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The article in the Journal of Cutaneous Pathology discusses a case of Spitz-Type Proliferative Nodules arising within a large congenital melanocytic nevus harboring a novel LMNA-RAF1 fusion. The patient, who had similar nodules develop and regress over time, underwent excisional biopsy of a growing nodule. Molecular and cytogenetic analysis revealed a novel fusion, supporting a Spitz pathway lesion, and failed to confirm a melanoma diagnosis. The article highlights the importance of accurate diagnosis and potential treatment options for similar cases. [Extracted from the article]

ABSTRACT Capicua transcriptional repressor (CIC)‐rearranged sarcoma (CRS) is a rare and recently described tumor that most commonly affects patients between 15 and 30 years of age. It is an undifferentiated round cell malignancy, with a disease defining CIC fusion, with double homeobox 4 (DUX4) being the most common partner. Here, we report a 77‐year‐old woman who presented with a cutaneous thigh mass with a clinical morphology suggesting Merkel cell carcinoma. Immunohistochemically, there was positivity for INSM1 (extensive) and synaptophysin (patchy) and granular expression of neurofilament (extensive), CAM5.2, and CK20 (focal, nonspecific). The majority of the tumor showed histopathologic features within the range of what can be seen in Merkel cell carcinoma, but there were divergent features, including a myxoid zone with corded and stranded tumor cells and a Ewing‐sarcoma‐like zone with confluent concentric membranous CD99 expression. WT‐1 was strongly expressed, prompting RNA‐based next generation sequencing for gene fusions, which identified the CIC:DUX4 [t(19;4)(19q13.2;4q35.2)]. A novel IRAK3:HMGA2 fusion was also identified. This example of CRS simulated MCC clinically, histopathologically, and immunohistochemically and represents a likely underrecognized diagnostic pitfall. [ABSTRACT FROM AUTHOR]

Oxford Nanopore Technologies sequencing, also referred to as Nanopore sequencing, stands at the forefront of a revolution in clinical genetics, offering the potential for rapid, long read, and real‐time DNA and RNA sequencing. This technology is currently making sequencing more accessible and affordable. In this comprehensive review, we explore its potential regarding precision cancer diagnostics and treatment. We encompass a critical analysis of clinical cases where Nanopore sequencing was successfully applied to identify point mutations, splice variants, gene fusions, epigenetic modifications, non‐coding RNAs, and other pivotal biomarkers that defined subsequent treatment strategies. Additionally, we address the challenges of clinical applications of Nanopore sequencing and discuss the current efforts to overcome them. [ABSTRACT FROM AUTHOR]

The article discusses two cases of low-grade myxoid spindle cell neoplasms with novel gene fusions involving MAP3K3 and MAP3K8 kinases. These gene fusions have not been previously identified in soft tissue tumors. The cases presented unique morphologic features that did not fit typical diagnoses, prompting further investigation. The study highlights the need for additional research to definitively classify and prognosticate these neoplasms. [Extracted from the article]

NTRK‐rearranged spindle cell neoplasm is a group of tumors characterized by NTRK1/2/3 gene fusion. Recently, tumors with other kinase fusion genes were reported to exhibit similar morphologies. Herein, we discuss an adult‐onset soft tissue tumor with similar histologic patterns as kinase gene fusion‐related tumors but with BRAF and NRAS mutations. A female in her 40s had a 40 mm tumor with an unclear border in the soft tissue of her foot joint. Short spindle‐shaped tumor cell proliferation with abundant capillaries and collagen fiber bundles were observed. The tumor infiltrated the subcutaneous adipose tissue, exhibiting a lipofibromatosis‐like pattern. Immunohistochemically, the tumor cells coexpressed CD34, S‐100, and BRAF V600E. Whole‐exome sequencing revealed BRAF p.V600E and NRAS p.Q61K mutations. Since BRAF activation occurs in BRAF fusion gene tumors and BRAF mutations, they could share a similar mechanism in tumorigenesis. This case suggests the further expansion of kinase‐related spindle cell tumors. [ABSTRACT FROM AUTHOR]

Aims Methods and Results Conclusion Although molecular tests developed for a growing list of oncogenic alterations have significantly aided in the classification of head and neck carcinomas, tumours in which prototypical histologic and immunophenotypic features are lacking or only partially developed continue to pose diagnostic challenges. Searching for known diagnostic and therapeutic targets by clinical next‐generation sequencing (NGS) assays can often lead to new discoveries.We present our institutional experience in applying targeted RNA NGS in 36 head and neck carcinomas that were morphologically difficult to classify between 2016 and 2023. The patients ranged in age from 5 to 83 years (median, 64), with the majority of tumors occurring in the major salivary glands and the sinonasal tract. Overall, seven (19%) cases showed unusual gene rearrangements, including five novel alterations: MON2::STAT6 in a hard palate adenocarcinoma with mucinous features, POC5::RAF1 in apocrine intraductal carcinoma of the lacrimal gland, EWSR1::CDADC1 fusion in a basaloid carcinoma of the submandibular gland, NFATC2::NUTM2B in myoepithelial carcinoma, and NSD3::NCOA2 fusion in a peculiar high‐grade carcinoma with a peritheliomatous growth pattern, and focal myogenic differentiation. Potential therapeutic actionability was identified in three cases (RAF1 and FGFR2 fusions).These findings broaden the current spectrum of gene rearrangements in head and neck carcinomas and support the utility of clinical NGS in identifying unusual, actionable alterations in diagnostically challenging cases. [ABSTRACT FROM AUTHOR]

Renal medullary carcinoma is a rare, high‐grade carcinoma arising in the renal medulla, which is usually associated with sickle cell trait, and there are very few documented cases in the Japanese population. We report a case of renal medullary carcinoma, immunohistochemically defined as SMARCB1 deficient, in a 67‐year‐old Japanese woman without a history of sickle cell trait. Somatic mutation of SMARCB1 and an EML4::ALK fusion gene were identified by comprehensive genomic profiling. Computed tomography revealed metastatic lesions in the retrocaval lymph nodes, liver, and bronchus. Six cycles of the dose‐dense methotrexate, vinblastine, adriamycin, and cisplatin‐combined chemotherapy were completed after an ultrasound‐guided percutaneous biopsy of the renal tumor. After chemotherapy, the size of the original tumor in the right kidney had decreased in size, as well as the other metastatic lesions. [ABSTRACT FROM AUTHOR]

NRAS Q61 mutations are driver genetic alterations associated with common melanocytic nevi. Herein, we describe a case of NRAS‐mutant melanocytic tumor with a blue nevus‐like morphology. A 71‐year‐old Japanese man presented with a 4.6‐mm nodule on his back. Histopathological examination revealed a dense distribution of spindle‐shaped melanocytes in the upper dermis and a sparse distribution of dendritic melanocytes in the mid‐dermis. The vertical periadnexal extension reached the deep dermis at the center of the tumor. A small junctional component, hyperpigmentation, sclerotic stroma, mild nuclear atypia, and a few mitotic figures were observed. Immunohistochemical examination revealed no PRAME expression and preserved p16 expression. Diffuse RASQ61R immunoreactivity was observed in these tumor cells. Nuclear β‐catenin expression was not observed. Targeted RNA sequencing revealed two mutations, NRAS c.182A>G (Q61R) and FGFR2 c.‐157A>G, but no other pathogenic alterations such as BRAF, GNAQ, GNA11, CTNNB1, PRKAR1A, or IDH1 mutations or kinase gene fusions. The histopathology fits that of compound‐type blue nevus, which is called "Kamino nevus"; however, this tumor was genetically considered to be on the spectrum of conventional acquired melanocytic nevi but not on that of blue nevi. Morphologically, NRAS‐driven melanocytic nevi resemble blue nevi without IDH1R132C coexistence. [ABSTRACT FROM AUTHOR]

Mesenchymal tumors may display morphologic and immunohistochemical overlap with melanocytic tumors, presenting a pitfall for misdiagnosis. We report a 62‐year‐old woman who presented with a recurrent dermal and subcutaneous tumor over the Achilles tendon 15 years following complete excision. Both the primary and the recurrent tumors were characterized by nests and sheets of epithelioid and spindle cells with eosinophilic cytoplasm and uniform ovoid nuclei. The tumor was positive for S100, SOX10, HMB45, cathepsin K, and p63 (weak), while negative for Melan‐A, MiTF, smooth muscle actin, and desmin. Gene fusion analysis of the recurrent tumor revealed a NONO::TFE3 fusion which has been recently reported in two similar cutaneous cases. Our case highlights the potential of a NONO::TFE3 cutaneous epithelioid and spindle cell tumor to recur after a prolonged disease‐free interval without evidence of high‐grade transformation or distant metastasis. Our findings support its classification as a cutaneous mesenchymal neoplasm of intermediate malignancy. [ABSTRACT FROM AUTHOR]

The article discusses a rare soft tissue and bone neoplasm called Xanthogranulomatous Epithelial Tumor (XGET) with unique characteristics. The diagnosis of XGET requires careful evaluation due to its aggressive clinical behavior. Only a few cases of XGET have been documented, primarily in the lower extremities and trunk. The management of XGET remains challenging, with surgical resection being the mainstay of treatment, although alternative modalities such as denosumab therapy are being explored. Further research is needed to establish optimal treatment guidelines for this rare entity. [Extracted from the article]

Aims: Chondromyxoid fibroma (CMF) is a rare, benign bone tumour which arises primarily in young adults and is occasionally diagnostically challenging. Glutamate metabotropic receptor 1 (GRM1) gene encodes a metabotropic glutamate receptor and was recently shown to be up‐regulated in chondromyxoid fibroma through gene fusion and promoter swapping. The aim of this study was to interrogate cases of CMF for the presence of GRM1 gene rearrangements, gene fusions and GRM1 protein overexpression. Methods and results: Selected cases were subjected to testing by fluorescent in‐situ hybridisation (FISH) with a GRM1 break‐apart probe, a targeted RNA sequencing method and immunohistochemical study with an antibody to GRM1 protein. Two cases were subjected to whole transcriptomic sequencing. In 13 of 13 cases, GRM1 protein overexpression was detected by immunohistochemistry using the GRM1 antibody. Of the 12 cases successfully tested by FISH, nine of 12 showed GRM1 rearrangements by break‐apart probe assay. Targeted RNA sequencing analysis did not detect gene fusions in any of the eight cases tested, but there was an increase in GRM1 mRNA expression in all eight cases. Two cases subjected to whole transcriptomic sequencing (WTS) showed elevated GRM1 expression and no gene fusions. Conclusion: GRM1 gene rearrangements can be detected using FISH break‐apart probes in approximately 75% of cases, and immunohistochemical detection of GRM1 protein over‐expression is a sensitive diagnostic method. The gene fusion was not detected by targeted RNA sequencing, due most probably to the complexity of fusion mechanism, and is not yet a reliable method for confirming a diagnosis of CMF in the clinical setting. [ABSTRACT FROM AUTHOR]

The histological similarities between pleomorphic adenomas (PAs) and cutaneous mixed tumors (CMTs) found in certain facial regions can create a diagnostic challenge. Molecular findings reveal common genetic profiles, particularly PLAG1 rearrangements in both PA and CMT. Although molecular distinctions have received limited attention, our observations indicate multiple cases of CMTs carrying the TRPS1::PLAG1 fusion. This clinical experience has driven our investigation into the potential diagnostic utility of TRPS1::PLAG1 fusions for determining tumor origin. Two cohorts consisting of 46 cases of CMT and 45 cases of PA of the salivary glands were obtained from French institutions and reviewed by specialists in each subspecialty. RNA sequencing analysis was conducted to identify the molecular features of cases harboring PLAG1. Clinical, pathological, and molecular data were collected. In this study, cases of CMT exhibited recurrent gene fusions, primarily TRPS1::PLAG1 (74%). These tumors shared characteristic histological features, including tubuloductal differentiation in 55% of cases and squamous metaplasia in varying proportions. In contrast, cases of PA had gene fusions involving PLAG1 with various gene partners, with only one case in which TRPS1::PLAG1 was identified. This disparity was also observed at the transcriptomic level between TRPS1::PLAG1 CMTs and other tumors. However, TRPS1 immunostaining did not correlate with TRPS1::PLAG1 fusion. In conclusion, we report that recurrent TRPS1::PLAG1 fusion CMTs exhibit similar characteristic histological features, including tubuloductal differentiation that is associated with squamous metaplasia in around half of cases. Detection of this fusion could be valuable in correctly identifying the origin of these tumors. © 2024 The Pathological Society of Great Britain and Ireland. [ABSTRACT FROM AUTHOR]

Summary Chronic eosinophilia leukaemia—not otherwise specified (CEL‐NOS) is a rare myeloproliferative neoplasm characterized by persistent clonal hypereosinophilia. Recent advances in genetics have refined diagnostic criteria, leading to the identification of CEL subtypes with specific cytogenetic and molecular abnormalities now classified as myeloid/lymphoid neoplasms with eosinophilia and tyrosine kinase gene fusions, which may benefit from targeted therapies. In contrast, CEL‐NOS lacks specific genetic drivers and intervention points to halt leukemogenesis. Molecular techniques have also enabled the definition of clonality in a considerable percentage of cases otherwise classified as idiopathic hypereosinophilic syndrome. CEL‐NOS poses a significant therapeutic challenge due to limited treatment options, poor prognosis and the risk of progression to acute leukaemia. Patients, often elderly and with comorbidities, face restricted access to transplantation, the only potentially curative treatment. Unfortunately, the prognosis remains poor even post‐transplant, with a 5‐year survival rate of only one‐third of patients. Other therapies, including steroids, cytoreductive and immunomodulatory treatments, offer limited and temporary responses with significant side effects. This review aims to consolidate current knowledge on CEL‐NOS, covering diagnostic approaches, genetic advancements and therapeutic challenges. It seeks to provide a comprehensive overview and highlight critical areas for future research. [ABSTRACT FROM AUTHOR]

ABSTRACT Background Methods Results Conclusions Inflammatory myofibroblastic tumor (IMT) is a rare intermediate‐grade neoplasm. It presents a great challenge in diagnosis and treatment. This study aims to identify the clinicopathological characteristics of IMT.A retrospective study was conducted, enrolling patients with IMT at Peking Union Medical College Hospital from January 2013 to October 2023. Clinical information, treatments, and efficacy were analyzed.A total of 72 patients were enrolled, including 38 men and 34 women, with a median age of 46.5 years. The most common primary site included the lung (n = 15, 20.8%), intestinal tract (n = 8, 11.1%), abdominal cavity (n = 7, 9.7%), and nasal sinus (n = 5, 6.9%). Thirty patients harbored anaplastic lymphoma kinase (ALK) fusion genes; Sixty‐five (90.3%) patients underwent surgical resection, and 11 of them had postoperative recurrence. Thirty patients received systemic therapy, including nonsteroidal anti‐inflammatory drugs (n = 1), steroids (n = 5), chemotherapy (n = 7), targeted therapy (n = 2), and immune checkpoint inhibitor (n = 1).The most common site of IMT is the lung. Surgery is the main treatment for IMT, and postoperative adjuvant therapy for ALK‐positive patients needs to be focused. The molecular testing is essential for all patients diagnosed with IMTs. Systemic treatment needs further research. [ABSTRACT FROM AUTHOR]

Angiocentric glioma (AG) is a supratentorial diffuse low‐grade glioma characterized by the MYB::QKI fusion gene, showing angiocentric growth of monomorphous spindle cells with astrocytic and ependymal immunophenotypes. We describe a rare case of MYB::QKI fusion‐positive diffuse cerebellar glioma in a 54‐year‐old male. The patient initially presented with a T2/FLAIR hyperintense lesion in the left cerebellar hemisphere and slowly progressive neurological symptoms. Histopathological evaluation revealed a diffuse glioma characterized by spindle‐shaped and small epithelioid cells with perivascular infiltration. Immunohistochemistry showed positivity for glial fibrillary acidic protein and only occasionally positive for Olig2. No dot‐ or ring‐like epithelial membrane antigen immunoreactivity was observed. In this case, the proliferative activity was higher than that in typical AG cases, as manifested by multiple mitoses (four mitoses/slide) and a Ki‐67 labeling index of 5%. The tumor cells were negative for IDH1 p.R132H and H3 p.K28M mutation‐specific antibodies. Fluorescence in situ hybridization showed a MYB break‐apart signal, and reverse transcription‐polymerase chain reaction analysis confirmed an in‐frame MYB (6q23.3, exon 11, NM_001161659.2)::QKI (6q26, exon 5, NM_006775.3) fusion. IDH1 p.R132, IDH2 p.R172, H3‐3A p.K28, H3C2 p.K28, and BRAF p.V600 were all wild type. DNA methylome profiling did not match any of the established methylation classes, including the four subtypes of diffuse glioma, MYB‐ or MYBL1‐altered. Considering the results of DNA methylome profiling, the question remains as to whether this case represents a subset of AG (diffuse glioma, MYB/MYBL1‐altered) or a distinct subtype. Although the morphological findings and the presence of fusion indicated that the tumor was a cerebellar AG, the DNA methylome profile did not match that of AG. An accumulation of more cases is needed to determine the precise nature of the tumor, which may lead to an expansion of the tumor concept. [ABSTRACT FROM AUTHOR]

Aims Methods and results Conclusion Sinonasal adenosquamous carcinoma (ASC) is a rare tumour classified as a variant of squamous cell carcinoma, exhibiting both squamous and glandular differentiation. ASC has a poorer prognosis compared to sinonasal mucoepidermoid carcinoma (MEC), another uncommon tumour in this region. ASC is believed to originate from metaplastic squamous epithelium, though it may also arise from respiratory epithelium in respiratory epithelial adenomatoid hamartoma (REAH) or seromucinous glands in seromucinous hamartoma (SH).Five cases of sinonasal ASC were retrieved from our registry. Initially, they were classified as sinonasal MEC (n = 3), ASC (n = 2), and carcinoma ex REAH (n = 1). All cases showed adenosquamous malignant proliferation beneath the surface respiratory epithelium with occasional squamous metaplasia, except for one case that showed dysplasia. The respiratory epithelium exhibited an inverted growth pattern consistent with REAH/SH, and displayed atypical sinonasal glands (ASGSH) arising within seromucinous hamartoma. Next‐generation sequencing (NGS) revealed multiple pathogenic mutations in two cases, and in case 4 GGA2::PRKCB and EYA2::SERINC3 gene fusions. One case was positive for high‐risk HPV. None of the cases exhibited CRTC1/3::MAML2 gene fusion.The connection between ASGSH and ASC has not been described in the literature. There is a growing need for additional studies on the morphological, immunohistochemical, and genetic aspects of these tumours. SH/REAH may serve as precursor lesions in the progression of atypical sinonasal glands to malignancy, and their role in tumour development deserves further investigation. [ABSTRACT FROM AUTHOR]

Aims Methods and results Conclusions Sebaceous neoplasms constitute a group of adnexal tumours, including sebaceous adenoma, sebaceoma and sebaceous carcinoma. Although mismatch repair deficiency may be observed, the nature of the genetic alterations contributing to the development of most of these tumours is still unknown. In the present study, we describe the clinical, microscopic, and molecular features of eight sebaceomas with GRHL gene rearrangement.Among these sebaceomas, four occurred in women and four in men; the median age was 63 years (range = 29–89). The tumours were located in the head and neck area in all cases. Microscopic examination revealed a well‐demarcated lesion located in the dermis with focal extension into the subcutaneous tissue (three cases). The neoplasms displayed macronodular (eight cases), cribriform (seven cases) and organoid (six cases) growth patterns, occurring in combination. The tumours were mainly composed of immature basophilic cells associated with scattered mature sebocytes. Numerous small infundibular cysts were present in seven cases. Mitotic activity was low (none/one to four mitoses/mm2). Immunohistochemistry showed positivity for androgen receptor and p63. Preserved expression of MLH1, PMS2, MSH2 and MSH6 was observed in all cases. RNA‐sequencing revealed RCOR1::GRHL2 (three cases), BCL6::GRHL1 (two cases), a BCOR::GRHL2 (one case), RCOR1::GRHL1 (one case) and TLE1::GRHL1 (one case) fusion transcript. Methylation analysis demonstrated that GRHL‐fused sebaceomas form an independent cluster and highlight the proximity of such tumours with poromas with folliculo‐sebaceous differentiation.In conclusion, we report recurrent fusions of the GRHL genes in a distinctive subset of sebaceomas harbouring infundibulocystic differentiation, a frequent organoid growth pattern and lack of mismatch repair deficiency. [ABSTRACT FROM AUTHOR]

ABSTRACT CIC::DUX4 fusion sarcoma represents a rare and aggressive subtype of undifferentiated small round blue cell tumors. We report on a 23‐year‐old African male who developed a rapidly enlarging inferolateral left buttock nodule with ulceration. After debulking excision of the lesion, histologic sections demonstrated sheets and lobules of atypical round blue cells with significant cytologic atypia. Prominent foci of atypical mitotic figures and tissue necrosis were present. Tumoral cells stained strongly and diffusely using MDM2, vimentin, WT1 and CD99 immunohistochemical (IHC) markers. Molecular testing was performed and highlighted CIC::DUX4 gene fusion positivity, making the diagnosis of a CIC::DUX4 sarcoma (CDS). Post‐surgical excision, the patient showed no disease on imaging and underwent five cycles of adjuvant chemotherapy with no recurrence observed at the eight‐month follow‐up. With fewer than 200 cases reported in the literature and somewhat nonspecific clinicopathologic characteristics, CIC::DUX4 sarcoma presents a diagnostic challenge. This case underlines the importance of molecular diagnostics in undifferentiated sarcomas and presents a rare primary cutaneous manifestation of CIC::DUX4 fusion sarcoma. Additionally, we provide a review of the literature to aid in recognition, diagnosis, and treatment of this rare entity. [ABSTRACT FROM AUTHOR]

Synovial Sarcomas (SS) are characterized by the presence of the SS18::SSX fusion gene, which protein product induce chromatin changes through remodeling of the BAF complex. To elucidate the genomic events that drive phenotypic diversity in SS, we performed RNA and targeted DNA sequencing on 91 tumors from 55 patients. Our results were verified by proteomic analysis, public gene expression cohorts and single‐cell RNA sequencing. Transcriptome profiling identified three distinct SS subtypes resembling the known histological subtypes: SS subtype I and was characterized by hyperproliferation, evasion of immune detection and a poor prognosis. SS subtype II and was dominated by a vascular‐stromal component and had a significantly better outcome. SS Subtype III was characterized by biphasic differentiation, increased genomic complexity and immune suppression mediated by checkpoint inhibition, and poor prognosis despite good responses to neoadjuvant therapy. Chromosomal abnormalities were an independent significant risk factor for metastasis. KRT8 was identified as a key component for epithelial differentiation in biphasic tumors, potentially controlled by OVOL1 regulation. Our findings explain the histological grounds for SS classification and indicate that a significantly larger proportion of patients have high risk tumors (corresponding to SS subtype I) than previously believed. [ABSTRACT FROM AUTHOR]

Summary: Rearrangement of NUTM1 gene (NUTM1r) is one of the most frequent aberrations occurring in infants (younger than 1 year at diagnosis) with B‐cell precursor Acute Lymphoblastic Leukaemia (BCP‐ALL). In this study we had the unique opportunity to analyze the umbilical cord blood (UCB) sample from one infant patient with NUTM1r BCP‐ALL. Herein we reported for the first time that NUTM1r infant ALL arise prenatally, as both the patient‐specific CUX1::NUTM1 fusion gene, as well as two IG/TR leukaemic markers were already present and detectable in the patient's UCB at birth. Our results clearly demonstrate the prenatal origin of NUTM1r infant BCP‐ALL. [ABSTRACT FROM AUTHOR]

Background: Activating BRAF gene alterations are central to melanocytic tumor pathogenesis. A small, emerging subset of melanocytic tumors driven by BRAF fusions has distinct therapeutic implications and has been described to have Spitzoid morphology patterns. However, such morphological patterns do not encompass all cases, and little is known about the functional molecular events. Materials and Methods: We conducted a retrospective search through our molecular archives to identify melanocytic tumors with BRAF fusions. We reviewed clinical, histopathological, and genomic features. We further explored transcriptomic and protein‐level findings. Results: Histopathologic patterns varied, with many cases without a distinctive pattern. We identified novel and diverse BRAF gene fusion partners. Differential transcriptomic analysis between low‐risk BRAF fusion tumors and reference BRAF V600E tumors showed no differentially expressed genes. However, quantitatively stronger MAPK pathway activation of BRAF fusion tumors over BRAF V600E tumors was demonstrated by statistically significant stronger staining of p‐ERK immunohistochemistry. Gene‐specific RNA analysis shows comparable BRAF transcript levels between the two groups. Discussion and Conclusion: The quantitatively stronger activation of the MAPK pathway of BRAF fusion tumors, instead of qualitatively different transcriptomes, may account for the morphology difference from conventional BRAF V600E tumors. BRAF fusions likely act through dysregulated protein function rather than RNA upregulation related to the characteristics of the fusion partners. [ABSTRACT FROM AUTHOR]

PRRX1‐fused mesenchymal neoplasm is a recently identified, rare subcutaneous soft tissue neoplasm that is characterized by fusion of PRRX1 (exon 1) with NCOA1 (exon 13) in the majority of reported cases. Although initially considered to be fibroblastic, a possibility of neural or neuroectodermal differentiation has been suggested in a subset of cases. We report a 26‐year‐old female with a 4.0 cm painless mass located in the subcutis of the left thigh. Microscopically, the tumor was well‐circumscribed and multinodular and was composed of relatively monomorphic ovoid to spindle cells arranged in loose fascicles, trabeculae, and cords within alternating myxoid and fibrous matrix, and vascularized stroma. Mitotic figures were scarce and necrosis was not observed. By immunohistochemistry, the neoplastic cells demonstrated focal co‐expression of S100 protein and SOX10 and were negative for epithelial membrane antigen, smooth muscle actin, desmin, CD34, STAT6, HMB45, Melan‐A, and MUC4. The expression of Rb1 was retained. Targeted RNA‐sequencing identified a novel transcript fusion of PRRX1 (exon 1)::NCOA1 (exon 15), which was further confirmed by reverse transcription polymerase chain reaction and Sanger sequencing. The tumor was narrowly excised and no tumor recurrence or metastasis was identified after 13 months of follow‐up. In summary, we report a new case of PRRX1‐fused mesenchymal neoplasm, expanding the molecular genetic spectrum and providing further support for possible neural or neuroectodermal differentiation of this emerging soft tissue tumor entity. [ABSTRACT FROM AUTHOR]

CIC‐rearranged sarcomas comprise a group of exceptionally aggressive round‐cell sarcomas. These tumors most commonly demonstrate CIC::DUX4 fusion and show similar histopathology to Ewing sarcomas, though lesions mimicking vascular neoplasms have recently been described. Here, we describe a case of a patient with CIC::DUX4 fusion sarcoma identified using RNA‐based molecular testing who was initially diagnosed with an endothelial neoplasm. The tumor showed extensive vasoformative growth, complete WT1 negativity, and global positive staining for ERG, CD31, and DUX4 by immunohistochemistry. Methylation testing of the tumor clustered more closely with angiosarcomas than with CIC‐rearranged sarcomas. Our findings suggest that CIC::DUX4 fused neoplasms may demonstrate a more diverse phenotypic range than previously appreciated and offer evidence that both molecular and immunohistochemical studies are needed for accurate diagnosis. [ABSTRACT FROM AUTHOR]

Aims: A subset of exceptionally rare primary renal perivascular epithelioid cell tumours (PEComas) that harbour Xp11.2 translocation have been reported, but no larger series devoted to this topic have been published. Methods and Results: We describe the clinicopathological and molecular features of 10 renal PEComas, collected from our routine and consultation files. There were five female and five male patients aged 14–65 (median: 32 years). One patient had a history of childhood neuroblastoma, but no patients were known to have a tuberous sclerosis complex or other hereditary disorder. Complete surgical excision was the treatment for all patients. The available follow‐up in five patients indicated a favourable outcome in 4/5 cases. Tumour size ranged from 2.8 to 15.2 cm (median, 5.2 cm). Immunohistochemistry revealed consistently strong TFE3 expression in all tumours, whereas PAX8 and keratin cocktails were uniformly negative. Other positive markers included HMB45 (7/9 tumours), CathepsinK (7/9 tumours), and CD117 (KIT) (3/5 tumours). TFE3 rearrangements were detected in 8/9 tumours (by targeted RNA sequencing in seven and by FISH in one). The identified fusion partners included SFPQ (n = 2) and one tumour each with ASPSCR1, ZC3H4, MED15, RBMX, and PRCC. One tumour that lacked TFE3 rearrangement by next‐generation sequencing (NGS) and fluorescence in situ hybridization (FISH) revealed a large intrachromosomal deletion involving PKD1 and TSC2 by DNA‐based NGS. Conclusion: This study highlights the morphologic and genetic diversity of TFE3‐rearranged primary renal PEComas and underlines the value of surrogate TFE3 immunohistochemistry in identifying them. The lack of PAX8 and keratin expression represents the mainstay for distinguishing these tumours from MiTF‐associated renal cell carcinomas. In addition, we report rare (ZC3H4, RBMX) and novel (MED15) TFE3 fusion partners in PEComa. [ABSTRACT FROM AUTHOR]

This article reports on two cases of testicular sclerosing stromal tumors (SSTs) that show GLI1 gene alterations. SSTs are neoplasms that were first described in the ovary in 1973 and are characterized by lobulated microscopic appearance. The patients in these cases were aged 35 and 65 years and presented with testicular masses. The tumors demonstrated large areas of hypocellular myxoid/oedematous stroma with scattered hypercellular areas. Both tumors expressed nuclear GLI1. The article suggests that these findings support the existence of rare SSTs in the testis and their potential pathogenesis related to ovarian SSTs. [Extracted from the article]

This article discusses a case of cellular congenital mesoblastic nephroma (CMN) with focal anaplasia in a 12-month-old male patient. The patient presented with constipation and was found to have a right renal mass. The nephrectomy specimen showed features of CMN with a single focus of anaplasia. Molecular testing confirmed the presence of an ETV6::NTRK3 fusion. The rarity of anaplasia in CMN makes this case noteworthy, and further studies are needed to determine the clinical significance of this finding. [Extracted from the article]

CREB gene family (ATF1, CREB1, CREM) fusions with either EWSR1 or FUS gene partners drive the pathogenesis of a wide range of neoplasms, including various soft tissue tumors, intracranial myxoid mesenchymal tumors (IMMTs), hyalinizing clear cell carcinoma (HCCC), and rare mesotheliomas. Recently, a SMARCA2::CREM fusion was reported in one case each of IMMT and HCCC. In this study, we expand the clinicopathologic and molecular spectrum of these neoplasms by describing three additional cases with SMARCA2::CREM and one with a novel SMARCA4::CREM fusion, highlighting the recurrent potential of additional CREB gene fusion partners beyond FET family members. To evaluate if these fusions define a new pathologic entity, we performed a comprehensive genomic and methylation analysis and compared the results to other related tumors. Tumors occurred in children and young adults (median age 20 years) and spanned a broad anatomic distribution, including soft tissue, intracranial, head and neck, and prostatic urethra. Microscopically, the tumors shared an undifferentiated round to epithelioid cell phenotype and a hyalinized fibrous stroma. Immunohistochemically, a polyphenotypic profile was observed, with variable expression of SOX10, desmin, and/or epithelial markers. No targetable genomic alterations were found using panel‐based DNA sequencing. By DNA methylation and transcriptomic analyses, tumors grouped closely to FET::CREB entities, but not with SMARCA4/SMARCB1‐deficient tumors. High expression of CREM by immunohistochemistry was also documented in these tumors. Patients experienced local recurrence (n = 2), locoregional lymph node metastases (n = 2), and an isolated visceral metastasis (n = 1). Overall, our study suggests that SMARCA2/4::CREM fusions define a distinct group of neoplasms with round cell to epithelioid histology, a variable immunoprofile, and a definite risk of malignancy. Larger studies are needed to further explore the pathogenetic relationship with the FET::CREB family of tumors. © 2024 The Pathological Society of Great Britain and Ireland. [ABSTRACT FROM AUTHOR]

Myxofibrosarcoma (MFS) and undifferentiated pleomorphic sarcoma (UPS) are two common and aggressive subtypes of soft tissue sarcoma. The aim of this study was to assess potential transcriptomic differences between MFS and UPS tumours and to evaluate the extent to which differences in gene expression profiles were associated with genomic and clinical features. The study included 162 patients with tumours diagnosed as MFS (N = 62) or UPS (N = 100). The patients had been diagnosed and treated at two Swedish sarcoma centres during a 30‐year period. For gene expression profiling and gene fusion detection all tumours were analysed using RNA‐sequencing and could be compared with data on clinical outcome (N = 155), global copy number profiles (N = 145), and gene mutations (N = 128). Gene expression profiling revealed three transcriptomic clusters (TCs) without any clear separation of MFS and UPS. One TC was associated with longer metastasis‐free survival. These tumours had lower tumour mutation burden (TMB), were enriched for a copy number signature representative of focal LOH and chromosomal instability on a diploid background, and were relatively immune‐depleted. MFS and UPS showed extensive genomic overlap, with whole genome doubling occurring more frequently among the latter. The results support the idea that MFS and UPS tumours have largely overlapping genomic and transcriptomic features, with UPS tumours showing more aggressive behaviour and more complex genomes. Independently of the tumour type, clinically relevant subgroups were revealed by gene expression analysis, and the finding of multiple genomic subgroups strongly suggest the existence of subgroups of relevance to treatment stratification. © 2024 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland. [ABSTRACT FROM AUTHOR]

Myxoid liposarcoma (MLPS) is a rare sarcoma, typically arising in deep soft tissues during the fourth to fifth decades of life. Histologically, MLPS is composed of uniform oval cells within a background of myxoid stroma and chicken‐wire capillaries. Genetically, MLPS is characterized by the FUS/EWSR1::DDIT3 fusion gene, which generally results from balanced interchromosomal translocation and is detectable via DDIT3 break‐apart fluorescence in situ hybridization (FISH). Here, we report an unusual intra‐articular MLPS case, negative for DDIT3 break‐apart FISH but positive for EWSR1::DDIT3. An 18‐year‐old female was referred to our hospital complaining of an intra‐articular mass in the right knee joint. Histologically, the tumor was mainly composed of mature adipocytes, brown fat‐like cells, and lipoblasts. Nanopore sequencing detected DNA rearrangements between EWSR1 and DDIT3 and clustered complex rearrangements involving multiple chromosomes, suggesting chromoplexy. Methylation classification using random forest, t‐distributed stochastic neighbor embedding, and unsupervised hierarchical clustering correctly classified the tumor as MLPS. The copy number was almost flat. The TERT promoter C‐124T was also detected. This report highlights, for the first time, the potential value of a fast and low‐cost nanopore sequencer for diagnosing sarcomas. [ABSTRACT FROM AUTHOR]

The dynamicity of the mitochondrial network is crucial for meeting the ever‐changing metabolic and energy needs of the cell. Mitochondrial fission promotes the degradation and distribution of mitochondria, while mitochondrial fusion maintains mitochondrial function through the complementation of mitochondrial components. Previously, we have reported that mitochondrial networks are tubular, interconnected, and well‐organized in young, healthy C. elegans, but become fragmented and disorganized with advancing age and in models of age‐associated neurodegenerative disease. In this work, we examine the effects of increasing mitochondrial fission or mitochondrial fusion capacity by ubiquitously overexpressing the mitochondrial fission gene drp‐1 or the mitochondrial fusion genes fzo‐1 and eat‐3, individually or in combination. We then measured mitochondrial function, mitochondrial network morphology, physiologic rates, stress resistance, and lifespan. Surprisingly, we found that overexpression of either mitochondrial fission or fusion machinery both resulted in an increase in mitochondrial fragmentation. Similarly, both mitochondrial fission and mitochondrial fusion overexpression strains have extended lifespans and increased stress resistance, which in the case of the mitochondrial fusion overexpression strains appears to be at least partially due to the upregulation of multiple pathways of cellular resilience in these strains. Overall, our work demonstrates that increasing the expression of mitochondrial fission or fusion genes extends lifespan and improves biological resilience without promoting the maintenance of a youthful mitochondrial network morphology. This work highlights the importance of the mitochondria for both resilience and longevity. [ABSTRACT FROM AUTHOR]

Solitary fibrous tumor (SFT) is a spindle cell tumor driven by the NAB2‐STAT6 fusion gene. While it can originate from any soft tissue, primary SFT of the pancreas is rare with limited reports. A 36‐year‐old man came to our department due to abdominal pain. Computed tomography revealed a circular mass with weak peripheral enhancement and an internal cyst in the pancreatic tail. Diagnosis was not confirmed through endoscopic ultrasound‐guided biopsy, and differential diagnoses included acinar cell carcinoma and pancreatic neuroendocrine tumor. A robotic distal pancreatectomy with splenectomy was performed, and the patient was discharged 11 days postoperatively. Histopathological examination showed an irregular arrangement of spindle cells, and immunohistochemical staining was positive for CD34 and STAT6, confirming an SFT diagnosis with low metastatic risk. Robotic surgery effectively managed this tumor. [ABSTRACT FROM AUTHOR]

Cleft lip and/or primary palate (CL/P) represent a prevalent congenital malformation, the aetiology of which is highly intricate. Although it is generally accepted that the condition arises from failed fusion between the upper lip and primary palate, the precise mechanism underlying this fusion process remains enigmatic. In this study, we utilized transposase‐accessible chromatin sequencing (scATAC‐seq) and single‐cell RNA sequencing (scRNA‐seq) to interrogate lambdoidal junction tissue derived from C57BL/6J mouse embryos at critical stages of embryogenesis (10.5, 11.5 and 12.5 embryonic days). We successfully identified distinct subgroups of mesenchymal and ectodermal cells involved in the fusion process and characterized their unique transcriptional profiles. Furthermore, we conducted cell differentiation trajectory analysis, revealing a dynamic repertoire of genes that are sequentially activated or repressed during pseudotime, facilitating the transition of relevant cell types. Additionally, we employed scATAC data to identify key genes associated with the fusion process and demonstrated differential chromatin accessibility across major cell types. Finally, we constructed a dynamic intercellular communication network and predicted upstream transcriptional regulators of critical genes involved in important signalling pathways. Our findings provide a valuable resource for future studies on upper lip and primary palate development, as well as congenital defects. [ABSTRACT FROM AUTHOR]

B‐cell acute lymphoblastic leukaemia (B‐ALL) is the most prevalent hematologic malignancy in children and a leading cause of mortality. Managing B‐ALL remains challenging due to its heterogeneity and relapse risk. This study aimed to delineate the molecular features of paediatric B‐ALL and explore the clinical utility of circulating tumour DNA (ctDNA). We analysed 146 patients with paediatric B‐ALL who received systemic chemotherapy. The mutational landscape was profiled in bone marrow (BM) and plasma samples using next‐generation sequencing. Minimal residual disease (MRD) testing on day 19 of induction therapy evaluated treatment efficacy. RNA sequencing identified gene fusions in 61% of patients, including 37 novel fusions. Specifically, the KMT2A‐TRIM29 novel fusion was validated in a boy who responded well to initial therapy but relapsed after 1 year. Elevated mutation counts and maximum variant allele frequency in baseline BM were associated with significantly poorer chemotherapy response (p = 0.0012 and 0.028, respectively). MRD‐negative patients exhibited upregulation of immune‐related pathways (p < 0.01) and increased CD8+ T cell infiltration (p = 0.047). Baseline plasma ctDNA exhibited high mutational concordance with the paired BM samples and was significantly associated with chemotherapy efficacy. These findings suggest that ctDNA and BM profiling offer promising prognostic insights for paediatric B‐ALL management. [ABSTRACT FROM AUTHOR]

The article discusses a rare case of an ectomesenchymal chondromyxoid tumor involving the hard palate, a location uncommon for this type of tumor. The patient, a 49-year-old man, presented with a painless mass on the hard palate, which was surgically removed and confirmed to have the characteristic RREB1::MRTFB gene fusion. Molecular testing using next-generation RNA sequencing was crucial in confirming the diagnosis and ruling out other similar neoplasms. The article emphasizes the importance of accurate diagnosis through a combination of histomorphology, immunophenotypical profile, and molecular genetic analysis. [Extracted from the article]

Aims Methods and Results Conclusion The PEComa family of tumours is defined by spindle/epithelioid cells with myomelanocytic differentiation. A small subset harbours TFE3 fusion; however, YAP1::TEE3 has not been reported. Clear cell stromal tumour of the lung (CCST‐L) is an emerging entity characterized by spindle to epithelioid cells with focal cytoplasmic clearing, inflammatory infiltrates, no myomelanocytic differentiation, and YAP1::TFE3 fusion. Herein, we report two cases of lung tumours with myomelanocytic differentiation that showed inflammatory spindle cell histology, focal epithelioid clear cells, as well as YAP1::TFE3 fusion.The patients were both men, aged 61 and 68 years. The tumours in both cases presented as well‐circumscribed solid masses involving the lung hilum. After lobectomy, no recurrence was observed at 7 and 32 months. Both tumours shared storiform to short fascicular growth of long spindle cells, with a minor component of epithelioid cells showing clear cytoplasm in the background of substantial intratumoral chronic inflammation and dilated blood vessels. One tumour showed focal melanin deposition. Both tumours were immunohistochemically positive for HMB45, Melan A, and h‐caldesmon. Fluorescence in situ hybridization assays indicated the presence of YAP1::TFE3 fusions, which was confirmed by RNA sequencing in one case tested, and by immunohistochemical TFE3 expression and loss of YAP1 C‐terminus staining.We present two cases of inflammatory spindle to epithelioid cell tumours of the lungs with myomelanocytic differentiation and YAP1::TFE3 fusion. This unique morphology and gene fusion suggest that these tumours may constitute a distinct subset of lung PEComa. Furthermore, morphological and molecular overlap with CCST‐L gives rise to a hypothesis of a potential inherent relationship between PEComa and CCST‐L. [ABSTRACT FROM AUTHOR]

Backgroud: Supernatants from various cytological samples, including body cavity effusion, sputum, bronchoalveolar lavage fluid (BALF), and needle aspiration, have been validated for detecting genetic alterations using cell‐free DNA (cfDNA) in patients with non‐small cell lung cancer (NSCLC). However, the sensitivity of fusion variations detection remains challenging. The protection of cell‐free RNA (cfRNA) is critical for resolving the issue. Methods: A protective solution (PS) was applied for preserving cfRNA in cytological supernatant (CS), and the quality of protected cfRNA was assessed by cycle threshold (CT) values from reverse transcription quantitative polymerase chain reaction (RT‐qPCR). Furthermore, we collected an additional set of malignant cytological and matched tumor samples from 84 NSCLC patients, cfDNA & cfRNA extraction and double detection for driver gene mutations was validated using the multi‐gene mutations detection by RT‐qPCR. Results: Under the optimal protection system, 91.0% (101/111) of cfRNA were protected effectively. Among the 84 NSCLC patient samples, seven cytological samples failed the tests. In comparison with tumor samples, the overall sensitivity and specificity of detecting driver genes of supernatant cfDNA and cfRNA were 93.8% (74/77) and 100% (77/77), respectively. Notably, when focusing exclusively on patients with fusion gene changes, both sensitivity and specificity reached 100% (11/11) for EML4‐ALK, ROS1, RET fusions, and MET ex14 skipping. Conclusion: These findings suggest that cfDNA & cfRNA extraction and double detection strategy recommended in this study improve the accuracy of driver genes mutations test, especially for RNA‐based assay. [ABSTRACT FROM AUTHOR]

Non‐small‐cell lung cancer (NSCLC) accounts for the majority of lung cancer cases worldwide, with a significant proportion of patients harbouring actionable oncogenic alterations. Among these alterations, the ROS1 rearrangement represents a distinct subset with therapeutic implications. Here, we present the case of a 52‐year‐old man diagnosed with advanced NSCLC harbouring the ROS1 fusion gene. Despite the initial poor response to conventional chemotherapy, the patient exhibited an exceptional and sustained response to crizotinib, with a progression‐free survival of 94 months and complete metabolic response on PET scan. This case underscores the importance of molecular profiling in guiding treatment decisions and highlights the efficacy of targeted therapies for ROS1‐positive NSCLC. [ABSTRACT FROM AUTHOR]

Myositis ossificans, a benign tumor composed of spindle cells and osteoblasts, can clinically and radiologically mimic osteosarcoma. While recognition and accurate diagnosis of myositis ossificans can be a challenge, this is critical as it may allow a conservative surgical approach to maximize functional outcomes. Herein, we present a patient with surface myositis ossificans confirmed genetically by the presence of COL1A1::USP6 gene fusion, along with a literature review. Due to the enhanced visualization of the bone matrix, computed tomography (CT) imaging may be a superior imaging modality to magnetic resonance (MR) imaging. Staged biopsies with samples obtained from the periphery and center of the lesions may allow pathologists to discern the zonal distribution histologically. Furthermore, immunohistochemistry fluorescence in situ hybridization and molecular testing can aid in the distinction of myositis ossificans from mimics. Because of their resemblance to other bone tumors, these cases of myositis ossificans highlight the importance of a multidisciplinary approach integrating clinical, radiologic, and pathologic analysis and involving serial imaging, sampling, and judicious use of ancillary immunohistochemical and molecular testing. [ABSTRACT FROM AUTHOR]

Background: The concept of gene fusion describes the process of fusing two genes into one, which is closely linked to tumour occurrence and development and may even be the direct cause of some tumours. Due to their tumour‐specific expression and ability to drive tumour occurrence and development, there is great potential for fusion genes to be used as diagnostic markers and targets for specific types of tumours. Main body: Although many fusion genes have been detected so far, they mainly focus on a small number of highly recurrent fusion genes detected in patients' tumours. There are few studies on the functional mechanism and clinical relevance of rare gene fusions. Our review discusses the generation mechanisms, detection methods, biological functions, and mechanisms of action of fusion genes. Additionally, we discuss the clinical significance of fusion gene detection in some tumour types. Conclusion: The function mechanism research of rare gene fusion is very necessary, and more functions of fusion genes independent of unfused/normal genes can be explored in future studies. There is still a long way to go in implementing precision tumour therapy targeting gene fusion. [ABSTRACT FROM AUTHOR]

Dermatofibrosarcoma protuberans (DFSP) is a rare cutaneous sarcoma characterized by the COL1A1‐PDGFB fusion gene. This study utilized single‐cell RNA sequencing to dissect the cellular and molecular landscape of primary DFSP. Distinct DFSP cell clusters, exhibiting fibroblast‐like traits, revealed variations in pathways associated with proliferation, inflammation and metabolism. Differential gene expression analysis during the differentiation from tumour stem cells to DFSP cells unveiled SMOC2, DCN and TGFBR3 as potential regulators of tumour invasion and immune infiltration through VEGF/TGF‐β signalling modulation. Cellular communication analysis highlighted interactions within DFSP cell clusters and with endothelial cells, implicating molecules such as NAMPT, ANGPT2 and PTN in pathogenesis and treatment resistance. These findings offer insights into DFSP intratumour heterogeneity, elucidate molecular mechanisms underlying tumour behaviour, and suggest potential therapeutic targets. [ABSTRACT FROM AUTHOR]

The ferric uptake regulator (Fur) is a global regulator that influences the expression of virulence genes in Klebsiella pneumoniae. Bioinformatics analysis suggests Fur may involve in iron acquisition via the identified regulatory box upstream of the yersiniabactin receptor gene fyuA. To observe the impact of the gene fyuA on the virulence of K. pneumoniae, the gene fyuA knockout strain and complementation strain were constructed and then conducted a series of phenotypic experiments including chrome azurol S (CAS) detection, crystal violet staining, and wax moth virulence experiment. To examine the regulatory relationship between Fur and the gene fyuA, green fluorescent protein (GFP) reporter gene fusion assay, real‐time quantitative reverse transcription polymerase chain reaction (RT‐qPCR), gel migration assay (EMSA), and DNase I footprinting assay were used to clarify the regulatory mechanism of Fur on fyuA. CAS detection revealed that the gene fyuA could affect the generation of iron carriers in K. pneumoniae. Crystal violet staining experiment showed that fyuA could positively influence biofilm formation. Wax moth virulence experiment indicated that the deletion of the fyuA could weaken bacterial virulence. GFP reporter gene fusion experiment and RT‐qPCR analysis revealed that Fur negatively regulated the expression of fyuA in iron‐sufficient environment. EMSA experiment demonstrated that Fur could directly bind to the promoter region of fyuA, and DNase I footprinting assay further identified the specific binding site sequences. The study showed that Fur negatively regulated the transcriptional expression of fyuA by binding to upstream of the gene promoter region, and then affected the virulence of K. pneumoniae. [ABSTRACT FROM AUTHOR]

Background: ZNF384‐fusion (Z‐fusion) genes were recently identified in B‐cell acute lymphoblastic leukemia (B‐ALL) and are frequent in Japanese adult patients. The frequency is about 20% in those with Philadelphia chromosome‐negative B‐ALL. ZNF384 is a transcription factor and Z‐fusion proteins have increased transcriptional activity; however, the detailed mechanisms of leukemogenesis of Z‐fusion proteins have yet to be clarified. Methods: We established three transfectants of cell lines expressing different types of Z‐fusion proteins, and analyzed their gene expression profile (GEP) by RNA‐seq. We also analyzed the GEP of clinical ALL samples using our previous RNA‐seq data of 323 Japanese ALL patients. We selected upregulated genes in both Z‐fusion gene‐expressing transfectants and Z‐fusion gene‐positive ALL samples, and investigated the binding of Z‐fusion proteins to regulatory regions of the candidate genes by ChIP‐qPCR. Results: We selected six commonly upregulated genes. After the investigation by ChIP‐qPCR, we finally identified CREB5 and RGS1 as direct and common target genes. RGS1 is an inhibitor of CXCL12‐CXCR4 signaling that is required for the homing of hematopoietic progenitor cells to the bone marrow microenvironment and development of B cells. Consistent with this, Z‐fusion gene transfectants showed impaired migration toward CXCL12. Conclusions: We identified CREB5 and RGS1 as direct and common transcriptional targets of Z‐fusion proteins. The present results provide novel insight into the aberrant transcriptional regulation by Z‐fusion proteins. [ABSTRACT FROM AUTHOR]

The article discusses a case of a rapidly enlarging ACTIN::MITF rearranged clear cell tumor with melanocytic differentiation in a 53-year-old male. The tumor exhibited unique clinicopathological features, including large size, rapid growth, marked ulceration, and increased mitotic activity. The study raises questions about the classification of these tumors and their relationship to PEComa, emphasizing the need for further research to understand their biological behavior and prognostic significance. [Extracted from the article]

The article in the journal "Histopathology" discusses a case of NTRK fusion cervical sarcoma with rhabdoid cells in a 42-year-old woman with a history of metastatic papillary thyroid carcinoma. The article details the histopathological findings, differential diagnosis, immunohistochemical studies, and molecular testing conducted to confirm the NTRK fusion sarcoma diagnosis. The study highlights the importance of comprehensive molecular testing in cases with rare morphological features and emphasizes the evolving nature of the diagnosis and classification of NTRK-rearranged gynaecological tumors. [Extracted from the article]

Introduction: A neurotrophic tropomyosin receptor kinase (NTRK)‐tyrosine kinase inhibitor (TKI) has shown dramatic efficacy against malignant tumors harboring an NTRK fusion gene. However, almost all tumors eventually acquire resistance to NTRK‐TKIs. Method: To investigate the mechanism of resistance to NTRK‐TKIs, we established cells resistant to three types of NTRK‐TKIs (larotrectinib, entrectinib, and selitrectinib) using KM12 colon cancer cells with a TPM3‐NTRK1 rearrangement. Result: Overexpression of 3‐hydroxy‐3‐methylglutaryl‐CoA synthase 2 (HMGCS2) was observed in three resistant cells (KM12‐LR, KM12‐ER, and KM12‐SR) by microarray analysis. Lower expression of sterol regulatory element‐binding protein 2 (SREBP2) and peroxisome proliferator activated receptor α (PPARα) was found in two cells (KM12‐ER and KM12‐SR) in which HMGCS2 was overexpressed compared to the parental KM12 and KM12‐LR cells. In resistant cells, knockdown of HMGCS2 using small interfering RNA improved the sensitivity to NTRK‐TKI. Further treatment with mevalonolactone after HMGCS2 knockdown reintroduced the NTRK‐TKI resistance. In addition, simvastatin and silibinin had a synergistic effect with NTRK‐TKIs in resistant cells, and delayed tolerance was observed after sustained exposure to clinical concentrations of NTRK‐TKI and simvastatin in KM12 cells. In xenograft mouse models, combination treatment with entrectinib and simvastatin reduced resistant tumor growth compared with entrectinib alone. Conclusion: These results suggest that HMGCS2 overexpression induces resistance to NTRK‐TKIs via the mevalonate pathway in colon cancer cells. Statin inhibition of the mevalonate pathway may be useful for overcoming this mechanistic resistance. [ABSTRACT FROM AUTHOR]

Background: Members of the neurotrophic tropomyosin receptor kinase (NTRK) gene family, NTRK1, NTRK2, and NTRK3 encode TRK receptor tyrosine kinases. Intra‐ or inter‐chromosomal gene rearrangements produce NTRK gene fusions encoding fusion proteins which are oncogenic drivers in various solid tumors. Methods: This study investigated the prevalence of NTRK fusion genes and identified fusion partners in Japanese patients with solid tumors recorded in the Center for Cancer Genomics and Advanced Therapeutics database of comprehensive genomic profiling test. Results: In the analysis population (n = 46,621), NTRK fusion genes were detected in 91 patients (0.20%). The rate was higher in pediatric cases (<18 years; 1.69%) than in adults (0.16%). NTRK gene fusions were identified in 21 different solid tumor types involving 38 different partner genes including 22 (57.9%) previously unreported NTRK gene fusions. The highest frequency of NTRK gene fusions was head and neck cancer (1.31%) and thyroid cancer (1.31%), followed by soft tissue sarcoma (STS; 0.91%). A total of 97 NTRK fusion gene partners were analyzed involving mainly NTRK1 (49.5%) or NTRK3 (44.2%) gene fusions. The only fusion gene detected in head and neck cancer was ETV6::NTRK3 (n = 22); in STS, ETV6::NTRK3 (n = 7) and LMNA::NTRK1 (n = 5) were common. Statistically significant mutual exclusivity of NTRK fusions with alterations was confirmed in TP53, KRAS, and APC. NTRK gene fusion was detected from 11 STS cases: seven unclassified sarcoma, three sarcoma NOS, and one Ewing sarcoma. Conclusions: NTRK gene fusion identification in solid tumors enables accurate diagnosis and potential TRK inhibitor therapy. [ABSTRACT FROM AUTHOR]

Background: Non‐small‐cell lung cancer (NSCLC) is the primary cause of brain metastases (BM). This study aimed to investigate differences in clinical and magnetic resonance imaging (MRI) features of BM between anaplastic lymphoma kinase (ALK) gene fusion (ALK+) and ALK wild‐type (ALK‐) NSCLC, and to preliminarily assess the efficacy of radiotherapy for treating BM. Methods: A retrospective analysis included 101 epidermal growth factor receptor (EGFR)‐ NSCLC patients with BM: 41 with ALK gene fusion and 60 being ALK‐. The brain MRI and clinical features were compared between different ALK status using the multivariate analysis, and a nomogram was constructed to predict ALK gene fusion. Fifty‐six patients who did not undergo cerebral surgery and had complete pre‐ and post‐ treatment data were further divided based on whether they received radiotherapy. Log‐rank test was used to compare the short‐term effect of treatment between the two groups under different genotypes. Results: ALK+ BM exhibited decreased peritumoral brain edema size, lower peritumoral brain edema index (PBEI), and a more homogeneous contrast enhancement pattern compared to ALK‐ BM. Age (OR = 1.04; 95%CI: 1.02–1.06), time to BM (OR = 1.50; 95% CI: 1.04–2.14), PBEI (OR = 1.26; 95% CI: 0.97–1.62), smoking status (smoking index >400 vs. non‐smoking status: OR = 1.42; 95% CI: 0.99–2.04) and contrast enhancement pattern (OR = 1.89; 95% CI: 1.28–2.78) were associated with ALK gene fusion. A nomogram based on these variables demonstrated acceptable predictive efficiency (AUC = 0.844). In the ALK+ group, patients who received radiotherapy did not show increased disease control rate (DCR) or progression‐free survival (PFS). In contrast, in the ALK‐ group, those who received radiotherapy had improved objective response rate (ORR), DCR, and PFS compared to those who were only treated with systemic therapy. Conclusions: The clinical and MRI features of BM can indicate the status of ALK in NSCLC. In the ALK‐ group, patients who received radiotherapy showed higher ORR, DCR, and PFS compared to those who did not. [ABSTRACT FROM AUTHOR]

Background: Cholangiocarcinoma (CCA) is a fatal cancer of the bile duct with a poor prognosis owing to limited therapeutic options. The incidence of intrahepatic CCA (iCCA) is increasing worldwide, and its molecular basis is emerging. Environmental factors may contribute to regional differences in the mutation spectrum of European patients with iCCA, which are underrepresented in systematic genomic and transcriptomic studies of the disease. Methods: We describe an integrated whole‐exome sequencing and transcriptomic study of 37 iCCAs patients in Germany. Results: We observed as most frequently mutated genes ARID1A (14%), IDH1, BAP1, TP53, KRAS, and ATM in 8% of patients. We identified FGFR2::BICC1 fusions in two tumours, and FGFR2::KCTD1 and TMEM106B::ROS1 as novel fusions with potential therapeutic implications in iCCA and confirmed oncogenic properties of TMEM106B::ROS1 in vitro. Using a data integration framework, we identified PBX1 as a novel central regulatory gene in iCCA. We performed extended screening by targeted sequencing of an additional 40 CCAs. In the joint analysis, IDH1 (13%), BAP1 (10%), TP53 (9%), KRAS (7%), ARID1A (7%), NF1 (5%), and ATM (5%) were the most frequently mutated genes, and we found PBX1 to show copy gain in 20% of the tumours. According to other studies, amplifications of PBX1 tend to occur in European iCCAs in contrast to liver fluke‐associated Asian iCCAs. Conclusions: By analyzing an additional European cohort of iCCA patients, we found that PBX1 protein expression was a marker of poor prognosis. Overall, our findings provide insight into key molecular alterations in iCCA, reveal new targetable fusion genes, and suggest that PBX1 is a novel modulator of this disease. [ABSTRACT FROM AUTHOR]

Gene fusions have emerged as crucial molecular drivers of oncogenesis in a subset of cutaneous adnexal neoplasms, including poroid neoplasms and hidradenomas. We present a unique case of primary cutaneous apocrine carcinoma harboring RARA::NPEPPS fusion, broadening the spectrum of fusion‐associated cutaneous adnexal neoplasms. A 77‐year‐old African American male presented with an ulcerated thigh nodule. Histopathologically, the predominantly dermal‐based adenocarcinoma exhibited papillary, micropapillary, cribriform, and solid growth patterns with central comedonecrosis, set in a fibrotic/desmoplastic stroma. Immunophenotypically, the neoplastic cells were positive for CK7, CK19, GATA3, TRPS1, HER2, CK5/6, calretinin, p63, and DPC4 (no loss), while lacking immunoreactivity for CK20, CDX2, TTF1, napsin‐A, PAX8, arginase‐1, adipophilin, NKX3.1, uroplakin II, and D2‐40. The immunoprofile and clinical and radiographic absence of any internal malignancy, including breast carcinoma, except for multiple lymphadenopathy, supported the diagnosis of primary cutaneous apocrine carcinoma. Next‐generation sequencing unveiled the novel RARA::NPEPPS fusion, concurrent ERBB2 amplification, and multiple somatic mutations involving TP53, CDKN2A, BRCA2, PIK3CA, PIK3R1, and others. The patient developed widespread metastases within a year after the initial diagnosis, indicating the tumor's aggressive behavior. This novel fusion, unprecedented in any human malignancies including primary cutaneous adnexal carcinomas, may suggest a potential new subtype within primary cutaneous adnexal carcinoma. [ABSTRACT FROM AUTHOR]