Alexander disease (AxD) is a rare and severe neurodegenerative disorder caused by mutations in glial fibrillary acidic protein (GFAP). While the exact disease mechanism remains unknown, previous studies suggest that mutant GFAP influences many cellular processes, including cytoskeleton stability, mechanosensing, metabolism, and proteasome function. While most studies have primarily focused on GFAP-expressing astrocytes, GFAP is also expressed by radial glia and neural progenitor cells, prompting questions about the impact of GFAP mutations on central nervous system (CNS) development. In this study, we observed impaired differentiation of astrocytes and neurons in co-cultures of astrocytes and neurons, as well as in neural organoids, both generated from AxD patient-derived induced pluripotent stem (iPS) cells with a GFAPR239C mutation. Leveraging single-cell RNA sequencing (scRNA-seq), we identified distinct cell populations and transcriptomic differences between the mutant GFAP cultures and a corrected isogenic control. These findings were supported by results obtained with immunocytochemistry and proteomics. In co-cultures, the GFAPR239C mutation resulted in an increased abundance of immature cells, while in unguided neural organoids and cortical organoids, we observed altered lineage commitment and reduced abundance of astrocytes. Gene expression analysis revealed increased stress susceptibility, cytoskeletal abnormalities, and altered extracellular matrix and cell-cell communication patterns in the AxD cultures, which also exhibited higher cell death after stress. Overall, our results point to altered cell differentiation in AxD patient-derived iPS-cell models, opening new avenues for AxD research.
- MeSH
- Alexanderova nemoc * genetika patologie metabolismus MeSH
- astrocyty * metabolismus patologie MeSH
- buněčná diferenciace * fyziologie MeSH
- gliový fibrilární kyselý protein * metabolismus genetika MeSH
- indukované pluripotentní kmenové buňky * metabolismus MeSH
- kokultivační techniky MeSH
- kultivované buňky MeSH
- lidé MeSH
- mutace MeSH
- nervové kmenové buňky metabolismus MeSH
- neurony metabolismus patologie MeSH
- organoidy metabolismus patologie MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
The forskolin-induced swelling assay (FIS) in patient-derived intestinal organoids (PDIOs), used to determine in vitro responsiveness to elexacaftor/tezacaftor/ivacaftor (ETI), showed variability in swelling among PDIOs obtained from people with CF (pwCF) carrying the same F508del/F508del CFTR genotype. We aimed to characterise the effect of ETI on the transcriptional activity of PDIOs-derived cells to understand the intracellular processes triggered by ETI and the differences in treatment response. Six high- and six low-responding PDIOs to ETI, derived from F508del/F508del pwCF, were incubated with or without ETI for 2 to 6 h. Gene expression was assessed using 3'-mRNA sequencing and modelled using negative binomial models. Incubation with ETI resulted in a significant upregulation of several biological processes: mostly related to chemokines and signalling, chemotaxis, and tissue development processes. No changes were observed in abundance of the CFTR transcripts or in CFTR-related gene sets and pathways. The genes and pathways associated with ETI did not overlap with those whose expression changed with time only. PDIOs with a high FIS response did not significantly differ in any interpretable gene from the FIS-low organoids. The changes in the PDIOs gene expression upon the exposure to ETI cannot explain differences in the magnitude of PDIOs FIS-measured response to ETI. In conclusion, on incubation with ETI, genes of the CFTR-related pathways do not change their transcriptional activity; instead, overexpression was observed in genes of inflammatory-like cytokine response and receptor activation pathways.
- MeSH
- aktivátory chloridových kanálů terapeutické užití farmakologie MeSH
- aminofenoly * terapeutické užití farmakologie MeSH
- benzodioxoly * terapeutické užití farmakologie MeSH
- chinolony * farmakologie terapeutické užití MeSH
- cystická fibróza * genetika farmakoterapie MeSH
- fixní kombinace léků MeSH
- indoly * farmakologie MeSH
- lidé MeSH
- organoidy * metabolismus MeSH
- protein CFTR genetika MeSH
- pyrazoly * farmakologie MeSH
- pyridiny farmakologie MeSH
- pyrrolidiny farmakologie MeSH
- pyrroly farmakologie MeSH
- stanovení celkové genové exprese metody MeSH
- střeva účinky léků MeSH
- transkriptom MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
As organoids and organ-on-chip (OoC) systems move toward preclinical and clinical applications, there is an increased need for method validation. Using a liquid chromatography-mass spectrometry (LC-MS)-based approach, we developed a method for measuring small-molecule drugs and metabolites in the cell medium directly sampled from liver organoids/OoC systems. The LC-MS setup was coupled to an automatic filtration and filter flush system with online solid-phase extraction (SPE), allowing for robust and automated sample cleanup/analysis. For the matrix, rich in, e.g., protein, salts, and amino acids, no preinjection sample preparation steps (protein precipitation, SPE, etc.) were necessary. The approach was demonstrated with tolbutamide and its liver metabolite, 4-hydroxytolbutamide (4HT). The method was validated for analysis of cell media of human stem cell-derived liver organoids cultured in static conditions and on a microfluidic platform according to Food and Drug Administration (FDA) guidelines with regards to selectivity, matrix effects, accuracy, precision, etc. The system allows for hundreds of injections without replacing chromatography hardware. In summary, drug/metabolite analysis of organoids/OoCs can be performed robustly with minimal sample preparation.
- MeSH
- chromatografie kapalinová metody MeSH
- extrakce na pevné fázi MeSH
- hmotnostní spektrometrie metody MeSH
- játra * metabolismus MeSH
- kapalinová chromatografie-hmotnostní spektrometrie MeSH
- knihovny malých molekul analýza metabolismus chemie MeSH
- laboratoř na čipu MeSH
- léčivé přípravky metabolismus analýza MeSH
- lidé MeSH
- organoidy * metabolismus cytologie MeSH
- tolbutamid metabolismus analýza MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- validační studie MeSH
Neural injuries in cerebral malaria patients are a significant cause of morbidity and mortality. Nevertheless, a comprehensive research approach to study this issue is lacking, so herein we propose an in vitro system to study human cerebral malaria using cellular approaches. Our first goal was to establish a cellular system to identify the molecular alterations in human brain vasculature cells that resemble the blood-brain barrier (BBB) in cerebral malaria (CM). Through transcriptomic analysis, we characterized specific gene expression profiles in human brain microvascular endothelial cells (HBMEC) activated by the Plasmodium falciparum parasites. We also suggest potential new genes related to parasitic activation. Then, we studied its impact at brain level after Plasmodium falciparum endothelial activation to gain a deeper understanding of the physiological mechanisms underlying CM. For that, the impact of HBMEC-P. falciparum-activated secretomes was evaluated in human brain organoids. Our results support the reliability of in vitro cellular models developed to mimic CM in several aspects. These systems can be of extreme importance to investigate the factors (parasitological and host) influencing CM, contributing to a molecular understanding of pathogenesis, brain injury, and dysfunction.
- MeSH
- endoteliální buňky metabolismus MeSH
- lidé MeSH
- mozek patologie MeSH
- mozková malárie * metabolismus parazitologie patologie MeSH
- organoidy metabolismus MeSH
- Plasmodium falciparum MeSH
- reprodukovatelnost výsledků MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem 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
It is currently challenging to adequately model the growth and migration of glioblastoma using two-dimensional (2D) in vitro culture systems as they quickly lose the original, patient-specific identity and heterogeneity. However, with the advent of three-dimensional (3D) cell cultures and human-induced pluripotent stem cell (iPSC)-derived cerebral organoids (COs), studies demonstrate that the glioblastoma-CO (GLICO) coculture model helps to preserve the phenotype of the patient-specific tissue. Here, we aimed to set up such a model using mature COs and develop a pipeline for subsequent analysis of cocultured glioblastoma. Our data demonstrate that the growth and migration of the glioblastoma cell line within the mature COs are significantly increased in the presence of extracellular matrix proteins, shortening the time needed for glioblastoma to initiate migration. We also describe in detail the method for the visualization and quantification of these migrating cells within the GLICO model. Lastly, we show that this coculture model (and the human brain-like microenvironment) can significantly transform the gene expression profile of the established U87 glioblastoma cell line into proneural and classical glioblastoma cell types.
- MeSH
- buněčné kultury metody MeSH
- buněčné linie MeSH
- glioblastom * genetika metabolismus MeSH
- lidé MeSH
- mozek MeSH
- nádorové mikroprostředí MeSH
- organoidy metabolismus MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
Východiska: Současné in vitro modelové systémy plně neodrážejí biologickou a klinickou diverzitu karcinomu prostaty (prostate cancer – PCa). Organoidy jsou 3D in vitro buněčné kultury, které mohou lépe rekapitulovat heterogenitu onemocnění a zachovat vlastnosti původního nádoru. Krátkodobá ex vivo kultivace PCa tkání může také usnadnit testování léčiv v personalizované medicíně. Materiál a metody: Pro organoidní kultivaci jsme zpracovali jak nádorovou, tak normální tkáň od 50 pacientů, kteří podstoupili radikální prostatektomii nebo transuretrální resekci prostaty. Kromě toho jsme využili techniku ex vivo tkáňové kultivace a provedli krátkodobý experiment s použitím gemcitabinu a inhibitoru Chk1 MU380 ve vzorcích od 10 pacientů. Výsledky: Celkem jsme byli schopni kultivovat organoidy z 58 % nádorových (29/50) a 69 % normálních tkání (20/29). Imunohistochemické barvení dvou reprezentativních případů odhalilo buněčnou pozitivitu na pan-cytokeratin potvrzující přítomnost epiteliálních buněk. Nadměrná exprese proteinů AMACR a ERG v nádorech však nebyla zachována v organoidech. Dalším omezením bylo udržení organoidů pouze do první pasáže, obvykle po dobu 3 týdnů. Dále byly provedeny krátkodobé testy v ex vivo kultuře nádorových tkání od deseti pacientů. Tkáňové vzorky z prostatektomií většinou vykazovaly nízkou míru proliferace a Ki-67 pozitivity. Další nevýhodou tohoto přístupu byla nekonzistentní morfologie mezi jednotlivými tkáňovými fragmenty. Pouze jeden případ vykazoval vysokou míru proliferace pro testování léčiv a nádorová tkáň byla přítomna ve všech testovaných vzorcích. V naší práci také poskytujeme přehled nedávných studií a podrobné srovnání kultivačních podmínek. Závěr: Podařilo se nám ustavit kultury organoidů i fragmentů tkání z primárních nádorů prostaty. Exprese nádorových markerů však nebyla zachována v získaných organoidech. Nekonzistentní morfologie a nízká proliferace ztěžovaly interpretaci výsledků testování léčiv u většiny případů. Přesto mohou být tyto přístupy slibné při použití tkání z metastatického kastračně rezistentního karcinomu prostaty.
Background: Current in vitro model systems do not fully reflect the biological and clinical diversity of prostate cancer (PCa). Organoids are 3D in vitro cell cultures that may better recapitulate disease heterogeneity and retain parental tumor characteristics. Short-term ex vivo culture of PCa tissues may also facilitate drug testing in personalized medicine. Materials and methods: For organoid culture, we have processed both cancer and normal tissues from 50 patients who underwent radical prostatectomy or transurethral resection of the prostate. In addition, we exploited the ex vivo tissue culture technique and performed short-term chemotherapy assay using gemcitabine and Chk1 inhibitor MU380 in 10 patient samples. Results: In total, we were able to cultivate organoids from 58% of tumors (29/50) and 69% of normal tissue (20/29). Immunohistochemical staining of two representative cases revealed cell positivity for pan-cytokeratin confirming the presence of epithelial cells. However, the overexpression of AMACR and ERG proteins in tumors was not recapitulated in organoids. Another limitation was the propagation of organoids only up to 3 weeks till the first passage. Next, a short-term drug test was performed for ten patients using ex vivo tissue culture. Samples from prostatectomies mostly presented a low proliferation rate as assessed by Ki-67 staining. Another drawback of this approach was inconsistent tissue morphology among particular tissue fragments. Only one case showed a high proliferation rate for drug testing and tumor tissue was present in all tested samples. In our work, we also provide an overview of recent studies and a detailed comparison of culture conditions. Conclusion: We have established cultures of both organoids and tissue fragments from PCa patient samples. However, the expression of tumor markers was not recapitulated in organoids. Inconsistent morphology among tissue fragments and low proliferation hampered the interpretation of the drug testing in most cases. Still, these approaches may be promising using tissues from metastatic castration-resistant prostate cancer.
- Klíčová slova
- ex vivo,
- MeSH
- individualizovaná medicína metody MeSH
- klinická studie jako téma MeSH
- kultivační techniky MeSH
- lidé MeSH
- nádorové buňky kultivované MeSH
- nádory prostaty * patologie MeSH
- organoidy metabolismus patologie MeSH
- transuretrální resekce prostaty MeSH
- Check Tag
- lidé MeSH
- mužské pohlaví MeSH
- Publikační typ
- práce podpořená grantem MeSH
The homeostasis of the gut epithelium relies upon continuous renewal and proliferation of crypt-resident intestinal epithelial stem cells (IESCs). Wnt/β-catenin signaling is required for IESC maintenance, however, it remains unclear how this pathway selectively governs the identity and proliferative decisions of IESCs. Here, we took advantage of knock-in mice harboring transgenic β-catenin alleles with mutations that specifically impair the recruitment of N- or C-terminal transcriptional co-factors. We show that C-terminally-recruited transcriptional co-factors of β-catenin act as all-or-nothing regulators of Wnt-target gene expression. Blocking their interactions with β-catenin rapidly induces loss of IESCs and intestinal homeostasis. Conversely, N-terminally recruited co-factors fine-tune β-catenin's transcriptional output to ensure proper self-renewal and proliferative behaviour of IESCs. Impairment of N-terminal interactions triggers transient hyperproliferation of IESCs, eventually resulting in exhaustion of the self-renewing stem cell pool. IESC mis-differentiation, accompanied by unfolded protein response stress and immune infiltration, results in a process resembling aberrant "villisation" of intestinal crypts. Our data suggest that IESC-specific Wnt/β-catenin output requires selective modulation of gene expression by transcriptional co-factors.
- MeSH
- algoritmy MeSH
- beta-katenin chemie metabolismus MeSH
- buněčná diferenciace MeSH
- chromatin metabolismus MeSH
- fenotyp MeSH
- genetická transkripce * MeSH
- homeostáza MeSH
- hyperplazie MeSH
- JNK mitogenem aktivované proteinkinasy metabolismus MeSH
- kmenové buňky metabolismus MeSH
- messenger RNA genetika metabolismus MeSH
- mutace genetika MeSH
- mutantní proteiny metabolismus MeSH
- myši MeSH
- organoidy metabolismus MeSH
- proliferace buněk MeSH
- restrukturace chromatinu MeSH
- sekvence nukleotidů MeSH
- signální transdukce MeSH
- střevní sliznice cytologie MeSH
- transkripční faktory metabolismus MeSH
- zvířata MeSH
- Check Tag
- myši MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
RATIONALE: Given the vast number of cystic fibrosis transmembrane conductance regulator (CFTR) mutations, biomarkers predicting benefit from CFTR modulator therapies are needed for subjects with cystic fibrosis (CF). OBJECTIVES: To study CFTR function in organoids of subjects with common and rare CFTR mutations and evaluate correlations between CFTR function and clinical data. METHODS: Intestinal organoids were grown from rectal biopsies in a cohort of 97 subjects with CF. Residual CFTR function was measured by quantifying organoid swelling induced by forskolin and response to modulators by quantifying organoid swelling induced by CFTR correctors, potentiator and their combination. Organoid data were correlated with clinical data from the literature. RESULTS: Across 28 genotypes, residual CFTR function correlated (r2=0.87) with sweat chloride values. When studying the same genotypes, CFTR function rescue by CFTR modulators in organoids correlated tightly with mean improvement in lung function (r2=0.90) and sweat chloride (r2=0.95) reported in clinical trials. We identified candidate genotypes for modulator therapy, such as E92K, Q237E, R334W and L159S. Based on organoid results, two subjects started modulator treatment: one homozygous for complex allele Q359K_T360K, and the second with mutation E60K. Both subjects had major clinical benefit. CONCLUSIONS: Measurements of residual CFTR function and rescue of function by CFTR modulators in intestinal organoids correlate closely with clinical data. Our results for reference genotypes concur with previous results. CFTR function measured in organoids can be used to guide precision medicine in patients with CF, positioning organoids as a potential in vitro model to bring treatment to patients carrying rare CFTR mutations.
Commensal microbiota contribute to gut homeostasis by inducing transcription of mucosal genes. Analysis of the impact of various microbiota on intestinal tissue provides an important insight into the function of this organ. We used cDNA microarrays to determine the gene expression signature of mucosa isolated from the small intestine and colon of germ-free (GF) mice and animals monoassociated with two E. coli strains. The results were compared to the expression data obtained in conventionally reared (CR) mice. In addition, we analyzed gene expression in colon organoids derived from CR, GF, and monoassociated animals. The analysis revealed that the complete absence of intestinal microbiota mainly affected the mucosal immune system, which was not restored upon monoassociation. The most important expression changes observed in the colon mucosa indicated alterations in adipose tissue and lipid metabolism. In the comparison of differentially expressed genes in the mucosa or organoids obtained from GF and CR mice, only six genes were common for both types of samples. The results show that the increased expression of the angiopoietin-like 4 (Angptl4) gene encoding a secreted regulator of lipid metabolism indicates the GF status.
- MeSH
- biologické markery metabolismus MeSH
- Escherichia coli fyziologie MeSH
- gnotobiologické modely genetika MeSH
- imunitní systém metabolismus MeSH
- kolon metabolismus MeSH
- mikrobiota MeSH
- myši inbrední BALB C MeSH
- organoidy metabolismus MeSH
- regulace genové exprese MeSH
- slizniční imunita MeSH
- stanovení celkové genové exprese * MeSH
- střevní sliznice metabolismus MeSH
- zvířata MeSH
- Check Tag
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
