Patent Application
20160215346
The present disclosure relates generally to blood biomarkers and their use for predicting mental state, and in particular, for predicting a subjects' risk of suicide (also referred to herein as “suicidality”). More particularly, the present disclosure relates to gene expression biomarkers, and to methods of screening for biomarkers, for identifying subjects who are at risk of committing suicide and methods for monitoring response to potential treatments by analyzing biomarkers.
Suicides are a leading cause of death in psychiatric patients, and in society at large. Particularly, suicide accounts for one million deaths worldwide each year. There are currently no objective tools to asses and track changes in suicidal risk without asking the subjects directly. Such tools, however, could prove substantially advantageous as the subjects at risk often choose not to share their suicidal ideation or intent with others, for fear of stigma, hospitalization, or that, in fact, their plans will be thwarted.
Conventionally, a convergence of methods assessing the subject's internal subjective feelings and thoughts, along with external, more objective, ratings of actions and behaviors, are used de facto in clinical practice, albeit not in a formalized and systematic way. Accordingly, there exists a need to develop more quantitative and objective ways for predicting and tracking suicidal states. More particularly, it would be advantageous if objective screening methods could be developed for determining expression levels of biomarkers to allow for determining suicidal risk and other psychotic depressed mood states, as well as monitoring a subject's response to treatments for lessening suicidal risk.
The present disclosure relates generally to predicting and tracking suicidality. Particularly, the present disclosure is directed to screening expression levels of biomarkers for predicting and tracking suicidality, and other psychotic depressed mood states, as well as for monitoring response to a treatment for suicidal risk. In one embodiment, the screening methods are useful in determining the suicidal risk of antidepressant treatment in a subject, which has been shown to be rare, but very serious in certain situations.
Biomarkers useful for identifying subjects at risk for suicide, as well as useful for monitoring the risk of suicide following treatment have been discovered. Accordingly, the present disclosure is directed to methods of identifying a subject at risk for suicide. The present disclosure is further directed to methods for monitoring response of a subject at risk for suicide to a treatment for suicide risk.
By monitoring and tracking changes in suicide state, the present disclosure allows for detection of an increased suicide risk prior to any suicide attempt by a subject, and further allows subjects at risk of suicide and other psychotic depressed mood states to be monitored and treated effectively. Accordingly, in another embodiment, the present disclosure relates to predicting future hospitalization for subjects being at risk for suicide and other psychotic depressed mood states such to provide sufficient monitoring and treatment to the subjects.
In one aspect, the present disclosure is directed to a method for identifying a subject at risk for suicide. The method includes obtaining a reference expression level of a blood biomarker; and determining an expression level of the blood biomarker in a sample obtained from the subject, wherein a change in the expression level of the blood biomarker in the sample obtained from the subject as compared to the reference expression level indicates a risk for suicide.
In another aspect, the present disclosure is directed to a method for monitoring response of a subject to a treatment for suicidal risk. The method includes obtaining an expression level of a biomarker from the subject; administering a treatment for suicidal risk to the subject; and determining an expression level of the biomarker in a sample obtained from the subject after the treatment is administered, wherein a change in the expression level of the biomarker in the sample obtained from the subject after the treatment is administered as compared to the expression level before administration indicates a response to the treatment.
In another aspect, the present disclosure is directed to a method for determining suicidal risk of an antidepressant, the method comprising: obtaining an expression level of a biomarker from a subject; administering an antidepressant to the subject; and determining an expression level of the biomarker in a sample obtained from the subject after the antidepressant is administered, wherein a change in the expression level of the biomarker in the sample obtained from the subject after the antidepressant is administered as compared to the expression level of the biomarker before the antidepressant is administered indicates a suicidal risk.
The disclosure will be better understood, and features, aspects and advantages other than those set forth above will become apparent when consideration is given to the following detailed description thereof. Such detailed description makes reference to the following drawings, wherein:
While the disclosure is susceptible to various modifications and alternative forms, specific embodiments thereof have been shown by way of example in the drawings and are herein described below in detail. It should be understood, however, that the description of specific embodiments is not intended to limit the disclosure to cover all modifications, equivalents and alternatives falling within the spirit and scope of the disclosure as defined by the appended claims.
Unless defined otherwise, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which the disclosure belongs. Although any methods and materials similar to or equivalent to those described herein may be used in the practice or testing of the present disclosure, the preferred materials and methods are described below.
In accordance with the present disclosure, biomarkers useful for objectively identifying subjects at risk for suicide, as well as for monitoring the risk of suicide following treatment and determining the risk of suicide following administration of antidepressants have been discovered. In one aspect, the present disclosure is directed to a method for identifying a subject at risk for suicide. The method includes obtaining a reference expression level of a blood biomarker; and determining an expression level of the blood biomarker in a sample obtained from the subject. A change in the expression level of the blood biomarker in the sample obtained from the subject as compared to the reference expression level indicates a risk for suicide. In some embodiments, the methods further include obtaining clinical risk factor information and clinical scale data such as for anxiety, mood and/or psychosis from the subject in addition to obtaining blood biomarker expression level in a sample obtained from the subject. This combined clinical data and blood biomarker expression level can further improve predictability of the risk of suicide as shown in
As used herein, “a subject at risk for suicide” refers to a subject diagnosed by one skilled in the art such as, for example, a clinician, using established protocols and methods for diagnosing suicidality. Such methods can include, for example, rigorous clinical interview using clinical standards for assessing and diagnosing whether a subject is at risk for suicide. Suicidality diagnosis can be established using, for example, questionnaires to identify suicidal ideation. Diagnosis can include diagnostic assessment using psychiatric rating scales including, for example, the Hamilton Rating Scale for Depression (HAMD-17), which includes a suicidal ideation rating item, Beck Scale for suicide ideation, Columbia Suicide Severity Rating Scale, The Kessler Psychological Distress Scale, and combinations thereof.
Particularly suitable subjects are humans. Suitable subjects can also be experimental animals such as, for example, monkeys and rodents, that display a behavioral phenotype associated with suicide, for example, a mood disorder or psychosis.
As used herein, “a reference expression level of a biomarker” refers to the expression level of a biomarker established for a subject with no suicidal ideation, expression level of a biomarker in a normal/healthy subject with no suicidal ideation as determined by one skilled in the art using established methods as described herein, and/or a known expression level of a biomarker obtained from literature. As known by those skilled in the art, “suicidal ideation” refers to thoughts, feelings, intent, external actions and behaviors about completing suicide. Suicidal ideation can vary from fleeting thoughts to unsuccessful attempts.
As used herein, “expression level of a biomarker” refers to the process by which a gene product is synthesized from a gene encoding the biomarker as known by those skilled in the art. The gene product can be, for example, RNA (ribonucleic acid) and protein. Expression level can be quantitatively measured by methods known by those skilled in the art such as, for example, northern blotting, amplification, polymerase chain reaction, microarray analysis, tag-based technologies (e.g., serial analysis of gene expression and next generation sequencing such as whole transcriptome shotgun sequencing or RNA-Seq), Western blotting, and combinations thereof.
Suitable biomarkers found to have a change in expression level include, for example, spermidine/spermine N1-acetyltransferase 1 (SAT1); forkhead box N3 (FOXN3); guanylate binding protein 1 (GBP1); phosphoinositide-3-kinase regulatory subunit 5 (PIK3R5); apolipoprotein L2 (APOL2); ATPase H+ transporting lysosomal 9 kDa, V0 subunit e1 (ATP6V0E1); GRINL1A complex locus (GCOM1); interleukin 1 beta (IL1B); lipoma HMGIC fusion partner (LHFP); lipase A (LIPA); myristoylated alanine-rich protein kinase C substrate (MARCKS); 6-phosphogluconolactonase (PGLS); phosphatase and tensin homolog (PTEN); reversion-inducing-cysteine-rich protein with kazal motifs (RECK); tumor necrosis factor (ligand) superfamily member 10 (TNFSF10); ATP-binding cassette, subfamily A (ABC1) member 1 (ABCA1); Rho guanine nucleotide exchange factor (GEF) 40 (ARHGEF4; FLJ10357); cancer susceptibility candidate 1 (CASC1); dehydrogenase/reductase (SDR family) member 9 (DHRS9); disrupted in schizophrenia 1 (DISC1); eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2); uncharacterized LOC727820 (LOC727820); mitogen-activated protein kinase kinase kinase 3 (MAP3K3); mitochondrially encoded NADH dehydrogenase 6 (MT-ND6; ND6); RNA binding motif protein 47 (RBM47); RPTOR independent companion of MTOR complex 2 (RICTOR); sterile alpha motif domain containing 9-like (SAMD9L); scavenger receptor class F member 1 (SCARF1); solute carrier family 36 (proton/amino acid symporter) member 1 (SLC36A1); signal transducer and activator of transcription 1, 91 kDa (STAT1); cytochrome c oxidase subunit Vb (COX5B); SWI/SNF related matrix associated actin dependent regulator of chromatin subfamily a member 1 (SMARCA1); ubiquitin-like modifier activating enzyme 6 (UBA6); zinc finger CCCH-type antiviral 1 (ZC3HAV1), CD24, ATP13A2, EPHX1, HTRA1, SPTBN1, MBNL2, OR2J3, RHEB, DBP, and combination thereof. Particularly suitable biomarkers include SAT1, MARCKS, PTEN, MAP3K3, and combinations thereof.
As used herein, a “change” in the expression level of the biomarker refers to an increase or a decrease of by about 1.2-fold or greater in the expression level of the biomarker as determined in a sample obtained from the subject as compared to the reference expression level of the biomarker. In one embodiment, the change in expression level is an increase or decrease by about 1.2 fold.
In one embodiment, the expression level of the blood biomarker in the sample obtained from the subject is increased as compared to the reference expression level of the biomarker. It has been found that an increase in the expression level of particular blood biomarkers in the sample obtained from the subject as compared to the reference expression level of the biomarker indicates a risk for suicide. Suitable biomarkers that indicate a risk for suicide when the expression level increases can be, for example, spermidine/spermine N1-acetyltransferase 1 (SAT1); forkhead box N3 (FOXN3); guanylate binding protein 1 (GBP1); phosphoinositide-3-kinase regulatory subunit 5 (PIK3R5); apolipoprotein L2 (APOL2); ATPase H+ transporting lysosomal 9 kDa, V0 subunit e1 (ATP6V0E1); GRINL1A complex locus (GCOM1); interleukin 1 beta (IL1B); lipoma HMGIC fusion partner (LHFP); lipase A (LIPA); myristoylated alanine-rich protein kinase C substrate (MARCKS); 6-phosphogluconolactonase (PGLS); phosphatase and tensin homolog (PTEN); reversion-inducing-cysteine-rich protein with kazal motifs (RECK); tumor necrosis factor (ligand) superfamily member 10 (TNFSF10); ATP-binding cassette, subfamily A (ABC1) member 1 (ABCA1); Rho guanine nucleotide exchange factor (GEF) 40 (ARHGEF4; FLJ10357); cancer susceptibility candidate 1 (CASC1); dehydrogenase/reductase (SDR family) member 9 (DHRS9); disrupted in schizophrenia 1 (DISC1); eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2); uncharacterized LOC727820 (LOC727820); mitogen-activated protein kinase kinase kinase 3 (MAP3K3); mitochondrially encoded NADH dehydrogenase 6 (MT-ND6; ND6); RNA binding motif protein 47 (RBM47); RPTOR independent companion of MTOR complex 2 (RICTOR); sterile alpha motif domain containing 9-like (SAMD9L); scavenger receptor class F member 1 (SCARF1); solute carrier family 36 (proton/amino acid symporter) member 1 (SLC36A1); signal transducer and activator of transcription 1, 91 kDa (STAT1); cytochrome c oxidase subunit Vb (COX5B); SWI/SNF related matrix associated actin dependent regulator of chromatin subfamily a member 1 (SMARCA1); ubiquitin-like modifier activating enzyme 6 (UBA6); zinc finger CCCH-type antiviral 1 (ZC3HAV1); tyrosine kinase, non-receptor 2 (TNK2), and combinations thereof. See, Table 5 for a list of biomarkers identified as showing an increase in expression level.
In another embodiment, the expression level of the blood biomarker in the sample obtained from the subject is decreased as compared to the reference expression level of the biomarker. Suitable biomarkers that indicate a risk for suicide when the expression level decreases as compared to the reference expression level have been found to include, for example, cluster 4 antigen (CD24; CD24 molecule); ATPase type 13A2 (ATP13A2); epoxide hydrolase 1, microsomal (xenobiotic) (EPHX1); HtrA serine peptidase 1 (HTRA1); leptin receptor (LEPR); spectrin beta non-erythrocytic 1 (SPTBN1); muscleblind-like 2 (MBNL2); olfactory receptor family 2 subfamily J member 3 (OR2J3); Ras homolog enriched in brain (RHEB); glutamate receptor, ionotropic, N-methyl D-aspartate-associated protein 1 (GRINA); D-box binding protein, promyelocytic leukemia (PML), potassium inwardly-rectifying channel, subfamily J, member 2 (KCNJ2), topoisomerase (DNA) 1 (TOP1) and combinations thereof. See, Table 5 for a list of biomarkers identified as showing a decrease in expression level.
In another embodiment, the method includes determining the expression level of a blood biomarker in the sample obtained from the subject that is increased as compared to the reference expression level of the biomarker and determining the expression level of the blood biomarker in the sample obtained from the subject that is decreased as compared to the reference expression level of the biomarker. For example, spermidine/spermine N1-acetyltransferase 1 (SAT1); forkhead box N3 (FOXN3); guanylate binding protein 1 (GBP1); phosphoinositide-3-kinase regulatory subunit 5 (PIK3R5); apolipoprotein L2 (APOL2); ATPase H+ transporting lysosomal 9 kDa, V0 subunit e1 (ATP6V0E1); GRINL1A complex locus (GCOM1); interleukin 1 beta (IL1B); lipoma HMGIC fusion partner (LHFP); lipase A (LIPA); myristoylated alanine-rich protein kinase C substrate (MARCKS); 6-phosphogluconolactonase (PGLS); phosphatase and tensin homolog (PTEN); reversion-inducing-cysteine-rich protein with kazal motifs (RECK); tumor necrosis factor (ligand) superfamily member 10 (TNFSF10); ATP-binding cassette, subfamily A (ABC1) member 1 (ABCA1); Rho guanine nucleotide exchange factor (GEF) 40 (ARHGEF4; FLJ10357); cancer susceptibility candidate 1 (CASC1); dehydrogenase/reductase (SDR family) member 9 (DHRS9); disrupted in schizophrenia 1 (DISC1); eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2); uncharacterized LOC727820 (LOC727820); mitogen-activated protein kinase kinase kinase 3 (MAP3K3); mitochondrially encoded NADH dehydrogenase 6 (MT-ND6; ND6); RNA binding motif protein 47 (RBM47); RPTOR independent companion of MTOR complex 2 (RICTOR); sterile alpha motif domain containing 9-like (SAMD9L); scavenger receptor class F member 1 (SCARF1); solute carrier family 36 (proton/amino acid symporter) member 1 (SLC36A1); signal transducer and activator of transcription 1, 91 kDa (STAT1); cytochrome c oxidase subunit Vb (COX5B); SWI/SNF related matrix associated actin dependent regulator of chromatin subfamily a member 1 (SMARCA1); ubiquitin-like modifier activating enzyme 6 (UBA6); zinc finger CCCH-type antiviral 1 (ZC3HAV1); tyrosine kinase, non-receptor 2 (TNK2), and combinations thereof in the blood sample of the subject can be increased as compared to the reference expression level, and cluster 4 antigen (CD24; CD24 molecule); ATPase type 13A2 (ATP13A2); epoxide hydrolase 1, microsomal (xenobiotic) (EPHX1); HtrA serine peptidase 1 (HTRA1); leptin receptor (LEPR); spectrin beta non-erythrocytic 1 (SPTBN1); muscleblind-like 2 (MBNL2); olfactory receptor family 2 subfamily J member 3 (OR2J3); Ras homolog enriched in brain (RHEB); glutamate receptor, ionotropic, N-methyl D-aspartate-associated protein 1 (GRINA); D-box binding protein, promyelocytic leukemia (PML), potassium inwardly-rectifying channel, subfamily J, member 2 (KCNJ2), topoisomerase (DNA) 1 (TOP1) and combinations thereof in the blood sample of the subject can be decreased as compared to the reference expression level to indicate an increase in the risk of suicide in a subject.
A particularly suitable sample for which the expression level of a biomarker is determined can be, for example, blood, including whole blood, leukocytes, and megakaryocytes. Other suitable samples for which the expression level of a biomarker is determined can be, for example, brain, cerebrospinal fluid, olfactory epithelium cells, fibroblasts from skin biopsies, induced pluripotent stem cells, and neuronal-like cells derived therefrom.
While described herein as a change in expression level, in some embodiments, particular levels of one or more of the above-described biomarkers can be useful for objectively identifying subjects at risk for future suicide. For example, it has been found that levels of SAT1 at 2500 Affymetrix microarray fluorescence intensity units (AU) or greater, including 2600 AU or greater, including 2700 AU or greater, including 2800 AU or greater, including 2900 AU or greater, and including 3000 AU or greater, have been found to be at increased risk for future suicide.
In another aspect, the present disclosure is directed to a method for monitoring response of a subject to a treatment for suicidal risk. As used herein, “treatment for suicidal risk” refers to a drug, nutritional, pharmaceutical, or the like, and combinations thereof that can modify the likelihood of a subject attempting and/or completing suicide. The method includes obtaining an expression level of a biomarker; administering a treatment for suicidal risk to the subject; and determining the expression level of the biomarker in a sample obtained from the subject after the treatment is administered, wherein a change in the expression level of the biomarker in the sample obtained from the subject after the treatment is administered as compared to the expression level of the biomarker before the treatment is administered indicates a response to the treatment.
Administration of the treatment can be by any suitable method known by those skilled in the art such as, for example, topical administration, enteral administration and parenteral administration. Suitable methods of administration can be, for example, transdermal administration, oral administration, and injection.
Suitable treatments for suicidal risk can be, for example, clozapine, omega-3 fatty acids (e.g., docosahexaenoic acid (DHA)), lithium, IL-1 trap, canakinumab, nicorandil, amiodarone, arsenic trioxide, vemurafenib, elsamitrucin, T 0128, CT-2106, BN80927, tafluposide, TAS-103, beta-lapachone, irinotecan, topo tecan, 9-amino-20-camptothecin, rubitecan, gimatecan, karenitecin, and combinations thereof.
Response to the treatment can be a decrease in the expression level of a biomarker after treatment. Biomarkers for which a decrease in the expression level of the biomarker indicates a response to the treatment can be, for example, spermidine/spermine N1-acetyltransferase 1 (SAT1); forkhead box N3 (FOXN3); guanylate binding protein 1 (GBP1); phosphoinositide-3-kinase regulatory subunit 5 (PIK3R5); apolipoprotein L2 (APOL2); ATPase H+ transporting lysosomal 9 kDa, V0 subunit e1 (ATP6V0E1); GRINL1A complex locus (GCOM1); lipoma HMGIC fusion partner (LHFP); lipase A (LIPA); myristoylated alanine-rich protein kinase C substrate (MARCKS); 6-phosphogluconolactonase (PGLS); reversion-inducing-cysteine-rich protein with kazal motifs (RECK); tumor necrosis factor (ligand) superfamily member 10 (TNFSF10); ATP-binding cassette, subfamily A (ABC1) member 1 (ABCA1); Rho guanine nucleotide exchange factor (GEF) 40 (ARHGEF4; FLJ10357); cancer susceptibility candidate 1 (CASC1); dehydrogenase/reductase (SDR family) member 9 (DHRS9); disrupted in schizophrenia 1 (DISC1); eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2); uncharacterized LOC727820 (LOC727820); mitogen-activated protein kinase kinase kinase 3 (MAP3K3); mitochondrially encoded NADH dehydrogenase 6 (MT-ND6; ND6); RNA binding motif protein 47 (RBM47); RPTOR independent companion of MTOR complex 2 (RICTOR); sterile alpha motif domain containing 9-like (SAMD9L); scavenger receptor class F member 1 (SCARF1); solute carrier family 36 (proton/amino acid symporter) member 1 (SLC36A1); signal transducer and activator of transcription 1, 91 kDa (STAT1); cytochrome c oxidase subunit Vb (COX5B); SWI/SNF related matrix associated actin dependent regulator of chromatin subfamily a member 1 (SMARCA1); ubiquitin-like modifier activating enzyme 6 (UBA6); zinc finger CCCH-type antiviral 1 (ZC3HAV1); tyrosine kinase, non-receptor 2 (TNK2), and combinations thereof.
Response to the treatment can alternatively be an increase in the expression level of a biomarker after treatment. Biomarkers for which an increase in the expression level of the biomarker indicates a response to the treatment can be, for example, small cell lung carcinoma cluster 4 antigen (CD24; CD24 molecule); ATPase type 13A2 (ATP13A2); epoxide hydrolase 1, microsomal (xenobiotic) (EPHX1); HtrA serine peptidase 1 (HTRA1); leptin receptor (LEPR); spectrin beta non-erythrocytic 1 (SPTBN1); muscleblind-like 2 (MBNL2); olfactory receptor family 2 subfamily J member 3 (OR2J3); Ras homolog enriched in brain (RHEB); glutamate receptor, ionotropic, N-methyl D-aspartate-associated protein 1 (GRINA); D-box binding protein and combinations thereof.
Response to the treatment can be a decrease in the expression level of a first biomarker and an increase in a second biomarker. The first biomarker can be, for example, spermidine/spermine N1-acetyltransferase 1 (SAT1); forkhead box N3 (FOXN3); guanylate binding protein 1 (GBP1); phosphoinositide-3-kinase regulatory subunit 5 (PIK3R5); apolipoprotein L2 (APOL2); ATPase H+ transporting lysosomal 9 kDa, V0 subunit e1 (ATP6V0E1); GRINL1A complex locus (GCOM1); lipoma HMGIC fusion partner (LHFP); lipase A (LIPA); myristoylated alanine-rich protein kinase C substrate (MARCKS); 6-phosphogluconolactonase (PGLS); reversion-inducing-cysteine-rich protein with kazal motifs (RECK); tumor necrosis factor (ligand) superfamily member 10 (TNFSF10); ATP-binding cassette, subfamily A (ABC1) member 1 (ABCA1); Rho guanine nucleotide exchange factor (GEF) 40 (ARHGEF4; FLJ10357); cancer susceptibility candidate 1 (CASC1); dehydrogenase/reductase (SDR family) member 9 (DHRS9); disrupted in schizophrenia 1 (DISC1); eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2); uncharacterized LOC727820 (LOC727820); mitogen-activated protein kinase kinase kinase 3 (MAP3K3); mitochondrially encoded NADH dehydrogenase 6 (MT-ND6; ND6); RNA binding motif protein 47 (RBM47); RPTOR independent companion of MTOR complex 2 (RICTOR); sterile alpha motif domain containing 9-like (SAMD9L); scavenger receptor class F member 1 (SCARF1); solute carrier family 36 (proton/amino acid symporter) member 1 (SLC36A1); signal transducer and activator of transcription 1, 91 kDa (STAT1); cytochrome c oxidase subunit Vb (COX5B); SWI/SNF related matrix associated actin dependent regulator of chromatin subfamily a member 1 (SMARCA1); ubiquitin-like modifier activating enzyme 6 (UBA6); zinc finger CCCH-type antiviral 1 (ZC3HAV1); and combinations thereof. The second biomarker can be, for example, cluster 4 antigen (CD24; CD24 molecule); ATPase type 13A2 (ATP13A2); epoxide hydrolase 1, microsomal (xenobiotic) (EPHX1); HtrA serine peptidase 1 (HTRA1); leptin receptor (LEPR); spectrin beta non-erythrocytic 1 (SPTBN1); muscleblind-like 2 (MBNL2); olfactory receptor family 2 subfamily J member 3 (OR2J3); Ras homolog enriched in brain (RHEB); glutamate receptor, ionotropic, N-methyl D-aspartate-associated protein 1 (GRINA); D-box binding protein, interleukin 1 beta (IL1B), phosphatase and tensin homolog (PTEN), promyelocytic leukemia (PML), potassium inwardly-rectifying channel, subfamily J, member 2 (KCNJ2), topoisomerase (DNA) 1 (TOP1) and combinations thereof. See, Table 5.
In another aspect, the present disclosure is directed to a method for determining suicidal risk as a side-effect of an antidepressant. The method includes obtaining an expression level of a biomarker from the subject; administering an antidepressant to the subject; and determining an expression level of the biomarker in a sample obtained from the subject after the antidepressant is administered. A change in the expression level of the biomarker in the sample obtained from the subject after the antidepressant is administered as compared to the expression level of the biomarker before the antidepressant is administered indicates suicidal risk as a side-effect of the antidepressant.
It is known that suicide risk is a rare, but very serious side-effect of some drugs. Upon initiation of antidepressant therapy, subjects can sometimes experience a sudden onset of suicidal ideation (e.g., suicidal thoughts and behaviors) that accompanies treatment. Subjects can become suicidal in the first weeks of treatment, upon a dosage change and/or a combination thereof. This has caused the U.S. Food and Drug Administration to require manufacturers to place explicit warnings on the label of the drug stating that its use may cause a risk of suicide.
Suitable antidepressants can be, for example, bupropion, citalopram, escitalopram, fluoxetine, fluvoxamine, mirtazapine, nefazodone, paroxetine, sertraline, and venlafaxine.
Suitable biomarkers can be, for example, spermidine/spermine N1-acetyltransferase 1 (SAT1); forkhead box N3 (FOXN3); guanylate binding protein 1 (GBP1); phosphoinositide-3-kinase regulatory subunit 5 (PIK3R5); apolipoprotein L2 (APOL2); ATPase H+ transporting lysosomal 9 kDa, V0 subunit e1 (ATP6V0E1); GRINL1A complex locus (GCOM1); interleukin 1 beta (IL1B); lipoma HMGIC fusion partner (LHFP); lipase A (LIPA); myristoylated alanine-rich protein kinase C substrate (MARCKS); 6-phosphogluconolactonase (PGLS); phosphatase and tensin homolog (PTEN); reversion-inducing-cysteine-rich protein with kazal motifs (RECK); tumor necrosis factor (ligand) superfamily member 10 (TNFSF10); ATP-binding cassette, subfamily A (ABC1) member 1 (ABCA1); Rho guanine nucleotide exchange factor (GEF) 40 (ARHGEF4; FLJ10357); cancer susceptibility candidate 1 (CASC1); dehydrogenase/reductase (SDR family) member 9 (DHRS9); disrupted in schizophrenia 1 (DISC1); eukaryotic translation initiation factor 2-alpha kinase 2 (EIF2AK2); uncharacterized LOC727820 (LOC727820); mitogen-activated protein kinase kinase kinase 3 (MAP3K3); mitochondrially encoded NADH dehydrogenase 6 (MT-ND6; ND6); RNA binding motif protein 47 (RBM47); RPTOR independent companion of MTOR complex 2 (RICTOR); sterile alpha motif domain containing 9-like (SAMD9L); scavenger receptor class F member 1 (SCARF1); solute carrier family 36 (proton/amino acid symporter) member 1 (SLC36A1); signal transducer and activator of transcription 1, 91 kDa (STAT1); cytochrome c oxidase subunit Vb (COX5B); SWI/SNF related matrix associated actin dependent regulator of chromatin subfamily a member 1 (SMARCA1); ubiquitin-like modifier activating enzyme 6 (UBA6); zinc finger CCCH-type antiviral 1 (ZC3HAV1); tyrosine kinase, non-receptor 2 (TNK2); cluster 4 antigen (CD24; CD24 molecule); ATPase type 13A2 (ATP13A2); epoxide hydrolase 1, microsomal (xenobiotic) (EPHX1); HtrA serine peptidase 1 (HTRA1); leptin receptor (LEPR); spectrin beta non-erythrocytic 1 (SPTBN1); muscleblind-like 2 (MBNL2); olfactory receptor family 2 subfamily J member 3 (OR2J3); Ras homolog enriched in brain (RHEB); glutamate receptor, ionotropic, N-methyl D-aspartate-associated protein 1 (GRINA); D-box binding protein, promyelocytic leukemia (PML), potassium inwardly-rectifying channel, subfamily J, member 2 (KCNJ2), topoisomerase (DNA) 1 (TOP1) and combinations thereof. Particularly suitable biomarkers include SAT1, MARCKS, PTEN, MAP3K3, and combinations thereof.
In yet another aspect, the present disclosure is directed to a method of predicting hospitalization of a subject at risk of suicide. The method includes obtaining a first expression level of a blood biomarker in an initial sample obtained from the subject; and determining a second expression level of the blood biomarker in a subsequent sample obtained from the subject, wherein an increase in the expression level of the blood biomarker in the subsequent sample obtained from the subject as compared to the expression level of the initial sample indicates a higher risk of future hospitalizations due to suicidality.
Suitable biomarkers can be, for example, spermidine/spermine N1-acetyltransferase 1 (SAT1); myristoylated alanine-rich protein kinase C substrate (MARCKS); 6-phosphogluconolactonase (PGLS); phosphatase and tensin homolog (PTEN); mitogen-activated protein kinase kinase kinase 3 (MAP3K3); and combinations thereof.
In this Example, whole-genome gene expression profiling of blood samples was conducted to identify blood gene expression biomarkers for suicidality.
Human Subjects.
Male Caucasian subjects diagnosed with bipolar disorder (“Discovery Cohort”) were evaluated that had a diametrical change in suicidal ideation scores from no suicidal ideation to high suicidal ideation from visit to visit. The subjects were limited to minimize any potential gender-related and ethnicity-related state effects on gene expression. A demographic breakdown of the Discovery Cohort subjects is shown in Table 1A.
A “Validation Cohort”, in which the top biomarker findings from the Discovery Cohort testing were evaluated, consisted of an age-matched cohort of 9 male suicide completers obtained through the Marion County Coroner's Office (8 Caucasians, 1 African-American) (Table 1B). The subjects in the Validation Cohort were required to have a last observed alive post-mortem interval of 24 hours or less, and had to have completed suicide by means other than overdose, which could affect gene expression.
The Discovery Cohort subjects were on a variety of different psychiatric medications, including mood stabilizers, antidepressants, antipsychotics, benzodiazepines, and others as listed in Table 2A (Table 2B provides toxicology for subjects in the coroner's office test cohort-suicide completers). Medications can have a strong influence on gene expression. However, this Example tested differentially expressed genes based at on intra-subject analyses, which factor out not only genetic background, effects but also medication effects. Moreover, there was no consistent pattern found in any particular type of medication, or between any change in medications and suicidal ideation in the rare instances where there were changes in medications between visits. Subjects were excluded, however, if they had significant acute medical or neurological illnesses, or had evidence of active substance abuse or dependence.
The subjects were subjected to diagnostic assessments using Diagnostic Interview for Genetic Studies, which is the scale used by the Genetics Initiative Consortia for both bipolar disorder and major depression, at a baseline visit, followed by up to three testing visits, three to six months apart. Particularly, six subjects were subjected to three follow-up testing visits and three subjects were subjected to two follow-up testing visits, resulting in a total of 24 blood samples for subsequent microarray studies as discussed herein. At each testing visit, the subjects received a series of psychiatric rating scales, including the Hamilton Rating Scale for Depression (HAMD-17), which includes a suicidal ideation rating item (
Using the nine subjects with multiple visits, corresponding to 24 chips, from the Discovery Cohort a differential analysis was run using Partek Genomic Suites 6.6 software package (Partek Incorporated, St. Louis, Mo.). Normalization was performed on all 24 chips by robust multi-array analysis (RMA), background corrected with quartile normalization and a median polish probe set summarization of all 24 chips to obtain the normalized expression levels of all probe sets for each chip. Two analyses, an intra-subject analysis and an inter-subject analysis, were conducted to establish a list of differentially expressed probe sets.
RNA Extraction.
During each visit, from about 2.5 ml to about 5.0 ml of whole blood was collected from the subjects separately into two PaxGene tubes, treated to stabilize RNA, by routine venipuncture. The cells from the whole blood were concentrated by centrifugation, the pellet washed, resuspended and incubated in buffers containing proteinase K for protein digestion. A second centrifugation step was conducted to remove residual cell debris. Ethanol was added. After ethanol addition, the supernatant was applied to a silica-gel membrane/column. The column was centrifuged and contaminants were removed in three wash steps. RNA bound to the membrane was then eluted using DEPC-treated water.
Globin Reduction.
To remove globin mRNA, total RNA from the whole blood was mixed with a biotinylated Capture Oligo Mix that is specific for human globin mRNA. The mixture was then incubated for 15 minutes to allow the biotinylated oligonucleotides to hybridize with the globin mRNA. Streptavidin magnetic beads were then added, and the mixture was incubated for 30 minutes. During this incubation, streptavidin binds to the biotinylated oligonucleotides, thereby capturing the globin mRNA on the magnetic beads. The streptavidin magnetic beads were then pulled to the side of the tube with a magnet, and the RNA, depleted of the globin mRNA, was transferred to a fresh tube. The treated RNA was further purified using a rapid magnetic bead-based purification method consisting of adding an RNA binding bead suspension to the samples and using magnetic capture to wash and elute the globin-clear RNA.
Sample Labeling.
Samples were labeled using an Ambion MessageAmp II-BiotinEnhanced antisense RNA (aRNA) amplification kit. The procedure involved the following steps:
Microarrays.
Biotin-labeled aRNA was then hybridized to Affymetrix HG-U133 Plus 2.0 GeneChips (Affymetrix, Santa Clara, Calif.) with over 40,000 genes and expressed sequence tags (ESTs) according to manufacturer's protocols (http://www.affymetrix.com/support/technical/manual/expression_manual.affx). All GAPDH 3′/5′ ratios should be less than 2.0 and backgrounds under 50. Arrays were stained using standard Affymetrix protocols for antibody signal amplification and scanned on an Affymetrix GeneArray 2500 scanner with a target intensity set at 250. Present/absent calls were determined using GCOS software with thresholds set at default values. Quality control measures including 30/50 ratios for glyceraldehyde 3-phosphate dehydrogenase and b-actin, scale factors, background and Q values were within acceptable limits.
Analysis.
Each subject's suicidal ideation (SI) scores at time of blood collection (0—no SI compared to 2 and above—high SI) were used for analysis. Particularly, gene expression differences between the no SI and the high SI states using both an intra-subject and an inter-subject design as shown in
An intra-subject analysis using a fold change in expression of at least 1.2 between high and no suicidal ideation visits within each subject was performed. There were in total 15 comparisons. Probe sets that had a 1.2 fold change were then assigned either a 1 (increased in high suicidal ideation) or a −1 (decreased in high suicidal ideation) in each comparison. These values were then summed for each probe set across the 15 comparisons, yielding a range of scores between −11 and 12. Probe sets in the top 5% (1,269 probe sets, <5% of 54,675 total probe sets) had an absolute value of 7 and greater, receiving an internal Convergent Functional Genomics (CFG) score of 1 point. Those probe sets in the top 0.1% (24 probe sets, <0.1% of 54,675 total probe sets) had a total absolute value of 11 and greater and received an internal CFG score of 3 points.
Additionally, an inter-subject analysis using t-test (2-tailed, unequal variance) was performed to find probes differentially expressed between high suicidal ideation and no suicidal ideation chips (
Results were then further filtered by only selecting probe sets that overlapped between the intra-subject and the inter-subject analyses, resulting in 279 probe sets corresponding to 246 unique genes. Gene names for the probe sets were identified using Partek as well as NetAffyx (Affymetrix) for Affymetrix HG-U133 Plus 2.0 GeneChips, followed by GeneCards to confirm the primary gene symbol. In addition, for those probe sets that were not assigned a gene name by Partek or NetAffyx, the UCSC Genome Browser on Human February 2009 (GRCh37/hg19) was used to directly map them to known genes. Genes were then scored using manually curated CFG databases as described below and shown in
Manually curated databases were created in the Laboratory of Neurophenomics, Indiana University School of Medicine (www.neurophenomics.info) of all the human gene expression (postmortem brain, blood, cell cultures), human genetic (association, CNVs, linkage) and animal model gene expression and genetic studies published to date on psychiatric disorders. Only the findings deemed significant in the primary publication, by the study authors, using their particular experimental design and thresholds, were included in the databases. The databases included only primary literature data and did not include review papers or other secondary data integration analyses to avoid redundancy and circularity. These large and constantly updated databases have been used in previous CFG cross-validation and prioritization studies.
Human Postmortem Brain Gene Expression Evidence.
Information about genes was obtained and imported in the databases searching the primary literature with PubMed (http://ncbi.nlm.nih.gov/PubMed), using various combinations of keywords (e.g., gene name and suicide and human brain). Postmortem convergence was deemed to occur for a gene if there were published reports of human postmortem data showing changes in expression of that gene in brains from patients who died from suicide.
Human Genetic Evidence Association and Linkage.
To designate convergence for a particular gene, the gene had to have independent published evidence of association or linkage for suicide. For linkage, the location of each gene was obtained through GeneCards (http://www.genecards.org), and the sex averaged cM location of the start of the gene was then obtained through http://compgen.rutgers.edu/old/map-interpolator/. For linkage convergence, the start of the gene had to map within 5 cM of the location of a marker linked to the disorder.
CFG Scoring.
For CFG analysis, two external cross-validating lines of evidence were weighed such that findings in human postmortem brain tissue, the target organ, were prioritized over genetic findings. Human brain expression evidence was given 4 points, while human genetic evidence was given a maximum of 2 points for association, and 1 point for linkage. Each line of evidence was capped in such a way that any positive findings within that line of evidence resulted in maximum points regardless of how many different studies support that single line of evidence, to avoid potential popularity biases.
In addition to the above external CFG score, genes based upon the initial differential expression analyses used to identify them were also prioritized. Probe sets identified by differential expression analyses could receive a maximum of 6 points (1 or 3 points from intra-subject analyses, and 1 or 3 points from inter-subject analyses). Thus, the maximum possible total CFG score for each gene was 12 points (6 points for internal score+6 points for external score).
The above-described scoring system provided a good separation of genes based on differential expression and on independent cross-validating evidence in the field (
IPA 9.0 (Ingenuity Systems, www.ingenuity.com, Redwood City, Calif.) was used to analyze the biological roles, including top canonical pathways and diseases, of the candidate genes resulting from the above findings (Table 3), as well as used to identify genes in the data sets that were the target of existing drugs (Table 4). Pathways were identified from the IPA library of canonical pathways that were most significantly associated with genes in the data set. The significance of the association between the data set and the canonical pathway was measured in two ways: 1) a ratio of the number of molecules from the data set that map to the pathway divided by the total number of molecules that map to the canonical pathway is displayed; and 2) Fisher's exact test was used to calculate a p-value determining the probability that the association between the genes in the data set and the canonical pathway was explained by chance alone. A KEGG pathway analysis through the Partek Genomic Suites 6.6 software package was also conducted.
The nine Affymetrix microarray data files from the Validation Cohort was imported as .cel files into Partek Genomic Suites 6.6 software package (Partek Incorporated St. Louis, Mo.). A robust multi-array analysis (RMA), background corrected with quartile normalization and a median polish probe set summarization of all 24+9=33 chips was conducted to obtain the normalized expression levels of all probe sets for each chip. Partek normalizes expression data into a log base of 2 for visualization. The data was non-log by taking 2 to the power of the transformed expression value. The non-log transformed expression data was then used to compare expression levels of SAT1 and CD24 in the different groups (
Further, testing of the top candidate biomarkers for suicidality were conduct (see
Whole-genome gene expression profiling in blood samples from a longitudinally-followed homogeneous cohort of male subjects with a major mood disorder (bipolar disorder) that predisposes to suicidality was conducted. The samples were collected at repeated visits, 3 to 6 months apart. State information about suicidal ideation was collected from a questionnaire administered at the time of each blood draw. An intra-subject design was used to analyze data from 9 subjects that switched from no suicidal ideation to high suicidal ideation at different visits, which factors out genetic variability, as well as some medications, lifestyle and demographic variability. An inter-subject case-case analysis was also used to identify genes differentially expressed in the blood in no suicidal ideation states versus high suicidal ideation states. The top 0.1% and 5% of the gene expression probe sets distributions were considered and differentially scored. Overlap between the intra-subject and inter-subject analyses of gene expression changes was required. Such a restrictive approach was used as a way of minimizing false positives, even at the risk of having false negatives. For example, there were genes on each of the two lists, from intra- and inter-subject analyses, that had clear prior evidence for involvement in suicidality, such as MT1E (Sequeira A. et al., Gene expression changes in the prefrontral cortex, anterior cingulate cortex and nucleus accumbens of mood disorders subjects that committed suicide, PioS one 7, e35367, doi:10,1371/journal.pone.0035367 (2012)), respectively GSK3B (Karege F. et al., Alteration in kinase activity but not in protein levels of protein kinase B and glycogen synthase kinase-3beta in ventral prefrontal cortex of depressed suicide victims. Biol Psychiatry 61, 240-245, doi:10.1016/j.biopsych.2006.04.036 (2007)), but were not included in the subsequent analyses because they were not in the overlap.
A CFG approach was then used to cross-match the list of 246 overlapping top differentially expressed genes from the blood samples with other key lines of evidence (human postmortem brain data, human genetic data) implicating them in suicidality, as a way of identifying and prioritizing disease-relevant genomic biomarkers, extracting generalizable signal out of potential cohort-specific residual noise and genetic heterogeneity. Manually curated databases of the psychiatric genomic and proteomic literature to date was created and used in the CFG analyses. The CFG approach was thus a de facto field-wide collaboration. In essence, in a Bayesian fashion, the whole body of knowledge in the field was used to leverage findings from the Discovery Cohort data sets. Unlike the use of CFG in previous studies, no human peripheral tissue evidence from the literature was used as there was none directly matching the instant genes, reflecting perhaps the dearth of peripheral gene expression work done so far on suicides, and the need for a study like the instant Example. Animal model evidence was also not used as there were to date no clear studies in animal models of self-harm or suicidality. SAT1 (spermidine/spermine N1-acetyltransferase 1) was the top blood biomarker increased in suicidal states (i.e. the top risk marker), and CD24 (CD24 molecule; small cell lung carcinoma cluster 4 antigen) was the top blood biomarker decreased in suicidal states (i.e. the top protective marker) (
In order to validate the Discovery Cohort findings in the most stringent way possible, SAT1 levels in blood samples from the Validation Cohort of 9 consecutive male suicide completers obtained from the coroner's office were evaluated. SAT1 gene expression levels were found to be elevated in 9 out of 9 (100%) subjects who committed suicide. In each suicide completer, the increase in SAT1 was at least three standard deviations above the average levels in high suicidal ideation subjects. The results were further strengthened by using a panel of the two markers (SAT1 and CD24) (
As shown in
One of the other biomarkers identified to be decreased in high suicidal states in the current Example was the circadian clock gene DBP (D-box binding protein). Serendipitously, previous work showed that mice engineered to lack DBP were stress-reactive and displayed a behavioral phenotype similar to bipolar disorder and co-morbid alcoholism (Le-Niculescu H. et al., “Phenomic, convergent functional genomic, and biomarker studies in a stress-reactive genetic animal model of bipolar disorder and co-morbid alcoholism,” American Journal of Medical Genetics, Part B, Neuropsychiatric genetics: the official publication of the International Society of Psychiatric Genetics 147B, 134-166, doi:10.1002/ajmg.b.30707 (2008)). In addition to bipolar disorder, alcoholism is known to increase the risk for suicide. Treatment with omega-3 fatty acids normalized the phenotype of those mice. Low omega-3 levels have been previously correlated with increased suicidality in human epidemiological studies (see Sublette M. et al., “Omega-3 polyunsaturated essential fatty acid status as a predictor of future suicide risk,” Am J Psychiatry 163, 1100-1102, doi:10.1176/appi.ajp.163.6.110 (2006); Lewis M. D. et al., “Suicide deaths of active-duty US military and omega-3 fatty-acid status: a case-control comparison,” J Clin Psychiatry 72, 1585-1590, doi:10.4088/JCP.11m06879 (2011)). Pathway analyses of the instant suicidality biomarker data identified among the top pathways the omega-3 docosahexaenoic acid (DHA) signaling pathway. Several of the biomarkers from this Example (those bolded in Table 6 in “Modulated by DHA” column)) were changed in expression by omega-3 treatment in the blood of the DBP mouse model in opposite direction to our human suicidality data (Table 6). PTEN, a biomarker increased in suicidality in the current Example in the blood, as well as in the brain of suicide completers, was also increased in the amygdala and decreased in the pre-frontal cortex of DBP knock-out mice subjected to stress.
SAT1
spermidine/spermine N1-
I
8
(D) Blood
acetyl transferase 1
GBP1
guanylate nucleotide binding
I
8
(D) Blood
protein 1
IL1B
interleukin 1 beta
I
6
(D) Blood
LHFP
lipoma HMGIC fusion
I
6
(D) Blood
partner
SPTBN1
spectrin, beta, non-
D
6
(I) Blood, VT
erythrocytic 1
MAP3K3
mitogen-activated protein
I
4
(D) Blood
kinase kinase kinase 3
MBNL2
muscleblind-like 2
D
4
(I) Blood
ATG3
autophagy-related 3 (yeast)
I
2
(D) Blood
CCR1
chemokine (C-C motif)
I
2
(D) Blood
receptor 1
CD84
CD84 antigen
D
2
(I) Blood
CEACAM1
CEA-related cell adhesion
I
2
(D) Blood
molecule 1
CLEC4E
C-type lectin domain family
I
2
(D) Blood
4, member e
CLEC7A
C-type lectin domain family
I
2
(D) Blood
7, member a
FZR1
fizzy/cell division cycle 20
D
2
(I) Blood
related 1 (
)
IFIT2
interferon-induced protein
I
2
(D) Blood
with tetratricopeptide repeats
2
MDM4
transformed mouse 3T3 cell
I
2
(D) Blood
double minute 4
NUDT3
nudix (nucleotide
I
2
(D) Blood
diphosphate linked moiety
X)-type motif 3
R3HDM1
R3H domain 1 (binds single-
I
2
(I) VT
(D) Blood
stranded nucleic acids)
RASSF3
Ras association (RaIGDS/AF-
I
2
(I) VT
(D) Blood
6) domain family member 3
S100A8
S100 calcium binding protein
I
2
(D) Blood
(D) Blood
A8 (calgranulin A)
TMEM140
transmembrane protein 140
I
2
(I) Blood
(D) Blood
TMEM154
transmembrane protein 154
I
2
(D) Blood
cerevisiae)
Other circadian clock-modulated genes identified as biomarkers for suicidality were PIK3R5, MARCKS, IL1B, CASC1, CCRN4L, H3F3B, RBCK1, TNK2, and UBE2B. Additionally, biomarkers, as bolded in Table 6 in the “Modulated by Clozapine” column, provided evidence for modulation by clozapine in blood in opposite direction to the human suicidality data in previous independent animal model pharmacogenomics studies (Table 6). Clozapine is the only FDA approved treatment for suicidality. Thus, the convergent evidence for the instant biomarkers is strong in translational ways beyond those used for their discovery and selection. S100A8 may be a key biomarker to monitor in terms of response to treatment with classic (clozapine) and complementary (omega-3) agents. Other potential drugs to be studied for modulating suicidality were revealed by the above analyses (Tables 4 and 6).
SAT1, FOXN3, DISC1, MBNL2 and RHEB had genetic association evidence for suicidality, suggesting that they are not only state biomarkers but also trait factors influencing suicidal risk. DISC1 is also one of the top candidate genes for schizophrenia based on a large scale CFG analysis of schizophrenia GWAS recently conducted (Ayalew M. et al., “Convergent functional genomics of schizophrenia: from comprehensive understanding to genetic risk prediction,” Molecular Psychiatry 17, 887-905, doi:10.1038/mp.2012.37 (2012)), while DISC1 and MBNL2 are also among the top candidate genes for bipolar disorder based on a large scale CFG analysis of bipolar disorder GWAS (Patel S. D. et al., “Coming to grips with complex disorders: genetic risk prediction in bipolar disorder using panels of genes identified through convergence functional genomics,” American Journal of Medical Genetics Part b, Neuropsychiatric genetics: the official publication of the International Society of Psychiatric genetics 153B, 850-877, doi:10.1pp2/ajmg.b.31087 (2010)). Additionally, DISC1 has clear animal model data for the role of its interaction with environmental stress in the pathophysiology of psychotic depression. DISC1 and MBNL2 may thus be key state and trait factors for suicidality risk in psychotic mood disorder subjects, and an indication for clozapine treatment in such subjects.
Suicide biomarkers that were identified in this study were overlapped with biomarkers identified as mood biomarkers (Le-Niculescu H. et al., “Identifying blood biomarkers for mood disorders using convergent functional genomics,” Molecular Psychiatry 14, 156-174, doi:10.1111/ele.12064 (2009)) and psychosis biomarkers (Kurian S. M. et al., “Identification of blood biomarkers for psychosis using convergent functional genomics,” Molecular Psychiatry 16, 37-58, doi:10.1038/mp.2009.117 (2011)) (Table 7). DOCK5 and 4 other biomarkers (as bolded in Table 7 in the “Direction of change in Mood” column were changed in high suicidal states in opposite direction to their change in high mood states, and DOCK5 and 6 other biomarkers (as bolded in Table 7 in the “Direction of change in Hallucination” or “Direction of change in Delusions” columns) were changed in the same direction as their change in high psychosis states, suggesting that suicidality can indeed be viewed as a psychotic depressed state, and that DOCK5 may be an additional key biomarker reflecting that state.
LEPR
leptin receptor
6
D
DOCK5
dedicator of
2
I
cytokinesis 5
EPM2A
epilepsy,
2
D
progressive
myoclonus type
2A, Lafora disease
FKBP7
FK506 binding
2
D
protein 7
KIAA0494
KIAA0494
2
I
MXD1
MAX dimerization
2
I
protein 1
PID1
phosphotyrosine
2
D
interaction domain
containing 1
PML
promyelocytic
2
I
leukemia
PPP2R1B
protein
2
D
phosphatase 2,
regulatory subunit
A, beta
SLC2A13
solute carrier
2
I
family 2
transporter),
member 13
TRIM6
tripartite motif
2
I
containing 6
This Example shows overlap at a gene and pathway level with cancer and apoptosis (Table 3, Table 8). SAT1, for example, is a key catabolic enzyme for polyamines. Polyamine levels within cells control cell viability, and significant decreases in polyamine levels can result in apoptosis. They appear to reflect an endowment for cellular and organismal activity and growth, key characteristics of mood. SAT1, which increased in suicidal subjects of this Example, is highly inducible by a variety of stimuli, including toxins, cytokines, heat shock, ischemia, and other stresses.
CD24, the top biomarker decreased in suicidal subjects of this Example, also has roles in apoptosis. Mice lacking CD24 show an increased rate of apoptosis (Duckworth C. A. et al., “CD24 is expressed in gastric parietal cells and regulates apoptosis and the response to Helicobacter felis infection in the murine stomach,” American Journal of Physiology, Gastrointestinal and Liver Physiology 303, G915-926, doi:10.1152/ajpgi.00068.2012 (2012)). It could be that simpler mechanisms related to cellular survival and programed cell-death decision have been recruited by evolution for higher mental functions such as thoughts and behaviors leading to suicidality. In that sense, suicidality could be viewed as whole-organism self-poptosis. Interestingly, lithium, a medication with clinical evidence for preventing suicidality in bipolar disorder, has anti-apoptotic effects at a cellular level. Imaging studies have shown reduced gray matter volume in the brain of individuals with bipolar disorder and history of suicide attempts. Long-term lithium treatment was associated with increased gray matter volumes in the same areas where suicide was associated with decreased gray matter.
Taken together, the results of this Example have implications for the understanding of suicide, as well as for the development of objective laboratory tests and tools to diagnose and track suicidal risk and to monitor response to treatment.
More particularly, it was found that suicidality may be associated with dysphoric mood, as well as increased psychosis, anxiety and stress. SAT1 blood gene expression levels, in particular, showed a trend towards increase in low mood, high psychosis, high anxiety, and high stress in the bipolar subjects (see
In this Example, SAT1 was validated by analyzing subsequent hospitalizations with and without suicidalilty and to previous hospitalizations with and without suicidality in two live follow-up cohorts, one bipolar (n=42) and one psychosis (schizophrenia/schizoaffective; n=46).
Particularly, the bipolar follow-up cohort (Table 9A) consisted of male Caucasian subjects in which whole-genome blood gene expression data, including levels of SAT1, were obtained at the testing visits as described in Example 1. If the subjects had multiple testing visits, the visit with the highest SAT1 level was selected for this analysis. The subjects' subsequent number of hospitalizations with or without suicidality was tabulated from electronic medical records.
The psychosis (schizophrenia/schizoaffective) follow-up cohort (n=46) (Table 9B) similarly consisted of Caucasian subjects in which whole-genome blood gene expression data, including levels of SAT1, were obtained at testing visits as described for the bipolar follow-up cohort. If the subjects had multiple testing visits, the visit with the highest SAT1 level was selected for this analysis. The subjects' subsequent number of hospitalizations with or without suicidality was tabulated from electronic medical records. A hospitalization was deemed to be without suicidality if suicidality was not listed as a reason for admission, and no suicidal ideation was described in the admission and discharge medical notes. Conversely, a hospitalization was deemed to be due to suicidality if suicidal acts or intent was listed as a reason for admission, and suicidal ideation was described in the admission and discharge medical notes.
For future hospitalization analyses, robust multi-array analysis (RMA) as described in Example 1 was conducted and normalized for each cohort, prior to looking at biomarker levels in individual subjects. One-tail t-tests with equal variance were used for statistical comparisons. ROC curves were calculated using SPSS software for each of the four-dimensional analyses, predicting the state variable of hospitalizations due to suicidality.
Higher SAT1 levels compared to lower SAT1 levels at time of testing differentiated future as well as past hospitalizations due to suicidality in the bipolar disorder subjects (
Taken together, the prospective and retrospective hospitalization data suggests SAT1, PTEN, MARCKS and MAP3K3 may be not only a state marker but perhaps a trait marker as well.
A multi-dimensional approach was also conducted to predict future hospitalizations, by adding data about mood, anxiety, and psychosis to the data about SAT1 expression levels (
The multi-dimensional approach described above for SAT1 was also conducted to predict future hospitalizations, by adding data about mood, anxiety, and psychosis to the data about the six top biomarkers' expression levels (BioM 6, including the biomarkers SAT1, PTEN, MARCKS, MAP3K3, UBA6, and MT-ND6;
These results demonstrate that combining clinical scale data for anxiety and mood with the blood biomarker date improves predictability of increased suicide ideation and/or future hospitalization.
The psychosis information was based on combining of the scores on the hallucinations and delusions in the PANSS (
Using discovery in live subjects and validation in suicide completers, possible biomarkers for suicidality were found. The top biomarker finding, SAT1, as well as PTEN, MARCKS and MAP3K3, were additionally validated by prospective and retrospective analyses in live subjects, looking at ability to predict and differentiate future and past hospitalizations due to suicidality in bipolar disorder and psychosis (schizophrenia/schizoaffective) (Table 10).
Beyond predictions, as a window into the biology of suicidality, the current Examples show overlap at a gene and pathway level with apoptosis. SAT1, for example, is a key catabolic enzyme for polyamines. Polyamine levels within cells control cell viability, and significant decreases in polyamine levels can result in apoptosis. They seem to reflect an endowment for cellular and organismal activity and growth, key characteristics of mood. SAT1, which is increased in live suicidal ideation subjects and in suicide completers in the Examples, is highly inducible by a variety of stimuli, including toxins, cytokines, heat shock, ischemia, and other stresses. SAT1 overexpressing mice had alterations in their polyamine pool, hair loss, infertility and weight loss (Pietila et al., Activation of polyamine catabolism profoundly alters tissue polyamine pools and affects hair growth and female fertility in transgenic mice overexpressing spermidine/spermine N1-acetyltransferase. J Biol. Chem. 272, 18746-18751 (1997); Min et al., Altered levels of growth-related and novel gene transcripts in reproductive and other tissues of female mice overexpressing spermidien/spermine N1-actyltransferase (SSAT). J. Biol. Chem. 277, 3647-3657, doi:10.1074/jbc.M100751200 (2002)). Turecki and colleagues have provided compelling evidence for changes in the polyamine system in the brain of suicide completers (Fiori et al., Global gene expression profiling of the polyamine system in suicide completers. Int. J. Neuropsychopharmacol. 14, 595-605, doi:10.1017/S1461145710001574 (2011)).
CD24, the top biomarker found to decrease in suicidal subjects, also has roles in apoptosis. Specifically, mice lacking CD24 showed an increased rate of apoptosis (Duckworth et al. CD24 is expressed in gastric parietal cells and regulates apoptosis and the response to Helicobacter felis infection in the murine stomach. American Journal of Physiology. Gastrointestinal and liver physiology 303, G915-926, doi:10.1152/ajpgi.00068.2012 (2012)).
It could be that simpler mechanisms related to cellular survival and programed cell-death decision have been recruited by evolution for higher mental functions such as feelings, thoughts, actions and behaviors leading to suicidality. In that sense, suicidality could be viewed as whole-organism self-apoptosis. Apoptosis mechanisms have previously been implicated in mood disorders, and their inhibition in affective resilience (Malkesman et al. Targeting the BH3-interacting domain death agonist to develop mechanistically unique antidepressants. Mol. Psychiatry 17, 770-780, doi:10.1038/mp.2011.77 (2012)). Interestingly, lithium, a medication with clinical evidence for preventing suicidality in bipolar disorder, has anti-apoptotic effects at a cellular level (Lowthert et al., Increased ratio of anti-apoptotic to pro-apoptotic BcI2 gene-family members in lithium-responders one month after treatment initiation. Biology of Mood & Anxiety Disorders 2, 15, doi:10.1186/2045-5380-2-15 (2012)). Imaging studies have shown reduced gray matter volume in the brain of individuals with bipolar disorder and history of suicide attempts. Long-term lithium treatment was associated with increased gray matter volumes in the same areas where suicide was associated with decreased gray matter (Benedetti et al., Opposite effects of suicidality and lithium on gray matter volumes in bipolar depression. J Affect Disord 135, 139-147, doi:10.1016/j.jad.2011.07.006 (2011)).
In view of the above, it will be seen that the several advantages of the disclosure are achieved and other advantageous results attained. As various changes could be made in the above methods without departing from the scope of the disclosure, it is intended that all matter contained in the above description and shown in the accompanying drawings shall be interpreted as illustrative and not in a limiting sense.
When introducing elements of the present disclosure or the various versions, embodiment(s) or aspects thereof, the articles “a”, “an”, “the” and “said” are intended to mean that there are one or more of the elements. The terms “comprising”, “including” and “having” are intended to be inclusive and mean that there may be additional elements other than the listed elements.
This application is a continuation application of U.S. application Ser. No. 14/194,024 filed on Feb. 28, 2014, which claims priority to U.S. Provisional Patent Application No. 61/770,696 filed on Feb. 28, 2013, both of which are hereby incorporated by reference in their entireties.
This invention was made with government support under OD007363 awarded by the National Institutes of Health. The Government has certain rights in the invention.
| Number | Date | Country | |
|---|---|---|---|
| 61770696 | Feb 2013 | US |
| Number | Date | Country | |
|---|---|---|---|
| Parent | 14194024 | Feb 2014 | US |
| Child | 15091706 | US |
