A powerful way to discover key genes playing causal roles in oncogenesis is to identify genomic regions that undergo frequent alteration in human cancers. Here, we report high-resolution analyses of somatic copy-number alterations (SCNAs) from 3131 cancer specimens, belonging largely to 26 histological types. We identify 158 regions of focal SCNA that are altered at significant frequency across multiple cancer types, of which 122 cannot be explained by the presence of a known cancer target gene located within these regions. Several gene families are enriched among these regions of focal SCNA, including the BCL2 family of apoptosis regulators and the NF-κB pathway. We show that cancer cells harboring amplifications surrounding the MCL1 and BCL2L1 anti-apoptotic genes depend upon expression of these genes for survival. Finally, we demonstrate that a large majority of SCNAs identified in individual cancer types are present in multiple cancer types.

Accurate species-level identification from culture-independent techniques is of importance for microbial niches that are less well characterized, such as that of the bladder. 16S rRNA amplicon sequencing, a common culture-independent way to identify bacteria, is often critiqued for lacking species-level resolution. Here, we extensively evaluate classification schemes for species-level bacterial annotation of 16S amplicon data from bladder bacteria.

The mussel byssus thread is an extremely tough core-shelled fiber that dissipates substantial amounts of energy during tensile loading. The mechanical performance of the shell is critically reliant on 3,4-dihydroxyphenylalanine's (Dopa) ability to form reversible iron-catecholate complexes at pH 8. However, the formation of these coordinate cross-links is undercut by Dopa's oxidation to Dopa-quinone, a spontaneous process at seawater conditions. The large mechanical mismatch between the cuticle and the core lends itself to further complications. Despite these challenges, the mussel byssus thread performs its tethering function over long periods of time. Here, we address these two major questions: (1) how does the mussel slow/prevent oxidation in the cuticle, and (2) how is the mechanical mismatch at the core/ shell interface mitigated? By combining a number of microscopy and spectroscopy techniques we have discerned a previously undescribed layer. Our results indicate this interlayer is thiol rich and thus will be called the thiol-rich interlayer (TRL). We propose the TRL serves as a long-lasting redox reservoir as well as a mechanical barrier.

The human bladder contains bacteria in the absence of infection. Interest in studying these bacteria and their association with bladder conditions is increasing, but the chosen experimental method can limit the resolution of the taxonomy that can be assigned to the bacteria found in the bladder. 16S rRNA gene sequencing is commonly used to identify bacteria, but is typically restricted to genus-level identification. Our primary aim was to determine if accurate species-level identification of bladder bacteria is possible using 16S rRNA gene sequencing. We evaluated the ability of different classification schemes, each consisting of combinations of a 16S rRNA gene variable region, a reference database, and a taxonomic classification algorithm to correctly classify bladder bacteria. We show that species-level identification is possible, and that the reference database chosen is the most important component, followed by the 16S variable region sequenced.

ObjectiveAn approach for assessing the urinary microbiome is 16S rRNA gene sequencing, where analysis methods are rapidly evolving. This re-analysis of an existing dataset aimed to determine whether updated bioinformatic and statistical techniques affect clinical inferences.MethodsA prior study compared the urinary microbiome in 123 women with mixed urinary incontinence (MUI) and 84 controls. We obtained unprocessed sequencing data from multiple variable regions, processed operational taxonomic unit (OTU) tables from the original analysis, and de-identified clinical data. We re-processed sequencing data with DADA2 to generate amplicon sequence variant (ASV) tables. Taxa from ASV tables were compared to the original OTU tables; taxa from different variable regions after updated processing were also compared. Bayesian graphical compositional regression (BGCR) was used to test for associations between microbial compositions and clinical phenotypes (e.g., MUI versus control) while adjusting for clinical covariates. Several techniques were used to cluster samples into microbial communities. Multivariable regression was used to test for associations between microbial communities and MUI, again while adjusting for potentially confounding variables.ResultsOf taxa identified through updated bioinformatic processing, only 40% were identified originally, though taxa identified through both methods represented >99% of the sequencing data in terms of relative abundance. Different 16S rRNA gene regions resulted in different recovered taxa. With BGCR analysis, there was a low (33.7%) probability of an association between overall microbial compositions and clinical phenotype. However, when microbial data are clustered into bacterial communities, we confirmed that bacterial communities are associated with MUI. Contrary to the originally published analysis, we did not identify different associations by age group, which may be due to the incorporation of different covariates in statistical models.ConclusionsUpdated bioinformatic processing techniques recover different taxa compared to earlier techniques, though most of these differences exist in low abundance taxa that occupy a small proportion of the overall microbiome. While overall microbial compositions are not associated with MUI, we confirmed associations between certain communities of bacteria and MUI. Incorporation of several covariates that are associated with the urinary microbiome improved inferences when assessing for associations between bacterial communities and MUI in multivariable models.

Objective: An approach for assessing the urinary microbiome is 16S rRNA gene sequencing, where a segment of the bacterial genome is amplified and sequenced. Methods used to analyze these data are rapidly evolving, although the research implications are not known. This re-analysis of an existing dataset aimed to determine the impact of updated bioinformatic and statistical techniques. Methods: A prior Pelvic Floor Disorders Network (PFDN) study compared the urinary microbiome in 123 women with mixed urinary incontinence (MUI) and 84 controls. We used the PFDN unprocessed sequencing data of V1-V3 and V4-V6 16S variable regions, processed operational taxonomic unit (OTU) tables, and de-identified clinical data. We processed sequencing data with an updated bioinformatic pipeline, which used DADA2 to generate amplicon sequence variant (ASV) tables. Taxa from ASV tables were compared to OTU tables generated from the original processing; taxa from different variable regions (e.g., V1-V3 versus V4-V6) after updated processing were also compared. After updated processing, data were analyzed with multiple filtering thresholds. Several techniques were tested to cluster samples into microbial communities. Multivariable regression was used to test for associations between microbial communities and MUI, while controlling for potentially confounding variables. Results: Of taxa identified through updated bioinformatic processing, only 40% were identified originally, though taxa identified through both methods represented >99% of sequencing data in terms of relative abundance. When different 16S rRNA gene regions were sequenced from the same samples, there were differences noted in recovered taxa. When the original clustering methods were applied to reprocessed sequencing data, we confirmed differences in microbial communities associated with MUI. However, when samples were clustered with a different methodology, microbial communities were no longer associated with MUI. Conclusions: Updated bioinformatic processing techniques recover many different taxa compared to prior techniques, though most of these differences exist in low abundance taxa that occupy a small proportion of the overall microbiome. Detection of high abundance taxa are not significantly impacted by bioinformatic strategy. However, there are different biases for less abundant taxa; these differences as well as downstream clustering methodology and filtering thresholds may affect interpretation of overall results.

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