Isolating and cryopreserving pig skin cells for single-cell RNA sequencing study

Selective epithelial expression of KRASG12D in the Oncopig pancreas drives ductal proliferation and desmoplasia that is accompanied by an immune response

Pancreatic ductal adenocarcinoma (PDAC) remains a formidable challenge in oncology, characterized by a high mortality rate, largely attributable to delayed diagnosis and the intricacies of its tumor microenvironment. Innovations in modeling pancreatic epithelial transformation provide valuable insights into the pathogenesis and potential therapeutic strategies for PDAC. We employed a porcine (Oncopig) model, utilizing the Ad-K8-Cre adenoviral vector, to investigate the effects of variable doses (107 to 1010 pfu) on pancreatic epithelial cells. This vector, the expression from which being driven by a Keratin-8 promoter, will deliver Cre-recombinase specifically to epithelial cells. Intraductal pancreatic injections in transgenic Oncopigs (LSL-KRASG12D-TP53R167H) were performed with histologically based evaluation at 2 months post-injection. Specificity of the adenoviral vector was validated through Keratin-8 expression and Cre-recombinase activity. We confirmed that the Ad-K8-Cre adenoviral vector predominantly targets ductal epithelial cells lining both large and small pancreatic ducts, as evidenced by Keratin 8 and CAM5.2 staining. Higher doses resulted in significant tissue morphology changes, including atrophy, and enlarged lymph nodes. Microscopic examination revealed concentration-dependent proliferation of the ductal epithelium, cellular atypia, metaplasia, and stromal alterations. Transgene expression was confirmed with immunohistochemistry. Desmoplastic responses were evident through vimentin, α-SMA, and Masson's trichrome staining, indicating progressive collagen deposition, particularly at the higher vector doses. Our study suggests a distinct dose-response relationship of Ad-K8-Cre in inducing pancreatic epithelial proliferation and possible neoplasia in an Oncopig model. All doses of the vector induced epithelial proliferation; the higher doses also produced stromal alterations, metaplasia, and possible neoplastic transformation. These findings highlight the potential for site-specific activation of oncogenes in large animal models of epithelial tumors, with the ability to induce stromal alterations reminiscent of human PDAC.

A cost-effective protocol for single-cell RNA sequencing of human skin

Introduction

Single-cell RNA sequencing (scRNAseq) and flow cytometry studies in skin are methodologically complex and costly, limiting their accessibility to researchers worldwide. Ideally, RNA and protein-based analyses should be performed on the same lesion to obtain more comprehensive data. However, current protocols generally focus on either scRNAseq or flow cytometry of healthy skin.

Methods

We present a novel label-free sample multiplexing strategy, building on the souporcell algorithm, which enables scRNAseq analysis of paired blood and skin samples. Additionally, we provide detailed instructions for simultaneous flow cytometry analysis from the same sample, with necessary adaptations for both healthy and inflamed skin specimens.

Results

This tissue multiplexing strategy mitigates technical batch effects and reduces costs by 2-4 times compared to existing protocols. We also demonstrate the effects of varying enzymatic incubation durations (1, 3, and 16 hours, with and without enzyme P) on flow cytometry outcomes. Comprehensive explanations of bioinformatic demultiplexing steps and a detailed step-by-step protocol of the entire experimental procedure are included.

Discussion

The protocol outlined in this article will make scRNAseq and flow cytometry analysis of skin samples more accessible to researchers, especially those new to these techniques.

Single-Cell RNA Sequencing Reveals the Cellular Landscape of Longissimus Dorsi in a Newborn Suhuai Pig

The introduction of single-cell RNA sequencing (scRNA-seq) technology has spurred additional advancements in analyzing the cellular composition of tissues. The longissimus dorsi (LD) in pigs serves as the primary skeletal muscle for studying meat quality in the pig industry. However, the single-cell profile of porcine LD is still in its infancy stage. In this study, we profiled the transcriptomes of 16,018 cells in the LD of a newborn Suhuai pig at single-cell resolution. Subsequently, we constructed a cellular atlas of the LD, identifying 11 distinct cell populations, including endothelial cells (24.39%), myotubes (18.82%), fibro-adipogenic progenitors (FAPs, 18.11%), satellite cells (16.74%), myoblasts (3.99%), myocytes (5.74%), Schwann cells (3.81%), smooth muscle cells (3.22%), dendritic cells (2.99%), pericytes (1.86%), and neutrophils (0.33%). CellChat was employed to deduce the cell-cell interactions by evaluating the gene expression of receptor-ligand pairs across different cell types. The results show that FAPs and pericytes are the primary signal contributors in LD. In addition, we delineated the developmental trajectory of myogenic cells and examined alterations in the expression of various marker genes and molecular events throughout various stages of differentiation. Moreover, we found that FAPs can be divided into three subclusters (NR2F2-FAPs, LPL-FAPs, and TNMD-FAPs) according to their biological functions, suggesting that the FAPs could be associated with the differentiation of tendon cell. Taken together, we constructed the cellular atlas and cell communication network in LD of a newborn Suhuai pig, and analyzed the developmental trajectory of myogenic cells and the heterogeneity of FAPs subpopulation cells. This enhances our comprehension of the molecular features involved in skeletal muscle development and the meat quality control in pigs.

A single-cell transcriptome atlas of pig skin characterizes anatomical positional heterogeneity

Different anatomical locations of the body skin show differences in their gene expression patterns depending on different origins, and the inherent heterogeneous information can be maintained in adults. However, highly resolvable cellular specialization is less well characterized in different anatomical regions of the skin. Pig is regarded as an excellent model animal for human skin research in view of its similar physiology to human. In this study, single-cell RNA sequencing was performed on pig skin tissues from six different anatomical regions of Chenghua (CH) pigs, with a superior skin thickness trait, and the back site of large white (LW) pigs. We obtained 233,715 cells, representing seven cell types, among which we primarily characterized the heterogeneity of the top three cell types, including smooth muscle cells (SMCs), endothelial cells (ECs), and fibroblasts (FBs). Then, we further identified several subtypes of SMCs, ECs, and FBs, and discovered the expression patterns of site-specific genes involved in some important pathways such as the immune response and extracellular matrix (ECM) synthesis in different anatomical regions. By comparing differentially expressed genes of skin FBs among different anatomical regions, we considered TNN, COL11A1, and INHBA as candidate genes for facilitating ECM accumulation. These findings of heterogeneity in the main skin cell types from different anatomical sites will contribute to a better understanding of inherent skin information and place the potential focus on skin generation, transmission, and transplantation, paving the foundation for human skin priming.

Intestinal single-cell atlas reveals novel lymphocytes in pigs with similarities to human cells

Lymphocytes can heavily influence intestinal health, but resolving intestinal lymphocyte function is challenging as the intestine contains a vastly heterogeneous mixture of cells. Pigs are an advantageous biomedical model, but deeper understanding of intestinal lymphocytes is warranted to improve model utility. Twenty-six cell types were identified in the porcine ileum by single-cell RNA sequencing and further compared with cells in human and murine ileum. Though general consensus of cell subsets across species was revealed, some porcine-specific lymphocyte subsets were identified. Differential tissue dissection and in situ analyses conferred spatial context, revealing similar locations of lymphocyte subsets in Peyer's patches and epithelium in pig-to-human comparisons. Like humans, activated and effector lymphocytes were abundant in the ileum but not periphery of pigs, suggesting tissue-specific and/or activation-associated gene expression. Gene signatures for peripheral and ileal innate lymphoid cells newly discovered in pigs were defined and highlighted similarities to human innate lymphoid cells. Overall, we reveal novel lymphocyte subsets in pigs and highlight utility of pigs for intestinal research applications.