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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:APP-ABI1

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: APP-ABI1
FusionPDB ID: 5646
FusionGDB2.0 ID: 5646
HgeneTgene
Gene symbol

APP

ABI1

Gene ID

351

10006

Gene nameamyloid beta precursor proteinabl interactor 1
SynonymsAAA|ABETA|ABPP|AD1|APPI|CTFgamma|CVAP|PN-II|PN2|preA4ABI-1|ABLBP4|E3B1|NAP1BP|SSH3BP|SSH3BP1
Cytomap

21q21.3

10p12.1

Type of geneprotein-codingprotein-coding
Descriptionamyloid-beta precursor proteinalzheimer disease amyloid proteinamyloid beta (A4) precursor proteinamyloid beta A4 proteinamyloid precursor proteinbeta-amyloid peptidebeta-amyloid peptide(1-40)beta-amyloid peptide(1-42)beta-amyloid precursor proteiabl interactor 1Abelson interactor 1Abl-interactor protein 1 longabl-binding protein 4eps8 SH3 domain-binding proteininteractor protein AblBP4nap1 binding proteinspectrin SH3 domain-binding protein 1
Modification date2020032920200327
UniProtAcc

Q8NEU8

Main function of 5'-partner protein: FUNCTION: Multifunctional adapter protein that binds to various membrane receptors, nuclear factors and signaling proteins to regulate many processes, such as cell proliferation, immune response, endosomal trafficking and cell metabolism (PubMed:26583432, PubMed:15016378, PubMed:24879834). Regulates signaling pathway leading to cell proliferation through interaction with RAB5A and subunits of the NuRD/MeCP1 complex (PubMed:15016378). Plays a role in immune response by modulating phagocytosis, inflammatory and innate immune responses. In macrophages, enhances Fc-gamma receptor-mediated phagocytosis through interaction with RAB31 leading to activation of PI3K/Akt signaling. In response to LPS, modulates inflammatory responses by playing a key role on the regulation of TLR4 signaling and in the nuclear translocation of RELA/NF-kappa-B p65 and the secretion of pro- and anti-inflammatory cytokines. Also functions as a negative regulator of innate immune response via inhibition of AKT1 signaling pathway by forming a complex with APPL1 and PIK3R1 (By similarity). Plays a role in endosomal trafficking of TGFBR1 from the endosomes to the nucleus (PubMed:26583432). Plays a role in cell metabolism by regulating adiponecting ans insulin signaling pathways and adaptative thermogenesis (PubMed:24879834) (By similarity). In muscle, negatively regulates adiponectin-simulated glucose uptake and fatty acid oxidation by inhibiting adiponectin signaling pathway through APPL1 sequestration thereby antagonizing APPL1 action (By similarity). In muscles, negativeliy regulates insulin-induced plasma membrane recruitment of GLUT4 and glucose uptake through interaction with TBC1D1 (PubMed:24879834). Plays a role in cold and diet-induced adaptive thermogenesis by activating ventromedial hypothalamus (VMH) neurons throught AMPK inhibition which enhances sympathetic outflow to subcutaneous white adipose tissue (sWAT), sWAT beiging and cold tolerance (By similarity). Also plays a role in other signaling pathways namely Wnt/beta-catenin, HGF and glucocorticoid receptor signaling (PubMed:19433865) (By similarity). Positive regulator of beta-catenin/TCF-dependent transcription through direct interaction with RUVBL2/reptin resulting in the relief of RUVBL2-mediated repression of beta-catenin/TCF target genes by modulating the interactions within the beta-catenin-reptin-HDAC complex (PubMed:19433865). May affect adult neurogenesis in hippocampus and olfactory system via regulating the sensitivity of glucocorticoid receptor. Required for fibroblast migration through HGF cell signaling (By similarity). {ECO:0000250|UniProtKB:Q8K3G9, ECO:0000269|PubMed:15016378, ECO:0000269|PubMed:19433865, ECO:0000269|PubMed:24879834, ECO:0000269|PubMed:26583432}.

Q8IZP0

Main function of 5'-partner protein: FUNCTION: May act in negative regulation of cell growth and transformation by interacting with nonreceptor tyrosine kinases ABL1 and/or ABL2. May play a role in regulation of EGF-induced Erk pathway activation. Involved in cytoskeletal reorganization and EGFR signaling. Together with EPS8 participates in transduction of signals from Ras to Rac. In vitro, a trimeric complex of ABI1, EPS8 and SOS1 exhibits Rac specific guanine nucleotide exchange factor (GEF) activity and ABI1 seems to act as an adapter in the complex. Regulates ABL1/c-Abl-mediated phosphorylation of ENAH. Recruits WASF1 to lamellipodia and there seems to regulate WASF1 protein level. In brain, seems to regulate the dendritic outgrowth and branching as well as to determine the shape and number of synaptic contacts of developing neurons. {ECO:0000269|PubMed:11003655, ECO:0000269|PubMed:18328268}.
Ensembl transtripts involved in fusion geneENST idsENST00000346798, ENST00000348990, 
ENST00000354192, ENST00000357903, 
ENST00000358918, ENST00000359726, 
ENST00000439274, ENST00000474136, 
ENST00000440126, ENST00000448388, 
ENST00000473481, ENST00000346832, 
ENST00000376134, ENST00000376137, 
ENST00000376140, ENST00000490841, 
ENST00000536334, ENST00000355394, 
ENST00000359188, ENST00000376138, 
ENST00000376139, ENST00000376142, 
ENST00000376160, ENST00000376166, 
ENST00000376170, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score31 X 25 X 12=930014 X 8 X 5=560
# samples 3313
** MAII scorelog2(33/9300*10)=-4.81669278663694
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(13/560*10)=-2.10691520391651
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: APP [Title/Abstract] AND ABI1 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: APP [Title/Abstract] AND ABI1 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)APP(27542882)-ABI1(27066170), # samples:1
Anticipated loss of major functional domain due to fusion event.APP-ABI1 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.
APP-ABI1 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.
APP-ABI1 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.
APP-ABI1 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
HgeneAPP

GO:0001934

positive regulation of protein phosphorylation

11404397

HgeneAPP

GO:0008285

negative regulation of cell proliferation

22944668

HgeneAPP

GO:1905606

regulation of presynapse assembly

19726636

TgeneABI1

GO:0018108

peptidyl-tyrosine phosphorylation

17101133



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/chr21:27542882/chr10:27066170)
- 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 APP (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 ABI1 (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)
ENST00000346798APPchr2127542882-ENST00000376170ABI1chr1027066170-313991341161375
ENST00000346798APPchr2127542882-ENST00000359188ABI1chr1027066170-322691341248404
ENST00000346798APPchr2127542882-ENST00000376142ABI1chr1027066170-331091341332432
ENST00000346798APPchr2127542882-ENST00000376139ABI1chr1027066170-321491341236400
ENST00000346798APPchr2127542882-ENST00000376160ABI1chr1027066170-321191341233399
ENST00000346798APPchr2127542882-ENST00000376166ABI1chr1027066170-312491341146370
ENST00000346798APPchr2127542882-ENST00000376138ABI1chr1027066170-314291341164376
ENST00000346798APPchr2127542882-ENST00000355394ABI1chr1027066170-331091341335433
ENST00000354192APPchr2127542882-ENST00000376170ABI1chr1027066170-32321841271254375
ENST00000354192APPchr2127542882-ENST00000359188ABI1chr1027066170-33191841271341404
ENST00000354192APPchr2127542882-ENST00000376142ABI1chr1027066170-34031841271425432
ENST00000354192APPchr2127542882-ENST00000376139ABI1chr1027066170-33071841271329400
ENST00000354192APPchr2127542882-ENST00000376160ABI1chr1027066170-33041841271326399
ENST00000354192APPchr2127542882-ENST00000376166ABI1chr1027066170-32171841271239370
ENST00000354192APPchr2127542882-ENST00000376138ABI1chr1027066170-32351841271257376
ENST00000354192APPchr2127542882-ENST00000355394ABI1chr1027066170-34031841271428433
ENST00000348990APPchr2127542882-ENST00000376170ABI1chr1027066170-32522041471274375
ENST00000348990APPchr2127542882-ENST00000359188ABI1chr1027066170-33392041471361404
ENST00000348990APPchr2127542882-ENST00000376142ABI1chr1027066170-34232041471445432
ENST00000348990APPchr2127542882-ENST00000376139ABI1chr1027066170-33272041471349400
ENST00000348990APPchr2127542882-ENST00000376160ABI1chr1027066170-33242041471346399
ENST00000348990APPchr2127542882-ENST00000376166ABI1chr1027066170-32372041471259370
ENST00000348990APPchr2127542882-ENST00000376138ABI1chr1027066170-32552041471277376
ENST00000348990APPchr2127542882-ENST00000355394ABI1chr1027066170-34232041471448433
ENST00000357903APPchr2127542882-ENST00000376170ABI1chr1027066170-32722241671294375
ENST00000357903APPchr2127542882-ENST00000359188ABI1chr1027066170-33592241671381404
ENST00000357903APPchr2127542882-ENST00000376142ABI1chr1027066170-34432241671465432
ENST00000357903APPchr2127542882-ENST00000376139ABI1chr1027066170-33472241671369400
ENST00000357903APPchr2127542882-ENST00000376160ABI1chr1027066170-33442241671366399
ENST00000357903APPchr2127542882-ENST00000376166ABI1chr1027066170-32572241671279370
ENST00000357903APPchr2127542882-ENST00000376138ABI1chr1027066170-32752241671297376
ENST00000357903APPchr2127542882-ENST00000355394ABI1chr1027066170-34432241671468433
ENST00000358918APPchr2127542882-ENST00000376170ABI1chr1027066170-33052572001327375
ENST00000358918APPchr2127542882-ENST00000359188ABI1chr1027066170-33922572001414404
ENST00000358918APPchr2127542882-ENST00000376142ABI1chr1027066170-34762572001498432
ENST00000358918APPchr2127542882-ENST00000376139ABI1chr1027066170-33802572001402400
ENST00000358918APPchr2127542882-ENST00000376160ABI1chr1027066170-33772572001399399
ENST00000358918APPchr2127542882-ENST00000376166ABI1chr1027066170-32902572001312370
ENST00000358918APPchr2127542882-ENST00000376138ABI1chr1027066170-33082572001330376
ENST00000358918APPchr2127542882-ENST00000355394ABI1chr1027066170-34762572001501433
ENST00000359726APPchr2127542882-ENST00000376170ABI1chr1027066170-33052572001327375
ENST00000359726APPchr2127542882-ENST00000359188ABI1chr1027066170-33922572001414404
ENST00000359726APPchr2127542882-ENST00000376142ABI1chr1027066170-34762572001498432
ENST00000359726APPchr2127542882-ENST00000376139ABI1chr1027066170-33802572001402400
ENST00000359726APPchr2127542882-ENST00000376160ABI1chr1027066170-33772572001399399
ENST00000359726APPchr2127542882-ENST00000376166ABI1chr1027066170-32902572001312370
ENST00000359726APPchr2127542882-ENST00000376138ABI1chr1027066170-33082572001330376
ENST00000359726APPchr2127542882-ENST00000355394ABI1chr1027066170-34762572001501433
ENST00000439274APPchr2127542882-ENST00000376170ABI1chr1027066170-313991341161375
ENST00000439274APPchr2127542882-ENST00000359188ABI1chr1027066170-322691341248404
ENST00000439274APPchr2127542882-ENST00000376142ABI1chr1027066170-331091341332432
ENST00000439274APPchr2127542882-ENST00000376139ABI1chr1027066170-321491341236400
ENST00000439274APPchr2127542882-ENST00000376160ABI1chr1027066170-321191341233399
ENST00000439274APPchr2127542882-ENST00000376166ABI1chr1027066170-312491341146370
ENST00000439274APPchr2127542882-ENST00000376138ABI1chr1027066170-314291341164376
ENST00000439274APPchr2127542882-ENST00000355394ABI1chr1027066170-331091341335433

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
ENST00000346798ENST00000376170APPchr2127542882-ABI1chr1027066170-3.52E-050.99996483
ENST00000346798ENST00000359188APPchr2127542882-ABI1chr1027066170-4.20E-050.99995804
ENST00000346798ENST00000376142APPchr2127542882-ABI1chr1027066170-6.10E-050.99993896
ENST00000346798ENST00000376139APPchr2127542882-ABI1chr1027066170-4.19E-050.99995804
ENST00000346798ENST00000376160APPchr2127542882-ABI1chr1027066170-5.16E-050.9999484
ENST00000346798ENST00000376166APPchr2127542882-ABI1chr1027066170-3.42E-050.9999658
ENST00000346798ENST00000376138APPchr2127542882-ABI1chr1027066170-3.06E-050.99996936
ENST00000346798ENST00000355394APPchr2127542882-ABI1chr1027066170-9.02E-050.99990976
ENST00000354192ENST00000376170APPchr2127542882-ABI1chr1027066170-3.84E-050.9999616
ENST00000354192ENST00000359188APPchr2127542882-ABI1chr1027066170-4.57E-050.99995434
ENST00000354192ENST00000376142APPchr2127542882-ABI1chr1027066170-6.77E-050.9999323
ENST00000354192ENST00000376139APPchr2127542882-ABI1chr1027066170-4.62E-050.99995375
ENST00000354192ENST00000376160APPchr2127542882-ABI1chr1027066170-5.65E-050.9999435
ENST00000354192ENST00000376166APPchr2127542882-ABI1chr1027066170-3.76E-050.99996245
ENST00000354192ENST00000376138APPchr2127542882-ABI1chr1027066170-3.34E-050.9999666
ENST00000354192ENST00000355394APPchr2127542882-ABI1chr1027066170-0.0001008370.99989915
ENST00000348990ENST00000376170APPchr2127542882-ABI1chr1027066170-4.04E-050.9999596
ENST00000348990ENST00000359188APPchr2127542882-ABI1chr1027066170-4.84E-050.9999516
ENST00000348990ENST00000376142APPchr2127542882-ABI1chr1027066170-7.17E-050.99992824
ENST00000348990ENST00000376139APPchr2127542882-ABI1chr1027066170-4.89E-050.9999511
ENST00000348990ENST00000376160APPchr2127542882-ABI1chr1027066170-5.98E-050.99994016
ENST00000348990ENST00000376166APPchr2127542882-ABI1chr1027066170-3.96E-050.9999604
ENST00000348990ENST00000376138APPchr2127542882-ABI1chr1027066170-3.52E-050.99996483
ENST00000348990ENST00000355394APPchr2127542882-ABI1chr1027066170-0.0001067010.9998933
ENST00000357903ENST00000376170APPchr2127542882-ABI1chr1027066170-4.09E-050.9999591
ENST00000357903ENST00000359188APPchr2127542882-ABI1chr1027066170-4.89E-050.9999511
ENST00000357903ENST00000376142APPchr2127542882-ABI1chr1027066170-7.23E-050.99992764
ENST00000357903ENST00000376139APPchr2127542882-ABI1chr1027066170-4.93E-050.99995065
ENST00000357903ENST00000376160APPchr2127542882-ABI1chr1027066170-6.05E-050.99993956
ENST00000357903ENST00000376166APPchr2127542882-ABI1chr1027066170-4.01E-050.9999598
ENST00000357903ENST00000376138APPchr2127542882-ABI1chr1027066170-3.56E-050.99996436
ENST00000357903ENST00000355394APPchr2127542882-ABI1chr1027066170-0.0001074780.9998925
ENST00000358918ENST00000376170APPchr2127542882-ABI1chr1027066170-4.41E-050.9999559
ENST00000358918ENST00000359188APPchr2127542882-ABI1chr1027066170-5.27E-050.9999473
ENST00000358918ENST00000376142APPchr2127542882-ABI1chr1027066170-7.80E-050.99992204
ENST00000358918ENST00000376139APPchr2127542882-ABI1chr1027066170-5.32E-050.99994683
ENST00000358918ENST00000376160APPchr2127542882-ABI1chr1027066170-6.52E-050.9999348
ENST00000358918ENST00000376166APPchr2127542882-ABI1chr1027066170-4.34E-050.9999566
ENST00000358918ENST00000376138APPchr2127542882-ABI1chr1027066170-3.85E-050.9999615
ENST00000358918ENST00000355394APPchr2127542882-ABI1chr1027066170-0.0001155850.99988437
ENST00000359726ENST00000376170APPchr2127542882-ABI1chr1027066170-4.41E-050.9999559
ENST00000359726ENST00000359188APPchr2127542882-ABI1chr1027066170-5.27E-050.9999473
ENST00000359726ENST00000376142APPchr2127542882-ABI1chr1027066170-7.80E-050.99992204
ENST00000359726ENST00000376139APPchr2127542882-ABI1chr1027066170-5.32E-050.99994683
ENST00000359726ENST00000376160APPchr2127542882-ABI1chr1027066170-6.52E-050.9999348
ENST00000359726ENST00000376166APPchr2127542882-ABI1chr1027066170-4.34E-050.9999566
ENST00000359726ENST00000376138APPchr2127542882-ABI1chr1027066170-3.85E-050.9999615
ENST00000359726ENST00000355394APPchr2127542882-ABI1chr1027066170-0.0001155850.99988437
ENST00000439274ENST00000376170APPchr2127542882-ABI1chr1027066170-3.52E-050.99996483
ENST00000439274ENST00000359188APPchr2127542882-ABI1chr1027066170-4.20E-050.99995804
ENST00000439274ENST00000376142APPchr2127542882-ABI1chr1027066170-6.10E-050.99993896
ENST00000439274ENST00000376139APPchr2127542882-ABI1chr1027066170-4.19E-050.99995804
ENST00000439274ENST00000376160APPchr2127542882-ABI1chr1027066170-5.16E-050.9999484
ENST00000439274ENST00000376166APPchr2127542882-ABI1chr1027066170-3.42E-050.9999658
ENST00000439274ENST00000376138APPchr2127542882-ABI1chr1027066170-3.06E-050.99996936
ENST00000439274ENST00000355394APPchr2127542882-ABI1chr1027066170-9.02E-050.99990976

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 APP-ABI1

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
APPchr2127542882ABI1chr102706617018419LLLLAAWTARALETVDIHKEKVARRE
APPchr2127542882ABI1chr102706617020419LLLLAAWTARALETVDIHKEKVARRE
APPchr2127542882ABI1chr102706617022419LLLLAAWTARALETVDIHKEKVARRE
APPchr2127542882ABI1chr102706617025719LLLLAAWTARALETVDIHKEKVARRE
APPchr2127542882ABI1chr10270661709119LLLLAAWTARALETVDIHKEKVARRE

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Potential FusionNeoAntigen Information of APP-ABI1 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.
APP-ABI1_27542882_27066170.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)
APP-ABI1chr2127542882chr102706617091HLA-A30:08RALETVDIHK0.97790.706919
APP-ABI1chr2127542882chr102706617091HLA-A68:02WTARALETV0.99830.693615
APP-ABI1chr2127542882chr102706617091HLA-A69:01WTARALETV0.99530.7425615
APP-ABI1chr2127542882chr102706617091HLA-A69:01ETVDIHKEKV0.99520.67481222
APP-ABI1chr2127542882chr102706617091HLA-A30:01RALETVDIHK0.97510.8264919

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Potential FusionNeoAntigen Information of APP-ABI1 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.
APP-ABI1_27542882_27066170.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)
APP-ABI1chr2127542882chr102706617091DRB1-0303LETVDIHKEKVARRE1126
APP-ABI1chr2127542882chr102706617091DRB5-0106LETVDIHKEKVARRE1126
APP-ABI1chr2127542882chr102706617091DRB5-0205LETVDIHKEKVARRE1126

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Fusion breakpoint peptide structures of APP-ABI1

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
10547WTARALETVDIHKEAPPABI1chr2127542882chr102706617091

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of APP-ABI1

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-B14:023BVN10547WTARALETVDIHKE-6.33173-6.44513
HLA-B14:023BVN10547WTARALETVDIHKE-1.81046-2.84576
HLA-B52:013W3910547WTARALETVDIHKE-5.92784-6.04124
HLA-B52:013W3910547WTARALETVDIHKE-4.3074-5.3427
HLA-A24:025HGA10547WTARALETVDIHKE-6.68795-7.72325
HLA-A24:025HGA10547WTARALETVDIHKE-5.73606-5.84946
HLA-B44:053DX810547WTARALETVDIHKE-6.99493-8.03023
HLA-B44:053DX810547WTARALETVDIHKE-6.82556-6.93896
HLA-A02:016TDR10547WTARALETVDIHKE-4.47214-5.50744

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Vaccine Design for the FusionNeoAntigens of APP-ABI1

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
APP-ABI1chr2127542882chr10270661701222ETVDIHKEKVGAGACTGTGGATATTCATAAGGAGAAAGTG
APP-ABI1chr2127542882chr1027066170615WTARALETVTGGACGGCTCGGGCGCTGGAGACTGTG
APP-ABI1chr2127542882chr1027066170919RALETVDIHKCGGGCGCTGGAGACTGTGGATATTCATAAG

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
APP-ABI1chr2127542882chr10270661701126LETVDIHKEKVARRECTGGAGACTGTGGATATTCATAAGGAGAAAGTGGCACGAAGAGAG

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Information of the samples that have these potential fusion neoantigens of APP-ABI1

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
STADAPP-ABI1chr2127542882ENST00000346798chr1027066170ENST00000355394TCGA-CD-8525-01A

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Potential target of CAR-T therapy development for APP-ABI1

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 APP-ABI1

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 APP-ABI1

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
TgeneABI1C0019193Hepatitis, Toxic1CTD_human
TgeneABI1C0860207Drug-Induced Liver Disease1CTD_human
TgeneABI1C1262760Hepatitis, Drug-Induced1CTD_human
TgeneABI1C3658290Drug-Induced Acute Liver Injury1CTD_human
TgeneABI1C4277682Chemical and Drug Induced Liver Injury1CTD_human
TgeneABI1C4279912Chemically-Induced Liver Toxicity1CTD_human