Patent Grant
10991449
The present disclosure relates generally to biomarkers and their use for predicting a subject's risk of suicidality (e.g., suicide ideation and actions, future hospitalization due to suicidality, and suicide completion). 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, as well as for preventing and treating subjects for suicidality. The present disclosure further relates to quantitative clinical information assessments through questionnaires and mobile applications (referred to herein as “apps”) for assessing affective state (mood and anxiety), for assessing socio-demographic and psychological suicide risk factors, and for identifying subjects who are at risk of committing suicide. Finally, the present disclosure relates to an algorithm for combining biomarkers and apps for identifying subjects who are at risk for committing suicide.
Suicide is a leading cause of death in psychiatric patients, and in society at large. Particularly, suicide accounts for one million deaths worldwide each year. Worldwide, one person dies every 40 seconds through suicide, a potentially preventable cause of death. Further, although women have a lower rate of suicide completion as compared to men, due in part to the less-violent methods used, women have a higher rate of suicide attempts. A limiting step in the ability to intervene is the lack of objective, reliable predictors. One cannot just ask individuals if they are suicidal, as the desire to not be stopped or future impulsive changes of mind may make their self-report of feelings, thoughts and plans unreliable.
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 their plans will be thwarted. The ability to asses and track changes in suicidal risk without asking a subject directly would further allow for intervening prior to suicide attempt and suicide completion by the subject.
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 tools and 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 ability to asses and track changes in suicidal risk without asking a subject directly would further allow for intervening prior to suicide attempt and suicide completion by the subject.
The present disclosure is generally related to predicting state (suicidal ideation) and trait—future psychiatric hospitalizations for suicidality. The methods described herein increase the predictive accuracy for specifically identifying subjects who are at risk for committing suicide and for predicting future hospitalization due to suicidality. In one particular aspect, the methods described herein increase the predictive accuracy for specifically identifying subjects who are at risk for committing suicide and for predicting future hospitalization due to suicidality.
In one aspect, the present disclosure is directed to a method for predicting suicidality in a subject. The method comprises: obtaining an expression level of a blood biomarker in a sample obtained from the subject; obtaining a reference expression level of a blood biomarker; and identifying a difference between the expression level of the blood biomarker in a sample obtained from the subject and the reference expression level of a blood biomarker, wherein the difference in the expression level of the blood biomarker in the sample obtained from the subject and the reference expression level of the blood biomarker indicates a risk for suicide.
In another aspect, the present disclosure is directed to a method for mitigating suicidality in a subject in need thereof. The method comprises: obtaining an expression level of a blood biomarker in a sample obtained from the subject; obtaining a reference expression level of the blood biomarker; identifying a difference in the expression level of the blood biomarker in the sample and the reference expression level of the blood biomarker; and administering a treatment, wherein the treatment reduces the difference between the expression level of the blood biomarker in the sample and the reference expression level of the blood biomarker to mitigate suicidality in the subject.
In another aspect, the present disclosure is directed to a computer-implemented method for assessing mood, anxiety, and combinations thereof in the subject using a computer-implemented method for assessing mood, anxiety, and combinations thereof, the method implemented using a first computer device coupled to a memory device, the method comprising: receiving mood information, anxiety information, and combinations thereof into the first computer device; storing, by the first computer device, the mood information, anxiety information, and combinations thereof in the memory device; presenting, by the first computer device, in visual form the mood information, anxiety information, and combinations thereof to a second computer device; receiving a request from the second computer device for access to the mood information, anxiety information, and combinations thereof; and transmitting, by the first computer device, the mood information, anxiety information, and combinations thereof to the second computer device to assess mood, anxiety, and combinations thereof in the subject.
In another aspect, the present disclosure is directed to a computer-implemented method for assessing socio-demographic/psychological suicidal risk factors in the subject using a computer-implemented method for assessing socio-demographic/psychological suicidal risk factors in the subject, the method implemented using a first computer device coupled to a memory device, the method comprising: receiving socio-demographic/psychological suicidal risk factor information into the first computer device; storing, by the first computer device, the socio-demographic/psychological suicidal risk factor information in the memory device; presenting, by the first computer device, in visual form the socio-demographic/psychological suicidal risk factor information to a second computer device; receiving a request from the second computer device for access to socio-demographic/psychological suicidal risk factor information; and transmitting, by the first computer device, the socio-demographic/psychological suicidal risk factor information to the second computer device to assess the socio-demographic/psychological suicidal risk factors in the subject.
In one aspect, the present disclosure is directed to a method for predicting suicidality in a subject. The method comprises: identifying a difference in the expression level of a blood biomarker in a sample obtained from a subject and a reference expression level of the blood biomarker by obtaining the expression level of the blood biomarker in a sample obtained from a subject; obtaining a reference expression level of a blood biomarker; analyzing the blood biomarker in the sample obtained from the subject and the reference expression level of the blood biomarker to detect the difference between the blood biomarker in the sample and the reference expression level of the blood biomarker; assessing mood, anxiety, and combinations thereof in the subject, using a first computer device coupled to a memory device, wherein the first computer device receives mood information, anxiety information, and combinations thereof into the first computer device; storing, by the first computer device, the mood information, anxiety information, and combinations thereof in the memory device; computing, by the first computer device, of the mood information, anxiety information, and combinations thereof, a score that can be used to predict suicidality; presenting, by the first computer device, in visual form the mood information, anxiety information, and combinations thereof to a second computer device; receiving a request from the second computer device for access to the mood information, anxiety information, and combinations thereof; and transmitting, by the first computer device, the mood information, anxiety information, and combinations thereof to the second computer device to assess mood, anxiety, and combinations thereof in the subject; assessing socio-demographic/psychological suicidal risk factors in the subject using the first computer device coupled to a memory device, wherein the first computer device receives socio-demographic/psychological suicidal risk factor information into the first computer device; storing, by the first computer device, the socio-demographic/psychological suicidal risk factor information in the memory device; computing, by the first computer device, of the socio-demographic/psychological suicidal risk factor information, a score that can be used to predict suicidality; presenting, by the first computer device, in visual form the socio-demographic/psychological suicidal risk factor information to the second computer device; receiving a request from the second computer device for access to socio-demographic/psychological suicidal risk factor information; and transmitting, by the first computer device, the socio-demographic/psychological suicidal risk factor information to the second computer device to assess the socio-demographic/psychological suicidal risk factors in the subject; and predicting suicidality in the subject by the combination of the difference between the expression level of the biomarker in the subject and the reference expression level of the blood biomarker; the assessment of mood, anxiety, and combinations thereof; and the assessment of socio-demographic/psychological suicidal risk factor information.
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 can be used in the practice or testing of the present disclosure, the preferred methods and materials are described below.
New data for discovery, prioritization, validation and testing of next generation broader-spectrum blood biomarkers for suicidal ideation and behavior, across psychiatric diagnoses are disclosed. Also disclosed are two clinical information questionnaires in the form of apps, one for affective state (Simplified Affective Scale, SASS) and one for suicide risk factors (Convergent Functional Information for Suicide, CFI-S), that are useful in predicting suicidality. Both of these instruments do not directly ask about suicidal ideation. Also disclosed is a comprehensive universal predictor for suicide (UP-Suicide), composed of the combination of top biomarkers (from discovery, prioritization and validation), along with CFI-S, and SASS, which predicts in independent test cohorts suicidal ideation and future psychiatric hospitalizations for suicidality.
As disclosed herein, “patient psychiatric information” may include mood information, anxiety information, and other psychiatric symptom information and combinations thereof.
As used herein, “predicting suicidality in a subject” is used herein to indicate in advance that a subject will attempt suicide and/or complete suicide.
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. In some embodiments, the reference expression level of a biomarker can be obtained for a subject who has no suicidal ideation at the time the sample is obtained from the subject, but who later exhibits suicide ideation. As used herein, “suicidality” includes both suicide ideation and suicidal acts.
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. The reference expression level of the biomarker can further refer to the expression level of the biomarker established for a high suicide risk subject, including a population of high suicide risk subjects. The reference expression level of the biomarker can also refer to the expression level of the biomarker established for a low suicide risk subject, including a population of low suicide risk subjects. The reference expression level of the biomarker can also refer to the expression level of the biomarker established for any combination of subjects such as a subject with no suicidal ideation, expression level of the biomarker in a normal/healthy subject with no suicidal ideation, expression level of the biomarker for a subject who has no suicidal ideation at the time the sample is obtained from the subject, but who later exhibits suicide ideation, expression level of the biomarker as established for a high suicide risk subject, including a population of high suicide risk subjects, and expression level of the biomarker can also refer to the expression level of the biomarker established for a low suicide risk subject, including a population of low suicide risk subjects. The reference expression level of the biomarker can also refer to the expression level of the biomarker obtained from the subject to which the method is applied. As such, the change within a subject from visit to visit can indicate an increased or decreased risk for suicide. For example, a plurality of expression levels of a biomarker can be obtained from a plurality of samples obtained from the same subject and used to identify differences between the plurality of expression levels in each sample. Thus, in some embodiments, two or more samples obtained from the same subject can provide an expression level(s) of a blood biomarker and a reference expression level(s) of the blood biomarker.
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, enzyme linked immunosorbent assay (ELISA), and combinations thereof.
As used herein, a “difference” in the expression level of the biomarker refers to an increase or a decrease in the expression of a blood biomarker when analyzed against a reference expression level of the biomarker. In some embodiments, the “difference” refers to an increase or a decrease by about 1.2-fold or greater in the expression level of the biomarker as identified between a sample obtained from the subject and the reference expression level of the biomarker. In one embodiment, the difference in expression level is an increase or decrease by about 1.2 fold. As used herein “a risk for suicide” can refer to an increased (greater) risk that a subject will attempt to commit suicide and/or complete suicide For example, depending on the biomarker(s) selected, the difference in the expression level of the biomarker(s) can indicate an increased (greater) risk that a subject will attempt to commit suicide and/or complete suicide. Conversely, depending on the biomarker(s) selected, the difference in the expression level of the biomarker(s) can indicate a decreased (lower) risk that a subject will attempt to commit suicide and/or complete suicide.
In accordance with the present disclosure, biomarkers useful for objectively predicting, mitigating, and/or preventing suicidality in subjects have been discovered. In one aspect, the present disclosure is directed to a method for predicting suicidality in a subject. 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 suicidality. 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.
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, one or more biomarkers as listed in Table 1 and combinations thereof.
In one particularly suitable embodiment, the subject is a male and the blood biomarker that increases in expression level as compared to the reference expression level is selected from solute carrier family 4 (sodium bicarbonate cotransporter), member 4 (SLC4A4), cell adhesion molecule 1 CADM1, dystrobrevin, alpha (DTNA), spermidine/spermine N1-acetyltransferase 1 (SAT1), interleukin 6 (interferon, beta 2) (IL6) and combinations thereof. In another embodiment, the subject is a female and the blood biomarker that increases in expression level as compared to the reference expression level is selected from erythrocyte membrane protein band 4.1 like 5 (EPB41L5), HtrA serine peptidase 1 (HTRA1), deleted in primary ciliary dyskinesia homolog (DPCD), general transcription factor IIIC, polypeptide 3, 102 kDa (GTF3C3), period circadian clock 1 (PER1), pyridoxal-dependent decarboxylase domain containing 1 (PDXDC1), kelch-like family member 28 (KLHL28), ubiquitin interaction motif containing 1 (UIMC1), sorting nexin family member 27 (SNX27) and combinations thereof.
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, one or more biomarkers as listed in Table 2 and combinations thereof.
In one particularly suitable embodiment, the subject is a male and the blood biomarker that decreases in expression level as compared to the reference expression level is spindle and kinetochore associated complex subunit 2 (SKA2), CAP-GLY domain containing linker protein family, member 4 (CLIP4), kinesin family member 2C (KIF2C), kelch domain containing 3 (KLHDC3) and combinations thereof. In another embodiment, the subject is a female and the blood biomarker that decreases in expression level as compared to the reference expression level is selected from phosphatidylinositol 3-kinase, catalytic subunit type 3 (PIK3C3), aldehyde dehydrogenase 3 family, member A2 (ALDH3A2), ARP3 actin-related protein 3 homolog (yeast) (ACTR3), B-cell CLL (BCL2), MOB kinase activator 3B (MOB3B), casein kinase 1, alpha 1 (CSNK1A1), La ribonucleoprotein domain family, member 4 (LARP4), zinc finger protein 548 (ZNF548) and combinations thereof.
Table 3 further discloses the top biomarkers across gender having expression levels that increase or decrease (as indicated) as compared to the reference expression levels to predict suicidality.
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. In one particular aspect, the subject is a female human. In another particular aspect, the subject is a male human.
In another aspect, the subject can further be diagnosed with a psychiatric disorder as known in the art. In particular aspects, the psychiatric disorder can be bipolar disorder, major depressive disorder, schizophrenia, and schizoaffective disorder, post-traumatic stress disorder, and combinations thereof.
In one embodiment, the subject can be diagnosed as having or as suspected of having bipolar disorder (BP) and the biomarker can be selected from DTNA; HS3ST3B1; CADM1; Unknown gene; KSR1; CD44; DAPP1; OPRM1; SPTBN1; AKT1S1; SAT1; C20orf27; and combinations thereof. As summarized in
In another embodiment, the subject can be diagnosed as having or as suspected of having depression (MDD) and the biomarker can be selected from PHF20; EIF1B-AS1; TLN1; NUCKS1; DLK1; BBIP1; BDNF; SKA2; IL10; GATM; PRPF40A; and combinations thereof. As summarized in
In another embodiment, the subject can be diagnosed as having or as suspected of having schizoaffective disorder (SZA) and the biomarker can be selected from USP48; NPRL3; TSPYL1; TMSB15B; IL6; TNS1; TNF; S100B; JUN; BATF2; ANXA11; and combinations thereof. As summarized in
In another embodiment, the subject can be diagnosed as having or as suspected of having schizophrenia (SZ) and the biomarker can be selected from RP11-389C8.2; CYB561; LOC100128288; CDDC163P; C1orf61; SKA2; BDNF; HTR2A; SLC5A3; ATP6V0E1; JUN; LOC100131662; and combinations thereof. As summarized in
A particularly suitable sample for which the expression level of a biomarker is determined can be, for example, blood, including whole blood, serum, plasma, leukocytes, and megakaryocytes.
The method can further include assessing mood, anxiety, and other like psychiatric symptoms, and combinations thereof in the subject using questionnaires and/or a computer-implemented method for assessing mood, anxiety, other like psychiatric symptoms, and combinations thereof. In one aspect, the method is implemented using a first computer device coupled to a memory device, the method comprising: receiving mood information, anxiety information, and combinations thereof into the first computer device; storing, by the first computer device, the mood information, anxiety information, and combinations thereof in the memory device; computing, by the first computer device, of the mood information, anxiety information, and combinations thereof, a score that can be used to predict suicidality; presenting, by the first computer device, in visual form the mood information, anxiety information, and combinations thereof to a second computer device; receiving a request from the second computer device for access to the mood information, anxiety information, and combinations thereof; and transmitting, by the first computer device, the mood information, anxiety information, and combinations thereof to the second computer device to assess mood, anxiety, and combinations thereof in the subject. Suitable mood and anxiety information is described herein in more detail below.
The method can further include assessing socio-demographic/psychological suicidal risk factors in the subject using a computer-implemented method for assessing socio-demographic/psychological suicidal risk factors in the subject, the method implemented using a first computer device coupled to a memory device, the method comprising: receiving socio-demographic/psychological suicidal risk factor information into the first computer device; storing, by the first computer device, the socio-demographic/psychological suicidal risk factor information in the memory device; presenting, by the first computer device, in visual form the socio-demographic/psychological suicidal risk factor information to a second computer device; receiving a request from the second computer device for access to socio-demographic/psychological suicidal risk factor information; and transmitting, by the first computer device, the socio-demographic/psychological suicidal risk factor information to the second computer device to assess the socio-demographic/psychological suicidal risk factors in the subject. Suitable socio-demographic/psychological suicidal risk factors are described herein in more detail below.
In accordance with the present disclosure, biomarkers useful for objectively predicting future hospitalization due to suicidality in subjects have been discovered. In one aspect, the present disclosure is directed to a method for future hospitalization due to suicidality in a subject. 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. 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.
Suitable biomarkers for predicting future hospitalization due to suicidality in a subject wherein an increase in the expression level of the blood biomarker occurs can be, for example, the blood biomarker(s) set forth in Table 1.
In another 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. Suitable biomarkers that indicate a risk for future hospitalization due to suicidality when the expression level increases in males as compared to the reference expression level have been found to include, for example, solute carrier family 4 (sodium bicarbonate cotransporter), member 4 (SLC4A4), cell adhesion molecule 1 CADM1, dystrobrevin, alpha (DTNA), spermidine/spermine N1-acetyltransferase 1 (SAT1), interleukin 6 (interferon, beta 2) (IL6) and combinations thereof. Suitable biomarkers that indicate a risk for future hospitalization due to suicidality when the expression level increases in females as compared to the reference expression level have been found to include, for example, erythrocyte membrane protein band 4.1 like 5 (EPB41L5), HtrA serine peptidase 1 (HTRA1), deleted in primary ciliary dyskinesia homolog (DPCD), general transcription factor IIIC, polypeptide 3, 102 kDa (GTF3C3), period circadian clock 1 (PER1), pyridoxal-dependent decarboxylase domain containing 1 (PDXDC1), kelch-like family member 28 (KLHL28), ubiquitin interaction motif containing 1 (UIMC1), sorting nexin family member 27 (SNX27) and combinations thereof.
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 future hospitalization due to suicidality when the expression level decreases in males as compared to the reference expression level have been found to include, for example, spindle and kinetochore associated complex subunit 2 (SKA2), CAP-GLY domain containing linker protein family, member 4 (CLIP4), kinesin family member 2C (KIF2C), kelch domain containing 3 (KLHDC3) and combinations thereof. Suitable biomarkers that indicate a risk for future hospitalization due to suicidality when the expression level decreases in females as compared to the reference expression level have been found to include, for example, phosphatidylinositol 3-kinase, catalytic subunit type 3 (PIK3C3), aldehyde dehydrogenase 3 family, member A2 (ALDH3A2), ARP3 actin-related protein 3 homolog (yeast) (ACTR3), B-cell CLL (BCL2), MOB kinase activator 3B (MOB3B), casein kinase 1, alpha 1 (CSNK1A1), La ribonucleoprotein domain family, member 4 (LARP4), zinc finger protein 548 (ZNF548) 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. In one particular embodiment, the subject is a female human. In another particular aspect, the subject is a male human.
In another aspect, the subject can further be diagnosed with a psychiatric disorder. The psychiatric disorder can be bipolar disorder, major depressive disorder, schizophrenia, and schizoaffective disorder, post-traumatic stress disorder and combinations thereof.
A particularly suitable sample for which the expression level of a biomarker is determined can be, for example, blood, including whole blood, serum, plasma, leukocytes, and megakaryocytes.
Suitable biomarkers found to have a difference in expression level include, for example, spermidine/spermine N1-acetyltransferase 1 (SAT1), interleukin 6 (interferon beta 2) (IL6), solute carrier family 4 (sodium bicarbonate cotransporter), member 4 (SLC4A4), spindle and kinetochore associated complex subunit 2 (SKA2), jun proto-oncogen (JUN), cell adhesion molecule 1 (CADM1), dystrobrevin alpha (DTNA), monoamine oxidase B (MAOB), myristoylated alanine-rich protein kinase C substrate (MARCKS), phosphatase and tensin homolog (PTEN), fatty acid desaturase 1 (FADS1), Rho GTPase activating protein 26 (ARHGAP26), B-cell CLL/lymphoma 2 (BCL2), cadherin 4 type 1 R cadherin (retinal) (CDH4), chemokine (C-X-C motif) ligand 11 (CXCL11), EMI domain containing 1 (EMID1), family with sequence similarity 49 member B (FAM49B), GRINL1A complex locus (GCOM1), hippocalcin-like 1 (HPCAL1), mitogen-activated protein kinase 9 (MAPK9), nuclear paraspeckle assembly transcript 1 (NEAT1), protein tyrosine kinase 2 (PTK2), RAS-like family 11 member B (RASL11B), small nucleolar RNA H/ACA box 68 (SNORA68), superoxide dismutase 2 mitochondrial (SOD2), transcription factor 7-like 2 (T-cell specific HMG-box) (TCF7L2), v-raf murine sarcoma viral oncogene homolog (BRAF), Chromosome 1 Open Reading Frame 61 (C1orf61), calreticulin (CALR), calcium/calmodulin-dependent protein kinase II beta (CAMK2B), caveolin 1 caveolae proein 22 kDa (CAV1), chromodomain helicase DNA binding protein 2 (CHD2), cAMP responsive element modulators (CREM), cortactin (CTTN), disheveled associated activator of morphogenesis 2 (DAAM2), Dab mitogen responsive phosphoprotein homolog 2 (DAB2), GABA(A) receptor associated protein like 1 (GABARAPL1), glutamate-ammonia ligase (GLUL), helicase with zinc finger (HELZ), immunoglobulin heavy chain constant gamma 1 (IGHG1), interleukin 1 beta (IL1B), jun B proto-oncogen (JUNB), lipoma HMGIC fusion partner (LHFP), metallothionein 1 E (MT1E), metallothionein 1 H (MT1H), metallothionein 2 (MT2A), N-myc downstream regulated 1 (NDRG1), nucleobindin 2 (NUCB2), PHD finger protein 20-like 1 (PHF20L1), cysteine-rich protein with kazal motifs (RECK), shisa family member 2 (SHISA2), transmembrane 4 L six family member 1 (TM4SF1), trophoblast glycoprotein (TPBG), tumor protein D52-like 1 (TPD52L1), TSC22 domain family member 3 (TSC22D3), vacuole membrane protein 1 (VMP1), ZFP 36 ring finger protein (ZFP36), zink finger FYVE domain containing 21 (ZHX2), histone cluster 1 H2bo (HIST1H2BO), keratocan (KERA), transcription factor Dp-1 (TFDP1), Single-Stranded DNA Binding Protein 2 (SSBP2), Transcription Factor EC (TFEC), Diphosphoinositol Pentakisphosphate Kinase 1 (PPIP5K1), Fibroblast Growth Factor Receptor 1 Oncogene Partner 2 (FGFR1OP2), Zinc Finger MYND-Type Containing 8 (ZMYND8), Interferon Gamma (IFNG), Brain-Derived Neurotrophic Factor (BDNF), cAMP Responsive Element Binding Protein 1 (CREB1), Hes Family BHLH Transcription Factor 1 (HES1), Ankyrin Repeat And MYND Domain Containing 1 (ANKMY1), Aldehyde Dehydrogenase 3 Family Member A2 (ALDH3A2), Heparan Sulfate (Glucosamine) 3-O-Sulfotransferase 3B1 (HS3ST3B1), Kinase Suppressor Of Ras 1 (KSR1), Dual Adaptor Of Phosphotyrosine And 3-Phosphoinositides (DAPP1), Opioid Receptor Mu 1 (OPRM1), Spectrin Beta Non-Erythrocytic 1 (SPTBN1), PHD Finger Protein 20 (PHF20), EIF1B Antisense RNA 1 (EIF1B-AS1), Talin 1 (TLN1), Nuclear Casein Kinase And Cyclin-Dependent Kinase Substrate 1 (NUCKS1), Delta-Like 1 Homolog (DLK1), BBSome Interacting Protein 1 (BBIP1), Interleukin 10 (IL10), Glycine Amidinotransferase (GATM), PRP40 Pre-MRNA Processing Factor 40 Homolog A (PRPF40A), Ubiquitin Specific Peptidase 48 (USP48), Nitrogen Permease Regulator-Like 3 (NPRL3), Testis-Specific Y-Encoded-Like Protein-Like 1 (TSPYL1), thymosin beta 15B (TMSB15B), Minichromosome Maintenance Complex Component 8 (MCM8), tensin 1 (TNS1), Tumor Necrosis Factor (TNF), 5100 Calcium Binding Protein B (S100B), Basic Leucine Zipper Transcription Factor ATF-Like 2 (BATF2), Annexin A11 (ANX11), RP11-389C8.2, Cytochrome B561 (CYB561), LOC100128288 (Uncharacterized LOC100128288), Coiled-Coil Domain Containing 163 Pseudogene (CCDC163P), 5-Hydroxytryptamine (Serotonin) Receptor 2A, G Protein-Coupled (HTR2A), Annexin A11 (ANXA11), Uncharacterized LOC100131662 (LOC100131662), Prolylcarboxypeptidase (Angiotensinase C; PRCP), and combinations thereof. See,
In another aspect, the present disclosure is directed to a method for mitigating suicidality in a subject in need thereof. The method includes: obtaining an expression level of a blood biomarker in a sample obtained from the subject; obtaining a reference expression level of the blood biomarker; identifying a difference in the expression level of the blood biomarker in the sample as compared to the reference expression level of the blood biomarker; and administering a treatment, wherein the treatment reduces the difference between the expression level of the blood biomarker in the sample as compared to the reference expression level of the blood biomarker to mitigate suicidality in the subject. As used herein, “mitigate”, “mitigating”, and the like refer to making a condition less severe and/or preventing a condition. More particularly, the phrase “mitigate suicidality” refers to reducing suicide ideation in a subject and/or preventing suicide completion.
Suitable treatments can be a lifestyle modification, administering a therapy, and combinations thereof.
Suitable therapy can be a nutritional, a drug and psychotherapy.
Particularly suitable nutritionals can be omega-3 fatty acids, including, by way of example, docosahexaenoic acid (DHA).
Particularly suitable drugs include, for example, ketamine, lithium, clozapine, selegeline, tocilizumab, siltuximab, enkephalin, methionine, gevokizumab, gallium nitrate, vemurafenib, dabrafenib, oblimersen, rasagiline, (−)-gossypol, navitoclax, gemcitabine/paclitaxel, bortezomib/paclitaxel, ABT-199, paclitaxel/trastuzumab, paclitaxel/pertuzumab/trastuzumab, lapatinib/paclitaxel, doxorubicin/paclitaxel, epirubicin/paclitaxel, paclitaxel/topotecan, paclitaxel, canakinumab, tesevatinib, enzastaurin, fomepizole, miglitol, anakinra, and combinations thereof. Other suitable drugs, as well as biomarkers found to be changed in opposite direction in suicide versus in treatments with omega-3 fatty acids, lithium, clozapine, or antidepressants (MAOIs) as listed in Tables 4 & 5. These biomarkers could potentially be used to stratify patients to different treatment approaches, and monitor their responses.
More particularly, it has been found that BCL2, JUN, GHA1, ENTPD1, ITIH5, MBNL1, and SSBP2 are changed in expression by the above listed treatments, and in particular therapies such as nutritionals and drugs, suggesting these biomarkers may be core to the anti-suicidal mechanism of these drugs. Further, BCL2, CAT, and JUN may be useful blood pharmacogenomic markers of response to lithium. CD84, MBNL1, and RAB22A may be useful blood pharmacogenomic markers of response to clozapine. NDRG1, FOXP1, AFF3, ATXN1, CSNK1A1, ENTPD1, ITIH5, PRDX3, and SSBP2 may be useful blood pharmacogenomic markers of response to omega-3 fatty acids. Three existing drugs, used for other indications, have been identified as targeting the top suicide biomarkers identified in the present disclosure, and could potentially be re-purposed for testing in treatment of acute suicidality: anakinra (inhibiting ILR1), enzastaurin (inhibiting AKT3), and tesevatinib (inhibiting EPHB4). Additionally, Connectivity Map analyses (
In another aspect, the subject can further be diagnosed with a psychiatric disorder. The psychiatric disorder can be any psychiatric disorder known in the art, including, for example, bipolar disorder, major depressive disorder, schizophrenia, and schizoaffective disorder, post-traumatic stress disorder, and combinations thereof.
In another aspect, the present disclosure is directed to a questionnaire and/or a computer-implemented method for assessing mood, anxiety, and combinations thereof in the subject using a computer-implemented method for assessing mood, anxiety, and the like, and combinations thereof. In one aspect, the method is implemented using a computer device coupled to a memory device. The method implemented using a first computer device coupled to a memory device includes receiving mood information, anxiety information, and combinations thereof into the first computer device; storing, by the first computer device, the mood information, anxiety information, and combinations thereof in the memory device; presenting, by the first computer device, in visual form the mood information, anxiety information, and combinations thereof to a second computer device; receiving a request from the second computer device for access to the mood information, anxiety information, and combinations thereof; and transmitting, by the first computer device, the mood information, anxiety information, and combinations thereof to the second computer device to assess mood, anxiety, and combinations thereof in the subject.
Mood information includes information relating to a subject's mood, motivation, movement, thinking, self-esteem, interest, appetite, and combinations thereof. Anxiety information includes information relating to a subjects anxiety, uncertainty, fear, anger, and combinations thereof. Particular mood and anxiety information assessed can include: determining how good is the subject's mood; determining the subject's motivation, drive, determination to do things right now; determining how high is the subject's physical energy and the amount of moving about that the subject feels like doing right now; determining how high is the subject's mental energy and thinking activity going on in the subject's mind right now; determining how good the subject feels about himself/herself and his/her accomplishments right now; determining how high the subject's interest to do things that are fun and enjoyable right now; determining how high the subjects appetite and desire for food is right now; determining how anxious the subject is right now; determining how uncertain about things the subject is right now; determining how frightened about things the subject feels right now; determining how angry about things the subject feels right now; determining events or actions the subject thinks are influencing how the subject feels right now; determining additional feelings the subject has right now; and combinations thereof. As illustrated in
The subject of the method can further be diagnosed as having a psychiatric disorder selected from bipolar disorder, major depressive disorder, schizophrenia, and schizoaffective disorder, post-traumatic stress disorder, and combinations thereof.
In another aspect, the present disclosure is directed to a computer-implemented method for assessing socio-demographic/psychological suicidal risk factors in the subject using a computer-implemented method for assessing socio-demographic/psychological suicidal risk factors in the subject, the method implemented using a computer device coupled to a memory device. The method includes: receiving socio-demographic/psychological suicidal risk factor information into the first computer device; storing, by the first computer device, the socio-demographic/psychological suicidal risk factor information in the memory device; presenting, by the first computer device, in visual form the socio-demographic/psychological suicidal risk factor information to a second computer device; receiving a request from the second computer device for access to socio-demographic/psychological suicidal risk factor information; and transmitting, by the first computer device, the socio-demographic/psychological suicidal risk factor information to the second computer device to assess the socio-demographic/psychological suicidal risk factors in the subject.
Socio-demographic and clinical risk factors for suicide includes items for assessing the influence of mental health factors, as well as of life satisfaction, physical health, environmental stress, addictions, cultural factors known to influence suicidal behavior, and two demographic factors, age and gender. Socio-demographic/psychological suicidal risk factors assessed can include: lack of coping skills when faced with stress; dissatisfaction with current life; lack of hope for the future; current substance abuse; acute loss/grief; psychiatric illness diagnosed and treated; poor treatment compliance; family history of suicide in blood relatives; personally knowing somebody who committed suicide; history of abuse (such as physical abuse, sexual abuse, emotional abuse, and neglect); acute/severe medical illness (including acute pain); chronic stress (including perceived uselessness, not feeling needed, and burden to extended kin); history of excessive introversion/conscientiousness (including planned suicide attempts); past history of suicidal acts/gestures; lack of religious beliefs; rejection; lack of positive relationships/social isolation; history of excessive extroversion and impulsive behavior (including rage, anger, physical fights and seeking revenge); lack of children/not in touch with children/not helping care for children; history of command hallucinations of self-directed violence; age (older than 60 years or younger than 25 years); gender; and combinations thereof.
The socio-demographic/psychological suicidal risk factors can be assessed by having the subject provide an answer to the above factors such as a yes answer, a no answer and a not applicable answer.
The subject of the method can further be diagnosed as having a psychiatric disorder selected from bipolar disorder, major depressive disorder, schizophrenia, and schizoaffective disorder, post-traumatic stress disorder, and combinations thereof.
In another aspect, the present disclosure is directed to a method for predicting suicidality in a subject. The method includes: identifying a difference in the expression level of a blood biomarker in a sample obtained from a subject and a reference expression level of the blood biomarker by obtaining the expression level of the blood biomarker in a sample obtained from a subject; obtaining a reference expression level of a blood biomarker; analyzing the blood biomarker in the sample obtained from the subject and the reference expression level of the blood biomarker to detect the difference between the blood biomarker in the sample and the reference expression level of the blood biomarker; assessing mood, anxiety, and combinations thereof, using a first computer device coupled to a memory device, wherein the first computer device receives mood information, anxiety information, and combinations thereof into the first computer device; storing, by the first computer device, the mood information, anxiety information, and combinations thereof in the memory device; presenting, by the first computer device, in visual form the mood information, anxiety information, and combinations thereof to a second computer device; receiving a request from the second computer device for access to the mood information, anxiety information, and combinations thereof; and transmitting, by the first computer device, the mood information, anxiety information, and combinations thereof to the second computer device to assess mood, anxiety, and combinations thereof in the subject; assessing socio-demographic/psychological suicidal risk factors in the subject using the first computer device coupled to a memory device, wherein the first computer device receives socio-demographic/psychological suicidal risk factor information into the first computer device; storing, by the first computer device, the socio-demographic/psychological suicidal risk factor information in the memory device; presenting, by the first computer device, in visual form the socio-demographic/psychological suicidal risk factor information to the second computer device; receiving a request from the second computer device for access to socio-demographic/psychological suicidal risk factor information; and transmitting, by the first computer device, the socio-demographic/psychological suicidal risk factor information to the second computer device to assess the socio-demographic/psychological suicidal risk factors in the subject; and predicting suicidality in the subject by the combination of the difference between the expression level of the biomarker in the subject and the reference expression level of the blood biomarker; the assessment of mood, anxiety, and combinations thereof; and the assessment of socio-demographic/psychological suicidal risk factor information.
As used herein, while the methods are described as using a first and second computer device, it should be understood that more or less than two computer devices may be used to perform the methods of the present disclosure. Particularly, three computer devices, or four computer devices or even five or more computer devices can be used to perform the methods without departing from the scope of the present disclosure.
In one aspect, the present disclosure is directed to a method for predicting future hospitalization of a subject due to suicidality. The method includes: identifying a difference in the expression level of a blood biomarker in a sample obtained from a subject and a reference expression level of the blood biomarker by obtaining the expression level of the blood biomarker in a sample obtained from a subject; obtaining a reference expression level of a blood biomarker; analyzing the blood biomarker in the sample obtained from the subject and the reference expression level of the blood biomarker to detect the difference between the blood biomarker in the sample and the reference expression level of the blood biomarker; assessing mood, anxiety, and combinations thereof, using a first computer device coupled to a memory device, wherein the first computer device receives mood information, anxiety information, and combinations thereof into the first computer device; storing, by the first computer device, the mood information, anxiety information, and combinations thereof in the memory device; presenting, by the first computer device, in visual form the mood information, anxiety information, and combinations thereof to a second computer device; receiving a request from the second computer device for access to the mood information, anxiety information, and combinations thereof; and transmitting, by the first computer device, the mood information, anxiety information, and combinations thereof to the second computer device to assess mood, anxiety, and combinations thereof in the subject; assessing socio-demographic/psychological suicidal risk factors in the subject using the first computer device coupled to a memory device, wherein the first computer device receives socio-demographic/psychological suicidal risk factor information into the first computer device; storing, by the first computer device, the socio-demographic/psychological suicidal risk factor information in the memory device; presenting, by the first computer device, in visual form the socio-demographic/psychological suicidal risk factor information to a second computer device; receiving a request from the second computer device for access to socio-demographic/psychological suicidal risk factor information; and transmitting, by the first computer device, the socio-demographic/psychological suicidal risk factor information to the second computer device to assess the socio-demographic/psychological suicidal risk factors in the subject; and predicting future hospitalization of the subject due to suicidality by the combination of the difference between the expression level of the biomarker in the subject and the reference expression level of the blood biomarker; the assessment of mood, anxiety, and combinations thereof; and the assessment of socio-demographic/psychological suicidal risk factor information.
Suitable biomarkers for use in the method for predicting suicide ideation in a subject and the method for predicting future hospitalization a subject due to suicidality include those described herein.
Mood information for use in the method for predicting suicide ideation in a subject and the method for predicting future hospitalization of a subject due to suicidality includes information relating to a subject's mood, motivation, movement, thinking, self-esteem, interest, appetite, and combinations thereof as described herein. Anxiety information includes information relating to a subjects anxiety, uncertainty, fear, anger, and combinations thereof as described herein.
Socio-demographic and clinical risk factors for suicide for use in the method for predicting suicide ideation in a subject and the method for predicting future hospitalization of a subject due to suicidality include items for assessing the influence of mental health factors, as well as of life satisfaction, physical health, environmental stress, addictions, cultural factors known to influence suicidal behavior, and two demographic factors, age and gender as described herein.
Methods
Human Blood Gene Expression Experiments and Analyses
RNA Extraction.
Whole blood (2.5-5 ml) was collected into each PaxGene tube by routine venipuncture. PaxGene tubes contain proprietary reagents for the stabilization of RNA. RNA was extracted and processed.
Microarrays.
Biotin-labeled aRNAs were hybridized to Affymetrix HG-U133 Plus 2.0 GeneChips (Affymetrix; with over 40 000 genes and expressed sequence tags), according to the manufacturer's protocols. 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. Quality-control measures, including 30/50 ratios for glyceraldehyde 3-phosphate dehydrogenase and (3-actin, scale factors, background and Q-values, were within acceptable limits.
Analysis.
The participant's SI scores at the time of blood collection (0—no suicidal ideation (SI) compared with 2 and above—high SI) were used. Gene expression differences between the no SI and the high SI visits were analyzed using a within-participant design, then an across-participants summation (
Gene Expression Analysis in the Discovery Cohort
Data was analyzed in two ways: an Absent-Present (AP) approach and a differential expression (DE) approach. The AP approach may capture turning on and off of genes, and the DE approach may capture gradual changes in expression. For the AP approach, Affymetrix Microarray Suite Version 5.0 (MASS) was used to generate Absent (A), Marginal (M), or Present (P) calls for each probe set on the chip (Affymetrix U133 Plus 2.0 GeneChips) for all participants in the discovery cohort. For the DE approach, all Affymetrix microarray data was imported as Cel. files into Partek Genomic Suites 6.6 software package (Partek Incorporated, St Louis, Mo., USA). Using only the perfect match values, a robust multi-array analysis (RMA) was run, background corrected with quantile normalization and a median polish probe set summarization, to obtain the normalized expression levels of all probe sets for each chip. RMA was performed independently for each of the 6 diagnoses used in the study, to avoid potential artefacts due to different ranges of gene expression in different diagnoses (Niculescu et al. MP 2015). Then the participants' normalized data was extracted from these RMA and assembled for the different cohorts used in the Example.
A/P analysis.
For the longitudinal within participant AP analysis, comparisons were made within participant between sequential visits to identify changes in gene expression from Absent to Present that track changes in phene expression (suicidal ideation, “SI”) from No SI to High SI. For a comparison, if there was a change from A to P tracking a change from No SI to High SI, or a change from P to A tracking a change from High SI to No SI, that was given a score of +1 (increased biomarker in High SI). If the change was in opposite direction in the gene vs the phene (SI), that was given a score of −1 (decreased biomarker in High SI). If there was no change in gene expression between visits, despite a change of phene expression (suicidal ideation), or a change in gene expression between visits, despite no change in phene expression (suicidal ideation), that was given a score of 0 (not tracking as a biomarker). If there was no change in gene expression and no change in suicidal ideation between visits, that was given a score of +1 if there was concordance (P-P with High SI-High SI, or A-A with No SI-No SI), or a score of −1 if there was the opposite (A-A with High SI-High SI, or P-P with No SI-No SI). If the changes were to M (moderate) instead of P, the values used were 0.5 or −0.5. These values were then summed up across the comparisons in each participant, resulting in a participant score for each gene/probeset in each participant. A perfection bonus was also used. If the gene expression perfectly tracked the suicidal ideation in a participant that had at least two comparisons (3 visits), that probe set was rewarded by a doubling of its participant score. Additionally, a non-tracking correction was used. If there was no change in gene expression in any of the comparisons for a particular participant, that overall participant score for that probe set in that participant was zero.
DE Analysis.
For the longitudinal within participant DE analysis, fold changes (FC) in gene expression were calculated between sequential visits within each participant. Scoring methodology was similar to that used above for AP. Probe sets that had a FC≥1.2 were scored+1 (increased in High SI) or −1 (decreased in High SI). FC≥1.1 were scored+0.5 or −0.5. FC lower than 1.1 were considered no change. The only difference between the DE and the AP analyses was when scoring comparisons where there was no phene expression (SI) change between visits and no change in gene expression between visits (FC lower than 1.1). In that case, the comparison received the same score as the nearest preceding comparison where there was a change in SI from visit to visit. If no preceding comparison with a change in SI was available, then it was given the same score as the nearest subsequent comparison where there was a change in SI. Also for DE, a perfection bonus and a non-tracking correction was used. If the gene expression perfectly tracked the suicidal ideation in a participant who had at least two comparisons (3 visits), that probe set was rewarded by a doubling of its score. If there was no change in gene expression in any of the comparisons for a particular participant, that overall participant score for that probe set in that participant was zero.
Internal Score.
Once scores within each participant were calculated, an algebraic sum across all participants was obtained for each probe set. Probe sets were then given internal CFG points based upon these algebraic sum scores. Probe sets with scores above the 33% of the distribution (for increased probe sets and decreased probe sets) received 1 point, those above 50% of the distribution received 2 points, and those above 80% of the distribution received 4 points.
In Example 1, for AP analyses, 23 probe sets received 4 points, 581 probe sets received 2 points, and 2077 probe sets received 1 point, for a total of 2681 probe sets. For DE analyses, 31 probe sets received 4 points, 1294 probe sets received 2 points, and 5839 probe sets received 1 point, for a total of 7164 probe sets. The overlap between the two discovery methods is shown in
Different probe sets may be found by the two methods due to differences in scope (DE capturing genes that were present in both visits of a comparison (i.e. PP, but are changed in expression), thresholds (what makes the 33% change cutoff across participants varies between methods), and technical detection levels (what is considered in the noise range varies between the methods).
In total, 9413 probe sets were identified with an internal CFG score of 1. Gene names for the probe sets were identified using NetAffyx (Affymetrix) and Partek 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 NetAffyx or Partek, the UCSC Genome Browser was used to directly map them to known genes, with the following limitations. In case the probe set fell in an intron, that particular gene was assumed to be implicated. Only one gene was assigned to each probe set. Genes were then scored using manually curated CFG databases as described below (
Convergent Functional Genomics
Databases.
Manually curated databases of all the human gene expression (postmortem brain, blood and cell cultures), human genetics (association, copy number variations and linkage), and animal model gene expression and genetic studies published to date on psychiatric disorders was established (Laboratory of Neurophenomics, Indiana University School of Medicine, www.neurophenomics.info). The databases include only primary literature data and do not include review papers or other secondary data integration analyses to avoid redundancy and circularity. These large and constantly updated databases have been used for CFG cross validation and prioritization (
Human Postmortem Brain Gene Expression Evidence.
Converging evidence was scored for a gene if there were published reports of human postmortem data showing changes in expression of that gene or changes in protein levels in brains from participants who died from suicide.
Human Blood and Other Peripheral Tissue Gene Expression Data.
Converging evidence was scored for a gene if there were published reports of human blood, lymphoblastoid cell lines, CSF, or other peripheral tissue data showing changes in expression of that gene or changes in protein levels in participants who had a history of suicidality or 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/mapinterpolator. 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 (
Pathway Analyses
IPA 9.0 (Ingenuity Systems, Redwood City, Calif., USA), GeneGO MetaCore (Encinitas, Calif.), and Kyoto Encyclopedia of Genes and Genomes (through the Partek Genomics Suite 6.6 software package) were used to analyze the biological roles, including top canonical pathways, and diseases, of the candidate genes resulting from this work, as well as to identify genes in the dataset that are the target of existing drugs (
Validation Analyses
For validation of the candidate biomarker genes, which of the top candidate genes (CFG score of 4 or above) that were stepwise changed in expression from the No SI group to the High SI group to the suicide completers group, were examined. The empirical cutoff of 33% of the maximum possible CFG score of 12 was used, which also permits the inclusion of potentially novel genes with maximal internal CFG score, but no external CFG score. Statistical analyses were performed in SPSS using one-way ANOVA and Bonferonni corrections.
For the AP analyses, the Affymetrix microarray data files were imported from the participants in the validation cohort of suicide completers into MASS, alongside the data files from the participants in the discovery cohort.
For the DE analyses, Cel. files were imported into Partek Genomic Suites. A RMA was then run, background corrected with quantile normalization, and a median polish probe set summarization of all the chips from the validation cohort 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 purposes. Expression data was non-log-transformed 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 biomarkers in the different groups.
Testing Analyses
The test cohort for suicidal ideation and the test cohort for future hospitalizations analyses were assembled out of data that was RMA normalized by diagnosis. Phenomic (clinical) and gene expression markers used for predictions were z-scored by diagnosis, to be able to combine different markers into panels and to avoid potential artefacts due to different ranges of phene expression and gene expression in different diagnoses. Markers were combined by computing the average of the increased risk markers minus the average of the decreased risk markers. Predictions were performed using R-studio.
Predicting Suicidal Ideation.
Receiver-operating characteristic (ROC) analyses between marker levels and suicidal ideation (SI) were performed by assigning participants with a HAMD SI score of 0-1 into the no SI category, and participants with a HAMD-SI score of 2 and greater into the SI category. Additionally, ANOVA was performed between no (HAMD-SI 0), moderate (HAMD-SI 1), and high SI participants (HAMD-SI 2 and above) and Pearson R (one-tail) was calculated between HAMD-SI scores and marker levels.
Predicting Future Hospitalizations for Suicidality.
Analyses for hospitalizations in the first year following testing were conducted on data for all the participants for which data was collected. For each participant in the test cohort for future hospitalizations, the Example visit with highest levels for the marker or combination of markers was selected as index visit (or with the lowest levels, in the case of decreased markers). ROC analyses between marker levels and future hospitalizations were performed based on assigning if participants had been hospitalized for suicidality (suicide ideation, suicide attempts) or not following the index testing visit. Additionally, a one tailed t-test with unequal variance was performed between groups of participants with and without hospitalizations for suicidality. Pearson R (one-tail) correlation was performed between hospitalization frequency (number of hospitalizations for suicidality divided by duration of follow-up) and biomarker score. The correlation analysis for hospitalizations frequency was also conducted for all future hospitalizations due to suicide beyond one year, as this calculation, unlike the ROC and t-test, accounts for the actual length of follow-up, which varied beyond one year from participant to participant.
In this Example, male subjects were analyzed for predicting suicidal ideation and future hospitalizations for suicidality.
Human Participants
Data was obtained from four cohorts: one live psychiatric participants discovery cohort (within-participant changes in suicidal ideation; n=37 out of 217); one postmortem coroner's office validation cohort (suicide completers; n=26); and two live psychiatric participants test cohorts—one for predicting suicidal ideation (n=108) and one for predicting future hospitalizations for suicidality (n=157).
Live psychiatric participants were recruited from the patient population at the Indianapolis VA Medical Center. All participants understood and signed informed consent forms detailing the research goals, procedure, caveats and safeguards. Participants completed diagnostic assessments by an extensive structured clinical interview—Diagnostic Interview for Genetic Studies—at a baseline visit, followed by up to six testing visits, 3-6 months apart or whenever a hospitalization occurred. At each testing visit, they received a series of psychiatric rating scales, including the Hamilton Rating Scale for Depression-17, which includes a suicidal ideation (SI) rating item (
The within participant discovery cohort, from which the biomarker data were derived, consisted of 37 male participants with psychiatric disorders, with multiple visits, who each had at least one diametric change in SI scores from no SI to high SI from one testing visit to another testing visit. There was 1 participant with 6 visits, 1 participant with 5 visits, 1 participant with 4 visits, 23 participants with 3 visits each, and 11 participants with 2 visits each, resulting in a total of 106 blood samples for subsequent microarray studies (
The postmortem cohort, in which the top biomarker findings were validated, consisted of a demographically matched cohort of 24 male violent suicide completers obtained through the Marion County coroner's office (
The independent test cohort for predicting suicidal ideation consisted of 108 male participants with psychiatric disorders, demographically matched with the discovery cohort with one or multiple testing visits in the lab, with either no SI, intermediate SI, or high SI, resulting in a total of 223 blood samples in whom whole-genome blood gene expression data were obtained.
The test cohort for predicting future hospitalizations consisted of male participants in whom whole-genome blood gene expression data were obtained at testing visits over the years as part of a longitudinal study. If the participants had multiple testing visits, the visit with the highest marker (or combination of markers) levels was selected for the analyses. The participants' subsequent number of psychiatric hospitalizations, with or without suicidality, was tabulated from electronic medical records. All participants had at least one year of follow-up or more at the VA Medical Center since the time of the testing visits in the lab. Participants were evaluated for the presence of future hospitalizations for suicidality, and for the frequency of such hospitalizations. A hospitalization was deemed to be without suicidality if suicidality was not listed as a reason for admission, and no SI was described in the admission and discharge medical notes. Conversely, a hospitalization was deemed to be because of suicidality if suicidal acts or intent was listed as a reason for admission, and SI was described in the admission and discharge medical notes.
Medications
The participants in the discovery cohort were all diagnosed with various psychiatric disorders (e.g., BP, MDD, SZA, SZ, PTSD). The participants were on a variety of different psychiatric medications: mood stabilizer, antidepressants, antipsychotics, benzodiazepines and others. Medications can have a strong influence on gene expression. However, the identification of differentially expressed genes was based on within-participant analyses, which factor out not only genetic background effects but also medication effects, as the participants had no major medication changes between visits. Moreover, there was no consistent pattern in any particular type of medication, or between any change in medications and SI, in the rare instances where there were changes in medications between visits.
Results
The top increased and decreased biomarkers after the discovery for ideation (CADM1, CLIP4, DTNA, KIF2C), prioritization with CFG for prior evidence (SAT1, SKA2, SLC4A4), and validation for behavior in suicide completers (IL6, MBP, JUN, KLHDC3) steps were tested in a completely independent test cohort of psychiatric participants for prediction of suicidal ideation (n=108), and in a future follow-up cohort of psychiatric participants (n=157) for prediction of psychiatric hospitalizations due to suicidality. The best individual biomarker across psychiatric diagnoses for predicting suicidal ideation was SLC4A4, with 72% accuracy. For bipolar disorder in particular, SLC4A4 predicted suicidal ideation with 93% accuracy, and future hospitalizations with 70% accuracy. Two new clinical information apps, one for affective state (Simplified Affective Scale, SASS) and one for suicide risk factors (Convergent Functional Information for Suicide, CFI-S) are disclosed, and how well they predict suicidal ideation across psychiatric diagnoses (85% accuracy for SASS, 89% accuracy for CFI-S). Also disclosed is that the integration of the top biomarkers and the clinical information into a universal predictive measure (UP-Suicide) was able to predict suicidal ideation across psychiatric diagnoses with 92% accuracy. For bipolar disorder, it was able to predict suicidal ideation with 98% accuracy and future hospitalizations with 94% accuracy.
For discovery, two differential expression methodologies were used: Absent/Present (AP) (reflecting on/off of transcription) and Differential Expression (DE) (reflecting more subtle gradual changes in expression levels). Genes that tracked suicidal ideation in each participant were identified. Three thresholds were used for increased in expression genes and for decreased in expression genes: ≥33% (low), ≥50% (medium), and ≥80% (high) of the maximum scoring increased and decreased gene across participants. These differentially expressed genes were then prioritized using a Bayesian-like Convergent Functional Genomics (CFG) approach (
To understand the biology represented by the biomarkers identified, and derive some mechanistic and practical insights, unbiased biological pathway analyses and hypothesis driven mechanistic queries, overall disease involvement and specific neuropsychiatric disorders queries, and overall drug modulation along with targeted queries for omega-3, lithium and clozapine were conducted. Administration of omega-3s in particular may be a mass-deployable therapeutic and preventive strategy.
The sets of biomarkers identified have biological roles in immune and inflammatory response, growth factor regulation, mTOR signaling, stress, and perhaps overall the switch between cell survival and proliferation vs. apoptosis (
Evidence for the involvement of the biomarkers for suicidality was also examined for involvement in other psychiatric disorders, allowing for analysis of context and specificity
A 22-item scale and app for suicide risk, Convergent Functional Information for Suicidality (CFI-S), was also developed, which integrates information about known life events, mental health, physical health, stress, addictions, and cultural factors that can influence suicide risk. Clinical risk predictors and scales are of high interest in the military and in the general population at large. The scale disclosed herein builds on those excellent prior achievements, while aiming for comprehensiveness, simplicity and quantification similar to a polygenic risk score. CFI-S is able to distinguish between individuals who committed suicide (coroner's cases, information obtained from the next of kin, n=35) and those high risk participants who did not, but had experienced changes in suicidal ideation (e.g., the discovery cohort of psychiatric participants described herein). Items of the CFI-S scale that were the most significantly different were analyzed. Seven (7) items that were significantly different were identified, 5 of which survived Bonferroni correction: lack of coping skills when faced with stress (p=3.35E-11), dissatisfaction with current life (p=2.77E-06), lack of hope for the future (4.58E-05), current substance abuse (p=1.25E-04), and acute loss/grief (p=9.45E-4). The top item was inability to cope with stress, which was independently consistent with the biological mechanistic results discussed above.
CFI-S provided good accuracy (ROC AUC 0.70, p-value 0.006) at predicting future hospitalizations for suicidality in the first year, across diagnostic groups. CFI-Suicide had very good accuracy (AUC 0.89, p-value 3.53E-13) at predicting suicidal ideation in psychiatric participants across diagnostic groups. Within diagnostic groups, in affective disorders, the accuracy was even higher. CFI-S had excellent accuracy at predicting high suicidal ideation in bipolar participants (AUC 0.97, p-value 1.75E-06) and in depression participants (AUC 0.95, p-value 7.98E-06).
Previously, the TASS (Total Affective State Scale) was developed and described for measuring mood and anxiety. The wording used in TASS was simplified and a new app was developed for an 11 item scale for measuring mood and anxiety, the Simplified Affective State Scale (SASS). The SASS is a set of 11 visual analog scales (7 for mood, 4 for anxiety) that provides a number ranging from 0 to 100 for mood state and for anxiety state.
SASS had very good accuracy (AUC 0.85, 9.96E-11) at predicting suicidal ideation in psychiatric participants across diagnostic groups. Within diagnostic groups, in affective disorders, the accuracy was even higher (AUC 0.87) in both bipolar disorder and depression. SASS also had good accuracy (AUC 0.71, p-value 0.008) at predicting future hospitalizations for suicidality in the first year following testing.
The best single biomarker predictor for suicidal ideation state across all diagnostic groups was SLC4A4, the top increased biomarker from AP CFG prioritization (AUC 0.72, p-value 2.41E-05). Within diagnostic groups, the accuracy was even higher. SLC4A4 had very good accuracy at predicting future high suicidal ideation in bipolar participants (AUC 0.93, p-value 9.45E-06) and good accuracy in schizophrenia participants (AUC 0.76, p-value 0.030). SLC4A4 is a sodium-bicarbonate co-transporter that regulates intracellular pH, and possibly apoptosis. Very little is known to date about its roles in the brain, thus representing a completely novel finding.
SKA2, the top decreased biomarker from AP and DE CFG, had good accuracy at predicting suicidal ideation across all diagnostic groups (AUC 0.69), and even better accuracy in bipolar participants (AUC 0.76, p-value 0.011) and schizophrenia participants (AUC 0.82).
The best single top biomarker predictor for future hospitalizations for suicidal behavior in the first year across all diagnostic groups was SAT1, the top increased biomarker from the DE CFG (AUC 0.55). Within diagnostic groups, in affective disorders, the SAT1 prediction accuracies were higher (depression AUC 0.62, bipolar AUC 0.63).
The a priori primary endpoint was a combined universal predictor for suicide (UP-Suicide), composed of the top biomarkers from discovery, prioritization and validation (n=11), along with CFI-Suicide, and SASS. UP-Suicide is an excellent predictor of suicidal ideation across all disorders in the independent cohort of psychiatric participants (AUC 0.92). UP-Suicide also has good predictive ability for future psychiatric hospitalizations for suicidality in the first year of follow-up (AUC 0.70). The predictive ability of UP-Suicide is notably higher in affective disorder participants (bipolar, depression) (
In this Example, female subjects were analyzed for predicting suicidal ideation and future hospitalizations for suicidality.
Human Participants
Four cohorts were used: one live psychiatric participants discovery cohort (within-participant changes in suicidal ideation; n=12 out of 51); one postmortem coroner's office validation cohort (suicide completers; n=6); and two live psychiatric participants test cohorts—one for predicting suicidal ideation (n=33), and one for predicting future hospitalizations for suicidality (n=24).
The live psychiatric participants were part of a larger longitudinal cohort that was continuously being collected. Participants were recruited from the patient population at the Indianapolis VA Medical Center and Indiana University School of Medicine through referrals from care providers, the use of brochures left in plain sight in public places and mental health clinics, and through word of mouth. All participants understood and signed informed consent forms detailing the research goals, procedure, caveats and safeguards. Participants completed diagnostic assessments by an extensive structured clinical interview—Diagnostic Interview for Genetic Studies—at a baseline visit, followed by up to six testing visits, 3-6 months apart or whenever a new psychiatric hospitalization occurred. At each testing visit, they received a series of psychiatric rating scales, including the Hamilton Rating Scale for Depression-17, which includes a suicidal ideation (SI) rating item (
The within participant discovery cohort, from which the biomarker data were derived, consisted of 12 female participants with psychiatric disorders and multiple visits in the lab, who each had at least one diametric change in SI scores from no SI to high SI from one testing visit to another. There were 7 participants with 3 visits each, and 5 participants with 2 visits each, resulting in a total of 31 blood samples for subsequent microarray studies (
The postmortem cohort, in which the top biomarker findings were validated for behavior, consisted of a demographically matched cohort of 6 female violent suicide completers obtained through the Marion County coroner's office (
The independent test cohort for predicting suicidal ideation (
The test cohort for predicting future hospitalizations (
Medications
The participants in the discovery cohort were all diagnosed with various psychiatric disorders (
Clock Gene Database
In this Example, a database was compiled of genes associated with circadian function, by using a combination of review papers (Zhang et al. Cell 2009; 139(1):19-210, McCarthy and Welsh Journal of biological rhythms 2012; 27(5):339-352) and searches of existing databases CircaDB (circadb.hogeneschlab.org), GeneCards (www.genecards.org), and GenAtlas (genatlas.medecine.univ-paris5.fr). Using the data, a total of 1280 genes were identified that show circadian functioning. The genes were classified into “core” clock genes, i.e. those genes that are the main engine driving circadian function (n=18), “immediate” clock genes, i.e. the genes that directly input or output to the core clock (n=331), and “distant” clock genes, i.e. genes that directly input or output to the immediate clock genes (n=1,119).
Clinical Measures
The Simplified Affective State Scale (SASS) is an 11-item scale for measuring mood and anxiety. The SASS has a set of 11 visual analog scales (7 for mood, 4 for anxiety) that ends up providing a number ranging from 0 to 100 for mood state, and the same for anxiety state. Also developed is an Android app version.
In some embodiments, the systems and methods described utilize a computer implemented method for assessing suicidal risk factors based upon patient psychiatric information further including mood information, anxiety information, and other psychiatric symptom information. Any and all such patient psychiatric information may be represented as a quantitative rating on a defined analog scale, such as the ratings and scales described above. Further, as used herein, such patient psychiatric information may be processed using an associated processing algorithm. The associated processing algorithm may include calculating mean values for each component of patient psychiatric information and then assigning a suitable weighting to each calculated mean value. The processing algorithm may thus use the quantitative ratings of the patient psychiatric information as inputs to calculate a diagnostic output score. The diagnostic output score may be used to compare to reference scores (from a diagnostic database) associated with patients having psychiatric symptom information (e.g., psychiatric disorder diagnosis or lack thereof) similar to the patient. By such comparison, the diagnostic output score may be assigned a percentile. The diagnostic output score may also be compared to the reference scores in the diagnostic database associated with individuals with no suicidality and high suicidality. Thus, if the diagnostic output score meets or exceeds a high suicidality reference score, a patient may be marked as at risk for suicide. Conversely, if the diagnostic output score meets or falls below a low suicidality reference score, a patient may be marked as not at risk for suicide.
Convergent Functional Information for Suicidality (CFI-S) is a 22-item scale and Android app for suicide risk, which integrates, in a simple binary fashion (Yes—1, No—0), similar to a polygenic risk score, information about known life events, mental health, physical health, stress, addictions, and cultural factors that can influence suicide risk. The scale was administered at participant testing visits (n=39), or scored based on retrospective electronic medical record information and Diagnostic Interview for Genetic Testing (DIGS) information (n=48). When information was not available for an item, it was not scored (NA).
In other embodiments, the systems and methods described utilize a computer implemented method for assessing suicidal risk factors based upon socio-demographic/psychological suicidal risk factors. Any and all such socio-demographic/psychological suicidal risk factors may be represented as a quantitative rating on a defined analog scale, such as the ratings and scales described above. Further, as used herein, such socio-demographic/psychological suicidal risk factors may be processed using an associated processing algorithm. The associated processing algorithm may include calculating mean values for each component socio-demographic/psychological suicidal risk factor and then assigning a suitable weighting to each calculated mean value. The processing algorithm may thus use the quantitative ratings of the socio-demographic/psychological suicidal risk factors as inputs to calculate a diagnostic output score. The diagnostic output score may be used to compare to reference scores (from a diagnostic database) associated with patients having socio-demographic/psychological suicidal risk factors similar to the patient. By such comparison, the diagnostic output score may be assigned a percentile. The diagnostic output score may also be compared to the reference scores in the diagnostic database associated with individuals with no suicidality and high suicidality. Thus, if the diagnostic output score meets or exceeds a high suicidality reference score, a patient may be marked as at risk for suicide. Conversely, if the diagnostic output score meets or falls below a low suicidality reference score, a patient may be marked as not at risk for suicide.
In some computer-implemented methods described above and herein, multiple computing devices may interact with one another (e.g., first and second computer devices). To protect data and privacy, such requests and transmissions are made using data encryption.
Combining Gene Expression and Clinical Measures
The Universal Predictor for Suicide (UP-Suicide) construct, the primary endpoint, was decided upon as part of a apriori study design to be broad-spectrum, and combine the top Bonferroni validated biomarkers with the phenomic (clinical) markers (SASS and CFI-S).
Results
Discovery of Biomarkers for Suicidal Ideation
A whole-genome gene expression profiling was conducted in the blood samples from a longitudinally followed cohort of female participants with psychiatric disorders that predispose to suicidality. The samples were collected at repeated visits, 3-6 months apart. State information about suicidal ideation (SI) was collected from a questionnaire (HAMD) administered at the time of each blood draw. Out of 51 female psychiatric participants (with a total of 123 visits) followed longitudinally in this Example, with a diagnosis of BP, MDD, SZ and SZA, there were 12 participants that switched from a no SI (SI score of 0) to a high SI state (SI score of 2 and above) at different visits, which was the intended discovery group (
For discovery, two differential expression methodologies were used: Absent/Present (AP) (reflecting on/off of transcription), and Differential Expression (DE) (reflecting more subtle gradual changes in expression levels). The genes that tracked suicidal ideation in each participant were identified in the analyses. Three thresholds were used for increased in expression genes and for decreased in expression genes: ≥33.3% (low), ≥50% (medium), and ≥80% (high) of the maximum scoring increased and decreased gene across participants. 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 AP and DE analyses, that had clear prior evidence for involvement in suicidality, such as AKAP10 (31.7%) and MED28 (31.8%) from AP, and S100B (31.7%) and SKA2 (31.4%) for DE, but were not included in subsequent analyses because they did not meet the apriori set 33.3% threshold. Notably, SKA2 reproduces the results in males (Example 1).
Prioritization of Biomarkers Based on Prior Evidence in the Field
These differentially expressed genes were then prioritized using a Bayesian-like Convergent Functional Genomics (CFG) approach (
Validation of Biomarkers for Behavior in Suicide Completers
For validation in suicide completers, 1471 genes were used that had a CFG score of 4 and above, from AP and DE, reflecting either maximum internal score from discovery or additional external literature cross-validating evidence. Out of these, 882 did not show any stepwise change in suicide completers (NC—non-concordant). As such, they may be involved primarily in ideation and not in behavior. The remaining 589 genes (40.0%) had levels of expression that were changed stepwise from no suicidal ideation to high suicidal ideation to suicide completion. 396 of these genes (26.9%) were nominally significant, and 49 genes (50 probesets—two for JUN) (3.33%) survived Bonferroni correction for multiple comparisons (
Selection of Biomarkers for Testing of Predictive Ability
For testing, Bonferroni validated biomarkers (49 genes, 50 probesets) were focused on. A secondary analysis of the top scoring biomarkers from both discovery and prioritization (65 genes) was conducted so as to avoid potential false negatives in the validation step due to possible postmortem artefacts or extreme stringency of statistical cutoff. The top CFG scoring genes after the Bonferroni validation step were BCL2 and GSK3B. The top CFG scoring genes from the discovery and prioritization steps were FAM214A, CLTA, HSPD1, and ZMYND8. Notably, all have co-directional gene expression changes evidence in brains of suicide completers in studies form other groups.
Biological Understanding
Unbiased biological pathway analyses and hypothesis driven mechanistic queries, overall disease involvement and specific neuropsychiatric disorders queries, and overall drug modulation along with targeted queries for omega-3, lithium and clozapine were studied (
The sets of biomarkers identified have biological roles in inflammation, neurotrophins, inositol signaling, stress response, and perhaps overall the switch between cell survival and proliferation vs. apoptosis (
The involvement of these biomarkers for suicidality in other psychiatric disorders were also analyzed. FAM214A, MOB3B, ZNF548, and ARHGAP35 were relatively specific for suicide, based on the evidence to date in the field, and were also identified co-directionally in the previous male work (Example 1). BCL2, GSK3B, HSPD1, and PER1 were less specific for suicide, having equally high evidence for involvement in suicide and in other psychiatric disorders. BCL2 was also identified co-directionally in Example 1.
HSPD1, found to be a top biomarker in this Example, increased in expression in suicidality, and was also increased in expression in the blood following anti-depressant treatment. Thus, this may be a useful biomarker for treatment-emergent suicidal ideation (TESI).
Further, a number of the genes changed in expression in opposite direction in suicide in this Example vs. high mood in Example 1—SSBP2, ZNF596, suggesting that suicidal participants are in a low mood state. Also, some of the top suicide biomarkers are changed in expression in the same direction as in high psychosis participants in a previous psychosis biomarker study—HERC4, PIP5K1B, SLC35B3, SNX27, KIR2DL4, NUDT10, suggesting that suicidal participants may be in a psychosis-like state. Taken together, the data indicates that suicidality could be viewed as a psychotic dysphoric state. This molecularly informed view is consistent with the emerging clinical evidence in the field.
A number of top biomarkers identified have biological roles that are related to the core circadian clock (such as PER1), or modulate the circadian clock (such as CSNK1A1), or show at least some circadian pattern (such as HTRA1). To be able to ascertain all the genes in the dataset that were circadian and do estimates for enrichment, a database from literature was compiled of all the known genes that fall into these three categories, numbering a total of 1468 genes. Using an estimate of about 21,000 genes in the human genome, that gives about 7% of genes having some circadian pattern. Out of the 49 Bonferroni validated biomarker genes, 7 had circadian evidence (14.3%), suggesting a 2-fold enrichment for circadian genes.
Additionally, biological pathway analyses were conducted on the genes that, after discovery and prioritization, were stepwise changed in suicide completers (n=882) and may be involved in ideation and behavior vs. those that were not stepwise changed (n=589), and that may only be involved in ideation. The genes involved in ideation map to pathways related to PI3K signaling. The genes involved in behavior map to pathways related to glucocorticoid receptor signaling. This is consistent with ideation being related to neurotrophic factors, and behavior being related to stress.
Clinical Information
A 22-item scale and app were used for suicide risk, Convergent Functional Information for Suicidality (CFI-S), which scores in a simple binary fashion and integrates information about known life events, mental health, physical health, stress, addictions, and cultural factors that can influence suicide risk. Determining which items of the CFI-S scale were the most significantly different between no and high suicidal ideation live participants was analyzed (
Testing for Predictive Ability
The best single increased (risk) biomarker predictor for suicidal ideation state was EPB41L5 (ROC AUC 0.68, p-value 0.06; Pearson Correlation 0.22, p-value 0.03), an increased in expression, Bonferroni validated biomarker (
The best single increased (risk) biomarker predictor for future hospitalizations for suicidality was HTRA1 (ROC AUC 0.84, p-value 0.01; Cox Regression Hazard Ratio 4.55, p-value 0.01), an increased in expression, Bonferroni validated biomarker (
BCL2, the top CFG scoring biomarker from validation, had good accuracy at predicting future hospitalizations for suicidality (ROC AUC 0.89, p-value 0.007; Cox Regression Hazard Ratio 3.08, p-value 0.01) (
CFI-S had very good accuracy (ROC AUC 0.84, p-value 0.002; Pearson Correlation 0.39, p-value 0.001) at predicting suicidal ideation in psychiatric participants across diagnostic groups. The other app, SASS, also had very good accuracy (ROC AUC 0.81, p-value 0.003; Pearson Correlation 0.38, p-value 0.0005) at predicting suicidal ideation in women psychiatric participants. The combination of the apps was synergistic (ROC AUC 0.87, p-value 0.0009; Pearson Correlation 0.48, p-value 0.0001). Thus, even without the benefit of potentially more costly and labor intensive blood biomarker testing, clinically useful predictions could be made with the apps.
The apriori primary endpoint was a combined universal predictor for suicide (UP-Suicide), composed of CFI-S and SASS, along with the Bonferroni validated biomarkers (n=50) resulting from the sequential discovery for ideation, prioritization with CFG, and validation for behavior in suicide completers steps. UP-Suicide was a good predictor of suicidal ideation (ROC AUC 0.82, p-value 0.003; Pearson Correlation 0.43, p-value 0.0003) (
Discussion
The present Example identified markers involved in suicidal ideation and suicidal behavior, including suicide completion, in females. Markers involved in behavior may be on a continuum with some of the markers involved in ideation, varying in the degree of expression changes from less severe (ideation) to more severe (behavior). One cannot have suicidal behavior without suicidal ideation, but it may be possible to have suicidal ideation without suicidal behavior.
50 biomarkers were found to have survived Bonferroni correction (49 genes; one gene, JUN, had two different probesets that validated). Additionally, 65 other biomarkers that were non Bonferroni, but had maximum internal score of 4 in discovery and a CFG score of 6 and above, meaning that in addition to strong evidence in this Example, they also had prior independent evidence of involvement in suicide from other studies, were also studied. These additional biomarkers are likely involved in suicide, but did not make the Bonferroni validation cutoff due to its stringency or potential technical/postmortem artifact reasons (
Data validating the CFI-S in women in the combined discovery and test cohort of live psychiatric participants was analyzed (
In assessing anxiety and mood, it was shown that anxiety measures cluster with suicidal ideation and CFI-S, and mood measures are in the opposite cluster, suggesting that the participants have high suicidal ideation when they have high anxiety and low mood (
The rationale for identifying blood biomarkers as opposed to brain biomarkers is a pragmatic one—the brain cannot be readily accessed in live individuals. Other peripheral fluids, such as CSF, require more invasive and painful procedures. Nevertheless, it is likely that many of the peripheral blood transcriptomic changes are not necessarily mirroring what is happening in the brain, and vice-versa. The keys to finding peripheral biomarkers are, first, to have a powerful discovery approach, such as the within-participant design, that closely tracks the phenotype you are trying to measure and reduces noise. Second, cross-validating and prioritizing the results with other lines of evidence, such as brain gene expression and genetic data, are important in order to establish relevance and generalizability of findings. Third, it is important to validate for behavior in an independent cohort with a robust and relevant phenotype, in this case suicide completers. Fourth, testing for predictive ability in independent/prospective cohorts is a must.
Biomarkers that survive such a rigorous step-wise discovery, prioritization, validation and testing process are likely directly relevant to the disorder studied. As such, whether they are involved in other psychiatric disorders or are relatively specific for suicide, and whether they are the modulated by existing drugs in general, and drugs known to treat suicidality in particular were evaluated.
A series of biomarkers have been identified that seem to be changed in opposite direction in suicide vs. in treatments with omega-3 fatty acids, lithium, clozapine. These biomarkers could potentially be used to stratify patients to different treatment approaches, and monitor their response.
BCL2, JUN, GHA1, ENTPD1, ITIH5, MBNL1, and SSBP2 were changed in expression by two of these three treatments, suggesting they may be core to the anti-suicidal mechanism of these drugs. BCL2, CAT, and JUN may be useful blood pharmacogenomic markers of response to lithium. CD84, MBNL1, and RAB22A may be useful blood pharmacogenomic markers of response to clozapine. NDRG1, FOXP1, AFF3, ATXN1, CSNK1A1, ENTPD1, ITIH5, PRDX3, and SSBP2 may be useful blood pharmacogenomic markers of response to omega-3 fatty acids. Three existing drugs used for other indications have been identified as targeting the top suicide biomarkers identified, and could potentially be re-purposed for testing in treatment of acute suicidality: anakinra (inhibiting ILR1), enzastaurin (inhibiting AKT3), and tesevatinib (inhibiting EPHB4). Additionally, Connectivity Map (ref) analyses identified compounds that induced gene expression signatures that were the opposite of those present in suicide, and might generate leads and/or be tested for use to treat/prevent suicidality: betulin (an anti-cancer compound from the bark of birch trees), zalcitabine (an anti-HIV drug), and atractyloside (a toxic glycoside). Other common drugs identified by the Connectivity Map analyses were nafcillin, lansoprazole, mifepristone, LY294002, minoxidil, acetysalicilic acid, estradiol, buspirone, dicloxacillin, corticosterone, metformin, diphenhydramine, haloperidol, and fluoxetine.
Of note, a number of biomarkers from the current Example in women reproduced and were co-directional with previous findings in Example 1 (BCL2, ALDH3A2, FAM214A, CLTA, ZMYND8, JUN), whereas others had changes in opposite directions (GSK3B, HSPD1, AK2, CAT), underlying the issue of biological context and differences in suicidality between the two genders.
Disclosed herein are instruments (biomarkers and applications) for predicting suicidality, that do not require asking the person assessed if they have suicidal thoughts, as individuals who are truly suicidal often do not share that information with people close to them or with clinicians. The widespread use of such risk prediction tests as part of routine or targeted healthcare assessments will lead to early disease interception followed by preventive lifestyle modifications or treatment. Biomarkers identified herein for suicidal ideation are enriched for genes involved in neuronal connectivity and schizophrenia. Biomarkers identified herein also validated for suicide behavior are enriched for genes involved in neuronal activity and mood.
Worldwide, one person dies every 40 seconds through suicide, a potentially preventable tragedy. A limiting step in the ability to intervene is the lack of objective, reliable predictors. A powerful within-participant discovery approach is disclosed herein in which genes that change in expression between no suicidal ideation and high suicidal ideation states were identified. The methods disclosed herein do not require asking the person assessed if they have thoughts of suicide, as individuals who are truly suicidal often do not share that information with clinicians. The widespread use of such risk prediction tests as part of routine or targeted healthcare assessments will lead to early disease interception followed by preventive lifestyle modifications and proactive treatment.
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 national phase application of PCT/US2016/036985, filed Jun. 10, 2016, which claims priority to U.S. Provisional Application No. 62/278,707 filed Jan. 14, 2016 and U.S. Provisional Application No. 62/174,880 filed on Jun. 12, 2015, each of which are hereby incorporated by reference in their entireties.
This invention was made with government support under OD007363 awarded by National Institutes of Health. The Government has certain rights in the invention.
| Filing Document | Filing Date | Country | Kind |
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| PCT/US2016/036985 | 6/10/2016 | WO | 00 |
| Publishing Document | Publishing Date | Country | Kind |
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| WO2016/201299 | 12/15/2016 | WO | A |
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| Supplementary European search report dated Jan. 21, 2019 for EP Application No. 16808423. |
| Number | Date | Country | |
|---|---|---|---|
| 20180181701 A1 | Jun 2018 | US |
| Number | Date | Country | |
|---|---|---|---|
| 62278707 | Jan 2016 | US | |
| 62174880 | Jun 2015 | US |
