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Fusion Protein:CHST11-TRAC

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: CHST11-TRAC
	FusionPDB ID: 16691
	FusionGDB2.0 ID: 16691
		Hgene	Tgene
	Gene symbol	CHST11	TRAC
	Gene ID	50515	9612
	Gene name	carbohydrate sulfotransferase 11	nuclear receptor corepressor 2
	Synonyms	C4ST\|C4ST-1\|C4ST1\|HSA269537\|OCBMD	CTG26\|N-CoR2\|SMAP270\|SMRT\|SMRTE\|SMRTE-tau\|TNRC14\|TRAC\|TRAC-1\|TRAC1
	Cytomap	12q23.3	12q24.31
	Type of gene	protein-coding	protein-coding
	Description	carbohydrate sulfotransferase 11C4S-1IgH/CHST11 fusioncarbohydrate (chondroitin 4) sulfotransferase 11chondroitin 4-O-sulfotransferase 1	nuclear receptor corepressor 2CTG repeat protein 26T3 receptor-associating factorsilencing mediator for retinoid and thyroid hormone receptorsthyroid-, retinoic-acid-receptor-associated corepressor
	Modification date	20200313	20200313
	UniProtAcc	Q9NPF2 Main function of 5'-partner protein: FUNCTION: Catalyzes the transfer of sulfate to position 4 of the N-acetylgalactosamine (GalNAc) residue of chondroitin. Chondroitin sulfate constitutes the predominant proteoglycan present in cartilage and is distributed on the surfaces of many cells and extracellular matrices. Can also sulfate Gal residues in desulfated dermatan sulfate. Preferentially sulfates in GlcA->GalNAc unit than in IdoA->GalNAc unit. Does not form 4, 6-di-O-sulfated GalNAc when chondroitin sulfate C is used as an acceptor.	TAAR6 Main function of 5'-partner protein: 345
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000303694, ENST00000547956, ENST00000546689, ENST00000549260, ENST00000550711,	ENST00000478163,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	13 X 8 X 6=624	8 X 3 X 3=72
	# samples	15	8
	** MAII score	log2(15/624*10)=-2.05658352836637 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(8/72*10)=0.15200309344505 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Fusion gene context	PubMed: CHST11 [Title/Abstract] AND TRAC [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: CHST11 [Title/Abstract] AND TRAC [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	CHST11(104851307)-TRAC(23016447), # samples:1
Anticipated loss of major functional domain due to fusion event.

* 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	CHST11	GO:0030206	chondroitin sulfate biosynthetic process	11056388

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr12:104851307/chr14:23016447)
- 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 CHST11 (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 TRAC (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)

ENST00000547956

CHST11

chr12

104851307

ENST00000478163

TRAC

chr14

23016447

1536

562

986

323

ENST00000303694

CHST11

chr12

104851307

ENST00000478163

TRAC

chr14

23016447

1531

557

981

323

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
ENST00000547956	ENST00000478163	CHST11	chr12	104851307	+	TRAC	chr14	23016447	+	0.013570554	0.98642945
ENST00000303694	ENST00000478163	CHST11	chr12	104851307	+	TRAC	chr14	23016447	+	0.014022476	0.98597753

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 CHST11-TRAC

+/-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
CHST11	chr12	104851307	TRAC	chr14	23016447	557	182	ILVIFYFQSMLHPDIQNPDPAVYQLR
CHST11	chr12	104851307	TRAC	chr14	23016447	562	182	ILVIFYFQSMLHPDIQNPDPAVYQLR

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Potential FusionNeoAntigen Information of CHST11-TRAC 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.

CHST11-TRAC_104851307_23016447.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)
CHST11-TRAC	chr12	104851307	chr14	23016447	557	HLA-B13:02	FQSMLHPDI	0.5207	0.5694	6	15
CHST11-TRAC	chr12	104851307	chr14	23016447	557	HLA-B56:01	HPDIQNPDPA	0.9458	0.6109	11	21
CHST11-TRAC	chr12	104851307	chr14	23016447	557	HLA-B35:03	HPDIQNPDPAV	0.994	0.8688	11	22
CHST11-TRAC	chr12	104851307	chr14	23016447	557	HLA-B35:04	HPDIQNPDPAV	0.9915	0.9789	11	22
CHST11-TRAC	chr12	104851307	chr14	23016447	557	HLA-B35:02	HPDIQNPDPAV	0.9915	0.9789	11	22
CHST11-TRAC	chr12	104851307	chr14	23016447	557	HLA-B54:01	HPDIQNPDPA	0.9803	0.7889	11	21
CHST11-TRAC	chr12	104851307	chr14	23016447	557	HLA-B35:12	HPDIQNPDPAV	0.9915	0.9789	11	22
CHST11-TRAC	chr12	104851307	chr14	23016447	557	HLA-B39:10	HPDIQNPDPAV	0.9414	0.9725	11	22
CHST11-TRAC	chr12	104851307	chr14	23016447	557	HLA-B55:02	HPDIQNPDPA	0.9582	0.6257	11	21
CHST11-TRAC	chr12	104851307	chr14	23016447	557	HLA-B51:05	HPDIQNPDPAV	0.9943	0.8282	11	22
CHST11-TRAC	chr12	104851307	chr14	23016447	557	HLA-B35:09	HPDIQNPDPAV	0.9915	0.9789	11	22
CHST11-TRAC	chr12	104851307	chr14	23016447	557	HLA-B67:01	HPDIQNPDPAV	0.9576	0.9693	11	22

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Potential FusionNeoAntigen Information of CHST11-TRAC in HLA II

CHST11-TRAC_104851307_23016447.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)
CHST11-TRAC	chr12	104851307	chr14	23016447	557	DRB1-1476	QSMLHPDIQNPDPAV	7	22
CHST11-TRAC	chr12	104851307	chr14	23016447	557	DRB1-1479	QSMLHPDIQNPDPAV	7	22

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Fusion breakpoint peptide structures of CHST11-TRAC

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
2532	FQSMLHPDIQNPDP	CHST11	TRAC	chr12	104851307	chr14	23016447	557

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of CHST11-TRAC

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	2532	FQSMLHPDIQNPDP	-7.15543	-7.26883
HLA-B14:02	3BVN	2532	FQSMLHPDIQNPDP	-4.77435	-5.80965
HLA-B52:01	3W39	2532	FQSMLHPDIQNPDP	-6.80875	-6.92215
HLA-B52:01	3W39	2532	FQSMLHPDIQNPDP	-4.20386	-5.23916
HLA-A11:01	4UQ2	2532	FQSMLHPDIQNPDP	-7.5194	-8.5547
HLA-A11:01	4UQ2	2532	FQSMLHPDIQNPDP	-6.9601	-7.0735
HLA-A24:02	5HGA	2532	FQSMLHPDIQNPDP	-7.52403	-7.63743
HLA-A24:02	5HGA	2532	FQSMLHPDIQNPDP	-5.82433	-6.85963
HLA-B27:05	6PYJ	2532	FQSMLHPDIQNPDP	-3.28285	-4.31815
HLA-B44:05	3DX8	2532	FQSMLHPDIQNPDP	-5.91172	-6.94702
HLA-B44:05	3DX8	2532	FQSMLHPDIQNPDP	-4.24346	-4.35686

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Vaccine Design for the FusionNeoAntigens of CHST11-TRAC

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
CHST11-TRAC	chr12	104851307	chr14	23016447	11	21	HPDIQNPDPA	ACCCAGATATCCAGAACCCTGACCCTGCCG
CHST11-TRAC	chr12	104851307	chr14	23016447	11	22	HPDIQNPDPAV	ACCCAGATATCCAGAACCCTGACCCTGCCGTGT
CHST11-TRAC	chr12	104851307	chr14	23016447	6	15	FQSMLHPDI	TCCAAAGTATGTTGCACCCAGATATCC

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
CHST11-TRAC	chr12	104851307	chr14	23016447	7	22	QSMLHPDIQNPDPAV	AAAGTATGTTGCACCCAGATATCCAGAACCCTGACCCTGCCGTGT

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Information of the samples that have these potential fusion neoantigens of CHST11-TRAC

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	CHST11-TRAC	chr12	104851307	ENST00000303694	chr14	23016447	ENST00000478163	TCGA-BR-A4IY-01A

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Potential target of CAR-T therapy development for CHST11-TRAC

Predicted 3D structure. We used RoseTTAFold.

111_CHST11-TRAC_d1ce7_pred.pdb

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

Hgene

CHST11

chr12:104851307

chr14:23016447

ENST00000303694

17_37

353.0

Transmembrane

Helical%3B Signal-anchor for type II membrane protein

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
CHST11	chr12	104851307	ENST00000303694	TRAC	chr14	23016447	ENST00000478163

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Related Drugs to CHST11-TRAC

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 CHST11-TRAC

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)