scholarly journals Deciphering the Immune Microenvironment on A Single Archival Formalin-Fixed Paraffin-Embedded Tissue Section by An Immediately Implementable Multiplex Fluorescence Immunostaining Protocol

Cancers ◽  
2020 ◽  
Vol 12 (9) ◽  
pp. 2449 ◽  
Author(s):  
Adrien Guillot ◽  
Marlene S. Kohlhepp ◽  
Alix Bruneau ◽  
Felix Heymann ◽  
Frank Tacke
Keyword(s):  
Immune Cell ◽  
Simple Procedure ◽  
Parenchymal Cell ◽  
Ffpe Tissue ◽  
Immune Microenvironment ◽  
Tissue Samples ◽  
Tissue Organization ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Formalin Fixed

Technological breakthroughs have fundamentally changed our understanding on the complexity of the tumor microenvironment at the single-cell level. Characterizing the immune cell composition in relation to spatial distribution and histological changes may provide important diagnostic and therapeutic information. Immunostaining on formalin-fixed paraffin-embedded (FFPE) tissue samples represents a widespread and simple procedure, allowing the visualization of cellular distribution and processes, on preserved tissue structure. Recent advances in microscopy and molecular biology have made multiplexing accessible, yet technically challenging. We herein describe a novel, simple and cost-effective method for a reproducible and highly flexible multiplex immunostaining on archived FFPE tissue samples, which we optimized for solid organs (e.g., liver, intestine, lung, kidney) from mice and humans. Our protocol requires limited specific equipment and reagents, making multiplexing (>12 antibodies) immediately implementable to any histology laboratory routinely performing immunostaining. Using this method on single sections and combining it with automated whole-slide image analysis, we characterize the hepatic immune microenvironment in preclinical mouse models of liver fibrosis, steatohepatitis and hepatocellular carcinoma (HCC) and on human-patient samples with chronic liver diseases. The data provide useful insights into tissue organization and immune–parenchymal cell-to-cell interactions. It also highlights the profound macrophage heterogeneity in liver across premalignant conditions and HCC.

scholarly journals The Dutch National TissueArchive Portal enables efficient, consistent, and transparent procurement of diagnostic tissue samples for scientific use

2021 ◽  
Author(s):  
Robin Verjans ◽  
Annette H. Bruggink ◽  
Robby Kibbelaar ◽  
Jos Bart ◽  
Aletta Debernardi ◽  
...  
Keyword(s):  
The Netherlands ◽  
Tissue Sample ◽  
Ffpe Tissue ◽  
Tissue Samples ◽  
Internet Portal ◽  
Formalin Fixed Paraffin ◽  
Practical Support ◽  
Formalin Fixed Paraffin Embedded ◽  
The Rich ◽  
Formalin Fixed

AbstractBiobanks play a crucial role in enabling biomedical research by facilitating scientific use of valuable human biomaterials. The PALGA foundation—a nationwide network and registry of histo- and cytopathology in the Netherlands—was established to promote the provision of data within and between pathology departments, and to make the resulting knowledge available for healthcare. Apart from the pathology data, we aimed to utilize PALGA’s nationwide network to find and access the rich wealth of Formalin-Fixed Paraffin-Embedded (FFPE) tissue samples for scientific use.  We implemented the Dutch National TissueArchive Portal (DNTP) to utilize PALGA’s nationwide network for requesting FFPE tissue samples. The DNTP consists of (1) a centrally organized internet portal to improve the assessing, processing, harmonization, and monitoring of the procurement process, while (2) dedicated HUB-employees provide practical support at peripheral pathology departments. Since incorporation of the DNTP, both the number of filed requests for FFPE tissue samples and the amount of HUB-mediated support increased 55 and 29% respectively. In line, the sample procurement duration time decreased significantly (− 47%). These findings indicate that implementation of the DNTP improved the frequency, efficiency, and transparency of FFPE tissue sample procurement for research in the Netherlands. To conclude, the need for biological resources is growing persistently to enable precision medicine. Here, we access PALGA’s national, pathology network by implementation of the DNTP to allow for efficient, consistent, and transparent exchange of FFPE tissue samples for research across the Netherlands.

scholarly journals Tumor Immune Microenvironment Characterization of Primary Lung Adenocarcinoma and Lymph Node Metastases

2021 ◽  
Vol 2021 ◽  
pp. 1-14
Author(s):  
Yuan Zhou ◽  
Xinying Shi ◽  
Huan Chen ◽  
Beibei Mao ◽  
Xue Song ◽  
...  
Keyword(s):  
Immune Cell ◽  
Locally Advanced ◽  
Transcriptome Data ◽  
Immune Microenvironment ◽  
Formalin Fixed Paraffin ◽  
Primary Lung Adenocarcinoma ◽  
Tumor Immune Microenvironment ◽  
Formalin Fixed Paraffin Embedded ◽  
Ifn Γ ◽  
Formalin Fixed

Background. The essential roles of the tumor microenvironment (TME) have been recognized during the initiation and progression of primary lung adenocarcinoma (LUAD). The aim of the present study was to delineate the immune landscape in both primary cancer and matched lymph node metastasis from a cohort of locally advanced stage LUAD patients with distinct outcomes. Methods. Formalin-fixed, paraffin-embedded samples were collected from 36 locally advanced LUAD patients. Transcriptome data of the tumor immune microenvironment were resolved using an immune oncology panel RNA sequencing platform. Bioinformatics approaches were used to determine the differentially expressed genes (DEGs), dysregulated pathways, and immune cell fraction between patients with early recurrence (ER) and late recurrence (LR). Results. Here, we showed that in primary cancer tissues, 23 DEGs were obtained between patients with ER and LR. Functional analysis revealed that the LR in LUAD patients may be associated with enriched gene sets belonging to the antigen presentation and MHC protein complex, innate immune response, and IFN-γ signaling pathways. Next, the transcriptome data were adopted to quantify immune cell fractions, indicating that high infiltration of mast cells and neutrophils was correlated with ER. Interestingly, similar findings were observed in metastatic lymph nodes from patients suffering from ER or LR. By analyzing the shared immune features of primary cancers and lymphatic metastases, we unraveled the prognostic value and joint utility of two DEGs, CORO1A and S100A8. Conclusions. In LUAD, the enrichment in antigen presentation, MHC protein complex, and IFN-γ signaling, and low infiltration of neutrophils in primary or metastatic nodules may be indications for a favorable prognosis. Integrated with bioinformatics approaches, transcriptome data of immune-related genes from formalin-fixed, paraffin-embedded (FFPE) samples can effectively profile the landscape of the tumor immune microenvironment and help predict clinical outcomes.

HTAPP_Sectioning formalin fixed paraffin embedded (FFPE) tissue samples for MIBI assays v1 (protocols.io.bu34nyqw)

protocols.io ◽  
2021 ◽  
Author(s):  
Ana Lako ◽  
Kathleen L ◽  
Sizun Jiang ◽  
Xavier Rovira-Clave ◽  
Garry not provided ◽  
...  
Keyword(s):  
Ffpe Tissue ◽  
Tissue Samples ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Formalin Fixed

scholarly journals Detection of Merkel Cell Polyomavirus in Human Tumors and Sarcoidosis From Formalin-Fixed Paraffin-Embedded (FFPE) Tissue Samples

2015 ◽  
Vol 144 (suppl 2) ◽  
pp. A298-A298
Author(s):  
Brian Soles ◽  
Vasuki Anandan ◽  
Carol Freeman ◽  
Kenneth Muldrew
Keyword(s):  
Ffpe Tissue ◽  
Merkel Cell Polyomavirus ◽  
Human Tumors ◽  
Merkel Cell ◽  
Tissue Samples ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Formalin Fixed

scholarly journals Mass Spectrometry Amyloid Typing Is Reproducible across Multiple Organ Sites

2019 ◽  
Vol 2019 ◽  
pp. 1-9 ◽  
Author(s):  
Dusan Holub ◽  
Pavla Flodrova ◽  
Tomas Pika ◽  
Patrik Flodr ◽  
Marian Hajduch ◽  
...  
Keyword(s):  
Mass Spectrometry ◽  
Staining Intensity ◽  
Multiple Organ ◽  
Ffpe Tissue ◽  
Al Amyloidosis ◽  
Tissue Samples ◽  
Amyloid A ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Formalin Fixed

We have determined patient’s amyloid subtype through immunohistochemical and proteomic analyses of formalin-fixed, paraffin-embedded (FFPE) tissue samples from two affected organs per patient. Amyloid typing, via immunohistochemistry (IHC) and laser microdissection followed by the combination of liquid chromatography with mass spectrometry (LMD-LC-MS), was performed using tissue samples of the human heart, liver, kidney, tongue, and small intestine from 11 patients, and the results were compared with clinical data. LMD-LC-MS correctly typed AL amyloidosis in all 22 FFPE tissue samples despite tissue origin. In contrast, IHC was successful only in the analysis of eight FFPE tissue samples with differences between the examined organs. In the majority of LMD-LC-MS typed samples, the level of IHC staining intensity for transthyretin and serum amyloid A was the same as that for Ig κ and Ig λ antibodies, suggesting low Ig κ or Ig λ antibodies reactivity and the additional antibody clones were essential for correct typing. Both methods used in the study were found to be suitable for amyloid typing, although LMD-LC-MS yielded more promising results than IHC.

scholarly journals Gene-expression analysis of a colorectal cancer-specific discriminatory transcript set on formalin-fixed, paraffin-embedded (FFPE) tissue samples

2015 ◽  
Vol 10 (1) ◽  
Author(s):  
Alexandra Kalmár ◽  
Barnabás Wichmann ◽  
Orsolya Galamb ◽  
Sándor Spisák ◽  
Kinga Tóth ◽  
...  
Keyword(s):  
Gene Expression ◽  
Colorectal Cancer ◽  
Expression Analysis ◽  
Gene Expression Analysis ◽  
Ffpe Tissue ◽  
Tissue Samples ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Formalin Fixed

Su1872 Diagnosis of Normal, Colorectal Cancer and Adenoma Cases From Both Fresh Frozen Biopsy and Formalin-Fixed, Paraffin-Embedded (FFPE) Tissue Samples - Potential mRNA Biomarkers of Colorectal Dysplasia-Carcinoma Transition

2012 ◽  
Vol 142 (5) ◽  
pp. S-523-S-524
Author(s):  
Alexandra Kalmár ◽  
Orsolya Galamb ◽  
Ferenc Sipos ◽  
Barnabas Wichmann ◽  
Sándor Spisák ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Ffpe Tissue ◽  
Tissue Samples ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Fresh Frozen ◽  
Formalin Fixed
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