RNA sequencing of cancer reveals novel splicing alterations
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1 RNA sequencing of cancer reveals novel splicing alterations Jeyanthy Eswaran, Anelia Horvath, Sucheta Godbole, Sirigiri Divijendra Reddy, Prakriti Mudvari, Kazufumi Ohshiro, Dinesh Cyanam, Sujit Nair, Suzanne A. W. Fuqua, Kornelia Polyak, Liliana D. Florea & Rakesh Kumar
2 Supplemental Table 1: NBS global sequencing statistics and read distribution Normal breast sample global mrna sequencing statistics Global Statistics NBS1 NBS2 NBS3 Total Number of reads Unique Reads Aligned Reads Unique Exons Total Exons Transcripts (known and novel) Genes
3 Supplemental Table 2: The number of cancer specific isoforms that align (nblast) with the human open reading frame database, human ORFeome 8.1 ( Cancer group Total cancer specific isoforms that express only in cancer subtype The number of cancer specific isoforms that align with ORF above 90% identity Non HER-2 Positive
4 Supplemental Table 3: The number of genes involved in differential promoter usage and promoter switching events in breast cancers in comparison to NBS Differential promoter usage and promoter switching events (PSE) Differential promoter usage comparison Statistically significant PSE genes Number of primary transcripts vs NBS Non- vs NBS Genes that change coding region due to PSE HER-2 vs NBS
5 Supplement Table 4: Determination of alternative splice events in individual breast cancer samples in comparison to NBS 1 (A) 2 (B) and 3 (C) using Multivariate Analysis of Transcript Splicing (MATS). A. B.
6 C.
7 Supplement Table 5: Determination of alternative splice events found common in individual breast cancer type vs. normal breast sample 1, 2 and 3 using MATS. Comparisons used to identify cancer specific events Exon Skip Alternative 5' End Alternativ e 3' End Retained Intron vs. NBS Non- vs. NBS HER2-positive vs. NBS
8 Supplement Table 6A: Determination of alternative splice events in merged breast cancer samples in comparison to merged NBS using MATS Merged Groups taken for MATS Alternative 3 prime Alternative 5 prime Mutually exclusive exon Intron retention Exon skip vs. NBS Non- vs. NBS HER2-positive vs. NBS Supplement Table 6B: Determination of switch like event i.e. specific alternative splice events that occur only in merged breast cancer samples or in merged NBS using MATS Event Type Event Number of Events Group A vs NBS Group B vs NBS Group C vs NBS Exon Skip Exclusion in Cancer Inclusion in Cancer Exclusion in Normal Inclusion in Normal Alternative 3' end Exclusion in Cancer Inclusion in Cancer Exclusion in Normal Inclusion in Normal Alternative 5' end Exclusion in Cancer Inclusion in Cancer Exclusion in Normal Inclusion in Normal Mutually Exclusive Exon Exclusion in Cancer Inclusion in Cancer Exclusion in Normal Inclusion in Normal Intron Retention Inclusion in Cancer Exclusion in Normal Inclusion in Normal
9 Supplement Table 7: Annotation of splice events in individual breast cancer samples from, Non- and HER2-positive group and in comparison to normal breast samples using direct exon model comparison Group Samples Type of Splice Events TSS TTS SKIP_ON SKIP_OFF MSKIP_ON MSKIP_OFF Non- Group Samples Type of splice Events TSS TTS SKIP_ON SKIP_OFF MSKIP_ON MSKIP_OFF Non Non Non Non Non Non HER2-positive breast cancer Samples Type of Splice Events TSS TTS SKIP_ON SKIP_OFF MSKIP_ON MSKIP_OFF HER2_ HER2_ HER2_ HER2_ HER2_
10 Supplement Table 8: Annotation of Novel Splice Events that are common in individual breast cancer after eliminating all the splice events that occur in normal breast samples as well as reference human genome, hg19 using direct exon model comparison Common Splice Events in breast cancer groups after eliminating events similar to hg19 Groups Type of Splice Events TSS TTS SKIP_ON SKIP_OFF MSKIP_ON MSKIP_OFF Non HER2-positive
11 Supplemental Figure 1: Venn diagram showing the overlapping transcripts that are similar to reference between A. all three breast cancer types and B. normal breast sample (NBS) A Non HER2-positive B HER2-positive Non NBS
12 density Supplemental Figure 2: CummeRbund plots of the expression level distribution for all genes that are considered from individual experimental conditions shown as the A. csdensity plot B. dendrogram A genes B sample_name NBT Non_ HER log10(fpkm)
13 Supplemental Figure 3: Isoforms associated with statistically significant differentially spliced genes (p-value<0.05) identified through pairwise comparisons of vs NBS (A), non- vs NBS (B), and HER2-positive vs NBS (C).
14 log10(fpkm) HER2 log10(fpkm) HER2 Non_ NBT log10(fpkm) HER2 Non_ NBT Non_ NBT Supplemental Figure 4: The distributions of A. genes B. primary transcripts and C. Coding sequence FPKM across all four groups shown as csboxplot 3 A B C sample_name NBT 0 Non_ HER2 sample_name NBT Non_ 0-1 sample_name NBT Non_ HER2 HER sample_name sample_name sample_name
15 Supplemental Figure 5: FPKM Bins of de novo reassembled transcripts from cufflinks assembler that are classified as novel and reference like using cuffcompare program in A. B. Non- and C. HER2-positive D. Normal breast samples expression transcripts
16 FPKM + 1 FPKM + 1 FPKM + 1 GRIPAP1 P2RY10 PGK1 ENG DOCK8 TMEM71 ASAP1 DSCC1,TAF2 LMO7,UCHL3 CDK8 GCN1L1 RBM19 UTP20 HSPA8,SNORD14C SLC36A4 CTTN,PPFIA1 TEAD1 BTAF1 KIAA1274 EPHX1,SRP9 PGK1 MED12,NLGN3 ZER1 DPM2,FAM102A NCBP1 DSCC1,TAF2 ENPP2 PARP2 VPS36 RPLP0 GCN1L1 PEBP1 LRRK2 FGD4 HSPA8,SNORD14C NT5C2 PARD3 KIAA1217 MLLT10 CROCC THOC2 NUP62CL,RBM41 DOCK11 ALG13 PGK1 ATP7A ZMYND19 EPB41L4B SPTAN1 VPS13A KIAA1797 PRKDC SORL1 CTTN,PPFIA1 MARK2 FRA10AC1 PARD3 MAPK8 RBM17 INTS3,SLC27A3 A Supplemental Figure 6: The relative abundances (FPKM) of top 20 statistically significant splice genes identified from the pair wise comparison between normal breast samples vs. (A), (B) Non- and (C) HER2-positive breast cancers sample_name NBT Non_ HER2 10 0!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! B sample_name NBT Non_ HER2 10 0!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! C sample_name NBT Non_ HER !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
17 Supplemental Figure 7: The overlap of statistically significant splice genes identified from the pair wise comparison between (A) normal breast samples vs., Non- and HER2- positive breast cancers and (B) comparison among the cancer subtypes alone. A NBS vs. NBS vs. Non- B NBS vs. NBS vs. Non- NBS vs. HER-2 positive NBS vs. HER-2 positive
18 Supplemental Figure 8: A. The top panel shows the total number of differentially spliced genes associated known and novel isoforms in (red), non- (green) and HER2-positive (blue) breast cancers. The bottom panel presents the total number of differentially spliced isoforms that are expressed only in, non- and HER2-positive breast cancers. B. Top 20 genes with an abundant novel splice isoform that is not expressed in NBT. The genes are sorted by the highest abundance (FPKMs) for, Non- and HER2. The relative abundance of the novel isoform in the other two breast cancer subtypes is also shown (color coded). The exon models for the novel isoforms are shown in Supplemental file 11. A B
19 Supplemental Figure 9: Venn diagram showing the overlap among candidates identified from cuffdiff statistical test at the level of pre-mrna (TSS), Splicing (Splice), Promoter usage (Promoter) and Coding sequence (CDS) between the normal breast samples vs. (A) Non- (B) and HER2-positive (C) breast cancers. TSS Splice A B C Non- Non Promoter Non- HER2-positive HER2-positive HER2-positive D CDS Non HER2-positive
20 Supplemental Figure 10. Relative abundance of TFAP2A isoforms
21 Supplemental Figure 11: The pathway influenced by the differentially splicing genes NBS vs. differentially splicing genes Cell Death, Cellular Function and Maintenance, Cell Cycle 27 out of 35 molecules NBS vs. Non- differentially splicing genes Post-translational modification, digestive system development & function, embryonic development. 27 out of 35 molecules NBS vs. HER2-positive differentially splicing genes Cell Morphology, cellular function and maintenance, embryonic development 27 out of 35 molecules
22 Supplemental Figure 12: The pathway influenced by the differentially expressing primary transcripts Immunological Disease, Cell to cell Signaling and interaction, cellular movement 30 out of 35 molecules NBS vs. differentially expressing primary transcript genes Tissue morphology, Cell Cycle, Hair & Skin development and function 29 out of 35 molecules NBS vs. Non- differentially expressing primary transcript genes Infectious Disease, renal and urological disease, antimicrobial response 31 out of 35 molecules NBS vs. HER2-positive differentially expressing primary transcript genes
23 Supplemental Figure 13: The pathway influenced by the genes that are involved in differential promoter usage Cellular development, cell to cell signaling and interaction, hematological system development & function 14 molecules present out of 35 NBS vs. differential promoter usage genes Cell to cell signaling and interaction, connective tissue development and function, Cancer 11 out of 35 molecules NBS vs. Non- differential promoter usage genes NBS vs. HER2-positive differential promoter usage genes Tissue development, Cell death, cell morphology 19 out of 35 molecules
24 Supplemental Figure 14: Overlap between differential splice, primary transcripts, promoter usage and promoter switching that occur in, Non- and HER2-positive in comparison with NBS. A 58 B 36 Non- Promoter switching DYRK1A MSI2 MLL5 FTO LRBA PHF16 ABCG1 GRIPAP1 SEC15L1 PHF16 ENO1 KIAA0556 AC HSPA18 AC TSS C FGD4 NCAPD2 KIAA0664 TIAA1217 SNHG7 HER2-Positive TSS 107 ALDH1N1 CPSF7 TFAP2A HSPA8, SNORD14 FCHO2 FGD4 NCAPD2 KIAA0664 TIAA1217 SNHG TSS 135 SDCCAG8 SORL1 SFPQ ZC3H7a DICER1 CASP10 MBD5 CSDA FRYL PPP1R12A ASAP1 DDI2 GPATCH8 LTN1 TRAPPC10 DROSHADHX9 CCDC107 ATP11B INPP4B NF5B IKBKB FBXW7 TFAP2A BRE PHF14 RC3H2 HSPA8 MAMDC2 AC FCHO2 TRAF3IP1
25 Supplemental Figure 15: Exon model of the, Non- and HER2-positive validated novel isoforms Novel Isoform: validated candidate PHLPP2 Non- Novel Isoform: validated candidate LARP1 HER2-positive Novel Isoform: validated candidateadd3
26 Supplemental Figure 16: Predicted protein domain models of the validated novel hybrid isoforms, PHLPP2 (A), ADD3 (B) and LARP1 (C)
27 Supplemental Figure 17: Overlap between the mrna sequencing based alternatively splicing genes and the genes identified from the comparative analysis of normal vs. ductal carcinoma in situ or invasive breast cancer Microarray based Normal vs. DCIS resulting differentially splicing genes microarray mrna seq mrna sequencing based Normal vs., Non- and HER2-positive breast cancer differentially splicing genes Microarray based Normal vs. IBC resulting differentially splicing genes mrna sequencing based Normal vs., Non- and HER2-positive breast cancer differentially splicing genes microarray mrna seq
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