Improvement of Combined FISH and Immunofluorescence to Trace the Fate of Somatic Stem Cells after Transplantation

Recurrence of posterior polymorphous corneal dystrophy is caused by the overgrowth of the original diseased host endothelium

Posterior polymorphous corneal dystrophy (PPCD) is a rare, bilateral autosomal dominant disorder affecting primarily the corneal endothelium and descemet membrane (DM). The aim of this study was to establish the origin of abnormal endothelium in a patient with PPCD exhibiting cornea graft failure after keratoplasty surgery. A sex-mismatched graft obtained from a patient with PPCD who underwent repeat penetrating keratoplasty and the patient's original cornea were investigated. Combined fluorescent immunohistochemistry for cytokeratin (CK) 19 (a marker of aberrant PPCD endothelium) with fluorescence in situ hybridization (FISH) of the sex chromosomes were used in order to characterize the cells on the posterior graft surface. The pathological endothelium of the failed PPCD cornea revealed strong positivity for CK19 using fluorescent immunohistochemistry. In all the CK19-positive cells, both X and Y chromosomes were simultaneously detected using FISH. The results clearly showed the original cells of the patient (XY), within 3.5 years, almost totally overgrown the posterior corneal surface of the graft (XX). Moreover, an abnormal posterior collagenous layer populated by fibroblast-like cells was observed between DM and the endothelium in the failed graft, but its exact origin could not be established due to the low number of cells. Simultaneous detection of CK19 using fluorescent immunohistochemistry together with the detection of gonosomes using FISH was performed for the first time in the cornea and allowed us to prove that the recurrence of PPCD was caused by pathological abnormal proliferation and migration of recipient cells into donor graft.

Automated analysis of protein expression and gene amplification within the same cells of paraffin-embedded tumour tissue

BACKGROUND

The simultaneous detection of protein expression and gene copy number changes in patient samples, like paraffin-embedded tissue sections, is challenging since the procedures of immunohistochemistry (IHC) and Fluorescence in situ Hybridization (FISH) negatively influence each other which often results in suboptimal staining. Therefore, we developed a novel automated algorithm based on relocation which allows subsequent detection of protein content and gene copy number changes within the same cell.

METHODS

Paraffin-embedded tissue sections of colorectal cancers were stained for CD133 expression. IHC images were acquired and image coordinates recorded. Slides were subsequently hybridized with fluorescently labeled DNA probes. FISH images were taken at the previously recorded positions allowing for direct comparison of protein expression and gene copy number signals within the same cells/tissue areas. Relocation, acquisition of the IHC and FISH images, and enumeration of FISH signals in the immunophenotyped tumour areas were done in an automated fashion.

RESULTS

Automated FISH analysis was performed on 13 different colon cancer samples that had been stained for CD133; each sample was scored for MYC, ZNF217 and Chromosome 6 in CD133 positive and negative glands. From the 13 cases four (31%) showed amplification for the MYC oncogene and seven of 13 (54%) cases were amplified for ZNF217. There was no significant difference between CD133 positive tumour and CD133 negative tumour cells.

CONCLUSION

The technique and algorithm presented here enables an easy and reproducible combination of IHC and FISH based on a novel automated algorithm using relocation and automated spot counting.

SATB1 defines the developmental context for gene silencing by Xist in lymphoma and embryonic cells

The noncoding Xist RNA triggers silencing of one of the two female X chromosomes during X inactivation in mammals. Gene silencing by Xist is restricted to a special developmental context in early embryos and specific hematopoietic precursors. Here, we show that Xist can initiate silencing in a lymphoma model. We identify the special AT-rich binding protein SATB1 as an essential silencing factor. Loss of SATB1 in tumor cells abrogates the silencing function of Xist. In lymphocytes Xist localizes along SATB1-organized chromatin and SATB1 and Xist influence each other's pattern of localization. SATB1 and its homolog SATB2 are expressed during the initiation window for X inactivation in ES cells. Importantly, viral expression of SATB1 or SATB2 enables gene silencing by Xist in embryonic fibroblasts, which normally do not provide an initiation context. Thus, our data establish SATB1 as a crucial silencing factor contributing to the initiation of X inactivation.

Simultaneous phenotyping and genotyping (FICTION-methodology) on paraffin sections and cytologic specimens: a comparison of 2 different protocols

Combining immunofluorescence labeling with fluorescence in situ hybridization (FISH) is a powerful technique simultaneously studying immunophenotypic markers and genetic abnormalities present in tumor cells [the FICTION method (fluorescence immunophenotyping, and interphase cytogenetics as a tool for the investigation of neoplasms)]. However, few studies have been applied to the technical problems posed by antigen retrieval and accessibility of genetic probes to target-DNA, using formalin-fixed, paraffin-embedded tissue. In this study, we compared 2 immunofluorescence detection systems, the 3-step IF (TIF) method against the Tyramide Signal Amplification techniques (TSA). The FICTION-TSA technique significantly improved the sensitivity for detection of the immunophenotypic markers without influencing specific probe hybridization to target-DNA, compared with the results obtained with the TIF method. The reaction product of the TSA system was robust to the following FISH procedure in contrast to the TIF technique. The TSA technique used also allowed synchronous detection of nuclear antigens and FISH signals using both fusion (IgH/CCND1) and break-apart (CCND1) probes on formalin-fixed paraffin-embedded tissue.

LPA-induced mutually exclusive subcellular localization of active RhoA and Arp2 mRNA revealed by sequential FRET and FISH

We previously demonstrated that mRNAs for the subunits of the Arp2/3 complex localize to protrusions in fibroblasts (Mingle et al. in J Cell Sci 118:2425-2433, 2005). However, the signaling pathway that regulates Arp2/3 complex mRNA localization remains unknown. In this study we have identified lysophosphatidic acid (LPA) as a potent inducer of Arp2 mRNA localization to protrusions in fibroblasts via the RhoA-ROCK pathway. As RhoA is known to be activated locally in the cells, we sought to understand how spatial activation of Rho affects Arp2 mRNA localization. By sequentially performing fluorescence resonance energy transfer (FRET) and fluorescence in situ hybridization (FISH), we have visualized active RhoA and Arp2 mRNA in the same cells. Upon LPA stimulation, approximately two times more cells than those in the serum-free medium showed mutually exclusive localization of active RhoA and Arp2 mRNA. These results demonstrate the importance of localized activation of Rho in Arp2 mRNA localization and provide new insights as to how Rho regulates Arp2/3 complex mRNA localization. To our best knowledge, this is the first report in which FRET and FISH are combined to detect localized protein activity and mRNA in the same cells. This method should be easily adopted for the detection of other fluorescence protein based biosensors and DNA/RNA in the same cells.

Reduction of high background staining by heating unfixed mouse skeletal muscle tissue sections allows for detection of thermostable antigens with murine monoclonal antibodies

Antigen detection with indirect immunohistochemical methods is hampered by high background staining if the primary antibody is from the same species as the examined tissue. This high background can be eliminated in unfixed cryostat sections of mouse skeletal muscle by boiling sections in PBS, and several proteins including even the low abundant dystrophin protein can then be easily detected with murine monoclonal antibodies. However, not all antigens withstand the boiling procedure. Immunoreactivity of some of these antigens can be restored by subsequent washing in Triton X-100, whereas immunoreactivity of other proteins is not restored by this detergent treatment. When such thermolabile proteins are labeled with polyclonal primary antibodies followed by dichlorotriazinylaminofluorescein-conjugated secondary antibodies and boiled, the fluorescence signal persists, and sections can then be processed with a monoclonal antibody for double immunostaining of a protein unaffected by boiling. This stability of certain fluorochromes on heating can also be exploited for double immunofluorescence labeling of two different thermostable proteins with murine monoclonal antibodies as well as for combination with Y-chromosome fluorescence in situ hybridization. Our method should extend the range of monoclonal antibodies applicable to tissues derived from the same species as the monoclonal antibodies.

Fluorescence in situ hybridization using an old world monkey Y chromosome specific probe combined with immunofluorescence staining on rhesus monkey tissues

To date, there is no commercially available Y chromosome probe that can be used for fluorescence in situ hybridization (FISH) for the male rhesus monkey. We have recently generated a probe for FISH with high specificity to the short arm of the rhesus monkey Y chromosome. In this study, we further describe a method that keeps the integrity of tissue-specific antigenic structures for immunofluorescence staining subsequent to FISH on paraffin-embedded rhesus monkey tissues. We have examined this technique in combination with an epithelial cell-specific marker, cytokeratin 8/18 (CK8/18), on various tissues, including jejunum, liver, kidney, and pancreas. CK8/18 and Y chromosome signals were distinctly seen simultaneously on epithelial cells from the same tissue section from male but not female monkeys. These studies indicate that our FISH immunofluorescence technique can be reliably used to identify and phenotype male cells in paraffin-embedded rhesus monkey tissues.

Development of mammalian artificial chromosomes for the treatment of genetic diseases: Sandhoff and Krabbe diseases

Mammalian artificial chromosomes (MACs) are being developed as alternatives to viral vectors for gene therapy applications, as they allow for the introduction of large payloads of genetic information in a non-integrating, autonomously replicating format. One class of MACs, the satellite DNA-based artificial chromosome expression vehicle (ACE), is uniquely suited for gene therapy applications, in that it can be generated denovo in cells, along with being easily purified and readily transferred into a variety of recipient cell lines and primary cells. To facilitate the rapid engineering of ACEs, the ACE System was developed, permitting the efficient and reproducible loading of pre-existing ACEs with DNA sequences and/or target gene(s). As a result, the ACE System and ACEs are unique and versatile platforms for ex vivo gene therapy strategies that circumvent and alleviate existing safety and delivery limitations surrounding conventional gene therapy vectors. This review will focus on the status of MAC technologies and, in particular, the application of the ACE System towards an ex vivo gene therapy treatment of lysosomal storage diseases, specifically Sandhoff (MIM #268800) and Krabbe (MIM #245200) diseases.