GLI1 fusions involving ACTB, MALAT1 and PTCH1 genes have been recently reported in a subset of malignant soft tissue tumors with characteristic monomorphic nested epithelioid morphology and frequent S100 positivity. However, we encountered a group of morphologically similar soft tissue tumors lacking the canonical GLI1 gene fusions and sought to investigate their genetic abnormalities. A combined approach including RNA-sequencing, targeted exome sequencing and FISH methodologies were used to identify potential novel genetic abnormalities. Ten patients (5 females, 5 males) with an age range of 4–65 years (median 32.5) were identified. Tumors were located in the soft tissues of the limbs, trunk and head and neck, with one each in the tongue and lung. Histologically, tumors revealed ovoid to epithelioid cells arranged in a distinctive nested-trabecular pattern, separated by thin septa and a delicate vascular network. Two cases showed areas of increased nuclear pleomorphism and focal fascicular spindle cell growth. Four tumors showed a high mitotic count (≥15/10 HPFs), with necrosis seen in 3 of them. Lymphovascular invasion was noted in 2 cases. No consistent immunoprofile was detected, with positivity for CD56 (6 cases), S100 (4 cases), SMA (2 cases) and pan-CK (1 case). FISH showed GLI1 (12q13.3) gene amplification in all 10 cases, with co-amplification of CDK4 (12q14.1) in 9 (90%) and MDM2 (12q15) in 8 (80%) cases. Targeted exome sequencing performed in 3 cases confirmed the GLI1, CDK4 and MDM2 co-amplification. Only one case showed the presence of both GLI1 break-apart and amplification, although no gene partner was detected. Our findings suggest that GLI1 amplification, often associated with co-amplifications of CDK4 and MDM2 genes, may represent an alternative genetic mechanism of GLI1 oncogenic activation akin to GLI1 fusions, defining the pathogenesis of an emerging group of malignant soft tissue tumors with a distinctive nested growth pattern and variable immunoprofile.

We report the use of optical coherence tomography (OCT) to determine spatially localized optical attenuation coefficients of human axillary lymph nodes and their use to generate parametric images of lymphoid tissue. 3D-OCT images were obtained from excised lymph nodes and optical attenuation coefficients were extracted assuming a single scattering model of OCT. We present the measured attenuation coefficients for several tissue regions in benign and reactive lymph nodes, as identified by histopathology. We show parametric images of the measured attenuation coefficients as well as segmented images of tissue type based on thresholding of the attenuation coefficient values. Comparison to histology demonstrates the enhancement of contrast in parametric images relative to OCT images. This enhancement is a step towards the use of OCT for in situ assessment of lymph nodes.

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The identification of somatic mutations is crucial for guiding therapeutic decisions about personalized melanoma treatment. However, genetic analysis of tumors is usually performed on limited and often low-quality DNA from tumors with low tumor cellularity and high tumor heterogeneity. Different mutation-detection platforms exist, with varying analytical sensitivities. Here we evaluated the detection of common mutations in BRAF, NRAS, and TERT promoter in 40 melanoma FFPE tissues using Droplet Digital (dd)PCR, and compared the results to the detection rates obtained by Sanger sequencing and pyrosequencing. The cellularity of tumors analyzed ranged from 5% to 50% (n = 28) and 50% to 90% (n = 12). Overall, droplet digital (dd)PCR was more sensitive, detecting mutations in 12.5% and 23% of tumors deemed as wild-type by pyrosequencing and Sanger sequencing, respectively. The increased sensitivity of ddPCR was more apparent among tumors with <50% tumor cellularity. Implementation of ddPCR-based assays may facilitate analysis of early-stage tumors and support research into improving outcomes in melanoma patients.

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