Formalin-fixed Paraffin-embedded Sections Research Articles

The effect of storage time and temperature on the proteomic analysis of FFPE tissue sections

Formalin-fixed paraffin-embedded (FFPE) tissues present an important resource for cancer proteomics. They are more readily available than fresh frozen (FF) tissues and can be stored at ambient temperature for decades. FFPE blocks are largely stable for long-term preservation of tumour histology, but the antigenicity of some proteins in FFPE sections degrades over time resulting in deteriorating performance of immunohistochemistry (IHC). It is not known whether FFPE sections that have previously been cut from blocks and used for liquid chromatography-mass spectrometry (LC–MS) analysis at a later time are affected by storage time or temperature. We determined the stability of FFPE sections stored at room temperature (RT) versus − 80 °C over 48 weeks. The stored sections were processed at different timepoints (n = 11) and compared to sections that were freshly cut from FFPE blocks at each timepoint (controls). A total of 297 sections (rat brain, kidney and liver stored at RT, − 80 °C or freshly cut) were tryptically digested and analysed on TripleTOF 6600 mass spectrometers in data-dependent acquisition (DDA) mode. Kidney and liver digests were also analysed in data-independent acquisition (DIA) mode. The number of proteins and peptides identified by DDA with ProteinPilot and some common post-translational modifications (PTMs) were unaffected by the storage time or temperature. Nine of the most common FFPE-associated modifications were quantified using DIA data and all were unaffected by storage time or temperature. Therefore, FFPE tissue sections are suitable for proteomic studies for at least 48 weeks from the time of sectioning.

Utility of immunohistochemistry for immunoglobulin G4 in the diagnosis of pemphigus

Objectives: Direct immunofluorescence (DIF) is the diagnostic gold standard for pemphigus. However, it is limited by the requirement of additional fresh-frozen tissue, immediate processing, and availability of a fluorescent microscope. The present study aims to assess the role of immunoglobulin G4 (IgG4) immunohistochemistry (IHC) on formalin-fixed paraffin-embedded tissue for the diagnosis of pemphigus by comparing IgG4-IHC results to DIF. Materials and Methods: IgG4-IHC was performed on formalin-fixed paraffin-embedded sections of lesional and perilesional skin biopsies of 30 cases of DIF-proven pemphigus and 30 non-pemphigus controls. Sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and diagnostic accuracy were analyzed for IgG4-IHC on lesional and perilesional biopsies to compare their diagnostic significance. Statistical analysis: Data were analyzed using the Statistical Package for the Social Sciences version 29. Sensitivity, specificity, PPV, NPV, and diagnostic accuracy of IgG4-IHC were calculated using standard formulae. Receiver operator curve analysis was performed for IgG4-IHC in lesional and perilesional skin to compare their diagnostic significance. The youden index was calculated using the formula “sensitivity + specificity – 1.” P < 0.05 was considered statistically significant. Results: Out of 30 cases enrolled for the study, 26 (86.6%) were diagnosed as pemphigus vulgaris and four (13.4%) as pemphigus foliaceous. The sensitivity, specificity, PPV, NPV, and diagnostic accuracy of IgG4-IHC for pemphigus on lesional biopsy were 66.7%, 100%, 100%, 75%, and 83.3% while the sensitivity, specificity, PPV, NPV, and diagnostic accuracy for the perilesional biopsy were 56.7%, 100%, 69.8%, and 78.3%, respectively. Conclusions: Our study indicated that IgG4-IHC is highly specific, but not sufficiently sensitive to replace DIF to diagnose pemphigus. IgG4-IHC on lesional skin is likely to be particularly valuable in a setting where a frozen section or immunofluorescence facility is not available. Further studies on larger samples are warranted to validate the role of IgG4-IHC in pemphigus.

Fluorescence microscopy of parathyroid and thyroid tissues for localization of autofluorescent substances using near-infrared wavelengths.

The parathyroid gland emits autofluorescence with a peak at 822 nm when excited using near-infrared light at 785 nm; this observation of autofluorescence using a near-infrared detection device is useful for identifying the parathyroid gland during surgery. We aimed to clarify the localization of autofluorescent substances in parathyroid and thyroid tissues by observing them under a fluorescence microscope through filters that selectively pass specific near-infrared wavelengths. Four cases of parathyroid and three cases of thyroid were examined under a fluorescence microscope. The frozen, formalin-fixed paraffin-embedded, and unfixed, unstained sections of parathyroid were observed through filters that selectively pass specific near-infrared wavelengths. Images were acquired at excitation 775 ± 50 nm and absorption 845 ± 55 nm in five randomly selected fields of view, avoiding tumor and inflammatory areas. Autofluorescence was measured as the ratio of fluorescent area to tissue area using hybrid cell counting. Autofluorescence was observed in all sections. In the parathyroid tissue, the frozen sections showed significantly more autofluorescence than the formalin-fixed paraffin-embedded sections, and in the thyroid tissue, although no significant difference was observed, the frozen sections showed more autofluorescence than the formalin-fixed paraffin-embedded sections. In addition, the single unfixed, unstained section showed stronger autofluorescence than the frozen sections, although no significant difference was found. The areas of autofluorescence in the parathyroid and thyroid tissues were thought to be the Golgi area and lipofuscin, respectively. Fluorescence microscopy of parathyroid and thyroid tissues revealed the localization of autofluorescent substances in each tissue.

Spatial deconvolution from bulk DNA methylation profiles determines intratumoral epigenetic heterogeneity

BackgroundIntratumoral heterogeneity emerges from accumulating genetic and epigenetic changes during tumorigenesis, which may contribute to therapeutic failure and drug resistance. However, the lack of a quick and convenient approach to determine the intratumoral epigenetic heterogeneity (eITH) limit the application of eITH in clinical settings. Here, we aimed to develop a tool that can evaluate the eITH using the DNA methylation profiles from bulk tumors.MethodsGenomic DNA of three laser micro-dissected tumor regions, including digestive tract surface, central bulk, and invasive front, was extracted from formalin-fixed paraffin-embedded sections of colorectal cancer patients. The genome-wide methylation profiles were generated with methylation array. The most variable methylated probes were selected to construct a DNA methylation-based heterogeneity (MeHEG) estimation tool that can deconvolve the proportion of each reference tumor region with the support vector machine model-based method. A PCR-based assay for quantitative analysis of DNA methylation (QASM) was developed to specifically determine the methylation status of each CpG in MeHEG assay at single-base resolution to realize fast evaluation of epigenetic heterogeneity.ResultsIn the discovery set with 79 patients, the differentially methylated CpGs among the three tumor regions were found. The 7 most representative CpGs were identified and subsequently selected to develop the MeHEG algorithm. We validated its performance of deconvolution of tumor regions in an independent cohort. In addition, we showed the significant association of MeHEG-based epigenetic heterogeneity with the genomic heterogeneity in mutation and copy number variation in our in-house and TCGA cohorts. Besides, we found that the patients with higher MeHEG score had worse disease-free and overall survival outcomes. Finally, we found dynamic change of epigenetic heterogeneity based on MeHEG score in cancer cells under the treatment of therapeutic drugs.ConclusionBy developing a 7-loci panel using a machine learning approach combined with the QASM assay for PCR-based application, we present a valuable method for evaluating intratumoral heterogeneity. The MeHEG algorithm offers novel insights into tumor heterogeneity from an epigenetic perspective, potentially enriching current knowledge of tumor complexity and providing a new tool for clinical and research applications in cancer biology.

Enhanced detection of distinct honeycomb-structured neuronal SMARCC2 cytobodies in Parkinson's Disease via Cyclic Heat-Induced Epitope Retrieval (CHIER).

Antigen retrieval is crucial for immunohistochemistry, particularly in formalin-fixed paraffin-embedded brain tissue, where fixation causes extensive crosslinking that masks epitopes. Heat Induced Epitope Retrieval (HIER) reverses these crosslinks, improving access to nuclear and aggregated proteins. We introduce Cyclic Heat-Induced Epitope Retrieval (CHIER), an advanced technique that builds on HIER by incorporating repeated cycles of heating and cooling. CHIER optimises antigen retrieval and significantly improves detection. CHIER is particularly effective for detecting chromatin-binding proteins, such as SMARCC2, which are difficult to label using conventional IHC methods. Using CHIER on formalin-fixed paraffin-embedded human brain sections, we achieved robust detection of SMARCC2 in both the nucleus and cytoplasm. CHIER also enhanced the visualisation of large SMARCC2+ cytoplasmic bodies, termed cytobodies, which are increased in Parkinson's Disease (PD). Our findings suggest that SMARCC2 may translocate from the nucleus to the cytoplasm in PD, potentially implicating SMARCC2 aggregation in the disease's pathology. Furthermore, CHIER does not negatively impact the antigenicity of other antibodies, supporting its use for multiplex fluorescent immunohistochemistry and super-resolution imaging. These results highlight CHIER's potential for improving the detection of chromatin-binding and aggregated proteins in neurodegenerative disease research, offering new insights into SMARCC2's role in Parkinson's Disease.

RNA Polymerase II hypertranscription at histone genes in cancer FFPE samples.

Genome-wide hypertranscription is common in human cancer and predicts poor prognosis. To understand how hypertranscription might drive cancer, we applied our FFPE-CUTAC method for mapping RNA Polymerase II (RNAPII) genome-wide in formalin-fixed paraffin-embedded (FFPE) sections. We demonstrate global RNAPII elevations in mouse gliomas and assorted human tumors in small clinical samples and discover regional elevations corresponding to de novo HER2 amplifications punctuated by likely selective sweeps. RNAPII occupancy at replication-coupled histone genes correlated with WHO grade in meningiomas, accurately predicted rapid recurrence, and corresponded to whole-arm chromosome losses. Elevated RNAPII at histone genes in meningiomas and diverse breast cancers is consistent with histone production being rate-limiting for S-phase progression and histone gene hypertranscription driving overproliferation and aneuploidy in cancer, with general implications for precision oncology.

Automated Quantification of Tertiary Lymphoid Structures in Human Tumor Samples Using Immunofluorescence and AI-Powered Analysis Pipeline.

The tumor microenvironment (TME) is a complex entity comprising not only tumor cells but also immune, stromal, and endothelial cells. Preclinical and clinical studies indicate that the density, localization, function, and organization of immune infiltration can influence survival probability and treatment response in many cancers. Among these cell organizations, the clustering of T and B cells into tertiary lymphoid structures (TLS) has been associated with favorable clinical outcomes. In this protocol, we propose a protocol for 7-plex immunofluorescence staining for identifying six cell types enriched in TLS in formalin-fixed paraffin-embedded (FFPE) human tumor sections. Additionally, we provide a detailed methodology for quantifying these cell subtypes using the Halo-AI analysis software. This approach will enable a more precise and detailed characterization of TLS in the TME, opening new avenues for understanding their role in anticancer treatment response.

Laser Capture Microdissection of Tertiary Lymphoid Structures from Formalin-Fixed Paraffin-Embedded Sections of Canine Cutaneous and Subcutaneous Sarcomas for NanoString Direct RNA Counting.

Laser capture microdissection (LCM) of formalin-fixed, paraffin-embedded sections is a way to analyze gene expression of morphologically distinct areas of tissue, as microscopically visualized with stained tissue sections. Herein, I describe a method for laser dissecting lymphoid aggregates in canine cutaneous and subcutaneous sarcomas and their adjacent sarcoma tissue to determine the differential expression of RNA as determined by NanoString® nCounter technology. Canine soft tissue sarcomas (STS) are diversely derived mesenchymal neoplasms that, regardless of exact histogenesis, behave similarly and thus have been grouped together as a diagnostic entity. The risk of recurrence and/or metastasis depends on the extent of surgical excision and histologic grade. Lymphoid aggregates are described in these tumors but have not been characterized. In humans, lymphoid aggregates characterized as tertiary lymphoid structures (TLS) improve the prognosis of several tumors, including sarcomas. We sought to determine if RNA expressed by lymphoid aggregates in canine sarcomas was compatible with TLS RNA expression. This chapter describes tissue preparation, staining, laser capture microdissection, and RNA isolation in preparation for digital RNA counting.

TMOD-06. ESTABLISHMENT OF PITUITARY NEUROENDOCRINE TUMOR (PITNET) ORGANOID MODELS

Abstract Pituitary neuroendocrine tumors (PitNETs) are tumors that originate from the anterior pituitary gland. While they are mostly benign, they can cause various clinical symptoms due to hormonal secretion abnormalities. PitNET can be broadly categorized into three lineages, each of which has its differentiation controlled by specific transcription factors. Treatment options for PitNET include surgical resection and pharmacotherapy, but available drugs are limited, and their efficacy markers remain unclear. To develop novel drugs for PitNET and identify their efficacy markers, it is necessary to develop new research models. In recent years, organoid models have garnered attention as novel research models for various cancer types. In this study, we established novel organoid models derived from PitNET patients and analyzed their histological and endocrinological characteristics. Surgical specimens from 4 cases of somatotroph adenoma, 1 case of double adenoma, 1 case of gonadotroph adenoma, and 1 case of corticotroph adenoma were minced in dissection medium and embedded in Matrigel basement membrane matrix respectively. The organoids were cultured under 5% CO2 at 37°C using media supplemented with various growth factors. After 28 days of culture, formalin-fixed paraffin-embedded sections were prepared to examine histological homology with patient tumors. Hematoxylin and eosin staining results showed that all organoids maintained cell morphology and tissue structure similar to the original tumors. Immunohistochemical staining for markers specific to each PitNET revealed similar staining patterns between the organoids and the original tumors. Furthermore, analysis of hormone levels in the culture medium showed that hormone production capabilities, such as growth hormone and follicle stimulating hormone, were maintained even after long-term culture. In this study, we successfully established PitNET organoid models that retain histological and endocrinological characteristics. These models are expected to serve as useful research tools for elucidating the molecular mechanisms of PitNET and developing novel therapies targeting critical molecular abnormalities.

Modification of the hi-c technology for molecular genetic analysis of formalin-fixed paraffin-embedded sections of tumor tissues

Molecular genetic analysis of tumor tissues is the most important step towards understanding the mechanisms of cancer development, and it is also necessary for the choice of targeted therapy. Hi-C (high-throughput chromatin conformation capture) technology can be used to detect various types of genomic variants, including balanced chromosomal rearrangements: inversions and translocations. In this work, we propose a modification of the Hi-C method for the analysis of chromatin contacts in formalin-fixed paraffin-embedded (FFPE) sections of tumor tissues. Our results demonstrate that this protocol allow to generate high-quality Hi-C data and detect all types of chromosomal rearrangements. We have analyzed various databases to compile a comprehensive list of translocations that hold clinical importance for targeted therapy selection. The practical value of molecular genetic testing is its ability to influence patient treatment strategies and provide prognostic insights. Detecting specific chromosomal rearrangements can guide the choice of targeted therapies, which is a critical aspect of personalized medicine in oncology.

Recruitment of CCR5-positive T cells in pulmonary vascular lesions in idiopathic- and connective tissue disease associated- pulmonary arterial hypertension

Abstract Background C-C chemokine receptor type 5 (CCR5) is a chemokine receptor predominantly expressed on leukocytes including T cells, macrophages, and dendritic cells, and is involved in the process by which T cells are attracted to specific tissues and organs. Although CCR5 has been shown to be expressed on macrophages and pulmonary artery smooth muscle cells in lung samples from human idiopathic pulmonary arterial hypertension (PAH) and some animal models, its expression on T cells in human PAH lungs has not been investigated. Purpose To investigate the immunohistochemical expression of CCR5 on T cells infiltrating in pulmonary vascular lesions of human PAH tissues, particularly from patients with idiopathic PAH and PAH associated with connective tissue disease (CTD-PAH), where inflammation has been implicated in the pathogenesis. Methods Subjects included 25 postmortem cases of idiopathic PAH (14 cases, a mean age of 34 ± 10 years, 8 female cases) and CTD-PAH (11 cases, 48 ± 13 years, all female). We performed immunohistochemistry using antibodies against CCR5 and CD3 (for T cells) on formalin-fixed paraffin-embedded sections. To semi-quantify, we selected the three small muscular pulmonary arteries (80-150 µm in external diameter) with the strongest CCR5-positive cell infiltration in each case, counted the number of positive cells, and the average were shown as the number of cells per vessel. Results In all cases, regardless of whether IPAH or CTD-PAH, a subset of infiltrating inflammatory cells into or accumulating around vessels was CCR5-positive. Specifically, CCR5-positive inflammatory cells were found in remodelled pulmonary arteries, such as plexiform lesions and constrictive lesions with intimal thickening and/or medial hypertrophy, as well as perivascular space. The average number of CCR5-positive cells per small muscular pulmonary artery was 8.1/vessel. Where pulmonary venous occlusive lesions were seen, CCR5-positive cells were also present in and around them. The majority of CCR5-positive inflammatory cells appeared to be T cells, based on morphology and CD3 immunopositivity in the serial sections. Conclusion(s) Activated T cells showing CCR5 immunopositivity were recruited to remodelled pulmonary vascular lesions in both idiopathic PAH and CTD-PAH. This implicates CCR5-positive T cells as a common key player and that CCR5 signalling is involved in the pathogenesis of PAH in concert with other inflammatory cells, vascular endothelial cells, and pulmonary artery smooth muscle cells.

Evaluating glycocalyx morphology and composition in frozen and formalin-fixed liver tumor sections

BackgroundThe glycocalyx (GCX) is a glycan structure on the vascular endothelium and cancer cells. It is crucial for blood flow regulation, tumor invasion, and cancer drug resistance. Understanding the role of GCX in human tumors could help develop new cancer biomarkers and therapies. AimThis study aimed to demonstrate microstructural changes in human primary and metastatic liver tumors (henceforth termed liver tumors) by visualizing GCX using surgical specimens and comparing formalin-fixed paraffin-embedded sections (FFPEs) with frozen sections. The results of lectin staining were also compared between frozen and FFPE specimens to determine which was more useful for accurately assessing GCX structure and composition. MethodsLiver tumors and normal tissue samples from three patients were collected and processed into FFPEs and frozen sections, respectively. Lanthanum nitrate staining and scanning electron microscopy (SEM) were used to assess the GCX structures. Twenty lectins were analyzed for their glycan components in the samples. ResultsSEM revealed significant differences in GCX morphology among the cancer specimens. Frozen sections provided a more accurate GCX evaluation than FFPEs, showing distinct glycan compositions in hepatocellular carcinoma, colorectal carcinoma liver metastases, and melanoma liver metastases. Hepatocellular carcinoma samples exhibited a loss of N-acetylgalactosamine-related lectins. ConclusionThe results revealed that liver tumors have distinct and bulky GCX compared to normal liver tissue, while frozen sections are more reliable for GCX evaluation. These findings highlight glycan alterations in liver tumors and contribute to the development of new cancer therapies targeting GCX on tumor cell surfaces.

Single cell spatial profiling of FFPE splenic tissue from a humanized mouse model of HIV infection

BackgroundLatency remains a major obstacle to finding a cure for HIV despite the availability of antiretroviral therapy. Due to virus dormancy, limited biomarkers are available to identify latent HIV-infected cells. Profiling of individual HIV-infected cells is needed to explore potential latency biomarkers and to study the mechanisms of persistence that maintain the HIV reservoir.MethodsSingle cell spatial transcriptomic characterization using the CosMx Spatial Molecular Imager platform was conducted to analyze HIV-infected cells in formalin-fixed paraffin-embedded sections of splenic tissue surgically obtained from an HIV-infected humanized mouse model. Regulation of over a thousand human genes was quantified in both viremic and aviremic specimens. In addition, in situ hybridization and immunohistochemistry were performed in parallel to identify HIV viral RNA- and p24-containing cells, respectively. Finally, initial findings from CosMx gene profiling were confirmed by isolating RNA from CD4 + T cells obtained from a person living with HIV on antiretroviral therapy following either PMA/Ionomycin or DMSO treatment. RNA was quantified using qPCR for a panel of targeted human host genes.ResultsSupervised cell typing revealed that most of the HIV-infected cells in the mouse spleen sections were differentiated CD4 + T cells. A significantly higher number of infected cells, 2781 (1.61%) in comparison to 112 (0.06%), and total HIV transcripts per infected cell were observed in viremic samples compared to aviremic samples, respectively, which was consistent with the data obtained from ISH and IHC. Notably, the expression of 55 genes was different in infected cells within tissue from aviremic animals compared to viremic. In particular, both spleen tyrosine kinase (SYK) and CXCL17, were expressed approximately 100-fold higher. This data was further evaluated against bulk RNA isolated from HIV-infected human primary CD4 + T cells. A nearly 6-fold higher expression of SYK mRNA was observed in DMSO-treated CD4 + T cells compared to those stimulated with PMA/Ionomycin.ConclusionThis study found that the CosMx SMI platform is valuable for assessing HIV infection and providing insights into host biomarkers associated with HIV reservoirs. Higher relative expression of the SYK gene in aviremic-infected cells from the humanized mouse HIV model was consistent with levels found in CD4 + T cells of aviremic donors.

Histological methods for plant tissues

ABSTRACT Although many of the structures and organelles of vegetative cells are comparable to those of animal tissues, significant differences between the two kingdoms require modifications in histological techniques for both tissue processing steps and histochemical staining techniques. The authors investigated the challenges of working with plant tissues by collecting various flora to represent the four main plant organs: leaf, stem, root, and flower/fruit. Triplicate samples for each specimen were placed into formalin for paraffin embedding, placed into formalin for later frozen sections, and used fresh to undergo immediate frozen sectioning. Frozen sections of plant tissues were more difficult to obtain than formalin-fixed paraffin-embedded (FFPE) sections, exhibited tissue loss during staining, and were inferior morphologically to FFPE sections. Although, historically, plant tissue fixation and processing has employed several different reagents compared with those used in animal tissue processing and took significantly longer times, the current investigation determined reagents and protocols from a modern histology laboratory which processes mammalian tissues can be applied to plant tissue processing with only slight modifications in respect to reagent timing. Additionally, staining techniques were compared and while it is well known that plant cell walls stain well with safranin O, the current investigation determined the uptake of safranin O can be accelerated by incubating at 60°C.

Aspergillosis coinfection in patients with proven mucormycosis.

Although research on aspergillosis and mucormycosis confection is important to optimize antifungal therapy, data on this issue is scarce. Thus, we systematically investigated aspergillosis coinfection in patients with proven mucormycosis. Medical records of adult patients with proven mucormycosis whose formalin-fixed paraffin-embedded (FFPE) tissue sections were available, in a tertiary hospital from August 2007 to July 2023 were retrospectively reviewed to assess coinfection with aspergillosis. We noted cultures of fungi from sterile and non-sterile sites and performed polymerase chain reaction (PCR) assays on FFPE tissues to detect Aspergillus- and Mucorales-specific DNA. Sixty-seven patients with proven mucormycosis, including 12 (18%) with a positive culture of the mucormycosis agent from sterile site cultures, were enrolled. Fungal cultures from sterile and non-sterile sites revealed Aspergillus spp. growth in nine (13%) of the 67 patients, including two sterile and seven non-sterile cultures. The fungal PCR analysis from the FFPE sections was positive for Aspergillus-specific PCR in five (7%) and positive for both Aspergillus- and Mucorales-specific PCR results in eight (12%). Overall, 21 (31%) of the 67 patients with proven mucormycosis had microbiologic and/or molecular evidence of aspergillosis coinfection. Positive blood or bronchoalveolar lavage fluid galactomannan results were more common in the coinfection group (67% [14/21]) than in the mucormycosis group (37% [17/46], P=.024). No significant difference in mortality between the two groups was observed. Approximately one-third of patients with proven mucormycosis exhibited molecular and/or microbiologic evidence of aspergillosis coinfection. Further research is needed to identify patients with aspergillosis and mucormycosis coinfections, for optimal antifungal therapy.

Evaluation of femtosecond-LA-ICP-TOFMS for multi-elemental mapping at cellular resolution of human-tissue from cancer patients

The characterization of the multi-elemental distributions within a thin tissue section of a liver metastasis from colorectal cancer patient after oxaliplatin-based chemotherapy, is critically evaluated using Ultraviolet Femtosecond Laser Ablation Inductively Coupled Plasma-Time of Flight Mass Spectrometry (UV-fs-LA-ICP-TOFMS). Different femtosecond laser ablation conditions, in terms of spot size and energy per pulse, were investigated to achieve proper ablation of the formalin-fixed paraffin-embedded tumor sections, while also trying to minimize the ablation of the glass substrate. Moreover, histological images of the tissues before and after the ablation processes were combined with UV-fs-LA-ICP-TOFMS elemental mapping to achieve multi-elemental spatial distributions at cellular level. For instance, spatial distributions of endogenous 31P, 56Fe, 63Cu and 64Zn analytes were determined within the thin tissue section. Furthermore, spatial distribution of elements such as 24Mg, 28Si, and 40Ca were employed to study glass substrate ablation during tissue analysis. Additional analytes, which might be partially associated to compounds employed on hematoxylin and eosin tissue staining processes, such as 23Na, 27Al, 32S, 39K, 79Br and 127I, were also detected. Finally, the accumulation of the oxaliplatin-based chemotherapy products in the stroma was confirmed from the spatial distribution of 196Pt ion signals within the tissue.

Evaluation of bone marrow glucose uptake and adiposity in male rats after diet and exercise interventions.

Obesity impairs bone marrow (BM) glucose metabolism. Adult BM constitutes mostly of adipocytes that respond to changes in energy metabolism by modulating their morphology and number. Here we evaluated whether diet or exercise intervention could improve the high-fat diet (HFD) associated impairment in BM glucose uptake (BMGU) and whether this associates with the morphology of BM adipocytes (BMAds) in rats. Eight-week-old male Sprague-Dawley rats were fed ad libitum either HFD or chow diet for 24 weeks. Additionally after 12 weeks, HFD-fed rats switched either to chow diet, voluntary intermittent running exercise, or both for another 12 weeks. BMAd morphology was assessed by perilipin-1 immunofluorescence staining in formalin-fixed paraffin-embedded tibial sections. Insulin-stimulated sternal and humeral BMGU were measured using [18F]FDG-PET/CT. Tibial microarchitecture and mineral density were measured with microCT. HFD rats had significantly higher whole-body fat percentage compared to the chow group (17% vs 13%, respectively; p = 0.004) and larger median size of BMAds in the proximal tibia (815 µm2 vs 592 µm2, respectively; p = 0.03) but not in the distal tibia. Switch to chow diet combined with running exercise normalized whole-body fat percentage (p < 0.001) but not the BMAd size. At 32 weeks of age, there was no significant difference in insulin-stimulated BMGU between the study groups. However, BMGU was significantly higher in sternum compared to humerus (p < 0.001) and higher in 8-week-old compared to 32-week-old rats (p < 0.001). BMAd size in proximal tibia correlated positively with whole-body fat percentage (r = 0.48, p = 0.005) and negatively with humeral BMGU (r = -0.63, p = 0.02). HFD significantly reduced trabecular number (p < 0.001) compared to the chow group. Switch to chow diet reversed this as the trabecular number was significantly higher (p = 0.008) than in the HFD group. In this study we showed that insulin-stimulated BMGU is age- and site-dependent. BMGU was not affected by the study interventions. HFD increased whole-body fat percentage and the size of BMAds in proximal tibia. Switching from HFD to a chow diet and running exercise improved glucose homeostasis and normalized the HFD-induced increase in body fat but not the hypertrophy of BMAds.

A universal pipeline to combine spatial transcriptomics, proteomics, and diagnostic H&amp;E assays on a single tissue section to study tissue microenvironment.

e14657 Background: Spatial multi-omics approaches, including spatial transcriptomics (ST) and spatial proteomics (SP), that elucidate the complex tissue microenvironment (TME) are gaining traction in cancer research studies. However, combining these approaches onto one tissue section remains challenging. ST methods visualize, locate and quantify RNA targets, evaluating the transcriptome of the TME at the subcellular level while SP methods stain and visualize protein biomarkers at the cellular level. Here we show a pipeline that combines these ST and SP methods with Hematoxylin and Eosin (H&amp;E) approach on a single tissue section to achieve single slide multi-omics data with high resolution tissue morphology images. Methods: 5µm formalin-fixed paraffin-embedded sections of human lung cancer samples were placed on a Xenium (10x Genomics, Pleasanton, CA) slides and treated to expose RNA molecules. Probe hybridization was performed with a human lung panel kit containing 289 barcoded DNA padlock probes. Downstream ligation and amplification generated copies of the barcode and thereafter, the Xenium Analyzer performed imaging and data collection. The same tissue section was then stained and imaged in COMET (Lunaphore Technologies SA, Switzerland) using sequential immunofluorescence (seqIF) method to detect 40 protein targets in situ. Serial sections of the specimens were used for direct H&amp;E and seqIF staining for comparative validation. Results: Multi-omics images generated from Xenium and COMET were overlayed, jointly analyzed and interpreted. Staining specificity of the protein targets for the post-Xenium slides remain comparable with the direct COMET-stained slide. 40-plex COMET staining intensity in post-Xenium slide was minimally weaker compared to direct COMET-stained slide. Additionally, H&amp;E staining of the post-Xenium/COMET slide and direct COMET-stained slide were comparable to the direct H&amp;E-stained section, demonstrating discernable tissue landscape features despite a fainter hematoxylin stain. Overall, tissue integrity and cell morphology were well-preserved across the different workflows performed on each section, and the protein targets remain relatively stable for labelling after in situ RNA detection process. Conclusions: We present a pipeline that combines two spatial omics approaches with the diagnostic standard H&amp;E staining on a single tissue section, allowing the same cells to be assessed for their histological, proteomic, and transcriptomic information. A visual comparison of images showed minimal compromise to cellular morphology and protein stability at the end of the pipeline compared to direct staining of serial sections. This pipeline could be potentially generalized to most of the ST and SP approaches, thus advancing multi-omics cancer research and potentially clinical diagnostics in the future.

Exploiting spatial transcriptomics to investigate the molecular mechanisms involved in cardiac metastasis development

Abstract Funding Acknowledgements Type of funding sources: Foundation. Main funding source(s): IEO-Monzino Foundation Background Cardiac metastasis is considered a relatively rare malignancy, although an increasing prevalence is expected in the future due to the increasing life expectancy. Several cases of cardiac metastases remain untreatable, given the anatomical location that often hampers both surgical eradication and bioptic collection for biological characterization. Here, we use spatial transcriptomics to provide an unbiased molecular characterization of cardiac metastases, and identify novel targets for their treatment. Material and methods We performed spatial transcriptomics on samples of primary tumor, cardiac, and extra-cardiac metastasis from three different patients. First, we checked RNA integrity by means of DV200 analysis. Spatial transcriptomic analysis was performed by using the GeoMX technology (Nanostring), which provides whole-transcriptome data along with spatial distribution information of the preselected samples from the candidate regions of interest (ROIs). ROIs were selected on the formalin-fixed paraffin-embedded sections by means of geometric shapes in combination with cell markers specific for tumor cells, cardiomyocytes and endothelial cells, respectively. Differential gene expression analysis and Gene Set Enrichment Analysis (GSEA) were performed on the entire transcriptome. Cell-cell interactions between cardiac cells and cancer cells were then evaluated by means of InterCellaR. Results Differential expression analysis between cardiac metastases and extra-cardiac tumors (primary tumors + extra-cardiac metastases) identified 92 differentially expressed genes (DEGs). Of these, 53 genes were significantly overexpressed in cardiac metastases, while 39 genes were overexpressed in the extra-cardiac samples, regardless of the site of origin of the tumor. Unsupervised hierarchical clustering of protein-coding genes clearly separated the samples according to their anatomical location, in particular cardiac metastasis from extra-cardiac tumors. GSEA identified several pathways enriched in cardiac metastases compared to the extra-cardiac tumors, including mechanotransduction (e.g. keratinization and cell-matrix interaction) and triglyceride metabolism, suggesting a potential role of these signaling pathways in the development of cardiac metastasis. Interactome analysis revealed a rich plethora of receptor-ligand interactions in cardiac metastasis, especially between tumor cells and cardiomyocytes. Conclusions These results start shedding light on the mechanisms that allow cancer cell growth in the heart and pave the way to the development of novel therapies to treat this malignancy.

Emerging Approaches to Profile Accessible Chromatin from Formalin-Fixed Paraffin-Embedded Sections.

Nucleosomes are non-uniformly distributed across eukaryotic genomes, with stretches of 'open' chromatin strongly associated with transcriptionally active promoters and enhancers. Understanding chromatin accessibility patterns in normal tissue and how they are altered in pathologies can provide critical insights to development and disease. With the advent of high-throughput sequencing, a variety of strategies have been devised to identify open regions across the genome, including DNase-seq, MNase-seq, FAIRE-seq, ATAC-seq, and NicE-seq. However, the broad application of such methods to FFPE (formalin-fixed paraffin-embedded) tissues has been curtailed by the major technical challenges imposed by highly fixed and often damaged genomic material. Here, we review the most common approaches for mapping open chromatin regions, recent optimizations to overcome the challenges of working with FFPE tissue, and a brief overview of a typical data pipeline with analysis considerations.