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Fusion Protein:HDAC4-SATB2

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: HDAC4-SATB2
	FusionPDB ID: 35838
	FusionGDB2.0 ID: 35838
		Hgene	Tgene
	Gene symbol	HDAC4	SATB2
	Gene ID	9759	23314
	Gene name	histone deacetylase 4	SATB homeobox 2
	Synonyms	AHO3\|BDMR\|HA6116\|HD4\|HDAC-4\|HDAC-A\|HDACA	GLSS
	Cytomap	2q37.3	2q33.1
	Type of gene	protein-coding	protein-coding
	Description	histone deacetylase 4histone deacetylase A	DNA-binding protein SATB2SATB family member 2special AT-rich sequence-binding protein 2
	Modification date	20200329	20200313
	UniProtAcc	P56524 Main function of 5'-partner protein: FUNCTION: Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes. Involved in muscle maturation via its interaction with the myocyte enhancer factors such as MEF2A, MEF2C and MEF2D. Involved in the MTA1-mediated epigenetic regulation of ESR1 expression in breast cancer. Deacetylates HSPA1A and HSPA1B at 'Lys-77' leading to their preferential binding to co-chaperone STUB1 (PubMed:27708256). {ECO:0000269\|PubMed:10523670, ECO:0000269\|PubMed:24413532, ECO:0000269\|PubMed:27708256}.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000345617, ENST00000541256, ENST00000543185, ENST00000553145,	ENST00000260926, ENST00000457245, ENST00000417098, ENST00000428695, ENST00000443023, ENST00000484124,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	13 X 10 X 9=1170	4 X 6 X 3=72
	# samples	15	7
	** MAII score	log2(15/1170*10)=-2.96347412397489 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(7/72*10)=-0.0406419844973459 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: HDAC4 [Title/Abstract] AND SATB2 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: HDAC4 [Title/Abstract] AND SATB2 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	HDAC4(240158289)-SATB2(200325255), # samples:1 HDAC4(240158289)-SATB2(200298237), # samples:1
Anticipated loss of major functional domain due to fusion event.	HDAC4-SATB2 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. HDAC4-SATB2 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. HDAC4-SATB2 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. HDAC4-SATB2 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	HDAC4	GO:0000122	negative regulation of transcription by RNA polymerase II	10869435\|16236793
Hgene	HDAC4	GO:0006338	chromatin remodeling	18850004
Hgene	HDAC4	GO:0006476	protein deacetylation	27708256
Hgene	HDAC4	GO:0016575	histone deacetylation	10869435
Hgene	HDAC4	GO:0033235	positive regulation of protein sumoylation	17696781
Hgene	HDAC4	GO:0034983	peptidyl-lysine deacetylation	18614528
Hgene	HDAC4	GO:0045892	negative regulation of transcription, DNA-templated	10869435
Hgene	HDAC4	GO:0070932	histone H3 deacetylation	12590135
Hgene	HDAC4	GO:0070933	histone H4 deacetylation	12590135

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr2:240158289/chr2:200325255)
- 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 HDAC4 (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 SATB2 (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)

ENST00000345617

HDAC4

chr2

240158289

ENST00000417098

SATB2

chr2

200298237

5630

886

783

2918

711

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
ENST00000345617	ENST00000417098	HDAC4	chr2	240158289	-	SATB2	chr2	200298237	-	0.000729111	0.99927086

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 HDAC4-SATB2

+/-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
HDAC4	chr2	240158289	SATB2	chr2	200298237	886	34	LLNPARVNHMPSTGLMIPVFCVVEQL

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Potential FusionNeoAntigen Information of HDAC4-SATB2 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.

HDAC4-SATB2_240158289_200298237.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)
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B39:01	NHMPSTGL	0.9998	0.9619	7	15
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B39:24	NHMPSTGL	0.9998	0.6186	7	15
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B38:01	NHMPSTGL	0.9996	0.9748	7	15
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B38:02	NHMPSTGL	0.9996	0.9798	7	15
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B15:10	NHMPSTGL	0.9995	0.5786	7	15
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B39:06	NHMPSTGL	0.9993	0.8915	7	15
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B15:37	NHMPSTGL	0.994	0.6344	7	15
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B51:01	MPSTGLMI	0.99	0.5193	9	17
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B14:02	NHMPSTGL	0.9706	0.9521	7	15
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B14:01	NHMPSTGL	0.9706	0.9521	7	15
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B15:18	NHMPSTGL	0.923	0.649	7	15
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B39:01	NHMPSTGLM	0.9985	0.9647	7	16
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B39:24	NHMPSTGLM	0.9972	0.6091	7	16
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B15:10	NHMPSTGLM	0.9958	0.5472	7	16
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B38:02	NHMPSTGLM	0.9954	0.9815	7	16
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B38:01	NHMPSTGLM	0.9949	0.9771	7	16
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B39:06	NHMPSTGLM	0.9889	0.9022	7	16
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B15:37	NHMPSTGLM	0.9774	0.6155	7	16
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B15:17	STGLMIPVF	0.9674	0.8667	11	20
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B14:02	NHMPSTGLM	0.9232	0.9611	7	16
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B14:01	NHMPSTGLM	0.9232	0.9611	7	16
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B57:03	STGLMIPVF	0.8829	0.9668	11	20
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B15:18	NHMPSTGLM	0.7858	0.6316	7	16
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B39:01	NHMPSTGLMI	0.9979	0.9685	7	17
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B39:24	NHMPSTGLMI	0.9976	0.6202	7	17
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B39:06	NHMPSTGLMI	0.9973	0.9051	7	17
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B38:02	NHMPSTGLMI	0.9971	0.9809	7	17
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B38:01	NHMPSTGLMI	0.997	0.9738	7	17
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B15:37	NHMPSTGLMI	0.9451	0.5593	7	17
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B15:10	VNHMPSTGLM	0.8749	0.5545	6	16
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B38:01	VNHMPSTGLM	0.573	0.991	6	16
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B27:05	ARVNHMPSTGL	1	0.5688	4	15
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B27:04	ARVNHMPSTGL	1	0.8403	4	15
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B27:07	ARVNHMPSTGL	0.9998	0.7121	4	15
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B35:01	MPSTGLMIPVF	0.9995	0.9198	9	20
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B35:08	MPSTGLMIPVF	0.9993	0.8845	9	20
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B35:05	MPSTGLMIPVF	0.9988	0.7041	9	20
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B35:03	MPSTGLMIPVF	0.9979	0.9066	9	20
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B35:04	MPSTGLMIPVF	0.9895	0.9647	9	20
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B35:02	MPSTGLMIPVF	0.9895	0.9647	9	20
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B39:09	NHMPSTGL	0.9998	0.8865	7	15
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B39:12	NHMPSTGL	0.9997	0.9616	7	15
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B39:05	NHMPSTGL	0.9996	0.9512	7	15
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-C01:30	HMPSTGLM	0.7725	0.9787	8	16
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B14:03	NHMPSTGL	0.6004	0.9456	7	15
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B39:09	NHMPSTGLM	0.9986	0.8846	7	16
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B39:12	NHMPSTGLM	0.9983	0.9655	7	16
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B54:01	MPSTGLMIP	0.9957	0.5472	9	18
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B39:05	NHMPSTGLM	0.9955	0.957	7	16
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-C01:17	HMPSTGLMI	0.2821	0.9767	8	17
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B14:03	NHMPSTGLM	0.2269	0.9442	7	16
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B15:21	NHMPSTGLM	0.1882	0.8551	7	16
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-C01:30	HMPSTGLMI	0.147	0.9798	8	17
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B54:01	MPSTGLMIPV	0.9987	0.5996	9	19
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B39:05	NHMPSTGLMI	0.9962	0.9621	7	17
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B27:03	ARVNHMPSTGL	0.9987	0.6214	4	15
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B35:12	MPSTGLMIPVF	0.9895	0.9647	9	20
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B39:31	NHMPSTGL	0.9998	0.9619	7	15
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B38:05	NHMPSTGL	0.9996	0.9748	7	15
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B15:09	NHMPSTGL	0.9992	0.6786	7	15
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B39:11	NHMPSTGL	0.9912	0.8924	7	15
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B78:02	MPSTGLMI	0.9897	0.9177	9	17
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B51:21	MPSTGLMI	0.9843	0.5491	9	17
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-C01:02	HMPSTGLM	0.9829	0.9753	8	16
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B51:09	MPSTGLMI	0.9794	0.5233	9	17
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B59:01	MPSTGLMI	0.9487	0.5004	9	17
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B39:31	NHMPSTGLM	0.9981	0.9647	7	16
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B38:05	NHMPSTGLM	0.9949	0.9771	7	16
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B15:09	NHMPSTGLM	0.9844	0.6556	7	16
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B57:02	STGLMIPVF	0.8992	0.9215	11	20
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B39:11	NHMPSTGLM	0.893	0.8574	7	16
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-C01:02	HMPSTGLMI	0.1764	0.9763	8	17
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-C01:03	HMPSTGLMI	0.0886	0.9102	8	17
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B38:05	NHMPSTGLMI	0.997	0.9738	7	17
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B15:09	NHMPSTGLMI	0.9925	0.63	7	17
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B38:05	VNHMPSTGLM	0.573	0.991	6	16
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B15:09	VNHMPSTGLM	0.545	0.7207	6	16
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B27:08	ARVNHMPSTGL	1	0.547	4	15
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B27:10	ARVNHMPSTGL	1	0.8673	4	15
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B27:09	ARVNHMPSTGL	0.9999	0.5546	4	15
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B27:06	ARVNHMPSTGL	0.9999	0.8512	4	15
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B35:77	MPSTGLMIPVF	0.9995	0.9198	9	20
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B35:23	MPSTGLMIPVF	0.9995	0.934	9	20
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B35:17	MPSTGLMIPVF	0.9988	0.8517	9	20
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B35:30	MPSTGLMIPVF	0.9988	0.8517	9	20
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B35:11	MPSTGLMIPVF	0.9979	0.9455	9	20
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B55:04	MPSTGLMIPVF	0.9968	0.5115	9	20
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B35:09	MPSTGLMIPVF	0.9895	0.9647	9	20
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B35:24	MPSTGLMIPVF	0.9883	0.8942	9	20
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B15:08	MPSTGLMIPVF	0.961	0.918	9	20
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B35:43	MPSTGLMIPVF	0.9606	0.9193	9	20
HDAC4-SATB2	chr2	240158289	chr2	200298237	886	HLA-B15:11	MPSTGLMIPVF	0.9571	0.9064	9	20

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Potential FusionNeoAntigen Information of HDAC4-SATB2 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 HDAC4-SATB2

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
10138	VNHMPSTGLMIPVF	HDAC4	SATB2	chr2	240158289	chr2	200298237	886

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of HDAC4-SATB2

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	10138	VNHMPSTGLMIPVF	-7.9962	-8.1096
HLA-B14:02	3BVN	10138	VNHMPSTGLMIPVF	-5.70842	-6.74372
HLA-B52:01	3W39	10138	VNHMPSTGLMIPVF	-6.83737	-6.95077
HLA-B52:01	3W39	10138	VNHMPSTGLMIPVF	-4.4836	-5.5189
HLA-A11:01	4UQ2	10138	VNHMPSTGLMIPVF	-10.0067	-10.1201
HLA-A11:01	4UQ2	10138	VNHMPSTGLMIPVF	-9.03915	-10.0745
HLA-A24:02	5HGA	10138	VNHMPSTGLMIPVF	-6.56204	-6.67544
HLA-A24:02	5HGA	10138	VNHMPSTGLMIPVF	-5.42271	-6.45801
HLA-B44:05	3DX8	10138	VNHMPSTGLMIPVF	-7.85648	-8.89178
HLA-B44:05	3DX8	10138	VNHMPSTGLMIPVF	-5.3978	-5.5112
HLA-B35:01	1A1N	10138	VNHMPSTGLMIPVF	-6.27422	-6.38762
HLA-B35:01	1A1N	10138	VNHMPSTGLMIPVF	-5.27424	-6.30954
HLA-A02:01	6TDR	10138	VNHMPSTGLMIPVF	-3.37154	-4.40684

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Vaccine Design for the FusionNeoAntigens of HDAC4-SATB2

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
HDAC4-SATB2	chr2	240158289	chr2	200298237	11	20	STGLMIPVF	GCACGGGTTTGATGATTCCTGTCTTTT
HDAC4-SATB2	chr2	240158289	chr2	200298237	4	15	ARVNHMPSTGL	CCCGCGTGAACCACATGCCCAGCACGGGTTTGA
HDAC4-SATB2	chr2	240158289	chr2	200298237	6	16	VNHMPSTGLM	TGAACCACATGCCCAGCACGGGTTTGATGA
HDAC4-SATB2	chr2	240158289	chr2	200298237	7	15	NHMPSTGL	ACCACATGCCCAGCACGGGTTTGA
HDAC4-SATB2	chr2	240158289	chr2	200298237	7	16	NHMPSTGLM	ACCACATGCCCAGCACGGGTTTGATGA
HDAC4-SATB2	chr2	240158289	chr2	200298237	7	17	NHMPSTGLMI	ACCACATGCCCAGCACGGGTTTGATGATTC
HDAC4-SATB2	chr2	240158289	chr2	200298237	8	16	HMPSTGLM	ACATGCCCAGCACGGGTTTGATGA
HDAC4-SATB2	chr2	240158289	chr2	200298237	8	17	HMPSTGLMI	ACATGCCCAGCACGGGTTTGATGATTC
HDAC4-SATB2	chr2	240158289	chr2	200298237	9	17	MPSTGLMI	TGCCCAGCACGGGTTTGATGATTC
HDAC4-SATB2	chr2	240158289	chr2	200298237	9	18	MPSTGLMIP	TGCCCAGCACGGGTTTGATGATTCCTG
HDAC4-SATB2	chr2	240158289	chr2	200298237	9	19	MPSTGLMIPV	TGCCCAGCACGGGTTTGATGATTCCTGTCT
HDAC4-SATB2	chr2	240158289	chr2	200298237	9	20	MPSTGLMIPVF	TGCCCAGCACGGGTTTGATGATTCCTGTCTTTT

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 HDAC4-SATB2

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
BLCA	HDAC4-SATB2	chr2	240158289	ENST00000345617	chr2	200298237	ENST00000417098	TCGA-BL-A13J-01A

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Potential target of CAR-T therapy development for HDAC4-SATB2

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 HDAC4-SATB2

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 HDAC4-SATB2

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)