Treatment of HT29 Human Colorectal Cancer Cell Line with Nanocarrier-Encapsulated Camptothecin Reveals Histone Modifier Genes in the Wnt Signaling Pathway as Important Molecular Cues for Colon Cancer Targeting
Abstract
:1. Introduction
2. Results
2.1. Identification of Genes Involved in Histone Modifications following Treatment with CPT-CEF in HT29 Colon Cancer Cells
2.2. Identification of Epigenetic Modifier Genes Affecting the Wnt Signaling Pathway
2.3. Protein–Protein Interaction (PPI) Networks and Functional Annotation
2.4. TCGA and Trans-Regulatory Elements
3. Discussion
4. Materials and Methodology
4.1. Treatment of HT29 Colon Cancer Cells with a CPT-CEF Nanocompound
4.2. Isolation of Total RNA from HT29 Colon Cancer Cells
4.3. Library Preparation for RNA-Seq
4.4. RNA-Seq Data Processing and Annotation
4.5. Differentially Expressed Genes between CPT-CEF-Treated and Untreated Colon Cancer Cells
4.6. Over-Representation Analysis of Differentially Expressed Genes
4.7. Construction and Analysis of Protein–Protein Interaction (PPI) Networks and Functional Annotation
4.8. TCGA Database and cBioPortal
4.9. Identification of Transcription Factors and Their Interactions
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Term | Gene Overlap | p Value | Adj p Value | Odds Ratio | Combined Score |
---|---|---|---|---|---|
H3K36me3 C2C12 mm9 | 43/407 | 4.64 × 10−14 | 1.91 × 10−11 | 3.827939 | 117.5226 |
H3K36me3 H7 hg19 | 106/1851 | 2.28 × 10−13 | 4.70 × 10−11 | 2.074867 | 60.39654 |
H3K79me2 myocyte mm9 | 107/2000 | 1.21 × 10−11 | 1.67 × 10−9 | 1.938406 | 48.72071 |
H3K36me3 bronchial epithelial cell hg19 | 92/1681 | 1.40 × 10−10 | 1.44 × 10−8 | 1.982947 | 44.9936 |
H3K36me3 spleen mm9 | 100/2000 | 2.71 × 10−9 | 2.23 × 10−7 | 1.811594 | 35.73849 |
H3K79me3 C2C12 mm9 | 97/2000 | 2.28 × 10−8 | 1.57 × 10−6 | 1.757246 | 30.91872 |
H3K36me3 Caco-2 hg19 | 31/382 | 9.48 × 10−8 | 5.58 × 10−6 | 2.940284 | 47.54937 |
H3K36me3 thymus mm9 | 66/1235 | 1.91 × 10−7 | 9.84 × 10−6 | 1.936279 | 29.95479 |
H3K36me3 MCF-7 hg19 | 72/1395 | 1.93 × 10−7 | 8.86 × 10−6 | 1.870033 | 28.90747 |
H3K36me3 ES-Bruce4 mm9 | 92/2000 | 6.19 × 10−7 | 2.55 × 10−5 | 1.666667 | 23.82415 |
Symbol | Function |
---|---|
ADARB1 | RNA binding |
TXNIP | negative regulation of transcription by RNA polymerase II |
FTL | iron ion binding |
TIMP2 | protease binding |
USP9X | negative regulation of transcription by RNA polymerase II |
LAMC1 | extracellular matrix structural constituent |
SLC25A36 | mitochondrial genome maintenance |
TP53INP2 | autophagosome assembly |
RASSF10 | spindle pole |
TGM2 | blood vessel remodeling |
F2R | activation of MAPKK activity |
HMGA1 | DNA-binding transcription factor activity, RNA polymerase-II-specific |
IGFBP4 | regulation of cell growth |
TRAP1 | RNA binding |
FGF19 | MAPK cascade |
NME1 | magnesium ion binding |
PGAM5 | protein serine/threonine phosphatase activity |
DHCR7 | blood vessel development |
MCM2 | G1/S transition of mitotic cell cycle |
DNMT1 | negative regulation of transcription by RNA polymerase II |
CACYBP | protein binding |
TCF3 | negative regulation of transcription by RNA polymerase II |
RUVBL1 | Swr1 complex |
RANGAP1 | Kinetochore |
EMG1 | blastocyst development |
POP1 | ribonuclease MRP activity |
CEP250 | G2/M transition of mitotic cell cycle |
WDR74 | nuclear exosome (RNase complex) |
S100A4 | epithelial to mesenchymal transition |
Genes Associated with the Wnt Signaling Pathways of Colorectal Cancer | DEGs |
---|---|
MMP7 | NFAT5, CLIP1, MYO6, KIF1B, SETD2, SDC1, DDX21, NFAT5, TCF7L2, TCF4, SDC1 |
C-Myc | CDK4, FKBP4, LMNB1, ROCK1, FEN1, MCM3, SETD2, H2AF7USP9X, USP34, S100A4, RPS27A, RUVBL2, TNRC6B, TMEM97, KITLG |
Smad3 | ZFYVE16, ZMYM2, CITED2, USP9X, ZFYVE16 |
MAP3K7 | TRAF7, RPL21, TCF7L2, CF7L2, RPS27A, RPL21 |
C-JUN | H24FZ, TMEM97, SETD2 |
TP53 | PHB, TP53INF2, AC5L, H2AFZ, TNRC6B, SETD2, SDC, S100A4 |
SSRP1 | AFF4 |
SRSF3 | SCAF11, TEP1, EPR3A, YBX1, INRNPA3 |
CCND1 | PAM, H2AFZ, RPL21, RPS27A, SDC1 |
SRSF5 | DKC1 |
SRSF1 | RSP10 |
SMAD | ROCK1, LMNB1, MCM3, FEN1, FKBP4 |
A | B | Neither | A Not B | B Not A | Both | Log2 Odds Ratio | p-Value | q-Value | Tendency |
---|---|---|---|---|---|---|---|---|---|
TRAF7 | SETD2 | 1074 | 10 | 44 | 6 | >3 | <0.001 | <0.001 | Co-occurrence |
TCF7L2 | SETD2 | 782 | 97 | 29 | 12 | 1.738 | 0.002 | 0.005 | Co-occurrence |
TRAF7 | TCF7L2 | 803 | 8 | 105 | 4 | 1.935 | 0.043 | 0.068 | Co-occurrence |
CDK4 | SETD2 | 1078 | 6 | 48 | 2 | 2.904 | 0.045 | 0.068 | Co-occurrence |
CDK4 | TCF7L2 | 805 | 6 | 108 | 1 | 0.313 | 0.588 | 0.705 | Co-occurrence |
CDK4 | TRAF7 | 1110 | 8 | 16 | 0 | <−3 | 0.892 | 0.892 | Mutual exclusivity |
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Farhana, A.; Koh, A.E.-H.; Kothandan, S.; Alsrhani, A.; Mok, P.L.; Subbiah, S.K. Treatment of HT29 Human Colorectal Cancer Cell Line with Nanocarrier-Encapsulated Camptothecin Reveals Histone Modifier Genes in the Wnt Signaling Pathway as Important Molecular Cues for Colon Cancer Targeting. Int. J. Mol. Sci. 2021, 22, 12286. https://doi.org/10.3390/ijms222212286
Farhana A, Koh AE-H, Kothandan S, Alsrhani A, Mok PL, Subbiah SK. Treatment of HT29 Human Colorectal Cancer Cell Line with Nanocarrier-Encapsulated Camptothecin Reveals Histone Modifier Genes in the Wnt Signaling Pathway as Important Molecular Cues for Colon Cancer Targeting. International Journal of Molecular Sciences. 2021; 22(22):12286. https://doi.org/10.3390/ijms222212286
Chicago/Turabian StyleFarhana, Aisha, Avin Ee-Hwan Koh, Sangeetha Kothandan, Abdullah Alsrhani, Pooi Ling Mok, and Suresh Kumar Subbiah. 2021. "Treatment of HT29 Human Colorectal Cancer Cell Line with Nanocarrier-Encapsulated Camptothecin Reveals Histone Modifier Genes in the Wnt Signaling Pathway as Important Molecular Cues for Colon Cancer Targeting" International Journal of Molecular Sciences 22, no. 22: 12286. https://doi.org/10.3390/ijms222212286