Quantitation of cellular resolution in situ hybridization histochemistry in brain by image analysis

In situ hybridization in neuropathology

In situ hybridization (ISH) allows the demonstration and localization of deoxyribonucleic acid (DNA) and ribonucleic acid (RNA) in tissue sections, cells and chromosomes by utilizing a specific interaction with a labelled nucleotide probe of known composition. Although this technique has been employed for many years using radiolabelled probes, the recent development of nonisotopic labelling systems and the greatly increased availability of synthetic nucleic acids has allowed an enormous expansion in the potential applications of ISH. The technique is now applicable to unfixed and fixed tissues, including archival material. The use of enzyme-linked antibody techniques to detect labelled probes has greatly increased the sensitivity of non-isotopic ISH without a loss of specificity. The successful use of ISH demands careful selection of labelled probes, adequate tissue pretreatment to allow access of the probe, control of the stringency of probe binding and a sensitive reporter system, in addition to adequate controls. The accurate localization of nucleotides in the central nervous system (CNS) has many current research applications in the study of gene expression in multiple sclerosis and other inflammatory disorders, and a wide range of neurodegenerative disorders, viral infections and neoplasms. The technique is of diagnostic value in viral disorders, particularly where multiple infections occur. The combination of non-isotopic ISH with immunocytochemistry electron microscopy and quantitative image analysis greatly increases its research potential, while the development of a related method, the in situ polymerase chain reaction, offers an additional opportunity for further enhancing the sensitivity of this technique.

A digital brain atlas and its application to the visceral neuraxis

We describe the details and application of a digital brain atlas for the comparison and integration of graphical neurobiological data. The atlas consists of multiple sets of high-resolution video images acquired from histological tissue sections representing a 3-dimensional (3D) volume of an exemplar rat brain. Through an interactive graphical interface running on a standard computer workstation, experimental data is brought into register with the atlas. Once in the atlas, coordinate reference frame data can be compared, analyzed, and visualized in 3 dimensions. We demonstrate the validity and usefulness of the digital brain atlas with a series of results on the visceral neuraxis in the rat.

Development of laminar expression of the m2 muscarinic cholinergic receptor gene in rat visual cortex and the effect of monocular visual deprivation

The postnatal development of laminar pattern of the m2 muscarinic acetylcholine receptor subtype mRNA in the visual cortex of both normally raised and monocularly deprived rats (one eyelid sutured at the age of 11 days) was studied using in situ hybridization histochemistry and computer-assisted image analysis. In normally raised rats, on birth, the m2 transcript was found to be more concentrated in the superficial zones of the cortex. This laminar pattern alters to a more homogeneous distribution of the label throughout the cortex already detectable on day 7. From day 10 onwards a bimodal laminar pattern gradually develops with increased mRNA levels in layer IV and upper layer VI. From postnatal day 21 onwards the hybridization peak in layer VI decreases as compared to the peak level in layer IV resulting in an adult distribution with highest labeling in layer IV, low labeling in layer I to III and moderate labeling in layers V and VI. Monocular deprivation results in decreased m2 mRNA levels in visual cortical layers IV-VI in both deprived and non-deprived cortices already detectable at the age of 18 days and persisting up to the age of 21 days; but this effect disappears following further deprivation until adulthood. The data suggest that the changes in m2 receptor level from a more homogeneous distribution to a bimodal pattern during postnatal development seem to be related to synaptogenesis and final tuning of connectional pattern within the rat visual cortex.

Differential laminar expression of AMPA receptor genes in the developing rat visual cortex using in situ hybridization histochemistry. Effect of visual deprivation

The postnatal development of laminar pattern of AMPA receptor mRNA subtypes GluR-A through to GluR-D (flip variants) in the visual cortex of both normally raised and monocularly deprived rats (one eyelid sutured at the age of 11 days) was studied using in situ hybridization histochemistry and computer-assisted image analysis. The AMPA receptors GluR-A through to GluR-D transcripts exhibit a differential laminar expression pattern in the developing rat visual cortex. At birth the levels of GluR-A transcripts are lower by about 50% in each visual cortical layer as compared to the adult values. In contrast, GluR-B to GluR-D mRNAs are expressed in all cases at higher levels at birth than in the adult brain. Unilateral eyelid closure at postnatal day 11 for several periods of time resulted in both transient and permanent changes in the laminar development of GluR-A through to GluR-C transcripts but hardly affected the GluR-D mRNA subtype. The distinct laminar developmental pattern of AMPA receptor mRNAs in rat visual cortex as well as the differential effects of visual deprivation suggest specific roles of AMPA receptor subtypes during the early postnatal maturation of visual function.

Laminar expression of m1-, m3- and m4-muscarinic cholinergic receptor genes in the developing rat visual cortex using in situ hybridization histochemistry. Effect of monocular visual deprivation

The postnatal development of laminar pattern of m1-, m3- and m4-mRNA-muscarinic acetylcholine receptor subtypes in the visual cortex of both normally raised and monocularly deprived rats (one eyelid sutured at the age of 11 days) was studied using in situ hybridization histochemistry and computer-assisted image analysis. From birth until day 15 the level of m1-receptor transcript in layer II/III increases markedly as compared to deeper layers. From day 15 up to day 18 a transient bimodal pattern develops with peaks in layers II/III and VI. Already on day 35 a more homogeneous distribution of m1-receptor mRNA level is detectable persisting until adulthood. In contrast, the m3-receptor mRNA shows already at birth a bimodal distribution with peaks in layers II/III and VI. Further development until adulthood results in transient changes in the ratio of the mRNA levels in these layers. In the adult visual cortex a similar laminar pattern as at birth is observed. From day 1 up to day 10 a relative increase in the mRNA level of the m4-receptor in layers II to IV is observed. From day 10 until day 15 a bimodal distribution of receptor mRNA develops with peaks in layers III and VI which is similar to the adult stage. However, between days 18 and 35 a shift in the laminar receptor mRNA distribution occurs resulting in peaks in layers IV and VI. The labeling of the m5-receptor transcript in rat visual cortex was very weak and did not show any alteration with age. Unilateral eyelid closure from postnatal day 11 resulted in transient changes in the laminar distribution of m3- and m4-receptor mRNA between postnatal days 18 and 25, whereas the development of the laminar pattern of the m1-receptor mRNA was not affected regardless of the length of visual deprivation. The distinct laminar developmental pattern of mRNA muscarinic receptor subtypes in rat visual cortex suggests specific roles of the muscarinic receptor subtypes during the first weeks of postnatal maturation of visual function.

Semi-quantitative analysis of somatostatin mRNA distribution in the rat central nervous system using in situ hybridization

The distribution of somatostatin mRNA in the rat brain has been examined by in situ hybridization using 32P-labelled oligonucleotide probes. Numerous telencephalic and diencephalic areas contained labelled cells with the largest numbers of cells occurring in the anterior olfactory nucleus, olfactory and entorhinal cortices, hippocampus, neocortex, caudate nucleus, accumbens, septum, amygdala and periventricular nucleus. Fewer labelled cells occurred in the mesencephalon and rhombencephalon but groups were seen in the region of the central grey, lateral lemniscus, parabrachial and tegmental nuclei, medial longitudinal fasciculus and nucleus of the solitary tract. This distribution closely matches published maps of the distribution of somatostatin-immunoreactive cell bodies. The intensity of individual cell labelling has also been quantified using image analysis and compared with the intensity of somatostatin immunocytochemical cell staining. In situ hybridization cell labelling varied both within different regions and from region to region. Highest labelling was seen in the periventricular nucleus of the hypothalamus followed by telencephalic regions such as cortex, hippocampus and the medial nucleus of the amygdala. In contrast all brainstem areas had low levels of labelling with the lowest levels of the brain occurring in the dorsolateral tegmental nucleus. Somatostatin immunocytochemistry showed similar variations such that the intensity of cell immunostaining broadly paralleled the intensity of cell in situ hybridization labelling. Thus both peptide and mRNA levels were much lower in brainstem cells than in forebrain, although a close correlation between immunocytochemistry and in situ hybridization was not seen in all brain regions.

Quantitative non-radioactive in situ hybridization. Model studies and studies on pituitary proopiomelanocortin cells after adrenalectomy

Non-radioactive in situ hybridization using biotinylated oligodeoxynucleotides and a detection protocol involving monoclonal antibiotin antibodies and the alkaline phosphatase-anti-alkaline phosphatase system was employed for quantitation by image analysis. Calibrations of the image analysis system with neutral density filters revealed that the grey levels recorded were strongly linearly correlated to the absorbance (r2 = 0.97) in the range studied in tissue specimens (0-0.8 optical density or absorbance units). Several methodological parameters, including light source stability, section thickness, probe concentration and development time were initially optimized. Model systems revealed that the grey level measured varied linearly with the logarithm of the target concentration. Moreover, histophysiological studies on adrenalectomized and sham-operated rats documented that previous biochemical data on an 8- to 10-fold increase in anterior lobe proopiomelanocortin (POMC) mRNA levels 8 days after adrenalectomy are accounted for both by an increased ACTH cell concentration and content of POMC mRNA, as well as by increases in ACTH cell sizes and cell numbers. Also in agreement with biochemical data, image analysis did not reveal significant differences between OD's of melanotrophs in adrenalectomized and sham-operated animals. To our knowledge, these data are the first to document that non-radioactive in situ hybridization can be employed for relative quantitation. A particular advantage of this approach is the good morphological definition which permits parallel analyses of densitometric values, cell sizes and cell areas/cell numbers.

Increased muscarinic receptor messenger RNA in Alzheimer's disease temporal cortex demonstrated by in situ hybridization histochemistry

A 35S-labelled synthetic oligonucleotide directed against part of the mRNA coding for the M1 subtype muscarinic receptor was used for in situ hybridization histochemistry in sections of human temporal cortex. M1 receptor mRNA was found in cell populations throughout the grey matter, especially in pyramidal cells. Quantitative densitometric analysis of autoradiograms was used to compare levels of this mRNA between Alzheimer's disease and controls. A significant (2.7-fold) increase in hybridization signal was found in Alzheimer's disease cases, both in absolute terms and relative to total polyadenylated mRNA as determined by hybridization with an oligodeoxythymidine probe. Elevated levels of muscarinic receptor mRNA may reflect up-regulation of transcription of this gene in response to the cholinergic deficits occurring in the disease.

Neuronal localization of prosomatostatin mRNA in the rat brain with in situ hybridization histochemistry

Individual neurons containing prosomatostatin mRNA were identified with in situ hybridization histochemistry. Our results demonstrate a widespread distribution of prosomatostatin mRNA in several regions of the rat central nervous system. Neurons containing this transcript were most abundant in the anterior olfactory nucleus, hypothalamus, hippocampus, and amygdala as well as in all regions of the cerebral cortex. Moreover, the distribution of mRNA-containing perikarya was coextensive with the location of neurons containing somatostatin-like immunoreactivity in all areas of the brain examined. Somatostatin neurons varied in their morphology and amount of hybridization signal from region to region. The widespread distribution and regional variations in neuronal morphology and the amount of hybridization signal are consistent with a neurotransmitter and/or a neuromodulator role for somatostatin in addition to its well-established neuroendocrine role. These results demonstrate that both the peptide and its mRNA are found in perikarya in the same areas and that they are therefore the sites of synthesis for somatostatin.

Recent developments in the use of synthetic oligonucleotides for in situ hybridization histochemistry

Synthetic oligonucleotides have been used with increasing frequency as probes for the detection and study of the regulation of specific mRNAs by in situ hybridization histochemistry. These probes can be easily obtained and used by the nonmolecular biologist, and they have been shown to be effective for the study of a wide range of mRNAs in neuronal and neuroendocrine tissues. Considerations in oligonucleotide probe design, synthesis, purification, and labeling are described in this article, and current procedures for tissue preparation and hybridization are discussed. In addition, control procedures and methods for the quantitation of in situ hybridization by image analysis are discussed. Finally, the combination of this technique with immunocytochemistry and retrograde tract-tracing is reviewed. The coupling of quantitative in situ hybridization with other neuronal markers, e.g., of connectivity, provides an increasingly valuable technology for exploring the regulation of gene expression in a rich anatomical context.