Pan-Cancer Analysis of lncRNA Regulation Supports Their Targeting of Cancer Genes in Each Tumor Context

Long noncoding RNAs (lncRNAs) are commonly dys-regulated in tumors, but only a handful are known toplay pathophysiological roles in cancer. We inferredlncRNAs that dysregulate cancer pathways, onco-genes, and tumor suppressors (cancer genes) bymodeling their effects on the activity of transcriptionfactors, RNA-binding proteins, and microRNAs in5,185 TCGA tumors and 1,019 ENCODE assays.Our predictions included hundreds of candidateonco- and tumor-suppressor lncRNAs (cancerlncRNAs) whose somatic alterations account for thedysregulation of dozens of cancer genes and path-ways in each of 14 tumor contexts. To demonstrateproof of concept, we showed that perturbations tar-geting OIP5-AS1 (an inferred tumor suppressor) andTUG1 and WT1-AS (inferred onco-lncRNAs) dysre-gulated cancer genes and altered proliferation ofbreast and gynecologic cancer cells. Our analysis in-dicates that, although most lncRNAs are dysregu-lated in a tumor-specific manner, some, includingOIP5-AS1, TUG1, NEAT1, MEG3, and TSIX, synergis-tically dysregulate cancer pathways in multiple tumorcontexts

Genomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas

This integrated, multiplatform PanCancer Atlas study co-mapped and identified distinguishing molecular features of squamous cell carcinomas (SCCs) from five sites associated with smokin

Pan-cancer Alterations of the MYC Oncogene and Its Proximal Network across the Cancer Genome Atlas

Although theMYConcogene has been implicated incancer, a systematic assessment of alterations ofMYC, related transcription factors, and co-regulatoryproteins, forming the proximal MYC network (PMN),across human cancers is lacking. Using computa-tional approaches, we define genomic and proteo-mic features associated with MYC and the PMNacross the 33 cancers of The Cancer Genome Atlas.Pan-cancer, 28% of all samples had at least one ofthe MYC paralogs amplified. In contrast, the MYCantagonists MGA and MNT were the most frequentlymutated or deleted members, proposing a roleas tumor suppressors.MYCalterations were mutu-ally exclusive withPIK3CA,PTEN,APC,orBRAFalterations, suggesting that MYC is a distinct onco-genic driver. Expression analysis revealed MYC-associated pathways in tumor subtypes, such asimmune response and growth factor signaling; chro-matin, translation, and DNA replication/repair wereconserved pan-cancer. This analysis reveals insightsinto MYC biology and is a reference for biomarkersand therapeutics for cancers with alterations ofMYC or the PMN

Spatial Organization and Molecular Correlation of Tumor-Infiltrating Lymphocytes Using Deep Learning on Pathology Images

Beyond sample curation and basic pathologic characterization, the digitized H&E-stained images of TCGA samples remain underutilized. To highlight this resource, we present mappings of tumorinfiltrating lymphocytes (TILs) based on H&E images from 13 TCGA tumor types. These TIL maps are derived through computational staining using a convolutional neural network trained to classify patches of images. Affinity propagation revealed local spatial structure in TIL patterns and correlation with overall survival. TIL map structural patterns were grouped using standard histopathological parameters. These patterns are enriched in particular T cell subpopulations derived from molecular measures. TIL densities and spatial structure were differentially enriched among tumor types, immune subtypes, and tumor molecular subtypes, implying that spatial infiltrate state could reflect particular tumor cell aberration states. Obtaining spatial lymphocytic patterns linked to the rich genomic characterization of TCGA samples demonstrates one use for the TCGA image archives with insights into the tumor-immune microenvironment

Stable physical activity patterns predominate in a longitudinal study of physical activity among young adults in Canada from before to during the COVID-19 pandemic

We examined change in walking, moderate-to-vigorous physical activity (MVPA) and meeting MVPA guidelines from before to during the COVID-19 pandemic, and identified factors associated with newly meeting and no longer meeting MVPA guidelines during the pandemic. Complete data were available for 614 young adults participating in the ongoing Nicotine Dependence in Teens (NDIT) study pre-pandemically in 2010–12 and 2017–20, and during the pandemic in 2020–21. Change in physical activity was examined in four sub-groups (i. e., stable inactive, newly met MVPA guidelines, no longer met MVPA guidelines, stable active). Factors associated with newly and no longer met MVPA guidelines were identified in multivariable logistic regression. While walking and MVPA changed little from 2010-2 to 2017–20, both declined during the pandemic (median for both = -30 min/ week). 63.3% of participants reported no change in meeting MVPA guidelines during the pandemic, 11.4% newly met MVPA guidelines and 25.2% no longer met MVPA guidelines. Male sex, not university-educated, amotivated to engage in physical activity reported pre-pandemic, and endorsing physical activity as a COVID-19 coping strategy were associated with newly met MVPA guidelines. Male sex, not university-educated, higher problemfocused coping scores and endorsing physical activity as a COVID-19 coping strategy were protective of no longer met MVPA guidelines. Increased understanding of why some participants increased or decreased MVPA during the pandemic is needed to inform physical activity-related policy during pandemics

Social Dancing and Incidence of Falls in Older Adults: A Cluster Randomised Controlled Trial

Background The prevention of falls among older people is a major public health challenge. Exercises that challenge balance are recognized as an efficacious fall prevention strategy. Given that small-scale trials have indicated that diverse dance styles can improve balance and gait of older adults, two of the strongest risk factors for falls in older people, this study aimed to determine whether social dance is effective in i) reducing the number of falls and ii) improving physical and cognitive fall-related risk factors. Methods and Findings A parallel two-arm cluster randomized controlled trial was undertaken in 23 self-care retirement villages (clusters) around Sydney, Australia. Eligible villages had to have an appropriate hall for dancing, house at least 60 residents, and not be currently offering dance as a village activity. Retirement villages were randomised using a computer generated randomisation method, constrained using minimisation. Eligible participants had to be a resident of the village, be able to walk at least 50 m, and agree to undergo physical and cognitive testing without cognitive impairment. Residents of intervention villages (12 clusters) were offered twice weekly one-hour social dancing classes (folk or ballroom dancing) over 12 mo (80 h in total). Programs were standardized across villages and were delivered by eight dance teachers. Participants in the control villages (11 clusters) were advised to continue with their regular activities. Main outcomes: falls during the 12 mo trial and Trail Making Tests. Secondary outcomes: The Physiological Performance Assessment (i.e., postural sway, proprioception, reaction time, leg strength) and the Short Physical Performance Battery; health-related physical and mental quality of life from the Short-Form 12 (SF-12) Survey. Data on falls were obtained from 522 of 530 (98%) randomised participants (mean age 78 y, 85% women) and 424 (80%) attended the 12-mo reassessment, which was lower among folk dance participants (71%) than ballroom dancing (82%) or control participants (82%, p = 0.04). Mean attendance at dance classes was 51%. During the period, 444 falls were recorded; there was no significant difference in fall rates between the control group (0.80 per person-year) and the dance group (1.03 per person-year). Using negative binomial regression with robust standard errors the adjusted Incidence Rate Ratio (IRR) was 1.19 (95% CI: 95% CI = 0.83, 1.71). In exploratory post hoc subgroup analysis, the rate of falls was higher among dance participants with a history of multiple falls (IRR = 2.02, 95% CI: 1.15, 3.54, p = 0.23 for interaction) and with the folk dance intervention (IRR = 1.68, 95% CI: 1.03, 2.73). There were no significant between-group differences in executive function test (TMT-B = 2.8 s, 95% CI: −6.2, 11.8). Intention to treat (ITT) analysis revealed no between-group differences at 12-mo follow-up in the secondary outcome measures, with the exception of postural sway, favouring the control group. Exploratory post hoc analysis by study completers and style indicated that ballroom dancing participants apparently improved their gait speed by 0.07 m/s relative to control participants (95% CI: 0.00, 0.14, p = 0.05). Study limitations included allocation to style based on logistical considerations rather than at random; insufficient power to detect differential impacts of different dance styles and smaller overall effects; variation of measurement conditions across villages; and no assessment of more complex balance tasks, which may be more sensitive to changes brought about by dancing. Conclusions Social dancing did not prevent falls or their associated risk factors among these retirement villages' residents. Modified dance programmes that contain "training elements" to better approximate structured exercise programs, targeted at low and high-risk participants, warrant investigation

Can social dancing prevent falls in older adults? a protocol of the Dance, Aging, Cognition,Economics (DAnCE) fall prevention randomised controlled trial

Background:  Falls are one of the most common health problems among older people and pose a major economic burden on health care systems. Exercise is an accepted stand-alone fall prevention strategy particularly if it is balance training or regular participation in Tai chi. Dance shares the ‘holistic’ approach of practices such as Tai chi. It is a complex sensorimotor rhythmic activity integrating multiple physical, cognitive and social elements. Small-scale randomised controlled trials have indicated that diverse dance styles can improve measures of balance and mobility in older people, but none of these studies has examined the effect of dance on falls or cognition. This study aims to determine whether participation in social dancing: i) reduces the number of falls; and ii) improves cognitive functions associated with fall risk in older people. Methods/design: A single-blind, cluster randomised controlled trial of 12 months duration will be conducted. Approximately 450 participants will be recruited from 24 self-care retirement villages that house at least 60 residents each in Sydney, Australia. Village residents without cognitive impairment and obtain medical clearance will be eligible. After comprehensive baseline measurements including physiological and cognitive tests and self-completed questionnaires, villages will be randomised to intervention sites (ballroom or folk dance) or to a wait-listed control using a computer randomisation method that minimises imbalances between villages based on two baseline fall risk measures. Main outcome measures are falls, prospectively measured, and the Trail Making cognitive function test. Cost-effectiveness and cost-utility analyses will be performed. Discussion: This study offers a novel approach to balance training for older people. As a community-based approach to fall prevention, dance offers older people an opportunity for greater social engagement, thereby making a major contribution to healthy ageing. Providing diversity in exercise programs targeting seniors recognises the heterogeneity of multicultural populations and may further increase the number of taking part in exercise

Global mismatches in aboveground and belowground biodiversity

Human activities are accelerating global biodiversity change and have resulted in severely threatened ecosystem services. A large proportion of terrestrial biodiversity is harbored by soil, but soil biodiversity has been omitted from many global biodiversity assessments and conservation actions, and understanding of global patterns of soil biodiversity remains limited. In particular, the extent to which hotspots and coldspots of aboveground and soil biodiversity overlap is not clear. We examined global patterns of these overlaps by mapping indices of aboveground (mammals, birds, amphibians, vascular plants) and soil (bacteria, fungi, macrofauna) biodiversity that we created using previously published data on species richness. Areas of mismatch between aboveground and soil biodiversity covered 27% of Earth's terrestrial surface. The temperate broadleaf and mixed forests biome had the highest proportion of grid cells with high aboveground biodiversity but low soil biodiversity, whereas the boreal and tundra biomes had intermediate soil biodiversity but low aboveground biodiversity. While more data on soil biodiversity are needed, both to cover geographic gaps and to include additional taxa, our results suggest that protecting aboveground biodiversity may not sufficiently reduce threats to soil biodiversity. Given the functional importance of soil biodiversity and the role of soils in human well-being, soil biodiversity should be considered further in policy agendas and conservation actions by adapting management practices to sustain soil biodiversity and considering soil biodiversity when designing protected areas.Peer reviewe

Prosthesis-patient mismatch after aortic valve replacement in the PARTNER 2 trial and registry

Objectives This study aimed to compare incidence and impact of measured prosthesis-patient mismatch (PPMM) versus predicted PPM (PPMP) after surgical aortic valve replacement (SAVR) and transcatheter aortic valve replacement (TAVR). Background TAVR studies have used measured effective orifice area indexed (EOAi) to body surface area (BSA) to define PPM, but most SAVR series have used predicted EOAi. This difference may contribute to discrepancies in incidence and outcomes of PPM between series. Methods The study analyzed SAVR patients from the PARTNER (Placement of Aortic Transcatheter Valves) 2A trial and TAVR patients from the PARTNER 2 SAPIEN 3 Intermediate Risk registry. PPM was classified as moderate if EOAi ≤0.85 cm2/m2 (≤0.70 if obese: body mass index ≥30 kg/m2) and severe if EOAi ≤0.65 cm2/m2 (≤0.55 if obese). PPMM was determined by the core lab–measured EOAi on 30-day echocardiogram. PPMP was determined by 2 methods: 1) using normal EOA reference values previously reported for each valve model and size (PPMP1; n = 929 SAVR, 1,069 TAVR) indexed to BSA; and 2) using normal reference EOA predicted from aortic annulus size measured by computed tomography (PPMP2; n = 864 TAVR only) indexed to BSA. Primary endpoint was the composite of 5-year all-cause death and rehospitalization. Results The incidence of moderate and severe PPMP was much lower than PPMM in both SAVR (PPMP1: 28.4% and 1.2% vs. PPMM: 31.0% and 23.6%) and TAVR (PPMP1: 21.0% and 0.1% and PPMP2: 17.0% and 0% vs. PPMM: 27.9% and 5.7%). The incidence of severe PPMM and severe PPMP1 was lower in TAVR versus SAVR (P < 0.001). The presence of PPM by any method was associated with higher transprosthetic gradient. Severe PPMP1 was independently associated with events in SAVR after adjustment for sex and Society of Thoracic Surgeons score (hazard ratio: 3.18;95% CI: 1.69-5.96; P < 0.001), whereas no association was observed between PPM by any method and outcomes in TAVR. Conclusions EOAi measured by echocardiography results in a higher incidence of PPM following SAVR or TAVR than PPM based on predicted EOAi. Severe PPMP is rare (<1.5%), but is associated with increased all-cause death and rehospitalization after SAVR, whereas it is absent following TAVR