SYNCHRONIZED CELL CYCLE GENE EXPRESSION TEST FOR ALZHEIMER'S DISEASE AND RELATED THERAPEUTIC METHODS

BACKGROUND OF THE INVENTION

Alzheimer's disease (“AD”) has long been the subject of considerable efforts to develop accurate diagnostic methods, as well as therapeutic methods. Despite these efforts, there is an unmet need for methods of accurately diagnosing AD and differentiating it from non-Alzheimer's dementia (“non-ADD”). There is also an unmet need for effective methods of treating AD.

SUMMARY OF THE INVENTION

This invention provides a method for determining whether a human subject is afflicted with AD or non-ADD when the subject is suspected of being afflicted with AD or non-ADD, comprising the steps of

- (a) synchronizing a population of suitable cells derived from the subject; and
- (b) in the resulting synchronized cell population, measuring the expression level of a gene known to be differentially expressed between corresponding synchronized cells derived from AD patients and those derived from non-ADD patients,

This invention also provides a method for determining whether a human subject is afflicted with AD or non-ADD when the subject is suspected of being afflicted with AD or non-ADD, comprising the steps of

- (a) synchronizing a population of cultured skin cell fibroblasts derived from the subject, wherein the synchronizing comprises culturing the fibroblasts to over-confluence and then starving the resulting over-confluent fibroblasts; and
- (b) in the resulting synchronized fibroblast population, measuring the expression level of each of genes AC004057.1, AC092651.1, ACP6, ADAM20, ASXL2, C2CD5, CARNS1, FAM149B1, GLIS3-AS1, IL18R1, LINC01393, LZIC, MAP1LC3B2, NHLH1, NORAD, NPPA-AS1_3, OSMR-AS1, PAN3, PHBP8, PSMB9, RAB3IP, RDH16, RFESDP1, RPL5, SCG2, SDHD, SHISA5, SLC45A3, SNHG14, TTC26, URB2, USMG5, WASF2, ZCWPW2, ZNF444, and ZNF70, wherein measuring the expression level of each gene comprises measuring the number of its RNA transcripts per number of total transcripts,

whereby (i) the subject is afflicted with AD if the expression levels measured in step (b) are consistent with the genes' expression levels in corresponding synchronized cells derived from AD patients, and (ii) the subject is afflicted with non-ADD if the expression levels measured in step (b) are consistent with the genes' expression levels in corresponding synchronized cells derived from non-ADD patients.

This invention further provides a method for determining whether a human subject is afflicted with AD or non-ADD when the subject is suspected of being afflicted with AD or non-ADD, comprising the steps of

(a) synchronizing a population of cultured immortalized B lymphocytes derived from the subject, wherein the synchronizing comprises culturing the lymphocytes to over-confluence and then starving the resulting over-confluent lymphocytes; and

- (b) in the resulting synchronized lymphocyte population, measuring the expression level of each of genes AC004057.1, AC092651.1, ACP6, ADAM20, ASXL2, C2CD5, CARNS1, FAM149B1, GLIS3-AS1, IL18R1, LINC01393, LZIC, MAP1LC3B2, NHLH1, NORAD, NPPA-AS1_3, OSMR-AS1, PAN3, PHBP8, PSMB9, RAB31P, RDH16, RFESDP1, RPL5, SCG2, SDHD, SHISA5, SLC45A3, SNHG14, TTC26, URB2, USMG5, WASF2, ZCWPW2, ZNF444, and ZNF70, wherein measuring the expression level of each gene comprises measuring the number of its RNA transcripts per number of total transcripts,

This invention provides a method for determining whether a human subject is afflicted with AD or is a NDS when the subject is suspected of being afflicted with AD, comprising the steps of

- (a) synchronizing a population of suitable cells derived from the subject; and
- (b) in the resulting synchronized cell population, measuring the expression level of a gene known to be differentially expressed between corresponding synchronized cells derived from AD patients and those derived from NDS patients,

This invention also provides a method for determining whether a human subject is afflicted with AD or is a NDS when the subject is not suspected of being afflicted with AD, comprising the steps of

- (a) synchronizing a population of suitable cells derived from the subject; and
- (b) in the resulting synchronized cell population, measuring the expression level of a gene known to be differentially expressed between corresponding synchronized cells derived from AD patients and those derived from NDS patients,

Finally, this invention provides methods for treating a human subject afflicted with Alzheimer's disease comprising administering to the subject a therapeutically effective amount of carfilzomib, bortezomib, bumetanide, furosemide or torsemide.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1

This Figure, based on a first study (“Study 1”), shows statistically significant genes when comparing the AD group with the Non-ADD group. Study 1 revealed that there are 2103 statistically significant genes for a P level less than 0.1; 1099 statistically significant genes for a P level less than 0.05; 285 statistically significant genes for a P level less than 0.01; and 6 statistically significant genes for a P level less or equal than 0.001.

FIG. 2

This Figure, based on Study 1, shows the top 6 statistically significant genes (P<=0.001) for the 6 AD and 2 Non-ADD cases. Squares represent the AD population while circles represent the Non-ADD population.

FIG. 3

This Figure, based on Study 1, shows an example of the top 10 statistically significant genes (P<=0.01). (A) Raw TPM (transcripts per million) data showing with squares the AD population and with circles the Non-ADD population. (B) Average TPM data showing with squares the AD population and with circles the Non-ADD population. Error bars are standard deviations. (C) Percent change (% Ch) in gene expression when comparing the AD with control (Non-ADD), i.e., 100*(AD-Non-ADD)/Non-ADD.

FIG. 4

This Figure, based on Study 1, shows genes ranked 11 to 20 at the statistical significance of 1% overlap probability (P<=0.01). (A) Raw TPM data showing with squares the AD population and with circles the Non-ADD population. (B) Average TPM data showing with squares the AD population and with circles the Non-ADD population. Error bars are standard deviations. (C) Percent change (% Ch) in gene expression when comparing the AD with control (Non-ADD), i.e., 100*(AD-Non-ADD)/Non-ADD.

FIG. 5

This Figure, based on Study 1, shows genes ranked 21 to 30 at the statistical significance of 1% overlap probability (P<=0.01). (A) Raw TPM data showing with squares the AD population and with circles the Non-ADD population. (B) Average TPM data showing with squares the AD population and with circles the Non-ADD population. Error bars are standard deviations. (C) Percent change (% Ch) in gene expression when comparing the AD with control (Non-ADD), i.e., 100*(AD-Non-ADD)/Non-ADD.

FIG. 6

This Figure, based on Study 1, shows genes ranked 31 to 40 at the statistical significance of 1% overlap probability (P<=0.01). (A) Raw TPM data showing with squares the AD population and with circles the Non-ADD population. (B) Average TPM data showing with squares the AD population and with circles the Non-ADD population. Error bars are standard deviations. (C) Percent change (% Ch) in gene expression when comparing the AD with control (Non-ADD), i.e., 100*(AD-Non-ADD)/Non-ADD.

FIG. 7

This Figure, based on Study 1, shows the percent change (% Ch) in gene expression for the top 40 genes.

FIG. 8

This Figure, based on a second study (“Study 2”), shows the number of statistically significant differentially expressed genes for the training set (first cylinders-lighter shading) versus the number of statistically significant differentially expressed genes for the validation set (second cylinders-darker shading) for different levels of statistical significance P<0.001, 0.01, 0.05, and 0.10.

FIG. 9

This Figure, based on Study 2, shows gene networks for (A) PAN3, (B) PSMB9, (C) TTC26, (D) ZNF444, (E) NHLH1, (F) URB2 and (G) ADAM20.

FIG. 10

This Figure, based on Study 2, shows network measures for cross-validated genes: (A) number of edges; (B) average node degree; and (C) average local clustering coefficient.

FIG. 11

This Figure, based on Study 2, compares Non-ADD (n=3) with Non-Demented Controls (NDC; n=5), and shows the number of differentially expressed genes in the Non-ADD population when compared with the NDC population.

FIG. 12

This Figure shows the number of statistically significant dysregulated genes when comparing AD (n=6) and Non-Demented Controls (n=5). Gene numbers are shown for P<0.0001, P<0.001, P<0.01, and P<0.05.

FIG. 13

This Figure shows predicted gene expression profile changes with Alzheimer's disease severity. The current gene expression dysregulations for 26 cross-validated genes were ranked according to the percent change of the AD group FPKM (fragments per kilobase million) when compared with the FPKM for the Non-ADD group (blue). The gene CARNS1 has the largest percent change while the gene C2CD5 has the lowest percent change. The cylinders above zero indicate up-regulation for that specific gene while the cylinders below zero indicate down-regulation. The blue cylinders indicate the current data, which were obtained from patients with high severity of AD/Non-ADD disease. The red, grey, and yellow cylinders represent our prediction of how the pattern of the 26 dysregulated genes would look like for lower severities, i.e., ½, ¼, and ⅛ of the current data, based on the assumption that disease severity linearly correlates with the FPKM percent change.

DETAILED DESCRIPTION OF THE INVENTION
Definitions

In this application, certain terms are used which shall have the meanings set forth as follows.

As used herein, “administer”, with respect to an agent, means to deliver the agent to a subject's body via any known method. Specific modes of administration include, without limitation, intravenous, oral, sublingual, transdermal, subcutaneous, intraperitoneal and intrathecal administration.

In addition, in this invention, the various agents can be formulated using one or more routinely used pharmaceutically acceptable carriers. Such carriers are well known to those skilled in the art. For example, oral delivery systems include tablets and capsules. These can contain excipients such as binders (e.g., hydroxypropylmethylcellulose, polyvinyl pyrilodone, other cellulosic materials and starch), diluents (e.g., lactose and other sugars, starch, dicalcium phosphate and cellulosic materials), disintegrating agents (e.g., starch polymers and cellulosic materials) and lubricating agents (e.g., stearates and talc). Injectable drug delivery systems include, for example, solutions, suspensions, gels, microspheres and polymeric injectables, and can comprise excipients such as solubility-altering agents (e.g., ethanol, propylene glycol and sucrose) and polymers (e.g., polycaprylactones and PLGA's). Implantable systems include rods and discs and can contain excipients such as PLGA and polycaprylactone.

As used herein, “Alzheimer's disease” means a concurrent affliction with the following three symptoms: (i) dementia; (ii) amyloid plaques; and (iii) neurofibrillary tangles. Dementia can be diagnosed during life. Cerebral amyloid plaques and neurofibrillary tangles can, for example, be diagnosed during autopsy. This definition of Alzheimer's disease is the one provided by the National Institute of Neurological Disorders and Stroke (NINDS) of the National Institutes of Health (NIH), and is known as the “gold standard.” All disease-afflicted subjects from whom samples were taken and studied, and for which data are presented herein, are autopsy-confirmed AD, non-ADD patients, and NDCs (who were hypervalidated because they were not demented at the time of biopsy collection).

As used herein, a gene's expression level is “consistent” with that gene's expression level in corresponding synchronized cells derived from AD patients if it is the same as, or close to, that expression level. For example, assume that gene X's TPM measure in synchronized cells derived from AD patients is 10 and its TPM measure is 100 in the same type of cells derived from non-ADD (or NDC) patients that are synchronized in the same way. A subject's gene X expression level would be consistent with gene X's AD expression level if it were, for example, below 50, below 40, below 30, below 20 or, ideally, 10 or lower.

As used herein, “culturing” lymphocytes is achieved, for example, by conducting the culturing at a temperature and in a growth factor milieu permissive of cell growth. In another embodiment, “culturing” lymphocytes is performed under conditions (e.g., those described herein for proliferation) that preserve lymphocyte viability. In one embodiment, the temperature, salinity and protein milieu permissive of cell growth is 37° C., RPMI 1640 Medium with 10% fetal bovine serum (“FBS”) and 1% penicillin (“PS”). In one embodiment of this invention, the lymphocyte-culturing step is performed for more than three hours. Preferably, the lymphocyte-culturing step is performed for more than six hours (e.g., overnight). B-lymphocyte can be cultured to over-confluence, i.e., high density/μl. The high density is determined as the plateau that is typically more then 90% in the growth curve. Then, the lymphocytes are starved overnight.

Methods for obtaining lymphocytes from a subject's blood are known, and include, for example, flow cytometry, Ficoll (a hydrophilic polysaccharide that separates layers of blood), and gradient centrifugation. Additionally, in the subject methods, the lymphocytes (e.g., B lymphocytes) can be used in immortalized or primary (i.e., non-immortalized) form. Methods for immortalizing lymphocytes (e.g., B lymphocytes) are known, and include, for example, treating the lymphocytes with Epstein-Barr virus (“EBV”).

As used herein, “culturing” skin fibroblasts is achieved, for example, by conducting the culturing at a temperature and in a growth factor milieu permissive of cell growth. In another embodiment, “culturing” skin fibroblasts is performed under conditions (e.g., those described below for proliferation) that preserve skin fibroblasts viability. In one embodiment, the temperature, humidity and protein milieu permissive of cell growth is 37° C., DMEM Medium with 10% fetal bovine serum (“FBS”) and 1% penicillin (“PS”). In one embodiment of this invention, the skin fibroblast-culturing step is performed for more than three hours. Preferably, the skin fibroblast-culturing step is performed for more than six hours (e.g., overnight).

Methods for obtaining skin fibroblasts from a subject's blood are known, and include, for example, skin punch biopsy, and growing cells out of explants. When cell confluence reaches 100%, cells are passaged. Typically after two passages, fibroblasts are purified in a proportion greater than 95%.

As used herein, cells “derived” from a subject are cells that arise through culturing and/or other physical manipulation performed on cells directly removed from the subject. For example, cultured skin fibroblasts derived from a subject are those skin fibroblasts that arise through culturing a sample of skin cells (e.g., contained in a punch biopsy) directly removed from the subject.

As used herein, “diagnosing Alzheimer's disease”, with respect to a symptomatic human subject, means determining that there is greater than 50% likelihood that the subject is afflicted with Alzheimer's disease. Preferably, “diagnosing Alzheimer's disease” means determining that there is greater than 60%, 70%, 80% or 90% likelihood that the subject is afflicted with Alzheimer's disease. As used herein, the phrase “determining whether the subject is afflicted with Alzheimer's disease” is synonymous with the phrase “diagnosing Alzheimer's disease.”

As used herein, “diagnosing non-ADD”, with respect to a symptomatic human subject, means determining that there is greater than 50% likelihood that the subject is afflicted with non-ADD. Preferably, “diagnosing non-ADD” means determining that there is greater than 60%, 70%, 80% or 90% likelihood that the subject is afflicted with non-ADD. As used herein, the phrase “determining whether the subject is afflicted with non-ADD” is synonymous with the phrase “diagnosing non-ADD.”

As used herein, “expression level”, with respect to a gene, includes, without limitation, any of the following: (i) the rate and/or degree of transcription of the gene (i.e., the rate at which, and/or degree to which, the gene is transcribed into RNA); (ii) the rate and/or degree of processing of the RNA encoded by the gene; (iii) the rate and/or degree of maturation of non-protein-coding RNA encoded by the gene; (iv) the rate at which, and/or degree to which, the RNA encoded by the gene is exported; (v) the rate at which, and/or degree to which, the RNA encoded by the gene is translated (i.e., the rate at which, and/or degree to which, the RNA is translated into protein); (vi) the rate at which, and/or degree to which, the protein encoded by the gene folds; (vii) the rate at which, and/or degree to which, the protein encoded by the gene is translocated; and (viii) the level of function (e.g., enzymatic activity or binding affinity) of the protein encoded by the gene.

As used herein, a gene is “differentially expressed between corresponding synchronized cells derived from AD patients and those derived from non-ADD patients” if, for example, the gene's TPM measure in synchronized cells derived from AD patients is different than in the same type of cells derived from non-ADD patients that are synchronized in the same way. For example, gene X would be differentially expressed between corresponding synchronized cells derived from AD patients and those derived from non-ADD patients if its TPM measure in synchronized cells derived from AD patients were 10 and its TPM measure were 100 in the same type of cells derived from non-ADD patients that are synchronized in the same way.

As used herein, an agent “favorably” affects the expression level of a gene whose expression level correlates with AD if it either decreases or increases that expression toward a level correlative with a non-AD (e.g., disease-free) state. For example, if the expression level of gene X is lower in an AD patient than in a non-afflicted patient, an agent favorably affecting the expression level of that gene would increase its expression level. Similarly, if the expression level of gene X is higher in an AD patient than in a non-afflicted patient, an agent favorably affecting the expression level of that gene would decrease its expression level.

As used herein, “measuring” the expression level of a gene means quantitatively determining the expression level via any means for doing so (e.g., Total RNA Sequencing (20 million reads, 2x75 bp PE)). Preferably, measuring the expression level of a gene is accomplished by measuring the number of RNA transcripts for that gene per million total RNA transcripts (i.e., “TPM” via FastQ data, and FPKM estimation per sample) present in the cell-derived RNA population being studied. For example, measuring the expression level of gene X in a synchronized cell population might yield a result of 50 TPM. In another embodiment, measuring a gene's expression level is done via protein quantification (e.g., via the known method of Western blotting). In a further embodiment, measuring a gene's expression level is done via a quantitative assay for protein function (e.g., via known methods for measuring enzymatic activity and/or protein binding strength).

As used herein, a subject afflicted with “non-Alzheimer's dementia” means a subject showing dementia such as, for example, that which characterizes Parkinson's disease, Huntington's disease and frontotemporal dementia.

As used herein, a “population” of cells includes any number of cells permitting the manipulation and study required to assess gene expression. In one embodiment, the population of cells includes at least 1,000,000 cells. In another embodiment, the population of cells includes between 100,000 cells and 1,000,000 cells, between 10,000 cells and 100,000 cells, between 1,000 cells and 10,000 cells, between 100 cells and 1,000 cells, between 10 cells and 100 cells, and fewer than 10 cells (e.g., one cell).

As used herein, the term “subject” includes, without limitation, a mammal such as a human, a non-human primate, a dog, a cat, a horse, a sheep, a goat, a cow, a rabbit, a pig, a rat and a mouse. Where the subject is human, the subject can be of any age. For example, the subject can be 50 years or older, 55 years or older, 60 years or older, 65 or older, 70 or older, 75 or older, 80 or older, 85 or older, or 90 or older. The instant methods are envisioned for all subjects, preferably humans (and preferably symptomatic).

As used herein, a human subject who is “suspected of being afflicted with AD or non-ADD” is a subject displaying at least one symptom (e.g., dementia) consistent with both AD and non-ADD.

As used herein, “synchronizing” a population of cells means placing at least a majority of cells in that population in the same cell cycle stage (namely, in the G1, S, G2 or M stage, and preferably in the G1, S or G2 stage). In one embodiment, synchronizing a population of cells means placing at least 60%, at least 70%, at least 80%, at least 90%, at least 95% or preferably at least 99% of cells in that population in the same cell cycle stage. In another embodiment, synchronizing a population of cells means placing the cells in that population in the same cell cycle stage that they would be in if cultured to over-confluence and then starved. Cell confluence followed by serum starvation typically arrests the cells in the G0/G1 stage [1-3].

Doses, i.e., “therapeutically effective amounts”, used in connection with this invention include, for example, a single administration, and two or more administrations (i.e., fractions). In one embodiment, the therapeutically effective amount of a drug approved for a non-Alzheimer's indication is the dose and dosing regimen approved for that non-Alzheimer's indication.

As used herein, “treating” a subject afflicted with a disorder shall include, without limitation, (i) slowing, stopping or reversing the disorder's progression, (ii) slowing, stopping or reversing the progression of the disorder's symptoms, (iii) reducing the likelihood of the disorder's recurrence, and/or (iv) reducing the likelihood that the disorder's symptoms will recur. In the preferred embodiment, treating a subject afflicted with a disorder means (i) reversing the disorder's progression, ideally to the point of eliminating the disorder, and/or (ii) reversing the progression of the disorder's symptoms, ideally to the point of eliminating the symptoms.

The treatment of AD can be measured according to a number of clinical endpoints. These include, without limitation, (a) lowering, stabilizing or slowing progression of (i) dementia, (ii) synaptic loss, (iii) amyloid plaques and/or (iv) neurofibrillary tangles, and/or (b) favorably affecting the expression level of a gene whose expression level correlates with AD.

Embodiments of the Invention

This invention provides accurate gene-based methods for determining whether a human subject is afflicted with AD or non-ADD when the subject is suspected of being afflicted with AD or non-ADD. The subject methods are based, at least in part, on the surprising discovery that synchronizing a patient's suitable cell population (e.g., lymphocytes, skin fibroblasts, pluripotent cells (such as iPSCs, and any progeny thereof)) and then measuring the expression levels of genes that are differentially expressed between AD and non-ADD cells permits accurately diagnosing the patient as having either AD or non-ADD. This invention also provides methods for treating AD using certain gene expression-altering agents.

Specifically, this invention provides a method for determining whether a human subject is afflicted with AD or non-ADD when the subject is suspected of being afflicted with AD or non-ADD, comprising the steps of

- (a) synchronizing a population of suitable cells derived from the subject; and
- (b) in the resulting synchronized cell population, measuring the expression level of a gene known to be differentially expressed between corresponding synchronized cells derived from AD patients and those derived from non-ADD patients,

In one embodiment of the subject method, the suitable cells derived from the subject are cultured skin cell fibroblasts. In another embodiment, the suitable cells derived from the subject are cultured B lymphocytes (preferably immortalized B lymphocytes).

Methods for synchronizing cell populations are known in the art. In one embodiment of the subject method, synchronizing the population of suitable cells comprises culturing the cells to over-confluence and then starving the resulting over-confluent cells.

Ideally in the subject method, the gene is known to be differentially expressed by a significant margin. In one embodiment, the gene is known to be differentially expressed by at least 50% between corresponding synchronized cells derived from AD patients and those derived from non-ADD patients. Preferably, the gene is known to be differentially expressed by at least 100% between corresponding synchronized cells derived from AD patients and those derived from non-ADD patients. Another way of expressing the degree of differential expression is “% change” or “% Ch”, which is equal to [AD_expression−Non-ADD_expression/Non-ADD_expression].

In another preferred embodiment of the subject method, the gene is selected from the group consisting of CFAP97, LINC01393, ZNF623, HAUS2, PAN3, PSMB9, ZFP28, TTC26, RFESDP1, ZNF444, WASF2, NHLH1, NPPA-AS1_3, NORAD, URB2, ADAM20, ZCWPW2, AC004057.1, AC092651.1, ACP6, ACP2, C2CD5, CARNS1, FAM149B1, GLIS3-AS1, ASXL2 and IL18R1.

In one embodiment, the gene expression levels set forth in Table 9, taken individually or collectively (e.g., one, two or more, three or more, four or more, and the like), are indicative of AD. In a preferred embodiment, the gene expression levels set forth in Table 10, taken individually or collectively (e.g., one, two or more, three or more, four or more, and the like), are indicative of AD. For example, as shown in Table 10, a PSMB9 expression level greater than 18 TPM is indicative of AD. In yet another embodiment, AD-indicative expression levels for each other gene disclosed herein are readily determined based on the data presented.

In a further preferred embodiment of the subject method, step (b) comprises measuring the expression levels of a plurality of genes, each gene being known to be differentially expressed between corresponding synchronized cells derived from AD patients and those derived from non-ADD patients. The plurality of genes can be of any suitable size, such as at least two genes, at least five genes, at least 20 genes, at least 100 genes, and at least 1,000 genes. Preferably, each gene of the plurality of genes is known to be differentially expressed by at least 50% (and more preferably by at least 100%) between corresponding synchronized cells derived from AD patients and those derived from non-ADD patients. In yet another preferred embodiment of the subject method, the plurality of genes comprises two or more genes selected from the group consisting of AC004057.1, AC092651.1, ACP6, ADAM20, ASXL2, C2CD5, CARNS1, FAM149B1, GLIS3-AS1, IL18R1, LINC01393, LZIC, MAP1LC3B2, NHLH1, NORAD, NPPA-AS1_3, OSMR-AS1, PAN3, PHBP8, PSMB9, RAB31P, RDH16, RFESDP1, RPL5, SCG2, SDHD, SHISA5, SLC45A3, SNHG14, TTC26, URB2, USMG5, WASF2, ZCWPW2, ZNF444, and ZNF70.

In the subject method where the expression levels of a plurality of genes are measured, the expression levels measured in step (b) are “consistent” with those in corresponding synchronized cells derived from AD patients if, for example, for at least a majority of gene expression levels measured, each such level is independently consistent with that gene's expression level in corresponding synchronized cells derived from AD patients.

In the subject method, measuring the expression level of a gene can be accomplished by any suitable method known in the art. In the preferred embodiment, measuring the expression level of a gene comprises measuring the number of that gene's RNA transcripts per number of total transcripts.

In a preferred embodiment, the subject invention provides a method for determining whether a human subject is afflicted with AD or non-ADD when the subject is suspected of being afflicted with AD or non-ADD, comprising the steps of

- (a) synchronizing a population of cultured skin cell fibroblasts derived from the subject, wherein the synchronizing comprises culturing the fibroblasts to over-confluence and then starving the resulting over-confluent fibroblasts; and
- (b) in the resulting synchronized fibroblast population, measuring the expression level of each of genes AC004057.1, AC092651.1, ACP6, ADAM20, ASXL2, C2CD5, CARNS1, FAM149B1, GLIS3-AS1, IL18R1, LINC01393, LZIC, MAP1LC3B2, NHLH1, NORAD, NPPA-AS1_3, OSMR-AS1, PAN3, PHBP8, PSMB9, RAB3IP, RDH16, RFESDP1, RPL5, SCG2, SDHD, SHISA5, SLC45A3, SNHG14, TTC26, URB2, USMG5, WASF2, ZCWPW2, ZNF444, and ZNF70, wherein measuring the expression level of each gene comprises measuring the number of its RNA transcripts per number of total transcripts,

In another preferred embodiment, the subject invention provides a method for determining whether a human subject is afflicted with AD or non-ADD when the subject is suspected of being afflicted with AD or non-ADD, comprising the steps of

- (a) synchronizing a population of cultured immortalized B lymphocytes derived from the subject, wherein the synchronizing comprises culturing the lymphocytes to over-confluence and then starving the resulting over-confluent lymphocytes; and
- (b) in the resulting synchronized lymphocyte population, measuring the expression level of each of genes AC004057.1, AC092651.1, ACP6, ADAM20, ASXL2, C2CD5, CARNS1, FAM149B1, GLIS3-AS1, IL18R1, LINC01393, LZIC, MAP1LC3B2, NHLH1, NORAD, NPPA-AS1_3, OSMR-AS1, PAN3, PHBP8, PSMB9, RAB31P, RDH16, RFESDP1, RPL5, SCG2, SDHD, SHISA5, SLC45A3, SNHG14, TTC26, URB2, USMG5, WASF2, ZCWPW2, ZNF444, and ZNF70 wherein measuring the expression level of each gene comprises measuring the number of its RNA transcripts per number of total transcripts,

This invention further provides a method for determining whether a human subject is afflicted with AD, non-ADD, or a disorder which is neither (i.e., a non-demented subject (also referred to as “NDS”, “NDS patient”, “NDS subject”, “NDC” (i.e., non-demented control), “NDC patient”, and “NDC subject”)) when the subject is suspected of being afflicted with AD or non-ADD, comprising the steps of

- (a) synchronizing a population of suitable cells derived from the subject; and
- (b) in the resulting synchronized cell population, measuring the expression level of a gene known to be differentially expressed between corresponding synchronized cells derived from AD patients, those derived from non-ADD patients and those derived from NDS subjects,

whereby (i) the subject is afflicted with AD if the expression level measured in step (b) is consistent with that gene's expression level in corresponding synchronized cells derived from AD patients, (ii) the subject is afflicted with non-ADD if the expression level measured in step (b) is consistent with that gene's expression level in corresponding synchronized cells derived from non-ADD patients, and (iii) the subject is afflicted with neither AD not non-ADD if the expression level measured in step (b) is consistent with that gene's expression level in corresponding synchronized cells derived from NDS subjects. The various embodiments of the diagnostic methods above for determining whether a human subject is afflicted with AD or non-ADD apply, mutatis mutandis, to this method.

This invention provides a method for determining whether a human subject is afflicted with AD or is a NDS when the subject is suspected of being afflicted with AD, comprising the steps of

- (a) synchronizing a population of suitable cells derived from the subject; and
- (b) in the resulting synchronized cell population, measuring the expression level of a gene known to be differentially expressed between corresponding synchronized cells derived from AD patients and those derived from NDS patients,

This invention also provides a method for determining whether a human subject is afflicted with AD or is a NDS when the subject is not suspected of being afflicted with AD, comprising the steps of

- (a) synchronizing a population of suitable cells derived from the subject; and
- (b) in the resulting synchronized cell population, measuring the expression level of a gene known to be differentially expressed between corresponding synchronized cells derived from AD patients and those derived from NDS patients,

Ideally in the subject method, the gene is known to be differentially expressed by a significant margin. In one embodiment, the gene is known to be differentially expressed by at least 50% between corresponding synchronized cells derived from AD patients and those derived from NDS patients. Preferably, the gene is known to be differentially expressed by at least 100% between corresponding synchronized cells derived from AD patients and those derived from NDS patients. Another way of expressing the degree of differential expression is “% change” or “% Ch”, which is equal to [AD_expression−NDS_expression/NDS_expression].

This invention further provides a method for treating a human subject afflicted with Alzheimer's disease comprising administering to the subject a therapeutically effective amount of an agent known to favorably affect the expression level of one or more genes whose expression levels correlate with Alzheimer's disease. Preferably, the genes are selected from the group consisting of AC004057.1, AC092651.1, ACP6, ADAM20, ASXL2, C2CD5, CARNS1, FAM149B1, GLIS3-AS1, IL18R1, LINC01393, LZIC, MAP1LC3B2, NHLH1, NORAD, NPPA-AS1_3, OSMR-AS1, PAN3, PHBP8, PSMB9, RAB31P, RDH16, RFESDP1, RPL5, SCG2, SDHD, SHISA5, SLC45A3, SNHG14, TTC26, URB2, USMG5, WASF2, ZCWPW2, ZNF444, and ZNF70. In one embodiment, the genes are selected from the group consisting of IL18R1, PSMB9, TTC26, WASF2, ACP6, CARNS1, NPPA-AS1_3, SCG2 and SDHD. In another embodiment, the gene is IL18R1, PSMB9, TTC26, WASF2, ACP6, CARNS1, NPPA-AS1_3, SCG2 or SDHD.

This invention further provides methods for treating a human subject afflicted with Alzheimer's disease comprising administering to the subject a therapeutically effective amount of an agent selected from the group consisting of carfilzomib (Kyprolis®, Onyx Pharmaceuticals), bortezomib (Velcade®, Takeda Oncology), bumetanide (Bumexe, Hoffman-La Roche), furosemide (Lasixe), torsemide (Demadexe), flavin mononucleotide, phosphoric acid, riboflavin, gamma-aminobutyric acid, adenosine monophosphate, histidine, L-arginine, cisplatin, clozapine, cyclosporin A, dexamethasone, etanercept, ethanol, filgrastim, glucose, haloperidol, heparin, infliximab, leflunomide, nitric oxide, oxygen, polyethylene glycol, prednisolone, progesterone, tacrolimus, thalidomide, zinc, calcitriol, calcium, serine, acetylcholine, capsaicin, dopamine, histamine, lithium, norepinephrine, succinic acid, formic acid, tromethamine, citric acid, 10Z-hymenialdisine (Tocris), JIB 04 (Tocris), CRT 0066101 (Tocris), celastrol, dihydroeponemycin, noradrenaline bitartrate (Tocris), or any other drug listed in Tables 7A and 7B. In a preferred embodiment, the agent is carfilzomib which, in one embodiment, is administered in the manner stated on the FDA-approved label for one of its approved indications (e.g., in the manner approved for treating multiple myeloma, wherein the formulation is injectable and is administered at a dose of 30 mg or 60 mg). In another preferred embodiment, the agent is bortezomib which, in one embodiment, is administered in the manner stated on the FDA-approved label for one of its approved indications (e.g., in the manner approved for treating multiple myeloma, wherein the formulation is injectable and is administered at a dose of 3.5 mg, or 1.3 mg/m²). In another preferred embodiment, the agent is bumetanide which, in one embodiment, is administered in the manner stated on the FDA-approved label for one of its approved indications (e.g., in the manner approved for treating edema, wherein the formulation is oral and is administered at a dose of 0.5 mg, 1 mg or 2 mg daily, every other day, or daily for 3-4 days followed by a 1-2-day rest period). In another preferred embodiment, the agent is furosemide which, in one embodiment, is administered in the manner stated on the FDA-approved label for one of its approved indications (e.g., in the manner approved for treating edema or hypertension, wherein the formulation is oral and is administered at a dose of 20 mg, 40 mg, 60 mg or 80 mg per day (e.g., 40 mg 2× daily)). In another preferred embodiment, the agent is torsemide which, in one embodiment, is administered in the manner stated on the FDA-approved label for one of its approved indications (e.g., in the manner approved for treating edema or hypertension, wherein the formulation is oral and is administered at a dose of 5 mg, 10 mg, 15 mg or 20 mg per day).

In another preferred embodiment, the agent is any of cisplatin, clozapine, cyclosporin A, dexamethasone, etanercept, filgrastim, haloperidol, heparin, infliximab, leflunomide, prednisolone, progesterone, tacrolimus, thalidomide or calcitriol which, in one embodiment, is administered in the manner stated on the FDA-approved label for one of its approved indications.

As for each of 10Z-hymenialdisine, JIB 04, CRT 0066101, celastrol, dihydroeponemycin, noradrenaline bitartrate, and other non-FDA-approved drugs, the preferred route of administration is oral, and the preferred dosage is from 0.1 mg/kg to 100 mg/kg, from 1 mg/kg to 5 mg/kg, from 5 mg/kg to 10 mg/kg, from 10 mg/kg to 15 mg/kg, or from 15 mg/kg to 20 mg/kg.

This invention will be better understood by reference to the examples which follow, but those skilled in the art will readily appreciate that the specific examples detailed are only illustrative of the invention as described more fully in the claims which follow thereafter.

EXAMPLES
Example 1—Study 1

TABLE 1

Based on data from Study 1, the top 285 statistically significant genes with

less than 1% overlap probability between AD and Non-ADD.

Top 285 statistically significant genes with less than 1%

overlap probability between AD and Non-ADD

PTCD2
UVSSA
SPIN2B
IFT80
PLPP5

ST20
KIAA1551
NPM1P50
AL356277.2
PCSK4

AC090971.4
SLC43A3
MIR6501
FUCA1
PPP1R16B

EIF4A2P1
BZW1P2
MED26
HIST1H2BL
PREPL

CFAP97
HS6ST1P1
ZNF860
ZDHHC11B
ZNF106

AL157871.3
CYB561D2
AC099508.1
BATF2
ZNF383

AC007325.4
SULT1A4
MFN2
RAET1E
LEAP2

NR3C2
AC138623.1
ASAH1
TUBB2B
ARHGAP42

C6orf58
RHPN1
HDAC4
FOXRED2
NOXRED1

LINC01393
ST8SIA6
ZNF628
AK3P3
SFXN5

AL031432.5
TTC8
C16orf62
WASF2
AL365203.1

AC005495.1
IGDCC4
AC025594.2
LBHD1
BX322639.1

NR2C2
XPC
ADAMTSL4-AS1
BEX1
AC005837.1

AL589684.1
TDO2
TESK1
CNOT6L
PVT1

WDR17
KBTBD6
SFXN1
ANKFY1
AC073539.7

FCF1P6
AC004997.1
JCHAIN
ACOX2
PML

AC092818.1
AL592183.1
F2R
URAHP
KDELC2

FGR
AC226101.1
PLCB4
COX7A2L
AC109583.2

HNRNPA3P10
AC087672.3
CACUL1
LSS
AL158835.2

C17orf97
FOXN3
KRT8P33
LINC02126
AL591846.2

FAM13A
KANK2
IMPDH1P4
AL049840.5
DHRS4L2

ARMCX5-GPRASP2
ZNF107
MIR4653
PROCR
LINC02085

ZNF274
ZNF593
AL590428.1
AC097468.3
TERF2

IPO4
AC093752.1
ZFP28
NHLH1
PPP2R2D

CYB5D1
CPVL
TTC26
RAPGEF1
PRORSD1P

AC005077.2
TAS2R10
TMIE
B3GALT5-AS1
ABHD12

ZNF547
AC069528.2
AP000766.1
CCDC159
AC010894.5

HIC1
SLC25A34
ARPC5
KLHL4
DYNC1LI2

LINC01239
AC005674.2
SIPA1
MVD
AC015917.2

MALRD1
MAPK8IP3
AP001830.1
ELOVL6
EIF3C

HOXA-AS2
ADD3
TMEM167A
FAXC
FAM223A

NBR2
VPS72
RBSN
SYNPO
ZNF808

AC010336.1
CDC25B
CU634019.1
AC087276.2
PHF1

KATNB1
AC026464.3
BTF3P9
AC145343.1
OR7E22P

BTBD7
RASA3
GSC
LRRC37A4P
AC027796.3

UBE2FP1
MIR6808
CASTOR1
Z97634.1
AP001148.1

NPPA-AS1_3
SNORD36C
FLJ46284
ZNF321P
LAMB2

ANKRD36
NMT1
AC138150.2
AP000763.2
DMTN

AC124067.4
EML2
BEST4
AC093270.1
ASIC3

DDIT4L
PRDM15
AC002066.1
AC021087.3
PHBP19

PTK2
AC005363.1
RPE
AL022328.4
RNY1P16

NORAD
MYNN
COLGALT2
AKNA
AC022613.3

COX6A1P2
GSAP
NSMCE4A
CFAP43
ZNF300

UPK1A-AS1
TNFSF12
SNORD110
SUMO2P6
AF165147.1

AC005521.1
CATSPER2P1
C1orf174
HIST1H2BF
AC119403.1

AC097532.2
HSPA8P11
PARP14
SLIT1

EIF4BP5
FOXK2
AC007566.1
ZNF407

HPCA
KIAA0556
UBE2R2-AS1
CAMK1

TCAF2P1
ZNF688
CACHD1
MTCP1

URB2
CU633904.1
HCG20
SKP1P1

MICB
SLC25A32
AC091544.5
ERI1

ORC1
ATP6V1B2
SNORD45A
PUM2

AP000238.1
ZFP30
AL031728.1
CEP290

KDM7A
AL021707.8
KIAA1468
PLAC8

THAP7
FNDC3A
JPT2
SUPT16H

FBXL17
EIF3KP1
AC095055.1
HSF4

AL157895.1
PNPLA7
AC027097.1
AC245052.3

TBC1D14
GSTCD
AL356512.1
PAN3

PPFIA4
C8orf82
FAM196B
KAT2A

ANAPC13
FZD1
ARHGAP23
FAM223B

(P < 0.01 - two-tailed, unequal variance T-test)

TABLE 2

Based on data from Study 1, genes with functional relevance to PKC

and MAPK

Protein
Rank
Gene Name
T-test (2, 3)

Mitogen-Activated Protein Kinase 8
60
MAPK8IP3
0.0014

Interacting Protein 3

Heparin Binding EGF Like Growth
324
HBEGF
0.0112

Factor

Heparan Sulfate Proteoglycan 2
369
HSPG2
0.0138

Solute Carrier Family 9 Member A5
652
SLC9A5
0.0278

Mitogen-Activated Protein Kinase 11
747
MAPK11
0.0323

Fos Proto-Oncogene, AP-1
92
FOSL1P1
0.0383

Transcription Factor Subunit

TABLE 3

Based on data from Study 1, genes with functional relevance for cell

adhesion and cell division

T-test

Protein
Rank
Gene Name
(2, 3)

Pentatricopeptide Repeat Domain 2
1
PTCD2
0.0000

Coiled-Coil Domain Containing 159
117
CCDC159
0.0033

Cell Division Cycle 25B
183
CDC25B
0.0055

TNF Superfamily Member 12
194
TNFSF12
0.0061

Glutathione S-Transferase C-Terminal
208
GSTCD
0.0066

Domain Containing

TEN1-CDK3 Readthrough
332
TEN1-CDK3
0.0115

(NMD Candidate)

Programmed Cell Death 6
333
PDCD6
0.0117

CDC42 Effector Protein 5
407
CDC42EP5
0.0157

LMCD1 Antisense RNA 1 (Head
469
LMCD1-AS1
0.0186

To Head)

CD72 Molecule
470
CD72
0.0187

Cell Division Cycle 37
531
CDC37
0.0221

Cyclin Dependent Kinase 2
550
CDK2AP2P1
0.0232

Associated Protein

2 Pseudogene 1

Coiled-Coil Domain Containing 62
553
CCDC62
0.0234

Coiled-Coil Domain Containing 173
649
CCDC173
0.0277

Interleukin 18 Receptor 1
703
IL18R1
0.0298

Adenomatosis Polyposis Coli
784
APCDD1L
0.0338

Down-Regulated 1-Like

C2 Calcium Dependent Domain
840
C2CD5
0.0363

Containing 5

Interleukin 17 Receptor D
848
IL17RD
0.0366

Coiled-Coil Domain Containing 65
909
CCDC65
0.0393

Cell Division Cycle 27 Pseudogene 2
978
CDC27P2
0.0432

Coiled-Coil Domain Containing 158
1006
CCDC158
0.0446

Example 2—Study 2; Synchronized Cell Cycle Gene Expression Test for Alzheimer's Disease; Cross-Validation of Genetic Differential Expression

The initial findings of the gene differential expression in synchronized skin fibroblasts, between the Alzheimer's Disease patients (AD; n=6) and the Non-Alzheimer's Disease Demented patients (Non-ADD; n=2), were cross-correlated with the second batch of samples (AD; n=2; Non-AD n=3). For the purpose of separating the two batches of samples, we called the first set of samples the “Training Set” and the second set of samples the “Validation Set.”

Methods

The genes were ranked in decreasing statistical significance order, i.e., with the highest statistical significance first (examples in Tables 4 and 5). The ranking is based on the t-test (two tailed, unequal variance) for the two groups of samples AD and Non-ADD. The comparison of the two lists of genes was made as described below.

Results

The number of statistically significant genes is similar in the training and validation sets (FIG. 8), with smaller differences for lower statistical significance (P<0.10) and larger differences for higher statistical significance (P<0.001). The larger difference for the higher statistical significance (P<0.001) could be due not only to the different number of samples in the validation set (5) when compared to the training set (8), but also to the different types of Non-ADD samples in the two sets. This difference suggests a high diversity of dysregulated pathways.

The majority of the genes (n=53) presented in Tables 4 and 5 are under highest statistical significance (P<0.001), and all of them are under high statistical significance (P<0.01). The presence of the first 40 genes from the training set (Table 4) was checked in the list of 2,077 genes from the validation set (P<0.10; FIG. 8). Similarly, the presence of the first 40 genes from the validation set (Table 5) was checked in the list of 2,103 genes from the training set (P<0.10; FIG. 8). The first 40 genes from Tables 4 and 5 are under highest statistical significance therefore it is very likely to have the highest impact in Alzheimer's disease detection, treatment, and pathways dysregulation. The cross-correlation of the first 40 genes in each set was made with a larger pool of genes from the opposite set (P<0.10) to accommodate the diversity in Non-ADD samples as well as to compensate for different numbers of samples in the validation (5) and training sets (8). However, in the end only the genes with similar statistical significance are considered as representing the core of dysregulation for AD.

The results of these initial findings in the highest statistically significant 40 genes suggests that about 81% of the genes which are dysregulated the training set are also dysregulated in the validation set. However, only about 7.5% of these genes show the same statistical significance in both training and validation set (Table 6).

Those genes showing the same statistical significance in the training and validation sets are at the core of the dysregulated pathways and will be very likely at the core of the genetic biomarkers for AD and at the core of the therapeutic targets for AD.

TABLE 4

Data for Differentially Expressed Genes from Study 2

First 40 differentially expressed genes in the

Training Set (6AD, 2 Non-ADD).

Training Set (6AD versus 2 Non-ADD)

T-test Two tailed

Rank
Gene name
Unequal Variance

1
PTCD2
3.48E−05

2
ST20
6.09E−05

3
AC090971.4
9.92E−05

4
EIF4A2P1
1.28E−04

5
CFAP97
1.38E−04

6
AL157871.3
1.44E−04

7
AC007325.4
2.26E−04

8
NR3C2
2.37E−04

9
C6orf58
2.38E−04

10
LINC01393
2.58E−04

11
AL031432.5
2.87E−04

12
AC005495.1
2.96E−04

13
NR2C2
3.07E−04

14
AL589684.1
3.26E−04

15
WDR17
3.81E−04

16
FCF1P6
4.04E−04

17
AC092818.1
4.30E−04

18
FGR
4.36E−04

19
HNRNPA3P10
4.41E−04

20
C17orf97
4.73E−04

21
FAM13A
5.15E−04

22
ARMCX5-
5.17E−04

GPRASP2

23
ZNF274
6.17E−04

24
IPO4
6.62E−04

25
CYB5D1
6.96E−04

26
AC005077.2
7.29E−04

27
ZNF547
7.57E−04

28
HIC1
7.58E−04

29
LINC01239
7.59E−04

30
MALRD1
7.87E−04

31
UVSSA
8.09E−04

32
KIAA1551
8.13E−04

33
SLC43A3
8.17E−04

34
BZW1P2
8.21E−04

35
HS6ST1P1
8.89E−04

36
CYB561D2
9.04E−04

37
SULT1A4
9.57E−04

38
AC138623.1
9.58E−04

39
RHPN1
9.68E−04

40
ST8SIA6
9.82E−04

TABLE 5

Data for Differentially Expressed Genes from Study 2

First 40 differentially expressed genes in the

Validation Set (2AD, 3 Non-ADD)

Validation Set (2 AD versus 3 Non-ADD)

T-test Two tailed

Rank
Gene name
Unequal Variance

1
RPL13AP6
2.36E−05

2
ARHGEF7
7.59E−05

3
ZNF623
9.37E−05

4
MYL12B
3.47E−04

5
RP11-
3.79E−04

500C11.3

6
EEF1A1P9
4.17E−04

7
EIF3M
5.39E−04

8
NDUFB6
5.93E−04

9
PGAM4
7.27E−04

10
XXYLT1-
8.29E−04

AS2

11
PIGX
8.60E−04

12
FAM71F2
8.74E−04

13
MPLKIP
9.28E−04

14
NDUFA8
9.30E−04

15
TCP10L
1.06E−03

16
ATG9B
1.09E−03

17
FAM229B
1.15E−03

18
RPS18P12
1.15E−03

19
RP3-
1.16E−03

340B19.2

20
SHFM1
1.27E−03

21
bP-21264C1.2
1.31E−03

22
FRMD5
1.37E−03

23
ATOX1
1.39E−03

24
ZCWPW1
1.43E−03

25
NENF
1.46E−03

26
RPS15AP38
1.61E−03

27
RP11-
1.69E−03

568N6.1

28
ZNF786
1.71E−03

29
ZNF3
1.74E−03

30
AP000688.14
1.75E−03

31
RP5-
1.84E−03

1125A11.6

32
HAUS2
1.87E−03

33
NDUFS1
1.95E−03

34
CAPNS1
2.05E−03

35
STEAP4
2.08E−03

38
PAN3
2.09E−03

37
RP5-940J5.6
2.10E−03

38
RP11-
2.10E−03

266K4.14

39
ATP5L
2.21E−03

40
PSMB9
2.21E−03

TABLE 6

Data for Differentially Expressed Genes from Study 2

Differentially expressed genes with similar statistical significance

(P < 0.05; n = 36) in the Training and Validation sets.

Cross-Validated Genes under Statistical Significance of P < 0.05

Number
Gene name
T-test Training
T-test Validation

1
AC004057.1
0.0246
0.0199

2
AC092651.1
0.0307
0.0332

3
ACP6
0.0332
0.0169

4
ADAM20
0.0321
0.0082

5
ASXL2
0.0397
0.0298

6
C2CD5
0.0363
0.0256

7
CARNS1
0.0281
0.0316

8
FAM149B1
0.0370
0.0150

9
GLIS3-AS1
0.0206
0.0409

10
IL18R1
0.0298
0.0399

11
LINC01393
0.0003
0.0115

12
LZIC
0.0338
0.0479

13
MAP1LC3B2
0.0260
0.0271

14
NHLH1
0.0032
0.0119

15
NORAD
0.0050
0.0424

16
NPPA-AS1_3
0.0048
0.0080

17
OSMR-AS1
0.0393
0.0241

18
PAN3
0.0088
0.0021

19
PHBP8
0.0256
0.0198

20
PSMB9
0.0378
0.0022

21
RAB3IP
0.0137
0.0186

22
RDH16
0.0117
0.0434

23
RFESDP1
0.0237
0.0043

24
RPL5
0.0220
0.0422

25
SCG2
0.0408
0.0295

26
SDHD
0.0328
0.0463

27
SHISA5
0.0188
0.0169

28
SLC45A3
0.0265
0.0359

29
SNHG14
0.0292
0.0259

30
TTC26
0.0023
0.0269

31
URB2
0.0051
0.0219

32
USMG5
0.0384
0.0340

33
WASF2
0.0027
0.0476

34
ZCWPW2
0.0145
0.0107

35
ZNF444
0.0158
0.0056

36
ZNF70
0.0301
0.0311

TABLE 7A

Top Cross-Validated Genes (P < 0.05); Drugs, Disorders and Encoded Proteins (Study 2)

Top Cross-Validated Genes (P < 0.05); Drugs and Known Disorders and Phenotypes

Gene

#
name
Drugs
Company
Disorders and Phenotypes

1
AC004057.1
NA
NA
Increased risk of

alias for

cardiovascular disease

RPS26P25

(CVD)

2
AC092651.1
NA
NA
Phenotype: bilirubin

alias for

measurement, glomerular

LOC100420889

filtration rate, chronic

kidney disease

3
ACP6
Flavin Mononucleotide
Pharma,
Schizophrenia, congenital

(Approved,
Nutra
heart disease (CHD)

Investigational),

Phosphoric acid

(Approved), Riboflavin

(Approved,

Investigational), 4-

Nitropheno (Experimental)

4
ADAM20
NA
NA
May be involved in sperm

maturation and/or

fertilization; a disintegrin

and metalloprotease

(active) domain 20;

membrane anchored cell

surface adhesion protein;

testis-specific with similarity

to fertilin-alpha

5
ASXL2
NA
NA
Shashi-Pena syndrome;

therapy-related

myelodysplastic syndrome;

ASXL2 and ASXL1 genes

were predicted cancer-

associated genes

6
C2CD5
NA
NA
Dynamically associated

with GLUT4-containing

glucose storage vesicles

(GSV) and plasma

membrane in response to

insulin stimulation

7
CARNS1
Gamma-Aminobutyric acid
Pharma,
Phenotype: mean

(Approved,
Nutra
corpuscular volume, mean

Investigational),

corpuscular hemoglobin,

Phosphoric acid

sunburn, body height,

(Approved), Adenosine

histidine metabolism,

monophosphate

homocarnosine

(Approved,

biosynthesis, arginine and

Investigational), Histidine

proline metabolism, beta-

(Approved), L-Arginin

alanine metabolism

(Approved)

(KEGG), lysine,

phenylalanine, tyrosine,

proline and tryptophan

catabolism

8
FAM149B1
NA
NA
Phenotype: systolic blood

pressure, Heschl's gyrus, a

core region of the auditory

cortex with highly variable

morphology, morphology

measurement

9
GLIS3-AS1
NA
NA
Diabetes mellitus,

Neonatal, with congenital

hypothyroidism; ndh

syndrome neonatal

diabetes mellitus with

congenital hypothyroidism

neonatal diabetes-

congenital hypothyroidism-

congenital glaucoma-

hepatic fibrosis-polycystic

kidneys syndrome

10
IL18R1
(43) Drugs for IL18R1
Pharma,
Ordinary smallpox, Variola,

Gene, Cisplatin
Nutra
growth hormone

(Approved), Clozapine

insensitivity syndrome,

(Approved), Cyclosporin A

pituitary dwarfism, growth

(Approved,

hormone receptor

Investigational),

deficiency, laron dwarfism,

Dexamethasone

laron-type isolated

(Approved,

somatotropin defect, laron-

Investigational),

type dwarfism, laron type

Etanercept (Approved,

pituitary dwarfism, primary

Investigational), Ethanol

growth hormone

(Approved), Filgrastim

insensitivity, primary growth

(Approved), glucose

hormone resistance, gh-r

(Approved), Haloperidol

deficiency, growth hormone

(Approved), Heparin

receptor defect, laron-type

(Approved,

pituitary dwarfism, laron-

Investigational), Infliximab

type short stature, primary

(Approved), Leflunomide

gh resistance, severe gh

(Approved,

insensitivity, complete

Investigational), Nitric

growth hormone

Oxide (Approved), Oxygen

insensitivity, gh receptor

(Approved), Polyethylene

deficiency, primary gh

glycol (Approved),

insensitivity, short stature

Prednisolone (Approved),

due to growth hormone

Progesterone (Approved),

resistance, lars, acute

Tacrolimus (Approved,

basophilic leukemia,

Investigational),

ehrlichiosis chafeensis,

Thalidomide (Approved,

hme human ehrlichial

Investigational), Zinc

infection, human monocytic

(Approved,

type, pneumoconiosis,

Investigational), Calcitriol

black lung, coal miner's

(Approved), calcium

pneumoconiosis, coal

(Approved), Serine

workers' lung, coal workers'

(Approved), cyclic amp

pneumoconiosis,

(Experimental), thymidine

melanoedema, coal

(Experimental,

worker's pneumoconiosis,

Investigational),

black lung disease, coal

Vesnarinone

workers pneumoconiosis.

(Investigational),

Ceramide, estrogen,

LY294002, mometasone

furoate, NMDA,

Progestins, Rapamycin,

alanine, arginine, cysteine,

glutamine, leucine,

phenylalanine, proline,

threonine, tyrosine

11
LINC01393
NA
NA
Phenotype: cytotoxicity

measurement, response to

clozapine, obesity

12
LZIC
NA
NA
Thiazolidinedione-induced

edema in diabetes.

Phenotype: leukocyte

count, systolic blood

pressure, resting heart rate

13
MAP1LC3B2
NA
NA
Plays a role in mitophagy

which contributes to

regulating mitochondrial

quantity and quality by

eliminating the

mitochondria to a basal

level to fulfill cellular energy

requirements and

preventing excess ROS

production; whereas LC3s

are involved in elongation

of the phagophore

membrane, the GABARAP

14
NHLH1
NA
NA
Cleft palate, isolated,

physical disorder, orofacial

cleft, cleft lip/palate-

ectodermal dysplasia

syndrome, split-hand/foot

malformation; May serve as

DNA-binding protein and

may be involved in the

control of cell-type

determination, possibly

within the developing

nervous system. Nascent

helix loop helix protein 1,

binding the E-box motif,

transiently expressed

during neurogenesis,

involved in retinal

development. Also

expressed in

neuroblastoma cell line

15
NORAD
Noradrenaline bitartrate
Tocris
Pancreatic cancer, bladder

cancer, esophageal cancer,

breast cancer, colorectal

cancer. Non-Coding RNA

activated by DNA damage

16
NPPA-AS1_3
Bumetanide (Approved),
Genentech, Inc., Validus
Atrial fibrillation, atrial

Furosemide (Approved),
Pharmaceuticals LLC,
standstill, atrial

Torsemide (Approved)
Leo Pharma, Apotex
cardiomyopathy with heart

Corporation, Sanis Health
block

Inc, Watson Labs, Roche

17
OSMR-AS1
NA
NA
OSMR Antisense RNA 1

18
PAN3
10Z-Hymenialdisine, JIB 04,
Tocris
Phenotype: monocyte

AZD 1208, G 5555,

percentage of leukocytes,

CRT 0066101

granulocyte percentage of

myeloid white cells,

myeloid white cell count,

lymphocyte percentage of

leukocytes

19
PHBP8
NA
NA
Adolescent idiopathic

scoliosis, total cholesterol

measurement, high density

lipoprotein cholesterol

measurement, Alzheimer's

disease, hippocampal

volume

20
PSMB9
Carfilzomib (Approved,
Amgen,
Proteasome-associated

Investigational),
Teva, Pfizer
autoinflammatory

Bortezomib (Approved,

syndrome 3, eosinophilic

Investigational), Kyprolis

variant of chromophobe

(Approved July 2012),

renal cell carcinoma,

Celastrol,

nasopharyngeal disease,

Dihydroeponemycin

Waterhouse-Friderichsen

syndrome, cardiac

sarcoidosis, epstein-barr

virus-associated gastric

carcinoma

21
RAB3IP
NA
NA
Involved in actin

remodeling and polarized

membrane transport;

Diastolic blood pressure

and memory performance

22
RDH16
Farnesol (Experimental),
NA
Platelet count, erythrocyte

NAD, Androstanediol,

count, perceived

Androsterone

unattractiveness to

mosquitos measurement

23
RFESDP1
NA
NA
Chronic obstructive

pulmonary disease,

smoking cessation

24
RPL5
Zinc (Approved,
NA
Mutations in this gene have

Investigational),

been identified in patients

with Diamond-Blackfan

Anemia (DBA).

Hemangioma, interatrial

communication

25
SCG2
Calcium (Approved),
Pharma,
Intracranial primitive

Acetylcholine (Approved),
Nutra
neuroectodermal tumor

Capsaicin (Approved),

(intracranial

Dexamethasone

pnet; intracranial primitive

(Approved,

neuroectodermal

Investigational), Dopamine

neoplasm), lymph node

(Approved), Glucose

cancer (lymph node

(Approved), Histamine

neoplasm, neoplasm of

(Approved,

lymph node), collagenous

Investigational), Lithium

colitis (microscopic colitis,

(Approved),

collagenous type colitis,

Norepinephrine

collagenous),

(Approved), Cyclic amp

neuroendocrine tumor

(Experimental), ATP

(neuroendocrine neoplasm,

(Investigational), 5-

neuroendocrine carcinoma,

Hydroxytryptamine,

neuroendocrine cancer,

Forskolin, Cysteine,

neuroendocrine neoplasia,

Tyrosine

carcinoma neuroendocrine,

neuroendocrine tumors,

carcinoma

neuroendocrine),

pheochromocytoma

(pheochromocytoma,

susceptibility to

pheochromocytoma,

modifier of

sporadic

pheochromocytoma/

secreting paraganglioma

chromaffin cell tumor

medullary chromaffinoma

medullary paraganglioma

pheochromoblastoma

pcc chromaffin cell

neoplasm

pheochromocytoma,

malignant)

26
SDHD
Succinic acid (Approved),
Pharma,
Paraganglioma and gastric

Formic acid (Approved,
Nutra
stromal sarcoma,

Experimental,

Paragangliomas, Cowden

Investigational),

syndrome, mitochondrial

Tromethamine (Approved),

complex ii deficiency,

Citric Acid (Approved)

carcinoid tumors, intestinal;

hereditary paraganglioma-

pheochromocytoma

syndrome

27
SHISA5
NA
NA
Vasculopathy, retinal, with

cerebral leukodystrophy,

aicardi-goutières syndrome

1 (cree encephalitis,

aicardi-goutieres

syndrome, ags,

encephalopathy with basal

ganglia calcification,

encephalopathy with

intracranial calcification and

chronic lymphocytosis of

cerebrospinal fluid,

encephalopathy, familial

infantile, with calcification

of basal ganglia and

chronic cerebrospinal fluid

lymphocytosis

pseudotoxoplasmosis

syndrome familial infantile

encephalopathy with

intracranial calcification and

chronic cerebrospinal fluid

lymphocytosis)

28
SLC45A3
NA
NA
Prostate cancer,

suppression of

tumorigenicity 12 (st12;

prostate adenocarcinoma

1; pac1), male reproductive

organ cancer

29
SNHG14
NA
NA
Angelman syndrome

(happy puppet syndrome),

Prader-Willi syndrome

(Prader-Labhart-Willi

syndrome), Gastric cancer

30
TTC26
NA
NA
Joubert syndrome (Joubert-

boltshauser syndrome);

Cerebelloparenchymal

disorder, cerebellar vermis

agenesis, agenesis of

cerebellar vermis,

cerebello-oculo-renal

syndrome, familial aplasia

of the vermis, cerebello-

oculo-renal syndrome

31
URB2
NA
NA
Hepatocellular carcinoma,

Buruli ulcer (buruli ulcer,

susceptibility to

mycobacterium ulcerans,

Bairnsdale ulcer, Daintree

ulcer, Mossman ulcer,

Searl ulcer). Phenotype:

red blood cell distribution

width, triglyceride

measurement, lipoprotein

cholesterol measurement,

high density lipoprotein

cholesterol measurement,

mean corpuscular

hemoglobin

32
USMG5
NA
NA
Schizophrenia, autism

alias for

spectrum disorder, worry

ATP5MD

measurement, systemic

lupus erythematosus,

unipolar depression,

response to escitalopram,

response to citalopram,

mood disorder

33
WASF2
Tyrosine
NA
Wiskott-Aldrich syndrome

(eczema-

thrombocytopenia-

immunodeficiency

syndrome), narcissistic

personality disorder,

substance abuse, tobacco

addiction, avoidant

personality disorder

(anxious personality

disorder)

34
ZCWPW2
NA
NA
Multiple sclerosis, systolic

blood pressure, alcohol

drinking, uterine fibroid,

cognitive decline

35
ZNF444
NA
NA
Chondrosarcoma,

extraskeletal myxoid

(extraskeletal myxoid

chondrosarcoma, myxoid

extraosseous

chondrosarcoma), coronary

artery disease,

microalbuminuria,

periodontitis, venous

thromboembolism

36
ZNF70
NA
NA
Phenotype: serum IgG

glycosylation

measurement, fractional

shortening, parathyroid

hormone measurement,

ejection fraction

measurement, left

ventricular systolic function

measurement

TABLE 7B

Top Cross-Validated Genes (P < 0.05); Drugs, Disorders and Encoded Proteins (Study 2)

Top Cross-Validated Genes (P < 0.05); Encoded Proteins

#
Gene name

1
AC004057.1
Ankyrin 2, ANK2-212, 206, 205, 208, 202, 203, 202, 201, 214, 224, 227

alias for

RPS26P25

2
AC092651.1
Anaphase Promoting Complex Subunit 1 Pseudogene.

alias for

LOC100420889

3
ACP6
This gene encodes a member of the histidine acid phosphatase protein

family. The encoded protein hydrolyzes lysophosphatidic acid, which is

involved in G protein-coupled receptor signaling, lipid raft modulation,

and in balancing lipid composition within the cell. Alternative splicing

results in multiple transcript variants. ACP6-001-Acid phosphatase 6

4
ADAM20
This gene encodes a member of the ADAM (a disintegrin and

metalloprotease domain) family. Members of this family are membrane-

anchored proteins structurally related to snake venom disintegrins, and

have been implicated in a variety of biological processes involving cell-

cell and cell-matrix interactions, including fertilization, muscle

development, and neurogenesis. The expression of this gene is testis-

specific. Disintegrin and metalloproteinase domain-containing protein 20

5
ASXL2
This gene encodes a member of a family of epigenetic regulators that

bind various histone-modifying enzymes and are involved in the

assembly of transcription factors at specific genomic loci. Naturally

occurring mutations in this gene are associated with cancer in several

tissue types (breast, bladder, pancreas, ovary, prostate, and blood). This

gene plays an important role in neurodevelopment, cardiac function,

adipogenesis, and osteoclastogenesis. Putative Polycomb group protein

ASXL2

6
C2CD5
C2 domain-containing protein 5

7
CARNS1
CARNS1 (EC 6.3.2.11), a member of the ATP-grasp family of ATPases,

catalyzes the formation of carnosine (beta-alanyl-L-histidine) and

homocarnosine (gamma-aminobutyryl-L-histidine), which are found

mainly in skeletal muscle and the central nervous system, respectively

(Drozak et al., 2010). Carnosine synthase 1. Catalyzes the synthesis of

carnosine and homocarnosine. Carnosine is synthesized more efficiently

than homocarnosine.

8
FAM149B1
Protein FAM149B1. Predicted intracellular proteins

9
GLIS3-AS1
GLIS3 Antisense RNA 1.

10
IL18R1
The protein encoded by this gene is a cytokine receptor that belongs to

the interleukin 1 receptor family. This receptor specifically binds

interleukin 18 (IL18), and is essential for IL18 mediated signal

transduction. IFN-alpha and IL12 are reported to induce the expression

of this receptor in NK and T cells. This gene along with four other

members of the interleukin 1 receptor family, including IL1R2, IL1R1,

ILRL.2 (IL-1 Rrp2), and IL1RL1 (T1/ST2), form a gene cluster on

chromosome 2q. Alternatively spliced transcript variants encoding

different isoforms have been found for this gene. Interleukin-18 receptor

1.

11
LINC01393
Long Intergenic Non-Protein Coding RNA 1393.

12
LZIC
Leucine zipper and CTNNBIP1 domain containing, isoform CRA_a.

Protein LZIC.

13
IMAP1LC3B2
Microtubule associated protein 1 light chain 3 beta 2.

14
NHLH1
The helix-loop-helix (HLH) proteins are a family of putative transcription

factors, some of which have been shown to play an important role in

growth and development of a wide variety of tissues and species. Four

members of this family have been clearly implicated in tumorigenesis via

their involvement in chromosomal translocations in lymphoid tumors:

MYC (MUM 190080), LYL1 (MIM 151440), E2A (MIM 147141), and SCL

(MIM 187040). Helix-loop-helix protein 1.

15
NORAD
Non-Coding RNA Activated By DNA Damage. Lee et al. (2016) found

that DNA damage induced NORAD expression in a p53 (TP53; 191170)-

dependent manner in HCT116 human colon cancer cells. Conditional

knockout or knockdown of NORAD expression caused multiple mitotic

errors, including anaphase bridges, mitotic slippage, and significant

aneuploidy. Mass spectrometric analysis of proteins that bound to

NORAD identified Pumilio-2 (PUM2; 607205), a protein that destabilizes

mRNAs by binding to PREs in their 3-prime UTRs. NORAD functions as

a molecular decoy for Pumilio proteins and stabilizes Pumilio target

mRNAs. Using combined RNA antisense purification and quantitative

mass spectrometry, Munschauer et al. (2018) showed that NORAD

interacts with proteins involved in DNA replication and repair in steady-

state cells and localizes to the nucleus upon stimulation with replication

stress or DNA damage. Cells depleted for NORAD or RBMX displayed

an increased frequency of chromosome segregation defects, reduced

replication fork velocity, and altered cell-cycle progression.

16
NPPA-AS1_3
Non-protein coding gene

17
OSMR-AS1
An RNA Gene, and is affiliated with the non-coding RNA class. OSMR =

Oncostatin M receptor This gene encodes a member of the type I

cytokine receptor family. The encoded protein heterodimerizes with

interleukin 6 signal transducer to form the type II oncostatin M receptor

and with interleukin 31 receptor A to form the interleukin 31 receptor,

and thus transduces oncostatin M and interleukin 31 induced signaling

events. Mutations in this gene have been associated with familial

primary localized cutaneous amyloidosis.

18
PAN3
PAN3 poly(A) specific ribonuclease subunit.PAB-dependent poly(A)-

specific ribonuclease subunit PAN3. The N-terminal zinc finger binds to

poly(A) RNA. Belongs to the protein kinase superfamily. PAN3 family.

Regulatory subunit of the poly(A)-nuclease (PAN) deadenylation

complex, one of two cytoplasmic mRNA deadenylases involved in

general and miRNA-mediated mRNA turnover. PAN specifically shortens

poly(A) tails of RNA and the activity is stimulated by poly(A)-binding

protein (PABP). PAN deadenylation is followed by rapid degradation of

the shortened mRNA tails by the CCR4-NOT complex. Deadenylated

mRNAs are then degraded by two alternative mechanisms, namely

exosome-mediated 3′-5′ exonucleolytic degradation, or deadenlyation-

dependent mRNA decapping and subsequent 5′-3′ exonucleolytic

degradation by XRN1. PAN3S acts as a positive regulator for PAN

activity, recruiting the catalytic subunit PAN2 to mRNA via its interaction

with RNA and PABP, and to miRNA targets via its interaction with

GW182 family proteins.

19
PHBP8
Prohibitin Pseudogene 8.

20
PSMB9
Proteasome subunit beta 9

The proteasome is a multicatalytic proteinase complex with a highly

ordered ring-shaped 20S core structure. The core structure is composed

of 4 rings of 28 non-identical subunits; 2 rings are composed of 7 alpha

subunits and 2 rings are composed of 7 beta subunits. Proteasomes are

distributed throughout eukaryotic cells at a high concentration and

cleave peptides in an ATP/ubiquitin-dependent process in a non-

lysosomal pathway. An essential function of a modified proteasome, the

immunoproteasome, is the processing of class I MHC peptides. This

gene encodes a member of the proteasome B-type family, also known

as the T1B family, that is a 20S core beta subunit. This gene is located

in the class II region of the MHC (major histocompatibility complex).

Expression of this gene is induced by gamma interferon and this gene

product replaces catalytic subunit 1 (proteasome beta 6 subunit) in the

immunoproteasome. Proteolytic processing is required to generate a

mature subunit.

21
RAB3IP
RAB3A interacting protein is a Protein Coding gene. Among its related

pathways are Cargo trafficking to the periciliary membrane and Vesicle-

mediated transport.

22
RDH16
Retinol dehydrogenase 16

23
RFESDP1
Rieske (Fe—S) Domain Containing Pseudogene 1 is a Rieske (Fe—S)

Domain Containing Pseudogene 1.

24
RPL5
Ribosomal protein L5. Ribosomes, the organelles that catalyze protein

synthesis, consist of a small 40S subunit and a large 60S subunit.

Together these subunits are composed of four RNA species and

approximately 80 structurally distinct proteins. This gene encodes a

member of the L18P family of ribosomal proteins and component of the

60S subunit. The encoded protein binds 5S rRNA to form a stable

complex called the 5S ribonucleoprotein particle (RNP), which is

necessary for the transport of nonribosome-associated cytoplasmic 5S

rRNA to the nucleolus for assembly into ribosomes. The encoded protein

may also function to inhibit tumorigenesis through the activation of

downstream tumor suppressors and the downregulation of oncoprotein

expression. Mutations in this gene have been identified in patients with

Diamond-Blackfan Anemia (DBA). This gene is co-transcribed with the

small nucleolar RNA gene U21, which is located in its fifth intron. As is

typical for genes encoding ribosomal proteins, there are multiple

processed pseudogenes of this gene dispersed throughout the genome.

25
SCG2
Secretogranin II. The protein encoded by this gene is a member of the

chromogranin/secretogranin family of neuroendocrine secretory proteins.

Studies in rodents suggest that the full-length protein, secretogranin II, is

involved in the packaging or sorting of peptide hormones and

neuropeptides into secretory vesicles. The full-length protein is cleaved

to produce the active peptide secretoneurin, which exerts chemotaxic

effects on specific cell types, and EM66, whose function is unknown

26
SDHD
Succinate Dehydrogenase Complex Subunit D. This gene encodes a

member of complex II of the respiratory chain, which is responsible for

the oxidation of succinate. The encoded protein is one of two integral

membrane proteins anchoring the complex to the matrix side of the

mitochondrial inner membrane. Mutations in this gene are associated

with the formation of tumors, including hereditary paraganglioma.

Transmission of disease occurs almost exclusively through the paternal

allele, suggesting that this locus may be maternally imprinted. There are

pseudogenes for this gene on chromosomes 1, 2, 3, 7, and 18.

Alternative splicing results in multiple transcript variant

27
SHISA5
Shisa family member 5. This gene encodes a member of the shisa

family. The encoded protein is localized to the endoplasmic reticulum,

and together with p53 induces apoptosis in a caspase-dependent

manner. Alternative splicing results in multiple transcript variants.

Related pseudogenes of this gene are found on chromosome X. Can

induce apoptosis in a caspase-dependent manner and plays a role in

p53/TP53-dependent apoptosis. Induced in a p53/TP53-dependent

manner in response to cellular stress.

28
SLC45A3
Solute carrier family 45 member 3. Hexose transport. Transport of

glucose and other sugars, bile salts and organic acids, metal ions and

amine compounds. Phenotype: microRNAs in cancer, transcriptional

misregulation in cancer, and metabolism.

29
SNHG14
Small Nucleolar RNA Host Gene 14. This gene is located within the

Prader-Willi Syndrome critical region on chromosome 15 and is

imprinted and expressed from the paternal allele. It encodes a

component of the small nuclear ribonucleoprotein complex, which

functions in pre-mRNA processing and may contribute to tissue-specific

alternative splicing. Alternative promoter use and alternative splicing

result in a multitude of transcript variants encoding the same protein.

Transcript variants that initiate at the CpG island-associated imprinting

center may be bicistronic and also encode the SNRPN upstream reading

frame protein (SNURF) from an upstream open reading frame. In

addition, long spliced transcripts for small nucleolar RNA host gene 14

(SNHG14) may originate from the promoters at this locus and share

exons with this gene. Alterations in this region are associated with

parental imprint switch failure, which may cause Angelman syndrome or

Prader-Willi syndrome.

30
TTC26
Tetratricopeptide Repeat Domain 26. Cytoplasmic expression in few

tissues, distinct in cilia. Component of the intraflagellar transport (IFT)

complex B required for transport of proteins in the motile cilium.

Required for transport of specific ciliary cargo proteins related to motility,

while it is neither required for IFT complex B assembly or motion nor for

cilium assembly. Required for efficient coupling between the

accumulation of GLI2 and GLI3 at the ciliary tips and their dissociation

from the negative regulator SUFU. Plays a key role in maintaining the

integrity of the IFT complex B and the proper ciliary localization of the

IFT complex B components. Not required for IFT complex A ciliary

localization or function. Essential for maintaining proper microtubule

organization within the ciliary axoneme.

31
URB2
URB2 ribosome biogenesis 2 homolog. High density

32
USMG5 alias
Up-regulated during skeletal muscle growth 5 homolog. Plays a critical

for ATP5MD
role in maintaining the ATP synthase population in mitochondria.

USMG5_HUMAN, Q96IX5 Transactivated by SBP1.

33
WASF2
WASP Family Member 2, This gene encodes a member of the Wiskott-

Aldrich syndrome protein family. The gene product is a protein that

forms a multiprotein complex that links receptor kinases and actin.

Binding to actin occurs through a C-terminal verprolin homology domain

in all family members. The multiprotein complex serves to tranduce

signals that involve changes in cell shape, motility or function. The

published map location (PMID: 10381382) has been changed based on

recent genomic sequence comparisons, which indicate that the

expressed gene is located on chromosome 1, and a pseudogene may

be located on chromosome X. Two transcript variants encoding different

isoforms have been found for this gene. Downstream effector molecule

involved in the transmission of signals from tyrosine kinase receptors

and small GTPases to the actin cytoskeleton. Promotes formation of

actin filaments. Part of the WAVE complex that regulates lamellipodia

formation. The WAVE complex regulates actin filament reorganization

via its interaction with the Arp 2/3 complex.

34
ZCWPW2
Zinc Finger CW-Type And PWWP Domain Containing 2.

35
ZNF444
Zinc finger protein 444. This gene encodes a zinc finger protein that

activates transcription of a scavenger receptor gene involved in the

degradation of acetylated low density lipoprotein (Ac-LDL) (PMID:

11978792). This gene is located in a cluster of zinc finger genes on

chromosome 19 at q13.4. A pseudogene of this gene is located on

chromosome 15. Multiple transcript variants encoding different isoforms

have been found for this gene.

36
ZNF70
Zinc Finger Protein 70. May be involved in transcriptional regulation.

TABLE 8

Protein Networks (Study 2)

Average

Average
local

Number
Number
node
clustering

Number
Gene name
of nodes
of edges
degree
coefficient

1
AC004057.1
NA
NA
NA
NA

2
AC092651.1
NA
NA
NA
NA

3
ADAM20
26
64
4.92
0.681

4
ASXL2
26
212
16.3
0.876

5
C2CD5
26
239
18.4
0.98

6
CARNS1
26
209
16.1
0.84

7
FAM149B1
2

1
1

8
GLIS3-
NA
NA
NA
NA

AS1FAM149B1

9
IL18R1
20
90
9
0.768

10
LINC01393
NA
NA
NA
NA

11
LINC01393
NA
NA
NA
NA

12
LZIC
2
1
1
1

13
MAP1LC3B2
NA
NA
NA
NA

14
NHLH1
26
54
4.15
0.504

15
NORAD
NA
NA
NA
NA

16
NPPA-AS1_3
NA
NA
NA
NA

17
OSMR-AS1
NA
NA
NA
NA

18
PAN3
31
114
7.35
0.801

19
PHBP8
NA
NA
NA
NA

20
PSMB9
26
322
24.8
0.992

21
RAB3IP
26
301
23.2
0.997

22
RDH16
26
39
3
0.613

23
RFESDP1
NA
NA
NA
NA

24
RPL5
26
323
24.8
0.994

25
SCG2
18
27
3
0.586

26
SDHD
26
115
8.85
0.769

27
SHISA5
10
5
1
0.6

28
SLC45A3
14
6
0.857
0.381

29
SNHG14
NA
NA
NA
NA

30
TTC26
26
301
23.2
0.997

31
URB2
6
1
0.333
0.333

32
USMG5
26
325
25
1

33
WASF2
51
NA
NA
NA

34
ZCWPW2
NA
NA
NA
NA

35
ZNF444
26
99
7.62
0.675

36
ZNF70
26
126
9.69
0.612

Example 3—Study 2; TPM Values

Reference Intervals

The average and standard deviations were calculated for the transcripts per million (TPM) values for each of the two groups—Alzheimer's disease (AD) and Non-Alzheimer's Disease Demented (Non-ADD) for each gene. The reference intervals were then calculated according to Horn and Pesce (Reference Intervals: A User's Guide. Paul S. Horn and Amadeo J. Pesce. Washington, D.C.: AACC Press, 2005, ISBN 1-59425-035-9) as the average plus minus two standard deviations. The reference intervals calculated in this way assure that 95% of all the possible values in each population (AD or non-ADD) are considered.

Gap Between AD and Non-ADD

If there is no overlap between the reference intervals of AD and Non-ADD, there is a gap between the two bell-shaped curves and that indicates unequivocal diagnosis.

If there is an overlap in the reference intervals for AD and Non-ADD (light grey in Table 9), then there is a possibility of having a false positive or a false negative in the diagnosis. The genes that show overlap in the reference intervals, i.e., no gap (light grey) were eliminated from the final vector diagnosis. The genes that show an average of zero in one of the groups, either in the AD group or in the Non-ADD group, were also eliminated.

Cut-Off for Each Gene

The cut-offs for each of the remaining 26 genes (Table 10) was determined as the middle of the gap in the reference intervals.

Genetic Vector AD Diagnosis

The AD diagnosis is based on the 26 components/genes of the vector. For each one of the components, the greater than (>) or smaller than (<) the cut-off value is indicated for each gene, in the last column.

TABLE 9

Gene Expression Levels (TPM) Indicative of AD (Study 2)

Number
Gene name
Cut-Off
AD Diagnosis

1
AC004057.1
161.81
>161.81

2*
AC092651.1
5.40
>5.40

3
ACP6
2.84
<2.84

4
ADAM20
0.16
<0.16

5
ASXL2
0.74
<0.76

6
C2CD5
28.76
>28.76

7
CARNS1
0.16
>0.15

8
FAM149B1
22.60
<22.60

9**
GLIS3-AS1
0.11
>0.11

10*
IL18R1
1.21
<0.88

11
LINC01393
1.00
>0.86

12*
LZIC
7.14
>7.14

13
MAP1LC3B2
4.41
>4.41

14
NHLH1
0.27
<0.27

15*
NORAD
61.03
>61.03

16
NPPA-AS1_3
2.54
<2.54

17*
OSMR-AS1
1.37
>1.37

18
PAN3
15.98
<15.98

19
PHBP8
0.98
>0.98

20
PSMB9
18.00
>18.00

21
RAB3IP
0.50
<0.50

22*
RDH16
0.58
<0.58

23**
RFESDP1
0.14
<0.00

24
RPL5
794.93
>794.88

25
SCG2
0.68
<0.68

26*
SDHD
40.92
>40.92

27
SHISA5
107.32
>107.32

28
SLC45A3
1.11
<1.11

29*
SNHG14
26.70
<26.70

30
TTC26
2.41
>2.41

31
URB2
2.28
>2.28

32
USMG5
129.13
>129.13

33
WASF2
23.74
>23.74

34
ZCWPW2
1.15
>1.15

35
ZNF444
17.60
<16.73

36
ZNF70
0.87
>0.87

*= no gap

**= zero average in one group

TABLE 10A

Gene Expression Levels (TPM) Indicative of AD (Study 2)

Number
Gene name
Cut-Off
AD Diagnosis

1
AC004057.1
161.81
>161.81

2
ACP6
2.84
<2.84

3
ADAM20
0.16
<0.16

4
ASXL2
0.74
<0.76

5
C2CD5
28.76
>28.76

6
CARNS1
0.16
>0.15

7
FAM149B1
22.60
<22.60

8
LINC01393
1.00
>0.86

9
MAP1LC3B2
4.41
>4.41

10
NHLH1
0.27
<0.27

11
NPPA-AS1_3
2.54
<2.54

12
PAN3
15.98
<15.98

13
PHBP8
0.98
>0.98

14
PSMB9
18.00
>18.00

15
RAB3IP
0.50
<0.50

16
RPL5
794.93
>794.88

17
SCG2
0.68
<0.68

18
SHISA5
107.32
>107.32

19
SLC45A3
1.11
<1.11

20
TTC26
2.41
>2.41

21
URB2
2.28
>2.28

22
USMG5
129.13
>129.13

23
WASF2
23.74
>23.74

24
ZCWPW2
1.15
>1.15

25
ZNF444
17.60
<16.73

26
ZNF70
0.87
>0.87

TABLE 10B

Gene Expression Levels (TPM) Indicative of

AD (Study 2) (Ranked According to % Change)

Rank
Gene Name
Cut-Off
AD Diag.
% Change

1
CARNS1
0.16
>0.15
347

2
PHBP8
0.98
>0.98
299

3
ZCWPW2
1.15
>1.15
170

4
MAP1LC3B2
4.41
>4.41
142

5
LINC01393
1
>0.86
127

6
TTC26
2.41
>2.41
110

7
PSMB9
18
>18.00
99

8
AC004057.1
161.81
>161.81
94

9
RPL5
794.93
>794.88
94

10
NPPA-AS1_3
2.54
<2.54
−86

11
URB2
2.28
>2.28
85

12
SCG2
0.68
<0.68
−81

13
RAB3IP
0.5
<0.50
−80

14
ASXL2
0.74
<0.76
−77

15
NHLH1
0.27
<0.27
−75

16
PAN3
15.98
<15.98
−73

17
WASF2
23.74
>23.74
69

18
USMG5
129.13
>129.13
66

19
SLC45A3
1.11
<1.11
−65

20
ACP6
2.84
<2.84
−57

21
SHISA5
107.32
>107.32
53

22
ADAM20
0.16
<0.16
−51

23
ZNF70
0.87
>0.87
34

24
ZNF444
17.6
<16.73
−18

25
FAM149B1
22.6
<22.60
−16

26
C2CD5
28.76
>28.76
3

TABLE 11

AD/NDC Dysregulated Genes under a Statistical Significance of P < 0.05

AD vs NDC; Statistical Significance T-test, to tailed, unequal variance

Training
Validation

#
Gene name
Set
Set

1
ACIN1
9.77E−05
2.39E−02

2
ACO2
1.40E−02
3.54E−02

3
ACSL4
4.02E−05
1.25E−03

4
ACTR1A
8.44E−03
3.92E−02

5
ADAM20
3.17E−02
2.08E−02

6
ADAMTS14
2.85E−02
3.31E−02

7
ADIPOR2
5.62E−03
4.83E−02

8
AHCY
1.24E−04
1.40E−02

9
AL591845.1
2.86E−02
4.82E−02

10
ALG5
7.60E−04
4.24E−02

11
AMMECR1
2.48E−02
1.72E−02

12
ANAPC13
2.54E−04
4.01E−02

13
ANGPTL1
4.34E−02
4.87E−02

14
ANXA7
7.94E−03
4.77E−02

15
AOX1
3.60E−02
1.93E−03

16
ARAP3
1.09E−02
1.68E−02

17
ARF3
4.13E−06
6.92E−03

18
ARPP19
1.77E−04
4.06E−02

19
ARSD
6.72E−03
3.52E−02

20
ASAP3
1.98E−02
1.65E−02

21
ASTE1
2.71E−03
1.54E−02

22
ATF6
1.02E−02
2.17E−02

23
ATP11B
3.43E−02
1.98E−02

24
ATP5F1
2.43E−02
8.83E−03

25
AURKC
3.23E−04
2.34E−02

26
AVPI1
1.14E−02
1.20E−02

27
B4GALT4
2.79E−03
2.86E−02

28
BCORL1
2.53E−02
3.19E−02

29
BICC1
1.24E−03
7.26E−03

30
BLVRA
7.50E−05
2.98E−02

31
BTBD1
3.78E−03
1.29E−02

32
BZW2
1.19E−03
4.23E−03

33
C11orf63
1.13E−02
4.42E−02

34
C12orf49
7.61E−05
2.82E−02

35
C20orf24
1.17E−02
3.08E−02

36
C3orf14
1.03E−02
2.70E−04

37
CAPNS1
1.59E−02
1.50E−02

38
CAPRIN1
4.44E−05
1.16E−02

39
CCAR1
2.02E−02
4.63E−02

40
CCDC114
1.90E−02
3.22E−02

41
CCDC146
2.46E−06
2.44E−04

42
CCDC6
8.24E−04
3.96E−02

43
CCDC65
2.51E−02
2.34E−03

44
CD58
8.66E−03
3.21E−02

45
CDC42
1.77E−03
4.97E−02

46
CDK14
6.27E−05
7.92E−04

47
CDK4
9.89E−03
2.78E−03

48
CEP192
8.79E−03
2.84E−02

49
CHMP2B
1.98E−03
4.55E−02

50
CHMP4B
5.87E−04
4.13E−02

51
CLNS1A
2.20E−03
7.24E−03

52
CLTA
2.43E−03
1.95E−03

53
CNIH1
4.72E−02
3.93E−02

54
COPS3
1.72E−02
2.20E−03

55
CRKL
1.87E−03
2.38E−02

56
CSAD
9.34E−04
4.75E−02

57
CSE1L
7.75E−03
4.24E−02

58
CSNK2A2
1.06E−03
2.01E−02

59
CUL1
1.04E−02
4.55E−02

60
CYB5B
3.96E−05
4.98E−02

61
CYP19A1
3.52E−02
1.94E−02

62
CYP20A1
4.61E−05
1.07E−02

63
CYP2E1
2.10E−03
1.85E−02

64
DCTN6
4.62E−03
3.58E−02

65
DDHD1
4.19E−02
2.73E−03

66
DDX1
2.35E−03
4.13E−02

67
DERA
2.28E−02
2.46E−03

68
DESI2
3.05E−04
3.95E−02

69
DMAC2
4.73E−03
1.45E−03

70
DNAJB5
1.06E−02
3.50E−02

71
DNAJC1
2.30E−03
2.85E−02

72
DNASE2
1.07E−02
1.38E−02

73
DOCK3
4.97E−02
4.86E−02

74
EAPP
1.43E−02
3.95E−02

75
ECH1
7.14E−04
3.95E−02

76
ECHDC2
4.65E−04
4.59E−02

77
EDEM3
3.12E−02
2.62E−02

78
EEF1B2
1.06E−04
2.21E−02

79
EHD2
3.84E−05
2.07E−02

80
EIF2AK2
3.74E−05
2.39E−02

81
EIF2B3
1.82E−02
4.39E−02

82
EIF2S2P4
8.92E−03
4.07E−03

83
EIF3E
2.96E−06
4.92E−02

84
EIF3I
2.32E−05
3.55E−02

85
EIF4G2
2.44E−02
3.21E−02

86
ELOB
4.55E−04
1.32E−02

87
EML2
5.41E−03
2.37E−02

88
EPB41L3
8.58E−04
4.53E−02

89
ERH
1.75E−05
3.50E−03

90
ERI1
6.23E−05
4.43E−02

91
ERICH1
2.69E−02
4.36E−02

92
EXOC1
2.82E−03
4.05E−02

93
EXOC4
1.91E−03
3.91E−03

94
FAM160A2
3.69E−05
2.39E−03

95
FAM71F1
2.65E−02
2.04E−02

96
FAM8A1
1.76E−04
3.94E−02

97
FBL
5.86E−04
3.48E−02

98
FBXL8
5.21E−04
2.24E−02

99
FBXO9
1.73E−02
4.21E−03

100
FDX1
6.84E−05
4.10E−03

101
FER1L4
2.46E−02
4.64E−02

102
FGF7
7.15E−03
4.28E−02

103
FRG1
4.36E−04
4.32E−02

104
FUCA2
9.44E−05
3.40E−02

105
FUT8
7.94E−03
1.84E−02

106
GBE1
5.60E−04
3.44E−02

107
GDE1
1.00E−04
1.68E−02

108
GIMAP2
1.42E−02
4.27E−02

109
GINM1
2.45E−03
3.70E−02

110
GLUL
2.28E−03
8.91E−03

111
GOLGA5
3.99E−04
3.16E−03

112
GOLPH3
1.31E−04
9.79E−03

113
GPNMB
2.61E−02
3.06E−02

114
GTPBP10
6.60E−04
7.96E−03

115
GUCD1
9.65E−04
2.85E−02

116
HACD3
2.06E−02
3.43E−02

117
HADHA
3.06E−02
4.04E−02

118
HAUS2
7.22E−04
1.15E−02

119
HBP1
8.17E−04
4.56E−03

120
HEMK1
1.55E−03
4.40E−02

121
HGFAC
4.61E−03
4.10E−02

122
HNRNPC
1.47E−04
3.47E−02

123
HNRNPM
2.00E−02
1.75E−02

124
HNRNPUL1
4.17E−04
2.26E−02

125
HOOK2
6.32E−04
3.94E−02

126
HOXA11
9.67E−04
3.35E−02

127
HOXC8
1.09E−03
3.15E−02

128
HOXD3
1.99E−03
2.56E−02

129
HSP90AA1
1.11E−03
4.29E−02

130
HTATSF1
9.69E−03
3.51E−03

131
IARS2
2.48E−02
4.62E−02

132
ICAM1
3.19E−02
3.08E−02

133
ICMT
4.19E−03
8.11E−03

134
IK
1.41E−02
3.75E−02

135
IL1R1
3.92E−03
2.75E−03

136
IL6ST
1.43E−03
4.09E−02

137
JDP2
2.68E−02
7.30E−03

138
KCNK2
2.27E−03
1.16E−04

139
KCTD1
6.62E−06
1.36E−02

140
KIAA1468
1.89E−02
2.95E−02

141
LAMTOR5
8.82E−04
3.72E−02

142
LAP3
2.94E−02
3.90E−03

143
LAPTM4B
1.64E−02
1.18E−02

144
LRRC1
3.91E−03
2.36E−02

145
LRRC32
3.41E−02
4.93E−03

146
MAN1A1
9.85E−03
2.61E−02

147
MAP1LC3B
2.33E−05
4.30E−02

148
MAPK1
3.18E−04
2.99E−02

149
MAPKAP1
1.51E−03
6.43E−03

150
MAX
2.62E−02
9.70E−03

151
MED4
4.39E−04
3.60E−02

152
MFAP1
4.14E−02
3.95E−03

153
MICAL1
1.13E−02
3.27E−02

154
MRM2
1.01E−03
1.26E−02

155
MRO
2.60E−04
3.98E−03

156
MRPL3
6.54E−04
2.97E−02

157
MRPS15
3.63E−06
4.25E−02

158
MRPS35
7.52E−03
3.72E−02

159
MSH3
1.63E−05
2.00E−03

160
MTPN
3.87E−04
1.25E−02

161
NAA50
2.03E−03
3.88E−02

162
NAMPT
4.20E−03
3.18E−02

163
NCALD
4.79E−02
1.27E−02

164
NCBP1
4.18E−02
4.87E−02

165
NCL
2.31E−02
1.34E−02

166
NDFIP1
8.40E−06
9.05E−03

167
NDUFA8
1.49E−03
1.47E−02

168
NDUFS1
2.08E−02
1.06E−02

169
NINL
8.97E−04
3.97E−02

170
NOL10
2.66E−02
6.16E−03

171
NUCKS1
1.50E−04
2.57E−03

172
NUDT15
1.18E−04
8.12E−03

173
NUFIP2
3.64E−02
3.66E−02

174
OGFRL1
8.48E−05
2.19E−02

175
OLFML3
2.52E−02
7.71E−03

176
OMD
4.12E−02
2.69E−03

177
OSTF1
2.08E−04
3.00E−02

178
PARK7
1.11E−03
9.71E−03

179
PARP3
5.65E−03
4.87E−02

180
PCNA
5.00E−04
3.98E−03

181
PDE4C
4.49E−02
2.91E−02

182
PDE8A
3.73E−02
3.86E−02

183
PHF5A
9.88E−04
4.14E−02

184
PHKA2
9.25E−04
4.59E−02

185
POLA1
4.33E−03
3.38E−02

186
POLR1E
5.93E−03
2.14E−02

187
PPM1G
1.07E−02
4.36E−02

188
PPP3CA
5.33E−03
5.42E−03

189
PRCP
5.97E−03
9.55E−03

190
PRDX5
8.75E−06
9.88E−03

191
PRELID3B
2.07E−04
4.22E−02

192
PRKAR2A
6.46E−03
2.82E−02

193
PRKAR2B
3.37E−03
2.18E−02

194
PRPS2
2.74E−04
6.87E−03

195
PSMA4
1.38E−02
2.65E−02

196
PSMA6
8.45E−04
5.22E−03

197
PSMB7
2.65E−06
6.28E−03

198
PSMC1
3.34E−02
3.42E−02

199
PSMD10
2.00E−06
8.74E−03

200
PSMG2
3.96E−05
3.65E−02

201
PYGL
5.81E−03
9.89E−03

202
QRSL1
7.24E−03
9.83E−03

203
RAB11A
4.74E−05
2.11E−02

204
RAB22A
9.93E−05
1.48E−02

205
RAB7A
6.78E−05
5.44E−03

206
RALBP1
5.12E−03
2.80E−02

207
RANBP6
1.24E−02
3.49E−02

208
RASA4
1.86E−02
2.40E−02

209
RNF113A
1.46E−05
1.22E−02

210
ROMO1
1.53E−02
4.21E−02

211
RP2
1.09E−04
1.12E−02

212
RPGRIP1L
2.38E−02
3.66E−02

213
RPL18A
8.79E−06
4.89E−02

214
RPL19
2.65E−05
1.55E−02

215
RPL22
1.10E−05
1.65E−02

216
RPL24
2.46E−05
1.33E−02

217
RPL27
4.97E−03
3.09E−02

218
RPL31
4.91E−05
1.76E−02

219
RPL34
1.11E−05
2.06E−02

220
RPL35
2.46E−06
2.18E−02

221
RPL5
5.81E−07
1.27E−02

222
RPS10
9.28E−04
2.67E−03

223
RPS12
2.13E−03
2.73E−03

224
RPS13
9.36E−05
6.52E−03

225
RPS20
2.42E−03
2.69E−02

226
RPS25
1.55E−03
3.63E−02

227
RPS6
6.63E−07
1.53E−03

228
RRAGC
9.09E−05
3.51E−02

229
RRP36
2.58E−03
9.89E−03

230
RSL24D1
7.83E−04
2.26E−02

231
RTN3
6.00E−04
1.06E−02

232
SARAF
1.86E−02
2.60E−03

233
SCRN1
9.33E−04
2.90E−03

234
SDHB
1.10E−02
4.07E−02

235
SEH1L
4.17E−03
4.26E−02

236
SERINC1
2.30E−03
9.64E−03

237
SERINC3
8.05E−05
7.58E−04

238
SET
6.47E−04
6.63E−03

239
SF3A1
2.13E−02
3.64E−02

240
SF3B1
5.38E−06
3.94E−03

241
SGPP1
1.66E−05
3.69E−02

242
SKAP2
1.31E−02
3.64E−02

243
SLC17A5
4.10E−02
3.67E−02

244
SLC25A1
1.67E−02
5.94E−03

245
SLC31A2
9.74E−03
1.56E−05

246
SLC9A5
1.87E−03
1.89E−02

247
SLF2
4.46E−03
4.43E−02

248
SMAD9
1.94E−02
4.57E−02

249
SMC2
7.22E−03
4.87E−03

250
SMS
5.19E−04
7.28E−03

251
SNRPB2
2.32E−04
2.76E−02

252
SNRPF
1.96E−03
4.96E−02

253
SNW1
2.17E−02
2.31E−02

254
SNX6
1.41E−02
4.52E−02

255
SNX8
1.41E−02
2.39E−02

256
SOX6
2.04E−02
2.04E−02

257
SPA17
2.88E−03
4.12E−02

258
SPCS2
4.82E−04
4.60E−02

259
SQLE
2.40E−06
4.27E−02

260
SRI
2.15E−02
3.60E−02

261
STAU1
6.40E−04
3.47E−02

262
SUPT7L
4.59E−03
8.10E−03

263
TACO1
1.21E−02
1.09E−02

264
TAF12
2.82E−03
1.50E−02

265
TAF8
1.84E−03
4.47E−03

266
TAX1BP1
4.69E−03
3.79E−02

267
TBC1D9
1.77E−03
1.23E−02

268
TFPI
2.22E−02
4.33E−02

269
TGM1
5.91E−03
7.94E−03

270
THAP10
4.26E−03
1.97E−02

271
THG1L
2.54E−03
8.18E−03

272
TIMP2
3.90E−03
2.95E−03

273
TMEM14C
9.85E−03
2.50E−02

274
TMEM19
2.26E−04
7.78E−03

275
TMEM30A
3.46E−03
4.66E−02

276
TMEM54
3.80E−03
1.04E−04

277
TMPO
2.62E−02
2.98E−03

278
TNFRSF19
6.73E−03
2.11E−02

279
TPT1
8.28E−03
3.04E−03

280
TRAM1
2.91E−03
4.06E−02

281
TRIM24
2.95E−06
4.03E−02

282
TRIM35
1.46E−02
1.85E−02

283
TSNAXIP1
5.94E−03
3.39E−02

284
TTC17
1.06E−04
1.83E−02

285
TUSC3
2.95E−02
1.29E−02

286
TXLNG
4.91E−02
4.56E−02

287
TXN2
4.14E−04
1.16E−02

288
TXNL4B
1.53E−02
4.38E−02

289
UBE2G1
4.25E−03
7.21E−03

290
UBE2R2
8.94E−04
4.63E−02

291
UCHL5
6.11E−03
1.14E−02

292
UQCC2
3.53E−03
1.58E−02

293
USP35
2.29E−04
2.25E−02

294
USP8
2.96E−02
1.24E−03

295
VDR
2.90E−02
4.16E−02

296
VPS25
1.71E−02
1.44E−02

297
VPS26A
2.23E−04
7.27E−03

298
VPS35
9.43E−03
4.62E−03

299
WASL
4.29E−03
1.37E−02

300
WBP11
3.60E−03
2.32E−02

301
WIPI1
6.07E−03
2.99E−02

302
WISP2
1.67E−02
6.00E−04

303
XPNPEP2
1.67E−02
2.40E−06

304
YBX3
1.52E−02
6.04E−03

305
YY1
1.20E−02
1.69E−02

306
ZC3HAV1
4.36E−03
9.83E−04

307
ZCCHC6
4.55E−02
2.00E−02

308
ZNF211
8.64E−04
2.04E−02

309
ZNF227
2.64E−02
2.79E−02

310
ZNF337
1.11E−03
4.74E−02

311
ZZEF1
7.78E−03
4.55E−02

TABLE 12

Common dysregulated genes for AD/NDC and AD/Non-

ADD under a statistical significance of P < 0.05.

AD vs Non-ADD
AD vs NDC

Training

Training
Validation

#
Gene name
Set
Validation
Gene name
Set
Set

1
AC004057.1
0.0246
0.0199
AC004057.1
0.0048
0.0039

2
ACP6
0.0332
0.0169
ACP6
0.0173
0.0055

3
ADAM20
0.0321
0.0082
ADAM20
0.0317
0.0208

4
RPL5
0.022
0.0422
RPL5
0.0000
0.0127

5
SHISA5
0.0188
0.0169
SHISA5
0.0219
0.0462

6
SNHG14
0.0292
0.0259
SNHG14
0.0045
0.0071

7
WASF2
0.0027
0.0476
WASF2
0.0013
0.0196

8
ZNF444
0.0158
0.0056
ZNF444
0.0002
0.0145

REFERENCES

1. Chen M et al. “Serum Starvation Induced Cell Cycle Synchronization Facilitates Human Somatic Cells Reprogramming”, PLoS ONE 7(4) (2012).

2. Baghdadchi N. “The Effects of Serum Starvation on Cell Cycle Synchronization”, OSR Journal of Student Research (2013).

3. Hayes O et al. “Cell confluency is as efficient as serum starvation for inducing arrest in the G0/G1 phase of the cell cycle in granulosa and fibroblast cells of cattle”, Anim. Reprod. Sci. 87(3-4):181-92 (2005).

4. Spellman P T et al, “Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization” Mol. Biol. Cell. 9(12):3273-97(1998).

	Number	Date	Country
Parent	PCT/US2018/064322	Dec 2018	US
Child	16434362		US

SYNCHRONIZED CELL CYCLE GENE EXPRESSION TEST FOR ALZHEIMER'S DISEASE AND RELATED THERAPEUTIC METHODS

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Abstract

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