Patents

Abstract

The present invention relates to a method for measuring the activation of mTOR pathway in a subject suffering from a kidney disease associated with a dysregulation of the mTOR pathway comprising the following steps: i) Obtaining urine sample from said subject; ii) Detecting whether of one or more of the following members of AKT, mTOR, 4E- BP1/2 or PI3K pathway are phosphorylated in urine sample and iii) Concluding that the pathway of mTOR is activated when the phosphorylation of AKT, mTOR, 4E-BP1/2 or PI3K is detected or concluding that the pathway of mTOR is not activated when phosphorylation of AKT, mTOR, 4E-BP1/2 or PI3K is not detected. Inventors have found that patients that responded to everolimus as demonstrated by a decrease in the volume of the angiomyolipoma using MRI (patients 1 to 3), had a reduction in the phosphorylation of S6RP. On the other hand, patients with stable disease on MRI had similar amount of phosphorylation of S6RP (patients 4 to 5). Of course, in all these patients, urines were sterile without leucocyturia. They concluded that P-S6RP can be used as a biomarker to monitor the impact of mTOR inhibitors in patients with kidney disease activating the mTOR pathway.

Description

METHODS AND COMPOSITIONS FOR DETECTING THE ACTIVATION OF mTOR PATHWAY

FIELD OF THE INVENTION:

The invention relates to methods compositions for detecting the activation of mTOR pathway. More particularly, the invention relates to a method for predicting the disease progression in a subject suffering from kidney diseases associated with a dysregulation of the mTOR pathway (such as ADPKD or TSC).

BACKGROUND OF THE INVENTION:

Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited renal disease, occurring in 1 out of every 1000 people in the general population¹. Mutations in two genes, PKD1 (encoding polycystin-1, PC-1) and PKD2 (encoding poly cystin-2, PC-2), account for approximately 85% and 15% of all cases of ADPKD. The pathophysiology of polycystic kidney disease (PKD) is complex and remains largely unknown. Cystogenesis has been related to increased cell proliferation and apoptosis, abnormal secretion, remodeling of the extracellular matrix and abnormal planar cell polarityl. Many signaling pathways have been shown to be activated in PKD, including the mammalian target of rapamycin (mTOR) pathway¹. Cumulative evidence in rodent models has shown that mTOR inhibitors (e.g., sirolimus and everolimus) can significantly retard cyst expansion²’³. Furthermore, recent data from retrospective studies of ADPKD patients after kidney transplantation have shown a significant reduction in kidney and hepatic cyst volume in those treated with sirolimus as compared to those receiving calcineurin inhibitors. However, these encouraging data were not confirmed in randomized clinical trial⁴’⁵.

Tuberous sclerosis complex (TSC) is a rare multisystem autosomal dominant genetic disease that causes non-cancerous tumours to grow in the brain and on other vital organs such as the kidneys, heart, liver, eyes, lungs and skin. TSC is caused by a mutation of either of two genes, TSC1 and TSC2, which code for the proteins hamartin and tuberin respectively. Hamartin and tuberin function as a complex which is involved in the control of cell growth and cell division. The complex appears to interact with RHEB GTPase, thus sequestering it from activating mTOR signalling, part of the growth factor (insulin) signalling pathway. Unfortunately, patients are treated with mTOR inhibitors without having any tools to monitor the disease activity and observe whether the treatment targeting the mTOR pathway will be benefit for ADPKD or TSC patients.

SUMMARY OF THE INVENTION:

The present invention relates to a method for measuring the activation of mTOR pathway in a subject suffering from a kidney disease associated with a dysregulation of the mTOR pathway comprising the following steps: i) Obtaining urine sample from said subject; ii) Detecting whether of one or more of the following members of AKT, mTOR, 4E-BP1/2 or PI3K pathway are phosphorylated in urine sample and iii) Concluding that the pathway of mTOR is activated when the phosphorylation of AKT, mTOR, 4E-BP1/2 or PI3K is detected or concluding that the pathway of mTOR is not activated when phosphorylation of AKT, mTOR, 4E-BP1/2 or PI3K is not detected.

In particular, the present invention is defined by the claims.

DETAILED DESCRIPTION OF THE INVENTION:

Inventors showed that the dose of mTOR inhibitors used in ADPKD patients was probably not sufficient enough to inhibit the mTOR pathway as assessed by the persistent activation of the pathway on the kidney biopsies⁶ (phosphorylation of S6RP, downstream target of mTORCl). Activation of the mTOR pathway is known to induce cell proliferation and hypertrophy⁷. Indeed, they hypothesized that assessing the activation of the mTOR pathway in cells isolated from the urines of ADPKD patients will provide a unique tool to monitor disease activity, to identify patients that may benefit from therapeutic targeting the mTOR pathway and as biomarker of mTOR pathway inhibition in ADPKD patients treated with mTOR pathway inhibitors or others.

Accordingly, in a first aspect, the present invention relates to a method for measuring the activation of mTOR pathway in a subject suffering from a kidney disease associated with a dysregulation of the mTOR pathway comprising the following steps: i) Obtaining urine sample from said subject; ii) Detecting whether of one or more of the following members of AKT, mTOR, 4E-BP1/2 or PI3K pathway are phosphorylated in urine sample and iii) Concluding that the pathway of mTOR is activated when the phosphorylation of AKT, mTOR, 4E-BP1/2 or PI3K is detected or concluding that the pathway of mTOR is not activated when phosphorylation of AKT, mTOR, 4E-BP1/2 or PI3K is not detected.

As used herein, the term “disease associated with a dysregulation of the mTOR pathway” refers to any disease in which the regulation of the mTOR pathway is impaired or absent. In a particular embodiment, the dysregulation of the mTOR pathway according to the invention relates to an activation, in particular a constitutive activation or a hyper activation of the mTOR pathway, or to a lack of inhibition, in particular a constitutive lack of inhibition, of the mTOR pathway. In another embodiment, also the disease associated with a dysregulation of the mTOR pathway is a disease due to or caused by a dysregulation of the mTOR pathway.

In a particular embodiment, the disease associated with a dysregulation of the mTOR pathway is selected from the group consisting of but not limited to: tuberous sclerosis complex (TSC), Autosomal dominant polycystic kidney disease (ADPKD), PTEN-related hamartoma syndrome, Peutz-Jeghers syndrome, and kidney cancer.

In a particular embodiment, the disease associated with a dysregulation of the mTOR pathway is Autosomal dominant polycystic kidney disease (ADPKD). ADPKD is the most common inherited renal disease, occurring in 1 out of every 1000 people in the general population¹. Mutations in two genes, PKD1 (encoding polycystin-1, PC-1) and PKD2 (encoding poly cystin-2, PC-2), account for approximately 85% and 15% of all cases of ADPKD.

In another embodiment, the disease associated with a dysregulation of the mTOR pathway is Tuberous sclerosis complex (TSC).

As used herein, the terms "Tuberous sclerosis" (TS) or Tuberous sclerosis complex (TSC) also known as "Bourneville tuberous sclerosis" (BTS), "Bourneville's disease" refers to a rare multisystem autosomal dominant genetic disease that causes non-cancerous tumours to grow in the brain and on other vital organs such as the kidneys, heart, liver, eyes, lungs and skin. In a particular embodiment, the disease associated with a dysregulation of the mTOR pathway is kidney cancer.

As used herein, the terms "kidney cancer," "renal cancer," or "renal cell carcinoma" refer to cancer that has arisen from the kidney. The terms "renal cell cancer" or "renal cell carcinoma" (RCC), as used herein, refer to cancer which originates in the lining of the proximal convoluted tubule. More specifically, RCC encompasses several relatively common histologic subtypes: clear cell renal cell carcinoma, papillary (chromophil), chromophobe, collecting duct carcinoma, and medullary carcinoma. Clear cell renal cell carcinoma (ccRCC) is the most common subtype of RCC. In a particular embodiment, the cancer is a metastatic renal cell carcinoma.

As used herein, the term “subject” refers to any mammals, such as a rodent, a feline, a canine, and a primate. Particularly, in the present invention, the subject is a human afflicted with or susceptible to be afflicted with disease associated with a dysregulation of the mTOR pathway. In a particular embodiment, the subject afflicted with or susceptible to be afflicted with ADPKD. In a particular embodiment, the subject afflicted with or susceptible to be afflicted with TSC.

As used herein the term "mTOR pathway" relates to an intracellular signaling pathway regulating the cell cycle and involving the mTOR protein. "mTOR" relates to the mechanistic or mammalian Target Of Rapamycin and is also known as the F 506- binding protein 12- rapamycin-associafed protein 1 (FRAP 1). mTOR is encoded by the MTOR gene. As is well known to one of skill in the art, mTOR links with other proteins and serves as a core component of two distinct protein complexes, mTOR complex 1 (mTORC 1) and mTOR complex 2 (mTORC2), which regulate different cellular processes. In particular, as a core component of both complexes, mTOR functions as a serine/threonine protein kinase that regulates cell growth, cell proliferation, cell motility, cell survival, protein synthesis, autophagy, and transcription. As a core component of mTORC2, mTOR also functions as a tyrosine protein kinase that promotes the activation of insulin receptors and insulin-like growth factor 1 receptors. mTORC2 has also been implicated in the control and maintenance of the actin cytoskeleton. Examples of upstream regulators of the mTOR pathway, i.e. regulators upstream of mTOR, notably encompass PI3-AT. Examples of downstream effectors of the mTOR pathway, i.e. effectors downstream of mTOR, notably encompass the S6 kinase which phosphorylates ribosomal protein S6. The naturally occurring human mTOR gene has a nucleotide sequence as shown in Genbank Accession number NM 004958 and the naturally occurring human mTOR protein has an aminoacid sequence as shown in Genbank Accession number NP 004949. The murine nucleotide and amino acid sequences have also been described (Genbank Accession numbers NM_020009 and NP_064393).

As used herein, the term “activation of mTOR pathway” refers to the activation of different functions of mTOR such as lipid & nucleotide synthesis; protein synthesis; survival and proliferation of cells.

As used herein, the term “AKT” also known as Protein kinase B (PKB) is a serine/threonine-specific protein kinase that plays a key role in multiple cellular processes such as glucose metabolism, apoptosis, cell proliferation, transcription, and cell migration, is responsible for cell survival and biosynthetic responses via phosphorylation of diverse protein targets including p53, FoxO/FH transcription factors, and CREB. AKT is made up of 3 closely related serine/threonine-protein kinases (AKT1, AKT2, and AKT3) called the AKT kinase, which regulate many cellular processes including metabolism, proliferation, survival, growth, and angiogenesis.

As used herein, the term “4E-BP1/2” refers to Eukaryotic translation initiation factor 4E (eIF4E)-binding protein 1 (4E-BP1) and is a member of a family of translation repressor proteins. The naturally occurring human 4E-BP1/2 gene has a nucleotide sequence as shown in Genbank Accession number NM 004095 and the naturally occurring human mTOR protein has an aminoacid sequence as shown in Genbank Accession number NP 004086. The murine nucleotide and amino acid sequences have also been described (Genbank Accession numbers NM_007918 and NP_031944).

As used herein, the term “PI3K refers to phosphoinositide 3-kinases also called phophatidylinositide 3-kinases. PI3K belongs to a family of enzymes which phosphorylate the 3 ’hydroxyl group of the onositol ring of the phosphatidylinositol (Ptdins). The PI3K signalling pathway can be activated, resulting in the synthesis of PIP3 from PIP2.

As used herein, the term “phosphorylation” refers to the attachment of a phosphoryl group in a molecule. Typically, a protein kinase transfers phosphate groups from ATP to serine, threonine, or tyrosine residues on protein peptide substrates, directly affecting the activity and function of the target.

In the context of the invention, the phosphorylation is performed on mTOR.

In another embodiment, the phosphorylation is performed on AKT.

In another embodiment, the phosphorylation is performed on PI3K.

In another embodiment, the phosphorylation is performed on 4E-BP1/2.

In a further embodiment, the phosphorylation is performed on S6RP.

As used herein, the term “S6RP” refers to S6 Ribosomal Protein (S6RP). It is the S6 subunit of the 40S ribosome and it functions to increase translation of mRNA containing a 5' -terminal oligopyramidine tract (5' -TOP). 1 mRNA with a 5'-TOP generally encode proteins involved in the translational machinery, such as proteins involved in ribosome formation. S6RP functions to control translation of proteins which are constituents of the ribosome, and therefore helps to control overall levels of protein translation. The function of S6RP is phosphorylation dependent, and S6RP is phosphorylated by P70S6K in a mitogen dependent fashion.

In a particular embodiment, the invention relates to a method for measuring the activation of mTOR pathway in a subject suffering from a kidney disease associated with a dysregulation of the mTOR pathway comprising the following steps : i) Obtaining urine sample from said subject ; ii) Detecting S6RP phosphorylated (P-S6RP) in urine sample and iv) Concluding that the pathway of mTOR is activated when P-S6RP is detected or concluding that the pathway of mTOR is not activated when P-S6RP is not detected.

In a further embodiment, the method according to the invention comprises a step of detecting the phosphorylation state of one or more of the following members of AKT, mTOR, 4E-BP1/2 PI3K pathway or S6RP in urine sample.

As used herein, the term "phosphorylation state" of a protein refers to the degree of (total amount of) phosphorylation of a protein. This includes both the number of sites {e.g. suitable Ser, Thr or Tyr amino acid residues) of a protein that are phosphorylated, and the level of phosphorylation at any given acceptor site on the amino acid chain.

As used herein, the term "measuring" includes qualitative and/or quantitative detection (i.e. detecting and/or determining the expression level) with or without reference to a control or a predetermined value. As used herein, "detecting" means determining if the phosphorylation of AKT, mTOR, 4E-BP1/2, PI3K pathway or S6RP is present or not in urine sample and "measuring" means determining the level of phosphorylation in urine sample.

Typically, methodologies are well known in the art to detect and/or measure the phosphorylation of a protein: 1) Kinase Activity Assays: Protein kinases are often common elements in multiple signaling networks influencing numerous downstream effectors responsible for a biological response. Thus, assessing the activity of a single specific kinase may provide valuable information on parallel pathways. Kinase activity within a biological sample is commonly measured in vitro by incubating the immunoprecipitated kinase with an exogenous substrate in the presence of ATP. Measurement of the phosphorylated substrate by a specific kinase can be assessed by several reporter systems including colorimetric, radioactive, or fluorometric detection; 2) Phospho-Specific Antibody Development: it is a classical method of directly measuring protein phosphorylation involves the incubation of whole cells with radiolabeled 32P-orthophosphate, the generation of cellular extracts, separation of proteins by SDS-PAGE, and exposure to film. This labor-intensive method requires many multi-hour incubations and the use of radioisotopes. Other traditional methods include 2-dimensional gel electrophoresis, a technique that assumes phosphorylation will alter the mobility and isoelectric point of the protein; 3) Western Blot: it is the most common method used for assessing the phosphorylation state of a protein, and most cell biology laboratories possess the equipment necessary to perform these experiments. Following separation of the biological sample with SDS- PAGE and subsequent transfer to a membrane (usually PVDF or nitrocellulose), a phospho-specific antibody can be used to identify the protein of interest (View phospho-specific antibodies for Western blot analysis). The typical Western blot protocol eliminates the hazards and waste disposal requirements associated with the use of radioisotope; 4) Enzyme-Linked Immunosorbent Assay (ELISA): the format for this microplate-based assay typically utilizes a capture antibody specific for the desired protein, independent of the phosphorylation state. The target protein, either purified or as a component in a complex heterogeneous sample such as a cell lysate, is then bound to the antibody-coated plate. A detection antibody specific for the phosphorylation site to be analyzed is then added. These assays are typically designed using colorimetric or fluorometric detection. The intensity of the resulting signal is directly proportional to the concentration of phosphorylated protein present in the original sample.

In a particular embodiment, the detection of phosphorylation of AKT, mTOR, 4E- BP1/2 or PI3K pathway is performed by Western Blot.

In a particular embodiment, the detection of phosphorylation of AKT, mTOR, 4E- BP1/2 or PI3K pathway is performed by ELISA.

In the context of the invention, urine sample is used to detect and/or measure the phosphorylation of AKT, mTOR, 4E-BP1/2, PI3K pathway or S6RP. More particularly, the detection of phosphorylation of AKT, mTOR, 4E-BP1/2, PI3K pathway or S6RP is performed in urinary pellet.

In a further embodiment, the detection of phosphorylation of AKT, mTOR, 4E-BP1/2, PI3K pathway or S6RP is performed in supernatant obtained from urine sample.

In a further embodiment, the detection of phosphorylation of AKT, mTOR, 4E-BP1/2, PI3K pathway or S6RP is performed in exosomes obtained from urine sample.

Typically, fresh urines were collected, centrifugated and isolated the cell pellets. Cells were then lysed in RIPA buffer and proteins extracted as previously described. Protein extracts from pellets were resolved by SDS-PAGE before being transferred onto the appropriate membrane and incubated with anti-P-AKT (Ser473) (Cell Signaling Technology), anti-P-S6RP (Cell Signaling Technology), anti-a-tubulin (Merck), b-actin or total S6RP antibodies followed by the appropriate peroxidase-conjugated secondary antibodies. Chemiluminescence results were acquired using a Chemidoc MP, and bands were quantitated with Image Lab Software (Bio-Rad Laboratories).

In a second aspect, the invention relates to a method for predicting the disease progression in a subject suffering from a kidney disease associated with a dysregulation of the mTOR pathway comprising the following steps : i) Obtaining urine sample from said subject ; ii) Detecting whether of one or more of the following members of AKT, mTOR, 4E

BP 1/2 or PI3K pathway are phosphorylated in urine sample and iii) Concluding that the disease is progressing when the phosphorylation of AKT, mTOR,

4E-BP1/2 or PI3K pathway is detected or concluding that the disease is not progressed when the phosphorylation of AKT, mTOR, 4E-BP1/2 or PI3K pathway activation is not detected.

In a particular embodiment, the invention relates to a method for predicting the disease progression in a subject suffering from a kidney disease associated with a dysregulation of the mTOR pathway comprising the following steps: i) Obtaining urine sample from said subject; ii) Detecting S6RP phosphorylated (P-S6RP) in urine sample and i) Concluding that the disease is progressing when P-S6RP is detected or concluding that disease is not progressing when P-S6RP is not detected.

As used herein, the term "predicting" means that the subject to be analyzed by the method of the invention is allocated either into the group of subject who will have a disease progression, or into a group of subject who will not a disease progression. In the context of the invention, the risk of having a disease progression in a subject shall be predicted.

In another embodiment, the method according to the invention relates to a method for predicting the survival time of a subject suffering from a kidney disease associated with a dysregulation of the mTOR pathway comprising i) detecting in urine sample obtained from the subject whether of one or more of the following members of AKT, mTOR, 4E BP1/2 or PI3K pathway are phosphorylated and ii) providing a good prognosis when one or more of the following members of AKT, mTOR, 4E BP 1/2, PI3K pathway or S6RP are not phosphorylated, or providing a bad prognosis when the one or more of the following members of AKT, mTOR, 4E BP 1/2 , PI3K pathway or S6RP are phosphorylated.

In another embodiment, the method according to the invention relates to a method for predicting the overall survival (OS) of a subject suffering from a kidney disease associated with a dysregulation of the mTOR pathway comprising i) detecting in urine sample obtained from the subject whether of one or more of the following members of AKT, mTOR, 4E BP 1/2, PI3K pathway or S6RP are phosphorylated and ii) providing a good prognosis when one or more of the following members of AKT, mTOR, 4E BP1/2, PI3K pathway or S6RP are not phosphorylated, or providing a bad prognosis when the one or more of the following members of AKT, mTOR, 4E BP 1/2, PI3K pathway or S6RP are phosphorylated.

In another embodiment, the invention relates to a method for predicting the progression free survival (PFS) of a subject suffering from a kidney disease associated with a dysregulation of the mTOR pathway comprising i) detecting in urine sample obtained from the subject whether of one or more of the following members of AKT, mTOR, 4E BP1/2, PI3K pathway or S6RP are phosphorylated and ii) providing a good prognosis when one or more of the following members of AKT, mTOR, 4E BP 1/2 PI3K pathway or S6RP are not phosphorylated, or providing a bad prognosis when the one or more of the following members of AKT, mTOR, 4E BP 1/2 PI3K pathway or S6RP are phosphorylated.

As used herein, the term "Overall survival (OS)" denotes the percentage of people in a study or treatment group who are still alive for a certain period of time after they were diagnosed with or started treatment for a disease, such as a disease associated with a dysregulation of the mTOR pathway (according to the invention). The overall survival rate is often stated as a five-year survival rate, which is the percentage of people in a study or treatment group who are alive five years after their diagnosis or the start of treatment.

As used herein, the term "Progression Free Survival (PFS)"denotes the length of time after primary treatment for a cancer ends that the patient survives without any signs or symptoms of that disease or without disease progression.

As used herein, the term "Good Prognosis" denotes a subject with significantly enhanced probability of survival after treatment.

In a third aspect, the invention relates to a method for predicting whether a subject will achieve a response to a treatment with mTOR, AKT, 4E BP 1/2, PI3K or glucosylceramide synthase pathway inhibitor treatment comprising the following steps: i) Obtaining urine sample from said subject; ii) Detecting whether of one or more of the following members of AKT, mTOR, 4E

BP 1/2 or PI3K pathway are phosphorylated in urine sample; iii) Concluding that the subject will achieve a response to a mTOR, AKT, 4E BP 1/2, PI3K or glucosylceramide synthase pathway inhibitor treatment when one or more of the following members of AKT, mTOR, 4E BP 1/2 or PI3K pathway are not phosphorylated or concluding that the subject will not achieve a response to a mTOR, AKT, 4E BP1/2, PI3K or glucosylceramide synthase pathway inhibitor treatment when one or more of the following members of AKT, mTOR, 4E BP 1/2 or PI3K pathway are phosphorylated.

In a particular embodiment, the invention relates to a method for predicting whether a subject will achieve a response to a treatment with a mTOR, AKT, 4E BP 1/2, PI3K pathway or glucosylceramide synthase inhibitor treatment comprising the following steps: i) Obtaining urine sample from said subject; ii) Detecting S6RP phosphorylated (P-S6RP) in urine sample and iii) Concluding that subject will achieve a response to a treatment with a mTOR, AKT, 4E BP 1/2 or PI3K pathway inhibitor when P-S6RP is not detected or concluding that subject will not achieve a response to a treatment with a mTOR, AKT, 4E BP1/2, PI3K or glucosylceramide synthase pathway inhibitor when P-S6RP is detected.

As used herein, the term the terms "will achieve a response" or "respond" refer to the response to a treatment of the subject suffering from a disease associated with a dysregulation of the mTOR pathway. Typically, such treatment induces, ameliorates or otherwise causes an improvement in the pathological symptoms, disease progression or physiological conditions associated with or resistance to succumbing to a disease associated with a dysregulation of the mTOR pathway. In the context of the invention, the term "respond" refers to the ability of a mTOR, AKT, 4E BP1/2 or PI3K pathway inhibitor treatment to an improvement of the pathological symptoms, thus, the subject presents a clinical improvement compared to the subject who does not receive the treatment. The said subject is considered as a "responder" to the treatment. The term "not respond" refers to a subject who does not present any clinical improvement to the treatment with mTOR, AKT, 4E BP1/2 or PI3K pathway inhibitor treatment. This subject is considered as a "non-responder" to the treatment.

Accordingly, the subject as considered "non-responder" has a particular monitoring in the therapeutic regimen. In the context of the invention, when the subject is identified as responder, it means that said subject improves overall and progression- free survival (OS/PFS).

As used herein, the term “mTOR pathway inhibitor” refers to a class of drugs that inhibit the mTOR pathway. Such inhibitors inhibit the cellular metabolism, growth, and proliferation which are regulated by two protein complexes, mTORCl and mTORC2. More particularly, the mTOR inhibitors inhibit also the PI3K and AKT pathways. mTOR inhibitors are well known in the art.

In the context of the invention, mTOR inhibitor is selected from the group consisting of but not limited to: rapamycin and rapalogs (sirolimus; temsirolimus; everolimus; deforolimus); vincristine; dactolisib or BEZ235 (phase I/II of clinical trial; Novartis); alpelisib (BYL719 Novartis); or sapanisertib (phase II of clinical trial; NCI); or taselisib (GDC-0032; phase II of clinicial trial, Roche).

As used herein, the term "AKT inhibitor" refers to any inhibitor that blocks or reduces activity of the AKTprotein and includes perifosine and edelfosine and others described herein. Because of the homology of the various AKT isoforms as well as the mechanisms of action of AKT inhibitors, an AKT inhibitor typically is effective in inhibiting the activity of all of the isoforms, though perhaps to varying degrees.

As used herein, the term "PI3K pathway inhibitor" refers to a class of drugs that inhibit the PI3K pathway. Such inhibitors inhibit the cellular metabolism, growth, and proliferation. In the context of the invention, PI3K inhibitor is selected from the group consisting of but not limited to: Alpelisib (BYL719), Taselisib, Perifosine, Idelalisib, Buparlisib (BKM120), Duvelisib, (IPI-145), Umbralisib, (TGR 1202), Copanlisib (BAY SO- 6946), PX-866, Dactolisib, CUDC-907, Voxtalisib (SAR245409, XL765), Pilaralisib, Copanilisib, GDC-0077, TAK-117, AZD-8186, IPI-549 or PX-866.

In a particular embodiment, the PI3K pathway inhibitor is BYL719. As used herein, the term “BYL719” is an ATP-competitive oral PI3K inhibitor selective for the pl 10a isoform that is activated by a mutant PIK3CA gene (Furet P., et al. 2013; Fritsch C., et al 2014). As used herein, the term “glucosylceramide synthase” refers to a glucosyltransferase enzyme which is involved in the production of glucocerebroside. As used herein, the term “glucosylceramide synthase pathway inhibitor” refers to a class of drugs that inhibit glucosylceramide synthase. In the context of the invention, PI3K inhibitor is selected from the group consisting of but not limited to: venglustat. Miglustat, Eliglustat.

In a particular embodiment, the glucosylceramide synthase pathway inhibitor is Venglustat. Venglustat also known as Ibiglustat, GZ/SAR402671 or Genz-682452 is designed to reduce the production of glucosylceramide (GL-1) and to substantially reduce formation of glucosylceramide-based glycosphingolipids.

In a further embodiment, the invention is suitable to predict whether a subject will achieve a response to a treatment with Venglustat.

Accordingly, the invention relates to a method for predicting whether a subject will achieve a response to a treatment with Venglustat treatment comprising the following steps: i) Obtaining urine sample from said subject; ii) Detecting whether of one or more of the following members of AKT, mTOR, 4E BP 1/2 or PI3K pathway are phosphorylated in urine sample; iii) Concluding that the subject will achieve a response to Venglustat when one or more of the following members of AKT, mTOR, 4E BP 1/2 or PI3K pathway are not phosphorylated or concluding that the subject will not achieve a response to a Venglustat when one or more of the following members of AKT, mTOR, 4E BP1/2 or PI3K pathway are phosphorylated.

In a particular embodiment, the invention relates to a method for predicting whether a subject will achieve a response to a treatment with Venglustat treatment comprising the following steps: iv) Obtaining urine sample from said subject; v) Detecting S6RP phosphorylated (P-S6RP) in urine sample and vi) Concluding that subject will achieve a response to a treatment with Venglustat when P-S6RP is not detected or concluding that subject will not achieve a response to a treatment with Venglustat when P-S6RP is detected. In a fourth aspect, the invention relates to a method for treating a subject suffering from a kidney disease associated with a dysregulation of the mTOR pathway in need thereof with an mTOR, mTOR, AKT, 4E BP1/2,PI3K or glucosylceramide synthase pathway inhibitor, wherein said method comprises the following steps: i) identifying whether said subject will achieve a response to treatment with a mTOR AKT, 4E BP1/2, PI3K or glucosylceramide synthase pathway inhibitor as described above; and ii) treating with a mTOR, AKT, 4E BP 1/2, PI3K or glucosylceramide synthase pathway inhibitor the subject identified as responder.

In a particular embodiment, the invention relates to a method for treating a subject suffering from a kidney disease associated with a dysregulation of the mTOR pathway in need thereof with an mTOR, mTOR, AKT, 4E BP 1/2, PI3K or glucosylceramide synthase pathway inhibitor, wherein said method comprises the following steps: i) Obtaining urine sample from said subject; ii) Detecting whether of one or more of the following members of AKT, mTOR, 4E BP1/2 or PI3K pathway are phosphorylated in urine sample; iii) Concluding that the subject will achieve a response to a mTOR, AKT, 4E BP 1/2, PI3K or glucosylceramide synthase pathway inhibitor treatment when more of the following members of AKT, mTOR, 4E BP 1/2 or PI3K pathway are not phosphorylated or concluding that the subject will not achieve a response to a mTOR, AKT, 4E BP 1/2, PI3K pathway or glucosylceramide synthase inhibitor treatment when more of the following members of AKT, mTOR, 4E BP1/2 or PI3K pathway are phosphorylated; and iv) Treating with a mTOR, AKT, 4E BP 1/2, PI3K or glucosylceramide synthase pathway inhibitor the subject identified as responder.

In another embodiment, the invention relates to a method for treating a subject suffering from a kidney disease associated with a dysregulation of the mTOR pathway in need thereof with an mTOR, mTOR, AKT, 4E BP 1/2, PI3K pathway or glucosylceramide synthase inhibitor, wherein said method comprises the following steps: i) Obtaining urine sample from said subject; ii) Detecting S6RP phosphorylated (P-S6RP) in urine sample; iii) Concluding that the subject will achieve a response when S6RP is not phosphorylated or concluding that the subject will not achieve a response when S6RP is phosphorylated; and v) Treating with a mTOR, AKT, 4E BP 1/2 , PI3K or glucosylceramide synthase pathway inhibitor the subject identified as responder.

In another embodiment, the invention relates to a method for treating a subject suffering from a kidney disease associated with a dysregulation of the mTOR pathway in need thereof with Venglustat wherein said method comprises the following steps: i) identifying whether said subject will achieve a response to treatment with a Venglustat as described above; and ii) treating with Venglustat the subject identified as responder.

Typically, the invention relates to a method for treating a subject suffering from a kidney disease associated with a dysregulation of the mTOR pathway in need thereof with Venglustat, wherein said method comprises the following steps: i) Obtaining urine sample from said subject; ii) Detecting whether of one or more of the following members of AKT, mTOR, 4E BP1/2 or PI3K pathway are phosphorylated in urine sample; iii) Concluding that the subject will achieve a response to Venglustat when more of the following members of AKT, mTOR, 4E BP 1/2 or PI3K pathway are not phosphorylated or concluding that the subject will not achieve a response to Venglustat when more of the following members of AKT, mTOR, 4E BP 1/2 or PI3K pathway are phosphorylated; and iv) treating with Venglustat the subject identified as responder.

In another embodiment, the invention relates to a method for treating a subject suffering from a kidney disease associated with a dysregulation of the mTOR pathway in need thereof with Venglustat, wherein said method comprises the following steps: i) Obtaining urine sample from said subject; ii) Detecting S6RP phosphorylated (P-S6RP) in urine sample; iii) Concluding that the subject will achieve a response when S6RP is not phosphorylated or concluding that the subject will not achieve a response when S6RP is phosphorylated; and vi) Treating with Venglustat the subject identified as responder.

As used herein, the terms “treating” or “treatment” refer to both prophylactic or preventive treatment as well as curative or disease modifying treatment, including treatment of subject at risk of contracting the disease or suspected to have contracted the disease as well as subject who are ill or have been diagnosed as suffering from a disease or medical condition, and includes suppression of clinical relapse. The treatment may be administered to a subject having a medical disorder or who ultimately may acquire the disorder, in order to prevent, cure, delay the onset of, reduce the severity of, or ameliorate one or more symptoms of a disorder or recurring disorder, or in order to prolong the survival of a subject beyond that expected in the absence of such treatment. By "therapeutic regimen" is meant the pattern of treatment of an illness, e.g., the pattern of dosing used during therapy. A therapeutic regimen may include an induction regimen and a maintenance regimen. The phrase "induction regimen" or "induction period" refers to a therapeutic regimen (or the portion of a therapeutic regimen) that is used for the initial treatment of a disease. The general goal of an induction regimen is to provide a high level of drug to a subject during the initial period of a treatment regimen. An induction regimen may employ (in part or in whole) a "loading regimen", which may include administering a greater dose of the drug than a physician would employ during a maintenance regimen, administering a drug more frequently than a physician would administer the drug during a maintenance regimen, or both. The phrase "maintenance regimen" or "maintenance period" refers to a therapeutic regimen (or the portion of a therapeutic regimen) that is used for the maintenance of a subject during treatment of an illness, e.g., to keep the subject in remission for long periods of time (months or years). A maintenance regimen may employ continuous therapy (e.g., administering a drug at a regular intervals, e.g., weekly, monthly, yearly, etc.) or intermittent therapy (e.g., interrupted treatment, intermittent treatment, treatment at relapse, or treatment upon achievement of a particular predetermined criteria [e.g., pain, disease manifestation, etc.]).

A “therapeutically effective amount” is intended for a minimal amount of active agent which is necessary to impart therapeutic benefit to a subject. For example, a "therapeutically effective amount" to a subject is such an amount which induces, ameliorates or otherwise causes an improvement in the pathological symptoms, disease progression or physiological conditions associated with or resistance to succumbing to a disorder. It will be understood that the total daily usage of the compounds of the present invention will be decided by the attending physician within the scope of sound medical judgment. The specific therapeutically effective dose level for any particular subject will depend upon a variety of factors including the disorder being treated and the severity of the disorder; activity of the specific compound employed; the specific composition employed, the age, body weight, general health, sex and diet of the subject; the time of administration, route of administration, and rate of excretion of the specific compound employed; the duration of the treatment; drugs used in combination or coincidential with the specific compound employed; and like factors well known in the medical arts. For example, it is well within the skill of the art to start doses of the compound at levels lower than those required to achieve the desired therapeutic effect and to gradually increase the dosage until the desired effect is achieved. However, the daily dosage of the products may be varied over a wide range from 0.01 to 1,000 mg per adult per day. Typically, the compositions contain 0.01, 0.05, 0.1, 0.5, 1.0, 2.5, 5.0, 10.0, 15.0, 25.0, 50.0, 100, 250 and 500 mg of the active ingredient for the symptomatic adjustment of the dosage to the subject to be treated. A medicament typically contains from about 0.01 mg to about 500 mg of the active ingredient, preferably from 1 mg to about 100 mg of the active ingredient. An effective amount of the drug is ordinarily supplied at a dosage level from 0.0002 mg/kg to about 20 mg/kg of body weight per day, especially from about 0.001 mg/kg to 7 mg/kg of body weight per day.

The mTOR, AKT, 4E BP1/2, PI3K or glucosylceramide synthase pathway inhibitor as described above may be combined with pharmaceutically acceptable excipients, and optionally sustained-release matrices, such as biodegradable polymers, to form pharmaceutical compositions. "Pharmaceutically" or "pharmaceutically acceptable" refer to molecular entities and compositions that do not produce an adverse, allergic or other untoward reaction when administered to a mammal, especially a human, as appropriate. A pharmaceutically acceptable carrier or excipient refers to a non-toxic solid, semi-solid or liquid filler, diluent, encapsulating material or formulation auxiliary of any type. The pharmaceutical compositions of the present invention for oral, sublingual, subcutaneous, intramuscular, intravenous, transdermal, local or rectal administration, the active principle, alone or in combination with another active principle, can be administered in a unit administration form, as a mixture with conventional pharmaceutical supports, to animals and human beings. Suitable unit administration forms comprise oral-route forms such as tablets, gel capsules, powders, granules and oral suspensions or solutions, sublingual and buccal administration forms, aerosols, implants, subcutaneous, transdermal, topical, intraperitoneal, intramuscular, intravenous, subdermal, transdermal, intrathecal and intranasal administration forms and rectal administration forms. Typically, the pharmaceutical compositions contain vehicles which are pharmaceutically acceptable for a formulation capable of being injected. These may be in particular isotonic, sterile, saline solutions (monosodium or disodium phosphate, sodium, potassium, calcium or magnesium chloride and the like or mixtures of such salts), or dry, especially freeze-dried compositions which upon addition, depending on the case, of sterilized water or physiological saline, permit the constitution of injectable solutions. The pharmaceutical forms suitable for injectable use include sterile aqueous solutions or dispersions; formulations including sesame oil, peanut oil or aqueous propylene glycol; and sterile powders for the extemporaneous preparation of sterile injectable solutions or dispersions. In all cases, the form must be sterile and must be fluid to the extent that easy syringability exists. It must be stable under the conditions of manufacture and storage and must be preserved against the contaminating action of microorganisms, such as bacteria and fungi. Solutions comprising compounds of the invention as free base or pharmacologically acceptable salts can be prepared in water suitably mixed with a surfactant, such as hydroxypropylcellulose. Dispersions can also be prepared in glycerol, liquid polyethylene glycols, and mixtures thereof and in oils. Under ordinary conditions of storage and use, these preparations contain a preservative to prevent the growth of microorganisms. The polypeptide (or nucleic acid encoding thereof) can be formulated into a composition in a neutral or salt form. Pharmaceutically acceptable salts include the acid addition salts (formed with the free amino groups of the protein) and which are formed with inorganic acids such as, for example, hydrochloric or phosphoric acids, or such organic acids as acetic, oxalic, tartaric, mandelic, and the like. Salts formed with the free carboxyl groups can also be derived from inorganic bases such as, for example, sodium, potassium, ammonium, calcium, or ferric hydroxides, and such organic bases as isopropylamine, trimethylamine, histidine, procaine and the like. The carrier can also be a solvent or dispersion medium containing, for example, water, ethanol, polyol (for example, glycerol, propylene glycol, and liquid polyethylene glycol, and the like), suitable mixtures thereof, and vegetables oils. The proper fluidity can be maintained, for example, by the use of a coating, such as lecithin, by the maintenance of the required particle size in the case of dispersion and by the use of surfactants. The prevention of the action of microorganisms can be brought about by various antibacterial and antifungal agents, for example, parabens, chlorobutanol, phenol, sorbic acid, thimerosal, and the like. In many cases, it will be preferable to include isotonic agents, for example, sugars or sodium chloride. Prolonged absorption of the injectable compositions can be brought about by the use in the compositions of agents delaying absorption, for example, aluminium monostearate and gelatin. Sterile injectable solutions are prepared by incorporating the active polypeptides in the required amount in the appropriate solvent with several of the other ingredients enumerated above, as required, followed by filtered sterilization. Generally, dispersions are prepared by incorporating the various sterilized active ingredients into a sterile vehicle which contains the basic dispersion medium and the required other ingredients from those enumerated above. In the case of sterile powders for the preparation of sterile injectable solutions, the preferred methods of preparation are vacuum-drying and freeze-drying techniques which yield a powder of the active ingredient plus any additional desired ingredient from a previously sterile-filtered solution thereof. Upon formulation, solutions will be administered in a manner compatible with the dosage formulation and in such amount as is therapeutically effective. The formulations are easily administered in a variety of dosage forms, such as the type of injectable solutions described above, but drug release capsules and the like can also be employed. For parenteral administration in an aqueous solution, for example, the solution should be suitably buffered if necessary and the liquid diluent first rendered isotonic with sufficient saline or glucose. These particular aqueous solutions are especially suitable for intravenous, intramuscular, subcutaneous and intraperitoneal administration. In this connection, sterile aqueous media which can be employed will be known to those of skill in the art in light of the present disclosure. For example, one dosage could be dissolved in 1 ml of isotonic NaCl solution and either added to 1000 ml of hypodermoclysis fluid or injected at the proposed site of infusion. Some variation in dosage will necessarily occur depending on the condition of the subject being treated. The person responsible for administration will, in any event, determine the appropriate dose for the individual subject.

In another aspect, the invention relates to a kit for performing the method according to the invention, wherein said kit comprises (i) means for detecting whether of one or more of the following members of AKT, mTOR, 4E BP1/2 or PI3K pathway are phosphorylated in urine sample obtained from a subject suffering from a disease associated with a dysregulation of the mTOR pathway and ii) instructions for this purpose.

The instructions for this purpose may include at least one methodology to detect and/or measure the phosphorylation of a protein (such as AKT, mTOR, 4E BP1/2 or PI3K, S6RP) and indications when a least one of the following members of AKT, mTOR, 4E BP 1/2 or PI3K pathway is phosphorylated.

The invention will be further illustrated by the following figures and examples. However, these examples and figures should not be interpreted in any way as limiting the scope of the present invention.

FIGURES:

Figure 1: mTOR pathway activation in urines of ADPKD patients. Western blot (A) and quantification (B) of P-S6RP, Pactin, GAPDH and a-tubulin in the urinary pellets of patients with ADPKD. Patient with fast decline of the eGFR, named progressors, (N° 1,2,4, 519, 189, 89, 500, 57, 533, 53, 144, 207, 150, 40 and 626) had a higher degree of S6RP phosphorylation compared to non progressors. AU: arbitrary unit.

Figure 2: mTOR pathway activation in urines of TSC patients. Western blot of P- S6RP, P-actin, GAPDH and a-tubulin in the urinary pellets of patients with TSC disorders treated with everolimus during a 3 -month period. Patients with angiomyolipoma volume reduction, as assed by MRI, had a decreased phosphorylation of S6RP (patients 1, 2 and 3) compared to patients with stable volume of the angiomyolipoma (patients 4 and 5). This demonstrates that patients with TSC disorders and kidney anomalies have detectable activation of the mTOR pathway in the urine and this could serve to determine the good inhibition of the pathway while receiving treatments.

EXAMPLE:

Inventors studied 28 ADPKD patients with or without disease progression as assessed by the decrease of an estimated glomerular filtration rate of -5ml/min/1.73m2 over 12 months of follow up, and 4 healthy volunteers without ADPKD or kidney dysfunction.

They collected fresh urines, centrifugate them (3000 rpm, 20 min, 4°C) and isolated the cell pellets. Cells were then lysed in RIPA buffer and proteins extracted as previously described. Protein extracts from pellets were resolved by SDS-PAGE before being transferred onto the appropriate membrane and incubated with anti-P-S6RP (Cell Signaling Technology, ref# 5364), anti-GAPDH (Merck Millipore, ref#374), anti-a-tubulin (Merck, ref# 5168), anti- P-actin (Sigma- Aldrich, ref#A2228) or total S6RP (Cell Signaling Technology, ref# 2217) antibodies followed by the appropriate peroxidase-conjugated secondary antibodies. Chemiluminescence results were acquired using a Chemidoc MP, and bands were quantitated with Image Lab Software (Bio-Rad Laboratories).

They first observed that 4 healthy volunteers had no P-S6RP detectable in the urines. Interestingly, among the 28 ADPKD patients followed at Necker hospital (Paris), 15 of them had an activation of the mTOR pathway as assessed by the phosphorylation of S6RP (Fig. lA and IB). Some of these patients had a very important degree of activation as assed by western blot analysis. Importantly these patients with AKT/mTOR pathway activation in the urinary cells were the patients with declining eGFR over time. We fist concluded that P-S6RP or other marker of activation of the mTOR pathway in the urine may be a potential biomarker to predict disease progression in patients with ADPKD.

They then wondered if activation of P-S6RP in the urine could be used as a biomarker for monitoring patients under mTOR inhibitor treatment. To this aim, they explored the urinary pellet of a cohort of patients with Tuberous Sclerosis disorders followed at Necker hospital (Paris). In this disease, patients have a genetic defect in TSC1 or TSC2, two negative regulators of the mTOR pathway. These patients usually have kidney disorders such as angiomyolipoma and cysts. Everolimus (mTOR inhibitor) is approved for patients with TSC disorders and angiomyolipoma. They collected urines of 5 TSC patients before everolimus introduction and then 3 months after drug introduction. They also performed kidney imaging (Magnetic Resonance, RM) before and 3 months after drug introduction. Everolimus was started at 5 mg per day and maintained over a 3 -month period on that dosage. Proteins from urinary pellets were extracted from the pellets and resolved by SDS-PAGE before being transferred onto the appropriate membrane and incubated with anti-P-S6RP (Cell Signaling Technology, ref# 5364), anti-GAPDH (Merck Millipore, ref#374), anti-a-tubulin (Merck, ref# 5168), anti-P-actin (Sigma- Aldrich, ref#A2228) or total S6RP (Cell Signaling Technology, ref# 2217) antibodies followed by the appropriate peroxidase-conjugated secondary antibodies. Chemiluminescence results were acquired using a Chemidoc MP, and bands were quantitated with Image Lab Software (Bio-Rad Laboratories). Interestingly, they observed that patients with kidney diseases associated with TSC disorders had detectable P-S6RP in the urine (Fig.2). Importantly, they found that, patients that responded to everolimus as demonstrated by a decrease in the volume of the angiomyolipoma using MRI (patients 1 to 3), had a reduction in the phosphorylation of S6RP. On the other hand, patients with stable disease on MRI had similar amount of phosphorylation of S6RP (patients 4 to 5). Of course, in all these patients, urines were sterile without leucocyturia. They concluded that P-S6RP can be used as a biomarker to monitor the impact of mTOR inhibitors in patients with kidney disease activating the mTOR pathway.

REFERENCES:

Throughout this application, various references describe the state of the art to which this invention pertains. The disclosures of these references are hereby incorporated by reference into the present disclosure.

1. Wilson PD. Polycystic kidney disease. N Engl J Med 2004;350(2): 151-64. (In eng).

2. Tao Y, Kim J, Schrier RW, Edelstein CL. Rapamycin markedly slows disease progression in a rat model of polycystic kidney disease. J Am Soc Nephrol 2005;16(l):46-51. (In eng).

3. Shillingford JM, Murcia NS, Larson CH, et al. The mTOR pathway is regulated by polycystin-1, and its inhibition reverses renal cystogenesis in polycystic kidney disease. Proc Natl Acad Sci U S A 2006; 103 (14): 5466-71.

4. Walz G, Budde K, Mannaa M, et al. Everolimus in patients with autosomal dominant polycystic kidney disease. N Engl J Med 2010;363(9):830-40. (Multicenter Study

Randomized Controlled Trial

Research Support, Non-U. S. Gov't) (In eng). DOI: 10.1056/NEJMoal 003491.

5. Serra AL, Poster D, Kistler AD, et al. Sirolimus and kidney growth in autosomal dominant polycystic kidney disease. N Engl J Med 2010;363(9):820-9. (Randomized Controlled Trial

Research Support, Non-U. S. Gov't) (In eng). DOI: 10.1056/NEJMoa0907419.

6. Canaud G, Knebelmann B, Harris PC, et al. Therapeutic mTOR inhibition in autosomal dominant polycystic kidney disease: What is the appropriate serum level? Am J Transplant 2010; 10(7): 1701-6. (Case Reports) (In eng). DOI: 10.1111/j .1600- 6143.2010.03152.x.

7. Manning BD, Toker A. AKT/PKB Signaling: Navigating the Network. Cell 2017;169(3):381-405. (In eng). DOI: 10.1016/j .cell.2017.04.001.

Claims

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CLAIMS: A method for measuring the activation of mTOR pathway in a subject suffering from a kidney disease associated with a dysregulation of the mTOR pathway comprising the following steps: i) Obtaining urine sample from said subject; ii) Detecting whether of one or more of the following members of AKT, mTOR, 4E-BP1/2 or PI3K pathway are phosphorylated in urine sample and iii) Concluding that the pathway of mTOR is activated when the phosphorylation of AKT, mTOR, 4E-BP1/2 or PI3K is detected or concluding that the pathway of mTOR is not activated when phosphorylation of AKT, mTOR, 4E-BP1/2 or PI3K is not detected. A method for measuring the activation of mTOR pathway in a subject suffering from a kidney disease associated with a dysregulation of the mTOR pathway comprising the following steps: i) Obtaining urine sample from said subject ; ii) Detecting S6RP phosphorylated (P-S6RP) in urine sample and iii) Concluding that the pathway of mTOR is activated when P-S6RP is detected or concluding that the pathway of mTOR is not activated when P-S6RP is not detected. A method for predicting the disease progression in a subject suffering from a kidney disease associated with a dysregulation of the mTOR pathway comprising the following steps: i) Obtaining urine sample from said subject ; ii) Detecting whether of one or more of the following members of AKT, mTOR, 4E BP 1/2 or PI3K pathway are phosphorylated in urine sample and iii) Concluding that the disease is progressing when the phosphorylation of AKT, mTOR, 4E-BP1/2 or PI3K pathway is detected or concluding that the disease is not progressed when the phosphorylation of AKT, mTOR, 4E-BP1/2 or PI3K pathway activation is not detected. A method for predicting whether a subject will achieve a response to a treatment with mTOR, AKT, 4E BP1/2, PI3K or glucosylceramide synthase pathway inhibitor treatment comprising the following steps: i) Obtaining urine sample from said subject ; ii) Detecting whether of one or more of the following members of AKT, mTOR, 4E BP1/2 or PI3K pathway are phosphorylated in urine sample; iii) Concluding that the subject will achieve a response to a mTOR, AKT, 4E BP 1/2, PI3K or glucosylceramide synthase pathway inhibitor treatment when more of the following members of AKT, mTOR, 4E BP 1/2 or PI3K pathway are not phosphorylated or concluding that the subject will not achieve a response to a mTOR, AKT, 4E BP 1/2, PI3K or glucosylceramide synthase pathway inhibitor treatment when more of the following members of AKT, mTOR, 4E BP1/2 or PI3K pathway are phosphorylated. The method according to claims 1 to 4 wherein, the phosphorylation is detected by Western Blot or ELISA. The method according to claims 1 to 5 wherein, the phosphorylation of one or more of the following members of AKT, mTOR, 4E-BP1/2, PI3K pathway or S6RP is detected in pellet, supernatant or exosomes obtained from urine sample. A method for treating a subject suffering from a kidney disease associated with a dysregulation of the mTOR pathway in need thereof with an mTOR, mTOR, AKT, 4E BP 1/2, PI3K or glucosylceramide synthase pathway inhibitor, wherein said method comprises the following steps: i) Obtaining urine sample from said subject; ii) Detecting whether of one or more of the following members of AKT, mTOR, 4E BP1/2 or PI3K pathway are phosphorylated in urine sample; iii) Concluding that the subject will achieve a response to a mTOR, AKT, 4E BP 1/2, PI3K or glucosylceramide synthase pathway inhibitor treatment when more of the following members of AKT, mTOR, 4E BP 1/2 or PI3K pathway are not phosphorylated or concluding that the subject will not achieve a response to a mTOR, AKT, 4E BP 1/2, PI3K or glucosylceramide synthase pathway inhibitor treatment when more of the following members of AKT, mTOR, 4E BP1/2 or PI3K pathway are phosphorylated; and iv) Treating with a mTOR, AKT, 4E BP 1/2, PI3K or glucosylceramide synthase pathway inhibitor the subject identified as responder.

8. The method according to claim 6 wherein, the inhibitor of mTOR, AKT, 4E BP1/2, PI3K or glucosylceramide synthase pathway is selected from the group consisting of but not limited to: rapamycin and rapalogs (sirolimus; temsirolimus; everolimus; deforolimus); vincristine; dactolisib or BEZ235 (phase I/II of clinical trial; Novartis); alpelisib (BYL719 Novartis); or sapanisertib (phase II of clinical trial; NCI); or taselisib (GDC-0032; phase II of clinicial trial, Roche); Perifosine, Idelalisib, Idelalisib, Buparlisib (BKM120), Duvelisib, (IPI-145), Umbralisib, (TGR 1202), Copanlisib (BAY 80-6946), PX-866, Dactolisib, CUDC-907, Voxtalisib (SAR245409, XL765), Pilaralisib, Copanilisib, GDC-0077, TAK-117, AZD-8186, IPI-549, PX-866, Venglustat. Miglustat or Eliglustat.

9. The method according to claims 1 to 8, wherein the kidney disease associated with a dysregulation of the mTOR pathway is selected from the group consisting of but not limited to: tuberous sclerosis complex (TSC), Autosomal dominant polycystic kidney disease (ADPKD), PTEN-related hamartoma syndrome, Peutz-Jeghers syndrome, and kidney cancer.

10. A kit for performing the method according to claims 1 to 9, wherein said kit comprises (i) means for detecting whether of one or more of the following members of AKT, mTOR, 4E BP1/2 or PI3K pathway are phosphorylated in urine sample obtained from a subject suffering from a disease associated with a dysregulation of the mTOR pathway and ii) instructions for this purpose.