A novel PARD3B-NUTM1 fusion in an aggressive primary CNS embryonal tumor in a young adult.,Acta Neuropathologica Communications

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A novel PARD3B-NUTM1 fusion in an aggressive primary CNS embryonal tumor in a young adult.
Acta Neuropathologica Communications ( IF 6.2 ) Pub Date : 2020-07-17 , DOI: 10.1186/s40478-020-00991-w
Kyungmin Ko ₁ , Takashi Kitani _{2,

3} , Brent T Harris _{1,

2,

3} , Amjad N Anaizi ₄ , David Solomon ₅ , Arie Perry ₅ , Jeffrey Toretsky ₂ , Metin Ozdemirli ₁

Affiliation

We report a novel PARD3B-NUTM1 gene fusion in a primary embryonal tumor of the brain which had a very aggressive course. A 29-year-old female presented with worsening headache of three-weeks duration. CT and MRI showed a hemorrhagic mass involving the right inferior frontal lobe and temporal lobe (Fig. 1 a, b). The tumor was well-demarcated. It was surgically removed with no gross residual tumor. MRI on post-operative day 27 showed recurrence and additional tumor in the prepontine region and between cerebellar tonsils. Chemotherapy with vincristine, cisplatin, and cyclophosphamide was initiated and staged re-excisions were performed, but the patient expired due to intraventricular hemorrhage on post-operative day 34. A comprehensive postmortem examination revealed no residual viable tumor in the brain or any other extracranial tumor.

Microscopic sections showed a relatively well-circumscribed, moderately cellular neoplasm. The tumor had a variegated histology with foci showing primitive, spindle cells in a myxoid to fibrillar background, foci showing small epithelioid cells with clear cytoplasm around thin-walled vessels, and foci of microvascular proliferation and necrosis (Fig. 1 c-e). There was microscopic infiltration of adjacent brain parenchyma by single tumor cells and reactive gliosis. Mitoses were frequent. No well-differentiated islands of squamous epithelium characteristic of NUT midline carcinoma were observed. By immunohistochemistry (Figs. 1 f-k), there was diffuse CD56 expression, patchy dot-like and strong membranous expression of CD99, focal neurofilament expression and GFAP was positive in a small subset of epithelioid tumor cells. Synaptophysin was positive in single scattered cells (less than 1%). Chromogranin A, OLIG2, IDH1 R132H mutant protein, EMA, pan-keratin, p40, p63, CD34, progesterone receptor, HMB-45, Melan-A, SOX10, desmin, smooth muscle actin, muscle specific actin, CD10, L1CAM, and WT-1 were negative by immunohistochemistry. INI-1 and ATRX expression were retained. The tumor cells showed strong nuclear p53 and c-Myc expression in most tumor cells and had a high Ki-67 (MIB-1) proliferative index (approximated at 60%). We classified the tumor as “central nervous system embryonal tumor, not otherwise specified”. The tumor was negative for EWSR1 rearrangement by fluorescence in situ hybridization (FISH). Histology of post-chemotherapy re-excision specimens were similar to the original with focal minimal necrosis (in approximately 10% of the tumor).

Next-generation sequencing (NGS) using the UCSF500 panel was performed (as described in reference [1]), which revealed a novel PARD3B-NUTM1 gene fusion between PARD3B intron 3–4 and NUTM1 intron 1–2 resulting in an in-frame fusion of exons 1–3 of PARD3B and exons 2–8 of NUTM1. The sequence predicts a fusion protein comprising the N-terminal 132 amino acids of the partitioning defective 3 homolog B protein (PAR3-β) and almost the entire NUT protein (amino acids 3–1160 C -terminus) (Fig. 1 l). There was also a BRCA2 nonsense mutation (p.K944*, c.1830A > T), which was present at a heterozygous allele frequency. NGS also showed chromosomal copy number changes that included gains of 6p and interstitial 15q, and loss of 6q. However, NGS did not detect TP53 or MYC alterations including mutation, amplification or rearrangements despite p53 and c-myc protein overexpression. Subsequent immunohistochemistry showed diffuse strong nuclear expression of NUT protein.

NUT carcinoma is an aggressive midline carcinoma predominantly seen in the head and neck region with undifferentiated or poorly differentiated morphology characterized by NUT expression [2]. The prognosis of NUT carcinomas is poor, with a median survival of 9.8 months [3]. It is now apparent that NUTM1 gene fusions also characterize a subset of undifferentiated soft tissue and visceral tumors not restricted to carcinomas or to the midline [4] and also has been described in B-ALL [5] . NUTM1-rearranged tumors often exhibit rapid growth and spread. Histologically they are heterogeneous and sometimes variegated and have a poorly differentiated cytology. In the brain, several NUTM1 rearrangements have been reported (Table 1). Five of the six cases reported as examples of a newly defined entity called “CNS Ewing sarcoma family tumor with CIC alteration” were shown to express NUT protein by immunohistochemistry and two of these were shown to have CIC-NUTM1 fusion [6]. An exceptional case of a NUTM1-rearranged brain tumor resulted in a disease-free survival at 16 months [7]. Our case showed a very aggressive course in the setting of a novel PARD3B-NUTM1 fusion accompanied by chromosomal copy number changes. PAR3-beta, the product of PARD3B, regulates cell-cell contact and indirectly activates the Hippo pathway, but few studies implicate PARD3B in tumorigenesis [8, 9].

Table 1 Comparison of reported NUTM1-rearranged primary brain tumors

Full size table

The clinical and histopathologic features of the NUTM1-rearranged brain tumors reported to date are not specific and pose a diagnostic challenge. For the three cases with available histologic description, the tumors showed young age at presentation and hyperchromatic nuclei [4, 7]. Cytologic features were dissimilar. A myxoid background component was a common feature. GFAP expression varied from focal to diffuse. The reported cases were consistently negative for cytokeratin and chromogranin A, and at most focally positive for synaptophysin. There was strong nuclear expression of NUT protein expressed in all five cases. In contrast, some soft tissue and visceral NUTM1-rearranged tumors were negative for NUT expression by immunohistochemistry. The reported NUTM1-rearranged brain tumors were not designated as a specific entity. Based on the morphologic features, intra-axial location, lack of other primary site, diffuse CD99 and CD56 and focal GFAP and neurofilament positivity, lack of carcinoma and sarcoma markers, and lack of histologic and molecular alterations that define other specific CNS primitive neuroectodermal tumors, our case was classified as “CNS embryonal tumor, not otherwise classified” category in the current WHO classification system, which is equivalent to CNS primitive neuroectodermal tumor in previous WHO classification systems.

The reported cases of NUTM1-rearrangements in primary brain tumors were discovered by NGS (Table 1). RNA sequencing was performed either retrospectively or for research purposes for cases 1, 2, and 3. RNA sequencing was performed for diagnostic workup in case 4 (ATXN1-NUTM1). In the current case, DNA sequencing was performed for diagnostic workup, revealing additional chromosomal copy number changes.

To our best knowledge, PARD3B-NUTM1 fusion has not been reported in any tumor. As our case illustrates, utilization of NGS for routine diagnostic workup of primitive appearing CNS tumors may uncover more NUTM1-rearranged tumors with different fusion partners. Molecular analysis of these aggressive tumors may explain the differences seen in histopathologies and provide clues to prognosis and identification of novel therapies.

Not applicable.

FISH:: Fluorescence in-situ hybridization
NGS:: Next generation sequencing

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Affiliations

Department of Pathology and Laboratory Medicine, Georgetown University Hospital, 3900 Reservoir Rd NW, Washington, DC, 20007, USA
Kyungmin Ko, Brent T. Harris & Metin Ozdemirli
Departments of Oncology and Pediatrics, Georgetown University School of Medicine, 3970 Reservoir Rd NW, Washington, DC, 20057, USA
Takashi Kitani, Brent T. Harris & Jeffrey Toretsky
Department of Neurology, MedStar Georgetown University Hospital, 3800 Reservoir Rd NW, Washington, DC, 20007, USA
Takashi Kitani & Brent T. Harris
Department of Neurosurgery, MedStar Georgetown University Hospital, 3800 Reservoir Rd NW, Washington, DC, 20007, USA
Amjad N. Anaizi
Department of Pathology, University of California, San Francisco, 505 Parnassus Ave, San Francisco, CA, 94143, USA
David Solomon & Arie Perry

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Kyungmin KoView author publications
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Takashi KitaniView author publications
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Amjad N. AnaiziView author publications
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All authors contributed to clinical care of the patient and preparing and reviewing the manuscript.

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Correspondence to Metin Ozdemirli.

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The Georgetown University IRB has reviewed the case and determined that the above case study is exempt from IRB approval.

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Ko, K., Kitani, T., Harris, B.T. et al. A novel PARD3B-NUTM1 fusion in an aggressive primary CNS embryonal tumor in a young adult. acta neuropathol commun 8, 112 (2020). https://doi.org/10.1186/s40478-020-00991-w

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Received: 10 June 2020
Accepted: 08 July 2020
Published: 17 July 2020
DOI: https://doi.org/10.1186/s40478-020-00991-w

Keywords

CNS embryonal tumor
NUT carcinoma
NUTM1
Next-generation sequencing

中文翻译：

年轻成人侵袭性原发性中枢神经系统胚胎肿瘤中的新型 PARD3B-NUTM1 融合。

我们报告了大脑原发性胚胎肿瘤中的一种新型PARD3B-NUTM1基因融合，该肿瘤具有非常侵袭性的病程。一名 29 岁女性因头痛持续三周而恶化。 CT和MRI显示出血性肿块累及右下额叶和颞叶（图1a、b）。肿瘤边界清楚。经过手术切除，没有肉眼可见的残留肿瘤。术后第 27 天的 MRI 显示桥前区和小脑扁桃体之间有复发和额外肿瘤。开始用长春新碱、顺铂和环磷酰胺进行化疗，并进行分期再次切除，但患者在术后第34天因脑室内出血而死亡。全面的尸检显示脑内没有残留的活肿瘤或任何其他颅外肿瘤。

显微镜切片显示边界相对清楚、细胞中等的肿瘤。肿瘤的组织学多种多样，病灶显示粘液样至纤维状背景中的原始梭形细胞，病灶显示薄壁血管周围有透明细胞质的小上皮样细胞，以及微血管增殖和坏死的病灶（图 1 ce）。邻近脑实质存在单个肿瘤细胞和反应性神经胶质增生的微观浸润。有丝分裂很频繁。没有观察到 NUT 中线癌特征的分化良好的鳞状上皮岛。通过免疫组织化学（图1fk），在一小部分上皮样肿瘤细胞中存在弥漫性CD56表达、CD99的斑状点状和强膜性表达、局灶性神经丝表达和GFAP阳性。突触素在单个分散细胞中呈阳性（小于 1%）。嗜铬蛋白 A、OLIG2、IDH1 R132H 突变蛋白、EMA、泛角蛋白、p40、p63、CD34、黄体酮受体、HMB-45、Melan-A、SOX10、结蛋白、平滑肌肌动蛋白、肌肉特异性肌动蛋白、CD10、L1CAM 和免疫组织化学结果显示 WT-1 呈阴性。 INI-1 和 ATRX 表达被保留。大多数肿瘤细胞中的肿瘤细胞显示出强烈的核p53和c-Myc表达，并且具有高Ki-67（MIB-1）增殖指数（大约为60%）。我们将肿瘤归类为“中枢神经系统胚胎性肿瘤，未另有说明”。通过荧光原位杂交 (FISH) 检测，肿瘤的EWSR1重排呈阴性。化疗后再次切除标本的组织学与原始标本相似，有局灶性最小坏死（约占肿瘤的 10%）。

使用 UCSF500 panel 进行下一代测序 (NGS)（如参考文献 [1] 中所述），结果揭示了PARD3B内含子 3-4 和NUTM1内含子 1-2 之间的新型PARD3B-NUTM1基因融合，从而产生框内PARD3B的外显子 1-3 和NUTM1的外显子 2-8 融合。该序列预测融合蛋白包含分配缺陷3同源物B蛋白（PAR3-β）的N端132个氨基酸和几乎整个NUT蛋白（氨基酸3-1160 C端）（图1l）。还有一个BRCA2无义突变（p.K944*，c.1830A > T），以杂合等位基因频率存在。 NGS 还显示染色体拷贝数变化，包括 6p 和间质 15q 的增加以及 6q 的丢失。然而，尽管 p53 和 c-myc 蛋白过度表达，NGS 并未检测到 TP53 或 MYC 改变，包括突变、扩增或重排。随后的免疫组织化学显示 NUT 蛋白的弥漫性强核表达。

NUT 癌是一种侵袭性中线癌，主要见于头颈部，具有未分化或低分化形态，以 NUT 表达为特征 [2]。 NUT癌的预后较差，中位生存期为9.8个月[3]。现在很明显， NUTM1基因融合还表征了未分化软组织和内脏肿瘤的一个子集，不限于癌或中线 [4]，并且也在 B-ALL [5] 中进行了描述。 NUTM1重排的肿瘤通常表现出快速生长和扩散。在组织学上，它们是异质的，有时呈杂色，并且细胞学分化差。在大脑中，已经报道了几种NUTM1重排（表 1）。作为新定义实体（称为“具有CIC改变的 CNS 尤文肉瘤家族肿瘤”）的示例，报告的 6 例病例中有 5 例通过免疫组织化学显示表达 NUT 蛋白，其中 2 例显示具有CIC-NUTM1融合 [6]。一个NUTM1重排脑肿瘤的特殊病例导致 16 个月无病生存 [7]。我们的病例在新型PARD3B-NUTM1融合的背景下表现出非常激进的过程，并伴有染色体拷贝数变化。 PAR3-β 是PARD3B的产物，调节细胞间接触并间接激活 Hippo 通路，但很少有研究表明PARD3B与肿瘤发生有关 [8, 9]。

表1 已报道的NUTM1重排原发性脑肿瘤的比较

全尺寸桌子

迄今为止报道的NUTM1重排脑肿瘤的临床和组织病理学特征并不具体，并且构成了诊断挑战。对于具有可用组织学描述的三个病例，肿瘤表现出年轻且细胞核深染[4, 7]。细胞学特征不同。粘液样背景成分是一个常见特征。 GFAP 表达从局灶性到弥漫性不同。报告的病例细胞角蛋白和嗜铬粒蛋白 A 始终呈阴性，最多突触素局部呈阳性。所有 5 例病例中均有强烈的 NUT 蛋白核表达。相反，通过免疫组织化学检测，一些软组织和内脏NUTM1重排肿瘤的 NUT 表达呈阴性。所报道的 NUTM1 重排脑肿瘤并未被指定为特定实体。基于形态特征、轴内位置、缺乏其他原发部位、弥漫性 CD99 和 CD56 以及局灶性 GFAP 和神经丝阳性、缺乏癌和肉瘤标志物以及缺乏定义其他特定 CNS 原始神经外胚层肿瘤的组织学和分子改变，我们的病例在现行WHO分类系统中被归类为“中枢神经系统胚胎性肿瘤，未另行分类”类别，相当于此前世界卫生组织分类系统中的中枢神经系统原始神经外胚层肿瘤。

NGS 发现了原发性脑肿瘤中NUTM1重排的报告病例（表 1）。对病例 1、2 和 3 进行回顾性或出于研究目的进行 RNA 测序。对病例 4 ( ATXN1-NUTM1)进行 RNA 测序用于诊断检查。在当前病例中，进行了 DNA 测序以进行诊断检查，揭示了额外的染色体拷贝数变化。

据我们所知，尚未在任何肿瘤中报道PARD3B-NUTM1融合。正如我们的案例所示，利用 NGS 对原始中枢神经系统肿瘤进行常规诊断检查可能会发现更多具有不同融合伙伴的NUTM1重排肿瘤。这些侵袭性肿瘤的分子分析可以解释组织病理学中所见的差异，并为预后和新疗法的鉴定提供线索。

不适用。

鱼：: 荧光原位杂交
NGS：: 下一代测序

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隶属关系

乔治城大学医院病理学和实验医学系，3900 Reservoir Rd NW，华盛顿特区，20007，美国

高京民、布伦特·T·哈里斯和梅廷·奥兹德米尔利
乔治城大学医学院肿瘤科和儿科系，3970 Reservoir Rd NW，华盛顿特区，20057，美国

北谷隆、布伦特·T·哈里斯和杰弗里·托雷斯基
神经内科，MedStar 乔治敦大学医院，3800 Reservoir Rd NW，华盛顿特区，20007，美国

北谷隆 & 布伦特·T·哈里斯
神经外科，MedStar 乔治城大学医院，3800 Reservoir Rd NW，华盛顿特区，20007，美国
阿姆贾德·阿奈兹
病理学系，加州大学旧金山分校，505 Parnassus Ave，旧金山，CA，94143，美国

大卫·所罗门和阿里·佩里

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贡献

所有作者都为患者的临床护理以及手稿的准备和审阅做出了贡献。

通讯作者

通讯作者：Metin Ozdemirli。

道德批准并同意参与

乔治城大学 IRB 已审查该案例，并确定上述案例研究免于 IRB 批准。

同意发表

不适用。

利益争夺

作者声明不存在竞争利益。

出版商备注

施普林格·自然对于已出版的地图和机构隶属关系中的管辖权主张保持中立。

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