Transcript Understanding the Complexity of Genes and

UNDERSTANDING THE COMPLEXITY
OF GENES AND DISEASES IN
INDONESIAN ARCHIPELAGO
Herawati Sudoyo
Eijkman Institute for Molecular Biology
Jakarta, Indonesia
Health systems complexity: Bridging Physiome with Health Care through
Computational Modelling Symposium, NITH-NTU, Singapore, 26 January 2015
GENNEKA TUNGGAL IKA
Unity in diversity
Indonesia and Infectious Diseases – a Great
Challenge to Mitigate Biorisk
 Problems with emerging and
reemerging infectious diseases
 Most caused mainly by environmental,
ecological or demographic factors
spread by travel and trade – Indonesia
is a maritime country with 17.504
islands, 700 languages, 33 provinces,
230 million population
Problems with people movement
Recognize the need to develop, strengthen and
maintained the capacity to detect, report and respond to
public health events
WHAT ARE WE FACING?
Indonesia – A very diverse populations –
vast genome diversity – disease
management complex
Indonesia - A rapidly developing country
with serious challenges in infectious
(emerging and re-emerging) and zoonotic
diseases
New, re-emerging or drug-resistant
infections whose incidence in humans has
increased within the past two decades or
whose incidence threatens to increase in
the near future
Indonesia – A rapidly developing country
with serious problems in Infectious disease
Malaria:
15 million cases and 42,000 deaths/year (2005) - highest
case number and fatality rate in the world; increasing drug
resistant parasites
Tuberculosis:
ranked third in TB burden following India and China - TB is
third major causes of mortality
Estimation: 269 TB cases/100,000
Dengue:
Most important viralborne disease
2004: 78,690 cases (CFR- 1.2%)
2007: 123,174 cases,1,251 deaths
Hepatitis B:
10% of population are carriers
Moderate-to-high endemic (WHO)
DENV SEROTYPE DISTRIBUTION – SHOWED DIVERSITY
Management of Disease is Not Simple, Need a Strong Disease Surveillance
250000
C A S E
200000
150000
100000
50000
0
1985 1986 1987 1988 1989 1990 1991 1992 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006
Indonesia
South-east Asia Region
Palembang 1998
Jayapura 1994
Jakarta 2004
8%
8%
Yogyakarta 1996
20%
19%
Bandung 2002
Four antigenically distinct serotypes:
infection with one serotype does not
provide protection to the other three
42%
41%
30%
32%
Makassar 2007-2008
N = 111
Corwin 2001; Suwandono 2006; Porter 2005; Graham 1999; Richards 1997; Sukri 2003
Merauke 2001
4 1
3 2
Serotype Legend
SCIENCE & TECHNOLOGY IN HEALTH SECURITY –
PREPAREDNESS FOR PANDEMIC
RISK ASSESSMENTS
 Molecular Epidemiology:
• Cluster of viral isolates will indicate
the presence of new strain
• Surveillance - tracing sources of
infection
 Characteristics of Virus
• Alteration of interaction with host
receptors - pandemic need changing
in specificity of viral type receptor
into human-type
• Change of virulence
• Drug resistance
ALL ABOUT COLLABORATION
• Interdisciplinary collaboration between genetics,
language, culture and medicine
Medicine
Anthropology
Archeology
Linguistic
Genetics
Mathematic
THE AUSTRONESIAN DIASPORA
WMP
OCEANIC
WMP
SHWNG
CMP
PAPUA
OCEANIC
 One of the world largest language group.
 Covers a very wide area, from Madagascar Island as the
western most to the Easter Island of Polynesia
Eijkman Institute
EIJKMAN INSTITUTE and THE
POPULATION STRUCTURE of the
INDONESIAN ARCHIPELAGO
• More than 6,000 samples collected
• More than 3745 individuals from 35 ethnic
populations examined for mtDNA
• 2000 genetic samples from 25 isolated populations of
13 islands for Y STR
• Most extensive database on mtDNA sequence
polymorphisms in Indonesian archipelago
• Pan Asia SNP initiative – mapping 50K Asian
population using DNA microarray – 234 Indonesian
samples
• 200 male samples of Javanese and Batak origin for
Rapidly Mutating YSTR
• Forensic population database – STR marker 21 loci, Y
filer
 MtDNA and Y chr diversity of
2740 individuals, 70
communities, 12 islands
 Indonesian genetic diversity
is a direct outcome of
complex history of
immigration, transitory
migrants and populations
Tumonggor et al. J Hum Genet. 2013: 58
SETTLEMENT of ISLAND SOUTHEAST ASIA
THE FIRST WAVE: FROM AFRICA TO THE EAST
~50,000 ya
Mellars P (2006). Science
The first stage of Indonesian prehistory represent
the archipelago’s initial settlement as part of Africa
dispersal ~ 50kya
SETTLEMENT OF ISLAND SOUTHEAST ASIA
THE SECOND WAVE: THE AUSTRONESIAN EXPANSION
~8,000 ya
Taiwan ~6,000 ya
Austronesians
Polynesia
Madagascar
~50,000 ya
Neolithic movements into and around island SEA – may
involve population dispersals from (into) Taiwan, and
between Indonesian island groups
 The largest survey of Indonesian Y chromosome showed
the presence of multiple genetic strata that likely arose
through a series of distinct migratory process
 Paternal gene pool subdivided eastern and western part of
Indonesia
• 1928 individuals - 73 populations, 11 language families
• Autosomal marker 50K - HUGO Pan-Asian SNP Consortium -.
Science 326, 1541 (2009)
• Autosomal data strongly support large demographic
movements of Asian populations into eastern Indonesia
from around 4 kya (Xu et al & HUGO Pan-Asian SNP Consortium,
PNAS 109, 4574 (2012)
East Papuan and Alorese
Sumba, Flores, Lembata
Malay,Sumatra, Borneo,
Java (Mix with
Austroasiatic)
VARIATION OF
GENOTYPIC PATTERN OF DISEASES
HEPATITIS AND OVALOCYTOSIS AS A MODEL
•
•
•
Variation of ethnics in Indonesia:
1. The peopling of the Indonesian archipelago
using mitochondrial-DNA, Y and autosomal
chromosome
2. Anthropological and linguistic study Consistent with cultural and linguistic
characteristics
Variation of susceptibility and resistance to
disease (malaria, TB and others)
Variation of genotypic and phenotypic pattern of
diseases (infectious and non-infectious,
including hepatitis B/C, dengue,red blood cell
disorders )
HEPATITIS B VIRUS
GENETIC HETEROGENEITY
 Ten HBV genotypes - A to J have been identified
worldwide
 Shows different geographical distribution, viral
characteristics and possibly clinical outcomes and
response to treatment, , provide historical information
pattern of the local population
A: North-west Europe, North America, Central Africa; B: Southeast Asia; C: Far east; D:
Mediteranean, Middle East, India; E: Sub-Saharan Africa; F: American natives, Polynesian;
G.USA samples, H: Mexico
Miyakawa & Mizokami, Intervirology 2003;46:329-338
• Indonesian Archipelago:
Genotypes B and C are predominant, with subgenotype B3/adw unique to Indonesia
• Latin America:
Genotypes F and H are indigenous in this continent,
genotypes A and D might be a mere reflection of a past
European migration, and genotypes B and C could
represent a consequence of a recent Asian migration.
HEPATITIS B VIRUS GENOTYPE DISTRIBUTION IN
INDONESIAN ARCHIPELAGO
Nanning Shanghai
Korea
Hongkong
Japan
Taiwan
Bangkok
Chinese Indonesian
Philippines
A1
Medan
C1
C2
East Asia
Padang
Kotamoba
gu
C5 Philippines
Dayak
Benuaq
B1 Japan
Mandar,
Toraja
B2 China
B3 West Indonesia
B5 Philippines
Alor
Nias &
Mentawai
B9
Merauk
e
Nusa Tenggara
islands of Indonesia
Java
East Flores
Mataram
D1
D3
Jayapur
a
Sentani
Kajang,
Makasar
B7
B8
Ternate,
Ambon
Sumba
West Flores
A
100
100
68
100
100
B
100
100
97
92
100
100
AB033553C2
AB113879C2
AB202071C2
AP011098C2
X01587C2
92
92
C
100
D
100
99
G
100
100
F
100
100
0.02
H
E
100
AB032431E
AB205129E
AB106564E
X75657E
AB064311G
AB064312G
EF634480G
AB056513G
AB086397F1
AF223963F1
AF223962F2
AF223965F2
AB166850F2
AB214516F2
AY090455F1
AB179747H
AB205010H
AB266536H
AB059660H
100
100
Inuit populations in Arctic
Japanese, east Asia
B1
B2
B3
B7
B9
B5
B8
B4
C1
C2
Chinese, Asia mainland
Indonesian populations, Southeast Asia
Indonesian populations, Southeast Asia
Indonesian populations, Southeast Asia
Philippino and Indonesian populations, Southeast Asia
Indonesian populations, Southeast Asia
Vietnamese, Southeast Asia
East Asia, China mainland and Southeast Asia
East Asia, China mainland and Southeast Asia
PhLC14C5
PhLC03C5
AB241112C5
100
AP011101C5
AP011099C5
AP011100C5
PhCH24C5
M154
AP011105C7
AP011104C7
AP011107C7
AP011106C7
96
AP011108C
J022
STN013
AB493837
AB493847
AB493838
100
AB493840
AB493839
AP011102C6
AB105172
AB493844
AB493843
AB493842
100
AB493841
100
AP011103C6
M007
X75656C3
X75665C3
100
AB048705C4
AB048704C4
100
AF280817D1
AY161157D1
100
AY161150D1
M73D1
AF151735D1
100
AB078032D2
AB078033D2
AB090268D2
AB090269D2
100
100
AY090452D3
AB493848.
AB493845
AB493846
DQ315776D3
100
DQ315777D3
100
AB048702D4
AB048703D4
100
AB048701D4
AB033559D4
92
92
B6
AP011089B7
AB493833
100
AB493835
AB493836
AB493832
EIHB134B3
AB033555B3
AP011085B3
AB033554B3
D00331B3
2059B3
1839B3
M54923B3
LBY01B7
100
LBY041B7
Alr049B7
AP011090B7
LBY009B7
AP011091B7
FLT32B7
AP011092B7
100
KD048B7
CBL027B7
100
LAR070B7
AP011088B7
FLT020B7
100
AB493830
AB493828
AB493829
AB493827
AB493831.
100
KDI35B8
KDI43B8
100
KDI04B8
KD35B8
AB219426B5
AB219429B5
100
AB219427B5
AB219428B5
AP011087B5
100
AP011086B5
PAN09B9
PAN011B9
Alo36B9
100
PAN01B9
PAN037B9
AP011096B8
AB493834
100
AP011093B8
AP011095B8
100
AP011094B8
AY033073B4
AY033072B4
AB100695B4
AB073835B4
AB112066C1
AB112348C1
AB112471C1
AB074756C1
EIHB006C1
AP011097C1
SLK-126
92
92
A1
A2
DQ463787B6
DQ463790B6
DQ463791B6
DQ463792B6
DQ463788B6
DQ463793B6
DQ463794B6
DQ463789B6
D23678B1
AB073850B1
AB073848B1
D00329B1
DQ993700B2
EU139543B2
DQ993708B2
EIH21AB2
2061B2
DQ993711B2
EIH45AB2
AP011084B2
92
100
AY226578
M57663A1
AB246335A1
AB241115A1
AF297621A1
X70185A2
AB222707A2
AB126580A2
AB246337A2
100
C5
C7
C6
Philippino, East Asia
Indonesian populations, Southeast Asia
Indonesian populations, Southeast Asia
C3 Polynesia, New Caledonia, Pacific region
C4
Aborigine populations, Southern Australia
D1
D2
D3
D4
E
G
F1
F2
H
Figure 2
a
*
* Indonesian of Chinese ethnic origin
B9
B7
B5
B3
B9
B7
B3
Makasarese
C2
B2
C2
C1
B7
B5
B3
C5
C2
C1
Torajan and Mandar
Batak
b
C5
B3
C1
Minahasa
and Talaud
B7
Ternate and Ambonese
B9
B8
B5
B3
Nias and Mentawai
B9
B8
B5
B3
B2
C2
C1
Minang
B3
C2
Malay
B9
B7
B5
B9
B8
B3
C1
B5
B3
B2
Javanese
C2
C1
Indonesian of Chinese ethnic origin
B9
B2
B9
B7
B5
B3
B8
B3
C1
Balinese and Lombok
B7
B5
C2
C1
Sumbanese
B9
B8
B7
B5
B3
Flores
C2
C1
Alorese
C6
B7
C2 B3
C1
C2
C1
Papuan
HBV genotype is maintained in Javanese
ethnic population separated for centuries
HBV/B3 (adw)
Javanese
(Holland)
Javanese
(Suriname)
Javanese
(Java)
TWO TYPES HBV/C SUBGENOTYPES: THE ASIAN AND PAPUA-PACIFIC
(study on HBV isolates from the Asia-Pacific Region)
Papua-Pacific
GQ358156
AB493842
AB493840
GQ358155
AB493844
AB493838
AP011103
AB493837
AB493841
AP011105
AB493839
AP011104
GQ358157
AP011102
AP011107
AP011108
EU670263
AP011106
AP011099
7
AP011101
X75656
6
9
X75665
3
AB048705
North
Australia
8
4
AP011100
PhLC14
AB048704
H
5
AB266536
PhLC03
10
AB241112
PhCH24
AB540583
2
1
AF223957C1
AB202071
EAST ASIA
AND SEA
AP011098
AP011097
AY247031
AB113879
AB112471
AB033553
AF533983
AB074756
D23681
AF068756
X01587
AB112066
100
AB112348
AF223960
HBV genotype is maintained in Javanese
ethnic population separated for centuries
• Subgenotypes of HBV/B
in Indonesia:
– B3 (adw)
– B5 (adw)
– B7 (ayw)
– B2 (Chinese
Indonesian)
DNA Sequence:
• Subgenotypes of HBV/B
in Japan (Sugauchi et al):
– Bj
– B2 (Ba: prevalent in China)
Maintained Viral
Characteristics
In Chinese ethnic
population*
Clinical Implications?
*Have been living in
Indonesia for > 3
generations
CLINICAL AND PUBLIC HEALTH SIGNIFICANCE:
Detection failure of HepB virus in blood donors
309 regular blood donors (2005) from Medan (North Sumatra)
and Solo (Central Java) (HBsAg, anti-HCV and anti-HIV neg)
• anti-HBc (+) : 134 (43.4%)
• HBV DNA (+): 25 (8.09%)
• Variants were detected in 7 samples: T123A (1), M133L (1),
T143M (7)
‘a’ determinant (124-147)
Thedja MD et al. 2010. Occult hepatitis B in blood donors in Indonesia: alter
antigenicity of the hepatitis B virus surface protein. Hepatology Int.4, 608
• Malaria - caused by Plasmodium parasites- is
responsible for high mortality mortality. An
estimated 300-500 million cases each year result
in more than 1 million deaths
• Available preventive methods are not sufficient
• Humans have a number of genetic adaptations
that act to combat Plasmodium
• Understanding the mechanism of malaria
interactions with the erythrocytes membrane will
provide opportunities for new methods of disease
prevention and treatment
Rank
49
Country
INDONESIA
Mortality Rate
3.1
MALARIA AS A SELECTIVE AGENT IN HUMANS
Duffy negativity,
G6PD deficiency (A-),
HbS, HbC
WHO 2005
SAO, HbE,
Gerbich negativity,
α-thalassemia (many),
G6PD deficiency (many)
COMMON THEMES AMONG MALARIARESISTANCE ALLELES EXAMINED to DATE
(G6PD A-, HBC, HBS, DUFFY NEGATIVITY, HBE)
1) Recent origins (<<30,000 years)
2) Strong selection coefficients
3) Compatible with “Malarial Eve” Hypothesis
SOUTHEAST ASIA OVALOCYTOSIS
•
•
•
•
An uncommon variant of hereditary elliptocytosis
Caused by heterozygosity for a 27 bp del in the gene
encoding the erythrocyte membrane protein band 3
– the solute carrier family 4 (SLC4A1) protein on
chromosome 17
SAO erythrocytes are rigid because mutation
enhances the tightness of association between band
3, ankyrin and the spectrin lattice
The condition confers highly specific protection
against cerebral malaria
 Erythrocyte membrane contain variety of proteins –
(i) peripheral proteins of bands 1, 2, 4.1, 4.2, 5 and
6, and (ii) integral proteins of bands 3, 7 and PAS
1 - 4.
 Mutation in SLC4A1 gene enhances the tightness of
association between band 3, ankyrin and spectrin
lattice
SAO PROTECTS FROM MALARIARELATED MORTALITY.
• Strong correlation between SAO and malaria
prevalence (Mgone et al. 1996).
• Case-control studies suggest strong
(complete?) protection from cerebral malaria
(Genton et al. 1995, Allen et al. 1999).
SAO is A BALANCED POLYMORPHISM
 Heterozygote has greatly enhanced fitness
in malarial environments.
Heterozygotes have no negative clinical manifestations.
 SAO homozygote is inviable
When SAO is common, it can demonstrably increase
the miscarriage rate (Liu et al. 1994)
 SAO as a health burden
One in for of the pregnancies in these couples will be
lost due to SAO inviability.
With random mating 12.25% (=0.35x0.35) of couples
will both be heterozygous carriers of SAO.
SAO HAS A RESTRICTED
GEOGRAPHIC DISTRIBUTION.
GEOGRAPHICAL DISTRIBUTION of SAO in
INDONESIAN ARCHIPELAGO (as 2014)
0
0
4.6
8.6
1.8
0
3.3
4
6.6
4.6
0
0
0.9
30
27.2
11 0
2.6
20
1.4
2.9
10.5 13.4
0
FREQUENCY OF SAO VARIES SIGNIFICANTLY IN
DIFFERENT POPULATIONS (not revised)
Africa
13.4
Alor
27
Irian
Batak
0
Java
0
0
Makassar
2.9
Sasak
0
Bugis
0
Minahasa
10.5
Sumba
Sumbawa
0
Toraja
0
6.6
Kaili
0.9
Banjar
4.6
Palembang
0
Tengger
Dayak
3.3
Minang
1.8
Malay (P’baru)
0.1
8.6
Bali
1.4
0
10
20
FREQUENCY OF SAO (%)
30
Eijkman Institute
DISTRIBUTION OF PAPUAN GENETIC
CONTRIBUTION AND SAO PREVALENCE
SAO Prevalance (%)
50
40
 SAO is not
found in nonendemic area for
malaria; but not
all endemic area
shown SAO
30
20
10
0
0
5
10
15
20
25
30
Papuan Genetic Contribution (%)
•SAO is found mainly in two clades: a. Malay-related (low
prevalence) and b. Papuan-related (high prevalence)
Models of Coevolution between Plasmodium and
Humans May Need to Accommodate the
Existence of Ancient Malaria-resistance Alleles
P. falciparum emerges as
health threat ~10,000
years before present.
SAO likely evolved after
expansion of P. falciparum into
Southeast Asia.
FUTURE STUDY
 Bringing human and medical genetics and
computational biology together – to answer
the big question on how culture shaped the
human genome
 The answer is in your hands
Medicine
Anthropology
Archeology
Linguistic
Genetics
Mathematic
Acknowledgment
Steve Lansing, Complex Institute, NTU
Murray Cox and Elsa Guillot, Massey University, New
Zealand
Tatyana Karafet, University of Arizona
The HUGO Pan-Asian SNP Consortium
EIJKMAN INSTITUTE
David Mulyono,
Meta Dewi Tedja
Din Syafruddin
Helen Suryadi
Safarina Malik
Gludhug Purnomo
Windy Joanmawati
Alida Harahap
Dewi Megawati
Thank you and greetings from Indonesia