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Fibronectin 1 (FN1)-rearranged Mesenchymal Neoplasms: An Updated Review

JUN NISHIO, YOSHIRO CHIJIIWA, YUKI SHINOHARA, MIKIKO AOKI and KAORI KOGA
Cancer Genomics & Proteomics March 2026, 23 (2) 156-168; DOI: https://doi.org/10.21873/cgp.20569

Abstract

Fibronectin 1 (FN1), located on chromosome 2q35, encodes fibronectin, a high molecular weight glycoprotein of the extracellular matrix. Several histologically overlapping chondroid matrix-producing tumors are known to harbor FN1 rearrangements, including soft tissue chondroma, synovial chondromatosis, calcifying aponeurotic fibroma, calcified chondroid mesenchymal neoplasm and phosphaturic mesenchymal tumor. Over the past 10 years, fusions involving the FN1 gene have also been identified in other mesenchymal neoplasms such as lipofibromatosis and inflammatory myofibroblastic tumor. The current World Health Organization Classification of Soft Tissue and Bone Tumors suggests that FN1-rearranged lesions are typically benign or intermediate. This review provides an updated overview of the clinical, histological and molecular genetic features of FN1-rearranged mesenchymal neoplasms and discusses their relationships with one another.

Keywords:

Introduction

Fibronectin 1 (FN1), located on chromosome 2q35, is a protein coding gene and encodes fibronectin that is involved in a wide range of physiological processes, including cell adhesion and migration (1, 2). FN1 rearrangements have been implicated in the pathogenesis of a particular group of soft-tissue and bone tumors. This group of so called “FN1-rearranged mesenchymal neoplasms” has been increasing in recent years, mainly consisting of chondroid matrix-producing tumors such as soft tissue chondroma (STC) (3), synovial chondromatosis (SC) (3), calcifying aponeurotic fibroma (CAF) (4), calcified chondroid mesenchymal neoplasm (CCMN) (5) and phosphaturic mesenchymal tumor (PMT) (6). Histologically, these tumors generally exhibit a lobular or nodular growth pattern within a chondroid matrix with calcifications and often contain osteoclast-like giant cells. Most of these tumors occur in the distal extremities and behave in a benign fashion, generally amenable to surgical excision. Malignant transformation is extremely rare, except SC. More recently, various fusion partners for FN1 have been discovered in chondroid matrix-producing tumors (3-6). It has been recognized that a subset of these lesions harbor FN1-receptor tyrosine kinase (RTK) gene fusions (3, 5). Fusions involving the FN1 gene have also been described in other mesenchymal neoplasms such as lipofibromatosis (LPF) (7) and inflammatory myofibroblastic tumor (IMT) (8).

In this review, we present an updated overview of the clinical, histological and molecular genetic features of FN1-rearranged mesenchymal neoplasms, with an emphasis on differential diagnosis. The corresponding clinicopathological and molecular characteristics of these entities are summarized in Table I.

View this table:
Table I.

Clinicopathological and molecular characteristics of FN1-rearranged mesenchymal neoplasms.

Chondroid Matrix-producing Tumors

Chondroid matrix-producing tumors harboring FN1 rearrangements include STC, SC, CAF, CCMN and PMT. The diagnosis of these tumors is often challenging due to their rarity and histological overlap. To date, FN1-rearranged chondroid matrix-producing tumors have been reported to contain a fusion consisting of FN1 on the 5′ side and a protein kinase on the 3′ side of the fusion transcript.

STC, also known as chondroma of soft parts or extraskeletal chondroma, is a benign cartilaginous tumor that most commonly occurs in the hands and feet of middle-aged adults, with a slight male predominance (9). It typically presents as a small (usually <2 cm), solitary, slow-growing, painless mass, which may show radiographic evidence of calcification. Surgical excision is the treatment of choice for STC. Local recurrence occurs in 15-20% of cases (9), but malignant transformation has not been reported in the literature. Histologically, STC is composed of lobules of mature hyaline cartilage delineated by fibrous septa. The chondrocytes are arranged in clusters and cytologically bland (9). Coarse calcification may be observed. Chondroblastoma-like subtype is hypercellular and contains enlarged chondrocytes within a chondroid matrix and variable numbers of osteoclast-like giant cells (10), recently reclassified as CCMN (5). Immunohistochemically, the chondrocytes express S100, epidermal growth factor (EGF) and ETS transcription factor ERG (ERG) (4, 11). Cytogenetic studies have demonstrated clonal chromosomal abnormalities, including 12q13-15 rearrangements and trisomy 5 (12-17). In addition, one case exhibited a t(3;12)(q27;q15) translocation resulting in a high mobility group AT-hook 2 (HMGA2)-LIM domain containing preferred translocation partner in lipoma (LPP) gene fusion (17). More recently, FN1 alterations were detected by fluorescence in situ hybridization (FISH) in 50% of cases (3). Interestingly, all cases harboring FN1 rearrangements showed the presence of grungy calcification. Fusions of FN1 to fibroblast growth factor receptor 1 (FGFR1) or FGFR2 have also been identified in a subset of cases (3).

SC is a locally aggressive cartilaginous neoplasm that most commonly involve the large joints, especially the knee joint (approximately two-thirds of cases). It can be entirely extra-articular (also referred to as tenosynovial chondromatosis) (18). SC typically occurs in the third to fifth decades of life, with a male predominance (19). Common presenting symptoms include pain, swelling, reduced range of motion or joint locking, although patients can be asymptomatic. Arthroscopic or open removal of loose bodies with synovectomy is ideal for symptomatic patients (20); however, this may not be technically possible. Local recurrence occurs in 15-20% of cases (19), with higher rates in the tenosynovial cases (18). Malignant transformation to chondrosarcoma occurs in 1-10% of cases (21), usually in longstanding cases with multiple local recurrences. Histologically, SC is composed of nodules of hyaline cartilage lined by synovial membranes consisting of a layer of flattened cells (Figure 1A). The chondrocytes show characteristic clustering (Figure 1B). Double-nucleated cells are commonly found. Calcification or endochondral ossification may be seen in longstanding cases (20). Immunohistochemistry is not essential for diagnosis, but the chondrocytes express S100. Cytogenetic studies have revealed clonal chromosomal aberrations, including chromosome 6 anomalies, rearrangements of 1p22 and 1p13 and extra copies of chromosome 5 (22-24). Recently, FN1 and/or activin A receptor type 2A (ACVR2A) rearrangements were detected by FISH in 57-67% of cases (3, 25). Agaram et al. (25) confirmed the presence of FN1-ACVR2A fusion in 56% of cases. Moreover, a novel FN1-nuclear factor of activated T cells 2 (NFATC2) fusion was noted in one case (25). Mutations of isocitrate dehydrogenase [NADP(+)] 1 (IDH1) and isocitrate dehydrogenase [NADP(+)] 2 (IDH2) are absent (26).

Figure 1.
Figure 1.

Histological features of synovial chondromatosis. (A) Low-power appearance showing a nodule of hyaline cartilage lined by synovial membranes (hematoxylin and eosin staining, original magnification ×20). (B) The chondrocytes are arranged in clusters separated by a matrix of hyaline cartilage (hematoxylin and eosin staining, original magnification ×100).

CAF is a benign but locally aggressive soft-tissue tumor that most commonly occurs in the hands and feet of children and adolescents, with a male predominance (27). It typically presents as a slow-growing, painless, ill-circumscribed subcutaneous mass and is usually less than 3 cm in diameter (28). Surgical excision is the mainstay of treatment for CAF. Local recurrence occurs in up to 53% of cases (29, 30). Malignant transformation is extremely rare, and only one case has been reported in the literature (31). Histologically, CAF shows two components, a fibromatosis-like component and a nodular calcified component (27). The fibromatosis-like areas are moderately cellular and consist of uniform bland spindle cells. The nodular calcified areas are less cellular and contain epithelioid fibroblasts and occasional osteoclast-type giant cells. Immunohistochemically, the tumor cells are variably positive for S100, smooth muscle actin (SMA), muscle-specific actin (MSA) and CD99 (30). In the pericalcified areas, expression of EGF and ERG was detected in 89% and 100% of cases, respectively (4, 32). Recently, a recurrent FN1-EGF gene fusion, resulting from a presumed ins(2;4)(q35;q25), has been identified (4).

CCMN is a newly recognized entity that primarily occurs in the distal extremities and temporomandibular joint (TMJ) of middle-aged adults, with a slight female predominance (5, 33). It encompasses chondroblastoma-like STC, chondroid tenosynovial giant cell tumor (TSGCT) and tophaceous pseudogout (34). CCMN typically presents as a small, slow-growing, painless mass. Surgical excision is the treatment of choice for CCMN. Although extremely rare, local recurrence has been described in two cases (35, 36). Malignant transformation has not been reported in the literature. Histologically, CCMN exhibits multinodular architecture, chondroid to cartilaginous matrix and a proliferation of polygonal to stellate cells with abundant eosinophilic cytoplasm. The matrix can show varying types of calcifications from coarse or grungy to lacey (5). The immunophenotype is essentially non-specific, although the tumor cells may be variably positive for S100 in the chondroid areas (35). At the molecular genetic level, FN1 fusion is the most common alteration, involving various partners such as FGFR1, FGFR2, FGFR3, MER proto-oncogene, tyrosine kinase (MERTK), neurotrophic receptor tyrosine kinase 1 (NTRK1), TEK receptor tyrosine kinase (TEK), proteoglycan 4 (PRG4), bone morphogenetic protein receptor type 2 (BMPR2), ArfGAP with FG repeats 1 (AGFG1) and metastasis associated lung adenocarcinoma transcript 1 (MALAT1) (5, 33, 35, 37-43). These molecular studies indicate that the most frequent fusion partner of FN1 is FGFR2 in CCMN. It is of interest that all cases harboring FN1-TEK fusions showed chondroid TSGCT-like features and were located in the TMJ (37). A novel platelet derived growth factor receptor alpha (PDGFRA)-ubiquitin specific peptidase 8 (USP8) fusion, resulting from a t(4;15) (q12;q21) translocation, has also been identified in 11 cases (36, 37, 39, 44). Benard et al. (37) reported that a subset of cases with PDGFRA-USP8 fusions showed a predilection for larger joints and displayed multiple foci of bone formation. Moreover, fusions of FGFR1-PLAG1 zinc finger (PLAG1), collagen type I alpha 2 chain (COL1A2)-microRNA 29b-1 (MIR29B1), PDGFRA-USP35 and TIMP metallopeptidase inhibitor 3 (TIMP3)-zinc finger CCHC-type containing 7 (ZCCHC7) have been demonstrated each in one case (5, 37, 40).

PMT is an exceedingly rare soft-tissue or bone neoplasm that mainly affects middle-aged adults with no sexual predominance and typically causes tumor-induced osteomalacia (TIO) (45). Most PMT-associated TIOs are mediated through overproduction of FGF23. In the soft tissues, PMT most often involves the extremities and acral sites, whereas bone tumors commonly occur in the appendicular skeleton and cranial bones (46). Most PMTs present as small, inapparent lesions (45). Clinical symptoms are non-specific and include muscle pain, bone pain, pathological fractures and progressive weakness mostly related to TIO and chronic hypophosphatemia. The great majority of PMTs are benign, with complete surgical excision resulting in dramatic improvement of phosphate wasting and osteomalacia (45). Local recurrence occurs in 14.2% of cases (47). Although a unique case of PMT with de novo liver metastasis has been reported in the literature (48), malignant onset or transformation is quite rare. There are currently no definite clinical prognostic factors in PMT. Histologically, PMT is composed of bland, spindle to stellae cells with a well-developed capillary network (Figure 2A). In addition, mature adipose tissue and osteoclast-like giant cells may be present. The matrix of PMT typically exhibits grungy or flocculent calcification (45) (Figure 2B). A small number of histologically malignant PMTs have been described in both soft-tissue and bone (46); these lesions show high nuclear grade, high cellularity, increased mitotic activity and necrosis (49). Histologically malignant cases can behave aggressively (49), and long-term follow-up is necessary to monitor for any signs of local recurrence or metastasis. By immunohistochemistry, most PMTs express CD56 (Figure 2C), ERG, special AT-rich sequence-binding protein 2 (SATB2), somatostatin receptor 2A (SSTR2A) (Figure 2D) and FGFR1 (50, 51). Expression of FGF23 protein has been shown in some PMTs (49). More recently, frequent expression of CD99, neuron-specific enolase (NSE), Bcl-2 and D2-40 has been demonstrated in PMT (52). Cytogenetic abnormalities have been described in only two cases, with no shared aberration (53). At the molecular level, roughly half of PMTs show FN1-FGFR1 or, rarely, FN1-FGF1 fusions (54, 55) (Figure 3). Moreover, fusions of FN1-FGFR2, FN1-zinc activated ion channel (ZACN), FGFR1-USP33, FGFR1-talin 1 (TLN1), spectrin beta, non-erythrocytic 1 (SPTBN1)-tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein theta (YWHAQ), PDGFRA-USP35, general transcription factor IIi (GTF21)-Ral GEF with PH domain and SH3 binding motif 1 (RALGPS1), latent transforming growth factor beta binding protein 1 (LTBP1)-von Willebrand factor A domain containing 8 (VWA8), KIAA1549-B-Raf proto-oncogene, serine/threonine kinase (BRAF) and NIPBL cohesin loading factor (NIPBL)-BEN domain containing 2 (BEND2) have been identified in FN1-FGFR1/FGF1 fusion-negative cases (55-57). It remains unknown whether and how these rare fusions act as tumorigenic drivers. On the other hand, fusion-negative PMTs frequently show overexpression of klotho (KL) (57, 58). These fusion-negative cases with high KL expression may demonstrate distinctive clinicopathological features such as a predilection for skeletal or sinonasal locations and histological resemblance to cellular solitary fibrous tumor (57).

Figure 2.
Figure 2.

Histological and immunohistochemical features of phosphaturic mesenchymal tumor (PMT). (A) PMT consists of an admixture of bland, spindled to stellae cells and scattered osteoclast-like giant cells (hematoxylin and eosin staining, original magnification ×100). (B) The matrix of PMT shows grungy calcification (hematoxylin and eosin staining, original magnification ×20). Immunohistochemically, the neoplastic cells are positive for CD56 (C) and somatostatin receptor 2A (D) (original magnification ×100).

Figure 3.
Figure 3.

Interphase fluorescence in situ hybridization analysis of phosphaturic mesenchymal tumor with fibronectin 1 (FN1) split dual color probe shows one normal fusion signal (the red and green signals remain juxtaposed to each other) and one isolated green signal (a loss of the red signal), indicating disruption of FN1.

Lipofibromatosis (LPF)

LPF is a rare locally aggressive soft-tissue tumor that most commonly occurs in the hands and feet of infants and young children, with a male predominance (59). It typically presents as a slow-growing, painless, poorly demarcated subcutaneous mass. Skeletal muscle involvement can be seen (60). Surgical excision is the treatment of choice for LPF. Local recurrence occurs in 33-72% of cases (61, 62), but malignant transformation or distant metastasis has not been reported in the literature. Histologically, LPF is composed of a mixture of mature adipose tissue and bland spindle cells (Figure 4). The interface with adipose tissue exhibits characteristic univacuolated cells (60). Immunohistochemically, the spindle cells are positive for CD34 and CD99. Immunoreactivity for SMA is variable (60). Cytogenetic abnormalities have been described in only one case, displaying a three-way translocation t(4;9;6)(q21;q22;q2?4) (63). Recently, an FN1-EGF gene fusion has been detected in four cases (7). Moreover, fusions of FN1-transforming growth factor alpha (TGFA), early growth response 1 (EGR1)-glutamate ionotropic receptor AMPA type subunit 1 (GRIA1), translocated promoter region, nuclear basket protein (TPR)-ROS proto-oncogene 1, receptor tyrosine kinase (ROS1), secreted protein acidic and cysteine rich (SPARC)-platelet derived growth factor receptor beta (PDGFRB), epidermal growth factor receptor (EGFR)-BRAF, vinculin (VCL)-ret proto-oncogene (RET) and heparin binding EGF like growth factor (HBEGF)-RNA binding motif protein 27 (RBM27) have been demonstrated each in one case (7).

Figure 4.
Figure 4.

Histological features of lipofibromatosis consisting of a mixture of mature adipose tissue and bland spindle cells (hematoxylin and eosin staining, original magnification ×200).

Inflammatory Myofibroblastic Tumor (IMT)

IMT is an intermediate (rarely metastasizing) soft-tissue tumor that most commonly occurs in the children and young adults of abdominal cavity, with a slight female predominance (64, 65). The presenting symptoms are closely related to the site of origin. About 20-30% of patients with IMT present with fever, malaise, weight loss and abnormal laboratory findings such as microcytic hypochromic anemia, thrombocytosis, polyclonal hypergammaglobulinemia and elevated erythrocyte sedimentation rate and C-reactive protein levels (66). Surgical excision with negative margins remains the mainstay of treatment for patients with localized IMT. Local recurrence occurs in about 25% of extrapulmonary IMTs (64). Although rare, malignant transformation can occur (67-70). Distant metastasis is rare (<5%) and most commonly involves the lung, brain, liver and bone (66). Histologically, IMT is composed of plump or spindled myofibroblasts admixed with a characteristic inflammatory infiltrate of lymphocytes, plasma cells and eosinophiles in a variably myxoid to collagenous stroma (Figure 5A). Dystrophic calcification and osseous metaplasia are occasionally observed (64). In addition, a distinct subtype of IMT, epithelioid inflammatory myofibroblastic sarcoma, has been described, with a poor prognosis compared to conventional IMT (71). By immunohistochemistry, IMT shows variable staining for SMA (Figure 5B), MSA, calponin, desmin and cytokeratin (Figure 5C). Most notably, approximately 50-60% of IMTs express ALK receptor tyrosine kinase (ALK) (64). Cytogenetic studies have shown recurrent chromosomal rearrangements involving the short arm of chromosome 2, in particular 2p23 (72-74). At the molecular level, ALK rearrangements can be detected in 50-60% of cases, with various fusion partner genes (66). In addition, ROS proto-oncogene 1, receptor tyrosine kinase (ROS1) and neurotrophic receptor tyrosine kinase (NTRK3) gene rearrangements are each found in approximately 5-10% of ALK-negative IMTs (75-77). Fusions of FN1 to ALK, ROS1 or RET proto-oncogene (RET) have also been identified in a subset of cases (8, 76, 78-90). It is of interest that most urinary bladder IMTs harbor FN1-ALK fusions (8, 78-85).

Figure 5.
Figure 5.

Histological and immunohistochemical features of inflammatory myofibroblastic tumor (IMT). (A) IMT consists of spindled fibroblastic/myofibroblastic cells and a mixed inflammatory infiltrate in a hyalinized collagenous stroma (hematoxylin and eosin staining, original magnification ×100). Immunohistochemically, the neoplastic cells are diffusely positive for smooth muscle actin (B) and focally positive for cytokeratin (AE1/AE3) (C) (original magnification ×100).

FN1-RTK Fusions

As mentioned above, fusions of FN1 to RTKs have been detected in a variety of mesenchymal neoplasms (3-8). It is suggested that FN1 may contribute to aberrant signal activation by supplying strong promoter elements and mediating RTK dimerization through its structural domains (5, 6, 80). Importantly, the structure of these gene fusions indicates that RTK inhibitors may be promising therapeutic options for patients with unresectable or metastatic tumors.

Conclusion

Almost all of FN1-rearrangeted chondroid matrix-producing tumors have a benign clinical course. Over the past decade, a number of novel fusions involving the FN1 gene have been identified in STC, SC, CAF, CCMN, PMT, LPF and IMT. Diagnosis of these tumors can be challenging due to their rarity as well as their clinical and histological overlap. Further studies are required to determine whether different fusion partners are associated with distinct morphological features and biological behavior of FN1-rearranged mesenchymal neoplasms.

Footnotes

  • Conflicts of Interest

    The Authors declare no conflicts of interest associated with this article.

  • Authors’ Contributions

    JN drafted the article and searched the literature. YC and YS collected the data and reviewed the article. MA and KK performed the histological evaluation. All Authors read and approved the final article.

  • Artificial Intelligence (AI) Disclosure

    No artificial intelligence (AI) tools, including large language models or machine learning software, were used in the preparation, analysis, or presentation of this article.

  • Received November 6, 2025.
  • Revision received November 26, 2025.
  • Accepted December 29, 2025.

This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY-NC-ND) 4.0 international license (https://creativecommons.org/licenses/by-nc-nd/4.0).

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