This invention relates to methods of molecular medicine and molecular biology.
Polycystic kidney disease (PKD) is a common genetic disorder characterized by the formation of fluid-filled epithelial-lined cysts in the kidneys of patients over time (Park et al., BMB Reports 44:359-368, 2011). The cysts in a PKD patient can increase in size and number over the decades, and displace and destroy adjacent renal parenchyma, which can ultimately lead to end-stage renal disease in the patient (Chapin et al., J. Cell Biol. 191:701-710, 2010). Multiple mechanisms have been shown to contribute to PKD, including increased proliferation and apoptosis, in addition to loss of differentiation and polarity (Belibi et al., Expert. Opin. Invest. Drugs 19:315-328, 2010). Many end-stage PKD patients depend on transplantation or hemodialysis to attenuate renal failure (Park et al., 2011; supra).
There are two types of PKD: autosomal dominant PKD (ADPKD) and autosomal recessive PKD (ARPKD). In the year 2006, about 500,000 people were diagnosed as having PKD in the U.S., with ADPKD affecting about 1 person out of 500 to 1,000 people, and ARPKD affecting about 1 person out of 20,000 to 40,000 people. ADPKD is the most common inherited disorder of the kidneys and accounts for ˜5% of the end-stage renal disease patients in the U.S. (Pei et al., Adv. Chronic Kidney Dis. 17:140-152, 2010).
The present invention is based, at least in part, on the discovery that levels of Proliferating Cell Nuclear Antigen (PCNA), cyclin D1, cyclin D3, MAPK-ERK kinase 1 (MEK), ribosomal protein S6 (S6), phosphorylated ribosomal protein S6 (pS6), extracellular signal-regulated kinase (ERK), phosphorylated extracellular signal-regulated kinase (pERK), protein kinase B (Akt), phosphorylated protein kinase B (pAkt), caspase-2, total ribosomal protein S6 (S6+pS6) and retinoblastoma binding protein (RBBP) are elevated in samples containing a biological fluid (e.g., a urine sample or a urine sample enriched for exosomes) from patients having PKD, are increased in samples containing a biological fluid (e.g., a urine sample or a urine sample enriched for exosomes) from patients with later stages of PKD as compared to the levels in patients having early stages of PKD, and are decreased in samples containing a biological fluid (e.g., a urine sample or a urine sample enriched for exosomes) from PKD subjects administered a therapeutically effective treatment of PKD. In view of this discovery, provided herein are methods for determining the efficacy of a treatment for PKD in a patient, diagnosing PKD in a patient, staging PKD in a patient, and monitoring PKD in a patient that include determining a level of one or more of PCNA, cyclin D1, cyclin D3, MEK, S6, pS6, ERK, pERK, Akt, pAkt, caspase-2, total ribosomal protein S6, and RBBP.
Provided here are methods of determining the efficacy of treatment for polycystic kidney disease (PKD) in a PKD patient that include: (a) providing a first sample including a biological fluid obtained from the PKD patient at a first time point; (b) concentrating the first sample for exosomes; (c) determining the level(s) of at least one marker selected from the group of Proliferating Cell Nuclear Antigen (PCNA), cyclin D1, cyclin D3, MAPK-ERK kinase 1 (MEK), ribosomal protein S6 (S6), phosphorylated ribosomal protein S6 (pS6), extracellular signal-regulated kinase (ERK), phosphorylated extracellular signal-regulated kinase (pERK), protein kinase B (Akt), phosphorylated protein kinase B (pAkt), caspase-2, total ribosomal protein S6, and retinoblastoma binding protein (RBBP) in the first sample; (d) administering a treatment for PKD to the PKD patient; (e) providing a second sample comprising a biological fluid obtained from the PKD patient at a second time point after step (d) and performing steps (b) and (c) on the second sample; and (f) identifying the administered treatment as being effective if the level is decreased at the second time point as compared to the first time point. In some embodiments of any of the method described herein, the administered treatment is administration of a glucosyl ceramide synthase (GCS) inhibitor. In some embodiments of any of the method described herein, the GCS inhibitor is selected from the group of: (S)-quinuclidin-3-yl (2-(4′-(2-methoxyethoxy)-[1,1′-biphenyl]-4-yl)propan-2-yl)carbamate; 4-fluoro-1-(5-fluoro-4-(4-((2-methoxyethoxy)methyl)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo [3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-((2-methoxyethoxy) methyl)phenyl)pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-((2-methoxyethoxy)methyl)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(methoxymethyl) phenyl)pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(methoxymethyl)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-methoxyethoxy)phenyl)pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-methoxyethoxy)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-fluoroethoxy)phenyl)pyrimidin-2-yl)-N-(quinuclidin-3-yl)piperidine-4-carboxamide; and 4-fluoro-1-(4-(4-(2-fluoroethoxy)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide.
Some embodiments of any of the methods described herein further include after (f): (g) administering additional doses of the administered GCS inhibitor identified as being effective to the PKD patient. In some embodiments of any of the methods described herein, in step (g) the PKD patient is administered additional doses of: (S)-quinuclidin-3-yl (2-(4′-(2-methoxyethoxy)-[1,1′-biphenyl]-4-yl)propan-2-yl)carbamate; 4-fluoro-1-(5-fluoro-4-(4-((2-methoxyethoxy)methyl)phenyl) pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-((2-methoxyethoxy)methyl)phenyl)pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-((2-methoxyethoxy)methyl)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(methoxymethyl)phenyl) pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(methoxymethyl) phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-methoxyethoxy)phenyl) pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-methoxyethoxy)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-fluoroethoxy)phenyl) pyrimidin-2-yl)-N-(quinuclidin-3-yl)piperidine-4-carboxamide; or 4-fluoro-1-(4-(4-(2-fluoroethoxy)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide.
In some embodiments of any of the methods described herein, steps (c) and (e) include determining the levels of at least two markers selected from the group consisting of PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the administered treatment is identified as being effective if at least one of the two levels is decreased at the second time point as compared to the first time point. In some embodiments of any of the methods described herein, the administered treatment is identified as being effective if both levels are decreased at the second time point as compared to the first time point.
In some embodiments of any of the methods described herein, steps (c) and (e) include determining the levels of at least three markers selected from the group of PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the administered treatment is identified as being effective if at least one of the three levels is decreased at the second time point as compared to the first time point. In some embodiments of any of the methods described herein, the administered treatment is identified as being effective if all three levels are decreased at the second time point as compared to the first time point.
In some embodiments of any of the methods described herein, steps (c) and (e) include determining the levels of at least four markers selected from the group of PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the administered treatment is identified as being effective if at least one of the four levels is decreased at the second time point as compared to the first time point. In some embodiments of any of the methods described herein, the administered treatment is identified as being effective if all four levels are decreased at the second time point as compared to the first time point. In some embodiments of any of the methods described herein, the administered treatment is administration of a CDK inhibitor (e.g., R-roscovitine) to the PKD patient.
In some embodiments of any of the methods described herein, the concentrating in (b) and (e) includes ultracentrifuging the first and second samples, respectively. In some embodiments of any of the methods described herein, the first and second samples include urine.
In some embodiments of any of the methods described herein, determining the level(s) of at least one marker in (c) and (e) include determining the level of protein of the at least one marker. In some embodiments of any of the methods described herein, steps (c) and (e) include contacting the sample with antibodies that bind specifically to the protein of the at least one marker. In some embodiments of any of the methods described herein, steps (c) and (e) include determining the level of one or both of cyclin D1 and MEK.
Some embodiments of any of the methods described herein further include after (f): (g) administering additional doses of the administered treatment identified as being effective to the PKD patient. In some embodiments of any of the methods described herein, the administered treatment identified as being effective is a CDK inhibitor, and in step (g) the PKD patient is administered additional doses of the CDK inhibitor (e.g., S-CR8).
Also provided are methods of determining the efficacy of treatment in a patient identified as having polycystic kidney disease (PKD) that include: (a) providing a first sample including a biological fluid obtained from the PKD patient at a first time point; (b) determining the level(s) of at least one marker selected from the group of Proliferating Cell Nuclear Antigen (PCNA), cyclin D1, cyclin D3, MAPK-ERK kinase 1 (MEK), ribosomal protein S6 (S6), phosphorylated ribosomal protein S6 (pS6), extracellular signal-regulated kinase (ERK), phosphorylated extracellular signal-regulated kinase (pERK), protein kinase B (Akt), phosphorylated protein kinase B (pAkt), caspase-2, total S6, and retinoblastoma binding protein (RBBP) in the first sample; (c) administering a treatment for PKD to the PKD patient; (d) providing a second sample comprising a biological fluid obtained from the patient at a second time point after step (c) and performing step (b) on the second sample; and (e) identifying the administered treatment as being effective if the level is decreased at the second time point as compared to the level at the first time point. In some embodiments of any of the methods described herein, the administered treatment is administration of a glucosyl ceramide synthase (GCS) inhibitor. In some embodiments of any of the methods described herein, the GCS inhibitor is selected from the group consisting of: (S)-quinuclidin-3-yl (2-(4′-(2-methoxyethoxy)-[1,1′-biphenyl]-4-yl)propan-2-yl)carbamate; 4-fluoro-1-(5-fluoro-4-(4-((2-methoxyethoxy) methyl)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl) piperidine-4-carboxamide; 4-fluoro-1-(4-(4-((2-methoxyethoxy)methyl)phenyl) pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-((2-methoxyethoxy)methyl)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo [3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(methoxymethyl) phenyl)pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(methoxymethyl)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo [3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-methoxyethoxy) phenyl)pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-methoxyethoxy)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo [3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-fluoroethoxy) phenyl)pyrimidin-2-yl)-N-(quinuclidin-3-yl)piperidine-4-carboxamide; and 4-fluoro-1-(4-(4-(2-fluoroethoxy)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide.
Some embodiments of any of the methods described herein further include after (e): (f) administering additional doses of the administered GCS inhibitor identified as being effective to the PKD patient. In some embodiments of any of the methods described herein, in step (f) the PKD patient is administered additional doses of: (S)-quinuclidin-3-yl (2-(4′-(2-methoxyethoxy)-[1,1′-biphenyl]-4-yl)propan-2-yl)carbamate; 4-fluoro-1-(5-fluoro-4-(4-((2-methoxyethoxy)methyl)phenyl) pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-((2-methoxyethoxy)methyl)phenyl)pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-((2-methoxyethoxy) methyl)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo [3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(methoxymethyl) phenyl)pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(methoxymethyl)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo [3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-methoxyethoxy) phenyl)pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-methoxyethoxy)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-fluoroethoxy)phenyl)pyrimidin-2-yl)-N-(quinuclidin-3-yl)piperidine-4-carboxamide; or 4-fluoro-1-(4-(4-(2-fluoroethoxy)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide.
In some embodiments of any of the methods described herein, steps (b) and (d) include determining the levels of at least two markers selected from the group of PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the administered treatment is identified as being effective if at least one of the two levels is decreased at the second time point as compared to the first time point. In some embodiments of any of the methods described herein, the administered treatment is identified being effective if both levels are decreased at the second time point as compared to the first time point.
In some embodiments of any of the methods described herein, steps (b) and (d) include determining the levels of at least three markers selected from the group consisting of PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the administered treatment is identified as being effective if at least one of the three levels is decreased at the second time point as compared to the first time point. In some embodiments of any of the methods described herein, the administered treatment is identified as being effective if all three levels are decreased at the second time point as compared to the first time point.
In some embodiments of any of the methods described herein, steps (b) and (d) include determining the levels of at least four markers selected from the group of PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the administered treatment is identified as being effective if at least one of the four levels is decreased at the second time point as compared to the first time point. In some embodiments of any of the methods described herein, the administered treatment is identified as being effective if all four levels are decreased at the second time point as compared to the first time point. In some embodiments of any of the methods described herein, the administered treatment is administration of a CDK inhibitor or R-roscovitine.
In some embodiments of any of the methods described herein, determining the level(s) of at least one marker in (b) and (d) includes determining the level of protein of the at least one marker. In some embodiments of any of the methods described herein, steps (b) and (d) include contacting the sample with antibodies that bind specifically to the protein of the at least one marker. In some embodiments of any of the methods described herein, steps (b) and (d) include determining the level of at least two of PCNA, cyclin D3, pERK, and Akt. Some embodiments of any of the methods described herein further include after (e): (f) administering additional doses of the administered treatment identified as being effective to the PKD patient. In some embodiments of any of the methods described herein, the administered treatment identified as being effective is a CDK inhibitor, and in step (f) the PKD patient is administered additional doses of the CDK inhibitor. In some embodiments of any of the methods described herein, in step (f) the PKD patient is administered additional doses of roscovitine.
Also provided are methods of diagnosing polycystic kidney disease (PKD) in a patient that include: (a) providing a sample including a biological fluid from a patient suspected of having PKD; (b) concentrating the sample for exosomes; (c) determining the level(s) of at least one marker selected from the group of Proliferating Cell Nuclear Antigen (PCNA), cyclin D1, cyclin D3, MAPK-ERK kinase 1 (MEK), ribosomal protein S6 (S6), phosphorylated ribosomal protein S6 (pS6), extracellular signal-regulated kinase (ERK), phosphorylated extracellular signal-regulated kinase (pERK), protein kinase B (Akt), phosphorylated protein kinase B (pAkt), caspase-2, total S6, and retinoblastoma binding protein (RBBP) in the sample; and (d) identifying the patient as having PKD if the level is elevated as compared to a control level. In some embodiments of any of the methods described herein, step (c) includes determining the levels of at least two markers selected from the group of PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the patient is identified as having PKD if at least one of the two levels are elevated as compared to control level(s). In some embodiments of any of the methods described herein, the patient is identified as having PKD if both levels are elevated as compared to control levels.
In some embodiments of any of the methods described herein, step (c) includes determining the levels of at least three markers selected from the group consisting of PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the patient is identified as having PKD if at least one of the three levels are elevated as compared to control levels. In some embodiments of any of the methods described herein, the patient is identified as having PKD if all three levels are elevated as compared to control levels.
In some embodiments of any of the methods described herein, step (c) includes determining the levels of at least four markers selected from the group of PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the patient is identified as having PKD if at least one of the four levels are elevated as compared to control levels. In some embodiments of any of the methods described herein, the patient is identified as having PKD if all four levels are elevated as compared to control levels.
In some embodiments of any of the methods described herein, concentrating in (b) includes ultracentrifuging the sample. In some embodiments of any of the methods described herein, the sample includes urine. In some embodiments of any of the methods described herein, determining the level(s) of at least one marker in (c) includes determining the level of protein of the at least one marker. In some embodiments of any of the methods described herein, step (c) includes contacting the sample with antibodies that bind specifically to the protein of the at least one marker.
In some embodiments of any of the methods described herein, step (c) includes determining the level of at least two of PCNA, cyclin D1, cyclin D3, MEK, S6, and phosphorylated S6. Some embodiments of any of the methods described herein further include after step (d): (e) administering a treatment for PKD to a patient identified as having PKD. In some embodiments of any of the methods described herein, the treatment is administering a glucosyl ceramide synthase (GCS) inhibitor to the patient. In some embodiments of any of the methods described herein, the GCS inhibitor is selected from the group of: (S)-quinuclidin-3-yl (2-(4′-(2-methoxyethoxy)-[1,1′-biphenyl]-4-yl)propan-2-yl)carbamate; 4-fluoro-1-(5-fluoro-4-(4-((2-methoxyethoxy) methyl)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-((2-methoxyethoxy)methyl) phenyl)pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-((2-methoxyethoxy)methyl)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(methoxymethyl)phenyl)pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(methoxymethyl)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-methoxyethoxy)phenyl)pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-methoxyethoxy)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-fluoroethoxy)phenyl)pyrimidin-2-yl)-N-(quinuclidin-3-yl)piperidine-4-carboxamide; and 4-fluoro-1-(4-(4-(2-fluoroethoxy)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide.
In some embodiments of any of the methods described herein, the treatment is administering a CDK inhibitor to the patient (e.g., S-CR8). Some embodiments of any of the methods described herein further include after (d): (e) imaging one or both kidney(s) in a patient identified as having PKD. In some embodiments of any of the methods described herein, the control level is a threshold level or a level in a healthy subject or a population of healthy subjects.
Also provided are methods of diagnosing polycystic kidney disease (PKD) in a patient that include: (a) providing a sample including kidney tissue from a patient suspected of having PKD; (b) determining the level(s) of at least one marker selected from the group consisting of Proliferating Cell Nuclear Antigen (PCNA), cyclin D1, cyclin D3, MAPK-ERK kinase 1 (MEK), ribosomal protein S6 (S6), phosphorylated ribosomal protein S6 (pS6), extracellular signal-regulated kinase (ERK), phosphorylated extracellular signal-regulated kinase (pERK), protein kinase B (Akt), phosphorylated protein kinase B (pAkt), caspase-2, total S6, and retinoblastoma binding protein (RBBP) in the sample; and (c) identifying the patient as having PKD if the level is elevated as compared to a control level. In some embodiments of any of the methods described herein, step (b) includes determining the levels of at least two markers selected from the group of PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the patient is identified as having PKD if at least one of the two levels are elevated as compared to control level(s). In some embodiments of any of the methods described herein, the patient is identified as having PKD if both levels are elevated as compared to control levels.
In some embodiments of any of the methods described herein, step (b) includes determining the levels of at least three markers selected from the group of PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the patient is identified as having PKD if at least one of the three levels are elevated as compared to control levels. In some embodiments of any of the methods described herein, the patient is identified as having PKD if all three levels are elevated as compared to control levels.
In some embodiments of any of the methods described herein, step (b) includes determining the levels of at least four markers selected from the group of PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the patient is identified as having PKD if at least one of the four levels are elevated as compared to control levels. In some embodiments of any of the methods described herein, the patient is identified as having PKD if all four levels are elevated as compared to control levels. In some embodiments of any of the methods described herein, determining the level(s) of at least one marker in (b) includes determining the level of protein of the at least one marker. In some embodiments of any of the methods described herein, step (b) includes contacting the sample with antibodies that bind specifically to the protein of the at least one marker. In some embodiments of any of the methods described herein, step (b) includes determining the level of at least two of cyclin D1, MEK, ERK, pAkt, Akt, S6, and pS6.
Some embodiments of any of the methods described herein further include after step (c): (d) administering a treatment for PKD to a patient identified as having PKD. In some embodiments of any of the methods described herein, the treatment is administering a glucosyl ceramide synthase (GCS) inhibitor to the patient. In some embodiments of any of the methods described herein, the GCS inhibitor is selected from the group of: (S)-quinuclidin-3-yl (2-(4′-(2-methoxyethoxy)-[1,1′-biphenyl]-4-yl)propan-2-yl)carbamate; 4-fluoro-1-(5-fluoro-4-(4-((2-methoxyethoxy)methyl) phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-((2-methoxyethoxy)methyl)phenyl)pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-((2-methoxyethoxy)methyl)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(methoxymethyl)phenyl) pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(methoxymethyl) phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-methoxyethoxy)phenyl) pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-methoxyethoxy)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-fluoroethoxy)phenyl) pyrimidin-2-yl)-N-(quinuclidin-3-yl)piperidine-4-carboxamide; and 4-fluoro-1-(4-(4-(2-fluoroethoxy)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide.
In some embodiments of any of the methods described herein, the treatment is administering a CDK inhibitor (e.g., S-CR8) to the patient. Some embodiments of any of the methods described herein further include after (c): (d) imaging one or both kidney(s) in a patient identified as having PKD.
Also provided are methods of determining the stage of polycystic kidney disease (PKD) in a patient that include: (a) providing a sample including a biological fluid from a patient suspected of having PKD or identified as having PKD; (b) concentrating the sample for exosomes; (c) determining the level(s) of at least one marker selected from the group of Proliferating Cell Nuclear Antigen (PCNA), cyclin D1, cyclin D3, MAPK-ERK kinase 1 (MEK), ribosomal protein S6 (S6), phosphorylated ribosomal protein S6 (pS6), extracellular signal-regulated kinase (ERK), phosphorylated extracellular signal-regulated kinase (pERK), protein kinase B (Akt), phosphorylated protein kinase B (pAkt), caspase-2, total S6, and retinoblastoma binding protein (RBBP) in the sample; and (d) determining the stage of PKD in the patient from the level. In some embodiments of any of the methods described herein, step (c) includes determining the levels of at least two markers selected from the group of PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the stage of PKD in the patient is determined from at least one of the two levels. In some embodiments of any of the methods described herein, the stage of PKD in the patient is determined from both levels.
In some embodiments of any of the methods described herein, step (c) includes determining the levels of at least three markers selected from the group of PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the stage of PKD in the patient is determined from at least one of the three levels. In some embodiments of any of the methods described herein, the stage of PKD in the patient is determined from all three levels.
In some embodiments of any of the methods described herein, step (c) includes determining the levels of at least four markers selected from the group of PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the stage of PKD in the patient is determined from at least one of the four levels. In some embodiments of any of the methods described herein, the stage of PKD in the patient is determined from all four levels. In some embodiments of any of the methods described herein, the concentrating in step (b) includes ultracentrifuging the sample. In some embodiments of any of the methods described herein, the sample comprises urine. In some embodiments of any of the methods described herein, determining the level(s) of at least one marker in (c) includes determining the level of protein of the at least one marker. In some embodiments of any of the methods described herein, step (c) includes contacting the sample with antibodies that bind specifically to the protein of the at least one marker.
In some embodiments of any of the methods described herein, step (c) includes determining the level of at least two of PCNA, cyclin D3, MEK, and phosphorylated S6. Some embodiments of any of the methods described herein further include after (d): (e) administering a treatment for stage I, stage II, stage III, stage IV, or stage V PKD to a patient identified to have stage I, stage II, stage III, stage IV, or stage V PKD, respectively. Some embodiments of any of the methods described herein further include after (d): (e) imaging one or both kidney(s) in a patient after (d) to confirm the stage of PKD in the patient.
Also provided are methods of monitoring polycystic kidney disease (PKD) patient that include: (a) providing a first sample including a biological fluid obtained from the PKD patient at a first time point; (b) concentrating the first sample for exosomes; (c) determining the level(s) of at least one marker selected from the group of Proliferating Cell Nuclear Antigen (PCNA), cyclin D1, cyclin D3, MAPK-ERK kinase 1 (MEK), ribosomal protein S6 (S6), phosphorylated ribosomal protein S6 (pS6), extracellular signal-regulated kinase (ERK), phosphorylated extracellular signal-regulated kinase (pERK), protein kinase B (Akt), phosphorylated protein kinase B (pAkt), caspase-2, total S6, and retinoblastoma binding protein (RBBP) in the first sample; (d) providing a second sample including a biological fluid obtained from the PKD patient at a second time point after the first time point, and performing steps (b) and (c) on the second sample; and (e) identifying the patient as having improving or static PKD if the level is not elevated at the second time point as compared to the level at the first time point. In some embodiments of any of the methods described herein, steps (c) and (d) include determining the levels of at least two markers selected from the group consisting of PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the patient is identified as having improving or static PKD if at least one of the two levels is not elevated at the second time point as compared to the first time point. In some embodiments of any of the methods described herein, the patient is identified as having improving or static PKD if both levels are not elevated at the second time point as compared to the first time point.
In some embodiments of any of the methods described herein, steps (c) and (d) include determining the levels of at least three markers selected from the group of PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the patient is identified as having improving or static PKD if at least one of the three levels is not elevated at the second time point as compared to the first time point. In some embodiments of any of the methods described herein, the patient is identified as having improving or static PKD if all three levels are not elevated at the second time point as compared to the first time point.
In some embodiments of any of the methods described herein, steps (c) and (d) include determining the levels of at least four markers selected from the group of PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the patient is identified as having improving or static PKD if at least one of the four levels are not elevated at the second time point as compared to the first time point. In some embodiments of any of the methods described herein, the patient is identified as having improving or static PKD if all four levels are not elevated at the second time point as compared to the first time point. In some embodiments of any of the methods described herein, the concentrating in (b) and (d) includes ultracentrifuging the sample. In some embodiments of any of the methods described herein, the first and second samples comprise urine. In some embodiments of any of the methods described herein, determining the level(s) of at least one marker in steps (c) and (d) include determining the level of protein of the at least one marker. In some embodiments of any of the methods described herein, steps (c) and (d) include contacting the sample with antibodies that bind specifically to the protein of the at least one marker. In some embodiments of any of the methods described herein, steps (c) and (d) include determining the level of at least two of PCNA, cyclin D3, MEK, and phosphorylated S6. Some embodiments of any of the methods described herein further include after (e): (f) administering the same treatment to a patient identified as having improving or static PKD.
Also provided are kits that include, consist essentially of, or consist of at least three antibodies selected from the group of: an antibody that specifically binds to Proliferating Cell Nuclear Antigen (PCNA), an antibody that specifically binds to cyclin D1, an antibody that specifically binds to cyclin D3, an antibody that specifically binds to MAPK-ERK kinase 1 (MEK), an antibody that specifically binds to ribosomal protein S6 (S6), an antibody that specifically binds to phosphorylated ribosomal protein S6 (pS6), an antibody that specifically binds to extracellular signal-regulated kinase (ERK), an antibody that specifically binds to phosphorylated extracellular signal-regulated kinase (pERK), an antibody that specifically binds to protein kinase B, an antibody that specifically binds to phosphorylated protein kinase B (pAkt), an antibody that specifically binds to caspase-2, and an antibody that specifically binds to retinoblastoma binding protein (RBBP).
As used herein, the word “a” before a noun represents one or more of the particular noun. For example, the phrase “a marker” represents “one or more markers.”
The term “patient” means a vertebrate, including any member of the class mammalia, including humans, domestic and farm animals, and zoo, sports or pet animals, such as mouse, rabbit, pig, sheep, goat, cattle, horse (e.g., race horse), and higher primates. In preferred embodiments, the patient is a human.
The term “biological fluid” means any fluid obtained from a mammalian patient (e.g., blood, plasma, serum, or other blood fractions, lymph, urine, cerebrospinal fluid, ascites, saliva, breast milk, tears, vaginal discharge, amniotic fluid, lavage, semen, glandular secretions, exudate, and contents of cysts or feces). In preferred embodiments, the biological fluid is urine, blood, serum, or plasma.
The term “exosome” is art known and means a lipid-based microparticle or nanoparticle, or protein-rich aggregate, present in a sample (e.g., a biological fluid) obtained from a patient. Exosomes are also referred to in the art as extracellular vesicles, microvesicles, or nanovesicles. In the present disclosure, an extracellular vesicle can be between about 20 nm to about 1 m (e.g., 20 nm to about 90 nm) in diameter. The size of vesicles may also be much higher where the diameter is in the micron range, e.g. 1-10 m. Exosomes are secreted or shed from a variety of different mammalian cell types. Non-limiting examples of exosomes and methods for concentrating a sample (e.g., a biological fluid) for exosomes are described herein. Additional examples of exosomes and methods for concentrating a sample for exosomes are known in the art.
The phrase “concentrating a sample for exosomes” is art known and means one or more manipulations of a sample to increase the concentration of exosomes. The step of concentrating a sample for exosomes can, for example, include one or more of the following: centrifuging the sample (e.g, ultracentrifugation, optionally in a density gradient), passing the sample through a chromatography column (e.g., an affinity or molecular sieve chromatography column, such as a spin column), and the use of antibodies that specifically bind to an antigen on the surface of an exosome and/or a bead (e.g., a bead coated with the antibodies that specifically bind to the antigen on the surface of an exosome or a bead coated with a molecule that binds specifically to the antibody that specifically binds to the antigen on the surface of the exosome). Exemplary methods of concentrating a sample for examples are described herein and additional methods are known in the art.
Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Methods and materials are described herein for use in the present invention; other, suitable methods and materials known in the art can also be used. The materials, methods, and examples are illustrative only and not intended to be limiting. All publications, patent applications, patents, sequences, database entries, and other references mentioned herein are incorporated by reference in their entirety. In case of conflict, the present specification, including definitions, will control.
Other features and advantages of the invention will be apparent from the following detailed description and figures, and from the claims.
Provided herein are methods for determining the efficacy of treatment for PKD in a patient, diagnosing PKD in a patient, staging PKD in a patient, and monitoring PKD in a patient that include determining a single or multiple levels of one or more markers selected from the group of Proliferating Cell Nuclear Antigen (PCNA), cyclin D1, cyclin D3, MAPK-ERK kinase 1 (MEK), ribosomal protein S6 (S6), phosphorylated ribosomal protein S6 (pS6), extracellular signal-regulated kinase (ERK), phosphorylated extracellular signal-regulated kinase (pERK), protein kinase B (Akt), phosphorylated protein kinase B (pAkt), caspase-2, total ribosomal protein S6, and retinoblastoma binding protein (RBBP). Also provided are kits comprising at least three antibodies selected from the group consisting of: an antibody that specifically binds to PCNA, an antibody that specifically binds to cyclin D1, an antibody that specifically binds to cyclin D3, an antibody that specifically binds to MEK, an antibody that specifically binds to S6, an antibody that specifically binds to pS6, an antibody that specifically binds to ERK, an antibody that specifically binds to pERK, an antibody that specifically binds to Akt, an antibody that specifically binds to pAkt, an antibody that specifically binds to caspase-2, and an antibody that specifically binds to RBBP. Non-limiting aspects of these methods are described below. As can be appreciated in the art, the various aspects described below can be used in any combination without limitation.
The methods described herein can further include a step of identifying or diagnosing a patient as having PKD. Non-limiting examples of diagnosing a patient as having PKD are provided herein and are described below.
In other examples, a patient is identified as having PKD based on the observation or assessment of one or more symptoms of the following symptoms in a patient: high blood pressure, back or side pain, headache, increased size of abdomen, presence of blood in urine, frequent urination, kidney stones, kidney failure, urinary tract or kidney infections, cysts on the kidney, cysts on the liver, pancreatic cysts, mitral valve prolapse, aneurysms, nausea, vomiting, left ventricular hypertrophy, hernia, diverticulitis, fatigue, poor appetite, weight loss, trouble concentrating, dry/itchy skin, muscle cramps, swelling in feet and ankles, mild to moderate depression, and bubbly urine. PKD can also be diagnosed in a subject by performing a genetic test (see, e.g., PKD1 genetic diagnostic tests from a variety of vendors including Athena Diagnostics (Worcester, Mass.) and CGC Genetics (Porto, Portugal); PKD2 genetic diagnostic tests from a variety of ventors including Centrogene AG (Germany), PreventionGenetics (Marshfield, Wis.), GCG Genetics (Portugal), and InVitae Corporation (San Francisco, Calif.); and PKHD1 genetic diagnostic tests are available from a variety of vendors including Centrogene AG (Germany), Prevention Genetics (Marshfield, Wis.), Counsyl (San Francisco, Calif.), and Invitae (San Francisco, Calif.)). The detection of mutations or deletions of the PKD1 and/or PKD2 genes can be used to diagnose autosomal dominant PKD, and the detection of mutations or deletions in PKHD1 can be used to diagnose autosomal recessive PKD.
PKD (e.g., autosomal dominant PKD and autosomal recessive PKD) can be diagnosed by performing imaging studies. For example, ultrasound, computerized tomography (CT), and magnetic resonance imaging (MRI) can be used to look for cysts on the kidney(s) and to determine the total kidney volume (TKV) or height-adjusted total kidney volume (htTKV). For example, the detection of at least two cysts (e.g., at least three, four, five, or six cysts) on each kidney by age 30 in a patient (e.g., a patient with a family history of the disease) can confirm the diagnosis of PKD. The detection of a multicystic dysplastic kidney(s) in a fetus (e.g., a fetus that is greater than 14 weeks of gestation) can be used to diagnose autosomal recessive PKD. In addition, the amniotic fluid from a fetus can be used to detect a mutation or deletion in PKHD1 (e.g., using any of the genetic diagnostic tests for PKHD1 described herein or known in the art).
PKD can also be diagnosed or identified in a subject, in part, by determining a patient's kidney function. For example, PKD can be diagnosed and identified in part by measuring one or more of a patient's creatinine level (e.g., a level of creatinine greater than 1.3 mg/dL indicating that the patient has PKD), glomerular filtration rate (e.g., a rate that is below 80 mL/minutes indicates that the patient has PKD), and blood urea nitrogen (e.g., a blood urea nitrogen level of greater than 20 mg/dL).
The PKD patients described herein can be diagnosed or identified using any of the methods described or provided herein, or any methods known in the art. The PKD patient can be in utero (e.g., a fetus with a gestational age greater than 14 weeks, 15 weeks, 17 weeks, 20 weeks, 25 weeks, 30 weeks, or 35 weeks), an infant, an adolescent (between 13 and 18 years old (e.g., between 13 and 15 years old or between 15 and 18 years old), or an adult (greater than 18 years old (e.g., greater than 20, 22, 24, 26, 28, 30, 32, 34, 36, 38, 40, 45, 50, 55, 60, 65, 70, 75, 80, 85, 90, or 95 years old). The PKD patient can be a female (e.g., a pregnant female) or can be a male. The PKD patient may already be receiving a treatment for PKD. In other examples, the PKD patient may not have received a treatment for a PKD. In additional examples, the PKD patient may have received a previous treatment for PKD and the previous treatment was therapeutically unsuccessful (e.g., lead to the development of negative adverse side effects, did not reduce the rate of development and/or growth of cysts, and/or did not reduce the rate of loss in the function of the patient's kidney(s)). The PKD patient may be a participant in a clinical study.
Some examples of a treatment for PKD is the administration of one or more glucosylceramide synthase (GCS) inhibitors. Non-limiting examples of GSC inhibitors are described in Lee et al. (J. Biol. Chem. 274:14662-14669, 1999), Shayman et al. (Methods Enzymol. 311:373-387, 2000), Huang et al. (FASEB J. 25:3661-3673, 2011), Kolton et al. (Bioorg. Med. Chem. Lett. 21:6773-6777, 2011), Larsen et al. (J. Lipid Res. 53:282-291, 2012), Niino et al. (Biochem. Biophys. Res. Comm. 433:170-174, 2013), Richards et al. (J. Med. Chem. 55:4322-4325, 2012), Nietupski et al. (Mol. Genet. Metab. 105:621-628, 2012), Ashe et al. (PLoS One 6:e21758, 2011), Shayman (Drugs Future 35:613-620, 2010), Bijl et al. (J. Pharmacol. Exp. Ther 326:849-855, 2008), Treiber et al. (Xenobiotica 37:298-314, 2007), McEachern et al. (Mol. Genet. Metab. 91:259-267, 2007), Wennekes et al. (Diabetes 56:1341-1349, 2007), Jimbo et al. (J. Biochem. 127:485-291, 2000), Miura et al. (Bioorg. Med. Chem. 6:1481-1489, 1998), Abe et al. (J. Biochem. 111:191-196, 1992), Inokuchi et al. (J. Cell Physiol. 141:573-583, 1989), and Inokuchi et al. (J. Lipid Res. 28:565-571, 1987). Additional examples of GCS inhibitors are described in U.S. Patent Application Publication Nos. 2013/0225573, 2013/0137743, 2013/0095089, 2012/0322787, 2012/0322786, 2011/0184021, 2011/0166134, 2010/0256216, and 2007/0259918 (each of which is hereby incorporated by reference).
Additional examples of GCS inhibitors are described in WO 14/043068 (incorporated herein by reference). For example, a GCS inhibitor can have a structure represented by Formula I below.
wherein:
n is 1, 2, or 3;
m is 0 or 1;
p is 0 or 1;
t is 0, 1, or 2;
E is S, O, NH, NOH, NNO2, NCN, NR, NOR or NSO2R;
X1 is CR1 when m is 1 or N when m is 0;
X2 is O, —NH, —CH2, SO2, NH—SO2, CH(C1-C6) alkyl or —NR2;
X3 is a direct bond, O, —NH, —CH2—, CO, —CH(C1-C6) alkyl, SO2NH, —CO—NH—, or NR3;
X4 is a direct bond, CR4R5, CH2CR4R5 or CH2—(C1-C6) alkyl-CR4R5;
X5 is a direct bond, O, S, SO2, CR4R5, (C1-C6)alkyl, (C1-C6)alkyloxy, —O—(C1-C6)alkyl, (C1-C6)alkenyl, (C1-C6)alkenyloxy, —R7—(C3-C10)cycloalkyl, (C3-C10)cycloalkyl-R7—, —R7—(C6-C12)aryl, (C6-C12)aryl-R7—, —R7—(C2-C9)heteroaryl, (C2-C9)heteroaryl-R7—, —R7—(C2-C9)heterocycloalkyl, and (C2-C9)heterocycloalkyl-R7—, wherein R7 is a direct bond, O, S, SO2, CR4R5, (C1-C6)alkyl, (C1-C6)alkyloxy, —O—(C1-C6)alkyl, (C1-C6)alkenyl, (C1-C6)alkenyloxy; and further wherein when X5 is defined as —R7—(C3-C10)cycloalkyl, (C3-C10)cycloalkyl-R7—, —R7—(C6-C12)aryl, (C6-C12)aryl-R7—, —R7—(C2-C9)heteroaryl, (C2-C9)heteroaryl-R7—, —R7—(C2-C9) heterocycloalkyl, and (C2-C9)heterocycloalkyl-R7—, wherein the (C3-C10)cycloalkyl, (C6-C12) aryl, (C2-C9)heteroaryl, (C2-C9) heterocycloalkyl groups are optionally substituted by one or more substituents selected from the group consisting of halo, (C1-C6)alkyl, (C1-C6) alkylenyl, amino, (C1-C6) alkylamino, (C1-C6)dialkylamino, (C1-C6)alkoxy, O(C3-C6 cycloalkyl), (C3-C6) cycloalkoxy, nitro, CN, OH, (C1-C6)alkyloxy, (C3-C6) cycloalkyl, (C1-C6) alkoxycarbonyl, (C1-C6) alkylcarbonyl, (C1-C6)halo alkyl, (C2-C9)heterocycloalkyl, R8R9N—CO— wherein R8 and R9 are each independently selected from the group consisting of hydrogen and (C1-C6)alkyl or R8 and R9 can be taken together with the nitrogen to which they are attached to form a (C2-C9)heterocycloalkyl or (C2-C9)heterocycloalkyl group optionally substituted by one to three halo groups, (C1-C6)alkylsulfonyl optionally substituted by one or two groups selected from (C1-C6)alkoxy and (C3-C10)cycloalkyl;
(C1-C6)alkyl substituted by one to four substituents selected from the group consisting of halo, hydroxy, cyano, (C1-C6)alkoxy, (C1-C6)alkoxy(C1-C6)alkoxy, (C2-C9)heterocycloalkyl, (C2-C9)heteroaryl optionally substituted by (C1-C6)alkoxy; or (C3-C10)cycloalkoxy optionally substituted by (C1-C6)alkoxy; and
(C1-C6)alkyloxy substituted by one to four substituents selected from the group consisting of halo, hydroxy, cyano, (C1-C6)alkoxy, (C1-C6)alkoxy(C1-C6)alkoxy, (C2-C9)heterocycloalkyl, (C2-C9)heteroaryl optionally substituted by (C1-C6)alkoxy; or (C3-C10)cycloalkoxy optionally substituted by (C1-C6)alkoxy;
R is (C6-C12)aryl, (C2-C9)heteroaryl, (C1-C6)alkyl, (C2-C9)heteroaryl(C1-C6)alkyl; R1 is H, CN, (C1-C6)alkylcarbonyl, or (C1-C6)alkyl;
R2 and R3 are each independently —H, (C1-C6)alkyl optionally substituted by one or more substituents selected from the group consisting of halogen, (C1-C6)alkyl, (C6-C12)aryl, (C2-C9)heteroaryl, (C1-C6)alkyl(C6-C12)aryl, halo(C6-C12)aryl, and halo(C2-C9)heteroaryl, or optionally when X2 is —NR2 and X3 is —NR3, R2 and R3 may be taken together with the nitrogen atoms to which they are attached form a non-aromatic heterocyclic ring optionally substituted by with one or more substituents selected from halogen, (C1-C6)alkyl, (C6-C12)aryl, (C2-C9)heteroaryl, (C1-C6)alkyl(C6-C12)aryl, halo(C6-C12)aryl, and halo(C2-C9)heteroaryl;
R4 and R5 are independently selected from H, (C1-C6)alkyl, or taken together with the carbon to which they are attached to form a spiro (C3-C10)cycloalkyl ring or spiro (C3-C10)cycloalkoxy ring;
R6 is —H, halogen, —CN, (C6-C12)aryl, (C6-C12)aryloxy, (C1-C6)alkyloxy; (C1-C6)alkyl optionally substituted by one to four halo or (C1-C6)alkyl;
A1 is (C2-C6)alkynyl; (C3-C10)cycloalkyl, (C6-C12)aryl, (C2-C9)heteroaryl, (C2-C9)heterocycloalkyl or benzo(C2-C9)heterocycloalkyl wherein A1 is optionally substituted with one or more substituents selected from the group consisting of halo, (C1-C6)alkyl optionally substituted by one to three halo; (C1-C6)alkenyl, amino, (C1-C6)alkylamino, (C1-C6) dialkylamino, (C1-C6)alkoxy, nitro, CN, —OH, (C1-C6)alkyloxy optionally substituted by one to three halo; (C1-C6)alkoxycarbonyl, and (C1-C6) alkylcarbonyl;
A2 is H, (C3-C10)cycloalkyl, (C6-C12)aryl, (C2-C9)heteroaryl, (C2-C9)heterocycloalkyl or benzo(C2-C9)heterocycloalkyl wherein A2 is optionally substituted with one or more substituents selected from the group consisting of halo, (C1-C6)alkyl, (C1-C6)alkylenyl, amino, (C1-C6) alkylamino, (C1-C6)dialkylamino, (C1-C6)alkoxy, O(C3-C6 cycloalkyl), (C3-C6) cycloalkoxy, nitro, CN, OH, (C1-C6)alkyloxy, (C3-C6) cycloalkyl, (C1-C6)alkoxycarbonyl, (C1-C6) alkylcarbonyl, (C1-C6) halo alkyl, (C2-C9)heterocycloalkyl, R8R9N—CO—, wherein R8 and R9 are each independently selected from the group consisting of hydrogen and (C1-C6)alkyl or R8 and R9 can be taken together with the nitrogen to which they are attached to form a (C2-C9)heterocycloalkyl or (C2-C9)heterocycloalkyl group optionally substituted by one to three halo groups, (C1-C6)alkylsulfonyl optionally substituted by one or two groups selected from (C1-C6)alkoxy and (C3-C10)cycloalkyl;
(C1-C6)alkyl substituted by one to four substituents selected from the group consisting of halo, hydroxy, cyano, (C1-C6)alkoxy, (C1-C6)alkoxy(C1-C6)alkoxy, (C2-C9)heterocycloalkyl, (C2-C9)heteroaryl optionally substituted by (C1-C6)alkoxy; or (C3-C10)cycloalkoxy optionally substituted by (C1-C6)alkoxy; and
(C1-C6)alkyloxy substituted by one to four substituents selected from the group consisting of halo, hydroxy, cyano, (C1-C6)alkoxy, (C1-C6)alkoxy(C1-C6)alkoxy, (C2-C9)heterocycloalkyl, (C2-C9)heteroaryl optionally substituted by (C1-C6)alkoxy; or (C3-C10)cycloalkoxy optionally substituted by (C1-C6)alkoxy;
with the proviso that the sum of n+t+Y+z is not greater than 6;
with the proviso that when p is 0; X2 is NH—SO2 and X3 is NH;
with the proviso that when n is 1; t is O; y is 1; z is 1; X2 is NH; E is O; X3 is NH;
A2 is H and X5 is a direct bond; A1 is not unsubstituted phenyl, halophenyl or isopropenyl phenyl;
with the proviso that when n is 1; t is O; y is 1; z is 1; X2 is O; E is O; X3 is NH; A1 is (C6-C12)aryl and X5 is a direct bond; A2 is H and R4 is H then R5 is not cyclohexyl;
with the proviso that when n is 1; t is O; y is 1; z is 1; X2 is NH; E is O; X3 is CH2; R4 and R5 are both hydrogen; A2 is H and X5 is a direct bond; then A1 is not unsubstituted phenyl; and
with the proviso that when X3 is O, —NH, —CH2—, CO, —CH(C1-C6) alkyl, SO2NH, —CO—NH— or —NR3; and X4 is CR4R5, CH2CR4R5 or CH2—(C1-C6) alkyl-CR4R5; then A2 must be (C3-C10)cycloalkyl, (C6-C12)aryl, (C2-C9)heteroaryl, (C2-C9)heterocycloalkyl or benzo(C2-C9)heterocycloalkyl substituted with one or more substituents selected from the group consisting of (C2-C9)heterocycloalkyl, R8R9N—CO— wherein R8 and R9 are each independently selected from the group consisting of hydrogen and (C1-C6)alkyl or R8 and R9 can be taken together with the nitrogen to which they are attached to form a (C2-C9)heterocycloalkyl or (C2-C9)heterocycloalkyl group optionally substituted by one to three halo groups, (C1-C6)alkylsulfonyl optionally substituted by one or two groups selected from (C1-C6)alkoxy and (C3-C10)cycloalkyl;
(C1-C6)alkyl substituted by one to four substituents selected from the group consisting of hydroxy, cyano, (C1-C6)alkoxy, (C1-C6)alkoxy(C1-C6)alkoxy, (C2-C9)heterocycloalkyl, (C2-C9)heteroaryl optionally substituted by (C1-C6)alkoxy; or (C3-C10)cycloalkoxy optionally substituted by (C1-C6)alkoxy;
or (C1-C6)alkyloxy substituted by one to four substituents selected from the group consisting of hydroxy, cyano, (C1-C6)alkoxy, (C1-C6)alkoxy(C1-C6)alkoxy, (C2-C9)heterocycloalkyl, (C2-C9)heteroaryl optionally substituted by (C1-C6)alkoxy; or (C3-C10)cycloalkoxy optionally substituted by (C1-C6)alkoxy.
Additional exemplary GCS inhibitors include: 1-azabicyclo[2.2.2]oct-3-yl [2-(2,4′-difluorobiphenyl-4-yl)propan-2-yl]carbamate; 1-azabicyclo[2.2.2]oct-3-yl {2-[4-(1,3-benzothiazol-6-yl)phenyl]propan-2-yl} carbamate; 1-azabicyclo [3.2.2]non-4-yl {1-[5-(4-fluorophenyl)pyridin-2-yl] cyclopropyl} carbamate; 1-azabicyclo[2.2.2]oct-3-yl {1-[3-(4-fluorophenoxy)phenyl]cyclopropyl} carbamate; 1-azabicyclo[2.2.2]oct-3-yl {1-[4-(1,3-benzothiazol-5-yl)phenyl]cyclopropyl} carbamate; 1-azabicyclo[2.2.2]oct-3-yl [1-(4′-fluoro-3′-methoxybiphenyl-4yl)cyclopropyl] carbamate; 1-azabicyclo [2.2.2]oct-3-yl [3-(4′-fluorobiphenyl-4-yl)oxetan-3-yl] carbamate; 1-azabicyclo[2.2.2]oct-3-yl {1-[6-(4-fluorophenoxy) pyridin-2-yl]cyclopropyl} carbamate; 1-azabicyclo[2.2.2]oct-3-yl [3-(4′-fluorobiphenyl-4-yl)pentan-3-yl] carbamate; 1-azabicyclo[2.2.2]oct-3-yl {2-[2-(4-fluorophenyl)-2H-indazol-6-yl]propan-2-yl} carbamate; 1-azabicyclo[2.2.2]oct-3-yl {2-[2-(IH-pyrrol-1-yl)pyridin-4-yl]propan-2-yl} carbamate; 1-(3-ethyl-1-azabicyclo [2.2.2]oct-3-yl)-3-[1-(4′-fluorobiphenyl-4-yl)cyclopropyl]urea; N—(I-azabicyclo [2.2.2]oct-3-yl)-N′—[I-(4′-fluorobiphenyl-4yl)cyclopropyl]ethanediamide; 1-azabicyclo [2.2.2]oct-3-yl (1-{4[(4,4difluorocyclohexyl)oxy]phenyl} cyclopropyl) carbamate; 1-(4-methyl-1-azabicyclo[3.2.2]non-4-yl)-3-[1-(5-phenylpyridin-2-yl)cyclopropyl]urea; 1-[1-(4′-fluorobiphenyl-4-yl)cyclopropyl]-I-methyl-3-(3-methyl-1-azabicyclo [2.2.2]oct-3-yl)urea; 1-[1-(4′-fluorobiphenyl-4-yl)cyclopropyl]-I-methyl-3-(3-methyl-1-azabicyclo[2.2.2]oct-3-yl)urea; 1-{2-[4′-(2-methoxyethoxy)biphenyl-4-yl]propan-2-yl}-3-(3-methyl-1azabicyclo[2.2.2]oct-3-yl)urea; 2-(1-azabicyclo [3.2.2]non-4-yl)-N-[1-(5-phenylpyridin-2-yl)cyclopropyl] acetamide; 3-(4′-fluorobiphenyl-4-yl)-3-methyl-N-(4-methyl-1-azabicyclo[3.2.2]non-4-5yl)butanamide; N-[2-(biphenyl-4-yl)propan-2-yl]-N′-(3-methyl-1-azabicyclo [2.2.2]oct-3-yl)sulfuric diamide; N-[2-(4′-fluorobiphenyl-4-yl)propan-2-yl]-N′-(3-methyl-1-azabicyclo[2.2.2]oct-3-yl)sulfuric diamide; 1-(3-butyl-1-azabicyclo [2.2.2]oct-3-yl)-3-{2-[1-(4-fluorophenyl)-IH-pyrazol-4-yl]propan-2-yl} urea; 1-azabicyclo[2.2.2]oct-3-yl [4-(4-fluorophenyl)-2-methylbut-3-yn-2-yl]carbamate; 1-(3-butyl-1-azabicyclo[2.2.2]oct-3-yl)-3-[4-(4-fluorophenyl)-2-methylbut-3-yn-2-yl]urea; N—[I-(4′-fluorobiphenyl-4-yl)cyclopropyl]-1,4-diazabicyclo[3.2.2]nonane-4-carboxamide; 1-(2-(4′-fluoro-[I, 1′-biphenyl]-4-yl)propan-2-yl)-3-(3-methyl-1-azabicyclo[3.2.2]nonan-3-yl)urea; 1-(2-(4′-fluoro-[I, 1′-biphenyl]-4-yl)propan-2-yl)-3-(4-methyl-1-azabicyclo[4.2.2]decan-4-yl)urea; 1-(2-(4′-fluoro-[I, 1′-biphenyl]-4-yl)propan-2-yl)-3-(3-methyl-1-azabicyclo[4.2.2]decan-3-yl)urea; and 1-(2-(4′-fluoro-[1, 1′-biphenyl]-4-yl)propan-2-yl)-3-(5-methyl-1-azabicyclo[4.2.2]decan-5-yl)urea.
Additional examples of GCS inhibitors are listed below.
Some examples of a treatment for PKD include the administration of one or more cyclin dependent kinase (CDK) inhibitors. Non-limiting examples of CDK inhibitors include S-CR8, olomoucine, LEE011, palbociclib, P1446A-05, PD-0332991, and R-roscovitine. Additional examples of CDK inhibitors are described in Cicenas et al. (J. Cancer Res. Clin. Oncol. 138:1409-1418, 2011), Blachly et al. (Leuk. Lymphoma 54:2133-2143, 2013), Galons et al. (Expert Opin. Ther. Pat. 20:377-404, 2010), Geyer et al. (Biochim. Biophys. Acta 1754:160-170, 2005). Additional examples of CDK inhibitors are described in U.S. Patent Application Publication Nos. 2006/0178371, 2006/0173017, 2006/0173016, 2006/0135589, 2006/0128725, 2006/0106023, 2006/0041131, 2006/0040958, 2006/0030555, 2005/0261353, 2005/0130980, 2005/0004007, 2004/0248905, 2004/0209878, 2004/0198757, 2004/0116442, 2004/0110775, 2004/0106624, 2004/0102451, 2004/0097517, 2004/0097516, 2004/0073969, 2004/0072835, 2004/0063715, 2004/0048849, 2004/0006074, 2003/0073686, 2002/0065293, 2002/0042412, 2002/0013328, 2002/0002178, and 2001/0025379.
Another example of a treatment for PKD is hemodialysis or peritoneal dialysis. A further example of a treatment for PKD is the surgical transplantation of a kidney.
The methods provided herein include the determination of the level(s) of at least one marker selected from the group of: PCNA, cyclin D1, cyclin D3, MEK, S6, pS6, ERK, pERK, Akt, pAKT, caspase-2, total S6, and RBBP, in at least one sample from a patient (e.g., a PKD patient). For example, the level(s) of one or more marker can be determined in a sample containing a biological fluid (e.g., urine) from the patient (e.g., a PKD patient) (e.g., a sample containing a biological fluid that has been concentrated for exosomes). In some examples, the marker is a protein. In other examples, the marker is a mRNA encoding the marker protein.
Methods for determining the levels of the markers described herein are well understood in the art. For example, the protein level of each marker described herein can be determined using an antibody-based assay (e.g., an enzyme-linked immnosorbent assay, antibody array, antibody-labeled beads, and immunoblots). Exemplary antibodies that can be used in these antibody-based assays are described in the Examples. Additional antibodies that can be used in the antibody-based assays are known in the art. Methods of making antibodies that specifically bind to a marker are also well known in the art. Additional methods for determining the protein level of each marker include mass spectrometry, liquid chromatography (e.g., high performance liquid chromatography) mass spectrometry (LC-MS), and liquid chromatography (e.g., high performance liquid chromatography) tandem mass spectrometry (LC-MS/MS). Non-limiting examples of methods for determining the protein level of a marker in a sample containing a biological fluid (e.g., a sample containing a biological fluid that has been concentrated for exosomes) are described in Pisitkun et al. (Proteomics Clin. Appl. 6:268-278, 2012). These exemplary methods of determining the level(s) of the markers can be used in any of the methods provided herein.
The mRNA level of each marker described herein can be determined, e.g., using a polymerase chain reaction (PCR)-based assay (e.g., real-time PCR and reverse-transcriptase PCR). Additional methods for determining the mRNA level of each marker include the use of a gene chip. Further examples of methods for determining the mRNA level of a marker in a sample containing a biological fluid (e.g., a sample containing a biological fluid that has been concentrated for exosomes) are described in Chen et al. (Lab Chip 10:505-511, 2010), Schageman et al. (BioMed Res. Int., Article ID 253957, 2013), and Alvarez et al. (Kidney Inter. 82:1024-1032, 2012). Additional methods for determining an mRNA level of a marker are well known in the art.
In some examples, a sample (e.g., a sample comprising a biological fluid) from a subject can be stored for a period of time (e.g., stored at least 1 hour (e.g., at least 2, 4, 6, 8, 12, or 24 hours, or at least 1, 2, 3, 4, 5, 6, 7, 14, or 21 days, e.g., at a temperature of about 10° C., about 0° C., about −20° C., about −40° C., about −70° C., or about −80° C.) before the level(s) of the at least one marker are determined in the sample. For example, a sample comprising a biological fluid and concentrated for exosomes can be stored for a period of time (e.g., stored for any of the times and/or temperatures described herein) before the level(s) of the at least one marker are determined in the sample. Some examples further include a step of concentrating a sample containing a biological fluid before the level(s) of the at least one marker (e.g., any marker or any combination of marker described herein) is determined. Non-limiting examples of methods of concentrating a sample containing a biological fluid for exosomes are described herein. In some examples, a biological sample containing a biological fluid that is concentrated for exosomes is stored for a period of time (e.g., stored for any of the times and/or temperatures described herein) before the level(s) of the at least one marker are determined in the sample.
The level(s) of any marker or any combination of markers described herein can be determined in a sample (e.g., a sample containing a biological fluid or a sample containing a biological fluid that has been concentrated for exosomes) in any of the methods described herein. Examples of combinations of markers or single markers that can be determined (i.e., the level determined) in a sample (e.g., a sample containing a biological fluid or a sample containing a biological fluid that has been concentrated for exosomes) in any of the methods described herein are shown in Table 1. A description of each of the markers described herein is provided below.
Proliferating Cell Nuclear Antigen (PCNA) is a 28.8 kDa protein having 261 amino acids. The amino acid sequence of human PCNA is SEQ ID NO: 1. The protein level of PCNA described herein can include the forms of PCNA that are non-phosphorylated and phosphorylated at the tyrosine at amino acid position 248 in SEQ ID NO: 1, include only the form of PCNA phosphorylated at the tyrosine at amino acid position 248 in SEQ ID NO: 1, or include only the unphosphorylated form of PCNA.
Cyclin D1 is a 33.7 kDa protein having 295 amino acids. The amino acid sequence of human cyclin D1 is SEQ ID NO: 2. The protein level of cyclin D1 can include the forms of cyclin D1 that are non-phosphorylated and phosphorylated at the threonine at amino acid position 286 in SEQ ID NO: 2, include only the form of cyclin D1 phosphorylated at the threonine at amino acid position 286 in SEQ ID NO: 2, or include only the unphosphorylated form of cyclin D1.
Cyclin D3 is a protein having 292 amino acids. The amino acid sequence of human cyclin D3 is SEQ ID NO: 3. The protein level of cyclin D3 can include the forms of cyclin D3 that are non-phosphorylated and phosphorylated at the serine at amino acid position 279 in SEQ ID NO: 3, include only the form of cyclin D3 phosphorylated at the serine at amino acid position 279 in SEQ ID NO: 3, or include only the unphosphorylated form of cyclin D3.
MAPK-ERK kinase 1 (MEK) is a protein having two isoforms. The first isoform of human MEK has a sequence of 393 amino acids (SEQ ID NO: 4) and the second isoform of human MEK has a sequence of 367 amino acids (SEQ ID NO: 5). The protein level of MEK can include one or more of: the unphosphorylated form of the first isoform of MEK; the unphosphorylated form of the second isoform of MEK; one or more form(s) of the first isoform of MEK including one or more of a phosphorylation at the serine at amino acid position 218 in SEQ ID NO: 4, a phosphorylation at the serine at amino acid position 222 in SEQ ID NO: 4, a phosphorylation at the threonine at amino acid position 286 in SEQ ID NO: 4, a phosphorylation at the threonine at amino acid position 292 in SEQ ID NO: 4, and a phosphorylation at the serine at amino acid position 298 in SEQ ID NO: 4; and one or more form(s) of the second isoform of MEK including one or more of a phosphorylation at the serine at amino acid position 192 of SEQ ID NO: 5, a phosphorylation at the serine at amino acid position 196 of SEQ ID NO: 5, a phosphorylation at the threonine at amino acid position 260 in SEQ ID NO: 5, a phosphorylation at the threonine at amino acid position 266 in SEQ ID NO: 5, and a phosphorylation at the serine at amino acid position 272 in SEQ ID NO: 5.
S6, pS6, and total S6
Ribosomal protein S6 (S6) is a 28.7 kDa protein having 249 amino acids. The amino acid sequence of human S6 is SEQ ID NO: 6. The phrase “level of S6” or “level of ribosomal protein S6,” when referring to a protein level, means the sum of the levels of all detectable forms (e.g., all phosphorylated forms and the unphosphorylated form) of S6. The phosphorylated forms of S6 protein can include one or more of: a phosphorylation of the serine at amino acid position 235 in SEQ ID NO: 6, a phosphorylation of the serine at amino acid position 236 in SEQ ID NO: 6, a phosphorylation of the serine at amino acid position 240 in SEQ ID NO: 6, a phosphorylation at the serine at amino acid position 242 in SEQ ID NO: 6, a phosphorylation at serine at amino acid position 244 in SEQ ID NO: 6, and a phosphorylation at the serine at amino acid position 247 in SEQ ID NO: 6. In some embodiments, the level of S6 can be determined through the use of an antibody that binds to an antigen that is common to all detectable forms (e.g., all phosphorylated forms and the unphosphorylated form) of S6.
The phrase “level of pS6” or “level of ribosomal protein pS6,” when referring to a protein level, means the level (or sum of two or more of the levels) of one or more of a phosphorylated form of ribosomal S6 protein having a phosphorylation at serine at amino acid position 235 in SEQ ID NO: 6, a phosphorylation at serine at amino acid position 236 in SEQ ID NO: 6, or a phosphorylation in the serines at amino acid positions 235 and 236 in SEQ ID NO: 6. The level of pS6 can be determined, e.g., by using an antibody or antibodies that specifically bind to an epitope in S6 that includes the phosphorylated serine at amino acid position 235 in SEQ ID NO: 6 and/or the phosphorylated serine at amino acid position 236 in SEQ ID NO: 6.
The phrase “level of ERK,” when referring to a protein level, means the sum of the levels of all detectable forms of ERK1 (e.g., all phosphorylated forms and unphosphorylated forms of each isoform of ERK1) and/or all detectable forms of ERK2 (e.g., all phosphorylated forms and unphorylated forms). The first isoform of human ERK1 has a sequence of 379 amino acids (SEQ ID NO: 7). The second isoform of human ERK1 has a sequence of 335 amino acids (SEQ ID NO: 8). The third isoform of human ERK1 has a sequence of 357 amino acids (SEQ ID NO: 9). The first isoform of human ERK2 has a sequence of 360 amino acids (SEQ ID NO: 10). The second isoform of human ERK2 has a sequence of 316 amino acids (SEQ ID NO: 11).
The phosphorylated forms of the first isoform of ERK1 can include one or more of: a phosphorylation of the serine at amino acid position 170 in SEQ ID NO: 7, a phosphorylation of the threonine at amino acid position 198 in SEQ ID NO: 7, a phosphorylation of the threonine at amino acid position 202 in SEQ ID NO: 7, a phosphorylation of the tyrosine at amino acid position 204 in SEQ ID NO: 7, and a phosphorylation of the threonine at amino acid position 207 in SEQ ID NO: 7. The phosphorylated forms of the second isoform of ERK1 can include one or more of: phosphorylation of the serine at amino acid position 170 in SEQ ID NO: 8, a phosphorylation of the threonine at amino acid position 198 in SEQ ID NO: 8, a phosphorylation of the threonine at amino acid position 202 in SEQ ID NO: 8, a phosphorylation of the tyrosine at amino acid position 204 in SEQ ID NO: 8, and a phosphorylation of the threonine at amino acid position 207 in SEQ ID NO: 8. The phosphorylated forms of the third isoform of ERK1 can include one or more of: a phosphorylation of the serine at amino acid position 170 in SEQ ID NO: 9, a phosphorylation of the threonine at amino acid position 198 in SEQ ID NO: 9, a phosphorylation of the threonine at amino acid position 202 in SEQ ID NO: 9, a phosphorylation of the tyrosine at amino acid position 204 in SEQ ID NO: 9, and a phosphorylation of the threonine at amino acid position 207 in SEQ ID NO: 9. All detectable forms of ERK1 can be identified, e.g., by using an antibody that specifically binds to an epitope that is shared between the unphosphorylated forms of the first, second, and third isoforms of ERK1 and all of the various phosphorylated forms of the first, second, and third isoforms of ERK1.
The phosphorylated forms of the first isoform of ERK2 can include one or more of: a phosphorylation at the serine at amino acid position 29 in SEQ ID NO: 10, a phosphorylation of the threonine at amino acid position 185 in SEQ ID NO: 10, a phosphorylation of the tyrosine at amino acid position 187 in SEQ ID NO: 10, a phosphorylation of the threonine at the amino acid position 190 in SEQ ID NO: 10, a phosphorylation of the serine at the amino acid position 246 in SEQ ID NO: 10, a phosphorylation of the serine at amino acid position 248, and a phosphorylation of the serine at amino acid position 284 in SEQ ID NO: 10. The phosphorylated forms of the second isoform of ERK2 can include one or more of: a phosphorylation at the serine at amino acid position 29 in SEQ ID NO: 11, a phosphorylation of the threonine at amino acid position 185 in SEQ ID NO: 11, a phosphorylation of the tyrosine at amino acid position 187 in EQ ID NO: 11, and a phosphorylation of the threonine at the amino acid position 190 in SEQ ID NO: 11. All detectable forms of ERK2 can be identified, e.g., by using an antibody that specifically binds to an epitope that is shared between the unphosphorylated forms of the first and second isoforms of ERK2 and all of the various phosphorylated forms of the first and second isoforms of ERK2.
pERK
The phrase “level of pERK,” when referring to a protein level, means the level (or sum of two or more of the levels) of one or more of: a form of the first isoform of ERK1 having a phosphorylation at the threonine at amino acid position 202 in SEQ ID NO: 7, a form of the first isoform of ERK1 having a phosphorylation at the tyrosine at amino acid position 204 in SEQ ID NO: 7, a first isoform of ERK1 having a phosphorylation at threonine at amino acid position 202 and tyrosine at amino acid position 204 in SEQ ID NO: 7, a form of the second isoform of ERK1 having a phosphorylation at the threonine at amino acid position 202 in SEQ ID NO: 8, a form of the second isoform of ERK1 having a phosphorylation at the tyrosine at amino acid position 204 in SEQ ID NO: 8, a form of the second isoform of ERK1 having a phosphorylation at the threonine at amino acid position 202 and the tyrosine at amino acid position 204 of SEQ ID NO: 8, a form of the third isoform of ERK1 having a phosphorylation at the threonine at amino acid position 202 in SEQ ID NO: 9, a form of the third isoform of ERK1 having a phosphorylation at the tyrosine at amino acid position 204 in SEQ ID NO: 9, a form of the third isoform of ERK1 having a phosphorylation at the threonine at amino acid position 202 and the tyrosine at amino acid position 204 in SEQ ID NO: 9, a form of the first isoform of ERK2 having a phosphorylation at the threonine at amino acid position 185 in SEQ ID NO: 10, a form of the first isoform of ERK2 having a phosphorylation at the tyrosine at amino acid position 187 of SEQ ID NO: 10, a form of the first isoform of ERK2 having a phosphorylation at the threonine at amino acid position 185 and the tyrosine at amino acid position 187 of SEQ ID NO: 10, a form of the second isoform of ERK2 having a phosphorylation at the threonine at amino acid position 185 in SEQ ID NO: 11, a form of the second isoform of ERK2 having a phosphorylation at the tyrosine at amino acid position 187 in SEQ ID NO: 11, and a form of the second isoform of ERK2 having a phosphorylation at the threonine at amino acid position 185 and the tyrosine at amino acid position 187 in SEQ ID NO: 11. The level of pERK can be determined, e.g., by using an antibody that specifically binds to an epitope in the first, second, or third isoforms of ERK1 that includes the phosphorylated threonine at amino acid position 202 in SEQ ID NO: 7, 8, or 9 and/or the phosphorylated tyrosine at amino acid position 204 in SEQ ID NO: 7, 8, or 9, respectively, or an antibody that specifically binds to an epitope on the first or second isoforms of ERK2 that includes the phosphorylated threonine at amino acid position 185 in SEQ ID NO: 10 or 11 and/or the phosphorylated tyrosine at amino acid position 187 in SEQ ID NO: 10 or 11, respectively.
Akt is a 55.7 kDa protein having 480 amino acids (SEQ ID NO: 12). The protein level of Akt can include two or more of: the unphosphorylated form of Akt and one or more form(s) of Akt including one or more of a phosphorylation at the serine at amino acid position 124 in SEQ ID NO: 12, a phosphorylation at the serine at amino acid position 126 in SEQ ID NO: 12, a phosphorylation at the serine at amino acid position 129 in SEQ ID NO: 12, a phosphorylation at the tyrosine at amino acid position 176 in SEQ ID NO: 12, a phosphorylation at the threonine at amino acid position 308 in SEQ ID NO: 12, a phosphorylation at the threonine at amino acid position 450 in SEQ ID NO: 12, a phosphorylation at the serine at amino acid position 473 in SEQ ID NO: 12, and a phosphorylation at the tyrosine at amino acid position 474 in SEQ ID NO: 12.
pAkt
The phrase “level of pAkt,” when referring to a protein level, means the level (or sum of two or more of the levels) of one or more a form Akt having a phosphorylation at the serine at amino acid position 473 in SEQ ID NO: 12. The level of pAkt can be determined, e.g., by using an antibody that specifically binds to an epitope in Akt that includes the phosphorylated serine at amino acid position 473 in SEQ ID NO: 12.
There are three different isoforms of caspase-2 in humans. The first isoform of caspase-2 in its unprocessed form has a total of 452 amino acids (SEQ ID NO: 13). After processing, the first isoform of caspase-2 forms three subunit peptides: amino acids 170-325 of SEQ ID NO: 13 (caspase-2 subunit p18), amino acids 334-452 of SEQ ID NO: 13 (caspase-2 subunit p13), and amino acids 348-452 of SEQ ID NO: 13 (caspase-2 subunit p12). Amino acids 2-169 of SEQ ID NO: 13 represent the prosequence of the unprocessed form of caspase-2. The second isoform has a total of 313 amino acids (SEQ ID NO: 14). The third isoform has a total of 91 amino acids (SEQ ID NO: 15). A phosphorylated form of the first isoform of caspase-2 has a phosphorylation at the serine at amino acid position 340 in SEQ ID NO: 13. The protein level of caspase-2 can include one or more of the unprocessed form of the first isoform of caspase-2, the caspase-2 subunit p18, the caspase-2 subunit p13, the caspase-2 subunit p12, the form of the first isoform of caspase-2 having a phosphorylation at the serine at amino acid position 340 in SEQ ID NO: 13, and a form of the caspase-2 subunit p13 having a phosphorylation at the serine at amino acid position 7 in caspase-2 subunit p13.
Human retinoblastoma binding protein (RBBP) has 425 amino acids (SEQ ID NO: 16). A phosphorylated form of RBBP has a phosphorylation at the serine at amino acid position 110 in SEQ ID NO: 16. The protein level of RBBP can include one or both of: the unphosphorylated form of RBBP and a form of RBBP having a phosphorylation at the serine at amino acid position 110 in SEQ ID NO: 16.
Some of the methods described herein include a step of concentrating a biological sample containing a biological fluid (e.g., any of the biological fluids described herein) for exosomes. For example, a sample containing a biological fluid can be concentrated for exosomes by ultracentrifuging the sample (e.g., in a sucrose gradient or using differential centrifugation) (see, e.g., the methods described in Gonzalez et al., J. Am. Soc. Nephrol. 20:363-379, 2009, and Alvarez et al., Kidney Int. 82:1024-1032, 2012) and removing an aliquot of the sample or the entire sample containing concentrated exosomes. In other examples, a sample containing a biological fluid can be concentrated for exosomes through the use of ultrafiltration (e.g., nanofiltration) (see, e.g., the methods described in Cheruvanky et al., Am. J. Physiol. Renal Physiol. 292:F1657-F1661, 2007, and Alvarez et al., Kidney Int. 82:1024-1032, 2012), precipitation (see, e.g., the methods described in Alvarez et al., Kidney Int. 82:1024-1032, 2012), or affinity purification that includes the use of a chromatography resin (e.g., a heparin column) or bead that is coated with an antibody that specifically binds to an epitope on the surface of exosomes, microfluidics (see, e.g., the methods described in Chen et al., Lap Chip 10:505-511, 2010). Additional methods for concentrating a sample for exosomes is described in Schageman et al., BioMed Research Int., Article 253957, 2013.
Exemplary methods for concentrating a sample containing a biological fluid for exosomes are also described in the Examples. Additional methods for concentrating a sample containing a biological fluid for exosomes are known in the art.
Provided herein are methods of determining the efficacy of a treatment for PKD in a PKD subject. In some examples, these methods include: (a) providing a first sample comprising a sample including a biological fluid (e.g., urine) obtained from a PKD patient at a first time point; (b) concentrating the first sample for exosomes; (c) determining the level(s) of at least one (e.g., two, three, four, five, six, seven, eight, nine, ten, eleven, or twelve in any combination) marker selected from the group of: PCNA, cyclin D1, cyclin D3, MEK, S6, pS6, ERK, pERK, Akt, pAkt, caspase-2, total S6, and RBBP in the first sample; (d) administering a treatment for PKD to the PKD patient; (e) providing a second sample including a biological fluid obtained from the PKD patient as a second time point after step (d) and performing steps (b) and (c) on the second sample; and (f) identifying the administered treatment as being effective if the level is decreased at the second time point as compared to the first time point. Some embodiments further include after (f): (g) administering additional doses of the administered GCS inhibitor identified as being effective (e.g., (S)-quinuclidin-3-yl (2-(4′-(2-methoxyethoxy)-[1,1′-biphenyl]-4-yl)propan-2-yl)carbamate; 4-fluoro-1-(5-fluoro-4-(4-((2-methoxyethoxy)methyl)phenyl) pyrimidin-2-yl)-N-(4-methyl-1 azabicyclo[3.2.2] nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-((2-methoxyethoxy)methyl) phenyl)pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-((2-methoxyethoxy)methyl)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(methoxymethyl)phenyl) pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(methoxymethyl)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo [3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-methoxyethoxy) phenyl)pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-methoxyethoxy)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-fluoroethoxy)phenyl)pyrimidin-2-yl)-N-(quinuclidin-3-yl)piperidine-4-carboxamide; or 4-fluoro-1-(4-(4-(2-fluoroethoxy)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2] nonan-4-yl)piperidine-4-carboxamide) to the PKD patient. Some examples of the methods further include after (f): (g) administering additional doses of the administered treatment identified as being effective (e.g., a CDK inhibitor, such as S-CR8) to the PKD patient.
In some embodiments, the steps (c) and (e) include determining the levels of at least two (e.g., three, four, five, six, or seven) markers selected from the group of: PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the administered treatment is identified as being effective if at least one or both of the two levels is decreased at the second time point as compared to the first time point. In some embodiments, the steps (c) and (e) include determining the levels of at least three (e.g., four, five, six, or seven) markers selected from the group of: PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the administered treatment is identified as being effective if at least one, two, or all three of the three levels is decreased at the second time point as compared to the first time point. In some embodiments, the steps (c) and (e) include determining the levels of at least four (e.g., five, six, or seven) markers selected from the group of: PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the administered treatment is identified as being effective if at least one, two, three, or all four of the levels is decreased at the second time point as compared to the first time point.
In some embodiments of these methods, the concentrating in (b) and (e) includes ultracentrifuging (e.g., differential centrifuging or centrifuging in a density gradient) or filtering the first and second samples, respectively. In some examples, the concentrating in (b) and (e) includes precipitating exosomes in the first and second samples, respectively; passing the first and second samples, respectively through a microfluidic device, respectively; or contacting the first and second samples with an affinity resin that is labeled with an antibody that specifically binds to an epitope present on the surface of exosomes, respectively. Additional methods for concentrating a sample containing a biological fluid for exosomes are known in the art. In some examples, the first and second samples contain urine.
In some examples, determining the level(s) of the one or more marker(s) in (c) and (e) includes determining the level of protein of the at least one marker. For example, the determining in (c) and (e) can include contacting the sample with antibodies that bind specifically to the protein of the at least one marker. In some embodiments, (c) and (e) include determining the level of one or both of cyclin D1 and MEK.
Also provided herein are methods of determining the efficacy of a treatment for PKD in a PKD subject that include: (a) providing a first sample including a biological fluid obtained from the PKD patient at a first time point; (b) determining the level(s) of at least one (e.g., two, three, four, five, six, seven, eight, nine, ten, eleven, or twelve in any combination) marker selected from the group of: PCNA, cyclin D1, cyclin D3, MEK, S6, pS6, ERK, pERK, Akt, pAkt, caspase-2, total S6, and RBBP in the first sample; (c) administering a treatment for PKD to the PKD patient; (d) providing a second sample including a biological fluid obtained from the patient at a second time point after step (c) and performing step (b) on the second sample; and (e) identifying the administered treatment as being effective if the level is decreased at a second time point as compared to the first time point. Some embodiments further include after (e): (f) administering additional doses of the administered GCS inhibitor identified as being effective (e.g., (S)-quinuclidin-3-yl (2-(4′-(2-methoxyethoxy)-[1,1′-biphenyl]-4-yl)propan-2-yl)carbamate; 4-fluoro-1-(5-fluoro-4-(4-((2-methoxyethoxy) methyl)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-((2-methoxyethoxy)methyl)phenyl)pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-((2-methoxyethoxy)methyl) phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(methoxymethyl)phenyl)pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(methoxymethyl) phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-methoxyethoxy)phenyl)pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-methoxyethoxy)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-fluoroethoxy)phenyl)pyrimidin-2-yl)-N-(quinuclidin-3-yl)piperidine-4-carboxamide; or 4-fluoro-1-(4-(4-(2-fluoroethoxy)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide) to the PKD patient. Some examples of the methods further include after (e): (f) administering additional doses of the administered treatment identified as being effective (e.g., a CDK inhibitor, such as S-CR8) to the PKD patient.
In some embodiments, the steps (b) and (d) include determining the levels of at least two (e.g., three, four, five, six, or seven) markers selected from the group of: PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the administered treatment is identified as being effective if at least one or both of the two levels is decreased at the second time point as compared to the first time point. In some embodiments, the steps (b) and (d) include determining the levels of at least three (e.g., four, five, six, or seven) markers selected from the group of: PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the administered treatment is identified as being effective if at least one, two, or all three of the three levels is decreased at the second time point as compared to the first time point. In some embodiments, the steps (b) and (d) include determining the levels of at least four (e.g., five, six, or seven) markers selected from the group of: PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the administered treatment is identified as being effective if at least one, two, three, or all four of the levels is decreased at the second time point as compared to the first time point.
In some examples, determining the level(s) of the one or more marker(s) in (b) and (d) includes determining the level of protein of the at least one marker. For example, the determining in (b) and (d) can include contacting the sample with antibodies that bind specifically to the protein of the at least one marker. In some embodiments, (b) and (d) include determining the level of at least two of PCNA, cyclin D3, pERK, and Akt.
In some embodiments of any of the methods, the administered treatment is administration of a glucosyl ceramide synthase (GCS) inhibitor (e.g., any of the GCS inhibitors described herein or known in the art). For example, the GCS inhibitor is selected from the group of: (S)-quinuclidin-3-yl (2-(4′-(2-methoxyethoxy)-[1,1′-biphenyl]-4-yl)propan-2-yl)carbamate; 4-fluoro-1-(5-fluoro-4-(4-((2methoxyethoxy) methyl) phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo [3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-((2-methoxyethoxy)methyl)phenyl) pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-((2-methoxyethoxy) methyl)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo [3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(methoxymethyl) phenyl)pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(methoxymethyl)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-methoxyethoxy)phenyl)pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-methoxyethoxy)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-fluoroethoxy)phenyl)pyrimidin-2-yl)-N-(quinuclidin-3-yl)piperidine-4-carboxamide; and 4-fluoro-1-(4-(4-(2-fluoroethoxy)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide.
In some embodiments of any of the methods, the administered treatment is administration of a CDK inhibitor (e.g., any of the CDK inhibitors described herein or known in the art, such as R-roscovitine) to the PKD patient.
Some embodiments of any of the methods further include a step of selecting a patient having PKD or diagnosing a patient having PKD (e.g., using any of the exemplary methods of diagnosing PKD described herein). The patient in any of these methods can be any of the patients described herein. For example, a patient having PKD can have previously been administered a treatment for PKD and the treatment was unsuccessful. Some embodiments of any of the methods further include obtaining the first and/or second samples from the PKD patient.
Some embodiments further include recording the identified efficacy of the administered treatment in the patient's medical record (e.g., a computer readable medium). Some examples further include informing the patient, the patient's family, and/or the patient's primary care physician or attending physician of the identified efficacy of the administered treatment. Some embodiments further include authorization of a refill of an administered treatment identified as being effective.
The difference in time between the first and second time points can be, e.g., between 1 week and 40 weeks, between 1 week and 30 weeks, between 1 week and 20 weeks, between 1 week and 12 weeks, between 1 week and 8 weeks, between 1 week and 4 weeks, between 1 week and 2 weeks, between 2 weeks and 12 weeks, between 2 weeks and 8 weeks, or between 2 weeks and 4 weeks.
Also provided are methods of diagnosing PKD in a patient that include (a) providing a sample including a biological fluid from a patient suspected of having PKD; (b) concentrating the sample for exosomes; (c) determining the level(s) of at least one marker selected from the group of: PCNA, cyclin D1, cyclin D3, MEK, S6, pS6, ERK, pERK, Akt, pAkt, caspase-2, total S6, and RBBP in the sample; and (d) identifying the patient as having PKD if the level is elevated as compared to a control level. Some examples of these methods further include after (d): (e) administering a treatment for PKD (e.g., any of the exemplary treatments for PKD described herein) to a patient identified as having PKD. Some embodiments further include after (d): (e) administering a GCS inhibitor (e.g., (S)-quinuclidin-3-yl (2-(4′-(2-methoxyethoxy)-[1,1′-biphenyl]-4-yl)propan-2-yl)carbamate; 4-fluoro-1-(5-fluoro-4-(4-((2methoxyethoxy)methyl) phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo [3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-((2-methoxyethoxy) methyl)phenyl)pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-((2-methoxyethoxy) methyl)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(methoxymethyl)phenyl)pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(methoxymethyl)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-methoxyethoxy)phenyl)pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-methoxyethoxy)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-fluoroethoxy)phenyl)pyrimidin-2-yl)-N-(quinuclidin-3-yl)piperidine-4-carboxamide; or 4-fluoro-1-(4-(4-(2-fluoroethoxy)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide) to a patient identified as having PKD. Some embodiments further include after (d): (e) administering a CDK inhibitor (e.g., roscovitine) to a patient identified as having PKD. Some embodiments further include after (d): (e) performing one or more additional tests to confirm PKD in the patient (e.g., imaging one or both kidney(s) in a patient identified as having PKD).
In some embodiments, the step (c) includes determining the levels of at least two (e.g., three, four, five, six, or seven) markers selected from the group of: PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the patient is identified as having PKD if at least one or both of the two levels is elevated as compared to the control level. In some embodiments, step (c) includes determining the levels of at least three (e.g., four, five, six, or seven) markers selected from the group of: PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the patient is identified as having PKD if at least one, two, or all three of the three levels is elevated as compared to the control level. In some embodiments, step (c) includes determining the levels of at least four (e.g., five, six, or seven) markers selected from the group of: PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the subject is identified as having PKD if at least one, two, three, or all four of the levels is elevated at compared to the control level.
In some embodiments of these methods, the concentrating in (b) includes ultracentrifuging (e.g., differential centrifuging or centrifuging in a density gradient) or the sample. In some examples, the concentrating in (b) includes precipitating exosomes in the sample; passing the sample through a microfluidic device; or contacting the sample with an affinity resin that is labeled with an antibody that specifically binds to an epitope present on the surface of exosomes. Additional methods for concentrating a sample containing a biological fluid for exosomes are known in the art. In some examples, the sample contains urine.
In some examples, determining the level(s) of the one or more marker(s) in (c) includes determining the level of protein of the at least one marker. For example, the determining in (c) can include contacting the sample with antibodies that bind specifically to the protein of the at least one marker. In some embodiments, (c) includes determining the level of at least two of PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6.
Also provided are methods of diagnosing PKD in a patient that include (a) providing a sample including a biological fluid from a patient suspected of having PKD; (b) determining the level(s) of at least one marker selected from the group of: PCNA, cyclin D1, cyclin D3, MEK, S6, pS6, ERK, pERK, Akt, pAkt, caspase-2, total S6, and RBBP in the sample; and (c) identifying the patient as having PKD if the level is elevated as compared to a control level. Some examples of these methods further include after (c): (d) administering a treatment for PKD (e.g., any of the exemplary treatments for PKD described herein) to a patient identified as having PKD. Some embodiments further include after (c): (d) administering a GCS inhibitor (e.g., (S)-quinuclidin-3-yl (2-(4′-(2-methoxyethoxy)-[1,1′-biphenyl]-4-yl)propan-2-yl)carbamate; 4-fluoro-1-(5-fluoro-4-(4-((2methoxyethoxy)methyl)phenyl) pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-((2-methoxyethoxy)methyl)phenyl)pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-((2-methoxyethoxy) methyl)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(methoxymethyl)phenyl) pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(methoxymethyl) phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-methoxyethoxy)phenyl) pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-methoxyethoxy) phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-fluoroethoxy)phenyl) pyrimidin-2-yl)-N-(quinuclidin-3-yl)piperidine-4-carboxamide; or 4-fluoro-1-(4-(4-(2-fluoroethoxy)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide) to a patient identified as having PKD. Some embodiments further include after (c): (d) administering a CDK inhibitor (e.g., S-CR8) to a patient identified as having PKD. Some embodiments further include after (c): (d) performing one or more additional tests to confirm PKD in the patient (e.g., imaging one or both kidney(s) in a patient identified as having PKD).
In some embodiments, the step (b) includes determining the levels of at least two (e.g., three, four, five, six, or seven) markers selected from the group of: PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the patient is identified as having PKD if at least one or both of the two levels is elevated as compared to the control level. In some embodiments, step (b) includes determining the levels of at least three (e.g., four, five, six, or seven) markers selected from the group of: PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the patient is identified as having PKD if at least one, two, or all three of the three levels is elevated as compared to the control level. In some embodiments, step (b) includes determining the levels of at least four (e.g., five, six, or seven) markers selected from the group of: PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the subject is identified as having PKD if at least one, two, three, or all four of the levels is elevated As compared to the control level.
In some examples, determining the level(s) of the one or more marker(s) in (b) includes determining the level of protein of the at least one marker. For example, the determining in (b) can include contacting the sample with antibodies that bind specifically to the protein of the at least one marker. In some embodiments, (b) includes determining the level of at least two of cyclin D1, MEK, ERK, pAkt, S6, and pS6.
In any of these methods, a control level can be, e.g., a level of the at least one marker in a subject not presenting with one or more symptoms of PKD and/or not diagnosed as having PKD, a level of the at least one marker in a healthy subject or a population of healthy subjects, or a threshold level (e.g., a level above which indicates that the subject has PKD).
Some embodiments further include recording the identification of PKD in the patient in the patient's medical record (e.g., a computer readable medium). Some examples further include informing the patient, the patient's family, and/or the patient's primary care physician or attending physician of the identification of PKD in the patient. Some examples further include informing the patient's insurance provider of the identification of PKD in the patient.
Also provided herein are methods of determining the stage of PKD in a patient that include: (a) providing a sample including a biological fluid from a patient suspected of having PKD or identified as having PKD; (b) concentrating the sample for exosomes; (c) determining the level(s) of at least one marker selected from the group of: PCNA, cyclin D1, cyclin D3, MEK, S6, pS6, ERK, pERK, Akt, pAkt, caspase-2, total S6, and RBBP in the sample; and (d) determining the stage of PKD in the patient from the level. In some embodiments, the determining in (d) includes comparing the determined level of at least one marker to a range of values for a particular stage of PKD (e.g., stage I, stage II, stage III, stage IV, or stage V) and identifying a subject as having a particular stage of PKD if the at least one level falls within a range of values for the particular stage of PKD. Some embodiments further include after (d): (e) administering a treatment for stage I, stage II, stage III, stage IV, or stage V PKD to a patient identified as having stage I, stage II, stage III, stage IV, or stage V PKD, respectively. Some embodiments further include after (d): (e) performing one or more assays to confirm the stage of PKD (e.g., imaging one or both kidney(s) in a patient after (d) to confirm the stage of PKD in the patient). Some embodiments further include after (d): (e) hospitalizing a subject identified as having stage IV or stage V PKD. Ranges of levels of the at least one marker described herein in a sample including a biological fluid (e.g., urine or a sample comprising a biological fluid that has been enriched for exosomes) from a subject having a certain stage of PKD (e.g., stage I, stage II, stage III, stage IV, or stage PKD) can be determined using skills known in the art. The five stages of PKD are described on the Kidney Support webpage (kidney-support.org): stage 1 (emergence stage), stage 2 (growth stage), stage 3 (enlargement or swelling stage), stage 4 (cyst rupture stage), and stage 5 (end stage).
In some embodiments, step (c) includes determining the levels of at least two (e.g., three, four, five, six, or seven) markers selected from the group of: PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the stage of PKD is determined from at least one or both of the two levels. In some embodiments, step (c) includes determining the levels of at least three (e.g., four, five, six, or seven) markers selected from the group of: PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the stage of PKD is determined from at least one, two, or all three of the three levels. In some embodiments, step (c) includes determining the levels of at least four (e.g., five, six, or seven) markers selected from the group of: PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the stage of PKD is determined from at least one, two, three, or all four of the levels.
In some embodiments of these methods, the concentrating in (b) includes ultracentrifuging (e.g., differential centrifuging or centrifuging in a density gradient) or the sample. In some examples, the concentrating in (b) includes precipitating exosomes in the sample; passing the sample through a microfluidic device; or contacting the sample with an affinity resin that is labeled with an antibody that specifically binds to an epitope present on the surface of exosomes. Additional methods for concentrating a sample containing a biological fluid for exosomes are known in the art. In some examples, the sample contains urine.
In some examples, determining the level(s) of the one or more marker(s) in (c) includes determining the level of protein of the at least one marker. For example, the determining in (c) can include contacting the sample with antibodies that bind specifically to the protein of the at least one marker. In some embodiments, (c) includes determining the level of at least two of PCNA, cyclin D3, MEK, and phosphorylated S6.
Also provided herein are methods of determining the stage of PKD in a patient that include: (a) providing a sample including a biological fluid from a patient suspected of having PKD or identified as having PKD; (b) determining the level(s) of at least one marker selected from the group of: PCNA, cyclin D1, cyclin D3, MEK, S6, pS6, ERK, pERK, Akt, pAkt, caspase-2, total S6, and RBBP in the sample; and (c) determining the stage of PKD in the patient from the level. In some embodiments, the determining in (c) includes a comparing the determined level of the at least one marker to a range of values for a particular stage of PKD (e.g., stage I, stage II, stage III, stage IV, or stage V) and identifying a subject as having a particular stage of PKD if the at least one level falls within a range of values for the particular stage of PKD. Some embodiments further include after (c): (d) administering a treatment for stage I, stage II, stage III, stage IV, or stage V PKD to a patient identified as having stage I, stage II, stage III, stage IV, or stage V PKD, respectively. Some embodiments further include after (c): (d) performing one or more assays to confirm the stage of PKD (e.g., imaging one or both kidney(s) in a patient after (c) to confirm the stage of PKD in the patient). Some embodiments further include after (c): (d) hospitalizing a subject identified as having stage IV or stage V PKD.
In some embodiments, step (b) includes determining the levels of at least two (e.g., three, four, five, six, or seven) markers selected from the group of: PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the stage of PKD is determined from at least one or both of the two levels. In some embodiments, step (b) includes determining the levels of at least three (e.g., four, five, six, or seven) markers selected from the group of: PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the stage of PKD is determined from at least one, two, or all three of the three levels. In some embodiments, step (b) includes determining the levels of at least four (e.g., five, six, or seven) markers selected from the group of: PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the stage of PKD is determined from at least one, two, three, or all four of the levels.
In some examples, determining the level(s) of the one or more marker(s) in (b) includes determining the level of protein of the at least one marker. For example, the determining in (b) can include contacting the sample with antibodies that bind specifically to the protein of the at least one marker. In some embodiments, (b) includes determining the level of at least two of PCNA, cyclin D3, MEK, and phosphorylated S6.
Also provided are methods of monitoring a PKD patient that include: (a) providing a first sample including a biological fluid obtained from the PKD patient at a first time point; (b) concentrating the first sample for exosomes; (c) determining the level(s) of at least one marker (e.g., two, three, four, five, six, seven, eight, nine, ten, eleven, or twelve in any combination) marker selected from the group of: PCNA, cyclin D1, cyclin D3, MEK, S6, pS6, ERK, pERK, Akt, pAkt, caspase-2, total S6, and RBBP in the first sample; (d) providing a second sample including a biological fluid obtained from the PKD patient as a second time point after step (c) and performing steps (b) and (c) on the second sample; and (e) identifying the patient as having improving or static PKD if at least one of the two levels is not elevated at the second time point as compared to the first time point. In some embodiments, the steps (c) and (d) include determining the levels of at least two (e.g., three, four, five, six, or seven) markers selected from the group of: PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the patient is identified as having improving or static PKD if at least one or both of the two levels is/are not elevated at the second time point as compared to the first time point. In some embodiments, the steps (c) and (d) include determining the levels of at least three (e.g., four, five, six, or seven) markers selected from the group of: PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the patient is identified as having improving or static PKD if at least one, two, or all three of the three levels is/are not elevated at the second time point as compared to the first time point. In some embodiments, the steps (c) and (d) include determining the levels of at least four (e.g., five, six, or seven) markers selected from the group of: PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the patient is identified as having improving or static PKD if at least one, two, three, or all four of the levels is/are not elevated at the second time point as compared to the first time point.
In some embodiments of these methods, the concentrating in (b) and (d) includes ultracentrifuging (e.g., differential centrifuging or centrifuging in a density gradient) or filtering the first and second samples, respectively. In some examples, the concentrating in (b) and (d) includes precipitating exosomes in the first and second samples, respectively; passing the first and second samples, respectively through a microfluidic device, respectively; or contacting the first and second samples with an affinity resin that is labeled with an antibody that specifically binds to an epitope present on the surface of exosomes, respectively. Additional methods for concentrating a sample containing a biological fluid for exosomes are known in the art. In some examples, the first and second samples contain urine.
In some examples, determining the level(s) of the one or more marker(s) in (c) and (d) include determining the level of protein of the at least one marker. For example, the determining in (c) and (d) can include contacting the sample with antibodies that bind specifically to the protein of the at least one marker. In some embodiments, (c) and (d) include determining the level of at least two (e.g., three or four) of PCNA, cyclin D3, MEK, and phosphorylated S6. Some embodiments further include after (e): (f) administering the same treatment (e.g., any of the exemplary treatments of PKD described herein or known in the art) to a patient identified as having improving or static PKD. For example, the administering in (f) can be the administration of a GCS inhibitor (e.g., (S)-quinuclidin-3-yl (2-(4′-(2-methoxyethoxy)-[1,1′-biphenyl]-4-yl)propan-2-yl)carbamate; 4-fluoro-1-(5-fluoro-4-(4-((2methoxyethoxy)methyl) phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo [3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-((2-methoxyethoxy) methyl)phenyl)pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-((2-methoxyethoxy) methyl)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(methoxymethyl)phenyl)pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(methoxymethyl)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-methoxyethoxy)phenyl)pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-methoxyethoxy)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-fluoroethoxy)phenyl)pyrimidin-2-yl)-N-(quinuclidin-3-yl)piperidine-4-carboxamide; or 4-fluoro-1-(4-(4-(2-fluoroethoxy)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide).
Also provided are methods of monitoring a PKD patient that include: (a) providing a first sample including a biological fluid obtained from the PKD patient at a first time point; (b) determining the level(s) of at least one marker (e.g., two, three, four, five, six, seven, eight, nine, ten, eleven, or twelve in any combination) marker selected from the group of: PCNA, cyclin D1, cyclin D3, MEK, S6, pS6, ERK, pERK, Akt, pAkt, caspase-2, total S6, and RBBP in the first sample; (c) providing a second sample including a biological fluid obtained from the PKD patient as a second time point after step (b) and performing step (b) on the second sample; and (d) identifying the patient as having improving or static PKD if at least one of the two levels is not elevated at the second time point as compared to the first time point. In some embodiments, the steps (b) and (c) include determining the levels of at least two (e.g., three, four, five, six, or seven) markers selected from the group of: PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the patient is identified as having improving or static PKD if at least one or both of the two levels is/are not elevated at the second time point as compared to the first time point. In some embodiments, the steps (b) and (c) include determining the levels of at least three (e.g., four, five, six, or seven) markers selected from the group of: PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the patient is identified as having improving or static PKD if at least one, two, or all three of the three levels is/are not elevated at the second time point as compared to the first time point. In some embodiments, the steps (c) and (c) include determining the levels of at least four (e.g., five, six, or seven) markers selected from the group of: PCNA, cyclin D1, cyclin D3, MEK, S6, and pS6, and the patient is identified as having improving or static PKD if at least one, two, three, or all four of the levels is/are not elevated at the second time point as compared to the first time point.
In some examples, determining the level(s) of the one or more marker(s) in (b) and (c) include determining the level of protein of the at least one marker. For example, the determining in (b) and (c) can include contacting the sample with antibodies that bind specifically to the protein of the at least one marker. In some embodiments, (b) and (c) include determining the level of at least two (e.g., three or four) of PCNA, cyclin D3, MEK, and phosphorylated S6. Some embodiments further include after (d): (e) administering the same treatment (e.g., any of the exemplary treatments of PKD described herein or known in the art) to a patient identified as having improving or static PKD. For example, the administering in (e) can be the administration of a GCS inhibitor (e.g., (S)-quinuclidin-3-yl (2-(4′-(2-methoxyethoxy)-[1,1′-biphenyl]-4-yl)propan-2-yl)carbamate; 4-fluoro-1-(5-fluoro-4-(4-((2methoxyethoxy)methyl) phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo [3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-((2-methoxyethoxy) methyl)phenyl)pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-((2-methoxyethoxy) methyl)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(methoxymethyl)phenyl)pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(methoxymethyl)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-methoxyethoxy)phenyl)pyrimidin-2-yl)-N-(3-methylquinuclidin-3-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-methoxyethoxy)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide; 4-fluoro-1-(4-(4-(2-fluoroethoxy)phenyl)pyrimidin-2-yl)-N-(quinuclidin-3-yl)piperidine-4-carboxamide; or 4-fluoro-1-(4-(4-(2-fluoroethoxy)phenyl)pyrimidin-2-yl)-N-(4-methyl-1-azabicyclo[3.2.2]nonan-4-yl)piperidine-4-carboxamide).
Some embodiments of any of the methods further include a step of selecting a patient having PKD or diagnosing a patient having PKD (prior to step (a)) (e.g., using any of the exemplary methods of diagnosing PKD described herein). The patient in any of these methods can be any of the patients described herein. Some embodiments of any of the methods further include obtaining the first and/or second samples from the PKD patient.
Some embodiments further include recording the improving or static PKD status of the patient in the patient's medical record (e.g., a computer readable medium). Some examples further include informing the patient, the patient's family, and/or the patient's primary care physician or attending physician of improving or static PKD status of the patient. Some embodiments further include authorization of a refill of a treatment administered to the subject between the first and second time points, when the subject has been identified as having improving or static PKD. Some embodiments include discharging a subject from an inpatient facility (e.g., hospital) based on identification of the subject as having improving or static PKD.
The difference in time between the first and second time points can be, e.g., between 1 week and 40 weeks, between 1 week and 30 weeks, between 1 week and 20 weeks, between 1 week and 12 weeks, between 1 week and 8 weeks, between 1 week and 4 weeks, between 1 week and 2 weeks, between 2 weeks and 12 weeks, between 2 weeks and 8 weeks, or between 2 weeks and 4 weeks.
Also provided herein are kits that consist essentially of or consist of at least three (e.g., four, five, six, seven, eight, nine, ten, eleven, or twelve) antibodies selected from the group consisting of: an antibody that specifically binds to PCNA, an antibody that specifically binds to cyclin D1, an antibody that specifically binds to cyclin D3, an antibody that specifically binds to MEK, an antibody that specifically binds to S6, an antibody that specifically binds to pS6, an antibody that specifically binds to pERK, an antibody that specifically binds to protein kinase B (Akt), an antibody that specifically binds to pAkt, an antibody that specifically binds to caspase-2, and an antibody that specifically binds to RBBP. In some examples, any combination of the three or more antibodies are labeled (e.g., with a radioisotope, a fluorophore, or a quencher).
Some examples of the kits further include an antibody that specifically binds to one or more exosome protein markers (e.g., aquaporin-2, TSG101, and/or ALIX). Some examples of the kits further include one or more positive control recombinant proteins (e.g., an isolated recombinant PCNA, cyclin D1, cyclin D3, MEK, S6, pS6, pERK, Akt, pAkt, caspase-2, and RBBP. In some examples, the at least three antibodies are covalently attached to a solid surface (e.g., a chip, a bead, or a membrane) by the Fc domain.
Some examples of the kits described herein further include one or more reagents for use in concentrating a sample containing a biological fluid for exosomes (e.g., a nanomembrane filter and/or beads that are coated with an antibody that specifically binds to a epitope present on the surface of an exosome).
Some kits further contain a sample containing a biological fluid (e.g., a sample containing a biological fluid that has been concentrated for exosomes) from a PKD patient (e.g., a PKD patient with a known severity of PKD) or an animal model of PKD (e.g., any of the animal models described in the Examples).
The invention is further described in the following examples, which do not limit the scope of the invention described in the claims.
A set of experiments were performed to determine whether a set of biomarkers would be useful in methods of determining efficacy of treatment of PKD and the diagnosing, monitoring, and staging of PKD.
Animals and Urine Collection
C57BL/6J jck/+ mice were maintained for crossing. The cystic jck/jck mice were genotyped as previously described (Smith et al., J. Am. Soc. Nephrol. 17:2821-2831, 2006). Pcy mice were maintained on a CD1 genetic background as previously described (Takahashi et al., J. Am. Soc. Nephrol. 1:980-989, 1991). GCS inhibitor C9 was administered ad libitum to jck and pcy mice by mixing in powdered 5053 diet at 0.225% from 26 to 64 days and 4 to 30 weeks of age, respectively (as described in Natoli et al., Nature Medicine 16:788-792, 2010). Urine samples from the mice were collected in metabolic cages over a 24-hour period and stored at −80° C.
Human Patient Sample Collections
Normal and PKD human patient kidney samples were purchased from the National Disease Research Institute (NDRI). Autosomal dominant PKD urine samples were collected at the University of Toronto and all patients gave informed consent. Briefly, mid void morning urine specimens were collected and stabilized with Complete proteinase inhibitor cocktail (Roche, Basel, Switzerland). The urine was centrifuged at 2000×g for 10 minutes to remove cellular debris and stored at −80° C. Total kidney volume (TKV) was quantified in autosomal dominant PKD patients by magnetic resonance imaging (MRI) (without gadolinium). The profile of each human autosomal dominant PKD human patient who participated in the study is shown in Table 2 below.
1The study population includes both early and late stage autosomal dominant PKD human patients with TKVs ranging from 300 mL to 4,000 mL.
Isolation of Urinary Exosomes
Exosomes were isolated from pooled urine samples (animal studies) or mid void urine samples (human samples) by ultracentrifugation at 100,000 g for 2 hours. Following ultracentrifugation, the exosome pellet was resuspended in 2.5× Laemmli Buffer (5×: 15% SDS, 0.575 M sucrose, 0.325 M Tris, pH 6.8, 5% beta-mercapto ethanol, and 0.002% bromophenol blue) for sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and immunoblot analysis.
Immunoblot Analysis
Kidney samples were homogenized on ice in radioimmunoprecipitation assay (RIPA) buffer (Boston BioProducts, Ashland, Mass.) containing 1 mM dithiothreitol, 5 mM ethylenediaminetetraacetic acid (EDTA), 2 mM NaF, 1 mM Na3VO4 (all supplied by Sigma-Aldrich, St. Louis, Mo.), Pefabloc SC and Complete protease inhibitor cocktail (both from Roche, Basel, Switzerland). Protein concentration was determined by BCA protein assay (Pierce, Rockford, Ill.). The samples were loaded onto 4-12% NuPage Bis-Tris gels following the manufacturer's protocols (Invitrogen, Grand Island, N.Y.). Electrophoretic transfer of the proteins in the gel onto nitrocellulose was performed in a semi-dry apparatus according to the manufacturer's instructions (Invitrogen). After electrophoretic transfer, the resulting membranes were blocked with 5% non-fat milk in tris-buffered saline (TBS) containing 0.1% Tween-20 and incubated with primary antibodies overnight at 4° C. The primary antibodies were detected with horseradish peroxidase-labeled secondary antibodies at a 1:10,000 dilution (Promega, Fitchburg, Wis.). Immunoreactive proteins were revealed by enhanced chemiluminescence (GE Healthcare, Wauwatosa, Wis., and Thermo Scientific, Waltham, Mass.). The primary antibodies to the following antigenes were used: PCNA (DAKO, Carpinteria, Calif.), cyclin D1, S6, phospho-S6 (Ser235/236), phospho-AKT (ser473), total ERK, phospho-ERK (Thr202/Tyr204) (Cell Signaling Technology, Danvers, Mass.), cyclin D3, total AKT, caspase-2, RBBP (BD Biosciences, Billerica, Mass.), MEK1 (Upstate Biotechnology, Lake Placid, N.Y.), aquaporin-2 (Millipore, Billerica, Mass.) β-actin, TSG101 (Abcam, Cambridge, Mass.), ALIX (Santa Cruz Biotechnology, Dallas, Tex.), and GAPDH (US Biological, Salem, Mass.).
Markers that can be used for accurate diagnosis and assessment of PKD in human patients in both preclinical and clinical settings were identified using a three-step approach and samples from both PKD human patients and mouse models of PKD. In a first step, markers that were differentially expressed in jck mice (a mouse model of PKD) as compared to normal control mice were identified. Markers from several different pathways were identified, including the cell cycle, Akt/mTOR, and proteins in apoptosis and mitogenic cascades were significantly elevated in exosomes purified from the urine of jck mice as compared to control mice (
A further set of experiments was performed to determine whether the same markers could be used to determine the efficacy of a treatment for PKD in a patient having PKD. In these experiments, urine samples from jck mice that were treated with GCS inhibitor C9 continuously for 5 weeks were gathered (
A further set of experiments was performed to validate the use of the markers described herein for both diagnosing and determining the efficacy of treatment in human patients having PKD. In these experiments, another mouse model of PKD, pcy mice were used. The pcy mouse model is a slowly progressive adult form of PKD characterized by cyst formation and fibrosis. Treatment of pcy mice with GCS inhibitor C9 resulted in effective inhibition of cystogenesis and fibrogenesis (Natoli et al., Nature Medicine 16:788-792, 2010). In these experiments, pcy mice were left untreated or were treated with GCS inhibitor C9 for thirty weeks, and then the expression levels of the markers described herein were determined in both kidney lysate and urine exosome samples. The data from these experiments show the levels of the markers were decreased in both the kidney lysate samples and the urine exosome samples from pcy mice treated with GCS inhibitor C9 as compared to the corresponding levels in the untreated mice (
A further set of experiments was performed to determine whether levels of the markers described herein can be used to stage PKD in a patient. In these experiments, levels of markers described herein were determined in urinary exosomes from a population of thirteen human PKD patients having different stages of PKD (stages I through V, as evidenced by the total kidney volume and height-adjusted total kidney volume measured for each patient, and shown in
In sum, the data provided herein demonstrate that the markers described herein can be used to accurately determine the efficacy of a treatment of PKD in a patient and to accurately diagnose, monitor, and stage PKD in a patient.
It is to be understood that while the invention has been described in conjunction with the detailed description thereof, the foregoing description is intended to illustrate and not limit the scope of the invention, which is defined by the scope of the appended claims. Other aspects, advantages, and modifications are within the scope of the following claims.
This application claims priority to U.S. Provisional Patent Application Ser. No. 62/033,031, filed Aug. 4, 2014, the entire contents which are herein incorporated by reference.
Filing Document | Filing Date | Country | Kind |
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PCT/US2015/043497 | 8/3/2015 | WO | 00 |
Number | Date | Country | |
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62033031 | Aug 2014 | US |