Download Discovery Of Genetic Mutations That Cause Stuttering

Discovery of genetic
mutations that cause
stuttering
Dennis Drayna, PhD
NIDCD/National Institutes of Health
US Public Health Service, DHHS
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
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
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
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
Part I.
Human genetics for speechlanguage pathologists
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
How do we use genetics to
identify a gene that causes a
disorder?
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
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
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
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
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
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)
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
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
Part II.
Genetic studies of stuttering
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.
Stuttering – a tractable target?
• Is it genetic?
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 = 1.3-4.2%
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
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
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
Genetics of stuttering
- Large families • Family X
– Studied in the 1940’s
• The Utah Family
– Descendents of single affected individual
• Other families
– Cameroon
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
A complication – most
stuttering goes away
spontaneously
• Recovery from childhood developmental
stuttering is high, perhaps 75% or more
• Our strategy – study persistent stuttering
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?
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
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
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
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
Solution?
Specialized populations
• Take advantage of unusual population
structure
– Pakistan
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
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
Pakistani stuttering families
PKST 72
I:1
I:2
II:2
II:1
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:2
IV:1
IV:3
Aysha
V:1
Genotyped
Zahoor ahmad
IV:4
M.Din
Charagh bibi(hajan)
V:4
V:3
mukhtar
ghulam Fatima
VI:6
VI:3
VI:1
VI:2
VII:4
kalsoom
Bashiran
Imran
VII:1
VII:2
Yasmeen
Abdul Ghaffar
VII:3
Genotyped
M waqas
VII:5
VI:7
VI:8
Haneef haji Tufail haji yousaf
VII:19
VII:7
VII:8
VII:18
VII:17
Bushra
Sohail
Akram Surriya
VIII:2
VIII:3
VII:10 VII:11
VII:9
VII:12
Aslam Ilyas
IX:18
Atif
IX:2
Tahir
X:14 X:12
X:13
X:15
X:1
Genotyped
Abid
IX:5
Genotyped
Firdos Shagufta Tashfeen
IX:3
IX:4
IX:6
Genotyped
Kashif
IX:7
Genotyped
Yaseen
IX:8
Genotyped
Zulfiqar Ali
IX:9
Genotyped
M Tayyab
VII:13
VIII:6
Asad
IX:11
robina
awais
IX:12
Genotyped
M Hussain
IX:13
IX:14
shahid
hafeez
IX:15
IX:16
shazia Yasmeen
IX:17
Nazia
X:16
X:2
Genotyped
Haroon
X:3
Genotyped
Asif
X:4
X:5
X:6
shan
Iqra
Tayyaba
PKST 72
VI:10
VII:14
VII:21 VII:22 VII:23
VII:15
VII:16
Jameel
VIII:7
Asif
VIII:4
IX:10
VI:9
Reehana shafeeq Rukhsana
Usman
IX:1
VI:11
VII:20
VIII:5
VIII:1
M.Din
Amanat Rasheedan
VI:5
VI:4
Abdul Jabbar
VII:6
M Iqbal
V:5
Raj bibi
V:2
X:7
X:8
X:9
X:10
X:11
Amir
Ahmad
Fehmeeda
Jawwad
Hamza
Abdul Baree
Gene identification strategy
• Focus on this region on chromosome 12 in
Pakistani family PKST72
• 87 genes lie within this interval
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
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
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
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
GNPTAB
• Encodes part of an enzyme
• Enzyme involved in the normal
metabolism of all cells
• Functions as part of the cell’s “recycling
bin”
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
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
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
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
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
Discussion
• Mutations in these 3 genes may account for 510% 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
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
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
How does a disorder of cell
metabolism lead to stuttering?
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
Can we explain stuttering in
more individuals?
Newly identified Pakistani stuttering
families
Linkage analysis in PKST77
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
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