This work was supported by the philanthropic contributions of the John G. and Marie Stella Kenedy Memorial Foundation (Grant #0727033) and the Melanoma Research Alliance. The authors wish to thank the University of Texas MD Anderson Cancer Center Institutional Tissue Bank (ITB) for coordinating tissue distribution and collection and facilitating translational research, as well as Dr. Ignacio Wistuba, Dr. Victor Prieto, the MD Anderson Cancer Center Department of Pathology and the Melanoma Moon Shot Program. Finally, the authors wish to acknowledge all patients and families affected by melanoma.

Ethics statement: This protocol is approved by the University of Texas MD Anderson Cancer Center.
1. Specimen Procurement
<ol>
	<li>Collect research tissue samples from surplus tumor and related normal tissue10-12. Store specimens on wet ice to avoid autolysis.</li>
	<li>Send all tissues, medical devices and foreign bodies removed during a surgical procedure to the Department of Pathology for necessary examination in order to facilitate a pathologic diagnosis.</li>
	<li>Handle tissue allocated for research in accordance with applicable research and tissue banking policies and procedures. 
	NOTE: Biospecimen collection involves the coordination of pathologists, pathologists&#39; assistants, histotechnologists and tissue procurement specialists.</li>
</ol>
2. Pathology Quality Assurance (QA)&#160;
<ol>
	<li>Complete and verify patient records as an early QA measure and consult a pathologist to review diagnostic patient records (pathology reports, tissue slides, etc.) and tissue samples. Judge tissue samples on morphological characteristics of interest such as percentage of tumor, necrosis, tissue-tumor interface, etc. This is in accordance with biorepository best practices10-12.</li>
	<li>Following initial review, conduct periodic reviews of biorepository data and research samples during the entire length of stay of the biospecimen.</li>
	<li>Link results and annotations from histopathological and other investigations to the samples and provide this data to the researchers through a proprietary biorepository software system. &#160; 
	NOTE: QA processes ensure the integrity of both the clinical and technical aspects of biorepository operations.</li>
	<li>Perform genetic and molecular tests to verify and characterize the samples for clinical use.</li>
	<li>Collect and analyze data based on feedback from researchers who have been using the samples for laboratory experiments. Track samples using barcode technology. This electronic tracking system is also advocated in biorespository best practices10-12.</li>
</ol>
3. Specimen/Tissue Processing &#160;
<ol>
	<li>Always store fresh tissue specimens on wet ice, and process as quickly as possible, in order to limit changes induced by extraction of the tissue sample from its natural environment. Process normal tumor-matched and tumor tissue samples separately to avoid cross-contamination. 
	NOTE: Based on research protocols, biospecimen processing can involve collection of the specimens in one or more types of media.</li>
	<li>Before beginning the process, prepare a sterile Petri culture dish, a scalpel, as well as a needle or forceps for tissue processing. Ensure that tubes have been prepared, labeled, and laid out in order to limit time of sample processing (Figure 2).</li>
	<li>All relevant tissue information, such as patient name, number, treatment, date of surgery, and other relevant information as may be appropriate for the study, should be made readily accessible in an institutional tissue database. Limited patient information should be held in the lab in paper or spreadsheet form. 
	NOTE: Only collect biospecimen information relevant to the nature of the research viz., basic biomedical research, clinical research, translational research, etc. For disease-specific information, the biorepository staff should collect data deemed necessary by the current literature and governing organizations to ensure proper diagnosis and meaningful research. This includes but is not limited to tumor grades and cancer staging information.</li>
	<li>Plan all desired subsequent experiments in advance, to decide on the size of tissue sections required for each type of analysis, as well as the location of excisions. Ideally, although impossible, all analyses should be representative of the entire tissue section in order to account for tissue heterogeneity and limit bias of downstream analyses. Lay out all required items in advance as depicted in Figure 2.</li>
	<li>Place the tissue specimen in the open Petri culture dish, flat against the surface. 
	NOTE: Allow only authorized biorepository staff to handle identified samples and to review identified health data. Investigators should access only those patient identifiers as allowed by the signed informed consents and as regulated by the IRB. All specimens must be adequately labeled and should include at minimum, a unique tissue identification number and tissue type. Do not include any PHI in the labels, in accordance with HIPAA regulations.</li>
	<li>Inspect the sample from all angles, to gain a better understanding of its structure and dimensions. Pin the sample to the bottom of the dish with the needle, and proceed to bisect the tissue along its largest and best representative axis.</li>
	<li>Cut out a small piece of tissue and place it in a sterile 1.5 ml microcentrifuge tube containing 1ml of RNA-stabilizing solution. This sample can be placed on ice for the remainder of the process and stored at 4 &#176;C until needed. 
	NOTE: When working with RNA, gloves should always be worn, and RNAse-free filter tips should be used to limit chances of degradation and RNA contamination.</li>
	<li>Lay out an open and pre-labeled biopsy cassette in the lid of the Petri culture dish. Cut out a slice of tissue no thicker than 3 to 5 mm and transfer it to the cassette. Place the cassette in 10% Neutral Buffered Formalin (NBF) for a minimum of 72 hr. Transfer the cassette in 70% ethanol for long-term storage before paraffin-embedding. 
	NOTE: Labeling of cassettes should be carried out in pencil or with recommended markers as use of xylene during processing will otherwise erase labels.</li>
	<li>Cut out a piece of tissue and place it in a tissue mold. Cover the tissue section in optimal cutting temperature (OCT) compound, and freeze it immediately at -20 &#176;C for cryosectioning. This tissue section may be stored at -20 &#176;C until ready for cryosectioning.</li>
	<li>Cut out one or many pieces of tissue and transfer them to a 50 ml tube containing MACS buffer (1x phosphate buffered saline (PBS), 0.5% fetal bovine serum (FBS), 2 mM Ethylenediaminetetraacetic acid (EDTA)) for subsequent flow cytometry analysis. For flow cytometry, larger samples may be preferable as cells may be lost during tumor disassociation, cell fixation and permeabilization when required. Generally, this section may be taken at the end, once all other pieces have been processed. Leftover representative tumor sample may be used for flow cytometry. Optionally, this tube may be stored at 4 &#176;C O/N or used for flow cytometric staining immediately following digestion into a cell suspension (see Step 4 - Flow Cytometric Staining).</li>
	<li>Cut remainder of tissue into pieces no larger than a maximum size of 0.5 mm x 0.5 mm and transfer them to cryogenic vials for immediate freezing in liquid nitrogen. These snap-frozen samples may be used for future analyses and collaborative purposes. 
	NOTE: Extra care should be taken when working with liquid nitrogen as direct contact can cause severe injury. Eyes should be protected with safety glasses with side shields or with a face shield. Cryogenic gloves should also be worn to protect from liquid nitrogen burns caused by splashing and direct contact. Gloves should fit properly but be loose enough to be removed quickly should liquid nitrogen splash into them.</li>
</ol>
4. Flow Cytometric Staining
<ol>
	<li>Tissue Homogenization
	<ol>
		<li>Prepare digestion medium with DMEM (40 ml), DNase I (50 U/ml) and Collagenase I (2 mg/ml). Place fresh or O/N-stored tumor in MACS buffer in the lid of a Petri dish, and submerge with digestion medium. 
		NOTE: Different digestion methods exist, each with advantages (i.e., cell surface protein expression, viability). Ensure you have the proper method for your desired downstream application.</li>
		<li>Pin tumor to the bottom of the dish with a needle, and cut from the outside to center with a scalpel, until the tumor has a paste-like texture. Transfer tumor mix to a 50 ml tube, seal and place in a plastic bag to avoid leaks. Transfer tube to an incubator, and rotate at 225 RPM, 37 &#176;C, 1 hr.</li>
		<li>Filter tumor cell suspension through a 70&#181;m cell strainer. Centrifuge cell suspension at 250 x g, 4 &#176;C, 5 min. Resuspend cell pellet in 1 ml FACS buffer (500 ml PBS, 1 ml 0.5 M stock EDTA, 10 ml FCS or FBS).</li>
		<li>Count cells using a hemocytometer and re-suspend at a concentration of 1x107 cells/ml. Transfer 100 &#181;l per well (106 cells) in a 96 well round bottom plate for staining.</li>
	</ol>
	</li>
	<li>Viability and Antibody Staining
	<ol>
		<li>Add 200 &#181;l of viability stain solution to each well and mix. Incubate for 30 minutes, at 4 &#176;C, in the dark. Spin down cells at 250 x g, 4 &#176;C, 5 min, and aspirate supernatant.</li>
		<li>Add antibody mixture at recommended/titrated concentration (as per manufacturer) for surface antigens in 200 &#181;l of FACS buffer. Incubate cells at 4 &#176;C, 30 min, in the dark. Spin down cells at 250 x g, 4 &#176;C, 5 min, and aspirate supernatant.</li>
		<li>Wash with 200 &#181;l of FACS buffer, spin down cells at 250 x g, 4 &#176;C, 5 min, and aspirate supernatant. Resuspend cells in 200 &#181;l of FACS buffer and proceed to flow cytometer for acquisition and analysis. 
		NOTE : If performing intracellular flow cytometry staining, perform fixation and permeabilization steps and intracellular staining between steps 4.2.2 and 4.2.3. If performing cytokine staining, cells should be pre-activated preceding staining as recommended, and an inhibitor of intracellular protein transport and secretion such as monensin should be used during activation to ensure retention of soluble factors. Fixed cells may be stored short-term (one week) at 4 &#176;C in the dark prior to acquisition on a flow cytometer.</li>
	</ol>
	</li>
</ol>

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	<li>Lorsch, J. R., Collins, F. S., Lippincott-Schwartz, J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Cell+Biology.+Fixing+problems+with+cell+lines.">Cell Biology. Fixing problems with cell lines.</a> Science. 346, 1452-1453 (2014).</li><li>van der Worp, H. B., 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=Can+animal+models+of+disease+reliably+inform+human+studies.">Can animal models of disease reliably inform human studies.</a> , (2010).</li><li>McCabe, P. M., 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=Animal+models+of+disease.">Animal models of disease.</a> Physiol. Behav. 68, 501-507 (2000).</li><li>Woolf, S. H. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+meaning+of+translational+research+and+why+it+matters.">The meaning of translational research and why it matters.</a> JAMA. 299, 211-213 (2008).</li><li>Brockbank, K. G., Taylor, M. J. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Tissue+Preservation.">Tissue Preservation.</a> Advances in Biopreservation. , 157-159 (2006).</li><li>Bulmer, M., Gilbert, N. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=The+ethics+of+social+research.">The ethics of social research.</a> Researching social life. , 45-57 (2001).</li><li>Penslar, R. L. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> IRB guidebook. , (1993).</li><li>. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> MD Anderson Cancer Center Institutional Tissue Bank Standard Operating Procedures. 3, (2009).</li><li>Ruffell, B., 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=Leukocyte+composition+of+human+breast+cancer.">Leukocyte composition of human breast cancer.</a> Proc. of the Ntnl. Aca. of Sci. 109, 2796-2801 (2012).</li><li>Shapiro, H. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=.">.</a> Practical flow cytometry. , (2005).</li><li>Baker, A. F., 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=Stability+of+phosphoprotein+as+a+biological+marker+of+tumor+signaling.">Stability of phosphoprotein as a biological marker of tumor signaling.</a> Clin. Cancer Res. 11, 4338-4340 (2005).</li><li>Jacobs, S. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Sample+processing+considerations+for+detecting+copy+number+changes+in+formalin-fixed,+paraffin-embedded+tissues.">Sample processing considerations for detecting copy number changes in formalin-fixed, paraffin-embedded tissues.</a> Cold Spring Harbor protocols. 2012, 1195-1202 (2012).</li><li>Chung, J. -. Y., 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=Factors+in+tissue+handling+and+processing+that+impact+RNA+obtained+from+formalin-fixed,+paraffin-embedded+tissue.">Factors in tissue handling and processing that impact RNA obtained from formalin-fixed, paraffin-embedded tissue.</a> J. Histochem. Cytochem. 56, 1033-1042 (2008).</li><li>Guo, H., 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=An+efficient+procedure+for+protein+extraction+from+formalin-fixed,+paraffin-embedded+tissues+for+reverse+phase+protein+arrays.">An efficient procedure for protein extraction from formalin-fixed, paraffin-embedded tissues for reverse phase protein arrays.</a> Proteome Sci. 10, 1477-5956 (2012).</li><li>Feldman, A. 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=Advantages+of+mRNA+amplification+for+microarray+analysis.">Advantages of mRNA amplification for microarray analysis.</a> Biotechniques. 33, 906-914 (2002).</li><li>Francino, O., 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=Advantages+of+real-time+PCR+assay+for+diagnosis+and+monitoring+of+canine+leishmaniosis.">Advantages of real-time PCR assay for diagnosis and monitoring of canine leishmaniosis.</a> Vet Parasitol. 137, 214-221 (2006).</li><li>Grunberg-Manago, M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Messenger+RNA+stability+and+its+role+in+control+of+gene+expression+in+bacteria+and+phages.">Messenger RNA stability and its role in control of gene expression in bacteria and phages.</a> Annu. Rev. Genet. 33, 193-227 (1999).</li><li>Lesnik, E. A., Freier, S. M. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Relative+thermodynamic+stability+of+DNA,+RNA,+and+DNA:RNA+hybrid+duplexes:+relationship+with+base+composition+and+structure.">Relative thermodynamic stability of DNA, RNA, and DNA:RNA hybrid duplexes: relationship with base composition and structure.</a> Biochemistry. 34, 10807-10815 (1995).</li><li>MacBeath, G. <a target="_blank" href="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=PubMed&cmd=Search&doptcmdl=Citation&defaultField=Title+Word&term=Protein+microarrays+and+proteomics.">Protein microarrays and proteomics.</a> Nat Genet. 32, 526-532 (2002).</li></ol>

The authors have no conflicts of interest to disclose.

Ultimately, the methods of processing must be dictated by the desired hypothesis and anticipated technical assays to be performed (Figure 1). The following section serves as an overview to describe potential assays that may be performed on such tissue sections. It is by no means an exhaustive overview, but is intended to help guide sample processing methods and choice of downstream assays by describing techniques and listing their strengths and weaknesses.
Flow cytometry stain...

Medical research has benefited immensely from the study of both human cell lines and animal models. Cell lines allow for better control of components in a system, as well as use of cells from the proper organism. Working with human cells, while more representative, presents a drastically simplified snapshot of mechanisms which may be responsible for health and disease, because cell lines may not recapitulate the impact of other cells, stromal components, and organs which may affect responses1. On the other hand, animal models, although not entirely accurate in reproducing human disease and genetic heterogeneity, offer further insight by allowing for input of whole animal systems in most models2,3.
Shortcomings aside, both methods have their benefits and are complementary. However, the main goal remains to study human cells and organs, in a full body, multi-organ system. Accordingly, translational research has taken great strides in facilitating the study of human organs and tissues extracted from patients, in order to better grasp the mechanisms underlying disease. Translational research offers the advantage of studying the result of treatments and diseases in the entire body and in appropriate cells, thereby providing the best of both worlds between cell and animal work4.
Translational research is also not without flaws. Harvested specimens from human patients, upon removal from the host, are immediately subjected to ischemia and other external factors from which they would be otherwise protected. This may result in stress-induced molecular and genetic changes, and cause bias in subsequent studies. Therefore, much effort has been put into extracting and processing tissues through strict methods to best preserve organ and cell integrity for downstream studies5. Importantly, future applications must be considered closely when selecting methods of processing human samples, as certain methods may be detrimental to cellular components and signaling pathways while sparing others.
For any research involving human tissues, regulatory issues must be addressed. After the Tuskegee and Belmont reports, there was a growing acceptance of the fact that biomedical research was associated with inherent risks often resulting in unavoidable ethical dilemmas6. The need for national standards was recognized and the federal government created Institutional Review Boards (IRBs) as a means to uphold the principles of the Belmont Report (Respect for persons, Beneficence, Justice).
Any institution&#39;s IRB is a committee of doctors, researchers and community members who are responsible for protecting research participants. It requires that voluntary consent be obtained from all participants of biomedical research studies, and that this consent be documented in an informed consent form. The informed consent process aims to provide adequate information to a participant, so that an informed decision may be made on whether or not to enroll in a study, or to continue participation. In this regard, the informed consent document must have good readability and should be written in language that can be easily comprehended (6th to 8th grade reading level) by the target population. The possibility of coercion or undue influence must be minimized, and the subject must be given ample time to consider participation. The participant must also be allowed to exercise their right to withdraw consent at any stage during the course of the study without penalty. Voluntary informed consent is a mandatory pre-requisite for a subject&#39;s participation in research and it is also legally effective7.
As per the regulations for the protection of human subjects 21 CFR 50.25 (<a href="http://www.hhs.gov/ohrp/humansubjects/guidance/45cfr46.html">http://www.hhs.gov/ohrp/humansubjects/guidance/45cfr46.html</a>8), study participants must be informed of the purpose of the research, procedures involved in the research, alternatives to participation, all foreseeable risks and discomforts (including not only physical injury but also possible psychological, social, or economic harm, discomfort, or inconvenience), benefits of the research to society and possibly to the individual, length of time the subject is expected to participate, person to contact for answers to questions or in the event of a research-related injury or emergency, statement indicating that participation is voluntary and that refusal to participate will not result in any consequences or any loss of benefits such as a compromise in regular clinical care that the participant is otherwise entitled to receive as a result of his/her diagnoses, and finally a statement regarding the subject&#39;s right to confidentiality and right to withdraw from the study at any time without any consequences. Tissue specimens from participants who withdraw consent during the course of the study should not be banked and must be immediately exhausted. Waiver of one or more elements of informed consent may be obtained from the IRB for some research projects that could not practically be done without an alteration to the required elements or for studies where required elements are not applicable. Great care must be taken to ensure data confidentiality. The Health Insurance Portability and Accountability Act (HIPAA) is a federal law that prevents using or disclosing &#8220;Protected Health Information&#8221; (PHI) without written consent from the participants. PHI includes but is not limited to health information transmitted or maintained in any form or medium and includes fields that could be used to identify an individual9.
Through this work, we aim to outline the protocol that must be followed during tissue processing - including procurement, and storage and emphasize the importance of following these strict guidelines so as to minimize the biases that may result due to the stresses a tissue is subjected to upon extraction. We also endeavor to provide a brief overview of the downstream assays or analyses (Figure 1) that could be performed on such specimens so that readers may make a qualified judgment on what assay(s) best suits their needs.

<table><tbody><tr><td>Needles</td><td>BD</td><td>305167</td><td></td></tr><tr><td>Stainless steel disposable scalpels</td><td>Miltex</td><td>4-410</td><td></td></tr><tr><td>Tissue culture dish</td><td>Corning</td><td>353003</td><td></td></tr><tr><td>Biopsy Cassettes</td><td>Thermo Fisher</td><td>58931</td><td></td></tr><tr><td>RNA-stabilizing solution</td><td>Ambion</td><td>AM7021</td><td></td></tr><tr><td>1.5 ml Eppendorf tubes</td><td>Phenix</td><td>MAX-815</td><td></td></tr><tr><td>50 ml tubes</td><td>Corning</td><td>430290</td><td></td></tr><tr><td>10% Neutral Buffered Formalin</td><td>StatLab Medical Products</td><td>28600-5</td><td></td></tr><tr><td>Formalin Containers</td><td>Fisher Scientific</td><td>23-032-059</td><td></td></tr><tr><td>Optimal cutting temperature solution (OCT)</td><td>Sakura Finetek</td><td>4583</td><td></td></tr><tr><td>Tissue-Tek Cryomold</td><td>Sakura Finetek</td><td>4557</td><td></td></tr><tr><td>Dnase I</td><td>Roche</td><td>10104159001</td><td></td></tr><tr><td>Collagenase I</td><td>Roche</td><td>11088793001</td><td></td></tr><tr><td>70&amp;mu;m cell strainers</td><td>BD Bioscience</td><td>352350</td><td></td></tr><tr><td>96 well round bottom plates</td><td>Corning</td><td>3799</td><td></td></tr><tr><td>Live/Dead stain solution</td><td>Life Technologies</td><td>L34957</td><td></td></tr></tbody></table>

working with human tissues for translational cancer research

Medical research for human benefit is greatly impeded by the necessity for human tissues and subjects. However, upon obtaining consent for human specimens, precious samples must be handled with the greatest care in order to ensure integrity of organs, tissues, and cells to the highest degree. Unfortunately, tissue processing by definition requires extraction of tissues from the host, a change which can cause great cellular stress and have major repercussions on subsequent analyses. These stresses could result in the specimen being no longer representative of the site from which it was retrieved. Therefore, a strict protocol must be adhered to while processing these specimens to ensure representativeness. The desired assay(s) must also be taken into consideration in order to ensure that an optimal technique is used for sample processing. Outlined here is a protocol for tissue retrieval, processing and various analyses which may be performed on processed tissue in order to maximize downstream production from limited tissue samples.

The results displayed below depict flow cytometry gating strategy for broad immune phenotyping on a processed melanoma tumor. The day of staining, tissue sample was digested and homogenized with collagenase I and DNase I incubation for 60 min, at 37 &#176;C under 225 RPM rotation. Following digestion, cell suspension was filtered through a 70 &#181;m cell strainer to eliminate debris and cells were stained with fluorescence-labeled flow cytometry antibodies for immune cell phenotyping. Shown below (Figure 3</stro...

Watch this Scientific Journal Video about Working with Human Tissues for Translational Cancer Research at JoVE.com

Working with Human Tissues for Translational Cancer Research

Translational cancer research is dependent on extraction of human tissues. Much work has gone into optimizing extraction methods for ex vivo analysis. Here, we describe tissue processing methods allowing for maximal data output from limited samples.

Medical research for human benefit is greatly impeded by the necessity for human tissues and subjects. However, upon obtaining consent for human ...

working-with-human-tissues-for-translational-cancer-research

Universidad de Cartagena UDEC

Research

JoVE Journal

Medicine

9.8K Views.  University of Texas MD Anderson Cancer Center. Translational cancer research is dependent on extraction of human tissues. Much work has gone into optimizing extraction methods for ex vivo analysis. Here, we describe tissue processing methods allowing for maximal data output from limited samples.

Video: Working with Human Tissues for Translational Cancer Research

Utilization of Ultrasound Guided Tissue-directed Cellular Implantation for the Establishment of Biologically Relevant Metastatic Tumor Xenografts

Preclinical testing of anticancer therapies relies on relevant xenograft models that mimic the innate tendencies of cancer. Advantages of standard subcutaneous flank models include procedural ease and the ability to monitor tumor progression and response without invasive imaging. Such models are often inconsistent in translational clinical trials and have limited biologically relevant characteristics with low proclivity to produce metastasis, as there is a lack of a native microenvironment. In comparison, orthotopic xenograft models at native tumor sites have been shown to mimic the tumor microenvironment and replicate important disease characteristics such as distant metastatic spread. These models often require tedious surgical procedures with prolonged anesthetic time and recovery periods. To address this, cancer researchers have recently utilized ultrasound-guided injection techniques to establish cancer xenograft models for preclinical experiments, which allows for rapid and reliable establishment of tissue-directed murine models. Ultrasound visualization also provides a noninvasive method for longitudinal assessment of tumor engraftment and growth. Here, we describe the method for ultrasound-guided injection of cancer cells, utilizing the adrenal gland for NB and renal sub capsule for ES. This minimally invasive approach overcomes tedious open surgery implantation of cancer cells in tissue-specific locations for growth and metastasis, and abates morbid recovery periods. We describe the utilization of both established cell lines and patient derived cell lines for orthotopic injection. Pre-made commercial kits are available for tumor dissociation and luciferase tagging of cells. Injection of cell suspension using image-guidance provides a minimally invasive and reproducible platform for the creation of preclinical models. This method is utilized to create reliable preclinical models for other cancers such as bladder, liver and pancreas exemplifying its untapped potential for numerous cancer models.

Here, we present a protocol to utilize ultrasound-guided injection of neuroblastoma (NB) and Ewing's sarcoma (ES) cells (established cell lines and patient-derived tumor cells) at biologically relevant sites to create reliable preclinical models for cancer research.

Preclinical testing of anticancer therapies relies on relevant xenograft models that mimic the innate tendencies of cancer. Advantages of standard ...

Cancer Research

Tissue Engineering of a Human 3D in vitro Tumor Test System

Cancer is one of the leading causes of death worldwide. Current therapeutic strategies are predominantly developed in 2D culture systems, which inadequately reflect physiological conditions in vivo. Biological 3D matrices provide cells an environment in which cells can self-organize, allowing the study of tissue organization and cell differentiation. Such scaffolds can be seeded with a mixture of different cell types to study direct 3D cell-cell-interactions. To mimic the 3D complexity of cancer tumors, our group has developed a 3D in vitro tumor test system.	
	Our 3D tissue test system models the in vivo situation of malignant peripheral nerve sheath tumors (MPNSTs), which we established with our decellularized porcine jejunal segment derived biological vascularized scaffold (BioVaSc). In our model, we reseeded a modified BioVaSc matrix with primary fibroblasts, microvascular endothelial cells (mvECs) and the S462 tumor cell line. For static culture, the vascular structure of the BioVaSc is removed and the remaining scaffold is cut open on one side (Small Intestinal Submucosa SIS-Muc). The resulting matrix is then fixed between two metal rings (cell crowns).	
	Another option is to culture the cell-seeded SIS-Muc in a flow bioreactor system that exposes the cells to shear stress. Here, the bioreactor is connected to a peristaltic pump in a self-constructed incubator. A computer regulates the arterial oxygen and nutrient supply via parameters such as blood pressure, temperature, and flow rate. This setup allows for a dynamic culture with either pressure-regulated pulsatile or constant flow.	
	In this study, we could successfully establish both a static and dynamic 3D culture system for MPNSTs. The ability to model cancer tumors in a more natural 3D environment will enable the discovery, testing, and validation of future pharmaceuticals in a human-like model.

Tissue Engineering of a Human 3D in vitro Tumor Test System

Methods to create human 3D tumor tissues as test systems are described. These technologies are based on a decellularized Biological Vascularized Scaffold (BioVaSc), primary human cells and a tumor cell line, which can be cultured under static as well as under dynamic conditions in a flow bioreactor.

Cancer is one of the leading causes of death worldwide.  Current therapeutic strategies are predominantly developed in 2D culture  systems, which ...

Bioengineering

Preparation of Human Tissues Embedded in Optimal Cutting Temperature Compound for Mass Spectrometry Analysis

Sphingolipids are cellular components that have well-established roles in human metabolism and disease. Mass spectrometry can be used to determine whether sphingolipids are altered in a disease and investigate whether sphingolipids can be targeted clinically. However, properly powered prospective studies that acquire tissues directly from the surgical suite can be time consuming, and technically, logistically, and administratively challenging. In contrast, retrospective studies can take advantage of cryopreserved human specimens already available, usually in large numbers, at tissue biorepositories. Other advantages of procuring tissues from biorepositories include access to information associated with the tissue specimens including histology, pathology, and in some instances clinicopathological variables, all of which can be used to examine correlations with lipidomics data. However, technical limitations related to the incompatibility of optimal cutting temperature compound (OCT) used in the cryopreservation and mass spectrometry is a technical barrier for the analysis of lipids. However, we have previously shown that OCT can be easily removed from human biorepository specimens through cycles of washes and centrifugation without altering their sphingolipid content. We have also previously established that sphingolipids in human tissues cryopreserved in OCT are stable for up to 16 years. In this report, we outline the steps and workflow to analyze sphingolipids in human tissue specimens that are embedded in OCT, including washing tissues, weighing tissues for data normalization, the extraction of lipids, preparation of samples for analysis by liquid chromatography electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS), mass spectrometry data integration, data normalization, and data analysis.

Sphingolipids are bioactive metabolites with well-established roles in human disease. Characterizing alterations in tissues with mass-spectrometry can reveal roles in disease etiology or identify therapeutic targets. However, the OCT-compound used for cryopreservation in biorepositories interferes with mass-spectrometry. We outline methods to analyze sphingolipids in human tissues embedded in OCT with LC-ESI-MS/MS.

Sphingolipids are cellular components that have well-established roles in human metabolism and disease. Mass spectrometry can be used to determine whether ...

Testing Cancer Immunotherapeutics in a Humanized Mouse Model Bearing Human Tumors

Reversing the immunosuppressive nature of the tumor microenvironment is critical for the successful treatment of cancers with immunotherapy drugs. Murine cancer models are extremely limited in their diversity and suffer from poor translation to the clinic. To serve as a more physiological preclinical model for immunotherapy studies, this protocol has been developed to evaluate the treatment of human tumors in a mouse reconstituted with a human immune system. This unique protocol demonstrates the development of human immune system (HIS, &#34;humanized&#34;) mice, followed by implantation of a human tumor, either a cell-line derived xenograft (CDX) or a patient derived xenograft (PDX). HIS mice are generated by injecting CD34+ human hematopoietic stem cells isolated from umbilical cord blood into neonatal BRGS (BALB/c Rag2-/- IL2R&#947;C-/- NODSIRP&#945;) highly immunodeficient mice that are also capable of accepting a xenogeneic tumor. The importance of the kinetics and characteristics of the human immune system development and tumor implantation is emphasized. Finally, an in-depth evaluation of the tumor microenvironment using flow cytometry is described. In numerous studies using this protocol, it was found that the tumor microenvironment of individual tumors is recapitulated in HIS-PDX mice; &#34;hot&#34; tumors exhibit large immune infiltration while &#34;cold&#34; tumors do not. This model serves as a testing ground for combination immunotherapies for a wide range of human tumors and represents an important tool in the quest for personalized medicine.

This protocol outlines the generation of human immune system (HIS) mice for immuno-oncology studies. Instructions and considerations in the use of this model for testing human immunotherapeutics on human tumors implanted in this model are presented with an emphasis on characterizing the response of the human immune system to the tumor.

Reversing the immunosuppressive nature of the tumor microenvironment is critical for the successful treatment of cancers with immunotherapy drugs. Murine ...

Pancreatic Cancer-Derived Tumor Organoids and Fibroblasts from Fresh Tissue

Establishment of Pancreatic Cancer-Derived Tumor Organoids and Fibroblasts From Fresh Tissue

Tumor organoids are three-dimensional (3D) ex vivo tumor models that recapitulate the biological key features of the original primary tumor tissues. Patient-derived tumor organoids have been used in translational cancer research and can be applied to assess treatment sensitivity and resistance, cell-cell interactions, and tumor cell interactions with the tumor microenvironment. Tumor organoids are complex culture systems that require advanced cell culture techniques and culture media with specific growth factor cocktails and a biological basement membrane that mimics the extracellular environment. The ability to establish primary tumor cultures highly depends on the tissue of origin, the cellularity, and the clinical features of the tumor, such as the tumor grade. Furthermore, tissue sample collection, material quality and quantity, as well as correct biobanking and storage are crucial elements of this procedure. The technical capabilities of the laboratory are also crucial factors to consider. Here, we report a validated SOP/protocol that is technically and economically feasible for the culture of ex vivo tumor organoids from fresh tissue samples of pancreatic adenocarcinoma origin, either from fresh primary resected patient donor tissue or patient-derived xenografts (PDX). The technique described herein can be performed in laboratories with basic tissue culture and mouse facilities and is tailored for wide application in the translational oncology field.

Author Spotlight: Establishment of Pancreatic Cancer-Derived Tumor Organoids and Fibroblasts From Fresh Tissue  

Tumor organoids have revolutionized cancer research and the approach to personalized medicine. They represent a clinically relevant tumor model that allows researchers to stay one step ahead of the tumor in the clinic. This protocol establishes tumor organoids from fresh pancreatic tumor tissue samples and patient-derived xenografts of pancreatic adenocarcinoma origin.

Tumor organoids are three-dimensional (3D) ex vivo tumor models that recapitulate the biological key features of the original primary tumor tissues. ...

Preparing a Microfluidics-Based Vascularized Human Micro-Tumor Model

Establishing a Physiologic Human Vascularized Micro-Tumor Model for Cancer Research

A lack of validated cancer models that recapitulate the tumor microenvironment of solid cancers in vitro remains a significant bottleneck for preclinical cancer research and therapeutic development.&#160;To overcome this problem, we have developed the vascularized microtumor (VMT), or tumor chip, a microphysiological system that realistically models the complex human tumor microenvironment. The VMT forms de novo within a microfluidic platform by co-culture of multiple human cell types under dynamic, physiological flow conditions. This tissue-engineered micro-tumor construct incorporates a living perfused vascular network that supports the growing tumor mass just as newly formed vessels do in vivo. Importantly, drugs and immune cells must cross the endothelial layer to reach the tumor, modeling in vivo physiological barriers to therapeutic delivery and efficacy. Since the VMT platform is optically transparent, high-resolution imaging of dynamic processes such as immune cell extravasation and metastasis can be achieved with direct visualization of fluorescently labeled cells within the tissue. Further, the VMT retains in vivo tumor heterogeneity, gene expression signatures, and drug responses. Virtually any tumor type can be adapted to the platform, and primary cells from fresh surgical tissues grow and respond to drug treatment in the VMT, paving the way toward truly personalized medicine. Here, the methods for establishing the VMT and utilizing it for oncology research are outlined. This innovative approach opens new possibilities for studying tumors and drug responses, providing researchers with a powerful tool to advance cancer research.

Author Spotlight: Creating Human Vascularized Micro-Tumors as Models for Translational Cancer Research 

This protocol presents a physiologically relevant tumor-on-a-chip model to perform high-throughput basic and translational human cancer research, advancing drug screening, disease modeling, and personalized medicine approaches with a description of loading, maintenance, and evaluation procedures.

A lack of validated cancer models that recapitulate the tumor microenvironment of solid cancers in vitro remains a significant bottleneck for preclinical ...

Quantitative Mass Spectrometric Profiling of Cancer-cell Proteomes Derived From Liquid and Solid Tumors

In-depth analyses of cancer cell proteomes are needed to elucidate oncogenic pathomechanisms, as well as to identify potential drug targets and diagnostic biomarkers. However, methods for quantitative proteomic characterization of patient-derived tumors and in particular their cellular subpopulations are largely lacking. Here we describe an experimental set-up that allows quantitative analysis of proteomes of cancer cell subpopulations derived from either liquid or solid tumors. This is achieved by combining cellular enrichment strategies with quantitative Super-SILAC-based mass spectrometry followed by bioinformatic data analysis. To enrich specific cellular subsets, liquid tumors are first immunophenotyped by flow cytometry followed by FACS-sorting; for solid tumors, laser-capture microdissection is used to purify specific cellular subpopulations. In a second step, proteins are extracted from the purified cells and subsequently combined with a tumor-specific, SILAC-labeled spike-in standard that enables protein quantification. The resulting protein mixture is subjected to either gel electrophoresis or Filter Aided Sample Preparation (FASP) followed by tryptic digestion. Finally, tryptic peptides are analyzed using a hybrid quadrupole-orbitrap mass spectrometer, and the data obtained are processed with bioinformatic software suites including MaxQuant. By means of the workflow presented here, up to 8,000 proteins can be identified and quantified in patient-derived samples, and the resulting protein expression profiles can be compared among patients to identify diagnostic proteomic signatures or potential drug targets.

In-depth analyses of cancer cell proteomes facilitate identification of novel drug targets and diagnostic biomarkers. We describe an experimental workflow for quantitative analysis of (phospho-)proteomes in cancer cell subpopulations derived from liquid and solid tumors. This is achieved by combining cellular enrichment strategies with quantitative Super-SILAC-based mass spectrometry.

In-depth analyses of cancer cell proteomes are needed to elucidate oncogenic pathomechanisms, as well as to identify potential drug targets and diagnostic ...

Tumor Dissociation Protocol for Single-Cell RNA Sequencing Analysis

Dissociation of Human and Mouse Tumor Tissue Samples for Single-cell RNA Sequencing

Human tumor samples hold a plethora of information about their microenvironment and immune repertoire. Effective dissociation of human tissue samples into viable cell suspensions is a required input for the single-cell RNA sequencing (scRNAseq) pipeline. Unlike bulk RNA sequencing approaches, scRNAseq enables us to infer the transcriptional heterogeneity in tumor specimens at the single-cell level. Incorporating this approach in recent years has led to many discoveries, such as identifying immune and tumor cellular states and programs associated with clinical responses to immunotherapies and other types of treatments. Moreover, single-cell technologies applied to dissociated tissues can be used to identify accessible chromatin regions T and B cell receptor repertoire, and the expression of proteins, using DNA barcoded antibodies (CITEseq).
The viability and quality of the dissociated sample are critical variables when using these technologies, as these can dramatically affect the cross-contamination of single cells with ambient RNA, the quality of the data, and interpretation. Moreover, long dissociation protocols can lead to the elimination of sensitive cell populations and the upregulation of a stress response gene signature. To overcome these limitations, we devised a rapid universal dissociation protocol, which has been validated on multiple types of human and murine tumors. The process begins with mechanical and enzymatic dissociation, followed by filtration, red blood lysis, and live dead enrichment, suitable for samples with a low input of cells (e.g., needle core biopsies). This protocol ensures a clean and viable single-cell suspension paramount to the successful generation of Gel Bead-In Emulsions (GEMs), barcoding, and sequencing.

Author Spotlight: Exploring Strategies for Successful Immune Response Against Tumors

This protocol outlines the procedure for rapidly dissociating human and mouse tumor samples for single-cell RNA sequencing.

Human tumor samples hold a plethora of information about their microenvironment and immune repertoire. Effective dissociation of human tissue samples into ...

Methods for Culturing Human Femur Tissue Explants to Study Breast Cancer Cell Colonization of the Metastatic Niche

Bone is the most common site of breast cancer metastasis. Although it is widely accepted that the microenvironment influences cancer cell behavior, little is known about breast cancer cell properties and behaviors within the native microenvironment of human bone tissue.We have developed approaches to track, quantify and modulate human breast cancer cells within the microenvironment of cultured human bone tissue fragments isolated from discarded femoral heads following total hip replacement surgeries. Using breast cancer cells engineered for luciferase and enhanced green fluorescent protein (EGFP) expression, we are able to reproducibly quantitate migration and proliferation patterns using bioluminescence imaging (BLI), track cell interactions within the bone fragments using fluorescence microscopy, and evaluate breast cells after colonization with flow cytometry. The key advantages of this model include: 1) a native, architecturally intact tissue microenvironment that includes relevant human cell types, and 2) direct access to the microenvironment, which facilitates rapid quantitative and qualitative monitoring and perturbation of breast and bone cell properties, behaviors and interactions. A primary limitation, at present, is the finite viability of the tissue fragments, which confines the window of study to short-term culture. Applications of the model system include studying the basic biology of&#160;breast cancer and other bone-seeking malignancies within the metastatic niche, and developing therapeutic strategies to effectively target breast cancer cells in bone tissues.

Protocols are described for studying breast cancer cell migration, proliferation and colonization in a human bone tissue explant model system.

Bone is the most common site of breast cancer metastasis. Although it is widely accepted that the microenvironment influences cancer cell behavior, little ...

Long-term Culture of Human Breast Cancer Specimens and Their Analysis Using Optical Projection Tomography

Breast cancer is a leading cause of mortality in the Western world. It is well established that the spread of breast cancer, first locally and later distally, is a major factor in patient prognosis. Experimental systems of breast cancer rely on cell lines usually derived from primary tumours or pleural effusions. Two major obstacles hinder this research: (i) some known sub-types of breast cancers (notably poor prognosis luminal B tumours) are not represented within current line collections; (ii) the influence of the tumour microenvironment is not usually taken into account.
We demonstrate a technique to culture primary breast cancer specimens of all sub-types. This is achieved by using three-dimensional (3D) culture system in which small pieces of tumour are embedded in soft rat collagen I cushions. Within 2-3 weeks, the tumour cells spread into the collagen and form various structures similar to those observed in human tumours1. Viable adipocytes, epithelial cells and fibroblasts within the original core were evident on histology. Malignant epithelial cells with squamoid morphology were demonstrated invading into the surrounding collagen. Nuclear pleomorphism was evident within these cells, along with mitotic figures and apoptotic bodies.
We have employed Optical Projection Tomography (OPT), a 3D imaging technology, in order to quantify the extent of tumour spread in culture. We have used OPT to measure the bulk volume of the tumour culture, a parameter routinely measured during the neo-adjuvant treatment of breast cancer patients to assess response to drug therapy. 
Here, we present an opportunity to culture human breast tumours without sub-type bias and quantify the spread of those ex vivo. This method could be used in the future to quantify drug sensitivity in original tumour. This may provide a more predictive model than currently used cell lines.

We have developed a collagen-based in vitro assay which promotes proliferation and invasion from samples of all breast cancer subtypes. Optical Projection Tomography, a three dimensional microscopy technique was utilised to visualise and quantify tumour expansion. This assay may be used to quantify drug response of individual tumour samples.

Breast cancer is a leading cause of mortality in the Western world. It is well established that the spread of breast cancer, first locally and later ...

Working with Human Tissues for Translational Cancer Research

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Utilization of Ultrasound Guided Tissue-directed Cellular Implantation for the Establishment of Biologically Relevant Metastatic Tumor Xenografts

Tissue Engineering of a Human 3D in vitro Tumor Test System

Preparation of Human Tissues Embedded in Optimal Cutting Temperature Compound for Mass Spectrometry Analysis

Testing Cancer Immunotherapeutics in a Humanized Mouse Model Bearing Human Tumors

Establishment of Pancreatic Cancer-Derived Tumor Organoids and Fibroblasts From Fresh Tissue

Establishing a Physiologic Human Vascularized Micro-Tumor Model for Cancer Research

Quantitative Mass Spectrometric Profiling of Cancer-cell Proteomes Derived From Liquid and Solid Tumors

Dissociation of Human and Mouse Tumor Tissue Samples for Single-cell RNA Sequencing

Methods for Culturing Human Femur Tissue Explants to Study Breast Cancer Cell Colonization of the Metastatic Niche

Long-term Culture of Human Breast Cancer Specimens and Their Analysis Using Optical Projection Tomography