In
vivo and ex vivo comparative
transcriptional profiling of invasive and non-invasive Candida albicans
isolates identifies genes associated with tissue invasion
Sascha Thewes, Marianne Kretschmar, Hyunsook
Park, Martin Schaller, Scott G. Filler and Bernhard Hube
Mol Microbiol (2007)
Summary
The human pathogenic fungus Candida albicans can cause a wide range of infections and
invade multiple organs. To identify C. albicans genes that are expressed during invasion of the liver,
we used genome-wide transcriptional profiling in vivo and ex vivo. By analysing the different phases of intraperitoneal
infection from attachment to tissue penetration in a time course experiment
and by comparing the profiles of an invasive with those of a non-invasive
strain, we identified genes and transcriptional pattern which are associated
with the invasion process. This includes genes involved in metabolism, stress,
and nutrient uptake, as well as transcriptional programmes regulating morphology
and environmental sensing. One of the genes identified as associated with
liver invasion was DFG16, a gene crucial for pH-dependent hyphal formation,
correct pH-sensing, invasion at physiological pH and systemic infection.
These data were provided by Sascha Thewes1
and Bernhard Hube2, 1Robert Koch-Institut, Berlin,
Germany; 2Hans Knšll-Institut, Jena, Germany.
The provided data consist of four parts:
- supplementary
tables to the text
- raw data
from in vivo
transcriptional profiling (SC5314 and ATCC10231) after intraperitoneal
infection of mice
- raw data
from ex vivo
transcriptional profiling (SC5314 12h) after infection of haemoperfused
pig liver
- raw data
from in vitro
transcriptional profiling of ∆dfg16 vs. CAI4 + CIp10 (pH 7.4; 37 ˇC)
1. Supplementary
tables
2. Experimental Data in
vivo
transcriptional profiling
| Species |
Candida
albicans |
| |
|
| Strains |
wt: SC5314 (Gillum
et al., 1984) |
| ATCC10231 (http://www.lgcpromochem.com/atcc/) |
|
| Growth Conditions |
Intraperitoneal infection
of mice |
| RNA extraction |
Harvested cells were frozen
in liquid N2. RNA
was extracted using RNApure (Peqlab)
following the manual. |
| Labelling |
Direct labelling with Cy3/Cy5-dUTP
as described here
using the Agilent
Fluorescent Linear Amplification Kit. |
| Reference
RNA (refRNA) |
The reference (Cy3) on
each array was from a pool of SC5314 (Gillum et al., 1984) RNA samples from cells
grown in YPD at 37ˇC to mid-exponential phase. |
| Microarray |
Glass microarrays with
probes for 5907 C. albicans ORFs as
described. |
| Microarray Manufacturer
|
|
| Hybridisation Method
|
DIG EasyHyb hybridisation |
| Imaging & Data Capture
|
GenePix 4000B Scanner (Axon
Instruments, now Molecular Devices).
Software: GenePix
Pro 4.1 (Molecular Devices). |
| Normalisation Method
|
Intensity dependent (Lowess)
normalisation by GeneSpring
7.0 (Silicon Genetics). |
| Quality Analysis |
In GenePix Pro, signal
had to be at least 1 SD above
background |
| Statistical Analysis |
|
Microarray Data (in vivo)
|
Sample |
Cy3 Labelling |
Cy5 Labelling |
Microarray Batch No. |
Microarray Slide No. |
Image Files (.tif) |
GenePix Results file (.gpr) |
Data from GeneSpring (.xls) |
| S 0h (1) |
Common reference |
SC5314 preculture |
J160C |
9 |
J160C_9_532.tif J160C_9_635.tif |
J160C_9.gpr |
|
| S 0h (2) |
Common reference |
SC5314 preculture |
K030C |
18 |
K030C_18_532.tif K030C_18_635.tif |
K030C_18.gpr |
|
| A 0h (1) |
Common reference |
ATCC10231 preculture |
J160C |
10 |
J160C_10_532.tif J160C_10_635.tif |
J160C_10.gpr |
|
| A 0h (2) |
Common reference |
ATCC10231 preculture |
K030C |
19 |
K030C_19_532.tif K030C_19_635.tif |
K030C_19.gpr |
|
| S 0.5h (1) |
Common reference |
SC5314 lavage |
G300C |
20 |
G300C_20_532.tif G300C_20_635.tif |
G300C_20.gpr |
|
| S 0.5h (2) |
Common reference |
SC5314 lavage |
K030C |
11 (stripped) |
K030C_11_stripped_532.tif K030C_11_stripped_635.tif |
K030C_11_stripped.gpr |
|
| A 0.5h (1) |
Common reference |
ATCC10231 lavage |
H130C |
10 |
H130C_10_532.tif H130C_10_635.tif |
H130C_10.gpr |
|
| A 0.5h (2) |
Common reference |
ATCC10231 lavage |
J160C |
7 (stripped) |
J160C_7_stripped_532.tif J160C_7_stripped_635.tif |
J160C_7_stripped.gpr |
|
| S 3h (1) |
Common reference |
SC5314 3h |
H130C |
13 |
H130C_13_532.tif H130C_13_635.tif |
H130C_13.gpr |
|
| S 3h (2) |
Common reference |
SC5314 3h |
J160C |
7 |
J160C_7_532.tif J160C_7_635.tif |
J160C_7.gpr |
|
| A 3h (1) |
Common reference |
ATCC10231 3h |
H130C |
12 |
H130C_12_532.tif H130C_12_635.tif |
H130C_12.gpr |
|
| A 3h (2) |
Common reference |
ATCC10231 3h |
J160C |
8 |
J160C_8_532.tif J160C_8_635.tif |
J160C_8.gpr |
|
| S 5h (1) |
Common reference |
SC5314 5h |
H130C |
12 (stripped) |
H130C_12_stripped_532.tif H130C_12_stripped_635.tif |
H130C_12_stripped.gpr |
|
| S 5h (2) |
Common reference |
SC5314 5h |
H130C |
14 |
H130C_14_532.tif H130C_14_635.tif |
H130C_14.gpr |
|
| A 5h (1) |
Common reference |
ATCC10231 5h |
H130C |
15 |
H130C_15_532.tif H130C_15_635.tif |
H130C_15.gpr |
|
| A 5h (2) |
Common reference |
ATCC10231 5h |
H130C |
14 (stripped) |
H130C_14_stripped_532.tif H130C_14_stripped_635.tif |
H130C_14_stripped.gpr |
|
| |
|
|
|
|
|
3. Experimental Data ex
vivo
transcriptional profiling
| Species |
Candida
albicans |
| |
|
| Strains |
wt: SC5314 (Gillum
et al., 1984) |
| ATCC10231 (http://www.lgcpromochem.com/atcc/) |
|
| Growth Conditions |
Ex vivo infection of haemoperfused
pig liver (Thewes et al., 2007, J Med Microbiol) |
| RNA extraction |
Harvested cells were frozen
in liquid N2. RNA
was extracted using RNApure (Peqlab)
following the manual. |
| Labelling |
Direct labelling with Cy3/Cy5-dUTP
as described here
using the Agilent
Fluorescent Linear Amplification Kit. |
| Reference
RNA (refRNA) |
The reference (Cy3) on
each array was from a pool of SC5314 (Gillum et al., 1984) RNA samples from cells
grown in YPD at 37ˇC to mid-exponential phase. |
| Microarray |
Glass microarrays with
probes for 5907 C. albicans ORFs as
described. |
| Microarray Manufacturer
|
|
| Hybridisation Method
|
DIG EasyHyb hybridisation |
| Imaging & Data Capture
|
GenePix 4000B Scanner (Axon
Instruments, now Molecular Devices).
Software: GenePix
Pro 4.1 (Molecular Devices). |
| Normalisation Method
|
Intensity dependent (Lowess)
normalisation by GeneSpring
7.0 (Silicon Genetics). |
| Quality Analysis |
In GenePix Pro, signal
had to be at least 1 SD above
background |
| Statistical Analysis |
|
Microarray Data (ex vivo)
|
Sample |
Cy3 Labelling |
Cy5 Labelling |
Microarray Batch No. |
Microarray Slide No. |
Image Files (.tif) |
GenePix Results file (.gpr) |
Data from GeneSpring (.xls) |
| S 12h (1) |
Common reference |
SC5314 12h |
F280D |
23 |
F280D_23 _532.tif
F280D_23 _635.tif |
F280D_23.gpr |
|
| S 12h (2) |
Common reference |
SC5314 12h |
F280D |
28 |
F280D_28_532.tif
F280D_28_635.tif |
F280D_28.gpr |
|
|
|
|
|
|
|
|
4. Experimental Data in
vitro
transcriptional profiling
| Species |
Candida
albicans |
| |
|
| Strains |
CAI4 + CIp10
(Murad
et al., 2000) |
| ∆dfg16 |
|
| Growth Conditions |