Uncovering Novel Pre-Treatment Molecular Biomarkers for Anti-TNF Therapeutic Response in Patients with Crohn’s Disease
Abstract
:1. Introduction
2. Materials and Methods
2.1. Description of Datasets
2.2. Biological Function Analysis
2.3. Microenvironmental Feature Evaluation
2.4. Statistical Analyses
3. Results
3.1. Identification of the Target Gene Signatures Attributed to Anti-TNF Therapy Resistance
3.2. Functional Enrichment Analysis of the Top DEGs Associated with Anti-TNF Therapy Resistance
3.3. Tissue-Microenvironment Landscape Associated with Anti-TNF Therapy Resistance
3.4. Development of Biomarkers for Anti-TNF Therapy Resistance
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Immune Marker | Log FC | Average Expression | t-Statistic | p-Value | Adjusted p-Value | B-Statistic |
---|---|---|---|---|---|---|
Fibroblast | −1.233 | 9.062 | −4.284 | <0.001 | 0.001 | 1.170 |
Neutrophil | −0.758 | 7.115 | −4.052 | <0.001 | 0.001 | 0.486 |
Endothelial cell | −0.568 | 5.94 | −3.452 | 0.001 | 0.005 | −1.196 |
Monocyte | −0.594 | 7.101 | −3.045 | 0.004 | 0.009 | −2.252 |
Macrophage/Monocyte | −0.594 | 7.101 | −3.045 | 0.004 | 0.009 | −2.252 |
B cell | −0.476 | 7.407 | −1.434 | 0.159 | 0.291 | −5.432 |
NK cell | 0.218 | 4.652 | 1.299 | 0.201 | 0.315 | −5.608 |
Myeloid dendritic cell | −0.227 | 5.085 | −1.196 | 0.238 | 0.327 | −5.731 |
cytotoxicity score | −0.220 | 4.861 | −0.996 | 0.325 | 0.397 | −5.945 |
T cell CD8+ | −0.181 | 0.922 | −0.89 | 0.378 | 0.416 | −6.042 |
T cell | −0.061 | 5.295 | −0.349 | 0.729 | 0.729 | −6.373 |
Gene | Log FC | Average Expression | t-Statistic | p-Value | Adjusted p-Value | B-Statistic | GeneHancer Identifiers | Activity |
---|---|---|---|---|---|---|---|---|
CBR4 | 0.284 | 7.105 | 4.778 | <0.0001 | 0.236 | 2.232 | - | - |
ACAD10 | 0.215 | 7.08 | 3.981 | <0.0001 | 0.246 | 0.228 | GH12J112025 | Enhancer active in: |
CD4+ CD25− IL17− PMA Th | ||||||||
primary cells | ||||||||
BAIAP3 | −0.264 | 6.6 | −4.538 | <0.0001 | 0.246 | 1.618 | - | - |
BMP6 | −0.702 | 7.506 | −4.298 | <0.0001 | 0.246 | 1.013 | - | - |
DDX11L2 | −0.767 | 8.115 | −4.104 | <0.0001 | 0.246 | 0.532 | GH02J113885 | Enhancer active in: |
CD4+ CD25− IL17− PMA Th | ||||||||
primary cells | ||||||||
DYNLL2 | −0.317 | 8.359 | −4.292 | <0.0001 | 0.246 | 0.999 | GH17J058328 | Enhancer active in: |
CD4+ CD25− IL17− PMA Th | ||||||||
primary cells, CD4+ CD25− | ||||||||
IL17+ PMA Th17 primary cells | ||||||||
KAT2B | −0.587 | 9.99 | −3.945 | <0.0001 | 0.246 | 0.142 | GH03J020038 | Enhancer active in: |
GH03J020037 | CD4+ CD25− IL17+ PMA Th17 | |||||||
GH03J020048 | primary cells | |||||||
GH03J020047 | ||||||||
GH03J020060 | ||||||||
GH03J020053 | ||||||||
GH03J020070 | ||||||||
KLF9 | −0.29 | 7.425 | −3.859 | <0.0001 | 0.246 | −0.068 | GH09J070402 | Enhancer active in: |
GH09J070395 | CD4+ CD25− IL17- PMA Th | |||||||
GH09J070389 | primary cells, CD4+ CD25− | |||||||
GH09J070400 | IL17+ PMA Th17 primary cells | |||||||
GH09J070394 | ||||||||
SPTSSB | −0.465 | 5.504 | −4.024 | <0.0001 | 0.246 | 0.335 | - | - |
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Kwak, M.S.; Cha, J.M.; Jeon, J.W.; Yoon, J.Y.; Park, S.B. Uncovering Novel Pre-Treatment Molecular Biomarkers for Anti-TNF Therapeutic Response in Patients with Crohn’s Disease. J. Funct. Biomater. 2022, 13, 36. https://doi.org/10.3390/jfb13020036
Kwak MS, Cha JM, Jeon JW, Yoon JY, Park SB. Uncovering Novel Pre-Treatment Molecular Biomarkers for Anti-TNF Therapeutic Response in Patients with Crohn’s Disease. Journal of Functional Biomaterials. 2022; 13(2):36. https://doi.org/10.3390/jfb13020036
Chicago/Turabian StyleKwak, Min Seob, Jae Myung Cha, Jung Won Jeon, Jin Young Yoon, and Su Bee Park. 2022. "Uncovering Novel Pre-Treatment Molecular Biomarkers for Anti-TNF Therapeutic Response in Patients with Crohn’s Disease" Journal of Functional Biomaterials 13, no. 2: 36. https://doi.org/10.3390/jfb13020036
APA StyleKwak, M. S., Cha, J. M., Jeon, J. W., Yoon, J. Y., & Park, S. B. (2022). Uncovering Novel Pre-Treatment Molecular Biomarkers for Anti-TNF Therapeutic Response in Patients with Crohn’s Disease. Journal of Functional Biomaterials, 13(2), 36. https://doi.org/10.3390/jfb13020036