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).

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)
<ol>
	<li>Prepare Digest Buffer (see Table of Materials).</li>
	<li>Obtain the tissue of interest as soon as possible after tumor excision and transport the specimen in quench buffer (DMEM F-12 with ~5% fetal bovine serum) or 1x PBS on ice.</li>
	<li>Mince the tissue using clean forceps and scissors in 3-5 mL of Digest Buffer in a 90 mm Petri dish (Figure 2A).</li>
	<li>Transfer the minced tissue to a 50 mL conical tube and dissociate in ~10 mL of Digest Buffer for 30 min at 37 &#176;C using a water bath with shaking function or a dry agitator.</li>
	<li>Remove from the agitator and quench with ~20 mL of quench medium. Filter the solution through a 100 &#181;m cell strainer into a clean conical tube.</li>
	<li>Collect any remaining solid tissue from the strainer (re-mince remaining tissue pieces if needed), and place in ~10 mL of fresh Digest Buffer for another 30 min at 37 &#176;C with agitation. Repeat until all tumor tissue has been dissociated.</li>
	<li>Pool cell suspension aliquots and filter through a 70 &#181;m followed by a 40 &#181;m cell strainer into a clean conical tube on ice.</li>
	<li>Centrifuge to pellet cells at 500 &#215; g for 5 min at 4 &#176;C and then decant the supernatant.</li>
</ol>
2. Cryopreservation
<ol>
	<li>Rinse the cells by resuspending the pellet in 1 mL of 1x PBS.</li>
	<li>Transfer the cell suspension (~1-10 million cells/tube for optimal freezing) to a 1.5 mL cryovial on ice.</li>
	<li>Centrifuge to pellet cells at 500 &#215; g for 5 min at 4 &#176;C and then decant the supernatant.</li>
	<li>Resuspend the cells in 1 mL of Bambanker solution, transfer to a 1.5 or 2 mL cryovial (Figure 2B), and freeze using a -1 &#176;C/min cooling rate freezing container (containing 100% isopropyl alcohol) at -80 &#176;C, or transfer to liquid nitrogen if longer-term storage of the sample is anticipated.</li>
</ol>
3. Nuclei isolation
<ol>
	<li>Rapidly thaw the cryovial of cell suspension and place it on wet ice.</li>
	<li>Transfer the thawed cell suspension to a 2 mL microcentrifuge tube and top up the vial to 2 mL solution with 1x PBS to rinse the cells.</li>
	<li>Obtain a manual cell count using a hemocytometer to assess both the quantity and quality of the cells (Figure 2C).</li>
	<li>Centrifuge to pellet cells at 500 &#215; g for 5 min at 4 &#176;C and then gently decant the supernatant using progressively smaller pipette tips to leave behind a dry pellet and maintain it on ice.
	<ol>
		<li>Use a swing-bucket rotor for all centrifugation steps. For maximum cell yield, place the tubes in the centrifuge with the hinge facing outwards and then decant with the pipette tip directed towards the opposite side of the tube (Figure 2D). 
		NOTE: For decanting the supernatant, use progressively smaller pipette tips to remove fluid to limit disruption of the pellet while maximizing the volume of fluid decanted. This strategy is particularly helpful later in the protocol following nuclei extraction since the nuclei pellet is generally not visible.</li>
	</ol>
	</li>
	<li>Prepare 1x Cell Lysis Buffer, Cell Lysis Dilution Buffer, and Wash Buffer (Figure 3A) according to the published protocol with the following modifications (see Table 1,&#160;Table of Materials): 
	NOTE: Place the Digitonin on a heating block at 65 &#176;C prior to use to dissolve the precipitate (Figure 3B). This typically takes about 10 min.</li>
	<li>Prepare the 0.1x Cell Lysis Buffer by combining 100 &#181;L of 1x Cell Lysis Buffer and 900 &#181;L of Cell Lysis Dilution Buffer, pipette gently to mix, and place it on ice.</li>
	<li>Resuspend the cell pellet in 100 &#181;L of chilled 0.1x Cell Lysis Buffer and gently pipette to mix 5x.</li>
	<li>Incubate on ice for 3 min (Figure 3C).</li>
	<li>Add 1 mL of chilled Wash Buffer and pipette up and down to gently mix 5x.</li>
	<li>Centrifuge to pellet the nuclei at 500 &#215; g for 5 min at 4 &#176;C, gently decant the supernatant to a dry pellet, and maintain on ice. 
	NOTE: If the starting cell number is low (100,000-200,000 cells), perform the cell lysis and wash steps in a 200 &#181;L PCR tube instead of a 2 mL microcentrifuge tube to decrease the tube surface area and minimize losses. In this case, adjust the Wash Buffer volume down to accommodate the smaller tube volume.</li>
	<li>Repeat Steps 3.9-3.10 2x for a total of three washes.</li>
	<li>Manually count the nuclei using a hemocytometer slide under the microscope. Use trypan blue dye if desired to provide contrast for viewing the nuclei and to help discern nuclei from unlysed cells.</li>
	<li>Prepare the 1x Nuclei Buffer per the published protocol: 20x Nuclei Buffer stock, 1 mM DTT, 1 U/&#181;L RNase Inhibitor in nuclease-free water and keep on ice (see Table of Materials).</li>
	<li>Resuspend the nuclei pellet in 1x Nuclei Buffer based on goal-targeted nuclei recovery. 
	NOTE: If the concentration is high enough, aim for a targeted recovery of 10,000 or slightly higher at this step (3,230-8,060 nuclei/&#181;L) when determining the starting resuspension volume, given the anticipated volume loss of 25 &#181;L and the 20% decrease in concentration with filtering (Step 3.15).</li>
	<li>Gently pass the resuspended nuclei volume through a 40 &#181;m Pipette Tip Cell Strainer and place the nuclei on ice (Figure 3D).</li>
	<li>Recount the nuclei (Figure 4A-C). Dilute the final solution further with Nuclei Buffer if needed.</li>
	<li>Transport the nuclei on ice and immediately proceed with nuclei capture per published protocols.</li>
</ol>

Isolation of Nuclei for Multiome Sequencing in Solid Tumor Specimen

<ol>
	<li>Jain, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single-cell+RNA+sequencing+and+spatial+transcriptomics+reveal+cancer-associated+fibroblasts+in+glioblastoma+with+protumoral+effects.">Single-cell RNA sequencing and spatial transcriptomics reveal cancer-associated fibroblasts in glioblastoma with protumoral effects.</a> J Clin Invest. 133 (5), e147087 (2023).</li><li>Sahai, E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=A+framework+for+advancing+our+understanding+of+cancer-associated+fibroblasts.">A framework for advancing our understanding of cancer-associated fibroblasts.</a> Nat Rev Cancer. 20 (3), 174-186 (2020).</li><li>Foster, D. S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Multiomic+analysis+reveals+conservation+of+cancer-associated+fibroblast+phenotypes+across+species+and+tissue+of+origin.">Multiomic analysis reveals conservation of cancer-associated fibroblast phenotypes across species and tissue of origin.</a> Cancer Cell. 40 (11), 1392-1406 (2022).</li><li>Hasan, S., Buechler, M. B. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=What's+in+a+name?+An+emerging+framework+for+cancer-associated+fibroblasts,+myofibroblasts,+and+fibroblasts.">What's in a name? An emerging framework for cancer-associated fibroblasts, myofibroblasts, and fibroblasts.</a> Cancer Cell. 40 (11), 1273-1275 (2022).</li><li>. Nuclei isolation from complex tissues for single cell multiome ATAC + gene expression sequencing Available from: <a target="_blank" href="https://www.10xgenomics.com/support/single-cell-multiome-atac-plus-gene-expression/documentation/steps/sample-prep/nuclei-isolation-from-complex-tissues-for-single-cell-multiome-atac-plus-gene-expression-sequencing">https://www.10xgenomics.com/support/single-cell-multiome-atac-plus-gene-expression/documentation/steps/sample-prep/nuclei-isolation-from-complex-tissues-for-single-cell-multiome-atac-plus-gene-expression-sequencing</a> (2022)</li><li>. Nuclei isolation from embryonic mouse brain tissue for single cell multiome ATAC + gene expression sequencing Available from: <a target="_blank" href="https://www.10xgenomics.com/support/single-cell-multiome-atac-plus-gene-expression/documentation/steps/sample-prep/nuclei-isolation-from-embryonic-mouse-brain-tissue-for-single-cell-multiome-atac-plus-gene-expression-sequencing">https://www.10xgenomics.com/support/single-cell-multiome-atac-plus-gene-expression/documentation/steps/sample-prep/nuclei-isolation-from-embryonic-mouse-brain-tissue-for-single-cell-multiome-atac-plus-gene-expression-sequencing</a> (2022)</li><li>Januszyk, M., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Characterization+of+diabetic+and+non-diabetic+foot+ulcers+using+single-cell+RNA-sequencing.">Characterization of diabetic and non-diabetic foot ulcers using single-cell RNA-sequencing.</a> Micromachines (Basel). 11 (9), 815 (2020).</li><li>Foster, D. S., Jones, R. E., Ransom, R. C., Longaker, M. T., Norton, J. A. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+evolving+relationship+of+wound+healing+and+tumor+stroma.">The evolving relationship of wound healing and tumor stroma.</a> JCI Insight. 3 (18), e99911 (2018).</li><li>Nott, A., Schlachetzki, J. C. M., Fixsen, B. R., Glass, C. K. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nuclei+isolation+of+multiple+brain+cell+types+for+omics+interrogation.">Nuclei isolation of multiple brain cell types for omics interrogation.</a> Nat Protoc. 16 (3), 1629-1646 (2021).</li><li>Foster, D. S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Integrated+spatial+multiomics+reveals+fibroblast+fate+during+tissue+repair.">Integrated spatial multiomics reveals fibroblast fate during tissue repair.</a> Proc Natl Acad Sci U S A. 118 (41), e2110025118 (2021).</li><li>Leiz, J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nuclei+isolation+from+adult+mouse+kidney+for+single-nucleus+RNA-sequencing.">Nuclei isolation from adult mouse kidney for single-nucleus RNA-sequencing.</a> J Vis Exp. (175), (2021).</li><li>Narayanan, A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Nuclei+isolation+from+fresh+frozen+brain+tumors+for+single-nucleus+RNA-seq+and+ATAC-seq.">Nuclei isolation from fresh frozen brain tumors for single-nucleus RNA-seq and ATAC-seq.</a> J Vis Exp. (162), e61542 (2020).</li></ol>

The authors have no conflicts of interest to disclose.

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...

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.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>100, 70, and 40 &#956;m Falcon cell strainers&#160;</td>
			<td>&#160;ThermoFisher</td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>10x Genomics Nuclei Buffer (20x)</td>
			<td>10x Genomics</td>
			<td>2000153/2000207</td>
			<td></td>
		</tr>
		<tr>
			<td>Bambanker&#160;</td>
			<td>Wako, Fisher Scientitic</td>
			<td>NC9582225&#160;</td>
			<td></td>
		</tr>
		<tr>
			<td>BSA</td>
			<td>Miltenyi Biotec</td>
			<td>130-091-376</td>
			<td></td>
		</tr>
		<tr>
			<td>Calcium Chloride</td>
			<td>Sigma Aldrich</td>
			<td>499609</td>
			<td></td>
		</tr>
		<tr>
			<td>Collagenase (Collagenase Type IV)</td>
			<td>ThermoFisher</td>
			<td>17104019</td>
			<td></td>
		</tr>
		<tr>
			<td>Digitonin</td>
			<td>Thermo Fisher</td>
			<td>BN2006</td>
			<td></td>
		</tr>
		<tr>
			<td>DNase I</td>
			<td>Worthington</td>
			<td>LS006330</td>
			<td></td>
		</tr>
		<tr>
			<td>DTT</td>
			<td>Sigma Aldrich</td>
			<td>646563</td>
			<td></td>
		</tr>
		<tr>
			<td>Dulbecco&#8217;s Modified Eagle Medium F-12</td>
			<td>Thermo Fisher</td>
			<td>11320082</td>
			<td></td>
		</tr>
		<tr>
			<td>Fetal Bovine Serum</td>
			<td>Thermo Fisher</td>
			<td>10438026</td>
			<td></td>
		</tr>
		<tr>
			<td>Flowmi 40 &#956;m&#160; Pipette Tip Cell Strainer&#160;</td>
			<td>Sigma Aldrich</td>
			<td>BAH136800040</td>
			<td></td>
		</tr>
		<tr>
			<td>HEPES</td>
			<td>Sigma Aldrich</td>
			<td>H3375</td>
			<td></td>
		</tr>
		<tr>
			<td>Histopaque-1119 Gradient Cell Separation solution</td>
			<td>Sigma Aldrich</td>
			<td>11191</td>
			<td></td>
		</tr>
		<tr>
			<td>Medium 199</td>
			<td>Sigma Aldrich</td>
			<td>M2520</td>
			<td></td>
		</tr>
		<tr>
			<td>MgCl2</td>
			<td>Sigma Aldrich</td>
			<td>M1028</td>
			<td></td>
		</tr>
		<tr>
			<td>Miltenyi GentleMACSTM digest kit&#160;</td>
			<td></td>
			<td></td>
			<td></td>
		</tr>
		<tr>
			<td>NaCl</td>
			<td>Sigma Aldrich</td>
			<td>59222C</td>
			<td></td>
		</tr>
		<tr>
			<td>Nalgene Cryo &#34;Mr. Frosty&#34; Freezing Container</td>
			<td>&#160;ThermoFisher</td>
			<td>5100-0001</td>
			<td></td>
		</tr>
		<tr>
			<td>Nonident P40 Substitute</td>
			<td>Sigma Aldrich</td>
			<td>74385</td>
			<td></td>
		</tr>
		<tr>
			<td>Poloxamer 188</td>
			<td>Sigma</td>
			<td>P5556</td>
			<td></td>
		</tr>
		<tr>
			<td>Rnase inhibitor&#160;</td>
			<td>Sigma Aldrich</td>
			<td>3335399001</td>
			<td></td>
		</tr>
		<tr>
			<td>Tris-HCl</td>
			<td>Sigma Aldrich</td>
			<td>T2194</td>
			<td></td>
		</tr>
		<tr>
			<td>Tween-20</td>
			<td>Thermo Fisher</td>
			<td>85113</td>
			<td></td>
		</tr>
	</tbody>
</table>

optimized nuclei isolation from fresh and frozen solid tumor specimens for multiome sequencing

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.

Author Spotlight: Enhancing Nuclei Isolation for Multiome Sequencing in Challenging Tumor Microenvironments

Optimized Nuclei Isolation from Fresh and Frozen Solid Tumor Specimens for Multiome Sequencing

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<stron...

Watch this Scientific Journal Video about Author Spotlight: Enhancing Nuclei Isolation for Multiome Sequencing in Challenging Tumor Microenvironments at JoVE.com

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.

Multiome sequencing, which provides same-cell/paired single-cell RNA- and the assay for transposase-accessible chromatin with sequencing (ATAC-sequencing) ...

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835 Views.  Stanford University. 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. 