Gene Fusions in Differential Diagnosis of Salivary Gland Neoplasms: A Systematic Review
Authors:
Inka Kovářová 1,2; Martina Bradová 1,2; Jan Laco 3,4; Bacem Othman 2,5; Elaheh Mosaieby 1; Alena Skálová 1,2
Authors‘ workplace:
Šiklův ústav patologie, Lékařská fakulta Univerzity Karlovy v Plzni, Plzeň
1; Bioptická laboratoř, s. r. o., Plzeň
2; Fingerlandův ústav patologie, Lékařská fakulta Univerzity Karlovy v Hradci Králové, Hradec Králové
3; Fingerlandův ústav patologie, Fakultní nemocnice Hradec Králové, Hradec Králové
4; Ústav anatomie, Lékařská fakulta Univerzity Karlovy v Plzni, Plzeň
5
Published in:
Čes.-slov. Patol., 62, 2026, No. 2, p. 106-113
Category:
Reviews Article
Overview
Salivary gland tumors represent a rare and morphologically heterogeneous group of neoplasms, which represents a significant diagnostic challenge for histopathologists. Diagnosis is based primarily on morphological evaluation, but immunohistochemical methods are often a necessary complementary tool. However, due to immunophenotype overlap between different tumor entities, even immunohistochemistry may not always allow an unambiguous diagnosis. In recent years, characteristic genomic alterations, particularly gene fusions, have been identified in a number of salivary gland tumors. These alterations are tightly tumor type specific, and their detection may be crucial in diagnostically difficult cases. In addition, selected genetic changes may have prognostic and/ or potential therapeutic significance in the era of personalized medicine. The aim of this review article is to summarize current knowledge in this area.
Keywords:
review – gene fusion – head and neck pathology – salivary gland neoplasm
Sources
1. WHO Classification of Tumours Editorial Board. Head and neck tumours. 5th ed. Lyon (FR): International Agency for Research on Cancer; 2024. (WHO classification of tumours; vol. 9). Available from: https://publications. iarc.who.int/629.
2. Skalova A, Stenman G, Simpson RHW, et al. The role of molecular testing in the differential diagnosis of salivary gland carcinomas. Am J Surg Pathol 2018; 42(2): e11-e27.
3. Stenman G. Fusion oncogenes in salivary gland tumors: molecular and clinical consequences. Head Neck Pathol 2013; 7(Suppl 1): S12-S19.
4. Skalova A, Hyrcza MD, Vanecek T, et al. Fusion-positive salivary gland carcinomas. Genes Chromosomes Cancer 2022; 61(5): 228-243.
5. Moutasim KA, Thomas GJ. Salivary gland tumours: update on molecular diagnostics. Diagn Histopathol 2021; 26(4): 159-164.
6. Skalova A, Bradova M, Michal M Jr, et al. Molecular pathology in diagnosis and prognostication of head and neck tumors. Virchows Arch 2024; 484(2): 215-231.
7. Skalova A, Vanecek T, Sima R, et al. Mammary analogue secretory carcinoma of salivary glands, containing the ETV6-NTRK3 fusion gene: a hitherto undescribed salivary gland tumor entity. Am J Surg Pathol 2010; 34 : 599-608.
8. Skalova A, Vanecek T, Martinek P, et al. Molecular profiling of mammary analog secretory carcinoma revealed a subset of tumors harboring a novel ETV6-RET translocation: report of 10 cases. Am J Surg Pathol 2018; 42(2): 234-246.
9. Fujii K, Murase T, Beppu S, et al. MYB, MYBL1, MYBL2 and NFIB gene alterations and MYC overexpression in salivary gland adenoid cystic carcinoma. Histopathology 2017; 71(5): 823-834.
10. Jee KJ, Persson M, Heikinheimo K, et al. Genomic profiles and CRTC1-MAML2 fusion distinguish different subtypes of mucoepidermoid carcinoma. Mod Pathol 2013; 26(2): 213-222.
11. Okumura Y, Miyabe S, Nakayama T, et al. Impact of CRTC1/3-MAML2 fusions on histological classification and prognosis of mucoepidermoid carcinoma. Histopathology 2011; 59(1): 90-97. 12. Antonescu CR, Katabi N, Zhang L, et al. EWSR1-ATF1 fusion is a novel and consistent finding in hyalinizing clear-cell carcinoma of salivary gland. Genes Chromosomes Cancer 2011; 50(7): 559-570.
13. Chapman E, Skalova A, Ptakova N, et al. Molecular profiling of hyalinizing clear cell carcinomas revealed a subset of tumors harboring a novel EWSR1-CREM fusion: report of 3 cases. Am J Surg Pathol 2018; 42 : 1182-1189.
14. Bishop JA, Weinreb I, Swanson D, et al. Microsecretory adenocarcinoma: a novel salivary gland tumor characterized by a recurrent MEF2C-SS18 fusion. Am J Surg Pathol 2019; 43(8): 1023-1032.
15. Weinreb I, Hahn E, Dickson BC, et al. Microcribriform adenocarcinoma of salivary glands: a unique tumor entity characterized by an SS18::ZBTB7A fusion. Am J Surg Pathol 2023; 47(2): 194-201. 16. Cocco E, Scaltriti M, Drilon A. NTRK fusion - -positive cancers and TRK inhibitor therapy. Nat Rev Clin Oncol 2018; 15(12): 731-747. 17. Lassen U. How I treat NTRK gene fusion-positive cancers. ESMO Open 2019; 4(Suppl 2): e000612.
18. Drilon A. TRK inhibitors in TRK fusion-positive cancers. Ann Oncol 2019; 30(Suppl 8): viii23-viii30.
19. Drilon A, Hu ZI, Lai GGY, et al. Targeting RET - -driven cancers: lessons from evolving preclinical and clinical landscapes. Nat Rev Clin Oncol 2018; 15(3): 151-167.
20. Desilets A, Repetto M, Yang SR, et al. RET-altered cancers: a tumor-agnostic review of biology, diagnosis and targeted therapy activity. Cancers (Basel) 2023; 15(16): 4146.
21. Rooper LM, Karantanos T, Ning Y, et al. Salivary secretory carcinoma with a novel ETV6-MET fusion: expanding the molecular spectrum of a recently described entity. Am J Surg Pathol 2018; 42(8): 1121-1126.
22. Guilmette J, Dias-Santagata D, Nosé V, et al. Novel gene fusions in secretory carcinoma of the salivary glands: enlarging the ETV6 family. Hum Pathol 2019; 83 : 50-58.
23. Skálová A, Banečkova M, Thompson LDR, et al. Expanding the molecular spectrum of secretory carcinoma of salivary glands with a novel VIM-RET fusion. Am J Surg Pathol 2020; 44(10): 1295-1307.
24. Sasaki E, Masago K, Fujita S, et al. Salivary secretory carcinoma harboring a novel ALK fusion: expanding the molecular characterization of carcinomas beyond the ETV6 gene. Am J Surg Pathol 2020; 44(7): 962-969.
25. Nakagawara A. Trk receptor tyrosine kinases: a bridge between cancer and neural development. Cancer Lett 2001; 169(2): 107 - 114.
26. Doebele RC, Drilon A, Paz-Ares L, et al. Entrectinib in patients with advanced or metastatic NTRK fusion-positive solid tumours: integrated analysis of three phase 1-2 trials. Lancet Oncol 2020; 21(2): 271-282.
27. Nordkvist A, Gustafsson H, Juberg-Ode M, et al. Recurrent rearrangements of 11q14-22 in mucoepidermoid carcinoma. Cancer Genet Cytogenet 1994; 74(2): 77-83.
28. Seethala RR, Dacic S, Cieply K, et al. A reappraisal of the MECT1/MAML2 translocation in salivary mucoepidermoid carcinomas. Am J Surg Pathol 2010; 34(8): 1106-1121.
29. Nakayama T, Miyabe S, Okabe M, et al. Clinicopathological significance of the CRTC3-MAML2 fusion transcript in mucoepidermoid carcinoma. Mod Pathol 2009; 22(12): 1575-1581.
30. Möller E, Stenman G, Mandahl N, et al. POU5F1, encoding a key regulator of stem cell pluripotency, is fused to EWSR1 in hidradenoma of the skin and mucoepidermoid carcinoma of the salivary glands. J Pathol 2008; 215(1): 78-86.
31. Seethala RR, Chiosea SI. MAML2 status in mucoepidermoid carcinoma can no longer be considered a prognostic marker. Am J Surg Pathol 2016; 40(8): 1151-1153.
32. Othman BK, Steiner P, Leivo I, et al. Rearrangement of KMT2A characterizes a subset of pediatric parotid mucoepidermoid carcinomas arising metachronous to acute lymphoblastic leukemia. Fetal Pediatr Pathol 2023; 42(5): 796-807.
33. Persson M, Andrén Y, Mark J, et al. Recurrent fusion of MYB and NFIB transcription factor genes in carcinomas of the breast and head and neck. Proc Natl Acad Sci U S A 2009; 106(44): 18740-18744.
34. Wei S, Pei J, Zhang PJL. Molecular pathology of adenoid cystic carcinoma. Histol Histopathol 2025; 40(10): 1519-1528.
35. Klein Nulent TJW, van Es RJJ, Breimer GE, et al. MYB immunohistochemistry as a predictor of MYB::NFIB fusion in the diagnosis of adenoid cystic carcinoma of the head and neck. Oral Surg Oral Med Oral Pathol Oral Radiol 2024; 138(6): 772-780.
36. Xu B, Drill E, Ho A, et al. Predictors of outcome in adenoid cystic carcinoma of salivary glands: a clinicopathologic study with correlation between MYB fusion and protein expression. Am J Surg Pathol 2017; 41(10): 1422-1432.
37. Skálová A, Bradová M, Agaimy A, et al. Molecular profiling of sinonasal adenoid cystic carcinoma: canonical and noncanonical gene fusions and mutation. Am J Surg Pathol 2025; 49(3): 227-242.
38. Chu YH, Xu B, Sukhadia P, et al. Targeted RNA sequencing of head and neck adenoid cystic carcinoma reveals SEC16A::NOTCH1 fusion and MET exon 14 skipping as potentially actionable alterations. Head Neck Pathol 2024; 18(1): 119.
39. Bubola J, MacMillan CM, Demicco EG, et al. Targeted RNA sequencing in the routine clinical detection of fusion genes in salivary gland tumors. Genes Chromosomes Cancer 2021; 60(10): 695-708.
40. Skálová A, Klubíčková N, Bradová M, et al. Discovery of novel TULP4/ACTN4/EWSR1/ ACTB::MYB and ESRRG::DNM3 fusions expands molecular landscape of adenoid cystic carcinoma beyond fusions between MYB/ MYBL1 and NFIB genes. Am J Surg Pathol 2024; 48(12): 1503-1511.
41. Hanna GJ, Stathis A, Lopez-Miranda E, et al. A phase I study of the pan-Notch inhibitor CB-103 for patients with advanced adenoid cystic carcinoma and other tumors. Cancer Res Commun 2023; 3(9): 1853-1861.
42. Weinreb I. Hyalinizing clear cell carcinoma of salivary gland: a review and update. Head Neck Pathol 2013; 7(Suppl 1): S20-S29.
43. Weinreb I, Bishop JA, Chiosea SI, et al. Recurrent RET gene rearrangements in intraductal carcinomas of salivary gland. Am J Surg Pathol 2018; 42(4): 442-452.
44. Bishop JA, Rooper LM, Sangoi AR, et al. The myoepithelial cells of salivary intercalated duct-type intraductal carcinoma are neoplastic: a study using combined whole-slide imaging, immunofluorescence, and RET fluorescence in situ hybridization. Am J Surg Pathol 2021; 45(4): 507-515.
45. Skálová A, Ptáková N, Santana T, et al. NCOA4-RET and TRIM27-RET are characteristic gene fusions in salivary intraductal carcinoma, including invasive and metastatic tumors: is intraductal correct? Am J Surg Pathol 2019; 43(10): 1303-1313.
46. Rooper LM, Thompson LDR, Gagan J, et al. Salivary intraductal carcinoma arising within intraparotid lymph node: a report of 4 cases with identification of a novel STRN-ALK fusion. Head Neck Pathol 2021; 15(1): 179-185.
47. Skálová A, Vanecek T, Uro-Coste E, et al. Molecular profiling of salivary gland intraductal carcinoma revealed a subset of tumors harboring NCOA4-RET and novel TRIM27-RET fusions: a report of 17 cases. Am J Surg Pathol 2018; 42(11): 1445-1455.
48. Nakaguro M, Urano M, Suzuki H, et al. Low-grade intraductal carcinoma of the salivary gland with prominent oncocytic change: a newly described variant. Histopathology 2018; 73(2): 314-320.
49. Bishop JA, Nakaguro M, Whaley RD, et al. Oncocytic intraductal carcinoma of salivary glands: a distinct variant with TRIM33-RET fusions and BRAF V600E mutations. Histopathology 2021; 79(3): 338-346.
50. Mauramo M, Tarkkanen J, Skalova A, et al. Oncocytic intraductal carcinoma of parotid gland with a novel AGK::BRAF gene fusion. Virchows Arch 2024; 485(5): 925-929.
51. Bishop JA, Weinreb I, Swanson D, et al. Microsecretory adenocarcinoma: a novel salivary gland tumor characterized by a recurrent MEF2C-SS18 fusion. Am J Surg Pathol 2019; 43(8): 1023-1032.
52. Bishop JA, Sajed DP, Weinreb I, et al. Microsecretory adenocarcinoma of salivary glands: an expanded series of 24 cases. Head Neck Pathol 2021; 15(4): 1192-1201.
53. Michal M, Skalova A, Simpson RH, et al. Cribriform adenocarcinoma of the tongue: a hitherto unrecognized type of adenocarcinoma characteristically occurring in the tongue. Histopathology 1999; 35(6): 495-501.
54. Skalova A, Sima R, Kaspirkova-Nemcova J, et al. Cribriform adenocarcinoma of minor salivary gland origin principally affecting the tongue: characterization of new entity. Am J Surg Pathol 2011; 35(8): 1168-1176.
55. Michal M, Kacerovska D, Kazakov DV. Cribriform adenocarcinoma of the tongue and minor salivary glands: a review. Head Neck Pathol 2013; 7(Suppl 1): S3-S11.
56. Weinreb I, Zhang L, Tirunagari LM, et al. Novel PRKD gene rearrangements and variant fusions in cribriform adenocarcinoma of salivary gland origin. Genes Chromosomes Cancer 2014; 53(10): 845-856.
57. Jurmeister P, Leitheiser M, Arnold A, et al. DNA methylation profiling of salivary gland tumors supports and expands conventional classification. Mod Pathol 2024; 37(12): 100625.
58. Sebastiao APM, Xu B, Lozada JR, et al. Histologic spectrum of polymorphous adenocarcinoma of the salivary gland harbor genetic alterations affecting PRKD genes. Mod Pathol 2020; 33(1): 65-73.
59. Stenman G, Fehr A, Skálová A, et al. Chromosome translocations, gene fusions, and their molecular consequences in pleomorphic salivary gland adenomas. Biomedicines 2022; 10(8): 1970.
60. Katabi N, Xu B, Jungbluth AA, et al. PLAG1 immunohistochemistry is a sensitive marker for pleomorphic adenoma: a comparative study with PLAG1 genetic abnormalities. Histopathology 2018; 72(2): 285-293.
61. Katabi N, Ghossein R, Ho A, et al. Consistent PLAG1 and HMGA2 abnormalities distinguish carcinoma ex-pleomorphic adenoma from its de novo counterparts. Hum Pathol 2015; 46(1): 26-33.
62. Haller F, Bieg M, Will R, et al. Enhancer hijacking activates oncogenic transcription factor NR4A3 in acinic cell carcinomas of the salivary glands. Nat Commun 2019; 10(1): 368.
63. Klubíčková N, Grossmann P, Šteiner P, et al. A minority of cases of acinic cell carcinoma of the salivary glands are driven by an NR4A2 rearrangement: the diagnostic utility of the assessment of NR4A2 and NR4A3 alterations in salivary gland tumors. Virchows Arch 2023; 482(2): 339-345.
64. Haller F, Skálová A, Ihrler S, et al. Nuclear NR4A3 immunostaining is a specific and sensitive novel marker for acinic cell carcinoma of the salivary glands. Am J Surg Pathol 2019; 43(9): 1264-1272.
65. Barasch N, Gong X, Kwei KA, et al. Recurrent rearrangements of the Myb/SANT-like DNA-binding domain containing 3 gene (MSANTD3) in salivary gland acinic cell carcinoma. PLoS One 2017; 12(2): e0171265.
66. Nakaguro M, Tada Y, Faquin WC, et al. Salivary duct carcinoma: updates in histology, cytology, molecular biology, and treatment. Cancer Cytopathol 2020; 128(10): 693-703.
67. Williams L, Thompson LD, Seethala RR, et al. Salivary duct carcinoma: the predominance of apocrine morphology, prevalence of histologic variants, and androgen receptor expression. Am J Surg Pathol 2015; 39(5): 705 - 713.
68. Nagao T, Gaffey TA, Visscher DW, et al. Invasive micropapillary salivary duct carcinoma: a distinct histologic variant with biologic significance. Am J Surg Pathol 2004; 28(3): 319-326.
69. Nagao T, Gaffey TA, Serizawa H, et al. Sarcomatoid variant of salivary duct carcinoma: clinicopathologic and immunohistochemical study of eight cases with review of the literature. Am J Clin Pathol 2004; 122(2): 222-231.
70. Di Palma S, Simpson RH, Marchiò C, et al. Salivary duct carcinomas can be classified into luminal androgen receptor-positive, HER2 and basal-like phenotypes. Histopathology 2012; 61(4): 629-643.
71. Zhu S, Schuerch C, Hunt J. Review and updates of immunohistochemistry in selected salivary gland and head and neck tumors. Arch Pathol Lab Med 2015; 139(1): 55-66. 72. Chiosea SI, Thompson LD, Weinreb I, et al. Subsets of salivary duct carcinoma defined by morphologic evidence of pleomorphic adenoma, PLAG1 or HMGA2 rearrangements, and common genetic alterations. Cancer 2016; 122(20): 3136-3144.
73. Dalin MG, Desrichard A, Katabi N, et al. Comprehensive molecular characterization of salivary duct carcinoma reveals actionable targets and similarity to apocrine breast cancer. Clin Cancer Res 2016; 22(18): 4623-4633.
74. Agaimy A, Baněčková M, Ihrler S, et al. ALK rearrangements characterize 2 distinct types of salivary gland carcinomas: clinicopathologic and molecular analysis of 4 cases and literature review. Am J Surg Pathol 2021; 45(9): 1166-1178.
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Czecho-Slovak Pathology
2026 Issue 2
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