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The landscape and therapeutic relevance of cancer-associated transcript fusions
Open accessAbstract
Transcript fusions as a result of chromosomal rearrangements have been a focus of attention in cancer as they provide attractive therapeutic targets. To identify novel fusion transcripts with the potential to be exploited therapeutically, we analyzed RNA sequencing, DNA copy number and gene mutation data from 4366 primary tumor samples. To avoid false positives, we implemented stringent quality criteria that included filtering of fusions detected in RNAseq data from 364 normal tissue samples. Our analysis identified 7887 high confidence fusion transcripts across 13 tumor types. Our fusion prediction was validated by evidence of a genomic rearrangement for 78 of 79 fusions in 48 glioma samples where whole-genome sequencing data were available. Cancers with higher levels of genomic instability showed a corresponding increase in fusion transcript frequency, whereas tumor samples harboring fusions contained statistically significantly fewer driver gene mutations, suggesting an important role for tumorigenesis. We identified at least one in-frame protein kinase fusion in 324 of 4366 samples (7.4%). Potentially druggable kinase fusions involving ALK, ROS, RET, NTRK and FGFR gene families were detected in bladder carcinoma (3.3%), glioblastoma (4.4%), head and neck cancer (1.0%), low-grade glioma (1.5%), lung adenocarcinoma (1.6%), lung squamous cell carcinoma (2.3%) and thyroid carcinoma (8.7%), suggesting a potential for application of kinase inhibitors across tumor types. In-frame fusion transcripts involving histone methyltransferase or histone demethylase genes were detected in 111 samples (2.5%) and may additionally be considered as therapeutic targets. In summary, we described the landscape of transcript fusions detected across a large number of tumor samples and revealed fusion events with clinical relevance that have not been previously recognized. Our results support the concept of basket clinical trials where patients are matched with experimental therapies based on their genomic profile rather than the tissue where the tumor originated.
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“Finally, a low ratio of chimeric to wild-type reads in the vicinity of the fusion boundary may indicate spurious mis-mapping of reads from a highly expressed gene (the transcript allele fraction described by Yoshihara et al. [87]).”
From A survey of best practices for RNA-seq data analysis (2016) · cites this paper as [87]
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Items 301–400 of 450
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“For example, UBE2D2 forms multiple chimeras in Lung Adenocarcinoma (LUAD) [36].”
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“2 region centromeric to FUS contains ZNF267 , ITGAX , and ARMC5 that are involved in bladder transitional cell carcinoma with t(1; 16)(p33;p11), bladder transitional cell carcinoma with t(16; 16)(p11;p11), and breast adenocarcinoma with t(8; 16)(p11;p11), respectively [Dessen and Huret, 2012b; Yoshihara et al., 2015].”
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“To date, besides the first CCDC6 fusion with the tyrosine kinase RET identified in papillary thyroid cancer [17,18], additional CCDC6 fusions have been reported with PDGFRb [19,20], PTEN [21], FGFR2 [22,23] ANK3 [24], and UBE2D1 [25] and with other genes in different tumor types [26].”
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Chu, Y., Katabi, N., Sukhadia, P., Mullaney, K. A., Zaidinski, M., Cracchiolo, J. R., Xu, B., Ghossein, R. A., Ho, A. L., DiNapoli, S. E., et al. (2024) · Histopathology · doi:10.1111/his.15380 · Cited by 6
Utility of Retrospective Molecular Analysis in Diagnostically Challenging Mesenchymal Neoplasms
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“44,45 Furthermore, the presence of BRAF fusion was additionally supported by BRAF break-apart fl uorescence in situ hybridization showing translocation positivity throughout the tumor with concomitant ampli fi cation of 3 ′ BRAF locus.”
BackgroundD’Souza, D. P., Bik, L., Giwa, O. D., Cohen, S., Barazany, H. L., Siegal, T., & Frenkel‐Morgenstern, M. (2024) · Nucleic Acids Research · doi:10.1093/nar/gkae1126 · Cited by 6
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“…subunit of the CORVET complex), involved in endosomal trafficking, and LRBA (LPS-responsive beige-like anchor protein), functioning in the regulation of the immune system, have both been described in fusion transcripts with other gene partners in solid tumors but not in myeloid malignancies [36].”
Fisher, C. L., Dillon, R. J., Anguita, E., Morris-Rosendahl, D. J., & Awan, A. R. (2022) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2022.09.006 · Cited by 6
Recurrent fusion transcripts in squamous cell carcinomas of the vulva
Brunetti, M., Agostini, A., Davidson, B., Trope, C. G., Heim, S., Panagopoulos, I., & Micci, F. (2017) · Oncotarget · doi:10.18632/oncotarget.15167 · Cited by 6
“CELF1 has been found involved in previous fusions with five different partners: with MTCH2 and MYOM1 in SCC and adenocarcinoma of the lung, respectively; with LUZP2 and ARFGAP2 in adenocarcinoma of the breast; and with BBOX1 in grade I-II astrocytoma of the brain [13].”
BackgroundInfluentialPanagopoulos, I., Gorunova, L., Lobmaier, I. V. K., Bjerkehagen, B., & Heim, S. (2017) · Oncology Reports · doi:10.3892/or.2017.5628 · Cited by 6
“Dermatofibrosarcoma protuberans, another subtype of spindle cell sarcoma, is characterized cytogenetically by supernumerary ring chromosomes or the translocation t(17;22)(q22;q13) (5).”
BackgroundBossi, P., Siano, M., Bergamini, C., Rocca, M. C., Sponghini, A. P., Giannoccaro, M., Tonella, L., Paoli, A., Marchesi, E., Perrone, F., et al. (2017) · Disease Markers · doi:10.1155/2017/6870614 · Cited by 6
“The distribution and the gene partners of our 27 fusion transcripts were compared with the 382 and the 282 fusions detected by a whole genome approach in HNSCC [13] and OSCC [15], respectively; we recorded a 33% of fusions shared among more patients and no overlap with fusions previously identified in HNSCC/OSCC.”
BackgroundMethodResultPrecision Medicine for Primary Central Nervous System Tumors: Are We There Yet?
Ippen, F. M., Colman, H., van den Bent, M. J., & Brastianos, P. K. (2018) · American Society of Clinical Oncology Educational Book · doi:10.1200/edbk_199247 · Cited by 6
Identification of a MYCN and Wnt-related VANGL2-ITLN1 fusion gene in neuroblastoma
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“Two rearrangements producing fusion genes of C12orf4 with another gene have been reported in cancer (Rudin et al., 2012; Yoshihara et al., 2015), a condition known to overlap in genetic etiology with neurodevelopmental disorders (Crawley, Heyer, & LaSalle, 2016).”
Case Study: The Recurrent Fusion RNA DUS4L-BCAP29 in Noncancer Human Tissues and Cells
Tang, Y., Guan, F., & Li, H. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-9904-0_19 · Cited by 6
FGFR-gerichtete Therapie von Kopf-Hals-Karzinomen
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“So konnte in der HNSCCKohorte des The Cancer Genome Atlas nur in einem Tumor (0,3% aller untersuchter Fälle) eine NTRK-Genfusion gefunden werden [4].”
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Identification of an Immunogenic Medulloblastoma-Specific Fusion Involving EPC2 and GULP1
Paret, C., Lehmann, N., Bender, H. G., Sprang, M., Sommer, C., Cana, D., Seidmann, L., Wingerter, A., Neu, M. A., Malki, K. E., et al. (2021) · Cancers · doi:10.3390/cancers13225838 · Cited by 6
“Translocations have been used not only as markers for certain cancer types, but also as therapeutic targets, since the fusion transcript may include druggable structures such as protein kinases [8].”
BackgroundIdentification of novel fusion transcripts in multiple myeloma
Lin, M., Lee, P. L., Chiu, L., Chua, C., Ban, K. H.-K., Lin, A., Chan, Z. L., Chung, T., Yan, B., & Chng, W. J. (2018) · Journal of Clinical Pathology · doi:10.1136/jclinpath-2017-204961 · Cited by 6
Comprehensive genome and transcriptome analysis reveals genetic basis for gene fusions in cancerPreprint
Fonseca, N. A., He, Y., Greger, L., PCAWG3, Brāzma, A., & Zhang, Z. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/148684 · Cited by 5
“These include a known fusion TBL1XR1–PIK3CA in a breast tumour, in which the 3’ complete PIK3CA ORF is overexpressed by the promoter of the 5’ TBL1XR1 [11].”
BackgroundNohr, E., Kunder, C. A., Jones, C. D., Sutton, S. C., Fung, E., Zhu, H., Feng, S. J., Gojenola, L., Bustamante, C. D., Zehnder, J. L., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/870634 · Cited by 6
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“Primarily through studies of lllumina RNA-seq, large catalogs of fusions have been cataloged across large collections of tumor and normal tissues (Klijn et al. 2015; Yoshihara et al. 2015; Babiceanu et al. 2016; Hu et al. 2018; Dehghannasiri et al. 2019; Haas et al. 2023).”
BackgroundReal-World Clinical Utility of Targeted RNA Sequencing in Leukemia Diagnosis and Management
Kim, S. W., Kim, N., Choi, Y. J., Lee, S.-T., Choi, J. R., & Shin, S. (2024) · Cancers · doi:10.3390/cancers16132467 · Cited by 5
“For the fourth case, t(12;12)(p12;p13), suspected as TEAD4::C2CD5 [22], genes were not included in the 199-gene panel.”
BackgroundJung, D. E., Seo, M.-K., Jo, J. H., Kim, K., Kim, C., Kang, H., Park, S. B., Lee, H. S., Kim, S., & Song, S. Y. (2024) · npj Precision Oncology · doi:10.1038/s41698-024-00654-2 · Cited by 5
“0 43 , FusionCancer (a database of fusion genes in human cancers) 44 , fusionhub 45 , tumorfusion 46 , and a study by Gao et al. 47 , in which tumorfusionsweredetectedamongmultiplecancersfromTCGA.”
BackgroundOptical Genome Mapping for Detection of BCR::ABL1—Another Tool in Our Toolbox
Tang, Z., Wang, W., Törüner, G., Hu, S., Fang, H., Xu, J., You, M. J., Medeiros, L. J., Khoury, J. D., & Tang, G. (2024) · Genes · doi:10.3390/genes15111357 · Cited by 5
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A Novel t(1;9)(p36;p24.1) JAK2 Translocation and Review of the Literature
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Rapid and highly sensitive approach for multiplexed somatic fusion detection
Abbou, S. D., Finstuen-Magro, S., McDannell, B., Feenstra, M., Ward, A., Shulman, D. S., Geoerger, B., Duplan, J., Comeau, H., Janeway, K. A., et al. (2022) · Modern Pathology · doi:10.1038/s41379-022-01058-y · Cited by 5
Watkins, J. A., Tarpey, P. S., O’Donovan, M., Tadross, J. A., & Mohammed, N. (2025) · Genes Chromosomes and Cancer · doi:10.1002/gcc.70072 · Cited by 4
“TANC1 has previously been described as a fusion partner in a small number of cases of non-schwannomatous neoplasms [9, 10].”
Native and tagged CENP-A histones are functionally inequivalent
Bui, M., Baek, S., Bentahar, R. S., Melters, D. P., & Dalal, Y. (2024) · Epigenetics & Chromatin · doi:10.1186/s13072-024-00543-9 · Cited by 4
“Under high levels of genome instability, transcript fusions which are often a result of chromosomal rearrangements, can lead to expression of aberrant proteins as documented with in-frame protein kinases found in bladder carcinoma, glioblastoma, lung adenocarcinoma, etc [63].”
BackgroundThe Use of Crizotinib in Sclerosing Epithelioid Fibrosarcoma with ALK Mutation: A Case Report
Badran, A. A., Steele, C., Alquaydheb, H. N., Theeb, A. B., Bawazir, A., Elshenawy, M. A., & Atallah, J. P. (2023) · Case Reports in Oncology · doi:10.1159/000532099 · Cited by 4
“In ALK-rearranged tumours, however, an uncontrolled increased expression of intracellular-activated fusion kinases results in the upregulation of downstream oncogenic processes [13].”
BackgroundMolecular features and clinical actionability of gene fusions in colorectal cancer
Sullo, F. G., Garinet, S., Blons, H., Taïeb, J., Laurent‐Puig, P., & Gallois, C. (2025) · Critical Reviews in Oncology/Hematology · doi:10.1016/j.critrevonc.2025.104656 · Cited by 4
On the evaluation of the fidelity of supervised classifiers in the prediction of chimeric RNAs
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“However, only a limited number of chimeric transcripts and their associated protein products have been characterised to date, most of them resulting from chromosomal translocation and associated with cancer [2, 3].”
BackgroundCytogenetic Resources and Information
Braekeleer, E. D., Huret, J. L., Mossafa, H., & Dessen, P. (2016) · Methods in molecular biology · doi:10.1007/978-1-4939-6703-2_25 · Cited by 4
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Getting Your Laboratory on Track With Neurotrophic Receptor Tyrosine Kinase
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Okada, H., Nasti, A., Sakai, Y., Takeshita, Y., Iwabuchi, S., Ho, T. T. B., Hashiba, T., Takata, N., Sato, T., Urabe, T., et al. (2025) · Genes · doi:10.3390/genes16091075 · Cited by 3
“…from fusion genes specific to different organs, such as: FOXP1 :: EIF4E3 , ABI2 :: CYP20A1 , and CTSD :: IFITM10 , related to breast adenocarcinoma [33–36]; HAVCR1 :: TIMD4 and JAK3 :: INSL3 , related to kidney adenocarcinoma [34,36,37]; and HACL1 :: COLQ and SIDT2 :: TAGLN , related to lymph node…”
ESR1 fusion proteins in breast cancer: distinguishing oncogenic drivers from passenger events
Gherghelas, A.-M., & Toseland, C. P. (2026) · Oncogene · doi:10.1038/s41388-026-03813-w · Cited by 3
“Their prevalence is currently estimated at 1 – 10% of breast cancer cases [18, 20, 25].”
Conjoined Genes as Common Events in Childhood Acute Lymphoblastic Leukemia
Severgnini, M., D’Angiò, M., Bungaro, S., Cazzaniga, G., Cifola, I., & Fazio, G. (2022) · Cancers · doi:10.3390/cancers14143523 · Cited by 3
“Moreover, the fusion involving MAEA::CTBP1 (detected in one SR B-ALL case from our cohort), although with different breakpoints, has already been described in colon adenocarcinoma and acute myeloid leukemia [25].”
BackgroundDarabi, S., Zuazo, C. E., Braxton, D. R., Eisenberg, B. L., & Demeure, M. J. (2023) · Biologics · doi:10.3390/biologics3030011 · Cited by 3
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Recent advances in the investigation of fusion RNAs and their role in molecular pathology of cancer
Xu, S.-M., Cheng, Y., Fisher, H., & Janitz, M. (2024) · The International Journal of Biochemistry & Cell Biology · doi:10.1016/j.biocel.2024.106529 · Cited by 3
Discovering predisposing genes for hereditary breast cancer using deep learning
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“SCP2 was also involved in recurrent fusions with ECHDC2 and FAF1 in breast adenocarcinomas [44, 45].”
BackgroundZhao, Y. D., Du, R., Chen, M., & Chen, Z. (2025) · Translational Oncology · doi:10.1016/j.tranon.2025.102384 · Cited by 3
“For example, RET fusions are present in approximately 1 – 2 % of NSCLC cases and up to 10 – 20 % of papillary thyroid carcinomas [7,13,14].”
Risk Factors for Lung Cancer in Never Smokers: A Recent Review Including Genetics
Quinn, A. M., Newman, W. G., & Hasleton, P. S. (2015) · Current Respiratory Medicine Reviews · doi:10.2174/1573398x11666151028205957 · Cited by 3
Transcriptional configurations of myeloproliferative neoplasms
Schischlik, F. (2022) · International review of cytology · doi:10.1016/bs.ircmb.2021.07.003 · Cited by 2
Fusion Genes in Prostate Cancer: A Comparison in Men of African and European Descent
Morgan, R. A., Keeley, D., Hazard, E. S., Allott, E. H., Wolf, B. J., Savage, S. J., Halbert, C. H., Gattoni‐Celli, S., & Hardiman, G. (2022) · Biology · doi:10.3390/biology11050625 · Cited by 3
“This fusion has previously been detected in thyroid cancer [66].”
BackgroundThe Pan-TRK Antibody is a Sensitive and Specific Tool for the Detection of NTRK Fusion Genes
Bautista-Wong, C., Mojica-González, Z., Hop-García, K., & Quevedo, L. B. (2023) · Applied immunohistochemistry & molecular morphology · doi:10.1097/pai.0000000000001116 · Cited by 3
Genome-wide Detection of Chimeric Transcripts in Early-stage Non-small Cell Lung Cancer
Ilnytskyy, Y., Petersen, L. F., McIntyre, J. B., Konno, M., D’Silva, A., Dean, M. L., Elegbede, A. A., Golubov, A., Kovalchuk, O., Kovalchuk, I., et al. (2023) · Cancer Genomics & Proteomics · doi:10.21873/cgp.20394 · Cited by 3
Novel gene fusions in human oropharyngeal carcinoma
Masago, K., Kuroda, H., Sasaki, E., Fujita, Y., Fujita, S., Horio, Y., Endo, M., Ishihara, H., Hanai, N., & Matsushita, H. (2024) · Cancer Genetics · doi:10.1016/j.cancergen.2024.06.004 · Cited by 3
All-in-one bimodal DNA and RNA next-generation sequencing panel for integrative diagnosis of glioma
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RetractedA Comprehensive Method for Detecting Fusion Genes in Paediatric Brain Tumours
Kondo, A., Shimizu, Y., Adachi, S., Ogino, I., Suzuki, M., Akiyama, O., & Arai, H. (2018) · Cancer Genomics & Proteomics · doi:10.21873/cgp.20093 · Cited by 3
Interchromosomal Translocations as a Means to Map Chromosome Territories in Breast Cancer
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Escalante, D. A., Wang, H., & Fundakowski, C. (2016) · Cancer Biology & Therapy · doi:10.1080/15384047.2016.1219823 · Cited by 3
“Kinase fusions play a prominent role in thyroid neoplasms, as evidenced by identification of a high percentage of recurrent fusions involving the ALK, NRTK, ROS, BRAF, RET and FGFR gene families.(2,4) Although the kinase fusions reported in in thyroid malignancies are numerous, they operate via mechanisms with a commo…”
BackgroundResultInfluentialThe landscape of gene fusions in hepatocellular carcinomaPreprint
Zhu, C., Lv, Y., Wu, L., Guan, J., Bai, X., Lin, J., Liu, T., Zhang, H., Anqiang, W., Yuan, X., et al. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/055376 · Cited by 3
“Transcriptome analysis has been widely used to identify gene fusions in human cancers (Bao et al. 2014; Stransky et al. 2014; Yoshihara et al. 2015).”
BackgroundMethodInfluentialEvaluating the ‘ARID’ landscape of SWI/SNF complexes with relevance to cancer
Hore, P., Sarkar, S., & Bashyam, M. D. (2025) · Gene · doi:10.1016/j.gene.2025.149664 · Cited by 4
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ALK Rearrangement in Anaplastic Thyroid Carcinoma: A Discovery Towards a Personalized Approach?
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Establishment of Novel Prostate Cancer Risk Subtypes and A Twelve-Gene Prognostic Model
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“Gene fusions are clinically relevant because they provide important information on tumorigenesis that pave the way for the development of targeted therapies for patients with speci fi c fusions (39).”
BackgroundPediatric Mesenchymal Tumor With MN1::TAF3 Fusion
Sato, C., Sugiyama, M., Mori, T., Nishino, S., Tao, K., Ogawa, C., & Yoshida, A. (2024) · Genes Chromosomes and Cancer · doi:10.1002/gcc.70009 · Cited by 2
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“Although the majority of fusion events are considered to be passenger mutations, a sub-set is expected to play pivotal roles in tumorigenesis and progression [8].”
BreCAN-DB: a repository cum browser of personalized DNA breakpoint profiles of cancer genomes
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Biologic Basis of Personalized Therapy in Head and Neck Squamous Cell Carcinoma
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Genomic Analysis in the Practice of Surgical Neuropathology: The Emory Experience
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Pathology of Primary Brain Tumors—Gliomas
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“According to the authors’ knowledge, this variation has not been previously described in the literature, which hampers the interpretation of its significance [7,8].”
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HPV ‐Associated Adenosquamous Carcinoma of the Oropharynx With a PARD3B :: ERBB4 Fusion
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The Role of Machine Learning in Finding Chimeric RNAs
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PPP1R7 Is a Novel Translocation Partner of CBFB via t(2;16)(q37;q22) in Acute Myeloid Leukemia
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Metadata
- Authors
- Yoshihara, K., Wang, Q., Torres-Garcia, W., Zheng, S., Vegesna, R., Kim, H., & Verhaak, R. G. W.
- Affiliations
- The University of Texas MD Anderson Cancer Center (US)
- Corresponding author
- Verhaak, R G W
- Venue
- Oncogene
- Published
- 2014-12-15
- Volume
- 34
- Issue
- 37
- Pages
- 4845-4854
- ISSN
- 0950-9232 (ISSN-L)
- 1476-5594
- PMC
- PMC4468049
- OpenAlex
- W2042337609
- Cited by
- 450
- References
- 56
- Citations by year
- 2026: 8 · 2025: 26 · 2024: 38 · 2023: 23 · 2022: 41 · 2021: 59 · 2020: 37 · 2019: 56 · 2018: 43 · 2017: 54 · 2016: 48 · 2015: 16 · 2014: 1
- FWCI
- 12.71
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Oncogene (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- Mary K. Chapman Foundation
- California Department of Transportation
- National Cancer Institute (CA083639, CA143883, U24CA143883, P50CA083639, P30CA016672)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Keywords
- fusion transcripts, chromosomal rearrangements, kinase fusions, anaplastic lymphoma kinase, reactive oxygen species, RET, NTRK, fibroblast growth factor receptor, genomic instability, driver mutations, kinase inhibitors, glioma, bladder cancer, thyroid cancer, lung adenocarcinoma, lung squamous cell carcinoma, head and neck cancer, low-grade glioma, glioblastoma
- MeSH terms
- Cell Transformation, Neoplastic, DNA Mutational Analysis, Humans, Neoplasms, RNA, Messenger, RNA, Neoplasm, Oncogene Proteins, Fusion, Sequence Alignment, Genetic Heterogeneity, Computational Biology, Gene Expression Profiling, Chromatin Assembly and Disassembly, Molecular Targeted Therapy
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