Comprehensive Analysis of Regulatory Factors and Immune-Associated Patterns to Decipher Common and BRCA1/2 Mutation-Type-Specific Critical Regulation in Breast Cancer.

Background: BRCA1/2 mutations are closely related to high lifetime risk of breast cancer (BC). The objective of this study was to identify the genes, regulators, and immune-associated patterns underlying disease pathology in BC with BRCA1/2 somatic mutations and their associations with clinical traits. Methods: RNA sequencing data and clinical information from The Cancer Genome Atlas (TCGA; N = 36 BRCA1-mutant BC; N = 49 BRCA2-mutant BC; and N = 117 BRCA1/2-wild-type BC samples) were used for discovery, which included consensus network analysis, function enrichment, and analysis of hub genes; other TCGA data (N = 117 triple-negative BC) and two Gene Expression Omnibus database expression profiles were used as validation cohorts. Results: Consensus network analysis helped to identify specific co-expressed modules that showed positive correlations with tumor stage, number of positive lymph nodes, and margin status in BRCA1/2-mutant BC but lacking correlations in BRCA1/2-wild-type BC. Functional enrichment suggested potential mechanisms in BRCA1/2 carriers that could regulate the cell cycle, immune response, cellular metabolic processes, and cell migration, via enriched pathways including p53 and JAK-STAT signaling. Consensus network analysis identified the specific and common carcinogenic mechanisms involving BRCA mutations. Regulators cross-linking these modules include E2F or IRF transcription factor family, associated with cell cycle or immune response regulation module, respectively. Eight hub genes, including ISG15, BUB1, and TTK, were upregulated in several BRCA1/2-mutant BC datasets and showed prognostic value in BC. Furthermore, their genetic expression was related to higher levels of immune infiltration in BRCA1/2-mutant BC, which manifested as recruitment of T helper cells (Th1 cells), follicular helper T cells, and regulatory T cells, and T cell exhaustion. Moreover, important indicators for evaluation of BC immunotherapy, tumor mutational burden and neoantigen load also positively correlated with expression of some hub genes. Conclusion: We constructed a BRCA1/2 mutation-type-specific co-expressed gene network with related transcription factors and immune-associated patterns that could regulate and influence tumor metastasis and immune microenvironment, providing novel insights into the pathological process of this disease and the corresponding BRCA mutations.

Drought resistance of ten ground cover seedling species during roof greening.

Roof greening is an important national policy for maintaining the hydrological balance in China; however, plant growth is limited by drought stress. This study aims to identify strong drought resistant plant species for roof greening from ten common species: Paeonia lactiflora, Hemerocallis dumortieri, Meehania urticifolia, Iris lactea var. chinensis, Hylotelephium erythrostictum, Sedum lineare, Iris germanica, Cosmos bipinnata, Hosta plantaginea, and Dianthus barbatus. By controlling the soil relative water content (RWC), we designed three treatments: moderate drought stress (40±2% < RWC < 45±2%), severe drought stress (RWC < 30±2%) and well-watered control (RWC > 75±2%). After the seedlings were provided different levels of water, their membrane permeability (MP), chlorophyll concentration (Chl), and superoxide dismutase (SOD), peroxidase (POD) and ascorbate peroxidase (APX) activity were measured. Finally, the membership function method was used to assess the drought resistance of these species. The results showed that C. bipinnata and M. urticifolia were not suitable for moderate or severe drought stress and did not survive. The other species presented variations in physiological and biochemical parameters. The MP of He. dumortieri, I. lactea and Ho. plantaginea showed minor changes between the well-watered control and drought stress. Most of the species showed reduced SOD activity under moderate drought stress but increased activity under severe stress. All of the plant species showed decreases in the protective enzymes POD and APX with increasing drought stress. The membership function method was applied to calculate the plant species' drought resistance, and the following order of priority of the roof-greening plant species was suggested: He. dumortieri > I. germanica > I. lactea > D. barbatus > Hy. erythrostictum > S. lineare > Ho. plantaginea > P. lactiflora.

miR-380-3p regulates melanogenesis by targeting SOX6 in melanocytes from alpacas (Vicugna pacos).

BACKGROUND: Melanocytes are derived from neural crest stem cells in the embryonic stage. In mature melanocytes, a series of complex enzyme-catalyzed reactions leads to the production of melanins, which determine the hair and skin colors of animals. The process of melanogenesis is complex and can be regulated by mRNA, microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) genes. MiRNAs are a type of endogenous noncoding RNA approximately 22 nt in size that predominantly regulate gene expression by inhibiting translation. miR-380-3p is a candidate miRNA potentially related to melanogenesis. To better understand the mechanism of miR-380-3p melanogenesis regulation, plasmids to overexpress or knockdown miR-380-3p were transfected into alpaca melanocytes, and their effects on melanogenesis were evaluated. RESULTS: In situ hybridization identified a positive miR-380-3p signal in alpaca melanocyte cytoplasm. Luciferase activity assays confirmed that SOX6 is targeted by miR-380-3p. miR-380-3p overexpression and knockdown in alpaca melanocytes respectively downregulated and upregulated SOX6 expression at the mRNA and protein levels. Additionally, miR-380-3p overexpression and knockdown, respectively, in alpaca melanocytes decreased and increased the mRNA levels of melanin transfer-related genes, including microphthalmia-associated transcription factor (MITF), tyrosinase (TYR), tyrosine-related protein-1 (TYRP1), and dopachrome tautomerase (DCT). In contrast, miR-380-3p overexpression and knockdown respectively increased and decreased the mRNA levels of ß-catenin. Additionally, the effect of miR-380-3p on melanogenesis was assessed by Masson-Fontana melanin staining. CONCLUSIONS: The results demonstrated that miR-380-3p targeted SOX6 to regulate melanogenesis by influencing ß-catenin and MITF transcription and translation, which reduced the expression of downstream genes, including TYR, TYRP1, and DCT. These results provide insights into the mechanisms through which miR-380-3p controls melanogenesis.

The role of sex-determining region Y-box 6 in melanogenesis in alpaca melanocytes.

BACKGROUND: Sex-determining region Y-box (SOX) proteins function as transcriptional regulators. The derivation of melanocytes from nerve crest cells has been reported to depend on SOX proteins, including SOX10 and SOX5. Whether SOX6 is expressed and has a functional role in melanocytes is unknown. OBJECTIVE: We aimed to study the effect of transcription factor SOX6 on melanogenesis in alpaca melanocytes. METHODS: We verified the role of SOX6 in melanogenesis by overexpressing and inhibiting SOX6 in melanocytes. Co-immunoprecipitation (co-IP) experiments were performed to further explore the function of SOX6 in melanogenesis and its mechanism of melanin production. We found that SOX6 interacted with cyclin-dependent kinase （CDK5）, ß-catenin, and Cyclin D1. RESULTS: Bioinformatics analysis suggested that SOX6 has a phosphorylation site for CDK5, which regulates melanogenesis, suggesting that SOX6 might play a role in melanogenesis. Co-IP experiments indicated that SOX6 interacted with CDK5, ß-catenin, and Cyclin D1. Quantitative real-time polymerase chain reaction and western blot analyses of SOX6-overexpressing melanocytes revealed increased mRNA and protein expression of Cyclin D1, CDK5, microphthalmia transcription factor (MITF), tyrosinase (TYR), tyrosine related protein-1 (TYRP1), and dopachrome-tautomerase (DCT), whereas ß-catenin levels decreased in SOX6-overexpressing melanocytes. The opposite results were observed upon SOX6 knockdown. The melanin content was significantly increased or decreased, respectively, by SOX6 overexpression or knockdown. CONCLUSION: Our results suggest that SOX6 might enhance melanogenesis by binding with ß-catenin to increase Cyclin D1 and MITF expression.

Correlation of increased Th17/Treg cell ratio with endoplasmic reticulum stress in chronic kidney disease.

To investigate the relationship between the regulatory immune network and endoplasmic reticulum stress (ERS) in patients with different stages of chronic kidney disease (CKD).A total of 91 patients diagnosed with CKD were divided into different groups according to the stage of disease and treatment with hemodialysis (HD) or peritoneal dialysis (PD). Routine blood and biochemical tests were performed in patients in the different CKD groups and in healthy controls (n = 20). The frequencies of T helper type 17 (Th17) and regulatory T (Treg) cells in the overall T cell population were measured by flow cytometric analysis. Levels of Th17 cell (IL-17) and Treg cell (IL-10) cytokines and the ERS markers CCAAT-enhancer-binding protein homologous protein (CHOP) and glucose-regulated protein 78 (GRP78) were measured by enzyme-linked immunosorbent assay in serum samples collected from controls and patients. Correlations between each parameter and serum creatinine were analyzed by Spearman rank correlation and regression test.CKD stage showed a positive correlation with serum creatinine level, and increased and decreased percentages of Th17 and Treg cells, respectively, reflected in an increased Th17/Treg cell ratio. Consistent with this, CKD stage was positively correlated with serum concentrations of IL-17 and negatively correlated with serum IL-10 levels. Moreover, serum levels of CHOP and GRP78 increased with advancing CKD stage. These correlations were most pronounced in patients in the CKD5 group, who also had the poorest response to HD and PD treatment, compared with CKD5 patients in the nondialysis group. Correlation analysis showed that serum levels of CHOP and GRP78 were independently and positively correlated with the ratio of Th17/Treg cells.We have found that an increased Th17/Treg cell ratio and increased serum levels of ERS markers correlate with the progression of CKD. Our results indicate that the interplay between regulation of the immune network and management of ERS is closely associated with the pathogenesis of CKD. Although HD and PD treatment manage chronic kidney conditions and prevent further deterioration of renal function, they have limited effects on improving the immune disorder and relieving ERS. Our study suggests a potential new direction for development of therapeutic strategies in CKD.

MicroRNA 143-5p regulates alpaca melanocyte migration, proliferation and melanogenesis.

microRNAs (miRNAs) have been shown to be closely involved in the control of melanogenesis and hair colour in mammals. Previous data also indicate that miR-143 regulates cell growth in melanoma. Here, we aimed to investigate the role of miR-143-5p in alpaca melanocytes. We found that miR-143-5p was highly expressed in the cytoplasm of alpaca melanocytes as demonstrated by an in situ hybridization assay. Prediction analysis revealed that miR-143-5p could regulate TGF-ß-activated kinase 1 (TAK1) expression, which we confirmed by luciferase reporter assay, indicating that miR-143-5p controls TAK1 expression by directly targeting its 3' untranslated region (UTR). miR-143-5p overexpression decreased TAK1 expression, which led to increased melanocyte migration and proliferation, and downregulation of microphthalmia-associated transcription factor (MITF), which regulates melanin production. These results support a functional role for miR-143-5p in regulating alpaca melanocyte migration, proliferation and melanogenesis through direct targeting of TAK1.

Cyclin-dependent kinase 5 regulates MAPK/ERK signaling in the skin of mice.

Cyclin-dependent kinase 5 (CDK5) is a proline-directed serine/threonine kinase that has been shown to play important roles in many tissues except the nervous system. We previously reported that CDK5 showed differential expression in the transcriptome profiles of the skin of alpacas with different hair colors. To understand the functional role of CDK5 in hair color determination, we constructed CDK5-knockdown mice and identified the effect on the mitogen-activated protein kinase (MAPK) pathway in the mouse skin. Quantitative real-time polymerase chain reaction, co-immunoprecipitation, and western blotting were performed to analyze the effects of CDK5-knockdown on the MAPK pathway in mice. The results showed that MAP3K6 was inhibited by phosphorylated CDK5 through its activator CDK7. The decrease in MAP3K6 levels caused down-regulation of MEK1 and ERK expression, leading to the up-regulation of miR-143-3p, which targets MAP3K6 via Dicer. Taken together, our findings indicate that CDK5 functions in regulating the MAPK pathway. Given that MAP3K6 was inhibited in two directions, this mechanism can provide insight into the contributions of the MAPK/ERK pathway to the inhibition of melanin production.

Pollution resistance assessment of existing landscape plants on Beijing streets based on air pollution tolerance index method.

Various plant species of green belt in urban traffic area help to reduce air pollution and beautify the city environment. Those plant species growing healthily under long-term atmospheric pollution environment are considered to be resilient. This study aims to identify plant species that are more tolerant to air pollution from traffic and to give recommendations for future green belt development in urban areas. Leaf samples of 47 plant species were collected from two heavy traffic roadside sites and one suburban site in Beijing during summer 2014. Four parameters in leaves were separately measured including relative water content (RWC), total chlorophyll content (TCH), leaf-extract pH (pH), and ascorbic acid (AA). The air pollution tolerance index (APTI) method was adopted to assess plants' resistance ability based on the above four parameters. The tolerant levels of plant species were classified using two methods, one by comparing the APTI value of individual plant to the average of all species and another by using fixed APTI values as standards. Tolerant species were then selected based on combination results from both methods. The results showed that different tolerance orders of species has been found at the three sampling sites due to varied air pollution and other environmental conditions. In general, plant species Magnolia denudata, Diospyros kaki, Ailanthus altissima, Fraxinus chinensis and Rosa chinensis were identified as tolerant species to air pollution environment and recommend to be planted at various location of the city, especially at heavy traffic roadside.