Widespread and Functional RNA Circularization in Localized Prostate Cancer.

The cancer transcriptome is remarkably complex, including low-abundance transcripts, many not polyadenylated. To fully characterize the transcriptome of localized prostate cancer, we performed ultra-deep total RNA-seq on 144 tumors with rich clinical annotation. This revealed a linear transcriptomic subtype associated with the aggressive intraductal carcinoma sub-histology and a fusion profile that differentiates localized from metastatic disease. Analysis of back-splicing events showed widespread RNA circularization, with the average tumor expressing 7,232 circular RNAs (circRNAs). The degree of circRNA production was correlated to disease progression in multiple patient cohorts. Loss-of-function screening identified 11.3% of highly abundant circRNAs as essential for cell proliferation; for ∼90% of these, their parental linear transcripts were not essential. Individual circRNAs can have distinct functions, with circCSNK1G3 promoting cell growth by interacting with miR-181. These data advocate for adoption of ultra-deep RNA-seq without poly-A selection to interrogate both linear and circular transcriptomes.

The Evolutionary Landscape of Localized Prostate Cancers Drives Clinical Aggression.

The majority of newly diagnosed prostate cancers are slow growing, with a long natural life history. Yet a subset can metastasize with lethal consequences. We reconstructed the phylogenies of 293 localized prostate tumors linked to clinical outcome data. Multiple subclones were detected in 59% of patients, and specific subclonal architectures associate with adverse clinicopathological features. Early tumor development is characterized by point mutations and deletions followed by later subclonal amplifications and changes in trinucleotide mutational signatures. Specific genes are selectively mutated prior to or following subclonal diversification, including MTOR, NKX3-1, and RB1. Patients with low-risk monoclonal tumors rarely relapse after primary therapy (7%), while those with high-risk polyclonal tumors frequently do (61%). The presence of multiple subclones in an index biopsy may be necessary, but not sufficient, for relapse of localized prostate cancer, suggesting that evolution-aware biomarkers should be studied in prospective studies of low-risk tumors suitable for active surveillance.

Optically Driven Rotation of Exciton-Polariton Condensates.

The rotational response of quantum condensed fluids is strikingly distinct from rotating classical fluids, especially notable for the excitation and ordering of quantized vortex ensembles. Although widely studied in conservative systems, the dynamics of rotating open-dissipative superfluids such as exciton-polariton condensates remains largely unexplored, as it requires high-frequency rotation while avoiding resonantly driving the condensate. We create a rotating polariton condensate at gigahertz frequencies by off-resonantly pumping with a rotating optical stirrer composed of the time-dependent interference of two frequency-offset, structured laser modes. Acquisition of angular momentum exceeding the critical 1ℏ/particle is directly measured, accompanied by the deterministic nucleation and capture of quantized vortices with a handedness controlled by the pump rotation direction. The demonstration of controlled optical rotation of a spontaneously formed polariton condensate enables new opportunities for the study of open dissipative superfluidity, ordering of non-Hermitian quantized vortex matter, and topological states in a highly nonlinear, photonic platform.

Revealing the Role of CO during CO2 Hydrogenation on Cu Surfaces with In Situ Soft X-Ray Spectroscopy.

The reactions of H2, CO2, and CO gas mixtures on the surface of Cu at 200 °C, relevant for industrial methanol synthesis, are investigated using a combination of ambient pressure X-ray photoelectron spectroscopy (AP-XPS) and atmospheric-pressure near edge X-ray absorption fine structure (AtmP-NEXAFS) spectroscopy bridging pressures from 0.1 mbar to 1 bar. We find that the order of gas dosing can critically affect the catalyst chemical state, with the Cu catalyst maintained in a metallic state when H2 is introduced prior to the addition of CO2. Only on increasing the CO2 partial pressure is CuO formation observed that coexists with metallic Cu. When only CO2 is present, the surface oxidizes to Cu2O and CuO, and the subsequent addition of H2 partially reduces the surface to Cu2O without recovering metallic Cu, consistent with a high kinetic barrier to H2 dissociation on Cu2O. The addition of CO to the gas mixture is found to play a key role in removing adsorbed oxygen that otherwise passivates the Cu surface, making metallic Cu surface sites available for CO2 activation and subsequent conversion to CH3OH. These findings are corroborated by mass spectrometry measurements, which show increased H2O formation when H2 is dosed before rather than after CO2. The importance of maintaining metallic Cu sites during the methanol synthesis reaction is thereby highlighted, with the inclusion of CO in the gas feed helping to achieve this even in the absence of ZnO as the catalyst support.

Genomic hallmarks of localized, non-indolent prostate cancer.

Prostate tumours are highly variable in their response to therapies, but clinically available prognostic factors can explain only a fraction of this heterogeneity. Here we analysed 200 whole-genome sequences and 277 additional whole-exome sequences from localized, non-indolent prostate tumours with similar clinical risk profiles, and carried out RNA and methylation analyses in a subset. These tumours had a paucity of clinically actionable single nucleotide variants, unlike those seen in metastatic disease. Rather, a significant proportion of tumours harboured recurrent non-coding aberrations, large-scale genomic rearrangements, and alterations in which an inversion repressed transcription within its boundaries. Local hypermutation events were frequent, and correlated with specific genomic profiles. Numerous molecular aberrations were prognostic for disease recurrence, including several DNA methylation events, and a signature comprised of these aberrations outperformed well-described prognostic biomarkers. We suggest that intensified treatment of genomically aggressive localized prostate cancer may improve cure rates.

Understanding Factors Influencing Decision Making by State Health Officials in a Public Health Emergency.

State and territorial health officials (STHOs) play a critical role in leading public health emergency response in their respective states. Through an exploratory qualitative study with 21 current or former STHOs, we sought to understand the issues that impact STHO decision making in public health responses. Initial findings suggest the need for structured decision making tools for use by leaders responding to public health emergencies, including COVID-19. Such tools could lead to more systematic responses by STHOs during public health crises.

Weaving and Layering Funding: A Territorial Health Agency's Guide to Effective Health Financing.

CONTEXT: State and territorial health agencies can optimize programmatic funding through braiding and layering strategies. IMPLEMENTATION: The Commonwealth Healthcare Corporation, a territorial health agency located on the Pacific Island of Saipan, Commonwealth of the Northern Mariana Islands (CNMI), restructured its Non-Communicable Disease Bureau into 4 new units. Existing funding streams were braided and layered to support the restructuring. A shared vision of strengthening crosscutting connections to improve population health outcomes helped guide the restructuring process. Vision planning with leaders and funding partners, establishing buy-in within agency and external partners, and assessing immediate impacts were a few of the steps taken by the agency to ensure a successful restructuring. IMPACT: The immediate impact of the restructure has been positive. In both the CNMI and select states that have undertaken similar efforts, braiding and layering funding has facilitated more streamlined processes, coordinated approaches across programs and funding partners, and provided deeper levels of trust in partnerships. Although it is still too early to draw long-term assessments in the CNMI, the agency projects that coordinated funds will strengthen its foundational capabilities and promote a more community-centered, collaborative, and effective approach to public health. Restructuring the Non-Communicable Disease Bureau through braiding and layering funds gives the agency the flexibility it needs to more effectively address the social determinants of health and local population health priorities through a client-centered approach, ultimately improving health outcomes for the commonwealth. LESSONS LEARNED AND IMPLICATIONS: The agency experienced several challenges throughout the restructuring process that offer lessons learned for addressing effective health financing. For example, ample time is needed at the beginning of the braiding and layering process to establish policies and procedures for efficient accounting, documenting, and reporting. In addition, ongoing support and training opportunities for programmatic teams can smooth out the transition from siloed to braided and layered funding structures. These lessons, in addition to key elements mapped out by experienced state health agencies, can guide and prepare other agencies interested in implementing innovative funding mechanisms.

Variation Among Public Health Interventions in Initial Efforts to Prevent and Control the Spread of COVID-19 in the 50 States, 29 Big Cities, and the District of Columbia.

US states and big cities acted to protect the residents of their jurisdictions from the threat of SARS-CoV-2 infection and reduce COVID-19 transmission. As there were no known pharmacologic interventions to prevent COVID-19 at the outset of the pandemic, public health and elected leaders implemented a host of nonpharmaceutical interventions (NPIs) to slow the spread of the virus. This article discusses variation among states and cities in their implementation of 3 NPIs: stay-at-home/shelter-in-place orders, gathering restrictions, and mask mandates. We illustrate how frequently each was used by states and big cities, discuss state and local authorities to implement such interventions, and consider how these NPIs and accompanying public adherence to public health orders may vary considerably in different regions of the country and by local and state laws specific to state preemption of public health authority.

COVID-19 Case Investigation and Contact Tracing: Early Lessons Learned and Future Opportunities.

CONTEXT: Case investigation and contact tracing are fundamental public health strategies for controlling and preventing the spread of infectious diseases. Although the principles behind these strategies are not new, the capacity and operational requirements needed to support disease investigation during the SARS-CoV-2 (COVID-19) pandemic are unprecedented. This article analyzes the implementation of case investigation and contact tracing in controlling COVID-19 transmission during the early stages of the US pandemic response (January 20 through August 31, 2020). PROGRAM IMPLEMENTATION: Governmental public health agencies mobilized to expand case investigation and contact tracing programs in the early months of the pandemic. In doing so, they encountered a range of challenges that included rapidly scaling up the workforce; developing and subsequently revising guidance and protocols specific to COVID-19 as more was learned about the virus over time; defining job functions; encouraging public acceptance of and participation in case investigation and contact tracing; and assessing the utility of these activities during both the containment and mitigation phases of outbreak response. COVID-19 case investigation and contact tracing programs presented an array of opportunities for health departments to innovate, especially around technology to support public health efforts, as well as opportunities to address health equity and advance community resilience. CONCLUSION: Lessons learned from disease intervention specialists, guidance and resources from federal agencies and national partners, and peer-to-peer exchange of promising practices can support jurisdictions encountering early implementation challenges. Further research is needed to assess COVID-19 case investigation and contact tracing program models and innovations, as well as strategies for implementing these activities during containment and mitigation phases.

Identification of intraductal carcinoma of the prostate on tissue specimens using Raman micro-spectroscopy: A diagnostic accuracy case-control study with multicohort validation.

BACKGROUND: Prostate cancer (PC) is the most frequently diagnosed cancer in North American men. Pathologists are in critical need of accurate biomarkers to characterize PC, particularly to confirm the presence of intraductal carcinoma of the prostate (IDC-P), an aggressive histopathological variant for which therapeutic options are now available. Our aim was to identify IDC-P with Raman micro-spectroscopy (RµS) and machine learning technology following a protocol suitable for routine clinical histopathology laboratories. METHODS AND FINDINGS: We used RµS to differentiate IDC-P from PC, as well as PC and IDC-P from benign tissue on formalin-fixed paraffin-embedded first-line radical prostatectomy specimens (embedded in tissue microarrays [TMAs]) from 483 patients treated in 3 Canadian institutions between 1993 and 2013. The main measures were the presence or absence of IDC-P and of PC, regardless of the clinical outcomes. The median age at radical prostatectomy was 62 years. Most of the specimens from the first cohort (Centre hospitalier de l'Université de Montréal) were of Gleason score 3 + 3 = 6 (51%) while most of the specimens from the 2 other cohorts (University Health Network and Centre hospitalier universitaire de Québec-Université Laval) were of Gleason score 3 + 4 = 7 (51% and 52%, respectively). Most of the 483 patients were pT2 stage (44%-69%), and pT3a (22%-49%) was more frequent than pT3b (9%-12%). To investigate the prostate tissue of each patient, 2 consecutive sections of each TMA block were cut. The first section was transferred onto a glass slide to perform immunohistochemistry with H&E counterstaining for cell identification. The second section was placed on an aluminum slide, dewaxed, and then used to acquire an average of 7 Raman spectra per specimen (between 4 and 24 Raman spectra, 4 acquisitions/TMA core). Raman spectra of each cell type were then analyzed to retrieve tissue-specific molecular information and to generate classification models using machine learning technology. Models were trained and cross-validated using data from 1 institution. Accuracy, sensitivity, and specificity were 87% ± 5%, 86% ± 6%, and 89% ± 8%, respectively, to differentiate PC from benign tissue, and 95% ± 2%, 96% ± 4%, and 94% ± 2%, respectively, to differentiate IDC-P from PC. The trained models were then tested on Raman spectra from 2 independent institutions, reaching accuracies, sensitivities, and specificities of 84% and 86%, 84% and 87%, and 81% and 82%, respectively, to diagnose PC, and of 85% and 91%, 85% and 88%, and 86% and 93%, respectively, for the identification of IDC-P. IDC-P could further be differentiated from high-grade prostatic intraepithelial neoplasia (HGPIN), a pre-malignant intraductal proliferation that can be mistaken as IDC-P, with accuracies, sensitivities, and specificities > 95% in both training and testing cohorts. As we used stringent criteria to diagnose IDC-P, the main limitation of our study is the exclusion of borderline, difficult-to-classify lesions from our datasets. CONCLUSIONS: In this study, we developed classification models for the analysis of RµS data to differentiate IDC-P, PC, and benign tissue, including HGPIN. RµS could be a next-generation histopathological technique used to reinforce the identification of high-risk PC patients and lead to more precise diagnosis of IDC-P.

A Brief History of the Prevention and Public Health Fund: Implications for Public Health Advocates.

The nation's first broad-based, mandatory investment in public health and prevention, the Prevention and Public Health Fund (the Fund), has had a brief and controversial history. Advocates for the Fund have had to defend it from both Democratic and Republican threats, including being used as an offset for administration priorities, and from congressional efforts to repeal and replace the Patient Protection and Affordable Care Act. Lessons learned from efforts to sustain the Fund are instructive in addressing current and future challenges faced by advocates for public health programs and prevention policies.

Prostate Cancer Genomic Subtypes.

Over the last decade, advancements in massively-parallel DNA sequencing and computational biology have allowed for unprecedented insights into the fundamental mutational processes that underlie virtually every major cancer type. Two major cancer genomics consortia-The Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC)-have produced rich databases of mutational, pathological, and clinical data that can be mined through web-based portals, allowing for correlative studies and testing of novel hypotheses on well-powered patient cohorts.In this chapter, we will review the impact of these technological developments on the understanding of molecular subtypes that promote prostate cancer initiation, progression, metastasis, and clinical aggression. In particular, we will focus on molecular subtypes that define clinically-relevant patient cohorts and assess how a better understanding of how these subtypes-in both somatic and germline genomes-may influence the clinical course for individual men diagnosed with prostate cancer.

Unleashing the Creativity and Innovation of Our Greatest Resource-The Governmental Public Health Workforce.

CONTEXT: Creativity and innovation in the governmental public health workforce will be required to generate new ideas to solve complex problems that extend beyond traditional public health functions such as disease surveillance and monitoring. Creativity and innovation can promote and advance necessary organizational transformation as well as improve organizational culture and workplace environment by motivating employees intrinsically. However, there is little empirical evidence on how rewarding creativity and innovation in governmental public health departments is associated with organizational culture and workplace environments. OBJECTIVE: This study describes (1) the degree to which creativity and innovation are rewarded in governmental public health agencies and (2) associations between rewarding creativity and innovation and worker satisfaction, intent to leave, and workplace characteristics. DESIGN: The cross-sectional Public Health Workforce Interests and Needs Survey (PH WINS) was administered using a Web-based platform in fall 2017. SETTINGS AND PARTICIPANTS: Data used for these analyses were drawn from the 2017 PH WINS of governmental health department employees. This included state health agency and local health department staff. PH WINS included responses from 47 604 staff members, which reflected a 48% overall response rate. PH WINS excludes local health departments with fewer than 25 staff or serving fewer than 25 000 people. RESULTS: Fewer than half of all workers, regardless of demographic group and work setting, reported that creativity and innovation were rewarded in their workplace. Most measures of worker satisfaction and workplace environment were significantly more positive for those who reported that creativity and innovation were rewarded in their workplace. CONCLUSION: This research suggests that promoting creativity and innovation in governmental public health agencies not only could help lead the transformation of governmental public health agencies but could also improve worker satisfaction and the workplace environment in governmental public health agencies.

Valection: design optimization for validation and verification studies.

BACKGROUND: Platform-specific error profiles necessitate confirmatory studies where predictions made on data generated using one technology are additionally verified by processing the same samples on an orthogonal technology. However, verifying all predictions can be costly and redundant, and testing a subset of findings is often used to estimate the true error profile. RESULTS: To determine how to create subsets of predictions for validation that maximize accuracy of global error profile inference, we developed Valection, a software program that implements multiple strategies for the selection of verification candidates. We evaluated these selection strategies on one simulated and two experimental datasets. CONCLUSIONS: Valection is implemented in multiple programming languages, available at: http://labs.oicr.on.ca/boutros-lab/software/valection.

Comparison of pre-processing methods for Infinium HumanMethylation450 BeadChip array.

MOTIVATION: Microarrays are widely used to quantify DNA methylation because they are economical, require only small quantities of input DNA and focus on well-characterized regions of the genome. However, pre-processing of methylation microarray data is challenging because of confounding factors that include background fluorescence, dye bias and the impact of germline polymorphisms. Therefore, we present valuable insights and a framework for those seeking the most optimal pre-processing method through a data-driven approach. RESULTS: Here, we show that Dasen is the optimal pre-processing methodology for the Infinium HumanMethylation450 BeadChip array in prostate cancer, a frequently employed platform for tumour methylome profiling in both the TCGA and ICGC consortia. We evaluated the impact of 11 pre-processing methods on batch effects, replicate variabilities, sensitivities and sample-to-sample correlations across 809 independent prostate cancer samples, including 150 reported for the first time in this study. Overall, Dasen is the most effective for removing artefacts and detecting biological differences associated with tumour aggressivity. Relative to the raw dataset, it shows a reduction in replicate variances of 67% and 76% for ß- and M-values, respectively. Our study provides a unique pre-processing benchmark for the community with an emphasis on biological implications. AVAILABILITY AND IMPLEMENTATION: All software used in this study are publicly available as detailed in the article. CONTACT: paul.boutros@oicr.on.ca. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Cribriform and intraductal prostate cancer are associated with increased genomic instability and distinct genomic alterations.

BACKGROUND: Invasive cribriform and intraductal carcinoma (CR/IDC) is associated with adverse outcome of prostate cancer patients. The aim of this study was to determine the molecular aberrations associated with CR/IDC in primary prostate cancer, focusing on genomic instability and somatic copy number alterations (CNA). METHODS: Whole-slide images of The Cancer Genome Atlas Project (TCGA, N = 260) and the Canadian Prostate Cancer Genome Network (CPC-GENE, N = 199) radical prostatectomy datasets were reviewed for Gleason score (GS) and presence of CR/IDC. Genomic instability was assessed by calculating the percentage of genome altered (PGA). Somatic copy number alterations (CNA) were determined using Fisher-Boschloo tests and logistic regression. Primary analysis were performed on TCGA (N = 260) as discovery and CPC-GENE (N = 199) as validation set. RESULTS: CR/IDC growth was present in 80/260 (31%) TCGA and 76/199 (38%) CPC-GENE cases. Patients with CR/IDC and ≥ GS 7 had significantly higher PGA than men without this pattern in both TCGA (2.2 fold; p = 0.0003) and CPC-GENE (1.7 fold; p = 0.004) cohorts. CR/IDC growth was associated with deletions of 8p, 16q, 10q23, 13q22, 17p13, 21q22, and amplification of 8q24. CNAs comprised a total of 1299 gene deletions and 369 amplifications in the TCGA dataset, of which 474 and 328 events were independently validated, respectively. Several of the affected genes were known to be associated with aggressive prostate cancer such as loss of PTEN, CDH1, BCAR1 and gain of MYC. Point mutations in TP53, SPOP and FOXA1were also associated with CR/IDC, but occurred less frequently than CNAs. CONCLUSIONS: CR/IDC growth is associated with increased genomic instability clustering to genetic regions involved in aggressive prostate cancer. Therefore, CR/IDC is a pathologic substrate for progressive molecular tumour derangement.

SeqControl: process control for DNA sequencing.

As high-throughput sequencing continues to increase in speed and throughput, routine clinical and industrial application draws closer. These 'production' settings will require enhanced quality monitoring and quality control to optimize output and reduce costs. We developed SeqControl, a framework for predicting sequencing quality and coverage using a set of 15 metrics describing overall coverage, coverage distribution, basewise coverage and basewise quality. Using whole-genome sequences of 27 prostate cancers and 26 normal references, we derived multivariate models that predict sequencing quality and depth. SeqControl robustly predicted how much sequencing was required to reach a given coverage depth (area under the curve (AUC) = 0.993), accurately classified clinically relevant formalin-fixed, paraffin-embedded samples, and made predictions from as little as one-eighth of a sequencing lane (AUC = 0.967). These techniques can be immediately incorporated into existing sequencing pipelines to monitor data quality in real time. SeqControl is available at http://labs.oicr.on.ca/Boutros-lab/software/SeqControl/.