Scientists Discover PINNED, a Previously Unrecognized Tumor of the Pineal Gland

A team of neuropathologists and neuro-oncology researchers has identified a previously unrecognized type of brain tumor that arises in the pineal gland, the small neuroendocrine organ deep in the epithalamus that produces melatonin and regulates the circadian rhythm. The new entity, provisionally named Pineal Neoplasm with Neuroendocrine and Epithelial Differentiation, or PINNED, was described in a study published in Acta Neuropathologica. The researchers assembled a cohort of 27 tumors whose genome-wide DNA methylation profiles formed a unique and highly consistent signature that did not match any established class of central nervous system tumor and was distinct from all currently recognized pineal tumor entities. The discovery adds a sixth candidate entity to a tumor family that the 2021 World Health Organization classification currently recognizes as five distinct types, and it may change how pathologists diagnose rare masses in this anatomically crowded region of the brain.

Pineal region tumors are among the rarest neoplasms in neuro-oncology. They account for approximately 3 to 11 percent of pediatric brain tumors but constitute less than 1 percent of intracranial CNS tumors in adults, and they occur at all ages. The recognized entities span a wide biological spectrum: pineocytoma, a slow-growing WHO grade 1 tumor with a favorable prognosis that most often affects patients between 30 and 60 years; pineal parenchymal tumor of intermediate differentiation, a WHO grade 2 to 3 neoplasm characterized by small in-frame insertions in the KBTBD4 gene in up to 80 percent of cases; pineoblastoma, a highly aggressive WHO grade 4 tumor that predominantly strikes young children, particularly those under 2 years of age, and divides into five molecular subgroups; papillary tumor of the pineal region, or PTPR, a WHO grade 2 or 3 neuroepithelial tumor with an epithelial-like papillary growth pattern; and the very rare desmoplastic myxoid tumor of the pineal region, SMARCB1-mutant. Diagnosis remains challenging because these entities overlap histopathologically, which is precisely where genome-wide DNA methylation profiling has transformed the field, improving diagnostic accuracy and enabling subclassification of tumor entities that look deceptively similar under the microscope.

The PINNED cohort emerged through the CNS Tumor Methylation Classifier, a random forest-based tool that evaluates global DNA methylation patterns and returns a calibrated score indicating the similarity between a sample and trained reference datasets. When the researchers analyzed their 27 tumors using classifier version v12.8, none reached the recommended match threshold of 0.9 or higher. Instead, the tumors consistently returned a result of no match, with the highest calibrated scores often assigned to medullomyoblastoma or Non-WNT/Non-SHH medulloblastoma. Unsupervised analyses using t-SNE plots and hierarchical clustering, visualized against 242 pineal reference cases drawn from published work and previously unpublished material, showed that the tumors formed a clearly separate cluster within the spectrum of pineal region tumors while epigenetically falling outside the medulloblastoma spectrum. These clustering results remained robust across multiple visualizations and reference cohorts of different sizes, supporting the conclusion that the tumors represent a biologically distinct group rather than an underrepresented subset of an existing class.

Clinically, the cohort displayed a balanced sex distribution, with 52 percent male patients, and a broad age range with a mean of 35 years, spanning 7 to 75 years. This demographic profile is more similar to PTPR than to pineoblastoma, which predominantly affects young children and often shows a male predominance. The clinical course, however, appeared concerning: gross total resections were achieved in less than half of the patients, and available follow-up data showed death of disease in four cases and progressive disease in an additional seven, with a 5-year progression-free survival below 25 percent. The authors note that this figure appears lower than both PTPR and pineoblastoma, although the cohort size is limited and long-term prognosis cannot yet be defined due to sparse follow-up data.

Under the microscope, PINNED tumors proved strikingly heterogeneous. All were highly cellular, and the cases recurrently demonstrated solid architecture with sharp demarcation from adjacent nervous tissue, overt mitotic figures, necrosis in 5 of 16 analyzable tumors (31 percent), and calcifications in 2 of 11 tumors (18 percent). Some cases showed a nested growth pattern, packed tubes with true lumina producing a pseudoglandular architecture, epithelioid cytology, or densely packed undifferentiated tumor tissue. Signet-ring morphology appeared diffusely in some tumors without relation to distinct architectures, and multinucleated, vacuolated, or rhabdoid cells were visible in some specimens, with rhabdoid cells showing some association with pseudopapillary structures. Where true rosettes were present, they were frequent and found in all parts of the tumor. The mean Ki-67 proliferation index was 10 percent.

The immunohistochemical profile proved more consistent than the morphology. The tumors uniformly expressed synaptophysin, OTX2, and cytokeratin 18, with these markers present even in less differentiated tumor cells. Synaptophysin showed strong and diffuse cytoplasmic expression in a fraction of tumor cells, including signet-ring cells, either as single positive cells or as foci, sometimes with a periluminal appearance. Chromogranin A was expressed in the majority of cases, often in a dot-like or granular pattern, and in some areas appeared stronger and broader; in some tumors only single cells showed strong cytoplasmic staining, and vacuolated signet-ring cells displayed eccentric chromogranin A expression. A subset of tumors contained single desmin-positive cells. In contrast, CRX, a transcription factor specific to the retina and pineal gland, was uniformly absent, and only one tumor showed focal SPDEF expression, a marker reported in 79 percent of PTPRs. Immunohistochemistry revealed loss of ATRX protein expression in 4 of 16 tumors, or 25 percent.

The original diagnoses assigned by referring institutions underscore how easily PINNED evades classification. Fourteen of the 27 tumors, or 52 percent, had originally been signed out as PTPR or as a high-grade neuroepithelial neoplasm of the pineal region or with descriptions consistent with PTPR, most likely because of focal papillary growth patterns, occasional rosettes, and epithelioid cytology. Four tumors were described as primitive neuroectodermal tumors consistent with pineoblastoma, three were classified only as pineal tumors, and one was said to most closely resemble a choroid plexus carcinoma. In at least four cases, the diagnosis of a metastatic neuroendocrine tumor in the pineal region had been discussed, a particularly important differential diagnosis for adult patients, since primary intracranial neuroendocrine neoplasms are exceedingly rare and the cytokeratin expression of PINNED may also resemble metastatic carcinoma.

Several findings argue against classifying PINNED as a PTPR subgroup despite the partial morphological overlap. The cohort consistently showed convincing synaptophysin and chromogranin A expression and mostly lacked SPDEF. Upon central review, the tumoral architecture was mostly solid, with papillary structures absent or only focal and less well-delineated. Single-nucleus RNA sequencing performed on four PINNED tumors, processed from formalin-fixed paraffin-embedded tissue using the 10x Genomics Chromium Fixed RNA Profiling assay, confirmed the molecular distinctiveness: when pseudobulk neoplastic nuclei data were compared with 34 other pineal and pineal region tumor samples based on gene co-expression patterns, PINNED showed the greatest transcriptomic similarity to PTPR but formed a distinct group, diverging before branching into any established PTPR subgroup in unsupervised hierarchical clustering. Copy-number profiling reinforced the separation. PINNED tumors showed multiple copy number alterations but no recurrent focal amplifications or deletions, in contrast to PTPR, which exhibited chromosome 10 loss in all analyzed tumors as well as recurrent losses of chromosomes 3 and 22q and gains of chromosome 8p. Recurrent mutations observed in PTPR, pineoblastoma, or PPTID, such as variants in PTEN, RB1, DROSHA, or KBTBD4, were absent in PINNED.

Targeted sequencing using the TruSight Oncology 500 panel in 13 tumors identified ATRX mutations in two cases, both of which also exhibited loss of ATRX protein expression by immunohistochemistry, making ATRX alterations the most common molecular abnormality in the cohort at 25 percent of analyzed tumors. No clinically relevant gene fusions were detected among the 17 tumors analyzed by bulk RNA sequencing. ATRX alterations have previously been reported in two pineal tumors diagnosed as PPTID independent of this cohort, but they have not emerged as a recurrent defining feature of established pineal tumor entities, making their relatively high frequency in PINNED particularly intriguing. The presence of secretory and neuroendocrine architectural features, including nested growth patterns, rosette formation, and signet-ring cells, suggests neuroendocrine differentiation, and both previously reported neuroendocrine tumors of the pineal gland showed expression of synaptophysin, chromogranin A, and cytokeratin, findings that overlap noticeably with the PINNED phenotype.

To probe the cellular origin of the tumors, the researchers projected their transcriptomic data onto an atlas of the developing murine pineal gland. The closest proximity of PINNED tumor cells, analyzed across 2,568 neoplastic nuclei, was with pinealocyte progenitors. A similar relationship to pineal gland development has been observed for pineoblastomas of different subgroups, whereas PTPRs show transcriptional similarities to the pineal primordium, further supporting the notion that PINNED is not a subset of PTPR. The picture is not entirely resolved: pinealocyte progenitor cells demonstrate CRX expression, although to a lesser extent than mature pinealocytes, and it remains unclear why CRX is strong in pineoblastoma but absent in PINNED even though both entities show the highest similarities to pinealocyte progenitor cells. Nevertheless, the authors conclude that PINNED most likely arises from within the pineal developmental lineage and represents a pineal tumor entity rather than an ectopic neoplasm merely located in the pineal region. The study has limitations: the total number of cases remains limited, independent external validation cohorts are warranted, the genetic drivers underlying tumor development remain largely unclear, and long-term prognosis cannot yet be defined. Still, recognition of PINNED appears important for the accurate diagnosis of pineal region tumors and may have implications for future tumor classification and treatment strategies.

Subject of Research: Discovery and molecular characterization of the novel pineal region tumor entity PINNED

Article Title: Identification and characterization of a novel distinct Pineal Neoplasm with Neuroendocrine and Epithelial Differentiation (PINNED)

Article References: Bode, H., Suwala, A. K., Gudenas, B., Fürst, A., Geisemeyer, N., Altendorf, L., Hack, K., Giannini, C., Abdullaev, Z., Brandner, S., Beckervordersandforth, J., Snuderl, M., Radke, J., Rodríguez-Antolín, C., Villa, C., Godfraind, C., Lowder, L., Mammoser, A., Kenning, T. J., … Schüller, U. (2026). Identification and characterization of a novel distinct Pineal Neoplasm with Neuroendocrine and Epithelial Differentiation (PINNED). Acta Neuropathologica, 152(1), Article 62. https://doi.org/10.1007/s00401-026-03111-5

Image Credits: AI Generated

DOI: 10.1007/s00401-026-03111-5

Keywords: PINNED, pineal gland, brain tumor, DNA methylation profiling, neuropathology, ATRX, tumor classification, Acta Neuropathologica, single-nucleus RNA sequencing, pinealocyte progenitors, Identification, characterization