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Fusion Protein:CYP20A1-ABI2

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: CYP20A1-ABI2
	FusionPDB ID: 21023
	FusionGDB2.0 ID: 21023
		Hgene	Tgene
	Gene symbol	CYP20A1	ABI2
	Gene ID	57404	10152
	Gene name	cytochrome P450 family 20 subfamily A member 1	abl interactor 2
	Synonyms	CYP-M	ABI-2\|ABI2B\|AIP-1\|AIP1\|AblBP3\|SSH3BP2\|argBP1\|argBPIA\|argBPIB
	Cytomap	2q33.2	2q33.2
	Type of gene	protein-coding	protein-coding
	Description	cytochrome P450 20A1cytochrome P450 monooxygenasecytochrome P450, family 20, subfamily A, polypeptide 1	abl interactor 2abelson interactor 2abl binding protein 3abl-interacting protein 1 (SH3-containing protein)abl-interactor protein 2barg protein tyrosine kinase-binding proteinarg-binding protein 1
	Modification date	20200313	20200327
	UniProtAcc	Q6UW02 Main function of 5'-partner protein:	Q9NYB9 Main function of 5'-partner protein: FUNCTION: Regulator of actin cytoskeleton dynamics underlying cell motility and adhesion. Functions as a component of the WAVE complex, which activates actin nucleating machinery Arp2/3 to drive lamellipodia formation (PubMed:21107423). Acts as regulator and substrate of nonreceptor tyrosine kinases ABL1 and ABL2 involved in processes linked to cell growth and differentiation. Positively regulates ABL1-mediated phosphorylation of ENAH, which is required for proper polymerization of nucleated actin filaments at the leading edge (PubMed:7590236, PubMed:8649853, PubMed:10498863). Contributes to the regulation of actin assembly at the tips of neuron projections. In particular, controls dendritic spine morphogenesis and may promote dendritic spine specification toward large mushroom-type spines known as repositories of memory in the brain (By similarity). In hippocampal neurons, may mediate actin-dependent BDNF-NTRK2 early endocytic trafficking that triggers dendrite outgrowth (By similarity). Participates in ocular lens morphogenesis, likely by regulating lamellipodia-driven adherens junction formation at the epithelial cell-secondary lens fiber interface (By similarity). Also required for nascent adherens junction assembly in epithelial cells (PubMed:15572692). {ECO:0000250\|UniProtKB:P62484, ECO:0000269\|PubMed:10498863, ECO:0000269\|PubMed:15572692, ECO:0000269\|PubMed:21107423, ECO:0000269\|PubMed:7590236, ECO:0000269\|PubMed:8649853}.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000461371, ENST00000356079, ENST00000429815,	ENST00000261016, ENST00000261017, ENST00000295851, ENST00000422511, ENST00000424558, ENST00000430418, ENST00000261018, ENST00000430574,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	4 X 4 X 3=48	5 X 5 X 4=100
	# samples	4	5
	** MAII score	log2(4/48*10)=-0.263034405833794 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(5/100*10)=-1 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0
Fusion gene context	PubMed: CYP20A1 [Title/Abstract] AND ABI2 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: CYP20A1 [Title/Abstract] AND ABI2 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	ABI2(204193354)-CYP20A1(204154488), # samples:2 CYP20A1(204144836)-ABI2(204267299), # samples:1
Anticipated loss of major functional domain due to fusion event.	CYP20A1-ABI2 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. CYP20A1-ABI2 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. CYP20A1-ABI2 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. CYP20A1-ABI2 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. ABI2-CYP20A1 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. ABI2-CYP20A1 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. ABI2-CYP20A1 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. ABI2-CYP20A1 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF. ABI2-CYP20A1 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target 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	ABI2	GO:0016601	Rac protein signal transduction	21107423
Tgene	ABI2	GO:0018108	peptidyl-tyrosine phosphorylation	17101133
Tgene	ABI2	GO:2000601	positive regulation of Arp2/3 complex-mediated actin nucleation	21107423

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr2:204193354/chr2:204154488)
- 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 CYP20A1 (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 ABI2 (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)
ENST00000356079	CYP20A1	chr2	204144836	+	ENST00000295851	ABI2	chr2	204267299	+	21853	973	15536	13566	656
ENST00000356079	CYP20A1	chr2	204144836	+	ENST00000261017	ABI2	chr2	204267299	+	6390	973	108	1568	486
ENST00000356079	CYP20A1	chr2	204144836	+	ENST00000430418	ABI2	chr2	204267299	+	1658	973	108	1481	457
ENST00000356079	CYP20A1	chr2	204144836	+	ENST00000424558	ABI2	chr2	204267299	+	2078	973	108	1481	457
ENST00000356079	CYP20A1	chr2	204144836	+	ENST00000261016	ABI2	chr2	204267299	+	2078	973	108	1481	457
ENST00000356079	CYP20A1	chr2	204144836	+	ENST00000422511	ABI2	chr2	204267299	+	2726	973	108	1481	457
ENST00000429815	CYP20A1	chr2	204144836	+	ENST00000295851	ABI2	chr2	204267299	+	21835	955	15518	13548	656
ENST00000429815	CYP20A1	chr2	204144836	+	ENST00000261017	ABI2	chr2	204267299	+	6372	955	66	1550	494
ENST00000429815	CYP20A1	chr2	204144836	+	ENST00000430418	ABI2	chr2	204267299	+	1640	955	66	1463	465
ENST00000429815	CYP20A1	chr2	204144836	+	ENST00000424558	ABI2	chr2	204267299	+	2060	955	66	1463	465
ENST00000429815	CYP20A1	chr2	204144836	+	ENST00000261016	ABI2	chr2	204267299	+	2060	955	66	1463	465
ENST00000429815	CYP20A1	chr2	204144836	+	ENST00000422511	ABI2	chr2	204267299	+	2708	955	66	1463	465

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
ENST00000356079	ENST00000295851	CYP20A1	chr2	204144836	+	ABI2	chr2	204267299	+	7.59E-05	0.99992406
ENST00000356079	ENST00000261017	CYP20A1	chr2	204144836	+	ABI2	chr2	204267299	+	6.05E-05	0.99993944
ENST00000356079	ENST00000430418	CYP20A1	chr2	204144836	+	ABI2	chr2	204267299	+	0.000299498	0.99970055
ENST00000356079	ENST00000424558	CYP20A1	chr2	204144836	+	ABI2	chr2	204267299	+	0.000250004	0.99974996
ENST00000356079	ENST00000261016	CYP20A1	chr2	204144836	+	ABI2	chr2	204267299	+	0.000250004	0.99974996
ENST00000356079	ENST00000422511	CYP20A1	chr2	204144836	+	ABI2	chr2	204267299	+	0.00017867	0.99982136
ENST00000429815	ENST00000295851	CYP20A1	chr2	204144836	+	ABI2	chr2	204267299	+	6.64E-05	0.9999336
ENST00000429815	ENST00000261017	CYP20A1	chr2	204144836	+	ABI2	chr2	204267299	+	5.77E-05	0.9999423
ENST00000429815	ENST00000430418	CYP20A1	chr2	204144836	+	ABI2	chr2	204267299	+	0.000288419	0.9997116
ENST00000429815	ENST00000424558	CYP20A1	chr2	204144836	+	ABI2	chr2	204267299	+	0.000237288	0.9997627
ENST00000429815	ENST00000261016	CYP20A1	chr2	204144836	+	ABI2	chr2	204267299	+	0.000237288	0.9997627
ENST00000429815	ENST00000422511	CYP20A1	chr2	204144836	+	ABI2	chr2	204267299	+	0.000162622	0.9998374

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 CYP20A1-ABI2

+/-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 CYP20A1-ABI2 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 CYP20A1-ABI2 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 CYP20A1-ABI2

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 CYP20A1-ABI2

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 CYP20A1-ABI2

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 CYP20A1-ABI2

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 CYP20A1-ABI2

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

Hgene

CYP20A1

chr2:204144836

chr2:204267299

ENST00000356079

4_24

283

463.0

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 CYP20A1-ABI2

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 CYP20A1-ABI2

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)