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Fusion Protein:NSD1-DPEP2

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: NSD1-DPEP2
	FusionPDB ID: 60416
	FusionGDB2.0 ID: 60416
		Hgene	Tgene
	Gene symbol	NSD1	DPEP2
	Gene ID	64324	64174
	Gene name	nuclear receptor binding SET domain protein 1	dipeptidase 2
	Synonyms	ARA267\|KMT3B\|SOTOS\|SOTOS1\|STO	MBD2
	Cytomap	5q35.3	16q22.1
	Type of gene	protein-coding	protein-coding
	Description	histone-lysine N-methyltransferase, H3 lysine-36 and H4 lysine-20 specificH3-K36-HMTaseH4-K20-HMTaseNR-binding SET domain-containing proteinandrogen receptor coactivator 267 kDa proteinandrogen receptor-associated coregulator 267androgen receptor-as	dipeptidase 2
	Modification date	20200321	20200313
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000347982, ENST00000354179, ENST00000439151, ENST00000361032, ENST00000511258,	ENST00000393847, ENST00000412757, ENST00000572888,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	23 X 14 X 17=5474	2 X 4 X 2=16
	# samples	37	2
	** MAII score	log2(37/5474*10)=-3.88699825884864 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(2/16*10)=0.321928094887362 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Fusion gene context	PubMed: NSD1 [Title/Abstract] AND DPEP2 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: NSD1 [Title/Abstract] AND DPEP2 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	NSD1(176619020)-DPEP2(68023301), # samples:3
Anticipated loss of major functional domain due to fusion event.	NSD1-DPEP2 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. NSD1-DPEP2 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. NSD1-DPEP2 seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF. NSD1-DPEP2 seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF. NSD1-DPEP2 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. NSD1-DPEP2 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF. NSD1-DPEP2 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted 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	NSD1	GO:0045893	positive regulation of transcription, DNA-templated	11509567

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr5:176619020/chr16:68023301)
- 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 NSD1 (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 DPEP2 (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)
ENST00000354179	NSD1	chr5	176619020	+	ENST00000393847	DPEP2	chr16	68023301	-	995	416	160	882	240
ENST00000354179	NSD1	chr5	176619020	+	ENST00000412757	DPEP2	chr16	68023301	-	992	416	160	882	240
ENST00000354179	NSD1	chr5	176619020	+	ENST00000572888	DPEP2	chr16	68023301	-	883	416	160	882	241
ENST00000439151	NSD1	chr5	176619020	+	ENST00000393847	DPEP2	chr16	68023301	-	1687	1108	45	1574	509
ENST00000439151	NSD1	chr5	176619020	+	ENST00000412757	DPEP2	chr16	68023301	-	1684	1108	45	1574	509
ENST00000439151	NSD1	chr5	176619020	+	ENST00000572888	DPEP2	chr16	68023301	-	1575	1108	45	1574	509
ENST00000347982	NSD1	chr5	176619020	+	ENST00000393847	DPEP2	chr16	68023301	-	936	357	101	823	240
ENST00000347982	NSD1	chr5	176619020	+	ENST00000412757	DPEP2	chr16	68023301	-	933	357	101	823	240
ENST00000347982	NSD1	chr5	176619020	+	ENST00000572888	DPEP2	chr16	68023301	-	824	357	101	823	241

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
ENST00000354179	ENST00000393847	NSD1	chr5	176619020	+	DPEP2	chr16	68023301	-	0.039437227	0.96056277
ENST00000354179	ENST00000412757	NSD1	chr5	176619020	+	DPEP2	chr16	68023301	-	0.03794371	0.9620562
ENST00000354179	ENST00000572888	NSD1	chr5	176619020	+	DPEP2	chr16	68023301	-	0.034769185	0.9652308
ENST00000439151	ENST00000393847	NSD1	chr5	176619020	+	DPEP2	chr16	68023301	-	0.001335093	0.99866486
ENST00000439151	ENST00000412757	NSD1	chr5	176619020	+	DPEP2	chr16	68023301	-	0.001322155	0.9986778
ENST00000439151	ENST00000572888	NSD1	chr5	176619020	+	DPEP2	chr16	68023301	-	0.001487408	0.99851257
ENST00000347982	ENST00000393847	NSD1	chr5	176619020	+	DPEP2	chr16	68023301	-	0.037301667	0.9626984
ENST00000347982	ENST00000412757	NSD1	chr5	176619020	+	DPEP2	chr16	68023301	-	0.03557727	0.96442276
ENST00000347982	ENST00000572888	NSD1	chr5	176619020	+	DPEP2	chr16	68023301	-	0.033639025	0.96636105

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 NSD1-DPEP2

+/-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
NSD1	chr5	176619020	DPEP2	chr16	68023301	1108	354	CSDPLINTHSKMKDHFDHIKAVIGSK
NSD1	chr5	176619020	DPEP2	chr16	68023301	357	85	CSDPLINTHSKMKDHFDHIKAVIGSK
NSD1	chr5	176619020	DPEP2	chr16	68023301	416	85	CSDPLINTHSKMKDHFDHIKAVIGSK

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Potential FusionNeoAntigen Information of NSD1-DPEP2 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.

NSD1-DPEP2_176619020_68023301.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)
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	HLA-A30:08	KMKDHFDHI	0.9761	0.6137	10	19
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	HLA-A02:04	KMKDHFDHI	0.8849	0.5311	10	19
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	HLA-B39:01	THSKMKDHF	0.8735	0.6743	7	16
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	HLA-A02:11	KMKDHFDHI	0.8718	0.5191	10	19
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	HLA-B38:01	THSKMKDHF	0.7825	0.8498	7	16
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	HLA-B38:02	THSKMKDHF	0.7799	0.8553	7	16
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	HLA-B15:18	THSKMKDHF	0.2855	0.5473	7	16
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	HLA-B13:02	KMKDHFDHI	0.028	0.6227	10	19
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	HLA-B13:01	KMKDHFDHI	0.0182	0.9248	10	19
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	HLA-B52:01	KMKDHFDHI	0.0048	0.8533	10	19
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	HLA-A30:08	KMKDHFDHIK	0.9935	0.6718	10	20
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	HLA-B39:06	KDHFDHIKAV	0.755	0.7641	12	22
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	HLA-B38:01	NTHSKMKDHF	0.2312	0.7784	6	16
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	HLA-B38:02	NTHSKMKDHF	0.2084	0.8129	6	16
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	HLA-B39:06	MKDHFDHIKAV	0.9995	0.9047	11	22
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	HLA-B15:04	KMKDHFDHI	0.9534	0.9226	10	19
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	HLA-B39:12	THSKMKDHF	0.9044	0.6883	7	16
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	HLA-B39:05	THSKMKDHF	0.7198	0.6664	7	16
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	HLA-B14:03	THSKMKDHF	0.029	0.5984	7	16
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	HLA-B15:73	KMKDHFDHI	0.9165	0.7497	10	19
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	HLA-B39:31	THSKMKDHF	0.8705	0.6844	7	16
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	HLA-A02:14	KMKDHFDHI	0.8625	0.5016	10	19
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	HLA-B15:30	KMKDHFDHI	0.8133	0.8083	10	19
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	HLA-B38:05	THSKMKDHF	0.7825	0.8498	7	16
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	HLA-C07:04	KMKDHFDHI	0.2763	0.7899	10	19
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	HLA-B15:09	THSKMKDHF	0.2698	0.5782	7	16
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	HLA-B39:11	THSKMKDHF	0.2026	0.635	7	16
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	HLA-A30:01	KMKDHFDHIK	0.9939	0.7645	10	20
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	HLA-B38:05	NTHSKMKDHF	0.2312	0.7784	6	16

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Potential FusionNeoAntigen Information of NSD1-DPEP2 in HLA II

NSD1-DPEP2_176619020_68023301.msa

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)
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-0101	MKDHFDHIKAVIGSK	11	26
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-0103	MKDHFDHIKAVIGSK	11	26
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-0105	MKDHFDHIKAVIGSK	11	26
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-0107	MKDHFDHIKAVIGSK	11	26
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-0109	MKDHFDHIKAVIGSK	11	26
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-0111	MKDHFDHIKAVIGSK	11	26
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-0113	MKDHFDHIKAVIGSK	11	26
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-0113	KMKDHFDHIKAVIGS	10	25
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-0115	MKDHFDHIKAVIGSK	11	26
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-0117	MKDHFDHIKAVIGSK	11	26
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-0117	KMKDHFDHIKAVIGS	10	25
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-0119	MKDHFDHIKAVIGSK	11	26
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-0121	MKDHFDHIKAVIGSK	11	26
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-0121	KMKDHFDHIKAVIGS	10	25
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-0125	MKDHFDHIKAVIGSK	11	26
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-0127	MKDHFDHIKAVIGSK	11	26
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-0129	MKDHFDHIKAVIGSK	11	26
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-0131	MKDHFDHIKAVIGSK	11	26
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-0447	MKDHFDHIKAVIGSK	11	26
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-0454	MKDHFDHIKAVIGSK	11	26
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1001	MKDHFDHIKAVIGSK	11	26
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1003	MKDHFDHIKAVIGSK	11	26
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1130	MKDHFDHIKAVIGSK	11	26
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1304	DPLINTHSKMKDHFD	2	17
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1304	SDPLINTHSKMKDHF	1	16
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1304	CSDPLINTHSKMKDH	0	15
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1304	PLINTHSKMKDHFDH	3	18
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1332	DPLINTHSKMKDHFD	2	17
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1332	SDPLINTHSKMKDHF	1	16
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1332	CSDPLINTHSKMKDH	0	15
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1332	PLINTHSKMKDHFDH	3	18
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1338	DPLINTHSKMKDHFD	2	17
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1338	SDPLINTHSKMKDHF	1	16
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1338	CSDPLINTHSKMKDH	0	15
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1343	DPLINTHSKMKDHFD	2	17
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1348	DPLINTHSKMKDHFD	2	17
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1348	SDPLINTHSKMKDHF	1	16
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1348	CSDPLINTHSKMKDH	0	15
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1348	PLINTHSKMKDHFDH	3	18
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1365	DPLINTHSKMKDHFD	2	17
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1365	SDPLINTHSKMKDHF	1	16
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1365	CSDPLINTHSKMKDH	0	15
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1375	DPLINTHSKMKDHFD	2	17
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1375	SDPLINTHSKMKDHF	1	16
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1375	CSDPLINTHSKMKDH	0	15
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1376	DPLINTHSKMKDHFD	2	17
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1376	SDPLINTHSKMKDHF	1	16
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1393	DPLINTHSKMKDHFD	2	17
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1393	SDPLINTHSKMKDHF	1	16
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1393	CSDPLINTHSKMKDH	0	15
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1393	PLINTHSKMKDHFDH	3	18
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1416	DPLINTHSKMKDHFD	2	17
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1416	SDPLINTHSKMKDHF	1	16
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1601	MKDHFDHIKAVIGSK	11	26
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1603	MKDHFDHIKAVIGSK	11	26
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1604	MKDHFDHIKAVIGSK	11	26
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1608	MKDHFDHIKAVIGSK	11	26
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1609	MKDHFDHIKAVIGSK	11	26
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB1-1610	MKDHFDHIKAVIGSK	11	26
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB5-0102	MKDHFDHIKAVIGSK	11	26
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB5-0103	MKDHFDHIKAVIGSK	11	26
NSD1-DPEP2	chr5	176619020	chr16	68023301	357	DRB5-0108N	MKDHFDHIKAVIGSK	11	26

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Fusion breakpoint peptide structures of NSD1-DPEP2

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
6415	NTHSKMKDHFDHIK	NSD1	DPEP2	chr5	176619020	chr16	68023301	357

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of NSD1-DPEP2

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-B52:01	3W39	6415	NTHSKMKDHFDHIK	-7.90165	-7.90165
HLA-B44:05	3DX8	6415	NTHSKMKDHFDHIK	-5.81679	-5.81679

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Vaccine Design for the FusionNeoAntigens of NSD1-DPEP2

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
NSD1-DPEP2	chr5	176619020	chr16	68023301	10	19	KMKDHFDHI	AAATGAAAGATCACTTCGACCACATCA
NSD1-DPEP2	chr5	176619020	chr16	68023301	10	20	KMKDHFDHIK	AAATGAAAGATCACTTCGACCACATCAAGG
NSD1-DPEP2	chr5	176619020	chr16	68023301	11	22	MKDHFDHIKAV	TGAAAGATCACTTCGACCACATCAAGGCTGTCA
NSD1-DPEP2	chr5	176619020	chr16	68023301	12	22	KDHFDHIKAV	AAGATCACTTCGACCACATCAAGGCTGTCA
NSD1-DPEP2	chr5	176619020	chr16	68023301	6	16	NTHSKMKDHF	ACACACATTCAAAAATGAAAGATCACTTCG
NSD1-DPEP2	chr5	176619020	chr16	68023301	7	16	THSKMKDHF	CACATTCAAAAATGAAAGATCACTTCG

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
NSD1-DPEP2	chr5	176619020	chr16	68023301	0	15	CSDPLINTHSKMKDH	GTTCTGATCCGTTGATTAACACACATTCAAAAATGAAAGATCACT
NSD1-DPEP2	chr5	176619020	chr16	68023301	1	16	SDPLINTHSKMKDHF	CTGATCCGTTGATTAACACACATTCAAAAATGAAAGATCACTTCG
NSD1-DPEP2	chr5	176619020	chr16	68023301	10	25	KMKDHFDHIKAVIGS	AAATGAAAGATCACTTCGACCACATCAAGGCTGTCATTGGATCCA
NSD1-DPEP2	chr5	176619020	chr16	68023301	11	26	MKDHFDHIKAVIGSK	TGAAAGATCACTTCGACCACATCAAGGCTGTCATTGGATCCAAGT
NSD1-DPEP2	chr5	176619020	chr16	68023301	2	17	DPLINTHSKMKDHFD	ATCCGTTGATTAACACACATTCAAAAATGAAAGATCACTTCGACC
NSD1-DPEP2	chr5	176619020	chr16	68023301	3	18	PLINTHSKMKDHFDH	CGTTGATTAACACACATTCAAAAATGAAAGATCACTTCGACCACA

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Information of the samples that have these potential fusion neoantigens of NSD1-DPEP2

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
CESC	NSD1-DPEP2	chr5	176619020	ENST00000347982	chr16	68023301	ENST00000393847	TCGA-C5-A7UH-01A

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Potential target of CAR-T therapy development for NSD1-DPEP2

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 NSD1-DPEP2

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 NSD1-DPEP2

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)