depart seminar 11_18_15_truncated
TRANSCRIPT
Gerry Higgins PhD, MDAdjunct Research Professor, Computational Medicine and
Bioinformatics, University of Michigan Medical School;Vice President, Pharmacogenomic Science, Assurex Health, Inc.
PSYCHIATRIC PHARMACOGENOMICS:
Clinical Translation & Novel Variant Discovery
Conflict of interest statement:
Dr. Gerald A. Higgins is an employee of AssureRx Health, Inc. (Mason, OH) and holds options in the company. He serves as an Adjunct Research Professor at the University of Michigan Medical School. He states that he has no financial interest in the response to this presentation.
CLINICAL TRANSLATION
The Impact of Psychiatric Disease→More than 350 million people are affected by
depression;→It is the number 1 cause of disability, U.S. and
worldwide;→Almost 2/3 of those who commit suicide have
depression; →34% of female patients diagnosed with bipolar
disorder attempt suicide, 19% of male bipolar patients attempt suicide;
→Majority of perpetrators of mass shootings in the U.S. since 1970 displayed psychiatric symptoms including paranoia, delusions, and depression, and 74% were on psychiatric medications; but
→In the new 2016 NIH budget, $5.6 B is earmarked for cancer research, only $404 M for depression research and $259 M for research on schizophrenia.
Challenges in Psychiatric Pharmacogenomics→ No usable objective diagnostic measures in clinical
practice, must rely on surrogate phenotypes and rating scales;
→Comorbid psychiatric conditions and comorbid non-psychiatric conditions confound differential diagnosis;
→Most psychiatric medications were developed in the 1950’s, including lithium, chlorpromazine and imipramine;
→There has been virtually no CNS drug development since 2000, with the exception of ketamine-like antidepressants;
→79 M Americans were prescribed psychiatric medications in 2014 - 25% of the U.S. population;
→Psychiatric medications exhibit unacceptably high levels of adverse events – 90,000 annual visits to the ER in the U.S. – 50% of all prescription drug-related hospitalizations.
David Mrazek, Psychiatric Pharmacogenomics & Assurex Health, Inc.
CYP2C19
CYP2D6
Use with Caution
CYP1A2
SLC6A4
5HTR2A
Genotype Phenotype Interpretive Drug Sorting
Medication Binning
Effect of Composite
Phenotype on Each Drug
Use as Directed
Use with Caution and More Frequent
Monitoring
Metabolizer Status
Metabolizer Status
Metabolizer Status
Transporter Activity
Receptor Activity
CYP2C9 Metabolizer Status
One reason why pharmacogenomic testing is adopted in psychiatry, but not in cardiology
(e.g., warfarin, clopidogrel)
Cardiologists:17% in solo practice in U.S.
Psychiatrists:85% in solo practice in U.S.
Another reason why pharmacogenomic testing is being adopted in psychiatry?
ANXIETY DISORDERS DEPRESSIVE DISORDERS COMORBID DISORDERS$0.00
$2,000.00
$4,000.00
$6,000.00
$8,000.00
$10,000.00
$12,000.00
$14,000.00
INCONGRUENT WITH GENESIGHT TEST RESULTS CONGRUENT WITH GENESIGHT TEST RESULTS
p <0.0001
$6874 $3579
p <0.007 p <0.0001
$4056
Winner, JG et al. Combinatorial pharmacogenomic guidance for psychiatric medications reduces overall pharmacy costs in a 1 year prospective evaluation. Current Med. Res. & Opinion. 2015. 1–11. doi:10.1185/03007995.2015.1063483
ANOVA one way test
Status – Clinical Translation, Assurex PGx testsTo date: Several published trials → Demonstration of clinical validity & utility, albeit with small numbers of patients;
Ongoing:Almost 30 clinical trials underway, many investigator-initiated, including 1 large RCT involving the National Network of Depression Centers (NNDC) and many other sites;
Reimbursement:Only genotype-based test in pharmacogenomics approved for reimbursement by the Centers for Medicare and Medicaid Services (CMS) nationwide;
Challenges:How to keep improving the science – success fosters competition;FDA regulation of LDTs is on the horizon.
PHARMACOGENOMIC VARIANT DISCOVERY
Novel Pharmacogenomic Variants & Pathways→Higgins GA, Allyn-Feuer A, Handelman S, Sadee W, Athey BD. The
epigenome, 4D nucleome and next-generation neuropsychiatric pharmacogenomics. Pharmacogenomics. 16(14), 1649–1669 (2015).
→Higgins GA, Allyn-Feuer A, Athey BD. Epigenomic mapping and effect sizes of noncoding variants associated with psychotropic drug response. Pharmacogenomics. 16(14), 1565–1583 (2015).
→Higgins GA, Allyn-Feuer A, Barbour E, Athey BD. A glutamatergic network mediates lithium response in bipolar disorder as defined by epigenome pathway analysis. Pharmacogenomics. 16(14), 1547–1563 (2015).
→Wiley JW, Higgins GA, Athey BD. Stress and glucocorticoid receptor transcriptional programming in time and space: Implications for the brain–gut axis. In press
→Higgins GA, Allyn-Feuer A, Barbour E, Austic E, Athey BD. Candidate pharmacodynamic variants for stratification of ketamine antidepressant response are associated with chromatin-mediated neuroplasticity. In preparation
→Higgins GA, Allyn-Feuer A, Barbour E, Athey BD. A novel antidepressant network in human brain mediates antidepressant response. In preparation
Collaborators
Brian D. Athey, Ph.D.
Ari Allyn-Feurer Edward Barbour
John W. Wiley, M.D. Wolfgang Sadee, Dr.rer.nat
The majority of assignable SNPs from GWAS in neuropsychiatric pharmacogenomics are located
within putative enhancers
Intron; 1161; 57%
Intergenic; 228; 11%
5'UTR; 324; 16%
3'UTR, 190, 9%Coding variant; 121; 6%
A. Location of lead SNPs and small indels reported in pharmacogenomic GWAS (from NHGRI)
Enhancer; 23Enhancer boundary, 1
Promoter boundary; 3
Promoter, 3
Transcribed; 3
B. SNPs that could be assigned using our bioinformatics pipeline & the Epigenome Roadmap
Effect sizes of pharmacogenomic SNPs are large
DILI: Drug-induced liver injury;SAE: Safety and adverse events;SSR: Selective serotoninergic reuptake inhibitors.
Used with permission from:Lilian Warren, Statistical Genetics,
GlaxoSmithKline.
Effect sizes of SNPs from neuropsychiatric GWAS are large
Higgins GA, Allyn-Feuer A, Athey BD. Epigenomic mapping and effect sizes of noncoding variants associated with psychotropic drug response. Pharmacogenomics. 16(14), 1565–1583 (2015).
Tagging SNPs for enhancers that cause drug-induced cutaneous injury
Addiction SNPs for enhancers
Analgesia SNPs
Lithium-response SNP that disrupts a promoter
Spatial associations elucidate adverse drug events in trans & cisA. The SNP rs4959235 within an intron of
SLC22A23 is significantly associated with Seroquel® (quetiapine)-induced prolonged QT interval in some patients [1]. It identifies a known enhancer.
B. In trans, this enhancer contacts the transcription start site of the NOS1AP gene.
C. Mutations in the NOS1AP gene, as well as altered expression, mediate drug-induced prolonged QT syndrome:
• Chang KC et al. Nitric oxide synthase 1 adaptor protein, an emerging new genetic marker for QT prolongation and sudden cardiac death. Acta Cardiol. Sin. 29:217–225. (2013)
• Jamshidi Y et al. Common variation in the NOS1AP gene is associated with drug-induced QT prolongation and ventricular arrhythmia. J. Amer. Coll. Cardiol. 60: 841-850. (2012)
• Kapoor A et al. QT Interval-International GWAS Consortium: An enhancer polymorphism at the cardiomyocyte intercalated disc protein NOS1AP locus is a major regulator of the QT interval. Amer. J. Human Genet. 94: 854-869. (2014)
• Tomás M, Napolitano C, De Giuli L et al. Priori Polymorphisms in the NOS1AP gene modulate QT interval duration and risk of arrhythmias in the long QT syndrome. J. Amer. Coll. Cardiol. 55: 2745-2752. (2010)
[1] Aberg K et al. Genome-wide association study of antipsychotic-induced QTc interval prolongation. Pharmacogenomics. 12:165–72. (2012).
Epigenome pathway analysis identifies a lithium-response network in human
brain
SNPs from 13 published studies on gene-SNP association and 2 GWAS of lithium response in bipolar disorder.
SNPs from 18 GWAS on bipolar disorder, other psychiatric disorders, and adverse events associated with lithium response.
19 SNPs after LD pruning, in non-coding domains of 10 genes
Set of 23,312 SNPs in LD (r2>0.8) with reported lead SNPs in same populations
Impute SNPs using genetic and epigenetic fine mapping
Lithium Response
802
217LithiumRespons
e SNPs
[1] Higgins GA, Allyn-Feuer A, Barbour E, Athey BD. A glutamatergic network mediates lithium response in bipolar disorder as defined by epigenome pathway analysis. Pharmacogenomics. 16(14), 1547–1563 (2015).
SNP Imputation and Bioinformatics Pipeline [1]
Gene set enrichment followed by ‘blinded’ pathway analysis using IPA®
shows that they are associated with a single CNS network (p = 1 x 10-26)
Subsequent publications by members of the NIH-funded Consortium on Lithium Genetics (ConLiGen)
In press, Nature
Same gene set and subset of the same SNPs, tested in a clinical population of lithium-responsive bipolar patients & controls.
SNP rs116323614 within an intron of the SESTD1 gene reached p < 2.47 x 10-08 in a GWAS of lithium-responders versus controls. SNP rs201013542 in high LD, is found in human brain.
“SESTD1: SEC14 and spectrin domains 1, a calcium channel regulator that regulates neurite elongation. Protein acts in the phosphoinositide signaling pathway, and interacts with RAC1 and GSK3B.” –TransFac Pro
Top pathway hit in Panther/ GO when entire gene set was entered:
Labeled as phosphoinositide signaling pathway by Panther/GO
PI3K
ATK1
PDK1
RAC1
SESTD1
Adverse events of treatment with lithium salts:Correlations with genes in this pathway
1.SBSN (Subsarin) & alopecia universalis: • Patel, Mansi, Shannon Harrison, and Rodney Sinclair. Drugs and hair
loss. (2013). Dermatologic Clin. 31(1), 67-73.• Lesiak, K., Bartlett, J. R., & Frieling, G. W. (2015). ‘Drug-Induced
Alopecia’. In Cutaneous Drug Eruptions (pp. 215-227). Springer London.
2.HTR1A (5-hydroxytryptamine (Serotonin) Receptor 1A) & weight gain:• Murphy E & McMahon FJ. Pharmacogenetics of antidepressants, mood
stabilizers, and antipsychotics in diverse human populations. Dis. Med. (2013). 16(87), 113-122.
• Wysokinski A & Kloszewska I. Mechanisms of increased appetite and weight gain induced by psychotropic medications. (2014). J. Advanced Clin. Pharmacol. 1.1, 12-33.
• Can A et al (2014). Molecular actions and clinical pharmacogenetics of lithium therapy. Pharmacol. Biochem. Behavior. 123, 3-16.
3. SLC1A2 (Solute Carrier Family 1 Member 2) & hand tremor:
• Their S et al. Polymorphisms in the glial glutamate transporter SLC1A2 are associated with essential tremor. Neurology. 79(3), 243-248 (2012);
• Brandler WM. Common variants in left/right asymmetry genes and pathways are associated with relative hand skill. PLoS Genetics. 9(9):e1003751 (2013);
• Their S et al. Polymorphisms in the glial glutamate transporter SLC1A2 are associated with essential tremor. Neurology. 79(3), 243-248 (2012).
4. CACNA1c (Subsarin) & Brugada Syndrome (lithium unmasking of long QT and sudden cardiac death)-
SNP rs1016388 located within an intron of the CACNA1C gene
is significantly associated with Brugada Syndrome
[1] Invitae® Brugada syndrome panel: https://www.invitae.com/en
SNP POSITION LOCATIONCHROMATIN
STATE
Left Ventricle
rs4756764 11: 13280971 Intron of ARNTL Enhancer
rs2314339 17: 40096958 Intron of NR1D1 Genic enhancer
rs12412727 10: 62113906 Intron of ANK3 Enhancer
rs1016388 12: 2322118 Intron of CACNA1C Enhancer
rs4354668 11:35440726 5’UTR, SLC1A2 Promoter- TSS
“Brugada syndrome is a disorder characterized by sudden death associated with one of several ECG patterns characterized by incomplete right bundle-branch block and ST-segment elevation. It can be drug-induced, with lithium accounting for the majority of the cases. Lithium “un-masks” an inherent heart defect, commonly in carriers of the intronic CACNA1C SNP rs1016388 [1].”
SNPs in bipolar risk genes SNPs in lithium response genes = Pharmacogenomic: Disease Coupling
GENE SIGNIFICANT LITHIUM HITS SIGNIFICANT BIPOLAR HITS
ANK3PMID:19448189; PMID:23378337; PMID: 24625017; PMID:25377609; PMID:14609504
PMID:18711365; PMID:20351715;PMID:21926972; PMID:22182935; PMID:23453885PMID:24618891
ARNTL PMID:22384149; PMID:24636202; PMID:24679394
PMID: 16528748; PMID: 18228528;PMID: 19839995; PMID: 24679394
CACNA1C
PMID: 25194313; PMID: 25445986;PMID: 25678966; PMID: 26476274
PMID: 18711365; PMID: 20351715; PMID: 21926972; PMID: 23453885; PMID: 24280982; PMID: 25056061
CANG2 PMID: 18408563 PMID: 18408563; PMID: 23038240
DLG4 PMID: 26297903 PMID: 21559497; PMID: 23759419;PMID: 22005598
GRIA2 PMID: 19448189; PMID: 24885933 PMID: 22122651; PMID: 25308386
GSK3B
PMID: 17628506; PMID: 19754466; PMID: 22990942; PMID: 24033914; PMID: 24677591 PMID: 24992082; PMID: 25345732; PMID: 26267417
PMID: 20492846; PMID:20668436; PMID: 14729229; PMID: 21886606 PMID: 21922001;PMID: 23449817; PMID: 25041379; PMID: 25435019
HTR1A PMID: 10893489; PMID: 10758249; PMID: 20159346; PMID: 24534415
PMID: 20594600; PMID: 22752684; PMID: 23926239
NR1D1 PMID: 19818381; PMID: 21781277; PMID: 24625017 PMID: 19267705; PMID: 18804497
SLC1A2
PMID: 23023733; PMID: 24354796 PMID: 24534415 PMID: 23023733; PMID: 25406999
Candidate pharmacodynamic variants for stratification of ketamine antidepressant response are associated with chromatin-
mediated neuroplasticity
Regulatory variants were examined in pharmacodynamic targets
Bioinformatics pipelineImpute SNPs from GWAS and gene association studies using epigenetic fine
mapping SNPs from clinical trials using knowledge –based discoverywww.clinical-trials.gov
Learning machine to detect regulatory variants [2]
Transcription factor annotation and Hi-C mapping [4]
Phylogenetic module complexity analysis to detect causal SNPs [6]Learning machine to detect splice
variants [5]
Examine GTEx data on normal RNA-Seq [3]
Map mRNA using Allen Brain Atlas [1]
OUTPUT
[1] Sunkin SM et al. Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system. Nuc. Acids Res. 41, D996-D1008 (2013).
[2] Lee D et al. A method to predict the impact of regulatory variants from DNA sequence. Nature Genet. (2015) doi:10.1038/ng.3331
[3] Pirinen M et al. Assessing allele-specific expression across multiple tissues from RNA-seq read data. Bioinformatics. btv074 (2015).
[4] Higgins GA et al. Epigenomic mapping and effect sizes of noncoding variants associated with psychotropic drug response. Pharmacogenomics. 16(14), 1565–1583 (2015).
[5] Vaquero-Garcia J et al. A new view of transcriptome complexity and regulation through the lens of local splicing variations, preprint
[6] Claussnitzer M et al. Leveraging cross-species transcription factor binding site patterns: From diabetes risk loci to disease mechanisms. Cell. 156, 343–358 (2014). doi:10.1016/j.cell.2013.10.058
Microarray analysis suggests that several pharmacodynamic genes are targets
Hippocampal formation, parahippocampal gyrus and inferior temporal cortex:
Dorsolateral frontal cortex:
Microarray shows that CYP2B6 and CYP2D6 are expressed in brain as well
Putative Pharmacogenomic Variants that may Impact Transcription
Putative Pharmacogenomic Variants that may Impact Transcription
Promoter_BoundaryGRIN2B. rs3764028_G;SK-N-SH cells.
Gene Set Enrichment of Spatial Contacts by Hi-C
Others have found similar results
Bharadwaj R et al. Conserved higher order chromatin regulates NMDA receptor gene expression and cognition. Neuron. 84, 997–1008 (2014):
Thakurela S et al. Dynamics and function of distal regulatory elements during neurogenesis and neuroplasticity. Genome Res. 25, 1–16 (2015):
Summary – Novel Variant Discovery→ These are methodological approaches for discovery of
candidate pharmacoepigenomic variants – their function and clinical utility must be demonstrated in biological experiments and clinical studies;
→For the lithium response pathway we discovered using bioinformatics analysis, there are indications that others have found similar results using the same variants in the pathway, or closely related to the pathway, in a subsequent clinical study and a GWAS;
→ We believe that these strategies will uncover what some have called “missing hereditability” in pharmacogenomic response and adverse events, and how the epigenome impacts variation in gene regulation through presumptive environmental effects.
Is lithium response an inherited trait?
From: Song J et al. Genome-wide association study identifies SESTD1 as a novel risk gene for lithium responsive bipolar disorder. Mol. Psychiatry. 1–8 (October 2015). doi:10.1038/mp.2015.165
Lithium response in bipolar disorder is a genetic trait: PCA analysis of familial clusters
Excellent lithium-responders
Poor lithium response, but excellent response to lamotrigine
Poor lithium-responders, may respond with antipsychotics
Goldstein D et al. Principal component analysis of lithium and lamotrigine-responsive and treatment-resistant pedigrees in bipolar disorder reveals distinct pharmacogenomic population structure. Genomics. 106 (2015).
Lithium rescues loss of brain tissue loss in bipolar disorder
Amygdala and hippocampus: → 15 studies published between 2009 and 2015 to datePrefrontal cortex: → 6 studies published between 2009 and 2015 to dateAnterior caudate, striatum, thalamus and/or nucleus accumbens: → 4 studies published between 2009 and 2015 to dateCingulate cortex: → 3 studies published between 2009 and 2015 to dateInsular cortex: → 2 studies published between 2009 and 2015 to dateAngular gyrus: → 2 studies published between 2009 and 2015 to dateInferior temporal cortex: → 1 study published between 2009 and 2015 to dateOccipital cortex: → 1 study published between 2009 and 2015 to dateCerebellum: → 1 study published between 2009 and 2015 to date
From: Burmeister M, McInnis MG, Zöllner S. Psychiatric genetics: progress amid controversy. Nature Rev. Genet. 9, 527-540 (2008).
The 4D nucleome
“Most causal variants are located in the regulatory part of the genome, not in the exome.”
[1] Kellis M et al. PNAS. 111:6131–6138 (2014).[2] Albert, FW, Kruglyak L. Nature Reviews Genetics (2015).
PHARMACOEPIGENOMIC VARIANT DISCOVERY