Work was supported by National Institutes of Health, (NIH/NINDS) Grants: R37-NS094804, R01-NS105556, R21-NS107894 to M.G.C.; (NIH/NINDS) Grants R01-NS076991, R01-NS096756, R01-NS082311 to P.R.L.; (NIH/NIBI): R01-EB022563; (NIH/NCI) U01CA224160; the Department of Neurosurgery, Rogel Cancer Center at The University of Michigan, ChadTough Foundation, and Leah&#39;s Happy Hearts Foundation to M.G.C. and P.R.L. RNA Biomedicine Grant F046166 to M.G.C. National Institutes of Health, UL1 TR002240 for Michigan Institute for Clinical and Health Research (MICHR), Postdoctoral Translational Scholars Program (PTSP) grant, Project F049768 to A.C. University of Michigan Forbes Cancer Research Institute, a Physician-Scientist Award from Research to Prevent Blindness, Inc. (RPB), grant R01 EY022633 from the NEI of the NIH (AK), and an unrestricted grant from RPB to the Department of Ophthalmology and Visual Sciences. This research utilized the Vision Research Core (P30 EY007003), and the Cancer Center Research Core (P30 CA046592). AK is supported by the Mrs. William Davidson Emerging Scholar Award from the A. Alfred Taubman Medical Research Institute.

<ol>
	<li>Reifenberger, G., Wirsching, H. G., Knobbe-Thomsen, C. B., Weller, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Advances+in+the+molecular+genetics+of+gliomas+-+implications+for+classification+and+therapy.">Advances in the molecular genetics of gliomas - implications for classification and therapy.</a> Nature Reviews Clinical Oncology. 14 (7), 434-452 (2017).</li><li>Espina, V., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Laser-capture+microdissection.">Laser-capture microdissection.</a> Nature Protocols. 1 (2), 586-603 (2006).</li><li>Rabien, A., Kristiansen, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tissue+Microdissection.">Tissue Microdissection.</a> Methods in Molecular Biology. 1381, 39-52 (2016).</li><li>Lovatt, D., Bell, T., Eberwine, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Single-neuron+isolation+for+RNA+analysis+using+pipette+capture+and+laser+capture+microdissection.">Single-neuron isolation for RNA analysis using pipette capture and laser capture microdissection.</a> Cold Spring Harbor Protocols. 2015 (1), (2015).</li><li>Erickson, H. S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Quantitative+RT-PCR+gene+expression+analysis+of+laser+microdissected+tissue+samples.">Quantitative RT-PCR gene expression analysis of laser microdissected tissue samples.</a> Nature Protocols. 4 (6), 902-922 (2009).</li><li>Cheng, L., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Laser-assisted+microdissection+in+translational+research:+theory,+technical+considerations,+and+future+applications.">Laser-assisted microdissection in translational research: theory, technical considerations, and future applications.</a> Applied Immunohistochemistry &amp; Molecular Morphology. 21 (1), 31-47 (2013).</li><li>Butler, A. E., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Recovery+of+high-quality+RNA+from+laser+capture+microdissected+human+and+rodent+pancreas.">Recovery of high-quality RNA from laser capture microdissected human and rodent pancreas.</a> Journal of Histotechnology. 39 (2), 59-65 (2016).</li><li>Clement-Ziza, M., Munnich, A., Lyonnet, S., Jaubert, F., Besmond, C. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Stabilization+of+RNA+during+laser+capture+microdissection+by+performing+experiments+under+argon+atmosphere+or+using+ethanol+as+a+solvent+in+staining+solutions.">Stabilization of RNA during laser capture microdissection by performing experiments under argon atmosphere or using ethanol as a solvent in staining solutions.</a> RNA. 14 (12), 2698-2704 (2008).</li><li>van Dijk, M. C., Rombout, P. D., Dijkman, H. B., Ruiter, D. J., Bernsen, M. R. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Improved+resolution+by+mounting+of+tissue+sections+for+laser+microdissection.">Improved resolution by mounting of tissue sections for laser microdissection.</a> Molecular Pathology. 56 (4), 240-243 (2003).</li><li>N&#250;&#241;ez, F. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=IDH1-R132H+acts+as+a+tumor+suppressor+in+glioma+via+epigenetic+up-regulation+of+the+DNA+damage+response.">IDH1-R132H acts as a tumor suppressor in glioma via epigenetic up-regulation of the DNA damage response.</a> Science Translational Medicine. 11 (479), (2019).</li><li>Calinescu, A. A., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Transposon+mediated+integration+of+plasmid+DNA+into+the+subventricular+zone+of+neonatal+mice+to+generate+novel+models+of+glioblastoma.">Transposon mediated integration of plasmid DNA into the subventricular zone of neonatal mice to generate novel models of glioblastoma.</a> Journal of Visualized Experiments. (96), (2015).</li><li>Koschmann, C., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=ATRX+loss+promotes+tumor+growth+and+impairs+nonhomologous+end+joining+DNA+repair+in+glioma.">ATRX loss promotes tumor growth and impairs nonhomologous end joining DNA repair in glioma.</a> Science Translational Medicine. 8 (328), (2016).</li><li>Brat, D. J., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Comprehensive,+Integrative+Genomic+Analysis+of+Diffuse+Lower-Grade+Gliomas.">Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas.</a> The New England Journal of Medicine. 372 (26), 2481-2498 (2015).</li><li>Datta, S., et al. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Laser+capture+microdissection:+Big+data+from+small+samples.">Laser capture microdissection: Big data from small samples.</a> Histology and Histopathology. 30 (11), 1255-1269 (2015).</li><li>Lein, E., Borm, L. E., Linnarsson, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+promise+of+spatial+transcriptomics+for+neuroscience+in+the+era+of+molecular+cell+typing.">The promise of spatial transcriptomics for neuroscience in the era of molecular cell typing.</a> Science. 358 (6359), 64-69 (2017).</li><li>Gagner, J. P., Zagzag, D. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Probing+Glioblastoma+Tissue+Heterogeneity+with+Laser+Capture+Microdissection.">Probing Glioblastoma Tissue Heterogeneity with Laser Capture Microdissection.</a> Methods in Molecular Biology. 1741, 209-220 (2018).</li></ol>

All authors of this paper declare no potential conflicts of interest.

Understanding the molecular mechanisms underlying glioma heterogeneity and invasion are of critical importance to uncover novel therapeutic targets13. In this manuscript, we describe a detailed and optimized method to analyze the molecular landscape of glioma heterogeneity and invasion using laser capture microdissection (LMD) followed by transcriptomic analysis.
Laser capture microdissection (LMD) can be used to identify different areas or single cells within the tumor...

Gliomas are the most aggressive primary tumors of the central nervous system. They are highly invasive and heterogeneous1. Analysis of cellular and molecular components of the tumor will reveal novel therapeutic targets.
Among different methods currently available, laser capture microdissection (LMD) of frozen brain tumor tissue is a cost-effective, reliable technique that allows the isolation of discrete anatomical areas or specific cell populations from tumor tissues to study their molecular profile2,3. LMD allows the analysis of mRNA gene expression profiles of selected single cells or multicellular structures4,5. LMD can be utilized to gain in-depth mechanistic knowledge about the molecular events that take place during tumor progression. Improvement in processing of tumor tissues is necessary to obtain optimal optical resolution of tissue morphology and RNA-quality6. Although paraformaldehyde fixation is the best option for morphological analysis, RNA quality is affected and degraded under these conditions, resulting in poor RNA quality for RNA-seq analysis. The use of frozen tissue sections avoids ice crystal formation, which could break cell membranes and produce holes within cells, and remains the best option for RNA-Seq analysis7.
Here, we describe an optimized section fixation and staining method to process frozen mouse brain tumor tissues for LMD. To prevent ice crystals from forming in the tissue, we perfused mice with a solution of 30% sucrose. This solution disrupts interactions between polar water molecules and prevents the formation of ice crystals, preserving the tissue morphology. Tissue staining is necessary to differentiate and obtain specific population of cells or anatomically distinct areas within the tumor. It is essential to fix and stain the tissue with innocuous dyes to maintain RNA integrity. It has been previously shown that staining tissue with hematoxylin/eosin (H&#38;E) deteriorates RNA integrity8. We fixed and stained the tissue of interest with ethanol, Cresyl violet 4% and eosin Y 0.5% solutions. Cresyl violet is an acidophilic dye that stains the cell nucleus with a dark blue color. Eosin Y is a basophilic dye that stains basic components of the cells, providing a distinction between cytoplasm and other cellular structures8. Both dyes are soluble in ethanol and do not deteriorate RNA quality. To avoid tissue damage and maintain high optical resolution of the cellular structures, we mounted the tissue sections prior to LMD9.

<table><tbody><tr><td>Accutase Cell Detachment Solution</td><td>Biolegend</td><td>423201</td><td></td></tr><tr><td>Animal-Free Recombinant Human EGF</td><td>Peprotech</td><td>AF-100-15</td><td></td></tr><tr><td>Antibiotic-Antimycotic (100X)</td><td>Gibco</td><td>15240062</td><td></td></tr><tr><td>B-27 Supplement (50X), serum free</td><td>Gibco</td><td>17504044</td><td></td></tr><tr><td>Buffer RLT</td><td>Qiagen</td><td>79216</td><td></td></tr><tr><td>Corning PCR Tubes</td><td>Sigma Aldrich</td><td>CLS6530</td><td></td></tr><tr><td>Cresyl Violet Acetate</td><td>Sigma Aldrich</td><td>C5042</td><td></td></tr><tr><td>DMEM/F12 - Dulbecco&#039;s Modified Eagle Medium: Nutrient Mixture F-12</td><td>Gibco</td><td>11330057</td><td></td></tr><tr><td>Eosin Y</td><td>Sigma Aldrich</td><td>E4009</td><td></td></tr><tr><td>HiSeq 4000</td><td>Illumina</td><td>N/A</td><td></td></tr><tr><td>Laser Microdissection (LMD) System</td><td>Leica</td><td>LMD7000</td><td></td></tr><tr><td>N-2 Supplement (100X)</td><td>Gibco</td><td>17502048</td><td></td></tr><tr><td>Normocin - Antimicrobial Reagent</td><td>Invivogen</td><td>ant-nr-1</td><td></td></tr><tr><td>Peel Away Disposable Embedding Molds</td><td>Electron Microscopy Sciences</td><td>70182</td><td></td></tr><tr><td>PEN Membrane Glass Slide (2 &amp;micro;m)</td><td>Lieca</td><td>1150518</td><td></td></tr><tr><td>Pinpoint Solution</td><td>Zymo Research</td><td>D3001-1</td><td></td></tr><tr><td>Recombinant Human FGF-basic</td><td>Peprotech</td><td>100-18B-1MG</td><td></td></tr><tr><td>Research Cryostat</td><td>Leica</td><td>CM3050s</td><td></td></tr><tr><td>RNaseZap RNase Decontamination Solution</td><td>Fisher Scientific</td><td>AM9780</td><td></td></tr><tr><td>RNeasy Plus Micro Kit</td><td>Qiagen</td><td>74034</td><td></td></tr><tr><td>SMARTer Stranded Total RNA-Seq Kit v2 - Pico Input Mammalian</td><td>Takara Bio</td><td>634411</td><td></td></tr><tr><td>Tissue-Plus O.C.T. Compound</td><td>Fisher Scientific</td><td>23-730-571</td><td></td></tr></tbody></table>

laser capture microdissection of glioma subregions for spatial and molecular characterization of intratumoral heterogeneity, oncostreams, and invasion

Gliomas are primary brain tumors characterized by their invasiveness and heterogeneity. Specific histological patterns such as pseudopalisades, microvascular proliferation, mesenchymal transformation and necrosis characterize the histological heterogeneity of high-grade gliomas. Our laboratory has demonstrated that the presence of high densities of mesenchymal cells, named oncostreams, correlate with tumor malignancy. We have developed a unique approach to understand the mechanisms that underlie glioma&#39;s growth and invasion. Here, we describe a comprehensive protocol that utilizes laser capture microdissection (LMD) and RNA sequencing to analyze differential mRNA expression of intra-tumoral heterogeneous multicellular structures (i.e., mesenchymal areas or areas of tumor invasion). This method maintains good tissue histology and RNA integrity. Perfusion, freezing, embedding, sectioning, and staining were optimized to preserve morphology and obtain high-quality laser microdissection samples. The results indicate that perfusion of glioma bearing mice using 30% sucrose provides good morphology and RNA quality. In addition, staining tumor sections with 4% Cresyl violet and 0.5% eosin results in good nuclear and cellular staining, while preserving RNA integrity. The method described is sensitive and highly reproducible and it can be utilized to study tumor morphology in various tumor models. In summary, we describe a complete method to perform LMD that preserves morphology and RNA quality for sequencing to study the molecular features of heterogeneous multicellular structures within solid tumors.

Our laboratory has generated a genetically engineered mouse models (GEMMs) using the sleeping beauty transposase system (Figure 1A). This system incorporates specific genetic alterations into the genome of neural progenitor cells in neonatal mice. These altered progenitor cells form endogenous glioma tumors. Plasmid sequences used to generate the tumors were: (1) pT2C-LucPGK-SB100X for Sleeping Beauty transposon &#38; luciferase expression, (2) pT2-NRASSV12 for NRAS express...

Watch this Scientific Journal Video about Laser Capture Microdissection of Glioma Subregions for Spatial and Molecular Characterization of Intratumoral Heterogeneity, Oncostreams, and Invasion at JoVE

Laser Capture Microdissection of Glioma Subregions for Spatial and Molecular Characterization of Intratumoral Heterogeneity, Oncostreams, and Invasion

Laser microdissection (LMD) is a sensitive and highly reproducible technique that can be used to uncover pathways that mediate glioma heterogeneity and invasion. Here, we describe an optimized protocol to isolate discrete areas from glioma tissue using laser LMD followed by transcriptomic analysis.

Gliomas are primary brain tumors characterized by their invasiveness and heterogeneity. Specific histological patterns such as pseudopalisades, ...

laser-capture-microdissection-glioma-subregions-for-spatial-molecular

Research

JoVE Journal

Neuroscience

6.8K Views.  University of Michigan Medical School. Dit protocol maakt gebruik van lasermicrodissection en RNA sequencing om het differentiële mRNA-expressie van intratumor heterogeniteit te analyseren, zoals gebieden van accumulatie van mesenchymale cellen of gebieden van tumorinvasie. Deze methode is geoptimaliseerd om een goede kwaliteit weefsel histologie en RNA integriteit te behouden om de verwerving van hoge kwaliteit laser microdissection monsters te vergemakkelijken. Deze methode is gevoelig en zeer reproduceerbaar.Het kan wor...

Video: Laser Capture Microdissection of Glioma Subregions for Spatial and Molecular Characterization of Intratumoral Heterogeneity, Oncostreams, and Invasion

Multi-photon Imaging of Tumor Cell Invasion in an Orthotopic Mouse Model of Oral Squamous Cell Carcinoma

Loco-regional invasion of head and neck cancer is linked to metastatic risk and presents a difficult challenge in designing and implementing patient management strategies. Orthotopic mouse models of oral cancer have been developed to facilitate the study of factors that impact invasion and serve as model system for evaluating anti-tumor therapeutics. In these systems, visualization of disseminated tumor cells within oral cavity tissues has typically been conducted by either conventional histology or with in vivo bioluminescent methods. A primary drawback of these techniques is the inherent inability to accurately visualize and quantify early tumor cell invasion arising from the primary site in three dimensions. Here we describe a protocol that combines an established model for squamous cell carcinoma of the tongue (SCOT) with two-photon imaging to allow multi-vectorial visualization of lingual tumor spread. The OSC-19 head and neck tumor cell line was stably engineered to express the F-actin binding peptide LifeAct fused to the mCherry fluorescent protein (LifeAct-mCherry). Fox1nu/nu mice injected with these cells reliably form tumors that allow the tongue to be visualized by ex-vivo application of two-photon microscopy. This technique allows for the orthotopic visualization of the tumor mass and locally invading cells in excised tongues without disruption of the regional tumor microenvironment. In addition, this system allows for the quantification of tumor cell invasion by calculating distances that invaded cells move from the primary tumor site. Overall this procedure provides an enhanced model system for analyzing factors that contribute to SCOT invasion and therapeutic treatments tailored to prevent local invasion and distant metastatic spread. This method also has the potential to be ultimately combined with other imaging modalities in an in vivo setting.

A comprehensive overview of the techniques involved in generating a mouse model of oral cancer and quantitative monitoring of tumor invasion within the tongue through multi-photon microscopy of labeled cells is presented. This system can serve as a useful platform for the molecular assessment and drug efficacy of anti-invasive compounds.

Loco-regional invasion of head and neck cancer is linked to metastatic risk and presents a difficult challenge in designing and implementing patient ...

Medicine

Characterization of the Effects of Migrastatic Inhibitors on 3D Tumor Spheroid Invasion by High-resolution Confocal Microscopy

Drug discovery and development in cancer research is increasingly being based on drug screens in a 3D format. Novel inhibitors targeting the migratory and invasive potential of cancer cells, and consequently the metastatic spread of disease, are being discovered and considered as complementary treatments in highly invasive cancers such as gliomas. Thus, generating data enabling the detailed analyses of cells in a 3D environment following the addition of a drug is required. The methodology described here, combining spheroid invasion assays with high-resolution image capture and data analysis by confocal laser scanning microscopy (CLSM), enabled detailed characterization of the effects of the potential anti-migratory inhibitor MI-192 on glioma cells. Spheroids were generated from cell lines for invasion assays in low adherent 96-well plates and then prepared for CLSM analysis. The described workflow was preferred over other commonly used spheroid-generating techniques due to both ease and reproducibility. This, combined with the enhanced image resolution attained by confocal microscopy compared to conventional wide-field approaches, allowed the identification and analysis of distinct morphological changes in migratory cells in a 3D environment following treatment with the migrastatic drug MI-192.

The effects of migrastatic inhibitors on glioma cancer cell migration in three-dimensional (3D) invasion assays using a histone deacetylase (HDAC) inhibitor are characterized by high-resolution confocal microscopy.

Drug discovery and development in cancer research is increasingly being based on drug screens in a 3D format. Novel inhibitors targeting the migratory and ...

Cancer Research

Quantifying the Brain Metastatic Tumor Micro-Environment using an Organ-On-A Chip 3D Model, Machine Learning, and Confocal Tomography

Brain metastases are the most lethal cancer lesions; 10-30% of all cancers metastasize to the brain, with a median survival of only ~5-20 months, depending on the cancer type. To reduce the brain metastatic tumor burden, gaps in basic and translational knowledge need to be addressed. Major challenges include a paucity of reproducible preclinical models and associated tools. Three-dimensional models of brain metastasis can yield the relevant molecular and phenotypic data used to address these needs when combined with dedicated analysis tools. Moreover, compared to murine models, organ-on-a-chip models of patient tumor cells traversing the blood brain barrier into the brain microenvironment generate results rapidly and are more interpretable with quantitative methods, thus amenable to high throughput testing. Here we describe and demonstrate the use of a novel 3D microfluidic blood brain niche (&#181;mBBN) platform where multiple elements of the niche can be cultured for an extended period (several days), fluorescently imaged by confocal microscopy, and the images reconstructed using an innovative confocal tomography technique; all aimed to understand the development of micro-metastasis and changes to the tumor micro-environment (TME) in a repeatable and quantitative manner. We demonstrate how to fabricate, seed, image, and analyze the cancer cells and TME cellular and humoral components, using this platform. Moreover, we show how artificial intelligence (AI) is used to identify the intrinsic phenotypic differences of cancer cells that are capable of transit through a model &#181;mBBN and to assign them an objective index of brain metastatic potential. The data sets generated by this method can be used to answer basic and translational questions about metastasis, the efficacy of therapeutic strategies, and the role of the TME in both.

Here, we present a protocol for preparing and culturing a blood brain barrier metastatic tumor micro-environment and then quantifying its state using confocal imaging and artificial intelligence (machine learning).

Brain metastases are the most lethal cancer lesions; 10-30% of all cancers metastasize to the brain, with a median survival of only ~5-20 months, ...

Digital Spatial Profiling for Characterization of the Microenvironment in Adult-Type Diffusely Infiltrating Glioma

Diffusely infiltrating gliomas are associated with high morbidity and mortality due to the infiltrative nature of tumor spread. They are morphologically complex tumors, with a high degree of proteomic variability across both the tumor itself and its heterogenous microenvironment. The malignant potential of these tumors is enhanced by the dysregulation of proteins involved in several key pathways, including processes that maintain cellular stability and preserve the structural integrity of the microenvironment. Although there have been numerous bulk and single-cell glioma analyses, there is a relative paucity of spatial stratification of these proteomic data. Understanding differences in spatial distribution of tumorigenic factors and immune cell populations between the intrinsic tumor, invasive edge, and microenvironment offers valuable insight into the mechanisms underlying tumor proliferation and propagation. Digital spatial profiling (DSP) represents a powerful technology that can form the foundation for these important multilayer analyses.
DSP is a method that efficiently quantifies protein expression within user-specified spatial regions in a tissue specimen. DSP is ideal for studying the differential expression of multiple proteins within and across regions of distinction, enabling multiple levels of quantitative and qualitative analysis. The DSP protocol is systematic and user-friendly, allowing for customized spatial analysis of proteomic data. In this experiment, tissue microarrays are constructed from archived glioblastoma core biopsies. Next, a panel of antibodies is selected, targeting proteins of interest within the sample. The antibodies, which are preconjugated to UV-photocleavable DNA oligonucleotides, are then incubated with the tissue sample overnight. Under fluorescence microscopy visualization of the antibodies, regions of interest (ROIs) within which to quantify protein expression are defined with the samples. UV light is then directed at each ROI, cleaving the DNA oligonucleotides. The oligonucleotides are microaspirated and counted within each ROI, quantifying the corresponding protein on a spatial basis.

Proteomic dysregulation plays an important role in the spread of diffusely infiltrating gliomas, but several relevant proteins remain unidentified. Digital spatial processing (DSP) offers an efficient, high-throughput approach for characterizing the differential expression of candidate proteins that may contribute to the invasion and migration of infiltrative gliomas.

Diffusely infiltrating gliomas are associated with high morbidity and mortality due to the infiltrative nature of tumor spread. They are morphologically ...

Industrialized, Artificial Intelligence-guided Laser Microdissection for Microscaled Proteomic Analysis of the Tumor Microenvironment

The tumor microenvironment (TME) represents a complex ecosystem comprised of dozens of distinct cell types, including tumor, stroma, and immune cell populations. To characterize proteome-level variation and tumor heterogeneity at scale, high-throughput methods are needed to selectively isolate discrete cellular populations in solid tumor malignancies. This protocol describes a high-throughput workflow, enabled by artificial intelligence (AI), that segments images of hematoxylin and eosin (H&#38;E)-stained, thin tissue sections into pathology-confirmed regions of interest for selective harvest of histology-resolved cell populations using laser microdissection (LMD). This strategy includes a novel algorithm enabling the transfer of regions denoting cell populations of interest, annotated using digital image software, directly to laser microscopes, thus enabling more facile collections. Successful implementation of this workflow was performed, demonstrating the utility of this harmonized method to selectively harvest tumor cell populations from the TME for quantitative, multiplexed proteomic analysis by high-resolution mass spectrometry. This strategy fully integrates with routine histopathology review, leveraging digital image analysis to support enrichment of cellular populations of interest and is fully generalizable, enabling harmonized harvests of cell populations from the TME for multiomic analyses.

This protocol describes a high-throughput workflow for artificial intelligence-driven segmentation of pathology-confirmed regions of interest from stained, thin tissue section images for enrichment of histology-resolved cell populations using laser microdissection. This strategy includes a novel algorithm enabling the transfer of demarcations denoting cell populations of interest directly to laser microscopes.

The tumor microenvironment (TME) represents a complex ecosystem comprised of dozens of distinct cell types, including tumor, stroma, and immune cell ...

Molecular Profiling of the Invasive Tumor Microenvironment in a 3-Dimensional Model of Colorectal Cancer Cells and Ex vivo Fibroblasts

Invading colorectal cancer (CRC) cells have acquired the capacity to break free from their sister cells, infiltrate the stroma, and remodel the extracellular matrix (ECM). Characterizing the biology of this phenotypically distinct group of cells could substantially improve our understanding of early events during the metastatic cascade.

Tumor invasion is a dynamic process facilitated by bidirectional interactions between malignant epithelium and the cancer associated stroma. In order to examine cell-specific responses at the tumor stroma-interface we have combined organotypic co-culture and laser micro-dissection techniques.
Organotypic models, in which key stromal constituents such as fibroblasts are 3-dimentioanally co-cultured with cancer epithelial cells, are highly manipulatable experimental tools which enable invasion and cancer-stroma interactions to be studied in near-physiological conditions.

Laser microdissection (LMD) is a technique which entails the surgical dissection and extraction of the various strata within tumor tissue, with micron level precision.
By combining these techniques with genomic, transcriptomic and epigenetic profiling we aim to develop a deeper understanding of the molecular characteristics of invading tumor cells and surrounding stromal tissue, and in doing so potentially reveal novel biomarkers and opportunities for drug development in CRC.&#160;&#160;&#160;

Molecular Profiling of the Invasive Tumor Microenvironment in a 3-Dimensional Model of Colorectal Cancer Cells and Ex vivo Fibroblasts

Molecular profiling of laser microdissected cells and stroma from synthetic, tissue-engineered colorectal cancer models represents a novel and manipulatable approach to characterize and dissect the distinctive biology at the interface between tumor cells at the invasive front and cancer associated stromal cells. &#160;

Invading colorectal cancer (CRC) cells have acquired the capacity to break free from their sister cells, infiltrate the stroma, and remodel the ...

An Immunocompetent Murine Model for Laser Interstitial Thermal Therapy of Glioblastoma

Glioblastoma (GB), the most aggressive form of primary brain cancer, accounts for approximately half of all high-grade primary brain tumors in adults and has no cure. Laser interstitial thermal therapy (LITT) is a Food and Drug Administration (FDA)-approved treatment for GB and is used in patients who may not be candidates for conventional surgical resection. While the clinical efficacy of LITT has been established, research beyond clinical case studies and case series is limited and hindered by the lack of an established animal model. This protocol uses C57BL/6 mice and syngeneic CT2A glioma cancer cell line to closely recapitulate human GB&#160;while also using a 1064 nm Neodymium-doped Yttrium Aluminum Garnet (Nd:YAG) laser, such as is used in one of the two FDA-approved LITT systems, providing excellent pre-clinical relevance. The successful establishment of this LITT murine model will provide a valuable platform for investigating the unique features of LITT ablation and its effects on the tumor microenvironment, potentially leading to improved therapeutic strategies.

Glioblastoma is a devastating form of primary brain cancer, and laser interstitial thermal therapy is emerging as a promising alternative to conventional surgical resection for inoperable glioblastoma. This protocol describes an optimized pre-clinical mouse model that can be used to study treatment effects or adjuvant and combinatorial treatments.

Glioblastoma (GB), the most aggressive form of primary brain cancer, accounts for approximately half of all high-grade primary brain tumors in adults and ...

A Human Glioblastoma Organotypic Slice Culture Model for Study of Tumor Cell Migration and Patient-specific Effects of Anti-Invasive Drugs

Glioblastoma (GBM) continues to carry an extremely poor clinical prognosis despite surgical, chemotherapeutic, and radiation therapy. Progressive tumor invasion into surrounding brain parenchyma represents an enduring therapeutic challenge. To develop anti-migration therapies for GBM, model systems that provide a physiologically relevant background for controlled experimentation are essential. Here, we present a protocol for generating slice cultures from human GBM tissue obtained during surgical resection. These cultures allow for ex vivo experimentation without passaging through animal xenografts or single cell cultures. Further, we describe the use of time-lapse laser scanning confocal microscopy in conjunction with cell tracking to quantitatively study the migratory behavior of tumor cells and associated response to therapeutics. Slices are reproducibly generated within 90 min of surgical tissue acquisition. Retrovirally-mediated fluorescent cell labeling, confocal imaging, and tumor cell migration analyses are subsequently completed within two weeks of culture. We have successfully used these slice cultures to uncover genetic factors associated with increased migratory behavior in human GBM. Further, we have validated the model&#39;s ability to detect patient-specific variation in response to anti-migration therapies. Moving forward, human GBM slice cultures are an attractive platform for rapid ex vivo assessment of tumor sensitivity to therapeutic agents, in order to advance personalized neuro-oncologic therapy.

Current ex vivo models of glioblastoma (GBM) are not optimized for physiologically relevant study of human tumor invasion. Here, we present a protocol for generation and maintenance of organotypic slice cultures from fresh human GBM tissue. A description of time-lapse microscopy and quantitative cell migration analysis techniques is provided.

Glioblastoma (GBM) continues to carry an extremely poor clinical prognosis despite surgical, chemotherapeutic, and radiation therapy. Progressive tumor ...

Quantitative Immunohistochemistry of the Cellular Microenvironment in Patient Glioblastoma Resections

With the growing interest in the tumor microenvironment, we set out to develop a method to specifically determine the microenvironment components within patient samples of glioblastoma, the deadliest and most invasive brain cancer. Not only are quantitative methods beneficial for accurately describing diseased tissues, they can also potentially contribute to more accurate prognosis, diagnosis, and the development of tissue-engineered systems and replacements. In glioblastoma, glial cells, such as microglia and astrocytes, have been independently correlated with poor prognosis based on pathologist grading. However, the state of these cells and other glial cell components has not been well-described quantitatively. This can be difficult due to the large processes that mark these glial cells. Furthermore, most histological analyses focus on the overall tissue sample or only within the bulk of the tumor, as opposed to delineating quantifications based on regions within the highly heterogeneous tissue. Here, we describe a method for identifying and quantitatively analyzing the populations of glial cells within the tumor bulk and adjacent regions of tumor resections from glioblastoma patients. We used chromogenic immunohistochemistry to identify the glial cell populations in patient tumor resections and ImageJ to analyze percent coverage of staining for each glial population. With these techniques we are able to better describe the glial cells throughout regions of the glioma tumor microenvironment.

This protocol was developed to quantitatively identify tumor microenvironment components in glioblastoma patient resections using chromogenic immunohistochemistry and ImageJ.

With the growing interest in the tumor microenvironment, we set out to develop a method to specifically determine the microenvironment components within ...

Capturing Oral Submucous Fibrosis Tissue Samples for Spatial-Omics Analysis

Isolation of Cells with Morphological and Spatial Information from Oral Submucous Fibrosis Samples by Laser Capture Microdissection

Oral submucous fibrosis (OSF) is a common type of potentially malignant disorder in the oral cavity. The atrophy of epithelium and fibrosis of the lamina propria and the submucosa are often found on histopathological slides. Epithelial dysplasia, epithelial atrophy, and senescent fibroblasts have been proposed to be associated with the malignant transformation of OSF. However, because of the heterogeneity of potentially malignant oral disorders and oral squamous cell carcinoma, it is difficult to identify the specific molecular mechanisms of malignant transformation in OSF. Here, we present a method to obtain a small number of epithelial or mesenchymal cells carrying morphological data and spatial information by laser capture microdissection on formalin-fixed paraffin-embedded tissue slides. Using a microscope, we can precisely capture microscale (~500 cells) dysplastic or atrophic epithelial tissue and fibrotic subepithelial tissue. The extracted cells can be evaluated by genome or transcriptome sequencing to acquire genomic and transcriptomic data with morphological and spatial information. This approach removes the heterogeneity of bulk OSF tissue sequencing and the interference caused by cells in non-lesioned areas, allowing for precise spatial-omics analysis of OSF tissue.

Author Spotlight: Unlocking the Mysteries of Oral Potential Malignancies 

Laser capture microdissection of oral submucous fibrosis tissues allows for precise extraction of cells from histological regions of interest for the analysis of multi-omics data with morphological and spatial information.

Oral submucous fibrosis (OSF) is a common type of potentially malignant disorder in the oral cavity. The atrophy of epithelium and fibrosis of the lamina ...

Laser Capture Microdissection of Glioma Subregions for Spatial and Molecular Characterization of Intratumoral Heterogeneity, Oncostreams, and Invasion

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