MicroRNA Methylome Signature and Their Functional Roles in Colorectal Cancer Diagnosis, Prognosis, and Chemoresistance
Abstract
:1. Introduction
2. MicroRNA Methylation with Diagnostic and Prognostic Markers
2.1. MiRNA-124a
2.2. MiRNA-137
2.3. MiRNA-34
2.4. Other microRNA Genes
MicroRNA(s) and Reference | MicroRNA Methylation Detection Method | Types of Specimens | Key Findings |
---|---|---|---|
miR-124a [17] Known targets: STAT3, IASPP PRRX1, KITENIN, PRPS1, RPIA PTB1/PKM1/PKM2, DNMT3B, DNMT1, ROCK1, PRRX1, PLCB1 | Methylation-specific PCR (MSP) and bisulfite sequencing | Cell line model with disrupted DNA methyltransferase |
|
miR-34b/c [19] Known targets: SATB2 | Methylation-specific PCR (MSP) and bisulfite sequencing | CRC cell lines |
|
miR-133b [20] Known targets: CXCR4, HOXA9 | Methylation-specific PCR (MSP) and combined bisulfite restriction analysis (COBRA) | Screening using CRC cell lines and validation in the tissues (6 CRCs, 2 adjacent non-tumors, and 2 healthy colorectal tissues) |
|
miR-324 [21] Known targets: ELAVL1 | Methylation-specific PCR (MSP) and bisulfite sequencing | 42 CRCs, 9 colorectal adenomas, and 16 normal mucosae in patients with and without CRC |
|
miR-137, miR- 342 [36] Known targets: miR-137: TCF4, FMNL2, Aurora-A miR-342: DNMT1, FOXM1, FOXQ1 | Methylation-specific PCR (MSP) | Fresh-frozen tissues (51 polyps, 8 tumors, and 14 normal mucosa) |
|
miR-9, miR-129, miR-137 [52] Known targets: miR-9: TM4SF1, FOXP2, ANO1 miR-129: MALAT1 miR-137: TCF4, FMNL2, Aurora-A | Methylation-specific PCR (MSP) and bisulfite sequencing | CRC cell lines and 50 primary CRCs with adjacent normal tissues |
|
miR-345 [54] No known target | Methylation-specific PCR (MSP) and bisulfite sequencing | CRC cell lines and 31 CRC patients |
|
miR-129-2, miR-345, miR-132 [56] Known targets: miR-129: MALAT1 miR-345: No known target miR-132: ZEB2, ERK1 | Bisulfite sequencing and Methylation-Specific Multiplex Ligation-Dependent Probe Amplification (MS-MLPA) | CRC cell lines treated with 5-aza-2′deoxycytidine followed by validation in 205 CRCs |
|
miR-132 [57] Known targets: miR-132: ZEB2, ERK1 | Methylation-specific PCR (MSP) and bisulfite sequencing | CRC cell lines and 36 CRCs with adjacent normal tissues |
|
miR-1, miR-9, miR-124, miR-137 [29] Known targets: miR-1: SMAD3 miR-9: TM4SF1, FOXP2, ANO1 miR-124: STAT3, IASPP PRRX1, KITENIN, PRPS1, RPIA. PTB1/PKM1/PKM2, DNMT3B, DNMT1, ROCK1, PRRX1, PLCB1. miR-137: TCF4, FMNL2, Aurora-A | Quantitative bisulfite pyrosequencing | 387 colorectal epithelial specimens (362 non-neoplastic and 25 neoplastic tissues) |
|
miR-125 [58] Known targets: BCL2, BCL2L12, MCL1, SMURF1, VEGFA, TAZ, CXCL12/CXCR4 | Bisulfite sequencing PCR | CRC tissues and adjacent normal tissues from 68 CRC patients |
|
miR-941 [59] No known target | Bisulfite sequencing | CRC cell lines |
|
miR-1237 [59] No known target | Bisulfite sequencing | CRC cell lines |
|
miR-1247 [60] No known target | Methylation-specific PCR (MSP) and bisulfite sequencing | CRC cell lines and patients (hypermethylated and non-methylated CRCs) |
|
miR-128 [61] Known targets: IRS1, Galectin-3 | Bisulfite sequencing PCR | CRC cell lines and patients |
|
miR-148a [62] Known targets: BCL2, ERBB3 | Bisulfite pyrosequencing | 273 CRC patients (76 stage II, 125 stage III, 72 stage IV) |
|
miR-126 [63] Known targets: CXCR4 | Methylation-specific PCR (MSP) and bisulfite sequencing | CRC cell lines and patients |
|
miR-27b [64] Known targets: RAB3D | Methylation-specific PCR (MSP) | CRC cell lines |
|
miR-149 [65] Known targets: FOXM1, EPHB3 | Methylation-specific PCR (MSP) | CRC cell lines |
|
miR-497/195 [66] Known targets: IGF1R, NRDP1, KSR1, FRA-1, PTPN3, CARMA3, FGF2 | Combined bisulfite restriction analysis (COBRA) and bisulfite genomic sequencing (BGS) | CRC cell lines and patients |
|
miR-212 [67] Known targets: MnSOD | Methylation-specific PCR (MSP) and bisulfite sequencing | CRC cell lines and tissues |
|
miR-200c/141 [68] Known targets: ZEB1, DLC1, TRAF5 | Methylation-specific PCR (MSP) | CRC tissues |
|
miR-373 [69] No known targets | Methylation-specific PCR (MSP) and bisulfite sequencing | CRC cell lines and 40 CRC patients |
|
3. MicroRNA Methylation in CRC Chemoresistance
4. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Baharudin, R.; Rus Bakarurraini, N.Q.; Ismail, I.; Lee, L.-H.; Ab Mutalib, N.S. MicroRNA Methylome Signature and Their Functional Roles in Colorectal Cancer Diagnosis, Prognosis, and Chemoresistance. Int. J. Mol. Sci. 2022, 23, 7281. https://doi.org/10.3390/ijms23137281
Baharudin R, Rus Bakarurraini NQ, Ismail I, Lee L-H, Ab Mutalib NS. MicroRNA Methylome Signature and Their Functional Roles in Colorectal Cancer Diagnosis, Prognosis, and Chemoresistance. International Journal of Molecular Sciences. 2022; 23(13):7281. https://doi.org/10.3390/ijms23137281
Chicago/Turabian StyleBaharudin, Rashidah, Nurul Qistina Rus Bakarurraini, Imilia Ismail, Learn-Han Lee, and Nurul Syakima Ab Mutalib. 2022. "MicroRNA Methylome Signature and Their Functional Roles in Colorectal Cancer Diagnosis, Prognosis, and Chemoresistance" International Journal of Molecular Sciences 23, no. 13: 7281. https://doi.org/10.3390/ijms23137281