GENETICS OF EARLY-ONSET ALZHEIMER’S DISEASE IN ASIA

Eva Bagyinszky, Ph.D

Department of BioNano Technology

Gachon University

2018.11.08.

Disclosure

There are no conflicts of interest and nothing to disclose

Increasing Global Burden of AD: Cultures differ in their dealing with dementia

The number of people with dementia will roughly double every 20 years,

with the biggest increases in developing countries as Asia.

What Is Alzheimer's disease?

1. AD is the most common age-related neurodegenerative disease

2. Abnormal proteins damage and destroy neurons and their connections in the brain

3. AD is characterized by marked decline in memory and other cognitive abilities

4. No disease modifying treatment is available to slow or stop its progression

1. Every 70 seconds, someone develops AD

2. 5.3 million Americans have AD

3. One in eight persons of age 65 and older develops AD

4. AD is the 6th leading cause of death

5. The national cost of caring for people with AD is estimated to be 300 billion dollars in 2018

Alzheimer's disease

Patients with AD is rapidly increasing with increasing aging

population, this figure is expected to be three times larger compared to

the present.

Tip of the Iceberg

Biomarker & Clinical Change in AD

Time (years)

Detection

Threshold

Cognitive

impairment

Functional/ Behavioral

changes = dementia

Asymptomatic stage – Genetic risk

& increasing biomarker signal

Clinical symptom stages –

Occurrence dependent on degree of

reserve capacity

Genetic risk factor Jack CR, et al. Lancet Neurol (2013)

Genetic Risk Factors for AD

1. Genetic variants may be more strongly related to the specific brain

function, biological mechanisms, or pathways in the development of AD

2. A better understanding of the genetic susceptibility factors of AD would

advance strategies for early detection and treatment

3. The heritability for AD is predicted to be as high as 80% based on twin

studies

Alzheimer’s disease

Alzheimer’s disease: 2 types of AD: EOAD (familial) & LOAD

EOAD (familial): Genetic background well defined

3 genes in EOAD: APP, PSEN1 and PSEN2

20 years 30 years 40 years 50 years 60 years

PSEN1

PSEN2

APP

APOE + other genes

Age

EOAD

(5%)

LOAD

(95%)

65 years

Down syndrome

AD Mutation frequencies

• Familial AD: 5-10% of all AD cases

• Issue: in the most patients, the disease causing factors remained unexplained

• Goal: finding out the missing etiology of EOAD

Genes penetrance Reported mutations

APP 1-1.5% of all familial AD

55

PSEN1 3-7% of all familial AD 270

PSEN2 less than 1% 48

(http://www.alzforum.org/mutations, accessed in August 2018)

Our previous approach on EOAD with 50 genes

• We designed a panel of 50 genes in

NGS

• Due to the pathological overlap,

different disease causing genes were

included.

• IonProton sequencer was used by

Theragen company

Dx Nr Genes

AD 19 PSEN2, S100A9, CR1, BIN1, TREM2, CLU, CTNNA3,

DNMBP, SORL1, BACE1, PICALM, BACE1, LPR6, PSEN1, ADAM10, ABCA7, CD33, TOMM40, APP

PD 7 PINK1, PARK7, PARK9, GBA, SNCA, PARK2, LRRK2

ALS & FTD

18 TDP43, CHMP2B, SIGMAR1, VCP, FUS, GRN, MAPT, UBQLN2, ALS2, TAF15, FIG4, OPTN, DAO, HNRNPA1, SOD1, ANG, VAPB, SQSTM1

Others 6 SPAST, CYP7B1, SPG11, CSF1R, NOTCH3, PRNP

ADAM-gene study by NGS No. CH Gene symbol Missense mutations Silent mutations

common Rare Common Rare

1 1 PSEN2 1 4 1

2 1 S100A9 1

3 1 CR1 5 3 1

4 2 BIN1 1 3 2

5 6 TREM2 1

6 8 CLU 3 1 1

7 10 CTNNA3 1 3 2 2

8 10 DNMBP 1 3 4

9 11 SORL1 9 2

10 11 BACE1 1 1

11 11 PICALM 1 2

12 11 GAB2 6 3 2

13 12 LRP6 1 3 1

14 14 PSEN1 5 1

15 15 ADAM10 3 1

16 19 ABCA7 8 24 11 7

17 19 CD33 2 5

18 19 TOMM40 2 2

19 21 APP 2 2

20 1 PINK1 1 4 2

21 1 PARK7 2 1

22 1 ATP13A2 1 4 1 3

23 1 GBA 1

24 4 SNCA 1

25 6 PARK2 1 2

26 12 LRRK2 9 4

27 1 TDP-43 2

28 3 CHMP2B 3

29 5 SQSTM1 2 2

30 9 SIGMAR1 1 2 1 1

31 9 VCP None

32 16 FUS 1 2 3

33 17 GRN 2 1 2

34 17 MAPT 1 3 1

35 17 TAF15 2 2 4

36 X UBQLN2 None

37 2 ALS2 1 5 3 3

38 6 FIG4 1 2

39 10 OPTN 2

40 12 DAO 2 1

41 12 HNRNPA1 1

42 14 ANG 1

43 20 VAPB None

44 21 SOD1 None

45 2 SPAST 1 3 1

46 8 CYP7B1 2

47 15 SPG11 2 5 1 1

48 5 CSF1R 1 9 4 3

49 19 NOTCH3 1 14 6

50 20 PRNP 2 2 1

Current approach: Whole exome sequencing

Diagnosis of patients with early onset dementia

(NINCDS-ADRDA)

APOE genotyping

Sample preparation

WHOLE EXOME SEQUENCING

Extensive genetic analysis for neurodegenerative disease-associated candidate genes (100)

Verification (standard sequencing)

Functional studies

In silico predictions

DISEASE ASSOCIATED MUTATION

Disease No Additional genes to our gene panel

AD

40 PSEN2, S100A9, CR1, BIN1, TREM2, CLU, CTNNA3, DNMBP, SORL1, BACE1, PICALM, LPR6, PSEN1, ADAM10, ABCA7, CD33, TOMM40, APP, MS4A4A, MS4A6E, TM2D3, CD2AP, EPHA1, CASS4, PLD3, HLA-DRB5, HLA-DRB1, INPP5D, DSG2, CDH12, CDH18, MEF2C, NME8, PTK2B, SLC24A4, RIN3, ZCWPW1, ACE, MTHFD1L

PD 22 PINK1, PARK7, PARK9, GBA, SNCA, PARK2, LRRK2; ACMSD, CD157/BST1,

FBXO7, FGF20, GAK, GIGYF2, GPNMB, HIP1R, LAMP3, PLA2G6, STBD1, STK39, STX1B, SYT11, VPS35

ALS & FTD

30 TDP43, CHMP2B, SIGMAR1, VCP, FUS, GRN, MAPT, UBQLN2, ALS2, TAF15, FIG4, OPTN, DAO, HNRNPA1, SOD1, ANG, VAPB, SQSTM1; ATXN1, ATXN2, EWSR1, HNRNPA2B1, PFN1, SETX, TMEM106B, CCNF, PPT1, TBK1, DCTN1, NEK1

Other disease

8 SPAST, CYP7B1, SPG11, CSF1R, NOTCH3, PRNP; CTSA; HTRA1

Exon Mutation Country

5 225 Val>Ala Korea

7 297 Thr->Met Korea

10 484 Pro->Ser Korea

14 604 Val>Met Thailand

16

669 Val>Leu Korea

678 Asp>Asn Japan

678 Asn->His Taiwan

17

693 Glu (deletion) Japan

710 Val>Gly China

715 Val>Met Korea

717 Val>Ile Japan, China

Thailand 718 Ile>Leu Taiwan

720 Leu>Ser Taiwan

722 Met->Lys China

APP mutations in Asia

APP mutations in Asia

Bagyinszky et al., 2016

V

b-secretase

b’-secretase

a-secretase

g-secretase

• Pathogenic APP mutations are located

in exon 16-17

• Mutations may disturb the a-b or g

secretase cleavage

• Several mutations were also

discovered outside of amyloid

cleavage regions

• Their pathogenic nature is currently

unclear

61-year-old man with dementia with

language problem.

He started to forget progressively since

age of 55.

3D protein structure modeling revealed

that p.Val604Met exchange could result in

significant changes in the APP protein due

to the increased hydrophobicity of

methionine in the helix

APP Val604Met (Thailand)

APP Val669Leu

• APP Val669Leu: novel mutation

• Was found in an AD patient and 2 relatives

• Not found in ExAC

• Located near the beta secretase cleavage site

• Nearest mutation: KM670/671VL (“Swedish APP”)

• PolyPhen2 revealed it as benign

• In vitro studies will be performed

• MRI revealed the pronounced hippocampal atrophy

FDG-PET showed bilateral and temporoparietal

hypometabolism

APP Val669Leu

MRI revealed the pronounced hippocampal

atrophy

3D model in APP V669L mutation. Orientation of

protein was changed by the leucine mutation.

PSEN1 mutations in Asia Exon Mutation Country

4

85 Leu>Pro Japan

96 Val>Phe Japan, Malaysia

97 Val>Leu China

99 Thr->Ala Japan

105 Phe>Cys China

5

116 Thr>Ile Korea

119 Thr>Ile Korea

123 Glu>Lys Japan

131 His->Arg Japan

136 Ala>Gly China

139 Met>Ile Korea

143 Ile>Thr Japan

154 Tyr>Asn Japan

6

163 His>Arg Japan, Korea

163 His>Pro Korea

165 Trp>Gly Korea

167 Ile (deletion) China

169 Ser (deletion) China

169 Ser>Leu Japan

173 Leu>Phe Japan

11

378 Gly>Glu Japan

381 Leu>Val Japan

384 Gly>Ala Japan

386 Leu->Ile China

388 Phe>Leu China

392 Leu>Val Japan

405 Asn>Ser Japan

Exon Mutation Country

7

184 Glu>Asp Japan

184 Glu>Gly Thailand

206 Gly>Ser Korea

209 Gly->Ala Korea

209 Gly>Arg Japan

213 Ile>Thr Japan

217 Gly>Asp Japan

219 Leu->Arg Japan

226 Leu>Phe Korea

232 Leu>Pro Korea

233 Met>Thr Korea

237 Phe>Ile Japan

248 Leu>Pro China

250 Leu>Val Japan

8

266 Ala>Val Japan

266 Gly>Ser Japan

269 Arg>His Japan

273 Glu>Ala Japan

280 Glu>Ala Japan

280 Glu>Lys Malaysia

282 Leu>Phe Japan

284 Pro>Leu Japan

285 Ala>Val Japan, Korea

286 Leu>Val Japan

9 Deletion Japan

10 352 Arg>Cys China

12

417 Gly>Ala Korea

431 Ala>Val Japan

434 Ala>Thr China

440 T deletion Japan

Bagyinszky et al., 2016

PSEN1 mutations in Asia

• PSEN1 mutations seems to be

the most common among Asians,

especially in Japan

• Emerging studies discover

additional mutations in Korean

and Chinese AD patients

• PSEN1 mutations may disturb the

gamma secretase mechanism,

resulting in impaired amyloid beta

production

PSEN1 Thr116Ile

• First cases in Asia

• Two unrelated families in Korea

• Similar AOO and symptoms, as in the European families

PSEN1 Thr116Ile

• Family 1: MRI: Atrophy could be seen in the right temporal and parietal regions. A vascular abnormality also appeared in the left frontal area.

• Family 2: MRI: no atrophy or vascular ischemic lesion

• Family 2: FDG-PET revealed but mild bitemporal hypometabolism

PSEN1 Thr116Ile

PSEN1 Thr116Ile

• 3D modeling on PSEN1 Thr116Ile could disturb significantly the HL-I loop structure.

• PSEN1 Thr116Ile mutation, in terms intramolecular interactions:

• Tyr116Ile may disturb the hydrogen bonds and hydrophobic interactions.

PSEN1 Leu226Phe

• Novel mutations among Korean patients

• Patient developed dementia in her 30s

• Disease progression was rapid

• This case may be a de novo case of AD

• Mutation may result in additional stress inside the helix

PSEN1 Leu226Phe

• MRI: bilateral hippocampal and distinct bilateral parietal cortical atrophy

• PET: severe hypometabolism in bilateral parietal regions.

• CT: diffuse severe brain atrophy

PSEN1 Leu226Phe

• Novel mutation, located in TM-V

• May result in a kink in the helix

PSEN1 Leu232Pro

MRI images showed bilateral

symmetric cerebral atrophy, mostly

affecting the parietotemporal region.

PSEN1 Glu280Lys (Malaysia)

• Novel mutation, located in the membrane associated HL-VI of PS1

• Two other pathogenic mutations: Glu280Ala (Paisa, Columbia) & Glu280Gly

• Probably pathogenic mutation, but missing heritability

• A novel PRNP Gly127Ser mutation was found in a step-niece of the three siblings harboring the PSEN1 Glu280Lys mutation.

PSEN1 Glu280Lys (Malaysia)

3D modeling suggested that mutation

may result in significant disturbances in

the membrane-associated long loop

function, and may result in extra helices

Several relatives were diagnosed with

either learning difficulties or with

epilepsy

PSEN1 Gly417Ala

• Discovered in a 37 years old Korean

male patient with dementia and

parkinsonism

• The patient showed mild Parkinsonian

symptoms, including generalized

bradykinesia, mild rigidity on his right

side, and stooped posture.

PSEN1 Gly417Ala

Novel presenilin-1 mutation

(c.1250G>C; p.Gly417Ala) was

discovered

May disturb the TM-VIII, and/or

the splicing of PSEN1 exon 12

3D model for PSEN1

p.Gly417Ala, alanine could

significantly disturb the protein

structure, since it is the higher

hydrophobicity of alanine than

glycine.

PSEN1 Gly417Ala could be a

probable pathogenic mutation in

Alzheimer’s disease

PSEN2 mutations in Asia

Exon Mutation Country

4 62 Arg>Cys Korea

82 Lys>Arg China

5 141 Asn>Tyr China

123 Pro>Leu China

6 169 His>Asn Korea

China

7 214 Val>Leu Korea

China

PSEN2 mutations in Asia

• PSEN2 mutations seems to be

rare among Asians

• From 2014, mutations were

discovered among Korean and

Chinese patients

• Patient had memory decline in his late 40s w/

problems with disorientation and speaking.

• Known mutation, but 1st in Asia

• Located in the N -terminal region of PS2 protein

PSEN2 Arg62Cys

PSEN2 His169Asn

Discovered in a 50 years old Korean

female patient with EOAD

PolyPhen-2 and SIFT software analyses

predicted this mutation to be a probable

damaging variant

3D model predicted the p.His169Asn may

result in major helix torsion due to histidine

to asparagine substitution.

PSEN2 Val214Leu

• Found in 3 unrelated patients with AD

• In silico software analyses predicted this mutation to be a probable damaging

variant

• 3D model revealed significant structural changes in the region.

Summary

• Several mutations were found in APP, PSEN1 and PSEN2

• However, these mutations appeared only in small % of patients

• A more complex genetic screening should be performed for risk genes or

other genetic factors, involved in neurodegenerative diseases

• Functional studies will be performed to verify the pathogenic nature of

mutations

Future directions

• Cell studies on the variants to find our

their possible role in neurodegeneration

• Transcriptomic analysis

• More deep analysis of WES data to find

possible novel candidate genes for AD

and dementia risk

• Comparison of mutations in AD and

CJD sets

• Screening the family members of AD

patients and compare their data

Thank you for the attention