1. integrative analysis of activity, blood lipids, and ... · scelo et al., 2014 and jelakovic et...
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Steven G RozenProfessor of Cancer & Stem Cell Biology, Duke-NUS Medical School Singapore
Director, Duke-NUS Centre for Computational Biology
Associate Dean of Research Informatics
1. Integrative analysis of activity, blood lipids,
and cardiac imaging in healthy volunteers
2. Widespread exposure to an herbal
medicine mutagen in Asian cancers
Sept 7, 2017Weekly Precision Medicine Forum, Duke University
Part 1 from Weng Khong LIMChief Bioinformatics Lead, PRISM (SingHealth and Duke-NUS Precision Medicine Institute)
Singapore
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• Small: 50 km (31 mi) east-west26 km (16 mi) north-south
• 5.8 million people
• Rich: per capita GDP > US (purchasing power parity, includes non-citizens)
• Good public health
• Life expectancy at birth 85 (US is 79.8)
• Infant mortality: 2.4/1,000 (US is 5.8/1,000)http://kids.britannica.com/comptons/art-55105/Singapore
(From CIA World Factbook, https://www.cia.gov/library/publications/the-world-factbook, Mar 2017)
Duke-NUS Medical School
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• Nonprofit partnership– Duke in North Carolina, USA– National University of Singapore (NUS)– SingHealth, largest public healthcare
provider, 3 hospitals, 3,100 beds• Same campus as National Cancer Centre,
National Heart Centre, National Eye Centre, etc.
• 60 MDs / year• 15 PhD students / year• PhD program in biostatistics and
bioinformatics: tinyurl.com/dnus-ibb
Precision Medicine In Singapore
• Strong interest on the part of Ministry of Health and Ministry of Trade and Industry (Biomedical Research Council)
• There is a National Precision Medicine Alliance
• Research community in process of “self-organizing” with several early-stage initiatives (many are genomics oriented), including PRISM (Patrick Tan will visit in October [?])
• Singapore does not have a single-payor system; EHR not centralized
• Trying to learn from other small countries (e.g. Finland) – “fast follower”
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Part 1
Integrative analysis of activity, blood lipids,
and cardiac imaging in healthy volunteers
Weng Khong LIMChief Bioinformatics Lead, PRISM (SingHealth and Duke-NUS Precision Medicine Institute)
Serum
Lipidomics
Activity/Sleep
Monitoring
(Wearables)
SPECTRA – A Genome/Phenome
Encyclopedia for Asian Patient Normality
Collaboration with National Heart Centre Biobank, SingHEART and
Singapore Infocom Development Authority (PIs : Stuart Cook and Yeo Khung
Keong)
Consented for Research,
Incidental Findings,
and Long Term Follow UpVolunteer
Lifestyle Factors
and clinical tests incl. ECGImaging
Studies
(MRI, Calcium)
Volunteer Characteristics
Characteristic Female (n=137, 58.8%) Male (n=96, 41.2%) Test
Age, years 47.49 (11.44) 44.36 (12.63) 0.051
Ethnicity 0.257
Chinese 127 (92.7) 85 (88.5)
Malay 4 ( 2.9) 3 ( 3.1)
Indian 2 ( 1.5) 6 ( 6.2)
Others 4 ( 2.9) 2 ( 2.1)
BMI, kg/m2 22.68 (3.89) 24.65 (3.98) <0.001
Waist Circumference, cm 78.33 (10.14) 88.54 (10.88) <0.001
SBP, mmHg 122.80 (17.36) 133.81 (15.64) <0.001
DBP, mmHg 72.88 (12.50) 83.12 (11.51) <0.001
RestingHR, (Fitbit, bpm) 70.37 (6.85) 68.72 (6.80) 0.07
ECG HR, bpm 64.87 (9.58) 63.45 (11.13) 0.304
Total Cholesterol, mmol/l 5.33 (1.02) 5.26 (0.85) 0.581
LDL, mmol/l 3.28 (0.84) 3.37 (0.92) 0.471
HDL, mmol/l 1.60 (0.34) 1.33 (0.32) <0.001
Triglycerides, mmol/l 0.98 (0.49) 1.34 (0.88) <0.001
Glucose, mmol/L 5.24 (0.41) 5.44 (0.64) 0.005
DailySteps, (Fitbit, x1000) 10.74 (4.13) 11.00 (3.66) 0.612
Fitbit ActivityClass 0.799
Cat I 14 (10.2) 10 (10.4)
Cat II 57 (41.6) 36 (37.5)
Cat III 54 (39.4) 38 (39.6)
Cat IV 12 ( 8.8) 12 (12.5)
GPPAQ Score 1.25 (1.12) 1.84 (1.15) <0.001
LVM, g 64.13 (14.49) 93.16 (21.29) <0.001
LVEDV, ml 107.79 (16.90) 137.36 (25.37) <0.001
RVEDV, ml 106.21 (19.00) 141.74 (22.65) <0.001
AoF, ml 65.62 (9.37) 78.39 (12.72) <0.001
Volunteer Characteristics
Characteristic Female (n=137, 58.8%) Male (n=96, 41.2%) Test
Age, years 47.49 (11.44) 44.36 (12.63) 0.051
Ethnicity 0.257
Chinese 127 (92.7) 85 (88.5)
Malay 4 ( 2.9) 3 ( 3.1)
Indian 2 ( 1.5) 6 ( 6.2)
Others 4 ( 2.9) 2 ( 2.1)
BMI, kg/m2 22.68 (3.89) 24.65 (3.98) <0.001
Waist Circumference, cm 78.33 (10.14) 88.54 (10.88) <0.001
SBP, mmHg 122.80 (17.36) 133.81 (15.64) <0.001
DBP, mmHg 72.88 (12.50) 83.12 (11.51) <0.001
RestingHR, (Fitbit, bpm) 70.37 (6.85) 68.72 (6.80) 0.07
ECG HR, bpm 64.87 (9.58) 63.45 (11.13) 0.304
Total Cholesterol, mmol/l 5.33 (1.02) 5.26 (0.85) 0.581
LDL, mmol/l 3.28 (0.84) 3.37 (0.92) 0.471
HDL, mmol/l 1.60 (0.34) 1.33 (0.32) <0.001
Triglycerides, mmol/l 0.98 (0.49) 1.34 (0.88) <0.001
Glucose, mmol/L 5.24 (0.41) 5.44 (0.64) 0.005
DailySteps, (Fitbit, x1000) 10.74 (4.13) 11.00 (3.66) 0.612
Fitbit ActivityClass 0.799
Cat I 14 (10.2) 10 (10.4)
Cat II 57 (41.6) 36 (37.5)
Cat III 54 (39.4) 38 (39.6)
Cat IV 12 ( 8.8) 12 (12.5)
GPPAQ Score 1.25 (1.12) 1.84 (1.15) <0.001
LVM, g 64.13 (14.49) 93.16 (21.29) <0.001
LVEDV, ml 107.79 (16.90) 137.36 (25.37) <0.001
RVEDV, ml 106.21 (19.00) 141.74 (22.65) <0.001
AoF, ml 65.62 (9.37) 78.39 (12.72) <0.001
Physical Activity Questionnaire
Left ventricular mass, g
Left ventricular end-diastolic vol. ml
Right ventricular end-diastolic vol. ml
Aortic forward flow, ml
Wearable Activity Tracker Data Collected
•Step counts (15-minute resolution)
•Heart rate (5-minute resolution)
•Sleep sessions (session start/end time)
• Volunteers tracked for:•Average of 5 days•With 3 days of complete data
Wearable activity trackers provide insights on behavioral and demographic stratification of volunteers --3 clusters based on daily activity patterns
High activity
Low activity
Clu
ster
Mid
Day
PM
A
M
Average of Each Activity Cluster
Association between Age and Activity Cluster
* (p < 0.05)
** (p < 0.01)
Dai
ly s
tep
s (1
,00
0s)
Relationships among Daily Steps, Age and
Gender
Wearable activity trackers correlate with
clinical heart rate measurements and self-
reported activity levels
Ele
ctro
card
iogr
amR
esti
ng
HR
(b
pm
)
Activity Tracker Resting HR (bm)
Trac
ker
HR
(b
pm
)
Self-reported activity level
Association of Daily Steps with
Cardiovascular and Metabolic Disease Risk Markers
OR for each additional 1000 steps
High Fasting Blood Glucose
Association of Activity Tracker
Resting Heart Rate with Cardiovascular and
Metabolic Disease Risk Markers
OR for each additional BPM
High Fasting Blood Glucose
Association of Cardiac Remodeling with
Daily Steps Activity
Left Ventricular MassLeft Ventricular
End-Diastolic Volume
Association of Cardiac Remodeling with
Daily Steps Activity
Right VentricularEnd-Diastolic Volume Aortic Forward Flow
Consistent with Previous Larger Study
Association with on Cardiac Remodeling
Lipidomics: Sphingolipids Correlated with Daily Steps
SphingolipidDailySteps (x1000) FBG
p-value β rs p-value β rs
Cer(d18:1/20:0)* 0.002 -0.073 -0.284 0.031 0.112 0.208
Cer(d18:0/20:0) 0.004 -0.066 -0.282 0.434 0.044 -0.001
Cer(d18:1/24:1(15Z)) 0.004 -0.067 -0.278 0.391 0.045 0.083
Cer(d18:1/18:0)* 0.005 -0.071 -0.305 0.024 0.112 0.197
Cer(d18:0/24:1(15Z)) 0.009 -0.062 -0.268 0.502 0.035 0.042
Cer(d18:1/16:0) 0.013 -0.061 -0.270 0.575 0.028 0.117
Cer(d18:1/22:0) 0.014 -0.060 -0.277 0.055 0.095 0.197
SM(36:0)* 0.015 -0.056 -0.233 0.024 0.123 0.204
Cer(d18:1/24:0) 0.023 -0.053 -0.204 0.188 0.067 0.081
SM(36:1)* 0.027 -0.051 -0.202 0.045 0.109 0.189
GlcCer(d18:1/16:0) 0.043 -0.043 -0.175 0.066 -0.113 -0.144
SM(36:2)* 0.048 -0.045 -0.211 0.021 0.125 0.215
Cer, ceramide; SM, sphingomyelin; GlcCer, glucosylceramide
Lipidomics: Sphingolipids Correlated
with Daily Steps and Blood Glucose
Cer, ceramide; SM, sphingomyelin; GlcCer, glucosylceramide
Conclusions
This proof of concept study looked at activity questionnaire and clinical lab tests, consumer grade wearable activity trackers, cardiac imaging, serum lipidomics
Consumer grade activity trackers provide useful data linked to other information
Activity tracker resting heart rate seems more informative than daily steps (integrates activity and other parameters over months / years?)
Acknowledgements
PRISM
• Patrick Tan (PI)• Stuart Cook (PI)• TEH Bin Tean• Steve Rozen• Sonia Davila• Teo Jing Xian• YANG Chengxi• Chris Bloecker• LIM Jing Quan
National Heart ResearchInstitute Singapore andNational Heart Centre Singapore
• YEO Khung Keong (PI)• Calvin Chin• Anders Sahlen• Tan Swee Yaw• Jonathan Yap• Edmund Pua• Kong Siew Ching (CRC)• Ho Pei Yi (CRC)
Part 2
Widespread exposure
to an herbal medicine mutagenin Asian cancers
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Herbal remedy – contains aristolochic acids and related compounds – collectively “AA”
Aristolochia PlantsHerbal remedies
Aristolochic acid IAA
(multiple variants)
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AdenineDNA adducts,
Adenine > Thymine mutations
Adapted from Poon et al, Science Translational Medicine, 2013
Also a nephrotoxin –causes kidney failure
Mutation signature analysis enabled by cheapnext generation sequencing of cancer genomes
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htt
p:/
/ww
w.g
eno
me.
gov/
seq
uen
cin
gco
sts/
Co
st p
er h
um
an g
eno
me
(US
$)
Year
$10 millionIn 2007
$1.5 thousandtoday
6,000 Xdrop in price
Mutational signature in an AA-exposed upper tracturothelial carcinoma (UTUC)
30Poon et al, Science Translational Medicine, 2013
CAG>CTG
CAA>CTATAG>TTG
Transcriptional strand bias
T > A ontranscribedstrand
T > A On NONtranscribedstrand
A few years ago:AA exposure in upper tract urothelial cancer
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Upper Tract Urothelial (Taiwan)
A year ago: AA exposure in multiple tumor types
Upper Tract Urothelial (Taiwan)
Bile duct (Singapore)
Liver (China)
Poon et al., 2013 and subsequent data (HCC)Zou et al., 2015 (CCA)Scelo et al., 2014 and Jelakovic et al., 2014 (RCC)Poon et al., 2013, Hoang et al., 2013 (UTUC)Poon et al., 2015 (Bladder)
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Kidney (Taiwan)
Bladder (Taiwan)
Why look for AA exposure in Taiwan liver cancer?
• AA signature in Taiwan
– Upper tract urothelial
– Bladder
– Kidney
• AA signature in other geographical regions in
– Liver (China)
– Bile duct cancer (China, Singapore)
– Kidney (Balkans)
• Taiwan a likely hotspot for AA exposure, but liver cancer not examined
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AA signature in Taiwan HCCs
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Principal components analysis shows many Taiwan HCCs have spectra similar to AA bladder and AA UTUC from Taiwan
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Overlays of mutations due to different exogenous mutagens or endogenous mutagenic processes-- Computational separation
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Bladder spectrum from Poon et al, Genome Medicine, 2015
AA
Overlays of mutations due to different exogenous mutagens or endogenous mutagenic processes-- Computational separation
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Bladder spectrum from Poon et al, Genome Medicine, 2015
AA
+ ABOBEC signatures
+ background signature
Non-negative matrix factorization andrelated approaches
New statistical approach
• mSigAct (mutational signature activity)
• Determines whether the observed mutations are significantly better explained with a contribution from the AA mutational signature than without
• Uses likelihood ratio test – compares likelihood under
– Null hypothesis: AA signature did not contribute to the observed mutations
– Alternative hypothesis: AA signature did contribute to the observed mutations
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78% of Taiwan liver cancers have the AA signature
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78% of Taiwan liver cancers have the AA signature
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78% of Taiwan liver cancers have the AA signature
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How extensive is AA exposure in liver cancer? • A great deal of publicly available somatic mutation data from
liver cancers
• Examined somatic mutations from 1,400 HCCs
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43
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Proportions of liver cancers with AA
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Numbers of mutations due to AA (log scale)
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Taiw
an
Ch
ina
SE A
sia
Vie
tnam
Kore
a
Jap
an
No
rth
Am
eri
ca
Euro
pe
May
o C
linic
No
info
rmat
ion
Asia, especially Taiwan most affected
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Non-molecular evidence thatAA exposure might be more widespread
• India / South Asia, Aristolochia indica plants used in traditional medicine (population > 1 billion)
• South / Central America, Aristolochia plants used in traditional medicine; extent unclear
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Evidence of use of AA-containing plants in South Asia
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Evidence of use of AA-containing plants in South Asia
Cultivated AA plant or AA plant
product purchased in market
AA inCentral American “snake bottle”
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Photograph by Donald HallUniversity of Florida
Aristolochia trilobata Battus polydamas
Photograph: Kimera Corporation
AA
AA containing plants readily available on the internet
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Theoretically banned/restricted but multiple plant species and parts readily available on web(广防己, guǎng fáng jǐ)
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漢防己/汉防己, hàn fáng jǐ(Stephania – no AA)
Theoretically banned/restricted but multiple plantspecies and parts readily available on web(马兜铃mǎ dōu líng)
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Asarum sp. 细辛, xì xīn
2017 07 19
http://qiherbs.com/xi-xin.html
Clinical implications of widespread AA exposure
• Primary prevention (avoiding AA)
– Regulation, education
– Possible: unlike tobacco, presumably non-addictive
– Possible: unlike aflatoxin, ingested deliberately
• Secondary prevention: focused screening for people with known or likely exposure based on
– Geography
– Use of AA-containing remedies
– Kidney failure
– Previous AA-related cancer (e.g. based on signature)
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Part 2 AcknowledgementsSingapore (Duke NUS, National Cancer Centre Singapore, and others)Song Ling PoonWillie YuMi Ni HuangAlvin NgApinya JusakulJohn McPhersonSwe Swe MyintLay Guat NgJohn SP YuenPatrick TanBen Tean TehAlex Chang
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Chang Gung Memorial HospitalJacob See-Tong PangSen-Yung HisehHao-Yi HuangMing-Chin YuYing-Hsu ChangKai-Jie YuKwai-Fong NgChing-Fang WuCheng-Lung HsuCheng-Keng Chuang
FundingSingapore National Medical Research Council; A*STAR and the Singapore Ministry of Health through the Duke-NUS Signature Research Programs; Singapore Millennium Foundation; Lee Foundation, the National Cancer Centre Research Fund; The Verdant Foundation; Cancer Science Institute Singapore
END
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Non negative matrix factorization (NMF)
Mutation signaturesMutations
contributed by
each signature
Mutations not
present in the
reconstructed
catalog
Observed somatic
mutation catalog of a
tumor genome
W X
≈N signatures
96
mu
tati
on
typ
es
96
mu
tati
on
typ
es
N s
ign
atu
resT tumors
T tumors
Level of exposure of 1 tumor to 1 signature
H
V (observed mutations)
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Important points on NMF
• NMF is only a tool – best (lowest error) approximate factorization does not necessarily correspond to any biological reality
• Models derived by NMF should be useful – provide information on exposures or mutational processes; "All models are wrong but some are useful.“1
• Signature extraction and activity (exposure) assignment are separate; can have good signature extraction but poor activity assignment, because factorization is usually underdetermined
• Must combine NMF with additional information to find useful models
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1 George E. P Box, G. E. P. (1979), "Robustness in the strategy of scientific model building", in Launer, R. L.; Wilkinson, G. N., Robustness in Statistics, Academic Press, pp. 201–236.