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The translational value of patient-derived primary melanoma cell cultures depends on the concentration of Tyrosine in the medium.

ABSTRACT: The translational value of patient-derived primary melanoma cell cultures depends on the concentration of Tyrosine in the medium.

PROVIDER: PRJNA719727 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14141960.fastq.gz	Fastqsanger.gz
	SRR14141961.fastq.gz	Fastqsanger.gz
	SRR14141962.fastq.gz	Fastqsanger.gz
	SRR14141963.fastq.gz	Fastqsanger.gz
	SRR14141964_1.fastq.gz	Fastqsanger.gz

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The translational value of patient-derived primary melanoma cell cultures depends on the concentration of Tyrosine in the medium.

Project description:The use of patient-derived primary cell cultures in cancer preclinical assays, including drug screens and genotoxic studies, has increased in recent years. However, their translational value is constrained by several limitations, including variability that can be caused by the culture conditions. Here, we show that the medium composition commonly used to propagate primary melanoma cultures has limited their representability of their tumor of origin, their cellular plasticity and modified their sensitivity to therapy. We established and compared cultures from different melanoma patients propagated in parallel in low-tyrosine (Ham’s F10) or, in high-tyrosine (Ham’s F10 supplemented with tyrosine, RPMI/DMEM) media. Tyrosine is the precursor of melanin biosynthesis, a process particularly active in differentiated melanocytes and melanoma cells. Unexpectedly, we found that the high tyrosine concentrations promoted an early phenotypic drift towards either a mesenchymal-like or senescence-like phenotype, and prevented the establishment of cultures of melanoma cells harboring differentiated features, which we show are frequently present in human clinical biopsies. Moreover, the invasive phenotype emerging in these culture conditions appeared irreversible and, as expected, associated with intrinsic resistance to MAPKi. In sharp contrast, differentiated melanoma cell cultures retained their phenotypes upon propagation in low-tyrosine medium, and importantly their phenotypic plasticity, a key hallmark of melanoma cells. Our findings underline the importance of culturing melanoma cells in low-tyrosine-containing medium in order to preserve their phenotypic identity of origin and cellular plasticity.

2021-11-03 | GSE171456 | GEO

RapiGest Precipitation Depends on Peptide Concentration

Project description:The mass spectrometry-compatible surfactant RapiGest promotes the enzymatic digestion of proteins by facilitating their unfolding while retaining enzymatic activity. RapiGest consists of a hydrophilic head and a hydrophobic tail, which can be separated by acid hydrolysis. This allows for removal of RapiGest prior to mass spectrometric analysis via precipitation and solid phase extraction. During in-solution digestion experiments with RapiGest, we noticed a high variability in the formation of precipitates after acid hydrolysis, implying that RapiGest precipitation is sample-dependent. We show that RapiGest hydrolyzes efficiently under acidic conditions and that differences in precipitation are solely due to protein/peptide concentration. Furthermore, we demonstrate that RapiGest precipitation can be triggered by the addition of intact proteins, providing a strategy for its efficient removal from highly diluted samples.

2021-09-07 | PXD025982 | Pride

high concentration sample

Project description:high concentration sample Raw sequence reads

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Tyrosine Kinase Inhibitor Cardiotoxicity

Project description:Tyrosine Kinase Inhibitor Cardiotoxicity

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Dose-dependent effects of dibutyl phthalate on embryonic development in zebrafish (Danio rerio): The value of integrating concentration gradients in transcriptomic analyses

Project description:Dose-dependent effects of dibutyl phthalate on embryonic development in zebrafish (Danio rerio): The value of integrating concentration gradients in transcriptomic analyses

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Tyrosine-Dependent Phenotype Switching Occurs Early in Many Primary Melanoma Cultures Limiting Their Translational Value.

Project description:The use of patient-derived primary cell cultures in cancer preclinical assays, including drug screens and genotoxic studies, has increased in recent years. However, their translational value is constrained by several limitations, including variability that can be caused by the culture conditions. Here, we show that the medium composition commonly used to propagate primary melanoma cultures has limited their representability of their tumor of origin and their cellular plasticity, and modified their sensitivity to therapy. Indeed, we established and compared cultures from different melanoma patients propagated in parallel in low-tyrosine (Ham's F10) or in high-tyrosine (Ham's F10 supplemented with tyrosine or RPMI1640 or DMEM) media. Tyrosine is the precursor of melanin biosynthesis, a process particularly active in differentiated melanocytes and melanoma cells. Unexpectedly, we found that the high tyrosine concentrations promoted an early phenotypic drift towards either a mesenchymal-like or senescence-like phenotype, and prevented the establishment of cultures of melanoma cells harboring differentiated features, which we show are frequently present in human clinical biopsies. Moreover, the invasive phenotype emerging in these culture conditions appeared irreversible and, as expected, associated with intrinsic resistance to MAPKi. In sharp contrast, differentiated melanoma cell cultures retained their phenotypes upon propagation in low-tyrosine medium, and importantly their phenotypic plasticity, a key hallmark of melanoma cells. Altogether, our findings underline the importance of culturing melanoma cells in low-tyrosine-containing medium in order to preserve their phenotypic identity of origin and cellular plasticity.

| S-EPMC8635994 | biostudies-literature

Dose-dependent effects of dibutyl phthalate on embryonic development in zebrafish (Danio rerio): The value of integrating concentration gradients in transcriptomic analyses

Project description:This study investigates the effects of dibutyl phthalate (DBP)—a plasticizer commonly detected in surface waters worldwide—on zebrafish (Danio rerio) embryos exposed to a concentration gradient from 0 to 120 hours post-fertilization (’protuding mouth’ stage). The primary objective was to assess the utility of integrating concentration gradients into transcriptomic analyses to uncover the mechanisms of action of environmental contaminants, such as DBP. Using this experimental design, dose-response modelling was applied to estimate the sensitivity and shape of transcriptomic responses across the DBP gradient. Following optimized over-representation analysis, we revealed that the retinoid signaling pathway may be the most sensitive pathway affected by DBP during zebrafish development, potentially leading to significant morphological changes.

2024-12-18 | GSE283957 | GEO

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Improving Patient to Patient CT Value Uniformity with an Individualized Contrast Medium Protocol Tailored to Body Weight and Contrast Medium Concentration in Coronary CT Angiography.

Project description:To determine whether body weight and concentration dependent contrast medium (CM) injection protocols can improve patient to patient CT value uniformity more than the conventional injection protocols with fixed injection parameters in coronary CT angiography (CCTA), one hundred and sixty patients who underwent CCTA were prospectively randomized into two groups. Group A (n = 80) used individualized-protocol with adjusted injection rate based on patient weight and contrast medium concentration to obtain constant iodine load of 280 mgI/kg while group B (n = 80) followed the conventional contrast injection protocol with total injection volume of 80ml and constant injection rate of 5.5ml/s. For both groups, patients were further divided into four subgroups with different CM concentrations: A1, B1 (300 mg I/ml); A2, B2 (320 mg I/ml); A3, B3 (350 mg I/ml) and A4 and B4 (370 mg I/ml). For each patient, the CT values of the ascending aorta, left ventricle and coronary arteries were measured. One-way analysis of variance was used to compare CT values among subgroups. Among the subgroups of A, sufficient attenuation of greater than 300HU was obtained in all target vessels with no difference among them. Among the subgroups of B, the CT values had significant difference in left ventricle, left circumflex branch, proximal and distal segment of the right coronary artery (all p < 0.05), and the attenuation with 300 mg I/ml CM concentration was significantly lower than that with 370 mg I/ml. Compared with group B, group A used less volume (62.83 ml vs. 80.00 ml, P<0.001) and lower rate (5.21 ml/s vs. 5.50 ml/s, P<0.001) of CM. Compared with the conventional contrast medium injection protocol with fixed volume and injection rate, the individualized-protocol based on patient weight and contrast concentration provides overall contrast dose reduction and achieves more homogenous attenuation among different coronary vessels and patients.

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Effect of NaCl concentration on the transcriptional network of E. coli in glucose minimal medium with glycine betaine

Project description:The growth rate of E. coli decrease continuously with NaCl concentration, however the pattern for metabolic efficiency as measured by optical density is corralated to a change in pattern in transcription data and proteomics.The analysis of the data suggest that between 4.5 and 5% NaCl, the metabolism switched from aerobic to fermentative pathways. The response to osmotic stress is similar to a response to oxidative stress. An example how a stagewise metabolic answer may be the result of continuously increasing stress.

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