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Fusion Protein:STK11-HMHA1

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: STK11-HMHA1
	FusionPDB ID: 87450
	FusionGDB2.0 ID: 87450
		Hgene	Tgene
	Gene symbol	STK11	HMHA1
	Gene ID	6794	23526
	Gene name	serine/threonine kinase 11	Rho GTPase activating protein 45
	Synonyms	LKB1\|PJS\|hLKB1	HA-1\|HLA-HA1\|HMHA1
	Cytomap	19p13.3	19p13.3
	Type of gene	protein-coding	protein-coding
	Description	serine/threonine-protein kinase STK11liver kinase B1polarization-related protein LKB1renal carcinoma antigen NY-REN-19serine/threonine-protein kinase 11serine/threonine-protein kinase LKB1	rho GTPase-activating protein 45histocompatibility (minor) HA-1minor histocompatibility antigen HA-1minor histocompatibility protein HA-1
	Modification date	20200329	20200313
	UniProtAcc	.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000326873, ENST00000585748,	ENST00000590577, ENST00000591169, ENST00000592335, ENST00000313093, ENST00000536472, ENST00000539243, ENST00000543365, ENST00000586866, ENST00000590214,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	13 X 3 X 8=312	5 X 8 X 6=240
	# samples	17	9
	** MAII score	log2(17/312*10)=-0.876011282724546 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(9/240*10)=-1.41503749927884 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: STK11 [Title/Abstract] AND HMHA1 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: STK11 [Title/Abstract] AND HMHA1 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	HMHA1(1066162)-STK11(1218416), # samples:1 STK11(1222005)-HMHA1(1080254), # samples:2
Anticipated loss of major functional domain due to fusion event.	STK11-HMHA1 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. STK11-HMHA1 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. STK11-HMHA1 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. STK11-HMHA1 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	STK11	GO:0006468	protein phosphorylation	12805220\|25329316
Hgene	STK11	GO:0007050	cell cycle arrest	12805220\|17216128
Hgene	STK11	GO:0046777	protein autophosphorylation	11430832
Hgene	STK11	GO:0071493	cellular response to UV-B	25329316
Hgene	STK11	GO:0072332	intrinsic apoptotic signaling pathway by p53 class mediator	11430832

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr19:1066162/chr19:1218416)
- 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 STK11 (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 HMHA1 (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)
ENST00000326873	STK11	chr19	1222005	+	ENST00000539243	HMHA1	chr19	1080253	+	4061	2093	1011	3800	929
ENST00000326873	STK11	chr19	1222005	+	ENST00000313093	HMHA1	chr19	1080253	+	4423	2093	1011	3800	929
ENST00000326873	STK11	chr19	1222005	+	ENST00000536472	HMHA1	chr19	1080253	+	3971	2093	1011	3884	957
ENST00000326873	STK11	chr19	1222005	+	ENST00000590214	HMHA1	chr19	1080253	+	4421	2093	1011	3800	929
ENST00000326873	STK11	chr19	1222005	+	ENST00000586866	HMHA1	chr19	1080253	+	4423	2093	1011	3800	929
ENST00000326873	STK11	chr19	1222005	+	ENST00000543365	HMHA1	chr19	1080253	+	4423	2093	1011	3800	929
ENST00000326873	STK11	chr19	1222005	+	ENST00000539243	HMHA1	chr19	1080254	+	4061	2093	1011	3800	929
ENST00000326873	STK11	chr19	1222005	+	ENST00000313093	HMHA1	chr19	1080254	+	4423	2093	1011	3800	929
ENST00000326873	STK11	chr19	1222005	+	ENST00000536472	HMHA1	chr19	1080254	+	3971	2093	1011	3884	957
ENST00000326873	STK11	chr19	1222005	+	ENST00000590214	HMHA1	chr19	1080254	+	4421	2093	1011	3800	929
ENST00000326873	STK11	chr19	1222005	+	ENST00000586866	HMHA1	chr19	1080254	+	4423	2093	1011	3800	929
ENST00000326873	STK11	chr19	1222005	+	ENST00000543365	HMHA1	chr19	1080254	+	4423	2093	1011	3800	929

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
ENST00000326873	ENST00000539243	STK11	chr19	1222005	+	HMHA1	chr19	1080253	+	0.005945915	0.99405414
ENST00000326873	ENST00000313093	STK11	chr19	1222005	+	HMHA1	chr19	1080253	+	0.004719691	0.9952803
ENST00000326873	ENST00000536472	STK11	chr19	1222005	+	HMHA1	chr19	1080253	+	0.005659892	0.9943401
ENST00000326873	ENST00000590214	STK11	chr19	1222005	+	HMHA1	chr19	1080253	+	0.004752926	0.99524707
ENST00000326873	ENST00000586866	STK11	chr19	1222005	+	HMHA1	chr19	1080253	+	0.004719691	0.9952803
ENST00000326873	ENST00000543365	STK11	chr19	1222005	+	HMHA1	chr19	1080253	+	0.004719691	0.9952803
ENST00000326873	ENST00000539243	STK11	chr19	1222005	+	HMHA1	chr19	1080254	+	0.005945915	0.99405414
ENST00000326873	ENST00000313093	STK11	chr19	1222005	+	HMHA1	chr19	1080254	+	0.004719691	0.9952803
ENST00000326873	ENST00000536472	STK11	chr19	1222005	+	HMHA1	chr19	1080254	+	0.005659892	0.9943401
ENST00000326873	ENST00000590214	STK11	chr19	1222005	+	HMHA1	chr19	1080254	+	0.004752926	0.99524707
ENST00000326873	ENST00000586866	STK11	chr19	1222005	+	HMHA1	chr19	1080254	+	0.004719691	0.9952803
ENST00000326873	ENST00000543365	STK11	chr19	1222005	+	HMHA1	chr19	1080254	+	0.004719691	0.9952803

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 STK11-HMHA1

+/-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
STK11	chr19	1222005	HMHA1	chr19	1080253	2093	360	PAKRFSIRQIRQHRSPVMRARKSSFN
STK11	chr19	1222005	HMHA1	chr19	1080254	2093	360	PAKRFSIRQIRQHRSPVMRARKSSFN

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Potential FusionNeoAntigen Information of STK11-HMHA1 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.

STK11-HMHA1_1222005_1080253.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)
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-B39:06	HRSPVMRA	0.9984	0.8642	12	20
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-B15:03	RQHRSPVM	0.954	0.5697	10	18
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-B39:13	RQHRSPVM	0.8611	0.7505	10	18
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-B27:05	HRSPVMRAR	0.9971	0.7979	12	21
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-A30:08	RQHRSPVMR	0.9901	0.5473	10	19
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-B08:09	QIRQHRSPV	0.9901	0.6803	8	17
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-B39:06	QHRSPVMRA	0.9869	0.8112	11	20
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-B14:02	IRQHRSPVM	0.9701	0.5343	9	18
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-B14:01	IRQHRSPVM	0.9701	0.5343	9	18
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-B15:37	QHRSPVMRA	0.2215	0.538	11	20
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-A31:02	RFSIRQIRQHR	0.9762	0.6112	3	14
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-A31:02	RQHRSPVMRAR	0.9607	0.6077	10	21
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-B73:01	HRSPVMRA	0.9938	0.9098	12	20
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-B15:04	RQHRSPVM	0.9902	0.8072	10	18
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-B27:14	HRSPVMRAR	0.9974	0.8181	12	21
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-C07:05	IRQHRSPVM	0.9958	0.941	9	18
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-C07:95	IRQHRSPVM	0.9939	0.5511	9	18
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-C07:27	IRQHRSPVM	0.9912	0.9265	9	18
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-C07:13	IRQHRSPVM	0.9776	0.8797	9	18
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-C07:29	IRQHRSPVM	0.9754	0.8776	9	18
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-B39:12	IRQHRSPVM	0.9733	0.746	9	18
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-C07:46	IRQHRSPVM	0.9522	0.8352	9	18
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-B27:03	HRSPVMRAR	0.9281	0.8265	12	21
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-C07:80	IRQHRSPVM	0.927	0.9325	9	18
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-C07:67	IRQHRSPVM	0.927	0.9325	9	18
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-C07:19	IRQHRSPVM	0.9143	0.6218	9	18
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-C07:10	IRQHRSPVM	0.8434	0.9366	9	18
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-B14:03	IRQHRSPVM	0.5805	0.7029	9	18
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-B73:01	QHRSPVMRA	0.5763	0.8043	11	20
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-B15:04	RQIRQHRSP	0.3946	0.8105	7	16
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-C12:16	IRQHRSPVM	0.2146	0.9562	9	18
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-B27:14	HRSPVMRARK	0.9977	0.8869	12	22
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-B15:04	RQHRSPVMRA	0.9054	0.7909	10	20
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-A31:01	RQHRSPVMRAR	0.9851	0.5617	10	21
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-A31:01	RFSIRQIRQHR	0.9819	0.5742	3	14
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-B15:54	RQHRSPVM	0.994	0.7353	10	18
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-B15:73	RQHRSPVM	0.969	0.7158	10	18
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-B27:10	HRSPVMRAR	0.9959	0.8569	12	21
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-A30:01	RQHRSPVMR	0.9905	0.7154	10	19
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-C07:17	IRQHRSPVM	0.9741	0.9532	9	18
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-A30:01	SIRQIRQHR	0.974	0.7935	5	14
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-C06:08	IRQHRSPVM	0.9497	0.9819	9	18
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-C07:02	IRQHRSPVM	0.927	0.9325	9	18
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-C07:04	IRQHRSPVM	0.8648	0.8895	9	18
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-C07:22	IRQHRSPVM	0.8333	0.6289	9	18
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-B15:09	QHRSPVMRA	0.4042	0.705	11	20
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-C03:67	IRQHRSPVM	0.3742	0.935	9	18
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-C06:06	IRQHRSPVM	0.2316	0.9863	9	18
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-C06:17	IRQHRSPVM	0.2216	0.9902	9	18
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-C06:02	IRQHRSPVM	0.2216	0.9902	9	18
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	HLA-B27:10	HRSPVMRARK	0.9981	0.9081	12	22

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Potential FusionNeoAntigen Information of STK11-HMHA1 in HLA II

STK11-HMHA1_1222005_1080253.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)
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	DRB1-1331	IRQIRQHRSPVMRAR	6	21
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	DRB1-1367	IRQIRQHRSPVMRAR	6	21
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	DRB1-1457	IRQIRQHRSPVMRAR	6	21
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	DRB1-1510	IRQIRQHRSPVMRAR	6	21
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	DRB1-1510	SIRQIRQHRSPVMRA	5	20
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	DRB1-1510	RQIRQHRSPVMRARK	7	22
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	DRB1-1535	IRQIRQHRSPVMRAR	6	21
STK11-HMHA1	chr19	1222005	chr19	1080253	2093	DRB1-1537	IRQIRQHRSPVMRAR	6	21

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Fusion breakpoint peptide structures of STK11-HMHA1

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
3954	IRQIRQHRSPVMRA	STK11	HMHA1	chr19	1222005	chr19	1080253	2093

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of STK11-HMHA1

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	3954	IRQIRQHRSPVMRA	-6.35597	-6.46937
HLA-B14:02	3BVN	3954	IRQIRQHRSPVMRA	-5.80319	-6.83849
HLA-B52:01	3W39	3954	IRQIRQHRSPVMRA	-6.67268	-6.78608
HLA-B52:01	3W39	3954	IRQIRQHRSPVMRA	-5.72753	-6.76283
HLA-A11:01	4UQ2	3954	IRQIRQHRSPVMRA	-7.31441	-7.42781
HLA-A11:01	4UQ2	3954	IRQIRQHRSPVMRA	-7.25126	-8.28656
HLA-A24:02	5HGA	3954	IRQIRQHRSPVMRA	-8.41244	-8.52584
HLA-A24:02	5HGA	3954	IRQIRQHRSPVMRA	-5.27978	-6.31508
HLA-B44:05	3DX8	3954	IRQIRQHRSPVMRA	-4.03348	-4.14688
HLA-B44:05	3DX8	3954	IRQIRQHRSPVMRA	-3.56413	-4.59943
HLA-A02:01	6TDR	3954	IRQIRQHRSPVMRA	-6.72173	-7.75703

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Vaccine Design for the FusionNeoAntigens of STK11-HMHA1

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
STK11-HMHA1	chr19	1222005	chr19	1080253	10	18	RQHRSPVM	GCAGCACAGGTCCCCCGTCATGCG
STK11-HMHA1	chr19	1222005	chr19	1080253	10	19	RQHRSPVMR	GCAGCACAGGTCCCCCGTCATGCGTGC
STK11-HMHA1	chr19	1222005	chr19	1080253	10	20	RQHRSPVMRA	GCAGCACAGGTCCCCCGTCATGCGTGCCCG
STK11-HMHA1	chr19	1222005	chr19	1080253	10	21	RQHRSPVMRAR	GCAGCACAGGTCCCCCGTCATGCGTGCCCGGAA
STK11-HMHA1	chr19	1222005	chr19	1080253	11	20	QHRSPVMRA	GCACAGGTCCCCCGTCATGCGTGCCCG
STK11-HMHA1	chr19	1222005	chr19	1080253	12	20	HRSPVMRA	CAGGTCCCCCGTCATGCGTGCCCG
STK11-HMHA1	chr19	1222005	chr19	1080253	12	21	HRSPVMRAR	CAGGTCCCCCGTCATGCGTGCCCGGAA
STK11-HMHA1	chr19	1222005	chr19	1080253	12	22	HRSPVMRARK	CAGGTCCCCCGTCATGCGTGCCCGGAAGAG
STK11-HMHA1	chr19	1222005	chr19	1080253	3	14	RFSIRQIRQHR	GTTCTCCATCCGGCAGATCCGGCAGCACAGGTC
STK11-HMHA1	chr19	1222005	chr19	1080253	5	14	SIRQIRQHR	CATCCGGCAGATCCGGCAGCACAGGTC
STK11-HMHA1	chr19	1222005	chr19	1080253	7	16	RQIRQHRSP	GCAGATCCGGCAGCACAGGTCCCCCGT
STK11-HMHA1	chr19	1222005	chr19	1080253	8	17	QIRQHRSPV	GATCCGGCAGCACAGGTCCCCCGTCAT
STK11-HMHA1	chr19	1222005	chr19	1080253	9	18	IRQHRSPVM	CCGGCAGCACAGGTCCCCCGTCATGCG

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
STK11-HMHA1	chr19	1222005	chr19	1080253	5	20	SIRQIRQHRSPVMRA	CATCCGGCAGATCCGGCAGCACAGGTCCCCCGTCATGCGTGCCCG
STK11-HMHA1	chr19	1222005	chr19	1080253	6	21	IRQIRQHRSPVMRAR	CCGGCAGATCCGGCAGCACAGGTCCCCCGTCATGCGTGCCCGGAA
STK11-HMHA1	chr19	1222005	chr19	1080253	7	22	RQIRQHRSPVMRARK	GCAGATCCGGCAGCACAGGTCCCCCGTCATGCGTGCCCGGAAGAG

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Information of the samples that have these potential fusion neoantigens of STK11-HMHA1

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
LUAD	STK11-HMHA1	chr19	1222005	ENST00000326873	chr19	1080253	ENST00000313093	TCGA-NJ-A4YF

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Potential target of CAR-T therapy development for STK11-HMHA1

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 STK11-HMHA1

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 STK11-HMHA1

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)