EML4::RET, a novel transcript fusion in papillary thyroid cancer

Abstract

Fusion genes are the most common genetic alterations found in pediatric papillary thyroid cancers (PTCs). Pediatric PTCs harboring fusion genes are generally associated with more aggressive disease than those without. RET (rearranged during transfection) rearrangements are the most common fusion genes in thyroid cancers. EML4 (human echinoderm microtubule-associated protein-like 4) was reported to be a fusion partner of ALK (anaplastic lymphoma kinase), NTRK (neurotrophic tyrosine receptor kinase), and MET (mesenchymal epithelial transition) fusion genes, but not of RET. We report a 16-year-old patient with PTC staged as pT3bN1bM1, who presented with lung metastases at diagnosis. RNA sequencing using our institution's next-generation sequencing panel revealed a novel EML4::RET transcript fusion. Between 2021 and 2024, the patient underwent 4 radioiodine (RAI) treatments for distant RAI-avid metastases, with remarkable response on posttherapeutic whole-body scans and by declining serum thyroglobulin levels. EML4::RET transcript fusion needs to be recognized as a novel rearrangement in PTC.

Introduction

Papillary thyroid cancers (PTCs) account for >90% of pediatric thyroid cancers [1]. Neck lymph nodes (LNs) are frequently observed, and lung metastases occur in up to 25% of young patients [1]. Metastases in pediatric differentiated thyroid cancers (DTCs) are almost always radioiodine (RAI)–avid, and the prognosis is excellent. Unlike in adults, fusion genes are the most common genetic alterations observed in pediatric PTCs. The RET (rearranged during transfection) gene encodes for a tyrosine kinase receptor. RET rearrangements (ie, chromosomal rearrangement between the RET gene and its partner gene) are drivers of oncogenesis in DTC and the most common fusion genes in thyroid cancers. More than 20 partner genes have been reported so far in RET fusions [2, 3]. RET/PTC fusions were identified in 6 out of 9 children or adolescents aged 4 to 19 years (67%) [4]. Fenton et al [5] found a RET/PTC fusion in 45% of 33 patients, including children and young adults. RET fusions were identified in 25% to 37% of patients with sporadic pediatric PTC [2, 6-8]. CCDC6::RET (RET/PTC1) and NCOA4::RET (RET/PTC3) are involved in the development of pediatric thyroid cancers and account for approximately 90% of RET fusion transcripts [3]. RET/PTC1 occurs most frequently in sporadic pediatric PTC, whereas RET/PTC3 is more common in radiation-induced PTC [9-11]. Pediatric PTCs harboring a fusion gene are generally associated with more aggressive disease than those without [8], particularly those with RET/PTC3 [9, 10].

Human echinoderm microtubule-associated protein (MAP)–like 4 (EML4) is a member of the echinoderm MAPs family that promotes microtubule stability. The EML4-ALK fusion protein is observed in patients with lung adenocarcinoma as well as breast and colorectal cancers. In DTC, EML4 has been identified as a fusion partner of ALK (anaplastic lymphoma kinase) [12-17], NTRK3 (neurotrophic tyrosine receptor kinase) [13, 15, 18, 19], NTRK2 [20], and MET (mesenchymal epithelial transition) [8, 21] fusion genes, but not of RET [16, 22]. We describe a novel RET fusion involving EML4 in a young patient with PTC.

Case presentation

A 16-year-old male from Mali who had been in France for a year was referred for diagnostic workup of a thyroid nodule. His past medical history was notable for neck surgery at age 8 owing to lymphadenopathy; however, he had no details about the pathology. The patient had no history of radiation exposure or family history of thyroid disease or DTC.

Diagnostic assessment

Physical examination revealed a firm left thyroid nodule and isolateral cervical lymphadenopathy. The serum thyrotropin (thyroid-stimulating hormone [TSH]) level was 1.12 mIU/L (normal reference range, 0.27-4.2 mIU/L). Thyroid peroxidase antibodies and thyroglobulin (Tg) antibodies were within the normal reference ranges. The serum calcitonin level was normal at 5.9 pg/mL (SI [Système International]: 1.72 pmol/L) (normal reference range, <10 pg/mL [SI: <2.92 pmol/L]). Thyroid scan showed a left cold nodule (Fig. 1A). Ultrasound (US) examination depicted a 34-mm solid hypoechoic left thyroid nodule with irregular margins, taller than wide in shape and with increased intranodular and perinodular blood flow, with a European Thyroid Imaging Reporting and Data System score of 5 (Fig. 1B). Ultrasound also depicted neck lymphadenopathy in the central and left lateral compartments (Fig. 1C and 1D). The largest node (27 mm) was observed in the left lateral compartment. Ultrasound-guided fine-needle aspiration was performed for cytology in the left thyroid nodule and in an 18-mm lymphadenopathy at left level III with Tg measurement in the aspiration sample. According to the Bethesda System for Reporting Thyroid Cytopathology, cytology was malignant (Bethesda class VI) in the left thyroid nodule and also malignant in the LN. Thyroglobulin measurement in the LN was markedly elevated at 15 322 ng/mL. Computed tomography (CT) scan showed more than 10 bilateral pulmonary micronodules suggesting metastases. Total thyroidectomy with bilateral central and left lateral compartment LN dissection was performed in August 2021. Pathology revealed a 34-mm nonencapsulated PTC with numerous psammomas and muscle extension (Fig. 1E and 1F), lymphatic and perineural invasion in the left lobe, and a 1-mm papillary microcarcinoma in the right lobe. Among the 18 LNs removed, 8 were malignant including 7 with extracapsular nodal extension (Fig. 1G). Papillary thyroid cancer was staged as pT3bN1bM1. Using our in-house next-generation sequencing (NGS) panel, no point mutation was found in BRAF, KRAS, HRAS, NRAS, and RET genes. RNA sequencing revealed an EML4::RET fusion. Although the 2015 American Thyroid Association (ATA) management guidelines for children with DTC [1] did not recommend routine use of 18-fluorodeoxyglucose positron emission tomography with CT (¹⁸FDG PET/CT), it was performed in this case because the 17-year-old patient was considered at high-risk per the 2015 ATA management guidelines for adult patients and was nearly an adult [23]. ¹⁸FDG PET/CT showed moderate uptake in a 6-mm nodule in the right lung (maximal standardized uptake value [SUVmax] = 2.5) and in a 7-mm nodule in the left lung (SUVmax = 1.7) (Fig. 2A-C). There was no significant ¹⁸FDG uptake in the other bilateral lung micronodules, all measuring ≤5 mm.

Figure 1.

Ultrasound and histologic features. The thyroid scan shows a cold nodule on the left lobe (A, arrow). Ultrasound (US) reports a 34-mm solid nodule with features suggesting high malignancy risk. Transverse US image depicts this hypoechoic nodule (arrows) with a taller-than-wide shape (B). Microcalcifications along with irregular margins were also observed (not shown). US images of the left central (C) and left lateral (D) nodes reveal patterns strongly indicative of malignancy, including peripheral vascularity, hyperechogenicity, round shape, and microcalcifications. Pathology confirmed a 34-mm nonencapsulated papillary thyroid carcinoma (PTC) (E, hematoxylin and eosin–stained [HES] sections; magnification ×10), featuring psammoma bodies (E, arrows), muscle extension (F, HES, arrows; magnification ×2.5), and lymphatic and perineural invasion. One central and 7 lateral lymph nodes exhibited involvement, with extracapsular nodal extension seen in 7 nodes (G, HES; magnification ×1.5), indicated by the arrow.

Figure 2.

In November 2021, a PET/CT scan performed 2 days before the first RAI treatment revealed moderate ¹⁸FDG uptake only in the 2 largest lung nodules: a 6-mm nodule in the upper part of the right inferior lobe (blue arrow) and a 7-mm nodule in the upper part of the left inferior lobe (red arrow). This is shown in (A) the maximum intensity projection (MIP) image of the ¹⁸FDG PET/CT, (B) the axial ¹⁸FDG PET image, and (C) the fused axial ¹⁸FDG PET/CT image. In September 2020, a CT scan detected bilateral lung micronodules, over 10 in number, with the largest measuring 7 mm in the upper part of the left inferior lobe (D, red arrow). In July 2025, a follow-up CT scan showed that most of the lung micronodules had disappeared while the others had decreased in size, with the largest remaining measuring 4 mm in the upper part of the left inferior lobe (E, red arrow).

Treatment

In November 2021, the patient received 3718 MBq (100 mCi) of RAI after thyroid hormone withdrawal (THW). The stimulated serum Tg level was 164 ng/mL. Throughout management, serum Tg antibodies stayed within the normal range. A whole-body scan (WBS) with neck and thorax ¹³¹I-single photon emission CT with CT (¹³¹I SPECT/CT), performed 5 days after RAI therapy, showed RAI-avid LNs in the right neck and bilateral RAI-avid lung metastases (Fig. 3A and 3E). According to the 2015 ATA management guidelines for adult and children patients with DTC, RAI therapy was administered every 6 to 12 months [1, 23]. In May 2022, the patient received a second RAI treatment with 3707 MBq (100 mCi) after THW. The stimulated serum Tg level dropped to 86 ng/mL. Posttherapy WBS with ¹³¹I SPECT/CT showed a partial response, with regression of the RAI-avid neck and lung metastases (Fig. 3B and 3F). In March 2023, the patient received a third RAI dose of 3699 MBq (100 mCi) after THW. The stimulated serum Tg level decreased to 45.8 ng/mL. Whole-body scan showed reduction in RAI uptake in the lungs (Fig. 3C and 3G). In February 2024, the patient received a fourth RAI dose of 3588 MBq (97 mCi) after THW. The stimulated Tg level was stable at 47.2 ng/mL. Posttreatment WBS revealed a moderate reduction in RAI uptake (Fig. 3D and 3H).

Figure 3.

Posttherapy WBS (A-D, anterior views from November 2021, May 2022, March 2023, and February 2024; D, black arrow shows false-positive skin uptake [24]) with neck and thorax ¹³¹I SPECT/CT (E-H, fused axial images from 2021 to 2024) performed 5 days after each of the 4 RAI treatments showed a marked decrease in RAI-avid lung metastases and neck LN on each acquisition (red arrows).

Outcome and follow-up

The patient was followed up every 4 to 6 months. During the last follow-up visit in November 2025, he still presented a biochemical incomplete response, with a Tg level of 2 ng/mL on levothyroxine. A CT scan showed that some lung nodules had shrunk (Fig. 2D and 2E), while other lung micronodules had disappeared.

Discussion

RNA sequencing identified a novel RET rearrangement involving EML4 in a 16-year-old patient with metastatic PTC. Next-generation sequencing has improved the detection of genetic alterations in DTC, especially chromosomal rearrangements. In clinical practice, using a custom RNA-based NGS panel requires identifying key fusion events. The fusion genes included in our NGS panel are described in a previous report [25]. RET rearrangements are the most common gene fusions in pediatric PTCs and are key oncogenic drivers. When the chromosomal translocation occurs, the 5′ region of a gene encoding a protein expressed in the thyrocyte is juxtaposed to the kinase encoding the 3′ end of the RET gene, leading to constitutive tyrosine kinase activation [3, 26] that triggers tumorigenesis. Figure 4 indicates that the breakpoints of the RET protooncogene are identical to those previously reported [15]. EML4::RET fusion was previously identified in a patient with lung cancer and leptomeningeal metastases, involving exon 19 of the EML4 partner gene, whereas in this case, exon 14 was involved [27].

Figure 4.

EML4::RET transcript fusion structure (figure generated by Arriba tools [doi:10.1101/gr.257246.119]). (A) Circos plot of EML4 and RET gene translocation. (B) Depth of coverage from RNA sequencing data of transcripts of EML4 and RET genes, with the presence of split reads between exon 14 of EML4 gene and exon 12 of RET gene.

So far, EML4 has been reported as a fusion partner of ALK, NTRK, and MET in DTC. Of these driver events, 6 rearrangements occurred in young patients aged 9 to 24 years [8, 15, 18]. This 16-year-old patient's case provides new pathological and clinical evidence regarding RET rearrangements involving EML4 in this disease. Pathology showed a multifocal PTC with psammoma bodies and muscle extension. These features are consistent with previous findings in RET fusion tumors, especially the presence of psammomas, multifocality, and lymphovascular involvement [2, 8, 21]. In a series of pediatric PTC cases, Pekova et al [8] showed that unlike fusion gene-negative PTCs, RET fusion-positive PTCs are associated with multifocality, extrathyroid extension, and the presence of psammoma bodies. Our patient also had LN involvement, extracapsular nodal extension, and lung metastases. These clinical features are in line with previous studies reporting that (1) there is a correlation between RET fusion-positive PTCs and LN metastases [2, 8] and (2) compared with other gene fusions, RET fusions are associated with distant metastases and more aggressive tumor behavior [8]. Furthermore, Pekova et al [8] reported a MET fusion with EML4 as partner gene in a 15-year-old girl who presented with pathologically and clinically aggressive features. Remission was obtained after a cumulative RAI activity of 700 mCi. The present case report shows that EML4::RET transcript fusion can be associated with more aggressive pathological and clinical features, and high-risk staging. Consequently, detecting this transcript fusion could play a crucial role in informing RAI treatment decisions postsurgery.

As is customary in pediatric patients with metastatic disease, high RAI avidity was observed in LN and lung metastases, with little or no ¹⁸FDG uptake, showing a notable response after several RAI treatments. A biochemically incomplete response was achieved, and no additional systemic therapy has been necessary to date. However, according to the 2025 ATA management guidelines for adult patients with DTC, there is a 20% to 53% risk of recurrence [28]. If a recurrence happens, it is unclear whether the disease will remain RAI-avid or become RAI-refractory. In the latter case, targeted therapy using selective RET inhibitors could be a treatment option. Of note, Lee et al [29] observed that RAI uptake was restored in the RAI-refractory progressive disease of a 7-year-old girl with PTC who was treated with selpercatinib. Additional case reports have shown that tumoral RAI uptake can be restored in adult patients with RET fusions following treatment with selpercatinib or pralsetinib. Nonetheless, the results of ongoing prospective multicenter trials investigating redifferentiation with selective RET inhibitors are still awaited. van der Tuin et al [13] reported targeted gene fusions in 12% of adult patients with RAI-refractory DTC, including RET rearrangements. In such patients with high tumor volume and progressive disease, selective RET inhibitors can be administered as first- or second-line therapy according to guidelines and availability [28, 30]. In conclusion, EML4::RET transcript fusion needs to be recognized as a novel rearrangement, particularly in young patients with PTC.

Learning points

• Fusion genes are the most common genetic alterations in pediatric PTCs and are generally associated with more aggressive disease. RET rearrangements represent the most common fusion transcripts.

• The EML4 protein promotes microtubule stability. In DTC, EML4 has been identified as a fusion partner of ALK, NTRK, and MET gene rearrangements but not of RET.

• We describe a novel EML4::RET transcript fusion found in a 16-year-old patient with PTC staged as pT3bN1bM1, who showed a remarkable response in RAI-avid lung metastases after 4 RAI treatments.

• The EML4::RET transcript fusion was associated with more aggressive pathological features, nodal and distant metastases. Papillary thyroid cancer was classified as high risk. Persistent disease demonstrated RAI sensitivity.

• EML4::RET transcript fusion is a novel rearrangement and oncogenic driver in PTC.

Contributors

R.C., V.L.H., and S.B. contributed to the patient's diagnosis and management. R.C. authored the initial draft of the manuscript, and R.C. and S.B. revised it. R.L. and L.C. contributed to the genetics section, while M.D. handled the histopathology section and prepared the histology images. All authors reviewed and approved the final version.

Funding

No public or commercial funding.

Disclosures

The authors have no conflicts of interest to disclose.

Informed patient consent for publication

The patient, now an adult, provided signed informed consent directly.

Data availability

Data sharing is not applicable to this article as no datasets were generated or analyzed during the current study.