Molecular correlates of male germ cell tumors with overgrowth of components resembling somatic malignancies

MicroRNA-371-373 cluster and methylome analysis suggests that a subset of 'somatic-type' malignancies arising in germ cell tumors may originate in yolk sac tumor components

Somatic-type malignancies (SMs) arising in germ cell tumors (GCTs) are aggressive neoplasms resistant to systemic treatment. Most are diagnosed in metastatic sites after chemotherapy; however, they have also been well-documented in primary testicular GCTs. Historically, SMs were thought to originate in components of teratoma that acquire molecular alterations equivalent to those that characterize their true somatic counterparts. However, recent studies have shown that SMs typically lack the hallmark molecular alterations seen in similar somatic tumors. Additionally, clinicopathologic and molecular data suggest that a subset may derive from yolk sac tumor (YST) rather than teratoma. In this study, we evaluated the relationship between conventional histological types of GCTs and SMs by comparing expression of microRNA (miR)-371-373 and genomic methylation profiles. A total of 96 samples (including multiple paired conventional GCT-SM samples from individual tumors) were assessed for miR-371-373 expression by RT-qPCR and genomic DNA methylation using a clinically validated assay. Expression of miR-371-373 was higher in conventional GCTs than in SMs (considered as a single category encompassing all histological subtypes). However, miR-371-373 expression was heterogeneous among SMs, with significantly higher levels in sarcomatoid YST (SYST) and glandular neoplasms than in other SMs. Genomic DNA methylation analysis showed that SMs (considered as a single category) did not form a distinct cluster. Instead, they grouped into multiple clusters that did not show perfect correspondence with histology and often included conventional GCTs. Genome-wide methylation assessment showed a higher abundance of hypermethylated regions in SMs than in conventional GCTs. Analysis of paired conventional GCT and 'somatic-type' components that did not meet size criteria for SMs dissected from individual tumors demonstrated separation according to histology, suggesting that epigenetic processes play a role in the transition from conventional GCT to 'somatic-type' phenotypes. Gene-level and pathway-level analyses identified MAPK/RAS signaling, mitosis/proliferation, differentiation towards neural tissue/neuroectoderm, epithelial-to-mesenchymal transition, and DNA repair as key differentially regulated processes in components with somatic-type histology, suggesting mechanisms of progression from conventional to 'somatic' phenotypes in GCT. These results support the hypothesis that a subset of SMs derive from YST and suggest that some subtypes (such as SYST) may represent 'intermediate' phenotypes. Additionally, analysis of differentially methylated promoter regions in SM identified genes and biologic processess that may underlie 'somatic tranformation' in GCTs. © 2025 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Molecular Diversity of Embryonic-Type Neuroectodermal Tumors Arising From Testicular Germ Cell Tumors

Embryonic-type neuroectodermal tumors (ENTs) arising from testicular germ cell tumors (GCTs) are a relatively common type of somatic transformation in GCTs with poor prognosis and limited therapeutic options, particularly when patients develop disease recurrence or metastasis. Knowledge of key events driving this transformation is limited to the paucity of comprehensive genomic data. We performed a retrospective database search in a Clinical Laboratory Improvement Amendments- and College of American Pathologists-certified laboratory for testicular GCT-derived ENTs that had previously undergone next-generation sequencing-based comprehensive genomic profiling during the course of clinical care. Clinicopathological and genomic data were centrally rereviewed. Here, we report the molecular features of 10 ENTs of testicular GCT origin. All tumors harbored gain of chromosome 12p, often with KRAS, CCND2, and KMD5A coamplification, supporting a germ cell origin. The tumors were microsatellite-stable and exhibited a low tumor mutational burden. Three tumors (30%) exhibited MYCN or MYC amplification with co-occurring inactivation of the p53 pathway via either TP53 mutations or MDM2 amplification in 2 tumors. Three additional tumors (30%) had activation of the PI3K pathway via PIK3CA and PIK3CG mutations or PIK3C2B amplification; 1 tumor with co-occurring CDK4 amplification. Gene rearrangements were detected in 3 tumors (30%), with novel BRD4::MAU2 and BCOR::CLIP2 fusions as well as an internal truncating ATRX rearrangement, respectively. In summary, ENTs arising from GCTs are molecularly heterogeneous; however, a large fraction of testicular ENTs could be stratified by 2 distinct sets of genetic alterations, including MYCN/MYC amplification with concurrent suppression of the p53 pathway, and activation of the PI3K pathway with co-occurring CDK4 amplification. Moreover, the novel gene fusions identified in a subset of testicular GCT-derived ENTs overlap with molecularly defined tumors of embryonic-type neuroectodermal features in the central nervous system, indicating the potential common driving events for tumorigenesis from different anatomical sites.

Somatic-type Malignancies of Germ Cell Origin: Molecular, Pathologic, and Clinical Features

Somatic-type malignancies (STMs) arising in germ cell tumors are relatively rare, affecting 3% to 8% of patients. These neoplasms show aggressive clinical behavior and are frequently resistant to systemic therapy. In the current review, we provide a comprehensive clinicopathologic overview of these tumors, emphasizing new molecular findings that have improved our understanding of their pathogenesis. In all areas, we highlight special considerations related to the different histologic subtypes. We conclude with a brief mention of areas of uncertainty and areas that require further study.

Clinicopathologic and molecular characterization of primitive neuroectodermal tumors (PNET) in the female genital tract: a retrospective study of 8 cases

AIMS

This study aimed to investigate the molecular alterations in primitive neuroectodermal tumors (PNET) of the female genital tract.

METHODS

We retrospectively analyzed the clinicopathologic and immunohistochemical features of 8 gynecologic PNET cases (3 cervical, 1 vaginal, and 4 ovarian). Fluorescence in situ hybridization and targeted next-generation sequencing (NGS) were performed to identify molecular alterations in these tumors.

RESULTS

The cohort included 5 FIGO stage I, 1 stage III, and 2 stage IV tumors. Two patients with stage IV disease died at 8 and 12 months. The cervical/vaginal tumors consisted of small round blue cells arranged in sheets, with EWSR1 rearrangements and concurrent diffuse expression of membranous CD99 and nuclear FLI1. The ovarian tumors displayed diverse morphologic features resembling central nervous system (CNS) tumors, including embryonal tumor with multilayered rosettes (case 5), medulloblastoma (case 6), glioblastoma (case 7), and ependymoma (case 8). Three ovarian tumors were associated with teratomas. None of the ovarian tumors exhibited EWSR1 rearrangements or i(12p)/12p overrepresentation. NGS identified an EWSR1::exon11∼FLI1::exon6 fusion in one cervical PNET, with no additional molecular alterations. In contrast, three ovarian tumors lacked common genetic changes seen in CNS tumors but harbored several significant variants, including NTRK2 exon11 c.1019C > T (p.T340 M) (case 6), INPP4B exon23 c.2221G > A (p.V741 M) (case 7), and FANCG exon7 c.882_883insA (p.D295Rfs∗14) with MET 7q31 polysomy (case 8).

CONCLUSIONS

Our findings confirm that cervical/vaginal and ovarian PNET represent two distinct tumor types. Ovarian PNET have different pathogenetic pathways from their CNS and testicular counterparts most likely.

Analysis of HNF1β expression suggests that its downregulation is involved in the sarcomatoid transformation of yolk sac tumor

Sarcomatoid yolk sac tumor postpubertal-type (YSTpt) is a rare phenotype of germ cell tumor that occurs mostly after chemotherapy. Its diagnosis is clinically relevant but challenging, due to its somewhat inconspicuous histologic features and negative/low expression of classical YSTpt makers (α-fetoprotein (AFP), glypican-3 (GPC3), and GATA3)). HNF1β is likely a key inducer of the YSTpt phenotype, acting in part by regulating the binding of FOXA2 to its target genomic sequences. Recently, immunohistochemical studies have shown that HNF1β has a sensitivity comparable to FOXA2 (higher than GPC3 and AFP) for non-sarcomatoid YSTpt. We found that sarcomatoid YSTpt did not express HNF1β (0: 8/8 (100%)), suggesting that combined downregulation of FOXA2 and HNF1β may underlie the sarcomatoid transformation in this rare phenotype of germ cell tumor.

Deep learning-based classifier for carcinoma of unknown primary using methylation quantitative trait loci

Cancer of unknown primary (CUP) constitutes between 2% and 5% of human malignancies and is among the most common causes of cancer death in the United States. Brain metastases are often the first clinical presentation of CUP; despite extensive pathological and imaging studies, 20%-45% of CUP are never assigned a primary site. DNA methylation array profiling is a reliable method for tumor classification but tumor-type-specific classifier development requires many reference samples. This is difficult to accomplish for CUP as many cases are never assigned a specific diagnosis. Recent studies identified subsets of methylation quantitative trait loci (mQTLs) unique to specific organs, which could help increase classifier accuracy while requiring fewer samples. We performed a retrospective genome-wide methylation analysis of 759 carcinoma samples from formalin-fixed paraffin-embedded tissue samples using Illumina EPIC array. Utilizing mQTL specific for breast, lung, ovarian/gynecologic, colon, kidney, or testis (BLOCKT) (185k total probes), we developed a deep learning-based methylation classifier that achieved 93.12% average accuracy and 93.04% average F1-score across a 10-fold validation for BLOCKT organs. Our findings indicate that our organ-based DNA methylation classifier can assist pathologists in identifying the site of origin, providing oncologists insight on a diagnosis to administer appropriate therapy, improving patient outcomes.

Germ cell tumors in children

Pediatric germ cell tumors represent a rare but biologically diverse group of neoplasms arising from pluripotent primordial germ cells. The 2022 edition of the WHO Classification of Pediatric Tumors introduced the first organ independent classification of germ cell tumors, reflecting advances in molecular biology, histopathology, and clinical practice. This review highlights the key changes, including the refined distinctions between the different subtypes. These updates enhance diagnostic accuracy and provide a framework for understanding age-dependent differences in tumor biology and behavior. Emphasis is placed on integrating the new classification into multidisciplinary care, particularly in addressing diagnostic challenges in pre- and post-pubertal-type germ cell tumors. By bridging the gap between histopathology and oncology, the updated classification represents a pivotal step forward in improving outcomes for children with germ cell tumors.

Characterization of testicular embryonic-type neuroectodermal tumor and embryonic-type neuroectodermal tissue admixed with mature neuro-glial tissue using a broad immunohistochemical panel

Embryonic-type neuroectodermal tumor (ENT) is a somatic-type malignancy characterized by overgrowth of embryonic-type neuroectodermal tissue (EtNT). In germ cell tumors, EtNT is frequently intermingled with other components that may exhibit significant morphologic overlap [mature neuro-glial tissue (MNGT), nephroblastomatous tissues, and primitive endodermal-type glands]. Therefore, the quantification of EtNT (crucial for the diagnosis of ENT) can be challenging. In this study, we investigated the immunohistochemical profile of ENT, EtNT, and MNGT using a broad immunohistochemical panel. We found that SOX2 was the most sensitive marker for EtNT (100%), but it also stained MNGT (28.6%). GFAP and S100 were relatively sensitive (71.4%) and highly specific (GFAP 100%, S100 85.8%) for MNGT, whereas synaptophysin stained both. Combining our results with those of previous studies, we propose that a combination of SOX11, SOX2, GFAP, S100, AFP, villin, CDX2, PAX8, and nuclear WT1 may help to identify and quantify EtNT in germ cell tumors.

P53 Overexpression May Represent an Early Marker of Clinicopathologic Progression in Vasculogenic Mesenchymal Lesions of Germ Cell Tumor Origin

Vasculogenic mesenchymal lesions (VMLs) of germ cell tumor origin are thought to originate in postpubertal-type yolk sac tumor components and include a spectrum of lesions from teratoma with vasculogenic stroma (TVS), to low and high-grade vasculogenic mesenchymal tumors (VMTs). VMLs exhibit rudimentary to well-developed neoplastic vessels within primitive mesenchyme, being considered a neoplastic reiteration of embryonic vasculogenesis in the splanchnic mesoderm of the yolk sac. They occur in patients with primary mediastinal germ cell tumors after chemotherapy, and a subset progresses to "somatic-type" sarcomas [including angiosarcoma (AS)], with high-grade VMTs likely portending a higher risk. Recently, we encountered a low-grade VMT that progressed to metastatic AS during follow-up. In this case, both the low-grade VMT and the subsequent AS demonstrated p53 overexpression, suggesting that p53 alterations may precede histopathologic transformation. To test this hypothesis, we evaluated neoplasms representing the entire spectrum of VMLs using p53 immunohistochemistry (IHC; clone DO-7, Dako). Overexpression was defined as nuclear positivity in > 80% of neoplastic cells. Because the distinction between high-grade VMT and AS can be subjective in some cases, they were grouped together in a single category. Thirty-nine VMLs were assessed: 16 high-grade VMT/AS, 19 low-grade VMT, and 4 TVS. Patient age ranged from 19 to 46 years (mean, 30 years; male = 97%). Four high-grade VMT/AS and one low-grade VMT showed p53 overexpression (5/39 VMLs, 13%; 4/16 high-grade VMT/AS, 25%). These tumors included 1 unequivocal AS and 1 high-grade VMT/AS with progression to rhabdomyosarcoma. The only low-grade VMT with p53 overexpression demonstrated progression to AS. Another high-grade VMT that progressed to sarcoma demonstrated p53 overexpression in the sarcoma component, but it was excluded because the VMT was not represented in the material available at the time of the study. Lesions with intratumoral grade heterogeneity (classified based the highest grade), demonstrated more pronounced p53 overexpression in the high-grade components. P53 overexpression is associated with disease progression in a subset of VMTs and may precede morphologic transformation to sarcoma. Routine evaluation of VMTs with p53 IHC seems justified, with overexpressors likely requiring an close clinical surveillance.

Analysis of GATA3 and FOXA2 expression suggests that downregulation of genes involved in the maintenance of a mature yolk sac tumor phenotype may underlie sarcomatoid transformation

In the post-chemotherapy setting, germ cell tumors of the testis (GCTT) that resemble non-specific sarcomas and co-express cytokeratins and glypican-3 (GPC3) are diagnosed as "sarcomatoid yolk sac tumor postpubertal-type (YSTpt)". The diagnosis of sarcomatoid YSTpt is clinically relevant but challenging due to its rarity, non-specific histology, and negative α-fetoprotein (AFP) staining. Recently, FOXA2 has emerged as a key-gene in the reprogramming of GCTT (activating the transcription of several genes, among which GATA3), and immunohistochemical studies showed that GATA3 and FOXA2 have a higher sensitivity for non-sarcomatoid YSTpt than GPC3 and AFP. We found that sarcomatoid YSTpt did not express FOXA2 [0: 14/14 (100%)] and showed focal expression of GATA3 [0: 12/14 (85.7%), 1 + : 2/14 (14.3%)], thus suggesting that these markers are not useful in diagnosing this tumor. Furthermore, we proposed a potential mechanism of sarcomatoid transformation in the post-chemotherapy setting of GCTT, mediated by the downregulation of FOXA2 and GATA3.

SMARCB1-Deficient Skull Base Chondrosarcoma with 12p Duplication Presenting as Somatic-Type Malignancy Arising from Metastatic Seminoma

Somatic-type malignancy (STM) can occur infrequently within a primary or metastatic testicular germ cell tumor (TGCT) and is associated with dismal prognosis and survival. STM with chondrosarcomatous features is exceedingly rare and head and neck involvement has not been previously documented. A 39-year-old white man presented with nasal obstruction and epistaxis. Imaging disclosed a 6.9-cm expansile tumor involving the nasal cavity and skull base with intraorbital and intracranial extension. The histopathologic properties of the tumor were compatible with chondrosarcoma, grade II-III. Immunohistochemically, malignant cells were strongly and diffusely positive for S100 and epithelial markers, and showed loss of SMARCB1 expression. IDH1/2 mutations were not detected. Following whole-body PET scan, a 7.0-cm left testicular mass was discovered and diagnosed as seminoma with syncytiotrophoblastic cells, stage pT3NXM1b. Extensive retroperitoneal, mediastinal, and supraclavicular lymphadenopathy was also noticed. Histopathologic examination of the left supraclavicular lymph node revealed metastatic seminoma. By FISH, most metastatic nodal seminoma cells harbored 1 to 4 copies of isochromosome 12p, while the chondrosarcoma featured duplication of 12p. Presence of a malignant TGCT with disseminated supradiaphragmatic lymphadenopathy, the unique immunophenotypic properties of the skull-based chondrosarcoma and lack of IDH1/2 aberrations with gain of 12p strongly support the diagnosis of STM chondrosarcoma arising from metastatic TGCT. The patient did not respond to chemotherapy and succumbed three months after diagnosis. Although exceedingly uncommon, metastasis to the head and neck may occur in patients with TGCT. This case of STM chondrosarcoma demonstrated divergent immunophenotypic and molecular characteristics compared to "typical" examples of head and neck chondrosarcoma. High index of suspicion is advised regarding the diagnosis of lesions that present with otherwise typical histomorphology but unexpected immunohistochemical or molecular features.

Characterizing the mutational burden, DNA methylation landscape, and proteome of germ cell tumor-related somatic-type malignancies to identify the tissue-of-origin, mechanisms of therapy resistance, and druggable targets

BACKGROUND

Germ cell tumors (GCT) might undergo transformation into a somatic-type malignancy (STM), resulting in a cell fate switch to tumors usually found in somatic tissues, such as rhabdomyosarcomas or adenocarcinomas. STM is associated with a poor prognosis, but the molecular and epigenetic mechanisms triggering STM are still enigmatic, the tissue-of-origin is under debate and biomarkers are lacking.

METHODS

To address these questions, we characterized a unique cohort of STM tissues on mutational, epigenetic and protein level using modern and high-throughput methods like TSO assays, 850k DNA methylation arrays and mass spectrometry.

RESULTS AND CONCLUSIONS

For the first time, we show that based on DNA methylation and proteome data carcinoma-related STM more closely resemble yolk-sac tumors, while sarcoma-related STM resemble teratoma. STM harbor mutations in FGF signaling factors (FGF6/23, FGFR1/4) highlighting the corresponding pathway as a therapeutic target. Furthermore, STM utilize signaling pathways, like AKT, FGF, MAPK, and WNT to mediate molecular functions coping with oxidative stress, toxin transport, DNA helicase activity, apoptosis and the cell cycle. Collectively, these data might explain the high therapy resistance of STM. Finally, we identified putative novel biomarkers secreted by STM, like EFEMP1, MIF, and DNA methylation at specific CpG dinucleotides.

Testicular neoplasms: the interrelationships of serum levels of microRNA-371a-3p (M371) and classical tumor markers with histology, clinical staging, and age-a statistical analysis

PURPOSE

In testicular neoplasms, the interrelationship of elevations of the novel serum tumor marker microRNA-371a-3p (M371) and traditional markers with other clinical features is still incompletely understood. The present study evaluated marker expression rates in relation to various other clinical parameters.

METHODS

The following data were retrospectively registered from 641 consecutive patients with testicular neoplasms: histology, such as seminoma (n = 365), nonseminoma (n = 179), benign tumor (n = 79), other malignant tumor (n = 18); patients age (years); clinical stage (CS1, CS2a/b, CS2c, CS3); and preoperative elevation of beta HCG, AFP, LDH, M371 (yes/no). Descriptive statistical methods were employed with comparisons of various subgroups to disclose associations of marker expression rates with age, histology and CS, and of age with histology.

RESULTS

The histologic subgroups revealed significantly different expression rates of tumor markers. M371 performed best with expression rates of 82.69% and 93.58% in seminoma and in nonseminoma, respectively. In germ cell tumors, all markers had significantly higher expression rates in metastasized stages than in localized disease. All markers except LDH have significantly higher expression rates in younger than in older patients. Nonseminoma is most prevalent in the youngest age category, seminoma predominates in patients > 40 years, other malignancies were restricted to patients > 50 years.

CONCLUSION

The study documented significant associations of serum marker expression rates with histology, age and clinical staging, with highest rates in nonseminomas, young age and advanced clinical stages. M371 showed significantly higher expression rates than other markers suggesting its superior clinical usefulness.

Mediastinal high-grade vasculogenic mesenchymal tumour with seminoma: a case report and literature review

Germ cell tumours with somatic-type solid malignancy (GCT-STM) are a rare disease of the mediastinum. Recently, a cohort of vasculogenic mesenchymal tumour (VMT)-nonseminoma cases with different prognoses were recognized and reported. Here, we report a case of mediastinal high-grade VMT with a seminoma. A 16-year-old male had a fever, chest tightness and fatigue. Chest CT showed a 7.5 cm×5.3 cm solid mass in the right anterior mediastinum. The serum levels of alpha-fetoprotein (AFP), beta-human chorionic gonadotropin (β-HCG) and carcinoembryonic antigen (CEA) were within the normal range. Tumorectomy was performed. The tumour was irregular, and no capsule was found. The cut surface was greyish white and greyish brown with medium consistency. There were foci of bleeding and necrosis. Microscopic histology showed prominent vascular proliferation, which was lined by mildly atypical endothelial cells in a cellular stroma with significant cytologic atypia. The vascular spectrum varied from crevice-like or antler-like thin- to thick-walled vessels. Beyond the tumour area, inside the remnant thymus tissues, there were small clusters of polygonal tumour cells with clear cytoplasm, distinct cell membranes, and round to polygonal nuclei with prominent nucleoli that were positive for Oct4, PLAP, SALL4 and CD117. The patient did not receive any treatments pre- or postoperation, and his condition was stable without progression after 14 months of follow-up evaluation. Here, we added a new entity of GCT-STM of the mediastinum composed of VMT and seminoma. A better understanding of the pathological features of GCT-VMT could help pathologists improve their awareness of these rare diseases.