Some additional analysis for paper revision
Junyan Lu
2020 Sept. 3
Last updated: 2024-06-12
Checks: 6 1
Knit directory: BH3profiling/analysis/
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Load and pre-process datasets
Define interested genes
Genes will be considered in the analysis
BCL-2 MCL-1 BCL-xL BFL-1 BAX BAK BIM PUMA
"BCL2" "MCL1" "BCL2L1" "BCL2A1" "BAX" "BAK1" "BCL2L11" "BBC3"
NOXA COX5A COX5B SOD1 SOD2
"PMAIP1" "COX5A" "COX5B" "SOD1" "SOD2" The first row shows the commonly used protein names and the second row shows the corresponding official gene symbols
BH3 profiling data
RNAseq data
BCL2 MCL1 BCL2L1 BCL2A1 BAX BAK1 BCL2L11 BBC3 PMAIP1 COX5A
TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE TRUE
COX5B SOD1 SOD2
TRUE TRUE TRUE [1] 13 71Proteomics
BCL2 MCL1 BCL2L1 BCL2A1 BAX BAK1 BCL2L11 BBC3 PMAIP1 COX5A
TRUE FALSE FALSE FALSE TRUE FALSE TRUE FALSE FALSE TRUE
COX5B SOD1 SOD2
TRUE FALSE TRUE [1] 6 91Genomics
Prepare patient genomic background
[1] "IGHV.status" "del11q" "del13q" "del17p" "trisomy12"
[6] "NOTCH1" "SF3B1" "TP53" Correlation between the baseline mRNA expression of the interested genes and mutations in CLL
Result table
Plot associations with 10% FDR
Correlation between the protein expressions of the interested genes and mutations in CLL
Result table
Only the associations between BAX and trisomy12 passed 10% FDR
Plot associations with 10% FDR
Differential expression of the interested genes before and after ex-vivo Ibrutinib treatment
Load dataset
Preprocessing
Subset for DMSO and Ibr
Subset for interested genes
[1] 13 187Differential expression between Ibr treatment and DMSO
Plot associations with 10% FDR
Wether the expression of interested genes before and after ex-vivo ibrutinib treatment associated with ibrutinib responses?
Prepare drug response profile
Prepare gene expression
Association test
Table of significant associations (10%)
In the treatment column:
- Ibrutinib_48h means the gene expression after
Ibrutinib treatment for 48 hours
- DMSO_48h means the gene expression after 48h
incubation with just DMSO
- FoldChange means the log fold change between
Ibrutinib and DMSO after 48 hourse
Note that in this experiment, we don’t have the real baseline (0 hour)
Plot the significant associations
Wether the expression of interested genes before and after ex-vivo ibrutinib treatment associated with BH3 profiling data?
Prepare drug response profile
Association test
Table of significant associations (10%)
Plot the significant associations
It’s interesting to see that the gene expression after 48h DMSO
incubation show stronger association to BH3 profile than the real
baseline gene expression (0h) we used in the manuscript
This could be because the BH3 profiling data we are using is
also the BH3 profile after 48h DMSO incubation
You can see from the below longitudinal gene expression profile,
some of those genes show strong changes during culturing in
DMSO
Look at the longitudinal gene expression data
Visualize the time-course expression of the interested genes in DMSO and Ibrutinib treated samples
Correlate the protein expression with in-vivo Ibr treated patients (a smaller cohort from Heidelberg)
Load dataset
Subset for interested genes
[1] 6 10Result table
Plot associations with 10% FDR
Contrary to the gene expression after ex-vivo Ibr treatment, BCL2 protein level increased after in-vivo ibrutinib treatment
Correlate the protein expression with in-vivo Ibr treated patients (look at a larger cohort from Zurich)
Load dataset
Selected appropriate samples
[1] 9 30Differential expression
Result table
Plot associations with 10% FDR
The trend is similar to the smaller cohort from
Heidelberg
Correlate the gene expression with in-vivo Ibr treated patients (those are the sample samples as the ones above)
Load dataset
Selected appropriate samples
[1] 12 70Differential expression
Plot associations with 10% FDR
It seems the trend on mRNA level is not consistent with the
trend on protein level..
Analysis of Stephen’s Western Blot data
T-test
Boxplot
R version 4.2.0 (2022-04-22)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Big Sur/Monterey 10.16
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] latex2exp_0.9.4 forcats_0.5.1
[3] stringr_1.4.1 dplyr_1.1.4.9000
[5] purrr_0.3.4 readr_2.1.2
[7] tidyr_1.2.0 tibble_3.2.1
[9] ggplot2_3.4.1 tidyverse_1.3.2
[11] DESeq2_1.36.0 SummarizedExperiment_1.26.1
[13] Biobase_2.56.0 MatrixGenerics_1.8.1
[15] matrixStats_0.62.0 GenomicRanges_1.48.0
[17] GenomeInfoDb_1.32.2 IRanges_2.30.0
[19] S4Vectors_0.34.0 BiocGenerics_0.42.0
[21] jyluMisc_0.1.5
loaded via a namespace (and not attached):
[1] utf8_1.2.4 shinydashboard_0.7.2 tidyselect_1.2.1
[4] RSQLite_2.2.15 AnnotationDbi_1.58.0 htmlwidgets_1.5.4
[7] grid_4.2.0 BiocParallel_1.30.3 maxstat_0.7-25
[10] munsell_0.5.0 codetools_0.2-18 DT_0.23
[13] withr_3.0.0 colorspace_2.0-3 highr_0.9
[16] knitr_1.39 proDA_1.10.0 rstudioapi_0.13
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[34] ggbeeswarm_0.6.0 locfit_1.5-9.6 bitops_1.0-7
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[58] modelr_0.1.8 crosstalk_1.2.0 backports_1.4.1
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