Yu SY, Hu YW, Liu XY, Xiong W, Zhou ZT, Yuan ZH. Gene expression profiles in peripheral blood mononuclear cells of SARS patients. World J Gastroenterol 2005; 11(32): 5037-5043 [PMID: 16124062 DOI: 10.3748/wjg.v11.i32.5037]
Corresponding Author of This Article
Zheng-Hong Yuan, Key Laboratory of Medical Molecular Virology, Ministry of Education and Public Health, Shanghai Medical College of Fudan University, Shanghai 200032, China. zhyuan@shmu.edu.cn
Article-Type of This Article
Brief Reports
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World J Gastroenterol. Aug 28, 2005; 11(32): 5037-5043 Published online Aug 28, 2005. doi: 10.3748/wjg.v11.i32.5037
Table 1 Clinical characteristics of two SARS patients
P1
P2
Age (yr)
57
40
Gender
Male
Female
Body temperature (°C)
39.2
36.8
White cell count (×109/L)
13.3
4.67
Neutrophil (×109/L)
12.8
3.25
Lymphocyte (×109/L)
0.406
0.897
CD3+ (/µL)
359
791
CD4+CD3+/CD3+ (%)
86
58
CD8+CD3+/CD3+ (%)
13
36
CD4+CD8+CD3+/CD3+ (%)
4
2
CD4+/CD8+
6.38
1.62
Monocyte (×109/L)
0.122
0.442
Eosinophil (×109/L)
0.004
0.033
Basophil (×109/L)
0.009
0.041
Outcome
Death
Rehabilitation
Table 2 Primer sequence used in real-time quantitative PCR analysis
Accession number
Description
Forward primer (5’→3’)
Reverse primer (5’→3’)
NM_000634
IL-8R α
GGAACTGGTGTCTTCAGGG
CATCTAATGTCAGATTCGGGG
NM_003855
IL-18R1
GGGTATTACTCCTGCGTGCA
CCATTTTCTTCCCCGAACATCC
BC025925
GAPDH
GGTATCGTGGAAGGACTCATGAC
ATGCCAGTGAGCTTCCCGTTCAGC
Table 3 Comparison of microarray and real-time quantitative PCR analysis on selected genes (mean±SD)
Gene description
Techniques
P1
P2
IL-8R α
Microarray
73.52
–
Real-time qPCR
11.63±0.15
0.37±0.09
IL-18R1
Microarray
42.33
–
Real-time qPCR
48.55±0.36
0.38±0.27
Table 4 Functional categories of over 2.0-fold-regulated genes in two SARS patients
Classification
P1
P2
Cell communication
802 (518↑284↓)
288 (116↑172↓)
Cell differentiation
65 (33↑32↓)
24 (6↑12↓)
Cellular physiological process
1 056 (645↑411↓)
406 (188↑218↓)
Coagulation
42 (25↑17↓)
17 (6↑11↓)
Development
316 (202↑114↓)
132 (50↑82↓)
Death
166 (116↑50↓)
80 (45↑35↓)
Extracellular structure
3 (1↑2↓)
2 (2↓)
organization and biogenesis
Homeostasis
30 (13↑17↓)
11 (8↑3↓)
Metabolism
1 497 (867↑630↓)
512 (191↑330↓)
Obsolete biological process
1 (1↓)
1 (1↓)
Organismal physiological process
467 (278↑189↓)
198 (110↑88↓)
Pathogenesis
1 (1↑)
2 (2↑)
Regulation of cell process
57 (57↓)
88 (48↑40↓)
Response to stimulus
532 (317↑215↓)
232 (124↑108↓)
Viral life cycle
15 (7↑8↓)
10 (5↑5↓)
Behavior
14 (8↑6↓)
6 (1↑5↓)
Total
3 854 (2 273↑1 581↓)
1 380 (527↑853↓)
Table 5 Differentially expressed genes encoding pro- and anti-inflammatory cytokines are involved in IL-1 and TNF-α signaling cassettes in two patients
GenBank access
Definition
P1
P2
Pro- and anti-inflammatory cytokines and receptors
AF043337
IL-8
8
–2.46
NM_000634
IL-8 receptor, α
73.52
–
NM_001557
IL-8 receptor, β
51.98
4.29
NM_000575
IL-1, α
3.73
–
NM_000576
IL-1, β
6.5
11.31
NM_000877
IL-1 receptor, type I
18.38
–
NM_004633
IL-1 receptor, type II
362.04
3.84
U64094
Soluble type II IL-1 receptor
630.35
–
NM_003856
IL-1 receptor-like 1
11.31
3.25
U65590
IL-1 receptor antagonist IL-1Ra
14.93
–
AF051151
Toll/IL-1 receptor-like protein 3
14.93
–
NM_000418
IL-4 receptor
13.93
–
NM_000600
IL-6
–
3.03
NM_002184
IL-6 signal transducer gp130
–
–2.14
BC001903
IL-10 receptor, β
4
–
NM_004512
IL-11 receptor, α
–6.06
–2.30
NM_001560
IL-13 receptor, α1
3.25
–
U62858
IL-13 receptor
5.66
–
U81380.2
IL-13 receptor soluble form
4.29
–
NM_000585
IL-15
–3.03
2
NM_004513
IL-16
–
–2.83
NM_014339
IL-17 receptor
4.29
–
NM_003855
IL-18 receptor 1
42.22
–
NM_003853
IL-18 receptor accessory protein
19.7
–
AF269133
Novel interleukin receptor
–3.03
–
NM_004862
TNF-α
17.15
–
NM_001065
TNFRSF1A
4
–
NM_003841
TNFRSF10C
19.7
–
NM_000760
G-CSF 3 receptor
25.99
–
BC002635
GM-CSF 2 receptor, α, low-affinity
3.03
–
M64445
GM-CSF receptor
4.92
2.64
NM_002607
Platelet-derived growth factor α polypeptide
–2.46
–
NM_004347
Caspase 5
4.59
–
NM_000201
Intercellular adhesion molecule 1
17.15
–
NM_002162
Intercellular adhesion molecule 3
6.28
–
NM_003243
Transforming growth factor, β receptor III
–36.76
–4.59
NM_003242
Transforming growth factor, β receptor II
–
–2.30
NM_000358
Transforming growth factor, β-induced, 68 ku
–24.25
–
The genes involved in the IL-1 signaling pathway
NM_007199
IL-1 receptor-associated kinase M
19.7
–
NM_002182
IL-1 receptor accessory protein
25.99
–
AF167343
Soluble IL-1 receptor accessory protein
55.72
–
M87507
IL-1 β convertase
3.25
–
U13698
IL-1-β converting enzyme isoform γ
3.03
–
U13699
IL-1-β converting enzyme isoform δ
–
2.14
U13700
IL-1-β converting enzyme isoform ε
2.64
–
The TNF signal downstream genes
NM_004619
TNF receptor-associated factor 5
–
–2.00
NM_016614
TRAF and TNF receptor-associated protein
3.84
–2.30
NM_006290
TNF-α induced protein 3
5.66
–
NM_007115
TNF-α induced protein 6
45.25
4.92
AB034747
Small integral membrane protein of lysosome late endosome
7.46
–
U50062
RIP protein kinase
–
–2.00
Table 6 Differentially expressed genes involved in immune regulation in two SARS cases
GenBank access
Definition
P1
P2
IFN and IFN-induced genes
M29383
IFN-γ
–
2.14
NM_000416
IFN-γ receptor 1
4.59
–
NM_005534
IFN-γ receptor 2
3.84
–
NM_000629
IFN (α, β, and ω) receptor 1
4.29
–
NM_002198
IFN regulatory factor 1
–
3.84
NM_002460
IFN regulatory factor 4
–
–2.30
NM_004030
IFN regulatory factor 7
–
3.25
BC001356
IFN-induced protein 35
–
2.83
M34455
IFN-γ-inducible indoleamine 2,3-dioxygenase
–
5.66
NM_001548
IFN-induced protein with tetratricopeptide repeats 1
–
3.03
NM_001549
IFN-induced protein with tetratricopeptide repeats 4
–
6.06
NM_002053
Guanylate binding protein 1, IFN-inducible
–
3.03
NM_004120.2
Guanylate binding protein 2, IFN-inducible
–
3.73
NM_022873
IFN-α-inducible protein
–
6.5
NM_003641
IFN-induced transmembrane protein 1 (9-27)
–
2.3
NM_004509
IFN-induced protein 41
–
2.14
NM_005532
IFN-α inducible protein 27
–
14.93
NM_005101
IFN-stimulated protein, 15 ku
–
6.5
NM_006417
IFN-induced, hepatitis C-associated microtubular aggregate protein
–2.46
2.64
NM_002759
PKR
–
2.14
NM_002462
Mx1
–
2.14
Chemokines and receptors
NM_001511
GRO1
55.72
–
NM_002993
Granulocyte chemotactic protein 2
3.73
–
NM_001565
CXCL10
–
14.93
AF030514
CXCL11
–
18.38
AJ224869
CXCR4
6.5
2.83
M21121
RANTES
–13.93
–
NM_001295
CCR1
3.84
–
NM_000648
CCR2
–9.19
–3.25
NM_001837
CCR3
–
6.5
NM_000579
CCR5
–3.25
–4.00
NM_001838
CCR7
–3.73
–2.64
U20350
CX3CR1
–42.22
–
Toll-like receptors
NM_003264
Toll-like receptor 2
8
–
NM_003265
Toll-like receptor 3
–3.25
–2.30
NM_003266
Toll-like receptor 4
3.73
–2.64
NM_016562
Toll-like receptor 7
–17.15
2.3
Table 7 Differentially expressed genes involving MAPK or JAK-STAT signaling pathways in two SARS cases
GenBank access
Definition
P1
P2
U35002
JNK2 β1 protein kinase
–2.00
–2.14
U31601
JAK-3B
10.56
–
NM_007315
STAT-1
–
2.14
NM_005419
STAT-2
–
3.03
NM_003151
STAT-4
–2.30
–
NM_012448
STAT5B
8.57
–
AB005043
STAT induced STAT inhibitor 1
5.66
3.03
NM_003955
STAT induced STAT inhibitor 3
4.92
–
NM_002745
MAPK 1
4
–
NM_002748
MAPK 6
3.73
–
NM_001315
MAPK 14
9.19
–
NM_004759
MAPK-activated protein kinase 2
4.29
–
NM_003668
MAPK-activated protein kinase 5
–2.46
–
NM_001674
Activating transcription factor 3
2.46
5.27
NM_007348
Activating transcription factor 6
3.73
–
Citation: Yu SY, Hu YW, Liu XY, Xiong W, Zhou ZT, Yuan ZH. Gene expression profiles in peripheral blood mononuclear cells of SARS patients. World J Gastroenterol 2005; 11(32): 5037-5043