Name: single-cell suspension preparation from nile tilapia intestine for single-cell sequencing
Uploaded: 2023-02-10T14:00:00
Description: Watch this Scientific Journal Video about Single-Cell Suspension Preparation from Nile Tilapia Intestine for Single-Cell Sequencing at JoVE.com

The authors wish to acknowledge support from the Hainan Provincial Natural Science Foundation of China (NO. 320QN211) and the Research Fund Program of Guangdong Provincial Key Laboratory of Aquatic Animal Disease Control and Healthy Culture of China (NO. PBEA2021ZD01).

All animal protocols during this study were approved by the Hainan University Institutional Animal Care and Use Committee (Protocol number: HNUAUCC-2022-00063; Approval date: 2022-03-03). A list of the equipment and supplies used in this experiment can be found in the Table of Materials. A summary of the current protocol is illustrated in Figure 1.
1. Fish preparation
<ol>
	<li>Obtain 6 month old Nile tilapia with a mean body we...

This protocol describes the preparation of a high-quality single-cell suspension of Nile tilapia intestine. Before dissociation, the removal of fat and mesentery from the intestine is necessary, particularly for carnivorous fish intestines with much fat. Using a syringe instead of hard scraping to wash off the intestinal contents reduces the mechanical damage to the cells. To ensure cell viability, it is also essential to maintain the temperature at 20 &#176;C or below for the tissue dissection and rinsing steps. The was...

Cells are the fundamental units of organisms. Compared to bulk-tissue studies, single-cell level studies can reflect cell heterogeneity and provide higher-resolution information1. In recent years, researchers have applied single-cell sequencing technologies for genome, transcriptome, epigenome, or multi-omic studies at the single-cell level in mammals, zebrafish, and other model organisms and reported great breakthroughs2,3,4,5,6,7. While most studies have focused on model organisms, there are few reference protocols or commercial dissociation kits for single-cell sequencing in economic fish species, which limits the application of single-cell sequencing in aquaculture research. Therefore, developing tissue dissociation protocols that produce high-quality single-cell suspensions with high cell viability and nucleic acid integrity is crucial.
Optimizing the tissue dissociation protocol with the appropriate enzyme or enzyme combination to obtain enough viable cells with minimum damage is essential. The most effective enzyme for tissue dissociation varies depending on the tissue type. In mammals, several enzymes have been used to prepare single-cell suspensions for mammalian solid tissues, including collagenase, dispase, trypsin, papain, elastase, hyaluronidase, liberase, accutase, and trypLE8,9. Trypsin digestion combined with mechanical disruption has commonly been used to dissociate tissues for cell culture in fish10,11,12,13,14. Trypsin has also been used or added into the digestion cocktail for tissue dissociation in the rat intestine15 and zebrafish gill tissue16. However, for several reasons, trypsin is not the best option for single-cell sequencing. Trypsin alone is usually ineffective for tissue dissociation. Additionally, trypsin induces DNA strand breaks17,18 and RNA degradation19.
Papain degrades the proteins that make up the tight junctions between cells. In mammalian nerve and smooth muscle cells, papain is more efficient and less destructive than other proteases20,21. However, like trypsin, papain results in the free DNA-induced aggregation of cells due to the cell lysis that occurs during enzymatic digestion9. Elastase breaks down elastin, which is typically found in the skin, lungs, ligaments, tendons, and vascular tissues22. It is often used in combination with collagenase, dispase, or trypsin for dissociating lung tissue8. Hyaluronidase cleaves the glycosidic bonds of hyaluronan, contributing to the digestion of the extracellular matrix in various connective tissues and skin9,23.
In general, collagenase and dispase are good options for extracellular matrix breakdown. They have been used in the dissociation of human, mouse, and zebrafish intestines24,25,26,27. Collagenase destroys the peptide bond in collagen, promotes the digestion of the extracellular matrix, and releases the cells into suspension, and, thus, collagenase is often used for human and mouse solid tissue dissociation, including for the liver28,29, spleen30, pancreas31, and intestine25. Dispase is a protease that hydrolyzes the N-terminal peptide bonds of nonpolar amino acid residues and is milder than collagenase. It cleaves the extracellular matrix components, such as fibronectin, type IV collagen, and to a lesser extent, type I collagen, without affecting cell-cell junctions. Dispase is used separately or with other enzymes for tissue dissociation, such as for intestine25,32, brain33, liver34, etc. In addition, commercially available digestion cocktails, including liberase, accutase, and trypLE, are also good alternatives for solid tissue dissociation, especially for the skin, liver, and kidney8,9.
Nile tilapia (Oreochromis niloticus) belongs to the family Cichlidae of the order Perciformes. It is one of the most cultured freshwater fish species in tropical and subtropical areas, with an annual production of 4.5 million tons in 202235. It is one of the best-studied aquaculture fish species with a well-annotated genome. Nile tilapia is an ideal research model for aquaculture fish species due to its short generation time, ease of rearing, and adaptability to a wide range of rearing environments. The intestine is of great research interest as it is the organ of nutrition digestion and absorption, metabolism, and mucosal immunity. The intestine is the habitat of microbial populations and is an essential immune tissue36. It is immunologically active due to the presence of numerous immune cell types, including macrophages, B cells, granulocytes, and T cells.
In the current study, we developed a protocol for preparing a high-quality single-cell suspension from the Nile tilapia intestine to facilitate single-cell level studies in aquaculture fish species. According to the characteristics of these tissue-specific enzymes and preliminary work, collagenase/dispase is appropriate for dissociating tilapia intestine tissue. The final enzyme type to consider in preparing single-cell suspensions is DNase-I, which prevents cell aggregation by degrading free DNA released through dead cell lysis during enzymatic digestion without initiating apoptotic pathways9 and increases the live cell yield36. Additionally, bovine serum albumin (BSA) is added to the washing buffer to reduce cell clumping and improve cell viability. Several reagent companies describe BSA as an enzyme stabilizer. The addition of 0.04%-1% BSA to PBS (phosphate-buffered saline) has been used to develop a washing solution for preparing single-cell sequencing suspensions without adverse effects38. The addition of a low ratio of BSA could help maintain cell viability and avoid the free DNA-induced aggregation of cells due to cell lysis. This protocol can also provide a valuable reference for developing cell dissociation protocols from the intestines of other aquaculture fish species.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>0.22-&#956;m Sterile Filter</td>
			<td>Solarbio Life Sciences</td>
			<td>SLGV033RB</td>
			<td>It is used to filter and sterilize the enzyme solution.</td>
		</tr>
		<tr>
			<td>40-&#956;m Cell Strainer</td>
			<td>Solarbio Life Sciences</td>
			<td>F8200</td>
			<td>Cell Strainer is applied to eliminate undigested tissue pieces.</td>
		</tr>
		<tr>
			<td>Bovine serum albumin (BSA)</td>
			<td>Sigma-Aldrich</td>
			<td>SRE0098</td>
			<td>Powder; dilute 0.04 g BSA with 100 mL 1&#215; DPBS to prepare 0.04% BSA-DPBS washing bffer. Store at 2 - 8 &#176;C.</td>
		</tr>
		<tr>
			<td>Collagenase II</td>
			<td>Sangon Biotech</td>
			<td>A004202</td>
			<td>Dilute with PBS to a final concentration of 1 mg/mL.</td>
		</tr>
		<tr>
			<td>Collagenase/dispase</td>
			<td>Roche</td>
			<td>10269638-001</td>
			<td>Dilute with PBS to a final concentration of 1 mg/mL.</td>
		</tr>
		<tr>
			<td>Dispase</td>
			<td>Sigma-Aldrich</td>
			<td>D4818</td>
			<td>Dilute with PBS to a final concentration of 1 mg/mL.</td>
		</tr>
		<tr>
			<td>DNase I</td>
			<td>Sigma-Aldrich</td>
			<td>AMPD1</td>
			<td>DNase I helps reduce cell clumping.</td>
		</tr>
		<tr>
			<td>Dulbecco&#39;s phosphate-buffered saline (DPBS), Ca2+/Mg2+-free</td>
			<td>Solarbio Life Sciences</td>
			<td>E607009-0500</td>
			<td>Store at room temperature.</td>
		</tr>
		<tr>
			<td>Elastase</td>
			<td>Sangon Biotech</td>
			<td>A600438</td>
			<td>Dilute with PBS to a final concentration of 0.5 mg/mL.</td>
		</tr>
		<tr>
			<td>Fetal bovine serum (FBS)</td>
			<td>Gibco</td>
			<td>16000-044</td>
			<td>Serum, used at volume of 5% in digetstion solution.</td>
		</tr>
		<tr>
			<td>Inverted&#160;Microscope</td>
			<td>Leica</td>
			<td>qTOWER3G</td>
			<td>It is used to examine cell viability.</td>
		</tr>
		<tr>
			<td>Liberase</td>
			<td>Roche</td>
			<td>5401119001</td>
			<td>Dilute with PBS to a final concentration of 0.25 mg/mL.</td>
		</tr>
		<tr>
			<td>Nile tilpia (Oreochromis niloticus)</td>
			<td>ProGift Aquaculture Technology Co. Ltd.</td>
			<td>NA</td>
			<td>Healthy fish with no disease signs (Mean body weight: 100 g).&#160;</td>
		</tr>
		<tr>
			<td>Phosphate-buffered saline (PBS)</td>
			<td>Solarbio Life Sciences</td>
			<td>P1020</td>
			<td>Store at room temperature.</td>
		</tr>
		<tr>
			<td>Refrigerated Centrifuge</td>
			<td>Eppendorf</td>
			<td>5424</td>
			<td>It is used to spin down the tissue and cell petet.</td>
		</tr>
		<tr>
			<td>RNase inhibitor</td>
			<td>NEB</td>
			<td>M0314L</td>
			<td>Inhibit RNase activity</td>
		</tr>
		<tr>
			<td>Solid-phase RNase-Be-Gone Reagent</td>
			<td>Sangon Biotech</td>
			<td>B644201-0050</td>
			<td>It is used to remove the RNase from tools such as dissecting scissors and glass pipettes. Store at room temperature.</td>
		</tr>
		<tr>
			<td>Tricaine methanesulfonate (MS-222)</td>
			<td>Sigma-Aldrich</td>
			<td>E10521</td>
			<td>For fish euthanasia.&#160;</td>
		</tr>
		<tr>
			<td>Trypan Blue</td>
			<td>Invitrogen</td>
			<td>C0040</td>
			<td>It is used for staining dead cells.</td>
		</tr>
		<tr>
			<td>Trypsin</td>
			<td>Sangon Biotech</td>
			<td>E607001</td>
			<td>Dilute with PBS to a final concentration of 1 mg/mL.</td>
		</tr>
	</tbody>
</table>

single-cell suspension preparation from nile tilapia intestine for single-cell sequencing

Nile tilapia is one of the most commonly cultured freshwater fish species worldwide and is a widely used research model for aquaculture fish studies. The preparation of high-quality single-cell suspensions is essential for single-cell level studies such as single-cell RNA or genome sequencing. However, there is no ready-to-use protocol for aquaculture fish species, particularly for the intestine of tilapia. The effective dissociation enzymes vary depending on the tissue type. Therefore, optimizing the tissue dissociation protocol by selecting the appropriate enzyme or enzyme combination to obtain enough viable cells with minimum damage is essential. This study illustrates an optimized protocol to prepare a high-quality single-cell suspension from Nile tilapia intestine with an enzyme combination of collagenase/dispase. This combination is highly effective for dissociation with the utilization of bovine serum albumin and DNase to reduce cell aggregation after digestion. The cell output satisfies the requirements for single-cell sequencing, with 90% cell viability and a high cell concentration. This protocol can also be modified to prepare a single-cell suspension from the intestines of other fish species. This research provides an efficient reference protocol and reduces the need for additional trials in the preparation of single-cell suspensions for aquaculture fish species.

This protocol describes the preparation of a high-quality single-cell suspension of Nile tilapia intestine for single-cell sequencing (Figure 1). This research shows that the collagenase/dispase mix has a good dissociation effect and is mild for intestine tissue. The selection of the optimal digestion enzyme is essential for preparing a high-quality single-cell suspension. In the preliminary work, the dissociation efficiencies of several commonly used enzymes were compared, and the results a...

Watch this Scientific Journal Video about Single-Cell Suspension Preparation from Nile Tilapia Intestine for Single-Cell Sequencing at JoVE.com

Single-Cell Suspension Preparation from Nile Tilapia Intestine for Single-Cell Sequencing

Here, we demonstrate the preparation of a high-quality single-cell suspension of tilapia intestine for single-cell sequencing.

Nile tilapia is one of the most commonly cultured freshwater fish species worldwide and is a widely used research model for aquaculture fish studies. The ...

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