Comparison of fixation methods for preservation of morphology, RNAs, and proteins from paraffin-embedded human cancer cell-implanted mouse models

Unravelling the conundrum of nucleolar NR2F1 localization using antibody-based approaches in vitro and in vivo

As a transcription factor, NR2F1 regulates spatiotemporal gene expression in the nucleus particularly during development. Aberrant NR2F1 causes the rare neurodevelopmental disorder Bosch-Boonstra-Schaaf Optic Atrophy Syndrome. In addition, altered NR2F1 expression is frequently observed in various cancers and is considered a prognostic marker or potential therapeutic target. NR2F1 has been found in both the nucleus and nucleoli, suggesting a non-canonical and direct role in the latter compartment. Hence, we studied this phenomenon employing various in vitro and in vivo models using different antibody-dependent approaches. Examination of seven commonly used anti-NR2F1 antibodies in different human cancer and stem cells as well as in wild type and null mice revealed that NR2F1 nucleolar localization is artificial and has no functional role. Our subsequent comparative analysis demonstrated which anti-NR2F1 antibody best fits which approach. The data allow for correct data interpretation and underline the need to optimize any antibody-mediated technique.

Enhancing bone repair through improved angiogenesis and osteogenesis using mesoporous silica nanoparticle-loaded Konjac glucomannan-based interpenetrating network scaffolds

We have fabricated and characterized novel bioactive nanocomposite interpenetrating polymer network (IPN) scaffolds to treat bone defects by loading mesoporous silica nanoparticles (MSNs) into blends of Konjac glucomannan, polyvinyl alcohol, and polycaprolactone. By loading MSNs, we developed a porous nanocomposite scaffold with mechanical strengths comparable to cancellous bone. In vitro cell culture studies proved the cytocompatibility of the nanocomposite scaffolds. RT-PCR studies confirmed that these scaffolds significantly upregulated major osteogenic markers. The in vivo chick chorioallantoic membrane (CAM) assay confirmed the proangiogenic activity of the nanocomposite IPN scaffolds. In vivo studies were performed using Wistar rats to evaluate the scaffolds' compatibility, osteogenic activity, and proangiogenic properties. Liver and renal function tests confirmed that these scaffolds were nontoxic. X-ray and μ-CT results show that the bone defects treated with the nanocomposite scaffolds healed at a much faster rate compared to the untreated control and those treated with IPN scaffolds. H&E and Masson's trichrome staining showed angiogenesis near the newly formed bone and the presence of early-stage connective tissues, fibroblasts, and osteoblasts in the defect region at 8 weeks after surgery. Hence, these advantageous physicochemical and biological properties confirm that the nanocomposite IPN scaffolds are ideal for treating bone defects.

Intranasal Nose-to-Brain Drug Delivery via the Olfactory Region in Mice: Two In-Depth Protocols for Region-Specific Intranasal Application of Antibodies and for Expression Analysis of Fc Receptors via In Situ Hybridization in the Nasal Mucosa

A region-specific catheter-based intranasal administration method was successfully developed, established, and validated as reported previously. By using this method, drugs can be applicated specifically to the olfactory region. Thereby, intranasally administered drugs could be delivered via neuronal connections to the central nervous system. Here, we present a detailed protocol with a step-by-step procedure for nose-to-brain delivery via the olfactory mucosa.Fc receptors such as the neonatal Fc receptor (FcRn) and potentially Fcγ receptor IIb (FcγRIIb) are involved in the uptake and transport of antibodies via the olfactory nasal mucosa. To better characterize their expression levels and their role in CNS drug delivery via the nose, an in situ hybridization (ISH) protocol was adapted for nasal mucosa samples and described in abundant details.

Substantial decrease in SARS-CoV-2 RNA after fixation of cadavers intended for anatomical dissection

With the onset of the COVID-19 pandemic, a problem arose with classic body donation programmes for obtaining cadavers for anatomical dissections, science and research. The question has emerged whether bodies of individuals who died of COVID-19 or were infected by SARS-CoV-2 could be admitted to Departments of Anatomy. To determine the risk of SARS-CoV-2 transmission to employees or students, the presence and stability of SARS-CoV-2 RNA in cadavers after fixation agents' application and subsequent post-fixation baths over time were examined. The presence of viral RNA in swabs from selected tissues was assessed by the standardized routine RNA isolation protocol and subsequent real-time PCR analysis. To support the results obtained from the tissue swabs, samples of RNA were exposed in vitro to short and long-term exposure to the components of the injection and fixation solutions used for the bodies' conservation. Substantial removal of SARS-CoV-2 RNA was observed in post-mortem tissue following perfusion with 3.5% phenol, 2.2% formaldehyde, 11.8% glycerol and 55% ethanol, and subsequent post-fixation in an ethanol bath. In vitro experiments showed significant effects of formaldehyde on SARS-CoV-2 RNA, while phenol and ethanol showed only negligible effects. We conclude that cadavers subjected to fixation protocols as described here should not pose a considerable risk of SARS-CoV-2 infection while being handled by students and staff and are, therefore, suitable for routine anatomical dissections and teaching.

Differential Levels of Tryptophan-Kynurenine Pathway Metabolites in the Hippocampus, Anterior Temporal Lobe, and Neocortex in an Animal Model of Temporal Lobe Epilepsy

Glutamate-receptor-mediated hyperexcitability contributes to seizure generation in temporal lobe epilepsy (TLE). Tryptophan-kynurenine pathway (TKP) metabolites regulate glutamate receptor activity under physiological conditions. This study was designed to investigate alterations in the levels of TKP metabolites and the differential regulation of glutamatergic activity by TKP metabolites in the hippocampus, anterior temporal lobe (ATL), and neocortex samples of a lithium-pilocarpine rat model of TLE. We observed that levels of tryptophan were reduced in the hippocampus and ATL samples but unaltered in the neocortex samples. The levels of kynurenic acid were reduced in the hippocampus samples and unaltered in the ATL and neocortex samples of the TLE rats. The levels of kynurenine were unaltered in all three regions of the TLE rats. The magnitude of reduction in these metabolites in all regions was unaltered in the TLE rats. The frequency and amplitude of spontaneous excitatory postsynaptic currents were enhanced in hippocampus ATL samples but not in the neocortex samples of the TLE rats. The exogenous application of kynurenic acid inhibited glutamatergic activity in the slice preparations of all these regions in both the control and the TLE rats. However, the magnitude of reduction in the frequency of kynurenic acid was higher in the hippocampus (18.44 ± 2.6% in control vs. 30.02 ± 1.5 in TLE rats) and ATL (16.31 ± 0.91% in control vs. 29.82 ± 3.08% in TLE rats) samples of the TLE rats. These findings suggest the differential regulation of glutamatergic activity by TKP metabolites in the hippocampus, ATL, and neocortex of TLE rats.

Optimizing immunostaining of archival fish samples to enhance museum collection potential

Immunohistochemistry (IHC) is a powerful biochemical technique that uses antibodies to specifically label and visualize proteins of interests within biological samples. However, fluid-preserved specimens within natural history collection often use fixatives and protocols that induce high background signal (autofluorescence), which hampers IHC as it produces low signal-to-noise ratio. Here, we explored techniques to reduce autofluorescence using sodium borohydride (SBH), citrate buffer, and their combination on fish tissue preserved with paraformaldehyde, formaldehyde, ethanol, and glutaraldehyde. We found SBH was the most effective quenching technique, and applied this pretreatment to the gill or skin of 10 different archival fishes - including specimens that had been preserved in formaldehyde or ethanol for up to 65 and 37 years, respectively. The enzyme Na⁺/K⁺-ATPase (NKA) was successfully immunostained and imaged using confocal fluorescence microscopy, allowing for the identification and characterization of NKA-rich ionocytes essential for fish ionic and acid-base homeostasis. Altogether, our SBH-based method facilitates the use of IHC on archival samples, and unlocks the historical record on fish biological responses to environmental factors (such as climate change) using specimens from natural history collections that were preserved decades to centuries ago.

Intracellular flow cytometry staining of antibody-secreting cells using phycoerythrin-conjugated antibodies: pitfalls and solutions

Background

Antibody-secreting cells are terminally differentiated B cells that play a critical role in humoral immunity through immunoglobulin secretion along with possessing the potential to be long-lived. It is now appreciated that ASCs regulate multiple aspects of biology through the secretion of various cytokines. In this regard, ICFC is a key tool used to assess the presence of intracellular proteins such as cytokines and transcription factors.

Methods

Paraformaldehyde plus saponin or the eBioscience Foxp3/Transcription Factor Staining Buffer Set were used to evaluate the non-specific intracellular retention of phycoerythrin-containing antibody conjugates by ASCs.

Results

We showed that the use of phycoerythrin-containing antibody conjugates led to a false interpretation of ASC intracellular protein expression compared with other cell types. This was mainly due to the inappropriate retention of these antibodies specifically within ASCs. Furthermore, we demonstrated how to reduce this retention which allowed for a more accurate comparison of intracellular protein expression between ASCs and other cell types such as B lymphocytes. Using this methodology, our data revealed that spleen ASCs expressed toll-like receptor 7 as well as the pro-form of the inflammatory cytokine interleukin-1β.

Conclusion

Increasing the number of centrifugation steps performed on ASCs post-fixation leads to inappropriate retention of phycoerythrin-containing antibody conjugates during ICFC.

Perfusion with 10% neutral-buffered formalin is equivalent to 4% paraformaldehyde for histopathology and immunohistochemistry in a mouse model of experimental autoimmune encephalomyelitis

Intravascular (IV) perfusion of tissue fixative is commonly used in the field of neuroscience as the central nervous system tissues are exquisitely sensitive to handling and fixation artifacts which can affect downstream microscopic analysis. Both 10% neutral-buffered formalin (NBF) and 4% paraformaldehyde (PFA) are used, although IV perfusion with PFA is most commonly referenced. The study objective was to compare the severity of handling and fixation artifacts, semiquantitative scores of inflammatory and neurodegenerative changes, and quantitative immunohistochemistry following terminal IV perfusion of mice with either 10% NBF or 4% PFA in a model of experimental autoimmune encephalitis (EAE). The study included 24 mice; 12 were control animals not immunized and an additional 12 were immunized with PLP139-151 subcutaneously, harvested at day 20, and fixed in the same fashion. Equal numbers (4 per group) were perfused with 10% NBF or 4% PFA, and 4 were immersion-fixed in 10% NBF. NBF-perfused mice had less severe dark neuron artifact than PFA-perfused mice (P < .001). Immersion-fixed animals had significantly higher scores for oligodendrocyte halos, dark neuron artifact, and perivascular clefts than perfusion-fixed animals. Histopathology scores in EAE mice for inflammation, demyelination, and necrosis did not differ among fixation methods. Also, no significant differences in quantitative immunohistochemistry for CD3 and Iba-1 were observed in immunized animals regardless of the method of fixation. These findings indicate that IV perfusion of mice with 10% NBF and 4% PFA are similar and adequate fixation techniques in this model.

Effects of different fixatives over different fixation times, including Antigenfix, on immunohistochemical studies

Tissue fixation is an essential step in the performance of ancillary studies, including immunohistochemistry. The aim of this study was to compare the effect of various fixatives and fixative times on immunohistochemistry (IHC) in bovine and porcine endometrium using progesterone receptors and SOX2 antibodies. Immunohistochemical staining with progesterone receptors and SOX2 was performed on tissue samples fixed in formalin, Antigenfix, Greenfix, Bouin’s solution and methacarn at 1.5, 8.5, 15.5, 29.5, 64.5, 189.5, 249.5, 309.5 and 369.5 days of fixation. Formalin and Antigenfix proved to be the best fixative for both short-term and long-term fixation for IHC. Bouin’s solution was partially applicable for short-term (24 h) fixation. Greenfix and methacarn were absolutely inappropriate fixatives for IHC (completely negative staining using methacarn). These results were obtained on an automated immunostainer using EDTA buffer pH 8.4 as the antigen retrieval solution. When the staining procedure was performed manually and citrate buffer with different pH values was used, weakly positive results were obtained with both progesterone receptors (pH 8 and 9) and SOX2 (pH 7.2); however, significantly lower staining quality was obtained using the methacarn fixative compared to aldehyde fixatives. The reported findings demonstrated the superiority of aldehyde fixatives (formalin and Antigenfix) over alcohol fixatives (methacarn) and fixatives combining both denaturing and cross-linking proteins (Greenfix and Bouin’s solution) for IHC. Antigen retrieval-IHC using EDTA buffer was found to be excellent for aldehyde fixatives, but proved to be completely unsuitable for methacarn, Greenfix, and Bouin’s solution.

Assessing the quality of long-term stored tissues in formalin and in paraffin-embedded blocks for histopathological analysis

Introduction:

Formalin is the most commonly used fixative which enables for long-term storage of specimens and preserves morphologic features allowing the microscopic evaluation for future research analysis. Archival collections of the tissue serve as a reliable tool for diagnostic research purpose. They have an important role in on-going patient care, allows for evaluation of recurrent cases for diagnostic purpose and rare case specimens can also be used as an educational tool as well as for further biomedical research purposes. However, studies assessing quality and their usefulness for such purposes are scanty. Hence, the present study is aimed at evaluating and comparing the tissue changes after long-term storage in formalin as well as in paraffin-embedded blocks.

Methodology:

Three study groups include specimens stored in formalin for a minimum of 5 years (long-term fixed tissue) and their corresponding paraffin-embedded old tissue blocks along with freshly fixed tissues taken as controls which were subjected to routine histopathological procedures and were assessed for macroscopic and microscopic evaluation.Chi-square test and Z-proportion tests were considered for statistical analysis.

Results:

Prolonged storage of the tissues in formalin showed variation in color and consistency, difficulty in cutting during grossing with inadequate sectioning characters, loss of tissue integrity and architecture, and inadequate nuclear and cytoplasmic details.

Conclusion:

On histological analysis, prolonged formalin-stored specimens showed deleterious effects than archival blocks. Hence, it can be proposed that tissues are better preserved in paraffin blocks rather than in formalin for further biomedical research purposes.

Different fixatives influence morphology, antigen preservation, and TUNEL staining in chicken (Gallus gallus) testis

The optimized fixative for testis is still controversial. This study investigated the effects of Modified Davidson's Fluid (mDF), 4% Paraformaldehyde (4% PFA), and Bouin's Fluid (BF) fixatives on chicken testes in normal/cadmium (Cd) feeding groups using hematoxylin and eosin (HE), immunohistochemistry (IHC), and Terminal Transferase dUTP Nick End Labeling (TUNEL) staining. Compared to the mDF, we established that the testes fixed with 4% PFA and BF in the normal group had severe shrinkage in tubular and interstitial compartments. Moreover, compared with 4% PFA, the number of GATA4-positive Sertoli cells/mm² reduced by 67.61% in mDF and 80.57% in BF for one seminiferous tubule. The TUNEL assay illustrated that more positive cells/mm² in mDF group (28.47 ± 11.38) than in 4% PFA (10.49 ± 7.89). In Cd-treated testes, mDF showed more morphological details than 4% PFA and BF. In contrast, the number of GATA4-positive Sertoli cells/mm² of 4% PFA was higher than that of mDF by 65.78% and BF by 64.80% in a seminiferous tubule. The number of TUNEL positive cells/mm² in mDF (272.60 ± 34.41) were higher than in 4% PFA (175.91 ± 19.87). These results suggest that mDF fixative is suitable for normal and Cd-treated testis fixation for HE and TUNEL staining in chicken, whereas 4% PFA fixative is better for IHC examination.

Differential glutamate receptor expression and function in the hippocampus, anterior temporal lobe and neocortex in a pilocarpine model of temporal lobe epilepsy

Temporal lobe epilepsy (TLE) is the most common form of intractable epilepsy where hyperactive glutamate receptors may contribute to the complex epileptogenic network hubs distributed among different regions. This study was designed to investigate the region-specific molecular alterations of the glutamate receptors and associated excitatory synaptic transmission in pilocarpine rat model of TLE. We recorded spontaneous excitatory postsynaptic currents (EPSCs) from pyramidal neurons in resected rat brain slices of the hippocampus, anterior temporal lobe (ATL) and neocortex. We also performed mRNA and protein expression of the glutamate receptor subunits (NR1, NR2A, NR2B, and GLUR1-4) by qPCR and immunohistochemistry. We observed significant increase in the frequency and amplitude of spontaneous EPSCs in the hippocampal and ATL samples of TLE rats than in control rats. Additionally, the magnitude of the frequency and amplitude was increased in ATL samples compared to that of the hippocampal samples of TLE rats. The mRNA level of NR1 was upregulated in both the hippocampal as well as ATL samples and that of NR2A, NR2B were upregulated only in the hippocampal samples of TLE rats than in control rats. The mRNA level of GLUR4 was upregulated in both the hippocampal as well as ATL samples of TLE rats than in control rats. Immunohistochemical analysis demonstrated that the number of NR1, NR2A, NR2B, and GLUR4 immuno-positive cells were significantly higher in the hippocampal samples whereas number of NR1 and GLUR4 immuno-positive cells were significantly higher in the ATL samples of the TLE rats than in control rats. This study demonstrated the region-specific alterations of glutamate receptor subunits in pilocarpine model of TLE, suggesting possible cellular mechanisms contributing to generation of independent epileptogenic networks in different temporal lobe structures.

BIA-ALCL diagnosis on CytoLyt fixed ThinPrep, cell block and immunohistochemistry

Breast implant associated anaplastic large cell lymphoma (BIA-ALCL) is an emergent rare T cell non-Hodgkin lymphoma arising in association with a breast implant, particularly textured ones. Recent guidelines list cytopathological examination as the first essential step for diagnosis, routinely followed by CD30 immunohistochemistry (IHC) and flow cytometry (FC) for a T cell clone. The majority of BIA-ALCL literature regarding cytopathological evaluation describes morphology based on various preparation methods limited to cytospins and smears with the exception of at least one case report detailing cytomorphological and IHC findings on ThinPrep. This case report details initial diagnosis of BIA-ALCL rendered with CytoLyt prepared ThinPrep and cell block, including the specific antibodies used for IHC. The ThinPrep slide showed numerous singly dispersed large, atypical cells with abundant cytoplasm containing irregular nuclei with dispersed chromatin and prominent nucleoli in a background of macrophages, inflammatory cells and granular debris. TIA-1 and CD30 along with other T-cell markers, including specific antibodies, remains immunoreactive in tissue collected in CytoLyt solution. Cell size reduction, artifactual lymphoid cell aggregation and prominent nucleoli in benign and reactive conditions are among other ThinPrep cellular alterations pathologists should bear in mind.

Combination Treatment with GSK126 and Pomalidomide Induces B-Cell Differentiation in EZH2 Gain-of-Function Mutant Diffuse Large B-Cell Lymphoma

Enhancer of zeste 2 polycomb repressive complex 2 subunit (EZH2), the catalytic subunit of polycomb repressive complex 2 (PRC2), regulates genes involved in cell lineage and differentiation through methylating lysine 27 on histone H3 (H3K27me3). Recurrent gain-of-function mutations of EZH2 have been identified in various cancer types, in particular, diffuse large B-cell lymphoma (DLBCL), through large-scale genome-wide association studies and EZH2 depletion or pharmacological inhibition has been shown to exert an antiproliferative effect on cancer cells, both in vitro and in vivo. In the current study, a combination of pomalidomide and GSK126 synergistically inhibited the growth of EZH2 gain-of-function mutant Diffuse large B-cell lymphoma (DLBCL) cells. Furthermore, this synergistic effect appeared to be dependent on cereblon (CRBN), a cellular receptor of pomalidomide, but not degradation of IKAROS family zinc finger 1 (IKZF1) or IKAROS family zinc finger 3 (IKZF3). RNA sequencing analyses revealed that co-treatment with GSK126 and pomalidomide induced specific gene sets involved in B-cell differentiation and apoptosis. Synergistic growth inhibition and B-cell differentiation were further validated in xenograft mouse models. Our collective results provide a molecular basis for the mechanisms underlying the combined therapeutic effects of PRC2 inhibitors and pomalidomide on EZH2-mutated DLBCL.

The effects of tissue fixation on sequencing and transcript abundance of nucleic acids from microdissected liver samples of smallmouth bass (Micropterus dolomieu)

There is an increasing emphasis on effects-based monitoring to document responses associated with exposure to complex mixtures of chemicals, climate change, pathogens, parasites and other environmental stressors in fish populations. For decades aquatic monitoring programs have included the collection of tissues preserved for microscopic pathology. Consequently, formalin-fixed, paraffin-embedded (FFPE) tissue can be an important reservoir of nucleic acids as technologies emerge that utilize molecular endpoints. Despite the cross-linking effects of formalin, its impact on nucleic acid quality and concentration, amplification, and sequencing are not well described. While fresh-frozen tissue is optimal for working with nucleic acids, FFPE samples have been shown to be conducive for molecular studies. Laser capture microdissection (LCM) is one technology which allows for collection of specific regions or cell populations from fresh or preserved specimens with pathological alterations, pathogens, or parasites. In this study, smallmouth bass (Micropterus dolomieu) liver was preserved in three different fixatives, including 10% neutral buffered formalin (NBF), Z-Fix® (ZF), and PAXgene® (PG) for four time periods (24 hr, 48 hr, seven days, and 14 days). Controls consisted of pieces of liver preserved in RNALater® or 95% ethanol. Smallmouth bass were chosen as they are an economically important sportfish and have been utilized as indicators of exposure to endocrine disruptors and other environmental stressors. Small liver sections were cut out with laser microdissection and DNA and RNA were purified and analyzed for nucleic acid concentration and quality. Sanger sequencing and the NanoString nCounter® technology were used to assess the suitability of these samples in downstream molecular techniques. The results revealed that of the formalin fixatives, NBF samples fixed for 24 and 48 hr were superior to ZF samples for both Sanger sequencing and the Nanostring nCounter®. The non-formalin PAXgene® samples were equally successful and they showed greater stability in nucleic acid quality and concentration over longer fixation times. This study demonstrated that small quantities of preserved tissue from smallmouth bass can be utilized in downstream molecular techniques; however, future studies will need to optimize the methods presented here for different tissue types, fish species, and pathological conditions.

Impact of different stabilization methods on RT-qPCR results using human lung tissue samples

Aiming to increase the reproducibility of biomedical research results, biobanks obtain human tissues of the highest quality and carry out different storage methods adapted to the needs of analytical technique to be performed by the biomedical researchers. However, there is much controversy and little data concerning the real impact of different stabilization methods on tissue quality, integrity and functionality of derived biomolecules. The influence of four stabilization methods [RNAlater (RNL), snap freezing (SF), snap freezing using Optimal Cutting Tissue compound (SF-OCT) and formalin-fixed paraffin-embedded (FFPE)] on RNA quality and integrity was evaluated in paired samples of lung tissue. RNA integrity was evaluated through PCR-endpoint assays amplifying six fragments of different length of the HPRT1 gene and RNA Integrity Number (RIN). To evaluate the difference of tissue functionality among the stabilization methods tested, RT-qPCRs were performed focusing on the differential expression of the HPRT1, SNRPD3 and Jun genes. RNA from the samples preserved with the RNL or SF-OCT method showed better integrity compared to SF and FFPE, measured by PCR-endpoint and RT-qPCR assays. However, only statistically significant differences were observed between the RNA from FFPE and other stabilization methods when gene expression of HPRT1, SNRPD3 and Jun housekeeping genes were determined by RT-qPCR. For the three mentioned genes, Cq and RIN values were highly correlated. The present work describes the fragility of SF samples, being critical the moment just before RNA extraction, although further experiments of tissue RNA are needed. Standardization pre-analytic workflow can lead to improved reproducibility between biomedical research studies. The present study demonstrated clear evidences about the impact of the stabilization method on RNA derived from lung human tissue samples.

Effects of 4% paraformaldehyde and modified Davidson's fluid on the morphology and immunohistochemistry of Xiang pig testes

Modified Davidson’s fluid (mDF) is a good fixative for morphological and antigen preservation. However, recent studies have shown that 4% paraformaldehyde (PFA) can better preserve the actin structure in rodent testes. It remains controversial which of these fixatives is best for testicular tissue. This study investigated the effects of both mDF and 4% PFA on the morphology and antigen preservation of Xiang pig testes using hematoxylin-eosin (HE) staining and immunohistochemistry (IHC). The stronger testis penetration of mDF compared with that of 4% PFA was primarily manifested as testicular color change and decrease in tissue weight loss. Testes fixed with 4% PFA displayed a severe shrinkage of both the tubular and interstitial compartments and the seminiferous tubule area decreased by 12.02% compared with that in mDF-fixed tissues. In contrast, IHC results showed that 4% PFA fixation achieved better IHC-positive performance than mDF fixation for antigens specifically expressed in germ cells, Leydig cells and Sertoli cells. Due to this improved antigen preservation by 4% PFA fixation, the relative immunoreactions intensity significantly increased by 39.8%, 27.8%, and 76.4%, respectively, compared with that in mDF fixation. In summary, fixation of Xiang pig testes with mDF was suitable for HE staining, while fixation with 4% PFA was more suitable for IHC.

Cytology cell blocks are suitable for immunohistochemical testing for PD-L1 in lung cancer

Background

PD-L1 immunohistochemistry (IHC) testing is usually carried out on tissue blocks from core needle biopsy or surgical resections. In this study, we assessed the feasibility of using cytology cell blocks for PD-L1 IHC assay.

Methods

A total of 1419 consecutive cases of non-small-cell lung cancer (NSCLC), including 371 cytology cell blocks, 809 small biopsies, and 239 surgical specimens, were included in the study. The cytology cell blocks were prepared with formalin only, methanol/alcohol only or both. PD-L1 expression was examined by staining with Dako PD-L1 IHC 22C3 pharmDx kit. A Tumor Proportion Score (TPS) was categorized as <1%, 1%-49% and ≥50% tumor cells. A total of 100 viable tumor cells were required for adequacy.

Results

Of the cytology cell blocks, 92% of the specimens had an adequate number of tumor cells, not significantly different from small biopsies. The rate of TPS ≥50% differed between sample types and was observed in 42% of cytology cell blocks versus 36% of small biopsies (P = 0.04), and 29% of surgical resections (P = 0.001). The fixative methods did not affect the immunostaining, with overall PD-L1 high expression (TPS ≥50%) rates of 42% in formalin-fixed specimens versus 40% in specimens with combined fixation by methanol/alcohol and formalin (NS). The PD-L1 high expression rate was not associated with EGFR, ALK or KRAS molecular alterations. Higher stage (IV) was associated with higher PD-L1 TPS (P= 0.001).

Conclusion

Our results show that when the TPS ≥50% is used as the end point, PD-L1 IHC performs well with cytology cell blocks. Cell blocks should be considered as a valuable resource for PD-L1 testing in advanced NSCLC. The clinical significance of higher PD-L1 IHC scores in cytology specimens needs to be evaluated prospectively.

Comparison of Fixation Methods for Preservation Cytology Specimens of Cell Block Preparation Using 10% Neutral Buffer Formalin and 96% Alcohol Fixation in E-cadherin and Ki-67 Immunohistochemical Examination

BACKGROUND:

Cytological and molecular examinations are among the most important examinations in cancer diagnosis. 96% alcohol is a fixative solution commonly used by clinicians for cytological samples because of its accessibility and affordability. Cellblock preparation from cytology specimen may increase morphology detail and may be used for further biomarker analysis. E-cadherin is an adhesion protein expressed in the cell membrane of most carcinoma. Ki67 is a protein expressed in nuclei of malignant cells that used as a proliferation marker.

AIM:

This study was designed to investigate the effect of fixation duration in 96% alcohol on protein preservation for immunohistochemistry (IHC) evaluation compared to 10% neutral buffered formalin (NBF) as the gold standard.

METHODS:

Twenty-five fine-needle aspiration biopsy (FNAB) specimen diagnosed as carcinoma were fixed in 10% NBF and 96% alcohol for 1 hour, 6 hours, 24 hours, 48 hours and 72 hours. Cell blocks preparation were made from those 6 groups of specimens. E-cadherin and Ki67 IHC were done to cell blocks section and evaluated. The data were statistically analysed using the Friedman test with p-value < 0.05 of a significant level.

RESULTS:

There were significant differences between E-cadherin and Ki67 expression in cell block preparation from 96% alcohol-fixed cytology specimen for 1 hour, 6 hours, 24 hours, 48 hours and 72 hours to 10% NBF (p = 0.0001).

CONCLUSION:

The result indicated that 96% alcohol is not suitable as a fixative solution for cell block preparation in E-cadherin and Ki-67 IHC examination.

Evaluation of loop-mediated isothermal amplification assay for detection and typing of human papilloma virus 16 and 18 from endocervical samples

Background

Many human papillomavirus (HPV) types are associated with cervical cancer (CC). Therefore, HPV genotyping has both clinical and epidemiological importance. HPV 16 and 18 are two principal high-risk types responsible for more than 70% of all CC cases. Although several commercial and non-commercial genotyping assays are available, there is a need for a cost-effective and sensitive genotyping method for low- and middle-income countries.

Methods

The study was aimed at evaluation of loop-mediated isothermal amplification (LAMP) assay for HPV genotyping in cervical samples. A total of six primer sets for each HPV type were selected for the assay. The LAMP assay was standardised and validated with HPV control panel. Cervical biopsies were subjected to nested multiplex polymerase chain reaction (NM-PCR; as a part of routine diagnostic workup) and LAMP (HPV 16 and 18) simultaneously.

Results

A total of 225 clinical samples were processed during the study period. The sensitivity of the assay was determined using the 10-fold dilutions of positive controls. Both the HPV 16-LAMP and HPV 18-LAMP assays were shown to detect as low as 10 viral copies per reaction, which is similar to that of NM-PCR. The LAMP assay had a good agreement (new cases; 92%, post-chemoradiotherapy [post-CRT]; 89.1%) with NM-PCR for the detection of both HPV 16 and 18. As compared to histology (new cases; 79.8%, post-CRT; 51.3%), LAMP had better agreement with NM-PCR for detection of HPV from post-CRT cases.

Conclusions

We evaluated the LAMP assay for simultaneous detection and typing of HPV 16 and 18. The assay had good agreement with NM-PCR for detection of both HPV 16 and 18. The LAMP assay is a promising tool for HPV genotyping along with routine cervical cytology, especially in resource-constrained settings.

The impact of cell fixation on coherent anti-stokes Raman scattering signal intensity in neuronal and glial cell lines

A number of studies require sample fixation, aimed to preserve cells in a physiological state with minimal changes of morphology and intracellular molecular content. Sample fixation may significantly distort experimental data, which makes the data interpretation process more challenging. It is particularly important for study of lipid-related diseases, where the biochemical and morphological characteristics of the cells need to be well preserved for an accurate data analysis. This study investigates the effects of formaldehyde and ethanol (EtOH) fixatives on coherent anti-stokes Raman scattering (CARS) signal of proteins and lipids in major cellular compartments of neuronal and glial cells. We found that both fixatives induce alteration of proteins and lipids signal in studied cell lines. Furthermore, the impact of sample preservation methods on CARS signal varies between cell lines. For instance, our data reveals that EtOH fixation induces ~45% increase of CARS signal of proteins in the nucleolus of neuronal cells and ~35% decrease of CARS signal in glial cells. The results indicate that aldehyde fixation is a preferable method for preservation of neuronal and glial cells prior to CARS imaging, as it less affects both CARS signal and intracellular distribution of proteins and lipids.

From fix to fit into the autoptic human brains

Formalin-fixed, paraffinembedded (FFPE) human brain tissues are very often stored in formalin for long time. Formalin fixation reduces immunostaining, and the DNA/RNA extraction from FFPE brain tissue becomes suboptimal. At present, there are different protocols of fixation and several procedures and kits to extract DNA/RNA from paraffin embedding tissue, but a gold standard protocol remains distant. In this study, we analyzed four types of fixation systems and compared histo and immuno-staining. Based on our results, we propose a modified method of combined fixation in formalin and formic acid for the autoptic adult brain to obtain easy, fast, safe and efficient immunolabelling of long-stored FFPE tissue. In particular, we have achieved an improved preservation of cellular morphology and obtained success in postmortem immunostaining for NeuN. This nuclear antigen is an important marker for mapping neurons, for example, to evaluate the histopathology of temporal lobe epilepsy or to draw the topography of cardiorespiratory brainstem nuclei in sudden infant death syndrome (SIDS). However, NeuN staining is frequently faint or lost in postmortem human brain tissues. In addition, we attained Fluoro Jade C staining, a marker of neurodegeneration, and immunofluorescent staining for stem cell antigens in the postnatal human brain, utilizing custom fit fixation procedures.

New piperidine derivative DTPEP acts as dual-acting anti-breast cancer agent by targeting ERα and downregulating PI3K/Akt-PKCα leading to caspase-dependent apoptosis

OBJECTIVES

In our ongoing studies to develop ER targeting agents, we screened for dual-acting molecules with a hypothesis that a single molecule can also target both ER positive and negative groups of breast cancer.

MATERIALS AND METHODS

1-(2-(4-(Dibenzo[b,f]thiepin-10-yl)phenoxy)ethyl)piperidine (DTPEP) was synthesized and screened in both MCF-7 (ER+ve) and MDA-MB-231 (ER-ve) cells. Assays for analysis of cell cycle, ROS, apoptosis and MMP loss were carried out using flow cytometry. Its target was investigated using western blot, transactivation assay and RT-PCR. In vivo efficacy of DTPEP was validated in LA-7 syngeneic rat mammary tumour model.

RESULTS

Here, we report identification of dual-acting molecule DTPEP that downregualtes PI3K/Akt and PKCα expression, induces ROS and ROS-dependent apoptosis, loss of mitochondrial membrane potential, induces expression of caspase indicative of both intrinsic and extrinsic apoptosis in MCF-7 and MDA-MB-231 cells. In MCF-7 cells, DTPEP downregulates ERα expression and activation. In MDA-MB-231 cells, primary cellular target of DTPEP is not clearly known, but it downregualtes PI3K/Akt and PKCα expression. In vivo study showed regression of LA-7 syngeneic mammary tumour in SD rat.

CONCLUSIONS

We identified a new dual-acting anti-breast cancer molecules as a proof of concept which is capable of targeting both ER-positive and ER-negative breast cancer.

Nonformalin Fixative Agents: A Comparative Study of Fixative Efficacy and Histomorphology

OBJECTIVES

Formalin is a gold standard fixative agent. However, formalin possesses health hazards and is not always available in rural areas. The objective of this study was to compare tissue fixative efficacy of nonformalin fixative agents with formalin.

METHODS

Oral tissues obtained during impacted tooth removal were collected. The tissue fragments were sectioned and fixed in 4 different fixatives; 30% jaggery, 70% ethanol, 2% mepivacaine with 1:100 000 epinephrine, or formalin for 24 and 72 hours. All specimens were then immersed in formalin for another 24 hours and processed according to standard protocol. Hematoxylin and eosin-stained sections were evaluated by a pathologist. The cellular structure, cellular outline, and quality of staining were graded from 1 to 3 and average fixative efficacy scores were compared using 1-way analysis of variance. Fixative artifacts were described.

RESULTS

Fixative efficacy scores of 70% ethanol and 30% jaggery at 24 and 72 hours were not statistically different from those of formalin. Conversely, 2% mepivacaine demonstrated significantly lower fixative efficacy scores than other agents. Although efficacy of each fixative was not statistically different between 24 and 72 hours, efficacy of 70% ethanol was markedly reduced at 72 hours when compared with others. Acantholysis of epithelial cells was the most notable artifact at 72 hours when fixed with nonformalin fixative agents.

CONCLUSION

Both 70% ethanol and 30% jaggery provided acceptable fixative efficacy at 24 hours. However, only 30% jaggery maintained fixative efficacy at 72 hours. Nevertheless, negative effects on the epithelial cells were unavoidable and should be interpreted with caution.

Elucidating the Burden of HIV in Tissues Using Multiplexed Immunofluorescence and In Situ Hybridization: Methods for the Single-Cell Phenotypic Characterization of Cells Harboring HIV In Situ

Persistent tissue reservoirs of HIV present a major barrier to cure. Defining subsets of infected cells in tissues is a major focus of HIV cure research. Herein, we describe a novel multiplexed in situ hybridization (ISH) (RNAscope) protocol to detect HIV-DNA (vDNA) and HIV-RNA (vRNA) in formalin-fixed paraffin-embedded (FFPE) human tissues in combination with immunofluorescence (IF) phenotyping of the infected cells. We show that multiplexed IF and ISH (mIFISH) is suitable for quantitative assessment of HIV vRNA and vDNA and that multiparameter IF phenotyping allows precise identification of the cellular source of the ISH signal. We also provide semi-quantitative data on the impact of various tissue fixatives on the detectability of vDNA and vRNA with RNAscope technology. Finally, we describe methods to quantitate the ISH signal on whole-slide digital images and validation of the quantitative ISH data with quantitative real-time PCR for vRNA. It is our hope that this approach will provide insight into the biology of HIV tissue reservoirs and to inform strategies aimed at curing HIV.

Reduced graphene oxide-loaded nanocomposite scaffolds for enhancing angiogenesis in tissue engineering applications

Tissue engineering combines cells, scaffolds and signalling molecules to synthesize tissues in vitro. However, the lack of a functioning vascular network severely limits the effective size of a tissue-engineered construct. In this work, we have assessed the potential of reduced graphene oxide (rGO), a non-protein pro-angiogenic moiety, for enhancing angiogenesis in tissue engineering applications. Polyvinyl alcohol/carboxymethyl cellulose (PVA/CMC) scaffolds loaded with different concentrations of rGO nanoparticles were synthesized via lyophilization. Characterization of these scaffolds showed that the rGO-loaded scaffolds retained the thermal and physical properties (swelling, porosity and in vitro biodegradation) of pure PVA/CMC scaffolds. In vitro cytotoxicity studies, using three different cell lines, confirmed that the scaffolds are biocompatible. The scaffolds containing 0.005 and 0.0075% rGO enhanced the proliferation of endothelial cells (EA.hy926) in vitro. In vivo studies using the chick chorioallantoic membrane model showed that the presence of rGO in the PVA/CMC scaffolds significantly enhanced angiogenesis and arteriogenesis.

Cleavable Crosslinkers as Tissue Fixation Reagents for Proteomic Analysis

Formaldehyde fixation is widely used for long-term maintenance of tissue. However, due to formaldehyde-induced crosslinks, fixed tissue proteins are difficult to extract, which hampers mass spectrometry (MS) proteomic analyses. Recent years have seen the use of different combinations of high temperature and solubilizing agents (usually derived from antigen retrieval techniques) to unravel formaldehyde-fixed paraffin-embedded tissue proteomes. However, to achieve protein extraction yields similar to those of fresh-frozen tissue, high-temperature heating is necessary. Such harsh extraction conditions can affect sensitive amino acids and post-translational modifications, resulting in the loss of important information, while still not resulting in protein yields comparable to those of fresh-frozen tissue. Herein, the objective is to evaluate cleavable protein crosslinkers as fixatives that allow tissue preservation and efficient protein extraction from fixed tissue for MS proteomics under mild conditions. With this goal in mind, disuccinimidyl tartrate (DST) and dithiobis(succinimidylpropionate) (DSP) are investigated as cleavable fixating reagents. These compounds crosslink proteins by reacting with amino groups, leading to amide bond formation, and can be cleaved with sodium metaperiodate (cis-diols, DST) or reducing agents (disulfide bonds, DSP), respectively. Results show that cleavable protein crosslinking with DST and DSP allows tissue fixation with morphology preservation comparable to that of formaldehyde. In addition, cleavage of DSP improves protein recovery from fixed tissue by a factor of 18 and increases the number of identified proteins by approximately 20 % under mild extraction conditions compared with those of formaldehyde-fixed paraffin-embedded tissue. A major advantage of DSP is the introduction of well-defined protein modifications that can be taken into account during database searching. In contrast to DSP fixation, DST fixation followed by cleavage with sodium metaperiodate, although effective, results in side reactions that prevent effective protein extraction and interfere with protein identification. Protein crosslinkers that can be cleaved under mild conditions and result in defined modifications, such as DSP, are thus viable alternatives to formaldehyde as tissue fixatives to facilitate protein analysis from paraffin-embedded, fixed tissue.

A method for isolating cortical interneurons sharing the same birthdays for gene expression studies

The two neuronal populations in the cortex, pyramidal neurons and interneurons, can be separated based on neurotransmitter identity, however, within this segregation a large degree of diversity exists. Investigations into the molecular diversity of neurons are impeded by the inability to isolate cell populations born at different times for gene expression analysis. Developing interneurons may be distinguished by the expression of Glutamic Acid Decarboxylase-67 (GAD67). Neuronal birthdating using nucleoside analogs is an effective means of identifying coetaneous interneurons. Using these two features, neurotransmitter identity and birthdating, we have developed a method to isolate migrating interneurons using fluorescent-activated cell sorting (FACS) for RNA extraction and gene expression analysis. We utilized 5-ethynyl-2'-deoxyuridine (EdU) to birthdate interneuron cohorts and the GAD67 knock-in GFP transgenic mice to identify interneurons. In combination, we achieved simultaneous detection of GFP and EdU signals during FACS sorting of coetaneous interneurons with minimum loss of RNA integrity. RNA quality was deemed to be satisfactory by quantitative polymerase chain reaction (qPCR) for the interneuron-specific transcript Gad67.

Nestin phosphorylation at threonines 315 and 1299 correlates with proliferation and metastasis of human pancreatic cancer

The neuroepithelial stem cell marker nestin is a cytoskeletal protein that regulates cell proliferation, invasion, and stemness in various tumors, including pancreatic tumors. In the present study, we examined the expression and roles of phosphorylated nestin in pancreatic cancer cells. Nestin phosphorylation at threonines 315 (Thr315) and 1299 (Thr1299) was observed during mitosis in human pancreatic cancer cells. Nestin phosphorylation was positively correlated with a cell proliferation marker, MIB-1 expression in human pancreatic cancer samples. Transfection of MIA PaCa-2 cells with nestin mutated at Thr315 and/or Thr1299 (to suppress phosphorylation) resulted in lower proliferation rates than those in control groups. Transfecting MIA PaCa-2 cells with wild-type nestin or with nestin mutated at Thr315 increased migration and invasion. In contrast, transfection with nestin mutated at both phosphorylation sites (Thr315 and Thr1299) did not enhance cell migration or invasion. In an intra-splenic xenograft experiment using MIA PaCa-2 cells, tumors expressing the nestin double mutant formed fewer liver metastases than tumors expressing wild-type nestin. Nestin phosphorylation at these two sites was decreased upon treatment with inhibitors for cyclin dependent kinases, AKT, and Aurora in PANC-1 cells, which express a high baseline level of phosphorylated nestin. These findings suggest that phosphorylation of nestin at Thr315 and/or Thr1299 affects cell proliferation, and inhibition of both phosphorylation sites suppresses invasion and metastasis of human pancreatic cancer. Inhibiting nestin phosphorylation at these two sites may represent a novel therapeutic strategy for pancreatic cancer.

Analysis of the Germinal Center Reaction in Tissue Sections

Germinal centers are short-lived microanatomical compartments with essential roles in adaptive immunity. These lymphoid structures can be identified in secondary lymphoid organs using both flow cytometry and immunohistological analyses, but only the latter provides useful architectural and spatial information. Here we describe how to use immunofluorescence and immunohistochemistry with specific antibodies to precisely highlight the cellular and architectural features of germinal centers, both in human and mouse secondary lymphoid organs, and to study their normal development and disturbance in disease.

Evaluation of Histomorphometric Changes in Tissue Architecture in Relation to Alteration in Fixation Protocol - An Invitro Study

INTRODUCTION

Preparation of good tissue specimens for microscopy requires complete fixation. No ideal fixative has been found till date, with every fixative showing advantages and disadvantages. Appropriate fixation is required to maintain clear and consistent morphologic features for histologic examination. Pathologists mostly examine formalin fixed tissue sections and are less used to the morphologic changes induced by other fixatives. Underfixed and overfixed tissue in various fixatives can lead to tissue architectural changes which can affect its diagnostic value.

AIM

To assess sectioning ability, staining intensity and microscopic details of tissues kept in different fixatives at different time intervals.

MATERIALS AND METHODS

Fresh tissue specimen i.e., goat tongue was collected and its middle-third portion was used for the study purpose. The tissue was grossed into 10 equal pieces and kept in various fixatives (10% Buffered formalin, Carnoy's solution, Absolute ethyl alcohol, Bouin's fluid) for five different time intervals (6, 12, 18, 24 and 30 hours) and normal tissue processing steps were carried out followed by sectioning and staining. During sectioning, sectioning parameter was assessed. Following sectioning, sections were observed under light microscope and were histologically evaluated for staining and microscopic details. To calculate the sectioning parameter Fisher's exact test was used and to assess parameters for staining and microscopic details Mann-Whitney U test was used.

RESULTS

According to the study, 10% buffered formaldehyde is considered as a superior fixative under all parameters followed by Bouin's fluid, Carnoy's solution and Absolute alcohol.

CONCLUSION

In our study, it was concluded that 10% buffered formaldehyde should be continued as a routine fixative however, other fixatives can be used depending upon the non-availability of required fixative or in case of emergencies. Pathologist should be accustomed to histologic and morphologic changes of underfixed and overfixed tissue which can affect its diagnostic value.

Increased lymph node retrieval decreases adjuvant chemotherapy rate for stage II colon cancer

OBJECTIVE

Investigation of lymph nodes in colorectal specimens after surgery due to cancer is important for staging the cancer. There has to be an adequate number of lymph nodes to conclude a node-negative status. Our aim was to investigate if change in fixative could give increased lymph node yield, and if this could result in a potential decrease of adjuvant treatment for stage II patients. In addition, we wanted to evaluate if the change in fixative could potentially affect subsequent molecular testing.

MATERIAL AND METHODS

All resection specimens from one hospital were from 2011 fixed in GEWF while resection specimens from two other hospitals were fixed in conventional buffered formalin. Number of lymph nodes harvested were compared from two periods; 2009/2010 and 2012/2013. In addition, tumors fixed in GEWF and tumors fixed in formalin were tested separately with immunohistochemical staining and molecular testing.

RESULTS

There was a significant increase in lymph node retrieval in specimens fixed in GEWF compared to number of lymph nodes found before the implementation of this fixative (p < 0.001). For hospitals using only formalin, the number of nodes did not increase significantly. Number of positive lymph nodes did not increase. Immunohistochemical staining can be a problem with tumors fixed in GEWF, but DNA quality seems not affected by the changes.

CONCLUSIONS

GEWF enhances lymph node detection in colorectal cancer specimens, leading to fewer patients being falsely defined as high-risk stage II. The loss of stability when staining for MMR-proteins can be overcome by molecular analysis when needed.

Ret mouse very large tumors (VLTs) display altered ratios of infiltrating memory to naive T cells: Roles in tumor expansion

Melanoma is an aggressive skin cancer, however it is immunogenic. The size of the primary tumor is associated with the nodal metastases. Our goals were to characterize melanoma-associated antigens (MAAs) and tumor-infiltrating T-lymphocytes (TILs) subsets in the few very large tumors (VLTs) developing in ret transgenic mice of melanoma. Tumors >700mg (VLTs) were investigated for MAAs and subsets of TILs. Immunohistochemistry and flow cytometry-based studies were performed to determine the infiltration patterns of T-lymphocytes in VLTs. It was observed that zinc fixative restores the antigenicity of the cell-surface markers of lymphocyte subpopulations without the need of antigen retrieval, whereas formalin-based fixative fails to restore the antigenicity in the presence of antigen retrieval in the immunohistochemistry. VLTs from ret mice express MAAs, such as Tyrosinase, TRP-1, TRP-2 and gp-100. The mean±standard deviation (S.D.) T-cell infiltration per 400 times-high power field in VLTs; CD4(+) (2.33±1.3), CD8(+) (2.00±1.0), and CD4(+) Foxp3(+) (2.5±0.5) regulatory T cells infiltration was exclusively restricted to the tumor stroma. Moreover, our flow cytometry-based data reveal that % mean±S.D. naive CD3(+) CD4(+) T cell infiltration (32.8±4.0%) was significantly larger than effector (25.8±2.8%, p<0.01) and central memory cells (16.1±3.7%, p<0.001) in VLTs. Similarly, between CD3(+) CD8(+) T cells, naive cells infiltrate (57.7±2.3%) in a significantly larger frequency than effector (5.0±0.4%, p<0.0001) and central memory cell (4.8±1.7%, p<0.0001) subsets. These results suggest that the VLTs from ret mice display lowered infiltration ratios between memory and naive T cells, which could be associated with the relatively large growth of VLTs.

A simple and rapid method for combining fluorescent in situ RNA hybridization (FISH) and immunofluorescence in the C. elegans germline

Imaging of RNAs and proteins in specific tissues has opened ample avenues to understand gene expression during development. Recently, a fluorescent in situ RNA hybridization (FISH) method has been developed to analyze the spatio-temporal expression patterns of endogenous mRNAs. However, combining FISH with immunofluorescence is challenging as the reaction conditions for the two procedures conflict in multiple ways. In this report, we developed a simple and rapid method to detect both RNAs and associated proteins with better preservation of the fine structure in the C. elegans germline. This method will provide new tools for in vivo imaging of RNAs and their associated proteins in the same germline, which also enables simultaneous visualization of RNA/protein complex at the cellular level in vivo. •Developing a simple and rapid FISH method with better preservation of the fine structure.•Combining FISH with immunofluorescence in C. elegans germline.•Labeling extruded gonads, instead of the whole worms, to prevent non-specific somatic autofluorescence.

Correlative Synchrotron Fourier Transform Infrared Spectroscopy and Single Molecule Super Resolution Microscopy for the Detection of Composition and Ultrastructure Alterations in Single Cells

Single molecule localization microscopy (SMLM) and synchrotron Fourier transform infrared (S-FTIR) spectroscopy are two techniques capable of elucidating unique and valuable biological detail. SMLM provides images of the structures and distributions of targeted biomolecules at spatial resolutions up to an order of magnitude better than the diffraction limit, whereas IR spectroscopy objectively measures the holistic biochemistry of an entire sample, thereby revealing any variations in overall composition. Both tools are currently applied extensively to detect cellular response to disease, chemical treatment, and environmental change. Here, these two techniques have been applied correlatively at the single cell level to probe the biochemistry of common fixation methods and have detected various fixation-induced losses of biomolecular composition and cellular ultrastructure. Furthermore, by extensive honing and optimizing of fixation protocols, many fixation artifacts previously considered pervasive and regularly identified using IR spectroscopy and fluorescence techniques have been avoided. Both paraformaldehyde and two-step glutaraldehyde fixation were identified as best preserving biochemistry for both SMLM and IR studies while other glutaraldehyde and methanol fixation protocols were demonstrated to cause significant biochemical changes and higher variability between samples. Moreover, the potential complementarity of the two techniques was strikingly demonstrated in the correlated detection of biochemical changes as well as in the detection of fixation-induced damage that was only revealed by one of the two techniques.

Enhanced detection of Porcine reproductive and respiratory syndrome virus in fixed tissues by in situ hybridization following tyramide signal amplification

This study evaluated the sensitivity of biotinyl-tyramide-based in situ hybridization (TISH) method by comparison with chromogenic in situ hybridization (CISH) and immunohistochemical staining (IHC) methods. This study also determined the effect of fixative and fixation time on the detection of Porcine reproductive and respiratory syndrome virus (PRRSV) in paraffin-embedded tissues. Lung samples were fixed in 4% paraformaldehyde (PFA) or 10% neutral buffered formalin (NBF) for various times before paraffin embedding. Of 30 paraffin-embedded lung samples, fixed for 1 day in 4% PFA or 10% NBF, 18 (60%) were positive for PRRSV by nested reverse transcription polymerase chain reaction (nRT-PCR). All 18 lung samples (100%) also were positive for PRRSV by TISH, but only 10 of these 18 specimens (56%) were positive for PRRSV by IHC and CISH. We demonstrated that TISH can detect PRRSV RNA in paraffin-embedded tissues after up to 90 days of fixation. PRRSV nucleic acids and antigens were better preserved in 4% PFA than in 10% NBF. Compared with CISH and IHC testing methods, TISH appeared to be more sensitive for the detection of PRRSV in paraffin-embedded tissues.

Fixation methods for the preservation of morphology, RNAs, and proteins in paraffin-embedded human cervical cancer cell xenografts in mice

After various types of fixation, paraffin-embedded tissues are commonly used for histological analysis and pathological diagnosis; they are also suitable for long-term storage. Neutral buffered formalin, paraformaldehyde, and ethanol are common fixatives for histopathological analysis. For molecular biological analysis, fixed paraffin-embedded tissues are valuable resources; suitable fixative solutions and methods are needed to quantify and perform molecular biological analyses including immunohistochemistry, in situ hybridization, and quantitative polymerase chain reaction. Currently, 4 % paraformaldehyde is the recommended fixative for the preservation of RNAs and proteins, as well as for morphological study in paraffin-embedded human cervical cancer tissues that were xenografted in immunodeficient mice. Here, we describe the method for the fixation and preparation of paraffin-embedded tissue specimens for analysis of RNAs, proteins, and morphology.

Downregulation of fibroblast growth factor receptor 2 and its isoforms correlates with a high proliferation rate and poor prognosis in high-grade glioma

Fibroblast growth factor receptor 2 (FGFR-2) contributes to the progression of numerous types of cancers; however, its role in glioma has yet to be determined. We investigated the expression of FGFR-2 and its predominant isoforms, FGFR-2 IIIb and FGFR-2 IIIc, in gliomas of all histological grades. Using immunohistochemistry, we demonstrated that FGFR-2, FGFR-2 IIIb and FGFR-2 IIIc were expressed in the astrocytes of normal human brains. The percentages of cells expressing FGFR-2, FGFR-2 IIIb and FGFR-2 IIIc and the intensities of their staining in glioblastomas (grade IV) were significantly reduced when compared to these parameters in the low-grade tumors (grade I, II and III; P<0.05). A high MIB-1 index, indicated by Ki-67 expression in >20% of the cells, was also associated with low expression of each FGFR-2 protein. Lower expression of FGFR-2 and FGFR-2 IIIc was correlated with a reduced survival rate (P=0.02 and 0.0253, respectively). Quantitative PCR analysis confirmed that the mRNA levels of FGFR-2 IIIb and FGFR-2 IIIc in a high-grade glioma-derived cell line (YKG-1) were lower than levels in a low-grade glioma-derived cell line (KG-1-C). These findings suggest that the decrease or loss of FGFR-2, FGFR-2 IIIb and FGFR-2 III in high-grade gliomas correlates with poor prognosis, which we attribute to the high proliferation rate of the tumor.

Correlation of diffusion tensor, dynamic susceptibility contrast MRI and (99m)Tc-Tetrofosmin brain SPECT with tumour grade and Ki-67 immunohistochemistry in glioma

OBJECTIVE

Assessment of the grade and type of glioma is of paramount importance for prognosis. Tumour proliferative potentials may provide additional information on the behaviour of the tumour, its response to treatment and prognosis. The purpose of this study was to investigate the correlation between diffusion tensor imaging (DTI), dynamic susceptibility contrast (DSC) magnetic resonance imaging (MRI) and (99m)Tc-Tetrofosmin brain single-photon emission computed tomography (SPECT), and the tumour grade and Ki-67 labelling index in newly diagnosed gliomas.

METHODS

Study was made of patients with suspected glioma on brain MRI between December 2010 and January 2012, by DTI, DSC MRI and (99m)Tc-Tetrofosmin brain SPECT. The proliferative activity of each tumour was measured by deriving the Ki-67 proliferation index from immunohistochemical staining of tumour specimens.

RESULTS

Glioma was newly diagnosed in 25 patients (17 men, 8 women, aged 19-79 years, median 55 years). The Ki-67 index ranged from 1% to 80% (mean 19.4%). On evaluation of the relationship between the (99m)Tc-Tetrofosmin tumour uptake by gliomas was found to be significantly correlated with cellular proliferation (rho=0.924, p<0.0001). Regarding DTI, significant negative correlation was demonstrated between the apparent diffusion coefficient (ADC) ratio and the Ki-67 index (rho=-0.545, p=0.0087). Significant correlation was also observed between the fractional anisotropy (FA) ratio and the Ki-67 index (rho=0.489, p=0.02). Strong correlation was found between relative cerebral blood volume (rCBV) and Ki-67 index (rho=0.853, p<0.0001), and between the (99m)Tc-Tetrofosmin lesion-to-normal (L/N) uptake ratio and rCBV (rho=0.808, p ≤ 0.0001). Significant negative correlation was demonstrated between the (99m)Tc-Tetrofosmin L/N ratio and ADC ratio (rho=-0.513, p=0.014). These imaging techniques were able to distinguish between low-grade and high-grade gliomas.

CONCLUSIONS

Findings on DSC MRI and brain SPECT with (99m)Tc-Tetrofosmin metrics were more closely correlated with glioma cellular proliferation.

Detection of single influenza viral RNA in cells using a polymeric sequence probe

A polynucleotide probe, call a polymeric sequence probe (PSP), was used to detect influenza A (Influenza A/WSN/33) NA (Neuraminidase) viral RNA in Madin-Darby canine kidney (MDCK) cells. The PSP is a single-stranded DNA molecule with ~2,000 tandem repeat fluorescence binding sites and target binding sites that can bind with multiple fluorescence complementary oligos and target viral RNA using a fluorescence in situ hybridization (FISH) process. A single viral RNA labeled by PSP can be directly observed in MDCK cells. The simple FISH protocol enables the observation and quantitative analysis of the infectious process and drug effects with ultrahigh sensitivity and spatial resolution.