Colonic Tissue and Stool 16S rDNA Sequences11,831 sequences,395 OTUs, 240 (61%) novel,7 Phyla

Greater variability in diversity between, than within subjectsGreater variability in diversity between, than within subjects

Double principal coordinate analysis

A

C

B

Sources of variation in host response?

host geneticsmicrobial stimulustime, “dose”specimen

Kawasakisyndrome

http://www.mars.dti.ne.jp/~maachan/Kawasaki1.JPG

• Vasculitis of unknown etiology (infection?)• 90/100,000/yr Jap <5 yr old• 6-11/100,000/yr USA <5 yr old• Winter-Spring• Siblings w/in 10 days

Kawasaki20 pts: acute (A),subacute (SA), chronic (C)18 controls: acute

SA & C

(SA & C from same pt tend to group together)

-1.5

-0.5

0.5

1.5

2.5

0 10 20 30 40 50 60

Time-dependent transcript abundance

day since fever onset

fever inNepal

cancer

health

Whitney A et al, PNAS 2003; 100:1896-1901

Unsupervisedclustering

Fever in Nepalsubjects

0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0 200 400 600 800 1000

DxLymph%

Attributable variance in gene expression

gene

Frac

tion

var

ianc

e ex

plaine

d

diagnosis

lymphocyte%

SAM-Smallpox and Monkeypox Animal Models

CA2 Carbonic anhydraseEPB72 Erythrocyte membrane protein 7.2PLAUR Plasminogen activator, urokinase receptorDEFA1 Defensin, alpha 1BPI Bactericidal/permeability-increasing proteinALOX5 Arachidonate 5-lipoxygenaseMMP9 Matrix metalloproteinase 9VNN2 Vanin 2

GBP1/2 Guanylate binding protein 1 and 2SCYB10 IP-10TNFRSF10 Apo2 ligandCASP4/5 Caspase 4 and 5, apoptosis related UBE2L6 Ubiquitin-conjugating enzyme E2L 6PSMA3/E2/B8 Proteasome activator subunits

MHC classII HLA-DOB1, DRA, DRB1, DMA, DRB5CD74 Invariant chain of MHCII

CD38CX3CR1 Fractalkine receptorIL7

SmallpoxDay 2-4

MonkeypoxDay 2-4

Ig light chain/J chain

MHC Class II

B Cell/T Cell

IFN-induced genes

NRBCProliferation

BPI, Defensin

SERPIN, Vanin, MMP9

Upregulation Cluster

Smallpox in macaques: PBMCs

Rubins K et al., PNAS 2004; 101:15190-15195

TNFα, NFκB – Smallpox vs. EbolaD

0 D 1

D 2

D 3

D 4

D 5

D 6

D 7

D 9

D 1

0-42

D 0

D 1

D 2

D 3

D 4

D 5

D 6

NFκBIA

TNFα induced

NFκB2

Smallpox in vivo Ebola in vivo

TNFα

RelBNFκBIE

TNFαNFκB2

Poxvirus modulation of host defense

Seet B et al., Annu Rev Immunol. 2003;21:377-423

Viral protein Cell homolog Function MPV VAR VAC

TNF receptor,CrmB

TNF-R Secretedreceptor

J2RJ2L

G2R C22LB28R

TNF receptor,CrmC

TNF-R Secretedreceptor

A53R

TNF receptor,CrmE

TNF-R Secretedreceptor

K1R

Sources of variation in host response?

The pathogenic signature imparts specificity upon the host response.

Ebola “Pre-Symptomatic” Gene Expression

Day

2

Day

1

Day

0

EGR1FOSJUN

CD20IL1β

MX1/2SCYB10GBP1/2STAT1

Genes with at least a 2.0-fold induction or repression of expression from baseline (Day0) in at least three of the samples for Day 1 or Day 2 are shown. The expression patterns of 319 genes were hierarchically clustered.

Pathogens and commensals: conserved patterns and pathways

Sources of variation in host response?Future experimental paths

Data sets: temporal profiles of humans w/disease, controlsanimal models

Correlations between mucosal community structure and local response

Issues

ConclusionsConclusionsHost responses to microbial disease are

highly dynamicAt superficial level, conserved host response

patterns dominate picture of microbial diseaseClassification scheme of humans with

microbial disease will reflect virulence strategy (pathogenic community pattern?), host genetics, nature of specimen, etc.

Why disease? Timing, intensity, location, and features of response program

AcknowledgementsStanfordPaul Lepp

Karla LightfieldLes DethlefsenPaul EkburgElies Bik

Stephen PopperKate RubinsPat Brown

FundingNIDCR, NIAID, NHLBI, DARPA, Ellison

Medical Foundation

UCSFGary Armitage

TIGRSteve Gill

Karen Nelson

USAMRIIDPeter JahrlingLisa HensleyTom GeisbertJohn Huggins

U of ManitobaCharles Bernstein

UCSDJane Burns

DukeBarth Reller