The following is a summary of “Comprehensive Long-Read Sequencing Analysis Discloses the Transcriptome Features of Papillary Thyroid Microcarcinoma,” published in the May 2024 issue of Endocrinology by Wang, et al.
Papillary thyroid microcarcinoma (PTMC) emerged as the most prevalent form of thyroid cancer, with lymph node metastasis recognized as a significant prognostic factor. For a study, researchers sought to delineate the PTMC transcriptome profile and identify transcripts correlated with lateral neck lymph node metastasis in PTMC.
Full-length transcriptome sequencing was conducted on 64 PTMC samples. Standard bioinformatic protocols were employed to characterize and annotate the expression profiles of two PTMC subtypes. Functional open reading frame (ORF) annotation for known and novel transcripts was predicted using HMMER, DeepLoc, and DeepTMHMM tools. Transcription quantification and differential gene expression analyses identified candidate transcripts associated with the pN1b subtype.
Exon skipping constituted over 27.82% of the alternative splicing events observed—approximately 42.56% of discovered transcripts represented novel isoforms of annotated genes. A total of 39,193 ORFs in novel transcripts and 18,596 ORFs in known transcripts were identified. Predictions were made regarding the distribution patterns of characterized transcripts in functional domains, subcellular localization, and transmembrane structures. 1,033 and 1,204 differentially expressed genes were identified in the pN0 and pN1b groups, respectively. Furthermore, novel isoforms of FRMD3, NOD1, and SHROOM4 were highlighted for their association with the pN1b subtype.
The study offered insights into the global transcriptome landscape of PTMC and uncovered novel isoforms associated with PTMC aggressiveness.
Reference: academic.oup.com/jcem/article-abstract/109/5/1263/7457333
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