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Fusion Protein:CC2D2A-BST1

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: CC2D2A-BST1
	FusionPDB ID: 13508
	FusionGDB2.0 ID: 13508
		Hgene	Tgene
	Gene symbol	CC2D2A	BST1
	Gene ID	57545	683
	Gene name	coiled-coil and C2 domain containing 2A	bone marrow stromal cell antigen 1
	Synonyms	JBTS9\|MKS6	CD157
	Cytomap	4p15.32	4p15.32
	Type of gene	protein-coding	protein-coding
	Description	coiled-coil and C2 domain-containing protein 2A	ADP-ribosyl cyclase/cyclic ADP-ribose hydrolase 2ADP-ribosyl cyclase 2NAD(+) nucleosidasebone marrow stromal antigen 1bone marrow stromal cell antigen 1 variant 2cADPr hydrolase 2cyclic ADP-ribose hydrolase 2
	Modification date	20200313	20200313
	UniProtAcc	Q9P2K1 Main function of 5'-partner protein: FUNCTION: Component of the tectonic-like complex, a complex localized at the transition zone of primary cilia and acting as a barrier that prevents diffusion of transmembrane proteins between the cilia and plasma membranes. Required for ciliogenesis and sonic hedgehog/SHH signaling (By similarity). {ECO:0000250, ECO:0000269\|PubMed:18513680}.	Q10588 Main function of 5'-partner protein: FUNCTION: Synthesizes the second messengers cyclic ADP-ribose and nicotinate-adenine dinucleotide phosphate, the former a second messenger that elicits calcium release from intracellular stores. May be involved in pre-B-cell growth. {ECO:0000269\|PubMed:11866528}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000513811, ENST00000438599, ENST00000503658, ENST00000511544, ENST00000389652, ENST00000413206, ENST00000424120, ENST00000503292, ENST00000507954, ENST00000515124,	ENST00000265016, ENST00000382346,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	5 X 5 X 3=75	1 X 1 X 1=1
	# samples	6	1
	** MAII score	log2(6/75*10)=-0.321928094887362 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(1/1*10)=3.32192809488736
Fusion gene context	PubMed: CC2D2A [Title/Abstract] AND BST1 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: CC2D2A [Title/Abstract] AND BST1 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	CC2D2A(15482451)-BST1(15713430), # samples:2
Anticipated loss of major functional domain due to fusion event.	CC2D2A-BST1 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. CC2D2A-BST1 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. CC2D2A-BST1 seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene 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
Tgene	BST1	GO:0001952	regulation of cell-matrix adhesion	15328157
Tgene	BST1	GO:0008284	positive regulation of cell proliferation	8202488
Tgene	BST1	GO:0032956	regulation of actin cytoskeleton organization	15328157
Tgene	BST1	GO:0050727	regulation of inflammatory response	15328157
Tgene	BST1	GO:0050730	regulation of peptidyl-tyrosine phosphorylation	8941363
Tgene	BST1	GO:0090022	regulation of neutrophil chemotaxis	15328157

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr4:15482451/chr4:15713430)
- 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 CC2D2A (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 BST1 (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)
ENST00000424120	CC2D2A	chr4	15482451	+	ENST00000265016	BST1	chr4	15713430	+	1335	501	221	1006	261
ENST00000424120	CC2D2A	chr4	15482451	+	ENST00000382346	BST1	chr4	15713430	+	1949	501	221	1006	261
ENST00000413206	CC2D2A	chr4	15482451	+	ENST00000265016	BST1	chr4	15713430	+	1320	486	239	991	250
ENST00000413206	CC2D2A	chr4	15482451	+	ENST00000382346	BST1	chr4	15713430	+	1934	486	239	991	250
ENST00000503292	CC2D2A	chr4	15482451	+	ENST00000265016	BST1	chr4	15713430	+	1261	427	180	932	250
ENST00000503292	CC2D2A	chr4	15482451	+	ENST00000382346	BST1	chr4	15713430	+	1875	427	180	932	250
ENST00000389652	CC2D2A	chr4	15482451	+	ENST00000265016	BST1	chr4	15713430	+	1064	230	130	735	201
ENST00000389652	CC2D2A	chr4	15482451	+	ENST00000382346	BST1	chr4	15713430	+	1678	230	130	735	201
ENST00000507954	CC2D2A	chr4	15482451	+	ENST00000265016	BST1	chr4	15713430	+	1288	454	207	959	250
ENST00000507954	CC2D2A	chr4	15482451	+	ENST00000382346	BST1	chr4	15713430	+	1902	454	207	959	250
ENST00000515124	CC2D2A	chr4	15482451	+	ENST00000265016	BST1	chr4	15713430	+	1245	411	164	916	250
ENST00000515124	CC2D2A	chr4	15482451	+	ENST00000382346	BST1	chr4	15713430	+	1859	411	164	916	250

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
ENST00000424120	ENST00000265016	CC2D2A	chr4	15482451	+	BST1	chr4	15713430	+	0.002286875	0.9977131
ENST00000424120	ENST00000382346	CC2D2A	chr4	15482451	+	BST1	chr4	15713430	+	0.001316875	0.99868315
ENST00000413206	ENST00000265016	CC2D2A	chr4	15482451	+	BST1	chr4	15713430	+	0.002286212	0.9977138
ENST00000413206	ENST00000382346	CC2D2A	chr4	15482451	+	BST1	chr4	15713430	+	0.001402156	0.9985978
ENST00000503292	ENST00000265016	CC2D2A	chr4	15482451	+	BST1	chr4	15713430	+	0.002633196	0.99736685
ENST00000503292	ENST00000382346	CC2D2A	chr4	15482451	+	BST1	chr4	15713430	+	0.001329019	0.99867105
ENST00000389652	ENST00000265016	CC2D2A	chr4	15482451	+	BST1	chr4	15713430	+	0.002512589	0.9974874
ENST00000389652	ENST00000382346	CC2D2A	chr4	15482451	+	BST1	chr4	15713430	+	0.001107886	0.9988921
ENST00000507954	ENST00000265016	CC2D2A	chr4	15482451	+	BST1	chr4	15713430	+	0.002754215	0.9972458
ENST00000507954	ENST00000382346	CC2D2A	chr4	15482451	+	BST1	chr4	15713430	+	0.001314766	0.9986852
ENST00000515124	ENST00000265016	CC2D2A	chr4	15482451	+	BST1	chr4	15713430	+	0.002862838	0.9971372
ENST00000515124	ENST00000382346	CC2D2A	chr4	15482451	+	BST1	chr4	15713430	+	0.001452675	0.99854726

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 CC2D2A-BST1

+/-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

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Potential FusionNeoAntigen Information of CC2D2A-BST1 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.

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)

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Potential FusionNeoAntigen Information of CC2D2A-BST1 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 CC2D2A-BST1

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.

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of CC2D2A-BST1

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

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Vaccine Design for the FusionNeoAntigens of CC2D2A-BST1

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

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 CC2D2A-BST1

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

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Potential target of CAR-T therapy development for CC2D2A-BST1

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 CC2D2A-BST1

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 CC2D2A-BST1

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)