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Prostate cancer (PCa) can be highly heterogeneous and multifocal, and accurate assessment of the volume, grade, and stage of PCa in situ is not a simple task. Urine has been investigated as a source of PCa biomarkers for over 70 years, and there is now strong evidence that analysis of urine could provide more accurate diagnosis and a better risk stratification that could aid clinical decisions regarding disease surveillance and treatment. Urine diagnostics is a developing area, moving towards multi-omic biomarker integration for improved diagnostic performance. Urine tests developed by strong collaborations between scientists and clinicians have the potential to provide targeted and meaningful data that can guide treatment and improve men’s lives.

Genome-wide DNA sequencing was used to decrypt the phylogeny of multiple samples from distinct areas of cancer and morphologically normal tissue taken from the prostates of three men. Mutations were present at high levels in morphologically normal tissue distant from the cancer, reflecting clonal expansions, and the underlying mutational processes at work in morphologically normal tissue were also at work in cancer. Our observations demonstrate the existence of ongoing abnormal mutational processes, consistent with field effects, underlying carcinogenesis. This mechanism gives rise to extensive branching evolution and cancer clone mixing, as exemplified by the coexistence of multiple cancer lineages harboring distinct ERG fusions within a single cancer nodule. Subsets of mutations were shared either by morphologically normal and malignant tissues or between different ERG lineages, indicating earlier or separate clonal cell expansions. Our observations inform on the origin of multifocal disease and have implications for prostate cancer therapy in individual cases.

BackgroundThe Parent-focused Redesign for Encounters, Newborns to Toddlers (PARENT) intervention was created as a team-based approach to well-child care (WCC) that relies on a health educator (Parent Coach) to provide the bulk of WCC services, address specific needs faced by families in low-income communities, and decrease reliance on the clinician as the primary provider of WCC services. ObjectiveThis study aims to evaluate the impact of PARENT using a cluster randomized controlled trial. MethodsThis study tested the effectiveness of PARENT at 10 clinical sites in 2 federally qualified health centers in Tacoma, Washington, and Los Angeles, California. We conducted a cluster randomized controlled trial that included 916 families with children aged ≤12 months at the time of the baseline survey. Parents will be followed up at 6 and 12 months after enrollment. The Parent Coach, the main element of PARENT, provides anticipatory guidance, psychosocial screening and referral, developmental and behavioral surveillance, screening, and guidance at each WCC visit. The coach is supported by parent-focused previsit screening and visit prioritization, a brief, problem-focused clinician encounter for a physical examination and any concerns that require a clinician’s attention, and an automated text message parent reminder and education service for periodic, age-specific messages to reinforce key health-related information recommended by Bright Futures national guidelines. We will examine parent-reported quality of care (receipt of nationally recommended WCC services, family-centeredness of care, and parental experiences of care), and health care use (WCC, urgent care, emergency department, and hospitalizations), conduct a cost analysis, and conduct a separate time-motion study of clinician time allocation to assess efficiency. We will also collect data on exploratory measures of parent-and parenting-focused outcomes. Our primary outcomes were receipt of anticipatory guidance and emergency department use. ResultsParticipant recruitment began in March 2019. After recruitment, 6- and 12-month follow-up surveys will be completed. As of August 30, 2021, we enrolled a total of 916 participants. ConclusionsThis large pragmatic trial of PARENT in partnership with federally qualified health centers will assess its utility as an evidence-based and financially sustainable model for the delivery of preventive care services to children in low-income communities. Trial RegistrationClinicalTrials.gov: NCT03797898; https://clinicaltrials.gov/ct2/show/NCT03797898 International Registered Report Identifier (IRRID)DERR1-10.2196/27054

Urine from patients with prostate cancer (PCa) contains gene transcripts that have been used for PCa diagnosis and prognosis. Historically, patient urine samples have been collected after a digital rectal examination of the prostate, which was thought necessary to boost the levels of prostatic secretions in the urine. We herein describe methodology that allows urine to be collected by patients at home and then posted to a laboratory for analysis. RNA yields and quality were comparable to those for post digital rectal examination urine, and there was improved sensitivity for the detection of TMPRSS2:ERG transcripts by RT-PCR. The At-Home collection protocol has opened up the potential to perform large-scale PCa studies without the inconvenience, cost, discomfort and expense of patients having to visit the clinic.

Abstract Background Human tissue is increasingly being whole genome sequenced as we transition into an era of genomic medicine. With this arises the potential to detect sequences originating from microorganisms, including pathogens amid the plethora of human sequencing reads. In cancer research, the tumorigenic ability of pathogens is being recognized, for example, Helicobacter pylori and human papillomavirus in the cases of gastric non-cardia and cervical carcinomas, respectively. As of yet, no benchmark has been carried out on the performance of computational approaches for bacterial and viral detection within host-dominated sequence data. Results We present the results of benchmarking over 70 distinct combinations of tools and parameters on 100 simulated cancer datasets spiked with realistic proportions of bacteria. mOTUs2 and Kraken are the highest performing individual tools achieving median genus-level F1 scores of 0.90 and 0.91, respectively. mOTUs2 demonstrates a high performance in estimating bacterial proportions. Employing Kraken on unassembled sequencing reads produces a good but variable performance depending on post-classification filtering parameters. These approaches are investigated on a selection of cervical and gastric cancer whole genome sequences where Alphapapillomavirus and Helicobacter are detected in addition to a variety of other interesting genera. Conclusions We provide the top-performing pipelines from this benchmark in a unifying tool called SEPATH, which is amenable to high throughput sequencing studies across a range of high-performance computing clusters. SEPATH provides a benchmarked and convenient approach to detect pathogens in tissue sequence data helping to determine the relationship between metagenomics and disease.

Feminist cosmetic surgery scholars have been attentive to cosmetic breast surgeries as emblematic of a range of issues and questions. Breast implant and reduction surgeries have been analyzed by scholars as psychologically beneficial, as representative of unethical practices in the cosmetic surgery industry, as exemplar of the objectification of women’s bodies, and as connected to powerful cultural ideas about breasts. A curious dearth in previous scholarship is a sufficient engagement with the ubiquitous library of photographs that document these procedures. This essay discusses before and after photographs of cosmetic breast surgeries, which occupy a liminal space as medical and sexual, verification and fantasy. In this essay, I argue that before and after photographs of cosmetic breast surgeries should be read as revealing of the conditions under which patients and surgeons operate, rather than solely as proof of an operation’s results. To make this argument, I focus on two examples of before and after photographs – one of a breast augmentation and one of a breast reduction – and guide my analysis of the images in relation to narrative interviews with three women who underwent cosmetic breast surgeries.

Abstract Background Prevention of unnecessary biopsies and overtreatment of indolent disease remains a challenge in the management of prostate cancer. Novel non-invasive tests that can identify clinically significant (intermediate-risk and high-risk) diseases are needed to improve risk stratification and monitoring of prostate cancer patients. Here, we investigated a panel of six DNA methylation biomarkers in urine samples collected post-digital rectal exam from patients undergoing prostate biopsy, for their utility to guide decision making for diagnostic biopsy and early detection of aggressive prostate cancer. Results We recruited 408 patients in risk categories ranging from benign to low-, intermediate-, and high-risk prostate cancer from three international cohorts. Patients were separated into 2/3 training and 1/3 validation cohorts. Methylation biomarkers were analyzed in post-digital rectal exam urinary sediment DNA by quantitative MethyLight assay and investigated for their association with any or aggressive prostate cancers. We developed a Prostate Cancer Urinary Epigenetic (ProCUrE) assay based on an optimal two-gene (HOXD3 and GSTP1) LASSO model, derived from methylation values in the training cohort, and assessed ProCUrE’s diagnostic and prognostic ability for prostate cancer in both the training and validation cohorts. ProCUrE demonstrated improved prostate cancer diagnosis and identification of patients with clinically significant disease in both the training and validation cohorts. Using three different risk stratification criteria (Gleason score, D’Amico criteria, and CAPRA score), we found that the positive predictive value for ProCUrE was higher (59.4–78%) than prostate specific antigen (PSA) (38.2–72.1%) for all risk category comparisons. ProCUrE also demonstrated additive value to PSA in identifying GS ≥ 7 PCa compared to PSA alone (DeLong’s test p = 0.039), as well as additive value to the PCPT risk calculator for identifying any PCa and GS ≥ 7 PCa (DeLong’s test p = 0.011 and 0.022, respectively). Conclusions ProCUrE is a promising non-invasive urinary methylation assay for the early detection and prognostication of prostate cancer. ProCUrE has the potential to supplement PSA testing to identify patients with clinically significant prostate cancer.

The Prostate Urine Risk (PUR) biomarker is a four-group classifier for predicting outcome in patients prior to biopsy and for men on active surveillance. The four categories correspond to the probabilities of the presence of normal tissue (PUR-1), D’Amico low-risk (PUR-2), intermediate-risk (PUR-3), and high-risk (PUR-4) prostate cancer. In the current study we investigate how the PUR-4 status is linked to Gleason grade, prostate volume, and tumor volume as assessed from biopsy (n = 215) and prostatectomy (n = 9) samples. For biopsy data PUR-4 status alone was linked to Gleason Grade group (GG) (Spearman’s, ρ = 0.58, p < 0.001 trend). To assess the impact of tumor volume each GG was dichotomized into Small and Large volume cancers relative to median volume. For GG1 (Gleason Pattern 3 + 3) cancers volume had no impact on PUR-4 status. In contrast for GG2 (3 + 4) and GG3 (4 + 3) cancers PUR-4 levels increased in large volume cancers with statistical significance observed for GG2 (p = 0.005; Games-Howell). These data indicated that PUR-4 status is linked to the presence of Gleason Pattern 4. To test this observation tumor burden and Gleason Pattern were assessed in nine surgically removed and sectioned prostates allowing reconstruction of 3D maps. PUR-4 was not correlated with Gleason Pattern 3 amount, total tumor volume or prostate size. A strong correlation was observed between amount of Gleason Pattern 4 tumor and PUR-4 signature (r = 0.71, p = 0.034, Pearson’s). These observations shed light on the biological significance of the PUR biomarker and support its use as a non-invasive means of assessing the presence of clinically significant prostate cancer.

"Doing Feminist Theory Through Digital Video" is an assignment I designed for my undergraduate feminist theory course, where students created a short digital video on a concept in feminist theory. I outline the assignment and the pedagogical and epistemological frameworks that structured the assignment (digital storytelling, participatory video and feminist approaches to service learning) before presenting an analysis of its learning outcomes gleaned through interviews with students. I argue that incorporating creative and service learning components into a feminist theory course deepens student learning about praxis and subjectivity because it engages their spirit, mind and body, leading to a sustained engagement with feminist theory and an ability to imagine feminist theory outside of the university classroom. My objective for this paper is to share what I have learned as an educator from this project, and that this will be useful to others interested in adapting this kind of assignment to their own pedagogical contexts.