Genetics of Schizophrenia

1. Genetics of Schizophrenia Jon McClellan, MD University of Washington Disclosures: Grants from NIH, Stanley Medical Foundation, NARSAD No Industry Sponsored Research, Speaker’s Boards, or Consultation

2. Schizophrenia Genetics Until recently, most widely quoted model in Psychiatric Genetics: “Common Disease – Common Allele” Model “Polygenic model” • Combined impact of common genetic variants, each with small effect on risk, plus interactions with environmental risk factors, results in the illness

3. “Common Disease – Rare Variants” Model Rare large effect mutations are responsible for substantial portion of schizophrenia, autism, and perhaps most complex illnesses Individual mutations may be specific to single cases or families Many different genes involved, each with many different disease-causing mutations Human disease characterized by enormous genetic heterogeneity McClellan and King, Cell 2010

4. How can Rare Mutations Explain a Common Psychiatric Disorder? • The majority of human genes are involved with brain development • New mutations are common • Those that cause illnesses may only persist a few generations because of their negative consequences • Any gene important to an illness may be disrupted by 1000’s of different mutations • Each mutation may be rare, but collectively the gene may be responsible for a substantial portion of cases (BRCA1) • Different mutations in different genes may disrupt related neurobiological pathways, leading to the same disorder

5. Genetic causes of complex disease must reflect evolutionary forces shaping the human genome

6. Human Migration Adapted from Cavalli-Sforza & Feldman, Nature Genetics33, 266 – 275, 2003

7. A village of a few hundred families, anywhere. What % of all human variation is here? 10% 50% 80% 90%

8. Human Genetic Diversity Adapted from: Tishkoff & Verrelli Annu Rev Genomics Hum Genet 2003

9. Human Allelic Heterogeneity The exponential growth of the human population has resulted in a vast number of new mutations All possible mutations have occurred and will occur again Each person harbors ~ 175 de novo mutations Recent alleles usually rare and specific to one population (or even one family) Many are deleterious and do not persist beyond a few generations

10. Schizophrenia and Autism: Caused by recent rare large effect mutations? Illnesses persist with similar prevalence world-wide Familial Disorder, yet most cases sporadic Persistence of Illness Despite Impact on Fertility Environmental Exposures Increased Risk associated with Paternal Age Maternal Famine for Schizophrenia

11. 3.00 2.50 Paternal age Maternal age 2.00 Relative risk of Schizophrenia 1.50 1.00 < 30 30 - 35 - 40 - 45 - 50+ Parent’s age at childbirth Schizophrenia and Parental Age Malaspina et al., Arch Gen Psychiatry 2001

12. Reichenberg et al., 2006, Arch Gen Psychiatry

13. Dutch Hongerwinter 1944-45 Schizophrenia (%) 4.0 3.5 3.0 Jan-Jun 1944 Jul-Dec 1944 Jan-Sep 1945 Oct-Dec 1945 Jan-Jun 1946 Jun-Dec 1946 2.5 Birth month and year 2.0 1.5 1.0 0.5 0.0 Susser et al. Arch Gen Psych 1996

14. 2.50 2.00 1.50 Schizophrenia (%) 1.00 0.50 0.00 1955 1956 1957 1958 1959 1960 1961 1962 1963 1964 1965 1966 Chinese Famine of 1959-60 Wuhu region of Anhui Province St. Clair et al. JAMA 2005

15. Rare Structural Variants Disrupt Multiple Genes in Neurodevelopmental Pathways in Schizophrenia Tom Walsh, Jon M. McClellan, Shane E. McCarthy, Anjené M. Addington, Sarah B. Pierce, Greg M. Cooper, Alex S. Nord, Mary Kusenda, Dheeraj Malhotra,Abhishek Bhandari, Sunday M. Stray, Caitlin F. Rippey, Patricia Roccanova, Vlad Makarov, B. Lakshmi, Robert L. Findling, Linmarie Sikich, Thomas Stromberg, Barry Merriman, Nitin Gogtay, Philip Butler, Kristen Eckstrand, Laila Noory, Peter Gochman, Robert Long, Zugen Chen, Sean Davis, Carl Baker, Evan E. Eichler, Paul S. Meltzer, Stanley F. Nelson, Andrew B. Singleton, Ming K. Lee, Judith L. Rapoport, Mary-Claire King, Jonathan Sebat3 Science, 320:539-43, 2008

16. “Study Ties Genetic Variations to Schizophrenia” "You're basically screwing up the way that the regulation of brain growth occurs" Jon McClellan, MD “Dad, "screwed up" is not a very professional phrase, it makes you sound kind of stupid” Tessa McClellan

17. Hypothesis • Rare copy number mutations affecting genes in neurodevelopmental pathways will be more common among persons with schizophrenia than among controls

18. Subjects Cases 150 persons with schizophrenia or schizoaffective disorder Controls 268 persons age >35 Free of signs of neurological or psychiatric illness Same distribution of self-reported ethnicities as cases

19. Copy Number Variants Deletions Duplications

20. Copy Number Variants • Deletions, duplications and inversions of DNA • Can involve thousands, or even millions, of basepairs • Most Copy Number Variants are benign and common • Copying errors that disrupt normal gene function can lead to disease. Sebat et al., 2004

21. Definition of Rare CNVs • Not previously reported in Database of Genomic Variants (DGV) • Data from 1000’s of individuals • CNV found either only in cases or only in controls • Mutation impacts one or more genes • 100kb or larger in size

22. del Chr2:211,792,494-212,191,651 del Chr3:7,177,597-7,314,117 del Chr3:197,224,662-198,573,215 del Chr5:36,190,704-36,693,387 dup Chr7:77,358,702-77,857,149 dup Chr8:142,025,432-142,393,948 dup Chr18:7,070,926-7,565,943 dup Chr19:59,045,962-59,363,706 del Chr22:32,048,581-32,715,286 Subset of Rare structural variants detected using high density array CGH

23. Rare Structural Variants and Schizophrenia • Individuals with Schizophrenia significantly more likely to have a rare deletion or duplication (≥ 100 kb) impacting a gene 15 % vs 5 % of healthy controls • Rate of rare mutations higher in early onset cases (20%) • Each mutation was different, and impacted different genes • Genes disrupted in Schizophrenia cluster in pathways related to neurodevelopment, including glutamate and neuregulin pathways Walsh et al., Science, 2008

24. So… What about other studies?

25. Enrichment of Rare Structural Variants replicated by several independent groups • 8-fold increased risk of de novo structural mutations in Sporadic Schizophrenia (Xu et al., 2008) • Higher frequency of rare duplications and deletions found in large samples of patients with schizophrenia (Stefansson et al., 2008; International Schizophrenia Consortium, 2008) • Recurrent mutations at genomic “Hotspots” found in multiple cases Several-fold increased risk for disorder (OR’s > 5)

26. Genomic “Hotspots” Nonallelic Homologous Recombination due to Segmental Duplication Genomic “Hot Spots”

27. Cases N=3391 Controls N=3181 22q11.2 (VCFS) 13 0 9 0 15q13.3 10 1 1q21 ISC Nature 2008

28. Genomic Hotspots (so far…) • 1q21.1, 3q29, 15q11.2, 15q13.3, 16p11.2, 16p12.1, 16p13.11, 17p12, and 22q11.2 • Duplications in the neuropeptide receptor VIPR2 And with better sequencing tools… Rare deleterious point mutations and indels detected in genes important to neurodevelopmental pathways: • e.g., GRM1, MAP1A, GRIN2B, and NLGN • Critical pathways include glutamate functioning, synapse formation, signaling and brain development • Both rare De novo and inherited events may cause the disorder

29. Genomic Analysis of Schizophrenia (GENESIS) R01MH083989 NIMH series: >5000 cases, family members; >5000 controls Raquel Gur, MGI, U Pennsylvania David Braff, COGS, UC San Diego Robert Savage, PAARTNERS, U Alabama Vish Nimgaonkar, GSS, U Pittsburgh Genomic sequencing and analysis, U Washington, Seattle Tom Walsh, Jack McClellan, Ming K Lee, Anne Thornton, Amanda Watts, Sunday Stray

30. Genomic Analysis of Schizophrenia (GENESIS) Identification of de novo events Trios with sporadic schizophrenia Affected proband and unaffected parents Negative family history of schizophrenia, bipolar disorder, or major depression Exome sequencing of proband and both parents from blood-based DNA

31. Genomic Analysis of Schizophrenia (GENESIS) Eventually 300 trios, presently 92 trios in pipeline First 22 trios: 19 validated de novo mutations in 19 different genes

32. Strong Association of De Novo Copy Number Mutations with Autism Jonathan Sebat, B. Lakshmi, Dheeraj Malhotra, Jennifer Troge, Christa Lese-Martin, Tom Walsh, Boris Yamrom, Seungtai Yoon, Alex Krasnitz, Jude Kendall, Anthony Leotta, Deepa Pai,1 Ray Zhang, Yoon-Ha Lee, James Hicks, Sarah J. Spence, Annette T. Lee, Kaija Puura,6 Terho Lehtimäki, David Ledbetter, Peter K. Gregersen, Joel Bregman, James S. Sutcliffe, Vaidehi Jobanputra, Wendy Chung, Dorothy Warburton, Mary-Claire King, David Skuse, Daniel H. Geschwind, T. Conrad Gilliam, Kenny Ye, Michael Wigler Science, 316:445-449, 2007

33. Rare Structural Variants and Autism • 10 % of Individuals with Sporadic Autism have de novo duplications and deletions (> 100kb, Sebat et al., 2007) • 2 % of multiplex cases • 1 % of controls • 7 % of cases with Sporadic Autism vs 2 % of multiplex cases have de novo CNVs (Marshall et al., 2008) • Replicated several times by independent groups

34. Rare Mutations and Autism Genomic Hotspots • 1q21.1, 7q11.23, 15q13.3, 16p11.2, 16p13.11, 17p12, and 22q11.2 • 16p11.2 may explain ~ 1 % of cases

35. Rare Mutations and Autism • To date, rare deleterious mutations associated with Autism in > 100 genes and > 40 genomic loci • Genes disrupted associated with pathways critical for neurodevelopment, including synaptic development, neuronal cell-adhesion and ubiquitin degradation • Many of the same genes and hotspots are also associated with Schizophrenia

36. Rare Variants and Psychiatric Disease • Rare CNVs, point mutations and indels also reported for: Intellectual Disability Tourette Disorder ADHD Bipolar Disorder • Some mutations/genes same as those found in Schizophrenia • Includes Genomic Hotspots

37. Genomics and Psychiatry Autism, Schizophrenia , Intellectual Disability, Bipolar Disorder, ADHD and Tourette Disorder each associated with rare deleterious mutations that disrupt genes related to brain development Many disease specific mutations appear to be either de novo, or of recent origin Genes implicated involved in neural development

38. Genomics and Psychiatry Most individuals have a different mutation involving different gene(s) Genomic Hotspots may account for a higher proportion of cases Some individuals are found to have more than one deleterious mutation in different genes/loci: “Multi-hit” model explains how some events are inherited from nonaffected persons Adds further complexity to heritability of disorders

39. Same Gene, Different Disorder

40. Blackwood et al., 2001 AJHG DISC1 18/29

41. Different Gene(s), Same Disorder

42. 16p13.11 Developmental Delays ADHD Autism Schizophrenia 1q21.1 16p11.2 Macrocephaly Developmental Delays Autism Developmental Delays Autism Schizophrenia Bipolar Disorder Developmental Delays Epilepsy Microcephaly Developmental Delays Schizophrenia Developmental Delays Autism Developmental Delays Autism Schizophrenia Epilepsy 22q11.2 15q13.3 Developmental Delays Autism Developmental Delays Developmental Delays ADHD Autism Schizophrenia Bipolar Disorder Developmental Delays Autism Schizophrenia Epilepsy NRXN1 CNTNAP2

43. Meanwhile…. The search for common risk alleles Genome-wide Association Studies (GWAS) struggle with: Lack of replication Small dwindling effect sizes (< 1.5) Lack of demonstrated biological relevance for disorder

44. Neuropsychiatric disorders characterized by marked genetic heterogeneity Most affected individuals may have a different genetic cause Multiple different mutations in multiple different genes/genomic loci may ultimately act by disrupting neuronal homeostasis (Ramocki & Zoghbi, 2008) Phenotypic differences may be due to timing and impact of mutation on development, plus other epistatic, epigenetic and/or environmental factors

45. So… Psychiatric diagnoses have clinical marked heterogeneity and Marked genetic heterogeneity characterizes most complex illnesses Vast clinical and genetic heterogeneity likely explains why diagnostic issues are so complex and treatment response so variable across individuals with the same illness

46. Implications DSM diagnostic categories may be too heterogeneous for major advances in neurobiological understanding of disorders Research needs to focus on individuals grouped by disrupted neurobiological pathways/genes rather than by broadly defined syndromes

48. University of Washington Mary-Claire King Tom Walsh Jack McClellan Sarah Pierce Cait Rippey Diane Dickel Sunday Stray Ming K. Lee Greg Cooper Carl Baker Evan Eichler Cold Spring Harbor Laboratory Shane McCarthy Abishek Bhandari Mary Kusenda Dheeraj Malhotra Jonathan Sebat NIH - NIMH Anjene Addington Judith Rapoport NIH - NIA Andrew Singleton