Comprehensive proteogenomic characterization of rare kidney tumors.

Non-clear cell renal cell carcinomas (non-ccRCCs) encompass diverse malignant and benign tumors. Refinement of differential diagnosis biomarkers, markers for early prognosis of aggressive disease, and therapeutic targets to complement immunotherapy are current clinical needs. Multi-omics analyses of 48 non-ccRCCs compared with 103 ccRCCs reveal proteogenomic, phosphorylation, glycosylation, and metabolic aberrations in RCC subtypes. RCCs with high genome instability display overexpression of IGF2BP3 and PYCR1. Integration of single-cell and bulk transcriptome data predicts diverse cell-of-origin and clarifies RCC subtype-specific proteogenomic signatures. Expression of biomarkers MAPRE3, ADGRF5, and GPNMB differentiates renal oncocytoma from chromophobe RCC, and PIGR and SOSTDC1 distinguish papillary RCC from MTSCC. This study expands our knowledge of proteogenomic signatures, biomarkers, and potential therapeutic targets in non-ccRCC.

Differential chromatin accessibility and transcriptional dynamics define breast cancer subtypes and their lineages.

Breast cancer is a heterogeneous disease, and treatment is guided by biomarker profiles representing distinct molecular subtypes. Breast cancer arises from the breast ductal epithelium, and experimental data suggests breast cancer subtypes have different cells of origin within that lineage. The precise cells of origin for each subtype and the transcriptional networks that characterize these tumor-normal lineages are not established. In this work, we applied bulk, single-cell (sc), and single-nucleus (sn) multi-omic techniques as well as spatial transcriptomics and multiplex imaging on 61 samples from 37 breast cancer patients to show characteristic links in gene expression and chromatin accessibility between breast cancer subtypes and their putative cells of origin. We applied the PAM50 subtyping algorithm in tandem with bulk RNA-seq and snRNA-seq to reliably subtype even low-purity tumor samples and confirm promoter accessibility using snATAC. Trajectory analysis of chromatin accessibility and differentially accessible motifs clearly connected progenitor populations with breast cancer subtypes supporting the cell of origin for basal-like and luminal A and B tumors. Regulatory network analysis of transcription factors underscored the importance of BHLHE40 in luminal breast cancer and luminal mature cells, and KLF5 in basal-like tumors and luminal progenitor cells. Furthermore, we identify key genes defining the basal-like ( PRKCA , SOX6 , RGS6 , KCNQ3 ) and luminal A/B ( FAM155A , LRP1B ) lineages, with expression in both precursor and cancer cells and further upregulation in tumors. Exhausted CTLA4-expressing CD8+ T cells were enriched in basal-like breast cancer, suggesting altered means of immune dysfunction among breast cancer subtypes. We used spatial transcriptomics and multiplex imaging to provide spatial detail for key markers of benign and malignant cell types and immune cell colocation. These findings demonstrate analysis of paired transcription and chromatin accessibility at the single cell level is a powerful tool for investigating breast cancer lineage development and highlight transcriptional networks that define basal and luminal breast cancer lineages.

Epigenetic regulation during cancer transitions across 11 tumour types.

Chromatin accessibility is essential in regulating gene expression and cellular identity, and alterations in accessibility have been implicated in driving cancer initiation, progression and metastasis1-4. Although the genetic contributions to oncogenic transitions have been investigated, epigenetic drivers remain less understood. Here we constructed a pan-cancer epigenetic and transcriptomic atlas using single-nucleus chromatin accessibility data (using single-nucleus assay for transposase-accessible chromatin) from 225 samples and matched single-cell or single-nucleus RNA-sequencing expression data from 206 samples. With over 1 million cells from each platform analysed through the enrichment of accessible chromatin regions, transcription factor motifs and regulons, we identified epigenetic drivers associated with cancer transitions. Some epigenetic drivers appeared in multiple cancers (for example, regulatory regions of ABCC1 and VEGFA; GATA6 and FOX-family motifs), whereas others were cancer specific (for example, regulatory regions of FGF19, ASAP2 and EN1, and the PBX3 motif). Among epigenetically altered pathways, TP53, hypoxia and TNF signalling were linked to cancer initiation, whereas oestrogen response, epithelial-mesenchymal transition and apical junction were tied to metastatic transition. Furthermore, we revealed a marked correlation between enhancer accessibility and gene expression and uncovered cooperation between epigenetic and genetic drivers. This atlas provides a foundation for further investigation of epigenetic dynamics in cancer transitions.

Five state factors control progressive stages of freshwater salinization syndrome.

Factors driving freshwater salinization syndrome (FSS) influence the severity of impacts and chances for recovery. We hypothesize that spread of FSS across ecosystems is a function of interactions among five state factors: human activities, geology, flowpaths, climate, and time. (1) Human activities drive pulsed or chronic inputs of salt ions and mobilization of chemical contaminants. (2) Geology drives rates of erosion, weathering, ion exchange, and acidification-alkalinization. (3) Flowpaths drive salinization and contaminant mobilization along hydrologic cycles. (4) Climate drives rising water temperatures, salt stress, and evaporative concentration of ions and saltwater intrusion. (5) Time influences consequences, thresholds, and potentials for ecosystem recovery. We hypothesize that state factors advance FSS in distinct stages, which eventually contribute to failures in systems-level functions (supporting drinking water, crops, biodiversity, infrastructure, etc.). We present future research directions for protecting freshwaters at risk based on five state factors and stages from diagnosis to prognosis to cure.

Exercise tolerance, fatigue, mental health, and employment status at 5 and 12 months following COVID-19 illness in a physically trained population.

Failure to recover following severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) may have a profound impact on individuals who participate in high-intensity/volume exercise as part of their occupation/recreation. The aim of this study was to describe the longitudinal cardiopulmonary exercise function, fatigue, and mental health status of military-trained individuals (up to 12-mo postinfection) who feel recovered, and those with persistent symptoms from two acute disease severity groups (hospitalized and community-managed), compared with an age-, sex-, and job role-matched control. Eighty-eight participants underwent cardiopulmonary functional tests at baseline (5 mo following acute illness) and 12 mo; 25 hospitalized with persistent symptoms (hospitalized-symptomatic), 6 hospitalized and recovered (hospitalized-recovered); 28 community-managed with persistent symptoms (community-symptomatic); 12 community-managed, now recovered (community-recovered), and 17 controls. Cardiopulmonary exercise function and mental health status were comparable between the 5 and 12-mo follow-up. At 12 mo, symptoms of fatigue (48% and 46%) and shortness of breath (SoB; 52% and 43%) remain high in hospitalized-symptomatic and community-symptomatic groups, respectively. At 12 mo, COVID-19-exposed participants had a reduced capacity for work at anaerobic threshold and at peak exercise levels of deconditioning persist, with many individuals struggling to return to strenuous activity. The prevalence considered "fully fit" at 12 mo was lowest in symptomatic groups (hospitalized-symptomatic, 4%; hospitalized-recovered, 50%; community-symptomatic, 18%; community-recovered, 82%; control, 82%) and 49% of COVID-19-exposed participants remained medically nondeployable within the British Armed Forces. For hospitalized and symptomatic individuals, cardiopulmonary exercise profiles are consistent with impaired metabolic efficiency and deconditioning at 12 mo postacute illness. The long-term deployability status of COVID-19-exposed military personnel is uncertain.NEW & NOTEWORTHY Subjective exercise limiting symptoms such as fatigue and shortness of breath reduce but remain prevalent in symptomatic groups. At 12 mo, COVID-19-exposed individuals still have a reduced capacity for work at the anaerobic threshold (which best predicts sustainable intensity), despite oxygen uptake comparable to controls. The prevalence of COVID-19-exposed individuals considered "medically non-deployable" remains high at 47%.

Cardiopulmonary, Functional, Cognitive and Mental Health Outcomes Post-COVID-19, Across the Range of Severity of Acute Illness, in a Physically Active, Working-Age Population.

BACKGROUND: The COVID-19 pandemic has led to significant morbidity and mortality, with the former impacting and limiting individuals requiring high physical fitness, including sportspeople and emergency services. METHODS: Observational cohort study of 4 groups: hospitalised, community illness with on-going symptoms (community-symptomatic), community illness now recovered (community-recovered) and comparison. A total of 113 participants (aged 39 ± 9, 86% male) were recruited: hospitalised (n = 35), community-symptomatic (n = 34), community-recovered (n = 18) and comparison (n = 26), approximately five months following acute illness. Participant outcome measures included cardiopulmonary imaging, submaximal and maximal exercise testing, pulmonary function, cognitive assessment, blood tests and questionnaires on mental health and function. RESULTS: Hospitalised and community-symptomatic groups were older (43 ± 9 and 37 ± 10, P = 0.003), with a higher body mass index (31 ± 4 and 29 ± 4, P < 0.001), and had worse mental health (anxiety, depression and post-traumatic stress), fatigue and quality of life scores. Hospitalised and community-symptomatic participants performed less well on sub-maximal and maximal exercise testing. Hospitalised individuals had impaired ventilatory efficiency (higher VE/V̇CO2 slope, 29.6 ± 5.1, P < 0.001), achieved less work at anaerobic threshold (70 ± 15, P < 0.001) and peak (231 ± 35, P < 0.001), and had a reduced forced vital capacity (4.7 ± 0.9, P = 0.004). Clinically significant abnormal cardiopulmonary imaging findings were present in 6% of hospitalised participants. Community-recovered individuals had no significant differences in outcomes to the comparison group. CONCLUSION: Symptomatically recovered individuals who suffered mild-moderate acute COVID-19 do not differ from an age-, sex- and job-role-matched comparison population five months post-illness. Individuals who were hospitalised or continue to suffer symptoms may require a specific comprehensive assessment prior to return to full physical activity.

Changing characteristics of post-COVID-19 syndrome: Cross-sectional findings from 458 consultations using the Stanford Hall remote rehabilitation assessment tool.

BACKGROUND: In the UK, there have been multiple waves of COVID-19, with a five-tier alert system created to describe the transmission rate and appropriate restrictions. While acute mortality decreased, there continued to be a significant morbidity, with individuals suffering from persistent, life-restricting symptoms for months to years afterwards. A remote rehabilitation tool was created at the Defence Medical Rehabilitation Centre (DMRC) Stanford Hall to assess post-COVID-19 symptoms and their impact on the UK military.This study aims to understand changes in post-COVID-19 syndrome between wave 1 and wave 2, identify interactions between alert level and symptoms and investigate any predictive nature of acute symptoms for postacute symptomology in a young, physically active population. METHODS: Cross-sectional study of 458 consecutive remote rehabilitation assessments performed at DMRC Stanford Hall between 2 April 2020 and 29 July 2021. Consultations were coded, anonymised, and statistical analysis was performed to determine associations between acute and postacute symptoms, and between symptoms, alert levels and waves. RESULTS: 435 assessments were eligible; 174 in wave 1 and 261 in wave 2. Post-COVID-19 syndrome prevalence reduced from 43% to 2% between the waves. Acutely, widespread pain was more prevalent in wave 2 (p<0.001). Postacutely, there was increased anxiety (p=0.10) in wave 1 and increased sleep disturbance (p<0.001), memory/concentration issues (p<0.001) and shortness of breath/cough (p=0.017) in wave 2. Increasing alert level was associated with increased postacute symptom prevalence (p=0.046), with sleep disturbance increasing at higher alert level (p=0.016). Acute symptoms, including fatigue, sleep disturbance and myalgia, were associated with multiple postacute symptoms. CONCLUSIONS: This study reports the overall prevalence and symptom burden in the UK military in the first two waves of COVID-19. By reporting differences in COVID-19 in different waves and alert level, this study highlights the importance of careful assessment and contextual understanding of acute and postacute illnesses for individual management plans.

The effect of medium-term recovery status after COVID-19 illness on cardiopulmonary exercise capacity in a physically active adult population.

A failure to fully recover following coronavirus disease 2019 (COVID-19) may have a profound impact on high-functioning populations ranging from frontline emergency services to professional or amateur/recreational athletes. The aim of the study is to describe the medium-term cardiopulmonary exercise profiles of individuals with "persistent symptoms" and individuals who feel "recovered" after hospitalization or mild-moderate community infection following COVID-19 to an age, sex, and job-role matched control group. A total of 113 participants underwent cardiopulmonary functional tests at a mean of 159 ± 7 days (∼5 mo) following acute illness; 27 hospitalized with persistent symptoms (hospitalized-symptomatic), 8 hospitalized and now recovered (hospitalized-recovered); 34 community managed with persistent symptoms (community-symptomatic); 18 community managed and now recovered (community-recovered); and 26 controls. Hospitalized groups had the least favorable body composition (body mass, body mass index, and waist circumference) compared with controls. Hospitalized-symptomatic and community-symptomatic individuals had a lower oxygen uptake (V̇o2) at peak exercise (hospitalized-symptomatic, 29.9 ± 5.0 mL/kg/min; community-symptomatic, 34.4 ± 7.2 mL/kg/min; vs. control 43.9 ± 3.1 mL/kg/min, both P < 0.001). Hospitalized-symptomatic individuals had a steeper V̇e/V̇co2 slope (lower ventilatory efficiency) (30.5 ± 5.3 vs. 25.5 ± 2.6, P = 0.003) versus. controls. Hospitalized-recovered had a significantly lower oxygen uptake at peak (32.6 ± 6.6 mL/kg/min vs. 43.9 ± 13.1 mL/kg/min, P = 0.015) compared with controls. No significant differences were reported between community-recovered individuals and controls in any cardiopulmonary parameter. In conclusion, medium-term findings suggest that community-recovered individuals did not differ in cardiopulmonary fitness from physically active healthy controls. This suggests their readiness to return to higher levels of physical activity. However, the hospitalized-recovered group and both groups with persistent symptoms had enduring functional limitations, warranting further monitoring, rehabilitation, and recovery.NEW & NOTEWORTHY At 5 mo postinfection, community-treated individuals who feel recovered have comparable cardiopulmonary exercise profiles to the physically trained and active controls, suggesting a readiness to return to higher intensity/volumes of exercise. However, both symptomatic groups and the hospital-recovered group have persistent functional limitations when compared with active controls, supporting the requirement for ongoing monitoring, rehabilitation, and recovery.

Effectiveness of virtual reality-based gait education in enhancing the rehabilitation outcomes of injured military personnel.

INTRODUCTION: Correcting adverse biomechanics is key in rehabilitating musculoskeletal injuries. Verbal instruction remains the primary method for correcting biomechanics and therefore a patient's understanding of these instructions is believed to directly influence treatment outcomes. The aim of this study was to establish the patients' perceptions of virtual reality-based gait education (VR-GEd) and to assess its influence on the standard military rehabilitation outcomes. METHODS: A retrospective analysis using routinely collected data was performed. Twenty patients with lower-limb musculoskeletal injuries undertook a VR-GEd session on the commencement of a 3-week, multidisciplinary, inpatient course of rehabilitation. Patient outcomes were compared with a group of matched controls, completing the same standardised course of inpatient treatment. RESULTS: The VR-GEd group exhibited greater reductions the interference pain had on their mood (p=0.022). Improvements in generalised anxiety (p=0.029) were greater in the VR-GEd group but were not large enough to be clinically meaningful. VR-GEd did not influence functional outcomes. Patients rated the sessions highly in terms of enjoyment and perceived value. Patient feedback highlighted that they understood their injury better and felt the session could positively influence their recovery. CONCLUSION: VR-GEd was proven to be an enjoyable and valued means of educating military inpatients about their injury mechanics. This study found no contraindications for the inclusion of VR-GEd in current rehabilitation programmes. However, current evidence suggests a single VR-GEd session cannot act as a replacement for biofeedback interventions, due to the lack of enhanced improvement across rehabilitation outcomes.

Dysautonomia following COVID-19 is not associated with subjective limitations or symptoms but is associated with objective functional limitations.

BACKGROUND: Individuals who contract coronavirus disease 2019 (COVID-19) can suffer with persistent and debilitating symptoms long after the initial acute illness. Heart rate (HR) profiles determined during cardiopulmonary exercise testing (CPET) and delivered as part of a post-COVID recovery service may provide insight into the presence and impact of dysautonomia on functional ability. OBJECTIVE: Using an active, working-age, post-COVID-19 population, the purpose of this study was to (1) determine and characterize any association between subjective symptoms and dysautonomia; and (2) identify objective exercise capacity differences between patients classified "with" and those "without" dysautonomia. METHODS: Patients referred to a post-COVID-19 service underwent comprehensive clinical assessment, including self-reported symptoms, CPET, and secondary care investigations when indicated. Resting HR >75 bpm, HR increase with exercise <89 bpm, and HR recovery <25 bpm 1 minute after exercise were used to define dysautonomia. Anonymized data were analyzed and associations with symptoms, and CPET outcomes were determined. RESULTS: Fifty-one of the 205 patients (25%) reviewed as part of this service evaluation had dysautonomia. There were no associations between symptoms or perceived functional limitation and dysautonomia (P >.05). Patients with dysautonomia demonstrated objective functional limitations with significantly reduced work rate (219 ± 37 W vs 253 ± 52 W; P <.001) and peak oxygen consumption (V̇o2: 30.6 ± 5.5 mL/kg/min vs 35.8 ± 7.6 mL/kg/min; P <.001); and a steeper (less efficient) V̇e/V̇co2 slope (29.9 ± 4.9 vs 27.7 ± 4.7; P = .005). CONCLUSION: Dysautonomia is associated with objective functional limitations but is not associated with subjective symptoms or limitation.

Predicting surgical outcomes for chronic exertional compartment syndrome using a machine learning framework with embedded trust by interrogation strategies.

Chronic exertional compartment syndrome (CECS) is a condition occurring most frequently in the lower limbs and often requires corrective surgery to alleviate symptoms. Amongst military personnel, the success rates of this surgery can be as low as 20%, presenting a challenge in determining whether surgery is worthwhile. In this study, the data of 132 fasciotomies for CECS was analysed and using combinatorial feature selection methods, coupled with input from clinicians, identified a set of key clinical features contributing to the occupational outcomes of surgery. Features were utilised to develop a machine learning model for predicting return-to-work outcomes 12-months post-surgery. An AUC of 0.85 ± 0.08 was achieved using a linear-SVM, trained using 6 features (height, mean arterial pressure, pre-surgical score on the exercise-induced leg pain questionnaire, time from initial presentation to surgery, and whether a patient had received a prior surgery for CECS). To facilitate trust and transparency, interrogation strategies were used to identify reasons why certain patients were misclassified, using instance hardness measures. Model interrogation revealed that patient difficulty was associated with an overlap in the clinical characteristics of surgical outcomes, which was best handled by XGBoost and SVM-based models. The methodology was compiled into a machine learning framework, termed AITIA, which can be applied to other clinical problems. AITIA extends the typical machine learning pipeline, integrating the proposed interrogation strategy, allowing to user to reason and decide whether to trust the developed model based on the sensibility of its decision-making.

Biomechanical differences between military patients with patellar tendinopathy and asymptomatic controls during single-leg squatting and gait - A statistical parametric mapping study.

BACKGROUND: Prior identification of biomechanical differences between patients with patellar tendinopathy and healthy controls has utilised time-discrete analysis which is susceptible to type I error when multiple comparisons are uncorrected. We employ statistical parametric mapping to minimise the risk of such error, enabling more appropriate clinical decision-making. METHODS: Lower-limb biomechanics of 21 patients with patellar tendinopathy and 22 controls were captured during walking and three types of squats. A statistical parametric mapping two-sample t-test was used to identify kinematic and kinetic differences between groups for each joint. Paired t-tests were used to compare pain before and after tasks, in patients with patellar tendinopathy. FINDINGS: During walking, cases demonstrated reduced knee joint power during initial contact and hip joint power during terminal stance. In squatting, cases demonstrated increased knee abduction angles at various time points of the small knee bend and single-leg squat. Cases demonstrated reduced knee internal rotation moment during the deepest portion of the single-leg squat and single-leg decline squat. INTERPRETATION: Gait appears unaffected by patellar tendinopathy, likely due to low task difficulty. Elevated knee abductions angles during squatting were confirmed as a key difference in patients with patellar tendinopathy. Reduced knee internal rotation moments in patients were attributed to a potential reduction in hip external rotator strength and possible pain avoidance strategy; however further evidence is required to substantiate these claims. Findings provide a clear rationale for rehabilitation programs to focus on knee stabilisation and strengthening of the muscles surrounding the hip.

Evaluation of a multi-sensor Leap Motion setup for biomechanical motion capture of the hand.

The Leap Motion controller (LMC) offers a low-cost means of markerless hand tracking, however, its utility is limited by a small field of view and reliance on appropriate sensor positioning. A recent update from Leap Motion has enabled the use of a multiple LMC device on a single computer, allowing the tracking of hands from multiple orientations, potentially overcoming the aforementioned limitations. This study describes a method of implementing a multi-LMC setup and evaluates its effect on the validity and reliability of the derived kinematics. This study implemented a Kabsch algorithm and Kalman filter to re-orientate and fuse the trajectories captured by three LMC at different orientations. Reliability was assessed by comparing between-day differences in maximum joint angles (ΔMJA) and a calculated coefficient of multiple correlations (CMC). Validity was assessed by comparing the LMC to the gold standard, a Vicon markered motion capture (MMC) system, and calculating the ΔMJA and applying the linear fit method. The proposed method was evaluated by comparing the reliability and validity of the single-LMC setups to the multi-LMC setup. A multi-LMC setup proved successful in improving the reliability and validity of kinematic data, most notably where reliability and validity were poor and variation was high between the single-LMC setups. Findings suggest that through implementing the proposed method, limitations associated with single-LMC setups, notably its reliance on optimal sensor positioning, can be overcome.

Effects of sample pretreatment and particle size on the determination of nitrogen in soil by portable LIBS and potential use on robotic-borne remote Martian and agricultural soil analysis systems.

Field determination of nitrogen in soil is of interest for both terrestrial and Martian applications. Improved management of soil nitrogen levels on Earth could benefit global food production, whilst the determination of soil nitrogen on Mars is required to assess the planet's future habitability. In this study, a mobile laser induced breakdown spectroscopy (LIBS) system with a 1064 nm Nd:YAG laser delivering 25 mJ per pulse was used to assess the effects of sample pretreatment on the measurement of nitrogen in soil. Although pelletisation was preferred, simply milling the sample to <100 mm particle size - which may be more feasible on a remote rover-based analytical platform - improved the spectra obtained. Ablation craters formed in targets prepared from different particle size fractions of the same commercially-available topsoil showed a clear trend in morphology, with smaller particles yielding more uniform craters with fewer fractures. The LIBS emission intensity at 746.83 nm followed a similar trend to results obtained for total nitrogen content in the soil particle size fractions by microanalysis (Perkin Elmer CHN Elemental Analyser) and was well-correlated (R 2 = 0.94) with soil nitrate determined by ion chromatography (Dionex DX-100). Although correlations were less good when analysing field soil samples collected from central Scotland (R 2 = 0.82 for comparison between LIBS and microanalysis) the study nevertheless demonstrates the potential of portable LIBS for measurement of soil nitrogen content.