Tumor-derived DNA can be found in the plasma of cancer patients. In this study, we explored the use of shotgun massively parallel sequencing (MPS) of plasma DNA from cancer patients to scan a cancer ...genome noninvasively.
Four hepatocellular carcinoma patients and a patient with synchronous breast and ovarian cancers were recruited. DNA was extracted from the tumor tissues, and the preoperative and postoperative plasma samples of these patients were analyzed with shotgun MPS.
We achieved the genomewide profiling of copy number aberrations and point mutations in the plasma of the cancer patients. By detecting and quantifying the genomewide aggregated allelic loss and point mutations, we determined the fractional concentrations of tumor-derived DNA in plasma and correlated these values with tumor size and surgical treatment. We also demonstrated the potential utility of this approach for the analysis of complex oncologic scenarios by studying the patient with 2 synchronous cancers. Through the use of multiregional sequencing of tumoral tissues and shotgun sequencing of plasma DNA, we have shown that plasma DNA sequencing is a valuable approach for studying tumoral heterogeneity.
Shotgun DNA sequencing of plasma is a potentially powerful tool for cancer detection, monitoring, and research.
Context:
Congenital adrenal hyperplasia (CAH) is an autosomal recessive condition that arises from mutations in CYP21A2 gene, which encodes for the steroidogenic enzyme 21-hydroxylase. To prevent ...genital ambiguity in affected female fetuses, prenatal treatment with dexamethasone must begin on or before gestational week 9. Currently used chorionic villus sampling and amniocentesis provide genetic results at approximately 14 weeks of gestation at the earliest. This means that mothers who want to undergo prenatal dexamethasone treatment will be unnecessarily treating seven of eight fetuses (males and three of four unaffected females), emphasizing the desirability of earlier genetic diagnosis in utero.
Objective:
The objective of the study was to develop a noninvasive method for early prenatal diagnosis of fetuses at risk for CAH.
Patients:
Fourteen families, each with a proband affected by phenotypically classical CAH, were recruited.
Design:
Cell-free fetal DNA was obtained from 3.6 mL of maternal plasma. Using hybridization probes designed to capture a 6-Mb region flanking CYP21A2, targeted massively parallel sequencing (MPS) was performed to analyze genomic DNA samples from parents and proband to determine parental haplotypes. Plasma DNA from pregnant mothers also underwent targeted MPS to deduce fetal inheritance of parental haplotypes.
Results:
In all 14 families, the fetal CAH status was correctly deduced by targeted MPS of DNA in maternal plasma, as early as 5 weeks 6 days of gestation.
Conclusions:
MPS on 3.6 mL plasma from pregnant mothers could potentially provide the diagnosis of CAH, noninvasively, before the ninth week of gestation. Only affected female fetuses will thus be treated. Our strategy represents a generic approach for noninvasive prenatal testing for an array of autosomal recessive disorders.
In rodents, obesity and aging impair nicotinamide adenine dinucleotide (NAD
) biosynthesis, which contributes to metabolic dysfunction. Nicotinamide mononucleotide (NMN) availability is a ...rate-limiting factor in mammalian NAD
biosynthesis. We conducted a 10-week, randomized, placebo-controlled, double-blind trial to evaluate the effect of NMN supplementation on metabolic function in postmenopausal women with prediabetes who were overweight or obese. Insulin-stimulated glucose disposal, assessed by using the hyperinsulinemic-euglycemic clamp, and skeletal muscle insulin signaling phosphorylation of protein kinase AKT and mechanistic target of rapamycin (mTOR) increased after NMN supplementation but did not change after placebo treatment. NMN supplementation up-regulated the expression of platelet-derived growth factor receptor β and other genes related to muscle remodeling. These results demonstrate that NMN increases muscle insulin sensitivity, insulin signaling, and remodeling in women with prediabetes who are overweight or obese (clinicaltrial.gov NCT03151239).
MolProbity is a structure‐validation web service that provides broad‐spectrum solidly based evaluation of model quality at both the global and local levels for both proteins and nucleic acids. It ...relies heavily on the power and sensitivity provided by optimized hydrogen placement and all‐atom contact analysis, complemented by updated versions of covalent‐geometry and torsion‐angle criteria. Some of the local corrections can be performed automatically in MolProbity and all of the diagnostics are presented in chart and graphical forms that help guide manual rebuilding. X‐ray crystallography provides a wealth of biologically important molecular data in the form of atomic three‐dimensional structures of proteins, nucleic acids and increasingly large complexes in multiple forms and states. Advances in automation, in everything from crystallization to data collection to phasing to model building to refinement, have made solving a structure using crystallography easier than ever. However, despite these improvements, local errors that can affect biological interpretation are widespread at low resolution and even high‐resolution structures nearly all contain at least a few local errors such as Ramachandran outliers, flipped branched protein side chains and incorrect sugar puckers. It is critical both for the crystallographer and for the end user that there are easy and reliable methods to diagnose and correct these sorts of errors in structures. MolProbity is the authors' contribution to helping solve this problem and this article reviews its general capabilities, reports on recent enhancements and usage, and presents evidence that the resulting improvements are now beneficially affecting the global database.
Untargeted metabolomics provides a comprehensive platform for identifying metabolites whose levels are altered between two or more populations. By using liquid chromatography quadrupole ...time-of-flight mass spectrometry (LC-Q-TOF-MS), hundreds to thousands of peaks with a unique m/z ratio and retention time are routinely detected from most biological samples in an untargeted profiling experiment. Each peak, termed a metabolomic feature, can be characterized on the basis of its accurate mass, retention time and tandem mass spectral fragmentation pattern. Here a seven-step protocol is suggested for such a characterization by using the METLIN metabolite database. The protocol starts from untargeted metabolomic LC-Q-TOF-MS data that have been analyzed with the bioinformatics program XCMS, and it describes a strategy for selecting interesting features as well as performing subsequent targeted tandem MS. The seven steps described will require 2-4 h to complete per feature, depending on the compound.
Bacterial biofilms in the colon alter the host tissue microenvironment. A role for biofilms in colon cancer metabolism has been suggested but to date has not been evaluated. Using metabolomics, we ...investigated the metabolic influence that microbial biofilms have on colon tissues and the related occurrence of cancer. Patient-matched colon cancers and histologically normal tissues, with or without biofilms, were examined. We show the upregulation of polyamine metabolites in tissues from cancer hosts with significant enhancement of N1, N12-diacetylspermine in both biofilm-positive cancer and normal tissues. Antibiotic treatment, which cleared biofilms, decreased N1, N12-diacetylspermine levels to those seen in biofilm-negative tissues, indicating that host cancer and bacterial biofilm structures contribute to the polyamine metabolite pool. These results show that colonic mucosal biofilms alter the cancer metabolome to produce a regulator of cellular proliferation and colon cancer growth potentially affecting cancer development and progression.
Display omitted
•Colonic mucosal biofilms alter the cancer metabolome•N1, N12-diacetylspermine was significantly upregulated in tissues with biofilms•Biofilms create conditions conducive to oncogenic transformation in colon cells•Global isotope metabolomics reveals the metabolite fate of N1, N12-diacetylspermine
Johnson et al. examine the metabolomics of bacterial communities called biofilms and human colon cancers. The host and bacterial polyamine metabolites are proposed to act together to promote biofilm formation and cancer growth, creating conditions conducive for normal to cancer cell transformation.
The Pathosystems Resource Integration Center (PATRIC) is the bacterial Bioinformatics Resource Center (https://www.patricbrc.org). Recent changes to PATRIC include a redesign of the web interface and ...some new services that provide users with a platform that takes them from raw reads to an integrated analysis experience. The redesigned interface allows researchers direct access to tools and data, and the emphasis has changed to user-created genome-groups, with detailed summaries and views of the data that researchers have selected. Perhaps the biggest change has been the enhanced capability for researchers to analyze their private data and compare it to the available public data. Researchers can assemble their raw sequence reads and annotate the contigs using RASTtk. PATRIC also provides services for RNA-Seq, variation, model reconstruction and differential expression analysis, all delivered through an updated private workspace. Private data can be compared by 'virtual integration' to any of PATRIC's public data. The number of genomes available for comparison in PATRIC has expanded to over 80 000, with a special emphasis on genomes with antimicrobial resistance data. PATRIC uses this data to improve both subsystem annotation and k-mer classification, and tags new genomes as having signatures that indicate susceptibility or resistance to specific antibiotics.
► X-ray crystallography is a critical tool in the study of biological systems. ► Significant time and effort are required to determine and optimize many macromolecular structures. ► The Phenix ...software package provides a comprehensive system for structure solution with an emphasis on automation.
X-ray crystallography is a critical tool in the study of biological systems. It is able to provide information that has been a prerequisite to understanding the fundamentals of life. It is also a method that is central to the development of new therapeutics for human disease. Significant time and effort are required to determine and optimize many macromolecular structures because of the need for manual interpretation of complex numerical data, often using many different software packages, and the repeated use of interactive three-dimensional graphics. The Phenix software package has been developed to provide a comprehensive system for macromolecular crystallographic structure solution with an emphasis on automation. This has required the development of new algorithms that minimize or eliminate subjective input in favor of built-in expert-systems knowledge, the automation of procedures that are traditionally performed by hand, and the development of a computational framework that allows a tight integration between the algorithms. The application of automated methods is particularly appropriate in the field of structural proteomics, where high throughput is desired. Features in Phenix for the automation of experimental phasing with subsequent model building, molecular replacement, structure refinement and validation are described and examples given of running Phenix from both the command line and graphical user interface.
Purpose We compared outcomes in patients treated with nephroureterectomy vs nephron sparing endoscopic surgery for upper tract urothelial carcinoma. Materials and Methods Patients treated at our ...institution for upper tract urothelial carcinoma from 1996 to 2004 were monitored for upper tract and bladder recurrence, metastasis, and cancer specific and overall survival. Outcomes were compared between treatment groups by univariate and multivariate analyses based on pertinent pathological and demographic variables. Results Of 96 renal units 62 underwent immediate nephroureterectomy and 34 were managed endoscopically. Median followup in all survivors was 77 months. Overall nephroureterectomy and endoscopy complication rates were 29% and 9.3%, respectively. In patients with low grade tumors the 5-year metastasis-free survival rate after nephroureterectomy and endoscopy was 88% and 94%. The corresponding 5-year cancer specific and overall survival rates were 89% vs 100% and 72% vs 75%, respectively. Of endoscopic cases 84% had at least 1 ipsilateral recurrence. Multivariate analysis revealed that only tumor grade was significantly associated with metastasis-free survival while grade and body mass index correlated with cancer specific survival, and Charlson Comorbidity index and grade impacted overall survival. Treatment group was not associated with survival outcome. Conclusions When technically feasible and in select patients, endoscopic management provides cancer related and overall survival equivalent to that of nephroureterectomy in patients with low grade upper tract urothelial carcinoma at the cost of frequent re-treatments in many patients. Nephroureterectomy is standard treatment for high grade cancer when there is a normal contralateral kidney but endoscopy should be considered when there are imperative indications for nephron sparing.
PDF
