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Fusion Protein:STK3-MTDH

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: STK3-MTDH
	FusionPDB ID: 87574
	FusionGDB2.0 ID: 87574
		Hgene	Tgene
	Gene symbol	STK3	MTDH
	Gene ID	8428	92140
	Gene name	serine/threonine kinase 24	metadherin
	Synonyms	HEL-S-95\|MST3\|MST3B\|STE20\|STK3	3D3\|AEG-1\|AEG1\|LYRIC\|LYRIC/3D3
	Cytomap	13q32.2	8q22.1
	Type of gene	protein-coding	protein-coding
	Description	serine/threonine-protein kinase 24STE20-like kinase 3STE20-like kinase MST3epididymis secretory protein Li 95mammalian STE20-like protein kinase 3serine/threonine kinase 24 (STE20 homolog, yeast)sterile 20-like kinase 3	protein LYRIC3D3/LYRICastrocyte elevated gene 1astrocyte elevated gene-1 proteinlysine-rich CEACAM1 co-isolated proteinmetastasis adhesion protein
	Modification date	20200313	20200313
	UniProtAcc	.	Q86UE4 Main function of 5'-partner protein: FUNCTION: Downregulates SLC1A2/EAAT2 promoter activity when expressed ectopically. Activates the nuclear factor kappa-B (NF-kappa-B) transcription factor. Promotes anchorage-independent growth of immortalized melanocytes and astrocytes which is a key component in tumor cell expansion. Promotes lung metastasis and also has an effect on bone and brain metastasis, possibly by enhancing the seeding of tumor cells to the target organ endothelium. Induces chemoresistance. {ECO:0000269\|PubMed:15927426, ECO:0000269\|PubMed:16452207, ECO:0000269\|PubMed:18316612, ECO:0000269\|PubMed:19111877}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000523601, ENST00000419617, ENST00000521768,	ENST00000336273, ENST00000519934,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	24 X 16 X 11=4224	9 X 15 X 7=945
	# samples	30	16
	** MAII score	log2(30/4224*10)=-3.81557542886257 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(16/945*10)=-2.56224242422107 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: STK3 [Title/Abstract] AND MTDH [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: STK3 [Title/Abstract] AND MTDH [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	STK3(99718694)-MTDH(98673299), # samples:1
Anticipated loss of major functional domain due to fusion event.	STK3-MTDH 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. STK3-MTDH 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. STK3-MTDH 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. STK3-MTDH 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. STK3-MTDH seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF. STK3-MTDH seems lost the major protein functional domain in Hgene partner, which is a kinase 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	STK3	GO:0006468	protein phosphorylation	19604147
Hgene	STK3	GO:0042542	response to hydrogen peroxide	22291017
Hgene	STK3	GO:0046777	protein autophosphorylation	17046825\|17657516
Tgene	MTDH	GO:0000122	negative regulation of transcription by RNA polymerase II	15927426
Tgene	MTDH	GO:0010508	positive regulation of autophagy	21127263
Tgene	MTDH	GO:0043066	negative regulation of apoptotic process	17704808
Tgene	MTDH	GO:0043123	positive regulation of I-kappaB kinase/NF-kappaB signaling	16452207\|18316612
Tgene	MTDH	GO:0045766	positive regulation of angiogenesis	19940250
Tgene	MTDH	GO:0051092	positive regulation of NF-kappaB transcription factor activity	16452207\|18316612
Tgene	MTDH	GO:0051897	positive regulation of protein kinase B signaling	17704808

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr8:99718694/chr8:98673299)
- 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 STK3 (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 MTDH (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)

ENST00000419617

STK3

chr8

99718694

ENST00000336273

MTDH

chr8

98673299

6293

825

2192

715

ENST00000419617

STK3

chr8

99718694

ENST00000519934

MTDH

chr8

98673299

2667

825

2093

682

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
ENST00000419617	ENST00000336273	STK3	chr8	99718694	-	MTDH	chr8	98673299	+	0.000384093	0.9996159
ENST00000419617	ENST00000519934	STK3	chr8	99718694	-	MTDH	chr8	98673299	+	0.000822269	0.99917775

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 STK3-MTDH

+/-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
STK3	chr8	99718694	MTDH	chr8	98673299	825	260	EGKPPYADIHPMRPNGRTVEVAEGEA

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Potential FusionNeoAntigen Information of STK3-MTDH 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.

STK3-MTDH_99718694_98673299.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)
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B07:02	RPNGRTVEV	0.9996	0.7097	12	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B07:05	RPNGRTVEV	0.9996	0.611	12	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B07:10	RPNGRTVEV	0.9996	0.7298	12	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B08:09	RPNGRTVEV	0.9902	0.6592	12	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B14:01	RPNGRTVEV	0.8938	0.8535	12	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B14:02	RPNGRTVEV	0.8938	0.8535	12	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B35:04	RPNGRTVEV	0.643	0.9013	12	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B35:02	RPNGRTVEV	0.643	0.9013	12	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B82:01	RPNGRTVEV	0.356	0.5006	12	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B81:01	RPNGRTVEV	0.3422	0.5126	12	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B07:02	RPNGRTVEVA	0.9975	0.7298	12	22
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B07:05	RPNGRTVEVA	0.9974	0.6242	12	22
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B07:02	HPMRPNGRTV	0.996	0.6343	9	19
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B07:05	HPMRPNGRTV	0.9959	0.5567	9	19
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-A33:01	DIHPMRPNGR	0.9906	0.8538	7	17
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-A33:05	DIHPMRPNGR	0.9906	0.8538	7	17
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-A68:03	DIHPMRPNGR	0.9773	0.7045	7	17
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B08:09	HPMRPNGRTV	0.9697	0.7456	9	19
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B08:09	MRPNGRTVEV	0.9056	0.8071	11	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B35:03	HPMRPNGRTV	0.778	0.7655	9	19
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B82:01	MRPNGRTVEV	0.7132	0.6631	11	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B81:01	HPMRPNGRTV	0.6582	0.5792	9	19
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B82:01	HPMRPNGRTV	0.5966	0.6035	9	19
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B07:12	RPNGRTVEV	0.9983	0.7468	12	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-C08:15	YADIHPMRP	0.9965	0.9376	5	14
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B07:04	RPNGRTVEV	0.9892	0.642	12	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B14:03	RPNGRTVEV	0.9282	0.8271	12	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B54:01	RPNGRTVEV	0.9153	0.5266	12	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B35:12	RPNGRTVEV	0.643	0.9013	12	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B39:10	RPNGRTVEV	0.5553	0.7626	12	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B78:01	RPNGRTVEV	0.5498	0.5141	12	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-C04:14	RPNGRTVEV	0.2563	0.9637	12	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-C04:10	RPNGRTVEV	0.0064	0.9386	12	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-C04:07	RPNGRTVEV	0.0063	0.9367	12	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B54:01	HPMRPNGRTV	0.9885	0.6517	9	19
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B07:12	HPMRPNGRTV	0.9882	0.7302	9	19
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B07:12	RPNGRTVEVA	0.985	0.7413	12	22
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B42:02	HPMRPNGRTV	0.9819	0.6444	9	19
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B42:01	HPMRPNGRTV	0.9764	0.6403	9	19
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B07:04	RPNGRTVEVA	0.9752	0.6834	12	22
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B54:01	MRPNGRTVEV	0.9732	0.7008	11	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B07:04	HPMRPNGRTV	0.9697	0.5801	9	19
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B42:02	MRPNGRTVEV	0.9329	0.7984	11	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B56:04	HPMRPNGRTV	0.9242	0.5407	9	19
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B42:01	MRPNGRTVEV	0.9202	0.7868	11	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-A33:03	DIHPMRPNGR	0.8932	0.5482	7	17
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B54:01	RPNGRTVEVA	0.884	0.6499	12	22
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B39:10	HPMRPNGRTV	0.6915	0.911	9	19
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B78:01	MRPNGRTVEV	0.3424	0.7937	11	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-C06:02	MRPNGRTV	0.909	0.9917	11	19
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-C06:17	MRPNGRTV	0.909	0.9917	11	19
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B07:22	RPNGRTVEV	0.9996	0.7097	12	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B07:09	RPNGRTVEV	0.9996	0.6848	12	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B07:13	RPNGRTVEV	0.999	0.912	12	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-C08:02	YADIHPMRP	0.9965	0.9376	5	14
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B08:12	RPNGRTVEV	0.8962	0.5134	12	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B35:09	RPNGRTVEV	0.643	0.9013	12	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B67:01	RPNGRTVEV	0.6388	0.7525	12	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B35:13	RPNGRTVEV	0.6178	0.6975	12	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-C04:04	RPNGRTVEV	0.5474	0.9179	12	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B78:02	RPNGRTVEV	0.5267	0.621	12	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-C07:04	RPNGRTVEV	0.4027	0.9575	12	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B82:02	RPNGRTVEV	0.356	0.5006	12	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-C18:01	RPNGRTVEV	0.01	0.9493	12	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-C04:01	RPNGRTVEV	0.0063	0.9367	12	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B07:22	RPNGRTVEVA	0.9975	0.7298	12	22
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B07:09	RPNGRTVEVA	0.9963	0.6929	12	22
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B07:22	HPMRPNGRTV	0.996	0.6343	9	19
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B07:09	HPMRPNGRTV	0.9954	0.6125	9	19
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B55:04	MRPNGRTVEV	0.9902	0.6013	11	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B55:02	HPMRPNGRTV	0.973	0.5234	9	19
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B59:01	HPMRPNGRTV	0.9452	0.5556	9	19
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B55:04	HPMRPNGRTV	0.9435	0.5281	9	19
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B56:02	HPMRPNGRTV	0.9242	0.5407	9	19
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B78:02	HPMRPNGRTV	0.8254	0.5734	9	19
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B67:01	HPMRPNGRTV	0.7612	0.8162	9	19
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B82:02	MRPNGRTVEV	0.7132	0.6631	11	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	HLA-B82:02	HPMRPNGRTV	0.5966	0.6035	9	19

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Potential FusionNeoAntigen Information of STK3-MTDH in HLA II

STK3-MTDH_99718694_98673299.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)
STK3-MTDH	chr8	99718694	chr8	98673299	825	DRB1-1452	YADIHPMRPNGRTVE	5	20
STK3-MTDH	chr8	99718694	chr8	98673299	825	DRB5-0101	YADIHPMRPNGRTVE	5	20
STK3-MTDH	chr8	99718694	chr8	98673299	825	DRB5-0105	YADIHPMRPNGRTVE	5	20
STK3-MTDH	chr8	99718694	chr8	98673299	825	DRB5-0106	YADIHPMRPNGRTVE	5	20
STK3-MTDH	chr8	99718694	chr8	98673299	825	DRB5-0106	PYADIHPMRPNGRTV	4	19
STK3-MTDH	chr8	99718694	chr8	98673299	825	DRB5-0106	ADIHPMRPNGRTVEV	6	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	DRB5-0106	PPYADIHPMRPNGRT	3	18
STK3-MTDH	chr8	99718694	chr8	98673299	825	DRB5-0111	YADIHPMRPNGRTVE	5	20
STK3-MTDH	chr8	99718694	chr8	98673299	825	DRB5-0113	YADIHPMRPNGRTVE	5	20
STK3-MTDH	chr8	99718694	chr8	98673299	825	DRB5-0114	YADIHPMRPNGRTVE	5	20
STK3-MTDH	chr8	99718694	chr8	98673299	825	DRB5-0202	YADIHPMRPNGRTVE	5	20
STK3-MTDH	chr8	99718694	chr8	98673299	825	DRB5-0202	PYADIHPMRPNGRTV	4	19
STK3-MTDH	chr8	99718694	chr8	98673299	825	DRB5-0204	YADIHPMRPNGRTVE	5	20
STK3-MTDH	chr8	99718694	chr8	98673299	825	DRB5-0204	PYADIHPMRPNGRTV	4	19
STK3-MTDH	chr8	99718694	chr8	98673299	825	DRB5-0204	ADIHPMRPNGRTVEV	6	21
STK3-MTDH	chr8	99718694	chr8	98673299	825	DRB5-0205	YADIHPMRPNGRTVE	5	20
STK3-MTDH	chr8	99718694	chr8	98673299	825	DRB5-0205	PYADIHPMRPNGRTV	4	19
STK3-MTDH	chr8	99718694	chr8	98673299	825	DRB5-0205	ADIHPMRPNGRTVEV	6	21

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Fusion breakpoint peptide structures of STK3-MTDH

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
117	ADIHPMRPNGRTVE	STK3	MTDH	chr8	99718694	chr8	98673299	825

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of STK3-MTDH

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	117	ADIHPMRPNGRTVE	-8.60826	-8.72166
HLA-B14:02	3BVN	117	ADIHPMRPNGRTVE	-2.66483	-3.70013
HLA-B52:01	3W39	117	ADIHPMRPNGRTVE	-6.90747	-7.02087
HLA-B52:01	3W39	117	ADIHPMRPNGRTVE	-1.88432	-2.91962
HLA-A11:01	4UQ2	117	ADIHPMRPNGRTVE	-11.2418	-11.3552
HLA-A24:02	5HGA	117	ADIHPMRPNGRTVE	-9.24546	-9.35886
HLA-A24:02	5HGA	117	ADIHPMRPNGRTVE	-4.08507	-5.12037
HLA-B44:05	3DX8	117	ADIHPMRPNGRTVE	-7.05529	-7.16869
HLA-B44:05	3DX8	117	ADIHPMRPNGRTVE	-4.33606	-5.37136
HLA-A02:01	6TDR	117	ADIHPMRPNGRTVE	-6.57504	-6.68844

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Vaccine Design for the FusionNeoAntigens of STK3-MTDH

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
STK3-MTDH	chr8	99718694	chr8	98673299	11	19	MRPNGRTV	ATGAGGCCAAATGGGCGGACTGTT
STK3-MTDH	chr8	99718694	chr8	98673299	11	21	MRPNGRTVEV	ATGAGGCCAAATGGGCGGACTGTTGAAGTG
STK3-MTDH	chr8	99718694	chr8	98673299	12	21	RPNGRTVEV	AGGCCAAATGGGCGGACTGTTGAAGTG
STK3-MTDH	chr8	99718694	chr8	98673299	12	22	RPNGRTVEVA	AGGCCAAATGGGCGGACTGTTGAAGTGGCT
STK3-MTDH	chr8	99718694	chr8	98673299	5	14	YADIHPMRP	TATGCTGATATACATCCAATGAGGCCA
STK3-MTDH	chr8	99718694	chr8	98673299	7	17	DIHPMRPNGR	GATATACATCCAATGAGGCCAAATGGGCGG
STK3-MTDH	chr8	99718694	chr8	98673299	9	19	HPMRPNGRTV	CATCCAATGAGGCCAAATGGGCGGACTGTT

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
STK3-MTDH	chr8	99718694	chr8	98673299	3	18	PPYADIHPMRPNGRT	CCTCCTTATGCTGATATACATCCAATGAGGCCAAATGGGCGGACT
STK3-MTDH	chr8	99718694	chr8	98673299	4	19	PYADIHPMRPNGRTV	CCTTATGCTGATATACATCCAATGAGGCCAAATGGGCGGACTGTT
STK3-MTDH	chr8	99718694	chr8	98673299	5	20	YADIHPMRPNGRTVE	TATGCTGATATACATCCAATGAGGCCAAATGGGCGGACTGTTGAA
STK3-MTDH	chr8	99718694	chr8	98673299	6	21	ADIHPMRPNGRTVEV	GCTGATATACATCCAATGAGGCCAAATGGGCGGACTGTTGAAGTG

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Information of the samples that have these potential fusion neoantigens of STK3-MTDH

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
Non-Cancer	STK3-MTDH	chr8	99718694	ENST00000419617	chr8	98673299	ENST00000336273	135N

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Potential target of CAR-T therapy development for STK3-MTDH

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 STK3-MTDH

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 STK3-MTDH

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)