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Optimized Nuclei Isolation from Fresh and Frozen Solid Tumor Specimens for Multiome Sequencing
In This Article
Summary
The protocol provides a reliable and optimized approach to the isolation of nuclei from solid tumor specimens for multiome sequencing using the 10x Genomics platform, including recommendations for tissue dissociation conditions, cryopreservation of single-cell suspensions, and assessment of isolated nuclei.
Abstract
Multiome sequencing, which provides same-cell/paired single-cell RNA- and the assay for transposase-accessible chromatin with sequencing (ATAC-sequencing) data, represents a breakthrough in our ability to discern tumor cell heterogeneity-a primary focus of translational cancer research at this time. However, the quality of sequencing data acquired using this advanced modality is highly dependent on the quality of the input material.
Digestion conditions need to be optimized to maximize cell yield without sacrificing quality. This is particularly challenging in the context of solid tumors with dense desmoplastic matrices that must be gently broken down for cell release. Freshly isolated cells from solid tumor tissue are more fragile than those isolated from cell lines. Additionally, as the cell types isolated are heterogeneous, conditions should be selected to support the total cell population.
Finally, nuclear isolation conditions must be optimized based on these qualities in terms of lysis times and reagent types/ratios. In this article, we describe our experience with nuclear isolation for the 10x Genomics multiome sequencing platform from solid tumor specimens. We provide recommendations for tissue digestion, storage of single-cell suspensions (if desired), and nuclear isolation and assessment.
Introduction
As our knowledge of tumor biology grows, the importance of analyzing heterogeneous cells across the tumor microenvironment has also increased1,2. The ability to acquire single-cell RNA and the assay for transposase-accessible chromatin with sequencing (ATAC-sequencing) data from the same cell in a paired-cell fashion (multiome sequencing) provides a significant advance towards this end3,4. These experiments are expensive and time-consuming, however, and the quality and impact of the data acquired are highly dependent on the quality of the experimental ....
Protocol
Human pancreatic cancer (pancreatic ductal adenocarcinoma) samples were acquired according to an IRB-approved protocol in our laboratory. Informed consent was obtained from patients for tissue collection. Tissue was transported from the operating room to the laboratory and then processed as follows.
1. Tissue dissociation (digestion)
- Prepare Digest Buffer (see Table of Materials).
- Obtain the tissue of interest as soon as possible after tu.......
Representative Results
To isolate high-quality nuclei from patient solid tumor specimens for multiome sequencing (Figure 1), the tumor tissue was dissociated and a single-cell suspension was cryopreserved (Figure 2A-D). The cell suspension was then thawed at the time of planned multiome capture. Nuclei capture was conducted with optimized lysis buffer reagents and timing to maximize both quality and yield (Figure 3A
Discussion
Untangling the heterogeneous cell populations present in the tumor microenvironment is an active area of focus in cancer biology. Similarly, complex tissues exist in benign pathologies such as wound healing and fibrosis. Multiome sequencing has emerged as a powerful tool permitting the acquisition of same-cell paired scRNA- and ATAC-seq data. This protocol describes the isolation of nuclei, which demands optimization in the setting of processing fresh, fragile, small tumor specimens. Here we provide a protocol for nuclei.......
Acknowledgements
We would like to acknowledge the Stanford Functional Genomics Facility (SFGF), particularly Dhananjay Wagh and John Coller, and 10x Genomics for their assistance with optimizing our experiments. We would also like to thank Drs. George Poultsides, Monica Dua, Brendan Visser, and Byrne Lee for their assistance in acquiring patient specimens. We would like to acknowledge Art and Elaine Taylor, the Rantz Foundation, and Warren and Judy Kaplan for their generous support of our research efforts. Funding sources include NIH grants 1F32CA23931201A1 (D.S.F.), 1R01GM116892 (M.T.L.), 1R01GM136659 (M.T.L), Goldman Sachs Foundation (J.A.N., D.S.F., M.T.L.), the Damon Runyon Cancer....
Materials
| Name | Company | Catalog Number | Comments |
| 100, 70, and 40 μm Falcon cell strainers | ThermoFisher | ||
| 10x Genomics Nuclei Buffer (20x) | 10x Genomics | 2000153/2000207 | |
| Bambanker | Wako, Fisher Scientitic | NC9582225 | |
| BSA | Miltenyi Biotec | 130-091-376 | |
| Calcium Chloride | Sigma Aldrich | 499609 | |
| Collagenase (Collagenase Type IV) | ThermoFisher | 17104019 | |
| Digitonin | Thermo Fisher | BN2006 | |
| DNase I | Worthington | LS006330 | |
| DTT | Sigma Aldrich | 646563 | |
| Dulbecco’s Modified Eagle Medium F-12 | Thermo Fisher | 11320082 | |
| Fetal Bovine Serum | Thermo Fisher | 10438026 | |
| Flowmi 40 μm Pipette Tip Cell Strainer | Sigma Aldrich | BAH136800040 | |
| HEPES | Sigma Aldrich | H3375 | |
| Histopaque-1119 Gradient Cell Separation solution | Sigma Aldrich | 11191 | |
| Medium 199 | Sigma Aldrich | M2520 | |
| MgCl2 | Sigma Aldrich | M1028 | |
| Miltenyi GentleMACSTM digest kit | |||
| NaCl | Sigma Aldrich | 59222C | |
| Nalgene Cryo "Mr. Frosty" Freezing Container | ThermoFisher | 5100-0001 | |
| Nonident P40 Substitute | Sigma Aldrich | 74385 | |
| Poloxamer 188 | Sigma | P5556 | |
| Rnase inhibitor | Sigma Aldrich | 3335399001 | |
| Tris-HCl | Sigma Aldrich | T2194 | |
| Tween-20 | Thermo Fisher | 85113 |
References
- Jain, S., et al. Single-cell RNA sequencing and spatial transcriptomics reveal cancer-associated fibroblasts in glioblastoma with protumoral effects. J Clin Invest. 133 (5), e147087 (2023).
- Sahai, E., et al.
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