Amplification methods for the immunolocalization of rare molecules in cells and tissues

Radius measurement via super-resolution microscopy enables the development of a variable radii proximity labeling platform

The elucidation of protein interaction networks is critical to understanding fundamental biology as well as developing new therapeutics. Proximity labeling platforms (PLPs) are state-of-the-art technologies that enable the discovery and delineation of biomolecular networks through the identification of protein-protein interactions. These platforms work via catalytic generation of reactive probes at a biological region of interest; these probes then diffuse through solution and covalently "tag" proximal biomolecules. The physical distance that the probes diffuse determines the effective labeling radius of the PLP and is a critical parameter that influences the scale and resolution of interactome mapping. As such, by expanding the degrees of labeling resolution offered by PLPs, it is possible to better capture the various size scales of interactomes. At present, however, there is little quantitative understanding of the labeling radii of different PLPs. Here, we report the development of a superresolution microscopy-based assay for the direct quantification of PLP labeling radii. Using this assay, we provide direct extracellular measurements of the labeling radii of state-of-the-art antibody-targeted PLPs, including the peroxidase-based phenoxy radical platform (269 ± 41 nm) and the high-resolution iridium-catalyzed µMap technology (54 ± 12 nm). Last, we apply these insights to the development of a molecular diffusion-based approach to tuning PLP resolution and introduce a new aryl-azide-based µMap platform with an intermediate labeling radius (80 ± 28 nm).

Immunogold cytochemistry in neuroscience

The complexity of the central nervous system calls for immunocytochemical procedures that allow target proteins to be localized with high precision and with opportunities for quantitation. Immunogold procedures stand out as particularly powerful in this regard. Although these procedures have found wide application in the neuroscience community, they present limitations and pitfalls that must be taken into account. At the same time, these procedures offer potentials that remain to be fully realized.

Layered electrophoretic transfer - A method for pre-analytic processing of histological sections

Current technologies for measuring protein expression across a tissue section are based on MS or in situ detection such as immunohistochemistry. However, due to the inherent molecular complexity of tissue samples and the large dynamic range of protein expression in cells, current approaches are often unable to measure moderate- and low-abundant proteins. In addition, they do not provide information on the physico-chemical properties of the proteins studied. To address these problems, we are developing a new pre-analytic methodology termed layered electrophoretic transfer (LET) that selectively separates and processes proteins from an intact tissue section without compromising important two-dimensional histological information. LET offers two potential advantages over standard techniques: (i) A reduced complexity of the tissue proteome for subsequent analysis; (ii) An opportunity to assess the biochemical status of proteins as they exist in situ. As an initial proof-of-concept, we demonstrate here that the protein content from a mixture of molecular weight standards, human tissue lysates, and tissue sections can be successfully transferred and separated using LET, and further demonstrate that the method can be coupled with immunoblotting or MS for downstream measurements. LET technology represents a new pre-analytic tool for interrogating the proteome in tissue sections while preserving valuable spatial information.

Immunohistochemistry as an important tool in biomarkers detection and clinical practice

The immunohistochemistry technique is used in the search for cell or tissue antigens that range from amino acids and proteins to infectious agents and specific cellular populations. The technique comprises two phases: (1) slides preparation and stages involved for the reaction; (2) interpretation and quantification of the obtained expression. Immunohistochemistry is an important tool for scientific research and also a complementary technique for the elucidation of differential diagnoses which are not determinable by conventional analysis with hematoxylin and eosin. In the last couple of decades there has been an exponential increase in publications on immunohistochemistry and immunocytochemistry techniques. This review covers the immunohistochemistry technique; its history, applications, importance, limitations, difficulties, problems and some aspects related to results interpretation and quantification. Future developments on the immunohistochemistry technique and its expression quantification should not be disseminated in two languages—that of the pathologist and another of clinician or surgeon. The scientific, diagnostic and prognostic applications of this methodology must be explored in a bid to benefit of patient. In order to achieve this goal a collaboration and pooling of knowledge from both of these valuable medical areas is vital

Simultaneous visualization of multiple antigens with tyramide signal amplification using antibodies from the same species

After immunohistochemistry (IHC) began to be used routinely, a number of investigators worked on methods for staining multiple molecules in the same tissue sections or cells. Achieving this goal was not easy, however. One reason for this is that the majority of primary antibodies used in IHC reactions are raised in rabbits, and recognizing signals from two different rabbit antibodies is not trivial. Thus, all of the protocols described to date have serious limitations. Here we report a simple, quick, and inexpensive solution to the problem. It has two major advantages over existing methods. First, by using antibodies from the same host, two or more antigens can be visualized in the same section with commercially available fluorescent dyes. Second, because the technique relies on signal amplification, both rare and abundant antigens can be detected.

Heat-induced antigen retrieval: mechanisms and application to histochemistry

Since the introduction of the fluorescence-labeled antibody method by Coons et al. [Immunological properties of antibody containing a fluorescent group. Proc Soc Exp Biol Med 47, 200-2002], many immunohistochemical methods have been refined to obtain high sensitivity with low background staining at both light and electron microscopic levels. Heat-induced antigen retrieval (HIAR) reported by Shi et al. in the early 1990s has greatly contributed to immunohistochemical analysis for formalin-fixed and paraffin-embedded (FFPE) materials, particularly in the field of pathology. Although antigen retrieval techniques including enzyme digestion, treatment with protein denaturants and heating have been considered tricky and mysterious techniques, the mechanisms of HIAR have been rapidly elucidated. Heating cleaves crosslinks (methylene bridges) and add methylol groups in formaldehyde-fixed proteins and nucleic acids and extends polypeptides to unmask epitopes hidden in the inner portion of antigens or covered by adjacent macromolecules. In buffers having an appropriate pH and ion concentration, epitopes are exposed without entangling the extended polypeptides during cooling process, since polypeptides may strike a balance between hydrophobic attraction force and electrostatic repulsion force. Recent studies have demonstrated that HIAR is applicable for immunohistochemistry with various kinds of specimens, i.e., FFPE materials, frozen sections, plastic-embedded specimens, and physically fixed tissues at both the light- and electron-microscopic levels, and have suggested that the mechanism of HIAR is common to aldehyde-fixed and aldehyde-unfixed materials. Furthermore, heating has been shown to be effective for flow cytometry, nucleic acid histochemistry (fluorescein in situ hybridization (FISH), in situ hybridization (ISH), and terminal deoxynucleotidyl transferase-mediated nick labeling (TUNEL)), and extraction and analysis of macromolecules in both FFPE archive materials and specimens processed by other procedures. In this article, we review mechanism of HIAR and application of heating in both immunohistochemistry and other histochemical reactions.

Organisation of neoplastic haematopathology services: a UK perspective

The diagnosis of haematological malignancies has begun to emerge as a distinct pathological discipline in the United Kingdom. This has been driven by the recommendation of the National Institute for Clinical Excellence that diagnosis of leukaemia and lymphoma should take place in a specialist laboratory and in most cases this should be organised on a regional basis. The reason for this guidance was the perception that there was a considerable level of diagnostic inaccuracy and that this could be improved by better integration of the currently available technologies. This is one of a number of major changes in the way that services to patients are being delivered, all of which are centred on the development of multidisciplinary teams responsible for the provision of local services. The introduction of the WHO classification of haematological malignancy provides a structure for the development of integrated haemtopathology laboratories, with its emphasis on definition of disease entities based on clinical, morphological, phenotypical and molecular features. This means that these diagnostic modalities can be used systematically and in parallel to provide effective cross validation of a diagnosis. One of the challenges raised by this approach is the selection of the most informative panels of investigations both at presentation and subsequent follow up from the wide range of options that are now available. The introduction of specialist haematopathology services in the United Kingdom has highlighted a number of scientific and organisational issues that in time may have a wider impact on diagnostic laboratories in general. These include the relationship between size and cost effectiveness and the future role of clinical scientists and medically trained pathologists. Integrated laboratories of the type being developed challenge the prevailing model for delivery of pathological services in the United Kingdom, which is based around the traditional pathology disciplines. These speciality boundaries will become less relevant as long established diagnostic techniques are replaced by the new generation of diagnostic technologies and it is important to establish frameworks of service delivery that can deploy these developments for the benefit of patients.

Nucleoporins as components of the nuclear pore complex core structure and Tpr as the architectural element of the nuclear basket

The vertebrate nuclear pore complex (NPC) is a macromolecular assembly of protein subcomplexes forming a structure of eightfold radial symmetry. The NPC core consists of globular subunits sandwiched between two coaxial ring-like structures of which the ring facing the nuclear interior is capped by a fibrous structure called the nuclear basket. By postembedding immunoelectron microscopy, we have mapped the positions of several human NPC proteins relative to the NPC core and its associated basket, including Nup93, Nup96, Nup98, Nup107, Nup153, Nup205, and the coiled coil-dominated 267-kDa protein Tpr. To further assess their contributions to NPC and basket architecture, the genes encoding Nup93, Nup96, Nup107, and Nup205 were posttranscriptionally silenced by RNA interference (RNAi) in HeLa cells, complementing recent RNAi experiments on Nup153 and Tpr. We show that Nup96 and Nup107 are core elements of the NPC proper that are essential for NPC assembly and docking of Nup153 and Tpr to the NPC. Nup93 and Nup205 are other NPC core elements that are important for long-term maintenance of NPCs but initially dispensable for the anchoring of Nup153 and Tpr. Immunogold-labeling for Nup98 also results in preferential labeling of NPC core regions, whereas Nup153 is shown to bind via its amino-terminal domain to the nuclear coaxial ring linking the NPC core structures and Tpr. The position of Tpr in turn is shown to coincide with that of the nuclear basket, with different Tpr protein domains corresponding to distinct basket segments. We propose a model in which Tpr constitutes the central architectural element that forms the scaffold of the nuclear basket.

Sorting of furin in polarized epithelial and endothelial cells: expression beyond the Golgi apparatus

The conversion of proteins into their mature forms underlies the functionality of many fundamental cellular pathways. One posttranslational modification leading to maturation of precursor proteins consists of the cleavage of their prodomain at pairs of basic amino acids by enzymes of the subtilisin-like mammalian proprotein convertase family. One of these enzymes, furin, acts in the constitutive secretory pathway of almost every cell type. However, in spite of furin's major roles in many pathophysiological processes, the exact subcellular sites of processing and activation of its substrates remain elusive. In this study, furin antigenic sites were tracked in subcellular compartments of various tissues and corresponding cell lines by high-resolution immunogold electron microscopy, Western blotting, cell transfection, and in vivo gene delivery of the furin cDNA. In addition to the Golgi apparatus, furin was assigned to endosomes and plasma membranes of polarized intestinal and renal epithelial cells and endothelial cells of the continuous, fenestrated, and discontinuous capillaries. Roles of furin in endothelial permeability, basement membrane turnover, and shedding of transmembrane proteins are supported by our data.

Morphological and cytochemical aspects of capillary permeability

Transport of plasma soluble constituents across the capillary wall is of primordial importance in cardiovascular physiology. While physiological experiments have concluded with the existence of two sets of pores, a large one responsible for the transport of proteins and a small one designed for the diffusion of small solutes, the morphological counterparts have yet to get general agreement. In this review, we present the different proposed paths within and between the endothelial cells that do allow passage of plasma constituents and may respond to the definitions established by physiological means. The vesicular system existing in endothelial cells has been the first transendothelial path to be proposed. Several data have demonstrated the involvement of this system in transport, although others have systematically brought controversy. One alternative to the vesicles has been the demonstration of membrane-bound tubules creating, in certain cases, transendothelial channels that would allow diffusion of plasma proteins and other constituents across the capillary wall. Access to this tubulo-vesicular system could be restrained by the stomatal diaphragm and facilitated by specific membrane receptors. Further, we have demonstrated for the first time with morpho-cytochemical tools, that the intercellular clefts are the site of diffusion for small molecules such as peptides having a molecular weight inferior to 3,000. For the fenestrated capillary bed, we have shown that fenestrae are the site through which plasma constituents cross the capillary wall. However, and in spite of the existence of these large open pores, the endothelial cells still display the tubulo-vesicular system involved in transport of large molecules and their intercellular clefts are also the site of diffusion of small molecules. Making consensus on the existence of an intracellular tubulo-vesicular system in non-fenestrated capillaries, responsible for the transport of large molecules by the endothelial cells, and understanding the rational for the fenestrated capillary to have three paths for transport--the fenestrae, the tubulo-vesicular system, and the inter-endothelial clefts--require further investigation.