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Fusion Protein:POU2F1-CD46

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: POU2F1-CD46
	FusionPDB ID: 67231
	FusionGDB2.0 ID: 67231
		Hgene	Tgene
	Gene symbol	POU2F1	CD46
	Gene ID	5451	4179
	Gene name	POU class 2 homeobox 1	CD46 molecule
	Synonyms	OCT1\|OTF1\|oct-1B	AHUS2\|MCP\|MIC10\|TLX\|TRA2.10
	Cytomap	1q24.2	1q32.2
	Type of gene	protein-coding	protein-coding
	Description	POU domain, class 2, transcription factor 1NF-A1OTF-1Octamer-binding transcription factor-1POU class 2 homeobox 1 isoform Oct-1Roct-1octamer-binding protein 1octamer-binding transcription factor 1	membrane cofactor proteinCD46 antigen, complement regulatory proteinCD46 molecule, complement regulatory proteinantigen identified by monoclonal antibody TRA-2-10complement membrane cofactor proteinmeasles virus receptormembrane cofactor protein (CD
	Modification date	20200320	20200313
	UniProtAcc	.	P15529 Main function of 5'-partner protein: FUNCTION: Acts as a cofactor for complement factor I, a serine protease which protects autologous cells against complement-mediated injury by cleaving C3b and C4b deposited on host tissue. May be involved in the fusion of the spermatozoa with the oocyte during fertilization. Also acts as a costimulatory factor for T-cells which induces the differentiation of CD4+ into T-regulatory 1 cells. T-regulatory 1 cells suppress immune responses by secreting interleukin-10, and therefore are thought to prevent autoimmunity. {ECO:0000269\|PubMed:10843656, ECO:0000269\|PubMed:12540904}.; FUNCTION: (Microbial infection) A number of viral and bacterial pathogens seem to bind MCP in order to exploit its immune regulation property and directly induce an immunosuppressive phenotype in T-cells.; FUNCTION: (Microbial infection) Acts as a receptor for Adenovirus subgroup B2 and Ad3. {ECO:0000269\|PubMed:12915534, ECO:0000269\|PubMed:14566335, ECO:0000269\|PubMed:15047806, ECO:0000269\|PubMed:15078926, ECO:0000269\|PubMed:15919905, ECO:0000269\|PubMed:16254377}.; FUNCTION: (Microbial infection) Acts as a receptor for cultured Measles virus. {ECO:0000269\|PubMed:10972291}.; FUNCTION: (Microbial infection) Acts as a receptor for Herpesvirus 6/HHV-6. {ECO:0000269\|PubMed:12663806, ECO:0000269\|PubMed:12724329}.; FUNCTION: (Microbial infection) May act as a receptor for pathogenic bacteria Neisseria and Streptococcus pyogenes (PubMed:7708671, PubMed:9379894, PubMed:11260136, PubMed:11971006).
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000367865, ENST00000367862, ENST00000367866, ENST00000420254, ENST00000429375, ENST00000452019, ENST00000541643,	ENST00000322875, ENST00000322918, ENST00000354848, ENST00000358170, ENST00000361067, ENST00000367041, ENST00000367042, ENST00000441839, ENST00000360212, ENST00000469535, ENST00000480003, ENST00000357714, ENST00000367047,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	15 X 7 X 11=1155	16 X 13 X 7=1456
	# samples	17	17
	** MAII score	log2(17/1155*10)=-2.76428620016572 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(17/1456*10)=-3.098403704061 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: POU2F1 [Title/Abstract] AND CD46 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: POU2F1 [Title/Abstract] AND CD46 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	POU2F1(167301772)-CD46(207930358), # samples:1
Anticipated loss of major functional domain due to fusion event.	POU2F1-CD46 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. POU2F1-CD46 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. POU2F1-CD46 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. POU2F1-CD46 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	POU2F1	GO:0045892	negative regulation of transcription, DNA-templated	11891224\|11997177
Hgene	POU2F1	GO:0045944	positive regulation of transcription by RNA polymerase II	15252056
Tgene	CD46	GO:0008593	regulation of Notch signaling pathway	23086448
Tgene	CD46	GO:0010629	negative regulation of gene expression	23086448
Tgene	CD46	GO:0032613	interleukin-10 production	23086448
Tgene	CD46	GO:0032733	positive regulation of interleukin-10 production	12540904
Tgene	CD46	GO:0035581	sequestering of extracellular ligand from receptor	23086448
Tgene	CD46	GO:0042102	positive regulation of T cell proliferation	12540904
Tgene	CD46	GO:0043382	positive regulation of memory T cell differentiation	12540904
Tgene	CD46	GO:0045591	positive regulation of regulatory T cell differentiation	12540904
Tgene	CD46	GO:0071636	positive regulation of transforming growth factor beta production	12540904

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr1:167301772/chr1:207930358)
- 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 POU2F1 (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 CD46 (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)
ENST00000367866	POU2F1	chr1	167301772	+	ENST00000367042	CD46	chr1	207930358	+	3269	196	51	1232	393
ENST00000367866	POU2F1	chr1	167301772	+	ENST00000354848	CD46	chr1	207930358	+	3176	196	51	1253	400
ENST00000367866	POU2F1	chr1	167301772	+	ENST00000441839	CD46	chr1	207930358	+	3112	196	51	1193	380
ENST00000367866	POU2F1	chr1	167301772	+	ENST00000322875	CD46	chr1	207930358	+	3221	196	51	1298	415
ENST00000367866	POU2F1	chr1	167301772	+	ENST00000367041	CD46	chr1	207930358	+	3224	196	51	1187	378
ENST00000367866	POU2F1	chr1	167301772	+	ENST00000358170	CD46	chr1	207930358	+	3314	196	51	1277	408
ENST00000367866	POU2F1	chr1	167301772	+	ENST00000322918	CD46	chr1	207930358	+	3067	196	51	1148	365
ENST00000367866	POU2F1	chr1	167301772	+	ENST00000361067	CD46	chr1	207930358	+	3179	196	51	1256	401
ENST00000452019	POU2F1	chr1	167301772	+	ENST00000367042	CD46	chr1	207930358	+	3308	235	177	1271	364
ENST00000452019	POU2F1	chr1	167301772	+	ENST00000354848	CD46	chr1	207930358	+	3215	235	177	1292	371
ENST00000452019	POU2F1	chr1	167301772	+	ENST00000441839	CD46	chr1	207930358	+	3151	235	177	1232	351
ENST00000452019	POU2F1	chr1	167301772	+	ENST00000322875	CD46	chr1	207930358	+	3260	235	177	1337	386
ENST00000452019	POU2F1	chr1	167301772	+	ENST00000367041	CD46	chr1	207930358	+	3263	235	177	1226	349
ENST00000452019	POU2F1	chr1	167301772	+	ENST00000358170	CD46	chr1	207930358	+	3353	235	177	1316	379
ENST00000452019	POU2F1	chr1	167301772	+	ENST00000322918	CD46	chr1	207930358	+	3106	235	177	1187	336
ENST00000452019	POU2F1	chr1	167301772	+	ENST00000361067	CD46	chr1	207930358	+	3218	235	177	1295	372
ENST00000429375	POU2F1	chr1	167301772	+	ENST00000367042	CD46	chr1	207930358	+	3207	134	7	1170	387
ENST00000429375	POU2F1	chr1	167301772	+	ENST00000354848	CD46	chr1	207930358	+	3114	134	7	1191	394
ENST00000429375	POU2F1	chr1	167301772	+	ENST00000441839	CD46	chr1	207930358	+	3050	134	7	1131	374
ENST00000429375	POU2F1	chr1	167301772	+	ENST00000322875	CD46	chr1	207930358	+	3159	134	7	1236	409
ENST00000429375	POU2F1	chr1	167301772	+	ENST00000367041	CD46	chr1	207930358	+	3162	134	7	1125	372
ENST00000429375	POU2F1	chr1	167301772	+	ENST00000358170	CD46	chr1	207930358	+	3252	134	7	1215	402
ENST00000429375	POU2F1	chr1	167301772	+	ENST00000322918	CD46	chr1	207930358	+	3005	134	7	1086	359
ENST00000429375	POU2F1	chr1	167301772	+	ENST00000361067	CD46	chr1	207930358	+	3117	134	7	1194	395
ENST00000541643	POU2F1	chr1	167301772	+	ENST00000367042	CD46	chr1	207930358	+	3293	220	162	1256	364
ENST00000541643	POU2F1	chr1	167301772	+	ENST00000354848	CD46	chr1	207930358	+	3200	220	162	1277	371
ENST00000541643	POU2F1	chr1	167301772	+	ENST00000441839	CD46	chr1	207930358	+	3136	220	162	1217	351
ENST00000541643	POU2F1	chr1	167301772	+	ENST00000322875	CD46	chr1	207930358	+	3245	220	162	1322	386
ENST00000541643	POU2F1	chr1	167301772	+	ENST00000367041	CD46	chr1	207930358	+	3248	220	162	1211	349
ENST00000541643	POU2F1	chr1	167301772	+	ENST00000358170	CD46	chr1	207930358	+	3338	220	162	1301	379
ENST00000541643	POU2F1	chr1	167301772	+	ENST00000322918	CD46	chr1	207930358	+	3091	220	162	1172	336
ENST00000541643	POU2F1	chr1	167301772	+	ENST00000361067	CD46	chr1	207930358	+	3203	220	162	1280	372
ENST00000420254	POU2F1	chr1	167301772	+	ENST00000367042	CD46	chr1	207930358	+	3293	220	162	1256	364
ENST00000420254	POU2F1	chr1	167301772	+	ENST00000354848	CD46	chr1	207930358	+	3200	220	162	1277	371
ENST00000420254	POU2F1	chr1	167301772	+	ENST00000441839	CD46	chr1	207930358	+	3136	220	162	1217	351
ENST00000420254	POU2F1	chr1	167301772	+	ENST00000322875	CD46	chr1	207930358	+	3245	220	162	1322	386
ENST00000420254	POU2F1	chr1	167301772	+	ENST00000367041	CD46	chr1	207930358	+	3248	220	162	1211	349
ENST00000420254	POU2F1	chr1	167301772	+	ENST00000358170	CD46	chr1	207930358	+	3338	220	162	1301	379
ENST00000420254	POU2F1	chr1	167301772	+	ENST00000322918	CD46	chr1	207930358	+	3091	220	162	1172	336
ENST00000420254	POU2F1	chr1	167301772	+	ENST00000361067	CD46	chr1	207930358	+	3203	220	162	1280	372
ENST00000367862	POU2F1	chr1	167301772	+	ENST00000367042	CD46	chr1	207930358	+	3402	329	178	1365	395
ENST00000367862	POU2F1	chr1	167301772	+	ENST00000354848	CD46	chr1	207930358	+	3309	329	178	1386	402
ENST00000367862	POU2F1	chr1	167301772	+	ENST00000441839	CD46	chr1	207930358	+	3245	329	178	1326	382
ENST00000367862	POU2F1	chr1	167301772	+	ENST00000322875	CD46	chr1	207930358	+	3354	329	178	1431	417
ENST00000367862	POU2F1	chr1	167301772	+	ENST00000367041	CD46	chr1	207930358	+	3357	329	178	1320	380
ENST00000367862	POU2F1	chr1	167301772	+	ENST00000358170	CD46	chr1	207930358	+	3447	329	178	1410	410
ENST00000367862	POU2F1	chr1	167301772	+	ENST00000322918	CD46	chr1	207930358	+	3200	329	178	1281	367
ENST00000367862	POU2F1	chr1	167301772	+	ENST00000361067	CD46	chr1	207930358	+	3312	329	178	1389	403

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
ENST00000367866	ENST00000367042	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000147045	0.9998529
ENST00000367866	ENST00000354848	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000132306	0.9998677
ENST00000367866	ENST00000441839	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000154545	0.9998454
ENST00000367866	ENST00000322875	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000122099	0.9998779
ENST00000367866	ENST00000367041	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000139359	0.99986064
ENST00000367866	ENST00000358170	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000132662	0.9998673
ENST00000367866	ENST00000322918	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000129563	0.9998704
ENST00000367866	ENST00000361067	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000144672	0.9998553
ENST00000452019	ENST00000367042	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000229981	0.99977
ENST00000452019	ENST00000354848	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000225224	0.99977475
ENST00000452019	ENST00000441839	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000240328	0.9997596
ENST00000452019	ENST00000322875	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000326864	0.9996731
ENST00000452019	ENST00000367041	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000176301	0.99982375
ENST00000452019	ENST00000358170	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000303976	0.999696
ENST00000452019	ENST00000322918	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000218367	0.99978167
ENST00000452019	ENST00000361067	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000245169	0.99975485
ENST00000429375	ENST00000367042	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000148617	0.99985135
ENST00000429375	ENST00000354848	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000132354	0.9998677
ENST00000429375	ENST00000441839	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000156233	0.9998437
ENST00000429375	ENST00000322875	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000121325	0.99987864
ENST00000429375	ENST00000367041	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000140845	0.9998591
ENST00000429375	ENST00000358170	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.00013479	0.9998652
ENST00000429375	ENST00000322918	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000130425	0.9998696
ENST00000429375	ENST00000361067	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000145381	0.99985456
ENST00000541643	ENST00000367042	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000223409	0.99977654
ENST00000541643	ENST00000354848	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.00022009	0.9997799
ENST00000541643	ENST00000441839	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000233476	0.9997665
ENST00000541643	ENST00000322875	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000320314	0.9996797
ENST00000541643	ENST00000367041	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000171301	0.9998287
ENST00000541643	ENST00000358170	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000296406	0.9997036
ENST00000541643	ENST00000322918	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000212297	0.99978775
ENST00000541643	ENST00000361067	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000238896	0.99976116
ENST00000420254	ENST00000367042	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000223409	0.99977654
ENST00000420254	ENST00000354848	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.00022009	0.9997799
ENST00000420254	ENST00000441839	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000233476	0.9997665
ENST00000420254	ENST00000322875	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000320314	0.9996797
ENST00000420254	ENST00000367041	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000171301	0.9998287
ENST00000420254	ENST00000358170	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000296406	0.9997036
ENST00000420254	ENST00000322918	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000212297	0.99978775
ENST00000420254	ENST00000361067	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000238896	0.99976116
ENST00000367862	ENST00000367042	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000178129	0.99982184
ENST00000367862	ENST00000354848	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000181959	0.999818
ENST00000367862	ENST00000441839	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000160617	0.9998393
ENST00000367862	ENST00000322875	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000174606	0.9998254
ENST00000367862	ENST00000367041	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000135185	0.9998648
ENST00000367862	ENST00000358170	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000192481	0.99980754
ENST00000367862	ENST00000322918	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000152338	0.99984765
ENST00000367862	ENST00000361067	POU2F1	chr1	167301772	+	CD46	chr1	207930358	+	0.000204463	0.9997955

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 POU2F1-CD46

+/-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
POU2F1	chr1	167301772	CD46	chr1	207930358	134	42	TSKPSMESGDGNTDACEEPPTFEAME
POU2F1	chr1	167301772	CD46	chr1	207930358	196	48	TSKPSMESGDGNTDACEEPPTFEAME
POU2F1	chr1	167301772	CD46	chr1	207930358	220	19	TSKPSMESGDGNTDACEEPPTFEAME
POU2F1	chr1	167301772	CD46	chr1	207930358	235	19	TSKPSMESGDGNTDACEEPPTFEAME
POU2F1	chr1	167301772	CD46	chr1	207930358	329	50	TSKPSMESGDGNTDACEEPPTFEAME

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Potential FusionNeoAntigen Information of POU2F1-CD46 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.

POU2F1-CD46_167301772_207930358.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)
POU2F1-CD46	chr1	167301772	chr1	207930358	329	HLA-B45:01	MESGDGNTDA	0.8673	0.9565	5	15
POU2F1-CD46	chr1	167301772	chr1	207930358	329	HLA-C05:09	NTDACEEPPTF	1	0.9381	11	22
POU2F1-CD46	chr1	167301772	chr1	207930358	329	HLA-C05:01	NTDACEEPPTF	1	0.9381	11	22

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Potential FusionNeoAntigen Information of POU2F1-CD46 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 POU2F1-CD46

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
2125	ESGDGNTDACEEPP	POU2F1	CD46	chr1	167301772	chr1	207930358	329

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of POU2F1-CD46

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	2125	ESGDGNTDACEEPP	-7.15543	-7.26883
HLA-B14:02	3BVN	2125	ESGDGNTDACEEPP	-4.77435	-5.80965
HLA-B52:01	3W39	2125	ESGDGNTDACEEPP	-6.80875	-6.92215
HLA-B52:01	3W39	2125	ESGDGNTDACEEPP	-4.20386	-5.23916
HLA-A11:01	4UQ2	2125	ESGDGNTDACEEPP	-7.5194	-8.5547
HLA-A11:01	4UQ2	2125	ESGDGNTDACEEPP	-6.9601	-7.0735
HLA-A24:02	5HGA	2125	ESGDGNTDACEEPP	-7.52403	-7.63743
HLA-A24:02	5HGA	2125	ESGDGNTDACEEPP	-5.82433	-6.85963
HLA-B27:05	6PYJ	2125	ESGDGNTDACEEPP	-3.28285	-4.31815
HLA-B44:05	3DX8	2125	ESGDGNTDACEEPP	-5.91172	-6.94702
HLA-B44:05	3DX8	2125	ESGDGNTDACEEPP	-4.24346	-4.35686

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Vaccine Design for the FusionNeoAntigens of POU2F1-CD46

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
POU2F1-CD46	chr1	167301772	chr1	207930358	11	22	NTDACEEPPTF	ACACAGATGCCTGTGAGGAGCCACCAACATTTG
POU2F1-CD46	chr1	167301772	chr1	207930358	5	15	MESGDGNTDA	TGGAGAGTGGAGATGGCAACACAGATGCCT

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 POU2F1-CD46

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
STAD	POU2F1-CD46	chr1	167301772	ENST00000367862	chr1	207930358	ENST00000322875	TCGA-CD-A489

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Potential target of CAR-T therapy development for POU2F1-CD46

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

Tgene

CD46

chr1:167301772

chr1:207930358

ENST00000322875

344_366

400.0

Transmembrane

Helical

Tgene

CD46

chr1:167301772

chr1:207930358

ENST00000322918

344_366

350.0

Transmembrane

Helical

Tgene

CD46

chr1:167301772

chr1:207930358

ENST00000354848

344_366

385.0

Transmembrane

Helical

Tgene

CD46

chr1:167301772

chr1:207930358

ENST00000357714

344_366

370.0

Transmembrane

Helical

Tgene

CD46

chr1:167301772

chr1:207930358

ENST00000358170

344_366

973.6666666666666

Transmembrane

Helical

Tgene

CD46

chr1:167301772

chr1:207930358

ENST00000360212

344_366

356.0

Transmembrane

Helical

Tgene

CD46

chr1:167301772

chr1:207930358

ENST00000361067

344_366

386.0

Transmembrane

Helical

Tgene

CD46

chr1:167301772

chr1:207930358

ENST00000367041

344_366

943.6666666666666

Transmembrane

Helical

Tgene

CD46

chr1:167301772

chr1:207930358

ENST00000367042

344_366

958.6666666666666

Transmembrane

Helical

Tgene

CD46

chr1:167301772

chr1:207930358

ENST00000367047

344_366

337.0

Transmembrane

Helical

Tgene

CD46

chr1:167301772

chr1:207930358

ENST00000441839

344_366

365.0

Transmembrane

Helical

Tgene

CD46

chr1:167301772

chr1:207930358

ENST00000480003

344_366

371.0

Transmembrane

Helical

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 POU2F1-CD46

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 POU2F1-CD46

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)