Isolation and some characteristics of cell nuclei from brain cortex of adult cat

Nuclei on the Rise: When Nuclei-Based Methods Meet Next-Generation Sequencing

In the last decade, we have witnessed an upsurge in nuclei-based studies, particularly coupled with next-generation sequencing. Such studies aim at understanding the molecular states that exist in heterogeneous cell populations by applying increasingly more affordable sequencing approaches, in addition to optimized methodologies developed to isolate and select nuclei. Although these powerful new methods promise unprecedented insights, it is important to understand and critically consider the associated challenges. Here, we provide a comprehensive overview of the rise of nuclei-based studies and elaborate on their advantages and disadvantages, with a specific focus on their utility for transcriptomic sequencing analyses. Improved designs and appropriate use of the various experimental strategies will result in acquiring biologically accurate and meaningful information.

Mapping RNA-chromatin interactions by sequencing with iMARGI

RNA-chromatin interactions represent an important aspect of the transcriptional regulation of genes and transposable elements. However, analyses of chromatin-associated RNAs (caRNAs) are often limited to one caRNA at a time. Here, we describe the iMARGI (in situ mapping of RNA-genome interactome) technique, which is used to discover caRNAs and reveal their respective genomic interaction loci. iMARGI starts with in situ crosslinking and genome fragmentation, followed by converting each proximal RNA-DNA pair into an RNA-linker-DNA chimeric sequence. These chimeric sequences are subsequently converted into a sequencing library suitable for paired-end sequencing. A standardized bioinformatic software package, iMARGI-Docker, is provided to decode the paired-end sequencing data into caRNA-DNA interactions. Compared to its predecessor MARGI (mapping RNA-genome interactions), the number of input cells for iMARGI is 3-5 million (a 100-fold reduction), experimental time is reduced, and clear checkpoints have been established. It takes a few hours a day and a total of 8 d to complete the construction of an iMARGI sequencing library and 1 d to carry out data processing with iMARGI-Docker.

Mechanical property characterization of hundreds of single nuclei based on microfluidic constriction channel

As label-free biomarkers, the mechanical properties of nuclei are widely treated as promising biomechanical markers for cell type classification and cellular status evaluation. However, previously reported mechanical parameters were derived from only around 10 nuclei, lacking statistical significances due to low sample numbers. To address this issue, nuclei were first isolated from SW620 and A549 cells, respectively, using a chemical treatment method. This was followed by aspirating them through two types of microfluidic constriction channels for mechanical property characterization. In this study, hundreds of nuclei were characterized, producing passage times of 0.5 ± 1.2 s for SW620 nuclei in type I constriction channel (n = 153), 0.045 ± 0.047 s for SW620 nuclei in type II constriction channel (n = 215) and 0.50 ± 0.86 s for A549 nuclei in type II constriction channel. In addition, neural network based pattern recognition was used to classify the nuclei isolated from SW620 and A549 cells, producing successful classification rates of 87.2% for diameters of nuclei, 85.5% for passage times of nuclei and 89.3% for both passage times and diameters of nuclei. These results indicate that the characterization of the mechanical properties of nuclei may contribute to the classification of different tumor cells.

The search for true numbers of neurons and glial cells in the human brain: A review of 150 years of cell counting

For half a century, the human brain was believed to contain about 100 billion neurons and one trillion glial cells, with a glia:neuron ratio of 10:1. A new counting method, the isotropic fractionator, has challenged the notion that glia outnumber neurons and revived a question that was widely thought to have been resolved. The recently validated isotropic fractionator demonstrates a glia:neuron ratio of less than 1:1 and a total number of less than 100 billion glial cells in the human brain. A survey of original evidence shows that histological data always supported a 1:1 ratio of glia to neurons in the entire human brain, and a range of 40-130 billion glial cells. We review how the claim of one trillion glial cells originated, was perpetuated, and eventually refuted. We compile how numbers of neurons and glial cells in the adult human brain were reported and we examine the reasons for an erroneous consensus about the relative abundance of glial cells in human brains that persisted for half a century. Our review includes a brief history of cell counting in human brains, types of counting methods that were and are employed, ranges of previous estimates, and the current status of knowledge about the number of cells. We also discuss implications and consequences of the new insights into true numbers of glial cells in the human brain, and the promise and potential impact of the newly validated isotropic fractionator for reliable quantification of glia and neurons in neurological and psychiatric diseases. J. Comp. Neurol. 524:3865-3895, 2016. © 2016 Wiley Periodicals, Inc.

The search for true numbers of neurons and glial cells in the human brain: A review of 150 years of cell counting

For half a century, the human brain was believed to contain about 100 billion neurons and one trillion glial cells, with a glia:neuron ratio of 10:1. A new counting method, the isotropic fractionator, has challenged the notion that glia outnumber neurons and revived a question that was widely thought to have been resolved. The recently validated isotropic fractionator demonstrates a glia:neuron ratio of less than 1:1 and a total number of less than 100 billion glial cells in the human brain. A survey of original evidence shows that histological data always supported a 1:1 ratio of glia to neurons in the entire human brain, and a range of 40-130 billion glial cells. We review how the claim of one trillion glial cells originated, was perpetuated, and eventually refuted. We compile how numbers of neurons and glial cells in the adult human brain were reported and we examine the reasons for an erroneous consensus about the relative abundance of glial cells in human brains that persisted for half a century. Our review includes a brief history of cell counting in human brains, types of counting methods that were and are employed, ranges of previous estimates, and the current status of knowledge about the number of cells. We also discuss implications and consequences of the new insights into true numbers of glial cells in the human brain, and the promise and potential impact of the newly validated isotropic fractionator for reliable quantification of glia and neurons in neurological and psychiatric diseases. J. Comp. Neurol. 524:3865-3895, 2016. © 2016 Wiley Periodicals, Inc.

Rapid Isolation of Nuclei from Cells In Vitro

This protocol presents a rapid, efficient, and practical (REAP) method to separate nuclei from cultured cells in vitro with as little damage and contamination as possible. The REAP procedure is performed at low temperature and takes <2 min, which minimizes protein degradation, protein modification, and diffusion of soluble proteins out of the nuclear compartment while maintaining the integrity of protein complexes. A mild detergent, NP-40, is used together with mild mechanical shearing to disrupt the plasma membrane, leaving the nuclear membrane intact. The REAP method can be used with various cell lines grown in vitro and requires minimal optimization. The isolated nuclei are suitable for numerous downstream applications (e.g., western blotting, 2D gel electrophoresis, and immunoprecipitation). If desired, aliquots of whole-cell lysate and the cytoplasmic fraction can be saved for comparison.

Isolation of Nuclei

The isolation of nuclei is often the first step in studying processes such as nuclear-cytoplasmic shuttling, subcellular localization of proteins, and protein-chromatin or nuclear protein-protein interactions in response to diverse stimuli. Therefore, rapidly obtaining nuclei from cells with relatively high purity and minimal subcellular contamination, protein degradation, or postharvesting modification is highly desirable. Historically, the isolation of nuclei involved a homogenization step followed by centrifugation through high-density glycerol or sucrose. Although clean nuclei with little cytoplasmic contamination can be prepared using this method, it is typically time consuming and can allow protein degradation, protein modification, and leaching of components from the nuclei to occur. We have developed a rapid and simple fractionation method that is based on the selective dissolution of the cytoplasmic membrane (but not the nuclear membrane) using a low concentration of a nonionic detergent and rapid centrifugation steps. Here we describe important considerations when isolating nuclei from cells, introduce our rapid method, and compare this method to a more traditional protocol for isolating nuclei, noting the strengths and limitations of each approach.

Validation of the isotropic fractionator: comparison with unbiased stereology and DNA extraction for quantification of glial cells

BACKGROUND

The "isotropic fractionator" (IF) is a novel cell counting technique that homogenizes fixed tissue, recovers cell nuclei in solution, and samples and quantifies nuclei by extrapolation. Studies using this technique indicate that the ratio of glia to neurons in the human brain is approximately 1:1 rather than the 10:1 or 50:1 ratio previously assumed. Although some results obtained with the IF have been similar to those obtained by stereology, the IF has never been calibrated or validated. It is conceivable that only a fraction of glial cell nuclei are recovered intact or recognized after the homogenization step.

NEW METHOD

To rule out this simple explanation for the claim of a 1:1 glia-neuron ratio, we compared cell numbers obtained from adjacent, weight-normalized samples of human and macaque monkey white matter using three techniques: the IF, unbiased stereology of histological sections in exhaustively sectioned samples, and cell numbers calculated from DNA extraction.

RESULTS AND COMPARISON OF METHODS

In primate forebrains, the IF yielded 73,000-90,000 nuclei/mg white matter, unbiased stereology yielded 75,000-92,000 nuclei/mg, with coefficients of error ranging from 0.013 to 0.063, while DNA extraction yielded only 4000-23,000 nuclei/mg in fixed white matter tissues.

CONCLUSIONS

Since the IF revealed about 100% of the numbers produced by unbiased stereology, there is no significant underestimate of glial cells. This confirms the notion that the human brain overall contains glial cells and neurons with a ratio of about 1:1 - far from the originally assumed ratio of 10:1 in favor of glial cells.

Neuron enriched nuclear proteome isolated from human brain

The brain consists of diverse cell types including neurons, astrocytes, oligodendrocytes, and microglia. The isolation of nuclei from these distinct cell populations provides an opportunity to identify cell-type-specific nuclear proteins, histone modifications, and regulation networks that are altered with normal brain aging or neurodegenerative disease. In this study, we used a method by which intact neuronal and non-neuronal nuclei were purified from human post-mortem brain employing a modification of fluorescence activated cell sorting (FACS) termed fluorescence activated nuclei sorting (FANS). An antibody against NeuN, a neuron specific splicing factor, was used to isolate neuronal nuclei. Utilizing mass spectrometry (MS) based label-free quantitative proteomics, we identified 1755 proteins from sorted NeuN-positive and negative nuclear extracts. Approximately 20% of these proteins were significantly enriched or depleted in neuronal versus non-neuronal populations. Immunoblots of primary cultured rat neuron, astrocyte, and oligodendrocyte extracts confirmed that distinct members of the major nucleocytoplasmic structural linkage complex (LINC), nesprin-1 and nesprin-3, were differentially enriched in neurons and astrocytes, respectively. These comparative proteomic data sets also reveal a number of transcription and splicing factors that are selectively enriched in a cell-type-specific manner in human brain.

Nerve growth factor in the nucleus: interaction with receptors on the nuclear membrane

Cells of a continuous line of rat pheochromocytoma (PC12) were incubated with 125I-labeled beta nerve growth factor (beta NGF), and at given time intervals the cell nuclei were isolated by a procedure that used the detergent Triton X-100. NGF was detectable in the nucleus after 20 min and continued to accumulate in a linear fashion for several hours after the total binding to the cell had reached steady state. After 17 hr at 37 degrees C, about 60% of the NGF bound to the cell was in the nucleus, NGF was not translocated to the nucleus at 4 degrees C. When nuclei were purified from PC12 cells and incubated with 125I-labeled beta NGF, specific binding sites were found. Binding was saturable and consistent with two sites: a high-affinity site with a Kd of 0.08 nM (+/- nM) and a lower-affinity site with a Kd of 9.0 nM (+/- 2.0 nM). The receptors in the nucleus were shown to be localized to the nuclear membrane. Membrane-free chromatin did not bind NGF specifically. The translocation of NGF to the nucleus was accompanied by a commensurate decrease in the cell-surface binding capacity. In the nucleus, however, the receptor capacities of both sites were increased when PC12 cells were grown in the presence of NGF.

Experimental disintegration of the nuclear envelope. Evidence for pore-connecting fibrils

The disintegration of the nuclear envelope has been examined in nuclei and nuclear envelopes isolated from amphibian oocytes from amphibian oocytes and rat liver tissue, using different electron microscope techniques (ultrathin sections and negatively or positively stained spread preparations). Various treatments were studied, including disruption by surface tension forces, very low salt concentrations, and nonionic detergents such as Triton C-100 and Nonidet P-40. The highest local stability of the cylinders of nonmembranous pore complex material is emphasized. As progressive disintegration occurred in the membrane regions, a network of fibrils became apparent which interconnects the pore complexes and is distinguished from the pore complex-associated about 15-20 nm thick, located at the level of the inner nuclear membrane, which is recognized in thin sections to bridge the interpore distances. With all disintegraiton treatments a somewhat higher susceptibility of the outer nuclear membrane is notable, but a selective removal does not take place. Final stages of disintegration are generally characterized by the absence of identifiable, membrane-like structures. Analysis of detergent-treated nuclei and nuclear membrane fractions shows almost complete absence of lipid components but retention bo significant amount of glycoproteins with a typical endomembrane-type carbohydrate pattern. Various alternative interpretations of these observations are discussed. From the present observations and those of Aaronson and Blobel (1,2), we favor the notion that threadlike intrinsic membrane components are stabilized by their attachment to the pore complexes, and perhaps also to peripheral nuclear structures,and constitute a detergent-resistant, interpore skeleton meshwork.

Isolation of nuclear pore complexes in association with a lamina

Nuclear pore complexes have been isolated in association with a 150 A thick lamina by detergent and salt fractionation of nuclear envelopes from rat liver. The pore complexes exhibit characteristic morphology and appear to be attached in a highly specific orientation to the lamina, which extends over relatively large areas. The pore complex-lamina fraction is composed of three major and several minor polypeptides with little or no DNA, RNA, or phospholipid. It is suggested that the association of the pore complexes and the lamina reflects the structural arrangement of the nuclear periphery in vivo.

On the attachment of the nuclear pore complex

Electron microscope examination of isolated rat liver nuclei after treatment with the detergent Triton X-100 revealed the complete removal of both the inner and outer membranes of the nuclear envelope. The envelope-denuded nuclei did not show any change in either shape or internal ultrastructure. Most strikingly, the nuclear pore complexes, which in untreated nuclei appear to be integral components of the nuclear envelope, were retained in their characteristic location at the distal ends of the channels leading through the peripheral heterochromatin. Determination of the chemical composition of detergent-treated nuclei showed that over 95% of the nuclear phospholipid was solubilized, thus corroborating the morphological absence of nuclear membranes. Furthermore, detergent treatment also solubilized approximately 10% of the nuclear protein. Analysis of the solubilized protein by polyacrylamide gel electrophoresis in the presence of SDS indicated that these proteins belong to a few specific classes which presumably represent the major polypeptides of the nuclear membranes. The total absence of the nuclear envelope on both morphological and biochemical grounds supports the idea that the nuclear pore complex does not require the membranes either for attachment to the nucleus or for maintenance of its own structural integrity.

Observations on the nucleolar and total cell body nucleic acid of injured nerve cells

1. The nucleic acid content of neuronal nucleoli and the total cell body nucleic acid content of neurones of the hypoglossal nucleus were measured by ultraviolet absorption microspectrography.2. After nerve injury both the nucleolar nucleic acid and the total cell body nucleic acid increased: nucleolar changes preceded those of the cell body.3. The closer to the nerve cell body that the axon was injured the earlier was the onset and the decline of the nucleolar response.4. Actinomycin D was given to prevent DNA-primed RNA synthesis, and the rate of ;decay' of nucleolar RNA was measured. This rate varied after nerve injury and was closely related to the nucleolar nucleic acid content.5. The apparent rate of transfer of labelled RNA from the neuronal nucleus into the cytoplasm changed after nerve injury in a manner closely related to the changes in nucleolar nucleic acid content.6. It was demonstrated by making consecutive nerve injuries or by preventing or delaying nerve regeneration, that the nucleic acid changes were not induced by removal of contact between the neurone and its motor end-plate, and were not repressed by the restoration of such contact.7. When regeneration was prevented the nucleolar nucleic acid content and the total cell body nucleic acid ultimately decreased to values less than normal: this decrease was greater when more of the axon was initially removed.8. The results are discussed in relation to the factor responsible for derepression and repression of DNA cistrons for ribosome synthesis in injured nerve cells.

Isolation of cell nuclei from the mammalian cerebral cortex and their assortment on a morphological basis

An aqueous method is described for the isolation of highly purified nuclei from the cerebral cortex of adult guinea pigs. Erythrocytes were removed by a short-time perfusion of the brain, myelin fragments by a rapid mechanical method, and blood capillaries by a centrifugal sieving through dense sucrose solutions. The nuclear preparation retained the activity of ATP:NMN adenylyltransferase. Recoveries of DNA in the P4I, P4II, P(L) and P(S) preparations were 30, 43, 8, and 7%, respectively. Microscopy and phase contrast microscopy showed a satisfactory removal of erythrocytes, myelin fragments, capillaries, and cytoplasmic elements. Biochemical purity of samples was verified by the absence of several cytoplasmic enzyme activities. In the electron microscope, the majority of nuclei showed well-preserved nuclear membranes, with nuclear pores, and were provided with a finely textured nucleoplasm. Occasional contaminants were elements of endoplasmic reticulum and of the endothelium. Assortment of nuclei on a morphological basis showed that 55-65% and 47-53% of nuclei in the P4I and P4II preparations, respectively, consisted of neuronal nuclei. In the P(L) preparation, the population of neuronal nuclei ranged between 72 and 83%, while 94-99% of the nuclei in the P(S) preparation consisted of smaller nuclei, most likely of oligodendroglial origin.

Isolation and fractionation of rat brain nuclei

A method for isolating pure and unaltered nuclei from rat brain by means of differential centrifugation is described. The isolated nuclei are further separated into discrete fractions of neuronal, astrocytic, and glial nuclei, with a yield amounting to 20 to 25% of the DNA of the original homogenate. Both the morphology and size of the nuclei remained unchanged. Problems concerning the composition of the isolation media, the use of detergents, as well as those raised by density gradient centrifugation in sucrose, Ficoll, and Dextran are discussed. Some values for the density of each type of brain nuclei are suggested.