Changes In Human Cells Research Articles

Evaluation of a Deep Learning Based Approach to Computational Label Free Cell Viability Quantification.

One of the most common techniques found in a cell biology or tissue engineering lab is the cytotoxicity assay. This can be performed using a variety of different dyes and stains and various protocols to result in a clear indication of dead and live cells within a culture to quantify the viability of a culture and monitor for sudden drops or increases in viability by a drug, material, viral vector, etc introduced into the culture. This assay helps cell biologists determine the health of their culture and what toxicity added substances may add to the culture and whether they are appropriate and safe to use with human cells. However, many of the dyes and stains used for this process are eventually toxic to cells, rendering the cells useless after testing and preventing real time monitoring of the same culture over a period of hours or days. Computation biology is moving cell biology towards novel and innovative techniques such as in silico labeling and dye free labeling using deep learning algorithms. In this work, we investigate whether it is feasible to train a Resnet CNN model to detect morphological changes in human cells that indicate cell death in order to classify cells as live or dead without utilizing a stain or dye. This work also aims to train one CNN model to count all cells regardless of viability status to get a total cell count, and then one CNN model that specifically identifies and counts all of the dead cells for an accurate dead and live cell total by utilizing both pieces of data to determine a general viability percentage for the culture. Additionally, this work explores the use of various image enhancements to understand if this process helps or impedes the deep learning models in their detection of total cells and dead cells.

Comparative landscape of genetic dependencies in human and chimpanzee stem cells

Comparative studies of great apes provide a window into our evolutionary past, but the extent and identity of cellular differences that emerged during hominin evolution remain largely unexplored. We established a comparative loss-of-function approach to evaluate whether human cells exhibit distinct genetic dependencies. By performing genome-wide CRISPR interference screens in human and chimpanzee pluripotent stem cells, we identified 75 genes with species-specific effects on cellular proliferation. These genes comprised coherent processes, including cell-cycle progression and lysosomal signaling, which we determined to be human-derived by comparison with orangutan cells. Human-specific robustness to CDK2 and CCNE1 depletion persisted in neural progenitor cells and cerebral organoids, supporting the G1-phase length hypothesis as a potential evolutionary mechanism in human brain expansion. Our findings demonstrate that evolutionary changes in human cells reshaped the landscape of essential genes and establish a platform for systematically uncovering latent cellular and molecular differences between species.

Inhibition of Toxoplasma gondii by 1,2,4-triazole-based compounds: marked improvement in selectivity relative to the standard therapy pyrimethamine and sulfadiazine

A safer treatment for toxoplasmosis would be achieved by improving the selectivity profile of novel chemotherapeutics compared to the standard therapy pyrimethamine (PYR) and sulfadiazine (SDZ). We previously reported on the identification of the compounds with imidazole-thiosemicarbazide scaffold as potent and selective anti-Toxoplasma gondii (T. gondii) agents. In our current research, we report on the optimisation of this chemical scaffold leading to the discovery cyclic analogue 20 b with s-triazole core structure. This compound displayed prominent CC30 to IC50 selectivity index (SI) of 70.72, making it 160-fold more selective than SDZ, 11-fold more selective than PYR, and 4-fold more selective than trimethoprim (TRI). Additionally, this compound possesses prerequisite drug-like anti-Toxoplasma properties to advance into preclinical development; it showed ability to cross the BBB, did not induce genotoxic and haemolytic changes in human cells, and as well as it was characterised by low cellular toxicity.

In vitro toxicological prospection of fungicides containing Difenoconazole or Tebuconazole as active ingredients

The active ingredients (AI) tebuconazole and difenoconazole (classified as toxic to living organisms and potentially mutagen, carcinogen, or teratogen) are part of the composition of widely used fungicides in crops. In 2016 they were found in irregular quantities by ANVISA in their latest report emitted by the Program of Analysis of Agrochemical Waste in Food. Two commercial fungicides containing the active ingredients tebuconazole and difenoconazole were evaluated in cytogenotoxic assays and on different biological molecules. Both active ingredients altered the clotting time of the plasma, and were procoagulants in the majority of the evaluated doses. The two AI acted on blood thrombi exerting thrombotic action and confirming the observed procoagulant potential. In the proteolysis assay, the AI did not alter the structure of fibrinogen under the conditions evaluated. Tebuconazole and Difenoconazole were also cytotoxic to human erythrocytes, as well as induced phospholipid breakdown, confirming their toxicity on membranes. However, under the conditions evaluated, the AI did not alter significantly the mitochondrial succinate dehydrogenase activity and did not induce DNA fragmentation. Assuming that changes in human cells and molecules have a cumulative effect, the toxic potential of fungicides might be greater when chronic exposure to their active principles occurs.

Machine learning-based approaches for identifying human blood cells harboring CRISPR-mediated fetal chromatin domain ablations

Two common hemoglobinopathies, sickle cell disease (SCD) and β-thalassemia, arise from genetic mutations within the β-globin gene. In this work, we identified a 500-bp motif (Fetal Chromatin Domain, FCD) upstream of human ϒ-globin locus and showed that the removal of this motif using CRISPR technology reactivates the expression of ϒ-globin. Next, we present two different cell morphology-based machine learning approaches that can be used identify human blood cells (KU-812) that harbor CRISPR-mediated FCD genetic modifications. Three candidate models from the first approach, which uses multilayer perceptron algorithm (MLP 20-26, MLP26-18, and MLP 30-26) and flow cytometry-derived cellular data, yielded 0.83 precision, 0.80 recall, 0.82 accuracy, and 0.90 area under the ROC (receiver operating characteristic) curve when predicting the edited cells. In comparison, the candidate model from the second approach, which uses deep learning (T2D5) and DIC microscopy-derived imaging data, performed with less accuracy (0.80) and ROC AUC (0.87). We envision that equivalent machine learning-based models can complement currently available genotyping protocols for specific genetic modifications which result in morphological changes in human cells.

Deep Time Course Proteomics of SARS-CoV- and SARS-CoV-2-Infected Human Lung Epithelial Cells (Calu-3) Reveals Strong Induction of Interferon-Stimulated Gene Expression by SARS-CoV-2 in Contrast to SARS-CoV.

Severe acute respiratory syndrome (SARS)-CoV and SARS-CoV-2 infections are characterized by remarkable differences, including infectivity and case fatality rate. The underlying mechanisms are not well understood, illustrating major knowledge gaps of coronavirus biology. In this study, protein expression of the SARS-CoV- and SARS-CoV-2-infected human lung epithelial cell line Calu-3 was analyzed using data-independent acquisition–mass spectrometry. This resulted in a comprehensive map of infection-related proteome-wide expression changes in human cells covering the quantification of 7478 proteins across four time points. Most notably, the activation of interferon type-I response was observed, which is surprisingly absent in several proteome studies. The data reveal that SARS-CoV-2 triggers interferon-stimulated gene expression much stronger than SARS-CoV, which reflects the already described differences in interferon sensitivity. Potentially, this may be caused by the enhanced abundance of the viral M protein of SARS-CoV in comparison to SARS-CoV-2, which is a known inhibitor of type I interferon expression. This study expands the knowledge on the host response to SARS-CoV-2 infections on a global scale using an infection model, which seems to be well suited to analyze the innate immunity.

Impacts of p97 on Proteome Changes in Human Cells during Coronaviral Replication.

Human coronavirus (HCoV) similar to other viruses rely on host cell machinery for both replication and to spread. The p97/VCP ATPase is associated with diverse pathways that may favor HCoV replication. In this study, we assessed the role of p97 and associated host responses in human lung cell line H1299 after HCoV-229E or HCoV-OC43 infection. Inhibition of p97 function by small molecule inhibitors shows antiviral activity, particularly at early stages of the virus life cycle, during virus uncoating and viral RNA replication. Importantly, p97 activity inhibition protects human cells against HCoV-induced cytopathic effects. The p97 knockdown also inhibits viral production in infected cells. Unbiased quantitative proteomics analyses reveal that HCoV-OC43 infection resulted in proteome changes enriched in cellular senescence and DNA repair during virus replication. Further analysis of protein changes between infected cells with control and p97 shRNA identifies cell cycle pathways for both HCoV-229E and HCoV-OC43 infection. Together, our data indicate a role for the essential host protein p97 in supporting HCoV replication, suggesting that p97 is a therapeutic target to treat HCoV infection.

Gradual compaction of the central spindle decreases its dynamicity in PRC1 and EB1 gene-edited cells.

During mitosis, the spindle undergoes morphological and dynamic changes. It reorganizes at the onset of the anaphase when the antiparallel bundler PRC1 accumulates and recruits central spindle proteins to the midzone. Little is known about how the dynamic properties of the central spindle change during its morphological changes in human cells. Using gene editing, we generated human cells that express from their endogenous locus fluorescent PRC1 and EB1 to quantify their native spindle distribution and binding/unbinding turnover. EB1 plus end tracking revealed a general slowdown of microtubule growth, whereas PRC1, similar to its yeast orthologue Ase1, binds increasingly strongly to compacting antiparallel microtubule overlaps. KIF4A and CLASP1 bind more dynamically to the central spindle, but also show slowing down turnover. These results show that the central spindle gradually becomes more stable during mitosis, in agreement with a recent "bundling, sliding, and compaction" model of antiparallel midzone bundle formation in the central spindle during late mitosis.

Analysis of DNA methylation of E‐cadherin and p16ink4a in oral lichen planus/oral lichenoid lesions

ObjectivesEpigenetic phenomena are changes in gene expression not involving the DNA sequence. DNA methylation is a major occurrence underlying epigenetic changes in human cells. Although aberrant DNA methylation is well documented in malignant lesions, limited information has been shown on the involvement of DNA methylation in oral lichen planus and oral lichenoid lesions (OLP). The present study aimed to investigate DNA methylation of E‐cadherin and p16 in OLP, and compare the findings with those in non‐inflamed gingiva (Non), radicular cyst (RC), and oral squamous cell carcinoma (SCC).Materials and methodsParaffin‐embedded surgical biopsy specimens were sliced, DNA was extracted, bisulfite treatment was applied, and methylation‐specific polymerase chain reaction was performed. Immunohistochemistry was performed to observe the relative expression patterns of these genes.ResultsE‐cadherin was hypermethylated in OLP (p < 0.01), SCC (p < 0.01), and RC (p < 0.05), when compared with Non; DNA hypermethylation was confirmed in OLP and SCC when compared to Non and RC. Hypermethylation of p16ink4a was observed only in SCC (p < 0.01).ConclusionDNA methylation levels of E‐cadherin and p16ink4a were significantly higher in OLP than in normal tissues, and may be associated with the pathogenesis and progression of the disease.

Pervasive functional translation of noncanonical human open reading frames.

Ribosome profiling has revealed pervasive but largely uncharacterized translation outside of canonical coding sequences (CDSs). In this work, we exploit a systematic CRISPR-based screening strategy to identify hundreds of noncanonical CDSs that are essential for cellular growth and whose disruption elicits specific, robust transcriptomic and phenotypic changes in human cells. Functional characterization of the encoded microproteins reveals distinct cellular localizations, specific protein binding partners, and hundreds of microproteins that are presented by the human leukocyte antigen system. We find multiple microproteins encoded in upstream open reading frames, which form stable complexes with the main, canonical protein encoded on the same messenger RNA, thereby revealing the use of functional bicistronic operons in mammals. Together, our results point to a family of functional human microproteins that play critical and diverse cellular roles.

A meta-analysis of in vitro exposures to weak radiofrequency radiation exposure from mobile phones (1990–2015)

To function, mobile phone systems require transmitters that emit and receive radiofrequency signals over an extended geographical area exposing humans in all stages of development ranging from in-utero, early childhood, adolescents and adults. This study evaluates the question of the impact of radiofrequency radiation on living organisms in vitro studies. In this study, we abstract data from 300 peer-reviewed scientific publications (1990–2015) describing 1127 experimental observations in cell-based in vitro models. Our first analysis of these data found that out of 746 human cell experiments, 45.3% indicated cell changes, whereas 54.7% indicated no changes (p = 0.001). Realizing that there are profound distinctions between cell types in terms of age, rate of proliferation and apoptosis, and other characteristics and that RF signals can be characterized in terms of polarity, information content, frequency, Specific Absorption Rate (SAR) and power, we further refined our analysis to determine if there were some distinct properties of negative and positive findings associated with these specific characteristics. We further analyzed the data taking into account the cumulative effect (SAR × exposure time) to acquire the cumulative energy absorption of experiments due to radiofrequency exposure, which we believe, has not been fully considered previously. When the frequency of signals, length and type of exposure, and maturity, rate of growth (doubling time), apoptosis and other properties of individual cell types are considered, our results identify a number of potential non-thermal effects of radiofrequency fields that are restricted to a subset of specific faster-growing less differentiated cell types such as human spermatozoa (based on 19 reported experiments, p-value = 0.002) and human epithelial cells (based on 89 reported experiments, p-value < 0.0001). In contrast, for mature, differentiated adult cells of Glia (p = 0.001) and Glioblastoma (p < 0.0001) and adult human blood lymphocytes (p < 0.0001) there are no statistically significant differences for these more slowly reproducing cell lines. Thus, we show that RF induces significant changes in human cells (45.3%), and in faster-growing rat/mouse cell dataset (47.3%). In parallel with this finding, further analysis of faster-growing cells from other species (chicken, rabbit, pig, frog, snail) indicates that most undergo significant changes (74.4%) when exposed to RF. This study confirms observations from the REFLEX project, Belyaev and others that cellular response varies with signal properties. We concur that differentiation of cell type thus constitutes a critical piece of information and should be useful as a reference for many researchers planning additional studies. Sponsorship bias is also a factor that we did not take into account in this analysis.

A precisely positioned MED12 activation helix stimulates CDK8 kinase activity

The Mediator kinase module regulates eukaryotic transcription by phosphorylating transcription-related targets and by modulating the association of Mediator and RNA polymerase II. The activity of its catalytic core, cyclin-dependent kinase 8 (CDK8), is controlled by Cyclin C and regulatory subunit MED12, with its deregulation contributing to numerous malignancies. Here, we combine in vitro biochemistry, cross-linking coupled to mass spectrometry, and in vivo studies to describe the binding location of the N-terminal segment of MED12 on the CDK8/Cyclin C complex and to gain mechanistic insights into the activation of CDK8 by MED12. Our data demonstrate that the N-terminal portion of MED12 wraps around CDK8, whereby it positions an "activation helix" close to the T-loop of CDK8 for its activation. Intriguingly, mutations in the activation helix that are frequently found in cancers do not diminish the affinity of MED12 for CDK8, yet likely alter the exact positioning of the activation helix. Furthermore, we find the transcriptome-wide gene-expression changes in human cells that result from a mutation in the MED12 activation helix to correlate with deregulated genes in breast and colon cancer. Finally, functional assays in the presence of kinase inhibitors reveal that binding of MED12 remodels the active site of CDK8 and thereby precludes the inhibition of ternary CDK8 complexes by type II kinase inhibitors. Taken together, our results not only allow us to propose a revised model of how CDK8 activity is regulated by MED12, but also offer a path forward in developing small molecules that target CDK8 in its MED12-bound form.

4′‐Phosphopantetheine corrects CoA, iron, and dopamine metabolic defects in mammalian models of PKAN

Pantothenate kinase‐associated neurodegeneration (PKAN) is an inborn error of CoA metabolism causing dystonia, parkinsonism, and brain iron accumulation. Lack of a good mammalian model has impeded studies of pathogenesis and development of rational therapeutics. We took a new approach to investigating an existing mouse mutant of Pank2 and found that isolating the disease‐vulnerable brain revealed regional perturbations in CoA metabolism, iron homeostasis, and dopamine metabolism and functional defects in complex I and pyruvate dehydrogenase. Feeding mice a CoA pathway intermediate, 4′‐phosphopantetheine, normalized levels of the CoA‐, iron‐, and dopamine‐related biomarkers as well as activities of mitochondrial enzymes. Human cell changes also were recovered by 4′‐phosphopantetheine. We can mechanistically link a defect in CoA metabolism to these secondary effects via the activation of mitochondrial acyl carrier protein, which is essential to oxidative phosphorylation, iron–sulfur cluster biogenesis, and mitochondrial fatty acid synthesis. We demonstrate the fidelity of our model in recapitulating features of the human disease. Moreover, we identify pharmacodynamic biomarkers, provide insights into disease pathogenesis, and offer evidence for 4′‐phosphopantetheine as a candidate therapeutic for PKAN.

Preclinical evaluation of 1,2,4-triazole-based compounds targeting voltage-gated sodium channels (VGSCs) as promising anticonvulsant drug candidates.

Epilepsy is a chronic neurological disorder affecting nearly 65-70 million people worldwide. Despite the observed advances in the development of new antiepileptic drugs (AEDs), still about 30-40% of patients cannot achieve a satisfactory seizure control. In our current research, we aimed at using the combined results of radioligand binding experiments, PAMPA-BBB assay and animal experimentations in order to design a group of compounds that exhibit broad spectrum of anticonvulsant activity. The synthesized 4-alkyl-5-substituted-1,2,4-triazole-3-thione derivatives were primarily screened in the maximal electroshock-induced seizure (MES) test in mice. Next, the most promising compounds (17, 22) were investigated in 6 Hz (32 mA) psychomotor seizure model. Protective effect of compound 22 was almost similar to that of levetiracetam. Moreover, these compounds did not induce genotoxic and hemolytic changes in human cells as well as they were characterized by low cellular toxicity. Taking into account the structural requirements for good anticonvulsant activity of 4-alkyl-5-aryl-1,2,4-triazole-3-thiones, it is visible that small electron-withdrawing substituents attached to phenyl ring have beneficial effects both on affinity towards VGSCs and protective activity in the animal models of epilepsy.

Biophysical and biomechanical properties of neural progenitor cells as indicators of developmental neurotoxicity.

Conventional in vitro toxicity studies have focused on identifying IC50 and the underlying mechanisms, but how toxicants influence biophysical and biomechanical changes in human cells, especially during developmental stages, remain understudied. Here, using an atomic force microscope, we characterized changes in biophysical (cell area, actin organization) and biomechanical (Young's modulus, force of adhesion, tether force, membrane tension, tether radius) aspects of human fetal brain-derived neural progenitor cells (NPCs) induced by four classes of widely used toxic compounds, including rotenone, digoxin, N-arachidonoylethanolamide (AEA), and chlorpyrifos, under exposure up to 36h. The sub-cellular mechanisms (apoptosis, mitochondria membrane potential, DNA damage, glutathione levels) by which these toxicants induced biochemical changes in NPCs were assessed. Results suggest a significant compromise in cell viability with increasing toxicant concentration (p < 0.01), and biophysical and biomechanical characteristics with increasing exposure time (p < 0.01) as well as toxicant concentration (p < 0.01). Impairment of mitochondrial membrane potential appears to be the most sensitive mechanism of neurotoxicity for rotenone, AEA and chlorpyrifos exposure, but compromise in plasma membrane integrity for digoxin exposure. The surviving NPCs remarkably retained stemness (SOX2 expression) even at high toxicant concentrations. A negative linear correlation (R2 = 0.92) exists between the elastic modulus of surviving cells and the number of living cells in that environment. We propose that even subtle compromise in cell mechanics could serve as a crucial marker of developmental neurotoxicity (mechanotoxicology) and therefore should be included as part of toxicology assessment repertoire to characterize as well as predict developmental outcomes.

Studying the free radical scavenging activity using low concentration of nanogold particles

Radiation is the emission energy or transition through space or through material medium in the form of a particle or wave. The radiation affects human body in highly complied processes. Various degrees of biological effects, from degrees to death of living tissues, involve a number of pathological change in human cells due to produce free radicals which are chemical species such as an atom, a molecule or an ion which contains unpaired electrons. In this study, gold nanoparticles (AuNPs) were synthesized by reducing agent gel and inhibition to reduce Au+3 ions of chlorooric acid (HAuCl4.3H2O) to nano gold. Requires reactive heating about 70°C. NPs were monitored by UV spectroscopy. The UV spectra showed 524 nm wavelength. The AuNPs, such as size, shape and stability, AFM and TEM techniques indicating a volume of 20-50 nm. Evaluation of antioxidant properties of AuNPs residues was done using DPPH assay. These nanoparticles have been found to be highly capable of antioxidants and can therefore be used as potential radical contaminants against harmful damage caused by free radicals.

Biochemical Changes in Human Cells Exposed to Low Concentrations of Gold Nanoparticles Detected by Raman Microspectroscopy.

The toxicological implications of nanoparticles deserve accurate scientific investigation for the protection of human health. Although toxic effects involve specific organs, the events that cause them have their origin from biochemical modifications of some cellular constituents. Therefore, a first analysis to evaluate the effects due to the action of nanoparticles is achieved by investigation of in vitro cells, which allows the identification of the cellular modifications caused by nanoparticles (NPs) even at much lower doses than the lethal ones. This work evaluated the Raman microspectroscopy capability to monitor biochemical changes occurring in human cells as a consequence of exposure to a suspension of gold nanoparticles with a non-cytotoxic concentration. Human keratinocyte cells were used as a model cell line, because they are mainly involved in environmental exposure. A trypan blue assay revealed that the investigated concentration, 650 ng/mL, is non-cytotoxic (about 5% of cells died after 48 h exposure). Specific Raman spectral markers to represent the cell response to nanoparticle exposure were found (at 1450 and 2865 cm−1) in the cytoplasm spectra, with the aid of ratiometric and principal component analysis.

Four Food and Drug Administration draft guidance documents and the REGROW Act: A litmus test for future changes in human cell- and tissue-based products regulatory policy in the United States?

Modern regenerative medicine research has expanded well past the development of traditional drugs and medical devices with many promising new therapies encompassing an increasingly diverse range of substances, notably cell‐based therapies. These substantial recent developments and the progress in the health care and therapeutics fields necessitate a new regulatory framework agile enough to accommodate these unique therapies and acknowledge their differences with traditional pharmaceuticals. In the United States, recent proposed changes in the regulatory framework for autologous human cells, tissues, and cellular and tissue‐based products (HCT/Ps) and their perceived risk–benefit analysis for patients remain controversial in the scientific field. To provide perspective on of the current status of the most recent attempts to redefine and conceptualize these changes in the United States, we will examine 4 draft guidance documents implemented by the Food and Drug Administration in interpreting relevant concepts and terminology pertaining to HCT/Ps: the Bipartisan Policy Center think tank report, “Advancing Regenerative Cellular Therapy: Medical Innovation for Healthier Americans,” the proposed REGROW Act for HCT/Ps, and the current 24 Food and Drug Administration‐approved HCT/Ps and related products in the United States.

Цитогенетические и экспрессионные маркеры индивидуальной радиочувствительности человека

Воздействие ионизирующего излучения вызывает значительные функциональные изменения в клетках человека, выражающиеся в активации различных сигнальных путей и транскрипционного ответа множества генов. Величина этих изменений вариабельна у разных индивидов, составляя феномен индивидуальной радиочувствительности. В обзоре рассматриваются известные маркеры индивидуальной радиочувствительности человека, начиная от цитогенетических, позволяющих непосредственно оценить эффективность репарации радиационно-индуцированных повреждений ДНК в клетках, до маркеров, выделенных на основании полногеномных и полнотранскриптомных исследований дифференциально экспрессирующихся генов, обусловливающих различные аспекты клеточного и организменного ответа на радиационное воздействие. Exposure to ionizing radiation causes significant functional changes in human cells which lead to activation of various signaling pathways and transcriptional response of many genes. The magnitude of these changes is variable for different individuals, making the phenomenon of individual radiosensitivity. In the review, markers of individual radiosensitivity are described ranging from cytogenetic markers for assessing the efficiency of DNA repair of radiation-induced damage in cells to genome- and transcriptome-wide approaches to identify differentially expressed genes that determine various aspects of response to radiation exposure.

The fourth annual BRDS on genome editing and silencing for precision medicines.

Precision medicine is promising for treating human diseases, as it focuses on tailoring drugs to a patient's genes, environment, and lifestyle. The need for personalized medicines has opened the doors for turning nucleic acids into therapeutics. Although gene therapy has the potential to treat and cure genetic and acquired diseases, it needs to overcome certain obstacles before creating the overall prescription drugs. Recent advancement in the life science has helped to understand the effective manipulation and delivery of genome-engineering tools better. The use of sequence-specific nucleases allows genetic changes in human cells to be easily made with higher efficiency and precision than before. Nanotechnology has made rapid advancement in the field of drug delivery, but the delivery of nucleic acids presents unique challenges. Also, designing efficient and short time-consuming genome-editing tools with negligible off-target effects are in high demand for precision medicine. In the fourth annual Biopharmaceutical Research and Development Symposium (BRDS) held at the University of Nebraska Medical Center (UNMC) on September 7-8, 2017, we covered different facets of developing tools for precision medicine for therapeutic and diagnosis of genetic disorders.