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About OMICS Group OMICS Group is an amalgamation of Open Access publications and
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.
Genome-Wide Transcriptomes Integrate Animal Intra- and Inter-Organism Processes and Evoke the Ecoimmunological Concept in Animal Health
Yongming Sang, D.Sc., Ph.D.
College of Veterinary Medicine
Kansas State University, Manhattan, KS 66506, USA
(07/28/2015, Transcriptome-2015)
Antiviral regulation model (PRRSV, PEDV, SIV, DCoV, CSFV, ASFV)
Obesity model (Had-36)
Metabolism Immunity = Two Facets of
One task of animal health & nutrition
Google images
III. Integrative Strategy in Animal Health and Nutrition:
Current Projects
NIH: Rat obesity induced by high-fat-diet plus Had-36 infection (NIH pilot: $50,000; and R15 pending)
USDA: (1) Immunogenetics and immunoreagent development ($48,000, 2014-2018) (2) Macrophage-based antiviral regulation ($499,436, 2013-2017); (3) Molecular
and functional diversity of interferons (USDA pending)
Mediator: IFNγ LPS IL4/13 IL10 IFNα
Status: M1a M1b M2 IL10+ antiviral Classically activated Alternative activated Regulatory Antiviral state
Phenotype: ProinflammatoryHost defense Antitumor and antiviral (M1a); Antibacterial (M1b)
Wound healingSuppress host defense Suppress antitumor immunity
Anti-inflammatorySecrete IL-10Restore immune homeostasis
ProinflammatorySecrete type I IFNsAntiviral
++ + Tissue macrophage
CMP GMP CFU-M
Progenitor cells
RNA from pooled cells
mRNA selection
Library preparation
Cluster preparation
Illunima sequencing
Mapping clean reads
Data analysis and DEG confirmation
Read quality control
PR
RSV
5h
Our Macrophage Polarization and RNA-seq Procedure
IRF1 IRF2 IRF3 IRF4 IRF5 IRF6 IRF7 IRF8 IRF9
-10
-5
0
5
10
15
20 IFN
LPS
IL4
IL10
IFN
Exp
ressio
n in
de
x(2
-C
t )
rela
tive
to
DP
BS
co
ntr
ols
M0-PBS vs. M1-LPSM0-PBS vs. M2-IL4M0-PBS vs. M1-IFNγM0-PBS vs. M2-IL10M0-PBS vs. MaV-IFNα
From 6624 significant DEGs of >30,000 detected genesIR
F1IR
F2IR
F3IR
F5IR
F6IR
F7IR
F8IR
F9IR
F2B
P1
IRF2
BP
2
0.0
12
3.2
52
.6
M0-PBSM1-IFNγM2-IL4M1-LPSM2-IL10MaV-IFNα
0.0
97
.33
.2
CC
L1C
CL2
CC
L3C
CL4
CC
L5C
CL8
CC
L17
CC
L20
CC
L21
CC
L23
CC
L24
CC
L35
CC
L26
CC
L27
CX
CL2
CX
3C
L1C
XC
R3
CX
CL9
CX
CL1
0C
XC
L11
CX
CL1
3C
XC
L14
CX
CL1
6C
CR
L2C
CR
2C
CB
P2
CC
R4
CC
R5
CC
R7
CX
CR
1C
XC
R2
CX
CR
2L
CX
CR
4C
XC
R5
CX
CR
6C
XC
R7
CX
3C
R1
0.0
15
0.3
4.4
M0-PBSM1-IFNγM2-IL4M1-LPSM2-IL10MaV-IFNα
IL1A
IL1B
IL36
AIL1
F10
IL1R
NIL1
R2
IL2R
AIL2
RG
IL3R
AIL4
RA
IL4I1
IL5IL6IL6
RIL6
RB
IL7IL7
RA
IL8IL9
RIL1
0IL1
0R
AIL1
0R
BIL1
1R
AIL1
2A
IL12
RB
1IL1
2B
IL12
RB
2IL1
3R
AIL1
5IL1
5R
AIL1
6IL1
7B
IL17
RB
IL17
RC
IL17
RE
IL18
IL18
BP
IL19
IL20
RB
IL21
RIL2
3R
AIL2
2R
AIL2
3P
19
IL27
IL27
RA
IL27
BIL2
9IL3
3TN
FTN
FAIP
1M
CSF
CSF
CSF3
CSF2
RA
CSF1
RC
SF2R
BTG
FB
DEGs Related to Cytokines, Chemokines and IRFs, and RT-PCR Confirmation
IRF1
IRF2
IRF3
IRF5
IRF6
IRF7
IRF8
IRF9
IRF2
BP
1IR
F2B
P2
0.0
12
3.2
52
.6
M0-PBSM1-IFNγM2-IL4M1-LPSM2-IL10MaV-IFNα
pH 4.0 5.0 5.5 6.0 6.5 7.0 8.0 9.0
(kD
a)
6
13
4 5 6 7
89 10
11
2
12
18
19
1716
151413
37
22
2120
3029
28
272625
2423
36
353433
32
31
38
44
43
42
41
40
39
5051
59
49
4847
46
45
585756
5554
53
52
66
6564
6362
61
60
6768
69
75
7473
72
71
70
7978
77
7680
81
89
888786
85
848382
90
93
91
9495
9697
99
98
92
104
105
109
111
112
106
108
107
100
102
103
101
110
M1-I
FNγ
/ M0-P
BS
20
14
10
150 96
84 75
66
50
40
30
RP
KM
0
200
400
600
800
0
50
100
150
200
250
0
200
400
600
800
0
200
400
600
800
1000
1200
1400
*
*
*
*
*
*
*
* *
*
*
*
*
*
2-S
ND
13
0-W
AR
S4
7-P
LEK
77
-RA
N
42
-CK
B1
6-P
LOD
36
2-R
NF1
14
79
-HN
RN
PU
52
-AN
XA
16
6-A
TP6
V1
E19
1-U
BE2
D3
10
0-C
AN
X
18
-MX
14
9-M
x29
0-H
2B
3A
99
-MP
P5
M1-IFNγ vs.
M0-PBS
M2-IL4 vs.
M0-PBS
M2-IL10 vs.
M0-PBS
MaV-IFNα vs.
M0-PBS
Spence S, et al., Immunity. 2013 Jan 24;38(1):66-78.
KLF1
KLF2
KLF3
KLF4
KLF5
KLF6
KLF7
KLF8
KLF9
KLF1
0K
LF11
KLF1
2K
LF13
KLF1
4K
LF15
KLF1
6K
LF17
0.0
30
.72
.8
SOC
S1SO
CS2
SOC
S3SO
CS4
SOC
S5SO
CS6
SOC
S7
0.0
50
.51
0.6
M0-PBSM1-IFNγM2-IL4M1-LPSM2-IL10MaV-IFNα
PP
AR
AP
PA
RD
PP
AR
GP
PR
C1
PP
AR
GC
1B
CD
47
0.0
15
0.5
60
.2
Alder JK, et al. J Immunol. 2008 Apr 15;180(8):5645-52.
DEGs Related to Transcription Factors that are Important for Macrophage Activation, and Proteomic Confirmation
STRADA
STRADB
CAB39
PRKAA1
PRKAA2
PRKAB1
PLCB2
PLCB1
CAMKK1
CAMKK2
STK11
PRKACB
PRKACG
PRKAB2
PRKAG1
PRKAG2
PRKAG3 AMP kinase
HMGR
ACC1
ACC2
CPT1A (liver)
CPT1B (muscle)
CPT1C (brain)
HNF4
FASN LIPE
IFN
γ-M
1 v
s. P
BS
-M0
STRADA
STRADB
CAB39
PRKAA1
PRKAA2
PRKAB1
PLCB2
PLCB1
CAMKK1
CAMKK2
STK11
PRKACB
PRKACG
PRKAB2
PRKAG1
PRKAG2
PRKAG3AMP kinase
HMGR
ACC1
ACC2
CPT1A (liver)
CPT1B (muscle)
CPT1C (brain)
HNF4
FASN LIPE
STRADA
STRADB
CAB39
PRKAA1
PRKAA2
PRKAB1
PLCB2
PLCB1
CAMKK1
CAMKK2
STK11
PRKACB
PRKACG
PRKAB2
PRKAG1
PRKAG2
PRKAG3AMP kinase
HMGR
ACC1
ACC2
CPT1A (liver)
CPT1B (muscle)
CPT1C (brain)
HNF4
FASN LIPE
IFN
γ-M
1 v
s. P
BS
-M0
IL4-M
2 v
s. P
BS
-M0
PLCB1 PLCB2
CAMKK1 CAMKK2 STRADA STRADB
CAB39 STK11
PRKACB PRKAA2 PRKAB1 PRKAB2 PRKAG1 PRKAG2
HMGR ACC1
CPT1A CPT1B CPT1C
SREBP2 FASN
LIPE
0.0 70.9 20.9
M0
-PB
S M
1-I
FNγ
M2
-IL4
M
1-L
PS
M2
-IL1
0
MaV
-IFN
α
DEGs in AMPK Pathway in Mediation of Lipid Metabolism
Regulation of PRRSV infection via AMPK
Pathway and Lipid Metabolism
CTRL
Fluorescent
ToFA (2.5 μg/ml)
ToFA (5 μg/ml)
mDCs infected with DsRed-PRRSV for 48 h
Merged
ToFA (5-(Tetradecyloxy)-2-furoic acid), a competitive
inhibitor of acetyl-CoA carboxylase (ACC)
FL1 (PRRSV)
99.42 0.58
100 101 102 103 104
MФsMARC-145 mDCs
6.09 93.91
83.16 16.84
98.52 1.48
43.26 56.74
62.55 37.45
74.51 25.49
86.97 13.02
98.96 1.04
100 101 102 103 104 100 101 102 103 104
FS
C-H
1000
800
600
400
200
0
1000
800
600
400
200
0
1000
800
600
400
200
0
Mo
ck
PR
RS
VT
oF
A+
PR
RS
V
DN
A m
eth
yla
tran
sfe
rase
his
ton
e d
ea
ce
tyla
se
His
ton
e m
eth
yltra
nsfe
rase
MGMT DMAP
DNMT1 DNMT1L DNMT3A
DNMT3AL DNMT3B
0.0 10.2 3.6
M0
-PB
S M
1-I
FNγ
M2
-IL4
M
1-L
PS
M2
-IL1
0
MaV
-IFN
α
ASH1L DOT1
EHMT1 EHMT2
EZH1 MLL1 MLL2 MLL3 MLL4 MLL5 NSD1 NSD3
SETD1A SETD2 SETD8
SETDB1 SETDB2
SETMAR SUV39H1
SUV420H2 WHSC1
0.0 19.1 13.9
HADC1 HADC2 HADC3 HADC8 HADC5 HADC7 HADC9 HADC9L HADC6 HADC10 HADC11 SIRT1 SIRT2 SIRT3 SIRT4 SIRT5 SIRT6 SIRT7
0.0 42.9 6.7
M0
-PB
S M
1-I
FNγ
M2
-IL4
M
1-L
PS
M2
-IL1
0
MaV
-IFN
α
KDM2A KDM2B KDM3A KDM3B KDM4A KDM4B KDM4C KDM5A KDM5B KDM5C KDM6A KDM7 KDM8 NO66
0.0 21.0 11.0
His
ton
e d
em
eth
yla
se
DEGs Critical for Epigenetic Regulation
http://www.eusem.com/main/CH/epi
CT
RL
Azacytidine DNA (-methyltransferase)
BIX-01294(-histone methyltransferase)
Trichostatin A(-histone deacetylase)
UNC0638(-selective HMT G9a/GLP)
MA
RC
-14
5M
acro
ph
ag
es
10
μM
0.5
μM
10
μM
0.5
μM
0.5
μM
0.5
μM
10
μM
1 μ
M
Regulation of PRRSV infection via
Epigenetic Regulation
Tissue macrophages
Differential activation statuses PRRSV
Epigenetic regulation
Lipid metabolism
Interferon responses…
Deviation of activation statuses
Increase PRRSV permissiveness
Routes for preventing
Summary
1. Porcine monocytic cells at different activation statuses, interact differentially with PRRSV
2. Key genes in the pathways such as lipid metabolism, epigenetics and interferon signaling are revealed among significant DEGs.
3. Signature genes revealed in PRRSV—infected macrophages at each activation status infer the mechanism of PRRSV-cell interaction.
4. Understanding and modulating cell activation status of monocytic innate immune cells provides a framework for optimizing antiviral immunity
Objective and Approach
Aims:
1. Develop rat obesity model integratively induced by a high-fat diet and Had-36 infection
2. Validate obesity phenotypes including body weight, fat index, plasma leptin level, and
parameters associated with gut/adipose inflammation
3. Extract ileal RNA from LF lean, Had-36+LF, HF and Had-36+HF obese groups
4. Perform transcriptomic analyses using 8-wk ileal and hypothalamus samples
5. Analyze gene ontology and pathway integration, and determine obesity-linked innate
immune genes
Tissue samples taken
at 8, 15, 30 wks
Body weight measured and
blood samples taken weekly
High-fat diet (HF)* Control diet (LF)*
Male Wistar Rats: 6-wk old [Serum negative to Ad., Body Weight (BW): 125 5g]
Had-36 + HF
Negative control: 12 Integrative induction: 24 Positive control-II: 24
Had-36*+LF
Positive control-I: 24
(*human adenovirus 36
LF: LabDiet 5001 Fat 5.0%
HF: LabDiet 5SLA Fat 20.6%)
de La Serre CB, et al., Am J Physiol Gastrointest Liver Physiol. 2010 Aug;299(2):G440-8.
Results and Discussion
Total fat
8-week
Adip
osity index (
% o
f B
W)
2.0
4.0
6.0
8.0
10.0
Total fat EWAT
30-weekMAT PRAT
Low-fat diet (LF)
High-fat diet (HF)
LF + Had-36
HF + Had-36* **
*
**
*
* *
**
* p<0.05, ** p<0.005, n=6-7
EWAT, MAT and PRAT: epididymal , mesenteric, and perirenal white adipose tissue
1. LF 4.HF+36
HF + Had-36 infection synergistically increased adiposity indexes in total fat or visceral fats in three adipose depots
Results and Discussion Profiling of Significant Differential Expression Genes
Tlr2
Tlr3
Tlr4
Tlr5
Tlr6
Tlr7
Tlr1
0
Tlr1
1
Tlr1
2
Tlr1
3Lo
g2(f
old
ch
an
ge
to
LF
)
-2.0
-1.5
-1.0
-0.5
0.0
0.5
1.0
1.5HF
Had-36
HF+Had36
De
fa5
De
fa6
De
fa7
De
fa8
De
fa9
De
fa1
0
De
fa1
1
De
fa2
4
De
fa-r
s1Log
2(f
old
change t
o L
F)
-2.5
-2.0
-1.5
-1.0
-0.5
0.0
0.5
1.0HF
Had-36
HF+Had-36
* *
*
* *
* * *
*
* * * *
* p<0.05
Ifn
a5
Ifn
k
Ifn
ar1
Ifn
g
Ifn
gr1
Ifn
gr2
Isg
12
Isg
20
Isg
20
L2Lo
g2(f
old
change t
o L
F)
-2.5
-2.0
-1.5
-1.0
-0.5
0.0
0.5
1.0
HF
LF+Had
HF+Had
*
* p<0.05
*
*
* *
* * * *
*
Results and Discussion Profiling of Significant Differential Expression Genes
Il1
a
Il1
b
Il1
f9
Il1
rn
Il1
r1
Il1
r2 Il4
Il4
ra Il6
Il6
ra
Il1
0
Il1
0ra
Il1
0rb
Il1
2a
Il1
2b
Il1
2rb
1
Il1
2rb
2
Il1
3
Il1
3ra
1
Il1
3ra
2
Il1
7b
Il1
7c
Il1
7d
Il1
7f
Il1
7ra
Il1
7rb
Il1
7rc
Il1
7rd
Il1
7re
Il1
8
Il1
8r1
Il2
0ra
Il2
2ra
1
Il2
2ra
2
Tn
fsf1
0
Tn
frsf1
1a
Tn
faip
1
Csf1
Csf2
Nfil3L
og
2(f
old
ch
an
ge
to
LF
)
-4
-3
-2
-1
0
1
2
3 HF
LF+Had
HF+Had * p<0.005
*
*
*
*
* * * *
* * * *
* *
* *
* *
* * * *
*
HF+Had
LF+Had
HF
LF
*
Log10
(p value)
-6.0 -4.0 -2.0 0.0
rhythmic processPPAR signaling pathwaynegative regulation of receptor biosynthetic processCircadian rhythm
(Dow
n-D
EG
enrich
ed
)
Log10
(p value)
-6.0 -4.0 -2.0 0.0
multi-organism process
response to biotic stimulus
response to other organism
organelle
membrane-bounded organelle
intracellular
intracellular part
cytoplasm
intracellular organelle
intracellular membrane-bounded organelle
nucleus
RNA binding
binding
heterocyclic compound binding
small molecule binding
nucleoside phosphate binding
nucleotide binding
BioGRID interaction data
SNARE complex
MI:mmu-miR-568
CREB regulated
TNF signaling pathway
Apoptosis
Legionellosis
Herpes simplex infection
Influenza A
NOD-like receptor signaling pathway
RIG-I-like receptor signaling pathway
Hepatitis C
Cytosolic DNA-sensing pathway
(Up-D
EG
enrich
ed
)
Results and Discussion Pathway analysis and gene ontology (GO) analysis
HF + Had-36 infected group compared with control group
All 30, including 10 disease/immunity related (highlighted), pathways show little direct relation with lipid metabolic pathways but are highly relevant to intracellular and inter-organism communication (p<0.05)
1. Infection of Had-36 synergizes with the induction of obesity by high-fat diet in rats; however, Had-36 infection has little effect in obesity induction in rats fed the control diet.
2. Either high-fat diet or Had-36 infection increases gut permeability and inflammation but has no synergistic effect (actually having antagonistic effect)
3. At 8-wk post treatment, rat ileal transcriptome shows significant down-regulation of multiple families of immune and metabolic genes in the HF and HF+Had-36 groups, as well as reprograming of circadian rhythm pathway.
Chawla A, et al. Nat Rev Immunol. 2011, 11:738-49.
Summary
Acknowledgements
• Laboratory colleagues:
•Funding resources: • The studies are supported in part by (1) USDA-NIFA-COOP-2010-002475 (Co-PI: Sang, KSU); USDA NIFA AFRI 2015-67015-23216 (Co-PI: Sang, KSU), and in particular (3) USDA-NIFA-2013-67015-21236 (PI: Sang, KSU) •NIH 1R15HD066377-01 (Co-PI: Sang KSU), Pilot project (PI. Sang, KSU) of NIH NCRR-COBRE-P20-RR017686 (PD: Daniel Marcus, KSU)
Andrew Schade
Amy Hanson
Joe Bergkamp Wyatt Brichalli
Qinfang Liu
Samantha Lyman
Wenjing S. Fausnett Jinhwa Lee Luca Popescu
Lyndie Holmes
Immunophysilogy Lab
2011-2015
Lab manager:
Dr. Barbara Lutjemeier
•Collaborators: Dr. Frank Blecha, KSU Dr. Raymond R. R. Rowland, KSU Dr. Joan Lunney, USDA-ARS Dr. Jishu Shi, KSU Dr. Wenjun Ma, KSU Dr. Laura Millar, USDA-ARS Dr. Zhihua Jiang, WSU Dr. Christopher Tuggle, ISU Dr. Chris Netherton (Pirbright, UK) Dr. Bryan Charleston (Pirbright, UK) Dr. Linda Dixon (Pirbright, UK) Dr. Ruth Welti (Kansas Lipdomics) Dr. Robert Goodband (KSU, Animal Science)
and Mr. Frank Jennings Jr (KSU, Animal farms)
Visiting Scholar:
Dr. Xiaorong Zhang
Thank You!
Classification of Raw Reads (M0: PAM-PBS)
0.0 0.2 0.4 0.6 0.8 1.0
Relative Position in Gene (5’-3’, 100 windows) N
um
be
r o
f re
ad
s (
×10
3)
30
20
10
0
93
4
95
82
4
10
09
69
1
13
28
31
84
42
57
96
4
94
4
10
09
78
5
72
6
16
38
12
28
2405
153
1461
4667
1489
3744
4592
5303
2320 1655
4397
1904
1491
2842
4884
0
1000
2000
3000
4000
5000
6000
M0
-M1
a
M0
-M2
c
M0
-M2
a
M0
-M1
b
M0
-Mav
M2
a-M1
a
M2
b-M
1a
M2
b-M
2a
M2
c-M1
a
M2
c-M2
a
M2
c-M1
b
Mav-M
1a
Mav-M
2c
Mav-M
2a
Mav-M
1b
up-regulated down-regulated total DEGs
RNA-seq Data Quality Control and DEG Analysis
Table 1: Numbers of potential gene makers identified in each activation status.
Status DEG
number
(1) IFNg-M1 44
(2) IFNa-MaV 72
(3) Co-IFNg & IFNa 88
(4) IL4-M2 234
(5) LPS-M1 72
(6) IL10-M2 9
Total 519
Profiling Signature Genes of Each
Activation Status
Background and Hypothesis
Mucosal antimicrobials,
and cytokines
Gut viruses
Gut bacteria
Bacterial and lipid
sensors, eg. TLR4
High-fat diet
Intestinal
epithelial
barrier
Viral
sensors
IRFs
IFN-a/b Cytokines
Tight
junction
?
Gut low-grade chronic
inflammation
Adipose low-grade
chronic inflammation Obesity Peripheral
circulation
Mitra AK, Clarke K. Viral obesity: fact or fiction? Obes Rev. 2010 Apr;11(4):289-96. Dhurandhar NV. Insulin sparing action of adenovirus 36 and its E4orf1 protein. J Diabetes Complications. 2013 Mar-Apr;27(2):191-9.
Hypothesis: Viral infection and high-fat diet can induce obesity independently, and in particular may contribute to prevalence of obesity synergistically.
Results and Discussion
Week
0 2 4 6 8 10
Avera
ge w
eig
ht in
cre
ase (
%)
0
50
100
150
200
Low-fat diet (LF)
High-fat diet (HF) LF + Had-36 HF + Had-36
*
**
*
HF + Had-36 infection synergistically increased BW after 5 wk Had-36 infection without HF had little effect
Ave. BW diff: 20-30 g between HF groups with LF groups
Body w
eig
ht
(g)
200
400
600
800
1 2 3 4
Low-fat diet (LF)
High-fat diet (HF) LF + Had-36 HF + Had-36
8 week post treatment
* p<0.05
Vander Wal JS, Huelsing J, Dubuisson O, Dhurandhar NV. An observational study of the association between adenovirus 36 antibody status and weight loss among youth. Obes Facts. 2013;6(3):269-78.
Results and Discussion
Either high-fat diet or Had-36 infection increases gut permeability but has no synergistic effect (actually having antagonistic effect) . Thus, the development of obesity is associated but may not proportionally correlated with an increase in gut permeability.
LF HF
LF + Had-36
HF + Had-36
Dextr
an
-FIT
C (
g/m
l)
0.0
1.0
2.0
3.0
4.0
5.0
6.0**
**
*
2.HF
* p<0.05, ** p<0.005, n=6-7
Lo
g2(f
old
ch
an
ge
to
LF
) -14
-12
-10
-8
-6
-4
-2
0
2
4
6 HF DEGs: Total: 1483, Up 15
Results and Discussion Profiling of Significant Differential Expression Genes
Log 2(fo
ld change to
LF)
-14 -1
2 -10
-8-6
-4-2
02
46
810
12
HF+Had DEGs: Total: 626, Up 23
Log2(fold change to LF)
-6 -4 -2 0 2 4 6 8 10
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