Genomes and Genes
Summary: The GENETIC RECOMBINATION of the parts of two or more GENES, including an ONCOGENE as at least one of the fusion partners. Such gene fusions are often detected in neoplastic cells and are transcribed into ONCOGENE FUSION PROTEINS.
- Okumura Y, Miyabe S, Nakayama T, Fujiyoshi Y, Hattori H, Shimozato K, et al. Impact of CRTC1/3-MAML2 fusions on histological classification and prognosis of mucoepidermoid carcinoma. Histopathology. 2011;59:90-7 pubmed publisher..0032). For disease-free survival, 'molecular AFIP classification' was also selected as an independent prognostic factor (P = 0.0006). Molecular AFIP classification may be useful in predicting the prognosis of patients with MEC. ..
- Paulo P, Ribeiro F, Santos J, Mesquita D, Almeida M, Barros Silva J, et al. Molecular subtyping of primary prostate cancer reveals specific and shared target genes of different ETS rearrangements. Neoplasia. 2012;14:600-11 pubmed
- Fu J, Liang D, Shih L. Analysis of acute leukemias with MLL/ENL fusion transcripts: identification of two novel breakpoints in ENL. Am J Clin Pathol. 2007;127:24-30 pubmed
- Vernon S, Bejarano P. Low-grade fibromyxoid sarcoma: a brief review. Arch Pathol Lab Med. 2006;130:1358-60 pubmed..Because of similar clinical behavior and the common cytogenetic abnormality, some authors prefer to consider both lesions as a single entity within the spectrum of low-grade sarcomas. ..
- Ford A, Palmi C, Bueno C, Hong D, Cardus P, Knight D, et al. The TEL-AML1 leukemia fusion gene dysregulates the TGF-beta pathway in early B lineage progenitor cells. J Clin Invest. 2009;119:826-36 pubmed publisher..Collectively, these data suggest a plausible mechanism by which dysregulated immune responses to infection might promote the malignant evolution of TEL-AML1-expressing preleukemic clones. ..
- Perner S. [Dangerous liaisons in prostate cancer. Clinical and biological implications of recurrent gene fusions]. Pathologe. 2010;31 Suppl 2:121-5 pubmed publisher..This review describes the path from the identification of common ETS gene rearrangements in prostate cancer to possible applications in the treatment of patients, on to the potential scientific implications arising from their discovery. ..
- Wu C, Kannan K, Lin S, Yen L, Milosavljevic A. Identification of cancer fusion drivers using network fusion centrality. Bioinformatics. 2013;29:1174-81 pubmed publisher..To our best knowledge, this is the first network-based approach for identifying fusion drivers. Matlab code implementing the fusion centrality method is available upon request from the corresponding authors. ..
- Paulo P, Barros Silva J, Ribeiro F, Ramalho Carvalho J, Jeronimo C, Henrique R, et al. FLI1 is a novel ETS transcription factor involved in gene fusions in prostate cancer. Genes Chromosomes Cancer. 2012;51:240-9 pubmed publisher..015). We report that FLI1 is a novel ETS transcription factor involved in gene fusions in prostate cancer and that intratumor genetic heterogeneity of ETS rearrangements can occasionally be found in index primary tumors. ..
- Thway K, Rockcliffe S, Gonzalez D, Swansbury J, Min T, Thompson L, et al. Utility of sarcoma-specific fusion gene analysis in paraffin-embedded material for routine diagnosis at a specialist centre. J Clin Pathol. 2010;63:508-12 pubmed publisher..PCR is less sensitive than FISH, and the use of both techniques is optimal for maximising the detection rate of translocation-positive sarcomas. ..
- Gessi M, Lambert S, Lauriola L, Waha A, Collins V, Pietsch T. Absence of KIAA1549-BRAF fusion in rosette-forming glioneuronal tumors of the fourth ventricle (RGNT). J Neurooncol. 2012;110:21-5 pubmed publisher..Our data support the hypothesis that RGNT may represent a distinct entity among the glioneuronal tumors of the central nervous system, with molecular features different from pilocytic astrocytomas. ..
- Mani R, Tomlins S, Callahan K, Ghosh A, Nyati M, Varambally S, et al. Induced chromosomal proximity and gene fusions in prostate cancer. Science. 2009;326:1230 pubmed publisher..These results may help explain why TMPRSS2-ERG fusions are restricted to the prostate, which is dependent on androgen signaling. ..
- Li Y, Heavican T, Vellichirammal N, Iqbal J, Guda C. ChimeRScope: a novel alignment-free algorithm for fusion transcript prediction using paired-end RNA-Seq data. Nucleic Acids Res. 2017;45:e120 pubmed publisher..ChimeRScope is accessible as a standalone software at (https://github.com/ChimeRScope/ChimeRScope/wiki) or via the Galaxy web-interface at (https://galaxy.unmc.edu/). ..
- Desmeules P, Joubert P, Zhang L, Al Ahmadie H, Fletcher C, Vakiani E, et al. A Subset of Malignant Mesotheliomas in Young Adults Are Associated With Recurrent EWSR1/FUS-ATF1 Fusions. Am J Surg Pathol. 2017;41:980-988 pubmed publisher..Other features of this unique MM subset include young age at presentation, lack of asbestos exposure and retained BAP1 expression. ..
- Esteyries S, Perot C, Adelaide J, Imbert M, Lagarde A, Pautas C, et al. NCOA3, a new fusion partner for MOZ/MYST3 in M5 acute myeloid leukemia. Leukemia. 2008;22:663-5 pubmed
- Patnaik M, Gangat N, Knudson R, Keefe J, Hanson C, Pardanani A, et al. Chromosome 8p11.2 translocations: prevalence, FISH analysis for FGFR1 and MYST3, and clinicopathologic correlates in a consecutive cohort of 13 cases from a single institution. Am J Hematol. 2010;85:238-42 pubmed publisher..We conclude that neither the SCLL phenotype nor blood eosinophilia is a consistent feature of FGFR1-associated 8p11.2 translocations; conversely, FISH might not always reveal FGFR1 involvement in typical SCLL. ..
- Parker B, Engels M, Annala M, Zhang W. Emergence of FGFR family gene fusions as therapeutic targets in a wide spectrum of solid tumours. J Pathol. 2014;232:4-15 pubmed..Understanding the diverse mechanisms of FGFR fusion formation and their oncogenic potential will shed light on the impact of FGFR-derived therapy in the future. ..
- Nibu K, Otsuki N, Nakao K, Sugasawa M, Rothstein J. RET/PTC fusion gene rearrangements in Japanese thyroid carcinomas. Eur Arch Otorhinolaryngol. 2005;262:368-73 pubmed..RET rearrangements are restricted to a well-differentiated papillary carcinoma, suggesting that RET/PTC positive papillary carcinomas do not progress to undifferentiated carcinoma. ..
- Brassesco M, Valera E, Bonilha T, Scrideli C, Carvalho De Oliveira J, Pezuk J, et al. Secondary PSF/TFE3-associated renal cell carcinoma in a child treated for genitourinary rhabdomyosarcoma. Cancer Genet. 2011;204:108-10 pubmed publisher..The presence of the PSF-TFE3 fusion has only been described in a very limited number of cases. Our report expands the spectrum of tumors in which RCC can arise in the pediatric age group after chemotherapy. ..
- Luo D, Liu Y, Zhuang H, Li L, Xu F, Zhang F, et al. [Immunophenotypes and prognosis of diffuse large B-cell lymphoma: a study of 500 cases]. Zhonghua Bing Li Xue Za Zhi. 2011;40:235-9 pubmed..EBV-positive DLBCL of the elderly and DLBCL-NOS also do not have significant difference in overall survival. Fluorescence in situ hybridization technique is helpful in identification of DLBCL with rare phenotypes. ..
- Peterlongo P, Chikhi R. Mapsembler, targeted and micro assembly of large NGS datasets on a desktop computer. BMC Bioinformatics. 2012;13:48 pubmed publisher..As indexing is localized, the memory footprint of Mapsembler is negligible. Mapsembler is released under the CeCILL license and can be freely downloaded from http://alcovna.genouest.org/mapsembler/. ..
- Avirneni Vadlamudi U, GALINDO K, Endicott T, Paulson V, Cameron S, Galindo R. Drosophila and mammalian models uncover a role for the myoblast fusion gene TANC1 in rhabdomyosarcoma. J Clin Invest. 2012;122:403-7 pubmed publisher..Taken together, these findings identify misregulated myoblast fusion caused by ectopic TANC1 expression as a RMS neoplasia mechanism and suggest fusion molecules as candidates for targeted RMS therapy...
- Pang L, Li F, Chang B, Hu W, Lu T, Li X, et al. [Detection of ASPL-TFE3 fusion gene by reverse transcriptase polymerase chain reaction in paraffin-embedded tumor tissues of alveolar soft part sarcoma]. Zhonghua Bing Li Xue Za Zhi. 2004;33:508-12 pubmed..To investigate the significance of detecting chimeric mRNA resulting from t(X;17)(p11.2;q25) in paraffin-embedded tumor tissues of alveolar soft part sarcoma (ASPS)...
- Bridge J, Liu X, Sumegi J, Nelson M, Reyes C, Bruch L, et al. Identification of a novel, recurrent SLC44A1-PRKCA fusion in papillary glioneuronal tumor. Brain Pathol. 2013;23:121-8 pubmed publisher..The FISH and RT-PCR assays developed in this study can serve as valuable diagnostic adjuncts for this rare disease entity. ..
- Bousquet M, Brousset P. Myeloproliferative disorders carrying the t(8;9) (PCM1-JAK2) translocation. Hum Pathol. 2006;37:500; author reply 500-2 pubmed
- Singh D, Chan J, Zoppoli P, Niola F, Sullivan R, Castaño A, et al. Transforming fusions of FGFR and TACC genes in human glioblastoma. Science. 2012;337:1231-5 pubmed publisher..FGFR-TACC fusions could potentially identify a subset of GBM patients who would benefit from targeted FGFR kinase inhibition...
- Weissferdt A, Neuling K, English M, Arul S, McMullan D, Ely A, et al. Peripheral primitive neuroectodermal tumor with postchemotherapy neuroblastoma-like differentiation. Pediatr Dev Pathol. 2006;9:229-33 pubmed
- Jółkowska J, Derwich K, Dawidowska M. Methods of minimal residual disease (MRD) detection in childhood haematological malignancies. J Appl Genet. 2007;48:77-83 pubmed..Implementation of standardized approaches for MRD assessment into routine molecular diagnostics available in all oncohaematological centres should be regarded nowadays a crucial point in further MRD study development. ..
- O Neill I. New insights into the nature of Warthin's tumour. J Oral Pathol Med. 2009;38:145-9 pubmed publisher..The underlying molecular basis and the pivotal studies defining such events are discussed. ..
- Rizkalla H, Wildgrove H, Quinn F, Capra M, O Sullivan M. Congenital fibrosarcoma of the ileum: case report with molecular confirmation and literature review. Fetal Pediatr Pathol. 2011;30:156-60 pubmed publisher..The associated hallmark chromosomal translocation t(12;15)(q13;q25) was demonstrated by reverse transcriptase polymerase chain reaction...
- Bunting S, Nussenzweig A. End-joining, translocations and cancer. Nat Rev Cancer. 2013;13:443-54 pubmed publisher..The factors and pathways that promote translocations are becoming clearer, with non-homologous end-joining implicated as a key source of genomic rearrangements. ..
- Chang T, Carter R, Li Y, Li Y, Wang H, Edmonson M, et al. The neoepitope landscape in pediatric cancers. Genome Med. 2017;9:78 pubmed publisher..The source code of the workflow is available at GitHub ( https://github.com/zhanglabstjude/neoepitope ). ..
- Freeman S, Jovanovic J, Grimwade D. Development of minimal residual disease-directed therapy in acute myeloid leukemia. Semin Oncol. 2008;35:388-400 pubmed publisher..We consider the challenges involved in extending this concept, to develop a more tailored personalized medicine approach to improve the management and outcome of other forms of AML. ..
- Tomlins S, Bjartell A, Chinnaiyan A, Jenster G, Nam R, Rubin M, et al. ETS gene fusions in prostate cancer: from discovery to daily clinical practice. Eur Urol. 2009;56:275-86 pubmed publisher..Multiple promising strategies have been identified to potentially target ETS fusions. Together, these results suggest that ETS fusions will affect multiple aspects of prostate cancer diagnosis and management. ..
- Fiore A, Fuziwara C, Kimura E. High iodine concentration attenuates RET/PTC3 oncogene activation in thyroid follicular cells. Thyroid. 2009;19:1249-56 pubmed publisher..These findings contribute to a better understanding of the effect of iodine on thyroid follicular cells, particularly how it may play a protective role during RET/PTC3 oncogene activation. ..
- Jin Y, Möller E, Nord K, Mandahl N, Von Steyern F, Domanski H, et al. Fusion of the AHRR and NCOA2 genes through a recurrent translocation t(5;8)(p15;q13) in soft tissue angiofibroma results in upregulation of aryl hydrocarbon receptor target genes. Genes Chromosomes Cancer. 2012;51:510-20 pubmed publisher..Apart from providing a diagnostic marker for soft tissue angiofibroma, the results also suggest that this tumor constitutes an interesting model for evaluating the cellular effects of AHR signaling...
- Wang V, Laborde R, Asmann Y, Li Y, Ma J, Eckloff B, et al. Search for chromosome rearrangements: new approaches toward discovery of novel translocations in head and neck squamous cell carcinoma. Head Neck. 2013;35:831-5 pubmed publisher..However, these translocations were found only in the single tumor. We hope that this integrative methodology will elucidate key aspects of tumor biology as well as generate novel targets for cancer diagnoses and therapies. ..
- Guo C, Wang Y, Xiao L, Troncoso P, Czerniak B. The relationship of TMPRSS2-ERG gene fusion between primary and metastatic prostate cancers. Hum Pathol. 2012;43:644-9 pubmed publisher..The concordance of the ERG gene rearrangement status between the index primary tumor focus and metastasis suggests that metastasis most likely arises from the index tumor focus in multifocal prostate cancer. ..
- Dekking E, van der Velden V, Bottcher S, Bruggemann M, Sonneveld E, Koning Goedheer A, et al. Detection of fusion genes at the protein level in leukemia patients via the flow cytometric immunobead assay. Best Pract Res Clin Haematol. 2010;23:333-45 pubmed publisher..The immunobead assay can be run in parallel to routine immunophenotyping and is particularly attractive for clinical settings without direct access to molecular diagnostics. ..
- Shah A, Jeffus S, Stelow E. Squamous cell carcinoma variants of the upper aerodigestive tract: a comprehensive review with a focus on genetic alterations. Arch Pathol Lab Med. 2014;138:731-44 pubmed publisher..Further insight into the molecular alterations underlying those variants may lead to alterations in existing treatment approaches and to evolution of novel treatment modalities. ..
- Pérez González Y, García Esparza E, Conde E, Azorin D. Epiphyseal ewing sarcoma: first reported case with molecular confirmation. Int J Surg Pathol. 2013;21:173-6 pubmed publisher..This is the third case report about a primary epiphyseal Ewing sarcoma and the fist one with molecular confirmation. ..
- Walf Vorderwülbecke V, de Boer J, Horton S, van Amerongen R, Proost N, Berns A, et al. Frat2 mediates the oncogenic activation of Rac by MLL fusions. Blood. 2012;120:4819-28 pubmed publisher..This suggests a rationale for the paradoxical requirement of canonical Wnt signaling and glycogen synthase kinase 3 activity for MLL fusion oncogenicity and identifies novel therapeutic targets for this disease. ..
- Qiao J, Patel K, Lopez Terrada D, Fang H. Atrophic dermatofibrosarcoma protuberans: report of a case demonstrated by detecting COL1A1-PDGFB rearrangement. Diagn Pathol. 2012;7:166 pubmed publisher..This appears to be the first report of a fusion between COL1A1 exon 31 to exon 2 of PDGFB in atrophic dermatofibrosarcoma protuberans...
- Zhang Y, Zhang W, Wang Q, Ding S, Lv R, Meng L. [Construction of recombinant shuttle plasmid pIMP1-eHER2/neu and screening and identification of its stable Clostridium sporogenes transformants]. Xi Bao Yu Fen Zi Mian Yi Xue Za Zhi. 2011;27:1184-7 pubmed..Stable C.sporogenes transformants with the recombinant plasmid pIMP1-eHER2/neu are successfully acquired, which laid a foundation for further anti-tumor study. ..
- Yokoyama Y, Shimizu A, Okada E, Ishikawa O, Motegi S. A rapid and efficient newly established method to detect COL1A1-PDGFB gene fusion in dermatofibrosarcoma protuberans. Biochem Biophys Res Commun. 2012;425:353-6 pubmed publisher..Importantly, we detected a novel COL1A1 breakpoint in exon 5. The newly developed method is valuable to rapidly identify COL1A1-PDGFB fusion transcripts in DFSP. ..
- Tomić T, Olausson J, Wilzén A, Sabel M, Truvé K, Sjögren H, et al. A new GTF2I-BRAF fusion mediating MAPK pathway activation in pilocytic astrocytoma. PLoS ONE. 2017;12:e0175638 pubmed publisher..Moreover, the consistency and growing list of BRAF/RAF gene fusions suggests these rearrangements to be informative tumor markers in molecular diagnostics, which could guide future treatment strategies. ..
- Moses W, Weng J, Khanafshar E, Duh Q, Clark O, Kebebew E. Multiple genetic alterations in papillary thyroid cancer are associated with younger age at presentation. J Surg Res. 2010;160:179-83 pubmed publisher..Our findings suggest that multiple genetic alterations in thyroid cancer may be associated with earlier disease initiation and or progression. ..
- Brown L, Hanna D, Khaw S, Ekert P. Dysregulation of BCL-2 family proteins by leukemia fusion genes. J Biol Chem. 2017;292:14325-14333 pubmed publisher..We examine how these fusion genes dysregulate the BCL-2 family of proteins, preventing activation of the apoptotic effectors, BAX and BAK, and promoting cell survival. ..
- Smit F, Salagierski M, Jannink S, Schalken J. High-resolution ERG-expression profiling on GeneChip exon 1.0 ST arrays in primary and castration-resistant prostate cancer. BJU Int. 2013;111:836-42 pubmed publisher..The variation of gene fusion expression levels, particularly in CPRC, needs to be taken into account when using quantitative molecular diagnosis of prostate cancer. ..
- Italiano A, Sung Y, Zhang L, Singer S, Maki R, Coindre J, et al. High prevalence of CIC fusion with double-homeobox (DUX4) transcription factors in EWSR1-negative undifferentiated small blue round cell sarcomas. Genes Chromosomes Cancer. 2012;51:207-18 pubmed publisher..These results suggest the possibility of a newly defined subgroup of primitive round cell sarcomas characterized by CIC rearrangements, distinct from Ewing sarcoma family of tumors...