Analysis of the Major Patterns of B Cell Gene Expression
Changes in Response to Short-Term Stimulation with 33 Single
Xiaocui Zhu,* Rebecca Hart,* Mi Sook Chang,* Jong-Woo Kim,* Sun Young Lee,*
Yun Anna Cao,* Dennis Mock,†Eugene Ke,†Brian Saunders,†Angela Alexander,§
Joella Grossoehme,§Keng-Mean Lin,§Zhen Yan,§Robert Hsueh,§Jamie Lee,¶
Richard H. Scheuermann,§¶David A. Fruman,?William Seaman,#Shankar Subramaniam,†‡
Paul Sternweis,§Melvin I. Simon,* and Sangdun Choi2*
We examined the major patterns of changes in gene expression in mouse splenic B cells in response to stimulation with 33 single
ligands for 0.5, 1, 2, and 4 h. We found that ligands known to directly induce or costimulate proliferation, namely, anti-IgM
(anti-Ig), anti-CD40 (CD40L), LPS, and, to a lesser extent, IL-4 and CpG-oligodeoxynucleotide (CpG), induced significant ex-
pression changes in a large number of genes. The remaining 28 single ligands produced changes in relatively few genes, even
though they elicited measurable elevations in intracellular Ca2?and cAMP concentration and/or protein phosphorylation, in-
cluding cytokines, chemokines, and other ligands that interact with G protein-coupled receptors. A detailed comparison of gene
expression responses to anti-Ig, CD40L, LPS, IL-4, and CpG indicates that while many genes had similar temporal patterns of
change in expression in response to these ligands, subsets of genes showed unique expression patterns in response to IL-4, anti-Ig,
and CD40L. The Journal of Immunology, 2004, 173: 7141–7149.
attempt to determine: 1) which ligands will activate signaling path-
ways, and 2) how distinct are the ligands in their downstream
signaling responses (1, 2). A total of 33 ligands was chosen for
their known or suspected effects on purified mouse splenic B cells
(see supplementary Table I3for the full list of the ligands). These
ligands included those known to induce or costimulate prolifera-
tion, such as anti-Ig, CD40L, LPS, IL-4, and CpG (3–7). They also
included several chemotactic ligands, including B cell-attracting
he Alliance for Cellular Signaling recently completed a
screen of the responses of mouse splenic B lymphocytes
to the application of a panel of distinct single ligands in an
chemokine 1 (BLC4
(CCL19), secondary lymphoid-tissue chemokine (CCL21), and
stromal cell-derived factor-1? (SDF1? or CXCL12), which medi-
ate B cell migration at different stages of the B cell life cycle and
are critical for proper lymphoid organ development, germinal cen-
ter formation, and immune responses (8). In this study, we report
the characteristics of B cell gene expression changes in response to
these 33 ligands, as determined by custom Agilent (Agilent Tech-
nologies, Palo Alto, CA) two-color cDNA arrays. We identify the
most potent ligands in inducing gene expression changes as those
that promote proliferation (anti-Ig, CD40L, LPS, and, to a lesser
extent, IL-4 and CpG). We also delineate the patterns of gene
expression that are either shared by these ligands or are unique to
the individual ligands.
or CXCL13), Ebl1-ligand chemokine
Materials and Methods
Detailed information of procedures, ligands, and solutions used in the ex-
periments can be found at the Alliance for Cellular Signaling protocols
Mice, reagents, cell culture, and RNA preparation
Mice used in the experiments were 6- to 8-wk-old male C57BL/6 mice
(The Jackson Laboratory, Bar Harbor, ME). Splenic B cells (?96% B220
positive) were purified from RBC-depleted splenocytes by using anti-
CD43 and anti-Mac-1/CD11b mAbs coupled to magnetic microbeads
(Miltenyi Biotec, Bergisch Gladbach, Germany), as described in Alliance
for Cellular Signaling protocol PP00000016. Purified B cells were cultured
with ligands or medium alone for 0.5, 1, 2, and 4 h, and their RNA was
extracted following Alliance for Cellular Signaling protocol PP00000009.
Triplicate experiments were performed for each ligand at each time point,
and each RNA sample was processed and measured by a cDNA array. As
*Molecular Biology Laboratory, Alliance for Cellular Signaling, Division of Biology,
California Institute of Technology, Pasadena, CA 91125;†Bioinformatics and Data
Coordination Laboratory, Alliance for Cellular Signaling, San Diego Supercomputer
Center, and‡Department of Bioengineering, University of California, San Diego, CA
92122;§Cell Preparation and Analysis Laboratory, Alliance for Cellular Signaling,
Department of Pharmacology, and¶Department of Pathology, University of Texas
Southwestern Medical Center, Dallas, TX 75390;?Department of Molecular Biology
and Biochemistry, University of California, Irvine, CA 92697; and#Macrophage Bi-
ology Laboratory, Alliance for Cellular Signaling, Department of Medicine, Univer-
sity of California, San Francisco, CA 94143
Received for publication May 13, 2004. Accepted for publication September
The costs of publication of this article were defrayed in part by the payment of page
charges. This article must therefore be hereby marked advertisement in accordance
with 18 U.S.C. Section 1734 solely to indicate this fact.
1This work was supported by contributions from public and private sources, includ-
ing the National Institute of General Medical Sciences Glue Grant Initiative (U54
GM062114). A complete listing of the Alliance for Cellular Signaling sponsors can
be found at www.signaling-gateway.org/aboutus/sponsors.html.
2Address correspondence and reprint requests to Dr. Sangdun Choi, Division of
Biology, 147-75, California Institute of Technology, 1200 East California Boulevard,
Pasadena, CA 91125. E-mail address: firstname.lastname@example.org
3The on-line version of this article contains supplemental material.
4Abbreviations used in this paper: BLC, B cell-attracting chemokine 1; AKT, protein
kinase B; Ccnd2, cyclin D2; Hk2, hexokinase 2; Ldh, lactate dehydrogenase; Ltb,
lymphotoxin ?; MARCKS, myristoylated alanine-rich protein kinase C substrate;
PAF, platelet-activating factor; Plk, polo-like kinase; SAM, Significance Analysis of
Microarrays; SDF, stromal cell-derived factor; Xbp, X box-binding protein.
The Journal of Immunology
Copyright © 2004 by The American Association of Immunologists, Inc.0022-1767/04/$02.00
a reference for the cDNA array hybridization, RNA from total RBC-de-
pleted splenocytes was extracted in the same manner as RNA from purified
splenic B cells.
Agilent cDNA array fabrication and annotation
A total of 15,494 cDNA probes was printed on 15,832 spots on the custom-
made arrays. Ninety-six percent of the probes came from the Riken Fantom
collection (http://fantom.gsc.riken.jp; Yokohama, Kanagawa, Japan), with
the rest from collections of the National Institute on Aging (Bethesda,
MD), Research Genetics (Huntsville, AL), and Incyte Genomics (St. Louis,
MO). The probes were PCR amplified by the Simon Lab at the California
Institute of Technology (Pasadena, CA) and were inkjet printed onto glass
slides by Agilent. The entire collection of the cDNA probes represents
10,615 unique genes as of the annotation results generated on December
30, 2003. See Table II in the supplemental material for the annotation table
and a description of the annotation process.
Agilent cDNA array analysis
Each array was hybridized with Cy5-labeled cDNA prepared from the
RNA of splenic B cells and Cy3-labeled cDNA prepared from RNA of
total splenocytes that was used as an internal reference (Alliance for Cel-
lular Signaling protocol PP00000019). The arrays were scanned using Agi-
lent Scanner G2505A with the scan resolution set to 10 ?m and the laser
intensity adjusted so that both the maximum red and green (Cy5 and Cy3)
fluorescence intensity were ?20,000 pixels. The image files were extracted
with background-subtraction (the Local background subtraction method)
and dye-normalization (the Rank consistent filter and the LOWESS algo-
rithm) using the Agilent G2566AA Feature Extraction Software Version
A.6.1.1. The entire raw data sets collected from over 400 arrays are avail-
able through the B cell ligand screen link at the Alliance for Cellular
Signaling Data Center website: www.signaling-gateway.org/data/.
For each array, we removed the control features. For features that were
saturated (with Agilent glsSaturated and rlsSaturated flags), nonuniform
(with Agilent gIsFeatNonUnifOL and rIsFeatNonUnifOL flags), or below
background (with Agilent gIsWellAboveBG and rIsWellAboveBG flags),
their Cy5 and Cy3 fluorescence intensity and log2(Cy5/Cy3) value were
set to blank. Features were further filtered by a statistical method, Signif-
icance Analysis of Microarrays (SAM) (9). Features identified by SAM as
differentially expressed between treated and time-matched controls were
included for downstream analysis. Our inputs for SAM analysis were mea-
surements of the expression level of array features in B cells, represented
as the Cy5 fluorescence intensity, which has been background subtracted
and normalized for dye bias and interarray variance (see supplementary
material for details of data preparation for SAM analysis). Features with
fewer than two nonblank replicate measurements in treated or time-
matched control B cells were not used in SAM analysis. One hundred
random permutations were done for each comparison. A total of 3396
features was identified by SAM as differentially expressed in at least 1 of
the 132 conditions with varied levels of false discovery rate. Of these, 459
features appeared to show changes in expression that correlated with the
dates of RNA sample preparation and were excluded from downstream
Data clustering and identification of gene expression signatures
The input for clustering analysis was log2(treated/0 h) value, the fold
change of gene expression level in cultured B cells relative to that in 0-h
B cells in log2scale. The log2(treated/0 h) value was calculated by sub-
tracting log2(0 h/spleen) from log2(treated/spleen), in which the log2
(treated/spleen) is the average of at least two of three replicate log2(Cy5/
Cy3) measurements of cultured B cells and log2(0 h/spleen) the average of
at least 6 of the 26 replicate log2(Cy5/Cy3) measurements of 0-h B cells.
For features that did not have at least 2 replicate measurements in cultured
B cells or at least 6 replicate measurements in 0-h B cells, their log2(treat-
ed/0 h) value was set to blank (see supplementary Table III for log2(treat-
ed/0 h) values of all 2937 differentially expressed features, and supple-
mentary Table IV for log2(treated/0 h) values of all array features). For
each clustering analysis, only features that 1) were differentially expressed
in at least one of the conditions, 2) had a nonblank log2(treated/0 h) value
in 80% of the conditions, and 3) whose maximum and minimum expression
changes across the conditions had a difference greater than 1 were
To visualize the overall characteristics of gene expression profiles in
response to the 33 single ligands or all the nonmitogenic ligands, hierar-
chical clustering was performed with the Cluster and TreeView program
(10). Clustering was done one way across the features following gene-wise
median centering, with experimental conditions aligned in ligand (alpha-
betical) and time-course orders. Euclidean correlation coefficient and com-
plete linkage were used as similarity metrics.
To identify gene expression signatures in response to anti-Ig, CD40L,
CpG, IL-4, or LPS, we first conducted K-means clustering of gene expres-
sion change over the 0.5-, 1-, 2-, and 4-h time course for each ligand to
group features according to their temporal expression pattern. Then by
comparing gene expression patterns across different ligand responses, we
identified groups of features that showed unique expression changes in
response to individual single ligands, and those that showed similar ex-
pression change patterns in response to all ligands. The groupings were
further refined by removing features that had different expression patterns
from the majority in the same group as revealed by hierarchical clustering
using similar settings described above. K-means clustering and hierarchical
clustering used in this study were implemented in the Multiple Experiment
Robust expression changes induced by BLC, IFN-?, IL-10, platelet-
activating factor (PAF), and SDF1? and the signature expression change
patterns induced by anti-Ig, CD40L, CpG, IL-4, and LPS were vizualized
by hierarchical clustering implemented in the Multiple Experiment Viewer
(www.tigr.org/software/tm4/mev.html). Clustering was done one way
across the features following gene-wise median centering. Euclidean cor-
relation coefficient and complete linkage were used as similarity metrics.
Quantitative real-time PCR
A total of 1 ?g of total RNA from pooled duplicate or triplicate RNA
samples used for microarray experiments was treated with DNase I (In-
vitrogen Life Technologies, Carlsbad, CA) to remove contaminating
genomic DNA. First-strand cDNA was synthesized with SuperScript II
(Invitrogen Life Technologies) and random hexamer priming (Invitrogen
Life Technologies). Quantitative real-time PCR was performed by using
i-Cycler (Bio-Rad, Hercules, CA) and SYBR green detection. See supple-
mentary material for details of quantitative real-time PCR primers and the
amplicon length of selected genes. Reactions were performed in 25 ?l in
triplicate wells in 96-well plates with the following ingredients: 5? and 3?
primers (200 nM each), iQ SYBR Green Supermix (Bio-Rad), and cDNA
corresponding to 40 ng of total RNA. Mouse ?-actin was amplified in
separate reactions in the same plate to be used as an internal control for
variances in the amount of cDNA in PCR. See supplementary Table VIII
for primer sequences and amplicon lengths. PCR cycle setup was as fol-
lows: 95°C for 1 min, 95°C for 3 min, 40? (95°C for 30 s, 60°C for 10 s,
72°C for 10 s). The Pfaffl’s equation (11) was used to calculate the ex-
pression ratio (R) of ligand-treated vs control B cells. Briefly: R ?
((Etarget)?CPtarget (control ? treated))/((E?-actin)?CP?-actin (control ?
treated)), where E ? 10(?1/slope), with the slope being the slope of the
standard curve of the target genes or ?-actin; ?CP target (control ?
treated) is the average cross point cycle number of the control minus that
of the treated sample for the target gene; ?CP ?-actin (control ? treated)
is the average cross point cycle number of control minus the treated sample
To examine gene expression changes induced by the 33 single li-
gands, we cultured purified mouse splenic B cells with ligands in
serum-free medium for 0.5, 1, 2, and 4 h. cDNA synthesized from the
RNA of B cells was labeled with Cy5 and hybridized onto custom-
made two-color Agilent cDNA arrays with a Cy3-labeled cDNA pre-
relative to 0 h in response to ligand or medium alone was then cal-
had three considerations when choosing this experimental design.
First, we focused on early gene expression changes with the rationale
that these changes are likely to be regulated by signaling pathways
directly activated downstream of receptor engagement and, therefore,
best reflect the characteristics of ligand-specific signal transduction.
Second, we used serum-free medium to avoid signaling events that
might be triggered by serum growth factors. Finally, we used the
RNA of total splenocytes as the universal reference in the two-color
7142PATTERNS OF B CELL GENE EXPRESSION IN RESPONSE TO 33 SINGLE LIGANDS
cDNA array hybridization to control for the variance introduced dur-
ing different times of array processing and to allow easy cross-con-
dition comparisons (12).
Overview of characteristics of B cell gene expression profiles
The majority of the early gene expression changes were found in
the responses to anti-Ig, CD40L, CpG, IL-4, and LPS, ligands that
either directly induce or costimulate proliferation of resting B
cells. Of the 2937 features identified by SAM analysis to be dif-
ferentially expressed in response to the 33 single ligands during the
4-h period, 2625 features changed expression in response to anti-
Ig, CD40L, CpG, IL-4, or LPS, while 797 features showed signif-
icant changes in response to the other 28 ligands. The dendrogram
of the hierarchically clustered gene expression changes induced by
all 33 single ligands revealed that the dominant gene expression
pattern (Fig. 1A) shown by the intense red or green vertical strips
was similar in the anti-Ig, CD40L, and LPS responses, represent-
ing coordinated up- or down-regulations of multiple genes. A sim-
ilar pattern was detected in the CpG and IL-4 responses; however,
the changes were of a smaller magnitude. No prominent expression
pattern was observed in responses to the remaining 28 ligands (Fig.
1A). Because expression changes induced by the 28 ligands were
of smaller magnitude than those induced by anti-Ig, CD40L, CpG,
IL-4, and LPS, their patterns may be masked when all the expres-
sion changes are visualized together. To explore this possibility,
we performed hierarchical clustering using only gene expression
changes induced by the 28 ligands to look for significant patterns.
We found that there were small clusters of genes that showed
strong changes in response to BLC, SDF1?, IFN-?, IL-10, and
PAF (Fig. 1B), while the rest of the genes were expressed in
treated B cells at similar levels as they were in time-matched con-
trol B cells. See Fig. 2 for the expression changes of the genes in
these small clusters.
Of the responses to anti-Ig, CD40L, LPS, CpG, or IL-4, the
number of differentially expressed features identified by SAM
analysis increased with time, with a sharp jump at 4 h (Fig. 3). A
total of 2547 features changed expression at 4 h in contrast to a
changes induced by single ligands. Experimental conditions were aligned
along the horizontal axis, in which the medium alone (UNTR) time course
was followed by the time course of single ligands arranged according to the
ligand’s alphabetical order. Each time course consists of four time points:
0.5, 1, 2, and 4 h. Hierarchically clustered expression changes, calculated
as the ratio of expression level in cultured B cells at 0.5, 1, 2, and 4 h vs
that in 0-h B cells in the log2scale, were displayed along the vertical axis.
For details of data filtering, processing, and clustering, see Material and
Methods. A, Gene expression changes induced by all 33 single ligands.
UNTR and ligands promoting proliferation were labeled. B, Gene expres-
sion changes induced by 28 nonmitogenic ligands. The 28 ligands include
all single ligands, except anti-Ig, CD40L, CpG, IL-4, and LPS. Yellow
arrows point to examples of small clusters of strong expression changes.
UNTR and ligands inducing small clusters of changes were labeled.
Dendrograms ofhierarchically clustered expression
BLC, IFN-?, IL-10, PAF, and SDF1?. The symbol and LocusLink of the
genes are listed on the right side of the dendrogram. Each Œ under the
ligand labels represents a time course (0.5, 1, 2, and 4 h). Gene expression
changes in B cells cultured in medium alone (UNTR) were included as the
Features showing robust expression changes in response to
7143 The Journal of Immunology
total of 663 features at 0.5, 1, and 2 h. A previous study of anti-Ig
response in mouse splenic B cells also reported a sharp increase at
4 h in the number of affected genes (13). The kinetics of expression
change varied in response to different ligands. At 0.5, 1, and 2 h,
anti-Ig and CD40L induced greater numbers of changes than LPS,
CpG, and IL-4 (Fig. 3), and by 4 h, a large number of genes
changed expression in response to LPS, anti-Ig, and CD40L, while
considerably fewer genes were affected by CpG and IL-4. Thus,
anti-Ig and CD40L induced the most immediate early gene expres-
sion changes, but by 4 h, anti-Ig, CD40L, and LPS all had exten-
sive effects on gene expression, with lesser effects by CpG
The finding that the five proliferative ligands induced the stron-
gest gene expression changes among the 33 ligands led us to focus
on the proliferative ligands to examine more closely the similari-
ties and differences in their downstream gene expression re-
sponses. We sought to identify target genes that were uniquely
regulated by individual ligands or were coregulated by a group of
ligands. Four major expression patterns were identified in anti-Ig,
CD40L, CpG, IL-4, and LPS responses to date. We report in this
study the genes in each distinct pattern and, when information is
available, speculate on the pathways of signal transduction and on
the biological relevance of the expression changes observed.
Expression change patterns shared by anti-Ig, CD40L, IL-4,
CpG, and LPS responses
A large number of features showed a similar temporal pattern of
expression change in response to anti-Ig, CD40L, CpG, IL-4, or
LPS, while the magnitude of change varied from ligand to ligand
for some features. A total of 176 features (149 unique genes) de-
creased and 294 features (228 unique genes) increased their ex-
pression at least 30% in response to treatment with each of the five
ligands, relative to culture in medium (Fig. 4). See supplementary
Table V for expression fold changes of up-regulated and down-
regulated features. Although strong expression changes were ob-
served for some of the features at 2 h, almost all of the features
exhibited significant up- or down-regulation at 4 h. Several genes
regulating cell cycle entry and progression showed expected ex-
pression changes. For example, cyclin-dependent kinase 4, a gene
promoting cell cycle progression, was up-regulated (Fig. 4B);
Forkhead box O1 and cyclin G2, genes inhibiting cell cycle entry,
were down-regulated by the ligands. So was a transcription repres-
sor, basic Kruppel-like factor 3 (Fig. 4A) (14–19). Several genes
involved in signal transduction decreased expression with time in
response to the ligands. These include MAPK kinase 6, a kinase
that directly activates p38 MAPK (20); spleen tyrosine kinase, a
kinase that contributes to the activation of Bruton’s tyrosine kinase
and phospholipase C-?1 downstream of BCR (21); and the ? iso-
form of diacylglycerol kinase, a kinase suggested to attenuate re-
ceptor signaling in T cells by converting a secondary messenger,
diacylglycerol, to phosphatidic acid (22) (Fig. 4A). These changes
in gene expression may result in subsequent changes in cell sig-
naling responses, although the precise role of such gene expression
changes in regulating B cell activity is not clear.
We also found that several genes encoding enzymes of the gly-
colysis pathway, including hexokinase 2 (Hk2), phosphoglycerate
mutase 1, lactate dehydrogenase 2 (Ldh2), and lactate dehydroge-
nase 3 (Ldh3), were up-regulated. Glycolysis converts the 6-car-
bon glucose into 3-carbon pyruvate and NADH. Pyruvate is either
oxidized further through the TCA cycle into CO2and H2O in the
mitochondria aerobically, or is reduced by NADH to lactate anaer-
obically in the cytosol. Hk2 and phosphoglycerate mutase 1 pro-
teins catalyze two different steps of the pathway that leads to the
generation of pyruvate, while Ldh2 and Ldh3 proteins reduce
pyruvate to lactate. The up-regulation of these glycolysis genes
suggests that glycolysis activity increases and shifts toward the
anaerobic pathway in B cells stimulated with ligands promoting
cell growth and proliferation. In fact, several reports showed that
lymphocyte cell lines and primary cells up-regulated the activity of
multiple glycolysis enzymes including Hk2, and increased glyco-
lysis rate and lactate production, when stimulated with cytokines
or other mitogenic ligands such as anti-CD3 plus anti-CD28 (23,
24). Although glycolysis is generally thought to be regulated by
metabolic demands of the cells through feedback mechanisms,
these recent reports suggest that glycolysis activity can be directly
regulated by signal transduction pathways downstream of the re-
ceptors, such as the PI3K/protein kinase B (AKT) pathway (23,
24). The shift toward anaerobic glycolysis is not because the cells
lack the ability to undergo TCA cycle for maximal energy output,
but rather is due to the fact that the rate of pyruvate and NADH
generation from the high glycolysis activity and the ample supply
of glucose in the culture medium exceeds the rate of their con-
sumption in the mitochondria. As a result, pyruvate is reduced by
NADH to lactate and secreted by the cells (23, 24). In vivo when
nutrients such as glucose are limited, the up-regulation of glyco-
lysis by mitogenic signals can help stimulated B cells to mount
rapid cell growth and proliferation and allow them an advantage in
using nutrients over unstimulated cells.
Finally, consistent with a previous study on anti-Ig gene expres-
sion response in B cells (25), we found that a large number of
genes (64 features representing 46 unique genes) involved in
mRNA processing and translation were almost exclusively up-reg-
ulated. These expression changes are likely to lead to the up-reg-
ulation of protein synthesis, which is required for cell size in-
crease, DNA replication, and cell division. See supplementary
Table V for expression fold changes of genes involved in RNA
processing and translation.
Gene expression change patterns distinguishing IL-4
Genes in this group exhibited two expression change patterns: 1)
not changed by anti-Ig, CD40L, CpG, and LPS, while strongly
up-regulated by IL-4 (Fig. 5A), and 2) down-regulated by anti-Ig,
CD40L, CpG, and LPS, while up-regulated or not changed by IL-4
(Fig. 5B). See supplementary Table VI for expression fold changes
of features of known genes in this group. Three of the genes
uniquely up-regulated by IL-4, Caspase-6, X box-binding protein
by SAM in response to anti-Ig, CD40L, CpG, IL-4, and LPS. The y-axis
scales the number of differentially expressed features, and x-axis is for
ligand condition. The false discovery rate of the differentially expressed
feature list at each time point (0.5, 1, 2, and 4 h) is listed in the parenthesis.
The number of differentially expressed features identified
7144 PATTERNS OF B CELL GENE EXPRESSION IN RESPONSE TO 33 SINGLE LIGANDS
1 (Xbp-1), and the ? isoform of calcineurin catalytic subunit have
been suggested to be STAT6 targets in B cells and/or T cells in
published reports (26–28). Additional experiments are needed to
determine whether other genes up-regulated by IL-4 are also tran-
scriptional targets of STAT6. For genes whose expression was not
changed by IL-4 while down-regulated by other ligands, the sim-
plest explanation could be that they are target genes of transcrip-
tion repressors activated by anti-Ig, CD40L, CpG, LPS, but not by
IL-4. It is also possible that these are target genes of transcription
factors inactivated by anti-Ig and others, but not by IL-4.
We are only beginning to understand the biological relevance of
the IL-4-specific gene expression pattern. Xbp-1, which was
strongly up-regulated within 1 h of IL-4 stimulation, is a crucial
transcriptional factor for plasma cell differentiation (29). Intrigu-
ingly, Xbp-1 activation requires an mRNA splicing event triggered
by the unfolded protein response, which leads to a reading frame
shift and subsequent translation of an additional trans activation
domain (30–32). It was shown that while IL-4 was the only cy-
tokine that rapidly induces Xbp-1 in mouse B cells, long-term
treatment with anti-CD40 or LPS, up to 2 days, strongly induced
Xbp-1 mRNA processing as well as transcription (28, 29, 33).
Increased load of Ig in endoplasmic reticulum in response to anti-
CD40 and LPS may initiate the unfolded protein response and
subsequent Xbp-1 mRNA splicing. Indeed, Xbp-1 mRNA splicing
depends on IgM protein synthesis during B cell differentiation, and
the spliced form is in turn required for Ig production and secretion
(28, 34). Xbp-1 transcripts induced early by IL-4 may help to
ensure efficient processing of subsequently produced Ig, and may
have other as yet unknown biological significances (28). No
change in Xbp-1 expression in response to IL-4 was detected in
mouse T cells (27), suggesting that cell type-specific proteins and
possibly chromosome accessibility are involved in regulating
Xbp-1 expression. With regard to cell proliferation, we did not find
the induction of proliferation inhibitors or the lack of expression of
genes required for proliferation that can account for the lack of
direct proliferative effect of IL-4 compared with anti-Ig, CD40L,
CpG, and LPS. It is possible that quantitative characteristics in
gene expression in response to IL-4 could contribute to the lack of
proliferative effect of IL-4, notably, the generally smaller magni-
tude of expression changes (Fig. 3). Our results also suggest that
the ability of IL-4 to promote proliferation as a cofactor is not
solely attributed to the up-regulation of antiapoptotic genes, such
as Bcl-2, by IL-4 stimulation (35), but it may be due to the syn-
ergistic induction of many genes involved in cell proliferation
Gene expression change patterns distinguishing anti-Ig
Genes in this group demonstrate mainly two temporal expression
patterns: 1) strongly up-regulated by CD40L, IL-4, CpG, and LPS,
while not changed or only slightly up-regulated by anti-Ig (Fig.
terns in response to anti-Ig, CD40L, CpG, IL-4, and LPS. A, Features that
decreased expression with time. B, Features that increased expression with
time. Each Œ under the ligand labels represents a time course (0.5, 1, 2, and
4 h). Gene expression changes in B cells cultured in medium (UNTR) alone
were included as the controls. The symbol of genes discussed in the results
is labeled on the right side of the dendrogram.
Features showing similar temporal expression change pat-
Features strongly up-regulated by IL-4, while not changed by anti-Ig,
CD40L, CpG, and LPS. B, Features strongly up-regulated or not changed
by IL-4, while down-regulated by anti-Ig, CD40L, CpG, and LPS. Only
features representing known genes are shown. The symbol and LocusLink
of the genes are listed on the right side of the dendrogram. Genes discussed
in the results are pointed to by arrows. Each Œ under the ligand labels
represents a time course (0.5, 1, 2, and 4 h). Gene expression changes in B
cells cultured in medium alone (UNTR) were included as the controls.
Features exhibiting IL-4-specific expression patterns. A,
7145 The Journal of Immunology
6A), and 2) down-regulated by other ligands, mainly at 2 and 4 h,
while up-regulated by anti-Ig (Fig. 6B). See supplementary Table
VII for expression fold changes of features of known genes in this
group. Worth noting in Fig. 6A is the significantly weaker up-
regulation of two genes required for cell cycle entry and progres-
sion, namely cyclin D2 (Ccnd2) and polo-like kinase (Plk), in re-
sponse to anti-Ig compared with that in response to CD40L, IL-4,
CpG, and LPS (36–38). The comparatively modest increase in
Ccnd2 and Plk expression could reflect heterogeneity in the splenic
B cell population; although most splenic B cells are mature fol-
licular cells, they also include transitional immature cells and ma-
ture marginal zone cells (39, 40). It is known that immature B cells
undergo apoptosis and down-regulate Ccnd2 in response to anti-Ig
(39, 41, 42), but do proliferate to the other mitogen, LPS (39). It
is possible that different gene response patterns to anti-Ig in the B
cell subsets could dilute or cancel each other out at the population
level, contributing to less up-regulation of Ccnd2 and Plk. This
explanation also fits with the observation that mouse splenic B
cells showed more death in response to anti-Ig than to CD40L or
LPS (43–45). Another gene that was strongly induced by CD40L,
CpG, IL-4, and LPS, but not by anti-Ig, is myristoylated alanine-
rich protein kinase C substrate (MARCKS). MARCKS encodes a
membrane protein that can bind to members of protein kinase C
family proteins, actin, and the calmodulin-Ca2?complex (46, 47).
It was proposed that the MARCKS protein can bind and sequester
a significant fraction of phosphoinositol-4,5-biphosphate in lateral
membrane domains and can release the lipid when phosphorylated
by protein kinase C family members or when it binds to calmod-
ulin-Ca2?complex (48–50). Thus, the increased expression of
MARCKS may affect signaling by inositol phosphates.
Several genes involved in endocytosis and intracellular traffic
were up-regulated by anti-Ig and down-regulated by other ligands
(Fig. 6B). Atp6ap2, Atp6v0e, and Atp6v1c1 encode subunits of
H?-ATPases whose function is to transport H?from cytoplasm
into intracellular compartments, resulting in luminal acidification,
which is important in regulating various steps of endocytosis and
intracellular traffic (51). Other genes up-regulated by anti-Ig that
may be involved in endocytosis and intracellular trafficking in-
clude sorting nexin 5, a member of the nexin family proteins pos-
tulated to be involved in intracellular protein targeting (52), and
chloride channel 7, a member of the voltage-gated chloride chan-
nel family proteins that have been suggested to contribute to lu-
minal acidification by charge neutralization (53). It has been
shown that BCR signaling facilitates multiple steps of the Ag pre-
sentation pathway, in which BCR-Ag complexes are internalized
and targeted to the endosomal compartment, followed by Ag pro-
cessing and loading onto MHC class II complex, and finally pre-
sentation on the cell surface (54–58). Increasing the expression of
genes involved in endocytosis and intracellular traffic may be one
of the mechanisms by which BCR signaling accelerates Ag pre-
sentation, which is important for B cell expansion and selection
Nfatc1, encoding the C1 subunit of the NF-AT transcription
factor, was up-regulated at 2 and 4 h in response to anti-Ig while
remaining unchanged in response to other proliferative ligands
Features exhibited weaker up-regulation in response to anti-Ig than to
CD40L, CpG, IL-4, and LPS. B, Features up-regulated by anti-Ig and
down-regulated or not changed by CD40L, CpG, IL-4, and LPS. The de-
scription of the figure is the same as in Fig. 5.
Features showing anti-Ig-specific expression patterns. A,
CpG, IL-4, and LPS. The description of the figure is the same as in Fig. 5.
Features up-regulated by CD40L and not changed by anti-Ig,
7146PATTERNS OF B CELL GENE EXPRESSION IN RESPONSE TO 33 SINGLE LIGANDS
(Fig. 6B). This observation, together with the fact that anti-Ig ac-
tivates NF-AT, raises the possibility that Nfatc1 expression may be
regulated by a positive feedback loop, in which activated NF-AT
transcription factor induces Nfatc1 expression (59). This mecha-
nism may sustain NF-AT activation by anti-Ig. Lymphotoxin ?
(Ltb) was strongly down-regulated by anti-Ig (Fig. 6), an unex-
pected result given that Ltb produced by B cells is required for
normal T-dependent humoral responses (60). A smaller magnitude
of down-regulation was induced by IL-4. Whether Ltb expression
is up-regulated in later time points beyond 4 h is unknown. CD40L
was previously shown to induce strong and sustained up-regulation
of Ltb in B cells following 24 h of stimulation (61). It is possible
that costimulation with CD40L is required to up-regulate Ltb in B
cells during T-dependent immune response.
Gene expression changes distinguishing CD40L
Genes in this group in general exhibited greater up-regulation in
response to CD40L than in response to other ligands (Fig. 7). See
supplementary Table VIII for expression fold changes of features
of known genes in this group. Of particular interest is Nf?b2,
which showed strong and consistent up-regulation in response to
CD40L during the 4-h period. NF-?B2 is required for peripheral B
cell maintenance and for normal development of secondary lym-
phoid tissue architecture and humoral responses (62, 63). Several
reports demonstrated that NF-?B2, together with its binding part-
ner, RELB, is activated via an alternative pathway, whereby ex-
tracellular stimuli such as the B cell-activating factor of the TNF
family, CD40L, and LT? induce the processing of the p100 pre-
cursor form of NF-?B2 into p52, which subsequently translocates
into the nucleus with RELB to activate transcription (64–68). It is
conceivable that the increased expression of Nf?b2 in response to
CD40L may contribute to sustained activation of NF-?B2-RELB
pathway; however, the precise function of the pathway in CD40L-
mediated B cell activation remains to be defined.
Results of quantitative real-time PCR validation of selected
To validate the microarray data, we measured expression changes
of seven of the genes we discussed in our paper in response to 4-h
treatment with anti-Ig, CD40L, and IL-4 using quantitative real-
time PCR. As shown in Fig. 8, gene expression changes measured
by quantitative real-time PCR are in general comparable to those
determined by microarray. PCR measured Ltb expression changes
induced by anti-Ig, CD40L, and IL-4; Ntac1 expression change
induced by CD40L and IL-4; and Xbp-1 expression change in-
duced by anti-Ig were greater than those measured by microarray.
In three cases, PCR measured expression change of Xbp-1 induced
by CD40L, Atp6ap2 expression change induced by IL-4, and
Nf?b2 expression changes induced by anti-Ig are in a different
direction than those determined by microarray. In these cases, the
expression changes (in log2scale) measured using both approaches
are all smaller than 0.5. It is generally thought that measurement of
smaller expression changes by microarray tends to be more vari-
able. Despite the above-mentioned differences, ligand-specific ex-
pression change patterns determined by quantitative real-time PCR
are largely consistent with those revealed by microarray data. Spe-
cifically, spleen tyrosine kinase showed up-regulation in response
to all three ligands; ? isoform of calcinerin catalytic subunit and
Xbp-1 showed the strongest up-regulation in response to IL-4,
while showing little change or down-regulation in response to anti-
Ig and CD40L; Atp6ap2 and Nfatc1 were uniquely up-regulated by
anti-Ig, while showing little change or down-regulation in response
to CD40L and IL-4; Ltb showed the strongest down-regulation in
response to Anti-Ig; and finally, Nf?b2 was strongly up-regulated
In the present study, we described the first study of genome-wide
transcriptional responses in B cells to short-term stimulation with
a comprehensive set of 33 single ligands, almost all of which in-
duce measurable early upstream biochemical signals. Our first
finding is that 5 of the 33 ligands that directly induce or costimu-
late proliferation generated most of the significant gene expression
changes, while the remaining 28 ligands, many of which produce
short-term reversible responses, such as chemokines, tended not to
induce sustained robust gene expression changes. On one hand, it
makes sense that proliferative ligands need to induce immediate
early gene expression changes that can further drive cellular
changes required for proliferation, such as the increase of cell size,
DNA replication, and cell division. In contrast, chemotactic li-
gands, which generate only transient morphological changes that
allow cells to migrate along a chemokine gradient, need to avoid
expression patterns using quantitative real-time PCR. Duplicate or tripli-
cate total RNA samples used for microarray experiments of 4-h untreated,
4-h anti-Ig, 4-h CD40L, and 4-h IL-4-treated B cells were pooled, and 1-?g
aliquots were reverse transcribed and used as templates to amplify selected
genes by quantitative real-time PCR with SYBR green detection. The ratio
of the expression level of each gene in treated vs untreated control B cells
was determined with the Pfaffl method (see Materials and Methods), and
its value in the log2scale was plotted in u. Microarray-measured gene
expression changes, log2(4-h treated/4-h untreated), were calculated by
subtracting the average of triplicate log2(4-h untreated/0 h) from the aver-
age of triplicate log2(4-h treated/0 h) and were plotted in ?.
Validation of the expression of selected genes in different
7147The Journal of Immunology
inducing expression changes that would lead to long-term irrevers-
ible cellular alterations. On the other hand, the finding is intriguing
given the fact that chemotactic ligands, BLC, Ebl1-ligand chemo-
kine, secondary lymphoid-tissue chemokine, and SDF1?, induced
significant Ca2?flux, cAMP generation, and phosphorylation of
AKT, ERK1/2, and P90RSK, while mitogenic ligand CpG induced
little or no Ca2?flux, cAMP generation, and limited kinase phos-
phorylation (data available through the B cell ligand screen link at
the Alliance for Cellular Signaling Data Center website www.sig-
naling-gateway.org/data/). It appears then that the mere activation
of an upstream kinase or other signaling events does not neces-
sarily lead to the extensive expression of its downstream target
genes. In addition, a strong signature of classical signaling path-
ways is not always required for robust gene expression changes. It
is likely that gene expression is regulated by multiple upstream
inputs, including, but not limited to, the ones measured in our
study, in which the timing, duration, as well as intensity of each
input could possibly have synergistic effects.
Our second finding is that a large number of genes showed sim-
ilar temporal patterns of expression change in response to anti-Ig,
CD40L, CpG, IL-4, and LPS, while a few genes exhibited patterns
unique for anti-Ig, CD40L, or IL-4. It is intriguing that receptors
with distinct signal transduction pathways induced largely over-
lapping early gene expression change profiles. Anti-Ig, CD40L,
IL-4, and CpG/LPS receptors recruit unique kinases and/or adaptor
proteins to the membrane immediately downstream of ligand en-
gagement. Through intermediate steps that are not completely un-
derstood, unique as well as common signaling events are induced
further downstream. Although Ca2?release and NF-AT are in-
duced only by anti-Ig and STAT6 mostly by IL-4 (5–8, 69), AKT,
NF-?B, PI3K, ERK 1 and 2 (ERK1/2), JNK, and p38 MAPK can
be activated by all or a subset of the ligands. That distinct signal
transduction pathways can affect the expression of a common set
of immediate early genes has been reported before. It was found
that in NIH 3T3 cells, mutating the binding sites for activation of
the phospholipase C-?1, PI3K, Src homology region 2 domain-
containing phosphatase 1, and Ras GTPase-activating protein of
platelet-derived growth factor ? receptor only led to quantitative,
but not qualitative change in the expression of a common set of
immediate early genes in response to platelet-derived growth fac-
tor stimulation (70). This observation led to the suggestion that
distinct signal transduction pathways, rather than regulate the ex-
pression of specific subsets of immediate early genes, generate
largely overlapping effects on the immediate early genes (70, 71).
This can be achieved by a mechanism whereby distinct signal
transduction pathways activate multiple transcription factors, each
or subsets of which can exert qualitatively similar effects on the
expression of early genes. Other mechanisms include cross talks
between signal transduction pathways and the convergence of dif-
ferent signals to common regulatory mechanisms, such as the
MAPK pathways, which generate the shared early transcriptional
response. These possibilities are not mutually exclusive; each of
them can contribute to the overlapping effects of different ligands
on early gene expression. In any case, the specificity of the bio-
logical functions of different ligands can be mediated by either
qualitative differences in early gene expression and/or the unique
induction or repression of small subsets of genes. In future work,
combining these comprehensive gene expression change measure-
ments with the signaling studies conducted with these ligands will
allow a greater understanding about how signaling networks im-
pact gene expression. These inferences can be further strengthened
by perturbations induced in specific signaling pathways and by
computational prediction of transcription factor binding sites in the
promoters of shared and distinct target genes.
Note added in proof. The microarray data used in this paper were
deposited into GEO (www.ncbi.nlm.nih.gov/geo/, Gene Expression
Omnibus) under the accession numbers of GSM5420, GSM5422-
5428, GSM5437-5552, GSM5556, GSM5558, GSM5567-5851,
GSM15996-16100, and GSM16108-16164.
We thank Dr Gilberto R. Sambrano and other members of Alliance for
Cellular Signaling for their critical review and insightful input during the
preparation of this manuscript.
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7149The Journal of Immunology