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DMD Lecture 7.9.2020 (Lai PS)
DMD Lecture 7.9.2020 (Lai PS)
NGS 6882A
BIOLOGY OF DISEASE:
Duchenne Muscular Dystrophy
Copyright ©, 2020
Bridging Biology to Disease
Providing an understanding of
human disease from a bench to
bedside perspective
The patient has to use both his hands and arms to walk up his
own body from a squatting position due to lack of hip and thigh
muscle strength.
Sir William Richard Gowers’, 1879
Typical sign: Proximal weakness (lower limb muscles), use hands &
arms to walk up own body from prone or squatting position into upright
position instead of relying on their legs. “Gowers sign or manoeuvre”
What is the difference between DMD and BMD at the clinical level?
But females
can be
carriers
https://sites.google.com/site/hannahcgenetics/medical
Disease: DMD/BMD Gene: DMD gene Protein: Dystrophin
Mutations in same gene can cause either DMD or BMD (two phenotypes)
Frame-shift mutations
Severe phenotype (DMD): out-of-frame or truncating mutations
Milder phenotype (BMD): in-frame or missense mutations
Duplication mutation
Different
clinical outcomes
due to type
of mutations!
Point mutation
Le Rumeur 2015
Bos J Basic Med Sci 15(3): 14-20
3. DIAGNOSIS
- Different techniques and approaches -
DIAGNOSING DMD/BMD
Thinking point:
What are some of the limitations
with each of the above approaches?
(1) Clinical Presentations
http://drustapbio.wikia.com/wiki/Duchenne_Muscular_Dystrophy
(2) Biochemical assay
(serum creatine kinase)
Serum creatine kinase (CK) as a biochemical marker
Normal Patient
(4) Molecular diagnosis
DMD BMD
60-70% gross deletions 80% gross deletions
10% duplications 5% duplications
15-30% point mutations 10-15% small point mutations
GENE
Deletions and Duplications in DMD gene
Involve whole or multi-exons
Clustered around two hot spot regions (5’ and 3’)
Lupez-Hernandez et al (2015)
Int J Med Sci 16: 5334-5346
Multiplex PCR
19 48
3 44
8 51
43
45
50
53
13 47
1
42
6 60
4 52
5’ 3’
75.0%
63.0% 65.0%
60.2%
51.2% 50.0%
40.0%
32.4%
Detecting deletions
Detecting carriers
B. Screening for point mutations
DNA Diagnosis: detecting point mutations
1. Pre-screening to narrow location (exon)
and/or
2. Direct sequencing
Remember:
DMD is largest gene in human genome
Spans 2.3 Mb with 79 exons
Blood : DNA
Muscle biopsy : mRNA/CDNA
• Sanger Sequencing
• Nex-gen Sequencing
Spectrum of mutations in DMD/BMD patients
Standard symbols and lines are used to represent the family members and their relationships.
https://teaching.ncl.ac.uk/bms/wiki/index.php/Pedigree
Case 1
CASE STUDY 1
Father Mother
Fetus
Patient ?
11 weeks
Is fetus affected?
Gene deletion identified
(Gene promoter, Pm to exon 8)
F : Father Promoter
Patient has gene
M : Mother deletions from
MK + - F M S P CV Promoter to exon 8
S : Sister
P : Patient
CV : prenatal DNA
Exon 3 Exon 4
MK : marker
+ : control + - F M S P CV M +- F M S P CV
- : control
Exon 6 Exon 8
+ - F M S P CV M +- F M S P CV
12 weeks
?
Is fetus affected?
Deletion of two exons
(exons 48-49)
Prenatal diagnosis by MLPA analysis of all 79 coding exons
Control
Is fetus affected?
CARRIER SCREENING
http://www.biology-pages.info/R/RFLPs.html
Identifying carriers : 3 Case Studies
Case 1
Genetic implications (Counselling)
• Patient (75)
• Mother (77) is definite carrier
• Younger brother (78) of patient is also affected and he
presented with symptoms later at 6 years
• Future prenatal diagnosis possible Questions:
• Female carriers can be identified (future siblings) • Why is mother a definite carrier?
Dys I 4 3 4 Dys I • Why does father only have one
Dys III 4 2 4 Dys III
87-1/B
87-8/T
2
2
1
1
2
1
87-1/B
87-8/T
chromosome/haplotype?
87-15/B
87-15/X
1
1
2
1
1
1
87-15/B
87-15/X • Which is the affected X-
I24/P 2 2 1 I24/P
I38/T
Str 44
1
8
1
13
2
8
I38/T
Str 44
chromosome (haplotype)?
Str 45
E48/M
8
2 76 77
7
2
11
1
Str 45
E48/M • Is brother (78) affected?
Str 49 2 3 1 Str 49
Str 50
J66
1
2 CK = 412
3
3
5
2
Str 50
J66
• Why is brother (78) not shaded?
Bstr H1 4 CK = 365 (10/2/95) 4 4 Bstr H1
BStr62 2 2 2 BStr62
3 Dys I
Dys I 3
2 Dys III
Dys III 2
1 87-1/B
87-1/B 1
1 87-8/T
87-8/T 1
2 87-15/B
87-15/B 2
1 87-15/X
87-15/X 1
I24/P
I38/T
2
1
75 78
2
1
I24/P
I38/T
13 Str 44
Str 44
Str 45
13
7
7 Str 45 one X chromosome
2 E48/M
E48/M 2
CK = 30,654 U/L 3 Str 49
Str 49 3
Str 50 3 CK = 6,220 (10/2/95)
Patient
3
3
Str 50
J66
two X chromosomes
J66 3
4 Bstr H1
Bstr H1 4
2 BStr62
BStr62 2
Case 2
Questions:
GENETIC RECOMBINATION 5
4
4
4
DYSI
DYSIII
• Which is the affected
2 2 87-1/BstNI
chromosome?
2 1 87-8/TaqI
2 1 87-15/BamHI
2 1 87-15/XmnI
2
2
1
2
I24/PstI
I38/TaqI
• Why is III.4 not an
I 2
1 1
5
1
3
E48/MseI
STR50
affected male?
CK=128U/L 2 2 J66
• How many definite
4 4 4 4 5 4 5 4 5 4 4 4 female carriers in the
4 4 4
family?
4 4 4 4 4 4 4 4 4
2 1 2 1 2 1 2 1 2 1 2 2
1 2 1 2 2 2 2 2 2 2 1 2
II 2
2
1 2 2
2
1
1
3 4 5 2
2
2
2
6 2
2
2
2
7 2
2
2
2
2
2
1
1
8 9 2
2
• Are II.8 and III.6
1
2
2
2
1
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
2
1
2
carriers?
2 2 1 2 1 2 1 2 1 2 1 2
3 3 3 3 5 3 5 3 5 3 5 1
1 2 2 2 2 2 2 2 2 2 2 2
4 4 4 5 4 5 4 4 4
III 4 1 2 4 2 4 3 4 4 5 4 4 6 4 4
2 2 2 2 1 2 2 2 2
1 1 2 2 2 2 1 1 2
1 1 2 2 2 2 1 1 2
1 1 1 2 2 2 1 1 2
1 1 1 2 2 2 1 2 1
2 2 2 2 2 2 2 2 2
1 1 2 1 2 1 1 1 2
3 3 2 5 3 5 3 5 1
2 2 2 2 2 2 2 2 2
In this pedigree, II.2 was shown to be a carrier by linkage analysis while carrier
risk was excluded in II.5, II.6, II.7, III.3, III.5. Intragenic recombination was
found in II.8 between markers 87-15/XmnI and I24/PstI. Thus, her carrier risk
status and that for her daughter’s (III.6) cannot be clarified (ie. unknown).
Case 3
Linkage analysis using X-markers
Haplotypes (maternal and paternal)
DYSI 1 3 4
DYSIII 2 2 4
87-1/BstNI 2 2 2
87-8/TaqI 2 1 1
87-15/BamHI 1 1 2
I 87-15/XmnI
I24/PstI
1
1
1
1
2
1
I38/TaqI 2 1 2
E48/MseI 2 2 2
1
3 1
2
STR50 3
J66 1 3 1
4 4 3 4 4
4 4 2 4 4
2 2 2 2 2
1 2 1 2 1
II 2
1
1
1
1
1
1
1
1
1
1
1
2
1
1
2 2 1 2 2
2 2 2 2 2
1
1 I.1 I.2 3
2
3
3 I.3 3
2
1
1
5. THERAPY
Current Clinical Management For DMD
• There is no “cure" for DMD
Current clinical management of DMD
supportive, providing temporary relief of signs and
symptoms & management of pulmonary, cardiac, psychosocial issues, etc.
Multidisciplinary care
Physiotherapists, orthopaedics, respiratory physicians,
cardiologists, medical social workers/psychologists, neurologists
Aim at restoring muscle strength & motor function
Steroid treatment – start between 4 to 6 years old THERAPY?
Exercise (physiotherapy)
Posture & pain management (non-ambulatory stage)
Supportive treament for scoliosis & weak bones (calcium & Vit D
supplementation, bisphosphonates, etc.
Pumonary and cardiology surveillance
Alternative supplements: carnitine, Coenzyme Q10, creatine, etc.
Genetic counselling, carrier screening, prenatal & preimplantation diagnosis
APPROACHES FOR THERAPY
DNA
mRNA
Patient DMD (del exon 50)
mRNA
Patient treated with AO BMD (del exons 50-51)
• 100 mg/2 mL (50 mg/mL) in single-dose vial
• 500 mg/10 mL (50 mg/mL) in single-dose vial
Restoration of 4-15%
- mdx mice (exon 23)
- AAV-9 to deliver
CRSIP/Cas9 components
- Permanent change
- Blood-brain barrier?
- Off-target sites? Why is CRISP/Cas9
approach subject to such effects?
in Vitro and in vivo studies
CRISPR-Cpf1 correction of muscular dystrophy mutations
2017 First use of alternative in human cardiomyocytes and mice (Zhang et al 2017).
Cas9 endocuclease
called Cpf1 from - Streptococcus pyogenes cas9 (SpCas9) most widely used Cas9
Prevotella & Francisella 1 endonuclease
- Limitations : G-rich PAM, thus cannot do genome editing of AT-rich
regions
- Large size is disadvantage for packaging & delivery for AAV vectors
- Staphylococcus aureus cas9 (SpCas9) smaller but PAM sequence is
longer & complex
- Thus, a smaller CRISPR enzyme will enable higher cutting efficiency
- New RNA-guide endonuclease called Cpf1
- Prefers T-rich PAM at 5’ end of spacer
Generates sticky 5’ overhangs - Splice acceptor site is T-rich and offers ideal PAM sequence for
Able to target AT rich-regions
genome editing by Cpf1
Providing an understanding of
human disease from a bench to
bedside perspective
USEFUL GENERAL REFERENCES FOR YOUR OWN INTEREST
About the Disease
• Chamberlain (1991). Curr Opin Genet Dev 1:11-14
• Muntoni (2003). Lancet Neurol. 2:731-40
About Molecular Diagnosis
• Luce et al (2014). Muscle Nerve 49: 249-256
• Laing et al (2011). Clin Biochem Rev 32:129-34
About Clinical Management
• Manzur et al (2008). Arch Dis Child 2008;93: 986-990
• Bushby et al (2010). Lancet Neurol. 9(1):77-93
About Therapy
• Benedetti et al (2013). FEBS J. 280, 4263–4280
• Mah et al (2016). Neuropsychiatric Disease & Treatment 12: 1795-1807
• Aartsma-Rus & Krieg (2017). Nucleic Acids Therapeutics 27: 1-3
• Li et al (2015). Stem Cells Report 4: 143-154
• Ousterout et al (2015). Nature Comm. 6:6244
• Long et al (2016). Science 6271: 400-403
• Zhang et al (2020). Science Advances 6: 6812
• Mollanoori et al (2020). Genes & Diseases. https://doi.org/10.1016/j.gendis.2019.12.007
Overview on DMD in Singapore
• Tomar et al (2019). Am J Med Genetics (C)181: 230-244