TMIC-05. SINGLE-CELL MULTI-OMIC ANALYSIS OF SPORADIC VESTIBULAR SCHWANNOMAS REVEALS SCHWANN CELLS WITH AN INJURY PHENOTYPE AND AN ASSOCIATION BETWEEN TUMOR SIZE AND MACROPHAGE INFILTRATE

Vestibular schwannomas (VS) comprise 8% of primary brain tumors, with rising prevalence due to increased detection by imaging. How intertumoral heterogeneity and differences within the tumor microenvironment (TME) contribute to the pathogenesis of VS remains poorly understood. We performed single-cell RNA sequencing (scRNA-seq) on 15 sporadic VS with paired single-nucleus assay of transposase accessible chromatin sequencing (snATAC-seq) on 7 tumors. Dimension reduction analysis revealed diverse Schwann, immune—predominantly macrophage, and stromal cell populations. Schwann cells adopted multiple unique functional states, such as repair-like, myelinating, and hypoxia-response, reflecting undescribed intratumoral heterogeneity within VS-associated Schwann cells. Remarkably, VS-associated Schwann cells were found to be phenotypically similar to Schwann cells in the setting of peripheral nerve injury, which is robustly associated with macrophage recruitment. Indeed, using our scRNA-seq atlas to perform deconvolution analysis of a broader cohort of VS, including newly sequenced (n = 22) and published bulk RNA-sequencing datasets (n = 153), we found variation in proportion of immune cells was strongly correlated with the proportion of macrophage infiltrate (R,2 = 0.86, p < 0.001). Furthermore, we found that macrophage/monocyte lineage cells represent a disproportionately large number of cycling cells in the VS TME, a finding corroborated by immunohistochemistry. Clinically, tumors with high macrophage infiltrate were associated with larger tumor size (Fisher’s exact test p = 0.007). Together, these findings suggest macrophages play an important role in VS pathogenesis. We therefore sought to characterize potential cell-to-cell interactions between Schwann cells and macrophages in our scRNA-seq atlas. Ligand-receptor analysis revealed several cytokines expressed by Schwann cells with cognate receptors expressed by macrophages, including MIF, SPP1, MDK, SEMA3C and IL34, which may be responsible for recruiting macrophages. In summary, we describe previously uncharacterized cellular diversity within VS, highlight an association between macrophage infiltration and clinical phenotypes, and identify potential therapeutic targets for VS treatment.

Pollock: fishing for cell states

Motivation

The use of single-cell methods is expanding at an ever-increasing rate. While there are established algorithms that address cell classification, they are limited in terms of cross platform compatibility, reliance on the availability of a reference dataset and classification interpretability. Here, we introduce Pollock, a suite of algorithms for cell type identification that is compatible with popular single-cell methods and analysis platforms, provides a set of pretrained human cancer reference models, and reports interpretability scores that identify the genes that drive cell type classifications.

Results

Pollock performs comparably to existing classification methods, while offering easily deployable pretrained classification models across a wide variety of tissue and data types. Additionally, it demonstrates utility in immune pan-cancer analysis.

Availability and implementation

Source code and documentation are available at https://github.com/ding-lab/pollock. Pretrained models and datasets are available for download at https://zenodo.org/record/5895221.

Supplementary information

Supplementary data are available at Bioinformatics Advances online.

The effect of reconstruction on positive margin rates in oral cancer: Using length of stay as a proxy measure for flap reconstruction in a national database

PURPOSE

Planned flap reconstruction, allowing aggressive resections of oral cavity squamous cell carcinoma (OCSCC), may decrease positive surgical margins. The purpose of this study was to determine if length of stay (LOS), as a proxy measure for flap reconstruction, is associated with positive margin rates in OCSCC.

MATERIALS AND METHODS

Data from the National Cancer Database was retrospectively collected for patients undergoing surgery for previously untreated clinical T1-3 OCSCC. Post-operative LOS was dichotomized between ≤4 and >4 days as a proxy measure for whether patients may have received flap reconstruction. Patients with LOS >4 days represent a diverse group, but those with a LOS ≤4 days are less likely to have undergone an oral cavity flap reconstruction.

RESULTS

10,107 patients were included, of which 5290 (52%) were clinical T1 and 4852 (48%) were clinical T2-3. 771 (8%) patients had a positive surgical margin. On multivariable logistic regression analysis, LOS ≤4 days was significantly associated with a positive margin resection in patients with clinical T2-3 tumors (OR 1.68, 95%CI 1.37-2.06) compared to patients with LOS >4 days. LOS was not associated with surgical margin status in patients with clinical T1 disease (OR 0.76, 95%CI 0.55-1.06). Patients with positive margin resections demonstrated worse overall survival (cT1: OR 1.35, 95%CI 1.06-1.72; cT2-3: OR 1.52, 95%CI 1.33-1.74).

CONCLUSIONS

LOS >4 days after oral cavity cancer resection was significantly associated with negative surgical margins in clinical T2-3 oral cavity cancer, suggesting the possibility that patients undergoing flap reconstruction after resection have fewer positive surgical margins.