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Center for Computational Systems Medicine
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Fusion Gene and Fusion Protein Summary

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Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)

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Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)

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Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)

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Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)

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Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)

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Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)

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Potential target of CAR-T therapy development

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Information on the samples that have these potential fusion neoantigens

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Fusion Protein Targeting Drugs - (Manual Curation)

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Fusion Protein Related diseases - (Manual Curation)

Fusion Protein:PRDM2-BMP8B

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: PRDM2-BMP8B
FusionPDB ID: 68443
FusionGDB2.0 ID: 68443
HgeneTgene
Gene symbol

PRDM2

BMP8B

Gene ID

7799

656

Gene namePR/SET domain 2bone morphogenetic protein 8b
SynonymsHUMHOXY1|KMT8|KMT8A|MTB-ZF|RIZ|RIZ1|RIZ2BMP8|OP2
Cytomap

1p36.21

1p34.2

Type of geneprotein-codingprotein-coding
DescriptionPR domain zinc finger protein 2GATA-3 binding protein G3BMTE-binding proteinPR domain 2PR domain containing 2, with ZNF domainPR domain-containing protein 2lysine N-methyltransferase 8retinoblastoma protein-binding zinc finger proteinretinoblastombone morphogenetic protein 8Bbone morphogenetic protein 8 (osteogenic protein 2)osteogenic protein 2
Modification date2020031320200313
UniProtAcc.

P34820

Main function of 5'-partner protein: FUNCTION: Induces cartilage and bone formation. May be the osteoinductive factor responsible for the phenomenon of epithelial osteogenesis. Plays a role in calcium regulation and bone homeostasis (By similarity). {ECO:0000250}.
Ensembl transtripts involved in fusion geneENST idsENST00000502727, ENST00000343137, 
ENST00000413440, ENST00000503842, 
ENST00000505823, ENST00000235372, 
ENST00000311066, ENST00000376048, 
ENST00000372827, ENST00000397360, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score8 X 4 X 5=1602 X 2 X 2=8
# samples 72
** MAII scorelog2(7/160*10)=-1.1926450779424
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(2/8*10)=1.32192809488736
Fusion gene context

PubMed: PRDM2 [Title/Abstract] AND BMP8B [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: PRDM2 [Title/Abstract] AND BMP8B [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)PRDM2(14075982)-BMP8B(40240710), # samples:1
Anticipated loss of major functional domain due to fusion event.PRDM2-BMP8B 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.
PRDM2-BMP8B 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.
PRDM2-BMP8B 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.
PRDM2-BMP8B 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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgenePRDM2

GO:0045944

positive regulation of transcription by RNA polymerase II

8654390



check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr1:14075982/chr1:40240710)
- 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.
FGviewer

check buttonRetention 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.

check buttonFusion gene breakpoints across PRDM2 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across BMP8B (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Amino Acid Sequences


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)
ENST00000376048PRDM2chr114075982+ENST00000372827BMP8Bchr140240710-47496371201511463
ENST00000376048PRDM2chr114075982+ENST00000397360BMP8Bchr140240710-14876371201352410
ENST00000311066PRDM2chr114075982+ENST00000372827BMP8Bchr140240710-547913678502241463
ENST00000311066PRDM2chr114075982+ENST00000397360BMP8Bchr140240710-221713678502082410
ENST00000235372PRDM2chr114075982+ENST00000372827BMP8Bchr140240710-547913678502241463
ENST00000235372PRDM2chr114075982+ENST00000397360BMP8Bchr140240710-221713678502082410

check buttonDeepORF 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.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score
ENST00000376048ENST00000372827PRDM2chr114075982+BMP8Bchr140240710-0.0037387910.9962612
ENST00000376048ENST00000397360PRDM2chr114075982+BMP8Bchr140240710-0.0159506930.9840493
ENST00000311066ENST00000372827PRDM2chr114075982+BMP8Bchr140240710-0.0023007650.9976992
ENST00000311066ENST00000397360PRDM2chr114075982+BMP8Bchr140240710-0.0047592370.9952408
ENST00000235372ENST00000372827PRDM2chr114075982+BMP8Bchr140240710-0.0023007650.9976992
ENST00000235372ENST00000397360PRDM2chr114075982+BMP8Bchr140240710-0.0047592370.9952408

check button 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 PRDM2-BMP8B

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
PRDM2chr114075982BMP8Bchr1402407101367172SARSKRSSPKSRKVERDRALGHQEPH
PRDM2chr114075982BMP8Bchr140240710637172SARSKRSSPKSRKVERDRALGHQEPH

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Potential FusionNeoAntigen Information of PRDM2-BMP8B in HLA I

check button 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.
PRDM2-BMP8B_14075982_40240710.msa

check button Potential FusionNeoAntigen Information
* We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5)
Fusion geneHchrHbpTgeneTchrTbpHLA IFusionNeoAntigen peptideBinding scoreImmunogenic scoreNeoantigen start (at BP 13)Neoantigen end (at BP 13)
PRDM2-BMP8Bchr114075982chr1402407101367HLA-A30:08RSSPKSRKV0.98720.7477514
PRDM2-BMP8Bchr114075982chr1402407101367HLA-B14:01RKVERDRAL0.85850.5371120
PRDM2-BMP8Bchr114075982chr1402407101367HLA-B14:02RKVERDRAL0.85850.5371120
PRDM2-BMP8Bchr114075982chr1402407101367HLA-B39:13RKVERDRAL0.59150.77831120
PRDM2-BMP8Bchr114075982chr1402407101367HLA-B15:03RKVERDRAL0.31780.69081120
PRDM2-BMP8Bchr114075982chr1402407101367HLA-C01:17SSPKSRKV0.93480.8673614
PRDM2-BMP8Bchr114075982chr1402407101367HLA-C01:30SSPKSRKV0.91810.8884614
PRDM2-BMP8Bchr114075982chr1402407101367HLA-C15:04RSSPKSRKV0.99420.8779514
PRDM2-BMP8Bchr114075982chr1402407101367HLA-C15:06RSSPKSRKV0.99320.8968514
PRDM2-BMP8Bchr114075982chr1402407101367HLA-C02:06RSSPKSRKV0.68880.9502514
PRDM2-BMP8Bchr114075982chr1402407101367HLA-C06:03RSSPKSRKV0.65090.9873514
PRDM2-BMP8Bchr114075982chr1402407101367HLA-C12:04RSSPKSRKV0.64350.9866514
PRDM2-BMP8Bchr114075982chr1402407101367HLA-B14:03RKVERDRAL0.49590.61111120
PRDM2-BMP8Bchr114075982chr1402407101367HLA-C12:12RSSPKSRKV0.4240.876514
PRDM2-BMP8Bchr114075982chr1402407101367HLA-C01:02SSPKSRKV0.92530.8645614
PRDM2-BMP8Bchr114075982chr1402407101367HLA-C15:02RSSPKSRKV0.99580.8652514
PRDM2-BMP8Bchr114075982chr1402407101367HLA-C15:05RSSPKSRKV0.99460.8944514
PRDM2-BMP8Bchr114075982chr1402407101367HLA-C15:09RSSPKSRKV0.99420.8779514
PRDM2-BMP8Bchr114075982chr1402407101367HLA-A30:01RSSPKSRKV0.9870.8296514
PRDM2-BMP8Bchr114075982chr1402407101367HLA-C06:06RSSPKSRKV0.94310.9857514
PRDM2-BMP8Bchr114075982chr1402407101367HLA-C16:02RSSPKSRKV0.89680.9922514
PRDM2-BMP8Bchr114075982chr1402407101367HLA-B39:02RKVERDRAL0.82530.77471120
PRDM2-BMP8Bchr114075982chr1402407101367HLA-B58:06RSSPKSRKV0.68580.6341514
PRDM2-BMP8Bchr114075982chr1402407101367HLA-C06:17RSSPKSRKV0.66340.9862514
PRDM2-BMP8Bchr114075982chr1402407101367HLA-C06:02RSSPKSRKV0.66340.9862514
PRDM2-BMP8Bchr114075982chr1402407101367HLA-C07:04RSSPKSRKV0.66320.8865514
PRDM2-BMP8Bchr114075982chr1402407101367HLA-C16:04RSSPKSRKV0.6590.9419514
PRDM2-BMP8Bchr114075982chr1402407101367HLA-C16:01RSSPKSRKV0.53190.9718514
PRDM2-BMP8Bchr114075982chr1402407101367HLA-C06:08RSSPKSRKV0.52240.9804514
PRDM2-BMP8Bchr114075982chr1402407101367HLA-C12:03RSSPKSRKV0.33360.9604514
PRDM2-BMP8Bchr114075982chr1402407101367HLA-B15:68RKVERDRAL0.12160.62241120
PRDM2-BMP8Bchr114075982chr1402407101367HLA-B07:13RSSPKSRKV0.10870.7193514
PRDM2-BMP8Bchr114075982chr1402407101367HLA-B15:54RKVERDRAL0.04050.83111120

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Potential FusionNeoAntigen Information of PRDM2-BMP8B in HLA II

check button 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.
PRDM2-BMP8B_14075982_40240710.msa

check button Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).
Fusion geneHchrHbpTgeneTchrTbpHLA IIFusionNeoAntigen peptideNeoantigen start (at BP 13)Neoantigen end (at BP 13)
PRDM2-BMP8Bchr114075982chr1402407101367DRB1-0320SRKVERDRALGHQEP1025
PRDM2-BMP8Bchr114075982chr1402407101367DRB1-0326SRKVERDRALGHQEP1025
PRDM2-BMP8Bchr114075982chr1402407101367DRB1-0342SRKVERDRALGHQEP1025
PRDM2-BMP8Bchr114075982chr1402407101367DRB1-0342KSRKVERDRALGHQE924
PRDM2-BMP8Bchr114075982chr1402407101367DRB1-0422SRKVERDRALGHQEP1025
PRDM2-BMP8Bchr114075982chr1402407101367DRB1-1476SRKVERDRALGHQEP1025
PRDM2-BMP8Bchr114075982chr1402407101367DRB1-1479SRKVERDRALGHQEP1025
PRDM2-BMP8Bchr114075982chr1402407101367DRB3-0204SRKVERDRALGHQEP1025
PRDM2-BMP8Bchr114075982chr1402407101367DRB3-0204KSRKVERDRALGHQE924

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Fusion breakpoint peptide structures of PRDM2-BMP8B

check button3D 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 nameBPseqHgeneTgeneHchrHbpTchrTbpAAlen
9035SSPKSRKVERDRALPRDM2BMP8Bchr114075982chr1402407101367

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PRDM2-BMP8B

check buttonVirtual screening between 25 HLAs (from PDB) and FusionNeoAntigens
* We used Glide to predict the interaction between HLAs and neoantigens.
HLA allelePDB IDFile nameBPseqDocking scoreGlide score
HLA-B14:023BVN9035SSPKSRKVERDRAL-7.9962-8.1096
HLA-B14:023BVN9035SSPKSRKVERDRAL-5.70842-6.74372
HLA-B52:013W399035SSPKSRKVERDRAL-6.83737-6.95077
HLA-B52:013W399035SSPKSRKVERDRAL-4.4836-5.5189
HLA-A11:014UQ29035SSPKSRKVERDRAL-10.0067-10.1201
HLA-A11:014UQ29035SSPKSRKVERDRAL-9.03915-10.0745
HLA-A24:025HGA9035SSPKSRKVERDRAL-6.56204-6.67544
HLA-A24:025HGA9035SSPKSRKVERDRAL-5.42271-6.45801
HLA-B44:053DX89035SSPKSRKVERDRAL-7.85648-8.89178
HLA-B44:053DX89035SSPKSRKVERDRAL-5.3978-5.5112
HLA-A02:016TDR9035SSPKSRKVERDRAL-3.37154-4.40684

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Vaccine Design for the FusionNeoAntigens of PRDM2-BMP8B

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptide sequenceFusionNeoAntigen RNA sequence
PRDM2-BMP8Bchr114075982chr1402407101120RKVERDRALGGAAAGTGGAGCGAGACCGTGCCCTGG
PRDM2-BMP8Bchr114075982chr140240710514RSSPKSRKVGGAGCTCCCCCAAGAGCCGGAAAGTGG
PRDM2-BMP8Bchr114075982chr140240710614SSPKSRKVGCTCCCCCAAGAGCCGGAAAGTGG

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
PRDM2-BMP8Bchr114075982chr1402407101025SRKVERDRALGHQEPGCCGGAAAGTGGAGCGAGACCGTGCCCTGGGCCACCAGGAGCCCC
PRDM2-BMP8Bchr114075982chr140240710924KSRKVERDRALGHQEAGAGCCGGAAAGTGGAGCGAGACCGTGCCCTGGGCCACCAGGAGC

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Information of the samples that have these potential fusion neoantigens of PRDM2-BMP8B

check button 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 typeFusion geneHchrHbpHenstTchrTbpTenstSample
PAADPRDM2-BMP8Bchr114075982ENST00000235372chr140240710ENST00000372827TCGA-HZ-A9TJ

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Potential target of CAR-T therapy development for PRDM2-BMP8B

check button Predicted 3D structure. We used RoseTTAFold.

check buttonRetention 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'.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

check button 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.
HgeneHchrHbpHenstTgeneTchrTbpTenstDeepLoc result

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Related Drugs to PRDM2-BMP8B

check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to PRDM2-BMP8B

check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource