Heat-induced Epitope Retrieval Research Articles

A study of PGP 9.5 immunohistochemical labeling on formalin-fixed paraffin embedded tissues for epidermal nerve fiber density testing

ABSTRACT There have been several methods established for immunohistochemical labeling of the PGP 9.5 antigen in human tissue for the assessment of epidermal nerve fiber density, none of which uses neutral-buffered formalin as the preferred fixative for paraffin-embedded tissue. The literature maintains that formalin-fixed paraffin embedded tissues are unable to be used for this purpose and that other fixatives must be used due to the cross-linkages caused by formalin fixation. This study was undertaken to develop a standardized method for the use of formalin-fixed paraffin embedded tissues for immunohistochemical labeling and assessment of epidermal nerve fiber density. Formalin-fixed paraffin embedded tissues from the punch biopsies of patients suspected to have small fiber neuropathy were prepared for immunohistochemical labeling using heat-induced epitope retrieval for one hour at 92°C. The tissues were then stained with a polyclonal rabbit anti-human PGP 9.5 primary antibody. The resulting stains were then evaluated by a licensed pathologist who counted the number of epidermal nerve fibers stained and recorded the epidermal length in millimeters. Human foreskin was used as the tissue control in these studies. Satisfactory immunohistochemical labeling of epidermal nerve fibers was achieved from formalin-fixed paraffin embedded tissues through the use of heat-induced epitope retrieval. The authors of this paper have concluded that formalin-fixed paraffin embedded tissues may be used to achieve satisfactory immunohistochemical labeling for the assessment of epidermal nerve fiber density.

Comparison of Antigen Retrieval Methods for Immunohistochemical Analysis of Cartilage Matrix Glycoproteins Using Cartilage Intermediate Layer Protein 2 (CILP-2) as an Example.

The aim of this study was to compare different antigen retrieval methods to improve the outcome of immunohistochemistry (IHC) performed on osteoarthritic (OA) cartilage obtained from total knee replacement operation. A voluminous and dense extracellular matrix of articular cartilage inhibits antibody penetration, and therefore, proteins present at low concentrations and masked during fixation may need antigen retrieval to enhance an IHC outcome. We focused on the IHC detection of a minor but diagnostically promising cartilage glycoprotein, CILP-2 (cartilage intermediate layer protein 2), to demonstrate the effect of four different protocols: (1) heat-induced epitope retrieval (HIER), (2) proteolytic-induced epitope retrieval applying proteinase K and hyaluronidase (PIER), (3) HIER combined with PIER, and (4) no antigen retrieval (control). A semi-quantitative staining assessment based on the CILP-2 staining extent was applied. Out of the tested antigen retrieval protocols, the best CILP-2 IHC staining results were achieved by PIER. Combining PIER with HIER did not improve CILP-2 staining in the given experimental setting. Rather the opposite, the application of heat reduced the positive effect of PIER on CILP-2 staining and resulted in the frequent detachment of sections from the slides. Our findings emphasize the need for proper adaptation of antigen retrieval protocols for IHC to maximize the quantitative evaluation of minor matrix proteins in OA articular cartilage samples.

Abstract 3767: A novel method to minimize HIER-induced alterations on H&E staining in an integrated mIF-H&E workflow

Abstract Background: Hematoxylin and eosin staining (H&E) is widely used as an anatomical assay for clinical diagnosis. Researchers and clinicians also rely on molecular in situ techniques, such as multiplexed immunofluorescence (mIF), to gain deeper insights on cellular phenotypes and tissue microenvironment. As a result, there has been significant interest in combining anatomical stains with molecular imaging techniques, most commonly by using a terminal H&E stain after mIF staining. This allows a combination of the two assays but has been observed to show alterations in the H&E staining pattern. In this work we identify heat-induced epitope retrieval (HIER) as the root cause of alterations of the terminal H&E stain after mIF. We further demonstrate a new workflow combining an initial H&E stain with subsequent InSituPlex assay, to avoid these alterations and thus enable co-registration of highly sensitive multiplexed immunofluorescence with an unaltered H&E stain. Methods: FFPE tissue slides were stained using a standard HIER protocol or a full mIF assay, followed by a standard H&E stain. Slides were imaged using a Zeiss Axioscan.Z1 scanner. Additional H&E-stained slides were prepared, and the H&E stain removed using a destaining protocol before carrying out InSituPlex® mIF staining for multiple markers. Fluorescence and brightfield images of the same slide were overlaid using UltiStacker® to assess qualitative differences between pre- and post-mIF H&E, and UltiAnalyzer.AI® was used to quantify cell densities and signal intensities between mIF image pre- and post-H&E. Results: Alterations in H&E staining were observed between slides directly stained with H&E and slides stained with a terminal H&E after HIER alone or a full mIF assay. Calculated cell counts and tissue area were consistent throughout, but some tissue microstructures could be difficult to resolve after either HIER or full mIF. Our destaining protocol was successful in removing hematoxylin and eosin from directly-stained H&E slides and allowing subsequent mIF staining. For most biomarkers, qualitative and quantitative differences in InSituPlex mIF staining were minimal. Brightfield and fluorescent images were co-registered with sub-micron accuracy using UltiStacker, enabling molecularly defined cellular phenotyping within a traditional H&E image. Conclusions: While the mIF to H&E workflow is widely used and is capable of allowing combined anatomical and cellular phenotyping, alterations in the H&E stain exist due to the use of HIER in most mIF protocols. An alternative method is possible in which H&E-stained slides are destained and then restained for mIF or other spatial assays, providing the same valuable combination of assay information but without the HIER-induced alterations in H&E staining pattern. Citation Format: Kevin Hwang, Grace Vezeau, Edyta Olejnik, Douglas Wood, Ruben Cardenes, Lauren Duro, Gourab Chatterjee, Je H. Lee. A novel method to minimize HIER-induced alterations on H&E staining in an integrated mIF-H&E workflow [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3767.

Antigen retrieval assisted electrochemiluminescence imaging of surface antigens at single tissue section

Previously, our group has established an electrochemiluminescence (ECL) molecular imaging method to detect carcinoembryonic antigen (CEA) at single tissue sections of carcinoma patients. However, the tissue fixation blocks the binding sites of surface antigens affecting the antigen-antibody interaction and the resultant visualization sensitivity. Herein, we report an antigen retrieval assisted ECL imaging strategy that utilizes heat-induced epitope retrieval (HIER) to re-expose the binding sites of the antigens for more efficient interaction between surface antigen and ruthenium-labeled antibody. With more ruthenium complexes tagged with surface antigens, the ECL intensity at the tissue sections increases significantly which could more accurately reflect the amount and the distribution of surface CEA. Accordingly, the different distribution of CEA at the carcinoma and paracancerous regions of tissue sections from two patients with lung adenocarcinoma (LUAD) is visualized, which could not be easily distinguished without the HIER treatment. Eventually, the combination of antigen retrieval and ECL molecular imaging could improve the visualization sensitivity at single tissue section and minimize the false negative phenomenon, which will greatly advance the development of ECL-based tissue imaging for future application in pathological diagnosis.

A Standardized and Reproducible Workflow for Membrane Glass Slides in Routine Histology and Spatial Proteomics

Defining the molecular phenotype of single cells in situ is key for understanding tissue architecture in health and disease. Advanced imaging platforms have recently been joined by spatial omics technologies, promising unparalleled insights into the molecular landscape of biological samples. Furthermore, high-precision laser microdissection (LMD) of tissue on membrane glass slides is a powerful method for spatial omics technologies and single-cell type spatial proteomics in particular. However, current histology protocols have not been compatible with glass membrane slides and LMD for automated staining platforms and routine histology procedures. This has prevented the combination of advanced staining procedures with LMD. In this study, we describe a novel method for handling glass membrane slides that enables automated eight-color multiplexed immunofluorescence staining and high-quality imaging followed by precise laser-guided extraction of single cells. The key advance is the glycerol-based modification of heat-induced epitope retrieval protocols, termed “G-HIER.” We find that this altered antigen-retrieval solution prevents membrane distortion. Importantly, G-HIER is fully compatible with current antigen retrieval workflows and mass spectrometry–based proteomics and does not affect proteome depth or quality. To demonstrate the versatility of G-HIER for spatial proteomics, we apply the recently introduced deep visual proteomics technology to perform single-cell type analysis of adjacent suprabasal and basal keratinocytes of human skin. G-HIER overcomes previous incompatibility of standard and advanced staining protocols with membrane glass slides and enables robust integration with routine histology procedures, high-throughput multiplexed imaging, and sophisticated downstream spatial omics technologies.

A comparative analysis of two antigen retrieval techniques: Microwave oven and pressure cooker for immunoexpression of estrogen and progesterone receptors in breast cancer tissue

Objectives: Antigen retrieval (AR) is an important step in Immunohistochemistry (IHC) which is used to unmask the antigenic sites and facilitate antigen-antibody binding. Adequate fixation of tissue is necessary to achieve consistent demonstration of tissue antigens that can be masked by the chemical process involved in formalin fixation and tissue processing. Out of the various methods of AR, heat-induced epitope retrieval (HIER) methods have greatly improved the quality and reproducibility of IHC. In this study, a comparison of the two most commonly used HIER methods-pressure cooker and microwave oven was done on thirty cases of breast carcinoma. Materials and Methods: Appropriate tumor sections were taken and subjected to manual IHC testing for estrogen receptor (ER) and progesterone receptor (PR) receptors in each case. The results were divided into technique and microscopy-based. The parameters assessed on microscopy were uniformity of nuclear staining, quality of nuclear staining, internal control staining, presence of background staining, and Allred score. The sensitivity and specificity and positive and negative predictive values for each method were calculated. Results: The parameters assessed on microscopy were comparable for both methods. Using a microwave oven, the sensitivity and specificity for ER and PR were 94% and 100%, respectively. Using a pressure cooker, the sensitivity, and specificity for ER were 94% and 100%, respectively, and for PR were 88% and 100%, respectively. On technical aspects, the pressure cooker method offers the advantage of being more convenient due to the possibility of simultaneous handling of more slides and being more time efficient. Conclusion: Both the AR methods had comparable results on microscopy. However, the pressure cooker has the benefit of being both time and money efficient from a technical standpoint.

Extracellular Vesicle Antibody Microarray for Multiplexed Inner and Outer Protein Analysis

Proteins are found both outside and inside of extracellular vesicles (EVs) and govern the properties and functions of EVs, while also constituting a signature of the cell of origin and of biological function and disease. Outer proteins on EVs can be directly bound by antibodies to either enrich EVs, or probe the expression of a protein on EVs, including in a combinatorial manner. However, co-profiling of inner proteins remains challenging. Here, we present the high-throughput, multiplexed analysis of EV inner and outer proteins (EVPio). We describe the optimization of fixation and heat-induced protein epitope retrieval for EVs, along with oligo-barcoded antibodies and branched DNA signal amplification for sensitive, multiplexed, and high-throughput assays. We captured four subpopulations of EVs from colorectal cancer (CRC) cell lines HT29 and SW403 based on EpCAM, CD9, CD63, and CD81 expression, and quantified the co-expression of eight outer [integrins (ITGs) and tetraspanins] and four inner (heat shock, endosomal, and inner leaflet) proteins. The differences in co-expression patterns were consistent with the literature and known biological function. In conclusion, EVPio analysis can simultaneously detect multiple inner and outer proteins in EVs immobilized on a surface, opening the way to extensive combinatorial protein profiles for both discovery and clinical translation.

Use of Citrus limon Juice as an Alternative Antigen Retrieval Solution for Formalin Fixed Breast Cancer Tissue in Immunohistochemistry

Background: The potential of Citrus limon fruit as a source of antigen retrieval agent is a significant step in the locally made brand of antigen retrieval solution with its availability and potential use in research and diagnosis. The cost of Immunohistochemistry tests is on the high side in Nigeria as a developing country, and many cancer patients have lost their lives in the cause of seeking alternative remedies to their prevailing health challenges due to financial constrain encountered in the cost of Immunohistochemistry (IHC) test. Its relevance makes the diagnosis of cancer effective for proper treatment and prognosis. Methods: Fifty (50) positive formalin-fixed breast tissues previously diagnosed using commercially prepared antigen retrieval solution (Thermoscientific – ephredia) were randomly selected for this study. Heat-induced epitope retrieval method (HIER) was used along with breast markers, namely Estrogen receptor (ER), Progesterone receptor (PR), and Human Epidermal Growth Factor Receptor 2 (HER-2) antibodies. Haematoxylin and eosin Techniave were used to demonstrate the general tissue structures to show the pleomorphic appearance of the cells invading the stroma, revealing an irregular shape with hyperchromatic nuclei. Results: Nuclear and cytoplasmic meshwork exposed without any background stain was observed. Estrogen receptor marker results in C. limon juice antigen retrieval was positive with a brown intensity score of 3 and proportion of stain score 5, having Thirty five (35) sections positive (70%). Progesterone receptor results in C. limon juice antigen retrieval revealed positive with a brown intensity score of 3 and a proportion of stain 5, with Forty-one (41) sections positive (82%). HER-2 results showed seventeen (17) sections (34%) positive with complete and intense brown circumferential membrane staining within >10% of tumor cells in C. limon juice antigen retrieval. Conclusion: The use of citrus juice is another source of antigen retrieval solution that can be explored for the immunohistochemistry test.

Immunohistochemical Detection of Estrogen Receptor-Beta (ERβ) with PPZ0506 Antibody in Murine Tissue: From Pitfalls to Optimization.

The estrogen receptor beta (ERβ) is physiologically essential for reproductive biology and is implicated in various diseases. However, despite more than 20 years of intensive research on ERβ, there are still uncertainties about its distribution in tissues and cellular expression. Several studies show contrasts between mRNA and protein levels, and the use of knockout strategies revealed that many commercially available antibodies gave false-positive expression results. Recently, a specific monoclonal antibody against human ERβ (PPZ0506) showed cross-reactivity with rodents and was optimized for the detection of rat ERβ. Herein, we established an immunohistochemical detection protocol for ERβ protein in mouse tissue. Staining was optimized on murine ovaries, as granulosa cells are known to strongly express ERβ. The staining results were confirmed by western blot analysis and RT-PCR. To obtain accurate and reliable staining results, different staining conditions were tested in paraffin-embedded tissues. Different pitfalls were encountered in immunohistochemical detection. Strong heat-induced epitope retrieval (HIER) and appropriate antibody dilution were required to visualize specific nuclear expression of ERβ. Finally, the specificity of the antibody was confirmed by using ovaries from Esr2-depleted mice. However, in some animals, strong (non-specific) background staining appeared. These signals could not be significantly alleviated with commercially available additional blocking solutions and are most likely due to estrus-dependent expression of endogenous immunoglobulins. In summary, our study showed that the antibody PPZ0506, originally directed against human ERβ, is also suitable for reliable detection of murine ERβ. An established staining protocol mitigated ambiguities regarding the expression and distribution of ERβ in different tissues and will contribute to an improved understanding of its role and functions in murine tissues in the future.

Effect of Antigen Retrieval on Genomic DNA From Immunodissected Samples.

Immunohistochemical (IHC) staining is an established technique for visualizing proteins in tissue sections for research studies and clinical applications. IHC is increasingly used as a targeting strategy for procurement of labeled cells via tissue microdissection, including immunodissection, computer-aided laser dissection (CALD), expression microdissection (xMD), and other techniques. The initial antigen retrieval (AR) process increases epitope availability and improves staining characteristics; however, the procedure can damage DNA. To better understand the effects of AR on DNA quality and quantity in immunodissected samples, both clinical specimens (KRAS gene mutation positive cases) and model system samples (lung cancer patient-derived xenograft tissue) were subjected to commonly employed AR methods (heat induced epitope retrieval [HIER], protease digestion) and the effects on DNA were assessed by Qubit, fragment analysis, quantitative PCR, digital droplet PCR (ddPCR), library preparation, and targeted sequencing. The data showed that HIER resulted in optimal IHC staining characteristics, but induced significant damage to DNA, producing extensive fragmentation and decreased overall yields. However, neither of the AR methods combined with IHC prevented ddPCR amplification of small amplicons and gene mutations were successfully identified from immunodissected clinical samples. The results indicate for the first time that DNA recovered from immunostained slides after standard AR and IHC processing can be successfully employed for genomic mutation analysis via ddPCR and next-generation sequencing (NGS) short-read methods.

Bone marrow trephine immunohistochemistry is useful in characterizing malignancy-associated myelonecrosis: A retrospective observational study.

We aim to describe the utility of immunohistochemistry (IHC) in characterizing malignancy-associated myelonecrosis (MN) on bone marrow trephine biopsies (BMBx) as a part of initial workup. Patten and intensity of antigenic immunoexpression in necrotic tumor cells on BMBx were evaluated in a series of cases using standardized avidin-biotin-complex immunoperoxidase technique after heat-induced epitope retrieval and compared the same with viable tumor cells wherever available. Fifteen out of 2494 (0.6%) cases (median age: 28years; range: 4 to 66years) had evidence of MN (extensive in eight, moderate in five, and focal in two) secondary to hematological (N=9) and solid (N=6) malignancies. Five (33.3%) had pancytopenia, and eight (53.3%) had difficult and/or hemodiluted aspirate. Antigenic expression for CD10, CD79a, CD3, CD7, and CD20 was retained by necrotic leukemic blasts or lymphoma cells; CD34, TdT, and PAX5 showed heterogeneous expression; and a weak Golgi zone (dot like) CD30 positivity was noted in Reed-Sternberg (RS) or RS-like giant cells. Necrotic epithelial metastases retained pancytokeratin in all and showed variable positivity for prostate-specific antigen, carcinoembryonic antigen, CK20, ER, PR, and GATA3. Necrotic neuroblastomas (N=2) retained positivity for synaptophysin and chromogranin, whereas retained nuclear positivity for NKX2.2 in necrotic Ewing family of tumor (N=1) aided in early diagnosis. Myelonecrosis may retain tumor antigenicity, and immunohistochemistry using selected panel of antibodies should be tried in such challenging cases for an early presumptive diagnosis and further decision making.

Optimized protocols for in situ hybridization, immunohistochemistry, and immunofluorescence on skeletal tissue

Assessment of gene and protein expression in tissue sections is instrumental in medical research. However, this is often challenging to perform on skeletal tissues that require prolonged decalcification and have poor adhesion to slides. In this study, we optimized selected steps of in situ hybridization (ISH), immunohistochemistry (IHC), and immunofluorescence (IF) for formalin fixed and decalcified skeletal tissues. Sections from distal femur of 6-, 8- and 14- week-old rats injected with BrdU with or without a hemizygous eGFP transgene expressed under the control of a ubiquitous promotor were used. We report that proteinase K digestion is critical for the sensitivity of ISH, as concentrations that were too strong and too mild both resulted in loss of signal. In addition, intensified RNase A digestion removed nonspecific riboprobe-mRNA hybrids. Furthermore, enzymatic antigen retrieval using proteinase K provided more consistent results in IHC and can therefore be a useful alternative to heat induced epitope retrieval (HIER) for skeletal tissues where such treatment often damages the morphology. A mild proteinase K digestion also improved IF detection of GFP and worked well for double labeling IF of GFP and osteocalcin on frozen sections of formalin fixed and decalcified rat bones while maintaining morphology. In summary, this study provides strategies to improve protocols for enzymatic digestion in ISH, IHC, and IF for skeletal tissues and also demonstrates the importance of careful optimization and validation with the use of these techniques.

Preparing Paraffin Tissue Sections for Staining.

Most histological studies are performed on formalin-fixed, paraffin-embedded (FFPE) tissue samples. Therefore, there is an extensive atlas of most tissues and organs prepared from these sources, and comparing the location of antigens to these data is immediately informative. Fixation and embedding procedures for preparation of paraffin tissue sections are described here. Because of the harsh fixation, embedding, and preparation conditions used in this procedure, many antigens are not well preserved. Thus, cell staining of paraffin-embedded tissue sections usually requires sensitive detection methods and may require amplification using multiple-layer techniques. The protein cross-linking associated with these fixation conditions can mask epitopes. To uncover them and thus improve antibody-antigen binding, the epitopes can be unmasked by reversing the protein cross-linking. One thermal method, heat-induced epitope retrieval, is presented here.

Gelatin-coated indium tin oxide slides improve human cartilage-bone tissue adherence and N-glycan signal intensity for mass spectrometry imaging

Matrix-assisted laser desorption/ionisation mass spectrometry imaging (MALDI-MSI) has been successfully used to elucidate the relative abundance and spatial mapping of analytes in situ. Currently, sample preparation workflows for soft formalin-fixed paraffin-embedded (FFPE) tissues, such as brain, liver, kidney, and heart, have been successfully developed. However, hard tissues, such as cartilage-bone, tooth, and whole mouse body, have resulted in the loss of morphology or tissue during the heat-induced epitope retrieval (HIER) step on commercially available conductive indium tin oxide (ITO) slides. Therefore, we have successfully developed a novel and cost-effective sample preparation workflow in which commercial conductive ITO slides are pre-coated with gelatin and chromium potassium sulfate dodecahydrate to improve the adherence of FFPE human osteoarthritic cartilage-bone tissue sections. Gelatin-coated ITO slides also resulted in overall higher N-glycan signal intensity for not only FFPE osteoarthritic cartilage-bone tissue but also for FFPE hard-boiled egg white used as a quality control to assess the quality of sample preparation and MALDI-MSI acquisition. In summary, we present a novel straightforward workflow to improve slide adherence and morphological preservation of FFPE cartilage-bone tissue sections during HIER while improving the signal intensity of N-glycans spatially mapped from the same tissue sections by MALDI-MSI.

External Quality Assessments of CD31 Immunoassays – the NordiQC experience

Nordic Immunohistochemical Quality Control (NordiQC) performs proficiency testing for about 600 pathology laboratories in more than 50 countries. All general results are published on www.nordiqc.org. Over-all, about 30% of the staining results on circulated slides from tissue micro arrays have by an expert group been assessed as insufficient for diagnostic use. This paper describes the results from the two latest NordiQC runs for CD31. Out of 476 stains submitted, 30.5% were considered insufficient, mostly due to too weak or false negative staining reactions. The best results were obtained by use of mouse monoclonal antibody JC70A with an optimized protocol based on efficient heat induced epitope retrieval and a three-step polymer/multimer conjugate as visualization system. The mouse monoclonal antibody 1A10 gave unsatisfactory results in almost all cases.

Frequency of overexpression of Her2/neu in colorectal adenocarcinomas– A hospital based cross-sectional study

Frequency of overexpression of Her2/neu in colorectal adenocarcinomas– A hospital based cross-sectional study - IJPO- Print ISSN No: - 2394-6784 Online ISSN No:- 2394-6792 Article DOI No:- 10.18231/j.ijpo.2020.006, Indian Journal of Pathology and Oncology-Indian J Pathol Oncol

Extracellular vesicles derived from injured vascular tissue promote the formation of tertiary lymphoid structures in vascular allografts.

Tertiary lymphoid structures (TLS) accumulate at sites of chronic injury where they function as an ectopic germinal center, fostering local autoimmune responses. Vascular injury leads to the release of endothelial‐derived apoptotic exosome‐like vesicles (ApoExo) that contribute to rejection in transplanted organs. The purpose of the study was to evaluate the impact of ApoExo on TLS formation in a model of vascular allograft rejection. Mice transplanted with an allogeneic aortic transplant were injected with ApoExo. The formation of TLS was significantly increased by ApoExo injection along with vascular remodeling and increased levels of antinuclear antibodies and anti‐perlecan/LG3 autoantibodies. ApoExo also enhanced allograft infiltration by γδT17 cells. Recipients deficient in γδT cells showed reduced TLS formation and lower autoantibodies levels following ApoExo injection. ApoExo are characterized by proteasome activity, which can be blocked by bortezomib. Bortezomib treated ApoExo reduced the recruitment of γδT17 cells to the allograft, lowered TLS formation, and reduced autoantibody production. This study identifies vascular injury‐derived extracellular vesicles (ApoExo), as initiators of TLS formation and demonstrates the pivotal role of γδT17 in coordinating TLS formation and autoantibody production. Finally, our results suggest proteasome inhibition with bortezomib as a potential option for controlling TLS formation in rejected allografts.

Interrogating the Spatial Architecture of Human Bone Marrow Via Imaging Mass Cytometry

Hematopoietic stem cell (HSC) proliferation, self-renewal, differentiation, and trafficking are dependent, in part, upon signals generated by stromal cells in the bone marrow. Stromal cells are organized into niches that support specific subsets of hematopoietic progenitors. Intimate interactions between HSCs and neighboring stromal cells coordinate hematopoietic responses during periods of physiologic stress, while also maintaining the lifelong integrity of the hematopoietic stem cell pool. Hematopoietic niches are comprised of a heterogeneous population of stromal and hematopoietic cells. The identity and function of the known stromal cell subsets have primarily been gleaned through genetic manipulation of mouse models. In humans, the spatial organization of these stromal cells in bone marrow and the signals they generate to regulate hematopoiesis are poorly understood. Current methods to characterize bone marrow mesenchymal stromal cells in humans include: 1) immunostaining of bone sections; 2) analysis of flow sorted stromal cells; and 3) analysis of ex vivoexpanded mesenchymal stem/progenitors. Major limitations to all of these approaches exist that relate to the heterogeneity of bone marrow stromal cells, the lack of markers that reliably distinguish different stromal cell populations, and inherent technical limitations of the assays, such as the number of markers that can be analyzed at one time. Here we report our efforts to use imaging mass cytometry imaging (IMC) to interrogate the complex cellular architecture of human bone marrow. IMC allows for the simultaneous detection of up to 40 markers through the use of antibodies conjugated to elemental metal tags acquired by time-of-flight mass spectrometry. We first used standard immunostaining techniques to develop a panel of antibodies compatible with archived formalin-fixed paraffin-embedded (FFPE) human bone marrow specimens using a heat-induced epitope retrieval method. Hematopoietic lineages have been successfully identified using CD11b, CD68, CD15, CD14, CD16, CD11c, CD20, CD3, CD4, CD8a, CD38, CD45RA, CD45RO, CD235a, CD71, CD34, CD31; stromal cells and structures with CXCL12, alpha-smooth muscle actin, collagen I, vimentin; and nuclear staining using Ki67, Histone H3, and DNA intercalator. We used panels consisting of up to 18 of these antibodies each to test IMC on FFPE human bone marrow specimens. Imaging was performed using the Hyperion Imaging System (Fluidigm), which consists of a UV laser scanning module to capture regions of more than 10,000 cells with 1-micron resolution coupled with a Helios Mass Cytometer. Image analysis was performed by creation of a cell segmentation mask using CellProfiler software and high dimensional analysis in histoCAT. Representative images and corresponding dimensional reduction with t-SNE are shown in Figure 1A-H, demonstrating successful discrimination of distinct hematopoietic lineages. Gating on subpopulations within the t-SNE clusters can be projected on to the original image to illustrate spatial distribution and marker co-expression, as an example CD3+ and CD8+ cells are shown in Figure 1I. These data indicate that IMC allows for highly multiplexed analysis of bone marrow cell populations. Developing imaging techniques for analysis of tissue-banked FFPE bone marrow samples would have broad applications for translational research on hematologic diseases. In particular, this technology has tremendous potential to advance understanding of the spatial architecture of human bone marrow and to investigate alterations in the bone marrow environment in malignant hematopoiesis. Disclosures Oh: Incyte: Membership on an entity's Board of Directors or advisory committees; Blueprint Medicines: Membership on an entity's Board of Directors or advisory committees; Novartis: Consultancy.

Abstract 1243: Effect of antigen retrieval on immuno-based RNA microdissection methods

Abstract Introduction: Clinical applications and research studies routinely utilize immunohistochemistry (IHC) approaches on tissue sections. The aim is to selectively target antigens (proteins) in the cells of a tissue section by exploiting the principle of antibody binding, thus enabling target specificity. The antigen retrieval (AR) process employed at the beginning of most IHC protocols increases epitope availability and improves staining characteristics; however, the procedure can damage nucleic acids, in this case RNA, to an unknown extent. Experimental Procedures: To better understand the effects of AR on RNA quality and quantity, model system samples (lung cancer patient derived xenograft tissue) were subjected to a commonly employed AR method [heat induced epitope retrieval (HIER)] and the effects on RNA were assessed by Qubit, Fragment Analyzer, and digital droplet PCR (ddPCR). The ddPCR experiments were performed following reverse transcriptase (RT) product generation and construction of cDNA, which then served as input to the ddPCR assay. Absolute quantitation of gene expression levels and expressed mutations were evaluated by ddPCR. Data Summary: The results showed that HIER resulted in optimal staining characteristics, but induced significant damage to RNA, producing extensive fragmentation and decreased yields. In general, fragmentation showed an inflection point at ~200 nt transcript length. Variation in the HIER protocol mitigated but did not eliminate the negative effects. Apart from the AR procedure, the IHC process itself also resulted in a significant decreased yield of RNA. Of note, in these experiments DAB chromogen was used exclusively in the IHC process. However, in spite of the observed deleterious effects on RNA, none of the AR methods combined with IHC negatively affected RT product generation and PCR amplification of small amplicons. Regarding the detection of RT product under different conditions, the size of the amplicon was found to make a difference, with the detection of longer amplicons being more difficult. In addition to a number of successful human and mouse gene expression measurements, KRAS gene mutations were successfully identified in the clinical cases under all conditions. Conclusions: The data indicate that RNA recovered from histology slides after standard AR and IHC processing can be successfully employed for genomic applications utilizing RT product formation (cDNA) for gene expression and detection of expressed mutations, especially if the detection methods are based on relatively short length nucleic acids. Studies that require larger RNA fragments such as long-read sequencing should avoid the use of HIER. Citation Format: Donald J. Johann, Meeiyueh Liu, Adam Roberge, Sarah Laun, Michael Emmert-Buck, Michael Tangrea. Effect of antigen retrieval on immuno-based RNA microdissection methods [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1243.

Selecting an Optimal Positive IHC Control for Verifying Antigen Retrieval.

Positive immunohistochemistry (IHC) controls are intended to detect problems in both immunostaining and heat-induced epitope retrieval (HIER). However, it is not known what features in a control are important for verifying HIER. Contrary to expectation, the fact that a tissue is formalin-fixed does not necessarily render it suitable in verifying proper HIER. Some tissue controls, for some immunostains, strongly stain even without HIER. Consequently, the control may verify the immunostain but provide little or no information regarding the HIER step. To sort this out, we used formalin-fixed peptide epitopes, a model that provides for precise definition of analyte concentration, epitope composition, and degree of fixation. Our data demonstrate that formalin fixation generates a variable level of protein epitope masking, depending on the epitope recognized by the primary antibody. Some epitopes are highly masked while others hardly at all. Furthermore, the ability of amino acids in the epitope to react with formaldehyde can, at least in part, account for this variability. Most important, we demonstrate the importance of selecting a positive control with a low or intermediate analyte concentration (relative to the immunostain's analytic sensitivity). High analyte concentrations can be insensitive in verifying the HIER step.