Biomarkers for nanoparticle compositions

Abstract

To provide pharmaceutical compositions for intravenous administration for treating a locally advanced or metastatic tumor in a human individual.SOLUTION: A pharmaceutical composition comprises nanoparticles comprising sirolimus and albumin. The individual is selected for treatment on the basis of having a loss-of-function mutation in TSC1 or TSC2. The loss-of-function mutation is selected from the group consisting of a non-sense mutation, a frameshift mutation, a splicing mutation, and a deletion. The loss-of-function mutation in TSC1 or TSC2 is determined by sequencing nucleic acids from a sample of the individual. The ratio of sirolimus to albumin in the nanoparticles is between about 1:1 and about 9:1. The nanoparticles in the pharmaceutical composition have an average diameter of about 150 nm or less. The dose of sirolimus in the pharmaceutical composition is about 30 mg / m2 to about 100 mg / m2.SELECTED DRAWING: None

Description

Technical Field

[0001] Cross - Reference to Related Applications This application claims priority to U.S. Provisional Application No. 62 / 186,309, filed on Jun. 29, 2015, the content of which is incorporated herein by reference in its entirety.

[0002] The present invention relates to methods and compositions for treating hyperplasia such as cancer. In particular, the present invention relates to methods and compositions for determining the responsiveness and / or likelihood of treatment success, comprising the step of administering a composition comprising nanoparticles containing an mTOR inhibitor (e.g., a rapamycin drug) and albumin. The present invention also relates to methods and compositions for treating pediatric solid tumors.

Background Art

[0003] The mammalian target of rapamycin (mTOR) is a conserved serine / threonine kinase that acts as a center of signal transduction in cells, integrating intracellular and extracellular signals to regulate cell growth and homeostasis. Activation of the mTOR pathway is associated with cell proliferation and survival, while inhibition of mTOR signaling results in inflammation and cell death. Dysregulation of the mTOR signaling pathway is involved in an increasing number of human diseases, including cancer and autoimmune disorders. As a result, mTOR inhibitors have been found to be widely applicable in the treatment of various pathological conditions such as solid tumors, organ transplantation, restenosis, and rheumatoid arthritis. However, an urgent problem in the application of mTOR inhibitors is the variability of treatment responses in different individuals with the same disease or condition. Considering the numerous genes involved in the expansion of the mTOR signaling network, a reliable set of predictive biomarkers is highly needed to guide the selection of an effective treatment plan for individual patients.

[0004] Sirolimus (INN / USAN), also known as rapamycin, is an immunosuppressive drug used to prevent rejection in organ transplantation. It is particularly useful in kidney transplantation. A stent that elutes sirolimus has been approved in the United States for treating coronary artery restenosis. Additionally, sirolimus has been demonstrated as an effective inhibitor of tumor growth in various cell lines and animal models. Other rimos drugs, such as analogs of rapamycin, are designed to improve the pharmacokinetic and pharmacodynamic properties of sirolimus. For example, temsirolimus has been approved in the United States and Europe for the treatment of renal cell carcinoma. Everolimus has been approved in the United States for treating advanced breast cancer, pancreatic neuroendocrine tumors, advanced renal cell carcinoma, and subependymal giant cell astrocytomas (SEGAs) associated with tuberous sclerosis. The mode of action of rapamycin is to bind to the cytosolic protein FK-binding protein 12 (FKBP12), and the sirolimus-FKBP12 complex then inhibits the mTOR pathway by directly binding to mTOR complex 1 (mTORC1).

[0005] The disclosures of all publications, patents, patent applications, and patent application publications referred to herein are hereby incorporated by reference in their entirety into this specification.

Summary of the Invention

Means for Solving the Problems

[0006] The present invention provides a method for treating hyperplasia (e.g., cancer, restenosis, and pulmonary hypertension) in an individual, comprising administering to the individual an effective amount of a composition comprising an mTOR inhibitor (e.g., a rimos drug) and nanoparticles containing albumin, wherein the state of mTOR activation abnormality is used as a basis for selecting the individual for treatment.

[0007] In one aspect of the present application, there is provided a method for treating hyperplasia in an individual, the method comprising administering to the individual an effective amount of a composition comprising nanoparticles containing an mTOR inhibitor and albumin, wherein the individual is selected for treatment based on having an mTOR activation abnormality. In some embodiments, the method further comprises the step of evaluating an mTOR activation abnormality in the individual.

[0008] In another aspect of the present application, there is provided a method for selecting an individual having hyperplasia for treatment with a composition comprising nanoparticles containing an mTOR inhibitor and albumin, the method comprising the steps of evaluating an mTOR activation abnormality in the individual and selecting or recommending the individual for treatment based on the individual having an mTOR activation abnormality. In some embodiments, the method further comprises the step of administering to the selected individual a composition comprising nanoparticles containing an mTOR inhibitor and albumin.

[0009] In some embodiments according to any one of the above methods, the hyperplasia is selected from the group consisting of cancer, restenosis, and pulmonary hypertension. In some embodiments, the cancer is selected from the group consisting of pancreatic neuroendocrine cancer, endometrial cancer, breast cancer, renal cell carcinoma, lymphangioleiomyomatosis (LAM), prostate cancer, lymphoma, bladder cancer, endometrial cancer, and ovarian cancer.

[0010] In some embodiments according to any one of the above methods, the mTOR activation abnormality comprises a mutation in an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises a copy number variation in an mTOR-related gene. In some embodiments, the mTOR activation abnormality is evaluated by gene sequencing. In some embodiments, the gene sequencing is based on DNA sequencing in a tumor sample. In some embodiments, the gene sequencing is based on sequencing of circulating DNA or cell-free DNA isolated from a blood sample.

[0011] In some embodiments according to any one of the above methods, the mTOR activation abnormality includes an abnormal expression level of an mTOR-related gene.

[0012] In some embodiments according to any one of the above methods, the mTOR activation abnormality includes an abnormal phosphorylation level of a protein encoded by an mTOR-related gene. In some embodiments, the mTOR activation abnormality includes an abnormal phosphorylation level of a protein encoded by mTOR selected from the group consisting of AKT, S6K, S6, 4EBP1, and SPARC. In some embodiments, the abnormal phosphorylation level is determined by immunohistochemistry.

[0013] In some embodiments according to any one of the above methods, the mTOR activation abnormality includes an abnormal activity level of an mTOR-related gene.

[0014] In some embodiments according to any one of the above methods, the mTOR activation abnormality results in the activation of mTORC1 (including, for example, the activation of mTORC1 rather than mTORC2).

[0015] In some embodiments according to any one of the above methods, the mTOR activation abnormality results in the activation of mTORC2 (including, for example, the activation of mTORC2 rather than mTORC1).

[0016] In some embodiments according to any one of the above methods, the mTOR activation abnormality results in the activation of both mTORC1 and mTORC2.

[0017] In some embodiments according to any one of the above methods, the mTOR activation abnormality is an abnormality of at least one mTOR-related gene selected from the group consisting of AKT1, FLT3, MTOR, PIK3CA, PIK3CG, TSC1, TSC2, RHEB, STK11, NF1, NF2, PTEN, TP53, FGFR4, KRAS, NRAS, and BAP1. In some embodiments, the at least one mTOR-related gene includes MTOR. In some embodiments, the mTOR activation abnormality includes an activating mutation of MTOR. In some embodiments, the at least one mTOR-related gene includes TSC1 or TSC2. In some embodiments, the mTOR activation abnormality includes loss of heterozygosity in TSC1 or TSC2. In some embodiments, the mTOR activation abnormality includes a loss-of-function mutation in TSC1 or TSC2. In some embodiments, the at least one mTOR-related gene includes RHEB. In some embodiments, the mTOR activation abnormality includes a loss-of-function mutation in RHEB. In some embodiments, the at least one mTOR-related gene includes NF1. In some embodiments, the mTOR activation abnormality includes a loss-of-function mutation in NF1. In some embodiments, the at least one mTOR-related gene includes NF2. In some embodiments, the mTOR activation abnormality includes a loss-of-function mutation in NF2. In some embodiments, the at least one mTOR-related gene includes PTEN. In some embodiments, the at least one mTOR-related gene includes deletion of PTEN. In some embodiments, the at least one mTOR-related gene includes PIK3CA. In some embodiments, the mTOR activation abnormality includes a loss-of-function mutation in PIK3CA. In some embodiments, the at least one mTOR-related gene includes PIK3CG. In some embodiments, the mTOR activation abnormality includes a loss-of-function mutation in PIK3CG. In some embodiments, the at least one mTOR-related gene includes AKT1. In some embodiments, the at least one mTOR-related gene includes an activating mutation of AKT1. In some embodiments, the at least one mTOR-related gene includes TP53. In some embodiments, the mTOR activation abnormality includes a loss-of-function mutation in TP53.

[0018] In some embodiments according to any one of the above methods, the mutant state of TFE3 is further used as a basis for selecting an individual. In some embodiments, the mutant state of TFE3 includes a translocation of TFE3.

[0019] In some embodiments according to any one of the above methods, the method further includes administering to the individual an effective amount of a second therapeutic agent.

[0020] In some embodiments according to any one of the above methods, the individual is a human.

[0021] In some embodiments according to any one of the above methods, a composition comprising nanoparticles containing an mTOR inhibitor and albumin is administered intravenously. In some embodiments, a composition comprising nanoparticles containing an mTOR inhibitor and albumin is administered subcutaneously.

[0022] In some embodiments according to any one of the above methods, the nanoparticles in the composition contain an mTOR inhibitor associated with (i.e., coated with) albumin.

[0023] In some embodiments according to any one of the above methods, the nanoparticles in the composition have an average diameter of about 150 nm or less (including, for example, any one of about 120 nm or less or 100 nm or less).

[0024] In some embodiments according to any one of the above methods, the ratio of the mTOR inhibitor to albumin in the nanoparticles is from about 1:1 to about 9:1.

[0025] In some embodiments according to any one of the above methods, the albumin is human serum albumin.

[0026] In some embodiments according to any one of the above methods, the mTOR inhibitor is a rapamycin drug. In some embodiments, the rapamycin drug is sirolimus.

[0027] In some embodiments according to any one of the above methods, the dosage of the mTOR inhibitor in the composition is from about 10 mg / m2 to about 150 mg / m2 (e.g., including any one of about 20 mg / m2 to about 45 mg / m2, about 45 mg / m2 to about 100 mg / m2, about 75 mg / m2 to about 100 mg / m2, about 20 mg / m2, about 45 mg / m2, about 65 mg / m2, about 75 mg / m2, or about 100 mg / m2).

[0028] In one aspect of the present application, there is provided a kit comprising a composition comprising nanoparticles containing an mTOR inhibitor and albumin, and an agent for evaluating mTOR activation abnormalities.

[0029] Similarly, compositions (e.g., pharmaceutical compositions), drugs, kits, and unit dosages useful in the methods described herein are also provided.

[0030] These and other aspects and advantages of the present invention will become apparent from the following detailed description and the appended claims. It should be understood that one, some, or all of the characteristics of the various embodiments described herein can be combined to form other embodiments of the present invention.

Brief Description of the Drawings

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BRIEF DESCRIPTION OF THE INVENTION

[0056] The present invention provides a method for treating an individual having hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) using a nanoparticle composition comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, wherein the level and / or mutational status of one or more biomarkers associated with the mTOR pathway is used as a basis for selecting an individual for treatment. Abnormalities in the sequence, expression level, phosphorylation, and / or activity level of any one or combination of the biomarkers described herein are associated with hyperactivation of the mTOR pathway (hereinafter referred to as "mTOR activation abnormality") and correlate with the response of an individual to treatment with the nanoparticle composition.

[0057] In one aspect, there is provided a method for treating hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) in an individual having an mTOR activation abnormality, the method comprising administering to the individual an effective amount of a composition comprising a nanoparticle comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin.

[0058] In another aspect, there is provided a method for treating hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) in an individual, the method comprising administering to the individual an effective amount of a composition comprising a nanoparticle comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, wherein the individual is selected for treatment based on an individual having an mTOR activation abnormality.

[0059] In another aspect, there is provided a method for selecting (including identifying) an individual for treatment with a composition comprising a nanoparticle comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, the method comprising evaluating an mTOR activation abnormality.

[0060] Similarly, provided are compositions (e.g., pharmaceutical compositions), agents, kits, and unit doses that are useful in the described methods. Definitions

[0061] As used herein, "treating" or "treatment" refers to a procedure for obtaining a beneficial or desired result, including clinical results. For the purposes of the present invention, beneficial or desired clinical results include, but are not limited to, alleviating one or more symptoms resulting from a disease, reducing the severity of a disease, stabilizing a disease (e.g., preventing or delaying disease progression), preventing or delaying the spread (e.g., metastasis) of a disease, preventing or delaying the recurrence of a disease, delaying or slowing the progression of a disease, improving the disease state, achieving remission (partial or complete) of a disease, reducing the dosage of one or more other medications required to treat the disease, delaying the progression of a disease, improving the quality of life, and / or extending survival. Similarly, "treatment" includes reducing the pathological consequences of hyperplasia, e.g., cancer, restenosis, or pulmonary hypertension. The methods of the present invention contemplate any one or more of these aspects of treatment.

[0062] The term "individual" refers to a mammal and includes, but is not limited to, humans, cows, horses, cats, dogs, rodents, or primates. In some embodiments, the individual is a human.

[0063] As used herein, a "risky" individual is an individual at risk of developing hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension). A "risky" individual may or may not have a detectable disease, and may or may not exhibit a detectable disease prior to the treatment methods described herein. "Risky" means that an individual has one or more so-called risk factors, which are measurable parameters that correlate with the development of hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) described herein. An individual having one or more of these risk factors is at a higher risk of developing hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) than an individual without these risk factor(s).

[0064] "Adjuvant setting" refers to a clinical situation where an individual has a history of hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) and the treatment is generally responsive to the individual (although not necessarily so), which includes but is not limited to surgery (e.g., surgical resection), radiation therapy, and chemotherapy. However, due to their history of hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension), these individuals are considered at risk of developing the disease. Treatment or administration in the "adjuvant setting" refers to subsequent treatment regimens. The degree of risk (e.g., when an individual in the adjuvant setting is considered "high risk" or "low risk") depends on multiple factors and most commonly depends on the degree of the disease at the time of initial treatment.

[0065] "Neoadjuvant setting" refers to a clinical situation where a method is performed prior to primary / definitive treatment.

[0066] As used herein, "delaying" the onset of hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) means postponing, inhibiting, slowing, retarding, stabilizing, and / or delaying the onset of cancer. This delay can be of various lengths depending on the disease history and / or the individual being treated. As will be apparent to those skilled in the art, a sufficient or significant delay can, in effect, encompass prevention in that the individual does not develop the disease. A method of "delaying" the onset of hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) is a method that reduces the likelihood of disease onset within a given time frame and / or reduces the extent of the disease within a given time frame compared to not using the method. Such comparisons are typically based on clinical trials using a statistically significant number of subjects. The onset of hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) can be detected using standard methods including, but not limited to, computed tomography (CAT scan), magnetic resonance imaging (MRI), abdominal ultrasound, coagulation tests, arteriography, or biopsy. Onset may refer to the progression of hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) that is not detected initially and includes occurrence, recurrence, and onset.

[0067] As used herein, the term "effective amount" refers to an amount of a compound or composition sufficient to treat a specified disorder, condition, or disease, such as ameliorating, alleviating, reducing, and / or delaying one or more of its symptoms. In therapeutic use, beneficial or desired results include, for example, reduction of one or more symptoms (biochemical, histological, and / or behavioral) resulting from the disease, including complications of the disease and pathological intermediate phenotypes presented during the development of the disease, improvement of the quality of life of a human suffering from the disease, reduction of the dosage of other drug therapies required for treatment of the disease, enhancement of the effect of another drug therapy, delay of the progression of the disease, and / or extension of the survival period of the patient. For hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension), an effective amount includes an amount sufficient to reduce a hyperplastic tissue (e.g., a tumor) and / or decrease the growth rate of the hyperplastic tissue (such as inhibiting the growth of the hyperplasia or tumor), or to prevent or delay other undesired cell growth in the hyperplasia. In some embodiments, the effective amount is an amount sufficient to delay the onset of hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension). In some embodiments, the effective amount is an amount sufficient to prevent or delay recurrence. The effective amount can be administered in a single or multiple administrations. In the case of cancer, the effective amount of the drug or composition can (i) decrease the number of tumor cells, (ii) reduce the tumor size, (iii) inhibit, retard, slow down, preferably stop to some extent the invasion of tumor cells into peripheral organs, (iv) inhibit tumor metastasis (i.e., slow down to some extent, preferably stop), (v) inhibit tumor growth, (vi) prevent or delay the occurrence and / or recurrence of the tumor, and / or (vii) reduce to some extent one or more symptoms associated with cancer.

[0068] As used herein, the term "co - administration" means that in combination therapy, the first therapy and the second therapy are administered within a time interval not exceeding any one of about 15 minutes, for example, about 10 minutes, about 5 minutes or about 1 minute. When the first and second therapies are co - administered, the first therapy and the second therapy may be included in the same composition (for example, a composition containing both the first therapy and the second therapy) or in separate compositions (for example, the first therapy is included in one composition and the second therapy is included in another composition).

[0069] As used herein, the term "sequential administration" means that in combination therapy, the first therapy and the second therapy are administered at a time interval exceeding any one of about 15 minutes, for example, about 20 minutes, about 30 minutes, about 40 minutes, about 50 minutes, about 60 minutes or longer. Either the first therapy or the second therapy may be administered first. The first therapy and the second therapy are included in separate compositions, and they may be included in the same or different packages or kits.

[0070] As used herein, the term "concurrent administration" means that in combination therapy, the administration of the first therapy and the administration of the second therapy overlap with each other.

[0071] As used herein, "pharmaceutically acceptable" or "pharmacologically compatible" means a material that is biologically and otherwise desirable. For example, the material does not cause any significantly undesirable biological effects and can be incorporated into a pharmaceutical composition to be administered to a patient without interacting in a harmful manner with any of the other components of the composition in which it is contained. Pharmaceutically acceptable carriers or excipients preferably meet the requirements of toxicity and manufacturing tests and / or are included in the "Guidelines for Inactive Ingredients" prepared by the US Food and Drug Administration.

[0072] As used herein, "adverse event" or "AE" refers to any adverse medical occurrence in an individual to whom a commercial pharmaceutical product is administered, or an individual who participates in a clinical trial and is administered an investigational or non-investigational pharmaceutical product. An AE does not necessarily have a causal relationship with the treatment of the individual. Thus, an AE can be any undesirable and unintended sign, symptom, or disease temporally associated with the use of a pharmaceutical product, whether or not it is considered to be related to a particular pharmaceutical product. AEs include, but are not limited to, exacerbation of pre-existing disease; increased frequency or intensity of pre-existing acute events or conditions; conditions that were possibly present prior to the start of the study but were detected or diagnosed after administration of the study drug; and pre-existing, persistent diseases or symptoms that were present at baseline and worsened after the start of the study. AEs do not include common medical or surgical procedures (e.g., surgery, endoscopy, tooth extraction, or transfusion) (provided that the condition leading up to the procedure is not an adverse event); pre-existing diseases, conditions, or laboratory finding abnormalities that are present or detected at the start of the study and do not worsen; hospitalizations or procedures performed for non-treatment purposes not related to an adverse medical occurrence (e.g., hospitalization for cosmetic or elective surgery, or social / convenience hospitalization); diseases or signs / symptoms associated with the disease during the study that are not more severe than predicted for the individual's condition; and overdose of the study drug without any clinical signs or symptoms.

[0073] As used herein, "Serious Adverse Event" or (SAE) means a) fatal; b) life-threatening (if the event occurs, it is defined as the immediate risk of death due to that event); c) resulting in persistent or significant disability or incapacity; d) requiring hospitalization of the patient or prolonging an existing hospitalization (exclusion: Hospitalizations for the expectant management of existing conditions that did not worsen during the study are not considered adverse events. Complications that occur during hospitalization are AEs, and if the hospitalization is prolonged due to the complication, the event is serious); e) congenital anomalies / birth defects in the offspring of an individual who has received drug therapy; or f) any adverse medical event at any dose that includes, but is not limited to, conditions that may endanger the individual or may require intervention to prevent one of the previously listed outcomes, unless clearly related to the individual's underlying disease. "Lack of efficacy" (progressive disease) is not considered an AE or SAE. Signs and symptoms or clinical sequelae resulting from lack of efficacy should be reported if they meet the definition of an AE or SAE.

[0074] Using the following definitions, responses can be evaluated based on target lesions. "Complete Response" or "CR" refers to the disappearance of all target lesions. "Partial Response" or "PR" refers to at least a 30% decrease in the sum of the longest diameters (SLD) of the target lesions, with reference to the baseline sum of the longest diameters (SLD). "Stable Disease" or "SD" refers to the situation where, with reference to the nadir SLD since the start of treatment, the shrinkage of the target lesions is not sufficient to qualify for a PR and the increase in the target lesions is not sufficient to qualify for a PD. Also, "Progressive Disease" or "PD" refers to at least a 20% increase in the SLD of the target lesions, or the presence of one or more new lesions, with reference to the nadir SLD recorded since the start of treatment.

[0075] Using the following response evaluation definitions, non-target lesions can be evaluated. "Complete response" or "CR" refers to the disappearance of all non-target lesions. "Stable disease" or "SD" refers to the persistence of one or more non-target lesions that do not qualify for CR or PD. Also, "Progressive disease" or "PD" refers to "definite progression" of existing non-target lesion(s), or the appearance of one or more new lesion(s) is considered progressive disease (if the subject's PD is to be evaluated at a certain point based only on the progression of non-target lesion(s), additional criteria need to be met).

[0076] "Progression-free survival" (PFS) indicates the length of time during and after treatment that the cancer does not grow. Progression-free survival includes the amount of time an individual experiences a complete response or a partial response, as well as the amount of time an individual experiences stable disease.

[0077] "Correlate" or "correlation" means comparing the performance and / or results of a first analysis or protocol with the performance and / or results of a second analysis or protocol in any way. For example, the results of a first analysis or protocol can be used to determine whether to perform a second analysis or protocol. With respect to embodiments of a gene expression analysis or protocol, the results of that gene expression analysis or protocol can be used to determine whether to perform a particular treatment regimen.

[0078] "Predict" or "prediction" is used herein to refer to the likelihood that an individual is likely to respond favorably or unfavorably to a treatment regimen.

[0079] As used herein, "time of initiation of treatment" or "baseline" refers to the time of the first exposure to treatment or a period prior thereto.

[0080] As used herein, a method that "aids in the evaluation" refers to a method that helps in making a clinical decision and may or may not be decisive with respect to that evaluation.

[0081] As used herein, "likely to respond" or "responsiveness", which is not limited thereto, refers to any kind of clinical or non-clinical improvement or positive response selected from a measurable reduction in tumor size or evidence of disease or progression of disease, complete response, partial response, stable disease, increase or prolongation of progression-free survival, or increase or prolongation of overall survival.

[0082] As used herein, "sample" refers to a composition containing a molecule to be characterized and / or identified based on, for example, physical, biochemical, chemical, physiological, and / or genetic characteristics.

[0083] As used herein, "cell" is understood to refer not only to a particular target cell but also to the progeny or potential progeny of such a cell. Since a particular modification can give rise to subsequent generations due to mutations or environmental influences, such progeny may not actually be identical to the parental cell, but are included within the scope of this term as used herein.

[0084] The mTOR activation abnormality determined "before or at the start of treatment" is the mTOR activation abnormality determined in an individual before or at the time the individual receives the first administration of the treatment modality described herein.

[0085] An "eligible" individual, including an individual "suitable" for the treatment(s) described herein, is an individual who is more likely to benefit from the administration of said treatment than not. Conversely, an "ineligible" or "unsuitable" individual, including an individual "not suitable" for the treatment(s) described herein, is an individual who is more likely to not benefit from the administration of said treatment than to benefit.

[0086] As used herein, the "nanoparticle composition of an mTOR inhibitor" refers to a composition comprising nanoparticles containing an mTOR inhibitor (e.g., a rapamycin drug) and albumin. The "rapamycin nanoparticle composition" refers to a composition comprising nanoparticles containing a rapamycin drug (e.g., sirolimus) and albumin.

[0087] It should be understood that the aspects and embodiments of the invention described herein include "consisting of" and / or "consisting essentially of" the aspects and embodiments.

[0088] References to "about" values or parameters herein include (and describe) variations that are inherent in the value or parameter itself. For example, a description that refers to "about X" includes a description of "X".

[0089] As used herein, the term "about X to Y" has the same meaning as "about X to about Y".

[0090] As used in this specification and the appended claims, the singular forms "a", "or", and "the" include plural referents unless the context clearly dictates otherwise.

[0091] As will be apparent to those skilled in the art, the individuals who are evaluated for, selected for, and / or receive a treatment are those who require such activity. Method of treatment based on a state of abnormal mTOR activation

[0092] In one aspect, the present invention provides a method of treating hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) in an individual based on one or more states of abnormal mTOR activation in one or more mTOR-related genes.

[0093] In some embodiments, a method of treating hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) in an individual, comprising administering to the individual an effective amount of a composition comprising nanoparticles containing an mTOR inhibitor (e.g., a rapamycin drug) and albumin, wherein the individual is selected for treatment based on an individual having an mTOR activation abnormality, is provided. In some embodiments, a method of treating hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) in an individual, comprising administering to the individual an effective amount of a composition comprising nanoparticles containing a rapamycin drug (e.g., sirolimus) and albumin (the nanoparticles having an average diameter of about 150 nm or less), wherein the individual is selected for treatment based on an individual having an mTOR activation abnormality, is provided. In some embodiments, a method of treating hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) in an individual, comprising administering to the individual an effective amount of a composition comprising nanoparticles containing sirolimus associated with (e.g., coated with) albumin (the nanoparticles having an average diameter of about 150 nm or less and the weight ratio of albumin to sirolimus in the composition being about 9:1 or less), wherein the individual is selected for treatment based on an individual having an mTOR activation abnormality, is provided. In some embodiments, a method of treating hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) in an individual, comprising administering to the individual an effective amount of Nab-sirolimus, wherein the individual is selected for treatment based on an individual having an mTOR activation abnormality, is provided. In some embodiments, the mTOR activation abnormality comprises a mutation in an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises a copy number polymorphism in an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises an abnormal expression level of an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises an abnormal activity level of an mTOR-related gene. In some embodiments, the mTOR activation abnormality results in activation of mTORC1 (e.g., including activation of mTORC1 but not mTORC2).In some embodiments, mTOR activation abnormalities result in the activation of mTORC2 (including, for example, the activation of mTORC2 rather than mTORC1). In some embodiments, mTOR activation abnormalities result in the activation of both mTORC1 and mTORC2. In some embodiments, the mTOR activation abnormality is an abnormality of at least one mTOR-related gene selected from the group consisting of AKT1, FLT3, MTOR, PIK3CA, PIK3CG, TSC1, TSC2, RHEB, STK11, NF1, NF2, PTEN, TP53, FGFR4, KRAS, NRAS, and BAP1. In some embodiments, the mTOR activation abnormality is evaluated by gene sequencing. In some embodiments, the gene sequencing is based on DNA sequencing in a tumor sample. In some embodiments, the gene sequencing is based on the sequencing of circulating DNA or cell-free DNA isolated from a blood sample. In some embodiments, the mutation status of TFE3 is further used as a basis for selecting an individual. In some embodiments, the mutation status of TFE3 includes a translocation of TFE3. In some embodiments, the mTOR activation abnormality includes an abnormal phosphorylation level of a protein encoded by an mTOR-related gene. In some embodiments, the mTOR activation abnormality includes an abnormal phosphorylation level of a protein encoded by mTOR selected from the group consisting of AKT, S6K, S6, 4EBP1, and SPARC. In some embodiments, the abnormal phosphorylation level is determined by immunohistochemistry.

[0094] In some embodiments, a method of treating hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) in an individual, comprising: (a) evaluating mTOR activation abnormality in the individual; and (b) administering to the individual an effective amount of a composition comprising nanoparticles containing an mTOR inhibitor (e.g., a rapamycin drug) and albumin, wherein the individual is selected for treatment based on having an mTOR activation abnormality. In some embodiments, a method of treating hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) in an individual, comprising: (a) evaluating mTOR activation or more in the individual; (b) administering to the individual an effective amount of a composition comprising nanoparticles containing a rapamycin drug (e.g., sirolimus) and albumin (the nanoparticles having an average diameter of about 150 nm or less), wherein the individual is selected for treatment based on having an mTOR activation abnormality. In some embodiments, a method of treating hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) in an individual, comprising: (a) evaluating mTOR activation or more in the individual; (b) administering to the individual an effective amount of a composition comprising nanoparticles containing sirolimus associated with (e.g., coated with) albumin (the nanoparticles having an average diameter of about 150 nm or less, and the weight ratio of albumin to sirolimus in the composition being about 9:1 or less), wherein the individual is selected for treatment based on having an mTOR activation abnormality. In some embodiments, a method of treating hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) in an individual, comprising: (a) evaluating mTOR activation or more in the individual; (b) administering to the individual an effective amount of Nab-sirolimus, wherein the individual is selected for treatment based on having an mTOR activation abnormality. In some embodiments, the mTOR activation abnormality includes a mutation of an mTOR-related gene. In some embodiments, the mTOR activation abnormality includes a copy number polymorphism of an mTOR-related gene. In some embodiments, the mTOR activation abnormality includes an abnormal expression level of an mTOR-related gene. In some embodiments, the mTOR activation abnormality includes an abnormal activity level of an mTOR-related gene.In some embodiments, mTOR activation abnormalities result in the activation of mTORC1 (including, for example, the activation of mTORC1 rather than mTORC2). In some embodiments, mTOR activation abnormalities result in the activation of mTORC2 (including, for example, the activation of mTORC2 rather than mTORC1). In some embodiments, mTOR activation abnormalities result in the activation of both mTORC1 and mTORC2. In some embodiments, the mTOR activation abnormality is an abnormality of at least one mTOR-related gene selected from the group consisting of AKT1, FLT3, MTOR, PIK3CA, PIK3CG, TSC1, TSC2, RHEB, STK11, NF1, NF2, PTEN, TP53, FGFR4, KRAS, NRAS, and BAP1. In some embodiments, the mTOR activation abnormality is evaluated by gene sequencing. In some embodiments, the gene sequencing is based on DNA sequencing in a tumor sample. In some embodiments, the gene sequencing is based on the sequencing of circulating DNA or cell-free DNA isolated from a blood sample. In some embodiments, the mutation status of TFE3 is further used as a basis for selecting an individual. In some embodiments, the mutation status of TFE3 includes a translocation of TFE3. In some embodiments, the mTOR activation abnormality includes an abnormal phosphorylation level of a protein encoded by an mTOR-related gene. In some embodiments, the mTOR activation abnormality includes an abnormal phosphorylation level of a protein encoded by mTOR selected from the group consisting of AKT, S6K, S6, 4EBP1, and SPARC. In some embodiments, the abnormal phosphorylation level is determined by immunohistochemistry.

[0095] In some embodiments, a method of treating hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) in an individual, comprising: (a) evaluating mTOR activation above normal in the individual; (b) selecting (e.g., identifying or recommending) the individual for treatment based on the individual having an mTOR activation abnormality; and (c) administering to the individual an effective amount of a composition comprising nanoparticles containing an mTOR inhibitor (e.g., a rapamycin drug) and albumin. In some embodiments, a method of treating hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) in an individual, comprising: (a) evaluating mTOR activation above normal in the individual; (b) selecting (e.g., identifying or recommending) the individual for treatment based on the individual having an mTOR activation abnormality; and (c) administering to the individual an effective amount of a composition comprising nanoparticles containing a rapamycin drug (e.g., sirolimus) and albumin (the nanoparticles having an average diameter of about 150 nm or less). In some embodiments, a method of treating hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) in an individual, comprising: (a) evaluating mTOR activation above normal in the individual; (b) selecting (e.g., identifying or recommending) the individual for treatment based on the individual having an mTOR activation abnormality; and (c) administering to the individual an effective amount of a composition comprising nanoparticles containing sirolimus associated with (e.g., coated with) albumin (the nanoparticles having an average diameter of about 150 nm or less and the weight ratio of albumin to sirolimus in the composition being about 9:1 or less). In some embodiments, a method of treating hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) in an individual, comprising: (a) evaluating mTOR activation above normal in the individual; (b) selecting (e.g., identifying or recommending) the individual for treatment based on the individual having an mTOR activation abnormality; and (c) administering to the individual an effective amount of Nab-sirolimus. In some embodiments, the mTOR activation abnormality comprises a mutation in an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises a copy number polymorphism in an mTOR-related gene.In some embodiments, the mTOR activation abnormality includes an abnormal expression level of an mTOR-related gene. In some embodiments, the mTOR activation abnormality includes an abnormal activity level of an mTOR-related gene. In some embodiments, the mTOR activation abnormality results in the activation of mTORC1 (including, for example, the activation of mTORC1 rather than mTORC2). In some embodiments, the mTOR activation abnormality results in the activation of mTORC2 (including, for example, the activation of mTORC2 rather than mTORC1). In some embodiments, the mTOR activation abnormality results in the activation of both mTORC1 and mTORC2. In some embodiments, the mTOR activation abnormality is an abnormality of at least one mTOR-related gene selected from the group consisting of AKT1, FLT3, MTOR, PIK3CA, PIK3CG, TSC1, TSC2, RHEB, STK11, NF1, NF2, PTEN, TP53, FGFR4, KRAS, NRAS, and BAP1. In some embodiments, the mTOR activation abnormality is evaluated by gene sequencing. In some embodiments, the gene sequencing is based on DNA sequencing in a tumor sample. In some embodiments, the gene sequencing is based on the sequencing of circulating DNA or cell-free DNA isolated from a blood sample. In some embodiments, the mutation status of TFE3 is further used as a basis for selecting an individual. In some embodiments, the mutation status of TFE3 includes a translocation of TFE3. In some embodiments, the mTOR activation abnormality includes an abnormal phosphorylation level of a protein encoded by an mTOR-related gene. In some embodiments, the mTOR activation abnormality includes an abnormal phosphorylation level of a protein encoded by mTOR selected from the group consisting of AKT, S6K, S6, 4EBP1, and SPARC. In some embodiments, the abnormal phosphorylation level is determined by immunohistochemistry.

[0096] In one aspect, the present invention provides a method for treating hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) in an individual, the method comprising administering to the individual an effective amount of a composition comprising mTOR inhibitors (e.g., rapamycin drugs) and nanoparticles comprising albumin, wherein the individual is selected for treatment based on having an mTOR activation abnormality. In some embodiments, a method for treating hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) in an individual is provided, the method comprising administering to the individual an effective amount of a composition comprising a rapamycin drug (e.g., sirolimus) and nanoparticles comprising albumin (the nanoparticles having an average diameter of about 150 nm or less), wherein the individual is selected for treatment based on having an mTOR activation abnormality. In some embodiments, a method for treating hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) in an individual is provided, the method comprising administering to the individual an effective amount of a composition comprising nanoparticles comprising sirolimus associated with (e.g., coated with) albumin (the nanoparticles having an average diameter of about 150 nm or less and the weight ratio of albumin to sirolimus in the composition being about 9:1 or less), wherein the individual is selected for treatment based on having an mTOR activation abnormality. In some embodiments, a method for treating hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) in an individual is provided, the method comprising administering to the individual an effective amount of Nab-sirolimus, wherein the individual is selected for treatment based on having an mTOR activation abnormality. In some embodiments, the mTOR activation abnormality comprises a mutation in an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises a copy number polymorphism in an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises an abnormal expression level of an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises an abnormal activity level of an mTOR-related gene. In some embodiments, the mTOR activation abnormality results in activation of mTORC1 (e.g., including activation of mTORC1 but not mTORC2).In some embodiments, mTOR activation abnormalities result in activation of mTORC2 (including, for example, activation of mTORC2 rather than mTORC1). In some embodiments, mTOR activation abnormalities result in activation of both mTORC1 and mTORC2. In some embodiments, the mTOR activation abnormality is an abnormality of at least one mTOR-related gene selected from the group consisting of AKT1, FLT3, MTOR, PIK3CA, PIK3CG, TSC1, TSC2, RHEB, STK11, NF1, NF2, PTEN, TP53, FGFR4, KRAS, NRAS, and BAP1. In some embodiments, the mTOR activation abnormality is evaluated by gene sequencing. In some embodiments, the gene sequencing is based on DNA sequencing in a tumor sample. In some embodiments, the gene sequencing is based on sequencing of circulating DNA or cell-free DNA isolated from a blood sample. In some embodiments, the mutation status of TFE3 is further used as a basis for selecting an individual. In some embodiments, the mutation status of TFE3 includes a translocation of TFE3. In some embodiments, the mTOR activation abnormality includes an abnormal phosphorylation level of a protein encoded by an mTOR-related gene. In some embodiments, the mTOR activation abnormality includes an abnormal phosphorylation level of a protein encoded by an mTOR-related gene selected from the group consisting of AKT, S6K, S6, 4EBP1, and SPARC. In some embodiments, the abnormal phosphorylation level is determined by immunohistochemistry.

[0097] In some embodiments, a method of selecting (including identifying or recommending) an individual having hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) for treatment with a composition comprising nanoparticles containing an mTOR inhibitor (e.g., a rapamycin drug) and albumin, the method comprising: (a) evaluating mTOR activation abnormality in the individual; (b) selecting or recommending the individual for treatment based on the individual having an mTOR activation abnormality. In some embodiments, a method of selecting (including identifying or recommending) an individual having hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) for treatment with a composition comprising a rapamycin drug (e.g., sirolimus) and albumin (including nanoparticles having an average diameter of about 150 nm or less), the method comprising: (a) evaluating mTOR activation abnormality in the individual; (b) selecting or recommending the individual for treatment based on the individual having an mTOR activation abnormality. In some embodiments, a method of selecting (including identifying or recommending) an individual having hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) for treatment with a composition comprising nanoparticles containing sirolimus associated with (e.g., coated with) albumin (including nanoparticles having an average diameter of about 150 nm or less and the weight ratio of albumin to sirolimus in the composition being about 9:1 or less), the method comprising: (a) evaluating mTOR activation abnormality in the individual; (b) selecting or recommending the individual for treatment based on the individual having an mTOR activation abnormality. In some embodiments, a method of selecting (including identifying or recommending) an individual having hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) for treatment with Nab-sirolimus, the method comprising: (a) evaluating mTOR activation abnormality in the individual; (b) selecting or recommending the individual for treatment based on the individual having an mTOR activation abnormality. In some embodiments, the mTOR activation abnormality includes a mutation in an mTOR-related gene. In some embodiments, the mTOR activation abnormality includes a copy number polymorphism in an mTOR-related gene.In some embodiments, the mTOR activation abnormality includes an abnormal expression level of an mTOR-related gene. In some embodiments, the mTOR activation abnormality includes an abnormal activity level of an mTOR-related gene. In some embodiments, the mTOR activation abnormality results in the activation of mTORC1 (e.g., including the activation of mTORC1 rather than mTORC2). In some embodiments, the mTOR activation abnormality results in the activation of mTORC2 (e.g., including the activation of mTORC2 rather than mTORC1). In some embodiments, the mTOR activation abnormality results in the activation of both mTORC1 and mTORC2. In some embodiments, the mTOR activation abnormality is an abnormality of at least one mTOR-related gene selected from the group consisting of AKT1, FLT3, MTOR, PIK3CA, PIK3CG, TSC1, TSC2, RHEB, STK11, NF1, NF2, PTEN, TP53, FGFR4, KRAS, NRAS, and BAP1. In some embodiments, the mTOR activation abnormality is evaluated by gene sequencing. In some embodiments, the gene sequencing is based on DNA sequencing in a tumor sample. In some embodiments, the gene sequencing is based on sequencing of circulating DNA or cell-free DNA isolated from a blood sample. In some embodiments, the mutation status of TFE3 is further used as a basis for selecting an individual. In some embodiments, the mutation status of TFE3 includes a translocation of TFE3. In some embodiments, the mTOR activation abnormality includes an abnormal phosphorylation level of a protein encoded by an mTOR-related gene. In some embodiments, the mTOR activation abnormality includes an abnormal phosphorylation level of a protein encoded by mTOR selected from the group consisting of AKT, S6K, S6, 4EBP1, and SPARC. In some embodiments, the abnormal phosphorylation level is determined by immunohistochemistry.

[0098] In some embodiments, a method of selecting (including identifying or recommending) an individual having hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) for treatment with a composition comprising nanoparticles containing an mTOR inhibitor (e.g., a rapamycin drug) and albumin, the method comprising: (a) evaluating mTOR activation abnormality in the individual; (b) selecting or recommending the individual for treatment based on the individual having an mTOR activation abnormality; (c) administering to the selected individual an effective amount of a composition comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin. In some embodiments, a method of selecting (including identifying or recommending) an individual having hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) for treatment with a composition comprising a rapamycin drug (e.g., sirolimus) and albumin (including nanoparticles having an average diameter of about 150 nm or less), the method comprising: (a) evaluating mTOR activation abnormality in the individual; (b) selecting or recommending the individual for treatment based on the individual having an mTOR activation abnormality; (c) administering to the selected individual an effective amount of a composition comprising a rapamycin drug (e.g., sirolimus) and albumin. In some embodiments, a method of selecting (including identifying or recommending) an individual having hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) for treatment with a composition comprising nanoparticles containing sirolimus associated with (e.g., coated with) albumin (including nanoparticles having an average diameter of about 150 nm or less and having a weight ratio of albumin to sirolimus in the composition of about 9:1 or less), the method comprising: (a) evaluating mTOR activation abnormality in the individual; (b) selecting or recommending the individual for treatment based on the individual having an mTOR activation abnormality; (c) administering to the selected individual an effective amount of a composition comprising nanoparticles containing sirolimus associated with (e.g., coated with) albumin.In some embodiments, provided is a method of selecting (including identifying or recommending) an individual having hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) for treatment with Nab-sirolimus, the method comprising: (a) evaluating mTOR activation abnormality in the individual; (b) selecting or recommending the individual for treatment based on the individual having the mTOR activation abnormality; and (c) administering an effective amount of Nab-sirolimus to the selected individual. In some embodiments, the mTOR activation abnormality includes a mutation in an mTOR-related gene. In some embodiments, the mTOR activation abnormality includes a copy number polymorphism in an mTOR-related gene. In some embodiments, the mTOR activation abnormality includes an abnormal expression level of an mTOR-related gene. In some embodiments, the mTOR activation abnormality includes an abnormal activity level of an mTOR-related gene. In some embodiments, the mTOR activation abnormality results in activation of mTORC1 (e.g., including activation of mTORC1 but not mTORC2). In some embodiments, the mTOR activation abnormality results in activation of mTORC2 (e.g., including activation of mTORC2 but not mTORC1). In some embodiments, the mTOR activation abnormality results in activation of both mTORC1 and mTORC2. In some embodiments, the mTOR activation abnormality is an abnormality of at least one mTOR-related gene selected from the group consisting of AKT1, FLT3, MTOR, PIK3CA, PIK3CG, TSC1, TSC2, RHEB, STK11, NF1, NF2, PTEN, TP53, FGFR4, KRAS, NRAS, and BAP1. In some embodiments, the mTOR activation abnormality is evaluated by gene sequencing. In some embodiments, the gene sequencing is based on DNA sequencing in a tumor sample. In some embodiments, the gene sequencing is based on sequencing of circulating DNA or cell-free DNA isolated from a blood sample. In some embodiments, the mutation status of TFE3 is further used as a basis for selecting the individual. In some embodiments, the mutation status of TFE3 includes a translocation of TFE3. In some embodiments, the mTOR activation abnormality includes an abnormal phosphorylation level of a protein encoded by an mTOR-related gene.In some embodiments, the mTOR activation abnormality comprises an abnormal phosphorylation level of a protein encoded by mTOR selected from the group consisting of AKT, S6K, S6, 4EBP1, and SPARC. In some embodiments, the abnormal phosphorylation level is determined by immunohistochemistry.

[0099] Furthermore, a method for treating hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) in an individual, comprising administering to the individual an effective amount of a composition comprising nanoparticles containing an mTOR inhibitor (e.g., a rapamycin drug) and albumin, wherein the individual has an mTOR activation abnormality, is provided. In some embodiments, a method for treating hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) in an individual, comprising administering to the individual an effective amount of a composition comprising nanoparticles containing a rapamycin drug (e.g., sirolimus) and albumin (the nanoparticles having an average diameter of about 150 nm or less), wherein the individual has an mTOR activation abnormality, is provided. In some embodiments, a method for treating hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) in an individual, comprising administering to the individual an effective amount of a composition comprising nanoparticles containing sirolimus associated with (e.g., coated with) albumin (the nanoparticles having an average diameter of about 150 nm or less and the weight ratio of albumin to sirolimus in the composition being about 9:1 or less), wherein the individual has an mTOR activation abnormality, is provided. In some embodiments, a method for treating hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) in an individual, comprising administering to the individual an effective amount of Nab-sirolimus, wherein the individual has an mTOR activation abnormality, is provided. In some embodiments, the mTOR activation abnormality comprises a mutation in an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises a copy number polymorphism in an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises an abnormal expression level of an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises an abnormal activity level of an mTOR-related gene. In some embodiments, the mTOR activation abnormality results in activation of mTORC1 (e.g., including activation of mTORC1 but not mTORC2). In some embodiments, the mTOR activation abnormality results in activation of mTORC2 (e.g., including activation of mTORC2 but not mTORC1). In some embodiments, the mTOR activation abnormality results in activation of both mTORC1 and mTORC2.In some embodiments, the mTOR activation abnormality is an abnormality of at least one mTOR-related gene selected from the group consisting of AKT1, FLT3, MTOR, PIK3CA, PIK3CG, TSC1, TSC2, RHEB, STK11, NF1, NF2, PTEN, TP53, FGFR4, KRAS, NRAS, and BAP1. In some embodiments, the mTOR activation abnormality is evaluated by gene sequencing. In some embodiments, the gene sequencing is based on DNA sequencing in a tumor sample. In some embodiments, the gene sequencing is based on sequencing of circulating DNA or cell-free DNA isolated from a blood sample. In some embodiments, the mutation status of TFE3 is further used as a basis for selecting an individual. In some embodiments, the mutation status of TFE3 includes a translocation of TFE3. In some embodiments, the mTOR activation abnormality includes an abnormal phosphorylation level of a protein encoded by an mTOR-related gene. In some embodiments, the mTOR activation abnormality includes an abnormal phosphorylation level of a protein encoded by mTOR selected from the group consisting of AKT, S6K, S6, 4EBP1, and SPARC. In some embodiments, the abnormal phosphorylation level is determined by immunohistochemistry.

[0100] Similarly, this specification also provides a method for evaluating whether an individual having hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) is likely or unlikely to respond to a treatment comprising a composition comprising nanoparticles containing an mTOR inhibitor (e.g., a rapamycin drug) and albumin, based on the individual having an mTOR activation abnormality, the method comprising the step of evaluating the mTOR activation abnormality in the individual. In some embodiments, the method further comprises administering to the individual determined to be likely to respond to the treatment an effective amount of a composition comprising nanoparticles containing an mTOR inhibitor (e.g., a rapamycin drug) and albumin. In some embodiments, the presence of an mTOR activation abnormality indicates that the individual is more likely to respond to the treatment, and the absence of an mTOR activation abnormality indicates that the individual is less likely to respond to the treatment. In some embodiments, the amount of the mTOR inhibitor (e.g., a rapamycin drug) is determined based on the state of the mTOR activation abnormality.

[0101] Also, this specification provides a method for assisting in the evaluation of whether an individual having hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) is likely to respond to, or is suitable for, a treatment comprising an effective amount of a composition comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, based on the individual having an mTOR activation abnormality, the method comprising the step of evaluating the mTOR activation abnormality in the individual. In some embodiments, the presence of an mTOR activation abnormality indicates that the individual is more likely to respond to the treatment, and the absence of an mTOR activation abnormality indicates that the individual is less likely to respond to the treatment. In some embodiments, the method further comprises the step of administering an effective amount of a composition comprising nanoparticles containing an mTOR inhibitor (e.g., a rapamycin drug) and albumin.

[0102] Further provided herein is a method of identifying an individual likely to respond to a treatment comprising an effective amount of a composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, the method comprising: (a) evaluating mTOR activation abnormalities in the individual; and (b) identifying the individual based on the individual having mTOR activation abnormalities, for hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension). In some embodiments, the method further comprises: i) administering an effective amount of a composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin. In some embodiments, the amount of the mTOR inhibitor (e.g., a rapamycin drug) is determined based on the state of the mTOR activation abnormality.

[0103] Also provided herein is a method of adjusting a therapeutic treatment of an individual having hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) who has received an effective amount of a composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, the method comprising: evaluating mTOR activation abnormalities in a sample isolated from the individual; and adjusting the therapeutic treatment based on the state of the mTOR activation abnormality. In some embodiments, the amount of the mTOR inhibitor (e.g., a rapamycin drug) is adjusted.

[0104] Also provided herein is a method of marketing a treatment comprising an effective amount of a composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin for use in hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) in a subpopulation of individuals, the method comprising providing information to a target population regarding the use of the treatment for treating such a subpopulation of individuals characterized by individuals in the subpopulation having samples with mTOR activation abnormalities.

[0105] In some embodiments of any of the methods described herein, the method predicts and / or results in a measurable reduction in abnormal cell growth (including tumor size, degree of stenosis, and pulmonary pressure), evidence of disease or disease progression, an objective response (e.g., in the case of cancer, including complete response, partial response, and stable disease), an increase or prolongation of progression-free survival, and / or an increase or prolongation of overall survival. In some embodiments of any of the above methods, an individual, if having an mTOR-activating abnormality, is likely to respond to a nanoparticle composition of an mTOR inhibitor (e.g., a rimosome nanoparticle composition containing Nab-sirolimus) alone or in combination with another agent, and the response of the individual to the treatment is evidenced by a measurable reduction in abnormal cell growth (including tumor size, degree of stenosis, and pulmonary pressure), evidence of disease or disease progression, an objective response (e.g., in the case of cancer, including complete response, partial response, and stable disease), an increase or prolongation of progression-free survival, and / or an increase or prolongation of overall survival.

[0106] In some embodiments of any of the methods described herein, a method of inhibiting abnormal cell growth (e.g., tumor growth, abnormal cell growth in blood vessels or lungs) in an individual, comprising administering to the individual an effective amount of a composition comprising nanoparticles containing an mTOR inhibitor (e.g., a rimos drug) and albumin, wherein the individual is selected based on an individual having an mTOR-activating abnormality, is provided. In some embodiments, at least about 10% (e.g., including any of at least about 20%, about 30%, about 40%, about 60%, about 70%, about 80%, about 90%, or about 100%) of the abnormal cell growth is inhibited.

[0107] In some embodiments of any of the methods described herein, a method of reducing tumor size in an individual, comprising administering to the individual an effective amount of a composition comprising a nanoparticle comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, wherein the individual is selected based on an individual having an mTOR activation abnormality, is provided. In some embodiments, the tumor size is reduced by at least about 10% (e.g., including any of at least about 20%, about 30%, about 40%, about 60%, about 70%, about 80%, about 90%, or about 100%).

[0108] In some embodiments of any of the methods described herein, a method of maintaining the lumen diameter or cross-sectional area of a blood vessel of an individual after an intravascular procedure, comprising administering to the individual an effective amount of a composition comprising a nanoparticle comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, wherein the individual is selected based on an individual having an mTOR activation abnormality, is provided. In some embodiments, at least about 50% (e.g., including any of at least about 60%, about 70%, about 80%, about 90%, or about 100%) of the lumen diameter or cross-sectional area of the blood vessel is maintained after the intravascular procedure. In some embodiments, the lumen diameter or cross-sectional area of the blood vessel is maintained for at least about 1 year, about 2 years, about 3 years, about 4 years, about 5 years, about 6 years, about 7 years, about 8 years, about 9 years, about 10 years, or more than that over any one of them during the intravascular procedure.

[0109] In some embodiments of any of the methods described herein, a method of reducing the pulmonary pressure of an individual, comprising administering to the individual an effective amount of a composition comprising a nanoparticle comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, wherein the individual is selected based on an individual having an mTOR activation abnormality, is provided. In some embodiments, the pulmonary pressure is reduced by at least about 10% (e.g., including any of at least about 20%, about 30%, about 40%, about 60%, about 70%, about 80%, or about 90%).

[0110] In some embodiments of any of the methods described herein, a method of inhibiting tumor metastasis in an individual, comprising administering to the individual an effective amount of a composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, wherein the individual is selected based on an individual having an mTOR activation abnormality, is provided. In some embodiments, at least about 10% (e.g., including any of at least about 20%, about 30%, about 40%, about 60%, about 70%, about 80%, about 90%, or about 100%) of the metastases are inhibited. In some embodiments, this method inhibits metastasis to lymph nodes.

[0111] In some embodiments of any of the methods described herein, a method of prolonging the progression-free survival period of hyperplasia (e.g., cancer, restenosis or pulmonary hypertension) in an individual, comprising administering to the individual an effective amount of a composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, wherein the individual is selected based on an individual having an mTOR activation abnormality, is provided. In some embodiments, this method prolongs the time to disease progression where the hyperplasia is cancer for at least about 1 month, about 2 months, about 3 months, about 4 months, about 5 months, about 6 months, about 7 months, about 8 months, about 9 months, about 10 months, about 11 months, about 12 months. In some embodiments, this method prolongs the time to disease progression where the hyperplasia is restenosis or pulmonary hypertension for at least about 3 months, about 6 months, about 1 year, about 2 years, about 3 years, about 4 years, about 5 years, about 6 years or more.

[0112] In some embodiments of any of the methods described herein, a method of extending the survival period of an individual having hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension), the method comprising administering to the individual an effective amount of a composition comprising nanoparticles containing an mTOR inhibitor (e.g., a rapamycin drug) and albumin, wherein the individual is selected based on an individual having mTOR activation abnormality, is provided. In some embodiments, the method extends the survival period of an individual with hyperplasia being cancer for any of at least about 1 month, about 2 months, about 3 months, about 4 months, about 5 months, about 6 months, about 7 months, about 8 months, about 9 months, about 10 months, about 11 months, about 12 months, about 18 months, or about 24 months. In some embodiments, the method extends the survival period of an individual with hyperplasia being restenosis or pulmonary hypertension for any of at least about 3 months, about 6 months, about 1 year, about 2 years, about 3 years, about 4 years, about 5 years, about 6 years or more.

[0113] In some embodiments of any of the methods described herein, a method of alleviating one or more (including any of about 1, about 2, about 3, about 4, about 5, about 6 or more) of the symptoms associated with hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension), the method comprising administering to the individual an effective amount of a composition comprising nanoparticles containing an mTOR inhibitor (e.g., a rapamycin drug) and albumin, wherein the individual is selected based on an individual having mTOR activation abnormality, is provided. In some embodiments, one or more of the symptoms associated with hyperplasia are alleviated by at least about 10% (including any of at least about 20%, about 30%, about 40%, about 60%, about 70%, about 80%, about 90%, or about 100%).

[0114] In some embodiments of any of the methods described herein, a method of improving the quality of life of an individual having hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension), the method comprising administering to the individual an effective amount of a composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, wherein the individual is selected based on an individual having mTOR activation abnormalities.

[0115] In some embodiments of any of the methods described herein, a method of reducing AE and SAE in an individual having hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension), the method comprising administering to the individual an effective amount of a composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, wherein the individual is selected based on an individual having mTOR activation abnormalities.

[0116] In some embodiments of any of the methods described herein, the method predicts and / or results in an objective response (e.g., a partial response or a complete response).

[0117] In some embodiments of any of the methods described herein, the method predicts and / or results in an improved quality of life.

[0118] "Abnormal mTOR activation" refers to genetic abnormalities, abnormal expression levels, and / or abnormal activity levels of one or more mTOR-related genes that can lead to overactivation of the mTOR signaling pathway. "Overactivate" refers to an improvement in the activity level of a molecule (e.g., a protein or protein complex) or a signaling pathway (e.g., the mTOR signaling pathway) to a level that exceeds a reference activity level or range, e.g., at least about 10%, about 20%, about 30%, about 40%, about 60%, about 70%, about 80%, about 90%, about 100%, about 200%, about 500% or higher than the median of the reference activity level or reference activity range. In some embodiments, the reference activity level is the clinically acceptable normal activity level in a standardized test or the activity level in a healthy individual (or tissue or cells isolated from an individual) without abnormal mTOR activation.

[0119] The mTOR-activating abnormalities contemplated herein can include one type of abnormality in one mTOR-related gene, more than one type of abnormality in one mTOR-related gene (e.g., at least about 2, about 3, about 4, about 5, about 6 or more of any), one type of abnormality in more than one mTOR-related gene (e.g., at least about 2, about 3, about 4, about 5, about 6 or more of any), or more than one type of abnormality in more than one mTOR-related gene (e.g., at least about 2, about 3, about 4, about 5, about 6 or more of any). Different types of mTOR-activating abnormalities can include, but are not limited to, genetic abnormalities, abnormal expression levels (e.g., overexpression or underexpression), abnormal activity levels (e.g., high activity level or low activity level), and abnormal phosphorylation levels. In some embodiments, the genetic abnormality includes a change to a nucleic acid (e.g., DNA or RNA), or protein sequence (i.e., a mutation), or an abnormal epigenetic feature related to an mTOR-related gene, including but not limited to those related to the coding, non-coding, regulatory, enhancer, silencer, promoter, intron, exon, and untranslated regions of the mTOR-related gene. In some embodiments, the mTOR-activating abnormality includes a mutation of an mTOR-related gene, including but not limited to deletions, frameshifts, insertions, missense mutations, nonsense mutations, point mutations, silent mutations, splice site mutations and translocations. In some embodiments, the mutation can be a loss-of-function mutation to a negative regulator of the mTOR signaling pathway, or a gain-of-function mutation of a positive regulator of the mTOR signaling pathway. In some embodiments, the genetic abnormality includes a copy number polymorphism of an mTOR-related gene. In some embodiments, the copy number polymorphism of an mTOR-related gene is caused by a genomic structural rearrangement including deletions, duplications, inversions and translocations.In some embodiments, the genetic abnormality includes abnormal epigenetic features of mTOR-related genes, including but not limited to DNA methylation, hydroxymethylation, increased or decreased histone binding, chromatin remodeling, and the like.

[0120] Aberrant mTOR activation is determined by comparison to a control or reference, such as a reference sequence (e.g., nucleic acid or protein sequence), a control expression (e.g., RNA or protein expression) level, a control activity (e.g., activation or inhibition of a downstream target) level, or a phosphorylation level of a control protein. An abnormal expression level or abnormal activity level in an mTOR-related gene may be above the control level (e.g., by any of about 10%, about 20%, about 30%, about 40%, about 60%, about 70%, about 80%, about 90%, about 100%, about 200%, about 500% or higher than the control level) if the mTOR-related gene is a positive regulator (i.e., activator) of the mTOR signaling pathway, or may be below the control level (e.g., by any of about 10%, about 20%, about 30%, about 40%, about 60%, about 70%, about 80%, about 90% or less than the control level) if the mTOR-related gene is a negative regulator (i.e., inhibitor) of the mTOR signaling pathway. In some embodiments, the control level (e.g., expression level or activity level) is the median of the levels (e.g., expression level or activity level) of a control population. In some embodiments, the control population is a population having the same hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) as the individual being treated. In some embodiments, the control population is a healthy population that does not have hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) and optionally has comparable demographic characteristics (e.g., gender, age, ethnicity, etc.) as the individual being treated. In some embodiments, the control level (e.g., expression level or activity level) is the level (e.g., expression level or activity level) of healthy tissue from the same individual. Genetic abnormalities can be determined by comparison to a reference sequence, including an epigenetic pattern of the reference sequence in a control sample.In some embodiments, the reference array is present in a healthy population of individuals who do not have hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension), and may optionally have similar demographic characteristics (such as gender, age, ethnicity, etc.) as the individual being treated, and corresponds to a sequence (DNA, RNA, or protein sequence) of a fully functional allele of an mTOR-related gene, such as an allele of an mTOR-related gene (e.g., a common allele). Exemplary mTOR-related genes and their reference sequences (i.e., wild-type sequences) are described in the "Biomarkers" section below.

[0121] The "state" of abnormal mTOR activation can refer to the presence or absence of abnormal mTOR activation in one or more mTOR-related genes, or the abnormal levels (expression or activity levels, including protein phosphorylation levels) of one or more mTOR-related genes. In some embodiments, the presence of genetic abnormalities (e.g., mutations or copy number polymorphisms) in one or more mTOR-related genes compared to a control indicates that (a) the individual is more likely to respond to treatment, or (b) the individual is selected for treatment. In some embodiments, the absence of genetic abnormalities in mTOR-related genes or wild-type mTOR-related genes compared to a control indicates that (a) the individual is less likely to respond to treatment, or (b) the individual is not selected for treatment. In some embodiments, abnormal levels (e.g., expression levels or activity levels including protein phosphorylation levels) of one or more mTOR-related genes are associated with the likelihood that an individual may respond to treatment. For example, a greater deviation of the levels (e.g., expression levels or activity levels including protein phosphorylation levels) of one or more mTOR-related genes in a direction of overactivating the mTOR signaling pathway indicates that the individual is more likely to respond to treatment. In some embodiments, a predictive model based on the levels (e.g., expression levels or activity levels including protein phosphorylation levels) of one or more mTOR-related genes is used to predict (a) the likelihood that an individual will respond to treatment, and (b) whether to select the individual for treatment. For example, the predictive model, including coefficients for each level, can be obtained by statistical analysis such as regression analysis using clinical trial data.

[0122] The expression level and / or activity level of one or more mTOR-related genes, and / or the phosphorylation level of one or more proteins encoded by one or more mTOR-related genes, and / or the presence or absence of one or more genetic abnormalities of one or more mTOR-related genes can be useful for determining any of (a) the likelihood that an individual may be suitable or highly likely to initially receive treatment, (b) the likelihood that an individual may be unsuitable or highly likely to initially receive treatment, (c) responsiveness to treatment, (d) the likelihood that an individual may be suitable or highly likely to continue receiving treatment, (e) the likelihood that an individual may be unsuitable or highly likely to continue receiving treatment, (f) adjustment of dosage, (g) prediction of the likelihood of clinical benefit.

[0123] In some embodiments, the mutation status, expression level, or activity level of one or more resistance biomarkers (e.g., TFE3) is used to select an individual for any of the treatment methods described herein and / or to determine any of (a) the likelihood that an individual may be suitable or highly likely to initially receive treatment, (b) the likelihood that an individual may be unsuitable or highly likely to initially receive treatment, (c) responsiveness to treatment, (d) the likelihood that an individual may be suitable or highly likely to continue receiving treatment, (e) the likelihood that an individual may be unsuitable or highly likely to continue receiving treatment, (f) adjustment of dosage, (g) prediction of the likelihood of clinical benefit. In some embodiments, the resistance biomarker is a gene selected from the ONCOPANEL™ assay. See, for example, Wagle N. et al., Cancer discovery, Vol. 2.1 (2012): pages 82-93.

[0124] In some embodiments according to any one of the treatment methods described herein, the mutation status of TFE3 in an individual is used as a basis for selecting the individual. In some embodiments, the mutation status of TFE3 is used in combination with one or more mTOR activating abnormalities in the individual as a basis for selecting the individual for treatment. In some embodiments, the mutation status of TFE3 includes a translocation of TFE3. In some embodiments, the translocation of TFE3 is used to exclude an individual from treatment. In some embodiments, the translocation of TFE3 in a sample of an individual is evaluated by fluorescence in-situ hybridization (FISH). In some embodiments, the sample is a blood sample. In some embodiments, the sample is a tumor biopsy. In some embodiments, the sample is obtained before the start of the treatment method described herein. In some embodiments, the sample is obtained after the start of the treatment method described herein.

[0125] As used herein, "based on" includes (and preferably, selecting an individual suitable for treatment) evaluating, determining or measuring the characteristics of an individual described herein. Where the status of an mTOR activating abnormality is used as a "basis for" selecting, evaluating, measuring or determining the treatment method described herein, the mTOR activating abnormality in one or more mTOR-related genes is determined before and / or during the treatment, and the resulting status (including the presence, absence, expression level and / or activity level of the mTOR activating abnormality) is used by a clinician when evaluating any of the following: (a) the individual may or is likely to be suitable for receiving treatment initially, (b) the individual may or is likely to be unsuitable for receiving treatment initially, (c) responsiveness to treatment, (d) the individual may or is likely to be suitable for continuing treatment, (e) the individual may or is likely to be unsuitable for continuing treatment, (f) adjustment of the dosage, or (g) prediction of the likelihood of clinical benefit.

[0126] The methods described herein relate to the administration of a composition comprising nanoparticles containing an mTOR inhibitor (e.g., a rapamycin drug) and albumin (hereinafter also referred to as "nanoparticle composition of mTOR inhibitor"). As used herein, "mTOR inhibitor" refers to an inhibitor of mTOR. mTOR is a serine / threonine-specific protein kinase downstream of the phosphatidylinositol 3-kinase (PI3K) / Akt (protein kinase B) pathway and is a very important regulator of cell survival, proliferation, stress, and metabolism. Dysregulation of the mTOR pathway has been found in many human cancers, and mTOR inhibition has produced a substantial inhibitory effect on tumor progression. In some embodiments, the mTOR inhibitor is an mTOR kinase inhibitor. The mTOR inhibitors described herein include, but are not limited to, BEZ235 (NVP-BEZ235), everolimus (RAD001, Zortress, Certican, and also known as Afinitor), rapamycin (also known as sirolimus or Rapamune), AZD8055, temsirolimus (also known as CCI-779 and Torisel), PI-103, Ku-0063794, INK 128, AZD2014, NVP-BGT226, PF-04691502, CH5132799, GDC-0980 (RG7422), Torin 1, WAY-600, WYE-125132, WYE-687, GSK2126458, PF-05212384 (PKI-587), PP-121, OSI-027, Palomid 529, PP242, XL765, GSK1059615, WYE-354, eforolimus (also known as ridafolimus or deforolimus), CC115, and CC-223.

[0127] In some embodiments, the mTOR inhibitor is a rapamycin drug, which includes sirolimus and its analogs. Examples of rapamycin drugs include, but are not limited to, temsirolimus (CCI-779), everolimus (RAD001), ridaforolimus (AP-23573), deforolimus (MK-8669), zotarolimus (ABT-578), pimecrolimus, and tacrolimus (FK-506). In some embodiments, the rapamycin drug is selected from the group consisting of temsirolimus (CCI-779), everolimus (RAD001), ridaforolimus (AP-23573), deforolimus (MK-8669), zotarolimus (ABT-578), pimecrolimus, and tacrolimus (FK-506).

[0128] In some embodiments, the albumin is human serum albumin.

[0129] In some embodiments, the mTOR inhibitor (e.g., rapamycin drug) is associated with albumin (e.g., coated with albumin).

[0130] In some embodiments, the composition comprising nanoparticles containing an mTOR inhibitor (e.g., rapamycin drug) and albumin is substantially free of surfactant.

[0131] In some embodiments, the composition comprising nanoparticles containing an mTOR inhibitor and albumin is Nab-sirolimus. "Nab" represents binding to nanoparticle albumin, and "Nab-sirolimus" is an albumin-stabilized nanoparticle formulation of sirolimus. Nab-sirolimus is also known as Nab-rapamycin as already described. See, for example, WO2008109163A1, WO2014151853, WO2008137148A2, and WO2012149451A1.

[0132] In some embodiments, the treatment comprises administering a composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin for less than about 50 minutes, such as less than about 40 minutes, less than about 30 minutes, about 30 to about 40 minutes, or for about 30 minutes. In some embodiments, the dosage of the mTOR inhibitor (e.g., a rapamycin drug containing sirolimus) in the nanoparticle composition of the mTOR inhibitor is from about 10 mg / m2 to about 150 mg / m2 (including, for example, from about 10 mg / m2 to about 50 mg / m2, from about 50 mg / m2 to about 75 mg / m2, or from about 75 mg / m2 to about 150 mg / m2). In some embodiments, the dosage of the mTOR inhibitor (e.g., a rapamycin drug containing sirolimus) in the nanoparticle composition of the mTOR inhibitor is about 45 mg / m2, about 56 mg / m2, about 75 mg / m2, or about 100 mg / m2. In some embodiments, the treatment comprises parenterally administering a composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin. In some embodiments, the treatment comprises intravenously administering a composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin. In some embodiments, the treatment comprises administering a composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin weekly. In some embodiments, the treatment comprises administering a composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin three out of four weeks or two out of three weeks weekly. In some embodiments, the treatment comprises administering a composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin on days 1, 8, and 15 of a 28-day cycle. In some embodiments, the treatment comprises administering a composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin on days 1 and 8 of a 21-day cycle. In some embodiments, the treatment comprises administering a composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin for at least about two cycles (including any of at least about 3, about 4, about 5, about 6, about 7, about 8, about 9, about 10 or more).In some embodiments of any part of this method, the treatment comprises administering a composition comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin without any premedication (e.g., steroid premedication) and / or prophylactic administration of G-CSF.

[0133] mTOR activation abnormalities in an individual can be evaluated or determined by analyzing a sample from the individual. This evaluation can be based on a new tissue sample or a stored tissue sample. Suitable samples include, but are not limited to, hyperplastic (e.g., cancer including tumor stroma) tissue, normal tissue adjacent to hyperplastic (e.g., cancer) tissue, normal tissue distal to hyperplastic (e.g., cancer) tissue, or lymphocytes in peripheral blood. In some embodiments, the sample is hyperplastic (e.g., cancer) tissue. In some embodiments, the sample is a biopsy sample containing hyperplastic (e.g., cancer) cells, such as fine needle aspiration of hyperplastic (e.g., cancer) cells (e.g., cancer cells including tumor stroma) obtained by laparoscopy. In some embodiments, the biopsy cells are centrifuged to form a pellet, fixed, and embedded in paraffin before analysis. In some embodiments, the biopsy cells are snap frozen before analysis. In some embodiments, the sample is a plasma sample. In some embodiments, the sample is a blood sample. In some embodiments, the sample is a tumor biopsy.

[0134] In some embodiments, the sample comprises circulating metastatic cancer cells. In some embodiments, the sample is obtained by sorting circulating tumor cells (CTCs) from blood. In some further embodiments, the CTCs are detached from the primary tumor and circulate in the body fluid. In some further embodiments, the CTCs are detached from the primary tumor and circulate in the bloodstream. In some embodiments, the CTCs are an indicator of metastasis.

[0135] In some embodiments, the sample is mixed with an antibody that recognizes a molecule (e.g., a protein) or a fragment thereof encoded by an mTOR-related gene. In some embodiments, the sample is mixed with a nucleic acid that recognizes a nucleic acid or a fragment thereof associated with an mTOR-related gene (e.g., DNA or RNA). In some embodiments, the sample is used for sequencing analysis, such as next-generation DNA, RNA, and / or exome sequencing analysis.

[0136] mTOR activation abnormalities can be evaluated before the start of treatment, at any time during treatment, and / or at the end of treatment. In some embodiments, mTOR activation abnormalities are evaluated from about 3 days before administration of the mTOR inhibitor nanoparticle composition to about 3 days after administration of the mTOR inhibitor nanoparticle composition in each cycle of administration. In some embodiments, mTOR activation abnormalities are evaluated on day 1 of each cycle of administration. In some embodiments, mTOR activation abnormalities are evaluated in each cycle of administration. In some embodiments, mTOR activation abnormalities are further evaluated every 2 cycles after the first 3 cycles of administration.

[0137] In some embodiments, the hyperplasia is cancer. Examples of cancers that can be treated by the methods described herein include adrenocortical carcinoma, myeloid metaplasia of unknown origin, anal cancer, appendiceal cancer, astrocytoma (e.g., cerebellar and cerebral), basal cell carcinoma, bile duct cancer (e.g., extrahepatic), bladder cancer, bone cancer (osteosarcoma and malignant fibrous histiocytoma), brain tumor (e.g., glioma, brainstem glioma, cerebellar or cerebral astrocytoma (e.g., pilocytic astrocytoma, diffuse astrocytoma, undifferentiated (malignant) astrocytoma), malignant glioma, ependymoma, oligodendroglioma, meningioma, craniopharyngioma, hemangioblastoma, medulloblastoma, supratentorial primitive neuroectodermal tumor, glioma of the visual pathway and hypothalamus, and glioblastoma), breast cancer, bronchial adenoma / carcinoid, carcinoid tumor (e.g., gastrointestinal carcinoid tumor), cancer of unknown primary, central nervous system lymphoma, cervical cancer, colon cancer, colorectal cancer, chronic myeloproliferative disorder, endometrial cancer (e.g., uterine cancer), ependymoma, esophageal cancer, Ewing family of tumors, eye cancer (e.g., intraocular melanoma and retinoblastoma), gallbladder cancer, gastric (stomach) cancer, gastrointestinal carcinoid tumor, gastrointestinal stromal tumor (GIST), germ cell tumor (e.g., extracranial, extragonadal, ovarian), gestational trophoblastic tumor, head and neck cancer, hepatocellular (liver) cancer (e.g., liver carcinoma and heptoma), hypopharyngeal cancer, islet cell carcinoma (pancreatic endocrine), laryngeal cancer, leukemia (except T-cell leukemia), lip and oral cavity cancer, oral cancer, liver cancer, lung cancer (e.g., small cell lung cancer, non-small cell lung cancer, adenocarcinoma of the lung, and squamous cell carcinoma of the lung), lymphoma (except T-cell lymphoma), medulloblastoma, melanoma, mesothelioma, metastatic squamous neck cancer of unknown primary, oral cancer, multiple endocrine neoplasia syndrome, myelodysplastic syndrome, myelodysplastic / myeloproliferative disease, nasal and paranasal cavity cancer, nasopharyngeal carcinoma, neuroblastoma, neuroendocrine cancer, oropharyngeal cancer, ovarian cancer (e.g., ovarian epithelial cancer, ovarian germ cell tumor, low malignant potential tumor of the ovary), pancreatic cancer, parathyroid cancer, penile cancer, peritoneal cancer, pharyngeal cancer, pheochromocytoma, pineoblastoma and supratentorial primitive neuroectodermal tumor, pituitary tumor, pleuropulmonary blastoma, primary central nervous system lymphoma (microglioma), pulmonary lymphangioleiomyomatosis, rectal cancer, renal cancer, renal pelvis and ureteral cancer (transitional cell cancer), rhabdomyosarcoma,Salivary gland cancer, skin cancer (e.g., non-melanoma (e.g., squamous cell carcinoma), melanoma, and Merkel cell carcinoma), small intestine cancer, squamous cell carcinoma, testicular cancer, throat cancer, thyroid cancer, tuberous sclerosis, urethral cancer, vaginal cancer, vulvar cancer, Wilms tumor, abnormal blood vessel proliferation associated with nevus syndrome, edema (e.g., those associated with brain tumors), and Meigs syndrome, but not limited to these.,

[0138] Accordingly, in some embodiments, provided is a method of treating cancer in an individual, the method comprising administering to the individual an effective amount of a composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, wherein the individual is selected for treatment based on having an mTOR-activating abnormality. In some embodiments, provided is a method of treating cancer in an individual, the method comprising: (a) evaluating an mTOR-activating abnormality in the individual; (b) administering (e.g., intravenously) to the individual an effective amount of a composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, wherein the individual is selected for treatment based on having an mTOR-activating abnormality. In some embodiments, provided is a method of selecting an individual having cancer for treatment with a composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, the method comprising: (a) evaluating an mTOR-activating abnormality in the individual; (b) selecting or recommending the individual for treatment based on the individual having an mTOR-activating abnormality. In some embodiments, provided is a method of selecting an individual having cancer for treatment with a composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, the method comprising: (a) evaluating an mTOR-activating abnormality in the individual; (b) selecting or recommending the individual for treatment based on the individual having an mTOR-activating abnormality; (c) administering to the selected individual an effective amount of a composition comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin. In some embodiments, provided is a method of treating cancer (e.g., mTOR inhibitor-sensitive cancer) in an individual, the method comprising administering to the individual an effective amount of a composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, wherein the individual has an mTOR-activating abnormality. In some embodiments, the composition comprising nanoparticles comprises a rapamycin drug and albumin, and the rapamycin drug in the nanoparticles is associated with (e.g., coated with) albumin.In some embodiments, the composition comprising the nanoparticles comprises a rapamycin drug and albumin, and the nanoparticles have an average particle size of about 150 nm or less (e.g., about 120 nm or less). In some embodiments, the composition comprising the nanoparticles comprises sirolimus and human serum albumin, the nanoparticles comprise sirolimus associated with (e.g., coated with) human serum albumin, the nanoparticles have an average particle size of about 150 nm or less (e.g., about 120 nm or less, e.g., about 100 nm), and the weight ratio of human albumin to sirolimus in the composition is about 9:1 or less (e.g., about 9:1 or about 8:1). In some embodiments, the composition comprising the nanoparticles comprises Nab-sirolimus. In some embodiments, the mTOR activation abnormality comprises a mutation of an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises a copy number polymorphism of an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises an abnormal expression level of an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises an abnormal activity level of an mTOR-related gene. In some embodiments, the mTOR activation abnormality results in the activation of mTORC1 (e.g., including the activation of mTORC1 rather than mTORC2). In some embodiments, the mTOR activation abnormality results in the activation of mTORC2 (e.g., including the activation of mTORC2 rather than mTORC1). In some embodiments, the mTOR activation abnormality results in the activation of both mTORC1 and mTORC2. In some embodiments, the mTOR activation abnormality is an abnormality of at least one mTOR-related gene selected from the group consisting of AKT1, FLT3, MTOR, PIK3CA, PIK3CG, TSC1, TSC2, RHEB, STK11, NF1, NF2, PTEN, TP53, FGFR4, KRAS, NRAS, and BAP1. In some embodiments, the mTOR activation abnormality is evaluated by gene sequencing. In some embodiments, the gene sequencing is based on DNA sequencing in a tumor sample. In some embodiments, the gene sequencing is based on sequencing of circulating DNA or cell-free DNA isolated from a blood sample.In some embodiments, the mutant state of TFE3 is further used as a basis for selecting an individual. In some embodiments, the mutant state of TFE3 includes a translocation of TFE3. In some embodiments, the mTOR activation abnormality includes an abnormal phosphorylation level of a protein encoded by an mTOR-related gene. In some embodiments, the mTOR activation abnormality includes an abnormal phosphorylation level of a protein encoded by mTOR selected from the group consisting of AKT, S6K, S6, 4EBP1, and SPARC. In some embodiments, the abnormal phosphorylation level is determined by immunohistochemistry.

[0139] In some embodiments, the cancer is selected from the group consisting of pancreatic neuroendocrine cancer, endometrial cancer, ovarian cancer, breast cancer, renal cell carcinoma, lymphangioleiomyomatosis (LAM), prostate cancer, lymphoma, and bladder cancer. This method is applicable to cancers at all stages, including stages I, II, III, and IV according to the American Joint Committee on Cancer (AJCC) for cancers determining the stage of a group. In some embodiments, the cancer is an early-stage cancer, a non-metastatic cancer, a primary cancer, a progressive cancer, a locally advanced cancer, a metastatic cancer, a cancer in remission, a cancer in an adjuvant therapy situation, or a cancer in a neoadjuvant therapy situation. In some embodiments, the cancer is a solid tumor. In some embodiments, the solid tumor is locally resected, locally unresectable, or unresectable. In some embodiments, the solid tumor is locally resected or the resectability is on the borderline. In some embodiments, the cancer is refractory to prior treatment. In some embodiments, the cancer is resistant to treatment with a non-nanoparticle formulation of a chemotherapeutic agent (e.g., a non-nanoparticle formulation of a rime drug). In some embodiments, the cancer is a liquid cancer.

[0140] In some embodiments, provided is a method of treating pancreatic neuroendocrine cancer in an individual, the method comprising administering to the individual an effective amount of a composition comprising an mTOR inhibitor (e.g., a rapamycin drug) and nanoparticles comprising albumin, wherein the individual is selected for treatment based on having an mTOR activation abnormality. In some embodiments, provided is a method of treating pancreatic neuroendocrine cancer in an individual, the method comprising: (a) evaluating an mTOR activation abnormality in the individual; (b) administering (e.g., intravenously) to the individual an effective amount of a composition comprising an mTOR inhibitor (e.g., a rapamycin drug) and nanoparticles comprising albumin, wherein the individual is selected for treatment based on having an mTOR activation abnormality. In some embodiments, provided is a method of selecting an individual having pancreatic neuroendocrine cancer for treatment with a composition comprising an mTOR inhibitor (e.g., a rapamycin drug) and nanoparticles comprising albumin, the method comprising: (a) evaluating an mTOR activation abnormality in the individual; (b) selecting or recommending the individual for treatment based on the individual having an mTOR activation abnormality. In some embodiments, provided is a method of selecting an individual having pancreatic neuroendocrine cancer for treatment with a composition comprising an mTOR inhibitor (e.g., a rapamycin drug) and nanoparticles comprising albumin, the method comprising: (a) evaluating an mTOR activation abnormality in the individual; (b) selecting or recommending the individual for treatment based on the individual having an mTOR activation abnormality; (c) administering to the selected individual an effective amount of a composition comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin. In some embodiments, provided is a method of treating pancreatic neuroendocrine cancer (e.g., mTOR inhibitor-sensitive pancreatic neuroendocrine cancer) in an individual, the method comprising administering to the individual an effective amount of a composition comprising an mTOR inhibitor (e.g., a rapamycin drug) and nanoparticles comprising albumin, wherein the individual has an mTOR activation abnormality. In some embodiments, the composition comprising nanoparticles comprises a rapamycin drug and albumin, and the rapamycin drug in the nanoparticles is associated with (e.g., coated with) albumin.In some embodiments, the composition comprising the nanoparticles comprises a rapamycin drug and albumin, and the nanoparticles have an average particle size of about 150 nm or less (e.g., about 120 nm or less). In some embodiments, the composition comprising the nanoparticles comprises sirolimus and human serum albumin, the nanoparticles comprise sirolimus associated with (e.g., coated with) human serum albumin, the nanoparticles have an average particle size of about 150 nm or less (e.g., about 120 nm or less, e.g., about 100 nm), and the weight ratio of human albumin to sirolimus in the composition is about 9:1 or less (e.g., about 9:1 or about 8:1). In some embodiments, the composition comprising the nanoparticles comprises Nab-sirolimus. In some embodiments, the mTOR activation abnormality comprises a mutation of an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises a copy number polymorphism of an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises an abnormal expression level of an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises an abnormal activity level of an mTOR-related gene. In some embodiments, the mTOR activation abnormality results in the activation of mTORC1 (e.g., including the activation of mTORC1 rather than mTORC2). In some embodiments, the mTOR activation abnormality results in the activation of mTORC2 (e.g., including the activation of mTORC2 rather than mTORC1). In some embodiments, the mTOR activation abnormality results in the activation of both mTORC1 and mTORC2. In some embodiments, the mTOR activation abnormality is an abnormality of at least one mTOR-related gene selected from the group consisting of AKT1, FLT3, MTOR, PIK3CA, PIK3CG, TSC1, TSC2, RHEB, STK11, NF1, NF2, PTEN, TP53, FGFR4, KRAS, NRAS, and BAP1. In some embodiments, the mTOR activation abnormality is evaluated by gene sequencing. In some embodiments, the gene sequencing is based on DNA sequencing in a tumor sample. In some embodiments, the gene sequencing is based on the sequencing of circulating DNA or cell-free DNA isolated from a blood sample.In some embodiments, the mutant state of TFE3 is further used as a basis for selecting an individual. In some embodiments, the mutant state of TFE3 includes a translocation of TFE3. In some embodiments, the mTOR activation abnormality includes an abnormal phosphorylation level of a protein encoded by an mTOR-related gene. In some embodiments, the mTOR activation abnormality includes an abnormal phosphorylation level of a protein encoded by mTOR selected from the group consisting of AKT, S6K, S6, 4EBP1, and SPARC. In some embodiments, the abnormal phosphorylation level is determined by immunohistochemistry. In some embodiments, pancreatic neuroendocrine cancer is a functional or non-functional pancreatic neuroendocrine tumor. In some embodiments, pancreatic neuroendocrine cancer is an insulinoma, glucagonoma, somatostatinoma, gastrinoma, VIP-producing tumor, GRFoma, or ACTHoma.

[0141] In some embodiments, provided is a method of treating endometrial cancer in an individual, the method comprising administering to the individual an effective amount of a composition comprising a nanoparticle comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, wherein the individual is selected for treatment based on having an mTOR activation abnormality. In some embodiments, provided is a method of treating endometrial cancer in an individual, the method comprising: (a) evaluating an mTOR activation abnormality in the individual; (b) administering (e.g., intravenously) to the individual an effective amount of a composition comprising a nanoparticle comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, wherein the individual is selected for treatment based on having an mTOR activation abnormality. In some embodiments, provided is a method of selecting an individual having endometrial cancer for treatment with a composition comprising a nanoparticle comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, the method comprising: (a) evaluating an mTOR activation abnormality in the individual; (b) selecting or recommending the individual for treatment based on the individual having an mTOR activation abnormality. In some embodiments, provided is a method of selecting an individual having endometrial cancer for treatment with a composition comprising a nanoparticle comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, the method comprising: (a) evaluating an mTOR activation abnormality in the individual; (b) selecting or recommending the individual for treatment based on the individual having an mTOR activation abnormality; (c) administering to the selected individual an effective amount of a composition comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin. In some embodiments, provided is a method of treating an individual's endometrial cancer (e.g., mTOR inhibitor-sensitive endometrial cancer), the method comprising administering to the individual an effective amount of a composition comprising a nanoparticle comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, wherein the individual has an mTOR activation abnormality. In some embodiments, the composition comprising the nanoparticle comprises a rapamycin drug and albumin, and the rapamycin drug in the nanoparticle is associated with (e.g., coated with) albumin.In some embodiments, the composition comprising the nanoparticles comprises a rapamycin drug and albumin, and the nanoparticles have an average particle size of about 150 nm or less (e.g., about 120 nm or less). In some embodiments, the composition comprising the nanoparticles comprises sirolimus and human serum albumin, the nanoparticles comprise sirolimus associated with (e.g., coated with) human serum albumin, the nanoparticles have an average particle size of about 150 nm or less (e.g., about 120 nm or less, e.g., about 100 nm), and the weight ratio of human albumin to sirolimus in the composition is about 9:1 or less (e.g., about 9:1 or about 8:1). In some embodiments, the composition comprising the nanoparticles comprises Nab-sirolimus. In some embodiments, the mTOR activation abnormality comprises a mutation in an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises a copy number polymorphism in an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises an abnormal expression level of an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises an abnormal activity level of an mTOR-related gene. In some embodiments, the mTOR activation abnormality results in the activation of mTORC1 (e.g., including the activation of mTORC1 but not mTORC2). In some embodiments, the mTOR activation abnormality results in the activation of mTORC2 (e.g., including the activation of mTORC2 but not mTORC1). In some embodiments, the mTOR activation abnormality results in the activation of both mTORC1 and mTORC2. In some embodiments, the mTOR activation abnormality is an abnormality in at least one mTOR-related gene selected from the group consisting of AKT1, FLT3, MTOR, PIK3CA, PIK3CG, TSC1, TSC2, RHEB, STK11, NF1, NF2, PTEN, TP53, FGFR4, KRAS, NRAS, and BAP1. In some embodiments, the mTOR activation abnormality is evaluated by gene sequencing. In some embodiments, the gene sequencing is based on DNA sequencing in a tumor sample. In some embodiments, the gene sequencing is based on sequencing of circulating DNA or cell-free DNA isolated from a blood sample.In some embodiments, the mutant state of TFE3 is further used as a basis for selecting an individual. In some embodiments, the mutant state of TFE3 includes a translocation of TFE3. In some embodiments, the mTOR activation abnormality includes an abnormal phosphorylation level of a protein encoded by an mTOR-related gene. In some embodiments, the mTOR activation abnormality includes an abnormal phosphorylation level of a protein encoded by mTOR selected from the group consisting of AKT, S6K, S6, 4EBP1, and SPARC. In some embodiments, the abnormal phosphorylation level is determined by immunohistochemistry.

[0142] In some embodiments, a method of treating breast cancer in an individual, comprising administering to the individual an effective amount of a composition comprising an mTOR inhibitor (e.g., a rimos drug) and nanoparticles comprising albumin, wherein the individual is selected for treatment based on having an mTOR activation abnormality, is provided. In some embodiments, a method of treating breast cancer in an individual, comprising: (a) evaluating an mTOR activation abnormality in the individual; and (b) administering (e.g., intravenously) to the individual an effective amount of a composition comprising an mTOR inhibitor (e.g., a rimos drug) and nanoparticles comprising albumin, wherein the individual is selected for treatment based on having an mTOR activation abnormality, is provided. In some embodiments, a method of selecting an individual having breast cancer for treatment with a composition comprising an mTOR inhibitor (e.g., a rimos drug) and nanoparticles comprising albumin, comprising: (a) evaluating an mTOR activation abnormality in the individual; and (b) selecting or recommending the individual for treatment based on the individual having an mTOR activation abnormality, is provided. In some embodiments, a method of selecting an individual having breast cancer for treatment with a composition comprising an mTOR inhibitor (e.g., a rimos drug) and nanoparticles comprising albumin, comprising: (a) evaluating an mTOR activation abnormality in the individual; (b) selecting or recommending the individual for treatment based on the individual having an mTOR activation abnormality; and (c) administering to the selected individual an effective amount of a composition comprising an mTOR inhibitor (e.g., a rimos drug) and albumin, is provided. In some embodiments, a method of treating breast cancer (e.g., mTOR inhibitor-sensitive breast cancer) in an individual, comprising administering to the individual an effective amount of a composition comprising an mTOR inhibitor (e.g., a rimos drug) and nanoparticles comprising albumin, wherein the individual has an mTOR activation abnormality. In some embodiments, the composition comprising nanoparticles comprises a rimos drug and albumin, and the rimos drug in the nanoparticles is associated with (e.g., coated with) albumin.In some embodiments, the composition comprising the nanoparticles comprises a rapamycin drug and albumin, and the nanoparticles have an average particle size of about 150 nm or less (e.g., about 120 nm or less). In some embodiments, the composition comprising the nanoparticles comprises sirolimus and human serum albumin, the nanoparticles comprise sirolimus associated with (e.g., coated with) human serum albumin, the nanoparticles have an average particle size of about 150 nm or less (e.g., about 120 nm or less, e.g., about 100 nm), and the weight ratio of human albumin to sirolimus in the composition is about 9:1 or less (e.g., about 9:1 or about 8:1). In some embodiments, the composition comprising the nanoparticles comprises Nab-sirolimus. In some embodiments, the mTOR activation abnormality comprises a mutation of an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises a copy number polymorphism of an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises an abnormal expression level of an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises an abnormal activity level of an mTOR-related gene. In some embodiments, the mTOR activation abnormality results in the activation of mTORC1 (e.g., including the activation of mTORC1 rather than mTORC2). In some embodiments, the mTOR activation abnormality results in the activation of mTORC2 (e.g., including the activation of mTORC2 rather than mTORC1). In some embodiments, the mTOR activation abnormality results in the activation of both mTORC1 and mTORC2. In some embodiments, the mTOR activation abnormality is an abnormality of at least one mTOR-related gene selected from the group consisting of AKT1, FLT3, MTOR, PIK3CA, PIK3CG, TSC1, TSC2, RHEB, STK11, NF1, NF2, PTEN, TP53, FGFR4, KRAS, NRAS, and BAP1. In some embodiments, the mTOR activation abnormality is evaluated by gene sequencing. In some embodiments, the gene sequencing is based on DNA sequencing in a tumor sample. In some embodiments, the gene sequencing is based on the sequencing of circulating DNA or cell-free DNA isolated from a blood sample.In some embodiments, the mutant state of TFE3 is further used as a basis for selecting an individual. In some embodiments, the mutant state of TFE3 includes a translocation of TFE3. In some embodiments, the mTOR activation abnormality includes an abnormal phosphorylation level of a protein encoded by an mTOR-related gene. In some embodiments, the mTOR activation abnormality includes an abnormal phosphorylation level of a protein encoded by mTOR selected from the group consisting of AKT, S6K, S6, 4EBP1, and SPARC. In some embodiments, the abnormal phosphorylation level is determined by immunohistochemistry.

[0143] In some embodiments, breast cancer is early-stage breast cancer, non-metastatic breast cancer, locally advanced breast cancer, metastatic breast cancer, hormone receptor-positive metastatic breast cancer, breast cancer in remission, breast cancer in the context of adjuvant therapy, ductal carcinoma in situ (DCIS), invasive ductal carcinoma (IDC), or breast cancer in the context of neoadjuvant therapy. In some embodiments, breast cancer is hormone receptor-positive metastatic breast cancer. In some embodiments, breast cancer is ductal carcinoma in situ. In some embodiments, the individual can be a human having a gene, gene mutation or polymorphism associated with breast cancer (e.g., BRCA1, BRCA2, ATM, CHEK2, RAD51, AR, DIRAS3, ERBB2, TP53, AKT, PTEN, and / or PI3K), or a human having one or more extra copies of a gene associated with breast cancer (e.g., one or more extra copies of the HER2 gene). In some embodiments, breast cancer is negative for at least one of estrogen receptor ("ER"), progesterone receptor ("PR") or human epidermal growth factor receptor 2 ("HER2"). In some embodiments, breast cancer is ER-negative, PR-negative and HER2-negative. In some embodiments, breast cancer is positive for ER, PR and / or HER2. In some embodiments, breast cancer is ER-positive.

[0144] In some embodiments, a method of treating renal cell carcinoma in an individual, comprising administering to the individual an effective amount of a composition comprising a nanoparticle comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, wherein the individual is selected for treatment based on having an mTOR activation abnormality, is provided. In some embodiments, a method of treating renal cell carcinoma in an individual, comprising: (a) evaluating an mTOR activation abnormality in the individual; (b) administering (e.g., intravenously) to the individual an effective amount of a composition comprising a nanoparticle comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, wherein the individual is selected for treatment based on having an mTOR activation abnormality, is provided. In some embodiments, a method of selecting an individual having renal cell carcinoma for treatment with a composition comprising a nanoparticle comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, comprising: (a) evaluating an mTOR activation abnormality in the individual; (b) selecting or recommending the individual for treatment based on the individual having an mTOR activation abnormality, is provided. In some embodiments, a method of selecting an individual having renal cell carcinoma for treatment with a composition comprising a nanoparticle comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, comprising: (a) evaluating an mTOR activation abnormality in the individual; (b) selecting or recommending the individual for treatment based on the individual having an mTOR activation abnormality; (c) administering to the selected individual an effective amount of a composition comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, is provided. In some embodiments, a method of treating renal cell carcinoma (e.g., mTOR inhibitor-sensitive renal cell carcinoma) in an individual, comprising administering to the individual an effective amount of a composition comprising a nanoparticle comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, wherein the individual has an mTOR activation abnormality. In some embodiments, the composition comprising the nanoparticle comprises a rapamycin drug and albumin, and the rapamycin drug in the nanoparticle is associated with (e.g., coated with) albumin.In some embodiments, the composition comprising the nanoparticles comprises a rapamycin drug and albumin, and the nanoparticles have an average particle size of about 150 nm or less (e.g., about 120 nm or less). In some embodiments, the composition comprising the nanoparticles comprises sirolimus and human serum albumin, the nanoparticles comprise sirolimus associated with (e.g., coated with) human serum albumin, the nanoparticles have an average particle size of about 150 nm or less (e.g., about 120 nm or less, e.g., about 100 nm), and the weight ratio of human albumin to sirolimus in the composition is about 9:1 or less (e.g., about 9:1 or about 8:1). In some embodiments, the composition comprising the nanoparticles comprises Nab-sirolimus. In some embodiments, the mTOR activation abnormality comprises a mutation in an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises a copy number polymorphism in an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises an abnormal expression level of an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises an abnormal activity level of an mTOR-related gene. In some embodiments, the mTOR activation abnormality results in the activation of mTORC1 (e.g., including the activation of mTORC1 but not mTORC2). In some embodiments, the mTOR activation abnormality results in the activation of mTORC2 (e.g., including the activation of mTORC2 but not mTORC1). In some embodiments, the mTOR activation abnormality results in the activation of both mTORC1 and mTORC2. In some embodiments, the mTOR activation abnormality is an abnormality in at least one mTOR-related gene selected from the group consisting of AKT1, FLT3, MTOR, PIK3CA, PIK3CG, TSC1, TSC2, RHEB, STK11, NF1, NF2, PTEN, TP53, FGFR4, KRAS, NRAS, and BAP1. In some embodiments, the mTOR activation abnormality is evaluated by gene sequencing. In some embodiments, the gene sequencing is based on DNA sequencing in a tumor sample. In some embodiments, the gene sequencing is based on the sequencing of circulating DNA or cell-free DNA isolated from a blood sample.In some embodiments, the mutated state of TFE3 is further used as a basis for selecting an individual. In some embodiments, the mutated state of TFE3 includes a translocation of TFE3. In some embodiments, the mTOR activation abnormality includes an abnormal phosphorylation level of a protein encoded by an mTOR-related gene. In some embodiments, the mTOR activation abnormality includes an abnormal phosphorylation level of a protein encoded by mTOR selected from the group consisting of AKT, S6K, S6, 4EBP1, and SPARC. In some embodiments, the abnormal phosphorylation level is determined by immunohistochemistry.

[0145] In some embodiments, renal cell carcinoma is an adenocarcinoma. In some embodiments, renal cell carcinoma is clear cell renal cell carcinoma, papillary renal cell carcinoma (also called chromophilic renal cell carcinoma), chromophobic renal cell carcinoma, collecting duct renal cell carcinoma, granular renal cell carcinoma, mixed granular renal cell carcinoma, and spindle renal cell carcinoma. In some embodiments, renal cell carcinoma is associated with (1) von Hippel-Lindau (VHL) syndrome, (2) hereditary papillary renal carcinoma (HPRC), (3) familial renal oncocytoma (FRO) associated with Birt-Hogg-Dubé syndrome (BHDS), or (4) hereditary renal carcinoma (HRC).

[0146] In some embodiments, a method of treating lymphangioleiomyomatosis (LAM) in an individual, comprising administering to the individual an effective amount of a composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, wherein the individual is selected for treatment based on having an mTOR activation abnormality, is provided. In some embodiments, a method of treating lymphangioleiomyomatosis in an individual, comprising: (a) evaluating an mTOR activation abnormality in the individual; (b) administering (e.g., intravenously) to the individual an effective amount of a composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, wherein the individual is selected for treatment based on having an mTOR activation abnormality, is provided. In some embodiments, a method of selecting an individual having lymphangioleiomyomatosis for treatment with a composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, comprising: (a) evaluating an mTOR activation abnormality in the individual; (b) selecting or recommending the individual for treatment based on the individual having an mTOR activation abnormality, is provided. In some embodiments, a method of selecting an individual having lymphangioleiomyomatosis for treatment with a composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, comprising: (a) evaluating an mTOR activation abnormality in the individual; (b) selecting or recommending the individual for treatment based on the individual having an mTOR activation abnormality; (c) administering to the selected individual an effective amount of a composition comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, is provided. In some embodiments, a method of treating LAM (e.g., mTOR inhibitor-sensitive LAM) in an individual, comprising administering to the individual an effective amount of a composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, wherein the individual has an mTOR activation abnormality. In some embodiments, the composition comprising nanoparticles comprises a rapamycin drug and albumin, and the rapamycin drug in the nanoparticles is associated with (e.g., coated with) albumin.In some embodiments, the composition comprising the nanoparticles comprises a rapamycin drug and albumin, and the nanoparticles have an average particle size of about 150 nm or less (e.g., about 120 nm or less). In some embodiments, the composition comprising the nanoparticles comprises sirolimus and human serum albumin, the nanoparticles comprise sirolimus associated with (e.g., coated with) human serum albumin, the nanoparticles have an average particle size of about 150 nm or less (e.g., about 120 nm or less, e.g., about 100 nm), and the weight ratio of human albumin to sirolimus in the composition is about 9:1 or less (e.g., about 9:1 or about 8:1). In some embodiments, the composition comprising the nanoparticles comprises Nab-sirolimus. In some embodiments, the mTOR activation abnormality comprises a mutation in an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises a copy number polymorphism in an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises an abnormal expression level of an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises an abnormal activity level of an mTOR-related gene. In some embodiments, the mTOR activation abnormality results in the activation of mTORC1 (e.g., including the activation of mTORC1 but not mTORC2). In some embodiments, the mTOR activation abnormality results in the activation of mTORC2 (e.g., including the activation of mTORC2 but not mTORC1). In some embodiments, the mTOR activation abnormality results in the activation of both mTORC1 and mTORC2. In some embodiments, the mTOR activation abnormality is an abnormality in at least one mTOR-related gene selected from the group consisting of AKT1, FLT3, MTOR, PIK3CA, PIK3CG, TSC1, TSC2, RHEB, STK11, NF1, NF2, PTEN, TP53, FGFR4, KRAS, NRAS, and BAP1. In some embodiments, the mTOR activation abnormality is evaluated by gene sequencing. In some embodiments, the gene sequencing is based on DNA sequencing in a tumor sample. In some embodiments, the gene sequencing is based on sequencing of circulating DNA or cell-free DNA isolated from a blood sample.In some embodiments, the mutated state of TFE3 is further used as a basis for selecting an individual. In some embodiments, the mutated state of TFE3 includes a translocation of TFE3. In some embodiments, the mTOR activation abnormality includes an abnormal phosphorylation level of a protein encoded by an mTOR-related gene. In some embodiments, the mTOR activation abnormality includes an abnormal phosphorylation level of a protein encoded by mTOR selected from the group consisting of AKT, S6K, S6, 4EBP1, and SPARC. In some embodiments, the abnormal phosphorylation level is determined by immunohistochemistry.

[0147] In some embodiments, lymphangioleiomyomatosis is hereditary. In some embodiments, lymphangioleiomyomatosis is characteristic of tuberous sclerosis. In some embodiments, lymphangioleiomyomatosis is solitary or sporadic. In some embodiments, lymphangioleiomyomatosis causes cysts in the lungs, lymphatics, and / or kidneys.

[0148] In some embodiments, provided is a method of treating prostate cancer in an individual, the method comprising administering to the individual an effective amount of a composition comprising an mTOR inhibitor (e.g., a rapamycin drug) and nanoparticles comprising albumin, wherein the individual is selected for treatment based on having an mTOR activation abnormality. In some embodiments, provided is a method of treating prostate cancer in an individual, (a) Evaluating the mTOR activation abnormality in an individual; (b) Administering (e.g., intravenously) to the individual an effective amount of a composition comprising nanoparticles containing an mTOR inhibitor (e.g., a rapamycin drug) and albumin, wherein the individual is selected for treatment based on having an mTOR activation abnormality. A method is provided. In some embodiments, a method of selecting an individual having prostate cancer for treatment with a composition comprising nanoparticles containing an mTOR inhibitor (e.g., a rapamycin drug) and albumin, comprising: (a) Evaluating the mTOR activation abnormality in the individual; (b) Selecting or recommending the individual for treatment based on the individual having an mTOR activation abnormality. A method is provided. In some embodiments, a method of selecting an individual having prostate cancer for treatment with a composition comprising nanoparticles containing an mTOR inhibitor (e.g., a rapamycin drug) and albumin, comprising: (a) Evaluating the mTOR activation abnormality in the individual; (b) Selecting or recommending the individual for treatment based on the individual having an mTOR activation abnormality; (c) Administering to the selected individual an effective amount of a composition comprising nanoparticles containing an mTOR inhibitor (e.g., a rapamycin drug) and albumin. A method is provided. In some embodiments, a method of treating prostate cancer (e.g., mTOR inhibitor-sensitive prostate cancer) in an individual, comprising administering to the individual an effective amount of a composition comprising nanoparticles containing an mTOR inhibitor (e.g., a rapamycin drug) and albumin, wherein the individual has an mTOR activation abnormality. In some embodiments, the composition comprising nanoparticles comprises a rapamycin drug and albumin, and the rapamycin drug in the nanoparticles is associated with (e.g., coated with) albumin. In some embodiments, the composition comprising nanoparticles comprises a rapamycin drug and albumin, and the nanoparticles have an average particle size of about 150 nm or less (e.g., about 120 nm or less).In some embodiments, the composition comprising the nanoparticles comprises sirolimus and human serum albumin, the nanoparticles comprise sirolimus associated with (e.g., coated with) human serum albumin, the nanoparticles have an average particle size of about 150 nm or less (e.g., about 120 nm or less, e.g., about 100 nm), and the weight ratio of human albumin to sirolimus in the composition is about 9:1 or less (e.g., about 9:1 or about 8:1). In some embodiments, the composition comprising the nanoparticles comprises Nab-sirolimus. In some embodiments, the mTOR activation abnormality comprises a mutation in an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises a copy number polymorphism in an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises an abnormal expression level of an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises an abnormal activity level of an mTOR-related gene. In some embodiments, the mTOR activation abnormality results in activation of mTORC1 (e.g., including activation of mTORC1 but not mTORC2). In some embodiments, the mTOR activation abnormality results in activation of mTORC2 (e.g., including activation of mTORC2 but not mTORC1). In some embodiments, the mTOR activation abnormality results in activation of both mTORC1 and mTORC2. In some embodiments, the mTOR activation abnormality is an abnormality in at least one mTOR-related gene selected from the group consisting of AKT1, FLT3, MTOR, PIK3CA, PIK3CG, TSC1, TSC2, RHEB, STK11, NF1, NF2, PTEN, TP53, FGFR4, KRAS, NRAS, and BAP1. In some embodiments, the mTOR activation abnormality is evaluated by gene sequencing. In some embodiments, the gene sequencing is based on DNA sequencing in a tumor sample. In some embodiments, the gene sequencing is based on sequencing of circulating DNA or cell-free DNA isolated from a blood sample. In some embodiments, the mutation status of TFE3 is further used as a basis for selecting an individual. In some embodiments, the mutation status of TFE3 comprises a translocation of TFE3.In some embodiments, the mTOR activation abnormality includes abnormal phosphorylation levels of proteins encoded by mTOR-related genes. In some embodiments, the mTOR activation abnormality includes abnormal phosphorylation levels of proteins encoded by mTOR selected from the group consisting of AKT, S6K, S6, 4EBP1, and SPARC. In some embodiments, the abnormal phosphorylation levels are determined by immunohistochemistry.

[0149] In some embodiments, the prostate cancer is adenocarcinoma. In some embodiments, the prostate cancer is a sarcoma, neuroendocrine tumor, small cell cancer, ductal cancer, or lymphoma. In some embodiments of any of this method, the prostate cancer can be androgen-independent prostate cancer (AIPC). In some embodiments, the prostate cancer can be androgen-dependent prostate cancer. In some embodiments, the prostate cancer can be refractory to hormone therapy. In some embodiments, the prostate cancer can be substantially refractory to hormone therapy. In some embodiments, the individual can be a human having a gene, gene mutation, or polymorphism associated with prostate cancer (e.g., RNASEL / HPC1, ELAC2 / HPC2, SR-A / MSR1, CHEK2, BRCA2, PON1, OGG1, MIC-1, TLR4, and / or PTEN), or a human having one or more extra copies of a gene associated with prostate cancer.

[0150] In some embodiments, a method of treating lymphoma in an individual, the method comprising administering to the individual an effective amount of a composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, wherein the individual is selected for treatment based on having an mTOR activation abnormality, is provided. In some embodiments, a method of treating lymphoma in an individual, the method comprising: (a) evaluating an mTOR activation abnormality in the individual; (b) administering (e.g., intravenously) to the individual an effective amount of a composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, wherein the individual is selected for treatment based on having an mTOR activation abnormality, is provided. In some embodiments, a method of selecting an individual having lymphoma for treatment with a composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, the method comprising: (a) evaluating an mTOR activation abnormality in the individual; (b) selecting or recommending the individual for treatment based on the individual having an mTOR activation abnormality, is provided. In some embodiments, a method of selecting an individual having lymphoma for treatment with a composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, the method comprising: (a) evaluating an mTOR activation abnormality in the individual; (b) selecting or recommending the individual for treatment based on the individual having an mTOR activation abnormality; (c) administering to the selected individual an effective amount of a composition comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, is provided. In some embodiments, a method of treating lymphoma (e.g., mTOR inhibitor-sensitive lymphoma) in an individual, the method comprising administering to the individual an effective amount of a composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, wherein the individual has an mTOR activation abnormality. In some embodiments, the composition comprising nanoparticles comprises a rapamycin drug and albumin, and the rapamycin drug in the nanoparticles is associated with (e.g., coated with) albumin.In some embodiments, the composition comprising the nanoparticles comprises a rapamycin drug and albumin, and the nanoparticles have an average particle size of about 150 nm or less (e.g., about 120 nm or less). In some embodiments, the composition comprising the nanoparticles comprises sirolimus and human serum albumin, the nanoparticles comprise sirolimus associated with (e.g., coated with) human serum albumin, the nanoparticles have an average particle size of about 150 nm or less (e.g., about 120 nm or less, e.g., about 100 nm), and the weight ratio of human albumin to sirolimus in the composition is about 9:1 or less (e.g., about 9:1 or about 8:1). In some embodiments, the composition comprising the nanoparticles comprises Nab-sirolimus. In some embodiments, the mTOR activation abnormality comprises a mutation of an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises a copy number polymorphism of an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises an abnormal expression level of an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises an abnormal activity level of an mTOR-related gene. In some embodiments, the mTOR activation abnormality results in the activation of mTORC1 (e.g., including the activation of mTORC1 rather than mTORC2). In some embodiments, the mTOR activation abnormality results in the activation of mTORC2 (e.g., including the activation of mTORC2 rather than mTORC1). In some embodiments, the mTOR activation abnormality results in the activation of both mTORC1 and mTORC2. In some embodiments, the mTOR activation abnormality is an abnormality of at least one mTOR-related gene selected from the group consisting of AKT1, FLT3, MTOR, PIK3CA, PIK3CG, TSC1, TSC2, RHEB, STK11, NF1, NF2, PTEN, TP53, FGFR4, KRAS, NRAS, and BAP1. In some embodiments, the mTOR activation abnormality is evaluated by gene sequencing. In some embodiments, the gene sequencing is based on DNA sequencing in a tumor sample. In some embodiments, the gene sequencing is based on the sequencing of circulating DNA or cell-free DNA isolated from a blood sample.In some embodiments, the mutant state of TFE3 is further used as a basis for selecting an individual. In some embodiments, the mutant state of TFE3 includes a translocation of TFE3. In some embodiments, the mTOR activation abnormality includes an abnormal phosphorylation level of a protein encoded by an mTOR-related gene. In some embodiments, the mTOR activation abnormality includes an abnormal phosphorylation level of a protein encoded by mTOR selected from the group consisting of AKT, S6K, S6, 4EBP1, and SPARC. In some embodiments, the abnormal phosphorylation level is determined by immunohistochemistry.

[0151] In some embodiments, the lymphoma is a B-cell lymphoma. Examples of B-cell lymphomas include precursor B-cell neoplasms (e.g., precursor B-lymphoblastic leukemia / lymphoma) and peripheral B-cell neoplasms (e.g., B-cell chronic lymphocytic leukemia / prolymphocytic leukemia / small lymphocytic lymphoma (small lymphocytic (SL) NHL), lymphoplasmacytic lymphoma / immunocytoma, mantle cell lymphoma, follicular center lymphoma, follicular lymphoma (e.g., cytologic grade: I (small cells), II (mixed small and large cells), III (large cells) and / or subtype: diffuse and small cell predominant), low-grade / follicular non-Hodgkin lymphoma (NHL), intermediate-grade / follicular NHL, marginal zone B-cell lymphoma (e.g., extranodal (e.g., MALT type + / - monocytoid B cells) and / or nodular (e.g., + / - monocytoid B cells)), splenic marginal zone lymphoma (e.g., + / - hairy lymphocytes), hairy cell leukemia, plasmacytoma / plasma cell myeloma (e.g., myeloma and multiple myeloma), diffuse large B-cell type lymphoma (e.g., primary mediastinal (thymic) B-cell lymphoma), intermediate-grade diffuse NHL, Burkitt lymphoma, high-grade B-cell lymphoma, Burkitt-like, high-grade immunoblastic NHL, high-grade lymphoblastic NHL, high-grade small non-cleaved cell NHL, large tumor lesion NHL, AIDS-related lymphoma, and Waldenström macroglobulinemia), but are not limited thereto. In some embodiments, the lymphoma is mantle cell lymphoma. In some embodiments, the lymphoma is a T-cell and / or putative NK-cell lymphoma.Examples of T cell and / or putative NK cell lymphomas include precursor T cell neoplasms (precursor T lymphoblastic lymphoma / leukemia) and peripheral T cell and NK cell neoplasms (e.g., T cell chronic lymphocytic leukemia / prolymphocytic leukemia, and large granular lymphocyte leukemia (LGL) (e.g., T cell type and / or NK cell type), cutaneous T cell lymphoma (e.g., mycosis fungoides / Sézary syndrome), unspecified primary T cell lymphoma (e.g., cytological classification (e.g., medium-sized cells, mixture of medium and large cells), large cells, lymphoepitheloid cells, subtype of hepatosplenic γδ T cell lymphoma, and panniculitic T cell lymphoma), angioimmunoblastic T cell lymphoma (AILD), angiocentric lymphoma, enteropathy-associated T cell lymphoma (e.g., + / - enteropathy-associated), adult T cell lymphoma / leukemia (ATL), anaplastic large cell type lymphoma (ALCL) (e.g., CD30+, T- and null cell types), anaplastic large cell lymphoma, and Hodgkin-like), but are not limited thereto. In some embodiments, the lymphoma is Hodgkin's disease. For example, Hodgkin's disease can be lymphocyte-predominant type, nodular sclerosis type, mixed cellularity type, lymphocyte depletion type, and / or lymphocyte-rich type. In some embodiments, the lymphoma is non-Hodgkin's disease.

[0152] In some embodiments, a method of treating bladder cancer in an individual, comprising administering to the individual an effective amount of a composition comprising an mTOR inhibitor (e.g., a rapamycin drug) and nanoparticles comprising albumin, wherein the individual is selected for treatment based on having an mTOR activation abnormality, is provided. In some embodiments, a method of treating bladder cancer in an individual, comprising: (a) evaluating an mTOR activation abnormality in the individual; (b) administering (e.g., intravenously) to the individual an effective amount of a composition comprising an mTOR inhibitor (e.g., a rapamycin drug) and nanoparticles comprising albumin, wherein the individual is selected for treatment based on having an mTOR activation abnormality, is provided. In some embodiments, a method of selecting an individual having bladder cancer for treatment with a composition comprising an mTOR inhibitor (e.g., a rapamycin drug) and nanoparticles comprising albumin, comprising: (a) evaluating an mTOR activation abnormality in the individual; (b) selecting or recommending the individual for treatment based on the individual having an mTOR activation abnormality, is provided. In some embodiments, a method of selecting an individual having bladder cancer for treatment with a composition comprising an mTOR inhibitor (e.g., a rapamycin drug) and nanoparticles comprising albumin, comprising: (a) evaluating an mTOR activation abnormality in the individual; (b) selecting or recommending the individual for treatment based on the individual having an mTOR activation abnormality; (c) administering to the selected individual an effective amount of a composition comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, is provided. In some embodiments, a method of treating bladder cancer (e.g., mTOR inhibitor-sensitive bladder cancer) in an individual, comprising administering to the individual an effective amount of a composition comprising an mTOR inhibitor (e.g., a rapamycin drug) and nanoparticles comprising albumin, wherein the individual has an mTOR activation abnormality. In some embodiments, the composition comprising nanoparticles comprises a rapamycin drug and albumin, and the rapamycin drug in the nanoparticles is associated with (e.g., coated with) albumin.In some embodiments, the composition comprising the nanoparticles comprises a rapamycin drug and albumin, and the nanoparticles have an average particle size of about 150 nm or less (e.g., about 120 nm or less). In some embodiments, the composition comprising the nanoparticles comprises sirolimus and human serum albumin, the nanoparticles comprise sirolimus associated with (e.g., coated with) human serum albumin, the nanoparticles have an average particle size of about 150 nm or less (e.g., about 120 nm or less, e.g., about 100 nm), and the weight ratio of human albumin to sirolimus in the composition is about 9:1 or less (e.g., about 9:1 or about 8:1). In some embodiments, the composition comprising the nanoparticles comprises Nab-sirolimus. In some embodiments, the mTOR activation abnormality comprises a mutation in an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises a copy number polymorphism in an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises an abnormal expression level of an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises an abnormal activity level of an mTOR-related gene. In some embodiments, the mTOR activation abnormality results in the activation of mTORC1 (e.g., including the activation of mTORC1 but not mTORC2). In some embodiments, the mTOR activation abnormality results in the activation of mTORC2 (e.g., including the activation of mTORC2 but not mTORC1). In some embodiments, the mTOR activation abnormality results in the activation of both mTORC1 and mTORC2. In some embodiments, the mTOR activation abnormality is an abnormality in at least one mTOR-related gene selected from the group consisting of AKT1, FLT3, MTOR, PIK3CA, PIK3CG, TSC1, TSC2, RHEB, STK11, NF1, NF2, PTEN, TP53, FGFR4, KRAS, NRAS, and BAP1. In some embodiments, the mTOR activation abnormality is evaluated by gene sequencing. In some embodiments, the gene sequencing is based on DNA sequencing in a tumor sample. In some embodiments, the gene sequencing is based on sequencing of circulating DNA or cell-free DNA isolated from a blood sample.In some embodiments, the mutated state of TFE3 is further used as a basis for selecting an individual. In some embodiments, the mutated state of TFE3 includes a translocation of TFE3. In some embodiments, the mTOR activation abnormality includes an abnormal phosphorylation level of a protein encoded by an mTOR-related gene. In some embodiments, the mTOR activation abnormality includes an abnormal phosphorylation level of a protein encoded by mTOR selected from the group consisting of AKT, S6K, S6, 4EBP1, and SPARC. In some embodiments, the abnormal phosphorylation level is determined by immunohistochemistry.

[0153] In some embodiments, the bladder cancer is low-grade bladder cancer. In some embodiments, the bladder cancer is high-grade bladder cancer. In some embodiments, the bladder cancer is invasive. In some embodiments, the bladder cancer is non-invasive. In some embodiments, the bladder cancer is non-muscle invasive bladder cancer (NMIBC). In some embodiments, the bladder cancer is BCG-unresponsive or recurrent non-muscle invasive bladder cancer. In some embodiments, the bladder cancer is a transitional cell carcinoma or urothelial carcinoma (e.g., metastatic urothelial carcinoma) including, but not limited to, papillary tumors and flat carcinomas. In some embodiments, the bladder cancer is metastatic urothelial carcinoma. In some embodiments, the bladder cancer is urothelial carcinoma of the bladder. In some embodiments, the bladder cancer is urothelial carcinoma of the ureter. In some embodiments, the bladder cancer is urothelial carcinoma of the urethra. In some embodiments, the bladder cancer is urothelial carcinoma of the renal pelvis. In some embodiments, the bladder cancer is squamous cell carcinoma. In some embodiments, the bladder cancer is non-squamous cell carcinoma. In some embodiments, the bladder cancer is adenocarcinoma. In some embodiments, the bladder cancer is small cell carcinoma.

[0154] In some embodiments, provided is a method of treating ovarian cancer in an individual, the method comprising administering to the individual an effective amount of a composition comprising a mTOR inhibitor (e.g., a rimos drug) and nanoparticles comprising albumin, wherein the individual is selected for treatment based on having an mTOR activation abnormality. In some embodiments, provided is a method of treating ovarian cancer in an individual, the method comprising: (a) evaluating an mTOR activation abnormality in the individual; (b) administering (e.g., intravenously) to the individual an effective amount of a composition comprising a mTOR inhibitor (e.g., a rimos drug) and nanoparticles comprising albumin, wherein the individual is selected for treatment based on having an mTOR activation abnormality. In some embodiments, provided is a method of selecting an individual having ovarian cancer for treatment with a composition comprising a mTOR inhibitor (e.g., a rimos drug) and nanoparticles comprising albumin, the method comprising: (a) evaluating an mTOR activation abnormality in the individual; (b) selecting or recommending the individual for treatment based on the individual having an mTOR activation abnormality. In some embodiments, provided is a method of selecting an individual having ovarian cancer for treatment with a composition comprising a mTOR inhibitor (e.g., a rimos drug) and nanoparticles comprising albumin, the method comprising: (a) evaluating an mTOR activation abnormality in the individual; (b) selecting or recommending the individual for treatment based on the individual having an mTOR activation abnormality; (c) administering to the selected individual an effective amount of the composition comprising a mTOR inhibitor (e.g., a rimos drug) and albumin. In some embodiments, provided is a method of treating ovarian cancer (e.g., mTOR inhibitor-sensitive ovarian cancer) in an individual, the method comprising administering to the individual an effective amount of a composition comprising a mTOR inhibitor (e.g., a rimos drug) and nanoparticles comprising albumin, wherein the individual has an mTOR activation abnormality. In some embodiments, the composition comprising nanoparticles comprises a rimos drug and albumin, and the rimos drug in the nanoparticles is associated with (e.g., coated with) albumin.In some embodiments, the composition comprising the nanoparticles comprises a rapamycin drug and albumin, and the nanoparticles have an average particle size of about 150 nm or less (e.g., about 120 nm or less). In some embodiments, the composition comprising the nanoparticles comprises sirolimus and human serum albumin, the nanoparticles comprise sirolimus associated with (e.g., coated with) human serum albumin, the nanoparticles have an average particle size of about 150 nm or less (e.g., about 120 nm or less, e.g., about 100 nm), and the weight ratio of human albumin to sirolimus in the composition is about 9:1 or less (e.g., about 9:1 or about 8:1). In some embodiments, the composition comprising the nanoparticles comprises Nab-sirolimus. In some embodiments, the mTOR activation abnormality comprises a mutation of an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises a copy number polymorphism of an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises an abnormal expression level of an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises an abnormal activity level of an mTOR-related gene. In some embodiments, the mTOR activation abnormality results in the activation of mTORC1 (e.g., including the activation of mTORC1 but not mTORC2). In some embodiments, the mTOR activation abnormality results in the activation of mTORC2 (e.g., including the activation of mTORC2 but not mTORC1). In some embodiments, the mTOR activation abnormality results in the activation of both mTORC1 and mTORC2. In some embodiments, the mTOR activation abnormality is an abnormality of at least one mTOR-related gene selected from the group consisting of AKT1, FLT3, MTOR, PIK3CA, PIK3CG, TSC1, TSC2, RHEB, STK11, NF1, NF2, PTEN, TP53, FGFR4, KRAS, NRAS, and BAP1. In some embodiments, the mTOR activation abnormality is evaluated by gene sequencing. In some embodiments, the gene sequencing is based on DNA sequencing in a tumor sample. In some embodiments, the gene sequencing is based on the sequencing of circulating DNA or cell-free DNA isolated from a blood sample.In some embodiments, the mutated state of TFE3 is further used as a basis for selecting an individual. In some embodiments, the mutated state of TFE3 includes a translocation of TFE3. In some embodiments, the mTOR activation abnormality includes an abnormal phosphorylation level of a protein encoded by an mTOR-related gene. In some embodiments, the mTOR activation abnormality includes an abnormal phosphorylation level of a protein encoded by mTOR selected from the group consisting of AKT, S6K, S6, 4EBP1, and SPARC. In some embodiments, the abnormal phosphorylation level is determined by immunohistochemistry.

[0155] In some embodiments, the ovarian cancer is ovarian epithelial cancer. Exemplary histological classifications of ovarian epithelial cancer include serous cysts (e.g., serous benign cystadenomas, serous cystadenomas with proliferative activity of epithelial cells and nuclear abnormalities but without invasive destructive growth, or serous cystadenocarcinomas), mucinous cysts (e.g., mucinous benign cystadenomas, mucinous cystadenomas with proliferative activity of epithelial cells and nuclear abnormalities but without invasive destructive growth, or mucinous cystadenocarcinomas), endometrioid tumors (e.g., endometrioid benign cysts, endometrioid tumors with proliferative activity of epithelial cells and nuclear abnormalities but without invasive destructive growth, or endometrioid adenocarcinomas), clear cell (mesonephric) tumors (e.g., benign clear cell tumors, clear cell tumors with proliferative activity of epithelial cells and nuclear abnormalities but without invasive destructive growth, or clear cell cystadenocarcinomas), unclassified tumors that cannot be assigned to one of the above groups, or other malignant tumors. In some embodiments, the individual can be a human having a gene, genetic mutation, or polymorphism associated with ovarian cancer (e.g., BRCA1 or BRCA2), or a human having one or more extra copies of a gene associated with ovarian cancer (e.g., one or more extra copies of the HER2 gene). In some embodiments, the ovarian cancer is an ovarian germ cell tumor. Exemplary histological subtypes include undifferentiated germ cell tumors or other germ cell tumors (e.g., endodermal sinus tumors, e.g., hepatoid or enteric tumors, pulmonary carcinomas, polyembryomas, choriocarcinomas, teratomas, or tumors of mixed morphology). Exemplary teratomas are immature teratomas, mature teratomas, solid teratomas, and cystic teratomas (e.g., dermoid cysts, e.g., mature cystic teratomas, and dermoid cysts with malignant transformation). Some teratomas are unidermal and highly restricted teratomas, e.g., struma ovarii, carcinoids, struma ovarii and carcinoids, or other teratomas (e.g., malignant neuroectodermal tumors and epitheliomas).

[0156] In some embodiments, the hyperplasia is restenosis. Thus, provided is a method of treating restenosis in an individual, the method comprising administering to the individual an effective amount of a composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, wherein the individual is selected for treatment based on having an mTOR activation abnormality. In some embodiments, provided is a method of treating restenosis in an individual, the method comprising: (a) evaluating an mTOR activation abnormality in the individual; (b) administering (e.g., intravenously) to the individual an effective amount of a composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, wherein the individual is selected for treatment based on having an mTOR activation abnormality. In some embodiments, provided is a method of selecting an individual having restenosis for treatment with a composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, the method comprising: (a) evaluating an mTOR activation abnormality in the individual; (b) selecting or recommending the individual for treatment based on the individual having an mTOR activation abnormality. In some embodiments, provided is a method of selecting an individual having restenosis for treatment with a composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, the method comprising: (a) evaluating an mTOR activation abnormality in the individual; (b) selecting or recommending the individual for treatment based on the individual having an mTOR activation abnormality; (c) administering to the selected individual an effective amount of a composition comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin. In some embodiments, provided is a method of treating restenotic cancer (e.g., mTOR inhibitor-sensitive restenosis) in an individual, the method comprising administering to the individual an effective amount of a composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin, wherein the individual has an mTOR activation abnormality. In some embodiments, the composition comprising nanoparticles comprises a rapamycin drug and albumin, and the rapamycin drug in the nanoparticles is associated with (e.g., coated with) albumin.In some embodiments, the composition comprising the nanoparticles comprises a rapamycin drug and albumin, and the nanoparticles have an average particle size of about 150 nm or less (e.g., about 120 nm or less). In some embodiments, the composition comprising the nanoparticles comprises sirolimus and human serum albumin, the nanoparticles comprise sirolimus associated with (e.g., coated with) human serum albumin, the nanoparticles have an average particle size of about 150 nm or less (e.g., about 120 nm or less, e.g., about 100 nm), and the weight ratio of human albumin to sirolimus in the composition is about 9:1 or less (e.g., about 9:1 or about 8:1). In some embodiments, the composition comprising the nanoparticles comprises Nab-sirolimus. In some embodiments, the mTOR activation abnormality comprises a mutation in an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises a copy number polymorphism in an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises an abnormal expression level of an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises an abnormal activity level of an mTOR-related gene. In some embodiments, the mTOR activation abnormality results in the activation of mTORC1 (e.g., including the activation of mTORC1 rather than mTORC2). In some embodiments, the mTOR activation abnormality results in the activation of mTORC2 (e.g., including the activation of mTORC2 rather than mTORC1). In some embodiments, the mTOR activation abnormality results in the activation of both mTORC1 and mTORC2. In some embodiments, the mTOR activation abnormality is an abnormality in at least one mTOR-related gene selected from the group consisting of AKT1, FLT3, MTOR, PIK3CA, PIK3CG, TSC1, TSC2, RHEB, STK11, NF1, NF2, PTEN, TP53, FGFR4, KRAS, NRAS, and BAP1. In some embodiments, the mTOR activation abnormality is evaluated by gene sequencing. In some embodiments, the gene sequencing is based on DNA sequencing in a tumor sample. In some embodiments, the gene sequencing is based on the sequencing of circulating DNA or cell-free DNA isolated from a blood sample.In some embodiments, the mutant state of TFE3 is further used as a basis for selecting an individual. In some embodiments, the mutant state of TFE3 includes a translocation of TFE3. In some embodiments, the mTOR activation abnormality includes an abnormal phosphorylation level of a protein encoded by an mTOR-related gene. In some embodiments, the mTOR activation abnormality includes an abnormal phosphorylation level of a protein encoded by mTOR selected from the group consisting of AKT, S6K, S6, 4EBP1, and SPARC. In some embodiments, the abnormal phosphorylation level is determined by immunohistochemistry.

[0157] In some embodiments, restenosis is in a coronary artery. In some embodiments, restenosis is in a peripheral blood vessel, such as the popliteal artery of the leg, the pudendal artery of the pelvis, and / or the carotid artery of the neck. In some embodiments, restenosis ensues from an endovascular or extravascular procedure or vascular trauma including, but not limited to, vascular surgery, cardiac surgery, antheroectomy, coronary artery bypass graft procedure, stent procedure, and angioplasty. In some embodiments, restenosis is in-stent restenosis. In some embodiments, restenosis is restenosis after angioplasty. In some embodiments, restenosis results from a vascular disease including atherosclerosis, vascular stenosis or atrophy, cerebral vascular stenosis disease, etc. In some embodiments, restenosis includes reducing the percentage diameter of stenosis by at least about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90% or more. In some embodiments, restenosis is binary restenosis.

[0158] In some embodiments, the method maintains an increase in the luminal diameter or cross-sectional area of a blood vessel after an intravascular procedure. In some embodiments, the luminal diameter or cross-sectional area of the blood vessel is maintained at at least about 50% (including any of, for example, at least about 60%, about 70%, about 80%, about 90%, or about 100%) of the luminal diameter or cross-sectional area of the blood vessel after the intravascular procedure. In some embodiments, the method inhibits and / or reduces abnormal cell growth in the blood vessel. In some embodiments, the method inhibits abnormal cell growth by at least about 10% (including any of, for example, at least about 20%, about 30%, about 40%, about 60%, about 70%, about 80%, about 90%, or about 100%). In some embodiments, the method alleviates one or more of the symptoms associated with restenosis. In some embodiments, the method delays restenosis. In some embodiments, the method prevents restenosis.

[0159] In some embodiments, the hyperplasia is pulmonary hypertension. Accordingly, there is provided a method of treating pulmonary hypertension in an individual, the method comprising administering to the individual an effective amount of a composition comprising an mTOR inhibitor (e.g., a rapamycin drug) and nanoparticles comprising albumin, wherein the individual is selected for treatment based on having an mTOR activation abnormality. In some embodiments, there is provided a method of treating pulmonary hypertension in an individual, the method comprising: (a) evaluating an mTOR activation abnormality in the individual; (b) administering (e.g., intravenously) to the individual an effective amount of a composition comprising an mTOR inhibitor (e.g., a rapamycin drug) and nanoparticles comprising albumin, wherein the individual is selected for treatment based on having an mTOR activation abnormality. In some embodiments, there is provided a method of selecting an individual having pulmonary hypertension for treatment with a composition comprising an mTOR inhibitor (e.g., a rapamycin drug) and nanoparticles comprising albumin, the method comprising: (a) evaluating an mTOR activation abnormality in the individual; (b) selecting or recommending the individual for treatment based on the individual having an mTOR activation abnormality. In some embodiments, there is provided a method of selecting an individual having pulmonary hypertension for treatment with a composition comprising an mTOR inhibitor (e.g., a rapamycin drug) and nanoparticles comprising albumin, the method comprising: (a) evaluating an mTOR activation abnormality in the individual; (b) selecting or recommending the individual for treatment based on the individual having an mTOR activation abnormality; (c) administering to the selected individual an effective amount of a composition comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin. In some embodiments, there is provided a method of treating pulmonary hypertension (e.g., mTOR inhibitor-sensitive pulmonary hypertension) in an individual, the method comprising administering to the individual an effective amount of a composition comprising an mTOR inhibitor (e.g., a rapamycin drug) and nanoparticles comprising albumin, wherein the individual has an mTOR activation abnormality. In some embodiments, the composition comprising nanoparticles comprises a rapamycin drug and albumin, and the rapamycin drug in the nanoparticles is associated with (e.g., coated with) albumin.In some embodiments, the composition comprising the nanoparticles comprises a rapamycin drug and albumin, and the nanoparticles have an average particle size of about 150 nm or less (e.g., about 120 nm or less). In some embodiments, the composition comprising the nanoparticles comprises sirolimus and human serum albumin, the nanoparticles comprise sirolimus associated with (e.g., coated with) human serum albumin, the nanoparticles have an average particle size of about 150 nm or less (e.g., about 120 nm or less, e.g., about 100 nm), and the weight ratio of human albumin to sirolimus in the composition is about 9:1 or less (e.g., about 9:1 or about 8:1). In some embodiments, the composition comprising the nanoparticles comprises Nab-sirolimus. In some embodiments, the mTOR activation abnormality comprises a mutation in an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises a copy number polymorphism in an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises an abnormal expression level of an mTOR-related gene. In some embodiments, the mTOR activation abnormality comprises an abnormal activity level of an mTOR-related gene. In some embodiments, the mTOR activation abnormality results in the activation of mTORC1 (e.g., including the activation of mTORC1 rather than mTORC2). In some embodiments, the mTOR activation abnormality results in the activation of mTORC2 (e.g., including the activation of mTORC2 rather than mTORC1). In some embodiments, the mTOR activation abnormality results in the activation of both mTORC1 and mTORC2. In some embodiments, the mTOR activation abnormality is an abnormality in at least one mTOR-related gene selected from the group consisting of AKT1, FLT3, MTOR, PIK3CA, PIK3CG, TSC1, TSC2, RHEB, STK11, NF1, NF2, PTEN, TP53, FGFR4, KRAS, NRAS, and BAP1. In some embodiments, the mTOR activation abnormality is evaluated by gene sequencing. In some embodiments, the gene sequencing is based on DNA sequencing in a tumor sample. In some embodiments, the gene sequencing is based on the sequencing of circulating DNA or cell-free DNA isolated from a blood sample.In some embodiments, the mutated state of TFE3 is further used as a basis for selecting an individual. In some embodiments, the mutated state of TFE3 includes a translocation of TFE3. In some embodiments, the mTOR activation abnormality includes an abnormal phosphorylation level of a protein encoded by an mTOR-related gene. In some embodiments, the mTOR activation abnormality includes an abnormal phosphorylation level of a protein encoded by mTOR selected from the group consisting of AKT, S6K, S6, 4EBP1, and SPARC. In some embodiments, the abnormal phosphorylation level is determined by immunohistochemistry.

[0160] In some embodiments, pulmonary hypertension is pulmonary arterial hypertension (PAH). In some embodiments, PAH is idiopathic PAH. In some embodiments, PAH is familial PAH. In some variant forms, PAH is associated with persistent pulmonary hypertension of the newborn. In some embodiments, PAH is associated with pulmonary veno-occlusive disease. In some embodiments, PAH is associated with pulmonary capillary hemangiomatosis. In some embodiments, pulmonary hypertension is pulmonary venous hypertension. In some embodiments, pulmonary hypertension is pulmonary hypertension associated with a respiratory disorder and / or hypoxemia. In some embodiments, pulmonary hypertension is pulmonary hypertension caused by chronic thromboembolic disease and / or embolic disease. In some embodiments, pulmonary hypertension is various pulmonary hypertensions. In some embodiments, various pulmonary hypertensions are associated with sarcoidosis, eosinophilic granuloma, histiocytosis X, lymphangiolomyomatosis, or pulmonary vascular compression (e.g., adenopathy, tumor, or fibrosing mediastinitis). In some embodiments, pulmonary hypertension is associated with chronic obstructive pulmonary disease (COPD). In some embodiments, pulmonary hypertension is associated with pulmonary fibrosis. In some embodiments, pulmonary hypertension is early-stage pulmonary hypertension or progressive pulmonary hypertension. In some embodiments, pulmonary hypertension is severe progressive pulmonary arterial hypertension.

[0161] In some embodiments, the method reduces pulmonary pressure. In some embodiments, the pulmonary pressure is reduced by at least about 10% (including, for example, any of at least about 20%, about 30%, about 40%, about 60%, about 70%, about 80%, about 90%, or about 100%). In some embodiments, the method inhibits and / or reduces abnormal cell growth in the pulmonary artery. In some embodiments, the method inhibits abnormal cell growth by at least about 10% (including, for example, any of at least about 20%, about 30%, about 40%, about 60%, about 70%, about 80%, about 90%, or about 100%). In some embodiments, the method alleviates one or more of the symptoms associated with pulmonary hypertension. In some embodiments, the method delays pulmonary hypertension. In some embodiments, the method prevents pulmonary hypertension.

[0162] In some embodiments according to any of the methods for treating restenosis or pulmonary hypertension as described above, the method inhibits negative remodeling in the blood vessels of an individual. In some embodiments, the blood vessel is an artery. In some embodiments, the artery is a coronary artery or a peripheral artery. In some embodiments, the artery is a pulmonary artery. Negative remodeling includes the physiological or pathological response of a blood vessel to a stimulus that results in a reduction in blood vessel diameter and lumen diameter. Such a stimulus may be caused, for example, by a change in blood flow or an angioplasty procedure. In some embodiments, the administration of the nanoparticle composition of the mTOR inhibitor increases the blood vessel diameter by about 10%, about 20%, about 30%, about 40%, about 60%, about 70%, about 80%, about 95% or more compared to the blood vessel diameter without injection. Negative remodeling can be angiographically quantified, for example, as the percentage diameter stenosis at the lesion site (or disease site). Another method of determining the degree of remodeling involves using intravascular ultrasound (IVUS) to measure the external elastic lamina area within the lesion. IVUS is a technique capable of imaging the external elastic lamina as well as the blood vessel lumen. In some embodiments, negative remodeling is associated with a vascular intervention procedure, such as angioplasty, stent placement, or atherectomy. Thus, the nanoparticle composition can be injected during or after a vascular intervention procedure.

[0163] In some embodiments according to any of the methods for treating restenosis or pulmonary hypertension as described above, the method inhibits vascular fibrosis (e.g., medial fibrosis or adventitial fibrosis) in a blood vessel in an individual. In some embodiments, the blood vessel is an artery. In some embodiments, the artery is a coronary artery or a peripheral artery. In some embodiments, the artery is a pulmonary artery.

[0164] As used herein, vascular fibrosis refers to extensive fibrous (connective) tissue formation in a blood vessel, which includes, for example, medial fibrosis or adventitial fibrosis. Vascular fibrosis is frequently associated with a large amount of deposition of extracellular matrix, as well as the proliferation of myofibroblasts and fibroblasts. Thus, in some embodiments, the methods described herein inhibit fibrous tissue formation in a blood vessel, for example, inhibiting fibrous tissue formation by about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80% or about 90% compared to a blood vessel without injection. In some embodiments, the method inhibits the deposition of extracellular matrix in a blood vessel, for example, inhibiting the deposition of extracellular matrix by about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80% or about 90% compared to a blood vessel without injection. In some embodiments, the method inhibits the proliferation of myofibroblasts in a blood vessel, for example, inhibiting the proliferation of myofibroblasts by about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80% or about 90% compared to a blood vessel without injection. In some embodiments, the method inhibits the proliferation of fibroblasts in a blood vessel, for example, inhibiting the proliferation of fibroblasts by about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80% or about 90% compared to a blood vessel without injection. In some embodiments, vascular fibrosis is associated with a vascular intervention procedure, such as angioplasty, stent placement, or atherectomy.

[0165] The methods provided herein can be used to treat an individual (e.g., a human) diagnosed with or suspected of having hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension). In some embodiments, the individual is a human. In some embodiments, the individual is at least about 20 years old, about 25 years old, about 30 years old, about 35 years old, about 40 years old, about 45 years old, about 50 years old, about 55 years old, about 60 years old, about 65 years old, about 70 years old, about 75 years old, about 80 years old, or about 85 years old. In some embodiments, the individual is male. In some embodiments, the individual is female. In some embodiments, the individual has undergone resection of hyperplastic tissue (e.g., a tumor). In some embodiments, the individual has refused surgery. In some embodiments, the individual is medically inoperable. In some embodiments of the invention, the individual is genetically or otherwise (e.g., having risk factors) predisposed to hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension). These risk factors include, but are not limited to, age, gender, race, diet, previous medical history, presence of a precursor disease, genetic considerations, and environmental exposures. In some embodiments, individuals at risk of hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) include, for example, those having relatives who have experienced hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension), and those whose risk has been determined by analysis of their genetic or biochemical markers.

[0166] The methods provided herein can be practiced in the context of adjuvant therapy. In some embodiments, the method is practiced in the context of neoadjuvant therapy, i.e., the method can be performed prior to primary / definitive treatment. In some embodiments, the method is used to treat an individual who has been previously treated. In some embodiments, the individual is resistant, non-responsive, partially responsive, initially responsive, or refractory to a prior treatment. In some embodiments, the individual is at the time of treatment, with a prior treatment ongoing. In some embodiments, the individual is not suitable to continue a prior treatment, for example, due to inability to respond and / or due to toxicity. In some embodiments, the individual has not been previously treated. In some embodiments, the method is used as first-line treatment. In some embodiments, the method is used as second-line treatment.

[0167] The methods described herein for treating hyperplasia can be used in monotherapy as well as in combination therapy with another agent. In some embodiments, a composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin is administered as a single agent. In some embodiments, the method further comprises administering to the individual an effective amount of at least one other therapeutic agent. The at least one other therapeutic agent can be a chemotherapeutic agent or an antibody. In some embodiments, the at least one other therapeutic agent is selected from the group consisting of an alkylating agent, an anthracycline antibiotic, a DNA cross-linking agent, an antimetabolite, an indolequinone, a taxane, or a platinum-based agent.

[0168] Also provided is a pharmaceutical composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug, such as sirolimus) for use in any of the methods of treating an individual having hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) described herein. In some embodiments, the composition comprises nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug, such as sirolimus) and albumin (e.g., human serum albumin). Biomarker

[0169] The present invention uses biomarkers to select individuals for treatment with nanoparticle compositions of mTOR inhibitors. Deviations from the normal sequence, expression level, and / or activity level of the biomarkers described herein can be used as a basis for selecting individuals for treatment.

[0170] As used herein, "biomarker" can refer to a molecule (typically a protein, nucleic acid, carbohydrate, or lipid) encoded or expressed by a hyperplastic cell (e.g., a cancer cell, or an abnormally proliferative cell in pulmonary hypertension or restenosis) that is useful for diagnosis, prognosis, and / or preferential targeting of nanoparticle compositions of mTOR inhibitors to hyperplastic cells. Biomarkers described herein include mTOR-related genes, molecules encoded by mTOR-related genes, or derivatives of mTOR-related genes or molecules encoded by mTOR-related genes, such as nucleic acids (DNA or RNA), proteins, or the native modified forms of nucleic acids or proteins corresponding to mTOR-related genes. Abnormalities in the sequence, expression level, and / or activity level of the biomarker correlate with mTOR signaling levels that exceed normal mTOR signaling levels in hyperplastic cells. mTOR signaling pathway

[0171] The mTOR signaling pathway is mediated by multiple upstream proteins that sense various signal sources and relay signals to the mTOR complex. The mTOR complex integrates upstream signals and regulates cell growth and proliferation by activating or inhibiting downstream effector proteins. The mTOR signaling pathway has been previously described. See, e.g., Laplante et al., Journal of cell science 122, no. 20 (2009): 3589-3594.

[0172] The mTOR complex is a multi-subunit protein complex that includes the mTOR protein, a 289 kDa serine-threonine kinase, as its catalytic subunit. There are at least two structurally and functionally distinct mTOR complexes, mTOR complex 1 (mTORC1) and mTOR complex 2 (mTORC2), each containing a distinct set of protein components. mTORC1 and mTORC2 are known to have distinct biochemical properties, including their affinity for mTOR inhibitors and their signaling characteristics (e.g., upstream and downstream interaction partners). For example, rapamycin (or a rapalog) binds to the 12 kDa (FKBP12) FK506-binding protein, thereby interacting with the FKBP12-rapamycin binding domain (FRB) of mTOR and thus inhibiting mTORC1 function. mTORC2 is characterized as being rapamycin-insensitive; that is, rapamycin (or a rapalog) produces only a small amount (e.g., less than about 1%) of inhibition of mTORC2 activity at low concentrations sufficient to completely inhibit mTORC1. Rapamycin (or a rapalog) may be toxic to the treated individual at concentrations that inhibit mTORC2 activity by a significant amount (e.g., any of at least about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90% or more).

[0173] mTORC1 contains at least five proteins, including the mTOR protein, the regulatory-associated protein of mTOR (RAPTOR), mammalian lethal with Sec13 protein 8 (mLST8, also known as GβL), proline-rich AKT substrate 40 kDa (PRAS40), and DEP domain-containing mTOR-interacting protein (DEPTOR). The signals integrated by mTORC1 include growth factors, energy status, oxygen levels, and amino acids. Important axes that sense upstream signals and regulate mTORC1 activity include TSC1 / 2 and RHEB (Ras homolog enriched in brain). TSC1 / 2 is a heterodimeric protein complex composed of TSC1 and TSC2 and functions as a GTPase-activating protein (GAP) for the small GTPase RHEB. RHEB can stimulate mTORC1 activity through direct interaction, while TSC1 / 2 can convert RHEB to its inactive GDP-bound state, thereby negatively regulating mTORC1 activity. Furthermore, TSC1 / 2-independent signaling pathways exist to mediate upstream signals and regulate mTORC1 activity.

[0174] Upstream signals from different sources are relayed to mTORC1 via various signaling pathways. For example, growth factors stimulate mTORC1 via insulin activation and the Ras signaling pathway. The insulin signaling pathway is initiated by the binding of insulin (e.g., IGF-1) to its cell surface receptor, thereby stimulating the tyrosine kinase activity of the insulin receptor and phosphorylating insulin receptor substrate 1 (IRS1). Phosphorylated IRS-1 activates PI3K to generate phosphatidylinositol (3,4,5)-trisphosphate (PtdIns(3,4,5)P3, or PIP3). PTEN (phosphatase and tensin homolog) negatively regulates the intracellular levels of PIP3 by dephosphorylating PIP3 to PIP2 (PtdIns(4,5)P2), thereby inhibiting the insulin signaling pathway. PIP3 recruits AKT (also known as protein kinase B, or PKB) to the plasma membrane and activates AKT by phosphorylation via PDK1 (protein kinase 3-phosphoinositide-dependent protein kinase-1). Next, activated AKT phosphorylates TSC2 to inactivate TSC1 / 2, thus activating mTORC1. Alternatively, AKT activation can activate mTORC1 by promoting phosphorylation and dissociation of PRAS40 from mTORC1 in a TSC1 / 2-independent manner.

[0175] In addition, growth factors that bind to cell surface receptors can signal to mTORC1 via the Ras signaling pathway. For example, the binding of an extracellular ligand (e.g., EGF) can activate a tyrosine kinase receptor (e.g., EGFR), phosphorylate the cytoplasmic domain of the receptor, thereby recruiting docking proteins such as GRB2 and activating the guanine nucleotide exchange factor SOS. Activated SOS can promote the removal of GDP from Ras, bind Ras to GTP, and activate it. Neurofibromin (NF)-1 becomes a negative regulator of the Ras pathway by stimulating the GTPase activity of Ras. NF-2 is another negative regulator of Ras signaling and acts downstream of the Grb2-SOS complex. Activated Ras activates the downstream protein kinase RAF, thereby phosphorylating and activating MEK. MEK phosphorylates and activates MAPK (mitogen-activated protein kinase, also known as ERK or extracellular signal-regulated kinase). ERK1 / 2 can directly phosphorylate TSC2 or activate p90 ribosomal S6 kinase 1 (RSK1), thereby phosphorylating TSC2, inactivating TSC1 / 2, and activating mTORC1.

[0176] AMP-activated protein kinase (AMPK) is a very important sensor for the intracellular energy state and is a regulator of mTORC1. Among the different activation mechanisms in the AMPK pathway, STK11 (serine / threonine kinase 11, also known as LKB1) can act as a major upstream kinase of AMPK, thereby activating AMPK during energy depletion. Activated AMPK phosphorylates TSC2, thereby activating the TSC1 / 2 GAP activity, inactivating Rheb, and thereby reducing mTORC1 activation. In addition, AMPK can directly phosphorylate RAPTOR, thereby inhibiting mTORC1 activity.

[0177] Similarly, hypoxia (low oxygen levels) can signal to mTORC1 via activation of AMPK. Alternatively, hypoxia can activate TSC1 / 2 via transcriptional regulation of DNA damage response 1 (REDD1). Also, hypoxia can reduce mTORC1 signaling by disrupting the RHEB-mTOR interaction via PML (a tumor suppressor in promyelocytic leukemia) or BNIP3 (BCL2 / adenovirus E1B 19 kDa protein-interacting protein 3).

[0178] Amino acids positively regulate mTORC1 activity, and the signaling of amino acid deprivation to mTORC1 can be independent of TSC1 / 2. RAG proteins, including the RAGA, RAGB, RAGC, and RAGD family of small GTPases, can bind to RAPTOR in an amino acid-sensitive manner and promote the activation of mTORC1.

[0179] Additional upstream signals that regulate mTORC1 activity include, but are not limited to, genotoxic stress, inflammation, Wnt ligands, and phosphatidic acid (PA). For example, pro-inflammatory cytokines such as TNFα activate IκB kinase-β (IKKβ), thereby inactivating TSC1 and activating mTORC1. Activation of the Wnt pathway can inhibit glycogen synthase kinase 3 (GSK3), thereby phosphorylating TSC2, activating TSC1 / 2, and thereby reducing mTORC1 activity.

[0180] mTORC2 contains at least six proteins, including the mTOR protein, the rapamycin-insensitive companion of mTOR (RICTOR), mammalian stress-activated protein kinase interacting protein (mSIN1), protein observed to have Rictor-1 (PROTOR-1), mLST8, and DEPTOR. mTORC2 is involved in the activation of AKT at residue Ser473 and the downstream phosphorylation of some AKT substrates. Also, mTORC2 regulates cytoskeletal organization, for example, by promoting the phosphorylation of protein kinase Cα (PKCα), paxillin phosphorylation, and the GTP loading of RhoA and RAC1.

[0181] The output of the mTOR signaling pathway includes diverse molecular, cellular, and physiological effects. For example, when mTORC1 is activated, many downstream activities occur, including the promotion of the biosynthesis of proteins, lipids, and organelles (e.g., mitochondria), as well as the inhibition of autophagy. For example, mTORC1 promotes protein synthesis by phosphorylating eukaryotic initiation factor 4E (eIF3E)-binding protein 1 (4EBP1) and p70 ribosomal S6 kinase I (S6K1). Phosphorylated 4EBP1 (p-4EBP1) prevents its binding to eIF4E and can promote cap-dependent translation by eIF4E. When S6K1 is phosphorylated, the kinase activity of S6K1 is activated, thereby promoting mRNA biosynthesis, cap-dependent translation, and elongation, and promoting the translation of ribosomal proteins by regulating the activities of many protein targets such as S6K1 aly / REF-like target (SKAR), programmed cell death 4 (PDCD4), eukaryotic elongation factor 2 kinase (eEF2K), and ribosomal protein S6. Also, activated mTORC1 can phosphorylate and suppress ULK1 and ATG13, thereby suppressing autophagy. When mTORC2 is activated, the activation of forkhead box protein O1 (FoxO1) and FoxO3a transcription factors can occur, thereby controlling the expression of genes involved in stress resistance, metabolism, cell cycle arrest, and apoptosis. mTOR-related genes

[0182] The biomarkers and mTOR activation abnormalities described herein relate to mTOR-related genes. As used herein, "mTOR-related genes" encode molecules such as proteins involved in the mTOR signaling pathway. The mTOR-related genes contemplated by the present invention include, but are not limited to, the genes described in the section on the "mTOR signaling pathway". mTOR-related genes can function as part of the mTORC1 and / or mTORC2 complex or regulate the mTORC1 and / or mTORC2 complex by mediating upstream signals. In some embodiments, the mTOR-related genes are selected from MTOR, TSC1, TSC2, RHEB, AKT (e.g., AKT1), PI3K (e.g., PIK3CA and PIK3CG), PTEN, NF1, NF2, STK11, TP53, FGFR4, BAP1, RAS, SOS, GRB2, IRS1, PDK1, RAF, MEK, ERK1, ERK2, RSK1, GSK3, REDD1, BNIP3, PML, AMPK, RAPTOR, DEPTOR, mLST8, PRAS40, VPS34, RAGA, RAGB, RAGC, RAGD, PAXILLIN, RHOA, RAC1, mSIN1, RICTOR (e.g., RICTOR-1), PROTOR-1, PKCα, PLD, IKKβ, and combinations thereof. In some embodiments, the mTOR-related genes are selected from AKT1, FLT3, MTOR, PIK3CA, PIK3CG, TSC1, TSC2, RHEB, STK11, NF1, NF2, PTEN, TP53, FGFR4, KRAS, NRAS, BAP1, and combinations thereof. Exemplary reference (i.e., wild-type) sequences of some mTOR-related genes and molecules encoded by mTOR-related genes (e.g., RNA and proteins) are described below. mTOR

[0183] mTOR is also known as serine / threonine-protein kinase mTOR, FK506-binding protein 12-rapamycin complex-associated protein 1, FKBP12-rapamycin complex-associated protein, mammalian target of rapamycin, mechanistic target of rapamycin, rapamycin and FKBP12 target 1, rapamycin target protein 1, FRAP, FRAP1, FRAP2, RAFT1, and RAPT1. In some embodiments, the nucleic acid sequence of the wild-type MTOR gene is specified by Genbank accession number NC_000001.11 from nucleotide 11106531 to nucleotide 11262557 on the reverse strand of chromosome 1 according to the GRCh38.p2 assembly of the human genome. The wild-type MTOR gene contains 59 exons, and mutations in the MTOR gene can occur in any one or any combination of its 59 exons, or in any intron or non-coding region of the MTOR gene.

[0184] In some embodiments, the amino acid sequence of the wild-type mTOR protein is specified by Genbank accession number NP_004949.1. The wild-type mTOR protein contains various domains including HEAT repeats, FAT domain, FKBP12-rapamycin (rapamyicn) binding (FRB) domain, serine / threonine kinase catalytic domain, and carboxy-terminal FATC domain. Mutations in the mTOR protein can occur in any one or any combination of the protein domains.

[0185] In some embodiments, the nucleic acid sequence of the cDNA encoding the wild-type mTOR protein is specified by Genbank accession number NM_004958.3. AKT

[0186] AKT, also known as protein kinase B (PKB), and its human genome encodes Akt1, Akt2, and Akt3, which are three AKT family members. This application contemplates abnormal mTOR activation in any member of the AKT family. In some embodiments, the mTOR-related gene is AKT1.

[0187] AKT1 is also known as RAC-alpha serine / threonine protein kinase, protein kinase B, protein kinase B alpha, PKB alpha, proto-oncogene c-Akt, AKT, RAC, CWS6, PRKBA, and RAC-alpha. In some embodiments, the nucleic acid sequence of the wild-type AKT1 gene is identified by Genbank accession number NC_000014.9 from nucleotide 104769349 to nucleotide 104795743 on the reverse strand of chromosome 14 according to the GRCh38.p2 assembly of the human genome. The wild-type AKT1 gene contains 17 exons. Mutations in the AKT1 gene can occur in any one or any combination of its 17 exons, or in any intron or non-coding region of the AKT1 gene.

[0188] In some embodiments, the amino acid sequence of the wild-type AKT1 protein is identified by Genbank accession number NP_001014431.1. The wild-type AKT1 protein contains various domains, including a PH domain, a protein kinase domain, and an AGC-kinase C-terminal domain. Mutations in the AKT1 protein can occur in any one or any combination of the protein domains.

[0189] In some embodiments, the nucleic acid sequence of the cDNA encoding wild-type AKT1 protein is identified by Genbank accession number NM_001014431.1. In some embodiments, the nucleic acid sequence of the cDNA encoding wild-type AKT1 protein is identified by Genbank accession number NM_001014432.1. In some embodiments, the nucleic acid sequence of the cDNA encoding wild-type AKT1 protein is identified by Genbank accession number NM_005163.2. PI3K

[0190] PI3K is a family of related lipid kinases that can phosphorylate the hydroxyl group at the 3-position of the inositol ring of phosphatidylinositol. There are four classes of PI3K, including class I, class II, class III, and class IV. Class IA PI3K is composed of a heterodimer between a p110 catalytic subunit and a p85 regulatory subunit. The p85 regulatory subunit has five variants designated p85α, p55α, p50α, p85β, and p55γ. In the human genome, p85α, p55α, and p50α are splice variants encoded by the same gene (PIK3R1), while p85β is encoded by the gene PIK3R2 and p55γ is encoded by the gene PIK3R3. The p110 catalytic subunit has three variants designated p110α, p110β, and p110δ, which are encoded by three separate genes. In the human genome, the gene PIK3CA encodes p110α, the gene PIK3CB encodes p110β, and the gene PIK3CD encodes p110δ. Similar to class IA PI3K, class IB PI3K is composed of a catalytic subunit and a regulatory subunit. Class IA PI3K is activated by receptor tyrosine kinases (RTKs), while class IB PI3K is activated by G protein-coupled receptors (GPCRs). The only known class IB PI3K catalytic subunit is p110γ encoded by the gene PIK3CG. There are two known regulatory subunits of p110γ, including p101 and p84 / p87 PIKAP. This application contemplates mTOR activation abnormalities in any class, member, complex, subunit, variant, or combination of variants of PI3K. In some embodiments, the mTOR-related gene is PIK3CA. In some embodiments, the mTOR-related gene is PIK3CG.

[0191] PIK3CA is also known as phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha isoform, PI3-kinase subunit alpha, PI3K-alpha, PtdIns-3-kinase subunit alpha, phosphatidylinositol-4,5-bisphosphate 3-kinase 110 kDa catalytic subunit alpha, PtdIns-3-kinase subunit p110-alpha, p110 alpha, MCM, CWS5, MCAP, PI2K, CLOVE, and MCMTC. In some embodiments, the nucleic acid sequence of the wild-type PIK3CA gene is identified by Genbank accession number NC_000003.12 from nucleotide 179148114 to nucleotide 179240084 on the forward strand of chromosome 3 according to the GRCh38.p2 assembly of the human genome. The wild-type PIK3CA gene contains 23 exons. Mutations in the PIK3CA gene can occur in any one or any combination of its 23 exons, or in any intron or non-coding region of the PIK3CA gene.

[0192] In some embodiments, the amino acid sequence of the wild-type PIK3CA protein is identified by Genbank accession number NP_006209.2. The wild-type PIK3CA protein contains various domains including a PI3K-ABD domain, a PI3K-RBD domain, a C2-PI3K-type domain, a PIK helical domain, and a PI3K / PI4K domain. Mutations in the PIK3CA protein can occur in any one or any combination of the protein domains.

[0193] In some embodiments, the nucleic acid sequence of the cDNA encoding the wild-type PIK3CA protein is identified by Genbank accession number NM_006218.2.

[0194] PIK3CG is also known as phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit gamma; PI3K, PIK3, PI3CG; PI3Kγ; p110γ, and p120-PI3K. In some embodiments, the nucleic acid sequence of the wild-type PIK3CG gene is identified by Genbank accession number NC_000007.14 from nucleotide 106865278 to nucleotide 106908978 on the forward strand of chromosome 7 according to the GRCh38.p2 assembly of the human genome. The wild-type PIK3CG gene contains 14 exons. Mutations in the PIK3CG gene can occur in any one or any combination of its 14 exons, or in any intron or non-coding region of the PIK3CG gene.

[0195] In some embodiments, the amino acid sequence of the wild-type PIK3CG protein is identified by Genbank accession number NP_002640.2. The wild-type PIK3CG protein contains various domains including a PI3K-ABD domain, a PI3K-RBD domain, a C2-PI3K-type domain, a PIK helical domain and a PI3K / PI4K domain. Mutations in the PIK3CG protein can occur in any one or any combination of the protein domains.

[0196] In some embodiments, the nucleic acid sequence of the cDNA encoding the wild-type PIK3CG protein is identified by Genbank accession number NM_001282426.1. In some embodiments, the nucleic acid sequence of the cDNA encoding the wild-type PIK3CG protein is identified by Genbank accession number NM_002649.3. In some embodiments, the nucleic acid sequence of the cDNA encoding the wild-type PIK3CG protein is identified by Genbank accession number NM_001282427.1. TSC1

[0197] TSC1 is also known as hamartin, tuberous sclerosis 1 protein, TSC, KIAA0243, and LAM. The TSC1 protein functions as part of a complex with TSC2 by negatively regulating mTORC1 signaling. In some embodiments, the nucleic acid sequence of the wild-type TSC1 gene is identified by Genbank accession number NC_000009.12 from nucleotide 132891348 to nucleotide 132945370 on the reverse strand of chromosome 9 according to the GRCh38.p2 assembly of the human genome. The wild-type TSC1 gene contains 25 exons. Mutations in the TSC1 gene can occur in any one or any combination of its 25 exons, or in any intron or non-coding region of the TSC1 gene.

[0198] In some embodiments, the amino acid sequence of the wild-type TSC1 protein is identified by Genbank accession number NP_000359.1. In some embodiments, the amino acid sequence of the wild-type TSC1 protein is identified by Genbank accession number NP_001155898.1. In some embodiments, the amino acid sequence of the wild-type TSC1 protein is identified by Genbank accession number NP_001155899.1.

[0199] In some embodiments, the nucleic acid sequence of the cDNA encoding the wild-type TSC1 protein is identified by Genbank accession number NM_000368.4. In some embodiments, the nucleic acid sequence of the cDNA encoding the wild-type TSC1 protein is identified by Genbank accession number NM_001162426.1. In some embodiments, the nucleic acid sequence of the cDNA encoding the wild-type TSC1 protein is identified by Genbank accession number NM_001162427.1. TSC2

[0200] TSC2 is also known as tuberin, tuberous sclerosis 2 protein, protein phosphatase 1 regulatory subunit 160, TSC4, PPP1R160, and LAM. The TSC2 protein functions as part of a complex with TSC1 by negatively regulating mTORC1 signaling. In some embodiments, the nucleic acid sequence of the wild-type TSC2 gene is identified by Genbank accession number NC_000016.10 from nucleotide 2047936 to nucleotide 2088712 on the forward strand of chromosome 16 according to the GRCh38.p2 assembly of the human genome. The wild-type TSC2 gene contains 42 exons. Mutations in the TSC2 gene can occur in any one or any combination of its 42 exons, or in any intron or non-coding region of the TSC2 gene.

[0201] In some embodiments, the amino acid sequence of the wild-type TSC2 protein is identified by Genbank accession number NP_000539.2. In some embodiments, the amino acid sequence of the wild-type TSC2 protein is identified by Genbank accession number NP_001070651.1. In some embodiments, the amino acid sequence of the wild-type TSC2 protein is identified by Genbank accession number NP_001107854.1.

[0202] In some embodiments, the nucleic acid sequence of the cDNA encoding the wild-type TSC2 protein is identified by Genbank accession number NM_000548.3. In some embodiments, the nucleic acid sequence of the cDNA encoding the wild-type TSC2 protein is identified by Genbank accession number NM_001077183.1. In some embodiments, the nucleic acid sequence of the cDNA encoding the wild-type TSC2 protein is identified by Genbank accession number NM_001114382.1. RHEB

[0203] RHEB is a member of the small GTPase superfamily that shuttles between an inactive form bound to GDP and an active form bound to GTP to regulate mTORC1 signaling. The human genome also has three pseudogenes of RHEB, including RHEBP1 on chromosome 10. Additionally, the RHEBL1 (Ras homolog enriched in brain-like-1) gene encodes a homolog of RHEB that is also a downstream target of the TSC1 / 2 complex and promotes signaling through mTOR. This application contemplates abnormal mTOR activation in all genes related to RHEB, including RHEB, RHEB pseudogenes, and RHEBL1. In some embodiments, the mTOR-related gene is RHEB.

[0204] RHEB is also known as Ras homolog enriched in brain, GTP-binding protein Rheb, and RHEB2. In some embodiments, the nucleic acid sequence of the wild-type RHEB gene is specified by Genbank accession number NC_000007.14 from nucleotide 151466012 to nucleotide 151519924 on the reverse strand of chromosome 7 according to the GRCh38.p2 assembly of the human genome. The wild-type RHEB gene contains 9 exons. Mutations in the RHEB gene can occur in any one or any combination of its 9 exons, or in any intron or non-coding region of the RHEB gene.

[0205] In some embodiments, the amino acid sequence of the wild-type RHEB protein is specified by Genbank accession number NP_005605.1. In some embodiments, the nucleic acid sequence of the cDNA encoding the wild-type RHEB protein is specified by Genbank accession number NM_005614.3. STK11

[0206] STK11 is also known as serine / threonine-protein kinase STK11, liver kinase B1, renal carcinoma antigen NY-REN-19, PJS, LKB1, and hLKB1. In some embodiments, the nucleic acid sequence of the wild-type STK11 gene is identified by Genbank accession number NC_000019.10 from nucleotide 1205799 to nucleotide 1228435 on the forward strand of chromosome 19 according to the GRCh38.p2 assembly of the human genome. The wild-type STK11 gene contains 13 exons. Mutations in the STK11 gene can occur in any one or any combination of its 13 exons, or in any intron or non-coding region of the STK11 gene.

[0207] In some embodiments, the amino acid sequence of the wild-type STK11 protein is identified by Genbank accession number NP_000446.1. In some embodiments, the nucleic acid sequence of the cDNA encoding the wild-type STK11 protein is identified by Genbank accession number NM_000455.4. NF1

[0208] NF1 is also known as the neurofibromatosis-related protein, neurofibromin 1, WSS, NFNS, and VRNF. In some embodiments, the nucleic acid sequence of the wild-type NF1 gene is identified by Genbank accession number NC_000017.11 from nucleotide 31007873 to nucleotide 31377677 on the forward strand of chromosome 17 according to the GRCh38.p2 assembly of the human genome. The wild-type NF1 gene contains 73 exons. Mutations in the NF1 gene can occur in any one or any combination of its 73 exons, or in any intron or non-coding region of the NF1 gene.

[0209] In some embodiments, the amino acid sequence of the wild-type NF1 protein is specified by Genbank accession number NP_001035957.1. In some embodiments, the amino acid sequence of the wild-type NF1 protein is specified by Genbank accession number NP_000258.1. In some embodiments, the amino acid sequence of the wild-type NF1 protein is specified by Genbank accession number NP_001121619.1. In some embodiments, wild-type NF1 is a naturally truncated NF1 protein that lacks the C-terminal 1534 amino acids from the full-length NF1 protein. The NF1 protein contains a Ras-GAP domain and a CRAL-TRIO domain. Mutations in the NF1 protein can occur in one or both of those protein domains.

[0210] In some embodiments, the nucleic acid sequence of the cDNA encoding the wild-type NF1 protein is specified by Genbank accession number NM_001042492.2. In some embodiments, the nucleic acid sequence of the cDNA encoding the wild-type NF1 protein is specified by Genbank accession number NM_000267.3. In some embodiments, the nucleic acid sequence of the cDNA encoding the wild-type NF1 protein is specified by Genbank accession number NM_001128147.2. In some embodiments, the wild-type mRNA encoding the NF1 protein undergoes RNA editing (CGA>UGA→Arg1306Term), resulting in premature translational termination and generating a naturally truncated NF1 protein. NF2

[0211] NF2 is also known as Merlin, Moesin-ezrin-radixin-like protein, Neurofibromin-2, Schwannomerlin, Schwannomin, SCH, CAN, and BANF. In some embodiments, the nucleic acid sequence of the wild-type NF2 gene is specified by Genbank accession number NC_000022.11 from nucleotide 29603556 to nucleotide 29698600 on the forward strand of chromosome 22 according to the GRCh38.p2 assembly of the human genome. The wild-type NF2 gene contains 18 exons. Mutations in the NF2 gene can occur in any one or any combination of its 18 exons, or in any intron or non-coding region of the NF2 gene.

[0212] In some embodiments, the amino acid sequence of the wild-type NF2 protein is specified by Genbank accession number NP_000259.1. In some embodiments, the amino acid sequence of the wild-type NF2 protein is specified by Genbank accession number NP_057502.2. In some embodiments, the amino acid sequence of the wild-type NF2 protein is specified by Genbank accession number NP_861546.1. In some embodiments, the amino acid sequence of the wild-type NF2 protein is specified by Genbank accession number NP_861966.1. In some embodiments, the amino acid sequence of the wild-type NF2 protein is specified by Genbank accession number NP_861967.1. In some embodiments, the amino acid sequence of the wild-type NF2 protein is specified by Genbank accession number NP_861968.1. In some embodiments, the amino acid sequence of the wild-type NF2 protein is specified by Genbank accession number NP_861969.1. In some embodiments, the amino acid sequence of the wild-type NF2 protein is specified by Genbank accession number NP_861970.1. In some embodiments, the amino acid sequence of the wild-type NF2 protein is specified by Genbank accession number NP_861971.1.

[0213] In some embodiments, the nucleic acid sequence of the cDNA encoding the wild-type NF2 protein is identified by Genbank accession number NM_000268.3. In some embodiments, the nucleic acid sequence of the cDNA encoding the wild-type NF2 protein is identified by Genbank accession number NM_016418.5. In some embodiments, the nucleic acid sequence of the cDNA encoding the wild-type NF2 protein is identified by Genbank accession number NM_181825.2. In some embodiments, the nucleic acid sequence of the cDNA encoding the wild-type NF2 protein is identified by Genbank accession number NM_181828.2. In some embodiments, the nucleic acid sequence of the cDNA encoding the wild-type NF2 protein is identified by Genbank accession number NM_181829.2. In some embodiments, the nucleic acid sequence of the cDNA encoding the wild-type NF2 protein is identified by Genbank accession number NM_181830.2. In some embodiments, the nucleic acid sequence of the cDNA encoding the wild-type NF2 protein is identified by Genbank accession number NM_181831.2. In some embodiments, the nucleic acid sequence of the cDNA encoding the wild-type NF2 protein is identified by Genbank accession number NM_181832.2. In some embodiments, the nucleic acid sequence of the cDNA encoding the wild-type NF2 protein is identified by Genbank accession number NM_181833.2. PTEN

[0214] PTEN is also known as phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase and dual specificity phosphatase PTEN, mutated in multiple advanced cancers 1, phosphatase and tensin homolog, MMAC1, TEP1, BZS, DEC, CWS1, GLM2, MHAM, and PTEN1. In some embodiments, the nucleic acid sequence of the wild-type PTEN gene is identified by Genbank accession number NC_000010.11 from nucleotide 87863438 to nucleotide 87971930 on the forward strand of chromosome 10 according to the GRCh38.p2 assembly of the human genome. The wild-type PTEN gene contains 16 exons. Mutations in the PTEN gene can occur in any one or any combination of its 16 exons, or in any intron or non-coding region of the PTEN gene.

[0215] In some embodiments, the amino acid sequence of the wild-type PTEN protein is identified by Genbank accession number NP_000305.3. In some embodiments, the amino acid sequence of the wild-type PTEN protein is identified by Genbank accession number NP_001291646.2. In some embodiments, the amino acid sequence of the wild-type PTEN protein is identified by Genbank accession number NP_001291647.1. The wild-type PTEN protein contains a phosphatase tensin-type domain and a C2 tensin-type domain. Mutations in the PTEN protein can occur in either one or both of the protein domains.

[0216] In some embodiments, the nucleic acid sequence of the cDNA encoding the wild-type PTEN protein is identified by Genbank accession number NM_000314.6. In some embodiments, the nucleic acid sequence of the cDNA encoding the wild-type PTEN protein is identified by Genbank accession number NM_001304717.2. In some embodiments, the nucleic acid sequence of the cDNA encoding the wild-type PTEN protein is identified by Genbank accession number NM_001304718.1. Genes that crosstalk with the mTOR pathway

[0217] Also, the mTOR-related genes contemplated by the present application include genes of pathways that crosstalk with the mTOR pathway and thereby modulate the activity of the mTOR signaling pathway (e.g., mediated via mTORC1 and / or mTORC2). For example, non-limiting examples of genes that can crosstalk with the mTOR pathway are described below: TP53, FGFR4, BAP1, FLT3, KRAS, and NRAS.

[0218] TP53, also known as tumor protein p53, P53, BCC7, LFS1, or TRP53, is a tumor suppressor protein that responds to various cellular stresses to regulate the expression of target genes, thereby inducing cell cycle arrest, apoptosis, senescence, DNA repair, or metabolic changes. TP53 crosstalks with the mTOR signaling pathway by inhibiting mTOR activity. In some embodiments, the nucleic acid sequence of the wild-type TP53 gene is specified by Genbank accession number NC_000017.11 from nucleotide 7668402 to nucleotide 7687550 of the complementary strand of chromosome 17 according to the GRCh38.p2 assembly of the human genome. The wild-type TP53 gene contains 12 exons. Mutations in the TP53 gene can occur in any one or any combination of its 12 exons, or in any intron or non-coding region of the TP53 gene. The wild-type protein encoded by TP53 includes multiple isoforms, such as isoforms a - l. Mutations can affect any of the TP53 isoforms. In some embodiments, the amino acid sequence of the wild-type TP53 protein is specified by Genbank accession number NP_000537.3. In some embodiments, the nucleic acid sequence of the cDNA encoding the wild-type TP53 protein is specified by Genbank accession number NM_000546.5.

[0219] FGFR4 is also known as fibroblast growth factor receptor 4, TKF, JTK2, and CD334. FGFR4 is a member of the fibroblast growth factor receptor family. The extracellular domain of the protein encoded by FGFR4 interacts with fibroblast growth factors and initiates a cascade of downstream signals involved in mitogenesis and differentiation. FGFR4 cross-talks with the mTOR signaling pathway. For example, RAS is known as a common regulator of FGFR4 and mTOR. In some embodiments, the nucleic acid sequence of the wild-type FGFR4 gene is specified by Genbank accession number NC_000005.10 from nucleotide 177086872 to nucleotide 177098142 on the forward strand of chromosome 5 according to the GRCh38.p2 assembly of the human genome. The wild-type FGFR4 gene contains 19 exons. Mutations in the FGFR4 gene can occur in any one or any combination of its 19 exons, or in any intron or non-coding region of the FGFR4 gene. In some embodiments, the amino acid sequence of the wild-type TP53 protein is specified by Genbank accession number NP_002002.3. In some embodiments, the nucleic acid sequence of the cDNA encoding the wild-type FGFR4 protein is specified by Genbank accession number NM_002011.4.

[0220] BAP1 is also known as BRCA1-associated protein-1, UCHL2, hucep-6, or HUCEP-13. BAP1 belongs to the ubiquitin C-terminal hydrolase subfamily of deubiquitinating enzymes that are involved in the removal of ubiquitin from proteins. The encoded enzyme binds to BRCA1 via the RING finger domain of breast cancer type 1 susceptibility protein (BRCA1) and acts as a tumor suppressor. Further, the enzyme may be involved in the regulation of transcription, the regulation of the cell cycle and cell growth, the response to DNA damage, and chromatin dynamics. In some embodiments, the nucleic acid sequence of the wild-type BAP1 gene is identified by Genbank accession number NC_000003.12 from nucleotide 52401004 to nucleotide 52410105 of the complementary strand of chromosome 3 according to the GRCh38.p2 assembly of the human genome. The wild-type BAP1 gene contains 17 exons. Mutations in the BAP1 gene can occur in any one or any combination of its 17 exons, or in any intron or non-coding region of the BAP1 gene. In some embodiments, the amino acid sequence of the wild-type BAP1 protein is identified by Genbank accession number NP_004647.1. In some embodiments, the nucleic acid sequence of the cDNA encoding the wild-type BAP1 protein is identified by Genbank accession number NM_004656.3.

[0221] FLT3 is also known as tyrosine kinase 3 related to fms, FLK2, STK1, CD135 or FLK-2. FLT3 encodes a class III receptor tyrosine kinase. In some embodiments, the nucleic acid sequence of the wild-type FLT3 gene is identified by Genbank accession number NC_000013.11 from nucleotide 28003274 to nucleotide 28100592 of the complementary strand of chromosome 13 according to the GRCh38.p2 assembly of the human genome. The wild-type FLT3 gene contains 27 exons. Mutations in the FLT3 gene can occur in any one or any combination of its 27 exons, or in any intron or non-coding region of the FLT3 gene. In some embodiments, the amino acids encoding the FLT3 protein are identified by Genbank accession number NP_004110.2. In some embodiments, the nucleic acid sequence of the cDNA encoding the wild-type NRAS protein is identified by Genbank accession number NM_004119.2.

[0222] KRAS is also known as Kirsten rat sarcoma viral oncogene homolog, NS, NS3, CFC2, KRAS1, KRAS2, RASK2, KI-RAS, C-K-RAS, K-RAS2A, K-RAS2B, K-RAS4A, or K-RAS4B. In some embodiments, the nucleic acid sequence of the wild-type KRAS gene is specified by Genbank accession number NC_000012.12 from nucleotide 25204789 to nucleotide 25250931 of the complementary strand of chromosome 12 according to the GRCh38.p2 assembly of the human genome. The wild-type KRAS gene contains 6 exons. Mutations in the KRAS gene can occur in any one or any combination of its 6 exons, or in any intron or non-coding region of the KRAS gene. In some embodiments, the amino acids encoding the KRAS protein are specified by Genbank accession number NP_004976.2. In other embodiments, the amino acids encoding the KRAS protein are specified by Genbank accession number NP_203524.1. In some embodiments, the nucleic acid sequence of the cDNA encoding the wild-type KRAS protein is specified by Genbank accession number NM_004985.3. In other embodiments, the nucleic acid sequence of the cDNA encoding the wild-type KRAS protein is specified by Genbank accession number NM_033360.2.

[0223] NRAS is also known as neuroblastoma RAS viral (v-ras) oncogene homolog, NS6, CMNS, NCMS, ALPS4, N-ras or NRAS1. In some embodiments, the nucleic acid sequence of the wild-type NRAS gene is specified by Genbank accession number NC_000001.11 from nucleotide 114704464 to nucleotide 114716894 of the complementary strand of chromosome 1 according to the GRCh38.p2 assembly of the human genome. The wild-type NRAS gene contains 7 exons. Mutations in the NRAS gene can occur in any one or any combination of its 7 exons, or in any intron or non-coding region of the NRAS gene. In some embodiments, the amino acids encoding the NRAS protein are specified by Genbank accession number NP_002515.1. In some embodiments, the nucleic acid sequence of the cDNA encoding the wild-type NRAS protein is specified by Genbank accession number NM_002524.4.

[0224] Abnormal mTOR activation This application contemplates abnormal mTOR activation in any one or more of the above mTOR-related genes, including deviations from reference sequences (i.e., genetic abnormalities), abnormal expression levels and / or abnormal activity levels of one or more mTOR-related genes. This application contemplates treatments and methods based on any one or more states of abnormal mTOR activation disclosed herein.

[0225] The mTOR activation abnormalities described in this specification are related to an improvement in the mTOR signaling level or activity level (i.e., overactivation). The mTOR signaling level or mTOR activity level described in this application can include mTOR signaling in response to any one or any combination of the upstream signals described above, and can include mTOR signaling by mTORC1 and / or mTORC2, whereby a measurable change in any one or combination of downstream molecular processes, cellular processes or physiological processes (e.g., protein synthesis, autophagy, metabolism, cell cycle arrest, apoptosis, etc.) can be brought about. In some embodiments, the mTOR activation abnormality overactivates mTOR activity by at least about 10%, about 20%, about 30%, about 40%, about 60%, about 70%, about 80%, about 90%, about 100%, about 200%, about 500% or higher than the level of mTOR activity without the mTOR activation abnormality. In some embodiments, the overactivation of mTOR activity is mediated only by mTORC1. In some embodiments, the overactivation of mTOR activity is mediated only by mTORC2. In some embodiments, the overactivation of mTOR activity is mediated by both mTORC1 and mTORC2.

[0226] Methods for determining mTOR activity are known in the art. See, for example, Brian CG et al., Cancer Discovery, 2014, Vol. 4: pp. 554-563. mTOR activity can be measured by quantifying any one of the outputs downstream of the mTOR signaling pathway described above (e.g., at the molecular, cellular, and / or physiological levels). For example, mTOR activity by mTORC1 can be measured by determining the level of phosphorylated 4EBP1 (e.g., P-S65-4EBP1), and / or the level of phosphorylated S6K1 (e.g., P-T389-S6K1), and / or the level of phosphorylated AKT1 (e.g., P-S473-AKT1). mTOR activity by mTORC2 can be measured by determining the level of phosphorylated FoxO1 and / or FoxO3a. The level of phosphorylated protein can be determined using any method known in the art, such as a Western blot assay, using an antibody that specifically recognizes the phosphorylated protein of interest.

[0227] Candidate mTOR-activating abnormalities can be identified by a variety of methods, such as by searching the literature or by experimental methods known in the art, including but not limited to gene expression profiling experiments (e.g., RNA sequencing experiments or microarray experiments), quantitative proteomics experiments, and gene sequencing experiments. For example, gene expression profiling experiments and quantitative proteomics experiments performed on samples collected from individuals with hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) compared to control samples can provide a list of genes and gene products (e.g., RNA, proteins, and phosphorylated proteins) that are present at abnormal levels. In some examples, gene sequencing (e.g., exome sequencing) experiments performed on samples collected from individuals with hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) compared to control samples can provide a list of genetic abnormalities. Statistical association analysis (e.g., genome-wide association analysis) is performed on experimental data collected from a population of individuals with hyperplasia, and in this experiment, the abnormalities identified with hyperplasia (abnormal levels or genetic abnormalities) can be related. In some embodiments, targeted sequencing experiments (e.g., the ONCOPANEL™ test) are performed, and a list of genetic abnormalities in individuals with hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) is provided.

[0228] The ONCOPANEL™ test can be used to examine the exon DNA sequences and intron regions of cancer-related genes for the detection of genetic abnormalities, including somatic mutations, copy number polymorphisms, and structural rearrangements, in DNA from samples of various sources (e.g., tumor biopsies or blood samples), thereby providing a list of candidate genetic abnormalities that may be mTOR-activating abnormalities. In some embodiments, the abnormalities in these mTOR-related genes are genetic abnormalities or abnormal levels (e.g., expression levels or activity levels) in genes selected from the ONCOPANEL™ test. See, for example, Wagle N. et al., Cancer discovery 2, no. 1 (2012):82-93.

[0229] An exemplary version of the ONCOPANEL (trademark) test includes 300 cancer genes and 113 introns across 35 genes. The 300 genes included in the exemplary ONCOPANEL (trademark) test are ABL1, AKT1, AKT2, AKT3, ALK, ALOX12B, APC, AR, ARAF, ARID1A, ARID1B, ARID2, ASXL1, ATM, ATRX, AURKA, AURKB, AXL, B2M, BAP1, BCL2, BCL2L1, BCL2L12, BCL6, BCOR, BCORL1, BLM, BMPR1A, BRAF, BRCA1, BRCA2, BRD4, BRIP1, BUB1B, CADM2, CARD11, CBL, CBLB, CCND1, CCND2, CCND3, CCNE1, CD274, CD58, CD79B, CDC73, CDH1, CDK1, CDK2, CDK4, CDK5, CDK6, CDK9, CDKN1A, CDKN1B, CDKN1C, CDKN2A, CDKN2B, CDKN2C, CEBPA, CHEK2, CIITA, CREBBP, CRKL, CRLF2, CRTC1, CRTC2, CSF1R, CSF3R, CTNNB1, CUX1, CYLD, DDB2, DDR2, DEPDC5, DICER1, DIS3, DMD, DNMT3A, EED, EGFR, EP300, EPHA3, EPHA5, EPHA7, ERBB2, ERBB3, ERBB4, ERCC2, ERCC3, ERCC4, ERCC5, ESR1, ETV1, ETV4, ETV5, ETV6, EWSR1, EXT1, EXT2, EZH2, FAM46C, FANCA, FANCC, FANCD2, FANCE, FANCF, FANCG, FAS, FBXW7, FGFR1, FGFR2, FGFR3, FGFR4, FH, FKBP9, FLCN, FLT1, FLT3, FLT4, FUS, GATA3, GATA4, GATA6, GLI1, GLI2, GLI3, GNA11, GNAQ, GNAS, GNB2L1, GPC3, GSTM5, H3F3A, HNF1A, HRAS, ID3, IDH1, IDH2, IGF1R, IKZF1, IKZF3, INSIG1, JAK2, JAK3, KCNIP1, KDM5C, KDM6A, KDM6B, KDR, KEAP1, KIT, KRAS, LINC00894, LMO1, LMO2, LMO3, MAP2K1, MAP2K4, MAP3K1,MAPK1, MCL1, MDM2, MDM4, MECOM, MEF2B, MEN1, MET, MITF, MLH1, MLL (KMT2A), MLL2 (KTM2D), MPL, MSH2, MSH6, MTOR, MUTYH, MYB, MYBL1, MYC, MYCL1 (MYCL), MYCN, MYD88, NBN, NEGR1, NF1, NF2, NFE2L2, NFKBIA, NFKBIZ, NKX2-1, NOTCH1, NOTCH2, NPM1, NPRL2, NPRL3, NRAS, NTRK1, NTRK2, NTRK3, PALB2, PARK2, PAX5, PBRM1, PDCD1LG2, PDGFRA, PDGFRB, PHF6, PHOX2B, PIK3C2B, PIK3CA, PIK3R1, PIM1, PMS1, PMS2, PNRC1, PRAME, PRDM1, PRF1, PRKAR1A, PRKCI, PRKCZ, PRKDC, PRPF40B, PRPF8, PSMD13, PTCH1, PTEN, PTK2, PTPN11, PTPRD, QKI, RAD21, RAF1, RARA, RB1, RBL2, RECQL4, REL, RET, RFWD2, RHEB, RHPN2, ROS1, RPL26, RUNX1, SBDS, SDHA, SDHAF2, SDHB, SDHC, SDHD, SETBP1, SETD2, SF1, SF3B1, SH2B3, SLITRK6, SMAD2, SMAD4, SMARCA4, SMARCB1, SMC1A, SMC3, SMO, SOCS1, SOX2, SOX9, SQSTM1, SRC, SRSF2, STAG1, STAG2, STAT3, STAT6, STK11, SUFU, SUZ12, SYK, TCF3, TCF7L1, TCF7L2, TERC, TERT, TET2, TLR4, TNFAIP3, TP53, TSC1, TSC2, U2AF1, VHL, WRN, WT1, XPA, XPC, XPO1, ZNF217, ZNF708, ZRSR2. The intron regions investigated in the exemplary ONCOPANEL (trademark) test are ABL1, AKT3, ALK, BCL2, BCL6, BRAF, CIITA, EGFR, ERG, ETV1, EWSR1, FGFR1, FGFR2, FGFR3, FUS, IGH, IGL, JAK2, MLL, MYC, NPM1, NTRK1, PAX5, PDGFRA, PDGFRB, PPARG, RAF1, RARA, RET,It is spread over specific introns of ROS1, SS18, TRA, TRB, TRG, and TMPRSS2. Any mTOR-activating abnormalities (e.g., genetic abnormalities and abnormal levels) of any of the genes included in any embodiment or version of the ONCOPANEL™ test, including but not limited to the genes and intron regions listed above, are contemplated by this application to function as a basis for selecting an individual for treatment with an mTOR inhibitor nanoparticle composition.,

[0230] Whether a candidate genetic abnormality or abnormal level is an mTOR-activating abnormality can be determined using methods known in the art. Genetic experiments can be performed in cells (e.g., cell lines) or animal models, and it can be confirmed that the hyperplasia-related abnormalities identified from all the abnormalities observed in the experiments are mTOR-activating abnormalities. For example, genetic abnormalities can be cloned and generated in cell lines or animal models, and the mTOR activity of these generated cell lines or animal models can be measured and compared with corresponding cell lines or animal models without the genetic abnormality. An increase in mTOR activity in such experiments can indicate that the genetic abnormality is a candidate mTOR-activating abnormality that can be tested in clinical trials.

[0231] Genetic abnormality Genetic abnormalities of one or more mTOR-related genes can include changes to nucleic acids (e.g., DNA or RNA) associated with mTOR-related genes, including but not limited to coding, non-coding, regulatory, enhancer, silencer, promoter, intron, exon, and untranslated regions of mTOR-related genes, or protein sequences (i.e., mutations), or epigenetic features.

[0232] These genetic abnormalities can be germline mutations (including chromosomal rearrangements) or somatic mutations (including chromosomal rearrangements). In some embodiments, the genetic abnormalities are present in all tissues, including normal and hyperplastic tissues of the individual. In some embodiments, the genetic abnormalities are present only in the hyperplastic tissues of the individual (e.g., tumor tissues, or abnormal proliferating cells in pulmonary hypertension or restenosis). In some embodiments, the genetic abnormalities are present only in a portion of the hyperplastic tumor tissue.

[0233] In some embodiments, the mTOR-activating abnormalities include, but are not limited to, mutations in mTOR-related genes, such as deletions, frameshifts, insertions, indels, missense mutations, nonsense mutations, point mutations, single nucleotide polymorphisms (SNPs), silent mutations, splice site mutations, splice variants, and translocations. In some embodiments, the mutations can be loss-of-function mutations in negative regulators of the mTOR signaling pathway, or gain-of-function mutations in positive regulators of the mTOR signaling pathway.

[0234] In some embodiments, the genetic abnormalities include copy number polymorphisms of mTOR-related genes. Typically, there are two copies of each mTOR-related gene per genome. In some embodiments, the copy number of the mTOR-related gene is amplified by the genetic abnormality, resulting in at least about 3, about 4, about 5, about 6, about 7, about 8, or more copies of the mTOR-related gene in the genome. In some embodiments, the genetic abnormality of the mTOR-related gene results in the loss of one or both copies of the mTOR-related gene in the genome. In some embodiments, the copy number polymorphism of the mTOR-related gene is a loss of heterozygosity of the mTOR-related gene. In some embodiments, the copy number polymorphism of the mTOR-related gene is a deletion of the mTOR-related gene. In some embodiments, the copy number polymorphism of the mTOR-related gene is caused by a structural rearrangement of the genome, including deletions, duplications, inversions, and translocations of chromosomes or fragments thereof.

[0235] In some embodiments, the genetic abnormality includes abnormal epigenetic features associated with mTOR-related genes, including but not limited to DNA methylation, hydroxymethylation, abnormal histone binding, chromatin remodeling, etc. In some embodiments, the promoter of the mTOR-related gene is hypermethylated in an individual by, for example, at least about 10%, about 20%, about 30%, about 40%, about 50%, about 60%, about 70%, about 80%, about 90% or higher, compared to a control level (e.g., a clinically shared normal level in a standardized test).

[0236] In some embodiments, the mTOR-activating abnormality is a genetic abnormality (e.g., a mutation or copy number polymorphism) in any one of the above mTOR-related genes. In some embodiments, the mTOR-activating abnormality is a mutation or copy number polymorphism in one or more genes selected from AKT1, MTOR, PIK3CA, PIK3CG, TSC1, TSC2, RHEB, STK11, NF1, NF2, PTEN, TP53, FGFR4 and BAP1.

[0237] Genetic abnormalities in mTOR-related genes have been identified in various human cancers, including hereditary and sporadic cancers. For example, germline-inactivating mutations in TSC1 / 2 cause tuberous sclerosis, and patients with this condition present with lesions including skin and brain hamartomas, renal angiomyolipomas, and renal cell carcinoma (RCC) (Krymskaya VP et al., 2011, FASEB Journal 25(6):1922-1933). PTEN hamartoma tumor syndrome (PHTS) is linked to inactivating germline PTEN mutations and is associated with a range of clinical manifestations, including breast cancer, endometrial cancer, follicular thyroid cancer, hamartomas, and RCC (Legendre C. et al., 2003, Transplantation proceedings 35(Suppl 3):151S-153S). Furthermore, sporadic kidney cancer has also been shown to harbor somatic mutations in several genes in the PI3K-Akt-mTOR pathway (e.g., AKT1, MTOR, PIK3CA, PTEN, RHEB, TSC1, TSC2) (Power LA, 1990, AmJHospPharm475(5):1033-1049; Badesch DB et al., 2010, Chest 137(2):376-387l; Kim JC and Steinberg GD, 2001, The Journal of urology, 165(3):745-756; McKiernan J. et al., 2010, JUrol183(Suppl 4)). Among the top 50 genes with substantial mutations identified by the Cancer Genome Atlas in clear cell renal cell carcinoma, the mutation rate is approximately 17% for gene mutations that converge on mTORC1 activation (Cancer Genome Atlas Research Network., "Comprehensive molecular characterization of clear cell renal cell carcinoma.", 2013 Nature 499:43-49). Genetic abnormalities in mTOR-related genes have been found to confer sensitivity to treatment with rapamycin drugs in individuals with cancer.For example, see Wagle et al., N Engl J Med 2014, 371:1426-33; Iyer et al., Science 2012, 338:221; Wagle et al., Cancer Discovery 2014, 4:546-553; Grabiner et al., Cancer Discovery 2014, 4:554-563; Dickson et al., Int J Cancer 2013, 132(7):1711-1717 and Lim et al., J Clin Oncol 33, 2015, Suppl; abstr 11010. The genetic abnormalities of mTOR-related genes described by the above references are incorporated herein. Exemplary genetic abnormalities in some mTOR-related genes are described below, and it is understood that the present application is not limited to the exemplary genetic abnormalities described herein.

[0238] In some embodiments, mTOR activation abnormalities include genetic abnormalities in MTOR. In some embodiments, the genetic abnormalities include activating mutations in MTOR. In some embodiments, the activating mutations in MTOR are at one or more positions (e.g., any one of about 1, about 2, about 3, about 4, about 5, about 6 or more positions) in the protein sequence of MTOR selected from the group consisting of N269, L1357, N1421, L1433, A1459, L1460, C1483, E1519, K1771, E1799, F1888, I1973, T1977, V2006, E2014, I2017, N2206, L2209, A2210, S2215, L2216, R2217, L2220, Q2223, A2226, E2419, L2431, I2500, R2505, and D2512. In some embodiments, the activating mutations in MTOR are one or more missense mutations (e.g., any one of about 1, about 2, about 3, about 4, about 5, about 6 or more mutations) selected from the group consisting of N269S, L1357F, N1421D, L1433S, A1459P, L1460P, C1483F, C1483R, C1483W, C1483Y, E1519T, K1771R, E1799K, F1888I, F1888I L, I1973F, T1977R, T1977K, V2006I, E2014K, I2017T, N2206S, L2209V, A2210P, S2215Y, S2215F, S2215P, L2216P, R2217W, L2220F, Q2223K, A2226S, E2419K, L2431P, I2500M, R2505P, and D2512H. In some embodiments, the activating mutations in MTOR disrupt the binding of MTOR to RHEB. In some embodiments, the activating mutations in MTOR disrupt the binding of MTOR to DEPTOR.

[0239] In some embodiments, the mTOR activation abnormality includes genetic abnormalities in TSC1 or TSC2. In some embodiments, the genetic abnormality includes loss of heterozygosity in TSC1 or TSC2. In some embodiments, the genetic abnormality includes loss-of-function mutations in TSC1 or TSC2. In some embodiments, the loss-of-function mutation is a frameshift mutation or a nonsense mutation in TSC1 or TSC2. In some embodiments, the loss-of-function mutation is the frameshift mutation c.1907_1908del in TSC1. In some embodiments, the loss-of-function mutation is the splice variant TSC1:c.1019+1G>A. In some embodiments, the loss-of-function mutation is the nonsense mutation c.1073G>A in TSC2 and / or the nonsense mutation p.Trp103* in TSC1. In some embodiments, the loss-of-function mutation includes missense mutations in TSC1 or TSC2. In some embodiments, the missense mutation is at position A256 of TSC1 and / or position Y719 of TSC2. In some embodiments, the missense mutation includes A256V in TSC1 or Y719H in TSC2.

[0240] In some embodiments, the mTOR activation abnormality includes genetic abnormalities in RHEB. In some embodiments, the genetic abnormality includes loss-of-function mutations in RHEB. In some embodiments, the loss-of-function mutation is at one or more positions in the protein sequence of RHEB selected from Y35 and E139. In some embodiments, the loss-of-function mutation in RHEB is selected from Y35N, Y35C, Y35H, and E139K.

[0241] In some embodiments, the mTOR activation abnormality includes genetic abnormalities in NF1. In some embodiments, the genetic abnormality includes loss-of-function mutations in NF1. In some embodiments, the loss-of-function mutation in NF1 is the missense mutation at position D1644 in NF1. In some embodiments, the missense mutation is D1644A in NF1.

[0242] In some embodiments, the mTOR activation abnormality includes a genetic abnormality in NF2. In some embodiments, the genetic abnormality includes a loss-of-function mutation in NF2. In some embodiments, the loss-of-function mutation in NF2 is a nonsense mutation. In some embodiments, the nonsense mutation in NF2 is c.863C>G.

[0243] In some embodiments, the mTOR activation abnormality includes a genetic abnormality in PTEN. In some embodiments, the genetic abnormality includes a deletion of PTEN in the genome.

[0244] In some embodiments, the mTOR activation abnormality includes a genetic abnormality in PI3K. In some embodiments, the genetic abnormality includes a loss-of-function mutation in PIK3CA or PIK3CG. In some embodiments, the loss-of-function mutation includes a missense mutation at a position of PIK3CA selected from the group consisting of E542, I844, and H1047. In some embodiments, the loss-of-function mutation includes a missense in PIK3CA selected from the group consisting of E542K, I844V, and H1047R.

[0245] In some embodiments, the mTOR activation abnormality includes a genetic abnormality in AKT1. In some embodiments, the genetic abnormality includes an activating mutation in AKT1. In some embodiments, the activating mutation is a missense mutation at position H238 of AKT1. In some embodiments, the missense mutation is H238Y in AKT1.

[0246] In some embodiments, the mTOR activation abnormality includes a genetic abnormality in TP53. In some embodiments, the genetic abnormality includes a loss-of-function mutation in TP53. In some embodiments, the loss-of-function mutation is a frameshift mutation in TP53, such as A39fs*5.

[0247] In some embodiments, the mTOR activation abnormality includes genetic abnormalities of KRAS. In some embodiments, the mTOR activation abnormality includes mutations in exon 2 or exon 3 of the KRAS gene. In some embodiments, the mTOR activation abnormality includes KRAS mutations at one or more positions selected from the group consisting of G12, G13, S17, P34, Q61, K117, or A146 of the KRAS amino acid sequence. In some embodiments, the mTOR activation abnormality includes KRAS mutations selected from the group consisting of G12C, G12S, G12R, G12F, G12L, G12N, G12A, G12D, G12V, G13R, G13C, G13S, G13A, G13D, G13V, G13P, S17G, P34S, Q61K, Q61L, Q61R, Q61H, K117N, A146P, A146T, and A146V.

[0248] Genetic abnormalities of mTOR-related genes can be evaluated based on samples such as samples derived from an individual and / or reference samples. In some embodiments, the sample is a tissue sample or nucleic acid extracted from a tissue sample. In some embodiments, the sample is a cell sample (e.g., CTC sample) or nucleic acid extracted from a cell sample. In some embodiments, the sample is a tumor biopsy. In some embodiments, the sample is a tumor sample or nucleic acid extracted from a tumor sample. In some embodiments, the sample is a biopsy sample or nucleic acid extracted from a biopsy sample. In some embodiments, the sample is a formalin-fixed paraffin-embedded (FFPE) sample or nucleic acid extracted from an FFPE sample. In some embodiments, the sample is a blood sample. In some embodiments, cell-free DNA is isolated from a blood sample. In some embodiments, the biological sample is a plasma sample or nucleic acid extracted from a plasma sample.

[0249] Genetic abnormalities of mTOR-related genes can be determined by any method known in the art. See, for example, Dickson et al., Int J Cancer, 2013, 132(7):1711-1717; Wagle N, Cancer Discovery, 2014, 4:546-553; and Cancer Genome Atlas Research Network, Nature, 2013, 499:43-49. Exemplary methods include genomic DNA sequencing using Sanger sequencing or next-generation sequencing platforms, bisulfite sequencing, or other DNA sequencing-based methods; polymerase chain reaction assays; in-situ hybridization assays; and DNA microarrays, but are not limited thereto. Epigenetic features (e.g., DNA methylation, histone binding or chromatin modification) of one or more mTOR-related genes derived from a sample isolated from an individual may be compared to epigenetic features of one or more mTOR-related genes derived from a control sample. Nucleic acid molecules extracted from the sample may be sequenced or analyzed for the presence of mTOR-activating genetic abnormalities compared to a reference sequence, such as the wild-type sequence of AKT1, MTOR, PIK3CA, PIK3CG, TSC1, TSC2, RHEB, STK11, NF1, NF2, PTEN, TP53, FGFR4, KRAS, NRAS, and / or BAP1 described in the "mTOR-related genes" section.

[0250] In some embodiments, genetic abnormalities of mTOR-related genes are evaluated using a cell-free DNA sequencing method. In some embodiments, genetic abnormalities of mTOR-related genes are evaluated using next-generation sequencing. In some embodiments, genetic abnormalities of mTOR-related genes isolated from a blood sample are evaluated using next-generation sequencing. In some embodiments, genetic abnormalities of mTOR-related genes are evaluated using exome sequencing. In some embodiments, genetic abnormalities of mTOR-related genes are evaluated using fluorescence in-situ hybridization analysis. In some embodiments, genetic abnormalities of mTOR-related genes are evaluated before initiation of the treatment methods described herein. In some embodiments, genetic abnormalities of mTOR-related genes are evaluated after initiation of the treatment methods described herein. In some embodiments, genetic abnormalities of mTOR-related genes are evaluated before and after initiation of the treatment methods described herein.

[0251] Abnormal level The abnormal level of an mTOR-related gene can refer to an abnormal expression level or an abnormal activity level.

[0252] The abnormal expression level of an mTOR-related gene includes an increase or decrease in the level of a molecule encoded by the mTOR-related gene as compared to a control level. The molecule encoded by the mTOR-related gene can include an RNA transcript (e.g., mRNA), a protein isoform, the phosphorylation and / or dephosphorylation state of the protein isoform, the ubiquitination and / or deubiquitination state of the protein isoform, the membrane localization (e.g., myristoylation, palmitoylation, etc.) state of the protein isoform, other post-transcriptional modification states of the protein isoform, or any combination thereof.

[0253] Abnormal activation levels of mTOR-related genes include enhancement or suppression of molecules encoded by any target genes downstream of the mTOR-related genes, including epigenetic regulation, transcriptional regulation, translational regulation, post-translational regulation, or any combination thereof, of the downstream target genes. Furthermore, the activity of mTOR-related genes includes downstream cellular and / or physiological effects in response to mTOR activation abnormalities, including, but not limited to, protein synthesis, cell growth, proliferation, signaling, mitochondrial metabolism, mitochondrial biogenesis, stress response, cell cycle arrest, autophagy, microtubule organization, and lipid metabolism.

[0254] Abnormal levels of mTOR-related genes (including gene products encoded by mTOR-related genes) are associated with hyperplasia, including cancer, restenosis, and pulmonary hypertension. For example, mTOR expression has been shown to increase according to disease stage in the progression from superficial disease to invasive bladder cancer, as demonstrated by activation of pS6-kinase, which was activated in 54 of 70 cases (77%) of T2 muscle-invasive bladder tumors (Seager CM et al., (2009) Cancer PrevRes. (Phila) 2, 1008-1014). The mTOR signaling pathway is also known to be overactivated in pulmonary arterial hypertension.

[0255] The level of an mTOR-related gene (e.g., expression level and / or activity level) in an individual can be determined based on a sample (e.g., a sample derived from the individual or a reference sample). In some embodiments, the sample is derived from a tissue, an organ, a cell, or a tumor. In some embodiments, the sample is a biological sample. In some embodiments, the biological sample is a biological fluid sample or a biological tissue sample. In further embodiments, the biological fluid sample is a body fluid. In some embodiments, the sample is a hyperplastic (e.g., tumor) tissue, a normal tissue adjacent to the solid tumor tissue, a normal tissue distal to the hyperplastic (e.g., tumor) tissue, a blood sample, or another biological sample. In some embodiments, the sample is a fixed sample. Fixed samples include, but are not limited to, formalin-fixed samples, paraffin-embedded samples, or frozen samples. In some embodiments, the sample is a biopsy containing hyperplastic (e.g., cancer) cells. In further embodiments, the biopsy is a fine needle aspirate of hyperplastic (e.g., cancer) cells. In further embodiments, the biopsy is hyperplastic (e.g., cancer) cells obtained by laparoscopy. In some embodiments, the biopsy cells are centrifuged to form a pellet, fixed, and embedded in paraffin. In some embodiments, the biopsy cells are snap frozen. In some embodiments, the biopsy cells are mixed with an antibody that recognizes a molecule encoded by the mTOR-related gene. In some embodiments, the biopsy is taken to determine whether an individual has hyperplasia (e.g., cancer, pulmonary hypertension, or restenosis) and is then used as a sample. In some embodiments, the sample contains surgically obtained hyperplastic (e.g., cancer) cells. In some embodiments, the sample can be obtained at a time different from when the determination of the expression level of the mTOR-related gene is made.

[0256] In some embodiments, the sample comprises circulating metastatic cancer cells. In some embodiments, the sample is obtained by sorting circulating tumor cells (CTCs) from blood. In further embodiments, the CTCs detach from the primary tumor and circulate in the body fluid. In further embodiments, the CTCs detach from the primary tumor and circulate in the bloodstream. In further embodiments, the CTCs are an indicator of metastasis.

[0257] In some embodiments, the level of the protein encoded by the mTOR-related gene is determined to evaluate the abnormal expression level of the mTOR-related gene. In some embodiments, the level of the protein encoded by the target gene downstream of the mTOR-related gene is determined to evaluate the abnormal activity level of the mTOR-related gene. In some embodiments, the protein level is determined using one or more antibodies specific to one or more epitopes of the individual protein or its proteolytic fragments. Suitable detection methods for use in the practice of the present invention include, but are not limited to, immunohistochemistry, enzyme-linked immunosorbent assay (ELISA), Western blotting, mass spectrometry, and immunological PCR. In some embodiments, the level of the protein encoded by the mTOR-related gene and / or its downstream target gene in the sample is normalized (e.g., divided) by the level of a housekeeping protein (e.g., glyceraldehyde 3-phosphate dehydrogenase, i.e., GAPDH) in the same sample.

[0258] In some embodiments, the level of mRNA encoded by an mTOR-related gene is determined to evaluate the abnormal expression level of the mTOR-related gene. In some embodiments, the level of mRNA encoded by a target gene downstream of the mTOR-related gene is determined to evaluate the abnormal activity level of the mTOR-related gene. In some embodiments, reverse transcription (RT)-polymerase chain reaction (PCR) assays (including quantitative RT-PCR assays) are used to determine the mRNA level. In some embodiments, gene chips or next-generation sequencing methods (e.g., RNA (cDNA) sequencing or exome sequencing) are used to determine the level of RNA (e.g., mRNA) encoded by the mTOR-related gene and / or its downstream target gene. In some embodiments, the mRNA level of the mTOR-related gene and / or its downstream target gene in a sample is normalized (e.g., divided) by the mRNA level of a housekeeping protein (e.g., GAPDH) in the same sample.

[0259] The level of the mTOR-related gene can be a high level or a low level compared to a control or reference. In some embodiments where the mTOR-related gene is a positive regulator of mTOR activity (e.g., mTORC1 and / or mTORC2 activity), the abnormal level of the mTOR-related gene is a high level compared to the control. In some embodiments where the mTOR-related gene is a negative regulator of mTOR activity (e.g., mTORC1 and / or mTORC2 activity), the abnormal level of the mTOR-related gene is a low level compared to the control.

[0260] In some embodiments, the level of the mTOR-related gene in an individual is compared to the level of the mTOR-related gene in a control sample. In some embodiments, the level of the mTOR-related gene in an individual is compared to the levels of the mTOR-related gene in a plurality of control samples. In some embodiments, the plurality of control samples are used to generate a statistic used to classify the level of the mTOR-related gene in individuals having hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension).

[0261] The classification or ranking of the level of an mTOR-related gene (i.e., high or low) can be determined relative to the statistical distribution of the control level. In some embodiments, the classification or ranking is relative to a control sample such as normal tissue (e.g., peripheral blood mononuclear cells), or a normal epithelial cell sample (e.g., a buccal swap or a skin punch) obtained from an individual. In some embodiments, the level of the mTOR-related gene is classified or ranked relative to the statistical distribution of the control level. In some embodiments, the level of the mTOR-related gene is classified or ranked relative to the level derived from a control sample obtained from an individual.

[0262] Control samples can be obtained using the same source and method as the non-control samples. In some embodiments, control samples are obtained from a variety of individuals (e.g., individuals without hyperplasia such as cancer, restenosis, or pulmonary hypertension, individuals with a benign or less advanced form of a disease corresponding to hyperplasia, and / or individuals sharing a similar ethnicity, age, and gender). In some embodiments, when the sample is a tumor tissue sample, the control sample can be a non-cancerous sample from the same individual. In some embodiments, multiple control samples (e.g., from different individuals) are used to determine the range of levels of the mTOR-related gene in a particular tissue, organ, or cell population.

[0263] In some embodiments, the control sample is cultured tissue or cells determined to be an appropriate control. In some embodiments, the control is a cell that does not have an mTOR activation abnormality. In some embodiments, the clinically acceptable normal level in a standardized test is used as the control level for determining an abnormal level of the mTOR-related gene. In some embodiments, the level of the mTOR-related gene or its downstream target gene in an individual is classified as high, intermediate, or low according to a scoring system such as an immunohistochemistry-based scoring system.

[0264] In some embodiments, the level of an mTOR-related gene is determined by measuring the level of the mTOR-related gene in an individual and comparing it to a control or reference (e.g., the median level of a given patient population, or the level of a second individual). For example, if it is determined that the level of an mTOR-related gene in a single individual is above the average level of a patient population, that individual is determined to have a high expression level of the mTOR-related gene. Alternatively, if it is determined that the level of an mTOR-related gene in a single individual is below the median level of a patient population, that individual is determined to have a low expression level of the mTOR-related gene. In some embodiments, an individual is compared to a second individual and / or patient population that responds to treatment. In some embodiments, an individual is compared to a second individual and / or patient population that does not respond to treatment. In some embodiments, the level is determined by measuring the level of nucleic acid encoded by the mTOR-related gene and / or its downstream target genes. For example, for a single individual, if it is determined that the level of a molecule (e.g., mRNA or protein) encoded by an mTOR-related gene is above the median level of a patient population, that individual is determined to have a high expression level of the molecule (e.g., mRNA or protein) encoded by the mTOR-related gene. Alternatively, for a single individual, if it is determined that the level of a molecule (e.g., mRNA or protein) encoded by an mTOR-related gene is below the median level of a patient population, that individual is determined to have a low level of the molecule (e.g., mRNA or protein) encoded by the mTOR-related gene.

[0265] In some embodiments, a control level of an mTOR-related gene is determined by obtaining a statistical distribution of the levels of the mTOR-related gene. In some embodiments, the level of the mTOR-related gene is classified or ranked relative to the control level, or a statistical distribution of the control level.

[0266] In some embodiments, the bioinformatics method is used to determine and classify the levels of mTOR-related genes, including the levels of target genes downstream of the mTOR-related genes, as a measure of the activity levels of the mTOR-related genes. A number of bioinformatics techniques have been developed to evaluate gene set expression profiles using gene expression profiling data. Examples of such methods include, but are not limited to, those described in Segal, E. et al., Nat Genet 34:66-176 (2003); Segal, E. et al., Nat Genet 36:1090-1098 (2004); Barry, WT. et al., Bioinformatics 21:1943-1949 (2005); Tian, L. et al., Proc Nat’l Acad Sci USA 102:13544-13549 (2005); Novak B A and Jain A N Bioinformatics 22:233-41 (2006); Maglietta R et al., Bioinformatics 23:2063-72 (2007); Bussemaker H J, BMC Bioinformatics 8 Suppl 6:S6 (2007).

[0267] In some embodiments, the control level is a predetermined threshold level. In some embodiments, mRNA is determined, and low levels are mRNA levels that are about 1-fold, about 0.9-fold, about 0.8-fold, about 0.7-fold, about 0.6-fold, about 0.5-fold, about 0.4-fold, about 0.3-fold, about 0.2-fold, about 0.1-fold, about 0.05-fold, about 0.02-fold, about 0.01-fold, about 0.005-fold, about 0.002-fold, about 0.001-fold or less lower than those considered clinically normal or those obtained from a control. In some embodiments, high levels are mRNA levels that are about 1.1-fold, about 1.2-fold, about 1.3-fold, about 1.5-fold, about 1.7-fold, about 2-fold, about 2.2-fold, about 2.5-fold, about 2.7-fold, about 3-fold, about 5-fold, about 7-fold, about 10-fold, about 20-fold, about 50-fold, about 70-fold, about 100-fold, about 200-fold, about 500-fold, about 1000-fold or more than 1000-fold higher than those considered clinically normal or those obtained from a control.

[0268] In some embodiments, the protein expression level is determined, for example, by Western blot or enzyme-linked immunosorbent assay (ELISA). For example, the criteria for low or high levels are based on the total intensity of the band on the protein gel corresponding to the protein encoded by the mTOR-related gene, which is blotted by an antibody that specifically recognizes the protein encoded by the mTOR-related gene, and can be normalized (e.g., divided) by the band of the same protein gel of the same sample corresponding to the housekeeping protein (e.g., GAPDH), which is blotted by an antibody that specifically recognizes the housekeeping protein (e.g., GAPDH). In some embodiments, the protein level is low if it is lower than any of about 1-fold, about 0.9-fold, about 0.8-fold, about 0.7-fold, about 0.6-fold, about 0.5-fold, about 0.4-fold, about 0.3-fold, about 0.2-fold, about 0.1-fold, about 0.05-fold, about 0.02-fold, about 0.01-fold, about 0.005-fold, about 0.002-fold, about 0.001-fold or less of that of what is considered clinically normal or that obtained from a control. In some embodiments, the protein level is high if it is higher than any of about 1.1-fold, about 1.2-fold, about 1.3-fold, about 1.5-fold, about 1.7-fold, about 2-fold, about 2.2-fold, about 2.5-fold, about 2.7-fold, about 3-fold, 5-fold, about 7-fold, about 10-fold, about 20-fold, about 50-fold or 100-fold or more than 100-fold of that of what is considered clinically normal or that obtained from a control.

[0269] In some embodiments, the protein expression level is determined, for example, by immunohistochemistry. For example, the criteria for low or high levels can be established based on the number of positively stained cells and / or the intensity of staining, for example, by using an antibody that specifically recognizes a protein encoded by an mTOR-related gene. In some embodiments, this biomarker level is low if less than about 1%, less than about 5%, less than about 10%, less than about 15%, less than about 20%, less than about 25%, less than about 30%, less than about 35%, less than about 40%, less than about 45% or less than about 50% of the cells have positive staining. In some embodiments, this biomarker level is low if the staining is 1%, 5%, 10%, 15%, 20%, 25%, 30%, 35%, 40%, 45% or 50% less intense than the positive control staining. In some embodiments, this biomarker level is high if more than about 40%, more than about 45%, more than about 50%, more than about 55%, more than about 60%, more than about 65%, more than about 70%, more than about 75%, more than about 80%, more than about 85% or more than about 90% of the cells have positive staining. In some embodiments, this biomarker level is high if the staining is of equal intensity to the positive control staining. In some embodiments, this biomarker level is high if the staining is 80%, 85% or 90% of the intensity of the positive control staining.

[0270] In some embodiments, the scoring is based on the "H-Score" described in U.S. Patent Application No. 2013 / 0005678. The H-Score is obtained by the formula: 3 × the proportion of cells with strong staining + 2 × the proportion of cells with moderate staining + the proportion of cells with weak staining, and is given in the range of 0 to 300.

[0271] In some embodiments, strong staining, moderate staining, and weak staining are calibrated levels of staining where ranges are established and the intensity of the staining is binned within those ranges. In some embodiments, strong staining is staining in an intensity range above the 75th percentile, moderate staining is staining in an intensity range from the 25th percentile to the 75th percentile, and low staining is staining in an intensity range below the 25th percentile. In some aspects, one of ordinary skill in the art familiar with a particular staining technique adjusts the size of the bins and defines the staining categories.

[0272] In some embodiments, if more than 50% of the stained cells show strong reactivity, a label of high staining is assigned; if no staining is observed in less than 50% of the stained cells, a label of no staining is assigned; and for all other cases, a label of low staining is assigned.

[0273] In some embodiments, the evaluation and / or scoring of genetic abnormalities or levels of mTOR-related genes in a sample, patient, etc. is performed by one or more experienced clinicians, i.e., clinicians experienced in the staining patterns of mTOR-related gene expression and the products of mTOR-related genes. For example, in some embodiments, the clinician is blinded to the clinical characteristics and outcomes regarding the sample, patient, etc. being evaluated and scored. Abnormal phosphorylation levels

[0274] In some embodiments, mTOR activation abnormalities (e.g., abnormal expression levels or abnormal activity levels) include abnormal protein phosphorylation levels. In some embodiments, the abnormal phosphorylation levels are present in proteins encoded by mTOR-related genes selected from the group consisting of AKT, TSC2, mTOR, PRAS40, S6K, S6, 4EBP1, and SPARC. Exemplary phosphorylation species of mTOR-related genes that can act as related biomarkers include, but are not limited to, AKT S473 phosphorylation, PRAS40 T246 phosphorylation, mTOR S2448 phosphorylation, 4EBP1 T36 phosphorylation, S6K T389 phosphorylation, 4EBP1 T70 phosphorylation, and S6 S235 phosphorylation. In some embodiments, an individual is selected for treatment if a protein in the individual is phosphorylated. In some embodiments, an individual is selected for treatment if a protein in the individual is not phosphorylated. In some embodiments, an individual is selected for treatment based on the phosphorylation levels of one or more proteins encoded by one or more mTOR-related genes. In some embodiments, the phosphorylation state of the protein is determined by immunohistochemistry.

[0275] Abnormal phosphorylation levels of proteins encoded by mTOR-related genes are associated with hyperplasia, including cancer, restenosis, and pulmonary hypertension. For example, high levels (74%) of phosphorylated mTOR expression were found in a human bladder cancer tissue array, and the intensity of phosphorylated mTOR was associated with reduced survival (Hansel DE et al., (2010) Am J Pathol 176:3062-3072).

[0276] In some embodiments, the protein phosphorylation levels of one or more mTOR-related genes are determined. The phosphorylation state of the protein can be evaluated from various sample sources. In some embodiments, the sample is a tumor biopsy. The phosphorylation state of the protein can be evaluated by various methods. In some embodiments, the phosphorylation state is evaluated using immunohistochemistry. The phosphorylation state of the protein can be site-specific. The phosphorylation state of the protein can be compared to a control sample. The control sample can be any one of the control samples described in the previous section for methods involving determination of the expression level or activity level of an mTOR-related gene. In some embodiments, the phosphorylation state is evaluated before the initiation of the treatment method described herein. In some embodiments, the phosphorylation state is evaluated after the initiation of the treatment method described herein. In some embodiments, the phosphorylation state is evaluated before and after the initiation of the treatment method described herein.

[0277] Also provided herein are methods of instructing treatment of hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension) by delivering a sample to a diagnostic laboratory to determine the level of an mTOR-related gene; providing a control sample with a known level of the mTOR-related gene; providing an antibody to a molecule encoded by the mTOR-related gene, or an antibody to a molecule encoded by a target gene downstream of the mTOR-related gene; contacting these samples and the control sample individually with the antibody(s), and / or detecting the relative amount of antibody binding, and presenting a conclusion that a patient should receive treatment by any one of the methods described herein using the level of the sample.

[0278] A method of indicating treatment of hyperplasia (e.g., cancer, restenosis, or pulmonary hypertension), the method further comprising examining or analyzing data related to the state of mTOR activation abnormality (e.g., its presence / absence, or level) in a sample, and presenting a conclusion based on the examination or analysis of the data to an individual such as a healthcare provider or healthcare administrator regarding the likelihood or suitability of an individual to respond to the treatment. In one aspect of the invention, the conclusion is the transmission of data over a network.

[0279] Resistance biomarker Genetic abnormalities and abnormal levels of certain genes may be associated with resistance to the treatment methods described herein. In some embodiments, individuals having an abnormality (e.g., a genetic abnormality or abnormal level) in a resistance biomarker are excluded from treatment methods using the mTOR inhibitor nanoparticles described herein. In some embodiments, the state of a resistance biomarker in combination with one or more states of mTOR activation abnormality is used as a basis for selecting an individual for any one of the treatment methods using the mTOR inhibitor nanoparticles described herein.

[0280] For example, TFE3, also known as a transcription factor that binds to IGHM enhancer 3, TFEA, RCCP2, RCCX1, or bHLHe33, is a transcription factor that specifically recognizes and binds to the MUE3-type E-box sequence in the promoter of a gene. TFE3 promotes the expression of genes downstream of the transforming growth factor beta (TGF-beta) signaling pathway. Translocations of TFE3 are associated with renal cell carcinoma and other cancers. In some embodiments, the nucleic acid sequence of the wild-type TFE3 gene is identified by Genbank accession number NC_000023.11 from nucleotide 49028726 to nucleotide 49043517 of the complementary strand of the X chromosome according to the GRCh38.p2 assembly of the human genome. Exemplary translocations of TFE3 that may be associated with resistance to treatment using the mTOR inhibitor nanoparticles described herein include, but are not limited to, Xp11 translocations such as t(X;1)(p11.2;q21), t(X;1)(p11.2;p34), (X;17)(p11.2;q25.3), and inv(X)(p11.2;q12). Translocations of the TFE3 locus can be evaluated using immunohistochemical methods or fluorescence in-situ hybridization (FISH). Other treatment methods

[0281] One aspect of the present application provides a method and composition for treating muscle-invasive non-invasive bladder cancer (NMIBC, such as BCG-refractory NMIBC), peripheral artery disease (PAD, such as restenotic lesions after revascularization of the superficial femoral artery above or below the knee), and pulmonary arterial hypertension (PAH, such as severe progressive PAH in which the currently available maximal medical therapy is ongoing) in an individual in need thereof, the method comprising administering to the individual an effective amount of a composition comprising nanoparticles comprising an mTOR inhibitor (e.g., a rapamycin drug) and albumin. The individual to be treated may or may not have the mTOR-activating abnormality described above. In some embodiments, the individual is selected for treatment based on having the mTOR-activating abnormality described above. In some embodiments, any of the mTOR-activating abnormalities described above are not used as a basis for selecting an individual for treatment.

[0282] In some embodiments, a method of treating muscle-invasive non-invasive bladder cancer (NMIBC, e.g., BCG-refractory or recurrent NMIBC) in an individual (e.g., a human) includes administering to the individual an effective amount of a composition comprising nanoparticles comprising a rimus drug and albumin, wherein the composition is administered intracystically at a dose of about 100 mg. In some embodiments, a method of treating muscle-invasive non-invasive bladder cancer (NMIBC, e.g., BCG-refractory or recurrent NMIBC) in an individual (e.g., a human) includes administering to the individual an effective amount of a composition comprising nanoparticles comprising a rimus drug and albumin, wherein the composition is administered at a dose of about 100 mg and the composition is administered weekly (e.g., for about 6 weeks). In some embodiments, a method of treating muscle-invasive non-invasive bladder cancer (NMIBC, e.g., BCG-refractory or recurrent NMIBC) in an individual (e.g., a human) includes administering to the individual an effective amount of a composition comprising nanoparticles comprising a rimus drug and albumin, wherein the composition is administered at a dose of about 100 mg and the composition is administered weekly (e.g., for about 6 weeks), and the dose is administered intracystically. In some embodiments, a method of treating muscle-invasive non-invasive bladder cancer (NMIBC, e.g., BCG-refractory or recurrent NMIBC) in an individual (e.g., a human) includes administering to the individual an effective amount of a composition comprising nanoparticles comprising a rimus drug and albumin, wherein the composition is administered at a dose of about 100 mg and the composition is administered weekly (e.g., for about 6 weeks), and the dose is administered intracystically by aseptic urethral catheterization after resection of a visible tumor during cystoscopy. In some embodiments, the composition is retained in the bladder for about 2 hours before urination. In some embodiments, the individual is administered a maintenance dose of the composition about 6 weeks later, and the maintenance dose is administered monthly. In some embodiments, the composition is administered as a single agent. In some embodiments, the composition is administered in combination with a second agent. In some embodiments, the second agent is a chemotherapeutic agent selected from the group consisting of mitomycin C, cisplatin, gemcitabine, valrubicin, and docetaxel. In some embodiments, the second agent is gemcitabine.In some embodiments, the second agent and the nanoparticle composition are administered sequentially. In some embodiments, the second agent and the nanoparticle composition are administered simultaneously. In some embodiments, the second agent and the nanoparticle composition are co-administered. In some embodiments, the nanoparticles in the composition have an average particle size of about 150 nm or less (e.g., about 120 nm or less). In some embodiments, the nanoparticles in the composition comprise a rapamycin drug associated with albumin (e.g., albumin-coated), and these nanoparticles have an average particle size of about 150 nm or less (e.g., about 120 nm or less). In some embodiments, the nanoparticles in the composition comprise sirolimus associated with human albumin (e.g., human albumin-coated). The nanoparticles have an average particle size of about 150 nm or less (e.g., about 120 nm or less, e.g., about 100 nm), and the weight ratio of human albumin to sirolimus in the composition is about 9:1 or less (e.g., about 9:1 or about 8:1). In some embodiments, the composition comprises Nab-sirolimus. In some embodiments, the composition is Nab-sirolimus.

[0283] In some embodiments, a method of treating non-muscle-invasive bladder cancer (NMIBC, e.g., BCG-unresponsive or recurrent NMIBC) in an individual (e.g., a human) comprising administering to the individual an effective amount of a composition comprising nanoparticles comprising a rimus drug and albumin, wherein the composition is administered intracystically at a dose of about 100 mg, and wherein the composition is administered twice a week (e.g., for about 6 weeks) is provided. In some embodiments, a method of treating non-muscle-invasive bladder cancer (NMIBC, e.g., BCG-unresponsive or recurrent NMIBC) in an individual (e.g., a human) comprising administering to the individual an effective amount of a composition comprising nanoparticles comprising a rimus drug and albumin, wherein the composition is administered at a dose of about 100 mg, and wherein the composition is administered twice a week (e.g., for about 6 weeks), and wherein the dose is administered intracystically is provided. In some embodiments, a method of treating non-muscle-invasive bladder cancer (NMIBC, e.g., BCG-unresponsive or recurrent NMIBC) in an individual (e.g., a human) comprising administering to the individual an effective amount of a composition comprising nanoparticles comprising a rimus drug and albumin, wherein the composition is administered at a dose of about 100 mg, and wherein the composition is administered twice a week (e.g., for about 6 weeks), and wherein the composition is administered intracystically by sterile urethral catheterization after resection of visible tumors during cystoscopy is provided. In some embodiments, the composition is retained in the bladder for about 2 hours prior to urination. In some embodiments, the individual is administered a maintenance dose of the composition about 6 weeks later, and the maintenance dose is administered monthly. In some embodiments, the composition is administered as a single agent. In some embodiments, the composition is administered in combination with a second agent. In some embodiments, the second agent is a chemotherapeutic agent selected from the group consisting of mitomycin C, cisplatin, gemcitabine, valrubicin, and docetaxel. In some embodiments, the second agent is gemcitabine. In some embodiments, the second agent and the nanoparticle composition are administered sequentially. In some embodiments, the second agent and the nanoparticle composition are administered simultaneously. In some embodiments, the second agent and the nanoparticle composition are co-administered. In some embodiments, the nanoparticles in the composition have an average particle size of about 150 nm or less (e.g., about 120 nm or less).In some embodiments, the nanoparticles in the composition comprise a rapamycin drug associated with (e.g., coated with) albumin, and these nanoparticles have an average particle size of about 150 nm or less (e.g., about 120 nm or less). In some embodiments, the nanoparticles in the composition comprise sirolimus associated with (e.g., coated with) human albumin, the nanoparticles have an average particle size of about 150 nm or less (e.g., about 120 nm or less, e.g., about 100 nm), and the weight ratio of human albumin to sirolimus in the composition is about 9:1 or less (e.g., about 9:1 or about 8:1). In some embodiments, the composition comprises Nab-sirolimus. In some embodiments, the composition is Nab-sirolimus.

[0284] In some embodiments, a method of treating muscle-invasive bladder cancer (NMIBC, e.g., BCG-refractory or recurrent NMIBC) in an individual (e.g., a human) comprising administering to the individual an effective amount of a composition comprising nanoparticles comprising a rimus drug and albumin, wherein the composition is administered intracellularly at a dose of about 300 mg, is provided. In some embodiments, a method of treating muscle-invasive bladder cancer (NMIBC, e.g., BCG-refractory or recurrent NMIBC) in an individual (e.g., a human) comprising administering to the individual an effective amount of a composition comprising nanoparticles comprising a rimus drug and albumin, wherein the composition is administered at a dose of about 300 mg, and wherein the composition is administered weekly (e.g., for about 6 weeks), is provided. In some embodiments, a method of treating muscle-invasive bladder cancer (NMIBC, e.g., BCG-refractory or recurrent NMIBC) in an individual (e.g., a human) comprising administering to the individual an effective amount of a composition comprising nanoparticles comprising a rimus drug and albumin, wherein the composition is administered at a dose of about 300 mg, and wherein the composition is administered weekly (e.g., for about 6 weeks), and wherein the dose is administered intravesically, is provided. In some embodiments, a method of treating muscle-invasive bladder cancer (NMIBC, e.g., BCG-refractory or recurrent NMIBC) in an individual (e.g., a human) comprising administering to the individual an effective amount of a composition comprising nanoparticles comprising a rimus drug and albumin, wherein the composition is administered at a dose of about 300 mg, and wherein the composition is administered weekly (e.g., for about 6 weeks), and wherein the dose is administered intravesically by sterile urethral catheterization after resection of visible tumors during cystoscopy, is provided. In some embodiments, the composition is retained in the bladder for about 2 hours before urination. In some embodiments, the individual is administered a maintenance dose of the composition about 6 weeks later, and the maintenance dose is administered monthly. In some embodiments, the composition is administered as a single agent. In some embodiments, the composition is administered in combination with a second agent. In some embodiments, the second agent is a chemotherapeutic agent selected from the group consisting of mitomycin C, cisplatin, gemcitabine, valrubicin, and docetaxel. In some embodiments, the second agent is gemcitabine.In some embodiments, the second agent and the nanoparticle composition are administered sequentially. In some embodiments, the second agent and the nanoparticle composition are administered simultaneously. In some embodiments, the second agent and the nanoparticle composition are co-administered. In some embodiments, the nanoparticles in the composition have an average particle size of about 150 nm or less (e.g., about 120 nm or less). In some embodiments, the nanoparticles in the composition comprise a rapamycin drug associated with albumin (e.g., coated with albumin), and these nanoparticles have an average particle size of about 150 nm or less (e.g., about 120 nm or less). In some embodiments, the nanoparticles in the composition comprise sirolimus associated with human albumin (e.g., coated with human albumin), the nanoparticles have an average particle size of about 150 nm or less (e.g., about 120 nm or less, e.g., about 100 nm), and the weight ratio of human albumin to sirolimus in the composition is about 9:1 or less (e.g., about 9:1 or about 8:1). In some embodiments, the composition comprises Nab-sirolimus. In some embodiments, the composition is Nab-sirolimus.

[0285] In some embodiments, a method of treating muscle-invasive bladder cancer (NMIBC, e.g., BCG-refractory or recurrent NMIBC) in an individual (e.g., a human) includes administering to the individual an effective amount of a composition comprising nanoparticles comprising a rimus drug and albumin, wherein the composition is administered intracellularly at a dose of about 200 mg. In some embodiments, a method of treating muscle-invasive bladder cancer (NMIBC, e.g., BCG-refractory or recurrent NMIBC) in an individual (e.g., a human) includes administering to the individual an effective amount of a composition comprising nanoparticles comprising a rimus drug and albumin, wherein the composition is administered at a dose of about 200 mg, and wherein the composition is administered twice a week (e.g., for about 6 weeks). In some embodiments, a method of treating muscle-invasive bladder cancer (NMIBC, e.g., BCG-refractory or recurrent NMIBC) in an individual (e.g., a human) includes administering to the individual an effective amount of a composition comprising nanoparticles comprising a rimus drug and albumin, wherein the composition is administered at a dose of about 200 mg, and wherein the composition is administered twice a week (e.g., for about 6 weeks), and wherein the dose is administered intravesically. In some embodiments, a method of treating muscle-invasive bladder cancer (NMIBC, e.g., BCG-refractory or recurrent NMIBC) in an individual (e.g., a human) includes administering to the individual an effective amount of a composition comprising nanoparticles comprising a rimus drug and albumin, wherein the composition is administered at a dose of about 200 mg, and wherein the composition is administered twice a week (e.g., for about 6 weeks), and wherein the dose is administered intravesically by aseptic urethral catheterization after resection of a visible tumor during cystoscopy. In some embodiments, the composition is retained in the bladder for about 2 hours before urination. In some embodiments, the individual is administered a maintenance dose of the composition about 6 weeks later, and the maintenance dose is administered monthly. In some embodiments, the composition is administered as a single agent. In some embodiments, the composition is administered in combination with a second agent. In some embodiments, the second agent is a chemotherapeutic agent selected from the group consisting of mitomycin C, cisplatin, gemcitabine, valrubicin, and docetaxel. In some embodiments, the second agent is gemcitabine.In some embodiments, the second agent and the nanoparticle composition are administered sequentially. In some embodiments, the second agent and the nanoparticle composition are administered simultaneously. In some embodiments, the second agent and the nanoparticle composition are co-administered. In some embodiments, the nanoparticles in the composition have an average particle size of about 150 nm or less (e.g., about 120 nm or less). In some embodiments, the nanoparticles in the composition comprise a rapamycin drug associated with albumin (e.g., albumin-coated), and these nanoparticles have an average particle size of about 150 nm or less (e.g., about 120 nm or less). In some embodiments, the nanoparticles in the composition comprise sirolimus associated with human albumin (e.g., human albumin-coated), the nanoparticles have an average particle size of about 150 nm or less (e.g., about 120 nm or less, e.g., about 100 nm), and the weight ratio of human albumin to sirolimus in the composition is about 9:1 or less (e.g., about 9:1 or about 8:1). In some embodiments, the composition comprises Nab-sirolimus. In some embodiments, the composition is Nab-sirolimus.

[0286] In some embodiments, a method of treating muscle-invasive bladder cancer (NMIBC, e.g., BCG-unresponsive or recurrent NMIBC) in an individual (e.g., a human) is provided, the method comprising administering to the individual an effective amount of a composition comprising nanoparticles comprising a rimus drug and albumin, wherein the composition is administered intravesicularly at a dose of about 400 mg. In some embodiments, a method of treating muscle-invasive bladder cancer (NMIBC, e.g., BCG-unresponsive or recurrent NMIBC) in an individual (e.g., a human) is provided, the method comprising administering to the individual an effective amount of a composition comprising nanoparticles comprising a rimus drug and albumin, wherein the composition is administered at a dose of about 400 mg and the composition is administered weekly (e.g., for about 6 weeks). In some embodiments, a method of treating muscle-invasive bladder cancer (NMIBC, e.g., BCG-unresponsive or recurrent NMIBC) in an individual (e.g., a human) is provided, the method comprising administering to the individual an effective amount of a composition comprising nanoparticles comprising a rimus drug and albumin, wherein the composition is administered at a dose of about 400 mg, the composition is administered weekly (e.g., for about 6 weeks), and the dose is administered intravesicularly. In some embodiments, a method of treating muscle-invasive bladder cancer (NMIBC, e.g., BCG-unresponsive or recurrent NMIBC) in an individual (e.g., a human) is provided, the method comprising administering to the individual an effective amount of a composition comprising nanoparticles comprising a rimus drug and albumin, wherein the composition is administered at a dose of about 400 mg, the composition is administered weekly (e.g., for about 6 weeks), and the dose is administered intravesicularly by aseptic urethral catheterization after resection of visible tumors during cystoscopy. In some embodiments, the composition is retained in the bladder for about 2 hours before urination. In some embodiments, the individual is administered a maintenance dose of the composition about 6 weeks later, and the maintenance dose is administered monthly. In some embodiments, the composition is administered as a single agent. In some embodiments, the composition is administered in combination with a second agent. In some embodiments, the second agent is a chemotherapeutic agent selected from the group consisting of mitomycin C, cisplatin, gemcitabine, valrubicin, and docetaxel. In some embodiments, the second agent is gemcitabine.In some embodiments, the second agent and the nanoparticle composition are administered sequentially. In some embodiments, the second agent and the nanoparticle composition are administered simultaneously. In some embodiments, the second agent and the nanoparticle composition are co-administered. In some embodiments, the nanoparticles in the composition have an average particle size of about 150 nm or less (e.g., about 120 nm or less). In some embodiments, the nanoparticles in the composition comprise a rapamycin drug associated with albumin (e.g., coated with albumin), and these nanoparticles have an average particle size of about 150 nm or less (e.g., about 120 nm or less). In some embodiments, the nanoparticles in the composition comprise sirolimus associated with human albumin (e.g., coated with human albumin), the nanoparticles have an average particle size of about 150 nm or less (e.g., about 120 nm or less, e.g., about 100 nm), and the weight ratio of human albumin to sirolimus in the composition is about 9:1 or less (e.g., about 9:1 or about 8:1). In some embodiments, the composition comprises Nab-sirolimus. In some embodiments, the composition is Nab-sirolimus.

[0287] In some embodiments, provided is a method of treating muscle-invasive bladder cancer (NMIBC, e.g., BCG-refractory or recurrent NMIBC) in an individual (e.g., a human), the method comprising administering to the individual an effective amount of a composition comprising Nab-sirolimus, wherein the composition is administered intracystically at a dose of about 100 mg. In some embodiments, provided is a method of treating muscle-invasive bladder cancer (NMIBC, e.g., BCG-refractory or recurrent NMIBC) in an individual (e.g., a human), the method comprising administering to the individual an effective amount of a composition comprising Nab-sirolimus, wherein the composition is administered at a dose of about 100 mg and wherein the composition is administered weekly (e.g., for about 6 weeks). In some embodiments, provided is a method of treating muscle-invasive bladder cancer (NMIBC, e.g., BCG-refractory or recurrent NMIBC) in an individual (e.g., a human), the method comprising administering to the individual an effective amount of a composition comprising Nab-sirolimus, wherein the composition is administered at a dose of about 100 mg and wherein the composition is administered weekly (e.g., for about 6 weeks) and wherein the dose is administered intracystically. In some embodiments, provided is a method of treating muscle-invasive bladder cancer (NMIBC, e.g., BCG-refractory or recurrent NMIBC) in an individual (e.g., a human), the method comprising administering to the individual an effective amount of a composition comprising Nab-sirolimus, wherein the composition is administered at a dose of about 100 mg and wherein the composition is administered weekly (e.g., for about 6 weeks) and wherein the dose is administered intracystically by sterile urethral catheterization after resection of visible tumors during cystoscopy. In some embodiments, the composition is retained in the bladder for about 2 hours before urination. In some embodiments, the individual is administered a maintenance dose of the composition about 6 weeks later, and the maintenance dose is administered monthly. In some embodiments, the composition is administered as a single agent. In some embodiments, the composition is administered in combination with a second agent. In some embodiments, the second agent is a chemotherapeutic agent selected from the group consisting of mitomycin C, cisplatin, gemcitabine, valrubicin, and docetaxel. In some embodiments, the second agent is gemcitabine. In some embodiments, the second agent and the nanoparticle composition are administered sequentially.In some embodiments, the second agent and the nanoparticle composition are administered simultaneously. In some embodiments, the second agent and the nanoparticle composition are co-administered.

[0288] In some embodiments, a method of treating muscle-invasive non-invasive bladder cancer (NMIBC, e.g., BCG-resistant or recurrent NMIBC) in an individual (e.g., a human) includes administering to the individual an effective amount of a composition comprising Nab-sirolimus, the composition being administered intracystically at a dose of about 100 mg, the composition being administered twice a week (e.g., for about 6 weeks). In some embodiments, a method of treating muscle-invasive non-invasive bladder cancer (NMIBC, e.g., BCG-resistant or recurrent NMIBC) in an individual (e.g., a human) includes administering to the individual an effective amount of a composition comprising Nab-sirolimus, the composition being administered at a dose of about 100 mg, the composition being administered twice a week (e.g., for about 6 weeks), the dose being administered intravesically. In some embodiments, a method of treating muscle-invasive non-invasive bladder cancer (NMIBC, e.g., BCG-resistant or recurrent NMIBC) in an individual (e.g., a human) includes administering to the individual an effective amount of a composition comprising nanoparticles comprising Nab-sirolimus, the composition being administered at a dose of about 100 mg, the composition being administered twice a week (e.g., for about 6 weeks), the dose being administered intravesically by sterile urethral catheterization after resection of visible tumors during cystoscopy. In some embodiments, the composition is retained in the bladder for about 2 hours before urination. In some embodiments, the individual is administered a maintenance dose of the composition about 6 weeks later, the maintenance dose being administered monthly. In some embodiments, the composition is administered as a single agent. In some embodiments, the composition is administered in combination with a second agent. In some embodiments, the second agent is a chemotherapeutic agent selected from the group consisting of mitomycin C, cisplatin, gemcitabine, valrubicin, and docetaxel. In some embodiments, the second agent is gemcitabine. In some embodiments, the second agent and the nanoparticle composition are administered sequentially. In some embodiments, the second agent and the nanoparticle composition are administered simultaneously. In some ...

Claims

1. 1. A method of treating hyperplasia in an individual, comprising administering to the individual an effective amount of a composition comprising nanoparticles comprising an mTOR inhibitor and albumin, wherein the individual is selected for treatment based on having an mTOR-activated abnormality.

2. 10. The method of claim 1, further comprising evaluating the individual for an mTOR activation abnormality.

3. 1. A method of selecting an individual having hyperplasia for treatment with a composition comprising nanoparticles comprising an mTOR inhibitor and albumin, comprising: (1) assessing an mTOR activation abnormality in the individual; (2) assessing the individual for treatment based on the individual having the mTOR activation abnormality. Steps to choose from A method comprising:

4. 4. The method of claim 3, further comprising administering to the selected individual the composition comprising nanoparticles comprising an mTOR inhibitor and albumin.

5. 5. The method of any one of claims 1 to 4, wherein the hyperplasia is selected from the group consisting of cancer, restenosis, and pulmonary hypertension.

6. 6. The method of claim 5, wherein the cancer is selected from the group consisting of pancreatic neuroendocrine cancer, endometrial cancer, breast cancer, renal cell carcinoma, lymphangioleiomyosarcoma (LAM), prostate cancer, lymphoma, bladder cancer, endometrial cancer, and ovarian cancer.

7. The method of any one of claims 1 to 6, wherein the mTOR activation abnormality comprises a mutation in an mTOR-associated gene.

8. The method of claim 7, wherein the mTOR activation abnormality comprises a copy number polymorphism of an mTOR-associated gene.

9. The method of claim 7 or claim 8, wherein the mTOR activation abnormality is assessed by gene sequencing.

10. The method of claim 9, wherein the gene sequencing is based on sequencing DNA in a tumor sample.

11. 10. The method of claim 9, wherein the gene sequencing is based on sequencing of circulating DNA or cell-free DNA isolated from a blood sample.

12. 12. The method of any one of claims 1 to 11, wherein the mTOR activation abnormality comprises an abnormal expression level of an mTOR-associated gene.

13. 12. The method of any one of claims 1 to 11, wherein the mTOR activation abnormality comprises an abnormal phosphorylation level of a protein encoded by the mTOR-associated gene.

14. The method of claim 13, wherein the mTOR activation abnormality comprises an abnormal phosphorylation level of a protein encoded by an mTOR-associated gene selected from the group consisting of AKT, S6K, S6, 4EBP1, and SPARC.

15. The method of claim 13 or claim 14, wherein the abnormal phosphorylation level is determined by immunohistochemistry.

16. 16. The method of any one of claims 1 to 15, wherein the mTOR activation abnormality comprises an abnormal activity level of an mTOR-associated gene.

17. The method of any one of claims 1 to 16, wherein the mTOR activation abnormality results in activation of mTORC1.

18. 18. The method of any one of claims 1 to 17, wherein the mTOR activation abnormality results in activation of mTORC2.

19. 19. The method of any one of claims 1 to 18, wherein the mTOR activation abnormality is an abnormality in at least one mTOR-related gene selected from the group consisting of AKT1, FLT3, MTOR, PIK3CA, PIK3CG, TSC1, TSC2, RHEB, STK11, NF1, NF2, PTEN, TP53, FGFR4, KRAS, NRAS, and BAP1.

20. 20. The method of claim 19, wherein the at least one mTOR associated gene comprises MTOR.

21. 21. The method of claim 20, wherein the mTOR activating abnormality comprises an activating mutation of MTOR.

22. 20. The method of claim 19, wherein the at least one mTOR associated gene comprises TSC1 or TSC2.

23. 23. The method of claim 22, wherein the mTOR activation abnormality comprises loss of heterozygosity in TSC1 or TSC2.

24. 23. The method of claim 22, wherein the mTOR activation abnormality comprises a loss-of-function mutation in TSC1 or TSC2.

25. 20. The method of claim 19, wherein the at least one mTOR associated gene comprises RHEB.

26. 26. The method of claim 25, wherein the mTOR activation abnormality comprises a loss-of-function mutation in RHEB.

27. 20. The method of claim 19, wherein the at least one mTOR associated gene comprises NF1.

28. 28. The method of claim 27, wherein the mTOR activation abnormality comprises a loss-of-function mutation in NF1.

29. 20. The method of claim 19, wherein the at least one mTOR associated gene comprises NF2.

30. 30. The method of claim 29, wherein the mTOR activation abnormality comprises a loss-of-function mutation in NF2.

31. 20. The method of claim 19, wherein the mTOR-associated gene comprises PTEN.

32. The method of claim 31 , wherein the mTOR activation abnormality comprises a deficiency of PTEN.

33. 20. The method of claim 19, wherein the mTOR-associated gene comprises PIK3CA.

34. 34. The method of claim 33, wherein the mTOR activation abnormality comprises a loss-of-function mutation in PIK3CA.

35. 20. The method of claim 19, wherein the mTOR-associated gene comprises PIK3CG.

36. 36. The method of claim 35, wherein the mTOR activation abnormality comprises a loss-of-function mutation in PIK3CG.

37. 20. The method of claim 19, wherein the mTOR-associated gene comprises AKT1.

38. 38. The method of claim 37, wherein the mTOR activation abnormality comprises an activating mutation of AKT1.

39. 20. The method of claim 19, wherein the mTOR-associated gene comprises TP53.

40. 40. The method of claim 39, wherein the mTOR activation abnormality comprises a loss-of-function mutation in TP53.

41. 41. The method of any one of claims 1 to 40, wherein the mutation status of TFE3 is further used as a basis for selecting the individual.

42. 42. The method of claim 41 , wherein the mutation status of TFE3 comprises a translocation of TFE3.

43. 43. The method of any one of claims 1 to 42, further comprising administering to the individual an effective amount of a second therapeutic agent.

44. 44. The method of any one of claims 1 to 43, wherein the individual is a human.

45. 45. The method of any one of claims 1-44, wherein the composition comprises nanoparticles comprising the mTOR inhibitor and the albumin is administered intravenously.

46. 45. The method of any one of claims 1 to 44, wherein the composition comprises nanoparticles comprising the mTOR inhibitor and the albumin is administered subcutaneously.

47. 47. The method of any one of claims 1 to 46, wherein the nanoparticles in the composition comprise the mTOR inhibitor in association with the albumin.

48. 48. The method of any one of claims 1 to 47, wherein the nanoparticles in the composition have an average diameter of about 150 nm or less.

49. 49. The method of any one of claims 1 to 48, wherein the ratio of said mTOR inhibitor to said albumin in said nanoparticles is from about 1:1 to about 9:

1.

50. 50. The method of any one of claims 1 to 49, wherein the albumin is human serum albumin.

51. 51. The method of any one of claims 1 to 50, wherein the mTOR inhibitor is a limus drug.

52. 52. The method of claim 51, wherein the limus drug is sirolimus.

53. The dosage of the mTOR inhibitor in the composition is about 10 mg / m ２ ~Approx. 100mg / m ２ 53. The method of any one of claims 1 to 52, wherein

54. A kit comprising: 1) a composition comprising nanoparticles comprising an mTOR inhibitor and albumin; and 2) an agent for assessing an mTOR-activated abnormality.

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