irGSEA: the integration of single-cell rank-based gene set enrichment analysis.

irGSEA is an R package designed to assess the outcomes of various gene set scoring methods when applied to single-cell RNA sequencing data. This package incorporates six distinct scoring methods that rely on the expression ranks of genes, emphasizing relative expression levels over absolute values. The implemented methods include AUCell, UCell, singscore, ssGSEA, JASMINE and Viper. Previous studies have demonstrated the robustness of these methods to variations in dataset size and composition, generating enrichment scores based solely on the relative gene expression of individual cells. By employing the robust rank aggregation algorithm, irGSEA amalgamates results from all six methods to ascertain the statistical significance of target gene sets across diverse scoring methods. The package prioritizes user-friendliness, allowing direct input of expression matrices or seamless interaction with Seurat objects. Furthermore, it facilitates a comprehensive visualization of results. The irGSEA package and its accompanying documentation are accessible on GitHub (https://github.com/chuiqin/irGSEA).

Association between radical versus conservative surgery and short-term outcomes of hepatic cystic echinococcosis in Nyingchi, China: a retrospective cohort study.

BACKGROUND: Radical or conservative surgical treatment for hepatic Cystic Echinococcosis (hepatic CE) is controversial. We aimed to measure the association between radical surgery (RS) versus conservative surgery (CS) and short-term outcomes in our cohort. METHODS: Medical records of hepatic CE patients' demographic, clinical, radiological, operative and postoperative details who underwent surgical treatment between January 3, 2017 and January 3, 2018 at the Department of General Surgery, Nyingchi People's Hospital, Nyingchi, China, were retrieved and analyzed. The primary outcome was overall morbidity. The secondary outcomes included: (i) bile leakage; (ii) complications of lung, pleura, heart, liver, pancreas and biliary tract; (iii) incision infection and residual cavity abscess formation; (iv) anaphylactic reaction and shock; (v) tear of surrounding tissues; (vi) hospital and post-operative length of stay (LOS); (vii) length of surgery; (viii) blood loss during surgery. Multivariable logistic/linear regression models with various adjustment strategies for confounders were performed to evaluate the association. RESULTS: A total of 128 hepatic CE patients were included with 82 (64.1%) and 46 (35.9%) receiving CS and RS, respectively. After fully adjusted, RS was associated with 60% lower risk of overall complication (aOR 0.4; 95%CI, 0.2-0.9) and 0.6-h shorter surgical time (aß 0.4; 95%CI,-0.0-0.8) comparing to CS. However, RS was associated with more blood loss during surgery (aß 179.3; 95%CI, 54.2-304.5). CONCLUSION: To conclude, RS was associated with a 60% reduction in developing overall complication in the short term, but may result in more blood loss during surgery than CS.

Single-Cell Transcriptome Integration Analysis Reveals the Correlation Between Mesenchymal Stromal Cells and Fibroblasts.

Background: Mesenchymal stromal cells (MSCs) and fibroblasts show similar morphology, surface marker expression, and proliferation, differentiation, and immunomodulatory capacities. These similarities not only blur their cell identities but also limit their application. Methods: We performed single-cell transcriptome sequencing of the human umbilical cord and foreskin MSCs (HuMSCs and FSMSCs) and extracted the single-cell transcriptome data of the bone marrow and adipose MSCs (BMSCs and ADMSCs) from the Gene Expression Omnibus (GEO) database. Then, we performed quality control, batch effect correction, integration, and clustering analysis of the integrated single-cell transcriptome data from the HuMSCs, FMSCs, BMSCs, and ADMSCs. The cell subsets were annotated based on the surface marker phenotypes for the MSCs (CD105 + , CD90 +, CD73 +, CD45 -, CD34 -, CD19 -, HLA-DRA -, and CD11b -), fibroblasts (VIM +, PECAM1 -, CD34 -, CD45 -, EPCAM -, and MYH11 -), and pericytes (CD146 +, PDGFRB +, PECAM1 -, CD34 -, and CD45 -). The expression levels of common fibroblast markers (ACTA2, FAP, PDGFRA, PDGFRB, S100A4, FN1, COL1A1, POSTN, DCN, COL1A2, FBLN2, COL1A2, DES, and CDH11) were also analyzed in all cell subsets. Finally, the gene expression profiles, differentiation status, and the enrichment status of various gene sets and regulons were compared between the cell subsets. Results: We demonstrated 15 distinct cell subsets in the integrated single-cell transcriptome sequencing data. Surface marker annotation demonstrated the MSC phenotype in 12 of the 15 cell subsets. C10 and C14 subsets demonstrated both the MSC and pericyte phenotypes. All 15 cell subsets demonstrated the fibroblast phenotype. C8, C12, and C13 subsets exclusively demonstrated the fibroblast phenotype. We identified 3,275 differentially expressed genes, 305 enriched gene sets, and 34 enriched regulons between the 15 cell subsets. The cell subsets that exclusively demonstrated the fibroblast phenotype represented less primitive and more differentiated cell types. Conclusion: Cell subsets with the MSC phenotype also demonstrated the fibroblast phenotype, but cell subsets with the fibroblast phenotype did not necessarily demonstrate the MSC phenotype, suggesting that MSCs represented a subclass of fibroblasts. We also demonstrated that the MSCs and fibroblasts represented highly heterogeneous populations with distinct cell subsets, which could be identified based on the differentially enriched gene sets and regulons that specify proliferating, differentiating, metabolic, and/or immunomodulatory functions.