This work was supported by a grant to Yong Yu from Johannes Kepler University Linz (BERM16108001).

1. DLBCL cell lines with mafosfamide or daunorubicin treatment to induce cellular senescence
NOTE: The protocol also works for adherent cancer cells. Depending on cell size, seed 1-2 &#215; 105 cells into one well of a 6-well plate and incubate the plate in a 5% CO2, 37 &#176;C incubator overnight before treatment. The protocol steps are the same as for suspension cells but with two exceptions. First, cells need to be trypsinized off the plate after step 3.4. Second, wash steps are performed without centrifugation before trypsinization.
<ol>
	<li>Count DLBCL cells and seed 1 &#215; 106 cells/mL in 4 mL of medium per well into a 6-well culture plate. Cultivate DLBCL cells in RPMI-1640 medium supplemented with 10% fetal bovine serum (FBS) and 100 U/mL penicillin/streptomycin.</li>
	<li>Add MAF (5 &#181;g/mL) or DN (20 ng/mL) into the cell culture and gently rock the plate to mix. 
	NOTE: MAF and DN are not stable. After dissolving in DMSO, the stock solution should be aliquoted and stored at -20 &#176;C. Freeze/thaw cycles should be avoided.</li>
	<li>Incubate the plate in a 5% CO2, 37 &#176;C incubator for 3 days.</li>
	<li>After a 3 day incubation, collect the DLBCL cells in 15 mL sterile centrifuge tubes and spin at 100 &#215; g, 4 &#176;C for 5 min.</li>
	<li>Discard the supernatant, resuspend the cell pellets with 4 mL of fresh medium, and add the suspensions back into the 6-well plate.</li>
	<li>Cultivate the cell plate in a 5% CO2, 37 &#176;C incubator for another 2 days before harvesting for analysis.</li>
</ol>
2. Prepare solutions for staining (Table 1)
3. Stain DLBCL cells with different senescence markers
NOTE: Cell samples stained with individual markers (i.e., pacific blue-EdU, C12FDG, or Alexa Fluor 647-&#947;H2AX) are prepared to generate a compensation matrix to correct the fluorescence spillover during measurement. Although highly suggested, this step could be suspended when there is an omittable overlap (compensation coefficient value &#8804; 0.1) of the emission spectra among different fluorophores. However, users must determine standardized compensation steps when using different instruments and fluorescent panels.
<ol>
	<li>Add 10 mM EdU solution at a ratio of 1:1,000 into the DLBCL cell culture generated from step 1.6 (final EdU concentration is 10 &#181;M). Gently rock the plate to mix and incubate in a 5% CO2, 37 &#176;C incubator for 3 h.</li>
	<li>Take the plate out of the incubator and add 100 mM chloroquine solution to a final concentration of 75 &#181;M (see discussion). Gently rock the plate to mix and incubate in a 5% CO2, 37 &#176;C incubator for 30 min.</li>
	<li>Take the plate out of the incubator and add 20 mM C12FDG solution at 1: 1,000 to a final C12FDG concentration of 20 &#181;M. Gently rock the plate to mix and incubate in a 5% CO2, 37 &#176;C incubator for 1 h.</li>
	<li>Take the plate out of the incubator and add 100 mM 2-phenylethyl-&#946;-D-thiogalactoside (PETG) solution at 1:50 to stop the fSA-&#946;-gal staining (final PETG concentration of 2 mM). Gently rotate the plate to mix.</li>
	<li>Transfer the cells to 15 mL sterile centrifuge tubes and spin at 100 &#215; g, 4 &#176;C for 5 min. Discard the supernatant and wash the cells with 4 mL of phosphate-buffered saline (PBS).</li>
	<li>Repeat the PBS washing step. Discard the supernatant and resuspend the cell pellets in 500 &#181;L of 4% paraformaldehyde fixation solution.</li>
	<li>After 10 min incubation at room temperature, centrifuge at 250 &#215; g, room temperature for 5 min. Discard the supernatant and wash cells with 4 mL of PBS.</li>
	<li>Repeat the PBS washing step. Discard the supernatant, resuspend the cell pellet in 200 &#181;L of saponin permeabilization buffer and transfer the suspension to a new 1.5 mL tube. After 10 min incubation at room temperature, centrifuge at 250 &#215; g, room temperature for 5 min.</li>
	<li>Discard the supernatant and resuspend the cell pellets in 200 &#181;L of primary antibody solution (1:500 &#947;H2AX antibody in antibody incubation solution). Incubate at 4 &#176;C overnight in the dark.</li>
	<li>Centrifuge the tubes at 250 &#215; g, 4 &#176;C for 5 min. Discard the supernatant and wash with 100 &#181;L of saponin wash solution.</li>
	<li>Repeat the washing step an additional two times. Discard the supernatant and resuspend the cell pellets in 500 &#181;L of EdU detection cocktail.</li>
	<li>Incubate at room temperature for 30 min in the dark. Centrifuge at 250 &#215; g, room temperature for 5 min. Discard the supernatant and wash with 1 mL of saponin wash solution.</li>
	<li>Repeat the washing step two times. Discard the supernatant and resuspend the cell pellets in 20-50 &#181;L of PBS. Proceed to section 4 for sample measurement.</li>
</ol>
4. Imaging senescence markers using the imaging flow cytometer system
<ol>
	<li>Empty the waste fluid bottle. Check the levels of speed beads, sterilizer, cleaner, debubbler, sheath, and rinse reagents (deionized water) to ensure sufficient fluids before turning on the instrument (see the Table of Materials).</li>
	<li>Turn on the instrument and imaging software (see the software interface in Figure 1A).</li>
	<li>Click on the Startup button to initialize fluidics and system calibration. 
	NOTE: This procedure takes approximately 45 min.</li>
	<li>Set the magnification to 40x, set fluidics speed to low, and turn on the lasers needed in the experiment. Turn on 405 nm, 488 nm, and 642 nm lasers to measure EdU-pacific blue, C12FDG, and Alexa Fluor 647-&#947;H2AX (or Alexa Fluor 647-Ki67), respectively. Set Ch6 for scatter channel, and Ch1 and Ch9 for brightfield.</li>
	<li>Start with the sample expected to have the highest fluorescence to set up the intensity of the lasers. Gently flip the sample tube to mix. Open the tube lid, and insert the sample tube onto the dock. Click on Load to start.</li>
	<li>Open a scatter plot and select the features Area_M01 and Aspect Ratio_M01 for the X- and Y-axes, respectively. Set a gate above aspect ratio of 0.5 to exclude doublets and cell aggregates below and on the right side, and the speed bead population on the left side (Figure 1B).</li>
	<li>Open a histogram plot and select the feature Gradient RMS_M01_Ch01 for the X-axis. Choose the singlet population and set the gate to select for focused cells (Figure 1C). 
	NOTE: The imaging system will automatically use speed beads to adjust the focus for imaging. However, it is recommended to select the right half of the histogram peak for the best-focused population.</li>
	<li>Open a histogram plot and select Raw Max Pixel Intensities for X-axis for each color channel (Ch2, 7, and 11). Adjust the laser powers (i.e., 488 nm, 405 nm, and 642 nm lasers for Ch2, 7, and 11, respectively), so each fluorochrome has a Raw Max Pixel value between 100 and 4,000 to avoid oversaturation. 
	NOTE: For this experiment, the laser power setting is 50 mW, 200 mW, and 50 mW for lasers 488 nm, 405 nm, and 642 nm, respectively.</li>
	<li>Choose the focused population to record and click on Acquire to measure the DLBCL samples with consistent settings. When changing samples for measurement, click on Return to recover the sample tube. Press Load to discard the sample.</li>
	<li>After all the samples are measured, turn off the brightfield and scatter laser. Measure single-color control samples to generate a compensation matrix.</li>
	<li>Click on Shutdown to close the imaging system.</li>
	<li>Analyze the data in the image analysis software.
	<ol>
		<li>Use the Spot Wizard tool of the image analysis software to automatically count and quantify nuclear &#947;H2AX foci in live-cell images. Select two cell populations (one with high and one with low spot count) to train the spot wizard for further automatic spot count analysis.</li>
	</ol>
	</li>
</ol>

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The authors have no conflicts of interest to disclose.

This method examined the senescence-entering capability of four different DLBCL cell lines upon chemotherapy treatment, with bright-field imaging and flow cytometry-based quantification. On a single-cell level, we successfully detected major C12FDG+EdU-Ki67+ senescent populations in treated KARPAS422 and WSU-DLCL2 cells, and to a lesser extent in OCI-LY1 cells, while the SU-DHL6 cell line was resistant to the treatment. The difference in senescence-entering capability among cel...

A variety of stimuli can trigger cellular senescence, causing cells to enter a state of stable cell cycle arrest. These stimuli include intrinsic signaling changes or extrinsic stresses. Intrinsic signals include progressive telomere shortening, changes in telomere structure, epigenetic modification, proteostasis disorders, mitochondrial dysfunction, and activation of oncogenes. Extrinsic stresses include inflammatory and/or tissue damage signals, radiation or chemical treatment, and nutritional deprivation1,2,3,4. Among distinct types of senescence, the most commonly seen and well-studied are replicative senescence, oncogene-induced senescence (OIS), radiation-induced senescence, and therapy-induced senescence (TIS). OIS is an acute cellular response to genotoxic damage caused by replicative stress generated by aberrant oncogene activation and can to some extent prevent the pathological progression from a preneoplastic lesion to a full-blown tumor. TIS happens when tumor cells are stressed by chemotherapeutic drugs or ionizing radiation5,6.
Senescence is considered a double-edged sword in pathology due to its highly dynamic nature. It was initially described as a beneficial tumor-suppressive mechanism to remove damaged cells from the circulating pool of dividing cells, safeguarding the normal function of organs and inhibiting tumor growth7,8,9. However, emerging evidence has suggested a dark side of senescence. Senescent cells secrete proinflammatory cytokines, known as senescence-associated secretory phenotype (SASP), leading to fibrosis and malfunctional organs and promoting tumor initiation and progression10. Moreover, senescent cancer cells undergo epigenetic and gene-expression reprogramming in parallel with chromatin remodeling and activation of a sustained DNA-damage response (DDR)11,12, newly acquiring new cancer-stem-cell properties3. Although senescence-capable tumors respond better to therapeutic intervention compared to senescence-incapable ones13, the persistence of senescent cells may lead to a poor long-term prognosis if they are not effectively identified and eliminated by senolytic drugs5. Either way, a reliable method to assess senescence is of significant clinical interest, not only for the prognosis of therapy treatment but also for the development of novel strategies targeting senescent cells.
Regardless of different triggers, senescent cells exhibit some common features, including enlarged, flattened, multinucleated morphology with big vacuoles, significantly expanded nuclei, formation of H3K9me3-rich senescence-associated heterochromatin (SAHF) in the nucleus, persistent accumulation of DNA damage marker &#947;H2AX foci, activated p53-p21CIP1 and Rb-p16INK4a cell cycle regulatory mechanisms, stable G1 cell cycle arrest, massive induction of SASP, and elevated senescence-associated &#946;-galactosidase (SA-&#946;-gal) activity14. Since no single marker is sufficient to define senescence, enzymatic staining for SA-&#946;-gal activity, which is considered the gold standard for senescence detection, is usually combined with immunohistochemical staining for H3K9me3 and Ki67 to detect TIS15. However, chemical chromogenic-based SA-&#946;-gal is difficult to quantify. Here, we combined 5-dodecanoylaminofluorescein-di-&#946;-D-galactopyranoside (C12FDG) fluorescence-based SA-&#946;-gal (fSA-&#946;-gal) detection with immunofluorescent staining for &#947;H2AX and EdU-incorporated DNA to identify C12FDG+EdU-&#947;H2AX+ senescent cells using the advanced imaging flow cytometer system, which combines the speed, sensitivity and detailed single-cell images with spatial information that cannot be provided by flow cytometry and microscopy. This method enables rapid generation of high-resolution images allowing for the positioning and quantification of fluorescent signals within cells, while licensing the swift analysis of multiple samples by building standard pipelines.

<table border="1" fo:keep-together.within-page="1" fo:keep-with-next.within-page="always">
	<tbody>
		<tr>
			<td>Alexa Fluor 647 anti-H2A.X Phospho (Ser139) Antibody</td>
			<td>Biolegend</td>
			<td>613407</td>
			<td></td>
		</tr>
		<tr>
			<td>Anti-Ki-67 Mouse Monoclonal Antibody (Alexa Fluor 647)</td>
			<td>Biolegend</td>
			<td>350509</td>
			<td></td>
		</tr>
		<tr>
			<td>C12FDG (5-Dodecanoylaminofluorescein Di-&#946;-D-Galactopyranoside)</td>
			<td>Fisher Scientific</td>
			<td>11590276</td>
			<td></td>
		</tr>
		<tr>
			<td>Chloroquin -diphosphat</td>
			<td>Sigma aldrich</td>
			<td>C6628</td>
			<td></td>
		</tr>
		<tr>
			<td>Cleanser (Coulter Clenz)</td>
			<td>Beckman Coulter</td>
			<td>8546929</td>
			<td></td>
		</tr>
		<tr>
			<td>Click-iT EdU Pacific Blue Flow Cytometry Assay Kit</td>
			<td>Thermo Scientific</td>
			<td>C10418</td>
			<td></td>
		</tr>
		<tr>
			<td>Daunorubicin</td>
			<td>Medchemexpress</td>
			<td>HY-13062A</td>
			<td></td>
		</tr>
		<tr>
			<td>Debubbler (70% Isopropanol)</td>
			<td>Millipore</td>
			<td>1.3704</td>
			<td></td>
		</tr>
		<tr>
			<td>Image Analysis software (Amnis&#160;IDEAS&#160;6.3)</td>
			<td>Luminex</td>
			<td>CN-SW69-12</td>
			<td></td>
		</tr>
		<tr>
			<td>Instrument and imaging software (Amnis&#160;ImageStreamX&#160;Mk II Imaging Flow Cytometer System and INSPIRE software)</td>
			<td>Luminex</td>
			<td>100220</td>
			<td></td>
		</tr>
		<tr>
			<td>KARPAS</td>
			<td>DSMZ</td>
			<td>ACC 31</td>
			<td></td>
		</tr>
		<tr>
			<td>mafosfamide cyclohexylamine</td>
			<td>Niomech</td>
			<td>D-17272</td>
			<td></td>
		</tr>
		<tr>
			<td>OCI-LY1</td>
			<td>DSMZ</td>
			<td>ACC 722</td>
			<td></td>
		</tr>
		<tr>
			<td>Paraformaldehyde</td>
			<td>Fisher Scientific</td>
			<td>11473704</td>
			<td></td>
		</tr>
		<tr>
			<td>PETG (2-Phenylethyl-&#946;-D-thiogalactosid)&#160;</td>
			<td>Sigma aldrich</td>
			<td>P4902</td>
			<td></td>
		</tr>
		<tr>
			<td>saponin</td>
			<td>Sigma aldrich</td>
			<td>47036</td>
			<td></td>
		</tr>
		<tr>
			<td>Sheath</td>
			<td>Millipore</td>
			<td>BSS-1006-B</td>
			<td></td>
		</tr>
		<tr>
			<td>SpeedBead Kit for ImageStream</td>
			<td>Luminex</td>
			<td>400041</td>
			<td></td>
		</tr>
		<tr>
			<td>Sterilizer (0.4-0.7% Hypochlorite)</td>
			<td>VWR</td>
			<td>JT9416-1</td>
			<td></td>
		</tr>
		<tr>
			<td>SU-DHL6</td>
			<td>DSMZ</td>
			<td>ACC 572</td>
			<td></td>
		</tr>
		<tr>
			<td>WSU-DLCL2</td>
			<td>DSMZ</td>
			<td>ACC 575</td>
			<td></td>
		</tr>
	</tbody>
</table>

simultaneous imaging and flow-cytometry-based detection of multiple fluorescent senescence markers in therapy-induced senescent cancer cells

Chemotherapeutic drugs can induce irreparable DNA damage in cancer cells, leading to apoptosis or premature senescence. Unlike apoptotic cell death, senescence is a fundamentally different machinery restraining&#160;propagation of cancer cells. Decades of scientific studies have revealed the complex pathological effects of senescent cancer cells in tumors and microenvironments that modulate cancer cells and stromal cells. New evidence suggests that senescence is a potent prognostic factor during cancer treatment, and therefore rapid and accurate detection of senescent cells in cancer samples is essential. This paper presents a method to visualize and detect therapy-induced senescence (TIS) in cancer cells. Diffuse large B-cell lymphoma (DLBCL) cell lines were treated with mafosfamide (MAF) or daunorubicin (DN) and examined for the senescence marker, senescence-associated &#946;-galactosidase (SA-&#946;-gal), the DNA synthesis marker 5-ethynyl-2&#8242;-deoxyuridine (EdU), and the DNA damage marker gamma-H2AX (&#947;H2AX). Flow cytometer imaging can help generate high-resolution single-cell images in a short period of time to simultaneously visualize and quantify the three markers in cancer cells.

A compensation matrix was generated using image analysis software by loading recorded data of single-color control samples. As shown in Supplemental Figure S1, a non-negligible (coefficient value &#8805; 0.1) light spillover from EdU to C12FDG was detected with crosstalk coefficient value 0.248, while the crosstalk among other channels was not significant. Four different DLBCL cell lines were treated with 5 &#181;g/mL MAF or 20 ng/mL DN to induce cellular senescence and analyzed using either c...

Watch this Scientific Journal Video about Simultaneous Imaging and Flow-Cytometry-based Detection of Multiple Fluorescent Senescence Markers in Therapy-Induced Senescent Cancer Cells at JoVE.com

Simultaneous Imaging and Flow-Cytometry-based Detection of Multiple Fluorescent Senescence Markers in Therapy-Induced Senescent Cancer Cells

Here we present a flow cytometry-based method for visualization and quantification of multiple senescence-associated markers in single cells.

Chemotherapeutic drugs can induce irreparable DNA damage in cancer cells, leading to apoptosis or premature senescence. Unlike apoptotic cell death, ...

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2.8K Views.  Johannes Kepler University Linz. Here we present a flow cytometry-based method for visualization and quantification of multiple senescence-associated markers in single cells.

Video: Simultaneous Imaging and Flow-Cytometry-based Detection of Multiple Fluorescent Senescence Markers in Therapy-Induced Senescent Cancer Cells

Fluorescent Orthotopic Mouse Model of Pancreatic Cancer

Pancreatic cancer remains one of the cancers for which survival has not improved substantially in the last few decades. Only 7% of diagnosed patients will survive longer than five years. In order to understand and mimic the microenvironment of pancreatic tumors, we utilized a murine orthotopic model of pancreatic cancer that allows non-invasive imaging of tumor progression in real time. Pancreatic cancer cells expressing green fluorescent protein (PANC-1 GFP) were suspended in basement membrane matrix, high concentration, (e.g., Matrigel HC) with serum-free media and then injected into the tail of the pancreas via laparotomy. The cell suspension in the high concentration basement membrane matrix becomes a gel-like substance once it reaches room temperature; therefore, it gels when it comes in contact with the pancreas, creating a seal at the injection site and preventing any cell leakage. Tumor growth and metastasis to other organs are monitored in live animals by using fluorescence. It is critical to use the appropriate filters for excitation and emission of GFP. The steps for the orthotopic implantation are detailed in this article so researchers can easily replicate the procedure in nude mice. The main steps of this protocol are preparation of the cell suspension, surgical implantation, and whole body fluorescent in vivo imaging. This orthotopic model is designed to investigate the efficacy of novel therapeutics on primary and metastatic tumors.

A procedure to implant green fluorescent protein-expressing pancreatic cancer cells (PANC-1 GFP) orthotopically into the pancreas of Balb-c Ola Hsd-Fox1nu mice to assess tumor progression and metastasis is presented here.

Pancreatic cancer remains one of the cancers for which survival has not improved substantially in the last few decades. Only 7% of diagnosed patients will ...

Flow Cytometry-based Drug Screening System for the Identification of Small Molecules That Promote Cellular Differentiation of Glioblastoma Stem Cells

Glioblastoma (GBM) is the most common and most lethal primary brain tumor in adults, causing roughly 14,000 deaths each year in the U.S. alone. Median survival following diagnosis is less than 15 months with maximal surgical resection, radiation, and temozolomide chemotherapy. The challenges inherent in developing more effective GBM treatments have become increasingly clear, and include its unyielding invasiveness, its resistance to standard treatments, its genetic complexity and molecular adaptability, and subpopulations of GBM cells with phenotypic similarities to normal stem cells, herein referred to as glioblastoma stem cells (GSCs). Because GSCs are required for tumor growth and progression, differentiation-based therapy represents a viable treatment modality for these incurable neoplasms. 
The following protocol describes a collection of procedures to establish a high throughput screening platform aimed at the identification of small molecules that promote GSC astroglial differentiation. At the core of the system is a glial fibrillary acidic protein (GFAP) differentiation reporter-construct. The protocol contains the following general procedures: (1) establishing GSC differentiation reporter lines; (2) testing/validating the relevance of the reporter to GSC self-renewal/clonogenic capacity; and (3) high-capacity flow-cytometry based drug screening. 
The screening platform provides a straightforward and inexpensive approach to identify small molecules that promote GSCs differentiation. Furthermore, utilization of libraries of FDA-approved drugs holds the potential for the identification of agents that can be repurposed more rapidly. Also, therapies that promote cancer stem cell differentiation are expected to work synergistically with current "standard of care" therapies that have been shown to target and eliminate primarily more differentiated cancer cells.

An efficient screening protocol is presented for the identification of small molecules that promote astroglial differentiation in glioblastoma stem cells (GSCs). The assay is based on a stem cell differentiation reporter whereby the expression of the enhanced GFP (eGFP) is driven by the human GFAP promoter.

Glioblastoma (GBM) is the most common and most lethal primary brain tumor in adults, causing roughly 14,000 deaths each year in the U.S. alone. Median ...

Multimodal Bioluminescent and Positronic-emission Tomography/Computational Tomography Imaging of Multiple Myeloma Bone Marrow Xenografts in NOG Mice

Multiple myeloma (MM) tumors engraft in the bone marrow (BM) and their survival and progression are dependent upon complex molecular and cellular interactions that exist within this microenvironment. Yet the BM microenvironment cannot be easily replicated in vitro, which potentially limits the physiologic relevance of many in vitro and ex vivo experimental models. These issues can be overcome by utilizing a xenograft model in which luciferase (LUC)-transfected 8226 MM cells will specifically engraft in the mouse skeleton. When these mice are given the appropriate substrate, D-luciferin, the effects of therapy on tumor growth and survival can be analyzed by measuring changes in the bioluminescent images (BLI) produced by the tumors in vivo. This BLI data combined with positronic-emission tomography/computational tomography (PET/CT) analysis using the metabolic marker 2-deoxy-2-(18F)fluoro-D-glucose (18F-FDG) is used to monitor changes in tumor metabolism over time. These imaging platforms allow for multiple noninvasive measurements within the tumor/BM microenvironment.

Here we use bioluminescent, X-ray, and positron-emission tomography/computed tomography imaging to study how inhibiting mTOR activity impacts bone marrow-engrafted myeloma tumors in a xenograft model. This allows for physiologically relevant, non-invasive, and multimodal analyses of the anti-myeloma effect of therapies targeting bone marrow-engrafted myeloma tumors in vivo.

Multiple myeloma (MM) tumors engraft in the bone marrow (BM) and their survival and progression are dependent upon complex molecular and cellular ...

Detection of Protease Activity by Fluorescent Peptide Zymography

The purpose of this method is to measure the proteolytic activity of complex biological samples. The samples are separated by molecular weight using electrophoresis through a resolving gel embedded with a degradable substrate. This method differs from traditional gel zymography in that a quenched fluorogenic peptide is covalently incorporated into the resolving gel instead of full length proteins, such as gelatin or casein. Use of the fluorogenic peptides enables direct detection of proteolytic activity without additional staining steps. Enzymes within the biological samples cleave the quenched fluorogenic peptide, resulting in an increase in fluorescence. The fluorescent signal in the gels is then imaged with a standard fluorescent gel scanner and quantified using densitometry. The use of peptides as the degradable substrate greatly expands the possible proteases detectable with zymographic techniques.

Here, we present a detailed protocol for a modified zymographic technique in which fluorescent peptides are used as the degradable substrate in place of native proteins. Electrophoresis of biological samples in fluorescent peptide zymograms enables detection of a wider range of proteases than previous zymographic techniques.

The purpose of this method is to measure the proteolytic activity of complex biological samples. The samples are separated by molecular weight using ...

Optimization, Design and Avoiding Pitfalls in Manual Multiplex Fluorescent Immunohistochemistry

Microenvironment evaluation of intact tissue for analysis of cell infiltration and spatial organization are essential in understanding the complexity of disease processes. The principle techniques used in the past include immunohistochemistry (IHC) and immunofluorescence (IF) which enable visualization of cells as a snapshot in time using between 1 and 4 markers. Both techniques have shortcomings including difficulty staining poorly antigenic targets and limitations related to cross-species reactivity. IHC is reliable and reproducible, but the nature of the chemistry and reliance on the visible light spectrum allows for only a few markers to be used and makes co-localization challenging. Use of IF broadens potential markers but typically relies on frozen tissue due to the extensive tissue autofluorescence following formalin fixation. Flow cytometry, a technique that enables simultaneous labeling of multiple epitopes, abrogates many of the deficiencies of IF and IHC, however, the need to examine cells as a single cell suspension loses the spatial context of cells discarding important biologic relationships. Multiplex fluorescent immunohistochemistry (mfIHC) bridges these technologies allowing for multi-epitope cellular phenotyping in formalin fixed paraffin embedded (FFPE) tissue while preserving the overall microenvironment architecture and spatial relationship of cells within intact undisrupted tissue. High fluorescent intensity fluorophores that covalently bond to the tissue epitope enables multiple applications of primary antibodies without worry of species specific cross-reactivity by secondary antibodies. Although this technology has been proven to produce reliable and accurate images for the study of disease, the process of creating a useful mfIHC staining strategy can be time consuming and exacting due to extensive optimization and design. In order to make robust images that represent accurate cellular interactions in-situ and to mitigate the optimization period for manual analysis, presented here are methods for slide preparation, optimizing antibodies, multiplex design as well as errors commonly encountered during the staining process.

Multiplex fluorescent immunohistochemistry is an emerging technology that enables the visualization of multiple cell types within intact formalin-fixed, paraffin embedded (FFPE) tissue. Presented are guidelines for ensuring a successful 7-color multiplex with instructions for optimizing antibodies and reagents, preparing slides, design and tips for avoiding common problems.

Microenvironment evaluation of intact tissue for analysis of cell infiltration and spatial organization are essential in understanding the complexity of ...

Detection of Lung Tumor Progression in Mice by Ultrasound Imaging

With ~1.6 million victims per year, lung cancer contributes tremendously to the worldwide burden of cancer. Lung cancer is partly driven by genetic alterations in oncogenes such as the KRAS oncogene, which constitutes ~25% of lung cancer cases. The difficulty in therapeutically targeting KRAS-driven lung cancer partly stems from having poor models that can mimic the progression of the disease in the lab. We describe a method that permits the relative quantification of primary KRAS lung tumors in a Cre-inducible LSL-KRAS G12D mouse model via ultrasound imaging. This method relies on brightness (B)-mode acquisition of the lung parenchyma. Tumors that are initially formed in this model are visualized as B-lines and can be quantified by counting the number of B-lines present in the acquired images. These would represent the relative tumor number formed on the surface of the mouse lung. As the formed tumors develop with time, they are perceived as deep clefts within the lung parenchyma. Since the circumference of the formed tumor is well-defined, calculating the relative tumor volume is achieved by measuring the length and width of the tumor and applying them in the formula used for tumor caliper measurements. Ultrasound imaging is a non-invasive, fast and user-friendly technique that is often used for tumor quantifications in mice. Although artifacts may appear when obtaining ultrasound images, it has been shown that this imaging technique is more advantageous for tumor quantifications in mice compared to other imaging techniques such as computed tomography (CT) imaging and bioluminescence imaging (BLI). Researchers can investigate novel therapeutic targets using this technique by comparing lung tumor initiation and progression between different groups of mice.

This protocol describes the steps taken to induce KRAS lung tumors in mice as well as the quantification of formed tumors by ultrasound imaging. Small tumors are visualized in early timepoints as B-lines. At later timepoints, relative tumor volume measurements are achieved by the measurement tool in the ultrasound software.

With ~1.6 million victims per year, lung cancer contributes tremendously to the worldwide burden of cancer. Lung cancer is partly driven by genetic ...

In Vivo Targeting of Xenografted Human Cancer Cells with Functionalized Fluorescent Silica Nanoparticles in Zebrafish

Developing nanoparticles capable of detecting, targeting, and destroying cancer cells is of great interest in the field of nanomedicine. In vivo animal models are required for bridging the nanotechnology to its biomedical application. The mouse represents the traditional animal model for preclinical testing; however, mice are relatively expensive to keep and have long experimental cycles due to the limited progeny from each mother. The zebrafish has emerged as a powerful model system for developmental and biomedical research, including cancer research. In particular, due to its optical transparency and rapid development, zebrafish embryos are well suited for real-time in vivo monitoring of the behavior of cancer cells and their interactions with their microenvironment. This method was developed to sequentially introduce human cancer cells and functionalized nanoparticles in transparent Casper zebrafish embryos and monitor in vivo recognition and targeting of the cancer cells by nanoparticles in real time. This optimized protocol shows that fluorescently labeled nanoparticles, which are functionalized with folate groups, can specifically recognize and target metastatic human cervical epithelial cancer cells labeled with a different fluorochrome. The recognition and targeting process can occur as early as 30 min postinjection of the nanoparticles tested. The whole experiment only requires the breeding of a few pairs of adult fish and takes less than 4 days to complete. Moreover, zebrafish embryos lack a functional adaptive immune system, allowing the engraftment of a wide range of human cancer cells. Hence, the utility of the protocol described here enables the testing of nanoparticles on various types of human cancer cells, facilitating the selection of optimal nanoparticles in each specific cancer context for future testing in mammals and the clinic.

Described here is a method for utilizing zebrafish embryos to study the ability of functionalized nanoparticles to target human cancer cells in vivo. This method allows for the evaluation and selection of optimal nanoparticles for future testing in large animals and in clinical trials.

Developing nanoparticles capable of detecting, targeting, and destroying cancer cells is of great interest in the field of nanomedicine. In vivo animal ...

Immunofluorescence Imaging of DNA Damage and Repair Foci in Human Colon Cancer Cells

The purpose of the manuscript is to provide a step-by-step protocol for performing immunofluorescence microscopy to study the radiation-induced DNA damage response induced by neutron-gamma mixed-beam used in boron neutron capture therapy (BNCT). Specifically, the proposed methodology is applied for the detection of repair proteins activation which can be visualized as foci using antibodies specific to DNA double-strand breaks (DNA-DSBs). DNA repair foci were assessed by immunofluorescence in colon cancer cells (HCT-116) after irradiation with the neutron-mixed beam. DNA-DSBs are the most genotoxic lesions and are repaired in mammalian cells by two major pathways: non-homologous end-joining pathway (NHEJ) and homologous recombination repair (HRR). The frequencies of foci, immunochemically stained, for commonly used markers in radiobiology like &#947;-H2AX, 53BP1 are associated with DNA-DSB number and are considered as efficient and sensitive markers for monitoring the induction and repair of DNA-DSBs. It was established that &#947;-H2AX foci attract repair proteins, leading to a higher concentration of repair factors near a DSB. To monitor DNA damage at the cellular level, immunofluorescence analysis for the presence of DNA-PKcs representative repair protein foci from the NHEJ pathway and Rad52 from the HRR pathway was planned. We have developed and introduced a reliable immunofluorescence staining protocol for the detection of radiation-induced DNA damage response with antibodies specific for repair factors from NHEJ and HRR pathways and observed radiation-induced foci (RIF). The proposed methodology can be used for investigating repair protein that is highly activated in the case of neutron-mixed beam radiation, thereby indicating the dominance of the repair pathway.

Radiation-induced DNA damage response activated by neutron mixed-beam used in boron neutron capture therapy (BNCT) has not been fully established. This protocol provides a step-by-step procedure to detect radiation-induced foci (RIF) of repair proteins by immunofluorescence staining in human colon cancer cell lines after irradiation with the neutron-mixed beam.

The purpose of the manuscript is to provide a step-by-step protocol for performing immunofluorescence microscopy to study the radiation-induced DNA damage ...

In Vitro Evaluation of Oncogenic Transformation in Human Mammary Epithelial Cells

Tumorigenesis is a multi-step process in which cells acquire capabilities&#160;that allow their growth, survival, and dissemination under hostile conditions. Different tests seek to identify and quantify these hallmarks of cancerous cells; however, they often focus on a single aspect of cellular transformation and, in fact, multiple tests are required for their proper characterization. The purpose of this work is to provide researchers with a set of tools to assess cellular transformation in vitro from a broad perspective, thereby making it possible to draw sound conclusions.
A sustained proliferative signaling activation is the major feature of tumoral tissues and can be easily monitored under in vitro conditions by calculating the number of population doublings achieved over time. Besides, the growth of cells in 3D cultures allows their interaction with surrounding cells, resembling what occurs in vivo. This enables the evaluation of cellular aggregation and, together with immunofluorescent labeling of distinctive cellular markers, to obtain information on another relevant feature of tumoral transformation: the loss of proper organization. Another remarkable characteristic of transformed cells is their capacity to grow without attachment to other cells and to the extracellular matrix, which can be evaluated with the anchorage assay.
Detailed experimental procedures to evaluate cell growth rate, to perform immunofluorescent labeling of cell lineage markers in 3D cultures, and to test anchorage-independent cell growth in soft agar are provided. These methodologies are optimized for Breast Primary Epithelial Cells (BPEC) due to its relevance in breast cancer; however, procedures can be applied to other cell types after some adjustments.

This protocol provides experimental in vitro tools to evaluate the transformation of human mammary cells. Detailed steps to follow-up cell proliferation rate, anchorage-independent growth capacity, and distribution of cell lineages in 3D cultures with basement membrane matrix are described.

Tumorigenesis is a multi-step process in which cells acquire capabilities&#160;that allow their growth, survival, and dissemination under hostile ...

Longitudinal Intravital Imaging Through Clear Silicone Windows

Intravital microscopy (IVM) enables visualization of cell movement, division, and death at single-cell resolution. IVM through surgically inserted imaging windows is particularly powerful because it allows longitudinal observation of the same tissue over days to weeks. Typical imaging windows comprise a glass coverslip in a biocompatible metal frame sutured to the mouse&#8217;s skin. These windows can interfere with the free movement of the mice, elicit a strong inflammatory response, and fail due to broken glass or torn sutures, any of which may necessitate euthanasia. To address these issues, windows for long-term abdominal organ and mammary gland imaging&#160;were developed from a thin film of polydimethylsiloxane (PDMS), an optically clear silicone polymer previously used for cranial imaging windows. These windows can be glued directly to the tissues, reducing the time needed for insertion. PDMS is flexible, contributing to its durability in mice over time&#8212;up to 35 days have been tested. Longitudinal imaging is imaging of the same tissue region during separate sessions. A stainless-steel grid was embedded within the windows to localize the same region, allowing the visualization of dynamic processes (like mammary gland involution) at the same locations, days apart. This silicone window also allowed monitoring of single disseminated cancer cells developing into micro-metastases over time. The silicone windows used in this study are simpler to insert than metal-framed glass windows and cause limited inflammation of the imaged tissues. Moreover, embedded grids allow for straightforward tracking of the same tissue region in repeated imaging sessions.

An approach is here presented for long-term intravital imaging using optically clear, silicone windows that can be glued directly to the tissue/organ of interest and the skin.&#160;These windows are cheaper and more versatile than others currently used in the field, and the surgical insertion causes limited inflammation and distress to the animals.

Intravital microscopy (IVM) enables visualization of cell movement, division, and death at single-cell resolution. IVM through surgically inserted imaging ...