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Cancer Research Mar 2024Epithelial-mesenchymal transition (EMT) is a fundamental cellular process frequently hijacked by cancer cells to promote tumor progression, especially metastasis. EMT is...
UNLABELLED
Epithelial-mesenchymal transition (EMT) is a fundamental cellular process frequently hijacked by cancer cells to promote tumor progression, especially metastasis. EMT is orchestrated by a complex molecular network acting at different layers of gene regulation. In addition to transcriptional regulation, posttranscriptional mechanisms may also play a role in EMT. Here, we performed a pooled CRISPR screen analyzing the influence of 1,547 RNA-binding proteins on cell motility in colon cancer cells and identified multiple core components of P-bodies (PB) as negative modulators of cancer cell migration. Further experiments demonstrated that PB depletion by silencing DDX6 or EDC4 could activate hallmarks of EMT thereby enhancing cell migration in vitro as well as metastasis formation in vivo. Integrative multiomics analysis revealed that PBs could repress the translation of the EMT driver gene HMGA2, which contributed to PB-meditated regulation of EMT. This mechanism is conserved in other cancer types. Furthermore, endoplasmic reticulum stress was an intrinsic signal that induced PB disassembly and translational derepression of HMGA2. Taken together, this study has identified a function of PBs in the regulation of EMT in cancer.
SIGNIFICANCE
Systematic investigation of the influence of posttranscriptional regulation on cancer cell motility established a connection between P-body-mediated translational control and EMT, which could be therapeutically exploited to attenuate metastasis formation.
Topics: Humans; Processing Bodies; Clustered Regularly Interspaced Short Palindromic Repeats; Early Detection of Cancer; Transcription Factors; Epithelial-Mesenchymal Transition; Colonic Neoplasms; Gene Expression Regulation, Neoplastic; Cell Movement; Cell Line, Tumor; Proteins
PubMed: 38190710
DOI: 10.1158/0008-5472.CAN-23-1693 -
International Journal of Biological... Feb 2024DEAD-box helicases are global regulators of liquid-liquid phase separation (LLPS), a process that assembles membraneless organelles inside cells. An outstanding member... (Review)
Review
DEAD-box helicases are global regulators of liquid-liquid phase separation (LLPS), a process that assembles membraneless organelles inside cells. An outstanding member of the DEAD-box family is DDX3X, a multi-functional protein that plays critical roles in RNA metabolism, including RNA transcription, splicing, nucleocytoplasmic export, and translation. The diverse functions of DDX3X result from its ability to bind and remodel RNA in an ATP-dependent manner. This capacity enables the protein to act as an RNA chaperone and an RNA helicase, regulating ribonucleoprotein complex assembly. DDX3X and its orthologs from mouse, yeast (Ded1), and C. elegans (LAF-1) can undergo LLPS, driving the formation of neuronal granules, stress granules, processing bodies or P-granules. DDX3X has been related to several human conditions, including neurodevelopmental disorders, such as intellectual disability and autism spectrum disorder. Although the research into the pathogenesis of aberrant biomolecular condensation in neurodegenerative diseases is increasing rapidly, the role of LLPS in neurodevelopmental disorders is underexplored. This review summarizes current findings relevant for DDX3X phase separation in neurodevelopment and examines how disturbances in the LLPS process can be related to neurodevelopmental disorders.
Topics: Animals; Humans; Mice; Autism Spectrum Disorder; Caenorhabditis elegans; DEAD-box RNA Helicases; Neurodevelopmental Disorders; RNA; Saccharomyces cerevisiae
PubMed: 38218270
DOI: 10.1016/j.ijbiomac.2024.129330 -
Medical Education Oct 2023Increasing recognition of autism is reflected in the growing awareness of autistic health care providers. Regulatory bodies including the UK General Medical Council and...
BACKGROUND
Increasing recognition of autism is reflected in the growing awareness of autistic health care providers. Regulatory bodies including the UK General Medical Council and the UK Medical Schools Council have published guidance fostering inclusion. Whilst many autistic doctors and students are thriving, many may not disclose their diagnosis unless difficulties arise, which perpetuates stereotypes. No studies have explored the experiences of autistic medical students. We aimed to do this.
METHODS
This was an interpretive phenomenological study. Autistic medical students were recruited using Facebook announcements. Participants underwent audio-recorded, loosely structured interviews. Recordings were transcribed verbatim and underwent an interpretive phenomenological analysis.
RESULTS
Five participated from five different UK medical schools. Constructed themes included: Autistic profiles and stereotypes-'I'm a lot better with patients than I am with my peers, with staff, which is hard for a lot of people to understand'; sensory processing and the learning environment-'noises really hurt my ears … It actually hurts'; me, myself and masking-'so, medicine's hard. But I'm also studying myself and I'm figuring myself out and that degree is harder'; the social world-'I always feel like I'm watching my back'; and navigating the system-'[they say] "but you're going to be a doctor one day, so you need to get used to it"'.
CONCLUSION
Participants longed for understanding and support from their medical schools. They reported experiences of isolation, bullying and anxiety. Most felt themselves to be victims of the system, whereby they were expected to adapt themselves in order to appear non-autistic. When participants reported not coping due to being autistic, most were advised to 'take time out'. None were offered personalised adjustments to their learning environment. All reported strengths associated with being autistic. This supports the assertion that autistic people can be safe, effective and skilled doctors.
Topics: Humans; Autistic Disorder; Students, Medical; Emotions; Anxiety; Learning
PubMed: 37264701
DOI: 10.1111/medu.15119 -
Ageing Research Reviews Sep 2023This systematic review aimed to evaluate previous studies which used near-infrared spectroscopy (NIRS) in dementia given its suitability as a diagnostic and... (Review)
Review
This systematic review aimed to evaluate previous studies which used near-infrared spectroscopy (NIRS) in dementia given its suitability as a diagnostic and investigative tool in this population. From 800 identified records which used NIRS in dementia and prodromal stages, 88 studies were evaluated which employed a range of tasks testing memory (29), word retrieval (24), motor (8) and visuo-spatial function (4), and which explored the resting state (32). Across these domains, dementia exhibited blunted haemodynamic responses, often localised to frontal regions of interest, and a lack of task-appropriate frontal lateralisation. Prodromal stages, such as mild cognitive impairment, revealed mixed results. Reduced cognitive performance accompanied by either diminished functional responses or hyperactivity was identified, the latter suggesting a compensatory response not present at the dementia stage. Despite clear evidence of alterations in brain oxygenation in dementia and prodromal stages, a consensus as to the nature of these changes is difficult to reach. This is likely partially due to the lack of standardisation in optical techniques and processing methods for the application of NIRS to dementia. Further studies are required exploring more naturalistic settings and a wider range of dementia subtypes.
Topics: Humans; Alzheimer Disease; Spectroscopy, Near-Infrared; Prodromal Symptoms; Brain; Cognitive Dysfunction
PubMed: 37356550
DOI: 10.1016/j.arr.2023.101992 -
Movement Disorders : Official Journal... May 2024Diffusion-weighted magnetic resonance imaging (dMRI) examines tissue microstructure integrity in vivo. Prior dementia with Lewy bodies (DLB) diffusion tensor imaging...
BACKGROUND
Diffusion-weighted magnetic resonance imaging (dMRI) examines tissue microstructure integrity in vivo. Prior dementia with Lewy bodies (DLB) diffusion tensor imaging studies yielded mixed results.
OBJECTIVE
We employed free-water (FW) imaging to assess DLB progression and correlate with clinical decline in DLB.
METHODS
Baseline and follow-up MRIs were obtained at 12 and/or 24 months for 27 individuals with DLB or mild cognitive impairment with Lewy bodies (MCI-LB). FW was analyzed using the Mayo Clinic Adult Lifespan Template. Primary outcomes were FW differences between baseline and 12 or 24 months. To compare FW change longitudinally, we included 20 cognitively unimpaired individuals from the Alzheimer's Disease Neuroimaging Initiative.
RESULTS
We followed 23 participants to 12 months and 16 participants to 24 months. Both groups had worsening in Montreal Cognitive Assessment (MoCA) and Movement Disorder Society-Unified Parkinson's Disease Rating Scale (MDS-UPDRS) scores. We found significant FW increases at both time points compared to baseline in the insula, amygdala, posterior cingulum, parahippocampal, entorhinal, supramarginal, fusiform, retrosplenial, and Rolandic operculum regions. At 24 months, we found more widespread microstructural changes in regions implicated in visuospatial processing, motor, and cholinergic functions. Between-group analyses (DLB vs. controls) confirmed significant FW changes over 24 months in most of these regions. FW changes were associated with longitudinal worsening of MDS-UPDRS and MoCA scores.
CONCLUSIONS
FW increased in gray and white matter regions in DLB, likely due to neurodegenerative pathology associated with disease progression. FW change was associated with clinical decline. The findings support dMRI as a promising tool to track disease progression in DLB. © 2024 International Parkinson and Movement Disorder Society.
Topics: Humans; Lewy Body Disease; Female; Male; Aged; Aged, 80 and over; Longitudinal Studies; Cognitive Dysfunction; Disease Progression; Diffusion Magnetic Resonance Imaging; Brain; Water; Diffusion Tensor Imaging; Middle Aged; White Matter
PubMed: 38477399
DOI: 10.1002/mds.29763 -
PloS One 2023The N190 is a body-sensitive ERP component that responds to images of human bodies in different poses. In natural settings, bodies vary in posture and appear within...
The N190 is a body-sensitive ERP component that responds to images of human bodies in different poses. In natural settings, bodies vary in posture and appear within complex, cluttered environments, frequently with other people. In many studies, however, such variability is absent. How does the N190 response change when observers see images that incorporate these sources of variability? In two experiments (N = 16 each), we varied the natural appearance of upright and inverted bodies to examine how the N190 amplitude, latency, and the Body-Inversion Effect (BIE) were affected by natural variability. In Experiment 1, we varied the number of people present in upright and inverted naturalistic scenes such that only one body, a subitizable number of bodies, or a "crowd" was present. In Experiment 2, we varied the natural body appearance by presenting bodies either as silhouettes or with photographic detail. Further, we varied the natural background appearance by either removing it or presenting individual bodies within a rich environment. Using component-based analyses of the N190, we found that the number of bodies in a scene reduced the N190 amplitude, but didn't affect the BIE (Experiment 1). Naturalistic body and background appearance (Experiment 2) also affected the N190, such that component amplitude was dramatically reduced by naturalistic appearance. To complement this analysis, we examined the contribution of spatiotemporal features (i.e., electrode × time point amplitude) via SVM decoding. This technique allows us to examine which timepoints across the entire waveform contribute the most to successful decoding of body orientation in each condition. This analysis revealed that later timepoints (after 300ms) contribute most to successful orientation decoding. These results demonstrate that natural appearance variability affects body processing at the N190 and that later ERP components may make important contributions to body processing in natural scenes.
Topics: Humans; Posture; Photic Stimulation; Pattern Recognition, Visual
PubMed: 37883414
DOI: 10.1371/journal.pone.0283673 -
Journal of Chromatography. B,... Nov 2023An important area within clinical research is in vivo metabolism of ketone bodies (β-hydroxybutyrate and acetoacetate) and in connection metabolites that may affect...
LC-MS/MS method for quantitative profiling of ketone bodies, α-keto acids, lactate, pyruvate and their stable isotopically labelled tracers in human plasma: An analytical panel for clinical metabolic kinetics and interactions.
An important area within clinical research is in vivo metabolism of ketone bodies (β-hydroxybutyrate and acetoacetate) and in connection metabolites that may affect their production and/or cellular transport such as the keto-acids from the branched-chain amino acids, lactate and pyruvate. To determine in vivo metabolite turnover, availability of accurate and sensitive methods for analyzing the plasma concentrations of these metabolites and their stable isotopically labeled enrichments is mandatory. Therefore, the present study describes a high-performance liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for simultaneous analysis of ketone bodies, α-keto acids, lactate, pyruvate, and their tracer enrichments in humans using 2 different derivatization techniques with 4-bromo-N-methylbenzylamine and O-benzylhydroxylamine as derivatization reagents, and 1-ethyl-3-dimethylaminopropyl carbodiimide as coupling compound followed by a single LC-MS/MS run. The method was validated for matrix effects, linearity, accuracy, precision, recovery, stability, and enrichment (ratio) analysis of a stable isotopically labelled analytes (tracers) continuously infused in humans divided by the unlabeled endogenous analyte (tracee) that makes it possible to quantify the analyte in vivo synthesis and degradation rates. The applied parallel derivatization procedure yielded good sensitivity for all analytes of interest and their tracers. Despite the double derivatization method, mixing the ethyl acetate portions at the final stage made it possible to simultaneously analyze all compounds in a single LC-MS/MS run. Moreover, the liquid chromatography method was optimized to robustly quantify the keto acids derived from leucine (α-keto-isocaproic acid) and isoleucine (α-keto-β-methylvaleric acid), the compounds with similar chemical structure and identical molecular weights. The presented method is designed and validated for human plasma. However, care should be taken in blood sampling and processing procedures as well as quick freezing and storage at -80 °C due to the instability of especially acetoacetate.
Topics: Humans; Lactic Acid; Pyruvic Acid; Acetoacetates; Ketone Bodies; Chromatography, Liquid; Tandem Mass Spectrometry; Keto Acids
PubMed: 37925904
DOI: 10.1016/j.jchromb.2023.123906 -
Diagnostics (Basel, Switzerland) Jan 2024Salivary DNA is widely used for genetic analyses because of its easy collection. However, its extracellular fraction in particular, similar to the extracellular DNA...
Salivary DNA is widely used for genetic analyses because of its easy collection. However, its extracellular fraction in particular, similar to the extracellular DNA (ecDNA) in plasma, could be a promising biomarker for oral or systemic diseases. In contrast to genetics, the quantity of salivary ecDNA is of importance and can be affected by the pre-analytical processing of samples, but the details are not known. The aim of our study was to analyze the effects of centrifugation and freezing of saliva on the concentration of ecDNA in saliva. Fifteen healthy volunteers, free of any known systemic or oral diseases, were asked to collect unstimulated saliva samples. Aliquots were centrifuged at 1600× and frozen or directly processed. The fresh or thawed cell-free saliva samples underwent subsequent centrifugation at 16,000× . The supernatants were used for DNA isolation and quantification using fluorometry and real-time PCR. While freezing had minimal effects on the salivary ecDNA concentration, another centrifugation step decreased ecDNA considerably in both fresh and frozen samples (by 97.8% and 98.4%, respectively). This was mirrored in the quantitative PCR targeting a nuclear (decrease by 93.5%) and mitochondrial (decrease by 97.7%) ecDNA sequence. In conclusion, in this first study focusing on the technical aspects of salivary ecDNA quantitation, we show that, regardless of its subcellular origin, the concentration of ecDNA in saliva is mainly affected by additional centrifugation and not by the freezing of centrifuged cell-free saliva samples. This suggests that most salivary ecDNA likely is associated with cell debris and apoptotic bodies. Which fraction is affected by a particular disease should be the focus of further targeted studies.
PubMed: 38337765
DOI: 10.3390/diagnostics14030249 -
Journal of Genetics and Genomics = Yi... Jan 2024The generation of mature and healthy oocytes is the most critical event in the entire female reproductive process, and the mechanisms regulating this process remain to...
The generation of mature and healthy oocytes is the most critical event in the entire female reproductive process, and the mechanisms regulating this process remain to be studied. Here, we demonstrate that Smith-like (LSM) family member 14B (LSM14B) regulates oocyte maturation, and the loss of LSM14B in mouse ovaries leads to abnormal oocyte MII arrest and female infertility. Next, we find the aberrant transcriptional activation, indicated by abnormal non-surrounded nucleolus and surrounded nucleolus oocyte proportions, and abnormal chromosome assembly and segregation in Lsm14b-deficient mouse oocytes. The global transcriptome analysis suggests that many transcripts involved in cytoplasmic processing body (P-body) function are altered in Lsm14b-deficient mouse oocytes. Deletion of Lsm14b results in the expression and/or localization changes of P-body components (such as LSM14A, DCP1A, and 4E-T). Notably, DDX6, a key component of the P-body, is downregulated and accumulates in the nuclei in Lsm14b-deficient mouse oocytes. Taken together, our data suggest that LSM14B links mouse oocyte maturation to female fertility through the regulation of the P-body.
Topics: Animals; Female; Mice; Oocytes; Oogenesis; Processing Bodies
PubMed: 37481122
DOI: 10.1016/j.jgg.2023.07.006 -
PloS One 2023Amazon streams present great biodiversity and offer several ecosystem services, but these systems are threatened by multiple land uses. The changes created by land use...
Amazon streams present great biodiversity and offer several ecosystem services, but these systems are threatened by multiple land uses. The changes created by land use are expected to drive the composition of species, ultimately changing the trophic relationships of several biological groups, including zooplankton. We investigated if land use changes the composition of zooplankton functional guilds in Amazon streams and which are the local (physical-chemical) variables driving the zooplankton functional guilds in the land-use gradient. Zooplankton and physical-chemical variables were sampled in 17 water bodies in the municipality of Barcarena, Pará, Brazil in 2018 and 2019, five sampling sites were in the Pará River and 12 in streams. Forest cover (a proxy for land use) was determined through digital image processing and converted in percentage. Zooplankton species were classified into five functional guilds (filter, raptorial, scraper, suctor, and predator feeders). We recorded 98 zooplankton taxa and filters were the most abundant functional guild. The composition of zooplankton functional guilds did not change in the land use gradient. However, the distribution of zooplankton functional guilds in Amazon streams was determined by local environmental variables related to the feeding strategies. Scraper-feeders (cladocerans) were positively related to greater canopy cover, suctor-feeders and predator-feeders (both rotifers) were related to greater total phosphorus, whereas filter-feeders (rotifers, cladocerans, and copepods) and raptorial (copepods) were related to total suspended solids. This study brings new information about zooplankton in Amazon streams that are under-studied. The functional approach clarifies the patterns observed and reflects the trophic relationships in which the zooplankton community is involved in streams under a degree of land use, i.e., scraper-cladocerans can represent more preserved streams under greater canopy cover, whereas the other functional guilds were related to variables that can represent more altered streams.
Topics: Animals; Ecosystem; Rivers; Zooplankton; Biodiversity; Rotifera
PubMed: 37527235
DOI: 10.1371/journal.pone.0288385