NEK Family Review and Correlations with Patient Survival Outcomes in Various Cancer Types

The Never in Mitosis Gene A (NIMA)–related kinases (NEKs) are a group of serine/threonine kinases that are involved in a wide array of cellular processes including cell cycle regulation, DNA damage repair response (DDR), apoptosis, and microtubule organization. Recent studies have identified the involvement of NEK family members in various diseases such as autoimmune disorders, malignancies, and developmental defects. Despite the existing literature exemplifying the importance of the NEK family of kinases, this family of protein kinases remains understudied. This report seeks to provide a foundation for investigating the role of different NEKs in malignancies. We do this by evaluating the 11 NEK family kinase gene expression associations with patients’ overall survival (OS) from various cancers using the Kaplan–Meier Online Tool (KMPlotter) to correlate the relationship between mRNA expression of NEK1-11 in various cancers and patient survival. Furthermore, we use the Catalog of Somatic Mutations in Cancer (COSMIC) database to identify NEK family mutations in cancers of different tissues. Overall, the data suggest that the NEK family has varying associations with patient survival in different cancers with tumor-suppressive and tumor-promoting effects being tissue-dependent

HOXA9 Reprograms the Enhancer Landscape to Promote Leukemogenesis

Aberrant expression of HOXA9 is a prominent feature of acute leukemia driven by diverse oncogenes. Here we show that HOXA9 overexpression in myeloid and B progenitor cells leads to significant enhancer reorganizations with prominent emergence of leukemia-specific de novo enhancers. Alterations in the enhancer landscape lead to activation of an ectopic embryonic gene program. We show that HOXA9 functions as a pioneer factor at de novo enhancers and recruits CEBPα and the MLL3/MLL4 complex. Genetic deletion of MLL3/MLL4 blocks histone H3K4 methylation at de novo enhancers and inhibits HOXA9/MEIS1-mediated leukemogenesis in vivo. These results suggest that therapeutic targeting of HOXA9-dependent enhancer reorganization can be an effective therapeutic strategy in acute leukemia with HOXA9 overexpressio

Radical-Initiated Brown Carbon Formation in Sunlit Carbonyl–Amine–Ammonium Sulfate Mixtures and Aqueous Aerosol Particles

Brown carbon (BrC) formed from glyoxal+ammonium sulfate (AS) and methylglyoxal+AS reactions photobleaches quickly, leading to the assumption that BrC formed overnight by Maillard reactions will be rapidly destroyed at sunrise. Here, we tested this assumption by reacting glyoxal, methylglyoxal, glycolaldehyde, or hydroxyacetone in aqueous mixtures with reduced nitrogen species at pH 4–5 in the dark and in sunlight (\u3e350 nm) for at least 10 h. The absorption of fresh carbonyl+AS mixtures decreased when exposed to sunlight, and no BrC formed, as expected from previous work. However, the addition of amines (either methylamine or glycine) allowed BrC to form in sunlight at comparable rates as in the dark. Hydroxyacetone+amine+AS aqueous mixtures generally browned faster in sunlight than in the dark, especially in the presence of HOOH, indicating a radical-initiated BrC formation mechanism is involved. In experiments with airborne aqueous aerosol containing AS, methylamine, and glyoxal or methylglyoxal, browning was further enhanced, especially in sunlight (\u3e300 nm), forming aerosol with optical properties similar to “very weak” atmospheric BrC. Liquid chromatography-electrospray ionization-mass spectrometry (LC-ESI-MS) analysis of aerosol filter extracts indicates that exposure of methylglyoxal+AS aqueous aerosol to methylamine gas, sunlight, and cloud processing increases incorporation of ammonia, methylamine, and photolytic species (e.g., acetyl radicals) into conjugated oligomer products. These results suggest that when amines are present, photolysis of first-generation, “dark reaction” BrC (imines and imidazoles) initiates faster, radical-initiated browning processes that may successfully compete with photobleaching, are enhanced in aqueous aerosol particles relative to bulk liquid solutions, and can produce BrC consistent with atmospheric observations

Kinetics, Products, and Brown Carbon Formation by Aqueous-Phase Reactions of Glycolaldehyde with Atmospheric Amines and Ammonium Sulfate

Glycolaldehyde (GAld) is a C2 water-soluble aldehyde produced during the atmospheric oxidation of isoprene and many other species and is commonly found in cloudwater. Previous work has established that glycolaldehyde evaporates more readily from drying aerosol droplets containing ammonium sulfate (AS) than does glyoxal, methylglyoxal, or hydroxyacetone, which implies that it does not oligomerize as quickly as these other species. Here, we report NMR measurements of glycolaldehyde’s aqueous-phase reactions with AS, methylamine, and glycine. Reaction rate constants are smaller than those of respective glyoxal and methylglyoxal reactions in the pH range of 3–6. In follow-up cloud chamber experiments, deliquesced glycine and AS seed particles were found to take up glycolaldehyde and methylamine and form brown carbon. At very high relative humidity, these changes were more than 2 orders of magnitude faster than predicted by our bulk liquid NMR kinetics measurements, suggesting that reactions involving surface-active species at crowded air–water interfaces may play an important role. The high-resolution liquid chromatography–electrospray ionization–mass spectrometric analysis of filter extracts of unprocessed AS + GAld seed particles identified sugar-like C6 and C12 GAld oligomers, including proposed product 3-deoxyglucosone, with and without modification by reactions with ammonia to diimine and imidazole forms. Chamber exposure to methylamine gas, cloud processing, and simulated sunlight increased the incorporation of both ammonia and methylamine into oligomers. Many C4–C16 imidazole derivatives were detected in an extract of chamber-exposed aerosol along with a predominance of N-derivatized C6 and C12 glycolaldehyde oligomers, suggesting that GAld is capable of forming brown carbon SOA

The United States COVID-19 Forecast Hub dataset

Academic researchers, government agencies, industry groups, and individuals have produced forecasts at an unprecedented scale during the COVID-19 pandemic. To leverage these forecasts, the United States Centers for Disease Control and Prevention (CDC) partnered with an academic research lab at the University of Massachusetts Amherst to create the US COVID-19 Forecast Hub. Launched in April 2020, the Forecast Hub is a dataset with point and probabilistic forecasts of incident cases, incident hospitalizations, incident deaths, and cumulative deaths due to COVID-19 at county, state, and national, levels in the United States. Included forecasts represent a variety of modeling approaches, data sources, and assumptions regarding the spread of COVID-19. The goal of this dataset is to establish a standardized and comparable set of short-term forecasts from modeling teams. These data can be used to develop ensemble models, communicate forecasts to the public, create visualizations, compare models, and inform policies regarding COVID-19 mitigation. These open-source data are available via download from GitHub, through an online API, and through R packages

Evaluation of individual and ensemble probabilistic forecasts of COVID-19 mortality in the United States

Short-term probabilistic forecasts of the trajectory of the COVID-19 pandemic in the United States have served as a visible and important communication channel between the scientific modeling community and both the general public and decision-makers. Forecasting models provide specific, quantitative, and evaluable predictions that inform short-term decisions such as healthcare staffing needs, school closures, and allocation of medical supplies. Starting in April 2020, the US COVID-19 Forecast Hub (https://covid19forecasthub.org/) collected, disseminated, and synthesized tens of millions of specific predictions from more than 90 different academic, industry, and independent research groups. A multimodel ensemble forecast that combined predictions from dozens of groups every week provided the most consistently accurate probabilistic forecasts of incident deaths due to COVID-19 at the state and national level from April 2020 through October 2021. The performance of 27 individual models that submitted complete forecasts of COVID-19 deaths consistently throughout this year showed high variability in forecast skill across time, geospatial units, and forecast horizons. Two-thirds of the models evaluated showed better accuracy than a naïve baseline model. Forecast accuracy degraded as models made predictions further into the future, with probabilistic error at a 20-wk horizon three to five times larger than when predicting at a 1-wk horizon. This project underscores the role that collaboration and active coordination between governmental public-health agencies, academic modeling teams, and industry partners can play in developing modern modeling capabilities to support local, state, and federal response to outbreaks

NEK Family Review and Correlations with Patient Survival Outcomes in Various Cancer Types

The Never in Mitosis Gene A (NIMA)–related kinases (NEKs) are a group of serine/threonine kinases that are involved in a wide array of cellular processes including cell cycle regulation, DNA damage repair response (DDR), apoptosis, and microtubule organization. Recent studies have identified the involvement of NEK family members in various diseases such as autoimmune disorders, malignancies, and developmental defects. Despite the existing literature exemplifying the importance of the NEK family of kinases, this family of protein kinases remains understudied. This report seeks to provide a foundation for investigating the role of different NEKs in malignancies. We do this by evaluating the 11 NEK family kinase gene expression associations with patients’ overall survival (OS) from various cancers using the Kaplan–Meier Online Tool (KMPlotter) to correlate the relationship between mRNA expression of NEK1-11 in various cancers and patient survival. Furthermore, we use the Catalog of Somatic Mutations in Cancer (COSMIC) database to identify NEK family mutations in cancers of different tissues. Overall, the data suggest that the NEK family has varying associations with patient survival in different cancers with tumor-suppressive and tumor-promoting effects being tissue-dependent

MAP3K Family Review and Correlations with Patient Survival Outcomes in Various Cancer Types

The mitogen-activated protein kinase (MAPK) pathways are ubiquitous in cellular signaling and are essential for proper biological functions. Disruptions in this signaling axis can lead to diseases such as the development of cancer. In this review, we discuss members of the MAP3K family and correlate their mRNA expression levels to patient survival outcomes in different cancers. Furthermore, we highlight the importance of studying the MAP3K family due to their important roles in the larger, overall MAPK pathway, relationships with cancer progression, and the understudied status of these kinases

Kinetics, Products, and Brown Carbon Formation by Aqueous-Phase Reactions of Glycolaldehyde with Atmospheric Amines and Ammonium Sulfate

International audienceGlycolaldehyde (GAld) is a C2 water-soluble aldehyde produced during the atmospheric oxidation of isoprene and many other species and is commonly found in cloudwater. Previous work has established that glycolaldehyde evaporates more readily from drying aerosol droplets containing ammonium sulfate (AS) than does glyoxal, methylglyoxal, or hydroxyacetone, which implies that it does not oligomerize as quickly as these other species. Here, we report NMR measurements of glycolaldehyde’s aqueous-phase reactions with AS, methylamine, and glycine. Reaction rate constants are smaller than those of respective glyoxal and methylglyoxal reactions in the pH range of 3–6. In follow-up cloud chamber experiments, deliquesced glycine and AS seed particles were found to take up glycolaldehyde and methylamine and form brown carbon. At very high relative humidity, these changes were more than 2 orders of magnitude faster than predicted by our bulk liquid NMR kinetics measurements, suggesting that reactions involving surface-active species at crowded air–water interfaces may play an important role. The high-resolution liquid chromatography–electrospray ionization–mass spectrometric analysis of filter extracts of unprocessed AS + GAld seed particles identified sugar-like C6 and C12 GAld oligomers, including proposed product 3-deoxyglucosone, with and without modification by reactions with ammonia to diimine and imidazole forms. Chamber exposure to methylamine gas, cloud processing, and simulated sunlight increased the incorporation of both ammonia and methylamine into oligomers. Many C4–C16 imidazole derivatives were detected in an extract of chamber-exposed aerosol along with a predominance of N-derivatized C6 and C12 glycolaldehyde oligomers, suggesting that GAld is capable of forming brown carbon SO

Photochemical Production of Light-absorbing Syringol Secondary Organic Aerosol in Droplets using an Atmospheric Simulation Chamber

International audienceThe photooxidation of syringol, a substituted phenol emitted primarily from lignin pyrolysis during wildfires, was used to explore the formation of secondary brown carbon (BrC) under dry, moist, and cloud-like conditions in aerosol and droplet-phase reactions using the CESAM multiphase atmospheric simulation chamber at the University of Paris-Est LISA in Créteil, France. Optical properties were monitored using a particle-into-liquid (PILS) waveguide with total organic carbon (TOC) analysis system while chemical properties were interrogated using two high-resolution aerosol time-of-flight mass spectrometers (HR-ToF-AMS, Aerodyne). Syringol oxidation produced brown, water-soluble products in deliquesced ammonium sulfate (AS) aerosol and in cloud droplets; the limited secondary organic aerosol (SOA) produced on dry AS seed aerosol did not absorb visible light. Browning occurred in simulated sunlight both with and without OH radicals generated by hydrogen peroxide photolysis, as well as in dark conditions with hydrogen peroxide. Brown products formed under dark conditions were different from those formed under light, while products formed in simulated sunlight were chemically and optically very similar whether or not HOOH was present. The aqueous BrC formed without light featured an absorbance peak at 470 nm consistent with a dimer observed previously in this chemical system and disappeared immediately upon illumination. HR-ESI-MS of chamber filter extracts indicates that most products detected by this technique contain N although HR-AMS spectra indicate only a very small contribution from N-containing fragments. UV/visible absorbance spectra and aerosol mass spectra suggest that the products formed in sunlit, OH-mediated reactions are highly similar to those formed under light without an OH radical source, suggesting that direct syringol photolysis may be capable of initiating similar radical-driven chemistry in the absence of additional oxidants like OH or 3C*. However, the actinic flux of the wavelengths of light necessary for this direct mechanism of syringol SOA formation (λ< 280 nm) is likely too small in the lower atmosphere to be relevant for most biomass burning plumes. Our findings from droplet phase reactions support earlier bulk phase studies suggesting that syringol is capable of forming light absorbing products rapidly in sunlit reactions, especially when liquid water is available