Improved protocol for single-nucleus RNA-sequencing of frozen human bladder tumor biopsies

This paper provides a laboratory workflow for single-nucleus RNA-sequencing (snRNA-seq) including a protocol for gentle nuclei isolation from fresh frozen tumor biopsies, making it possible to analyze biobanked material. To develop this protocol, we used non-frozen and frozen human bladder tumors and cell lines. We tested different lysis buffers (IgePal and Nuclei EZ) and incubation times in combination with different approaches for tissue and cell dissection: sectioning, semi-automated dissociation, manual dissociation with pestles, and semi-automated dissociation combined with manual dissociation with pestles. Our results showed that a combination of IgePal lysis buffer, tissue dissection by sectioning, and short incubation time was the best conditions for gentle nuclei isolation applicable for snRNA-seq, and we found limited confounding transcriptomic changes based on the isolation procedure. This protocol makes it possible to analyze biobanked material from patients with well-described clinical and histopathological information and known clinical outcomes with snRNA-seq.

Single-nucleus and Spatially Resolved Intratumor Subtype Heterogeneity in Bladder Cancer

Background

Current bulk transcriptomic classification systems for bladder cancer do not consider the level of intratumor subtype heterogeneity.

Objective

To investigate the extent and possible clinical impact of intratumor subtype heterogeneity across early and more advanced stages of bladder cancer.

Design setting and participants

We performed single-nucleus RNA sequencing (RNA-seq) of 48 bladder tumors and additional spatial transcriptomics for four of these tumors. Total bulk RNA-seq and spatial proteomics data were available from the same tumors for comparison, along with detailed clinical follow-up of the patients.

Outcome measurements and statistical analysis

The primary outcome was progression-free survival for non-muscle-invasive bladder cancer. Cox regression analysis, log-rank tests, Wilcoxon rank-sum tests, Spearman correlation, and Pearson correlation were used for statistical analysis.

Results and limitations

We found that the tumors exhibited varying levels of intratumor subtype heterogeneity and that the level of subtype heterogeneity can be estimated from both single-nucleus and bulk RNA-seq data, with high concordance between the two. We found that a higher class 2a weight estimated from bulk RNA-seq data is associated with worse outcome for patients with molecular high-risk class 2a tumors. The sparsity of the data generated using the DroNc-seq sequencing protocol is a limitation.

Conclusions

Our results indicate that discrete subtype assignments from bulk RNA-seq data may lack biological granularity and that continuous class scores may improve clinical risk stratification of patients with bladder cancer.

Patient summary

We found that several molecular subtypes can exist within a single bladder tumor and that continuous subtype scores can be used to identify a subgroup of patients with poor outcomes. Use of these subtype scores may improve risk stratification for patients with bladder cancer, which can help in making decisions on treatment.

Abstract 3483: Single-nucleus RNA-sequencing of human bladder tumors delineates intra-tumor cellular and subtype heterogeneity

Introduction: Single cell technologies now make it possible to study tumor ecosystems at single cell resolution and may improve our biological understanding of disease aggressiveness and tumor heterogeneity. Whereas single-cell RNA-sequencing of clinical tumor biopsies requires immediate processing after tissue acquisition, single-nucleus RNA-sequencing (snRNA-seq) allows profiling of single nuclei isolated from frozen tumor tissue from patients with long-term follow-up and known clinical outcomes.

Methods: We performed snRNA-seq of frozen tumors from 48 bladder cancer (BC) patients (10 Ta, 13 T1, 25 T2-4) using an optimized DroNc-seq protocol. Nuclei were isolated from frozen biopsies using IgePal lysis buffer and droplets were created using the Dolomite Bio platform followed by library generation and sequencing on an Illumina NovaSeq 6000. All epithelial nuclei were classified according to the UROMOL classes of non-muscle-invasive BC or the consensus classes of muscle-invasive BC. Bulk total RNA-sequencing (RNA-seq) was available for 44 of the tumors for comparison. Three tumors were additionally analyzed using 10x Chromium for validation and four tumors were analyzed using 10x Visium Spatial Transcriptomics.

Results: After pre-processing the raw sequencing data, we obtained data from 117,653 nuclei in total and 59,201 nuclei remained after quality control filtering (1,233 nuclei per tumor and 529 expressed genes per nuclei on average). We focused our analysis on the epithelial compartment, as it constituted the bulk of the tumors (99% of all nuclei). UMAP visualization and clustering of all tumors were mainly driven by patient origin indicating a high level of inter-tumor heterogeneity. To explore intra-tumor heterogeneity and the association to disease aggressiveness, we characterized the tumors individually using hallmark BC gene signatures. Finally, we explored the composition of transcriptomic classes for each tumor and found that 52% of tumors displayed profound intra-tumor class heterogeneity with less than 70% of all nuclei belonging to a single class. The dominating transcriptomic class of single nuclei was only consistent in 44% of the tumors when compared to the overall transcriptomic class from bulk RNA-seq. This may be explained by several levels of heterogeneity and method differences, including the technical challenges of applying a bulk classifier to single nuclei data. We are currently investigating whether specific epithelial subpopulations are associated to outcome and whether signatures derived from snRNA-seq data can be recovered in bulk RNA-seq data and used as prognostic predictors.

Conclusion: Our results highlight the biological complexity of bladder tumors and underline the importance of considering the extent of intra-tumor heterogeneity in the clinical management of BC patients.

Citation Format: Sia V. Lindskrog, Sofie S. Schmøkel, Iver Nordentoft, Philippe Lamy, Michael Knudsen, Jørgen B. Jensen, Lars Dyrskjøt. Single-nucleus RNA-sequencing of human bladder tumors delineates intra-tumor cellular and subtype heterogeneity [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3483.