Data on the clinicopathological features of NRG1 fusion-positive non-small cell lung cancer (NSCLC) are limited. We conducted a retrospective, multicenter study and included patients with NRG1 fusion-positive NSCLC diagnosed between January 2018 and February 2025. Six patients were identified; five were female (83.3%), two were never-smokers (33.3%), and four were former smokers (66.7%). Adenocarcinoma was the predominant histology (n = 5), comprising mucinous (n = 2), enteric (n = 2), and not otherwise specified (n = 1) variants, while one patient had squamous cell carcinoma. All were PD-L1-negative, and CD74-NRG1 was the most common fusion (50%). Three patients received afatinib; only one achieved a partial response with a progression-free survival of 8.7 months. Median overall survival was 6.7 months. Our study demonstrates the histologic and molecular heterogeneity of NRG1 fusion-positive NSCLC, encompassing mucinous and enteric variants of adenocarcinoma. Responses to afatinib were variable, underscoring the need for more effective therapies, including zenocutuzumab and emerging agents.
Pleomorphic liposarcoma (PLPS) is an aggressive high-grade sarcoma that often shows diverse morphological features and can mimic high-grade undifferentiated pleomorphic sarcoma (UPS)/spindle cell sarcoma or myxofibrosarcoma (MFS), especially when pleomorphic lipoblasts are sparse. The molecular profile of PLPS is distinct from well differentiated/dedifferentiated liposarcoma and myxoid liposarcoma. In this study, we investigate 39 cases of PLPS by comprehensive genomic profiling, occurring in 32 patients with available molecular data. Cases were reviewed and morphologic parameters-lipoblastic component, UPS-like, and MFS-like areas were estimated. The genomic findings were collected and compared to UPS and MFS groups studied using the same platform. The cohort included 15 females and 17 males, with a median age of 56.5 (range, 34-78). The lower extremity (n = 17) was the most common site involved, followed by upper extremity (n = 5) and pelvis (n = 5). UPS-like and MFS-like patterns were the most common morphologic variants, ranging from 15% to 95% and 20% to 90%, respectively. TP53 (87%) and RB1 (51%) mutations and copy number alterations were the most common alterations seen, followed by ATRX (36%). Compared to UPS and MFS, TP53 and RB1 gene alterations were significantly more common in PLPS. Conversely, CDKN2A/B deletions were infrequent in PLPS. Survival analysis showed that MYC amplification was associated with significantly shorter overall survival in PLPS. Among histologic variants, CYSLTR2 alterations were found to be highest in cases with predominantly pleomorphic lipoblasts; additionally, strong correlations were found between gene alteration frequencies of MFS and MFS-like PLPS, and between UPS and UPS-like PLPS. RB1 allele-specific copy number analysis showed loss of heterozygosity in 82% of cases. Our cohort of PLPS showed a complex molecular landscape with distinct genetic alterations, histologic correlations, and clinical outcomes, highlighting its unique position among genomically complex sarcomas and providing insights that may inform future diagnostic and therapeutic approaches.
Esophageal cancer (OC) is currently the eighth most common form of cancer worldwide with a 5-year survival rate of 10%-20%, with the primary risk factor of esophageal adenocarcinoma (OAC) being the development of Barrett's Esophagus (BO). Despite its clinical significance, the molecular pathogenesis underlying both BO and OC is not well understood. In recent years, epigenetic dysregulation, particularly aberrant DNA methylation, has emerged as a critical area of investigation, given its potential utility in the identification of diagnostic, prognostic, and therapeutic biomarkers. This review examines the evolving epigenetic landscape of esophageal cancer, including a focus on its origins in BO with a particular emphasis on DNA methylation, the most extensively researched epigenetic mechanism. Key DNA methylation-associated alterations involved in OAC and OSCC initiation and progression are discussed, alongside their potential clinical application as biomarkers for early detection, prognosis, and risk stratification in BO populations. Furthermore, the role of these epigenetically regulated genes in the disruption of Wnt signaling and cell cycle control pathways implicated in esophageal carcinogenesis is explored. The review concludes by outlining future research directions, current challenges, and the promise of epigenetic studies in advancing our understanding of OC pathogenesis and improving patient outcomes.
MITF-rearranged PEComas are rare, and their relationship to MITF-altered melanocytic tumors remains incompletely characterized. We report a malignant superficial soft tissue neoplasm of the thigh in a 45-year-old woman harboring a novel EEF1A1::MITF fusion. The tumor was composed of epithelioid to plump spindle cells arranged in sheets, nests, and short fascicles with prominent capillary vasculature. Significant cytologic atypia, brisk mitotic activity, and necrosis were present. The tumor cells showed diffuse strong nuclear MITF and diffuse GPNMB expression, with patchy SMA, scattered desmin, and multifocal cathepsin K positivity, while S100, SOX10, HMB45, Melan A, PRAME, tyrosinase, pancytokeratin, CD34, and TFE3 were negative. Although atypical for classic PEComa, this immunophenotype resembles that described in MITF-overexpressing PEComas. Molecular studies identified an ATRX frameshift mutation, homozygous CDKN2A/CDKN2B deletion, complex copy number alterations, and an in-frame EEF1A1::MITF fusion. No canonical TSC1, TSC2, or FLCN alteration was identified. These findings expand the molecular spectrum of PEComa and support the emerging concept that a subset of cutaneous PEComas may be driven by MITF rearrangements.
Previous studies have extensively examined the associations between CD133 gene polymorphisms (rs10022537, rs2286455, rs2240688, and rs3130) and cancer risk, but have yielded inconsistent results. This study aimed to investigate the potential contributions of these polymorphisms to the susceptibility of liver, lung, and gastric cancers through a replicated case-control study and a subsequent systematic meta-analysis. A total of 480 patients with liver cancer, 550 patients with lung cancer, 460 patients with gastric cancer, and 800 healthy controls from the Hubei population were enrolled. Sanger sequencing assay was applied to genotype the four target CD133 gene polymorphisms. The case-control study revealed that rs10022537 was significantly associated with the risk of liver cancer but not with the risk of lung or gastric cancer. In contrast, rs3130 was significantly associated with both lung and liver cancer risk, whereas no association was observed with gastric cancer risk. rs2240688 exhibited a significant association exclusively with lung cancer risk, and rs2286455 showed no significant association with any of the three cancer types. The meta-analysis further demonstrated that rs3130 was significantly associated with lung cancer risk in the Chinese population, and rs2240688 was significantly associated with gastric cancer risk. No significant association was found for rs10022537 or rs2286455 with liver, lung, or gastric cancer risk. Collectively, these findings suggested that rs3130 and rs2240688 in the CD133 gene may serve as susceptibility factors for risk of lung cancer and gastric cancer, respectively. Further validation studies in larger and more diverse populations are warranted.
BACKGROUND:Myelodysplastic syndromes (MDS) and acute myeloid leukemias (AML) harboring TP53 mutations are defined by extreme genomic instability, complex karyotypes (CK), and poor prognosis. While large-scale chromosomal imbalances are common in CK-MDS/AML, the synergy between focal amplifications of signaling drivers and the disruption of transcriptional regulators remains poorly elucidated. METHODS:We performed a comprehensive clinical, cytogenetic (GTG-banding, M-FISH, M-Band), and molecular (targeted FISH, NGS) analysis of seven patients with MDS and AML characterized by a recurrent and distinct genomic signature. RESULTS:All cases exhibited highly complex karyotypes on a TP53-mutated background. We identified high-level focal amplifications of EPOR (19p13.2) and JAK2 (9p24.1), predominantly manifesting as homogeneously staining regions (HSRs) or complex "sandwich-like" derivative chromosomes. Notably, these signaling alterations consistently co-occurred with monoallelic deletions of the TCF3 (E2A) tumor suppressor (19p13.3) and copy number gains of the ERG transcription factor (21q22). Detailed structural analysis indicates that TCF3 loss likely arises as a structural consequence of chromosome 19 rearrangements driving EPOR amplification. Based on this data, we propose a conceptual model of leukemogenesis where EPOR/JAK2 co-amplification potentially drives constitutive JAK2/STAT5 signaling, while concurrent ERG gain and TCF3 haploinsufficiency contribute to maturation delay. TP53 deficiency appears to be the primary permissive factor enabling the stabilization of these massive structural rearrangements. CONCLUSIONS:Our findings outline a recurrent and biologically coherent genomic pattern within the spectrum of TP53-mutated myeloid neoplasms, demonstrating significant phenotypic overlap with erythroid leukemia features in a subset of cases. Given the small cohort size, these findings are hypothesis-generating. However, this convergence of predicted JAK2/STAT5 pathway hyperactivation and transcriptional disinhibition points to a theoretical therapeutic vulnerability that warrants prospective validation in larger collaborative studies.
Soft tissue tumors with chondroid matrix represent a heterogeneous group with persistent diagnostic challenges. Advances in molecular diagnostics have identified recurrent gene fusions in several chondroid neoplasms, predominantly involving FN1. Here, we report two cases of chondroid tumors harboring a novel FOS::PABPN1 fusion. The patients were young and presented with small, deep, peri-osseous nodules located in the extremities. Histologically, the tumors were well-circumscribed and lobulated. Both cases presented fibro-cartilaginous and spindle cell areas. No cytonuclear atypia, mitoses, or necrosis were observed. Immunohistochemistry (performed in Case 2) revealed positivity for S100, CD34, and FOS, with negativity for MDM2, HMGA2, PLAG1, and desmin. RNA sequencing identified an identical in-frame FOS::PABPN1 fusion transcript in both tumors. Unsupervised transcriptomic clustering positioned the cases near synovial chondromatoses and other chondroid lesions, despite the absence of FN1 rearrangements. Massive overexpression of the WIF1 (Wnt Inhibitory Factor1) gene was also observed. To our knowledge, this is the first description of FOS rearrangement in mesenchymal tumors exhibiting chondroid differentiation. The FOS::PABPN1 fusion expands the spectrum of FOS-altered neoplasms beyond osteoblastic and vascular lesions and defines a potential new molecular subset of benign chondroid tumors. These findings highlight the utility of RNA sequencing in the diagnosis of chondroid neoplasms in order to identify rearrangement (of FN1, THBS1 or FOS) or IDH1/2. The consistent upregulation of WIF1 may represent a potential diagnostic biomarker.
Malignant peripheral nerve sheath tumors (MPNSTs) are aggressive soft tissue sarcomas and the most common cause of disease-associated death for neurofibromatosis type 1 (NF1) patients. In the context of NF1, MPNSTs develop from benign premalignant precursors and the transition to malignancy is typically accompanied by loss of the polycomb repressive complex 2 (PRC2), which results in aberrant upregulation of over 1200 genes due to global depletion of histone H3 lysine 27 trimethylation (H3K27me3). Previous studies suggest cells compensate for the loss of this repressive histone mark via hypermethylation of the genome. Here we analyzed genome-wide DNA methylation and the transcriptome in MPNST cell lines and isogenic PRC2-deficient and -proficient CRISPR-engineered immortalized human Schwann cells. In addition to effects of PRC2 status, we also measured the effects of two DNA methyltransferase inhibitors (DNMTi), decitabine and azacitidine. We found that PRC2 status does not affect global DNA methylation or average methylation levels across specific genomic features. Furthermore, decitabine and azacitidine have differential effects on MPNSTs. While both DNMTis hypomethylate the genome, they upregulate different targets. Azacitidine upregulates genes involved in RNA processing pathways and exhibits direct tumor cell cytotoxicity, while decitabine upregulates genes involved in the immune response, has no direct-cell killing effects, and likely suppresses tumor growth in vivo by altering the tumor microenvironment. We show that DNA hypomethylation alone is insufficient to kill MPNST cells, regardless of PRC2 status. Consequently, these findings suggest that DNMT inhibitors should be utilized in combination with other targeted therapies for MPNST patients.
Chondrosarcomas are malignant cartilage-forming bone tumors with heterogeneous behavior, making prognostication and clinical management challenging. Histological grading is the primary tool for predicting clinical outcomes in conventional chondrosarcoma. However, its high interobserver variability limits reliable distinction between low- and high-risk patients, potentially leading to suboptimal clinical management. Given the increasing use of DNA methylation profiling as a valuable tool in surgical pathology for tumor classification, we investigated its prognostic value in central conventional chondrosarcoma. We generated methylation data from 69 primary central conventional chondrosarcomas profiled with Illumina's Human MethylationEPIC Array (850 k sites), and identified methylation sites individually linked to patient outcome. A LASSO Cox regression model was applied to these methylation sites to identify an optimal set of eight informative sites. With the regression coefficients of these methylation sites, we constructed a risk score that predicts central conventional Chondrosarcoma Risk Outcome from Methylation (CHROME). CHROME stratifies patients into High or Low risk groups for disease recurrence, onset of metastasis and disease-specific mortality. Survival analysis in an independent validation cohort (n = 68) demonstrated strong discriminatory performance of CHROME, with complete separation of outcomes and no adverse events observed in the Low risk group. Overview of the clinico-pathological information showed that a low grade (ACT/G1) case with an event was correctly assigned to the High risk group, while nine high grade cases without events were classified as Low risk. CHROME provides accurate risk stratification in central conventional chondrosarcoma and may represent a valuable tool for improving its prognostication and clinical management.
BACKGROUND:There is morphological overlap between nodular necrotizing fibroblastic sarcoma (NNFS) and myxoinflammatory fibroblastic sarcoma (MIFS). Whether they represent neoplasms within the same tumor spectrum remains unclear. We performed a comparative clinicopathological, molecular, and epigenetic study of these two tumors. METHODS:We analyzed the clinicopathological features, immunophenotypes, and molecular profiles of three cases each of NNFS and MIFS. DNA methylation profiling was also performed. RESULTS:All three NNFS cases were located in the trunk, presenting as well-circumscribed subcutaneous nodules with central necrosis, whereas the three MIFS cases all arose in acral sites with an infiltrative or ill-defined growth pattern. Morphologically, both NNFS and MIFS were characterized by large polygonal to epithelioid cells with virocyte-like, ganglion cell-like, or Reed-Sternberg-like appearance. Unlike MIFS, NNFS did not exhibit prominent myxoid stroma or vacuolated pseudolipoblasts. On immunohistochemistry, NNFS cases uniformly showed focal positivity for pancytokeratin (AE1/AE3), whereas MIFS cases exhibited variable CD34 expression. Molecular analysis identified YAP1::MAML2 fusions in all three NNFS cases, while a BRAF rearrangement was detected in one of the three MIFS cases. DNA methylation profiling demonstrated that NNFS and MIFS cases clustered together forming a distinct group. CONCLUSIONS:Although NNFS and MIFS each harbor unique genetic alterations, our DNA methylation profiling demonstrates a potential relationship between these two morphologically similar entities.
The tumor suppressor gene TP53 is a key regulator of genomic stability, frequently altered across human cancers. In hematologic malignancies, TP53 lesions-typically mutations, deletions, and copy-neutral loss of heterozygosity-are associated with complex karyotypes, therapy resistance, and dismal prognosis. Amplifications of TP53, however, have not been systematically described in this context. We retrospectively analyzed cases submitted to our laboratory (09/2005-10/2025) by interphase FISH in which we suspected a TP53 amplification. Among these, eight cases exhibited TP53 amplification, all classified as myeloid neoplasms (n = 6 acute myeloid leukemia, AML; n = 2 myelodysplastic neoplasms, MDS). Median patient age was 72 years (range 48-83). Chromosome banding revealed highly complex karyotypes in all cases (4-12 aberrations), including 5q deletions (in 7/8 patients) and -7/7q- (4/8). Targeted sequencing demonstrated concurrent TP53 mutations in all patients (median variant allele frequency 48%, range 18%-91%) with few additional co-mutations. CNV (copy number variation) analysis confirmed focal TP53 copy number gains, but whole-transcriptome sequencing showed only modest TP53 expression increases, indicating that amplification did not translate into overexpression. Clinical data available for four AML cases revealed a median overall survival of 1 month. These findings indicate that TP53 amplification, although rare, constitutes a recurrent event in myeloid neoplasms, uniformly accompanied by TP53 mutation and complex cytogenetics. The combination of mutation and amplification likely confers biallelic TP53 inactivation, aligning these cases with multi-hit TP53 AML/MDS characterized by extreme genomic instability and highly adverse outcomes. Taken together, these data indicate that TP53 copy number assessment may be of potential diagnostic interest, although its role in risk stratification requires further studies.
Accurate detection of gene fusions is critical for the diagnosis of bone and soft tissue tumors, yet conventional gene panel testing remains costly and impractical when processing small sample numbers. Here, we present a cost-effective and scalable in-house workflow using a custom capture panel combined with nanopore sequencing and TEQUILA-based probe synthesis. We analyzed 24 sarcoma samples with known gene fusions, comprising frozen and formalin-fixed paraffin-embedded (FFPE) specimens. Expected fusions were detected in all 7 frozen samples and in 16 of 17 FFPE samples. Long-read sequencing enabled direct characterization of full-length fusion transcripts, providing structural information beyond fusion junctions. Gene expression quantification showed strong concordance with short-read sequencing (Spearman r = 0.770-0.976), supporting quantitative reliability. Down-sampling analysis demonstrated that 100-200 Mb of sequencing data per sample was sufficient for reliable fusion detection, while deeper sequencing improved sensitivity for lowly expressed fusions. In addition, reuse of flow cells supported flexible and efficient sequencing for small sample batches. This approach provides a practical and extensible framework for in-house fusion detection and improves the accessibility of molecular diagnostics for rare cancers.
Biphenotypic sinonasal sarcoma (BSNS) is a rare, low-grade spindle cell sarcoma of the sinonasal tract. It is characterized by dual neural and myogenic differentiation and classically shows fusions involving PAX3. MAML3, a co-activator in the Notch signaling pathway, is the most common fusion partner of PAX3. Here, we describe the first reported case, to our knowledge, of BSNS harboring a novel PAX3::MAML2 fusion in a polypoid lesion arising from the left ethmoid of a 61-year-old man. Microscopically, the tumor demonstrated bland spindle cell morphology. The cells were arranged in small fascicles and a vaguely whorled pattern without mitotic activity or cellular atypia. Immunohistochemistry displayed characteristic co-expression of S100 and smooth muscle actin as well as patchy nuclear positivity for beta-catenin. SOX10, AE1/AE3, EMA, and CD34 were negative. Ki-67 was expressed in less than 1% of tumor cells, consistent with a low-grade lesion. The RNA sequencing identified a novel PAX3::MAML2 fusion transcript. MAML2 fusion is commonly associated with other head and neck neoplasms, including mucoepidermoid carcinoma and NR1D1-rearranged tumors. These findings highlight the value of comprehensive fusion testing in BSNS and emphasize the evolving fusion landscape in this entity and related tumors.
PKMYT1 has emerged as a promising therapeutic target distinguished by its tumor-selective expression and essential role in replication stress management. Unlike WEE1, PKMYT1 is dispensable in normal cell cycles but critical for cancer cells coping with DNA damage, establishing a broad therapeutic window. This vulnerability is exemplified by synthetic lethality in CCNE1-amplified and TP53-deficient contexts, where PKMYT1 inhibition triggers catastrophic mitotic entry. Beyond canonical cell cycle regulation, PKMYT1 functions as a multifaceted oncoprotein modulating signaling networks, metabolic reprogramming, and immune evasion via cGAS-STING activation. With selective inhibitors like lunresertib (RP-6306) now in Phase I/II trials, often combined with ATR inhibitors or chemotherapy, the field stands at a translational inflection point. However, context-dependent roles (e.g., tumor-suppressive functions in LUAD) and undefined resistance mechanisms pose challenges. This review critically evaluates PKMYT1's mechanistic underpinnings, clinical landscape, and biomarker strategies. We advocate for precision targeting based on genetic signatures (CCNE1, TP53, ER) to optimize therapeutic efficacy and overcome resistance in replication stress-high malignancies.
Colorectal cancer (CRC) is a major global health burden with an increasing incidence among younger adults. High-glycemic food intake and biological aging have been proposed as potential risk factors for CRC, but their causal relationships and underlying mechanisms remain unclear. We conducted a two-sample Mendelian randomization (MR) study using large-scale genome-wide association study summary data to evaluate the genetic associations of 25 high-glycemic food intake traits and five aging-related indicators, including GrimAge acceleration, intrinsic epigenetic age acceleration, PhenoAge acceleration, Hannum age acceleration, and mitochondrial DNA copy number, with CRC risk. Two-step MR was used to explore potential mediating role of aging indicators. MR analyses showed nominally significant positive associations of intake of sugar added to tea (OR = 1.307, 95% CI: 1.033-1.655, p = 0.026, FDR = 0.216) and doughnut intake (OR = 2.524, 95% CI: 1.317-4.835, p = 0.005, FDR = 0.131) with CRC risk, whereas yogurt intake was nominally associated with lower CRC risk (OR = 0.755, 95% CI: 0.596-0.958, p = 0.020, FDR = 0.216). These food-CRC associations did not survive FDR correction and should therefore be interpreted as suggestive evidence. GrimAge acceleration showed a positive genetic association with CRC risk (OR = 1.102, 95% CI: 1.039-1.169, p = 0.001). Mediation analysis suggested that GrimAge acceleration may partly mediate the association between intake of sugar added to tea and CRC risk, with an estimated mediated proportion of 36.1%. These findings provide genetic evidence suggesting potential links among specific high-glycemic food intake traits, epigenetic aging, and CRC risk; however, mediation finding did not pass strict significance testing and requires validation in larger and independent datasets.
BACKGROUND:Alterations of the Y chromosome are frequent events in solid tumors, yet their biological and clinical significance remains incompletely understood. In colorectal cancer (CRC), recent studies have suggested context-dependent roles of Y-linked genes in tumor progression, while the impact of tumor-associated loss of the Y chromosome (LoY) in metastatic disease has not been clearly established. METHODS:We retrospectively analyzed primary tumor samples from 91 male patients with metastatic CRC treated at a single institution. Tumor LoY status was assessed using a droplet digital PCR-based assay. Associations between LoY, clinicopathological characteristics, KRAS/BRAF mutation status, and patient outcomes, including progression-free survival (PFS) and overall survival (OS), were evaluated. Exploratory analyses of TCGA-COAD/READ data were performed using chromosome Y copy-number segment data, mutation data, and survival information. RESULTS:Tumor LoY was detected in 46 cases (50.5%) and was more frequent in rectal cancers (p = 0.038). LoY was not associated with age, microsatellite instability status, KRAS or BRAF mutations. While PFS did not differ according to LoY status, OS was longer in patients with LoY-positive tumors (p = 0.046). In multivariable analysis, LoY showed a non-significant trend toward improved OS (HR = 0.52, 95% CI: 0.25-1.10; p = 0.07). In exploratory TCGA analyses, chromosome Y copy-number signal did not significantly differ between colon and rectal cancers, but lower chromosome Y signal was associated with worse OS, particularly in TCGA-COAD after adjustment for age and KRAS/BRAF status. CONCLUSIONS:LoY is a frequent chromosomal alteration in metastatic CRC and appears enriched in rectal primary tumors in our cohort. Its association with clinical outcome may depend on disease stage, molecular background, and analytical methodology. These findings support further investigation of Y chromosome loss as a context-dependent biomarker in CRC.
INTRODUCTION:Alterations involving RUNX1 are recurrent in hematologic malignancies and contribute to disease pathogenesis via dysregulation of transcriptional factors essential for hematopoiesis. Here, we report an acquired alteration in both alleles of RUNX1; one is a truncating mutation and the second is a novel RUNX1::ARID1B identified in acute myeloid leukemia. METHODS:Bone marrow samples were assessed by morphologic examination and flow cytometry. Cytogenetic analysis was performed using conventional G-banded karyotyping and fluorescence in situ hybridization (FISH). Molecular profiling was performed using next-generation sequencing (NGS) for single nucleotide changes, copy number variations, gene fusions, and expression. RESULTS:Morphology showed large-sized myeloblasts that are CD34+ and CD45+ (dim) consistent with acute myeloid leukemia. Genetic analysis of diagnostic specimen showed normal karyotype and FISH results but detected mutations in IDH1 and RUNX1. Cytogenetic analysis of a specimen at relapse showed complex abnormal karyotype and FISH detected RUNX1 rearrangement with 6q25. NGS identified this rearrangement as RUNX1::ARID1B. Thus, at this stage leukemia cells had "double-hit" abnormality in RUNX1. Gene transcript evaluation showed elevated levels of transcripts of both RUNX1 and ARIDB1. CONCLUSION:This study expands the spectrum of RUNX1 fusions and highlights the integral diagnostic value of morphology, flow cytometry, cytogenetics, FISH, and NGS analyses for broad structural variant detection in clinical practice. Furthermore, the truncating mutation in one allele of RUNX1 and RUNX1::ARID1B of the second allele detected with advanced disease suggests the possibility of combined transcriptional and chromatin regulatory alterations in disease recurrence in the patient.
Rhabdomyosarcoma with alveolar morphology is a diagnostically challenging tumor pattern, particularly in cases lacking canonical FOXO1-associated fusions. In the current WHO framework, molecular fusion status plays a central role in classification and risk stratification. However, a subset of tumors lacks canonical rearrangements and harbors alternative genetic events. We report a case of a 4-year-old girl with a massive parameningeal rhabdomyosarcoma presenting with cranial nerve dysfunction and airway compromise. Histological examination confirmed rhabdomyosarcoma with alveolar morphology. Fluorescence in situ hybridization revealed no rearrangements of FOXO1 or PAX3. Targeted RNA sequencing identified a novel NCOA1::ZNF143 fusion transcript. Despite intensive multimodal treatment including chemotherapy, radiotherapy, surgery, and metronomic therapy, the disease demonstrated multiple relapses with subsequent metastatic progression involving the spinal cord and central nervous system, ultimately leading to a fatal outcome.
Pulmonary spindle cell tumors are aggressive neoplasms with limited systemic treatment options, although a subset may harbor actionable genomic alterations. Because conventional fusion assays may miss rearrangements involving atypical or previously uncharacterized partners, we systematically investigated oncogenic fusions in pulmonary spindle cell tumors using anchored multiplex PCR-based targeted RNA sequencing. Formalin-fixed, paraffin-embedded tumor samples from 11 surgically resected pulmonary spindle cell tumors, excluding metastatic sarcomas, were analyzed using the FusionPlex Sarcoma panel supplemented with custom primers for RET, NTRK1, NTRK2, and NRG1. Two tumors (18.2%) harbored ALK fusions, identified as PPFIBP1::ALK and SYCL3::ALK. Both tumors showed positive ALK immunohistochemical staining. Histologically, the PPFIBP1::ALK-positive tumor was composed of spindle-shaped cells with a layered architecture, whereas the SYCL3::ALK-positive tumor showed relatively round cells arranged in clusters with collagenous stroma, highlighting the morphologic heterogeneity of ALK-rearranged pulmonary spindle cell tumors. These findings expand the molecular spectrum of pulmonary spindle cell tumors and identify rare ALK fusion partners in this setting. Our results support the incorporation of ALK immunohistochemistry as a screening tool and demonstrate the utility of anchored multiplex PCR-based RNA sequencing for the detection of therapeutically relevant fusions, particularly those with uncommon partners. This integrated approach may refine the diagnosis and support consideration of ALK-directed therapy in these rare tumors.
