A high-resolution map of human RNA translation.

Translated small open reading frames (smORFs) can have important regulatory roles and encode microproteins, yet their genome-wide identification has been challenging. We determined the ribosome locations across six primary human cell types and five tissues and detected 7,767 smORFs with translational profiles matching those of known proteins. The human genome was found to contain highly cell-type- and tissue-specific smORFs and a subset that encodes highly conserved amino acid sequences. Changes in the translational efficiency of upstream-encoded smORFs (uORFs) and the corresponding main ORFs predominantly occur in the same direction. Integration with 456 mass-spectrometry datasets confirms the presence of 603 small peptides at the protein level in humans and provides insights into the subcellular localization of these small proteins. This study provides a comprehensive atlas of high-confidence translated smORFs derived from primary human cells and tissues in order to provide a more complete understanding of the translated human genome.

Loss of C2orf69 defines a fatal autoinflammatory syndrome in humans and zebrafish that evokes a glycogen-storage-associated mitochondriopathy.

Human C2orf69 is an evolutionarily conserved gene whose function is unknown. Here, we report eight unrelated families from which 20 children presented with a fatal syndrome consisting of severe autoinflammation and progredient leukoencephalopathy with recurrent seizures; 12 of these subjects, whose DNA was available, segregated homozygous loss-of-function C2orf69 variants. C2ORF69 bears homology to esterase enzymes, and orthologs can be found in most eukaryotic genomes, including that of unicellular phytoplankton. We found that endogenous C2ORF69 (1) is loosely bound to mitochondria, (2) affects mitochondrial membrane potential and oxidative respiration in cultured neurons, and (3) controls the levels of the glycogen branching enzyme 1 (GBE1) consistent with a glycogen-storage-associated mitochondriopathy. We show that CRISPR-Cas9-mediated inactivation of zebrafish C2orf69 results in lethality by 8 months of age due to spontaneous epileptic seizures, which is preceded by persistent brain inflammation. Collectively, our results delineate an autoinflammatory Mendelian disorder of C2orf69 deficiency that disrupts the development/homeostasis of the immune and central nervous systems.

Paradigm Shifting Research: Key Studies in Urologic Oncology.

BACKGROUND: Genitourinary malignancies have a substantial impact on men and women in the USA as they include three of the ten most common cancers (prostate, renal, and bladder). Other urinary tract cancers are less common (testis and penile) but still have profound treatment implications related to potential deficits in sexual, urinary, and reproductive function. Evidenced-based practice remains the cornerstone of treatment for urologic malignancies. METHODS: The authors reviewed the literature in consideration of the four top articles influencing clinical practice in the prior calendar year, 2022. RESULTS: The PROTECT trial demonstrates favorable 15-years outcomes for active monitoring of localized prostate cancer. The SEMS trial establishes retroperitoneal lymph node dissection as a viable option for patients with seminoma of the testis with limited retroperitoneal lymph node metastases. CheckMate 274 supports adjuvant immunotherapy following radical cystectomy for muscle-invasive bladder cancer with a high risk of recurrence. Data reported from the IROCK consortium reinforce stereotactic ablative radiotherapy as an option for localized renal cell carcinoma. CONCLUSION: The care for patients with urologic cancers has been greatly improved through advances in surgical, medical, and radiation oncologic treatments realized through prospective randomized clinical trials and large multicenter collaborative groups.

Renal Pelvic Urothelial Carcinoma With Invasion Into Renal Medulla Can Be Redefined as pT2 to Improve Correlation With Survival.

According to the American Joint Cancer Committee, pT3 renal pelvic carcinoma is defined as tumor invading the renal parenchyma and/or peripelvic fat and is the largest pT category, with notable survival heterogeneity. Anatomical landmarks within the renal pelvis can be difficult to discern. Using glomeruli as a boundary to differentiate renal medulla invasion from renal cortex invasion, this study aimed to compare patient survival of pT3 renal pelvic urothelial carcinoma on the basis of the extent of renal parenchyma invasion and, thereafter, determine whether redefining pT2 and pT3 improves pT correlation with survival. Cases with primary renal pelvic urothelial carcinoma were identified through a review of pathology reports from nephroureterectomies completed at our institution from 2010 to 2019 (n = 145). Tumors were stratified by pT, pN, lymphovascular invasion, and invasion of the renal medulla versus invasion of the renal cortex and/or peripelvic fat. Overall survival between groups was compared using Kaplan-Meier survival models and Cox regression multivariate analysis. pT2 and pT3 tumors had similar 5-year overall survival, with multivariate analysis demonstrating an overlap between hazard ratios (HRs) for pT2 (HR, 2.20; 95% CI, 0.70-6.95) and pT3 (HR, 3.15; 95% CI, 1.63-6.09). pT3 tumors with peripelvic fat and/or renal cortex invasion had a 3.25-fold worse prognosis than pT3 tumors with renal medulla invasion alone. Furthermore, pT2 and pT3 tumors with only renal medulla invasion had similar overall survival, whereas pT3 tumors with peripelvic fat and/or renal cortex invasion had a worse prognosis (P = .00036). Reclassifying pT3 tumors with only renal medulla invasion as pT2 yielded greater separation between survival curves and HR. Thus, we recommend redefining pT2 renal pelvic carcinoma to include renal medulla invasion and restricting pT3 to peripelvic fat and/or renal cortex invasion to improve the prognostic accuracy of pT classification.

Robust Virus-Specific Adaptive Immunity in COVID-19 Patients with SARS-CoV-2 Δ382 Variant Infection.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOCs) that have become dominant as the pandemic progresses bear the ORF8 mutation together with multiple spike mutations. A 382-nucleotide deletion (Δ382) in the ORF7b and ORF8 regions has been associated with milder disease phenotype and less systemic inflammation in COVID-19 patients. However, its impact on host immunity against SARS-CoV-2 remains undefined. Here, RNA-sequencing was performed to elucidate whole blood transcriptomic profiles and identify contrasting immune signatures between patients infected with either wildtype or Δ382 SARS-CoV-2 variant. Interestingly, the immune landscape of Δ382 SARS-CoV-2 infected patients featured an increased adaptive immune response, evidenced by enrichment of genes related to T cell functionality, a more robust SARS-CoV-2-specific T cell immunity, as well as a more rapid antibody response. At the molecular level, eukaryotic initiation factor 2 signaling was found to be upregulated in patients bearing Δ382, and its associated genes were correlated with systemic levels of T cell-associated and pro-inflammatory cytokines. This study provides more in-depth insight into the host-pathogen interactions of ORF8 with great promise as a therapeutic target to combat SARS-CoV-2 infection.

Associations of self-efficacy, social support and coping strategies with health-related quality of life after radical cystectomy for bladder cancer: A cross-sectional study.

OBJECTIVES: Investigating associations between self-efficacy, social support and quality of life (HRQoL) and mediating effects of coping among bladder cancer (BC) patients treated with radical cystectomy (RC). METHODS: A cross-sectional study was conducted from January 2012 to December 2014 with 99 BC patients. An online survey assessed patient characteristics, HRQoL, coping strategies, self-efficacy and social support. A stepwise multiple linear regression model was used. RESULTS: Self-efficacy and social support were significantly associated with HRQoL. Complete mediation effects of adaptive/maladaptive coping strategies emerged for the associations between self-efficacy and social support with functional well-being (B = 0.247, 95% CI 0.119-0.374, p < 0.001; B = -0.414, 95% CI -0.526 to -0.302, p < 0.001) and total Functional Assessment of Cancer Therapy-Bladder (FACT-BI) (B = 0.779, 95% CI 0.351-1.207, p < 0.001; B = -1.969, 95% CI -2.344 to -1.594, p < 0.001). Maladaptive coping mediated the associations of self-efficacy and social support with physical well-being (B = -0.667, 95% CI -0.752 to -0.516, p < 0.001) and disease-specific symptoms (B = -0.413, 95% CI -0.521 to -0.304, p < 0.001). A partial mediation effect of adaptive coping was found for the association between self-efficacy and social well-being (B = 0.145, 95% CI 0.016-0.273, p < 0.05). Social support was significantly associated with emotional (B = 0.067, 95% CI 0.027-0.108, p < 0.001) and social well-being (B = 0.200, 95% CI 0.146-0.255, p < 0.001). CONCLUSION: Interventions should tackle self-efficacy, social support and coping strategies to improve BC patients' HRQoL.

Effects of a major deletion in the SARS-CoV-2 genome on the severity of infection and the inflammatory response: an observational cohort study.

BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants with a 382-nucleotide deletion (∆382) in the open reading frame 8 (ORF8) region of the genome have been detected in Singapore and other countries. We investigated the effect of this deletion on the clinical features of infection. METHODS: We retrospectively identified patients who had been screened for the ∆382 variant and recruited to the PROTECT study-a prospective observational cohort study conducted at seven public hospitals in Singapore. We collected clinical, laboratory, and radiological data from patients' electronic medical records and serial blood and respiratory samples taken during hospitalisation and after discharge. Individuals infected with the ∆382 variant were compared with those infected with wild-type SARS-CoV-2. Exact logistic regression was used to examine the association between the infection groups and the development of hypoxia requiring supplemental oxygen (an indicator of severe COVID-19, the primary endpoint). Follow-up for the study's primary endpoint is completed. FINDINGS: Between Jan 22 and March 21, 2020, 278 patients with PCR-confirmed SARS-CoV-2 infection were screened for the ∆382 deletion and 131 were enrolled onto the study, of whom 92 (70%) were infected with the wild-type virus, ten (8%) had a mix of wild-type and ∆382-variant viruses, and 29 (22%) had only the ∆382 variant. Development of hypoxia requiring supplemental oxygen was less frequent in the ∆382 variant group (0 [0%] of 29 patients) than in the wild-type only group (26 [28%] of 92; absolute difference 28% [95% CI 14-28]). After adjusting for age and presence of comorbidities, infection with the ∆382 variant only was associated with lower odds of developing hypoxia requiring supplemental oxygen (adjusted odds ratio 0·07 [95% CI 0·00-0·48]) compared with infection with wild-type virus only. INTERPRETATION: The ∆382 variant of SARS-CoV-2 seems to be associated with a milder infection. The observed clinical effects of deletions in ORF8 could have implications for the development of treatments and vaccines. FUNDING: National Medical Research Council Singapore.

Integrin α2 marks a niche of trophoblast progenitor cells in first trimester human placenta.

During pregnancy the trophoblast cells of the placenta are the only fetal cells in direct contact with maternal blood and decidua. Their functions include transport of nutrients and oxygen, secretion of pregnancy hormones, remodelling of the uterine arteries, and communicating with maternal cells. Despite the importance of trophoblast cells in placental development and successful pregnancy, little is known about the identity, location and differentiation of human trophoblast progenitors. We identify a proliferative trophoblast niche at the base of the cytotrophoblast cell columns in first trimester placentas that is characterised by integrin α2 (ITGA2) expression. Pulse-chase experiments with 5-iodo-2'-deoxyuridine indicate that these cells might contribute to both villous (VCT) and extravillous (EVT) lineages. These proliferating trophoblast cells can be isolated by flow cytometry using ITGA2 as a marker and express genes from both VCT and EVT. Microarray expression analysis shows that ITAG2+ cells display a unique transcriptional signature, including genes involved in NOTCH signalling, and exhibit a combination of epithelial and mesenchymal characteristics. ITGA2 thus marks a niche allowing the study of pure populations of trophoblast progenitor cells.

Scoping review: Facilitators and barriers in the adoption of teledentistry among older adults.

OBJECTIVE/BACKGROUND: Access to oral health care among older adults is a key issue in society, which has been exacerbated by social distancing measures and lockdowns during the COVID-19 pandemic. Older adults would greatly benefit from teledentistry, yet little information exists on the enablers and challenges of adopting this technology for use with this group. The aim of this scoping review is to summarise the applications and key factors associated with the adoption of teledentistry among older adults. MATERIALS AND METHODS: This scoping review was developed in accordance with Arksey and O'Malley's five-stage framework and the Joanna Briggs Institute scoping review protocol guidelines. Publications on teledentistry involving direct clinical services for older adults aged 60 and above were included. Publications that focused solely on teleeducation were excluded. A systematic search was carried out on major electronic databases until 25 August 2020. Out of 1084 articles screened, 25 articles were included. Facilitators and barriers were categorised using the socio-ecological model. RESULTS/DISCUSSION: Teleconsultation and telediagnosis were the most reported applications of teledentistry among older adults. Reported policy-level factors were data privacy issues (n = 7) and regulations (n = 17). Community-level facilitators and barriers included the availability of resources (n = 15) and support (n = 3). Familiar care settings (n = 2) and effective administration (n = 20) were key organisational-level factors. Staff attitudes and education (n = 23) and individual patient knowledge, attitudes and practices (n = 10) can influence teledentistry adoption while complex medical conditions (n = 8) may pose a challenge. CONCLUSION: Key factors in the uptake of teledentistry among older adults span across policy, community, organisational, interpersonal and individual factors. Commonly reported barriers included technical issues, lack of funding, consent issues and cognitive impairments.

Esrrb function is required for proper primordial germ cell development in presomite stage mouse embryos.

Estrogen related receptor beta (Esrrb) is an orphan nuclear receptor that is required for self-renewal and pluripotency in mouse embryonic stem (ES) cells. However, in the early post-implantation mouse embryo, Esrrb is specifically expressed in the extraembryonic ectoderm (ExE) and plays a crucial role in trophoblast development. Previous studies showed that Esrrb is also required to maintain trophoblast stem (TS) cells, the in vitro stem cell model of the early trophoblast lineage. In order to identify regulatory targets of Esrrb in vivo, we performed microarray analysis of Esrrb-null versus wild-type post-implantation ExE, and identified 30 genes down-regulated in Esrrb-mutants. Among them is Bmp4, which is produced by the ExE and known to be critical for primordial germ cell (PGC) specification in vivo. We further identified an enhancer region bound by Esrrb at the Bmp4 locus by performing Esrrb ChIP-seq and luciferase reporter assay using TS cells. Finally, we established a knockout mouse line in which the enhancer region was deleted using CRISPR/Cas9 technology. Both Esrrb-null embryos and enhancer knockout embryos expressed lower levels of Bmp4 in the ExE, and had reduced numbers of PGCs. These results suggested that Esrrb functions as an upstream factor of Bmp4 in the ExE, regulating proper PGC development in mice.

Inhibition of Phosphoinositide-3-Kinase Signaling Promotes the Stem Cell State of Trophoblast.

Trophoblast stem cells (TSCs) are a heterogeneous cell population despite the presence of fibroblast growth factor (FGF) and transforming growth factor ß (TGFB) as key growth factors in standard culture conditions. To understand what other signaling cascades control the stem cell state of mouse TSCs, we performed a kinase inhibitor screen and identified several novel pathways that cause TSC differentiation. Surprisingly, inhibition of phosphoinositide-3-kinase (PI3K) signaling increased the mRNA and protein expression of stem cell markers instead, and resulted in a tighter epithelial colony morphology and fewer differentiated cells. PI3K inhibition could not substitute for FGF or TGFB and did not affect phosphorylation of extracellular signal-regulated kinase, and thus acts independently of these pathways. Upon removal of PI3K inhibition, TSC transcription factor levels reverted to normal TSC levels, indicating that murine TSCs can reversibly switch between these two states. In summary, PI3K inhibition reduces the heterogeneity and seemingly heightens the stem cell state of TSCs as indicated by the simultaneous upregulation of multiple key marker genes and cell morphology. Stem Cells 2019;37:1307-1318.

Development and evaluation of a bladder Cancer specific survivorship care plan by patients and clinical care providers: a multi-methods approach.

BACKGROUND, CONTEXT AND PURPOSE: In spite of the mixed evidence for their impact, survivorship Care Plans (SCPs) are recommended to enhance quality of care for cancer survivors. Data on the feasibility of SCPs in bladder cancer (BC) is sparse. Using a mixed-methods approach, this study describes the iterative development, acceptability and feasibility of BC specific SCP (BC-SCP) in clinical settings. METHODS: In Phase I, we developed the BC-SCP. In Phase II, we conducted four focus groups with 19 patients and 15 providers to examine its acceptability and usability challenges. Data analyses using the Atlas.ti program, informed refinement of the BC-SCP. In Phase III, we conducted feasibility testing of the refined BC-SCP with 18 providers from 12 health-centers. An encounter survey was completed after each assessment to examine the feasibility of the BC-SCP. Chi-square and Fisher Exact tests were used for comparative analyses. RESULTS: During phase I, we observed high patient and provider acceptability of the BC-SCP and substantial engagement in improving its content, design, and structure. In Phase II, providers completed 59 BC-SCPs. Mean time for BC-SCP completion was 12.3 min. Providers reported that BC-SCP content was clear, did not hamper clinic flow and was readily completed with easy-to-access information. Comparative analyses to examine differences in SCP completion time by patient clinico-demographic characteristics and provider type revealed no significant differences. CONCLUSIONS: Our BC-SCP has clinical relevance, and can be used in an active practice setting. However, considerable progress will be necessary to achieve implementation of and sharing the BC-SCP with patients and care providers, particularly within the electronic medical record. In summary, BC-SCPs are essential to improve the follow up care of BC survivors. Clinical resources are required to ensure appropriate implementation of BC-SCPs. TRIAL REGISTRATION: Study HUM00056082.

Involving Patients in the Development and Evaluation of an Educational and Training Experiential Intervention (ETEI) to Improve Muscle Invasive Bladder Cancer Treatment Decision-making and Post-operative Self-care: a Mixed Methods Approach.

This study aims to describe the acceptability and feasibility of an educational and training experiential intervention (ETEI) we developed to enhance muscle invasive bladder cancer (MIBC) patients with treatment decision-making and post-operative self-care. Twenty-five patients were randomized to a control group (N = 8) or ETEI group (N = 17). ETEI group participated in a nurse-led session on MIBC education. The control group received diet and nutrition education. Study questionnaires were completed at baseline and at 1-month post-intervention. Our results showed acceptable recruitment (58%) and retention rates (68%). The ETEI group reported increased knowledge (82% vs. 50%), improved decisional support (64% vs. 50%), improved communication (73% vs. 50%), and increased confidence in treatment decisions (73% vs. 50%) compared to the control group. Patients in the control group reported improved diet (50% v. 27%) as well as maintaining a healthy lifestyle (67% vs. 45%) compared to the ETEI group. Patients in the ETEI group reported a significant decrease in cancer worries and increases in self-efficacy beliefs over time compared to the control group. The ETEI was feasible, acceptable, and showed a potential for inducing desired changes in cancer worries and efficacy beliefs.

Websites on Bladder Cancer: an Appropriate Source of Patient Information?

A growing number of patients search for health information online. An early investigation of websites about bladder cancer (BCa) revealed mostly incomplete and particularly inaccurate information. We analyzed the quality, readability, and popularity of the most frequented websites on BCa. An Internet search on www.google.com was performed for the term "bladder cancer." After selecting the most frequented websites for patient information, HONcode quality certification, Alexa popularity rank, and readability scores (according to US grade levels) were investigated. A 36-point checklist was used to assess the content according to the EAU guidelines on BCa, which was categorized into seven topics. The popularity of the 49 websites analyzed was average, with a median Alexa popularity rank of 41,698 (interquartile range [IQR] 7-4,671,246). The readability was rated difficult with 11 years of school education needed to understand the information. Thirteen (27%) websites were HONcode certified. Out of 343 topics (seven EAU guideline topics each on 49 websites), 79% were mentioned on the websites. Of these, 10% contained incorrect information, mostly outdated or biased, and 34% contained incomplete information. Publically provided websites mentioned more topics per website (median [IQR] 7 [5.5-7] vs. 5.5 [3.3-7]; p = 0.022) and showed less incorrect information (median [IQR] 0 [0-1] vs. 1 [0-1]; p = 0.039) than physician-provided websites. Our study revealed mostly correct but partially incomplete information on BCa websites for patients. Physicians and public organizations should strive to keep their website information up-to-date and unbiased to optimize patients' health literacy.

Prognostic importance of lymphovascular invasion in urothelial carcinoma of the renal pelvis.

BACKGROUND: The current study was conducted to assess the impact of lymphovascular invasion on the survival of patients with urothelial carcinoma of the renal pelvis. METHODS: Patients with urothelial carcinoma of the renal pelvis who underwent radical nephroureterectomy from 2010 through 2015 were identified in the National Cancer Data Base. Patients were characterized according to demographic and clinical factors, including pathologic tumor stage and lymphovascular invasion. Associations with overall survival were assessed through proportional hazards regression analysis. RESULTS: A total of 4177 patients were identified; 1576 had lymphovascular invasion. Patients with T3 disease and lymphovascular invasion had 5-year survival that was significantly worse than that of patients with T3 disease without lymphovascular invasion (34.7% vs 52.6; P < .001 by the log-rank test), and approached that of patients with T4 disease without lymphovascular invasion (34.7% vs 26.5%; P = .002). On multivariate analysis controlling for age, comorbidities, grade, lymph node status, surgical margin status, race, sex, and chemotherapy administration, patients with T3 disease and lymphovascular invasion also were found to have significantly worse survival compared with patients with T3 disease without lymphovascular invasion (hazard ratio, 1.7; 95% confidence interval, 1.4-1.91). CONCLUSIONS: Lymphovascular invasion status is a key prognostic marker that can stratify the risk of patients with pT3 upper tract urothelial carcinoma further. Patients with this pathologic feature should be carefully considered for clinical trials exploring existing and novel therapies. Cancer 2018;124:2507-14. © 2018 American Cancer Society.

Frailty and geriatric assessment in urologic oncology.

PURPOSE OF REVIEW: As the population ages, urologic oncologists are caring for older and more vulnerable patients that must withstand complex surgical treatments. Our healthcare environment emphasizes surgical quality, reductions in length of hospital stay, reduced readmission rates, and high patient satisfaction. So those who manage urologic malignancies must be able to optimize their patients. Understanding the concept of frailty, how to diagnose it in a timely and reliable manner, appreciate its perioperative impact, and consider interventions to reduce its effects may improve surgical outcomes. RECENT FINDINGS: There has been a recent swell of early research regarding frailty in urologic oncology and its related perioperative effects. Increasing degrees of frailty are associated with greater morbidity and mortality, and more adverse discharge disposition after surgical procedures. Clinicians are, thus, recognizing the value of geriatric assessment in their practice and exploring ways to integrate it using a team-based approach. Universal geriatric recommendations are now available in specific urologic populations to guide these efforts. Importantly, formal geriatric assessment outperforms physician discretion or the 'eyeball' test. SUMMARY: The current review offers a comprehensive study of the impact of frailty in urologic oncology, methods for its assessment, and active interventions to reduce it.

Bladder cancer in 2010: how far have we come?

Bladder cancer is the fourth most common cancer and ranks eighth as a cause of death from cancer among men in the United States. Although guidelines assist in treatment, the art of managing bladder cancer, such as the decision to use neoadjuvant chemotherapy and the timing of cystectomy, is still variable. Bladder cancer has a propensity to recur, and with recurrence, a significant number of cases progress, which makes the early detection of high-risk patients imperative. Advances in detection, surveillance, and treatment of bladder cancer are reviewed in this article.

A 10-Item Checklist Improves Reporting of Critical Procedural Elements during Transurethral Resection of Bladder Tumor.

PURPOSE: Previous studies have demonstrated significant variation in recurrence rates after transurethral resection of bladder tumor, likely due to differences in surgical quality. We sought to create a framework to define, measure and improve the quality of transurethral resection of bladder tumor using a surgical checklist. MATERIALS AND METHODS: We formed a multi-institutional group of urologists with expertise with bladder cancer and identified 10 critical items that should be performed during every high quality transurethral bladder tumor resection. We prospectively implemented a 10-item checklist into practice and reviewed the operative reports of such resections performed before and after implementation. Results at all institutions were combined in a meta-analysis to estimate the overall change in the mean number of items documented. RESULTS: The operative notes for 325 transurethral bladder tumor resections during checklist use were compared to those for 428 performed before checklist implementation. Checklist use increased the mean number of items reported from 4.8 to 8.0 per resection, resulting in a mean increase of 3.3 items (95% CI 1.9-4.7) on meta-analysis. With the checklist the percentage of reports that included all 10 items increased from 0.5% to 27% (p <0.0001). Surgeons who reported more checklist items tended to have a slightly higher proportion of biopsies containing muscle, although not at conventional significance (p = 0.062). CONCLUSIONS: The use of a 10-item checklist during transurethral resection of bladder tumor improved the reporting of critical procedural elements. Although there was no clear impact on the inclusion of muscle in the specimen, checklist use may enhance surgeon attention to important aspects of the procedure and be a lever for quality improvement.