PANDORA-Seq Unveils the Hidden Small Non-Coding RNA Landscape in Hypopharyngeal Carcinoma
Abstract
1. Introduction
2. Results
2.1. PANDORA-Seq Reveals a More Comprehensive Panoramic View of sncRNAs
2.2. Dynamic Changes in the Expression and Sequence Characteristics of sncRNA in Hypopharyngeal Carcinoma Tissues and Adjacent Normal Tissues
2.3. Expression Profiles of rsRNA and tsRNA in Hypopharyngeal Carcinoma Tissues and Adjacent Normal Tissues
2.4. Identification of Differentially Expressed sncRNAs
2.5. Validation of Differentially Expressed sncRNAs
3. Discussion
4. Materials and Methods
4.1. Sample Collection and Clinical Cohort
4.2. Total RNA Isolation and Quality Control
4.3. Treatment with Alkb and T4PNK
4.4. Small RNA Library Construction and Deep Sequencing
4.5. Annotation and Analysis of Small RNAs
4.6. RT-qPCR
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
sncRNAs | Small non-coding RNAs |
miRNAs | MicroRNAs |
tsRNAs | tRNA-derived small RNAs |
rsRNAs | rRNA-derived small RNAs |
ysRNAs | YRNA-derived small RNAs |
RNA-seq | RNA sequencing |
AUC | Area under the curve |
PANDORA-seq | Panoramic RNA display by overcoming RNA modification aborted sequencing |
Alkb | α-ketoglutarate-dependent hydroxylase |
T4PNK | T4 polynucleotide kinase |
GO | Gene Ontology |
KEGG | Kyoto Encyclopedia of Genes and Genomes |
CLL | Chronic lymphocytic leukemia |
AML | Acute myeloid leukemia |
PBMCs | Peripheral blood mononuclear cells |
HSCC | Hypopharyngeal squamous cell carcinoma |
UMIs | Unique molecular identifiers |
RT-qPCR | Reverse transcription quantitative polymerase chain reaction |
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Patients | Gender | Age (Years) | Tumor Size (mm) | TNM | Metastasis | Type | HPV |
---|---|---|---|---|---|---|---|
1 | Male | 79 | 46 × 28 × 50 | IVA | Yes | HSCC | Negative |
2 | Male | 67 | 35 × 20 × 31 | IVB | No | HSCC | Negative |
3 | Male | 76 | 31 × 17 × 32 | IVA | Yes | HSCC | Negative |
4 | Male | 52 | 17 × 18 × 15 | II | No | HSCC | Negative |
5 | Male | 70 | 17 × 16 × 11 | II | No | HSCC | Negative |
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Pu, M.; Shi, L.; Ma, H.; Tao, C.; Zhang, Y.; Bu, Y.; Ye, J. PANDORA-Seq Unveils the Hidden Small Non-Coding RNA Landscape in Hypopharyngeal Carcinoma. Int. J. Mol. Sci. 2025, 26, 5972. https://doi.org/10.3390/ijms26135972
Pu M, Shi L, Ma H, Tao C, Zhang Y, Bu Y, Ye J. PANDORA-Seq Unveils the Hidden Small Non-Coding RNA Landscape in Hypopharyngeal Carcinoma. International Journal of Molecular Sciences. 2025; 26(13):5972. https://doi.org/10.3390/ijms26135972
Chicago/Turabian StylePu, Miaoyan, Luyu Shi, Haiyu Ma, Chuntao Tao, Ying Zhang, Youquan Bu, and Junhong Ye. 2025. "PANDORA-Seq Unveils the Hidden Small Non-Coding RNA Landscape in Hypopharyngeal Carcinoma" International Journal of Molecular Sciences 26, no. 13: 5972. https://doi.org/10.3390/ijms26135972
APA StylePu, M., Shi, L., Ma, H., Tao, C., Zhang, Y., Bu, Y., & Ye, J. (2025). PANDORA-Seq Unveils the Hidden Small Non-Coding RNA Landscape in Hypopharyngeal Carcinoma. International Journal of Molecular Sciences, 26(13), 5972. https://doi.org/10.3390/ijms26135972