WO2007136822A2 - Methods to diagnose non-alcoholic steatohepatitis - Google Patents

Abstract

This invention relates, e.g., to a method to distinguish NASH (non-alcoholic steatohepatitis) from non-NASH types of NAFLD (non-alcoholic fatty liver disease), comprising (a) determining the phosphorylation state of one or more members of the AKT/mTOR/IRS pathway (e.g., IRS-1 (S612), AKT (S308), FKHR (T24), FKHRL (T32), GSK3 (S21/9), EIF4G (S1108), SHC (Y317), PKC-delta (T505), PKA (T197), CREB (S133), and/or FAK (Y397) in adipose tissue from a subject, wherein a significantly altered level of phosphorylation of the one or more members compared to a suitable reference standard indicates that the subject is likely to have NASH; and/or (b) determining the phosphorylation state of FAK (focal adhesion kinase) in adipose tissue from a subject, wherein a significantly increased level of phosphorylation in FAK compared to a suitable reference standard indicates that the subject is likely to have NASH. Treatment modalities based on this diagnostic method, and kits for carrying out a diagnostic method or a treatment method are also disclosed.

Description

LIVER DISEASE DIAGNOSTIC USING AKT/mTOR/IRS PATHWAY ACTIVATION

STATE IN FAT CELLS

This application claims the benefit of the filing date of U.S. Provisional applications 60/747,750, filed May 19, 2006, and 60/914,533, filed April 27, 2007, both of which are incorporated by reference herein in their entireties.

BACKGROUND INFORMATION

In fatty liver, fat accumulates in the liver cells. Simple fatty liver usually does not damage the liver, but is a condition that can be identified by taking a sample of liver tissue (liver biopsy) and examining it under a microscope. Simple fatty liver is not associated with any other liver abnormalities such as scarring or inflammation. It is a common finding in patients who are very overweight or have diabetes mellitus. Alcoholism can also result in inflammation of the liver (alcoholic hepatitis) and/or scarring (alcoholic cirrhosis); it can be differentiated from non- alcoholic liver inflammation by patient history. Possible explanations for fatty liver include the transfer of fat from other parts of the body, or an increase in the extraction of fat presented to the liver from the intestine. Another explanation is that the fat accumulates because the liver is unable to change it into a form that can be eliminated.

Non-alcoholic fatty liver disease (NAFLD) is an important cause of chronic liver disease worldwide. NAFLD is strongly associated with metabolic syndrome and insulin resistance and its prevalence is on the rise. NAFLD represent a spectrum ranging from simple steatosis (SS) to non-alcoholic steatohepatitis (NASH). Accumulating evidence suggests that NASH is potentially progressive, whereas simple steatosis, indicated by liver biopsies, follows a more benign course with little or no progression. NASH is described as inflammation of the liver associated with the accumulation of fat in the liver, and it differs significantly from the simple accumulation of fat in the liver (fatty Hver, or hepatic steatosis) in that the inflammation causes significant damage to the liver cells while simple fatty liver probably does not.

To diagnose NASH versus other forms of NAFLD, which is a critical clinical problem, a physician generally first eliminates other possible causes of chronic liver disease, especially alcohol abuse. Images of the liver obtained by an ultrasound test, a computed tomography (CT) scan, or a magnetic resonance imaging (MRI) scan, can suggest the presence of a fatty liver. However, the diagnosis must be confirmed. Currently, the confirmation is performed on a liver biopsy, a procedure in which a physician inserts a needle into the liver and extracts a sample of tissue, which is examined under a microscope. In NASH, which resembles alcoholic steatohepatitis, the inflammation of the liver is associated with an increase of fat deposits and typically occurs in middle-aged, overweight, and often diabetic patients who do not drink alcohol. It has also been connected with rapid weight loss, or in women taking hormones (estrogen). The fatty tissue in the liver may break up liver cells (steatonecrosis) and the patient may develop cirrhosis (scarring of the liver). Recent studies indicate that NASH can result in the development of fibrous tissue in the liver (fibrosis) in up to 40% of patients or cirrhosis in 5- 10% of patients. It is not certain why some NASH patients will progress to this serious form of chronic liver disease while others do not. Studies report that the progression to fibrosis or cirrhosis for NASH patients is variable but can occasionally occur in less than 20 years. Some studies have shown that 20% to 40% of people who are grossly overweight will develop NASH. If a patient is grossly overweight, however, it does not mean that he/she will develop NASH. Thus, there is significant clinical importance in identifying a diagnostic for NASH vs non- NASH forms of NAFLD, as well as identifying new therapeutic targets for NASH treatment strategies. Proteomics profiling is an attractive option among the available high-throughput technologies because almost all drugs target proteins. The profile of intracellular signaling events revealed by proteomics technology can help define pathways involved in the pathogenesis of NAFLD. Additionally, proteomics assays provide effective recapitulation of the post-translational and fluctuating phosphorylati on-driven signaling events that occur at the proteome level. Phosphorylation events in kinase-driven signal networks are particularly important for identifying disease pathogenesis and therapeutic targets.

In the past, it has been difficult to measure and quantify protein phosphorylation in cells and tissue specimens because of the transient nature of phosphorylation and the need for enzymatically based systems. Recently, however, antibodies have been developed that specifically recognize the phosphorylated isoform of cell signaling proteins, providing a means of directly assessing the state of activation of any signaling protein. Applying these antibodies to protein microarray platforms provides an opportunity to profile the ongoing cellular signaling pathway network within small numbers of human cells obtained by biopsy. A new type of protein microarray, the reverse-phase protein microarray (RPA), is particularly useful for such studies. One can isolate pure cell populations from hundreds of biopsy specimens, followed by spotting a protein lysate onto a suitable surface, such as a nitrocellulose-coated slide. Each array can then be incubated with one detection protein, such as an antibody, and a single analyte endpoint measured and directly compared across multiple samples. DESCRIPTION OF THE DRAWINGS

Figure 1 shows unsupervised molecular network analysis of cell signaling pathways. Baysean two-way clustering of endpoints (X-axis) and patients (Y-axis) is shown as a heatmap where degree of relative levels of phosphorylation are shown in medium grey, indicating the highest relative level of phosphorylation within the study set, light grey, the lowest relative level, and black indicating the median relative level. Three major clusters were formed, none of which correspond to liver disease pathology, and generally differed by degree of broad pathway activation. Cluster 1 contained patients with generally indolent adipocyte signaling, cluster 2 contained patients with generally broad signaling activation, and cluster 3 with a mixed phenotype. The ability of the RPA and clustering to faithfully recapitulate ongoing kinase driven signaling is demonstrated in the magnified box at the left, where the MEK-ERK pathway segregated into a unique family set. This clustering occurred without a priori training.

Figure 2 shows an analysis of specific signaling endpoints in adipose tissue taken from patients with progressive vs non-progressive NAFLD. Fig. 2A is a histogram that shows relative levels of phosphorylation of each of the signaling endpoints. Statistical significant differences (P < 0.001) between NASH and SS with or without NSI was seen with phosphorylation of FKHR (denoted by asterisk). Figure 2B shows an Rsquare partition plot of the most statistically significant phosphorylation endpoints obtained by analysis of adipose tissue taken from 14 obese patients with NASH vs 56 obese subjects with steatosis and underlying inflammation Fig. 2C shows a decision tree partition analysis of adipose tissue taken these same subjects and reveals that patients with NASH, the progressive form of NAFLD, can be distinguished from non-progressive forms of NAFLD (steatosis and inflammation) using a combination of a limited number of specific phosphoprotein measurements in white adipose tissue.

Figure 3 shows a pathway schematic of insulin signaling. A stylized representation of insulin- driven signaling within a cell is shown along with specific individual phosphorylated and signaling components of the pathway that were identified as differentially phosphorylated in progressive (NASH) vs non-progressive (steatosis with or without NSI) NAFLD in our study set (darkly outlined boxes).

Figure 4 shows a partition analysis of NAFLD vs obese controls. Figure 4A shows an Rsquare partition plot of the most statistically significant phosphorylation endpoints obtained by analysis of adipose tissue taken from 14 obese patients with NASH vs 29 obese subjects without any underlying liver disease, NAPLD, steatosis or underlying inflammation Fig. 4B shows a decision tree partition analysis of adipose tissue taken these same subjects and reveals that patients with NASH, the progressive form of NAFLD, can be distinguished from obese controls without underlying disease using a combination of a limited number of specific phosphoprotein measurements in white adipose tissue.

Figure 5 shows a partition analysis of simple steatosis vs obese controls. Fig. 5A shows an

Rsquare partition plot of the most statistically significant phosphorylation endpoints obtained by analysis of adipose tissue taken from 29 obese controls without underlying liver disease and 10 subjects with simple steatosis. Fig. 5B shows a decision tree partition representation of this plot.

DESCRIPTION OF THE INVENTION

The present invention relates, for example, to the identification of specific markers and signal transduction pathways that can be used to distinguish between subjects having NASH (non-alcoholic steatohepatitis), which is often a progressive form of liver disease, and subjects having non-NASH forms of NAPLD (non-alcoholic fatty liver disease), which are nonprogressive. Non-NASH forms of NAFLD include, e.g., simple steatosis (SS), with or without inflammation.

The inventors employed reverse phase protein microarray (RPA) technology to profile signaling events in adipose tissue from human patients with various forms of NAFLD and a matched group of obese controls. This multiplexed cell signaling analysis identified changes in specific signaling pathways active in adipose tissue in patients having various subtypes of

NAFLD. This analysis provided new biomarkers and therapeutic targets for disease mitigation.

The inventors report herein, e.g., the analysis of 54 different kinase substrates. Cell signaling endpoints revealed that an insulin signaling pathway is deranged in different locations in NAFLD patients. Furthermore, components of insulin receptor-mediated signaling differentiate most of the conditions on the NAFLD spectrum. For example, PKA and AKT/mTOR pathway derangement accurately discriminates patients with NASH from the nonprogressive forms of NAFLD. Furthermore, PKC delta, AKT, and SHC phosphorylation changes occur in patients with simple steatosis. Amounts of the FKHR phosphorylated at S256 residue were significantly correlated with AST/ ALT ratio in all morbidly obese patients. Furthermore, amounts of cleaved caspase 9 and pp90RSK S380 were positively correlated in patients with NASH. Thus, specific insulin pathway signaling events are altered in the adipose tissue of patients with NASH compared to patients with the non-progressive forms of NAFLD. The measurement of phosphorylation levels of such phospho-endpoints compared to suitable controls, reference standards, or known patterns of phosphorylation for subjects having NASH, form the basis of a method to distinguish NASH from non-NASH forms of NAFLD (e.g., non-progressive forms of NAFLD). The pathways identified are complex and involve a variety of forms of feedback inhibition. Thus, the particular proteins identified herein whose level of phosphorylation is increased or decreased in NASH compared to non-NASH forms of NAFLD was unpredictable and unexpected.

Furthermore, this analysis can identify new targets for the therapeutic treatment of NASH. This is now referred to as a "theranostic"- where the measured analytes serve both as a diagnostic as well as a therapeutic target. A current example of this is e-erbB2. This protein, a member of the EGF receptor family, is measured in breast cancer patients as a diagnostic endpoint for patients with poor prognosis, but is a drug target itself— for HERCEPTIN. Thus it serves to stratify and target therapy.

Advantages of a diagnostic method of the invention include that it is rapid, accurate and, importantly, is non- invasive. In addition to the elucidation of appropriate drug treatments, the diagnostic method of the invention, applied to fat biopsies from accessible sites, can be used to guide dietary, endocrine or supplement (vitamin) therapy, and exercise therapy for patients with metabolic syndrome, liver disease, diabetes, or other disorders.

The present invention provides, e.g., methods and kits for diagnosing NASH

(distinguishing NASH from non-NASH forms of NAFLD) in a subject in need thereof, and for identifying targets for the treatment of NASH, based on assessing the phosphorylation state (activation state) of one or more members of the AKT/mTOR/IRS signaling pathway and/or of FAK. One aspect of the invention is a method to distinguish NASH (nonalcoholic steatohepatitis) from non-NASH forms of NAFLD (non-alcoholic fatty liver disease (NAFLD), including simple steatosis (SS), with or without inflammation), in a subject in need thereof. The method comprises determining the amount of phosphorylation (the phosphorylation state) of one or more members of the AKT/mTOR/IRS pathway (e.g. IRS-I (S612), AKT (S308), FKHR (T24), FKHRL (T32), GSK3 (S21/9), EIF4G (Sl 108), SHC (Y317), PKC-delta (T505), PKA (T197) or CREB (S 133)) in adipose tissue from the subject. A significantly reduced level of phosphorylation of one or more of IRS-l (S612), AKT (S308), FKHR (T24), FKHRL (T32), GSK3 (S21/9), EIF4G (Sl 108), SHC (Y317) and/or PKC-delta (T505) compared to a positive reference standard, or a level that is statistically the same as a negative reference standard, indicates that the subject is likely to have NASH. A significantly increased level of phosphorylation of one or both of PKA (T197) or CREB (S133) compared to a negative reference standard, or statistically the same level compared to a positive reference standard, indicates that the subject is likely to have NASH. In embodiments of the method, at least about 2 of these 10 markers exhibit significantly altered levels of phosphorylation compared to a suitable reference standard; at least about 4 of these 10 markers exhibits significantly altered levels of phosphorylation compared to a suitable reference standard; at least about 7 of the markers exhibit significantly altered levels of phosphorylation; or about 10 of the markers exhibit significantly altered levels of phosphorylation. "About," as used herein, refers to plus or minus 10-20%. Thus, "about 4" includes 3-5, and "about 7" includes 6-8.

Another aspect of the invention is a method as above, which further comprises determining the amount of phosphorylation of one or more additional members of the AKT/mTOR/IRS pathway (e.g., AMPK, P70S6, LKB, SGK, BAD), wherein a significantly altered level of phosphorylation compared to a suitable (positive or negative) reference standard indicates that the subject is likely to have NASH.

Another aspect of the invention is a method to distinguish NASH (nonalcoholic •steatohepatitis) from non-NASH forms of NAFLD (non-alcoholic fatty liver disease (NAFLD), including simple steatosis (SS), with or without inflammation), in a subject in need thereof, comprising determining the amount of phosphorylation (the phosphorylation state) of FAK (focal adhesion kinase (Y397)) in adipose tissue from a subject, wherein a significantly increased level of phosphorylation of FAK (Y397) compared to a negative reference standard, or statistically the same level compared to a positive reference standard, indicates that the subject is likely to have NASH. Another aspect of the invention is a method to distinguish NASH (non-alcoholic steatohepatitis) from other forms of NAFLD (non-alcoholic fatty liver disease) in a subject in need thereof, comprising determining the phosphorylation state of one or more members of the AKT/mTOR/IRS pathway, and or of FAK (focal adhesion kinase), such as the markers discussed above, in adipose tissue from the subject, wherein if the phosphorylation pattern thus obtained is significantly similar to a phosphorylation pattern of markers that is indicative of NASH, the subject is likely to have NASH.

In methods of the invention, the phosphorylation state may be measured using an antibody against a phosphorylated isoform (at one or more defined phosphorylation sites) of the protein. The subject may be human. Another aspect of the invention is a kit for distinguishing NASH from other forms of NAFLD, comprising one or more reagents for detecting the phosphorylation state of at least one member of the AKT/mTOR/IRS pathway and/or of FAK. The reagents may be chosen from antibodies specific for a phosphorylated isoform (at one or more defined phosphorylation sites) of at least one member of the AKT/mTOR/IRS pathway and/or of FAK. Some suitable antibodies, and the phosphorylation sites they recognize, are indicated in Table 2.

Another aspect of the invention is a treatment method, wherein, if a subject is found to be likely to have NASH by a diagnostic method of the invention, the subject is treated with an effective amount of a modulatory agent (alone or in combination) as follows: (a) one or more stimulators or agonists of IRS-I, AKT, FKHR₅ FKHRL, GSK3, EIF4G,

SHC, and/or PKC-delta; and/or

(b) one or more inhibitors of PKA and/or CREB; and/or

(c) an inhibitor of FAK (Y397).

Another aspect of the invention is a method of treating NASH in a subject having or suspected of having a form of NAFLD, comprising determining if the subject is likely to have NASH by a diagnostic method of the invention; and if the subject is found to likely to NASH, administering to the subject an effective amount of a modulatory agent (stimulator or inhibitor) as above.

A treatment method of the invention may further comprise administering to the subject, in combination with the one or more agents as above, an effective amount of a conventional drug for treating NASH, e.g. interferon, insulin sensitizing agents such as Pioglitazone, etc. Experimental approaches under evaluation in patients with NASH include antioxidants, such as vitamin E, selenium, and betaine. These medications act by reducing the oxidative stress that appears to increase inside the liver in patients with NASH. Clinical trials in the next few years are expected to confirm that at least some of these substances are effective to treat the disease. Another experimental approach to treating NASH is the use of newer antidiabetic medications, including metformin, rosiglitazone, and pioglitazone, even in people without diabetes.

Another aspect of the invention is a pharmaceutical composition, comprising one or more of the modulatory agents as above, and a pharmaceutically acceptable carrier. Another aspect of the invention is a method to evaluate the effectiveness of a drug or treatment method for NASH in a subject, comprising determining the phosphorylation state of one or more members of the AKT/mTOR/IRS pathway and/or of FAK in adipose tissue from the subject, compared to positive and negative reference standards, at two or more times before and/or during treatment with the drug or treatment method; wherein, a reduction of an altered level of phosphorylation compared to the appropriate reference standard(s) over a period of time indicates that the drug or treatment method is effective for treating NASH in the subject. Any of the phospho-endpoints discussed herein may be used. Alternatively, or in addition, the phosphorylation patterns thus obtained from the sample from the subject may be compared to the phosphorylation pattern of markers that is indicative of NASH. If the phosphorylation pattern in the tissue from the subject becomes different from the NASH-indicative pattern (and more like the pattern in, e.g., a normal subject that does not have NASH), this indicates that the drug or treatment method is effective for treating NASH in the subject.

Another aspect of the invention is a method to follow the course of the disease in a subject having NASH, who is being treated for the disease, comprising determining the phosphorylation state of one or more members of the AKT/mTOR/IRS pathway and/or of FAK in adipose tissue from the subject, compared to positive and negative reference standards, at two or more times during the course of treatment; wherein, a reduction of an altered level of phosphorylation compared to the appropriate reference standard(s) over a period of time indicates that the subject is responding positively to the treatment. Any of the phospho- endpoints discussed herein may be used. Alternatively, or in addition, the phosphorylation patterns thus obtained from the sample from the subject may be compared to the phosphorylation pattern of markers that is indicative of NASH. If the phosphorylation pattern in the tissue from the subject becomes different from the NASH-indicative pattern (and more like the pattern in, e.g., a normal subject that does not have NASH), this indicates that the subject is responding positively to the treatment.

Another aspect of the invention is a method to prepare samples from fat tissue that are suitable for the analysis of phospho-proteins, comprising treating a fat sample under effective conditions with a denaturing ionic detergent (e.g., boiling the sample in about 1-3% (e.g., about 2%) SDS plus β-mercaptoethanol) and subjecting the treated sample to about 2-8 (e.g. about 5) cycles at a pressure of between about 30,000-40,000 (e.g., about 35,000) in a barocycler. (e.g. a Barocycler NEP3299).

Any of the diagnostic methods of the invention may further comprise presenting the measured values of phosphorylation in the form of a report. A method of the invention may be a method of personalized medicine. Methods of the invention may be readily adapted to high throughput methods.

Another aspect of the invention is a method comprising (a) obtaining an adipose tissue sample (e.g., from a subject, such as a subject having or suspected of having a form of NALDP); (b) obtaining data regarding the level of phosphorylation of IRS-I, AKT, FKHR, FKHRL, GSK3, EIF4G, SHC, PKC-delta, PKA, CREB and/or FAK and, optionally, of another member of the mTOR pathway in the sample; (c) comparing the phosphorylation state of the proteins in (b) to positive and negative reference standards, or to a phosphorylation pattern that is indicative of NASH; and (d) providing a report of the phosphorylation level(s) and/or of the comparison.

A "subject," as used herein, includes any animal that has a form of NAFLD. Suitable subjects (patients) include laboratory animals (such as mouse, rat, rabbit, or guinea pig), farm animals, and domestic animals or pets (such as a cat or dog). Non-human primates and, preferably, human patients, are included. A method of the invention can be used to stratify subjects with regard to how they fall in the spectrum of forms of NAFLD, ranging from simple steatosis (SS) to NASH. In particular, a method of the invention can distinguish subjects having NASH from subjects having other forms of NAFLD.

Suitable "samples" contain adipose tissue {e.g. white adipose tissue) from a subject. The adipose tissue can come from, e.g., omental or subcutaneous adipose tissue, or from a liver biopsy {e.g. a core needle biopsy). The use of omental tissue provides the advantage that obtaining such a sample is less invasive than obtaining it from other sources.

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

In a method of the invention, the phosphorylation levels of the phosphomarkers of the invention in a subject of interest are generally compared to negative and positive reference standards. To generate a "negative" reference standard, one can first process cells from adipose tissue from a subject (or a pool of subjects) that is known not to have NASH. The subject can be a lean and healthy control, or can have a non-NASH form of NAFLD. Protein extracts can be prepared from the adipose tissue and the level of phosphorylation at the phospho-endpoints of interest determined as described herein. The median value of such samples can serve as a negative reference standard.

To generate a "positive" reference standard, one can process cells from adipose tissue from a subject (or a pool of subjects) that is known to have NASH. Protein extracts can be prepared from the adipose tissue and the level of phosphorylation at the phospho-endpoints of interest determined as described herein. The median value of such samples can serve as a positive reference standard.

In variations of the above method, the determination of the positive or negative standard may be based on published data, retrospective studies of sick patients' tissues, and other information as would be apparent to a person of ordinary skill implementing the methods of the invention.

However, using adipose tissue from subjects as a clinical diagnostic reference standard is generally not practical on a routine basis. Instead, it is preferable to generate negative and positive reference standards by using lysates from cells in culture, and establishing a cut-point value by a direct comparison of the cell culture lysates to a true positive (e.g. endpoint values derived from fat from NASH subjects as described above) and true negative (e.g. endpoint values derived from fat from non-NASH or lean control subjects as described above). To accomplish this, one can first screen a variety of liver-based cells in culture, either primary cells or, preferably, cell lines (e.g., hepatocytes or stellate cells). The cells in culture can be propagated directly, under conventional conditions, so that members of the AKT/rnTOR/IRS pathway or FAK are not activated or are activated to a minimal degree; or they can be incubated under conventional conditions with a suitable mitogen that will globally activate the signaling networks, such as pervanadate or a growth factor (e.g, EGF or hepatocyte growth factor (HGF)), to activate specific pathways. Protein extracts are then prepared from the various cell lines, which have been incubated under the various conditions, using conventional procedures; and the level of phosphorylation at the phospho-endpoints of interest determined as described herein, and compared directly to the true positive and true negative clinical samples as a bridging experiment. In this way, one can establish conditions such that particular cells, cultured under particular defined conditions (stimulated or not), express an activation state value that is directly comparable to that of a subject that does not have NASH, or to a subject that does have NASH. Utilizing the cut-point values derived from median values of known true clinical positives and negatives, and bridging these values to a cell line reference standard can then provide a "negative reference standard" or a "positive reference standard," respectively.

The level of phosphorylation of the markers of the invention in a subject of interest is then determined as described herein. Any protein in a sample from a subject that exhibits a phosphorylation of statistically the same as the value in the "positive" reference standard, is considered to be hyper-phosphorylated, and to be indicative that the subject being tested is likely to have NASH. Any protein in a sample from a subject of interest that exhibits a phosphorylation value statistically the same as the value in the "negative" reference standard, is considered to be hypo-phosphorylated, and to be indicative that the subject being tested is likely not to have NASH.

In variants of this method, a negative or positive standard is used^' that is not directly comparable to the values in a non-NASH or a NASH subject, but which can be adjusted mathematically to reflect those values.

Alternatively, or in addition, a phosphorylation pattern (comprising a mathematical combination of one or more of the phosphoprotein endpoint values discussed herein) can be determined from an adipose sample from a subject (or a pool of subjects) that are known to have NASH, and from suitable controls (subjects having other forms of NAFLD, or free of liver disease). Individual proteins in a pattern which is indicative of NASH (the NASH-indicative pattern) may be hyper-phosphorylated or hypo-phosphoryated compared to the phosphorylation pattern from a subject (or pool of subjects) that have other forms of NAFLD, or that have no liver disease at all. These phosphorylation expression patterns can serve as comparison standards for the evaluation of subjects of interest. Example analytical tools and algorithms that are routinely used by person of ordinary skill implementing the methods of the invention to generate a combination of endpoints is k-means clustering, and random forest analysis.

For each protein whose level of phosphorylation is determined, the value can be normalized, e.g. to the total protein in the cell; or to the amount of a constitutively expressed protein (from a housekeeping gene), such as actin; or the amount of a phosphoprotein may be compared to the amount of its non-phosphorylated counterpart.

An increase in the amount of phosphorylation of a protein can reflect either an increase in the number of suitable amino acid residues of the protein {e.g., serines, threonines or tyrosines) that are phosphorylated, or an increased frequency of phosphorylations at a particular amino acid residue (e.g. on the amino acid side chain). Suitable controls for assays of the invention will be evident to the skiiled worker. For example, to provide for quality control, each set of proteins tested {e.g. in the form of a protein micro-array) may contain antigen controls, cell lysate controls, and/or a reference lysate. Each patient analyte sample can be normalized to total protein and quantitated in units relative to the reference "printed" on the same array. Each reference and control lysate can be printed in the same dilution series as patient samples and be immunostained at the same time, with identical reagents as the patient samples. All samples can be printed in duplicate in 4-point dilution curves.

The level of phosphorylation of a given amino acid residue can be measured qualitatively or quantitatively. The amount (quantity) of phosphorylation at a given residue may be higher or lower than is observed at other residues (e.g., other serine, threonine or tyrosine residues which are also phosphorylated), or at the same residue in a control sample (a reference Standard or baseline value). A residue may be hyper-phosphorylated (phosphorylated at a significantly increased level compared to a reference standard or baseline value) or hypo- phosphorylated (phosphorylated at a significantly decreased level compared to a reference standard or baseline value). Alternatively, a qualitative scale (such as a scale of 1 to 5) can be used.

A "significantly" elevated or decreased level of phosphorylation (compared to a reference standard) is a level whose difference from the value of the reference standard is statistically significant, using statistical methods that are appropriate and well-known in the art, generally with a probability value of less than five percent chance of the change being due to random variation. For example, the phosphorylation at a residue of interest of a member of the AKT/mTOR/IRS pathway of a subject having NASH may range from about 2-fold to 10-fold higher or lower (e.g. 5-fold), or more or less, respectively, than the level observed in a subject having a non-NASH form of NAFLD.

Methods for measuring the level of phosphorylation at an amino acid residue are conventional and routine. In general, the measurement relies on the existence of sets of ^■antibodies that are specific for either the non-phosphorylated or the phosphorylated isoforms of a particular amino acid residue of interest in the context of a protein of interest (such as a member of the AKT/mTOR7IRS pathway or FAK). Such antibodies are commercially available or can be generated routinely, using conventional procedures. In one embodiment, a synthetic peptide comprising an amino acid of interest from a protein of interest (either in the non- phosphorylated or phosphorylated form) is used as an antigen to prepare a suitable antibody. The antibody can be polyclonal or monoclonal. Antibodies are selected and verified to detect only the phosphorylated version of the protein but not the non-phosphorylated version of the native or denatured protein, and vice-versa.

Such antibodies can be used in a variety of ways. For example, one can prepare whole cell lysates from patient adipose tissue samples and spot them in an array format onto a suitable substrate, such as nitrocellulose strips or glass slides. Preferably, the proteins in the samples are denatured before spotting. In general, the cells are spotted at serial dilutions, such as two-fold serial dilutions, to provide a wide dynamic range. Suitable controls, such as positive controls or controls for base line values, can be included. Each array is then probed with a suitable detectable antibody, as described above, to determine and/or to quantitate which amino acid residue(s) in the various proteins of interest are phosphorylated. Methods for immuno- quantitation are conventional. For a further discussion of this method of reverse phase protein lysate microarrays (RPMA), see, e.g., Nishizuka et al. (2003) Proc. Natl. Acad. Sci. 100,14229- 14239.

Other suitable assays employing such antibodies to assess the level and/or degree of phosphorylation at a residue of interest include, e.g., Western blots, immunohistochemistry, immunoprecipitation, ELISA assays, assays based on fluorescent readouts, mass spectroscopy, suspension bead assays, and other conventional assays. Suitable methods include those that can detect the phosphoprotein in a very small sample {e.g. about 200 cells). Alternatively, methods can be used that are suitable for a large sample size (e.g. about 20,000-25,000 cells). Assays to measure the presence and/or amount of phosphorylated residues can be readily adapted to high throughput formats, e.g. using robotics.

As used herein, the singular forms "a," "an" and "the" include plural referents unless the context clearly dictates otherwise. For example, treatment with "an" agent that modulates the activation of "a" member of the AKT/mTOR pathway, as used herein, includes 2, 3, 4, 5 or more modulatory agents, that can alter the activation of 2, 3, 4, 5 or more members of the pathway.

The insulin receptor signaling pathway includes members of the downstream, interconnected pathways AKT (protein kinase B), mTOR (mammalian target of rapamycin) and IRS (insulin receptor substrate- 1). These pathways are referred to herein as the "AKT/mTOR/lRS" pathway or signaling pathway. Preferred markers from this pathway, for use in diagnostic assays of the invention, include, e.g., IRS-I (insulin receoptor substrate-1), AKT (protein kinase B), FKHR (forkhead transcription factor, or FoaOl), FKHRL (forkhead transcription factor ligand, or FoxO3a), GSK3 (glycogen synthase kinase-3), EIF4G (eukaryotic initiation factor 4G), SHC (src homology 2 domain-containing protein), PKC-delta (protein kinase C-delta), PKA (protein kinase A) and/or CREB (cAMP Response Element Binding Protein). Each of these markers is shown herein to be differentially phosphorylated in NASH as compared to non-NASH forms of NAFLD.

In subjects having NASH, one or more of IRS-I (S612), AKT (S308), FKHR (T24), FKHR (T32), GSK3 (S21/9), EIF4G (SI lOS), SHC (Y317), are hypo-phosphorylated; and/or one or more of PKA (T197) and/or CREB (Sl 33) are hyper-phosphorylated. One or more of these markers can be used in accordance with the present invention.

Other members of the AKT/mTOR/IRS pathway may also be used in assays to distinguish NASH from non-NASH forms of liver disease. These markers include other members or components that participate in the signal transduction cascade. These include, e.g., AMPK (AMP-activated protein kinase), P70S6 (ribosomal subunit 6 kinase of 70 kda), LKB (Hm kinase binding protein), SGK (serum and glucocorticoid-inducible kinase), and/or BAD (BcI activating domain). Other markers that may be used include, e.g., mTOR (mammalian target of rapamycin; also known as FRAP, RAFTl, or RAPTl) and other members of the mTOR pathway, including RAPTOR (regulatory associated protein of mTOR), 4E-BP 1 /PHAS- 1, p70s6k, TSC (tuberous sclerosis complex), 4E-BP1 /PHAS-I, p70s6k, eIF-4E, eIF-4G, and/or eIF4E complex; members of the AKT pathway, including PI3-kinase, PTEN (phosphatase and tensin homolog) and FKBP12; and members of the IRS pathway, including IRS-I and insulin growth factor (IGF) receptors {e.g. IGF-Rl, IGF-Rβ, and IGF-Rα). Members of other interconnected pathways include, e.g., pRb (the tumor suppressor, retinoblastoma protein); substrates of Akt, such as GSK3; and modulators of apoptosis, such as Bak. Other pathways that can be analyzed include, e.g., PTEN, PDKl, GSK3Beta, TSCl/2, ILK, Gab 1/2, p27Kipl, FKHRL, eNOS, ASKl, BAD, pRAS40, 14-3-3, or CHKl. Specific phosphorylation residues are indicated elsewhere herein. The nucleotide and amino acid sequences of the above-mentioned genes are well-known and can be determined routinely, as well as downloaded from various known databases. See, e.g. the world wide web site at ncbi.nlm.nih.gov.

If a subject is found to exhibit significantly altered (reduced or elevated) levels of phosphorylation of one or more members of the AKT/mTOR/IRS pathway, or significantly elevated levels in FAK, compared to a suitable control (reference standard), an effective amount of any of a variety of well-known inhibitors or stimulators (e.g. agonists) of activity of a member of the mTOR, AKT and/or IRS pathway, or inhibitors of FAK activity, can be administered. Such agents are sometimes referred to herein as "modulatory" agents. It will be evident to a skilled worker that a modulatory agent that is suitable to treat a subject having a reduced phosphorylation tevel of a diagnostic protein will be a stimulatory agent, such as an agonist, and that a modulatory agent that is suitable to treat a subject having an elevated phosphorylation level of a diagnostic protein will be an inhibitory agent. For example, one can administer one or more stimulators or agonists of IRS-I, AKT, FKHR, FKHRL, GSK3, EIF4G, SHC, and/or PKC-delta to a subject in which the relevant protein is hypo-phosphorylated compared to a "positive" control; and/or one can administer one or more inhibitors of PKA and/or CREB to a subject in which the relevant protein is hyper-phosphorylated compared to a "negative" control.

Tt is generally desirable to treat a subject with a combination of modulatory agents that affect different nodes of the AKT/mTOR/IRS pathway. In this way lower doses of each agent, with lower toxicity, may provide a more complete shut down of the pathway if used in combination. See, e.g., Araujo et al. (2007) Mathematical modeling of the cancer cell's control circuitry: Paving the way to patient-tailored combination therapy, Current Signal Transduction Therapies (in press); and Araujo et al. (2005), A mathematical model of combination therapy using the EGFR signaling network, Biosystems 80, 57-69.

As used herein, an "effective amount" of a modulatory agent is an amount that, when administered to a subject, brings about a measurable effect (therapeutic effect) in the subject over a reasonable time frame, and/or significantly alters the amount of phosphorylation of a marker of the invention. Although agents may be characterized as being, e.g., "FAK inhibitors," or "stimulators

(e.g. agonists) of the AKT/mTOR/IRS pathway," the present invention is not limited to the mechanism by which such agents achieve therapeutic efficacy. For example, a patient selected for treatment in accordance with the present invention may respond to an inhibitor of FAK or a stimulator of a member of the AKT/mTOR/IRS pathway, although the mechanism of action may not be related to, or completely related to, modulation of FAK or of the pathway.

Suitable agonists or stimulators of members of the AKT/mTOR/IRS pathway that are hypo-phosphorylated in NASH compared to a positive reference standard include, but are not limited to, any agent that increases the level of phosphorylation of one of the identified, hypo- phosphorylated, members of the AKT/mTOR/IRS pathway, such as a protein-specific phosphatase inhibitor. Such agents include, e.g., tautomycin and okadaic adic. Alternatively, agonists that work by other mechanisms can also be administered.

Suitable inhibitors of the members of the AKT/mTOR/IRS pathway that are hyper- phosphorylated in NASH compared to a negative reference standard include, but are not limited to, CC1779, LY294002, AP23573 and RAD-001. Furthermore, one or more of the following agents can be used:

Akt/mTOR inhibitors include, but are not limited to the following:

Examples of phosphatidylinositol-3-kinase (PT3-kinase) inhibitors, include, but are not limited to, e.g., celecoxib and analogs thereof, such as OSU-03012 and OSU-03013 {e.g., Zhu et al. (2004) Cancer Res. 64(12):4309-18);

3-deoxy-D-myo-inositol analogs (e.g., U.S. Application No. 20040192770; Meuillet et al. (2004) Oncol. Res. U, 513-27, 2004), such as PX-316;

2'-substituted, 3'-deoxy-phosphatidyl-myo-inositol analogs (e.g., Tabellini et al. (2004) Br. J. Haematol. 126(4), 574-82); fused heteroaryl derivatives (U.S. Pat. No. 6,608,056);

3-(imidazo[l,2-a]pyridin-3-yl) derivatives (e.g., U.S. Pat. Nos. 6,403,588 and 6,653,320);

Ly294002 (e.g., Vlahos et al. (1994) J. Biol, Chem. 269(7), 5241-5248); quinazoline-4-one derivatives, such as IC486068 (e.g., U.S. Application No.

20020161014; Geng et al. (2004) Cancer Res. 64, 4893-99);

3-(hetero)aryloxy substituted benzo(b)thiophene derivatives (e.g., WO 04 108715; also WO 04 108713); viridins, including semi-synthetic viridins such as such as PX-866 (acetic acid (lS,4E,10R,l lR,13S.14R)-[4-diallylaminoτnethylene-6-hydroxy-l-methoxymethyl-10,13- dimethyl-3,7,17-trioxo-l,3,4,7,10,l 1,12,13,14,15,16,17-dodecahydro-2-oxa- cyclopenta[a]phenanthren-l l-yl ester) (e.g., ThIe et al. (2004) MoI Cancer Ther. 3(7), 763-72; U.S. Application No. 20020037276; U.S. Pat. 5,726,167); and wortmannin and derivatives thereof (e.g., U.S. Pat. Nos. 5,504,103; 5,480,906, 5,468,773; 5,441,947; 5,378,725; 3,668,222).

Examples of Akt-kinase (also known as protein kinase B) inhibitors include, but are not limited to, e.g.,

Akt-1-1 (inhibits Aktl) (Barnett el al. (2005) Biochem. J., 385 (Pt.2), 399-408); Akt-1-1 ,2 (inhibits AkI and 2) (Barnett et al. (2005) Biochem. J. 385 (Pt.2), 399-408);

API-59CJ-Ome (e.g., Jin et al. (2004) Br. J. Cancer 91, 1808-12); l-H-imidazo[4,5-c]pyridinyl compounds (e.g., WO05011700); indole-3-carbinol and derivatives thereof (e.g., U.S. Pat. Nos. 6,656,963; Sarkar and Li (2004) JNutr. 134(12 Suppl), 3493S-3498S); perifosine (e.g., interferes with Akt membrane localization; Dasmahapatra et al. (2004)

Clin. Cancer Res. K)(15), 5242-52, 2004); phosphatidylinositol ether lipid analogues (e.g., Gills and Dennis (2004) Expert. Opin. Investig. Drugs U, 787-97); triciribine (TCN or API-2 or NCI identifier: NSC 154020; Yang et al. (2004) Cancer Res. 64, 4394-9).

Examples of mTOR inhibitors include, but are not limited to, e.g., FKBP 12 enhancer; rapamycins and derivatives thereof, including: CCI-779 (temsirolimus), RADOOl

(Everolimus; WO 9409010) and AP23573; rapalogs, e.g. as disclosed in WO 98/02441 and WO

01/14387, e.g. AP23573, AP23464, or AP23841; 40-(2-hydroxyethyl)rapamycin, 40-[3- hydroxy(hydroxymethyl) methylpropanoate]-rapamycin (also called CC 1779), 40-epi- (tetrazolyt)-rapamycin (also called ABT578), 32-deoxorapamycin, 16-pentynyloxy-32(S)- dihydrorapamycin, and other derivatives disclosed in WO 05005434; derivatives disclosed in

USP 5,258,389, WO 94/090101, WO 92/05179, USP 5,1 18,677, USP 5,118,678, USP

5,100,883, USP 5,151,413, USP 5,120,842, WO 93/111130, WO 94/02136, WO 94/02485, WO

95/14023, WO 94/02136, WO 95/16691, WO 96/41807, WO 96/41807 and USP 5,256, 790; phosphorus-containing rapamycin derivatives {e.g., WO 05016252);

4H-l-benzopyran-4-one derivatives (e.g., U.S. Provisional Application No. 60/528,340).

Examples of IRS pathway inhibitors include, but are not limited to, the following: Specific IGF-IR inhibition with neutralizing antibody, antagonistic peptide, or the selective kinase inhibitor NVP-AD W742. Proteasome inhibitors, MG 132 and lactacystin inhibit TRS-I phosphorylation. Proteasome inhibitors can regulate the tyrosine phosphorylation of IRS-I and the downstream insulin signaling pathway, leading to glucose transport. Inducible nitric oxide synthase, iNOS and NO donors induce IRS degradation. Serine phosphorylation of IRS-I is regulated by the inhibitor of kappa B kinase complex. Thapsigargin down-regulates IRS-I. PKC pathway and Akt inhibitors include Calphostin C, Staurosporine, and LY294002. STI571 is a further inhibitor of the cKit pathway related to the pathways of the present invention.

The mentioned proteins in their unphosphorylated and phosphorylated states can be used in accordance with the present invention, irrespective of the mechanism of action. Thus, although it is believed that NASH is correlated with certain phosphorylation patterns of the AKT/mTOR/IRS pathway and/or FAK, the present invention is not bound to any mechanism by which the theranostic, therapeutic, and/or prognostics methods achieve their success.

The modulatory agents (inhibitors, or stimulators (agonists)) discussed herein can be formulated into various compositions, e.g., pharmaceutical compositions, for use in therapeutic treatment methods. The pharmaceutical compositions can be assembled as a kit. Generally, a pharmaceutical composition of the invention comprises an amount of the inhibitor that is effective to ameliorate, at least to a detectable degree, one or more of the symptoms in a subject having NASH. That is, the amount is effective to effect at least a measurable amount of a therapeutic response in the subject over a reasonable time frame. The composition can comprise a carrier, such as a pharmaceutically acceptable carrier. By "pharmaceutically acceptable" is meant a material that is not biologically or otherwise undesirable, i.e., the material may be administered to a subject without causing any undesirable biological effects or interacting in a deleterious manner with any of the other components of the pharmaceutical composition in which it is contained. The carrier would naturally be selected to minimize any degradation of the active ingredient and to minimize any adverse side effects in the subject, as would be well known to one of skill in the art. For a discussion of pharmaceutically acceptable carriers and other components of pharmaceutical compositions, see, e.g., Remington's Pharmaceutical Sciences, 18th ed., Mack Publishing Company, 1990. A pharmaceutical composition or kit of the invention can contain other pharmaceuticals that are used to treat NASH (such as interferon, vitamin E, insulin sensitizing agents such as Pioglitazone, etc.), in addition to the stimulators(s) or inhibitor(s) of a member of the AKT/mTOR/IRS pathway, or inhibitor(s) of FAK. The other agent(s) can be administered at any suitable time during the treatment of the patient, either concurrently or sequentially, or the dosing can be staggered as desired. The drugs also can be combined in a composition. Doses of each can be less when used in combination than when any single agent is used alone.

One skilled in the art will appreciate that the particular formulation will depend, in part, upon the particular stimulatory or inhibitory agent of the invention, or other agent, that is employed, and the chosen route of administration. Accordingly, there is a wide variety of suitable formulations of compositions of the present invention.

Formulations suitable for oral administration (including sub-lingual administration) can consist of liquid solutions, such as an effective amount of the agent dissolved in diluents, such as water, saline, or fruit juice; capsules, sachets or tablets, each containing a predetermined amount of the active ingredient, as solid, granules or freeze-dried cells; solutions or suspensions in an aqueous liquid; and oil-in-water emulsions or water-in-oil emulsions. Tablet forms can include one or more of lactose, mannitol, corn starch, potato starch, microcrystalline cellulose, acacia, gelatin, colloidal silicon dioxide, croscarmellose sodium, talc, magnesium stearate, stearic acid, and other excipients, colorants, diluents, buffering agents, moistening agents, preservatives, flavoring agents, and pharmacologically compatible carriers. Suitable formulations for oral delivery can also be incorporated into synthetic and natural polymeric microspheres, or other means to protect the agents of the present invention from degradation within the gastrointestinal tract.

Formulations suitable for parenteral administration {e.g. intravenous, such as via the hepatic portal vein) include aqueous and non- aqueous, isotonic sterile injection solutions, which can contain anti-oxidants, buffers, bacteriostats, and solutes that render the formulation isotonic with the blood of the intended recipient, and aqueous and non-aqueous sterile suspensions that can include suspending agents, solubilizers, thickening agents, stabilizers, and preservatives. The formulations can be presented in unit-dose or multi-dose sealed containers, such as ampules and vials, and can be stored in a freeze-dried (lyophilized) condition requiring only the addition of the sterile liquid carrier, for example, water, for injections, immediately prior to use. Extemporaneous injection solutions and suspensions can be prepared from sterile powders, granules, and tablets of the kind previously described.

The modulatory agents of the invention, alone or in combination with other therapeutic agents, can be made into aerosol formulations to be administered via inhalation. These aerosol formulations can be placed into pressurized acceptable propellants, such as dichlorodifluoromethane, propane, nitrogen and the like.

The modulatory agents of the invention, alone or in combinations with other therapeutic agents, can be made into suitable formulations for transdermal {e.g. patch) application and absorption (Wallace et al., 1993, supra). Transdermal electroporation or iontophoresis also can be used to promote and/or control the systemic delivery of the agents and/or pharmaceutical compositions of the present invention through the skin {e.g., see Theiss et al. (1991), Meth. Find. Exp. Clin. Pharmacol. JJ, 353-359).

Formulations which are suitable for topical administration include lozenges comprising the active ingredient in a flavor, usually sucrose and acacia or tragacanth; pastilles comprising the active ingredient in an inert base, such as gelatin and glycerin, or sucrose and acacia; mouthwashes comprising the active ingredient in a suitable liquid carrier; or creams, emulsions, suspensions, solutions, gels, creams, pastes, foams, lubricants, sprays, suppositories, or the like. One skilled in the art will appreciate that a suitable or appropriate formulation can be selected, adapted or developed based upon the particular application at hand.

Dosages for an inhibitory agent of the invention can be in unit dosage form, such as a tablet or capsule. The term "unit dosage form" as used herein refers to physically discrete units suitable as unitary dosages for human and animal subjects, each unit containing a predetermined quantity of an inhibitor of the invention, alone or in combination with other therapeutic agents, calculated in an amount sufficient to produce the desired effect in association with a pharmaceutically acceptable diluent, carrier, or vehicle.

One skilled in the art can easily determine the appropriate dose, schedule, and method of administration for the exact formulation of the composition being used, in order to achieve the desired anti-cancer effective amount or effective concentration of the agent in the individual patient. One skilled in the art also can readily determine and use an appropriate indicator of the "effective concentration" of the compounds of the present invention by a direct or indirect analysis of appropriate patient samples.

The dose of a modulatory agent of the invention, or composition thereof, administered to an animal, particularly a human, in the context of the present invention should be sufficient to effect at least a measurable amount of a therapeutic response in the individual over a reasonable time frame. The exact amount of the dose will vary from subject to subject, depending on the species, age, weight and general condition of the subject, the severity or mechanism of any disorder being treated, the particular agent or vehicle used, its mode of administration and the like. The dose used to achieve a desired therapeutic concentration in vivo will be determined by the potency of the particular inhibitory agent employed, the pharmacodynamics associated with the agent in the host, the severity of the disease state of infected individuals, as well as, in the case of systemic administration, the body weight and age of the individual. The size of the dose also will be determined by the existence of any adverse side effects that may accompany the particular inhibitory agent, or composition thereof, employed. It is generally desirable, whenever possible, to keep adverse side effects to a minimum.

When given in combined therapy, the other therapeutic agent, for example, can be given at the same time as the inhibitor, or the dosing can be staggered as desired. The two drugs also can be combined in a composition. Doses of each can be less when used in combination than when either is used alone.

Any of the methods discussed herein can be adapted to other uses as well. For example, they can be used in a method for drug screening and reporting of drug effects on cell lines with extension into preclinical and clinical trials. In one embodiment, a cell line or tissue in a pathological condition is used as a control, and various putative inhibitors are administered, to determine if any of them restores a normal level of activity for the given marker {e.g., a member of the AKT/mTOR/IRS pathway or FAK), indicating that the putative inhibitor is potentially therapeutic. The effect of a putative inhibitor can be compared to the effect of a known therapeutic agent. The inventive methods can be used, e.g., to identify new drug targets, assess the effectiveness of drugs for treating NASH, improve the quality and reduce costs of clinical trials, discover the subset of positive responders to a particular drug (stratifying patient populations), improve therapeutic success rates, and reduce sample sizes, trial duration and costs of clinical trials. Methods of the invention can be adapted to high throughput methods (e.g., using robotics). Another embodiment of the invention is a kit useful for any of the methods disclosed herein. For example, a kit can comprise reagents for measuring the amount of phosphorylation of one or more of the proteins discussed herein. For example, a kit of the invention can comprise antibodies that are specific for particular unphosphorylated or phosphorylated isoforms of a member of the AKT/mTOR/IRS pathway and/or FAK. Furthermore, the kit may comprise reagents and/or devices for preparing a sample {e.g., for collecting a tissue and/or excising a sample from the tissue); for spotting test samples on a suitable surface, such as nitrocellulose strips; for performing immuno-quantitation {e.g., labeled antibodies, or reagents for labeling antibodies); instructions for performing a method of the invention; etc. The components of the kit may, optionally, be packaged in one or more containers.

In another embodiment, the kit is suitable for therapeutic treatment of NASH in a subject. Such a kit can comprise combinations of stimulatory agents and/or inhibitors {e.g. in the form of a pharmaceutical composition) as discussed elsewhere herein.

Among other uses, kits of the invention can be used in experimental applications {e.g., to evaluate the effectiveness of an agent of interest for the treatment of NASH or in clinical applications {e.g. to monitor the status of NASH in a subject undergoing treatment). A skilled worker will recognize components of kits suitable for carrying out any of the methods of the invention.

Optionally, a kit of the invention comprises include suitable buffers; pharmaceutically acceptable carriers; one or more containers or packaging materials; and/or instructions for performing the method. The reagents of the kit may be in containers in which the reagents are stable, e.g., in lyophilized form or stabilized liquids. The reagents may also be in single use form, e.g., in single dosage form. The reagents may also be in single use form, e.g., in single dosage form or in the form for carrying out a single diagnostic assay. Another aspect of the invention is a method for preparing samples from fat tissue that are suitable for the analysis of phospho-proteins, comprising treating a fat sample under effective conditions to solubilize the fat. For example, one can treat the sample with a denaturing ionic detergent {e.g., boil the sample in about 1-3% {e.g., about 2%) SDS plus β mercaptoethanol) and subject the treated sample to about 2-8 {e.g. about 5) cycles at a pressure of between about 30,000-40,000 {e.g., about 35,000) in a barocycler. {e.g. a Barocycler NEP3299).

In the Examples provided herein, two hundred mg of each adipose tissue sample was transferred to a specialized container (PULSE Tube) along with 1.2 ml of Lysis Buffer containing a 1 :1 mixture of 2X Tris-Glycine SDS Sample Buffer (Invitrogen Life Technologies, Carlsbad, CA) and Tissue Protein Extraction Reagent (Pierce, Rockford, IL) plus 2.5% β- mercaptoethanol, and subjected to five rapid pressure cycles in the Barocycler NEP3299 (Pressure BioSciences, West Bridgewater, MA). Each cycle consisted of 20 seconds at 35,000 psi followed by 20 seconds at ambient pressure. A test laboratory can utilize the following procedures:

To provide for quality assurance, samples can be processed and analyzed in real time, e.g. as they are received at a suitable processing facility that meets applicable regulatory standards. Samples may consist of Cytolyte preserved samples. A test set with matched frozen samples can verify the adequacy of specimen preservation. Techniques can be carried out at room temperature. Samples from adipose tissue can be obtained as discussed elsewhere herein.

Following the determination of the level of phosphorylation of a marker protein by a method as discussed herein, the values can be reported, e.g. in the form of a panel or suite of values, to physicians to improve therapy decisions for their patients. With such a report, various forms of NAFLD may be stratified at a molecular level, and therapies that are likely to be effective can be determined accordingly. This allows for optimal personalized patient therapies. Some suitable systems for reporting the data are described in co-pending provisional application, attorney docket number 65939-243694, filed March 27, 2007.

In the foregoing and in the following examples, all temperatures are set forth in uncorrected degrees Celsius; and, unless otherwise indicated, all parts and percentages are by weight.

EXAMPLES I. Materials and Methods A. Patient Population and pathology assessments Extensive clinical data and fasting serum samples (snap-frozen at the time of surgery) were obtained from patients undergoing bariatric surgery. Omental white adipose tissue specimens were collected during the surgery and immediately snap frozen for proteomic analysis. Finally, liver biopsies were also obtained at the time of surgery and reviewed by a single pathologist for NAFLD classification (ZG). Each liver biopsy was assessed for steatosis, inflammation, ballooning degeneration, fibrosis and other features. The degree of steatosis was assessed in hematoxylin-eosin-stained sections and graded as an estimate of the percentage of tissue occupied by fat vacuoles as follows: 0 = none; 1 = < 5%; 2 = 6% to 33%; 3 = 34% to 66%; 4 = 66%. Other histological features evaluated in hematoxylin-eosin sections included portal inflammation, lymphoplasmacytic lobular inflammation, polymorphonuclear lobular inflammation, Kupffer cell hypertrophy, apoptotic bodies, focal parenchymal necrosis, glycogen nuclei, hepatocellular ballooning, and Mallory bodies. These histological features were graded as follows: 0 = none; 1 = mild or few; 2 = moderate; or 3 = marked or many. Fibrosis was assessed with the Masson trichrome stain. Portal fibrosis and interlobular pericellular fibrosis were graded as follows: 0_none; 1 _ mild; 2 _ moderate; or 3 _ marked. When present, bridging fibrosis was noted as few or many bridges, and cirrhosis was identified when parenchymal nodules surrounded by fibrous tissue were noted. Cirrhosis was further categorized as incomplete or established, depending on the degree of loss of acinar architecture.

After assessing for each pathologic feature, liver biopsies were assigned to one of four diagnostic categories: (1) no fatty liver disease present, (2) simple steatosis, (3) steatosis with nonspecific inflammation, or (4) NASH. NAFLD was defined as a biopsy showing changes consistent with diagnostic categories 2 to 4. Patients were defined as having simple steatosis if they had hepatocellular fat accumulation as their sole pathology. Patients with steatosis and nonspecific inflammation had, in addition to fat, spotty hepatocellular dropout with focal inflammation or Kupffer cell hypertrophy. Nonalcoholic steatohepatitis was identified when, in addition to fat, lobular and hepatocellular inflammation and ballooning degeneration were identified on the hematoxylin-eosin stain. The presence of least one unequivocal Mallory body and some degree of zone 3 pericellular fibrosis or bridging fibrosis on the trichrome stain was also consistent with the diagnosis of NASH. This study was reviewed and approved by the institutional review board of Tnova Fairfax Hospital.

B. Adipose tissue processing and protein extraction

Two hundred mg of each adipose tissue sample was transferred to a specialized container (PULSE Tube) along with 1.2 ml of Lysis Buffer containing a 1:1 mixture of 2X Tris- Glycine SDS Sample Buffer (Invitrogen Life Technologies, Carlsbad, CA) and Tissue Protein Extraction Reagent (Pierce, Rockford, IL) plus 2.5% β-mercaptoethanol, and subjected to five rapid pressure cycles in the Barocycler NEP3299 (Pressure BioSciences, West Bridgewater, MA). Each cycle consisted of 20 seconds at 35,000 psi followed by 20 seconds at ambient pressure.

C. Reverse-phase protein microarrays

The protein lysates were loaded into 384-well plates and each serially diluted in Lysis Buffer to a five point dilution curve (neat, 1/2, 1/4, 1/8 and 1/16). Each dilution series was printed in duplicate onto nitrocellulose-coated glass slides (Whatman, Inc., Sanford, ME) with a 2470 Arrayer (Aushon BioSystems, Burlington, MA), outfitted with 350 μm pins, for a final deposited volume of approximately 33 nl per spot. Total protein in each spot ranged from 250 ng to 4 μg. Slides were dessicated and stored at -20°C. Total protein was quantified in selected arrays that were stained with Sypro Ruby Protein Blot Stain (Molecular Probes, Eugene, OR) according to the manufacturer's instructions and visualized on an Affymetrix 428 Array Scanner (Santa Clara, CA). Prior to antibody staining, the lysate arrays were treated with mild Reblot antibody stripping solution (Chemicon, Temecula, CA) for 15 min at room temperature, washed two x five min in PBS, and then incubated for at least 5 hours in blocking solution [Ig I-block (Tropix, Bedford, MA), 0.1% Tween-20 in 500 mL PBS] at room temperature with constant rocking.

D. Protein microarray staining

Blocked arrays were stained with antibodies on an automated slide stainer (Dako Cytomation, Carpinteria, CA) using the Catalyzed Signal Amplification System kit according to the manufacturer's recommendation (CSA; Dako Cytomation). Briefly, endogenous biotin was blocked for 10 min with the biotin blocking kit (Dako Cytomation), followed by application of protein block for 5 min; primary antibodies were diluted in antibody diluent and incubated on .slides for 30 min and biotinylated secondary antibodies were incubated for 15 min. Signal amplification involved incubation with a streptavidin-biotin-peroxidase complex provided in the CSA kit for 15 min, and amplification reagent, (biotinyl-tyramide/hydrogen peroxide, streptavidin-peroxidase) for 15 min each. Development was completed by using diaminobenzadine/ hydrogen peroxide as the chromogen/substrate. Slides were allowed to air dry following development.

We specifically chose 54 primary antibodies (Table 2) to analyze the following broad signaling pathways thought to be involved in adipokine signaling and tissue changes: a) cell survival/insulin-related signaling; b) cell proliferation; c) inflammation; d) apoptosis; e) cytokine and chemokine-related signaling. Secondary antibodies and dilutions included: biotinlyated goat anti-rabbit IgG (H+L) 1 :5000 (Vector Laboratories, Burlingame, CA, USA); and biotinylated rabbit anti-mouse IgG 1:10 (Dako Cytomation).

E. Image Analysis

Stained slides were scanned individually on a UMAX PowerLook III scanner (UMAX, Dallas, TX, USA) at 600 dpi and saved as TIF files in Photoshop 6.0 (Adobe, San Jose, CA, USA). The TlF images for antibody-stained slides and Sypro-stained slide images were analyzed with Micro Vigene image analysis software, version 2.200 (Vigenetech, North Billerica, MA) and Microsoft Excel 2000 software. Images were imported into Microvigene, which performed spot finding, local background subtraction, replicate averaging and total protein normalization, producing a single value for each sample at each endpoint. These numbers were then subjected to unsupervised hierarchical clustering analysis using JMP 5.0 (SAS Institute, Gary, NC).

F. Statistical procedures

Group comparisons were performed by non-parametric Mann-Whitney hypothesis tests. Associations between measurement pairs were tested with the use of Pearson correlation coefficients. The significance of these associations was assessed by computing the confidence interval of each correlation coefficient via Fisher's z-transform. Categorical data were subjected to univariate and multivariate ordered probit regression analysis. Unless otherwise noted, p- values < 0.05 were considered significant.

IT. Demographic and Clinical data

The study included 89 patients, 65 of whom had NAFLD and 24 who were designated as Obese Controls because their liver biopsies did not show any significant pathologic changes. Of the 65 NAFLD patients, 14 had biopsy-proven NASH and 51 had non-NASH fatty liver disease (7 with Simple Steatosis or SS and 44 with Steatosis and non-specific inflammation or NSI). Demographic and clinical data are summarized in Table 1.

Table 1

NAFLD Phenotve #

NASH 14

SS 10

NSI 46

Obese Control 29

TOTAL 99

III. Analysis of Human Adipose Tissue Phdspoproteome

Broad patient-specific heterogeneity of the active signaling events is revealed by unsupervised Bayesian clustering analysis of cellular signaling using the phospho-specifϊc endpoints listed in Table 2 (Figure 1). Although the underlying NAFLD phenotypes (e.g., NASH, SS, NSI) did not self-organize into specific clusters, cell signaling pathways fell into expected groupings corresponding to the time course of the changes in the activity the kinases and the levels of their phosphorylated substrates. Unsupervised Bayesian approaches allow separate assessment of the kinase phosphorylation levels and its cognate substrate (e.g., MEK and ERK). Even without an a priori training, many of the components of the MEK-ERK kinase pathway family were grouped in the same cluster, indicating that we were able to recapitulate active networks in lysed adipose cells. The inability of an unsupervised approach to segregate NAFLD phenotypes is not surprising, and probably results from the broad signaling differences between different NAFLD subtypes and the fact that many physiological links between adipose and liver tissues are relatively weak compared to changes within the liver itself.

To evaluate the potential for specific signaling pathways to provide for correlative outcomes, we took a more focused approach — studying and comparing the progressive form of NAFLD (NASH) with its relatively benign forms (SS and NSI) and evaluating each phosphorylation event as an independent variable.

Table 2

IV. Molecular Network Comparison of NASH vs. Non-NASH

To evaluate differences in molecular networks between patients with NASH and patients with the non-progressive form of NAFLD (Non-NASH), and to understand the influence of non-specific inflammation on any subsequent analysis, we studied each phospho-specific and signaling endpoint for significance of discrimination between NASH and SS, or between NASH and NSI. Histographical analysis revealed that phosphorylation of a member of the AKT/mTOR pathway, the forkhead transcription factor (FKHR), is elevated (P <0.001) in the adipose tissue of patients with SS compared to those with NASH (Figure 2A). Note that when all 89 morbidly obese patients were analyzed, amounts of the FKHR phosphorylated at S256 residue significantly correlated with AST/ALT ratio (R == 0.2706, p < 0.015). When the analysis is expanded to include patients with SS and NSI, decision tree partition analysis, which looks for linked principal distinguishing components, also identified the FKHR protein as an important classifier. Additionally, decision tree partitioning analysis pinpoints other members of the insulin and the AKT/mTOR pathways as being differentially phosphorylated in patients with non-progressive form of NAFLD and those with NASH (Figure 2B).

It is significant and' striking that although each of these endpoints was independently analyzed as an individual component of the pathway, whole pathways were highlighted, indicating broad, pathway wide differences between NASH and non-progressive forms of

NAFLD (Figure 3). The results indicate elevated phosphorylation of the insulin pathway in adipose tissue of patients with non-progressive forms of NAFLD (Non-NASH) compared to

NASH, except for focal adhesion kinase (FAK), for which phosphorylation appears to be relatively higher in NASH (Figure 2B). A comparison of SS to NSI revealed additional components of the AKT/mTOR pathway, GSK3 and E1F4G, and insulin signaling pathway,

SHC and PKCdelta (data not shown).

In summary, forkhead transcription factor (FKHR), AKT S3O8, and IRS-I (S612) are elevated (P <0.001) in the adipose tissue of patients with simple steatosis compared to those with NASH. Focal adhesion kinase (FAK) Y397, CREB S 133 and PKA Tl 97: phosphorylation is higher in NASH.

Interestingly, phosphorylation of the components of the insulin pathway was more pronounced in the adipose tissue of SS patients than in patients with NASH. A decrease in insulin signaling via the insulin receptor substrate (IRS)-l/phosphatidylinositol (PI) 3-kinase pathway should result in further reduction of glucose uptake and utilization in the livers of patients with NASH. Also, the levels of inactive, unphosphorylated IRSl were greater in the adipose tissue of patients with NASH than those with SS₃ perhaps because of compensatory regulation of total receptor upregulation in patients with a potentially progressive form of liver disease. Our observations suggest that the action of insulin in the adipose tissue of patients with non-progressive NAFLD is mediated mostly through CREB/FAK control of glucose metabolism, the PKC lipolysis pathway, and the AKT/mTOR pro-survival/apoptosis axis.

This signal pathway profiling of omental adipose specimens from patients with NAFLD appears to differentiate patients with NASH from those with the non-progressive forms of NAFLD (SS and NSI). Analysis of many disparate signaling pathways specifically highlighted the insulin signaling network as significantly affected in fatty liver disease pathogenesis.

V. Molecular Network Comparison of Patients with NAFLD vs. Obese Controls

We next analyzed phospho-signaling portraits in patients with NAFLD compared to Obese Controls without NAFLD to further understand pathway changes in adipose tissue, the relationship of these changes with liver pathology, and the specificity of the insulin pathway changes we observed in progressive NAFLD vs non-progressive NAFLD. Principal component analysis was also an effective tool for identifying key components of discrimination, with most Obese Controls segregated from subjects with NAFLD. However, although some components of the insulin pathway were part of the overall discrimination, a substantial component of the signaling differences corresponded to other pathways such as eNOS (obese control vs SS, Figure 5 A and 5B) and cAbl (obese control vs NASH, Figure 4A and 4B). Amounts of cleaved caspase 9 and pp90RSK S380 were positively correlated (R = 0.5444, p < 3.44e^"08) and were increased in patients with NASH and in those with NSI compared to the obese controls or those with SS (P < 0.05). The results indicate that the derangements in adipose tissue in patients with NASH vs non-progressive form of NAFLD are fairly specific, and that other signaling changes occur in the adipose tissue of NAFLD patients compared to the obese controls. VI. Validation of the identified endpoints with clinical studies

Each of the phosphorylated proteins is validated by using an independent and separate set of fat tissue specimens obtained from obese patients undergoing bariatric surgery. A liver biopsy is also procured and NAFLD, NASH, non-NASH, and diabetes status clinically and pathologically determined. The relative levels of the relevant phosphoproteins that correlate with NASH phenotype are measured and compared against a cut-point value as compared to a reference standard as described previously. This cut point can be a combination of values (a fingerprint) that are optimal for discrimination as determined by the discovery set. The classification of NASH vs non-NASH is then determined by the cut-point value and the results unblended. Sensitivity, specificity , receiver operating curves and hazard ratios can then be determined.

It is expected that, in view of the high statistical confidence level (95%) of the data described in examples I- V, each of the markers will be validated for characterizing a subject as having NASH rather than another form of NAFLD.

From the foregoing description, one skilled in the art can easily ascertain the essential characteristics of this invention, and without departing from the spirit and scope thereof, can make changes and modifications of the invention to adapt it to various usage and conditions and to utilize the present invention to its fullest extent. The preceding preferred specific embodiments are to be construed as merely illustrative, and not limiting of the scope of the invention in any way whatsoever. The entire disclosure of all applications, patents, and publications cited above, including U.S. Provisional application, 60/747,750, filed May 19, 2006, and U.S. Provisional application 60/914,533, filed April 27, 2007, and in the figures are hereby incorporated in their entirety by reference.

Claims

WE CLAIM:

1. A method to distinguish NASH (non-alcoholic steatohepatitis) from other forms of NAFLD (non-alcoholic fatty liver disease) in a subject in need thereof, comprising (a) determining the phosphorylation state of one or more of the following members of

AKT/mTOR/IRS pathway in adipose tissue from the subject: IRS-I (S612), AKT (S308), FKHR (T24), FKHRL (T32), GSK3 (S21/9), EIF4G (Sl 108), SHC (Y317) and/or PKC-delta (T505), wherein a significantly reduced level of phosphorylation of the one or more of the members of the pathway compared to a positive reference standard, or a level that is statistically the same as a negative reference standard, indicates that the subject is likely to have NASH, and/or

(b) determining the phosphorylation state of one or both of the following members of the AKT/mTOR/IRS pathway in adipose tissue from the subject: PKA (T197) and/or CREB (S 133), wherein a significantly increased level of phosphorylation of the one or both of the members of the pathway compared to a negative reference standard, or statistically the same level compared to a positive reference standard, indicates that the subject is likely to have NASH, and/or

(c) determining the phosphorylation state of FAK (Y397) in adipose tissue from the subject, wherein a significantly increased level of phosphorylation in FAK (Y397) compared to a negative reference standard, or statistically the same level compared to a positive reference standard, indicates that the subject is likely to have NASH.

2. The method of claim 1, wherein the determination of the phosphorylation state is of one or more of the 10 members of the AKT/mTOR.IRS pathway of (a) or (b).

3. The method of claim 1, wherein the determination of the phosphorylation state is of about 4 or more of the 10 members of the AKT/mTOR.IRS pathway of (a) or (b).

4. The method of claim 1, wherein the determination of the phosphorylation state is of about 7 or more of the 10 members of the AKT/mTOR.IRS pathway of (a) or (b).

10

5. The method of claim 1, wherein the determination is of the phosphorylation state of FAK.

6. The method of any of claims 1-5, further comprising determining the phosphorylation state of one or more of the following additional members of the AKT/mTOR/IRS pathway in adipose tissue from the subject: AMPK, P70S6, LKB, SGK, and/or BAD, wherein a significantly altered level of phosphorylation of the one or more additional members compared to a positive or negative reference standard further indicates that the subject is likely to have NASH.

7. The method of claim 6, further comprising determining the phosphorylation state of one or more additional members of the AKT/mTOR/IRS pathway, or of an interconnected pathway.

8. A method to distinguish NASH (non-alcoholic steatohepatitis) from other forms of NAFLD (non-alcoholic fatty liver disease) in a subject in need thereof, comprising determining the phosphorylation state of one or more members of the AKT/mTOR/IRS pathway, and or of FAK (focal adhesion kinase) in adipose tissue from the subject, wherein if the phosphorylation pattern thus obtained is statistically similar to a phosphorylation pattern of markers that is indicative of NASH, the subject is likely to have NASH.

9. The method of any of claims 1-8, wherein the non-NASH form of NAFLD is simple steatosis (SS), with or without inflammation.

10. The method of any of claims 1-9, wherein the phosphorylation state of a member of the AKT/mTOR/iRS pathway and/or of FAK is measured using an antibody against a phosphorylated isoform at a particular phosphorylation site of the protein.

11. The method of any of claims 1-10, wherein the subject is human.

12. A kit for distinguishing NASH from other forms of NAFLD, comprising one or more reagents for detecting the phosphorylation state of at least one member of the AKT/mTOR/IRS pathway and/or of FAK.

13. The kit of claim 12, wherein the phosphorylation state that is determined is of IRS-I (S612), AKT (S308), FKHR (T24), FKHRL (T32), GSK3 (S21/9), E1F4G (Sl 108), SHC (Y317), PKC-delta (T505), PKA (Tl 97), CREB (S 133), and/or FAK (Y397).

14. The kit of claim 12 or 13, wherein the reagents are chosen from antibodies specific for at least one phosphorylation site in at least one member of the AKT/mTOR/IRS pathway and/or of FAK.

15. The method of any of claims 1-11, further wherein, if the subject is found to be likely to have NASH, the subject is treated with an effective amount of the following modulatory agents, alone or in combination:

(a) one or more stimulators or agonists of IRS-I, AKT, FKHR, FKHRL, GSK3, EIF4G, SHC, and/or PKC-delta; and/or

(b) one or more inhibitors of PKA and/or CREB; and/or (c) an inhibitor of FAK (Y397).

16. A method of treating NASH in a subject having, or suspected of having, a form of NAFLD, comprising determining if the subject is likely to have NASH by the method of any of claims 1-11, and if the subject is found to likely to NASH, administering to the subject an effective amount of one of more of the following modulatory agents, alone or in combination:

(a) one or more stimulators or agonists of IRS-I, AKT, FKHR, FKHRL, GSK3, EIF4G, SHC, and/or PKC-delta; and/or (b) one or more inhibitors of PKA and/or CREB; and/or

(c) an inhibitor of FAK.

17. The method of claim 16, further comprising administering, in combination with the one or more modulatory agents of claim 16, an effective amount of a conventional drug for treating NASH.

18. The method of claim 17, wherein the conventional drug is the insulin sensitizer metformin, rosiglitazone, or vitamin E.

19. A pharmaceutical composition, comprising

(a) an inhibitor of FAK and

(b) one or more stimulators or agonists of IRS-I₇ AKT, FKHR, FKHRL, GSK3, EIF4G, SHC, and/or PKC-delta; and/or (c) one or more inhibitors of PKA and/or CREB, and a pharmaceutically acceptable carrier.

20. A method to evaluate the effectiveness of a drug or treatment method for NASH in a subject, comprising determining the phosphorylation state of one or more members of the AKT/mTOR/IRS pathway and/or of FAK in adipose tissue from the subject, at two or more times before and/or during treatment with a drug or treatment method, and comparing the phosphorylation patterns thus obtained to a phosphorylation pattern of markers that is indicative of NASH, wherein a change of the altered phosphorylation pattern in adipose tissue from the subject over time compared to the phosphorylation pattern of markers that is indicative of NASH indicates that the drug or treatment method is effective for treating NASH in the subject.

21. The method of claim 20, wherein the phosphorylation state is determined for one of more of IRS-I (S612), AKT (S308), FKHR (T24), FKHRL (T32), GSK3 (S21/9), E1F4G

(Sl 108), SHC (Y317), PKC-delta (T505), PKA (T 197), CREB (S 133) and/or FAK (Y397).

22. A method to follow the course of the disease in a subject having NASH, who is being treated for the disease, comprising determining the phosphorylation state of one or more members of the AKT/mTOR/IRS pathway and/or of FAK in adipose tissue from the subject, compared to a reference standard, at two or more times during the course of treatment, wherein, a change of the altered phosphorylation pattern in adipose tissue from the subject over time compared to the phosphorylation pattern of markers that is indicative of NASH indicates that the subject is responding positively to the treatment.

23. The method of claim 22, wherein the phosphorylation state is determined for one of more of IRS-I (S612), AKT (S308), FKHR (T24), FKHRL (T32), GSK3 (S21/9), EIF4G (Sl 108), SHC (Y317), PKC-delta (T505), PKA (T197), CREB (S133), and/or FAK (Y397).

24. A method to prepare samples from fat tissue that are suitable for the analysis of phospho-proteins, comprising treating a fat sample under effective conditions with a denaturing ionic detergent and subjecting the treated sample to about 5 cycles at a pressure of about 35,000 psi. in a barocycler.

25. The method of any of paragraphs 1-11, further wherein the measured values of phosphorylation are presented in the form of a report.

26. The method of any of paragraphs 1-11, which is a method of personalized medicine.

27. A method comprising

(a) obtaining an adipose tissue sample from a subject;

(b) obtaining data regarding the level of phosphorylation of one or more of TRS-I (S612), AKT (S308), FKHR (T24), FKHRL (T32), GSK3 (S21/9), EIF4G (Sl 108), SHC

(Y317), PKC-delta (T505), PKA (Tl 97), CREB (S 133), and/or FAK (Y397) and, optionally, of another member of the mTOR pathway in the sample;

(c) comparing the phosphorylation state of the proteins in (b) to positive and negative reference standards, or to a phosphorylation pattern indicative of NASH; and (d) providing a report of the phosphorylation level(s) and/or of the comparison.