colonic tissue and stool 16s rdna sequences/media/files/activity files... · colonic tissue and...
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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