Ligand-receptor interaction atlas within and between tumor cells and T cells in lung adenocarcinoma

Purpose: Lung adenocarcinoma (LUAD) is the leading cause of cancer-related deaths worldwide. Although tumor cell-T cell interactions are known to play a fundamental role in promoting tumor progression, these interactions have not been explored in LUAD.

Methods: The 10x genomics single-cell RNA sequencing (scRNA-seq) and gene expression data of LUAD patients were obtained from ArrayExpress, TCGA, and GEO databases. scRNA-seq data were analyzed and infiltrating tumor cells, epithelial cells, and T cells were identified in the tumor microenvironment. Differentially expressed ligand-receptor pairs were identified in tumor cells/normal epithelial cells and tumor T cells/non-tumor T cells based on corresponding scRNA-seq and gene expression data, respectively. These important interactions inside/across cancer cells and T cells in LUAD were systematically analyzed. Furthermore, a valid prognostic machine-learning model based on ligand-receptor interactions was built to predict the prognosis of LUAD patients. Flow cytometry and qRT-PCR were performed to validate the significantly differently expressed ligand-receptor pairs.

Results: Overall, 39,692 cells in scRNA-seq data were included in our study after quality filtering. A total of 65 ligand-receptor pairs (17 upregulated and 48 downregulated), including LAMB1-ITGB1, CD70-CD27, and HLA-B-LILRB2, and 96 ligand-receptor pairs (41 upregulated and 55 downregulated), including CCL5-CCR5, SELPLG-ITGB2, and CXCL13-CXCR5, were identified in LUAD cancer cells and T cells, respectively. To explore the crosstalk between cancer cells and T cells, 114 ligand-receptor pairs, including 11 ligand-receptor pair genes that could significantly affect survival outcomes, were identified in our research. A machine-learning model was established to accurately predict the prognosis of LUAD patients and ITGB4, CXCR5, and MET were found to play an important role in prognosis in our model. Flow cytometry and qRT-PCR analyses indicated the reliability of our study.

Conclusion: Our study revealed functionally significant interactions within and between cancer cells and T cells. We believe these observations will improve our understanding of potential mechanisms of tumor microenvironment contributions to cancer progression and help identify potential targets for immunotherapy in the future.

Systematic expression analysis of ligand-receptor pairs reveals important cell-to-cell interactions inside glioma

Background

Glioma is the most commonly diagnosed malignant and aggressive brain cancer in adults. Traditional researches mainly explored the expression profile of glioma at cell-population level, but ignored the heterogeneity and interactions of among glioma cells.

Methods

Here, we firstly analyzed the single-cell RNA-seq (scRNA-seq) data of 6341 glioma cells using manifold learning and identified neoplastic and healthy cells infiltrating in tumor microenvironment. We systematically revealed cell-to-cell interactions inside gliomas based on corresponding scRNA-seq and TCGA RNA-seq data.

Results

A total of 16 significantly correlated autocrine ligand-receptor signal pairs inside neoplastic cells were identified based on the scRNA-seq and TCGA data of glioma. Furthermore, we explored the intercellular communications between cancer stem-like cells (CSCs) and macrophages, and identified 66 ligand-receptor pairs, some of which could significantly affect prognostic outcomes. An efficient machine learning model was constructed to accurately predict the prognosis of glioma patients based on the ligand-receptor interactions.

Conclusion

Collectively, our study not only reveals functionally important cell-to-cell interactions inside glioma, but also detects potentially prognostic markers for predicting the survival of glioma patients.

Electronic supplementary material

The online version of this article (10.1186/s12964-019-0363-1) contains supplementary material, which is available to authorized users.

Transcriptomic analysis of overexpressed SOX4 and SOX8 in TM4 Sertoli cells with emphasis on cell-to-cell interactions

Sertoli cells are localized in seminiferous tubules within the testis. They are the first testicular cells to differentiate during male sex determination. In the adult, Sertoli cells provide nutrients to germ cells, control factors for spermatogenesis and protection by establishing the blood-testis barrier (BTB). This BTB is composed of tight junctions, basal ectoplasmic specializations, adherent junctions and gap junctions. The transcription factor SOX8 is necessary for the maintenance of spermatogenesis during adult life whereas SOX4 is involved in developmental processes. These factors are highly expressed in Sertoli cells. However, few of their target genes in adult Sertoli cells are known. Hence, we compared the transcriptomes of TM4 Sertoli cells overexpressing or not SOX4 or SOX8 using RNA-Seq followed by pathways and networks analyses. We found that SOX4 overexpression leads to downregulated genes enriched for cell junction organization and positive regulation of cell-to-cell adhesion. Upregulated genes in response to SOX8 overexpression were enriched for Sertoli cell development and differentiation. However, downregulated genes were enriched for cell-to-cell adhesion, tight junction interactions, gap junctions' assembly, as well as extracellular matrix binding. Hence, our results confirm that SOX8 is an important mediator of Sertoli cell maturation, whereas SOX4 and SOX8 influence gene expression related to regulation of blood-testis barrier assembly. In addition, TM4 cells can be considered as a useful model to better define the regulatory mechanisms of SOX4 or SOX8 on gene transcription in Sertoli cells.

Multifaceted Roles of Connexin 43 in Stem Cell Niches

Purpose of Review

Considerable progress has been made in the field of stem cell research; nonetheless, the use of stem cells for regenerative medicine therapies, for either endogenous tissue repair or cellular grafts post injury, remains a challenge. To better understand how to maintain stem cell potential in vivo and promote differentiation ex vivo, it is fundamentally important to elucidate the interactions between stem cells and their surrounding partners within their distinct niches.

Recent Findings

Among the vast array of proteins depicted as mediators for cell-to-cell interactions, connexin-comprised gap junctions play pivotal roles in the regulation of stem cell fate both in vivo and in vitro.

Summary

This review summarizes and illustrates the current knowledge regarding the multifaceted roles of Cx43, specifically, in various stem cell niches.

F-Actin is a marker of dorsal induction in earlyPatella embryos

The dorsal-ventral axis inPatella vulgata embryos is established at the 32-cell stage by an inductive interaction between the animal micromeres and one vegetal macromere. This vegetal macromere, once induced, is called the 3D macromere, and marks the future dorsal side of the embryo. We examined the pattern of filamentous (F) actin in such embryos using fluorescent phalloidin and found that this dorsal 3D macromere contains more F-actin than the remainder of the cells. In addition, only one of its two daughter cells, i.e. the 4D macromere, retains this higher density. In embryos in which the establishment of the dorsal-ventral axis has been experimentally inhibited via treatment with monensin, such differences in F-actin were not found. These results suggest that the appearance of an increased density of F-actin in the dorsal 3D and 4D macromeres of normal embryos requires the inductive interactions that establish the dorsal-ventral axis. We therefore conclude that F-actin is an early marker for dorsal induction in thePatella embryo.