Increasing evidence suggests that gut microbiota play a role in the pathogenesis of breast cancer. The composition and functional capacity of gut microbiota associated with breast cancer have not been studied systematically. We performed a comprehensive shotgun metagenomic analysis of 18 premenopausal breast cancer patients, 25 premenopausal healthy controls, 44 postmenopausal breast cancer patients, and 46 postmenopausal healthy controls. Microbial diversity was higher in breast cancer patients than in controls. Relative species abundance in gut microbiota did not differ significantly between premenopausal breast cancer patients and premenopausal controls. In contrast, relative abundance of 45 species differed significantly between postmenopausal patients and postmenopausal controls: 38 species were enriched in postmenopausal patients, including Escherichia coli, Klebsiella sp_1_1_55, Prevotella amnii, Enterococcus gallinarum, Actinomyces sp. HPA0247, Shewanella putrefaciens, and Erwinia amylovora, and 7 species were less abundant in postmenopausal patients, including Eubacterium eligens and Lactobacillus vaginalis. Acinetobacter radioresistens and Enterococcus gallinarum were positively but weakly associated with expression of high-sensitivity C-reactive protein; Shewanella putrefaciens and Erwinia amylovora were positively but weakly associated with estradiol levels. Actinomyces sp. HPA0247 negatively but weakly correlated with CD3+CD8+ T cell numbers. Further characterization of metagenome functional capacity indicated that the gut metagenomes of postmenopausal breast cancer patients were enriched in genes encoding lipopolysaccharide biosynthesis, iron complex transport system, PTS system, secretion system, and beta-oxidation. The composition and functions of the gut microbial community differ between postmenopausal breast cancer patients and healthy controls. The gut microbiota may regulate or respond to host immunity and metabolic balance. Thus, while cause and effect cannot be determined, there is a reproducible change in the microbiota of treatment-naive patients relative to matched controls.

A comprehensive cellular anatomy of normal human kidney is crucial to address the cellular origins of renal disease and renal cancer. Some kidney diseases may be cell type-specific, especially renal tubular cells. To investigate the classification and transcriptomic information of the human kidney, we rapidly obtained a single-cell suspension of the kidney and conducted single-cell RNA sequencing (scRNA-seq). Here, we present the scRNA-seq data of 23,366 high-quality cells from the kidneys of three human donors. In this dataset, we show 10 clusters of normal human renal cells. Due to the high quality of single-cell transcriptomic information, proximal tubule (PT) cells were classified into three subtypes and collecting ducts cells into two subtypes. Collectively, our data provide a reliable reference for studies on renal cell biology and kidney disease.

Significance Statement: Previous studies of bladder cell classification mostly relied on the cell’s morphology, location, electrophysiology, and function. However, it is difficult to classify bladder cells accurately and comprehensively using these methods. The authors created a single-cell transcriptomic map of human bladder cells using single-cell RNA sequencing. They also created a more detailed single-cell sequencing RNA map of the mouse bladder than what was previously available. Using these tools, the authors compare the similarities and differences between human and mouse bladder cells and found many cell types that are highly similar across the two. Additionally, the authors discovered two new types of human bladder cells. One may play a role in allergic reactions and nerve conduction, whereas the other may play a role in bladder emptying. The results may assist scientists studying the relationship between bladder cell types and diseases. Background: Having a comprehensive map of the cellular anatomy of the normal human bladder is vital to understanding the cellular origins of benign bladder disease and bladder cancer. Methods: We used single-cell RNA sequencing (scRNA-seq) of 12,423 cells from healthy human bladder tissue samples taken from patients with bladder cancer and 12,884 cells from mouse bladders to classify bladder cell types and their underlying functions. Results: We created a single-cell transcriptomic map of human and mouse bladders, including 16 clusters of human bladder cells and 15 clusters of mouse bladder cells. The homology and heterogeneity of human and mouse bladder cell types were compared and both conservative and heterogeneous aspects of human and mouse bladder evolution were identified. We also discovered two novel types of human bladder cells. One type is ADRA2A ⁺ and HRH2 ⁺ interstitial cells which may be associated with nerve conduction and allergic reactions. The other type is TNNT1 ⁺ epithelial cells that may be involved with bladder emptying. We verify these TNNT1 ⁺ epithelial cells also occur in rat and mouse bladders. Conclusions: This transcriptomic map provides a resource for studying bladder cell types, specific cell markers, signaling receptors, and genes that will help us to learn more about the relationship between bladder cell types and diseases.

Clear cell renal cell carcinoma (ccRCC) frequently features a high level of tumor heterogeneity. Elucidating the chromatin landscape of ccRCC at the single-cell level could provide a deeper understanding of the functional states and regulatory dynamics underlying the disease. Here, we performed single-cell RNA sequencing (scRNA-seq) and single-cell assay for transposase-accessible chromatin using sequencing (scATAC-seq) on 19 ccRCC samples, and whole-exome sequencing was used to understand the heterogeneity between individuals. Single-cell transcriptome and chromatin accessibility maps of ccRCC were constructed to reveal the regulatory characteristics of different tumor cell subtypes in ccRCC. Two long noncoding RNAs (RP11-661C8.2 and CTB-164N12.1) were identified that promoted the invasion and migration of ccRCC, which was validated with in vitro experiments. Taken together, this study comprehensively characterized the gene expression and DNA regulation landscape of ccRCC, which could provide new insights into the biology and treatment of ccRCC. Significance: A comprehensive analysis of gene expression and DNA regulation in ccRCC using scATAC-seq and scRNA-seq reveals the DNA regulatory programs of ccRCC at the single-cell level.

Previous studies have suggested that testosterone levels are linked to a variety of diseases, such as cardiovascular disease, type-2 diabetes, the metabolic syndrome, erectile dysfunction, depression, stroke and osteoporosis. Since cigarette smoking is a major health problem and highly prevalent among men, several groups have studied the effects of cigarette smoking on testosterone levels in men. However, the results have been conflicting. Our objectives were to examine the association of cigarette smoking and serum levels of sex hormone-binding globulin (SHBG), total testosterone (TT) and free testosterone (FT) in a large male population. Data from 2,021 men (989 nonsmokers and 1,032 smokers), aged 20-69, were collected from the Fangchenggang Area Male Health and Examination survey using an in-person interview and self-administered questionnaires from September to December, 2009. We have found the following: (a) smokers had significantly higher TT and FT levels compared to nonsmokers, even after stratification as per age, BMI, triglycerides and alcohol consumption. (b) Both TT (r = -0.083, P 0.05), although a positive association between increasing pack-years and SHBG level was observed (r = 0.174, P <0.001). More research is needed to elucidate the biological mechanisms and clinical significance of these associations.