Members of the casein kinase 1 (CK1) family are important regulators of multiple signaling pathways. CK1α is a well-known negative regulator of the Wnt/β-catenin pathway, which promotes the degradation of β-catenin via its phosphorylation of Ser45. In contrast, the closest paralog of CK1α, CK1α-like, is a poorly characterized kinase of unknown function. In this study, we show that the deletion of CK1α, but not CK1α-like, resulted in a strong activation of the Wnt/β-catenin pathway. Wnt-3a treatment further enhanced the activation, which suggests there are at least two modes, a CK1α-dependent and Wnt-dependent, of β-catenin regulation. Rescue experiments showed that only two out of ten naturally occurring splice CK1α/α-like variants were able to rescue the augmented Wnt/β-catenin signaling caused by CK1α deficiency in cells. Importantly, the ability to phosphorylate β-catenin on Ser45 in the in vitro kinase assay was required but not sufficient for such rescue. Our compound CK1α and GSK3α/β KO models suggest that the additional nonredundant function of CK1α in the Wnt pathway beyond Ser45-β-catenin phosphorylation includes Axin phosphorylation. Finally, we established NanoBRET assays for the three most common CK1α splice variants as well as CK1α-like. Target engagement data revealed comparable potency of known CK1α inhibitors for all CK1α variants but not for CK1α-like. In summary, our work brings important novel insights into the biology of CK1α, including evidence for the lack of redundancy with other CK1 kinases in the negative regulation of the Wnt/β-catenin pathway at the level of β-catenin and Axin.
- MeSH
- alternativní sestřih MeSH
- beta-katenin * metabolismus genetika MeSH
- fosforylace MeSH
- GSK3B metabolismus genetika MeSH
- HEK293 buňky MeSH
- kasein kinasa Ialfa * metabolismus genetika MeSH
- kinasa 3 glykogensynthasy metabolismus genetika MeSH
- lidé MeSH
- protein Wnt3A metabolismus genetika MeSH
- signální dráha Wnt * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- srovnávací studie MeSH
BACKGROUND & AIMS: Patient-derived organoid cancer models are generated from epithelial tumor cells and reflect tumor characteristics. However, they lack the complexity of the tumor microenvironment, which is a key driver of tumorigenesis and therapy response. Here, we developed a colorectal cancer organoid model that incorporates matched epithelial cells and stromal fibroblasts. METHODS: Primary fibroblasts and tumor cells were isolated from colorectal cancer specimens. Fibroblasts were characterized for their proteome, secretome, and gene expression signatures. Fibroblast/organoid co-cultures were analyzed by immunohistochemistry and compared with their tissue of origin, as well as on gene expression levels compared with standard organoid models. Bioinformatics deconvolution was used to calculate cellular proportions of cell subsets in organoids based on single-cell RNA sequencing data. RESULTS: Normal primary fibroblasts, isolated from tumor adjacent tissue, and cancer associated fibroblasts retained their molecular characteristics in vitro, including higher motility of cancer associated compared with normal fibroblasts. Importantly, both cancer-associated fibroblasts and normal fibroblasts supported cancer cell proliferation in 3D co-cultures, without the addition of classical niche factors. Organoids grown together with fibroblasts displayed a larger cellular heterogeneity of tumor cells compared with mono-cultures and closely resembled the in vivo tumor morphology. Additionally, we observed a mutual crosstalk between tumor cells and fibroblasts in the co-cultures. This was manifested by considerably deregulated pathways such as cell-cell communication and extracellular matrix remodeling in the organoids. Thrombospondin-1 was identified as a critical factor for fibroblast invasiveness. CONCLUSION: We developed a physiological tumor/stroma model, which will be vital as a personalized tumor model to study disease mechanisms and therapy response in colorectal cancer.
- MeSH
- fibroblasty asociované s nádorem * metabolismus MeSH
- fibroblasty metabolismus MeSH
- kokultivační techniky MeSH
- kolorektální nádory * patologie MeSH
- lidé MeSH
- nádorové mikroprostředí MeSH
- organoidy metabolismus MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
OBJECTIVES: The objective of this study was to determine the incidence of neoplastic diseases and associated risk factors in the early stages of life. METHODS: Data were retrospectively assessed in 730,000 live births between 2000 and 2019. The occurrence of tumors was monitored in the neonatal, infant (1-12 months), and toddler (13-24 months) periods. Risk factors were divided into demographic, internal, and environmental factors. The control group consisted of subjects in the same age category without oncological diseases. RESULTS: A total of 452 neoplastic diseases were diagnosed in the study sample. In total, 24% (110/452) manifested during the neonatal period, 45% (203/452) in infants, and 31% (139/452) at the age of 13-24 months. Any genetic disease (OR 26.68; 95% CI 7.64-93.12) and medications used by the mother (OR 3.07; 95% CI 1.32-7.15) were identified as risk factors. Without adjustment for all factors, asphyxia in the first minute, a younger age of the mother, lower pregnancy, and the presence of a congenital defect manifested themselves as risk factors. CONCLUSIONS: The highest risk factors for the development of early childhood tumors were identified as with medications used by the mother before or during pregnancy and genetic diseases.
- MeSH
- kojenec MeSH
- leukemie * epidemiologie etiologie MeSH
- lidé MeSH
- matky MeSH
- nádory * epidemiologie etiologie MeSH
- novorozenec MeSH
- předškolní dítě MeSH
- retrospektivní studie MeSH
- rizikové faktory MeSH
- těhotenství MeSH
- Check Tag
- kojenec MeSH
- lidé MeSH
- novorozenec MeSH
- předškolní dítě MeSH
- těhotenství MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
Manual visual review, annotation and categorization of electroencephalography (EEG) is a time-consuming task that is often associated with human bias and requires trained electrophysiology experts with specific domain knowledge. This challenge is now compounded by development of measurement technologies and devices allowing large-scale heterogeneous, multi-channel recordings spanning multiple brain regions over days, weeks. Currently, supervised deep-learning techniques were shown to be an effective tool for analyzing big data sets, including EEG. However, the most significant caveat in training the supervised deep-learning models in a clinical research setting is the lack of adequate gold-standard annotations created by electrophysiology experts. Here, we propose a semi-supervised machine learning technique that utilizes deep-learning methods with a minimal amount of gold-standard labels. The method utilizes a temporal autoencoder for dimensionality reduction and a small number of the expert-provided gold-standard labels used for kernel density estimating (KDE) maps. We used data from electrophysiological intracranial EEG (iEEG) recordings acquired in two hospitals with different recording systems across 39 patients to validate the method. The method achieved iEEG classification (Pathologic vs. Normal vs. Artifacts) results with an area under the receiver operating characteristic (AUROC) scores of 0.862 ± 0.037, 0.879 ± 0.042, and area under the precision-recall curve (AUPRC) scores of 0.740 ± 0.740, 0.714 ± 0.042. This demonstrates that semi-supervised methods can provide acceptable results while requiring only 100 gold-standard data samples in each classification category. Subsequently, we deployed the technique to 12 novel patients in a pseudo-prospective framework for detecting Interictal epileptiform discharges (IEDs). We show that the proposed temporal autoencoder was able to generalize to novel patients while achieving AUROC of 0.877 ± 0.067 and AUPRC of 0.705 ± 0.154.
We wanted to verify the effect of combining multi-echo (ME) functional magnetic resonance imaging (fMRI) with slice acceleration in simultaneous multi-slice acquisition. The aim was to shed light on the benefits of multiple echoes for various acquisition settings, especially for levels of slice acceleration and flip angle. Whole-brain ME fMRI data were obtained from 26 healthy volunteers (using three echoes; seven runs with slice acceleration 1, 4, 6, and 8; and two different flip angles for each of the first three acceleration factors) and processed as single-echo (SE) data and ME data based on optimal combinations weighted by the contrast-to-noise ratio. Global metrics (temporal signal-to-noise ratio, signal-to-noise separation, number of active voxels, etc.) and local characteristics in regions of interest were used to evaluate SE and ME data. ME results outperformed SE results in all runs; the differences became more apparent for higher acceleration, where a significant decrease in data quality is observed. ME fMRI can improve the observed data quality metrics over SE fMRI for a wide range of accelerated fMRI acquisitions.
- MeSH
- dospělí MeSH
- echoplanární zobrazování metody MeSH
- globus pallidus diagnostické zobrazování fyziologie MeSH
- lidé MeSH
- magnetická rezonanční tomografie metody MeSH
- mapování mozku metody MeSH
- mladý dospělý MeSH
- mozková kůra diagnostické zobrazování fyziologie MeSH
- počítačové zpracování obrazu metody MeSH
- psychomotorický výkon fyziologie MeSH
- Check Tag
- dospělí MeSH
- lidé MeSH
- mladý dospělý MeSH
- mužské pohlaví MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
OBJECTIVE: GDF11 is a member of the TGF-β superfamily that was recently implicated as potential "rejuvenating" factor, which can ameliorate metabolic disorders. The main objective of the presented study was to closely characterize the role of GDF11 signaling in the glucose homeostasis and in the differentiation of white adipose tissue. METHODS: We performed microscopy imaging, biochemical and transcriptomic analyses of adipose tissues of 9 weeks old ob/ob mice and murine and human pre-adipocyte cell lines. RESULTS: Our in vivo experiments employing GDF11 treatment in ob/ob mice showed improved glucose/insulin homeostasis, decreased weight gain and white adipocyte size. Furthermore, GDF11 treatment inhibited adipogenesis in pre-adipocytes by ALK5-SMAD2/3 activation in cooperation with the WNT/β-catenin pathway, whose inhibition resulted in adipogenic differentiation. Lastly, we observed significantly elevated levels of the adipokine hormone adiponectin and increased glucose uptake by mature adipocytes upon GDF11 exposure. CONCLUSION: We show evidence that link GDF11 to adipogenic differentiation, glucose, and insulin homeostasis, which are pointing towards potential beneficial effects of GDF11-based "anti-obesity" therapy.
- MeSH
- adipogeneze * MeSH
- adiponektin metabolismus MeSH
- beta-katenin * metabolismus MeSH
- buněčná diferenciace fyziologie MeSH
- glukosa metabolismus MeSH
- inzulin metabolismus MeSH
- kostní morfogenetické proteiny metabolismus MeSH
- lidé MeSH
- myši MeSH
- protein Smad2 MeSH
- protein Smad3 MeSH
- receptory regulované proteiny Smad MeSH
- růstové diferenciační faktory metabolismus MeSH
- signální dráha Wnt MeSH
- TGF-beta receptor I. typu MeSH
- transformující růstový faktor beta metabolismus MeSH
- tukové buňky metabolismus MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- myši MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
The volume of the hippocampus decreases more slowly than the volume of the cortex during normal aging. We explored changes in the hippocampus-to-cortex volume (HV:CTV) ratio with increasing age in non-demented Parkinson's disease (PD) patients as compared to healthy controls (HC). We also evaluated the association between the HV:CTV ratio and cognitive outcomes. Altogether 130 participants without dementia aged 51-88 years were consecutively enrolled, including 54 PD patients (mean age 67, standard deviation (SD) 8 years) and 76 HC (mean age 69, SD 7 years). All participants underwent structural magnetic resonance examination and psychological evaluation. Hippocampal and cortex volumes were determined from T1 and FLAIR scans using FreeSurfer software, and the HV:CTV ratio was calculated. Regression lines for age-dependence of the HV:CTV ratio for PD and HC groups were calculated. We further assessed the association between the HV:CTV ratio and cognitive tests examining hippocampus-related cognitive functions. PD patients and age-matched HC showed a significant difference in age-dependence of HV:CTV ratio (p value = 0.012), with a decreasing slope in PD and increasing slope in HC. In the PD group, a significant correlation (R = 0.561, p = 0.024) was observed between the HV:CTV ratio and the Digit Symbol-Coding test. The reduction of HV:CTV ratio is accelerated in pathological aging due to PD pathology. The HV:CTV ratio was associated with impaired processing speed, i.e., the cognitive function that is linked to subcortical alterations of both associated basal ganglia circuitry and the hippocampus.
The archiving and dissemination of protein and nucleic acid structures as well as their structural, functional and biophysical annotations is an essential task that enables the broader scientific community to conduct impactful research in multiple fields of the life sciences. The Protein Data Bank in Europe (PDBe; pdbe.org) team develops and maintains several databases and web services to address this fundamental need. From data archiving as a member of the Worldwide PDB consortium (wwPDB; wwpdb.org), to the PDBe Knowledge Base (PDBe-KB; pdbekb.org), we provide data, data-access mechanisms, and visualizations that facilitate basic and applied research and education across the life sciences. Here, we provide an overview of the structural data and annotations that we integrate and make freely available. We describe the web services and data visualization tools we offer, and provide information on how to effectively use or even further develop them. Finally, we discuss the direction of our data services, and how we aim to tackle new challenges that arise from the recent, unprecedented advances in the field of structure determination and protein structure modeling.
- MeSH
- databáze proteinů MeSH
- konformace proteinů MeSH
- nukleové kyseliny * MeSH
- proteiny * chemie MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- Evropa MeSH
The transcription factor c-Myb is an oncoprotein promoting cell proliferation and survival when aberrantly activated/expressed, thus contributing to malignant transformation. Overexpression of c-Myb has been found in leukemias, breast, colon and adenoid cystic carcinoma. Recent studies revealed its expression also in osteosarcoma cell lines and suggested its functional importance during bone development. However, the relevance of c-Myb in control of osteosarcoma progression remains unknown. A retrospective clinical study was carried out to assess a relationship between c-Myb expression in archival osteosarcoma tissues and prognosis in a cohort of high-grade osteosarcoma patients. In addition, MYB was depleted in metastatic osteosarcoma cell lines SAOS-2 LM5 and 143B and their growth, chemosensitivity, migration and metastatic activity were determined. Immunohistochemical analysis revealed that high c-Myb expression was significantly associated with poor overall survival in the cohort and metastatic progression in young patients. Increased level of c-Myb was detected in metastatic osteosarcoma cell lines and its depletion suppressed their growth, colony-forming capacity, migration and chemoresistance in vitro in a cell line-dependent manner. MYB knock-out resulted in reduced metastatic activity of both SAOS-2 LM5 and 143B cell lines in immunodeficient mice. Transcriptomic analysis revealed the c-Myb-driven functional programs enriched for genes involved in the regulation of cell growth, stress response, cell adhesion and cell differentiation/morphogenesis. Wnt signaling pathway was identified as c-Myb target in osteosarcoma cells. Taken together, we identified c-Myb as a negative prognostic factor in osteosarcoma and showed its involvement in the regulation of osteosarcoma cell growth, chemosensitivity, migration and metastatic activity.
- MeSH
- lidé MeSH
- myši MeSH
- nádorové buněčné linie MeSH
- nádory kostí * patologie MeSH
- osteosarkom * patologie MeSH
- pohyb buněk genetika MeSH
- prognóza MeSH
- proliferace buněk MeSH
- regulace genové exprese u nádorů MeSH
- retrospektivní studie MeSH
- signální dráha Wnt MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- myši MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Fanconi anemia (FA) is a chromosomal instability disorder of bone marrow associated with aplastic anemia, congenital abnormalities and a high risk of malignancies. The identification of more than two dozen FA genes has revealed a plethora of interacting proteins that are mainly involved in repair of DNA interstrand crosslinks (ICLs). Other important findings associated with FA are inflammation, oxidative stress response, mitochondrial dysfunction and mitophagy. In this work, we performed quantitative proteomic and metabolomic analyses on defective FA cells and identified a number of metabolic abnormalities associated with cancer. In particular, an increased de novo purine biosynthesis, a high concentration of fumarate, and an accumulation of purinosomal clusters were found. This was in parallel with decreased OXPHOS and altered glycolysis. On the whole, our results indicate an association between the need for nitrogenous bases upon impaired DDR in FA cells with a subsequent increase in purine metabolism and a potential role in oncogenesis.
- MeSH
- buněčné linie MeSH
- chromatografie kapalinová MeSH
- Fanconiho anemie metabolismus MeSH
- glykolýza MeSH
- lidé MeSH
- metabolické sítě a dráhy * MeSH
- metabolomika metody MeSH
- oprava DNA MeSH
- oxidativní fosforylace MeSH
- proteomika metody MeSH
- tandemová hmotnostní spektrometrie MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
