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Fusion Protein:FDFT1-DEFB135

Fusion Gene and Fusion Protein Summary

Fusion gene summary

Fusion partner gene information	Fusion gene name: FDFT1-DEFB135
	FusionPDB ID: 30043
	FusionGDB2.0 ID: 30043
		Hgene	Tgene
	Gene symbol	FDFT1	DEFB135
	Gene ID	2222	613209
	Gene name	farnesyl-diphosphate farnesyltransferase 1	defensin beta 135
	Synonyms	DGPT\|ERG9\|SQS\|SQSD\|SS	DEFB136
	Cytomap	8p23.1	8p23.1
	Type of gene	protein-coding	protein-coding
	Description	squalene synthaseFPP:FPP farnesyltransferasepresqualene-di-diphosphate synthasesqualene synthetase	beta-defensin 135beta-defensin 136
	Modification date	20200320	20200313
	UniProtAcc	P37268 Main function of 5'-partner protein: FUNCTION: Catalyzes the condensation of 2 farnesyl pyrophosphate (FPP) moieties to form squalene. Proceeds in two distinct steps. In the first half-reaction, two molecules of FPP react to form the stable presqualene diphosphate intermediate (PSQPP), with concomitant release of a proton and a molecule of inorganic diphosphate. In the second half-reaction, PSQPP undergoes heterolysis, isomerization, and reduction with NADPH or NADH to form squalene. It is the first committed enzyme of the sterol biosynthesis pathway. {ECO:0000269\|PubMed:10896663, ECO:0000269\|PubMed:24531458}.	.
Ensembl transtripts involved in fusion gene	ENST ids	ENST00000446331, ENST00000220584, ENST00000525777, ENST00000525900, ENST00000528643, ENST00000538689, ENST00000443614, ENST00000528812, ENST00000530664,	ENST00000382208,
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)	* DoF score	16 X 12 X 9=1728	5 X 2 X 6=60
	# samples	20	8
	** MAII score	log2(20/1728*10)=-3.11103131238874 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0	log2(8/60*10)=0.415037499278844 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0
Fusion gene context	PubMed: FDFT1 [Title/Abstract] AND DEFB135 [Title/Abstract] AND fusion [Title/Abstract]
Fusion neoantigen context	PubMed: FDFT1 [Title/Abstract] AND DEFB135 [Title/Abstract] AND neoantigen [Title/Abstract]
Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)	FDFT1(11696082)-DEFB135(11841930), # samples:2
Anticipated loss of major functional domain due to fusion event.	FDFT1-DEFB135 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF. FDFT1-DEFB135 seems lost the major protein functional domain in Hgene 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

Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr8:11696082/chr8:11841930)
- 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 FDFT1 (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 DEFB135 (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)
ENST00000538689	FDFT1	chr8	11679387	+	ENST00000382208	DEFB135	chr8	11841930	+	1020	850	376	933	185
ENST00000220584	FDFT1	chr8	11679387	+	ENST00000382208	DEFB135	chr8	11841930	+	902	732	222	815	197
ENST00000525900	FDFT1	chr8	11679387	+	ENST00000382208	DEFB135	chr8	11841930	+	726	556	67	639	190
ENST00000528812	FDFT1	chr8	11679387	+	ENST00000382208	DEFB135	chr8	11841930	+	1088	918	525	1001	158
ENST00000530664	FDFT1	chr8	11679387	+	ENST00000382208	DEFB135	chr8	11841930	+	956	786	345	869	174
ENST00000528643	FDFT1	chr8	11679387	+	ENST00000382208	DEFB135	chr8	11841930	+	830	660	369	743	124
ENST00000525777	FDFT1	chr8	11679387	+	ENST00000382208	DEFB135	chr8	11841930	+	894	724	433	807	124
ENST00000443614	FDFT1	chr8	11696082	+	ENST00000382208	DEFB135	chr8	11841930	+	1377	1207	94	1032	312
ENST00000528812	FDFT1	chr8	11696082	+	ENST00000382208	DEFB135	chr8	11841930	+	1997	1827	525	1475	316
ENST00000530664	FDFT1	chr8	11696082	+	ENST00000382208	DEFB135	chr8	11841930	+	1745	1575	345	1343	332
ENST00000538689	FDFT1	chr8	11667359	+	ENST00000382208	DEFB135	chr8	11841930	+	891	721	376	804	142
ENST00000220584	FDFT1	chr8	11667359	+	ENST00000382208	DEFB135	chr8	11841930	+	773	603	222	686	154
ENST00000443614	FDFT1	chr8	11667359	+	ENST00000382208	DEFB135	chr8	11841930	+	645	475	94	558	154
ENST00000525900	FDFT1	chr8	11667359	+	ENST00000382208	DEFB135	chr8	11841930	+	597	427	67	510	147
ENST00000528812	FDFT1	chr8	11667359	+	ENST00000382208	DEFB135	chr8	11841930	+	959	789	525	872	115
ENST00000530664	FDFT1	chr8	11667359	+	ENST00000382208	DEFB135	chr8	11841930	+	827	657	345	740	131
ENST00000528643	FDFT1	chr8	11667359	+	ENST00000382208	DEFB135	chr8	11841930	+	701	531	369	614	81
ENST00000525777	FDFT1	chr8	11667359	+	ENST00000382208	DEFB135	chr8	11841930	+	765	595	433	678	81

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
ENST00000538689	ENST00000382208	FDFT1	chr8	11679387	+	DEFB135	chr8	11841930	+	0.004440818	0.9955592
ENST00000220584	ENST00000382208	FDFT1	chr8	11679387	+	DEFB135	chr8	11841930	+	0.004799319	0.99520063
ENST00000525900	ENST00000382208	FDFT1	chr8	11679387	+	DEFB135	chr8	11841930	+	0.001739018	0.99826103
ENST00000528812	ENST00000382208	FDFT1	chr8	11679387	+	DEFB135	chr8	11841930	+	0.0053615	0.9946385
ENST00000530664	ENST00000382208	FDFT1	chr8	11679387	+	DEFB135	chr8	11841930	+	0.00501212	0.99498785
ENST00000528643	ENST00000382208	FDFT1	chr8	11679387	+	DEFB135	chr8	11841930	+	0.00996956	0.9900304
ENST00000525777	ENST00000382208	FDFT1	chr8	11679387	+	DEFB135	chr8	11841930	+	0.01595922	0.98404074
ENST00000443614	ENST00000382208	FDFT1	chr8	11696082	+	DEFB135	chr8	11841930	+	0.001281144	0.99871886
ENST00000528812	ENST00000382208	FDFT1	chr8	11696082	+	DEFB135	chr8	11841930	+	0.000323406	0.9996766
ENST00000530664	ENST00000382208	FDFT1	chr8	11696082	+	DEFB135	chr8	11841930	+	0.000394596	0.9996055
ENST00000538689	ENST00000382208	FDFT1	chr8	11667359	+	DEFB135	chr8	11841930	+	0.020664234	0.9793357
ENST00000220584	ENST00000382208	FDFT1	chr8	11667359	+	DEFB135	chr8	11841930	+	0.010395994	0.989604
ENST00000443614	ENST00000382208	FDFT1	chr8	11667359	+	DEFB135	chr8	11841930	+	0.008735449	0.9912646
ENST00000525900	ENST00000382208	FDFT1	chr8	11667359	+	DEFB135	chr8	11841930	+	0.004622113	0.9953779
ENST00000528812	ENST00000382208	FDFT1	chr8	11667359	+	DEFB135	chr8	11841930	+	0.027476922	0.9725231
ENST00000530664	ENST00000382208	FDFT1	chr8	11667359	+	DEFB135	chr8	11841930	+	0.027397243	0.9726027
ENST00000528643	ENST00000382208	FDFT1	chr8	11667359	+	DEFB135	chr8	11841930	+	0.070015855	0.9299842
ENST00000525777	ENST00000382208	FDFT1	chr8	11667359	+	DEFB135	chr8	11841930	+	0.27296746	0.7270326

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 FDFT1-DEFB135

+/-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 FDFT1-DEFB135 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 FDFT1-DEFB135 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 FDFT1-DEFB135

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 FDFT1-DEFB135

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 FDFT1-DEFB135

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 FDFT1-DEFB135

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 FDFT1-DEFB135

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 FDFT1-DEFB135

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 FDFT1-DEFB135

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)