Discovery of genetic mutations that cause stuttering

Transcription

1 Discovery of genetic mutations that cause stuttering Dennis Drayna, PhD NIDCD/National Institutes of Health US Public Health Service, DHHS

2 Who are we? National Institute on Deafness and Other Communication Disorders National Institutes of Health U.S. Public Health Services U.S. Department of Health and Human Services Your tax dollars at work

3 Stuttering The medical researcher s view Affects all populations and languages Common 4% lifetime prevalence, 0.5-1% of adults Poorly treated 1/3 long term success, 1/3 temporary success, 1/3 unsuccessful Profound effects; causes unknown

4 Fact #1- Not all stuttering is genetic Of the people who come to stuttering therapy, about half report a family history and half have no family history So, perhaps half of stuttering is due to genetic factors The other half is due to unknown causes Low birth weight, perinatal hypoxia

5 Fact #2 - Genes do not entirely control stuttering in anyone Severity varies from hour to hour, day to day, and in children, from month to month Stuttering therapy can largely eliminate stuttering Their genes have not changed

6 Part I. Human genetics for speechlanguage pathologists

7 Genetics The study of inheritance Our genes Individual units that code for specific products Together these products comprise the structure and functions of the body 21,000 different genes in humans Reside in structures inside the cell called chromosomes

8 How do we use genetics to identify a gene that causes a disorder?

9 The traditional paradigm 1. Identify stable variation a trait or a disorder 2. Demonstrate that variation is due to genetic factors 3. Perform studies in families with many cases of the disorder to identify the location of the causative gene(s) a linkage study 4. Search the location to identify a genetic variant carried by the affected family members and not by unaffected family members positional cloning

10 Positional cloning Refers to the isolation (cloning) of a specific gene based solely on its position in the genome Does not require knowledge about the pathology, physiology, or biochemistry of the disorder Agnostic with respect to disease mechanism

11 Positional cloning Produced a long line of successes in human genetics Identified the genes underlying all of the common single-genedisorders Cystic Fibrosis, Huntington Disease, neurofibromatosis, many others Extended to studies of complex genetic disorders

12 Complex disorders Caused by a combination of genetic and non-genetic factors Include most major classes of medical disorders Cardiovascular disease, psychiatric disorders, metabolic disorders

13 Linkage studies of complex disorders Generally disappointing Low linkage scores Failures to replicate across independent studies Produced many suggestive locations for genes underlying such disorders, but few convincing discoveries of causative genes

14 A solution? Population based association studies Case-control study design Test a very large number of genetic markers distributed across the human genome (100,000 2,000,000) Try to find markers that are more common in cases compared to controls Genome wide association study (GWAS)

15 GWAS experience GWAS works Can identify genetic variants that explain a small fraction of the disorder Problems Very large study populations needed Marginal odds ratios, frequently < 1.5 Majority of associated markers are not within genes

16 Whole-genome sequencing The next emerging genetic analysis method Enabled by technology developments Provide a complete enumeration of all genetic variants in a single individual Will require advances in information analysis for broad application in human disease gene finding

17 Part II. Genetic studies of stuttering

18 Why are genetic approaches so powerful? Capable of finding the genes that cause the disorder Ideal approach for inherited disorders that are difficult to study in other ways Once we have the gene(s), we can see what the gene codes for, and what it s function is, both normally and in people who stutter.

19 Stuttering a tractable target? Is it genetic?

20 Genetic Factors in Stuttering - Familial Aggregation - Inherited disorders tend to cluster in families Incidence of stuttering in first degree relatives = 20-74% Incidence of stuttering in general population = %

21 Genetic factors in stuttering - Twin Studies - Twins reared together Share 100% of early environment Share either 100% of genes (identicals) or 50% of their genes (fraternals) Five twin studies of stuttering published

22 Twin study results Identical twins are always more alike than fraternal twins Identical twin concordance = 20-63% Fraternal twin concordance = 3-19% Modeling using twin data concluded up to 70% of stuttering is due to genetic effects

23 Genetic factors in stuttering - Adoption studies - 2 adoption studies of stuttering have been published Both too small to reach statistically significant conclusions, however No evidence stuttering is learned

24 Family X Genetics of stuttering - Large families - Studied in the 1940 s The Utah Family Descendents of single affected individual Other families Cameroon

25 Genetic factors in stuttering - Segregation analyses - A disorder clusters in families. Does this clustering follow the rules for inherited disorders? Mixed results for stuttering Not possible to assign a specific mode of inheritance

26 A complication most stuttering goes away spontaneously Recovery from childhood developmental stuttering is high, perhaps 75% or more Our strategy study persistent stuttering

27 A common question If it s likely that variants in lots of different genes can cause stuttering, don t you need to find all of them?

28 The goal Find a variant in the genes a particular region of a particular chromosome that occurs in family members who stutter but not in family members who don t stutter Observe that or other variants in the same gene in the affected members of other stuttering families

29 Research plan Begin with genetic linkage studies Applicable to any inherited disorder Don t need to know anything about the underlying cause Identify the location of the gene or genes that cause the disorder Genes reside on structures inside cells called chromosomes which chromosome? Performed in families

30 North American linkage study Studied 70 modest sized nuclear families Found weak evidence of linkage on chromosome 18 Conclusion - there is no single common gene that causes stuttering in the general North American population

31 Similar results from studies by others Suggestive evidence for linkage on chromosomes 2, 3, 5, 7, 9, 12, 13, 15, and 21 Typical of linkage results for human complex traits Weak support for the findings Failures to find the same location across studies No direct identification of disease genes

32 Solution? Specialized populations Take advantage of unusual population structure Pakistan

33 Advantageous population structure - Pakistan 70% of all marriages between either 1st or 2nd cousins This marriage pattern has persisted over centuries Results in a population structure with greatly increased incidence of genetic disorders

34 Finding stuttering families in Pakistan Collaborated with the National Centre of Excellence in Molecular Biology (CEMB), University of Punjab, Lahore Sought stuttering families through the school system Identified 100 families, chose 44 for our linkage study

35 Pakistani stuttering families PKST 72 I:1 I:2 II:1 II:2 II:3 II:4 III:1 III:2 III:3 III:4 III:5 III:6 III:7 Sooban M.Din Bibi Rani Nizam Din Ali Muhammad Bagh Bare Roshan Din IV:1 IV:2 IV:3 IV:4 Aysha M.Din Charagh bibi(hajan) V:4 V:5 V:1 Genotyped Zahoor ahmad V:2 mukhtar V:3 ghulam Fatima Raj bibi M.Din VI:6 VI:7 VI:8 VI:11 VI:9 VI:10 VI:1 VI:2 VII:4 VI:3 VI:4 VI:5 Amanat Rasheedan kalsoom Bashiran Imran Haneef haji Tufail haji yousaf VII:19 VII:20 VII:21 VII:22 VII:23 VII:1 Yasmeen VII:2 Abdul Ghaffar VII:3 Genotyped M waqas VII:5 M Iqbal VII:6 VII:7 Abdul Jabbar VII:8 Bushra VII:18 Sohail VII:17 VII:9 Akram Surriya VII:10 VII:11 Aslam Ilyas VII:12 VII:13 VII:14 VII:15 Reehana shafeeq Rukhsana VII:16 Jameel VIII:5 VIII:7 VIII:1 VIII:2 VIII:3 VIII:4 Asif VIII:6 Abdul Baree Usman Asad IX:1 Atif IX:18 IX:2 Tahir IX:3 IX:4 FirdosShagufta IX:5 Genotyped Tashfeen IX:6 Genotyped Kashif IX:7 Genotyped Yaseen IX:8 Genotyped Zulfiqar Ali IX:9 Genotyped M Tayyab IX:10 robina IX:11 awais IX:12 Genotyped M Hussain IX:13 shahid IX:14 hafeez IX:15 IX:16 shazia Yasmeen IX:17 Nazia X:14 X:12 X:13 X:15 X:16 X:1 Genotyped Abid X:2 Genotyped Haroon X:3 Genotyped Asif X:4 X:5 X:6 X:7 Amir X:8 Ahmad X:9 Fehmeeda X:10 Jawwad X:11 Hamza shan Iqra Tayyaba PKST 72

36

37 Gene identification strategy Focus on this region on chromosome 12 in Pakistani family PKST72 87 genes lie within this interval

38 Variant of interest Variant that went along with stuttering in family PKST72 and did not appear in the normal Pakistani population This variant was an apparent mutation in a gene called GNPTAB This mutation changes an important part of the gene Invariant across all species known

39 Mutation associated with stuttering in family PKST72 The same mutation occurs in affected individuals in Pakistani families PKST 05, 25, 41 4/41 families suggests this mutation could account for ~10% of stuttering families in Pakistan The same mutation occurs in unrelated people who stutter from Pakistan and India Mutation not observed in normal North American individuals

40 The goal Find a variant in the genes a particular region of a particular chromosome that occurs in family members who stutter but not in family members who don t stutter Observe that or other variants in the same gene in the affected members of other stuttering families

41 Three other mutations in GNPTAB identified Found in affected individuals of South Asian and European descent All are mutations that make a change at a place in the gene an important place in the gene None ever found in normal control individuals

42 GNPTAB Encodes part of an enzyme Enzyme involved in the normal metabolism of all cells Functions as part of the cell s recycling bin

43 GNPTG Encodes another part of the same enzyme Identified 3 different mutations in 4 unrelated affected individuals All affect important parts of the gene All not observed in normals

44 GNPTAB/G Performs the first step in the lysosomal targeting pathway, which is responsible for directing ~ 60 enzymes to the cell s recycling bin, known as the lysosome

45 NAGPA The uncovering enzyme Performs the next step in the lysosomal targeting pathway Identified 3 mutations in 6 unrelated individuals All of European descent All affect important parts of the enzyme None observed in normal control individuals

46 GNPTAB/G mutations in known disorders Mutations in GNPTAB and GNPTG are known to cause mucolipidosis II and III (ML II and ML III) MLII is a severe disorder, fatal in the first decade of life MLIII is a less serious disease Both are rare lysosomal storage disorders with primary problems displayed in the skeletal system, joints, brain, liver, spleen

47 NAGPA mutations? No disorder in humans has been associated with NAGPA mutations This is surprising, because these might be expected to result in medical symptoms similar to those observed in ML II and III We hypothesize that the primary manifestation of NAGPA mutations is persistent stuttering

48 Discussion Mutations in these 3 genes may account for 5-10% of familial stuttering worldwide, and stuttering in more than 100,000 individuals in the U.S. alone Lysosomal targeting disorders are clearly no longer rare Indicates that stuttering now overlaps the field of medicine Pharmacologic therapies for lysosomal storage disorders now well established

49 Is stuttering a mild form of mucolipidosis? To date, we ve examined 4 affected individuals at the NIH Clinical Center No symptoms of ML II or ML III were observed in any of these individuals Other than stuttering, all 4 individuals were neurologically normal

50 Implications for Speech Language Pathology Our results explain a small fraction of stuttering Our results will allow us to ask questions about therapy Could underlying genetic differences explain differences in therapy outcomes? Our results suggest a coming partnership between SLP s and physicians

51 How does a disorder of cell metabolism lead to stuttering?

52 Working hypothesis A specific group of nerve cells in the brain are unique to speech production and also uniquely sensitive to this metabolic deficit Goal Identify these cells, discover what they do, determine what they re connected to, and understand how this inherited deficit uniquely affects them

53 Can we explain stuttering in more individuals?

54 Newly identified Pakistani stuttering families

55 Linkage analysis in PKST77

56 Acknowledgments NIDCD Changsoo Kang M. Hashim Raza Naveeda Riaz Eduardo Sainz Joe Kleinman Alison Fedyna NHGRI/NISC Alice Young Jim Mullikan Donna Krasnewich NIH Clinical Center Penelope Friedman NCBI Alejandro Schaffer Hollins Communications Research Institute Jennifer Mundorff CEMB/University of the Punjab Jamil Ahmad Shahid Khan S. Riazuddin Stuttering Foundation of America British Stammering Association National Stuttering Association Speak Clear Association of Cameroon Joseph Lukong Stuttering research subjects worldwide

57 Research volunteers needed! Individuals with: Persistent stuttering A family history of stuttering A willingness to provide blood and speech samples See me immediately following this talk