Recent single-cell RNA sequencing (scRNA-seq) analyses have offered much insight into the gene expression profiles in early-stage kidney development. However, comprehensive gene expression profiles from mid- and late-stage kidney development are lacking. In the present study, by using the scRNA-seq technique, we analyzed 54,704 rat kidney cells from just after birth to adulthood (six time points: postnatal days 0, 2, 5, 10, 20, and 56) including the mid and late stages of kidney development. Twenty-five original clusters and 13 different cell types were identified during these stages. Gene expression in these 13 cell types was mapped, and single cell atlas of the rat kidney from birth to maturity (http://youngbearlab.com) was built to enable users to search for a gene of interest and to evaluate its expression in different cells. The variation trend of six major types of kidney cells—intercalated cells of the collecting duct (CD-ICs), principal cells of the collecting duct (CD-PCs), cells of the distal convoluted tubules (DCTs), cells of the loop of Henle (LOH), podocytes (PDs), and cells of the proximal tubules (PTs)—during six postnatal time points was demonstrated. The trajectory of rat kidney development and the order of induction of the six major types of kidney cells from just after birth to maturity were determined. In addition, features of the dynamically changing genes as well as transcription factors during postnatal rat kidney development were identified. The present study provides a resource for achieving a deep understanding of the molecular basis of and regulatory events in the mid and late stages of kidney development.

Whether proline deficiency is a metabolic vulnerability in colorectal tumors is unknown. The aim of this study was to investigate the effects of proline metabolism‐related genes and exogenous proline on the progression of colorectal cancer (CRC). We aimed to further clarify the role of pyrroline‐5‐carboxylate reductase (PYCR) 2, a key enzyme of proline synthesis, in the regulation of colorectal intraperitoneal metastatic tumors. This study was carried out based on The Cancer Genome Atlas (TCGA) data, database analysis, single‐cell functional analysis, tissue microarray, cell experiments, and animal models. We found that, PYCR2 mRNA and protein levels were upregulated in CRC. The mRNA level of PYCR2 was closely related to the prognosis and tumor metastasis of CRC patients. The upregulated PYCR2 expression was at least partly due to low promoter methylation levels. The nomogram constructed based on PYCR2 expression and clinical characteristics of CRC showed good accuracy in predicting lymph node metastasis. Pycr2 knockdown inhibited epithelial–mesenchymal transition (EMT) of mouse CRC cells. Proline supplementation did not rescue the inhibition of mouse CRC cell proliferation and migration by Pycr2 knockdown. Proline supplementation also did not rescue the suppression of subcutaneous tumors and intraperitoneal metastatic tumors in mice by Pycr2 knockdown. PYCR2 co‐expressed genes in TCGA‐CRC were enriched in epigenetic modification‐related biological processes and molecular functions. Four small molecules with the lowest binding energy to the PYCR2 protein were identified. Collectively, Pycr2 knockdown inhibited mouse CRC progression in a proline‐independent approach. PYCR2 may be a promising tumor metastasis predictor and therapeutic target in CRC.

Analysis of the change of the cells in bile is an evolving research field in biliary pathophysiology and has potential value in diagnosis and therapy. However, laboratory studies of cell in bile across the world are scarce. Bile was collected from the clinical patients with cholangiocarcinoma (CC). To optimize the cell separation method in bile of patients with CC, we studied the factors that may affect cell vitality in bile including the dilution buffer, centrifugal force, centrifugal time, and store time and temperature. Then these factors were modified and performance was evaluated by flow cytometry with respect to the percentage and total yield of viable cells. The separated cells from bile were stained with CD3, CD4, CD8, CD56, TCRγ/δ, CD16, CD14, HLA-DR, CD33, CD15, CD11b, lineage cocktail (CD3, CD14, CD19, CD20, and CD56), CD66b, and CD45 antibodies. The different buffer solutions were joined in bile of patients with CC; experiment results show that the different dilutions have nearly no effect on the ratio of cells in bile by flow cytometry. The best centrifugal procedure was 300 g, 10 min. Bile should be stored at 4°C rather than at normal temperature. Our study further showed that the shorter time of the bile storage, the higher viability of the cell, and immune cells existed in cells isolated from bile. Evaluating bile cell viability is necessary to evaluate method performance.

Background: Ubiquitin-specific peptidase 20 (USP20) acts as oncogene or tumor suppressor gene in different types of cancer. But there are only a few reports about the effect of USP20 on colorectal cancer (CRC). This study aims to further explore the novel molecular mechanisms of USP20 in intraperitoneal metastasis of CRC. Methods: First, bioinformatics analyses were performed to discover the association between USP20 expression and the clinical characteristics of CRC. Subsequently, the mouse model was constructed using a USP20 knockout (USP20-KO) colon cell line to validate the effects of USP20 on intraperitoneal metastasis and immune cell infiltration. And then metabolomics study was performed on the USP20-KO cells to find the novel mechanisms of USP20. Finally, the relationship of prostaglandin E2 (PGE2) and USP20 was identified by enzyme-linked immunosorbent assay (ELISA) and Western blotting experiments. Results: Bioinformatics analyses showed that the USP20 expression was significantly upregulated in CRC and affected immune cell infiltration. The animal model study revealed that the intraperitoneal metastasis of tumor cell was inhibited by knocking out USP20, and the expression of USP20 could affect the proportions of CD8⁺ T cells and myeloid-derived suppressor cells (MDSCs) in tumor tissue and ascites. Metabolomics study found that PGE2 should be the key metabolite regulated by USP20 for affecting immune cell infiltration. Finally, it was validated that the expressions of 15-hydroxyprostaglandin dehydrogenase (15-PGDH) and microsomal prostaglandin E synthase-1 (mPGES-1) were regulated by the USP20 related ubiquitin-proteasome pathway. Conclusions: The USP20 expression is significantly upregulated in CRC, and can promote tumor metastasis by affecting immune cell infiltration. As an important tumor metabolite which can influence immune cell infiltration, PGE2 is regulated by USP20 through the protein degradation of mPGES-1 and 15-PGDH mediated by proteasome.