An accessible and high-throughput strategy of continuously monitoring apoptosis by fluorescent detection of caspase activation

Depth-enhanced high-throughput microscopy by compact PSF engineering

High-throughput microscopy is vital for screening applications, where three-dimensional (3D) cellular models play a key role. However, due to defocus susceptibility, current 3D high-throughput microscopes require axial scanning, which lowers throughput and increases photobleaching and photodamage. Point spread function (PSF) engineering is an optical method that enables various 3D imaging capabilities, yet it has not been implemented in high-throughput microscopy due to the cumbersome optical extension it typically requires. Here we demonstrate compact PSF engineering in the objective lens, which allows us to enhance the imaging depth of field and, combined with deep learning, recover 3D information using single snapshots. Beyond the applications shown here, this work showcases the usefulness of high-throughput microscopy in obtaining training data for deep learning-based algorithms, applicable to a variety of microscopy modalities.

Targeting senescent cells with NKG2D-CAR T cells

This study investigates the efficacy of NKG2D chimeric antigen receptor (CAR) engineered T cells in targeting and eliminating stress-induced senescent cells in vitro. Cellular senescence contributes to age-related tissue decline and is characterized by permanent cell cycle arrest and the senescence-associated secretory phenotype (SASP). Immunotherapy, particularly CAR-T cell therapy, emerges as a promising approach to selectively eliminate senescent cells. Our focus is on the NKG2D receptor, which binds to ligands (NKG2DLs) upregulated in senescent cells, offering a target for CAR-T cells. Using mouse embryonic fibroblasts (MEFs) and astrocytes (AST) as senescence models, we demonstrate the elevated expression of NKG2DLs in response to genotoxic and oxidative stress. NKG2D-CAR T cells displayed potent cytotoxicity against these senescent cells, with minimal effects on non-senescent cells, suggesting their potential as targeted senolytics. In conclusion, our research presents the first evidence of NKG2D-CAR T cells' ability to target senescent brain cells, offering a novel approach to manage senescence-associated diseases. The findings pave the way for future investigations into the therapeutic applicability of NKG2D-targeting CAR-T cells in naturally aged organisms and models of aging-associated brain diseases in vivo.

Cleaved caspase-3 is present in the majority of glial cells in the intact rat spinal cord during postnatal life

Cell death is an essential process that occurs during the development of the central nervous system. Despite the availability of a wide range of commercially produced antibodies against various apoptotic markers, data regarding apoptosis in intact spinal cord during postnatal development and adulthood are mostly missing. We investigated apoptosis in rat spinal cord at different stages of ontogenesis (postnatal days 8, 29, and 90). For this purpose, we applied immunofluorescent detection of two widely used apoptotic markers, cleaved caspase-3 (cC3) and cleaved poly(ADP-ribose) polymerase (cPARP). Surprisingly, we found significant discrepancy between the number of cC3+ cells and PARP+ cells, with a ratio between 500:1 and 5000:1 in rat spinal cord at all postnatal time points. The majority of cC3+ cells were glial cells and did not exhibit an apoptotic phenotype. In contrast with in vivo results, in vitro analysis of primary cell cultures derived from neonatal rat spinal cord and treated with the apoptotic inductor staurosporine revealed a similar onset of occurrence of both cC3 and cPARP in cells subjected to apoptosis. Gene expression analysis of spinal cord revealed elevated expression of the Birc4 (XIAP), Birc2, and Birc5 (Survivin) genes, which are known potent inhibitors of apoptosis. Our data indicate that cC3 is not an exclusive marker of apoptosis, especially in glial cells, owing its possible presence in inhibited forms and/or its participation in other non-apoptotic roles. Therefore, cPARP appears to be a more appropriate marker to detect apoptosis.

Multiplexed live-cell imaging for drug responses in patient-derived organoid models of cancer

Patient-derived organoid (PDO) models of cancer are a multifunctional research system that better recapitulates human disease as compared to cancer cell lines. PDO models can be generated by culturing patient tumor cells in extracellular basement membrane extracts (BME) and plating as three-dimensional domes. However, commercially available reagents that have been optimized for phenotypic assays in monolayer cultures often are not compatible with BME. Herein we describe a method to plate PDO models and assess drug effects using an automated live-cell imaging system. In addition, we apply fluorescent dyes that are compatible with kinetic measurements to simultaneously quantitate cell health and apoptosis. Image capture can be customized to occur at regular time intervals over several days. Users can analyze drug effects in individual Z-plane images or a Z Projection of serial images from multiple focal planes. Using masking, specific parameters of interest are calculated, such as PDO number, area, and fluorescence intensity. We provide proof-of-concept data demonstrating the effect of cytotoxic agents on cell health, apoptosis and viability. This automated kinetic imaging platform can be expanded to other phenotypic readouts to understand diverse therapeutic effects in PDO models of cancer.

Cholesterol biosynthesis modulates differentiation in murine cranial neural crest cells

Cranial neural crest cells (cNCC) are a multipotent embryonic cell population that give rise to a diverse set of cell types. These cells are particularly vulnerable to external metabolic stressors, as exemplified by the association between maternal hyperglycemia and congenital malformations. We were interested in studying the effect of various concentrations of glucose and pyruvate on cNCC metabolism, migration, and differentiation using an established murine neural crest cell model (O9-1). We unexpectedly observed a pattern of gene expression suggestive of cholesterol biosynthesis induction under glucose depletion conditions in O9-1 cells. We further showed that treatment with two different cholesterol synthesis inhibitors interfered with cell migration and differentiation, inhibiting chondrogenesis while enhancing smooth muscle cell differentiation. As congenital arhinia (absent external nose), a malformation caused by mutations in SMCHD1, appears to represent, in part, a defect in cNCC, we were also interested in investigating the effects of glucose and cholesterol availability on Smchd1 expression in O9-1 cells. Smchd1 expression was induced under high glucose conditions whereas cholesterol synthesis inhibitors decreased Smchd1 expression during chondrogenesis. These data highlight a novel role for cholesterol biosynthesis in cNCC physiology and demonstrate that human phenotypic variability in SMCHD1 mutation carriers may be related, in part, to SMCHD1's sensitivity to glucose or cholesterol dosage during development.

SynDISCO: A Mechanistic Modeling-Based Framework for Predictive Prioritization of Synergistic Drug Combinations Targeting Cell Signalling Networks

The widespread development of resistance to cancer monotherapies has prompted the need to identify combinatorial treatment approaches that circumvent drug resistance and achieve more durable clinical benefit. However, given the vast space of possible combinations of existing drugs, the inaccessibility of drug screens to candidate targets with no available drugs, and the significant heterogeneity of cancers, exhaustive experimental testing of combination treatments remains highly impractical. There is thus an urgent need to develop computational approaches that complement experimental efforts and aid the identification and prioritization of effective drug combinations. Here, we provide a practical guide to SynDISCO, a computational framework that leverages mechanistic ODE modeling to predict and prioritize synergistic combination treatments directed at signaling networks. We demonstrate the key steps of SynDISCO and its application to the EGFR-MET signaling network in triple negative breast cancer as an illustrative example. SynDISCO is, however, a network- and cancer-independent framework, and given a suitable ODE model of the network of interest, it could be leveraged to discover cancer-specific combination treatments.

Upconversion nanoparticles as an immunocomplexing agent for selective detection of caspases via sandwich-like supracomplexes

In this study, a nanoparticle-based sandwich-like immunoassay was designed in dispersion medium to precisely detect apoptosis over caspase antibodies in order to overcome the disadvantages of traditional apoptosis determination methods such as high cost, large sampling requirement, and appropriate laboratory and equipment conditions. For this purpose, a complementary particulate system including magnetic (MNPs) and upconversion silica (UC-SiNPs) nanoparticles while immobilizing antibodies (primary antibody to MNPs, secondary antibody to UC-SiNPs) were synthesized and characterized. Optimization and selectivity studies of the complex formed by primary antibody immobilized MNPs with standard caspase proteins were examined by the HPLC system. Within the scope of optimization studies, protein concentrations, optimal duration, and temperature parameters were evaluated. Optimal conditions were determined for pH, initial concentration, time, and temperature as 7.4, 5.6 μg/mL, 45 min, and room temperature, respectively. Furthermore, the adsorption of competitive proteins was investigated in selectivity studies as well. Moreover, the primary antibody immobilized MNPs were treated with standard caspase proteins under optimal conditions; subsequently, they were interacted with secondary antibody immobilized UC-SiNPs to demonstrate the supracomplex formation meanwhile zeta potential/size measurements and fluorescence emission spectrometry analyses were performed. As a result of these analyses, it was observed that the sandwich-like supracomplexes were successfully formed that significantly varied upconversion emission intensities of UC-SiNPs in dependence on the amounts of caspase proteins. Because this approach enabled a quantitative result, the nanoparticle-based sandwich-like immunoassay should be classified as an easy-to-handled, fast, and promising alternative to benchmark apoptosis assays.

High-throughput screening paradigms in ecotoxicity testing: Emerging prospects and ongoing challenges

The rapidly increasing number of new production chemicals coupled with stringent implementation of global chemical management programs necessities a paradigm shift towards boarder uses of low-cost and high-throughput ecotoxicity testing strategies as well as deeper understanding of cellular and sub-cellular mechanisms of ecotoxicity that can be used in effective risk assessment. The latter will require automated acquisition of biological data, new capabilities for big data analysis as well as computational simulations capable of translating new data into in vivo relevance. However, very few efforts have been so far devoted into the development of automated bioanalytical systems in ecotoxicology. This is in stark contrast to standardized and high-throughput chemical screening and prioritization routines found in modern drug discovery pipelines. As a result, the high-throughput and high-content data acquisition in ecotoxicology is still in its infancy with limited examples focused on cell-free and cell-based assays. In this work we outline recent developments and emerging prospects of high-throughput bioanalytical approaches in ecotoxicology that reach beyond in vitro biotests. We discuss future importance of automated quantitative data acquisition for cell-free, cell-based as well as developments in phytotoxicity and in vivo biotests utilizing small aquatic model organisms. We also discuss recent innovations such as organs-on-a-chip technologies and existing challenges for emerging high-throughput ecotoxicity testing strategies. Lastly, we provide seminal examples of the small number of successful high-throughput implementations that have been employed in prioritization of chemicals and accelerated environmental risk assessment.

Ibuprofen and diclofenac differentially affect cell viability, apoptosis and morphological changes in human cholangiocarcinoma cell lines

Objectives

Cholangiocarcinoma is a malignant biliary epithelial duct neoplasm caused by chronic inflammation after liver fluke infection. It is a major public health concern in the Greater Mekong sub-region in northeast Thailand. Herein, the effects of the non-steroidal anti-inflammatory drugs (NSAIDs) ibuprofen and diclofenac on the cell proliferation activity of the human cholangiocarcinoma cell lines KKU-M139 and KKU-213B were studied.

Methods

Cell viability was assessed with MTT assays. Inverted phase-contrast light microscopy, scanning electron microscopy and transmission electron microscopy were used to investigate the cells’ morphological alterations. Caspase 3/7 and Annexin V/PI were detected with a multimode microplate reader.

Results

Ibuprofen and diclofenac decreased viability in both cell lines, and ibuprofen-treated cells exhibited reversible cell injury. In both KKU-M139 and KKU-213B cell lines, the diclofenac-treated cells had the greatest injury. The cells exhibited features of irreversible cell injury. In addition, caspase 3/7 and Annexin V/PI detection revealed early cell apoptotic characteristics.

Conclusion

These findings suggest that NSAIDs may potentially suppress cell viability. Ibuprofen and diclofenac both induced morphological changes and apoptosis.

Quantitative Analysis of Apoptosis and Necrosis in Live Cells Using Flow Cytometry

Apoptosis and necrosis are the two sides of the cell death penumbra. Apoptosis is a well-studied model of cell death wherein the cell destroys itself employing a predefined form of active signaling without the release of soluble cytoplasmic contents to the external environment. Compared to apoptosis, necrosis is a nonspecific form of sudden cell death in response to an invasive external stimulus which in turn is devoid of active programmed intracellular signaling leading to the sudden release of the soluble cellular contents consequent to the rupture of the cell membrane. This fundamental difference between apoptosis and necrosis made us believe that the former is the safe form of cell death and the latter is an undesirable one which often elicits an inflammatory response to the adjacent cells. Recent studies have shown that necrosis also involves a few defined cellular and complex biochemical events similar to apoptosis rendering it difficult to distinguish these two events at the single-cell level using the currently used popular assays.Here we provide a newly described detailed methodology encompassing cell system development along with a multiparametric flow cytometry-based approach to discriminate apoptotic cells from necrotic cells using a stable cell line expressing genetically encoded probe for detecting caspase activation and DsRed targeted at the mitochondria.

Designing of various biosensor devices for determination of apoptosis: A comprehensive review

Apoptosis is a type of cell death caused by the occurrence of both pathological and physiological conditions triggered by ligation of death receptors outside the cell or triggered by DNA damage and/or cytoskeleton disruption. Timely monitoring of apoptosis can effectively help early diagnosis of related diseases and continuous assessment of the effectiveness of drugs. Detecting caspases, a protease family closely related to cellular apoptosis, and its identification as markers of apoptosis is a popular procedure. Biosensors are used for early diagnosis and play a very important role in preventing disease progression in various body sections. Recently, there has been a widespread increase in the desire to use materials made of paper (e.g. nitrocellulose membrane) for Point-of-Care (POC) testing systems since paper and paper-like materials are cheap, abundant and degradable. Microfluidic paper-based analytical devices (μPADs) are highly promising as they are cost-effective, easy to use, fast, precise and sustainable over time and under different environmental conditions. In this review, we focused our efforts on compiling the different approaches on identifying apoptosis pathway while giving brief information about apoptosis and biosensors. This review includes recent advantages in biosensing techniques to simply determine what happened in the cell life and which direction it would continue. As a conclusion, we believed that the review may help to researchers to compare/update the knowledge about diagnosis of the apoptosis pathway while reminding the basic definitions about the apoptosis and biosensor technologies.

Modelling and Prevention of Acute Kidney Injury through Ischemia and Reperfusion in a Combined Human Renal Proximal Tubule/Blood Vessel-on-a-Chip

Background

Renal ischemia/reperfusion injury (rIRI) is one of the major causes of AKI. Although animal models are suitable for investigating systemic symptoms of AKI, they are limited in translatability. Human in vitro models are crucial in giving mechanistic insights into rIRI; however, they miss out on crucial aspects such as reperfusion injury and the multitissue aspect of AKI.

Methods

We advanced the current renal proximal tubule-on-a-chip model to a coculture model with a perfused endothelial vessel separated by an extracellular matrix. The coculture was characterized for its three-dimensional structure, protein expression, and response to nephrotoxins. Then, rIRI was captured through control of oxygen levels, nutrient availability, and perfusion flow settings. Injury was quantified through morphologic assessment, caspase-3/7 activation, and cell viability.

Results

The combination of low oxygen, reduced glucose, and interrupted flow was potent to disturb the proximal tubules. This effect was strongly amplified upon reperfusion. Endothelial vessels were less sensitive to the ischemia-reperfusion parameters. Adenosine treatment showed a protective effect on the disruption of the epithelium and on the caspase-3/7 activation.

Conclusions

A human in vitro rIRI model was developed using a coculture of a proximal tubule and blood vessel on-a-chip, which was used to characterize the renoprotective effect of adenosine. The robustness of the model and assays in combination with the throughput of the platform make it ideal to advance pathophysiological research and enable the development of novel therapeutic modalities.

Evaluation In Vitro of Toxicity of Hydroalcoholic Extract of Leaves and Roots from Yacon (Smallanthus sonchifolius)

Yacon is an Andean plant that has been used in folk medicine for its medicinal properties. The beneficial effects of this plant are possibly due to the high content of phenolic compounds present in its leaves and roots. This study evaluated the in vitro toxicity of the hydroalcoholic extract of leaves and roots from yacon (1, 10, 50, and 100 μg/mL) through cell viability tests, genotoxic and mutagenic activity in leukocytes culture cells; and cytotoxicity and apoptosis cell death (1, 10, 50, 100, and 500 μg/mL) in cell line originally established from the primary mouse embryonic fibroblast cells that were cultured by the designated protocol, so-called 3T3 protocol "3-day transfer, inoculum 3 × 10⁵ cells" (3T3 cell line). No mutagenic and cytotoxic activities were observed in leukocyte cultures. Cytotoxic activity was evidenced in the highest concentrations of yacon leaf extract (50 and 100 μg/mL), whereas all concentrations tested with yacon leaf extract there was induction for apoptosis in the 3T3 cells. Genotoxic potential was observed only at higher doses of leaf (50 and 100 μg/mL) and root (100 μg/mL) extract. These results suggest that yacon leaf at high concentrations may present toxic potential showing concentration-dependent behavior; however, in vivo studies should be performed to validate these results.

Apoptosis Resistance in Fibroblasts Precedes Progressive Scarring in Pulmonary Fibrosis and Is Partially Mediated by Toll-Like Receptor 4 Activation

Inhalation of environmental toxicants such as cigarette smoke, metal or wood dust, silica, or asbestos is associated with increased risk for idiopathic pulmonary fibrosis (IPF). IPF involves progressive scarring of lung tissue, which interferes with normal respiration and is ultimately fatal; however, the complex cellular mechanisms of IPF pathogenesis remain unclear. Fibroblast apoptosis is essential in normal wound healing but is dysregulated in IPF. Recent studies suggest that Toll-like receptor 4 (TLR4) is key in the onset of IPF. Here, radiation-induced PF was used as a model for IPF because it very closely mimics the progressive and intractable nature of IPF. Female C57BL/6J (C57) and C57BL/6J TLR4-/- mice were exposed to a single dose of 13 Gy whole-thorax ionizing radiation. Although both strains showed similar levels of immediate radiation-induced damage, C57 mice exhibited more extensive fibrosis at 22-week postirradiation (PI) than TLR4-/- mice. Isolated C57 primary 1° MLFs showed decreased apoptosis susceptibility as early as 8-week postirradiation, a phenotype that persisted for the remainder of the radiation response. TLR4-/- 1° mouse lung fibroblasts did not exhibit significant apoptosis resistance at any point. Systemic release of high mobility group box 1, a TLR4 agonist, during the pneumonitis phase of the radiation response may act through TLR4 to contribute to fibroblast apoptosis resistance and thus interfere with wound resolution. These findings demonstrate that apoptosis resistance occurs earlier in pulmonary fibrosis pathogenesis than previously assumed, and that TLR4 signaling is a key mediator in this process.

Novel Insights into the Roles of Bcl-2 Homolog Nr-13 (vNr-13) Encoded by Herpesvirus of Turkeys in the Virus Replication Cycle, Mitochondrial Networks, and Apoptosis Inhibition

The Bcl-2 (B cell lymphoma 2)-related protein Nr-13 plays a major role in the regulation of cell death in developing avian B cells. With over 65% sequence similarity to the chicken Nr-13, herpesvirus of turkeys (HVT) vNr-13, encoded by the HVT079 and HVT096 genes, is the first known alphaherpesvirus-encoded Bcl-2 homolog. HVT-infected cells were reported to be relatively more resistant to serum starvation, suggested that vNr-13 could be involved in protecting the cells. Here, we describe CRISPR/Cas9-based editing of exon 1 of the HVT079 and HVT096 genes from the HVT genome to generate the mutant HVT-ΔvNr-13 to gain insights into its functional roles. Overall, wild-type HVT and HVT-ΔvNr-13 showed similar growth kinetics; however, at early time points, HVT-ΔvNr-13 showed 1.3- to 1.7-fold-lower growth of cell-associated virus and 3- to 6.2-fold-lower growth of cell-free virus. In transfected cells, HVT vNr-13 showed a mainly diffuse cytoplasmic distribution with faint nuclear staining. Further, vNr-13 localized to the mitochondria and endoplasmic reticulum (ER) and disrupted mitochondrial network morphology in the transfected cells. In the wild-type HVT-infected cells, vNr-13 expression appeared to be directly involved in the disruption of the mitochondrial network, as the mitochondrial network morphology was substantially restored in the HVT-ΔvNr-13-infected cells. IncuCyte S3 real-time apoptosis monitoring demonstrated that vNr-13 is unequivocally involved in the apoptosis inhibition, and it is associated with an increase of PFU, especially under serum-free conditions in the later stages of the viral replication cycle. Furthermore, HVT blocks apoptosis in infected cells but activates apoptosis in noninfected bystander cells.IMPORTANCE B cell lymphoma 2 (Bcl-2) family proteins play important roles in regulating apoptosis during homeostasis, tissue development, and infectious diseases. Several viruses encode homologs of cellular Bcl-2-proteins (vBcl-2) to inhibit apoptosis, which enable them to replicate and persist in the infected cells and to evade/modulate the immune response of the host. Herpesvirus of turkeys (HVT) is a nonpathogenic alphaherpesvirus of turkeys and chickens that is widely used as a live vaccine against Marek's disease and as recombinant vaccine viral vectors for protecting against multiple avian diseases. Identical copies of the HVT genes HVT079 and HVT096 encode the Bcl-2 homolog vNr-13. While previous studies have identified the potential ability of vNr-13 in inhibiting apoptosis induced by serum deprivation, there have been no detailed investigations on the functions of vNr-13. Using CRISPR/Cas9-based ablation of the vNr-13 gene, we demonstrated the roles of HVT vNr-13 in early stages of the viral replication cycle, mitochondrial morphology disruption, and apoptosis inhibition in later stages of viral replication.

Separase-triggered apoptosis enforces minimal length of mitosis

Prolonged mitosis often results in apoptosis¹. Shortened mitosis causes tumorigenic aneuploidy, but it is unclear whether it also activates the apoptotic machinery². Separase, a cysteine protease and trigger of all eukaryotic anaphases, has a caspase-like catalytic domain but has not previously been associated with cell death^3,4. Here we show that human cells that enter mitosis with already active separase rapidly undergo death in mitosis owing to direct cleavage of anti-apoptotic MCL1 and BCL-XL by separase. Cleavage not only prevents MCL1 and BCL-XL from sequestering pro-apoptotic BAK, but also converts them into active promoters of death in mitosis. Our data strongly suggest that the deadliest cleavage fragment, the C-terminal half of MCL1, forms BAK/BAX-like pores in the mitochondrial outer membrane. MCL1 and BCL-XL are turned into separase substrates only upon phosphorylation by NEK2A. Early mitotic degradation of this kinase is therefore crucial for preventing apoptosis upon scheduled activation of separase in metaphase. Speeding up mitosis by abrogation of the spindle assembly checkpoint results in a temporal overlap of the enzymatic activities of NEK2A and separase and consequently in cell death. We propose that NEK2A and separase jointly check on spindle assembly checkpoint integrity and eliminate cells that are prone to chromosome missegregation owing to accelerated progression through early mitosis.

High-Throughput Screening Technology in Industrial Biotechnology

Based on the development of automatic devices and rapid assay methods, various high-throughput screening (HTS) strategies have been established for improving the performance of industrial microorganisms. We discuss the most significant factors that can improve HTS efficiency, including the construction of screening libraries with high diversity and the use of new detection methods to expand the search range and highlight target compounds. We also summarize applications of HTS for enhancing the performance of industrial microorganisms. Current challenges and potential improvements to HTS in industrial biotechnology are discussed in the context of rapid developments in synthetic biology, nanotechnology, and artificial intelligence. Rational integration will be an important driving force for constructing more efficient industrial microorganisms with wider applications in biotechnology.