Browse
Submit Data
Databases
API
Help

Dataset Information

13 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Towards reliable diagnostics of prostate cancer via breath.

ABSTRACT: Early detection of cancer is a key ingredient for saving many lives. Unfortunately, cancers of the urogenital system are difficult to detect at early stage. The existing noninvasive diagnostics of prostate cancer (PCa) suffer from low accuracy (< 70%) even at advanced stages. In an attempt to improve the accuracy, a small breath study of 63 volunteers representing three groups: (1) of 19 healthy, (2) 28 with PCa, (3) with 8 kidney cancer (KC) and 8 bladder cancer (BC) was performed. Ultrabroadband mid-infrared Fourier absorption spectroscopy revealed eight spectral ranges (SRs) that differentiate the groups. The resulting accuracies of supervised analyses exceeded 95% for four SRs in distinguishing (1) vs (2), three for (1) vs (3) and four SRs for (1) vs (2) + (3). The SRs were then attributed to volatile metabolites. Their origin and involvement in urogenital carcinogenesis are discussed.

SUBMITTER: Maiti KS

PROVIDER: S-EPMC8443711 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

The phytoalexin camalexin mediates cytotoxicity towards aggressive prostate cancer cells via reactive oxygen species.

Project description:Camalexin is a phytoalexin that accumulates in various cruciferous plants upon exposure to environmental stress and plant pathogens. Besides moderate antibacterial and antifungal activity, camalexin was reported to also exhibit antiproliferative and cancer chemopreventive effects in breast cancer and leukemia. We studied the cytotoxic effects of camalexin treatment on prostate cancer cell lines and whether this was mediated by reactive oxygen species (ROS) generation. As models, we utilized LNCaP and its aggressive subline, C4-2, as well as ARCaP cells stably transfected with empty vector (Neo) control or constitutively active Snail cDNA that represents an epithelial to mesenchymal transition (EMT) model and displays increased cell migration and tumorigenicity. We confirmed previous studies showing that C4-2 and ARCaP-Snail cells express more ROS than LNCaP and ARCaP-Neo, respectively. Camalexin increased ROS, decreased cell proliferation, and increased apoptosis more significantly in C4-2 and ARCaP-Snail cells as compared to LNCaP and ARCaP-Neo cells, respectively, while normal prostate epithelial cells (PrEC) were unaffected. Increased caspase-3/7 activity and increased cleaved PARP protein shown by Western blot analysis was suggestive of increased apoptosis. The ROS scavenger N-acetyl cysteine (NAC) antagonized the effects of camalexin, whereas the addition of exogenous hydrogen peroxide potentiated the effects of camalexin, showing that camalexin is mediating its effects through ROS. In conclusion, camalexin is more potent in aggressive prostate cancer cells that express high ROS levels, and this phytoalexin has a strong potential as a novel therapeutic agent for the treatment of especially metastatic prostate cancer.

| S-EPMC3644009 | biostudies-literature

Reliable and accurate diagnostics from highly multiplexed sequencing assays.

Project description:Scalable, inexpensive, and secure testing for SARS-CoV-2 infection is crucial for control of the novel coronavirus pandemic. Recently developed highly multiplexed sequencing assays (HMSAs) that rely on high-throughput sequencing can, in principle, meet these demands, and present promising alternatives to currently used RT-qPCR-based tests. However, reliable analysis, interpretation, and clinical use of HMSAs requires overcoming several computational, statistical and engineering challenges. Using recently acquired experimental data, we present and validate a computational workflow based on kallisto and bustools, that utilizes robust statistical methods and fast, memory efficient algorithms, to quickly, accurately and reliably process high-throughput sequencing data. We show that our workflow is effective at processing data from all recently proposed SARS-CoV-2 sequencing based diagnostic tests, and is generally applicable to any diagnostic HMSA.

| S-EPMC7730459 | biostudies-literature

Toxicity of Carbon Nanomaterials-Towards Reliable Viability Assessment via New Approach in Flow Cytometry.

Project description:The scope of application of carbon nanomaterials in biomedical, environmental and industrial fields is recently substantially increasing. Since in vitro toxicity testing is the first essential step for any commercial usage, it is crucial to have a reliable method to analyze the potentially harmful effects of carbon nanomaterials. Even though researchers already reported the interference of carbon nanomaterials with common toxicity assays, there is still, unfortunately, a large number of studies that neglect this fact. In this study, we investigated interference of four bio-promising carbon nanomaterials (graphene acid (GA), cyanographene (GCN), graphitic carbon nitride (g-C3N4) and carbon dots (QCDs)) in commonly used LIVE/DEAD assay. When a standard procedure was applied, materials caused various types of interference. While positively charged g-C3N4 and QCDs induced false results through the creation of free agglomerates and intrinsic fluorescence properties, negatively charged GA and GCN led to false signals due to the complex quenching effect of the fluorescent dye of a LIVE/DEAD kit. Thus, we developed a new approach using a specific gating strategy based on additional controls that successfully overcame all types of interference and lead to reliable results in LIVE/DEAD assay. We suggest that the newly developed procedure should be a mandatory tool for all in vitro flow cytometry assays of any class of carbon nanomaterials.

| S-EPMC8305450 | biostudies-literature

Mobile Health Solutions for Prostate Cancer Diagnostics-A Systematic Review.

Project description:Prostate cancer, the most common cause of cancer in men in the UK and one of the most common around the world to date, has no consensus on screening. Multiple large-scale trials from around the world have produced conflicting outcomes in cancer-specific and overall mortality. A main part of the issue is the PSA test, which has a high degree of variability, making it challenging to set PSA thresholds, as well as limited specificity. Prostate cancer has a predisposition in men from black backgrounds, and outcomes are worse in men of lower socioeconomic groups. Mobile targeted case finding, focusing on high-risk groups, may be a solution to help those that most need it. The aim of this systematic review was to review the evidence for mobile testing for prostate cancer. A review of all mobile screening studies for prostate cancer was performed in accordance with the Cochrane guidelines and the PRISMA statement. Of the 629 unique studies screened, 6 were found to be eligible for the review. The studies dated from 1973 to 2017 and came from four different continents, with around 30,275 men being screened for prostate cancer. Detection rates varied from 0.6% in the earliest study to 8.2% in the latest study. The challenge of early diagnosis of potentially lethal prostate cancer remains an issue for developed and low- and middle-income countries alike. Although further studies are needed, mobile screening of a targeted population with streamlined investigation and referral pathways combined with raising awareness in those communities may help make the case for screening for prostate cancer.

| S-EPMC10453449 | biostudies-literature

Prostate cancer genomics: towards a new understanding.

Project description:Recent genetics and genomics studies of prostate cancer have helped to clarify the genetic basis of this common but complex disease. Genome-wide studies have detected numerous variants associated with disease as well as common gene fusions and expression 'signatures' in prostate tumours. On the basis of these results, some advocate gene-based individualized screening for prostate cancer, although such testing might only be worthwhile to distinguish disease aggressiveness. Lessons learned from these studies provide strategies for further deciphering the genetic causes of prostate cancer and other diseases.

| S-EPMC2721916 | biostudies-literature

Exhaled breath diagnostics of lung and gastric cancers in China using nanosensors.

Project description: Not available

| S-EPMC7307230 | biostudies-literature

Modular Breath Analyzer (MBA): Introduction of a Breath Analyzer Platform Based on an Innovative and Unique, Modular eNose Concept for Breath Diagnostics and Utilization of Calibration Transfer Methods in Breath Analysis Studies.

Project description:Exhaled breath analysis for early disease detection may provide a convenient method for painless and non-invasive diagnosis. In this work, a novel, compact and easy-to-use breath analyzer platform with a modular sensing chamber and direct breath sampling unit is presented. The developed analyzer system comprises a compact, low volume, temperature-controlled sensing chamber in three modules that can host any type of resistive gas sensor arrays. Furthermore, in this study three modular breath analyzers are explicitly tested for reproducibility in a real-life breath analysis experiment with several calibration transfer (CT) techniques using transfer samples from the experiment. The experiment consists of classifying breath samples from 15 subjects before and after eating a specific meal using three instruments. We investigate the possibility to transfer calibration models across instruments using transfer samples from the experiment under study, since representative samples of human breath at some conditions are difficult to simulate in a laboratory. For example, exhaled breath from subjects suffering from a disease for which the biomarkers are mostly unknown. Results show that many transfer samples of all the classes under study (in our case meal/no meal) are needed, although some CT methods present reasonably good results with only one class.

| S-EPMC8235513 | biostudies-literature

Towards reliable extreme weather and climate event attribution.

Project description:Climate change is shaping extreme heat and rain. To what degree human activity has increased the risk of high impact events is of high public concern and still heavily debated. Recent studies attributed single extreme events to climate change by comparing climate model experiments where the influence of an external driver can be included or artificially suppressed. Many of these results however did not properly account for model errors in simulating the probabilities of extreme event occurrences. Here we show, exploiting advanced correction techniques from the weather forecasting field, that correcting properly for model probabilities alters the attributable risk of extreme events to climate change. This study illustrates the need to correct for this type of model error in order to provide trustworthy assessments of climate change impacts.

| S-EPMC6465259 | biostudies-other

Towards reliable isoform quantification using RNA-SEQ data.

Project description:BACKGROUND: In eukaryotes, alternative splicing often generates multiple splice variants from a single gene. Here we explore the use of RNA sequencing (RNA-Seq) datasets to address the isoform quantification problem. Given a set of known splice variants, the goal is to estimate the relative abundance of the individual variants. METHODS: Our method employs a linear models framework to estimate the ratios of known isoforms in a sample. A key feature of our method is that it takes into account the non-uniformity of RNA-Seq read positions along the targeted transcripts. RESULTS: Preliminary tests indicate that the model performs well on both simulated and real data. In two publicly available RNA-Seq datasets, we identified several alternatively-spliced genes with switch-like, on/off expression properties, as well as a number of other genes that varied more subtly in isoform expression. In many cases, genes exhibiting differential expression of alternatively spliced transcripts were not differentially expressed at the gene level. CONCLUSIONS: Given that changes in isoform expression level frequently involve a continuum of isoform ratios, rather than all-or-nothing expression, and that they are often independent of general gene expression changes, we anticipate that our research will contribute to revealing a so far uninvestigated layer of the transcriptome. We believe that, in the future, researchers will prioritize genes for functional analysis based not only on observed changes in gene expression levels, but also on changes in alternative splicing.

| S-EPMC2863065 | biostudies-literature

Single nucleotide polymorphisms (SNPs) in prostate cancer: its implications in diagnostics and therapeutics.

Project description:Prostate cancer is one of the most frequently diagnosed malignancies in developed countries and approximately 248,530 new cases of prostate cancer are likely to be diagnosed in the United States in 2021. During the late 1990s and 2000s, the prostate cancer-related death rate has decreased by 4% per year on average because of advancements in prostate-specific antigen (PSA) testing. However, the non-specificity of PSA to distinguish between benign and malignant forms of cancer is a major concern in the management of prostate cancer. Despite other risk factors in the pathogenesis of prostate cancer, recent advancement in molecular genetics suggests that genetic heredity plays a crucial role in prostate carcinogenesis. Approximately, 60% of heritability and more than 100 well-recognized single-nucleotide-polymorphisms (SNPs) have been found to be associated with prostate cancer and constitute a major risk factor in the development of prostate cancer. Recent findings revealed that a low to moderate effect on the progression of prostate cancer of individual SNPs was observed compared to a strong progressive effect when SNPs were in combination. Here, in this review, we made an attempt to critically analyze the role of SNPs and associated genes in the development of prostate cancer and their implications in diagnostics and therapeutics. A better understanding of the role of SNPs in prostate cancer susceptibility may improve risk prediction, enhance fine-mapping, and furnish new insights into the underlying pathophysiology of prostate cancer.

| S-EPMC8129253 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data