A Trans-Kingdom Perspective
Skip Virgin
Pathology and Immunology
Washington University
School of Medicine
Saint Louis, Missouri USA
NIH, NIH Center for Excellence in Translational Research, NIH Primate Infectious Disease Resource,
Crohns and Colitis Foundation, Juvenile Diabetes Research Foundation
Chandni Desai
Lindsay Droit
Scott Handley
Guoyan Zhao
Tiffany Reese
UTSW
Megan Baldridge
WUSM
Tim Nice
OHSU
Outline
Virome- concept
Virome- substantial physiologic effects
Transkingdom interactions- components
of the microbiome cannot be considered in isolation
Potential transkingdom interactions in humans?
Can we improve mouse models
with this knowledge?
Resistance
to infection
and tumors
IFN
Chronic
Herpesvirus
Virome
Immunophenotype
GenotypePhenotype
Relationship
Atg16L1
Chronic
Norovirus
Susceptibility
to genetic
disease
Cadwell 2008 Nature 456:259
Cadwell 2010 Cell 141:1135
Resistance
to infection
and tumors
IFN
Chronic
Herpesvirus
Virome
Immunophenotype
GenotypePhenotype
Relationship
100
80
n=15
60
40
20
0
n=15
0
5
10
15
20
Day Post Listeria Challenge
Mock
Percent survival
Percent survival
100
80
60
n=10
40
n=10
20
0
10
20
Day Post Listeria Challenge
Latent HV68
Hoil-1-/-
Hoil-1-/-
Toxoplasma
gondii
Highlysusceptible
Listeria
monocytogenes
Highlysusceptible
Hoil-1-/-
Mycobacterium
tuberculosis
Resistant
Hoil-1-/-
MHV68
Resistant
MHV68
Day 28
Challenge with L.
monocytogenes
Resistance
to infection
and tumors
IFN
Chronic
Herpesvirus
Virome
Immunophenotype
GenotypePhenotype
Relationship
Atg16L1
Chronic
Norovirus
Susceptibility
to genetic
disease
Cadwell 2008 Nature 456:259
Cadwell 2010 Cell 141:1135
No Trigger
Barrier Raised
Atg16L1
Mutant mouse
Normal Paneth cell
No DSS-induced
villus blunting
MNV
Trigger
DSS-induced
villus blunting
Outline
Virome- concept
Virome- substantial physiologic effects
Transkingdom interactions- components
of the microbiome cannot be considered in isolation
Potential transkingdom interactions in humans?
Can we improve mouse models
with this knowledge?
IL4
Resistance
to infection
and tumors
IFN
IL13
H. polygyrus
Reese 2014 Science 6196:573
Chronic
Herpesvirus
Virome
Immunophenotype
GenotypePhenotype
Relationship
HOIL-1
IFN-
Bacterial
microbiome
STAT-1
IRF3
Atg16L1
Chronic
Norovirus
Susceptibility
to genetic
disease
Cadwell 2008 Nature 456:259
Cadwell 2010 Cell 141:1135
IL4
IFN
IL13
H. polygyrus
Reese 2014 Science 6196:573
Chronic
Herpesvirus
Resistance
to infection
and tumors
Barton 2007 Nature 447:326
White 2010 Blood, 115:4377
Canny 2013 J. Virol. 88:730
PBS
H. polygyrus
Day 7
Day 7
IL4 and IL13 activate the viral gene 50 promoter that is responsible
for triggering reactivation from latency
Transcription of gene 50
n.d.
n.d.
D48
Treat
D5
Image
antiIFN
IL-4c +
IL-4c anti-IFN
6.0
5.0
2.0
1.0
3.0
x10
4.0
HOIL-1
IFN-
Bacterial
microbiome
STAT-1
IRF3
Atg16L1
Chronic
Norovirus
Susceptibility
to genetic
disease
Cadwell 2008 Nature 456:259
Cadwell 2010 Cell 141:1135
CR6
Persistent
CW3
Non-persistent
CR6
0
Day
Analysis
14
CR6
-3 -2 -1 0
Day
Analysis
7
-14
CR6
Analysis
0
Day
14
Outline
Virome- concept
Virome- substantial physiologic effects
Transkingdom interactions- components
of the microbiome cannot be considered in isolation
Potential transkingdom interactions in humans?
Can we improve mouse models
with this knowledge?
250
200
200
200
150
100
Household controls
Ulcerative colitis
Crohn's disease
50
0
0
10
20
30
# of Samples
Ulcerative
colitisUC
N=36
78
42
8
114
40
Crohn's
disease
CD
N=16
64
8
150
100
Healthy controls
Ulcerative colitis
Crohn's disease
10 15 20 25 30
# of Samples
50
0
0
Ulcerative
colitisUC
N=18
29
13
31
107
Crohn's
disease
CD
N=7
71
29
Caudovirales
richness
250
Caudovirales
richness
Caudovirales
richness
Boston USA
Chicago USA
Cambridge UK
150
100
Healthy controls
Ulcerative colitis
Crohn's disease
10 15 20 25 30
# of Samples
50
0
0
Ulcerative
colitisUC
N=11
30
23
35
132
22
38
HHC
Household
controls
N=21
HHC
Healthy
controls
N=23
HHC
Healthy
controls
N=20
Crohn's
disease
CD
N=14
44
19
Disease-specific alteration
in the enteric virome in
inflammatory bowel disease
Norman et al., 2015 Cell 160:447
Virgin 2014 Cell 157:142
Clinical Outcome
1o
Collaborator
Country
Publication
Funding
Partner
IBD
Disease and
exacerbation
Parkes,
Handley
US, UK
CCFA
HIV/SIV
Enteropathy
Kwon
Uganda,
Botswana
NIH
Acquisition risk,
vaginal inflammation
Kwon
South
Africa
NIH
HIV/SIV
Barouch
Thailand,
Africa, US
PND NIH
Rotavirus
Harris
Ghana
--
Gates
T1D
Xavier
Finland
--
JDRF
Host genes
controlling
metagenome
Autophagy genes in
mice
Zhao
US
NIH
Diagnostics
Enteric disease in
monkeys
Lackner
US
NIH
Vaccine
Response
Outline
Virome- concept
Virome- substantial physiologic effects
Transkingdom interactions- components
of the microbiome cannot be considered in isolation
Potential transkingdom interactions in humans?
Can we improve mouse models
with this knowledge?
50
49
169 B6
mice
30
40
21 21
IFN response
IFN response
IL-1 expression
Memory CD8 response
Platelet formation
Coagulation/hemostasis
Wound healing
Tregs/Teffectors
ERK1/ERK2
Inflammation
Macrophage activation
Erythrocyte differentiation
Healthy vs. RSV
infected infant
Healthy vs St. aureus
infected infant
21 21
Outline
Virome- concept
Virome- substantial physiologic effects
Transkingdom interactions- components
of the microbiome cannot be considered in isolation
Potential transkingdom interactions in humans
Can we improve mouse models
with this knowledge?
Genome Databases
Biological Hypotheses
Animal Models
Mechanism
Of Course
Translation
Companion Diagnostics
Training
Chandni Desai
Lindsay Droit
Scott Handley
Guoyan Zhao
Tiffany Reese
UTSW
Megan Baldridge
WUSM
Tim Nice
OHSU
Bioinformaticsvirus
DNA + RNA
http://www.nature.com/nature/journal/v
534/n7606/images_article/nature18285f2.jpg
Controlling for
microbiome in
experiments
Additional
possible
tests
Computational
challenges for defining
the virome
Virgin, 2014 Cell 157:142
Sequences
Viruses
PCR
Confirmation
Key Findings:
Expansion of enteric virome
Many novel viruses
Confirmed by PCR
Adenovirus-induced epithelial
pathology
Enteric parvoviruses in
circulation
What is the Role of the Virome?
AIDs enteropathy?
Barrier breakdown?
PAMPS/antigens into tissue?
Systemic immune activation?
Progression to AIDS?
HV68/MHV68
Gammaherpesvirus
Genome/genes related to KSHV and EBV
Acute infection cleared by 12-14 days
Latency in B cells, macrophages, dendritic cells
Latency regulated by IFN and IL-4
LPD/Lymphoma
T and B cell
Immunity
Vasculitis
MHV68
28
Days
Celiac
Crohns
MS
WT
vs
WT + MNV
16HM
WT
16HM
Atg16L1HM
vs
Atg16L1HM + MNV
Immunoglobulin A (IgA)
IgA dimer
and secretory
component
Epithelial cell
poly-Ig
receptor
(Pigr)
Prevents bacterial
translocation
IgA
Protective in dextran
sodium sulfate (DSS)
challenge
Murthy et al. J. Gastroenterol. Hepatol. 2006.
Reikvam et al. Eur. J. Immunol. 2012.
low
high
high
low
low
low
low
+
Cohouse
14 days
low
low
Fecal
Transplant (FT)
high
Filtration
low
high
low
FT
high
low
WT
FT
high
low
Pigr-/-
FT
high
low
DSS effects appear to depend on IgA status and not the microbes themselves.
Moon, Baldridge et al. 2015. Nature. 521:90
# of
Adenovirus
readsa
WUHARV
Adenovir
usa
PCR
screena,b
Adenovirus
Enteritisc
SI
Adenoviru
s IHCc
LI
Adenovirus
IHCc
Other GI Pathologiesc
23
889
1,
othersd
Pos
Yes
Pos
Neg
Cytomegalovirus enteritis
25
26
27
0
0
n/a
n/a
Neg
Neg
No
No
Neg
Neg
Neg
Neg
653
5,
othersd
Pos
Yes
Pos
Neg
No
No
Balantidium typhlitis
14
1
0
52
4
0
0
othersd
othersd
n/a
othersd
othersd
n/a
n/a
Neg
Neg
Neg
Neg
Neg
Neg
Neg
No
No
No
No
No
No
No
Neg
Neg
Neg
Neg
Neg
Neg
Neg
Neg
Neg
Neg
Neg
Neg
Neg
Neg
640
othersd
Pos
Yes
Pos
Pos
29
30
31
32
33
37
38
41
B:Histologyfromanimal23
No
No
Balantidium sp. colitis
No
No
No
Balantidium sp. colitis
Balantidium sp.
typhlocolitis
C:Histologyfromanimal27
Week 32
or necropsy
Week 5
Week 32
or necropsy
Axis2[11.4%]
Axis1[19.6%]
Hoil-1-/-
Hoil-1-/-
Toxoplasma
gondii
Highlysusceptible
Listeria
monocytogenes
Highlysusceptible
Hoil-1-/-
Mycobacterium
tuberculosis
Resistant
Hoil-1-/-
MHV68
Resistant
Day 28
Harvest serum
for quantitation
of cytokines
MHV68
p<0.01
p<0.01
p<0.01
Addenbrookes
Cambridge UK
Miles Parkes
34 Subjects
17 Household controls
11 UC, 6 CD
73 Samples,
Many longitudinal
MGH, Boston
Ramnik Xavier
Dirk Gevers
45 Subjects
20 Controls
11 UC, 14 CD
45 Samples
None longitudinal
Rush, Chicago
Ali Keshvarzian
Ece Mutlu
42 Subjects
23 Controls
18 UC, 7 CD
48 samples
Few longitudinal
CD-Boston
Healthy-Boston
UC-Chicago
CD-Chicago
Healthy-Chicago
UC-Cambridge
CD-Cambridge
HHC-Cambridge
UC-Boston
CD-Boston
Healthy-Boston
UC-Chicago
CD-Chicago
Healthy-Chicago
UC-Cambridge
CD-Cambridge
HHC-Cambridge
Observed Species