Probing chromatin structure in the early phases of apoptosis

Somatic Mosaicism in Amyotrophic Lateral Sclerosis and Frontotemporal Dementia Reveals Widespread Degeneration from Focal Mutations

Although mutations in dozens of genes have been implicated in familial forms of amyotrophic lateral sclerosis (fALS) and frontotemporal degeneration (fFTD), most cases of these conditions are sporadic (sALS and sFTD), with no family history, and their etiology remains obscure. We tested the hypothesis that somatic mosaic mutations, present in some but not all cells, might contribute in these cases, by performing ultra-deep, targeted sequencing of 88 genes associated with neurodegenerative diseases in postmortem brain and spinal cord samples from 404 individuals with sALS or sFTD and 144 controls. Known pathogenic germline mutations were found in 20.6% of ALS, and 26.5% of FTD cases. Predicted pathogenic somatic mutations in ALS/FTD genes were observed in 2.7% of sALS and sFTD cases that did not carry known pathogenic or novel germline mutations. Somatic mutations showed low variant allele fraction (typically <2%) and were often restricted to the region of initial discovery, preventing detection through genetic screening in peripheral tissues. Damaging somatic mutations were preferentially enriched in primary motor cortex of sALS and prefrontal cortex of sFTD, mirroring regions most severely affected in each disease. Somatic mutation analysis of bulk RNA-seq data from brain and spinal cord from an additional 143 sALS cases and 23 controls confirmed an overall enrichment of somatic mutations in sALS. Two adult sALS cases were identified bearing pathogenic somatic mutations in DYNC1H1 and LMNA, two genes associated with pediatric motor neuron degeneration. Our study suggests that somatic mutations in fALS/fFTD genes, and in genes associated with more severe diseases in the germline state, contribute to sALS and sFTD, and that mosaic mutations in a small fraction of cells in focal regions of the nervous system can ultimately result in widespread degeneration.

Characterization of TaSPP-5A gene associated with sucrose content in wheat (Triticum aestivum L.)

BACKGROUND

Sucrose, the major product of photosynthesis and the primary sugar transported as a soluble carbohydrate via the phloem, is a critical determinant for harvest yield in wheat crops. Sucrose-phosphatase (SPP) catalyzes the final step in the sucrose biosynthesis pathway, implying its essential role in the plant.

RESULT

In this study, wheat SPP homologs genes were isolated from chromosomes 5A, 5B, and 5D, designated as TaSPP-5A, TaSPP-5B, and TaSPP-5D, respectively. Sequence alignment showed one 1-bp Insertion-deletion (InDel) and three single nucleotide polymorphisms (SNPs) at TaSPP-5A coding region, forming two haplotypes, TaSPP-5Aa and TaSPP-5Ab, respectively. A derived cleaved amplified polymorphism sequence (dCAPS) marker, TaSPP-5A-dCAPS, was developed to discriminate allelic variation based on the polymorphism at position 1242 (C-T). A total of 158 varieties were used to perform a TaSPP-5A marker-trait association analysis, where two haplotypes were significantly associated with sucrose content in two environments and with thousand-grain weight (TGW) and grain length (GL) in three environments. Quantitative real-time PCR further revealed that TaSPP-5Aa showed relatively higher expression than TaSPP-5Ab in wheat seedling leaves, generally associating with increased sucrose content and TGW. The expression of TaSPP-5A and sucrose content in TaSPP-5Aa haplotypes were also higher than those in TaSPP-5Ab haplotypes under both 20% PEG-6000 and 100 μM ABA treatment. Sequence alignment showed that the two TaSPP-5A haplotypes comprised 11 SNPs from -395 to -1962 bp at TaSPP-5A promoter locus, participating in the formation of several conserved sequences, may account for the high expression of TaSPP-5A in TaSPP-5Aa haplotypes. In addition, the distribution analysis of TaSPP-5A haplotypes revealed that TaSPP-5Aa was preferred in the natural wheat population, being strongly positively selected in breeding programs.

CONCLUSION

According to the SNPs detected in the TaSPP-5A sequence, two haplotypes, TaSPP-5Aa and TaSPP-5Ab, were identified among wheat accessions, which potential value for sucrose content selection was validated by association analysis. Our results indicate that the favorable allelic variation TaSPP-5Aa should be valuable in enhancing grain yield by improving the sucrose content. Furthermore, a functional marker, TaSPP-5A-dCAPS, can be used for marker-assisted selection to improve grain weight in wheat and provides insights into the biological function of TaSPP-5A gene.

Measurement of Cell Death in Mammalian Cells

Methods for assessing mammalian cell death are presented in this article, which is divided into six sections: (1) a brief overview of cytotoxicity and pathways of cell death; (2) a method to measure cell death using lactate dehydrogenase (LDH) release as a marker of membrane integrity; (3) a flow cytometry method that simultaneously measures two types of cell death, necrosis and apoptosis; (4) use of fluorescence microscopy and nuclear morphology to assess apoptosis and necrosis; (5) the use of multi-well plates and high-content analysis imaging systems to assess nuclear morphology; and (6) a discussion of the use of cytotoxicity assays to determine the mechanisms of cell death. © 2021 Wiley Periodicals LLC. Basic Protocol 1: Measurement of plasma membrane integrity and viability using LDH release Basic Protocol 2: Measurement of necrosis and apoptosis using flow cytometry Basic Protocol 3: Determination of nuclear morphology and membrane integrity Alternate Protocol 1: Assessment of nuclear morphology and membrane integrity using DAPI and PI Alternate Protocol 2: Assessment of nuclear morphology using multi-well plates Basic Protocol 4: Measurement of time-dependent toxicity using cell death markers.

A fluorogenic cyclic peptide for imaging and quantification of drug-induced apoptosis

Programmed cell death or apoptosis is a central biological process that is dysregulated in many diseases, including inflammatory conditions and cancer. The detection and quantification of apoptotic cells in vivo is hampered by the need for fixatives or washing steps for non-fluorogenic reagents, and by the low levels of free calcium in diseased tissues that restrict the use of annexins. In this manuscript, we report the rational design of a highly stable fluorogenic peptide (termed Apo-15) that selectively stains apoptotic cells in vitro and in vivo in a calcium-independent manner and under wash-free conditions. Furthermore, using a combination of chemical and biophysical methods, we identify phosphatidylserine as a molecular target of Apo-15. We demonstrate that Apo-15 can be used for the quantification and imaging of drug-induced apoptosis in preclinical mouse models, thus creating opportunities for assessing the in vivo efficacy of anti-inflammatory and anti-cancer therapeutics.

Programmed cell death or apoptosis is an essential biological process that is impaired in some diseases and can be used to assess the effectiveness of drugs. Here the authors design Apo-15 as a fluorogenic peptide for the detection and real-time imaging of apoptotic cells.

Measurement of cell death in mammalian cells

This unit presents methods used to assess cell death in mammalian cells. The unit is divided into five sections: (1) a brief overview of cytotoxicity and pathways of cell death, (2) an improved method to measure cell death using lactate dehydrogenase (LDH) release as a marker of membrane integrity, (3) a flow cytometry method that simultaneously measures two types of cell death, oncosis and apoptosis, (4) use of nuclear morphology to assess apoptosis and oncosis, and (5) a brief discussion of the use of cytotoxicity assays to determine the mechanisms of cell death.

Bystander-type effects mediated by long-lived inflammatory signaling in irradiated bone marrow

Radiation-induced bystander and abscopal effects, in which DNA damage is produced in nonirradiated cells as a consequence of communication with irradiated cells, indicate mechanisms of inducing damage and cell death additional to the conventional model of deposition of energy in the cell nucleus at the time of irradiation. In this study we show that signals generated in vivo in the bone marrow of mice irradiated with 4 Gy γ rays 18 h to 15 months previously are able to induce DNA damage and apoptosis in nonirradiated bone marrow cells but that comparable signals are not detected at earlier times postirradiation or at doses below 100 mGy. Bone marrow cells of both CBA/Ca and C57BL/6 genotypes exhibit responses to signals produced by either irradiated CBA/Ca or C57BL/6 mice, and the responses are mediated by the cytokines FasL and TNF-α converging on a COX-2-dependent pathway. The findings are consistent with indirect inflammatory signaling induced as a response to the initial radiation damage rather than to direct signaling between irradiated and nonirradiated cells. The findings also demonstrate the importance of studying tissue responses when considering the mechanisms underlying the consequences of radiation exposures.

Osmium carbonyl clusters: a new class of apoptosis inducing agents

Osmium carbonyl clusters, especially the cluster [Os(3)(CO)(10)(NCCH(3))(2)], were found to be active against four cancer cell lines, namely, ER+ breast carcinoma (MCF-7), ER- breast carcinoma (MDA-MB-231), metastatic colorectal adenocarcinoma (SW620), and hepatocarcinoma (Hep G2). The mode of action was studied in MCF-7 and MDA-MB-231 cell lines by a number of morphological and apoptosis assays, all of which pointed to the induction of apoptosis.

Nuclear chromatin texture and sensitivity to DNase I in human leukaemic CEM cells incubated with nanomolar okadaic acid

It is now known that the analysis of chromatin texture can be used in oncology as a sensitive detection method, either to define diagnostic classifications or to locate a lesion along a defined trend curve. However, the functional significance of these variations in textural features remains sometimes unclear. Several drugs have been shown to be able to modulate chromatin structure. Among them, the phosphatase inhibitor okadaic acid at low concentration can increase accessibility to DNA in chromatin of carcinoma cells. This paper demonstrates that short exposures (0-3 h) to a 10-nM dose of okadaic acid induced an increased sensitivity to DNase I digestion in human CEM leukaemic cell nuclei and that this sensitization was associated to variations of nuclear texture characteristics, as evaluated by image cytometry. CEM cells treated with okadaic acid for 0-3h displayed changes in chromatin supraorganization with a more homogeneous and fine chromatin texture, as compared to control cells. This suggests that the appearance of an open configuration of chromatin structure as evaluated by biochemical methods corresponds to a more decondensed texture of nuclei measured by image cytometry. Longer exposures (6-24h) of CEM cells to 10 nM okadaic acid lead to apoptosis. As reported previously for camptothecin-treated HL60 cells, okadaic acid-treated CEM cells display biphasic nuclear chromatin texture changes, i.e. a decondensation phase followed by the appearance of typical apoptotic cells with a smaller nuclear area and a highly condensed chromatin. Finally, using the multidrug-resistant CEM-VLB cell line, it was confirmed that these multidrug-resistant cells also display cross-resistance to okadaic acid, as this compound was unable to induce either increased DNase I sensitivity, apoptosis, or altered nuclear texture in this particular cell line.

Quercetin abrogates taxol-mediated signaling by inhibiting multiple kinases

Cell cycle block in G(2)/M initiates apoptosis, but the mechanism of this signaling cascade are largely unknown. The microtubule-perturbing agent Taxol has multiple effects on this signaling pathway and is a potent inducer of apoptosis. The specific pathways activated by low, clinically relevant concentrations of the drug are still largely unknown and are dependent on cell type and drug concentration. In this work, we have investigated why HeLa cells respond to Taxol by undergoing complete apoptosis, whereas MCF-7 cells remain in an intermediate phase with reduced death. Three phases were distinguished in these apoptotic pathways. The initial phase characterized by cellular detachment is followed by a second phase which includes the onset of apoptotic morphology, and p38 and Bcl-2 phosphorylation. These two phases are common to both cell lines. HeLa cells then proceed to the third and final execution phase, which culminates in death, whereas MCF-7 cells do not progress. Interestingly, the isoflavonoid Quercetin, a known general kinase inhibitor and an antioxidant, was able to prevent the onset of Taxol-induced cellular detachment and to protect from cell death. Moreover, it blocked Taxol-induced phosphorylation of p38 and Bcl-2, and prevented a Taxol-induced change in relative mobility of the apoptosis signal-regulating kinase 1 (Ask1). Our data elucidate the signaling pathways activated by Taxol at low clinically relevant concentrations.

Cell cycle checkpoint efficiency and cellular response to paclitaxel in prostate cancer cells

BACKGROUND

Defects in the cell cycle machinery of prostate cancer cells might impair the efficiency of cell cycle checkpoints and affect the cell response to chemotherapeutic drugs. We examined the relationship between the status of microtubule damage-activated checkpoints and the response of hormone-refractory prostate cancer cells to paclitaxel.

METHODS

The two cell lines DU145 and PC3 harboring defects at proteins involved in the regulation of checkpoints activated by microtubule damage were examined for cell sensitivity, apoptotic response, and efficiency of checkpoints in response to paclitaxel.

RESULTS

In spite of a comparable sensitivity to the antiproliferative effects of paclitaxel, DU145 and PC3 cells exhibited different cell cycle control at checkpoints activated by microtubule damage. A transient mitotic arrest was induced by the taxane in both cell lines. However, PC3 cells underwent a rapid mitotic slippage and displayed a defective postmitotic checkpoint as evidenced by the appearance of polyploid cells. In this cell line, paclitaxel-induced cell death was a slow and delayed event, occurring also after S-phase re-entry. The mitotic checkpoint appeared to be more stringent in DU145 cells compared to PC3 cells. Moreover, despite the expression of mutated proteins involved in the prevention of DNA endoreduplication (p53, pRb, and p16(INK4A)), these cells did not progress into the cell cycle but efficiently underwent apoptosis by 24 hr. Such a response of DU145 cells was associated with phosphorylation of the p21(WAF1) protein.

CONCLUSIONS

These observations evidence that activation of checkpoints following microtubule damage in prostate cancer may be regulated through complex mechanisms possibly involving p21(WAF1). Our findings support that the status of cell cycle checkpoints might affect the modality of cell death. However, the relevance of the mode of cell death for the sensitivity to taxanes remains to be determined.

Rb-independent induction of apoptosis by bovine papillomavirus type 1 E7 in response to tumor necrosis factor alpha

Bovine papillomavirus type 1 (BPV-1) is a small DNA virus that causes fibropapillomas of the host. BPV-1 has served as the prototype for studies of the molecular biology of the papillomaviruses. BPV-1 efficiently induces anchorage-independent growth and focus formation in murine C127 cells. The transforming properties of BPV-1 primarily reside in two genes, E5 and E6. Each of these genes is sufficient to transform cells. Although no independent transformation activity has been detected for E7, it was shown to be required for full transformation of C127 by BPV-1. We investigated the biological activities of BPV-1 E7 in several assays. Our results indicate that expression of BPV-1 E7 sensitizes cells to tumor necrosis factor alpha (TNF)-induced apoptosis. The TNF-induced apoptosis in E7-expressing cells was accompanied by increased release of arachidonic acid, indicating that phospholipase A(2) was activated. Unlike the E7 proteins from the cancer-related human papillomaviruses, the BPV-1 E7 protein does not associate efficiently with the retinoblastoma protein (pRB) in vitro, nor does it significantly affect the pRB levels in cultured cells. Furthermore, BPV-1 E7 sensitizes Rb-null cells to TNF-induced apoptosis. These studies indicate that BPV-1 E7 can sensitize cells to apoptosis through mechanisms that are independent of pRB.

Ethidium bromide staining reveals rapid cell dispersion in the rat dentate gyrus following ouabain-induced injury

The dentate gyrus of the hippocampal formation undergoes extensive network remodelling including progenitor cell proliferation, migration as well as apoptotic cell death in response to prolonged excitotoxic insults. Previous studies have shown that such a proliferative cell population may undergo aberrant migration and later persist in ectopically located positions within the molecular cell layer. In this study we have developed an experimental model to characterize the spatiotemporal patterns of such an injury-induced network remodelling. Ouabain (1 microl, 1 mM), a Na+, K+-ATPase blocker, was stereotactically co-injected into the rat dentate gyrus with ethidium bromide (1 microl, 40 microM). The latter is a fluorescent nucleic acid intercalating dye, which was used for labeling cells undergoing early phases of apoptosis or proliferation. Our results revealed that within an hour after the injection, a subpopulation of cells characterized by spindle- or ovoid-shaped somata and bipolar morphology, were intensely labeled with ethidium bromide. These cells were found initially clustered both inside and outside the dentate granule cell layer and later on markedly increased in number as well as spread radially in the next few hours into the dentate molecular layer. The unusual pattern of cell dispersion encountered in our study may represent aberrantly migrating progenitor cells consistent with earlier observations of ectopically-located granule cells in human temporal lobe epilepsy specimens and epilepsy animal models. Alternatively, the described phenomenon may represent dispersion of Cajal-Retzius cells that may be involved in post-lesion network remodelling.

Tamoxifen induces oxidative stress and apoptosis in oestrogen receptor-negative human cancer cell lines

Recent data have demonstrated that the anti-oestrogen tamoxifen (TAM) is able to facilitate apoptosis in cancer cells not expressing oestrogen receptor (ER). In an attempt to identify the biochemical pathway for this phenomenon, we investigated the role of TAM as an oxidative stress agent. In two ER-negative human cancer cell lines, namely T-leukaemic Jurkat and ovarian A2780 cancer cells, we have demonstrated that TAM is able to generate oxidative stress, thereby causing thiol depletion and activation of the transcriptional factor NF-kappaB. As described for other oxidative agents, TAM was able to induce either cell proliferation or apoptosis depending on the dose. When used at the lowest dose tested (0.1 microM), a slight proliferative effect of TAM was noticed in terms of cell counts and DNA synthesis rate, whereas at higher doses (10 microM) a consistent occurrence of apoptosis was detected. Importantly, the induction of apoptosis by TAM is not linked to down-regulation or functional inactivation by phosphorylation of the antiapoptotic bcl-2 protein.

The use of Apostain in identifying early apoptosis

Irradiated human peripheral blood lymphoid cells undergo apoptosis and progressively exhibit typical changes in light scatter and plasma membrane integrity that can be easily tracked by flow cytometry. Using this model, we assessed the capacity of a newly developed fluorochrome, Apostain, in identifying early apoptosis in unfixed samples. This probe is a plasma membrane permeant DNA dye that can be conveniently excited at 488 nm and has an emission wavelength > 650 nm. To identify apoptotic cells, Apostain relies on the transient changes of chromatin texture that allow to accommodate more of a DNA dye occurring in early apoptosis. As early as 4 h after irradiation a proportion of cells showed an enhanced Apostain uptake. Consistent with their initial apoptotic nature, these cells had a still integer plasma membrane, as assessed by ethidium bromide, and unaltered light scatter. With time, cells showing the enhanced Apostain uptake started to bind dimly Annexin-V and, later, reduced their forward scatter. After 18 h from irradiation, cells exhibiting a reduced forward scatter exhibited a bright staining with Annexin-V with a concomitant reduction in Apostain uptake, reflecting the gross chromatin disruption characterising the endpoint of apoptosis.