Bladder cancer is the fifth most prevalent cancer in the U.S., yet is understudied, and few laboratory models exist that reflect the biology of the human disease. Here, we describe a biobank of ...patient-derived organoid lines that recapitulates the histopathological and molecular diversity of human bladder cancer. Organoid lines can be established efficiently from patient biopsies acquired before and after disease recurrence and are interconvertible with orthotopic xenografts. Notably, organoid lines often retain parental tumor heterogeneity and exhibit a spectrum of genomic changes that are consistent with tumor evolution in culture. Analyses of drug response using bladder tumor organoids show partial correlations with mutational profiles, as well as changes associated with treatment resistance, and specific responses can be validated using xenografts in vivo. Our studies indicate that patient-derived bladder tumor organoids represent a faithful model system for studying tumor evolution and treatment response in the context of precision cancer medicine.
Display omitted
•Efficient generation of a biobank of patient-derived bladder cancer organoids•Organoids recapitulate the histological and molecular spectrum of human bladder cancer•Bladder tumor organoids display clonal evolution in culture and as xenografts•Drug response of organoids can be validated in xenografts
A biobank of patient-derived bladder tumor organoids faithfully recapitulates features of human cancer and enables analysis of clonal evolution and drug responses.
Temperate reefs from around the world are becoming tropicalised, as warm‐water species shift their distribution towards the poles in response to warming. This is already causing profound shifts in ...dominant foundation species and associated ecological communities as canopy seaweeds such as kelp are replaced by tropical species.
Here, we argue that the cascading consequences of tropicalisation for the ecosystem properties and functions of warming temperate reefs depend largely on the taxa that end up dominating the seafloor. We put forward three potential tropicalisation trajectories, that differ in whether seaweeds, turf or corals become dominant. We highlight potential gains to certain ecosystem functions for some tropicalisation endpoints. For example, local benthic fish productivity may increase in some tropicalised reefs as a higher proportion of primary production is directly consumed, but this will be at the expense of other functions such as carbon export. We argue that understanding these changes in flows of energy and materials is essential to formulate new conservation strategies and management approaches that minimise risks as well as capture potential opportunities.
Regardless of which trajectory is followed, tropicalised systems represent largely novel ecosystem configurations. This poses major challenges to traditional conservation and environmental management approaches, which typically focus on maintaining or returning species to particular locations. We outline management practices that may either mitigate predicted structural and functional changes or make the most of potential new opportunities in tropicalised reefs. These include marine protected areas to increase resilience and connectivity, the development of new fisheries that target range‐expanding invaders, and assisted evolution and migration strategies to facilitate the dominance of large habitat formers like corals or seaweeds.
We highlight important ecological and ethical challenges associated with developing novel approaches to manage tropicalised reefs, which may need to become increasingly interventionist. As technological innovations continue to emerge, having clear goals and considering the ethics surrounding interventions among the broader community are essential steps to successfully develop novel management approaches.
A plain language summary is available for this article.
Plain Language Summary
Droplet digital polymerase chain reaction (ddPCR) is a new technology that was recently commercialized to enable the precise quantification of target nucleic acids in a sample. ddPCR measures ...absolute quantities by counting nucleic acid molecules encapsulated in discrete, volumetrically defined, water-in-oil droplet partitions. This novel ddPCR format offers a simple workflow capable of generating highly stable partitioning of DNA molecules. In this study, we assessed key performance parameters of the ddPCR system. A linear ddPCR response to DNA concentration was obtained from 0.16% through to 99.6% saturation in a 20,000 droplet assay corresponding to more than 4 orders of magnitude of target DNA copy number per ddPCR. Analysis of simplex and duplex assays targeting two distinct loci in the Lambda DNA genome using the ddPCR platform agreed, within their expanded uncertainties, with values obtained using a lower density microfluidic chamber based digital PCR (cdPCR). A relative expanded uncertainty under 5% was achieved for copy number concentration using ddPCR. This level of uncertainty is much lower than values typically observed for quantification of specific DNA target sequences using currently commercially available real-time and digital cdPCR technologies.
Electroactive materials have been investigated as next-generation neuronal tissue engineering scaffolds to enhance neuronal regeneration and functional recovery after brain injury. Graphene, an ...emerging neuronal scaffold material with charge transfer properties, has shown promising results for neuronal cell survival and differentiation in vitro. In this in vivo work, electrospun microfiber scaffolds coated with self-assembled colloidal graphene, were implanted into the striatum or into the subventricular zone of adult rats. Microglia and astrocyte activation levels were suppressed with graphene functionalization. In addition, self-assembled graphene implants prevented glial scarring in the brain 7 weeks following implantation. Astrocyte guidance within the scaffold and redirection of neuroblasts from the subventricular zone along the implants was also demonstrated. These findings provide new functional evidence for the potential use of graphene scaffolds as a therapeutic platform to support central nervous system regeneration.
Extreme events have profound ecological impacts on species and ecosystems, including range contractions and collapse of entire ecosystems. Although theory predicts that extreme events cause loss of ...genetic diversity, empirical demonstrations are rare, obscuring implications for future adaptive capacity of species and populations. Here, we use rare genetic data from before an extreme event to empirically demonstrate massive and cryptic loss of genetic diversity across ∼800 km of underwater forests following the most severe marine heatwave on record. Two forest-forming seaweeds (Sargassum fallax and Scytothalia dorycarpa) lost ∼30%–65% of average genetic diversity within the 800-km footprint of the heatwave and up to 100% of diversity at some sites. Populations became dominated by single haplotypes that were often not dominant or present prior to the heatwave. Strikingly, these impacts were cryptic and not reflected in measures of forest cover used to determine ecological impact of the heatwave. Our results show that marine heatwaves can drive strong loss of genetic diversity, which may compromise adaptability to future climatic change.
•A marine heatwave caused massive loss of genetic diversity in underwater forests•Between 30% and 65% of average genetic diversity was lost across 800 km of coastline•Loss of genetic diversity was cryptic and not reflected in measures of forest cover•Marine heatwaves may compromise ability to respond to future climatic change
Extreme events have profound ecological impacts, but knowledge of how they affect underlying genetic diversity is scant. Gurgel et al. use rare empirical data from before a marine heatwave to demonstrate massive and cryptic loss of genetic diversity in underwater forests, which may compromise their ability to respond to future climatic change.
Currently there are few ideal methods for the characterization of nanoparticles in complex, environmental samples, leading to significant gaps in toxicity and exposure assessments of nanomaterials. ...Single particle-inductively coupled plasma-mass spectrometry (spICPMS) is an emerging technique that can both size and count metal-containing nanoparticles. A major benefit of the spICPMS method is its ability to characterize nanoparticles at concentrations relevant to the environment. This paper presents a practical guide on how to count and size nanoparticles using spICPMS. Different methods are investigated for measuring transport efficiency (i.e., nebulization efficiency), an important term in the spICPMS calculations. In addition, an alternative protocol is provided for determining particle size that broadens the applicability of the technique to all types of inorganic nanoparticles. Initial comparison, using well-characterized, monodisperse silver nanoparticles, showed the importance of having an accurate transport efficiency value when determining particle number concentration and, if using the newly presented protocol, particle size. Ultimately, the goal of this paper is to provide improvements to nanometrology by further developing this technique for the characterization of metal-containing nanoparticles.
Extreme events are increasing globally with devastating ecological consequences, but the impacts on underlying genetic diversity and structure are often cryptic and poorly understood, hindering ...assessment of adaptive capacity and ecosystem vulnerability to future change. Using very rare "before" data we empirically demonstrate that an extreme marine heatwave caused a significant poleward shift in genetic clusters of kelp forests whereby alleles characteristic of cool water were replaced by those that predominated in warm water across 200 km of coastline. This "genetic tropicalisation" was facilitated by significant mortality of kelp and other co-occurring seaweeds within the footprint of the heatwave that opened space for rapid local proliferation of surviving kelp genotypes or dispersal and recruitment of spores from warmer waters. Genetic diversity declined and inbreeding increased in the newly tropicalised site, but these metrics were relative stable elsewhere within the footprint of the heatwave. Thus, extreme events such as marine heatwaves not only lead to significant mortality and population loss but can also drive significant genetic change in natural populations.
Tumor-infiltrating immune cells have been linked to prognosis and response to immunotherapy; however, the levels of distinct immune cell subsets and the signals that draw them into a tumor, such as ...the expression of antigen presenting machinery genes, remain poorly characterized. Here, we employ a gene expression-based computational method to profile the infiltration levels of 24 immune cell populations in 19 cancer types.
We compare cancer types using an immune infiltration score and a T cell infiltration score and find that clear cell renal cell carcinoma (ccRCC) is among the highest for both scores. Using immune infiltration profiles as well as transcriptomic and proteomic datasets, we characterize three groups of ccRCC tumors: T cell enriched, heterogeneously infiltrated, and non-infiltrated. We observe that the immunogenicity of ccRCC tumors cannot be explained by mutation load or neo-antigen load, but is highly correlated with MHC class I antigen presenting machinery expression (APM). We explore the prognostic value of distinct T cell subsets and show in two cohorts that Th17 cells and CD8
T/Treg ratio are associated with improved survival, whereas Th2 cells and Tregs are associated with negative outcomes. Investigation of the association of immune infiltration patterns with the subclonal architecture of tumors shows that both APM and T cell levels are negatively associated with subclone number.
Our analysis sheds light on the immune infiltration patterns of 19 human cancers and unravels mRNA signatures with prognostic utility and immunotherapeutic biomarker potential in ccRCC.
PDF
