Optimized Nuclei Isolation from Fresh and Frozen Solid Tumor Specimens for Multiome Sequencing
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 conditions and materials. Standardized protocols for nuclei isolation have been published5,6. Fresh and heterogeneous tissues require protocol optimization since freshly isolated cells from solid tumor specimens are more fragile than those isolated from cell lines.
Another consideration is that for solid tumors, surgical specimens are often not available from the operating room until late in the day. As such, it is generally not feasible to proceed directly from sample acquisition to nuclei capture without a cryopreservation step. In our experience, freezing a single-cell suspension yields the highest-quality nuclei (rather than flash-frozen whole tissue or other modalities of preservation). This is particularly true for enzymatic tissue types with high RNase content such as the pancreas.
Tissue digestion conditions also need to be designed to maximize cell yield without sacrificing quality7. In the context of solid tumor types with dense desmoplastic matrices8, the extracellular matrix must be gently broken down for cell release. Additionally, because the cell types isolated are heterogeneous, conditions should be adjusted to support the total cell population. Human pancreatic cancer (pancreatic ductal adenocarcinoma) samples are used in the described protocol. Pancreatic cancer represents a highly desmoplastic tumor type, which portends relatively sticky tissue and cells. Moreover, as pancreatic tumor specimens available for research also tend to be relatively small, efforts are made to maximize the quantity of cells captured.
Isolation of nuclei requires the most optimization in terms of cell lysis conditions and timing, as well as reagent types and ratios. Handling the nuclei over the course of isolation also requires great care. In this article, we describe our experience optimizing nuclear isolation for the 10x Genomics multiome sequencing platform from solid tumor tissue (Figure 1). We provide recommendations for tissue digestion, cryopreservation of single-cell suspensions (if desired), and nuclear isolation.
Protocol
Representative Results
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…
Disclosures
The authors have nothing to disclose.
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 Research Foundation (D.D., M.T.L.), the Gunn/Olivier Fund, the California Institute for Regenerative Medicine, Stinehart/Reed Foundation, and the Hagey Laboratory for Pediatric Regenerative Medicine. Sequencing was obtained using machines purchased with NIH funds (S10OD025212, S10OD018220, and 1S10OD01058001A1).
Materials
| 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 |
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