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Fusion Protein:CSTB-PDE9A

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: CSTB-PDE9A
	FusionPDB ID: 19997
	FusionGDB2.0 ID: 19997
		Hgene	Tgene
	Gene symbol	CSTB	PDE9A
	Gene ID	1476	5152
	Gene name	cystatin B	phosphodiesterase 9A
	Synonyms	CPI-B\|CST6\|EPM1\|EPM1A\|PME\|STFB\|ULD	HSPDE9A2
	Cytomap	21q22.3	21q22.3
	Type of gene	protein-coding	protein-coding
	Description	cystatin-Bcystatin B (stefin B)epididymis secretory sperm binding proteinliver thiol proteinase inhibitor	high affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9ACGMP-specific 3',5'-cyclic phosphodiesterase type 9phosphodiesterase PDE9A21
	Modification date	20200313	20200327
	UniProtAcc	P04080 Main function of 5'-partner protein: FUNCTION: This is an intracellular thiol proteinase inhibitor. Tightly binding reversible inhibitor of cathepsins L, H and B.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000291568,	ENST00000291539, ENST00000328862, ENST00000335440, ENST00000349112, ENST00000380328, ENST00000398224, ENST00000398225, ENST00000398227, ENST00000398229, ENST00000398232, ENST00000398234, ENST00000398236, ENST00000470987, ENST00000335512, ENST00000539837,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	10 X 9 X 5=450	13 X 13 X 6=1014
	# samples	9	14
	** MAII score	log2(9/450*10)=-2.32192809488736 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(14/1014*10)=-2.85655892005837 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: CSTB [Title/Abstract] AND PDE9A [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: CSTB [Title/Abstract] AND PDE9A [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	CSTB(45196085)-PDE9A(44188298), # samples:1
Anticipated loss of major functional domain due to fusion event.	CSTB-PDE9A seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF. CSTB-PDE9A seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.

* DoF score (Degree of Frequency) = # partners X # break points X # cancer types
** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10)

Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner	Gene	GO ID	GO term	PubMed ID
Hgene	CSTB	GO:0010466	negative regulation of peptidase activity	6203523
Hgene	CSTB	GO:0045861	negative regulation of proteolysis	3488317
Tgene	PDE9A	GO:0046068	cGMP metabolic process	9624146
Tgene	PDE9A	GO:0046069	cGMP catabolic process	25799991

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr21:45196085/chr21:44188298)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.

Retention analysis results of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features, are available here.

Fusion gene breakpoints across CSTB (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion gene breakpoints across PDE9A (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

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Fusion Amino Acid Sequences

Fusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.

Henst

Tenst

Hgene

Hchr

Hbp

Hstrand

Tgene

Tchr

Tbp

Tstrand

Seq length
(transcript)

BP loci
(transcript)

Predicted start
(transcript)

Predicted stop
(transcript)

Seq length
(amino acids)

ENST00000291568

CSTB

chr21

45196085

ENST00000335512

PDE9A

chr21

44188298

884

242

667

218

ENST00000291568

CSTB

chr21

45196085

ENST00000539837

PDE9A

chr21

44188298

881

242

667

218

DeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated.

Henst	Tenst	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand	No-coding score	Coding score
ENST00000291568	ENST00000335512	CSTB	chr21	45196085	-	PDE9A	chr21	44188298	+	0.011490788	0.98850924
ENST00000291568	ENST00000539837	CSTB	chr21	45196085	-	PDE9A	chr21	44188298	+	0.012091844	0.9879082

Predicted full-length fusion amino acid sequences. For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among all the predicted ones.

Get the fusion protein sequences from here.

Fusion protein sequence information is available in the fasta format.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

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Fusion Protein Breakpoint Sequences for CSTB-PDE9A

+/-13 AA sequence from the breakpoints of the fusion protein sequences.

Hgene	Hchr	Hbp	Tgene	Tchr	Tbp	Length(fusion protein)	BP in fusion protein	Peptide
CSTB	chr21	45196085	PDE9A	chr21	44188298	242	76	TQPATAETQHIADQLKMILIKCCDIS

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Potential FusionNeoAntigen Information of CSTB-PDE9A in HLA I

Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.

CSTB-PDE9A_45196085_44188298.msa

Potential FusionNeoAntigen Information
* We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5)

Fusion gene	Hchr	Hbp	Tgene	Tchr	Tbp	HLA I	FusionNeoAntigen peptide	Binding score	Immunogenic score	Neoantigen start (at BP 13)	Neoantigen end (at BP 13)
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B52:01	DQLKMILI	0.9975	0.7434	12	20
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B48:01	TQHIADQL	0.9956	0.6489	7	15
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B39:13	TQHIADQL	0.9106	0.9019	7	15
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B39:01	QHIADQLKM	0.9988	0.9358	8	17
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B39:24	QHIADQLKM	0.9978	0.53	8	17
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B38:02	QHIADQLKM	0.9975	0.9714	8	17
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B38:01	QHIADQLKM	0.9971	0.9687	8	17
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B39:06	QHIADQLKM	0.9966	0.7704	8	17
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B15:10	QHIADQLKM	0.9854	0.5642	8	17
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B14:01	QHIADQLKM	0.9637	0.7525	8	17
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B14:02	QHIADQLKM	0.9637	0.7525	8	17
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B35:03	IADQLKMIL	0.9587	0.8437	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B15:18	QHIADQLKM	0.9436	0.6964	8	17
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B35:02	IADQLKMIL	0.8433	0.905	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B35:04	IADQLKMIL	0.8433	0.905	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B15:37	QHIADQLKM	0.7154	0.5407	8	17
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B44:03	AETQHIADQL	0.9839	0.9066	5	15
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B38:01	QHIADQLKMI	0.9827	0.966	8	18
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B38:02	QHIADQLKMI	0.9805	0.9682	8	18
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B44:05	AETQHIADQL	0.9586	0.5002	5	15
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B15:18	TQHIADQLKM	0.8297	0.6173	7	17
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B38:01	TQHIADQLKM	0.6546	0.9677	7	17
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B38:02	TQHIADQLKM	0.649	0.9693	7	17
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B15:37	TQHIADQLKM	0.5146	0.518	7	17
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B39:24	QHIADQLKMIL	0.9995	0.6215	8	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B39:01	QHIADQLKMIL	0.9995	0.9543	8	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B38:01	QHIADQLKMIL	0.9993	0.9792	8	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B38:02	QHIADQLKMIL	0.9992	0.9804	8	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B15:10	QHIADQLKMIL	0.999	0.5694	8	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B38:01	ETQHIADQLKM	0.716	0.9596	6	17
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B38:02	ETQHIADQLKM	0.6877	0.9614	6	17
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C05:09	IADQLKMI	1	0.9396	10	18
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C08:15	IADQLKMI	0.9999	0.9685	10	18
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B51:07	DQLKMILI	0.996	0.7372	12	20
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B48:03	TQHIADQL	0.956	0.524	7	15
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C04:07	IADQLKMIL	0.9999	0.7932	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C08:15	IADQLKMIL	0.9999	0.9687	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C04:10	IADQLKMIL	0.9999	0.7794	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C05:09	IADQLKMIL	0.9999	0.9377	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C01:17	IADQLKMIL	0.9998	0.9374	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C03:19	IADQLKMIL	0.9996	0.9805	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C03:07	IADQLKMIL	0.9995	0.9529	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C03:08	IADQLKMIL	0.999	0.8557	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B39:09	QHIADQLKM	0.9989	0.668	8	17
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C01:30	IADQLKMIL	0.9989	0.9514	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B39:12	QHIADQLKM	0.9984	0.9373	8	17
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C15:06	IADQLKMIL	0.998	0.8503	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B39:05	QHIADQLKM	0.9973	0.9292	8	17
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C04:06	IADQLKMIL	0.9925	0.8922	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C08:04	IADQLKMIL	0.9881	0.9461	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C08:13	IADQLKMIL	0.9881	0.9461	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C04:14	IADQLKMIL	0.9434	0.8574	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C07:13	IADQLKMIL	0.9291	0.8877	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C03:14	IADQLKMIL	0.9195	0.9594	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C08:03	IADQLKMIL	0.9045	0.9778	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C07:29	IADQLKMIL	0.8864	0.9355	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C02:06	IADQLKMIL	0.8501	0.9387	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B35:12	IADQLKMIL	0.8433	0.905	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B39:10	IADQLKMIL	0.7412	0.9028	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B15:21	QHIADQLKM	0.5404	0.8844	8	17
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B14:03	QHIADQLKM	0.2678	0.7978	8	17
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B44:10	AETQHIADQL	0.9772	0.6495	5	15
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B44:09	AETQHIADQL	0.9701	0.5376	5	15
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B39:08	AETQHIADQL	0.9579	0.8978	5	15
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B39:05	TQHIADQLKM	0.6361	0.9175	7	17
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B39:09	QHIADQLKMIL	0.9994	0.7219	8	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B39:05	QHIADQLKMIL	0.999	0.9484	8	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C04:03	IADQLKMI	1	0.8519	10	18
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C05:01	IADQLKMI	1	0.9396	10	18
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C08:02	IADQLKMI	0.9999	0.9685	10	18
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B39:02	TQHIADQL	0.9803	0.8993	7	15
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B40:12	TQHIADQL	0.956	0.524	7	15
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C05:01	IADQLKMIL	0.9999	0.9377	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C04:03	IADQLKMIL	0.9999	0.8372	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C18:01	IADQLKMIL	0.9999	0.8074	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C04:01	IADQLKMIL	0.9999	0.7932	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C01:03	IADQLKMIL	0.9999	0.9292	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C08:02	IADQLKMIL	0.9999	0.9687	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C01:02	IADQLKMIL	0.9998	0.9321	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C03:04	IADQLKMIL	0.9997	0.982	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C03:03	IADQLKMIL	0.9997	0.982	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C03:17	IADQLKMIL	0.9992	0.9604	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C03:05	IADQLKMIL	0.9992	0.92	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C03:67	IADQLKMIL	0.9991	0.9694	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B39:31	QHIADQLKM	0.9986	0.9363	8	17
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C03:02	IADQLKMIL	0.9979	0.9611	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C15:05	IADQLKMIL	0.9972	0.8743	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B38:05	QHIADQLKM	0.9971	0.9687	8	17
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C15:02	IADQLKMIL	0.996	0.8127	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C03:06	IADQLKMIL	0.992	0.9822	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C04:04	IADQLKMIL	0.9887	0.8644	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C16:01	IADQLKMIL	0.9819	0.9787	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B15:09	QHIADQLKM	0.9786	0.7701	8	17
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C16:02	IADQLKMIL	0.9688	0.9886	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C07:04	IADQLKMIL	0.9543	0.9095	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B35:13	IADQLKMIL	0.9448	0.8505	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-A02:03	HIADQLKMI	0.9143	0.5556	9	18
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C08:01	IADQLKMIL	0.9045	0.9778	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B35:09	IADQLKMIL	0.8433	0.905	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C12:02	IADQLKMIL	0.8334	0.9659	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-C17:01	IADQLKMIL	0.7936	0.7789	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B39:11	QHIADQLKM	0.732	0.9043	8	17
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B07:13	IADQLKMIL	0.6045	0.7434	10	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B40:04	AETQHIADQL	0.9982	0.7073	5	15
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B44:13	AETQHIADQL	0.9839	0.9066	5	15
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B44:26	AETQHIADQL	0.9839	0.9066	5	15
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B44:07	AETQHIADQL	0.9839	0.9066	5	15
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B38:05	QHIADQLKMI	0.9827	0.966	8	18
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B41:03	AETQHIADQL	0.8454	0.7307	5	15
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B38:05	TQHIADQLKM	0.6546	0.9677	7	17
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B15:09	TQHIADQLKM	0.4509	0.7508	7	17
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B38:05	QHIADQLKMIL	0.9993	0.9792	8	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B15:09	QHIADQLKMIL	0.9983	0.815	8	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B39:11	QHIADQLKMIL	0.9938	0.9312	8	19
CSTB-PDE9A	chr21	45196085	chr21	44188298	242	HLA-B38:05	ETQHIADQLKM	0.716	0.9596	6	17

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Potential FusionNeoAntigen Information of CSTB-PDE9A in HLA II

Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).

Fusion gene

Hchr

Hbp

Tgene

Tchr

Tbp

HLA II

FusionNeoAntigen peptide

Neoantigen start (at BP 13)

Neoantigen end (at BP 13)

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Fusion breakpoint peptide structures of CSTB-PDE9A

3D structures of the fusion breakpoint peptide of 14AA sequence that have potential fusion neoantigens
* The minimum length of the amino acid sequence in RoseTTAFold is 14AA. Here, we predicted the 14AA fusion protein breakpoint sequence not the fusion neoantigen peptide, which is shorter than 14 AA.

File name	BPseq	Hgene	Tgene	Hchr	Hbp	Tchr	Tbp	AAlen
2182	ETQHIADQLKMILI	CSTB	PDE9A	chr21	45196085	chr21	44188298	242

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of CSTB-PDE9A

Virtual screening between 25 HLAs (from PDB) and FusionNeoAntigens
* We used Glide to predict the interaction between HLAs and neoantigens.

HLA allele	PDB ID	File name	BPseq	Docking score	Glide score
HLA-B14:02	3BVN	2182	ETQHIADQLKMILI	-7.9962	-8.1096
HLA-B14:02	3BVN	2182	ETQHIADQLKMILI	-5.70842	-6.74372
HLA-B52:01	3W39	2182	ETQHIADQLKMILI	-6.83737	-6.95077
HLA-B52:01	3W39	2182	ETQHIADQLKMILI	-4.4836	-5.5189
HLA-A11:01	4UQ2	2182	ETQHIADQLKMILI	-10.0067	-10.1201
HLA-A11:01	4UQ2	2182	ETQHIADQLKMILI	-9.03915	-10.0745
HLA-A24:02	5HGA	2182	ETQHIADQLKMILI	-6.56204	-6.67544
HLA-A24:02	5HGA	2182	ETQHIADQLKMILI	-5.42271	-6.45801
HLA-B44:05	3DX8	2182	ETQHIADQLKMILI	-7.85648	-8.89178
HLA-B44:05	3DX8	2182	ETQHIADQLKMILI	-5.3978	-5.5112
HLA-A02:01	6TDR	2182	ETQHIADQLKMILI	-3.37154	-4.40684

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Vaccine Design for the FusionNeoAntigens of CSTB-PDE9A

mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is.

Fusion gene	Hchr	Hbp	Tchr	Tbp	Start in +/-13AA	End in +/-13AA	FusionNeoAntigen peptide sequence	FusionNeoAntigen RNA sequence
CSTB-PDE9A	chr21	45196085	chr21	44188298	10	18	IADQLKMI	GCCGACCAGCTGAAGATGATTTTG
CSTB-PDE9A	chr21	45196085	chr21	44188298	10	19	IADQLKMIL	GCCGACCAGCTGAAGATGATTTTGATA
CSTB-PDE9A	chr21	45196085	chr21	44188298	12	20	DQLKMILI	CAGCTGAAGATGATTTTGATAAAA
CSTB-PDE9A	chr21	45196085	chr21	44188298	5	15	AETQHIADQL	GAGACCCAGCACATCGCCGACCAGCTGAAG
CSTB-PDE9A	chr21	45196085	chr21	44188298	6	17	ETQHIADQLKM	ACCCAGCACATCGCCGACCAGCTGAAGATGATT
CSTB-PDE9A	chr21	45196085	chr21	44188298	7	15	TQHIADQL	CAGCACATCGCCGACCAGCTGAAG
CSTB-PDE9A	chr21	45196085	chr21	44188298	7	17	TQHIADQLKM	CAGCACATCGCCGACCAGCTGAAGATGATT
CSTB-PDE9A	chr21	45196085	chr21	44188298	8	17	QHIADQLKM	CACATCGCCGACCAGCTGAAGATGATT
CSTB-PDE9A	chr21	45196085	chr21	44188298	8	18	QHIADQLKMI	CACATCGCCGACCAGCTGAAGATGATTTTG
CSTB-PDE9A	chr21	45196085	chr21	44188298	8	19	QHIADQLKMIL	CACATCGCCGACCAGCTGAAGATGATTTTGATA
CSTB-PDE9A	chr21	45196085	chr21	44188298	9	18	HIADQLKMI	ATCGCCGACCAGCTGAAGATGATTTTG

mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.

Fusion gene

Hchr

Hbp

Tchr

Tbp

Start in +/-13AA

End in +/-13AA

FusionNeoAntigen peptide

FusionNEoAntigen RNA sequence

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Information of the samples that have these potential fusion neoantigens of CSTB-PDE9A

These samples were reported as having these fusion breakpoints. For individual breakpoints, we checked the open reading frames considering multiple gene isoforms and chose the in-frame fusion genes only. Then, we made fusion protein sequences and predicted the fusion neoantigens. These fusion-positive samples may have these potential fusion neoantigens.

Cancer type	Fusion gene	Hchr	Hbp	Henst	Tchr	Tbp	Tenst	Sample
SARC	CSTB-PDE9A	chr21	45196085	ENST00000291568	chr21	44188298	ENST00000335512	TCGA-3B-A9HO-01A

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Potential target of CAR-T therapy development for CSTB-PDE9A

Predicted 3D structure. We used RoseTTAFold.

Retention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, to provide the retention of the transmembrane domain, we only show the protein feature retention information of those transmembrane features

* Minus value of BPloci means that the break point is located before the CDS.

- In-frame and retained 'Transmembrane'.

Partner

Gene

Hbp

Tbp

ENST

Strand

BPexon

TotalExon

Protein feature loci

*BPloci

TotalLen

Protein feature

Protein feature note

Subcellular localization prediction of the transmembrane domain retained fusion proteins
* We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image.

Hgene

Hchr

Hbp

Henst

Tgene

Tchr

Tbp

Tenst

DeepLoc result

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Related Drugs to CSTB-PDE9A

Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Drug

Source

PMID

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Related Diseases to CSTB-PDE9A

Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)

Hgene

Tgene

Disease

Source

PMID

Diseases associated with fusion partners.
(DisGeNet 4.0)

Partner

Gene

Disease ID

Disease name

# pubmeds

Source

	Fusion Gene and Fusion Protein Summary
	Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)
	Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)
	Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)
	Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)
	Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)
	Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)
	Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)
	Potential target of CAR-T therapy development
	Information on the samples that have these potential fusion neoantigens
	Fusion Protein Targeting Drugs - (Manual Curation)
	Fusion Protein Related diseases - (Manual Curation)