Transcriptome Analysis Reveals the Induction of Apoptosis-Related Genes by a Monoclonal Antibody against a New Epitope of CD99 on T-Acute Lymphoblastic Leukemia
Abstract
1. Introduction
2. Materials and Methods
2.1. Cells, Cell Lines and Antibodies
2.2. Cell Apoptosis Assay
2.3. RNA Extraction
2.4. mRNA Library Constructing and Sequencing
2.5. RNA-Sequencing Data Analysis
2.6. Real-Time Quantitative RT-PCR
- FOS—Fw: 5′-CTTACTACCACTCACCCGCA-3′
- FOS—Rv: 5′-AGTGACCGTGGGAATGAAGT-3′
- TNF—Fw: 5′-TGCACTTTGGAGTGATCGGC-3′
- TNF—Rv: 5′-ACTCGGGGTTCGAGAAGATG-3′
- FASLG—Fw: 5′-TACCAGCCAGATGCACACAG-3′
- FASLG—Rv: 5′-GGCATGGACCTTGAGTTGGA-3′
- BCL2A1—Fw: 5′-GATAAGGCAAAACGGAGGCTG-3′
- BCL2A1—Rv: 5′-ATGGAGTGTCCTTTCTGGTCAA-3′
- JUNB—Fw: 5′-AACAGCCCTTCTACCACGAC-3′
- JUNB—Rv: 5′-CAGGCTCGGTTTCAGGAGTT-3′
- SOCS1—Fw: 5′-AGCTGCACGGCTCCTG-3′
- SOCS1—Rv: 5′-TGTGGAGACTGCATTGTCGG-3′
- IL27RA—Fw: 5′-ACTTGAACTGCTCGTGGGAG-3′
- IL27RA—Rv: 5′-CCTTAGTGCCCCAGACAAGG-3′
- PTPN6—Fw: 5′-ACCTCAAGTACCCGCTGAAC-3′
- PTPN6—Rv: 5′-GGCTCTCACGCACAAGAAAC-3′
- PDGFA—Fw: 5′-TACCTCGCCCATGTTCTGGC-3′
- PDGFA—Rv: 5′-TCCCTACGGAGTCTATCTCCAGG-3′
- NR4A1—Fw: 5′-CCACATTGTTGCCAAGACCTG-3′
- NR4A1—Rv: 5′-CTGGTGTCCCATATTGGGCTT-3′
- SGK1—Fw: 5′-GGCATGGTGGCAATTCTCATCG-3′
- SGK1—Rv: 5′-AGGTTGATTTGCTGAGAAGGACT-3′
- LPAR5—Fw: 5′-CGCAGAGCAACACGGA-3′
- LPAR5—Rv: 5′-GGTCATGGGAATGTGGGCTA-3′
- LTB—Fw: 5′-CAGCAAGGACTGGGGTTTC-3′
- LTB—Rv: 5′-GCCTGTTCCTTCGTCGTCT-3′
- GAPDH—Fw: 5′-GCAAATTCCATGGCACCGT-3′
- GAPDH—Rv: 5′-TCGCCCCACTTGATTTTGG-3′
2.7. Epitope Mapping via Phage Display Random Peptide Library
2.8. Epitope Mapping via Overlapping Peptide Libraries
2.9. Statistical Analysis
3. Results
3.1. mAb MT99/3 Strongly Induces Apoptosis in T-Acute Lymphoblastic Leukemia Cell Lines
3.2. mAb MT99/3-Induced Differential Gene Expression
3.3. Analysis of KEGG Pathway Enrichment of DEGs
3.4. DEGs Were Verified by RT-qPCR
3.5. Identification of CD99 Epitope Recognized by mAb MT99/3
4. Discussion
5. Limitations
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Pathway Term | Gene ID | Description | Gene Symbol | Control FPKM ※ | mAb MT99/3 FPKM ※ | Regulated by mAb MT99/3 |
---|---|---|---|---|---|---|
Apoptosis | ENSG00000170345 | Fos proto-oncogene, AP-1 transcription factor subunit | FOS | 0.35 | 6.16 | Up |
ENSG00000232810 | Tumor necrosis factor | TNF | 0.10 | 1.59 | Up | |
ENSG00000117560 | Fas ligand | FASLG | 0.00 | 0.56 | Up | |
ENSG00000140379 | BCL2-related protein A1 | BCL2A1 | 0.20 | 0.95 | Up | |
TNF signaling pathway | ENSG00000171223 | JunB proto-oncogene, AP-1 transcription factor subunit | JUNB | 21.47 | 48.43 | Up |
ENSG00000170345 | Fos proto-oncogene, AP-1 transcription factor subunit | FOS | 0.35 | 6.16 | Up | |
ENSG00000232810 | Tumor necrosis factor | TNF | 0.10 | 1.59 | Up | |
JAK-STAT signaling pathway | ENSG00000185338 | Suppressor of cytokine signaling 1 | SOCS1 | 1.19 | 7.21 | Up |
ENSG00000104998 | Interleukin 27 receptor subunit alpha | IL27RA | 3.18 | 7.19 | Up | |
ENSG00000111679 | Protein tyrosine phosphatase non-receptor type 6 | PTPN6 | 18.56 | 49.36 | Up | |
ENSG00000197461 | Platelet-derived growth factor subunit A | PDGFA | 1.36 | 3.13 | Up | |
PI3K-Akt signaling pathway | ENSG00000123358 | Nuclear receptor subfamily 4 group A member 1 | NR4A1 | 1.49 | 23.57 | Up |
ENSG00000118515 | Serum/glucocorticoid-regulated kinase 1 | SGK1 | 0.72 | 2.10 | Up | |
ENSG00000197461 | Platelet-derived growth factor subunit A | PDGFA | 1.36 | 3.13 | Up | |
ENSG00000117560 | Fas ligand | FASLG | 0.00 | 0.56 | Up | |
ENSG00000184574 | Lysophosphatidic acid receptor 5 | LPAR5 | 7.28 | 16.72 | Up | |
NF-kappa B signaling pathway | ENSG00000232810 | Tumor necrosis factor | TNF | 0.10 | 1.59 | Up |
ENSG00000227507 | Lymphotoxin beta | LTB | 2.47 | 5.18 | Up | |
ENSG00000140379 | BCL2-related protein A1 | BCL2A1 | 0.20 | 0.95 | Up |
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Takheaw, N.; Kotemul, K.; Chaiwut, R.; Pata, S.; Laopajon, W.; Rangnoi, K.; Yamabhai, M.; Kasinrerk, W. Transcriptome Analysis Reveals the Induction of Apoptosis-Related Genes by a Monoclonal Antibody against a New Epitope of CD99 on T-Acute Lymphoblastic Leukemia. Antibodies 2024, 13, 42. https://doi.org/10.3390/antib13020042
Takheaw N, Kotemul K, Chaiwut R, Pata S, Laopajon W, Rangnoi K, Yamabhai M, Kasinrerk W. Transcriptome Analysis Reveals the Induction of Apoptosis-Related Genes by a Monoclonal Antibody against a New Epitope of CD99 on T-Acute Lymphoblastic Leukemia. Antibodies. 2024; 13(2):42. https://doi.org/10.3390/antib13020042
Chicago/Turabian StyleTakheaw, Nuchjira, Kamonporn Kotemul, Ratthakorn Chaiwut, Supansa Pata, Witida Laopajon, Kuntalee Rangnoi, Montarop Yamabhai, and Watchara Kasinrerk. 2024. "Transcriptome Analysis Reveals the Induction of Apoptosis-Related Genes by a Monoclonal Antibody against a New Epitope of CD99 on T-Acute Lymphoblastic Leukemia" Antibodies 13, no. 2: 42. https://doi.org/10.3390/antib13020042
APA StyleTakheaw, N., Kotemul, K., Chaiwut, R., Pata, S., Laopajon, W., Rangnoi, K., Yamabhai, M., & Kasinrerk, W. (2024). Transcriptome Analysis Reveals the Induction of Apoptosis-Related Genes by a Monoclonal Antibody against a New Epitope of CD99 on T-Acute Lymphoblastic Leukemia. Antibodies, 13(2), 42. https://doi.org/10.3390/antib13020042