Explored differential gene expression of immuno-genes using breast cancer patients’ samples from the Cancer Gene Atlas (TCGA) database. Separated patients by their estrogen receptors (ER) status and discovered significant expression differences between two groups (ER+ and ER-) of patients for several immuno-genes, such as IL12RB2 and IL1F5.

1. Differential Gene Expression in
Breast Cancer
Shih Yin Chen
Michael Totagrande
Meriam Vejiga

2. Breast Cancer

5. Hypothesis

6. Are immuno-genes
differentially
expressed in Breast
Cancer patients?

7. Our Hypothesis
1. Mounting evidence associating viral infection
with some forms of breast cancer
2. Immunogenes alter expression upon viral
infection
3. Estrogen Receptor (ER) expression is one of the
key attributes for BRCA classification
a. ER status (+/-) has clinical significance

8. Some immuno-genes may
be differentially expressed
between ER+ and ER-
patients.

9. The Database

10. The Cancer
Genome Atlas
(TCGA)
National Institutes of Health
Repository of genomic and phenotypic data
for thousands of studies
TCGA-BRCA: Breast Cancer data
1,096 genotyped individuals
RNA-seq, mRNA, miRNA reads for ≈14,000
genes
Online portal very difficult to access and
utilize data
‘R’ packages - RTCGAToolbox, TCGAbiolinks,
RTCGA…
Script procedures to query, download, and analyze,
visualize data

11. Obtaining Data
Firehose
● “RNAseq pipeline”
● Quantile normalize and
log2 transform
TCGA Harmonized
● “Data generation &
harmonization
pipeline”
● GDC Portal Data
aligned to latest human
genome build
(GRCh38)
TCGA Legacy
● No preprocessing
● Raw data

12. Sample of the Data
113
patients
21 ER-
79 ER+
13 Other

13. Procedure
1. Download*
a. RTCGAToolbox or TCGABiolinks
2. Process
a. Split ER+/- patients, Split tumor/non-tumor
tissue per patient
3. Analyze
a. Differential Expression Analysis (DEA)
4. Visualize
a. Tables and Volcano Plots
ER+ ER-
tumor
non-tumor
tumor
non-tumor
tumor
non-tumor
DEA

14. Results

15. IL6 is an inflammatory cytokine that responds to various viruses (HCMV, EBV, and HPV).
Assuming HCMV, EBV, or HPV are involved in breast cancer, there would be higher
expression of IL6 in tumor cells
IL6 and IL6ST are overexpressed in breast cancer. Experimental evidence shows that down-
regulation of expression of IL6 and its receptor results in growth inhibition of MCF-7 breast
cancer cells.
IL8 is a primary cytokine responding to respiratory syncytial virus (RSV) infection. If RSV plays
a role in breast cancer, IL8 expression should increase in tumor tissue.
MUC1 encodes a mucin glycoprotein(s) which is basally expressed in most epithelial cells. In
breast adenocarcinoma and a variety of epithelial tumors its transcription is dramatically
upregulated
Hypothesis support

16. Volcano Plots

17. Gene LogFC LogFC.ER- LogFC.ER+ FDR.ER- FDR.ER+ Tumor.ER- Normal.ER- Tumor.ER+ Normal.ER+ LogFC.diff
NR0B1 0.338 -2.043 -0.025 5.57E-03 9.85E-01 2.52E+00 1.06E+01 1.75E+01 1.40E+01 2.018
ESR1 1.502 -0.152 1.526 8.91E-01 1.32E-13 6.80E+03 9.59E+03 3.62E+04 9.33E+03 1.678
MUC1 2.415 1.306 2.647 1.38E-02 2.17E-32 1.92E+04 7.53E+03 4.56E+04 5.63E+03 1.341
IL12B 1.159 2.293 4.85E-02 1.47E-11 1.18E+01 6.33E+00 1.69E+01 2.71E+00 1.134
FOS -2.659 -3.571 -2.48 1.59E-15 9.39E-29 6.85E+03 8.19E+04 1.79E+04 7.58E+04 1.091
IL17RD -1.739 -0.942 -1.978 3.92E-02 3.31E-30 2.42E+03 5.38E+03 1.82E+03 5.44E+03 -1.036
IL13 -0.965 -2.391 1.97E-01 1.43E-10 2.24E+00 5.43E+00 9.62E-01 4.51E+00 -1.426
IL17B -3.522 -2.45 -3.885 1.45E-03 4.08E-34 2.06E+01 1.77E+02 1.45E+01 1.63E+02 -1.435
MYC -1.095 0.076 -1.569 9.36E-01 1.81E-21 9.29E+03 1.10E+04 4.81E+03 1.17E+04 -1.645
IL1RL2 -1.081 0.224 -1.624 7.41E-01 9.23E-12 1.01E+02 9.81E+01 4.20E+01 1.04E+02 -1.848
IL1F9 3.429 1.063 1.45E-03 9.62E-02 1.92E+01 9.05E-01 3.00E+00 1.23E+00 -2.366
IL1F5 4.483 1.308 3.78E-04 1.08E-02 4.69E+01 1.10E+00 5.53E+00 1.68E+00 -3.175
IL12RB2 1.372 3.541 -0.046 1.54E-09 9.29E-01 8.41E+02 9.15E+01 9.41E+01 7.62E+01 -3.587
IL6 -2.883 -2.409 -3.082 2.36E-04 1.50E-22 2.67E+02 1.43E+03 1.60E+02 1.01E+03 -0.673

18. MUC1 (CD227/MCKD/EMA)
Polymorphic epithelial mucin
Cell surface glycoprotein with
expression in multiple organs
Heterodimer:
a subunit - cell
adhesion
b subunit - cell
signaling
MUC1 1.306 2.647

19. IL12RB2
Interleukin 12, subunit beta 2
Overexpression associated with
Crohn’s Disease and Leprosy
Inflammatory response
High expression in placenta
IL12RB2 3.541 -0.046

20. IL1F5 (IL36RN)
Inhibits NF-kB production
NF-kB promotes
protein expression
IL1F5 are associated with the
severe episodic inflammatory
skin disease known as
generalized pustular psoriasis
IL1F5 4.483 1.308

21. Summary
IL6 shows lower expression from our results, which is opposite from the hypothesis
IL8 expression does increase from the result, which matches our hypothesis
MUC1 is upregalated in tumor tissues, but especially in ER+ tumor tissues
ESR1 expressions match with the status of ER+ and ER-
IL12RB2 and IL1F5 have large differences in LogFC between ER+ and ER-