Integrative analysis of extracellular and intracellular bladder cancer cell line proteome with transcriptome: improving coverage and validity of -omics findings

Characterization of disease-associated proteins improves our understanding of disease pathophysiology. Obtaining a comprehensive coverage of the proteome is challenging, mainly due to limited statistical power and an inability to verify hundreds of putative biomarkers. In an effort to address these issues, we investigated the value of parallel analysis of compartment-specific proteomes with an assessment of findings by cross-strategy and cross-omics (proteomics-transcriptomics) agreement. The validity of the individual datasets and of a “verified” dataset based on crossstrategy/omics agreement was defined following their comparison with published literature. The proteomic analysis of the cell extract, Endoplasmic Reticulum/Golgi apparatus and conditioned medium of T24 vs. its metastatic subclone T24M bladder cancer cells allowed the identification of 253, 217 and 256 significant changes, respectively. Integration of these findings with transcriptomics resulted in 253 “verified” proteins based on the agreement of at least 2 strategies. This approach revealed findings of higher validity, as supported by a higher level of agreement in the literature data than those of individual datasets. As an example, the coverage and shortlisting of targets in the IL-8 signalling pathway are discussed. Collectively, an integrative analysis appears a safer way to evaluate -omics datasets and ultimately generate models from valid observations

A review of the ecology, palaeontology and distribution of atlantid heteropods (Caenogastropoda: Pterotracheoidea: Atlantidae)

Fewer than 1% of marine gastropod species live a holoplanktic life. Of these, the shelled heteropods of the family Atlantidae are among the most poorly understood. The atlantids potentially make up an important part of the ocean zooplankton, composing up to 69% of shelled holoplanktic gastropods in the Late Pleistocene to Recent fossil record. They are also likely to be at high risk from current and future global changes, including anthropogenic ocean acidification. However, due to their small size (<12 mm), difficulty of sampling and complicated morphology, we still lack key information about atlantid taxonomy and ecology. This makes it difficult to understand how important they are in the ocean foodweb and how they will be affected by environmental change. Although many studies have been carried out on the atlantids, these have generally been broad and unconnected. Here, we draw together this previous research, summarizing what is currently known about atlantid taxonomy, palaeontology, ecology and biogeography, and aiming to provide a foundation for future research on this group. The data indicate complex behaviours involving seasonal and vertical migration, and demonstrate extended geographical ranges, with implications for understanding the role of atlantids in the ocean foodweb and their sensitivity to environmental changes. This review highlights the urgent need for further taxonomic research on the atlantids, including molecular analysis, and for improved sampling techniques

Tracking Infant Development With a Smartphone:A Practical Guide to the Experience Sampling Method

The COVID-19 pandemic has forced developmental researchers to rethink their traditional research practices. The growing need to study infant development at a distance has shifted our research paradigm to online and digital monitoring of infants and families, using electronic devices, such as smartphones. In this practical guide, we introduce the Experience Sampling Method (ESM) – a research method to collect data, in the moment, on multiple occasions over time – for examining infant development at a distance. ESM is highly suited for assessing dynamic processes of infant development and family dynamics, such as parent-infant interactions and parenting practices. It can also be used to track highly fluctuating family dynamics (e.g., infant and parental mood or behavior) and routines (e.g., activity levels and feeding practices). The aim of the current paper was to provide an overview by explaining what ESM is and for what types of research ESM is best suited. Next, we provide a brief step-by-step guide on how to start and run an ESM study, including preregistration, development of a questionnaire, using wearables and other hardware, planning and design considerations, and examples of possible analysis techniques. Finally, we discuss common pitfalls of ESM research and how to avoid them

Integrative analysis of extracellular and intracellular bladder cancer cell line proteome with transcriptome: improving coverage and validity of –omics findings

Characterization of disease-associated proteins improves our understanding of disease pathophysiology. Obtaining a comprehensive coverage of the proteome is challenging, mainly due to limited statistical power and an inability to verify hundreds of putative biomarkers. In an effort to address these issues, we investigated the value of parallel analysis of compartment-specific proteomes with an assessment of findings by cross-strategy and cross-omics (proteomics-transcriptomics) agreement. The validity of the individual datasets and of a “verified” dataset based on cross-strategy/omics agreement was defined following their comparison with published literature. The proteomic analysis of the cell extract, Endoplasmic Reticulum/Golgi apparatus and conditioned medium of T24 vs. its metastatic subclone T24M bladder cancer cells allowed the identification of 253, 217 and 256 significant changes, respectively. Integration of these findings with transcriptomics resulted in 253 “verified” proteins based on the agreement of at least 2 strategies. This approach revealed findings of higher validity, as supported by a higher level of agreement in the literature data than those of individual datasets. As an example, the coverage and shortlisting of targets in the IL-8 signalling pathway are discussed. Collectively, an integrative analysis appears a safer way to evaluate -omics datasets and ultimately generate models from valid observations

A junctional PACSIN2/EHD4/MICAL-L1 complex coordinates VE-cadherin trafficking for endothelial migration and angiogenesis

Angiogenic sprouting relies on collective migration and coordinated rearrangements of endothelial leader and follower cells. VE-cadherin-based adherens junctions have emerged as key cell-cell contacts that transmit forces between cells and trigger signals during collective cell migration in angiogenesis. However, the underlying molecular mechanisms that govern these processes and their functional importance for vascular development still remain unknown. We previously showed that the F-BAR protein PACSIN2 is recruited to tensile asymmetric adherens junctions between leader and follower cells. Here we report that PACSIN2 mediates the formation of endothelial sprouts during angiogenesis by coordinating collective migration. We show that PACSIN2 recruits the trafficking regulators EHD4 and MICAL-L1 to the rear end of asymmetric adherens junctions to form a recycling endosome-like tubular structure. The junctional PACSIN2/EHD4/MICAL-L1 complex controls local VE-cadherin trafficking and thereby coordinates polarized endothelial migration and angiogenesis. Our findings reveal a molecular event at force-dependent asymmetric adherens junctions that occurs during the tug-of-war between endothelial leader and follower cells, and allows for junction-based guidance during collective migration in angiogenesis

Health economic evaluation of a nurse-assisted online eye screening in home healthcare to reduce avoidable vision impairment (iScreen):study protocol for a cluster randomized controlled trial

Background: Among older people undiagnosed and untreated vision impairment and blindness are common. The leading causes are uncorrected refractive errors and cataracts. Vision problems are associated with a lower quality of life, several health problems, and a higher chance of falling accidents and fractures. To eliminate avoidable vision impairment and blindness, targeted eye screening programs are recommended. Older patients, receiving home healthcare, have not yet been considered as a population at risk who could benefit from eye screening. Methods: A cluster-randomized controlled trial will be conducted to investigate the cost-effectiveness and cost-utility of online nurse-assisted eye screening in home healthcare, compared to care as usual, in reducing avoidable vision impairment. A healthcare and societal perspective will be used. The study will be performed in collaboration with several home healthcare organizations in the Netherlands. The online eye screening consists of near and distance visual acuity, followed by an Amsler grading test. Measurements in both groups will take place at baseline and after 6 and 12 months of follow-up. A total of 240 participants will be recruited. Older men and women (65 +), who receive home-based nursing and are cognitively able to participate, will be included. The primary outcome will be the change of two lines or more on the Colenbrander-1 M visual acuity chart between baseline and 12-month follow-up. Discussion: An eye screening for populations at risk contributes to the detection of undiagnosed and untreated vision impairment. This may reduce the health-related consequences of vision loss and the high economic burden associated with vision impairment. Trial registration: ClinicalTrials.gov NCT06058637. Registered on 27 September 2023.</p

A profusion of upstream open reading frame mechanisms in polyamine-responsive translational regulation

In many eukaryotic mRNAs one or more short ‘upstream’ open reading frames, uORFs, precede the initiator of the main coding sequence. Upstream ORFs are functionally diverse as illustrated by their variety of features in polyamine pathway biosynthetic mRNAs. Their propensity to act as sensors for regulatory circuits and to amplify the signals likely explains their occurrence in most polyamine pathway mRNAs. The uORF-mediated polyamine responsive autoregulatory circuits found in polyamine pathway mRNAs exemplify the translationally regulated dynamic interface between components of the proteome and metabolism

The Genetic Risk for COVID-19 Severity Is Associated With Defective Immune Responses

Recent genome-wide association studies (GWASs) of COVID-19 patients of European ancestry have identified genetic loci significantly associated with disease severity. Here, we employed the detailed clinical, immunological and multi-omics dataset of the Human Functional Genomics Project (HFGP) to explore the physiological significance of the host genetic variants that influence susceptibility to severe COVID-19. A genomics investigation intersected with functional characterization of individuals with high genetic risk for severe COVID-19 susceptibility identified several major patterns: i. a large impact of genetically determined innate immune responses in COVID-19, with ii. increased susceptibility for severe disease in individuals with defective cytokine production; iii. genetic susceptibility related to ABO blood groups is probably mediated through the von Willebrand factor (VWF) and endothelial dysfunction. We further validated these identified associations at transcript and protein levels by using independent disease cohorts. These insights allow a physiological understanding of genetic susceptibility to severe COVID-19, and indicate pathways that could be targeted for prevention and therapy

Safety and Outcome of High-Flow Nasal Oxygen Therapy Outside ICU Setting in Hypoxemic Patients With COVID-19∗

OBJECTIVE: High-flow nasal oxygen (HFNO) therapy is frequently applied outside ICU setting in hypoxemic patients with COVID-19. However, safety concerns limit more widespread use. We aimed to assess the safety and clinical outcomes of initiation of HFNO therapy in COVID-19 on non-ICU wards. DESIGN: Prospective observational multicenter pragmatic study. SETTING: Respiratory wards and ICUs of 10 hospitals in The Netherlands. PATIENTS: Adult patients treated with HFNO for COVID-19-associated hypoxemia between December 2020 and July 2021 were included. Patients with treatment limitations were excluded from this analysis. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: Outcomes included intubation and mortality rate, duration of hospital and ICU stay, severity of respiratory failure, and complications. Using propensity-matched analysis, we compared patients who initiated HFNO on the wards versus those in ICU. Six hundred eight patients were included, of whom 379 started HFNO on the ward and 229 in the ICU. The intubation rate in the matched cohort (n = 214 patients) was 53% and 60% in ward and ICU starters, respectively (p = 0.41). Mortality rates were comparable between groups (28-d [8% vs 13%], p = 0.28). ICU-free days were significantly higher in ward starters (21 vs 17 d, p &lt; 0.001). No patient died before endotracheal intubation, and the severity of respiratory failure surrounding invasive ventilation and clinical outcomes did not differ between intubated ward and ICU starters (respiratory rate-oxygenation index 3.20 vs 3.38; Pao2:Fio2ratio 65 vs 64 mm Hg; prone positioning after intubation 81 vs 78%; mortality rate 17 vs 25% and ventilator-free days at 28 d 15 vs 13 d, all p values &gt; 0.05). CONCLUSIONS: In this large cohort of hypoxemic patients with COVID-19, initiation of HFNO outside the ICU was safe, and clinical outcomes were similar to initiation in the ICU. Furthermore, the initiation of HFNO on wards saved time in ICU without excess mortality or complicated course. Our results indicate that HFNO initiation outside ICU should be further explored in other hypoxemic diseases and clinical settings aiming to preserve ICU capacity and healthcare costs.</p