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. 2020;10(3):652-654.e17.
doi: 10.1016/j.jcmgh.2020.04.011. Epub 2020 Apr 25.

Genome-Scale Analysis Identifies Novel Transcript-Variants in Esophageal Adenocarcinoma

B P D Purkayastha  1 , E R Chan  2 , D Ravillah  1 , L Ravi  1 , R Gupta  3 , M I Canto  4 , J S Wang  5 , N J Shaheen  6 , J E Willis  7 , A Chak  3 , V Varadan  1 , K Guda  8
Affiliations

Genome-Scale Analysis Identifies Novel Transcript-Variants in Esophageal Adenocarcinoma

B P D Purkayastha et al. Cell Mol Gastroenterol Hepatol. 2020.
No abstract available

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Figures

Figure 1
Figure 1
Characterization of COL10A1Var1. (A) Shown are the 5′ to 3′ exon (Ex)-introns (thin line) structures of COL10A1Var1 and canonical COL10A1. UTR, untranslated region. (B) Western blot analyses depicting COL10A1Var1 and COL10A1 proteins. IB, immunoblotting; IP, immunoprecipitation. CEMIP1 was used as positive control for secreted protein and Empty vector as a negative control. (C) Pie charts demonstrating the proportion (%) of samples positive for COL10A1Var1 transcript (top, red color) or canonical COL10A1 (bottom, blue color) in respective SQ, GAST, BM, HGD, and malignant (EAC) tissue biopsies. ∗∗∗P< .0001 indicates significant difference in the proportion COL10A1Var1 positivity between malignant (EAC) vs any of the respective non-EAC tissue groups, estimated by using a one-tailed Fisher exact test.
Figure 2
Figure 2
Impact of COL10A1/Var1on durotaxis of EAC cells. (A) PCR-based analysis showing COL10A1Var1 and canonical COL10A1 expression in normal esophageal squamous (Epc2), non-dysplastic BE (CP-A), dysplastic BE (CP-B, CP-C, CP-D), and EAC (OE19, OE33, FLO-1, EsoAd1, SKGT4) cell lines. B2M was used as the internal RNA control. BE, Barrett’s esophagus. (B) Representative images (left) demonstrating shRNA induction on doxycycline (Dox) treatment in stable OE19 cells, carrying either non-targeting control shRNA or shRNAs targeting both COL10A1Var1 and canonical COL10A1 transcripts (depicted as COL10A1/Var1). Note the specific induction of TurboRFP, a red fluorescent reporter of shRNA induction, on doxycyline treatment in these cells. PCR analysis (right) demonstrating knockdown of COL10A1/Var1 RNA on doxycycline treatment of the stable OE19 cells. B2M was used as an internal RNA control. (C) Representative images of durotaxis assay in stable OE19 cells. Quantitative analysis of cell migration (bar graph), measured as total fluorescence units (TFU, Y-axis) of TurboRFP-positive cells in the stiffer surface. All data are plotted as mean ± standard error of the mean, obtained from 3 replicate experiments. ∗∗P < .004 indicates significant differences in COL10A1/Var1 knockdown vs control shRNA cells, estimated by using a Student t test assuming unequal variances.
Supplementary Figure 1
Supplementary Figure 1
Full-length structure of novel transcript-variants identified in EACs. Shown are the complete mRNA sequences (5′ to 3′) of the respective candidate transcript-variants discovered in EACs. For each of the 7 candidates, variant-specific sequences are highlighted in blue font. Shown below each of the sequences are positions of individual exons and coding sequence. For each of the variants and their corresponding canonical genes, exon-intron structures along with their relative sizes-distances are illustrated on the right.
Supplementary Figure 1
Supplementary Figure 1
Full-length structure of novel transcript-variants identified in EACs. Shown are the complete mRNA sequences (5′ to 3′) of the respective candidate transcript-variants discovered in EACs. For each of the 7 candidates, variant-specific sequences are highlighted in blue font. Shown below each of the sequences are positions of individual exons and coding sequence. For each of the variants and their corresponding canonical genes, exon-intron structures along with their relative sizes-distances are illustrated on the right.
Supplementary Figure 1
Supplementary Figure 1
Full-length structure of novel transcript-variants identified in EACs. Shown are the complete mRNA sequences (5′ to 3′) of the respective candidate transcript-variants discovered in EACs. For each of the 7 candidates, variant-specific sequences are highlighted in blue font. Shown below each of the sequences are positions of individual exons and coding sequence. For each of the variants and their corresponding canonical genes, exon-intron structures along with their relative sizes-distances are illustrated on the right.
Supplementary Figure 1
Supplementary Figure 1
Full-length structure of novel transcript-variants identified in EACs. Shown are the complete mRNA sequences (5′ to 3′) of the respective candidate transcript-variants discovered in EACs. For each of the 7 candidates, variant-specific sequences are highlighted in blue font. Shown below each of the sequences are positions of individual exons and coding sequence. For each of the variants and their corresponding canonical genes, exon-intron structures along with their relative sizes-distances are illustrated on the right.
Supplementary Figure 1
Supplementary Figure 1
Full-length structure of novel transcript-variants identified in EACs. Shown are the complete mRNA sequences (5′ to 3′) of the respective candidate transcript-variants discovered in EACs. For each of the 7 candidates, variant-specific sequences are highlighted in blue font. Shown below each of the sequences are positions of individual exons and coding sequence. For each of the variants and their corresponding canonical genes, exon-intron structures along with their relative sizes-distances are illustrated on the right.
Supplementary Figure 1
Supplementary Figure 1
Full-length structure of novel transcript-variants identified in EACs. Shown are the complete mRNA sequences (5′ to 3′) of the respective candidate transcript-variants discovered in EACs. For each of the 7 candidates, variant-specific sequences are highlighted in blue font. Shown below each of the sequences are positions of individual exons and coding sequence. For each of the variants and their corresponding canonical genes, exon-intron structures along with their relative sizes-distances are illustrated on the right.
Supplementary Figure 1
Supplementary Figure 1
Full-length structure of novel transcript-variants identified in EACs. Shown are the complete mRNA sequences (5′ to 3′) of the respective candidate transcript-variants discovered in EACs. For each of the 7 candidates, variant-specific sequences are highlighted in blue font. Shown below each of the sequences are positions of individual exons and coding sequence. For each of the variants and their corresponding canonical genes, exon-intron structures along with their relative sizes-distances are illustrated on the right.
Supplementary Figure 1
Supplementary Figure 1
Full-length structure of novel transcript-variants identified in EACs. Shown are the complete mRNA sequences (5′ to 3′) of the respective candidate transcript-variants discovered in EACs. For each of the 7 candidates, variant-specific sequences are highlighted in blue font. Shown below each of the sequences are positions of individual exons and coding sequence. For each of the variants and their corresponding canonical genes, exon-intron structures along with their relative sizes-distances are illustrated on the right.
Supplementary Figure 1
Supplementary Figure 1
Full-length structure of novel transcript-variants identified in EACs. Shown are the complete mRNA sequences (5′ to 3′) of the respective candidate transcript-variants discovered in EACs. For each of the 7 candidates, variant-specific sequences are highlighted in blue font. Shown below each of the sequences are positions of individual exons and coding sequence. For each of the variants and their corresponding canonical genes, exon-intron structures along with their relative sizes-distances are illustrated on the right.
Supplementary Figure 1
Supplementary Figure 1
Full-length structure of novel transcript-variants identified in EACs. Shown are the complete mRNA sequences (5′ to 3′) of the respective candidate transcript-variants discovered in EACs. For each of the 7 candidates, variant-specific sequences are highlighted in blue font. Shown below each of the sequences are positions of individual exons and coding sequence. For each of the variants and their corresponding canonical genes, exon-intron structures along with their relative sizes-distances are illustrated on the right.
Supplementary Figure 1
Supplementary Figure 1
Full-length structure of novel transcript-variants identified in EACs. Shown are the complete mRNA sequences (5′ to 3′) of the respective candidate transcript-variants discovered in EACs. For each of the 7 candidates, variant-specific sequences are highlighted in blue font. Shown below each of the sequences are positions of individual exons and coding sequence. For each of the variants and their corresponding canonical genes, exon-intron structures along with their relative sizes-distances are illustrated on the right.
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