T gene isoform expression pattern is significantly different between chordomas and notochords

Pediatric Chordoma: A Tale of Two Genomes

Little is known about the genomic alterations in chordoma, with the exception of loss of SMARCB1, a core member of the SWI/SNF complex, in poorly differentiated chordomas. A TBXT duplication and rs2305089 polymorphism, located at 6q27, are known genetic susceptibility loci. A comprehensive genomic analysis of the nuclear and mitochondrial genomes in pediatric chordoma has not yet been reported. In this study, we performed WES and mtDNA genome sequencing on 29 chordomas from 23 pediatric patients. Findings were compared with that from whole-genome sequencing datasets of 80 adult patients with skull base chordoma. In the pediatric chordoma cohort, 81% of the somatic mtDNA mutations were observed in NADH complex genes, which is significantly enriched compared with the rest of the mtDNA genes (P = 0.001). In adult chordomas, mtDNA mutations were also enriched in the NADH complex genes (P < 0.0001). Furthermore, a progressive increase in heteroplasmy of nonsynonymous mtDNA mutations was noted in patients with multiple tumors (P = 0.0007). In the nuclear genome, rare likely germline in-frame indels in ARID1B, a member of the SWI/SNF complex located at 6q25.3, were observed in five pediatric patients (22%) and four patients in the adult cohort (5%). The frequency of rare ARID1B indels in the pediatric cohort is significantly higher than that in the adult cohort (P = 0.0236, Fisher's exact test), but they were both significantly higher than that in the ethnicity-matched populations (P < 5.9e-07 and P < 0.0001174, respectively). Implications: germline ARID1B indels and mtDNA aberrations seem important for chordoma genesis, especially in pediatric chordoma.

Current understanding of brachyury in chordoma

Chordomas are rare malignant tumors that pose significant challenges in terms of effective treatment options. Surgical resection remains the only established approach that has proven useful in the treatment of chordoma. However, recent evidence has shed light on the role of brachyury, also known as the T-gene and TBXT, as both a diagnostic marker and a potential therapeutic target in chordoma. Considering these developments, this review aims to provide a comprehensive summary of the current knowledge and understanding of brachyury in chordomas.

Single-molecule Real-time (SMRT) Sequencing Facilitates Transcriptome Research and Genome Annotation of the Fish Sillago sinica

As a newly described Sillaginidae species, Chinese sillago (Sillago sinica) needs a better understanding of gene annotation information. In this study, we reported the first full-length transcriptome data of S. sinica using the PacBio isoform sequencing Iso-seq and a description of transcriptome structure analysis. A total of 454,979 high-quality full-length transcripts were obtained by single-molecule real-time (SMRT) sequencing, which was corrected by Illumina sequencing data. After that, 66,948 non-redundant full-length transcripts were generated after mapping to the reference genome of S. sinica, including 49 fusion isoforms and 9,250 novel isoforms. 63,459 isoforms were successfully annotated by one of the Nr, Nt, SwissProt, Pfam, KOG, GO, and KEGG databases. Additionally, 30,987 alternative polyadenylation (APA) sites, 451,867 alternative splicing (AS) events, 21,928 long non-coding RNAs (lncRNAs) and 12,911 transcription factors (TFs) were identified. The full-length transcripts of S. sinica would provide a precious resource for characterizing the transcriptome of S. sinica and for the further study of gene function and regulatory mechanism of this species.

Identification of the Different Roles and Potential Mechanisms of T Isoforms in the Tumor Recurrence and Cell Cycle of Chordomas

Purpose

The roles of T (brachyury) isoforms in chordomas remain unclear. This study aimed to investigate the different roles and mechanisms of them in chordomas.

Patients and methods

The expression of T isoforms mRNAs in 57 chordomas was assessed, and a prognosis analysis was conducted. Cell apoptosis, proliferation and cell cycle assays were performed after specific T isoform mRNA knockdown. Whole-transcriptome sequencing, Gene Set Enrichment Analysis, Gene Ontology analysis, Kyoto Encyclopedia of Genes and Genomes analysis and competing endogenous RNA (ceRNA) analysis were conducted.

Results

As revealed in this study, the T-long isoform was a significant risk factor (hazard ratio [HR], 1.09; P=0.018) and the T-short isoform was a protective factor (HR, 0.24; P=0.012) associated with tumor recurrence. After T-long isoform knockdown, the cell cycle was arrested at G0/G1 phase and cell proliferation was significantly inhibited. A bioinformatic analysis revealed that the upregulation of H19, P21 and GADD45B; downregulation of SKP2 and CDK2; and accompanying changes in the P53 signaling pathway consistently contributed to G0/G1 arrest. After T-short isoform knockdown, the cell cycle was arrested at G2/M phase and cell apoptosis tended to increase slightly (P=0.067). The upregulation of YWHAZ and downregulation of E2F1 and its target genes might contribute to cell cycle arrest in G2/M phase and apoptosis. In addition, the ceRNA network, consisting of long noncoding RNAs, mRNAs and microRNAs, was established.

Conclusion

The T-long isoform was a risk factor and the T-short isoform was a protective factor for chordoma recurrence. In addition, the cell cycle was the main target of T isoforms knockdown, and the changes in the downstream transcriptome may contribute to the different effects of specific T isoform knockdown on the changes in the cell cycle distributions and apoptosis and proliferation of chordoma cells.

Expression of Cathepsin K in Skull Base Chordoma

OBJECTIVE

The aim of this study was to explore the association between cathepsin K and the clinical characteristics of skull base chordoma (SBC).

METHODS

This study included 58 paraffin-embedded samples and 85 frozen samples of 94 patients. All clinical data corresponding to these patients were available. Immunohistochemical staining and quantitative real-time polymerase chain reaction were performed. Positive rate of immunohistochemical staining slices and delta cycle threshold value of quantitative real-time polymerase chain reaction represented the cathepsin K expression level in protein and gene level separately.

RESULTS

In protein level, expression level (EL) of invasive tumors was increased compared with noninvasive tumors (P = 0.006), EL of tumors with dura erosion was increased compared with tumors without dura erosion (P = 0.001). Tumors with septa exhibited increased EL compared with tumors without septa (P = 0.001). Tumors with lobulation exhibited increased EL compared with tumors without lobulation (P = 0.000). Higher EL of cathepsin K was associated with reduced progression-free survival (PFS) (P = 0.015). In gene level, tumors with septa showed higher EL than tumors without septa (P = 0.015), and tumors with lobulation showed higher EL than tumors without lobulation (P = 0.049). Cathepsin K EL was an independent risk factor for reduced PFS, and an increased level of cathepsin K in SBC was associated with reduced PFS (P = 0.042).

CONCLUSIONS

Increased cathepsin K expression in SBC was associated with tumor invasion and reduced PFS. The cathepsin K level in SBC also was associated with tumor stage, tumor lobulation, and septa.