Current Achievements and Applications of Transcriptomics in Personalized Cancer Medicine
Abstract
:1. Introduction
2. Omics: Different Levels of Gene Expression
3. Transcriptome’s Components and Methods of Its Analysis
3.1. History of Gene Expression Measurement Methods
3.1.1. Microarrays
3.1.2. Large-Scale Real-Time Reverse Transcription PCR
3.1.3. RNA-Sequencing (RNA-Seq)
3.1.4. Next Generation Sequencing (NGS)
4. Applications of Transcriptome Analysis in Oncology
4.1. Applications in Clinical Classifications of Cancer
4.2. Identification of Early Detection Cancer Biomarkers
4.3. Creation of Cancer Prognostic and Predictive Panels
4.4. Intratumoral Heterogeneity (ITH) and Tumor Microenvironment (TME)-Related Research
4.5. RNA-Based Therapeutics
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Cancer Type Based on Origin Tissue | Molecular Classification | Reference | |
---|---|---|---|
Breast cancer | ER+/luminal-like | [87] | |
Basal-like | |||
Erb-B2+ | |||
Normal-like | |||
Luminal A | [91] | ||
Luminal B | |||
Colorectal cancer | CMS1 (microsatellite instability immune) | [95] | |
CMS2 (canonical) | |||
CMS3 (metabolic) | |||
CMS4 (mesenchymal) | |||
Gastric adenocarcinoma | EBV positive | [111] | |
MSI high | |||
GS | |||
CIN | |||
Glioblastoma | prognostic subtypes | Poor (invasive) | [112] |
Favorable (mitotic) | |||
Intermediate | |||
Proneural | [113] | ||
Mesenchymal | |||
Proliferative |
Cancer Type | Biomarkers | Expression in Cancer Tissue * | Reference |
---|---|---|---|
Breast cancer | miR-126-5p, miR-144-5p, miR-144-3p, miR-301a-3p, miR-126-3p, miR-101-3p, miR-664b-5p | up/down | [142] |
LINC00657 (lncRNA) | up | [143] | |
Colorectal cancer | ABCD3 | down | [144] |
piR-5937, piR-28876, piR-23210, piR-32159 | down | [140] | |
miR-17-92a, miR-135 | up | [145] | |
miR-21 | up | [141] | |
Esophageal cancer | CHI3L1, MMP13, SPP1 | up | [128] |
Gallbladder carcinoma | BIRC5 | up | [146] |
Gastric cancer | miR-106b, miR-20a, miR-21, miR-221, miR-451 | up | [132] |
miR-17-5p, miR-21, miR-106a, miR-106b | up | [147] | |
miR-1, miR-20a, miR-27a, miR-34a, miR-423-5p | up | [148] | |
piR-651 | down | [138] | |
Glioblastoma multiforme | Thymosin β4 (TMSB4X), S100A10 | up | [149] |
miR-20a, miR-106a | up | [150] | |
Hepatocellular cancer | piR-013306 | up | [136] |
Hogdkin lymphoma | piR-651 | down | [151] |
Melanoma | Ro-aassociated Y RNA (YRNAs): RNY3P1, RNY4P1, RNY4P25 (upregulation) miR-320a-3p, miR-134-5p (downregulation) | up/down | [152] |
miR-21 | up | [153] | |
Multiple myeloma | piR-823 | up | [154] |
Non-small cell lung carcinoma | 4-miRNA | up | [131] |
snoRNA | up | [130] | |
34 miRNA expression signature | up/down | [155] | |
Ovarian cancer | IGFBP-4 | up | [117] |
Pancreatic cancer | KRAS mRNA (as salivary biomarker) | up | [156] |
LAMC2 | up | [157] | |
Renal cancer | PIWIL1, piR-823 | down | [158] |
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Supplitt, S.; Karpinski, P.; Sasiadek, M.; Laczmanska, I. Current Achievements and Applications of Transcriptomics in Personalized Cancer Medicine. Int. J. Mol. Sci. 2021, 22, 1422. https://doi.org/10.3390/ijms22031422
Supplitt S, Karpinski P, Sasiadek M, Laczmanska I. Current Achievements and Applications of Transcriptomics in Personalized Cancer Medicine. International Journal of Molecular Sciences. 2021; 22(3):1422. https://doi.org/10.3390/ijms22031422
Chicago/Turabian StyleSupplitt, Stanislaw, Pawel Karpinski, Maria Sasiadek, and Izabela Laczmanska. 2021. "Current Achievements and Applications of Transcriptomics in Personalized Cancer Medicine" International Journal of Molecular Sciences 22, no. 3: 1422. https://doi.org/10.3390/ijms22031422