The relationship between oxidative balance score and erectile dysfunction in the U.S. male adult population.

Oxidative stress strongly influences the pathophysiology of erectile dysfunction (ED). In this study, we used the oxidative balance score (OBS), a composite index, to measure the effects of oxidative stress triggered by diet and lifestyle factors. Here, we conducted a cross-sectional study to determine the statistical relationship between OBS and ED among adult males in the U.S. The data from 3318 participants in the National Health and Nutrition Examination Survey (NHANES) 2001-2004 were analyzed. Weighted logistic regression was used to correct for confounding factors and acquire nationwide representative estimates. Generalized additive modeling was used to explore the nonlinear relationship. We also supplemented subgroup and sensitivity analysis to examine the robustness of the main results. Multivariate logistic regression indicated a consistent negative linear association between OBS and ED across all participants [OR (95% CI) = 0.96 (0.94, 0.98)]. After categorizing OBS into tertiles, participants in the highest tertile had 43% lower odds of having ED than those in the lowest tertile [OR (95% CI) = 0.57 (0.37, 0.87)]. The generalized additive model also visualized the linear trend of this association. Furthermore, this linear relationship remained relatively consistent, regardless of whether subgroup or sensitivity analyses were performed. Our findings suggest that adopting a lifestyle and diet pattern that promotes favorable OBS may effectively protect against the development of ED, regardless of the underlying causes.

Synthetic CRISPR/dCas9-KRAB system driven by specific PSA promoter suppresses malignant biological behavior of prostate cancer cells through negative feedback inhibition of PSA expression.

PSA is a type of proto-oncogene that is specifically and highly expressed in embryonic and prostate cancer cells, but not expressed in normal prostate tissue cells. The specific expression of prostate-specific antigen (PSA) is found to be related with the conditional transcriptional regulation of its promoter. Clustered regularly interspaced short palindromic repeats (CRISPR)-dCas9-KRAB is a newly developed transcriptional regulatory system that inhibits gene expression by interupting the DNA transcription process. Induction of CRISPR-dCas9-KRAB expression through the PSA promoter may help feedback inhibition of cellular PSA gene expression via single guide RNA (sgRNA), thereby monitoring and suppressing the malignant state of tumor cells. In this study, we examined the transcriptional activity of the PSA promoter in different prostate cancer cells and normal prostate epithelial cells and determined that it is indeed a prostate cancer cell-specific promoter.Then we constructed the CRISPR-dCas9-KRAB system driven by the PSA promoter, which can inhibit PSA gene expression in the prostate cancer cells at the transcriptional level, and therefore supress the malignant growth and migration of prostate cancer cells and promote their apoptosis in vitro. This study provides a potentially effective anti-cancer strategy for gene therapy of prostate cancer.

Fecal-related anthropogenic sources are key determinants of lake microbiomes through microbial source tracking.

Lake microbiomes are essential indicators of lake health and are strongly influenced by allochthonous microbial communities from various sources within the watershed. However, quantifying the contributions of multiple inputs to lake microbiomes is challenging because of the complex nature of river‒lake systems and the presence of many untraceable sources. Here, Jianhu Lake‒‒a geographically simple and closed plateau lake in southwestern China, was surveyed to disentangle the contributions of five distinct sources (three input rivers that receive town sewage, stormwater runoff, and creek spring water, as well as two nonpoint sources, duck ponds and dry farmland) to the overall lake microbiomes. We found that feces-loading sources, namely town sewage and duck aquaculture, accounted for 48.7% of the total variations in lake microbiomes. In contrast, the combined contribution of the remaining three sources amounted to 13.21%, despite these less-influential sources (e.g., stormwater runoff) may introduce an even larger volume of allochthonous materials into the lake. In addition, approximately 38.1% of the variations in the lake microbiomes were attributed to unknown sources. Sewage effluents also caused a significant loss of lake microbial diversity, and there was a tendency for large-scale microbial homogeneity in lake sediments that resembled those from duck ponds. We then used a targeted approach to track host-specific fecal pollution, and found that human feces were the primary source, followed by ruminant and chicken/duck feces, all of which can be successfully traced back to the feces-loading sources. In our further modelling of sediment transport from three rivers into the whole lake, we observed a significant relationship between sediment accumulation and adsorbed microorganisms only for the sewage-receiving river. Together, lines of evidence indicate that both point and nonpoint fecal-related anthropogenic sources possess discriminatory power for shaping microbial geographic patterns of the lake, posing threats to the survival of local indigenous lake microbiomes.

Climate Variations in the Low-Latitude Plateau Contribute to Different Sugarcane (Saccharum spp.) Yields and Sugar Contents in China.

In China, the main sugarcane (Saccharum spp.) planting areas can be found in the low-latitude plateau (21° N-25° N, 97° E-106° E), which has most of the natural ecological types. However, there is limited information on the climate conditions of this region and their influence on sugarcane yield and sucrose content. Monthly variations in the main climate factors, namely, average air temperature (AAT), average relative humidity (ARH), average rainfall amount (ARA), and average sunshine duration (ASD), from 2000 to 2019 and sugarcane yield and sucrose content of 26 major sugarcane-producing areas from 2001/2002 to 2018/2019 were collected from the low-latitude plateau in Yunnan for studying the impact of climate variations on sugarcane yield and sucrose content. The results showed that AAT in the mid-growth season had a significant positive correlation with sucrose content (p < 0.05), and AAT in the late-growth season had a very significant positive correlation with sucrose content (p < 0.01). ARH in the mid-growth season had a significant positive correlation with sugarcane yield (p < 0.05). ARA in the early-growth season showed a significant positive correlation with sugarcane yield (p < 0.05). ASD in the late-growth season had a significant positive correlation with sugarcane yield (p < 0.05) and sucrose content (p < 0.01). The rainy and humid sugarcane areas were characterized by high ARA and ARH during the entire growth period, low AAT and ASD in the mid-growth season, and low AAT in the late-growth season, contributing to a high sugarcane yield, but not a high sucrose content. The low temperature and sunshine semi-humid sugarcane areas were characterized by the lowest AAT in the early and middle stages of sugarcane growth, less ASD in the early and middle stages, and less ARA in the early and late stages, which are unfavorable for sugarcane yield and sucrose content. The high temperature and humidity sugarcane areas were characterized by higher AAT and ARA, and moderate ASD during the entire growth period, resulting in good sugarcane growth potential and contributing to the sugarcane yield and sucrose content. The semi-humid and multi-sunshine sugarcane areas were characterized by the lowest ARH in the entire growth period, the lowest ARA in the middle and late seasons, and the longest ASD, contributing to an increase in sucrose content. The humid and sunny areas were characterized by the longest ASD and high ARH in the early and late seasons of sugarcane growth and moderate AAT and ARA during the entire growth season, which are beneficial for high sugarcane yield and sucrose content. Overall, these findings suggest that the sugarcane variety layout should be based on the climate type (of which there are five in the plateau), and corresponding cultivation practices should be used to compensate for the climatic conditions in various growth stages.

[Effects of Different Planting Years of Dendrocalamus brandisii on Soil Fungal Community].

To explore the effect of soil fungal community under different planting years in Dendrocalamus brandisii, the soil samples from D. brandisii with different planting years (5, 10, 20, and 40 a) were taken as the research object. The soil fungal community structure, diversity, and its functional groups of different planting years were analyzed using high-throughput sequencing technology and the FUNGuild fungal function prediction tool, and the main soil environmental factors influencing the variations in soil fungal community were examined. The results showed that the dominant fungal communities at the phylum level were Ascomycota, Basidiomycota, Mortierellomycota, and Mucoromycota. The relative abundance of Mortierellomycota decreased and then increased with the increase in planting years, and there was a significant difference among different planting years (P<0.05). The dominant fungal communities at the class level were Sordariomycetes, Agaricomycetes, Eurotiomycetes, and Mortierellomycetes. The relative abundance of Sordariomycetes and Dothideomycetes decreased and then increased with the increase in planting years, and there were significant differences among different planting years (P<0.01). The Richness index and Shannon index of soil fungi increased and then decreased with the increase in planting years, and the Richness index and Shannon index in 10 a were significantly higher than those of other planting years. Non-metric multidimensional scaling (NMDS) and analysis of similarities (ANOSIM) showed that there were significant differences in soil fungal community structure with different planting years. The functional prediction with FUNGuild showed that the main functional trophic types of soil fungi in D. brandisii were pathotroph, symbiotroph, and saprotroph, and the most dominant functional group was endophyte-litter saprotroph-soil saprotroph-undefined saprotroph. The relative abundance of endophytes gradually increased with the increase in planting years. Correlation analysis showed that pH, total potassium (TK), and nitrate nitrogen (NO-3-N) were the main soil environmental factors affecting the change in fungal community. In summary, the planting year of D. brandisii has changed soil environmental factors and has thus changed the structure, diversity, and functional groups of soil fungal communities.

A Novel Intelligent System for Dynamic Observation of Cotton Verticillium Wilt.

Verticillium wilt is one of the most critical cotton diseases, which is widely distributed in cotton-producing countries. However, the conventional method of verticillium wilt investigation is still manual, which has the disadvantages of subjectivity and low efficiency. In this research, an intelligent vision-based system was proposed to dynamically observe cotton verticillium wilt with high accuracy and high throughput. Firstly, a 3-coordinate motion platform was designed with the movement range 6,100 mm × 950 mm × 500 mm, and a specific control unit was adopted to achieve accurate movement and automatic imaging. Secondly, the verticillium wilt recognition was established based on 6 deep learning models, in which the VarifocalNet (VFNet) model had the best performance with a mean average precision (mAP) of 0.932. Meanwhile, deformable convolution, deformable region of interest pooling, and soft non-maximum suppression optimization methods were adopted to improve VFNet, and the mAP of the VFNet-Improved model improved by 1.8%. The precision-recall curves showed that VFNet-Improved was superior to VFNet for each category and had a better improvement effect on the ill leaf category than fine leaf. The regression results showed that the system measurement based on VFNet-Improved achieved high consistency with manual measurements. Finally, the user software was designed based on VFNet-Improved, and the dynamic observation results proved that this system was able to accurately investigate cotton verticillium wilt and quantify the prevalence rate of different resistant varieties. In conclusion, this study has demonstrated a novel intelligent system for the dynamic observation of cotton verticillium wilt on the seedbed, which provides a feasible and effective tool for cotton breeding and disease resistance research.

An Intelligent Rice Yield Trait Evaluation System Based on Threshed Panicle Compensation.

High-throughput phenotyping of yield-related traits is meaningful and necessary for rice breeding and genetic study. The conventional method for rice yield-related trait evaluation faces the problems of rice threshing difficulties, measurement process complexity, and low efficiency. To solve these problems, a novel intelligent system, which includes an integrated threshing unit, grain conveyor-imaging units, threshed panicle conveyor-imaging unit, and specialized image analysis software has been proposed to achieve rice yield trait evaluation with high throughput and high accuracy. To improve the threshed panicle detection accuracy, the Region of Interest Align, Convolution Batch normalization activation with Leaky Relu module, Squeeze-and-Excitation unit, and optimal anchor size have been adopted to optimize the Faster-RCNN architecture, termed 'TPanicle-RCNN,' and the new model achieved F1 score 0.929 with an increase of 0.044, which was robust to indica and japonica varieties. Additionally, AI cloud computing was adopted, which dramatically reduced the system cost and improved flexibility. To evaluate the system accuracy and efficiency, 504 panicle samples were tested, and the total spikelet measurement error decreased from 11.44 to 2.99% with threshed panicle compensation. The average measuring efficiency was approximately 40 s per sample, which was approximately twenty times more efficient than manual measurement. In this study, an automatic and intelligent system for rice yield-related trait evaluation was developed, which would provide an efficient and reliable tool for rice breeding and genetic research.

An Intelligent Analysis Method for 3D Wheat Grain and Ventral Sulcus Traits Based on Structured Light Imaging.

The wheat grain three-dimensional (3D) phenotypic characters are of great significance for final yield and variety breeding, and the ventral sulcus traits are the important factors to the wheat flour yield. The wheat grain trait measurements are necessary; however, the traditional measurement method is still manual, which is inefficient, subjective, and labor intensive; moreover, the ventral sulcus traits can only be obtained by destructive measurement. In this paper, an intelligent analysis method based on the structured light imaging has been proposed to extract the 3D wheat grain phenotypes and ventral sulcus traits. First, the 3D point cloud data of wheat grain were obtained by the structured light scanner, and then, the specified point cloud processing algorithms including single grain segmentation and ventral sulcus location have been designed; finally, 28 wheat grain 3D phenotypic characters and 4 ventral sulcus traits have been extracted. To evaluate the best experimental conditions, three-level orthogonal experiments, which include rotation angle, scanning angle, and stage color factors, were carried out on 125 grains of 5 wheat varieties, and the results demonstrated that optimum conditions of rotation angle, scanning angle, and stage color were 30°, 37°, black color individually. Additionally, the results also proved that the mean absolute percentage errors (MAPEs) of wheat grain length, width, thickness, and ventral sulcus depth were 1.83, 1.86, 2.19, and 4.81%. Moreover, the 500 wheat grains of five varieties were used to construct and validate the wheat grain weight model by 32 phenotypic traits, and the cross-validation results showed that the R 2 of the models ranged from 0.77 to 0.83. Finally, the wheat grain phenotype extraction and grain weight prediction were integrated into the specialized software. Therefore, this method was demonstrated to be an efficient and effective way for wheat breeding research.

Cereal grain 3D point cloud analysis method for shape extraction and filled/unfilled grain identification based on structured light imaging.

Cereals are the main food for mankind. The grain shape extraction and filled/unfilled grain recognition are meaningful for crop breeding and genetic analysis. The conventional measuring method is mainly manual, which is inefficient, labor-intensive and subjective. Therefore, a novel method was proposed to extract the phenotypic traits of cereal grains based on point clouds. First, a structured light scanner was used to obtain the grains point cloud data. Then, the single grain segmentation was accomplished by image preprocessing, plane fitting, region growth clustering. The length, width, thickness, surface area and volume was calculated by the specified analysis algorithms for grain point cloud. To demonstrate this method, experimental materials included rice, wheat and corn were tested. Compared with manual measurement results, the average measurement error of grain length, width and thickness was 2.07%, 0.97%, 1.13%, and the average measurement efficiency was about 9.6 s per grain. In addition, the grain identification model was conducted with 25 grain phenotypic traits, using 6 machine learning methods. The results showed that the best accuracy for filled/unfilled grain classification was 90.184%.The best accuracy for indica and japonica identification was 99.950%, while for different varieties identification was only 47.252%. Therefore, this method was proved to be an efficient and effective way for crop research.

Targeted Methylation of the LncRNA NEAT1 Suppresses Malignancy of Renal Cell Carcinoma.

Long-chain non-coding RNA (LncRNA) has been found to play an important role in the regulation of the occurrence and progression of renal cell carcinoma (RCC). In this study, we demonstrated that LncRNA NEAT1 expression and m6A methylation level was decreased in RCC tissues. Further, the downregulated expression level of LncRNA NEAT1 was associated with poor prognosis for RCC patients. Then we used CRIPSR/dCas13b-METTL3 to methylate LncRNA NEAT1 in RCC cells. The results showed that the expression level of LncRNA NEAT1 was upregulated after methylated by dCas13b-METTL3 in RCC cells. And the proliferation and migration ability of RCC cells was decreased after methylated LncRNA NEAT1. Finally, we examined the effect of LncRNA NEAT1 hypermethylation on the transcriptome. We found differentially expressed genes in RCC cells were associated with "cGMP-PKG signaling pathway", "Cell adhesion molecules" and "Pathways in cancer". In conclusion, CRISPR/Cas13b-METTL3 targeting LncRNA NEAT1 m6A methylation activates LncRNA NEAT1 expression and provides a new target for treatment of RCC.

[Effects of plant community and soil properties on soil bacterial community in Bitahai Wetland, Southwest China]. / 植物群落和土壤理化性质对碧塔海湿地土壤细菌群落的影响.

Soil microorganism was the engine of the migration and transformation of biological elements in the soil-plant system of wetland ecosystems. Exploring the relationship between plant community, soil properties, and spatial structure with soil microorganisms is the key to maintain the health and stability of wetlands. In order to examine the effects of plant community, soil properties, and spatial structure on the bacterial community in wetlands, we used two-way indicator species analysis (TWINSPAN) to classify plant communities from 35 samples collected in Bitahai Wetland. We measured microbial community composition at the surface soil of the samples using high-throughput sequencing technology, and analyzed the relationship among plant community, soil pro-perties and spatial structure with bacterial community. The results showed that plant communities could classified into three different types by TWINSPAN. The physiognomy and structure of plant communities in same community type were relatively consistent. We found that quantitative classification had good applicability in vegetation classification of plateau wetland ecosystem. Acidobacteriota (21.0%), Chloroflexi (15.5%), Proteobacteria (15.3%) and Bacteroidetes (10.1%) had higher population densities (≥10%) in Bitahai Wetland. Analysis of similarities (ANOSIM) showed that different plant community types differed significantly in bacterial community composition, suggesting that plant communities could affect bacterial community. Cano-nical correspondence analysis (CCA) results showed that plant diversity, soil water content (SWC), pH, iron (Fe) and spatial structure were the dominated factors that significantly affecting bacterial community. The variance partitioning analysis (VPA) results showed that bacterial community was affected by single environment factors and their interactions. Our results highlighted that bacterial community is shaped by plant community, soil properties and spatial structure, with their effects being indivisible.

Patient-derived organoids of bladder cancer recapitulate antigen expression profiles and serve as a personal evaluation model for CAR-T cells in vitro.

OBJECTIVES: Recent advances in patient-derived cancer organoids have opened a new avenue for personalised medicine. We aimed to establish an in vitro technological platform to evaluate chimeric antigen receptor (CAR)-T cell-mediated cytotoxicity against bladder cancer. METHODS: Patient-derived bladder cancer organoids (BCOs) were derived using classic medium containing R-spondin 1 and noggin. The features of BCOs were characterised via H&E, whole-exome sequencing and immunofluorescence of specific markers. Surface antigen expression profiles of the recently identified CAR-recognisable targets were determined with a panel of antibodies via immunohistochemistry. A co-cultivation system consisting of BCOs and engineered T cells targeting a specific antigen was utilised to test its efficacy to model immunotherapy by cytotoxic assays and ELISA. RESULTS: Bladder cancer organoid lines of basal and luminal subtypes were established. The histopathological morphology, genomic alteration, and specific marker expression profiles showed that the BCO lines retained the characteristics of the original tumors. Among all tested CAR-recognisable antigens in other solid tumors, MUC1 was simultaneously expressed in organoids and parental tumor tissues. Given the surface antigen profiles, second-generation CAR-T cells targeting MUC1 were prepared for modelling in vitro immunotherapy responses in BCOs. Specific immune cytotoxicity occurred only in the MUC1+ organoids but not in the MUC1- organoids or control CAR-T cells. CONCLUSION: Patient-derived BCOs recapitulate the heterogeneity and key features of parental cancer tissues, and these BCOs could be useful for preclinical testing of CAR-T cells in vitro.

DNA barcoding and molecular phylogeny of Dumasia (Fabaceae: Phaseoleae) reveals a cryptic lineage.

Dumasia taxonomy and classification have long been problematic. Species within this genus have few morphological differences and plants without flowers or fruits are difficult to accurately identify. In this study, we evaluated the ability of six DNA barcoding sequences, one nuclear (ITS) and five chloroplast regions (trnH-psbA, matK, rbcL, trnL-trnF, psbB-psbF), to efficiently identify Dumasia species. Most single markers or their combinations identify obvious barcoding gaps between intraspecific and interspecific genetic variation. Most combined analyses including ITS showed good species resolution and identification efficiency. We therefore suggest that ITS alone or a combination of ITS with any cpDNA marker are most suitable for DNA barcoding of Dumasia. The phylogenetic analyses clearly indicated that Dumasia yunnanensis is not monophyletic and is separated as two independent branches, which may result from cryptic differentiation. Our results demonstrate that molecular data can deepen the comprehension of taxonomy of Dumasia and provide an efficient approach for identification of the species.

CRISPR-Cas13-Mediated Knockdown of lncRNA-GACAT3 Inhibited Cell Proliferation and Motility, and Induced Apoptosis by Increasing p21, Bax, and E-Cadherin Expression in Bladder Cancer.

The current study is to investigate the expression pattern and biological function of long non-coding RNA Focally gastric cancer-associated transcript3 (GACAT3) in bladder cancer. Real-time quantitative qPCR was used to detect the expression level of GACAT-3 in tumor tissues and paired normal tissues. Human bladder cancer T24 and 5637 cell lines were transiently transfected with specific CRISPR-Cas13 or negative control CRISPR-Cas13. Cell migration, proliferation, and apoptosis were measured by using wound healing assay CCK-8 assay and Caspase-3 ELISA assay, respectively. The expression changes of p21, Bax, and E-cadherin after knockdown of GACAT3 were detected by using Western blot. The results demonstrated that GACAT3 was up-regulated in bladder cancer tissues than that in the paired normal tissues. Inhibition of cell proliferation, increased apoptosis, and decreased motility were observed in T24 and 5637 cell lines transfected by CRISPR-Cas13 targeting GACAT3. Downregulation of GACAT3 increased p21, Bax, and E-cadherin expression and silencing these genes could eliminate the phenotypic changes induced by knockdown of GACAT3. A ceRNA mechanism for GACAT3 was also revealed. By using CRISPR-Cas13 biotechnology, we suggested that GACAT3 may be a novel target for diagnosis and treatment of bladder cancer.

Mixed adenocarcinoma, sarcomatoid carcinoma and adenosquamous carcinoma of the prostate: A case report.

Adenosquamous carcinoma (ASC) and sarcomatoid carcinoma (SC) of the prostate are rare, but highly aggressive tumors. The occurrence of mixed carcinomas in the prostate is even more rarely reported. The present study reports the case of a 62-year-old male who was diagnosed with prostatic adenocarcinoma accompanied by multiple bone metastases, as shown by a needle biopsy and skeletal computed tomography scan. The patient was treated with hormonal therapy, but thereafter, specimens from a transurethral resection of the prostate (TURP) were found to be composed of three histologically distinct elements: ASC, SC and adenocarcinoma. The level of p53 was evaluated by immunohistochemistry in detail, and it was found that this was significantly increased in the TURP samples compared with the needle biopsy samples. The abnormal level of p53 was likely associated with the prognosis of the patient; the patient succumbed to prostate carcinoma two months after the confirmation of the diagnosis.

[Knocking down TRPC1 expression by siRNA inhibits proliferation and invasiveness of human lung adenocarcinoma cell A549 in vitro].

OBJECTIVE: To evaluate the effects of down-regulated expression of transient receptor potential canonical (TRPC1) by RNA interference (RNAi) on proliferation and invasiveness of human lung adenocarcinoma cell A549 in vitro. METHODS: A549 cells were transfected with chemically synthesized small interfering RNA (siRNA) targeting TRPC1 gene. The mRNA and protein of TRPC1 were analyzed by real-time polymerase chain reaction (PCR) and Western blot respectively. To assess malignant phenotypes of transfected A549 cells, the assays of methyl thiazolyl tetrazolium (MTT), cell cycle and cell invasion were performed. RESULTS: siRNA targeting TRPC1 dramatically suppressed TRPC1 expression. In vitro study showed that siRNA targeting TRPC1 significantly inhibited cell proliferation of A549 cells with an inhibitory rate of 34.7% while negative control siRNA had no effect on cell proliferation. Flow cytometric analysis showed that siRNA targeting TRPC1 increased the number of cells in G0/G1 phase (P < 0.05) . Moreover, a knockdown of TRPC1 expression effectively inhibited cell invasiveness in A549 cells (P < 0.05) . CONCLUSION: Knocking down TRPC1 expression can inhibit proliferation and invasiveness of A549 cells in vitro.

Frequent mutations of genes encoding ubiquitin-mediated proteolysis pathway components in clear cell renal cell carcinoma.

We sequenced whole exomes of ten clear cell renal cell carcinomas (ccRCCs) and performed a screen of ∼1,100 genes in 88 additional ccRCCs, from which we discovered 12 previously unidentified genes mutated at elevated frequencies in ccRCC. Notably, we detected frequent mutations in the ubiquitin-mediated proteolysis pathway (UMPP), and alterations in the UMPP were significantly associated with overexpression of HIF1α and HIF2α in the tumors (P = 0.01 and 0.04, respectively). Our findings highlight the potential contribution of UMPP to ccRCC tumorigenesis through the activation of the hypoxia regulatory network.

Frequent mutations of chromatin remodeling genes in transitional cell carcinoma of the bladder.

Transitional cell carcinoma (TCC) is the most common type of bladder cancer. Here we sequenced the exomes of nine individuals with TCC and screened all the somatically mutated genes in a prevalence set of 88 additional individuals with TCC with different tumor stages and grades. In our study, we discovered a variety of genes previously unknown to be mutated in TCC. Notably, we identified genetic aberrations of the chromatin remodeling genes (UTX, MLL-MLL3, CREBBP-EP300, NCOR1, ARID1A and CHD6) in 59% of our 97 subjects with TCC. Of these genes, we showed UTX to be altered substantially more frequently in tumors of low stages and grades, highlighting its potential role in the classification and diagnosis of bladder cancer. Our results provide an overview of the genetic basis of TCC and suggest that aberration of chromatin regulation might be a hallmark of bladder cancer.

MicroRNA expression signatures of bladder cancer revealed by deep sequencing.

BACKGROUND: MicroRNAs (miRNAs) are a class of small noncoding RNAs that regulate gene expression. They are aberrantly expressed in many types of cancers. In this study, we determined the genome-wide miRNA profiles in bladder urothelial carcinoma by deep sequencing. METHODOLOGY/PRINCIPAL FINDINGS: We detected 656 differentially expressed known human miRNAs and miRNA antisense sequences (miRNA*s) in nine bladder urothelial carcinoma patients by deep sequencing. Many miRNAs and miRNA*s were significantly upregulated or downregulated in bladder urothelial carcinoma compared to matched histologically normal urothelium. hsa-miR-96 was the most significantly upregulated miRNA and hsa-miR-490-5p was the most significantly downregulated one. Upregulated miRNAs were more common than downregulated ones. The hsa-miR-183, hsa-miR-200b ∼ 429, hsa-miR-200c ∼ 141 and hsa-miR-17 ∼ 92 clusters were significantly upregulated. The hsa-miR-143 ∼ 145 cluster was significantly downregulated. hsa-miR-182, hsa-miR-183, hsa-miR-200a, hsa-miR-143 and hsa-miR-195 were evaluated by Real-Time qPCR in a total of fifty-one bladder urothelial carcinoma patients. They were aberrantly expressed in bladder urothelial carcinoma compared to matched histologically normal urothelium (p < 0.001 for each miRNA). CONCLUSIONS/SIGNIFICANCE: To date, this is the first study to determine genome-wide miRNA expression patterns in human bladder urothelial carcinoma by deep sequencing. We found that a collection of miRNAs were aberrantly expressed in bladder urothelial carcinoma compared to matched histologically normal urothelium, suggesting that they might play roles as oncogenes or tumor suppressors in the development and/or progression of this cancer. Our data provide novel insights into cancer biology.

Integrated profiling of microRNAs and mRNAs: microRNAs located on Xq27.3 associate with clear cell renal cell carcinoma.

BACKGROUND: With the advent of second-generation sequencing, the expression of gene transcripts can be digitally measured with high accuracy. The purpose of this study was to systematically profile the expression of both mRNA and miRNA genes in clear cell renal cell carcinoma (ccRCC) using massively parallel sequencing technology. METHODOLOGY: The expression of mRNAs and miRNAs were analyzed in tumor tissues and matched normal adjacent tissues obtained from 10 ccRCC patients without distant metastases. In a prevalence screen, some of the most interesting results were validated in a large cohort of ccRCC patients. PRINCIPAL FINDINGS: A total of 404 miRNAs and 9,799 mRNAs were detected to be differentially expressed in the 10 ccRCC patients. We also identified 56 novel miRNA candidates in at least two samples. In addition to confirming that canonical cancer genes and miRNAs (including VEGFA, DUSP9 and ERBB4; miR-210, miR-184 and miR-206) play pivotal roles in ccRCC development, promising novel candidates (such as PNCK and miR-122) without previous annotation in ccRCC carcinogenesis were also discovered in this study. Pathways controlling cell fates (e.g., cell cycle and apoptosis pathways) and cell communication (e.g., focal adhesion and ECM-receptor interaction) were found to be significantly more likely to be disrupted in ccRCC. Additionally, the results of the prevalence screen revealed that the expression of a miRNA gene cluster located on Xq27.3 was consistently downregulated in at least 76.7% of ∼50 ccRCC patients. CONCLUSIONS: Our study provided a two-dimensional map of the mRNA and miRNA expression profiles of ccRCC using deep sequencing technology. Our results indicate that the phenotypic status of ccRCC is characterized by a loss of normal renal function, downregulation of metabolic genes, and upregulation of many signal transduction genes in key pathways. Furthermore, it can be concluded that downregulation of miRNA genes clustered on Xq27.3 is associated with ccRCC.