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Dessources K, Ferrando L, Zhou QC, Iasonos A, Abu-Rustum NR, Reis-Filho JS, Riaz N, Zamarin D, Weigelt B. Impact of immune infiltration signatures on prognosis in endometrial carcinoma is dependent on the underlying molecular subtype. Gynecol Oncol 2023; 171:15-22. [PMID: 36804617 PMCID: PMC10040428 DOI: 10.1016/j.ygyno.2023.01.037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 01/04/2023] [Accepted: 01/30/2023] [Indexed: 02/18/2023]
Abstract
OBJECTIVES Increased numbers of tumor infiltrating lymphocytes (TIL) in endometrial cancer (EC) are associated with improved survival, but it is unclear how this prognostic significance relates to the underlying EC molecular subtype. In this explorative hypothesis-generating study, we sought to define the immune signatures associated with the molecular subtypes of EC (i.e., POLE-mutated, microsatellite unstable (MSI-high), copy number (CN)-low, and CN-high) and to determine their correlation with patient outcomes. METHODS RNA-sequencing and molecular subtype data of 232 primary ECs were obtained from The Cancer Genome Atlas. Deconvolution of bulk gene expression data was performed using single sample Gene Set Enrichment Analysis (ssGSEA) and Cell type Identification By Estimating Relative Subsets Of known RNA Transcripts (CIBERSORT). The association of the resultant immune signatures with overall survival was determined across molecular subtypes. RESULTS Statistically significant differences in enrichment were identified in 16/30 and 6/23 immune gene sets by ssGSEA and CIBERSORT, respectively. Signature of CD8+ cells in ECs of CN-high molecular subtype was associated with improved overall survival by ssGSEA (p = 0.0108), while CD8 signatures did not appear to be prognostic in MSI-high (p = 0.74) or CN-low EC molecular subtypes (p = 0.793). Of all molecular subtypes, CN-high ECs exhibited the lowest levels of CD8+ T cell infiltration. Consistent with antigen-induced T cell activation and exhaustion, enrichment for immunomodulatory receptors was predominantly observed in ECs of MSI-high and POLE-mutated molecular subtypes. CONCLUSIONS Deconvolution of bulk gene expression data can be used to identify populations of immune infiltrated endometrial cancers with improved survival. These data support the existence of unique mechanisms of immune resistance within molecular subgroups of the disease.
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Affiliation(s)
- Kimberly Dessources
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Lorenzo Ferrando
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Current address: IRCCS - Ospedale Policlinico San Martino, Genova, Italy
| | - Qin C Zhou
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alexia Iasonos
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nadeem R Abu-Rustum
- Gynecology Service, Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jorge S Reis-Filho
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Nadeem Riaz
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Dmitriy Zamarin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, USA.
| | - Britta Weigelt
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.
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2
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Gonzalez VD, Huang YW, Fantl WJ. Mass Cytometry for the Characterization of Individual Cell Types in Ovarian Solid Tumors. Methods Mol Biol 2022; 2424:59-94. [PMID: 34918287 PMCID: PMC10509819 DOI: 10.1007/978-1-0716-1956-8_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Mass cytometry aka Cytometry by Time-Of-Flight (CyTOF) is one of several recently developed multiparametric single-cell technologies designed to address cellular heterogeneity within healthy and diseased tissue. Mass cytometry is an adaptation of flow cytometry in which antibodies are labeled with stable heavy metal isotopes and the readout is by time-of-flight mass spectrometry. With minimal spillover between channels, mass cytometry enables readouts of up to 60 parameters per single cell. Critically, mass cytometry can identify minority cell populations that are lost in bulk tissue analysis. Mass cytometry has been used to great effect for the study of immune cells. We have extended its use to examine single cells within disaggregated solid tissues, specifically freshly resected tubo-ovarian high-grade serous tumors. Here we detail our protocols designed to ensure the production of high-quality single-cell datasets. The methodology can be modified to accommodate the study of other solid tissues.
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Affiliation(s)
- Veronica D Gonzalez
- Baxter Laboratory for Stem Cell Biology, Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, USA
- 10X Genomics, Pleasanton, CA, USA
| | - Ying-Wen Huang
- Department of Urology, Stanford University School of Medicine, Stanford, CA, USA
| | - Wendy J Fantl
- Department of Urology, Department of Obstetrics and Gynecology, Stanford Comprehensive Cancer Institute, Stanford, CA, USA.
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3
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Kashyap A, Rapsomaniki MA, Barros V, Fomitcheva-Khartchenko A, Martinelli AL, Rodriguez AF, Gabrani M, Rosen-Zvi M, Kaigala G. Quantification of tumor heterogeneity: from data acquisition to metric generation. Trends Biotechnol 2021; 40:647-676. [PMID: 34972597 DOI: 10.1016/j.tibtech.2021.11.006] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 01/18/2023]
Abstract
Tumors are unique and complex ecosystems, in which heterogeneous cell subpopulations with variable molecular profiles, aggressiveness, and proliferation potential coexist and interact. Understanding how heterogeneity influences tumor progression has important clinical implications for improving diagnosis, prognosis, and treatment response prediction. Several recent innovations in data acquisition methods and computational metrics have enabled the quantification of spatiotemporal heterogeneity across different scales of tumor organization. Here, we summarize the most promising efforts from a common experimental and computational perspective, discussing their advantages, shortcomings, and challenges. With personalized medicine entering a new era of unprecedented opportunities, our vision is that of future workflows integrating across modalities, scales, and dimensions to capture intricate aspects of the tumor ecosystem and to open new avenues for improved patient care.
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Affiliation(s)
- Aditya Kashyap
- IBM Research Europe -Säumerstrasse 4, Rüschlikon CH-8803, Zurich, Switzerland
| | | | - Vesna Barros
- Department of Healthcare Informatics, IBM Research, IBM R&D Labs, University of Haifa Campus, Mount Carmel, Haifa, 3498825, Israel; The Hebrew University, The Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Anna Fomitcheva-Khartchenko
- IBM Research Europe -Säumerstrasse 4, Rüschlikon CH-8803, Zurich, Switzerland; Eidgenössische Technische Hochschule (ETH-Zurich), Vladimir-Prelog-Weg 1-5/10, 8099 Zurich, Switzerland
| | | | | | - Maria Gabrani
- IBM Research Europe -Säumerstrasse 4, Rüschlikon CH-8803, Zurich, Switzerland
| | - Michal Rosen-Zvi
- Department of Healthcare Informatics, IBM Research, IBM R&D Labs, University of Haifa Campus, Mount Carmel, Haifa, 3498825, Israel; The Hebrew University, The Edmond J. Safra Campus - Givat Ram, Jerusalem, 9190401, Israel
| | - Govind Kaigala
- IBM Research Europe -Säumerstrasse 4, Rüschlikon CH-8803, Zurich, Switzerland.
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4
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Wopereis S, Walter LO, Vieira DSC, Ribeiro AAB, Fernandes BL, Wilkens RS, Santos-Silva MC. Evaluation of ER, PR and HER2 markers by flow cytometry for breast cancer diagnosis and prognosis. Clin Chim Acta 2021; 523:504-512. [PMID: 34762935 DOI: 10.1016/j.cca.2021.11.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 09/03/2021] [Accepted: 11/03/2021] [Indexed: 12/24/2022]
Abstract
BACKGROUND AND AIMS Laboratory diagnosis of breast cancer (BC) is done by morphological analysis and immunohistochemistry (IHC). However, this methodology still has some limitations. The aim of this study is to validate flow cytometry (FC) immunophenotyping to investigate diagnostic and prognostic markers of BC. METHODS Tumor samples from surgical specimens of patients previously diagnosed with BC, were first sliced and then macerated together with PBS. Then, sample was filtered and the single cell suspension obtained was labeled with antibodies against estrogen (ERα), progesterone (PR) and HER2 receptors and CD45. The results were compared, in terms of sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV), with reference methods. RESULTS Results obtained comparing FC with reference methods were: ERα detection (sensitivity: 75%; specificity: 90%; PPV: 96.7%; NPV: 47.4%); PR detection (sensitivity: 72%; specificity: 70%; PPV: 79.3%; NPV: 60.8%); HER2 detection (sensitivity: 80%; specificity: 90.2%; PPV: 66.7%; NPV: 94.9%). CONCLUSION The results obtained show the capacity of this methodology on BC markers differentiation. FC, together with morphological analysis and IHC can overcome individual limitations of each methodology and provide reliable results on a faster and efficient manner, resulting in improvements on BC diagnosis and prognosis.
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Affiliation(s)
- Sandro Wopereis
- Laboratory of Experimental Oncology and Hemopathies, Post-Graduation Program in Pharmacy, Health Sciences Center, Federal University of Santa Catarina, Florianópolis, SC 88040-900, Brazil; Polydoro Ernani de São Thiago University Hospital, Federal University of Santa Catarina, Florianópolis, SC 88036-800, Brazil
| | - Laura Otto Walter
- Laboratory of Experimental Oncology and Hemopathies, Post-Graduation Program in Pharmacy, Health Sciences Center, Federal University of Santa Catarina, Florianópolis, SC 88040-900, Brazil
| | - Daniella Serafin Couto Vieira
- Laboratory of Experimental Oncology and Hemopathies, Post-Graduation Program in Pharmacy, Health Sciences Center, Federal University of Santa Catarina, Florianópolis, SC 88040-900, Brazil; Polydoro Ernani de São Thiago University Hospital, Federal University of Santa Catarina, Florianópolis, SC 88036-800, Brazil
| | - Amanda Abdalla Biasi Ribeiro
- Laboratory of Experimental Oncology and Hemopathies, Post-Graduation Program in Pharmacy, Health Sciences Center, Federal University of Santa Catarina, Florianópolis, SC 88040-900, Brazil
| | - Bráulio Leal Fernandes
- Polydoro Ernani de São Thiago University Hospital, Federal University of Santa Catarina, Florianópolis, SC 88036-800, Brazil
| | - Renato Salerno Wilkens
- Polydoro Ernani de São Thiago University Hospital, Federal University of Santa Catarina, Florianópolis, SC 88036-800, Brazil
| | - Maria Cláudia Santos-Silva
- Laboratory of Experimental Oncology and Hemopathies, Post-Graduation Program in Pharmacy, Health Sciences Center, Federal University of Santa Catarina, Florianópolis, SC 88040-900, Brazil.
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5
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Costa AF, Ribeiro MGM, Onofre ASC, de Miranda Onofre FB. Aneuploidy detection for diagnostic and prognostic use in premalignant and malignant lesions of the uterine cervix: A systematic review. Diagn Cytopathol 2020; 49:335-346. [PMID: 33332763 DOI: 10.1002/dc.24683] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 11/25/2020] [Accepted: 12/07/2020] [Indexed: 12/09/2022]
Abstract
OBJECTIVE To systematically review the role of aneuploidy detection alone or in combination with other methods in cervical cancer screening and to evaluate the value of aneuploidy to predict the behavior of premalignant cervical lesions. METHOD We conducted a systematic review based on an electronic search for articles published between 2001 and 2020 across databases including MEDLINE/PubMed, Scopus, and Web of Science. Studies were subjected to data extraction, risk of bias, and narrative synthesis. RESULTS A total of 15 articles were included in the review. Eight out of 15 studies (53.3%) were judged to be at a high or unclear risk of bias. From the 15 included studies, the index test to detect aneuploidy was DNA image cytometry (DNA-ICM) in 12 studies and DNA flow cytometry (DNA-FCM) in three studies. Nine studies also evaluated the performance of cytology and/or human papillomavirus (HPV) tests. For DNA-ICM, sensitivity to detect cervical intraepithelial neoplasia or worse (CIN2+) varied between 59.0% and 95.9% and specificity varied between 54.1% and 100%. For DNA-FCM, sensitivity varied between 27.3% to 96.8% and specificity was 100%. For cytological evaluation, sensitivity varied between 25.0% and 70.4% and specificity varied between 70.6% and 99.9%. For HPV detection, sensitivity varied between 39.4% and 100% and specificity varied between 23.3% and 84.3%. CONCLUSION DNA ploidy along with atypical cells findings in cytology and/or HPV detection revealed great value to detect CIN2+ lesions and to predict which lesions are more likely to progress to cervical cancer.
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Affiliation(s)
- Ane Francyne Costa
- Department of Clinical Analysis, Federal University of Santa Catarina, Florianópolis, Brazil
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Gudbergsson JM, Christensen E, Kostrikov S, Moos T, Duroux M, Kjær A, Johnsen KB, Andresen TL. Conventional Treatment of Glioblastoma Reveals Persistent CD44 + Subpopulations. Mol Neurobiol 2020; 57:3943-3955. [PMID: 32632605 DOI: 10.1007/s12035-020-02004-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/26/2020] [Indexed: 02/06/2023]
Abstract
Glioblastoma (GBM) is the most frequent and devastating primary tumor of the central nervous system with a median survival of 12 to 15 months after diagnosis. GBM is highly difficult to treat due to its delicate location, inter- and intra-tumoral heterogeneity, and high plasticity in response to treatment. In this study, we intracranially implanted primary GBM cells into mice which underwent conventional GBM treatments, including irradiation, temozolomide, and a combination. We obtained single cell suspensions through a combination of mechanical and enzymatic dissociation of brain tissue and investigated in detail the changes in GBM cells in response to conventional treatments in vivo using multi-color flow cytometry and cluster analysis. CD44 expression was elevated in all treatment groups, which was confirmed by subsequent immunohistochemistry. High CD44 expression was furthermore shown to correlate with poor prognosis of GBM and low-grade glioma (LGG) patients. Together, these results indicate a key role for CD44 in glioma pathogenesis.
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Affiliation(s)
- Johann Mar Gudbergsson
- Neurobiology Research & Drug Delivery, Department of Health Science and Technology, Aalborg University, Fredrik Bajers Vej 3B, 9220, Aalborg, Denmark. .,Center for Nanomedicine and Theranostics, Department of Health Technology, Technical University of Denmark, Produktionstorvet, Building 423, 2800, Kongens Lyngby, Denmark.
| | - Esben Christensen
- Center for Nanomedicine and Theranostics, Department of Health Technology, Technical University of Denmark, Produktionstorvet, Building 423, 2800, Kongens Lyngby, Denmark
| | - Serhii Kostrikov
- Center for Nanomedicine and Theranostics, Department of Health Technology, Technical University of Denmark, Produktionstorvet, Building 423, 2800, Kongens Lyngby, Denmark
| | - Torben Moos
- Neurobiology Research & Drug Delivery, Department of Health Science and Technology, Aalborg University, Fredrik Bajers Vej 3B, 9220, Aalborg, Denmark
| | - Meg Duroux
- Molecular Pharmacology, Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Andreas Kjær
- Cluster for Molecular Imaging, Department for Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Physiology, Nuclear Medicine & PET, Rigshospitalet, University of Copenhagen, Copenhagen, Denmark
| | - Kasper Bendix Johnsen
- Center for Nanomedicine and Theranostics, Department of Health Technology, Technical University of Denmark, Produktionstorvet, Building 423, 2800, Kongens Lyngby, Denmark.
| | - Thomas Lars Andresen
- Center for Nanomedicine and Theranostics, Department of Health Technology, Technical University of Denmark, Produktionstorvet, Building 423, 2800, Kongens Lyngby, Denmark
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7
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Qiu J, Zhou F, Li X, Zhang S, Chen Z, Xu Z, Lu G, Zhu Z, Ding N, Lou J, Ye Z, Qian Q. Changes and Clinical Significance of Detailed Peripheral Lymphocyte Subsets in Evaluating the Immunity for Cancer Patients. Cancer Manag Res 2020; 12:209-219. [PMID: 32021437 PMCID: PMC6957005 DOI: 10.2147/cmar.s221586] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 12/03/2019] [Indexed: 11/25/2022] Open
Abstract
Objective The evaluation of lymphocyte subsets is widely regarded as an important factor for monitoring tumor progression and response to therapy. This study was designed to establish a comprehensive and detailed assessment of peripheral lymphocyte subsets with a multi-parametric flow cytometry assay for response prediction and prognosis evaluation of cancer patients. Methods Peripheral blood samples collected from 40 cancer patients and 23 age- and sex-matched healthy volunteers were tested for 29 lymphocyte subsets by flow cytometry. The univariate analysis was applied to establish the reference interval of healthy samples, and the ratio and proportion of 29 lymphocyte subsets between patient samples and healthy controls were compared to evaluate their clinical significance by Mann–Whitney U-test model. Results The reference ranges of 29 lymphocyte subsets were established with a normal distribution and no significant differences were observed between genders. Compared with healthy control group, lower proportion and ratio of specific parameters, such as Naïve Th cells (p<0.01), Naïve Tc cells (p<0.01), CM (central memory) Tc cells (p<0.01), Naïve T cells/Memory T cells (p<0.001), Naïve T cells/EM (effector memory) T cells (p<0.001) and Naive Th cells/Memory Th cells (p< 0.001), and higher proportion and ratio of EM Th cells (p<0.001), EM Tc cells (p<0.01), effector Tc cells (p<0.05), EM Th cells/CM Th cells (p<0.01) and EM Tc cells/CM Tc cells (p<0.01), as well as Breg (p<0.001), B cells (p<0.05) and CD16-NK cells (p<0.001) were found in cancer cohorts. Conclusion This study suggests that the changes in certain lymphocyte subsets might be helpful to evaluate the immunity of cancer patients, and holds great potential for clinical application.
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Affiliation(s)
- Jinrong Qiu
- Department of Biotherapy, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University of Chinese PLA, Shanghai, People's Republic of China
| | - Fuping Zhou
- Department of Biotherapy, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University of Chinese PLA, Shanghai, People's Republic of China
| | - Xinchun Li
- Shanghai Baize Medical Laboratory, Shanghai, People's Republic of China
| | - Sufang Zhang
- Shanghai Baize Medical Laboratory, Shanghai, People's Republic of China
| | - Zhuo Chen
- Shanghai Baize Medical Laboratory, Shanghai, People's Republic of China
| | - Zenghui Xu
- Shanghai Baize Medical Laboratory, Shanghai, People's Republic of China
| | - Gaoxiong Lu
- Shanghai Baize Medical Laboratory, Shanghai, People's Republic of China
| | - Zhi Zhu
- Department of Pathology, Changhai Hospital, The Second Military Medical University of Chinese PLA, Shanghai, People's Republic of China
| | - Na Ding
- Shanghai Baize Medical Laboratory, Shanghai, People's Republic of China
| | - Jinxing Lou
- Shanghai Mengchao Cancer Hospital, Shanghai, People's Republic of China
| | - Zhenlong Ye
- Shanghai Baize Medical Laboratory, Shanghai, People's Republic of China
| | - Qijun Qian
- Department of Biotherapy, Eastern Hepatobiliary Surgery Hospital, The Second Military Medical University of Chinese PLA, Shanghai, People's Republic of China.,Shanghai Baize Medical Laboratory, Shanghai, People's Republic of China.,Shanghai Mengchao Cancer Hospital, Shanghai, People's Republic of China
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8
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Dapic I, Baljeu-Neuman L, Uwugiaren N, Kers J, Goodlett DR, Corthals GL. Proteome analysis of tissues by mass spectrometry. MASS SPECTROMETRY REVIEWS 2019; 38:403-441. [PMID: 31390493 DOI: 10.1002/mas.21598] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 06/17/2019] [Indexed: 06/10/2023]
Abstract
Tissues and biofluids are important sources of information used for the detection of diseases and decisions on patient therapies. There are several accepted methods for preservation of tissues, among which the most popular are fresh-frozen and formalin-fixed paraffin embedded methods. Depending on the preservation method and the amount of sample available, various specific protocols are available for tissue processing for subsequent proteomic analysis. Protocols are tailored to answer various biological questions, and as such vary in lysis and digestion conditions, as well as duration. The existence of diverse tissue-sample protocols has led to confusion in how to choose the best protocol for a given tissue and made it difficult to compare results across sample types. Here, we summarize procedures used for tissue processing for subsequent bottom-up proteomic analysis. Furthermore, we compare protocols for their variations in the composition of lysis buffers, digestion procedures, and purification steps. For example, reports have shown that lysis buffer composition plays an important role in the profile of extracted proteins: the most common are tris(hydroxymethyl)aminomethane, radioimmunoprecipitation assay, and ammonium bicarbonate buffers. Although, trypsin is the most commonly used enzyme for proteolysis, in some protocols it is supplemented with Lys-C and/or chymotrypsin, which will often lead to an increase in proteome coverage. Data show that the selection of the lysis procedure might need to be tissue-specific to produce distinct protocols for individual tissue types. Finally, selection of the procedures is also influenced by the amount of sample available, which range from biopsies or the size of a few dozen of mm2 obtained with laser capture microdissection to much larger amounts that weight several milligrams.
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Affiliation(s)
- Irena Dapic
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | | | - Naomi Uwugiaren
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Jesper Kers
- Department of Pathology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam Cardiovascular Sciences (ACS), Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - David R Goodlett
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
- University of Maryland, 20N. Pine Street, Baltimore, MD 21201
| | - Garry L Corthals
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
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9
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Nowak-Sliwinska P, Alitalo K, Allen E, Anisimov A, Aplin AC, Auerbach R, Augustin HG, Bates DO, van Beijnum JR, Bender RHF, Bergers G, Bikfalvi A, Bischoff J, Böck BC, Brooks PC, Bussolino F, Cakir B, Carmeliet P, Castranova D, Cimpean AM, Cleaver O, Coukos G, Davis GE, De Palma M, Dimberg A, Dings RPM, Djonov V, Dudley AC, Dufton NP, Fendt SM, Ferrara N, Fruttiger M, Fukumura D, Ghesquière B, Gong Y, Griffin RJ, Harris AL, Hughes CCW, Hultgren NW, Iruela-Arispe ML, Irving M, Jain RK, Kalluri R, Kalucka J, Kerbel RS, Kitajewski J, Klaassen I, Kleinmann HK, Koolwijk P, Kuczynski E, Kwak BR, Marien K, Melero-Martin JM, Munn LL, Nicosia RF, Noel A, Nurro J, Olsson AK, Petrova TV, Pietras K, Pili R, Pollard JW, Post MJ, Quax PHA, Rabinovich GA, Raica M, Randi AM, Ribatti D, Ruegg C, Schlingemann RO, Schulte-Merker S, Smith LEH, Song JW, Stacker SA, Stalin J, Stratman AN, Van de Velde M, van Hinsbergh VWM, Vermeulen PB, Waltenberger J, Weinstein BM, Xin H, Yetkin-Arik B, Yla-Herttuala S, Yoder MC, Griffioen AW. Consensus guidelines for the use and interpretation of angiogenesis assays. Angiogenesis 2018; 21:425-532. [PMID: 29766399 PMCID: PMC6237663 DOI: 10.1007/s10456-018-9613-x] [Citation(s) in RCA: 419] [Impact Index Per Article: 69.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The formation of new blood vessels, or angiogenesis, is a complex process that plays important roles in growth and development, tissue and organ regeneration, as well as numerous pathological conditions. Angiogenesis undergoes multiple discrete steps that can be individually evaluated and quantified by a large number of bioassays. These independent assessments hold advantages but also have limitations. This article describes in vivo, ex vivo, and in vitro bioassays that are available for the evaluation of angiogenesis and highlights critical aspects that are relevant for their execution and proper interpretation. As such, this collaborative work is the first edition of consensus guidelines on angiogenesis bioassays to serve for current and future reference.
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Affiliation(s)
- Patrycja Nowak-Sliwinska
- Molecular Pharmacology Group, School of Pharmaceutical Sciences, Faculty of Sciences, University of Geneva, University of Lausanne, Rue Michel-Servet 1, CMU, 1211, Geneva 4, Switzerland.
- Translational Research Center in Oncohaematology, University of Geneva, Geneva, Switzerland.
| | - Kari Alitalo
- Wihuri Research Institute and Translational Cancer Biology Program, University of Helsinki, Helsinki, Finland
| | - Elizabeth Allen
- Laboratory of Tumor Microenvironment and Therapeutic Resistance, Department of Oncology, VIB-Center for Cancer Biology, KU Leuven, Louvain, Belgium
| | - Andrey Anisimov
- Wihuri Research Institute and Translational Cancer Biology Program, University of Helsinki, Helsinki, Finland
| | - Alfred C Aplin
- Department of Pathology, University of Washington, Seattle, WA, USA
| | | | - Hellmut G Augustin
- European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
- Division of Vascular Oncology and Metastasis Research, German Cancer Research Center, Heidelberg, Germany
- German Cancer Consortium, Heidelberg, Germany
| | - David O Bates
- Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham, UK
| | - Judy R van Beijnum
- Angiogenesis Laboratory, Department of Medical Oncology, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands
| | - R Hugh F Bender
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | - Gabriele Bergers
- Laboratory of Tumor Microenvironment and Therapeutic Resistance, Department of Oncology, VIB-Center for Cancer Biology, KU Leuven, Louvain, Belgium
- Department of Neurological Surgery, Brain Tumor Research Center, Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, USA
| | - Andreas Bikfalvi
- Angiogenesis and Tumor Microenvironment Laboratory (INSERM U1029), University Bordeaux, Pessac, France
| | - Joyce Bischoff
- Vascular Biology Program and Department of Surgery, Harvard Medical School, Boston Children's Hospital, Boston, MA, USA
| | - Barbara C Böck
- European Center for Angioscience, Medical Faculty Mannheim, Heidelberg University, Heidelberg, Germany
- Division of Vascular Oncology and Metastasis Research, German Cancer Research Center, Heidelberg, Germany
- German Cancer Consortium, Heidelberg, Germany
| | - Peter C Brooks
- Center for Molecular Medicine, Maine Medical Center Research Institute, Scarborough, ME, USA
| | - Federico Bussolino
- Department of Oncology, University of Torino, Turin, Italy
- Candiolo Cancer Institute-FPO-IRCCS, 10060, Candiolo, Italy
| | - Bertan Cakir
- Department of Ophthalmology, Harvard Medical School, Boston Children's Hospital, Boston, MA, USA
| | - Peter Carmeliet
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Leuven, Belgium
| | - Daniel Castranova
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Anca M Cimpean
- Department of Microscopic Morphology/Histology, Angiogenesis Research Center, Victor Babes University of Medicine and Pharmacy, Timisoara, Romania
| | - Ondine Cleaver
- Department of Molecular Biology, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - George Coukos
- Ludwig Institute for Cancer Research, Department of Oncology, University of Lausanne, Lausanne, Switzerland
| | - George E Davis
- Department of Medical Pharmacology and Physiology, University of Missouri, School of Medicine and Dalton Cardiovascular Center, Columbia, MO, USA
| | - Michele De Palma
- School of Life Sciences, Swiss Federal Institute of Technology, Lausanne, Switzerland
| | - Anna Dimberg
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Ruud P M Dings
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | | | - Andrew C Dudley
- Department of Microbiology, Immunology, and Cancer Biology, University of Virginia, Charlottesville, VA, USA
- Emily Couric Cancer Center, The University of Virginia, Charlottesville, VA, USA
| | - Neil P Dufton
- Vascular Sciences, Imperial Centre for Translational and Experimental Medicine, National Heart and Lung Institute, Imperial College London, London, UK
| | - Sarah-Maria Fendt
- Laboratory of Cellular Metabolism and Metabolic Regulation, VIB Center for Cancer Biology, Leuven, Belgium
- Laboratory of Cellular Metabolism and Metabolic Regulation, Department of Oncology, KU Leuven and Leuven Cancer Institute, Leuven, Belgium
| | | | - Marcus Fruttiger
- Institute of Ophthalmology, University College London, London, UK
| | - Dai Fukumura
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Bart Ghesquière
- Metabolomics Expertise Center, VIB Center for Cancer Biology, VIB, Leuven, Belgium
- Department of Oncology, Metabolomics Expertise Center, KU Leuven, Leuven, Belgium
| | - Yan Gong
- Department of Ophthalmology, Harvard Medical School, Boston Children's Hospital, Boston, MA, USA
| | - Robert J Griffin
- Department of Radiation Oncology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Adrian L Harris
- Molecular Oncology Laboratories, Oxford University Department of Oncology, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, Oxford, UK
| | - Christopher C W Hughes
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | - Nan W Hultgren
- Department of Molecular Biology and Biochemistry, University of California, Irvine, CA, USA
| | | | - Melita Irving
- Ludwig Institute for Cancer Research, Department of Oncology, University of Lausanne, Lausanne, Switzerland
| | - Rakesh K Jain
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Raghu Kalluri
- Department of Cancer Biology, Metastasis Research Center, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Joanna Kalucka
- Laboratory of Angiogenesis and Vascular Metabolism, Department of Oncology and Leuven Cancer Institute (LKI), KU Leuven, Leuven, Belgium
- Laboratory of Angiogenesis and Vascular Metabolism, Center for Cancer Biology, VIB, Leuven, Belgium
| | - Robert S Kerbel
- Department of Medical Biophysics, Biological Sciences Platform, Sunnybrook Research Institute, University of Toronto, Toronto, ON, Canada
| | - Jan Kitajewski
- Department of Physiology and Biophysics, University of Illinois, Chicago, IL, USA
| | - Ingeborg Klaassen
- Ocular Angiogenesis Group, Departments of Ophthalmology and Medical Biology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Hynda K Kleinmann
- The George Washington University School of Medicine, Washington, DC, USA
| | - Pieter Koolwijk
- Department of Ophthalmology, University of Lausanne, Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, Lausanne, Switzerland
| | - Elisabeth Kuczynski
- Department of Medical Biophysics, Biological Sciences Platform, Sunnybrook Research Institute, University of Toronto, Toronto, ON, Canada
| | - Brenda R Kwak
- Department of Pathology and Immunology, University of Geneva, Geneva, Switzerland
| | | | - Juan M Melero-Martin
- Department of Cardiac Surgery, Harvard Medical School, Boston Children's Hospital, Boston, MA, USA
| | - Lance L Munn
- Edwin L. Steele Laboratories, Department of Radiation Oncology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Roberto F Nicosia
- Department of Pathology, University of Washington, Seattle, WA, USA
- Pathology and Laboratory Medicine Service, VA Puget Sound Health Care System, Seattle, WA, USA
| | - Agnes Noel
- Laboratory of Tumor and Developmental Biology, GIGA-Cancer, University of Liège, Liège, Belgium
| | - Jussi Nurro
- Department of Biotechnology and Molecular Medicine, University of Eastern Finland, Kuopio, Finland
| | - Anna-Karin Olsson
- Department of Medical Biochemistry and Microbiology, Science for Life Laboratory, Uppsala Biomedical Center, Uppsala University, Uppsala, Sweden
| | - Tatiana V Petrova
- Department of oncology UNIL-CHUV, Ludwig Institute for Cancer Research Lausanne, Lausanne, Switzerland
| | - Kristian Pietras
- Division of Translational Cancer Research, Department of Laboratory Medicine, Lund, Sweden
| | - Roberto Pili
- Genitourinary Program, Indiana University-Simon Cancer Center, Indianapolis, IN, USA
| | - Jeffrey W Pollard
- Medical Research Council Centre for Reproductive Health, College of Medicine and Veterinary Medicine, University of Edinburgh, Edinburgh, UK
| | - Mark J Post
- Department of Physiology, Maastricht University, Maastricht, The Netherlands
| | - Paul H A Quax
- Einthoven Laboratory for Experimental Vascular Medicine, Department Surgery, LUMC, Leiden, The Netherlands
| | - Gabriel A Rabinovich
- Laboratory of Immunopathology, Institute of Biology and Experimental Medicine, National Council of Scientific and Technical Investigations (CONICET), Buenos Aires, Argentina
| | - Marius Raica
- Department of Microscopic Morphology/Histology, Angiogenesis Research Center, Victor Babes University of Medicine and Pharmacy, Timisoara, Romania
| | - Anna M Randi
- Vascular Sciences, Imperial Centre for Translational and Experimental Medicine, National Heart and Lung Institute, Imperial College London, London, UK
| | - Domenico Ribatti
- Department of Basic Medical Sciences, Neurosciences and Sensory Organs, University of Bari Medical School, Bari, Italy
- National Cancer Institute "Giovanni Paolo II", Bari, Italy
| | - Curzio Ruegg
- Department of Oncology, Microbiology and Immunology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Reinier O Schlingemann
- Ocular Angiogenesis Group, Departments of Ophthalmology and Medical Biology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
- Department of Ophthalmology, University of Lausanne, Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, Lausanne, Switzerland
| | - Stefan Schulte-Merker
- Institute of Cardiovascular Organogenesis and Regeneration, Faculty of Medicine, WWU, Münster, Germany
| | - Lois E H Smith
- Department of Ophthalmology, Harvard Medical School, Boston Children's Hospital, Boston, MA, USA
| | - Jonathan W Song
- Department of Mechanical and Aerospace Engineering, The Ohio State University, Columbus, OH, USA
- Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Steven A Stacker
- Tumour Angiogenesis and Microenvironment Program, Peter MacCallum Cancer Centre and The Sir Peter MacCallum, Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Jimmy Stalin
- Institute of Cardiovascular Organogenesis and Regeneration, Faculty of Medicine, WWU, Münster, Germany
| | - Amber N Stratman
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Maureen Van de Velde
- Laboratory of Tumor and Developmental Biology, GIGA-Cancer, University of Liège, Liège, Belgium
| | - Victor W M van Hinsbergh
- Department of Ophthalmology, University of Lausanne, Jules-Gonin Eye Hospital, Fondation Asile des Aveugles, Lausanne, Switzerland
| | - Peter B Vermeulen
- HistoGeneX, Antwerp, Belgium
- Translational Cancer Research Unit, GZA Hospitals, Sint-Augustinus & University of Antwerp, Antwerp, Belgium
| | - Johannes Waltenberger
- Medical Faculty, University of Münster, Albert-Schweitzer-Campus 1, Münster, Germany
| | - Brant M Weinstein
- Division of Developmental Biology, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Hong Xin
- University of California, San Diego, La Jolla, CA, USA
| | - Bahar Yetkin-Arik
- Ocular Angiogenesis Group, Departments of Ophthalmology and Medical Biology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Seppo Yla-Herttuala
- Department of Biotechnology and Molecular Medicine, University of Eastern Finland, Kuopio, Finland
| | - Mervin C Yoder
- Department of Pediatrics, Indiana University School of Medicine, Indianapolis, IN, USA
| | - Arjan W Griffioen
- Angiogenesis Laboratory, Department of Medical Oncology, VU University Medical Center, Cancer Center Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands.
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10
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Trifonova RT, Barteneva NS. Quantitation of IRF3 Nuclear Translocation in Heterogeneous Cellular Populations from Cervical Tissue Using Imaging Flow Cytometry. Methods Mol Biol 2018; 1745:125-153. [PMID: 29476467 DOI: 10.1007/978-1-4939-7680-5_8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Imaging flow cytometry (IFC) has become a powerful tool for studying the activation of transcriptional factors in heterogeneous cell populations in high-content imaging mode. With considerable interest to the clinical development of IFC, the question becomes how we can accelerate its application to solid tissues. We developed the first IFC-based procedure to quantify the nuclear translocation of interferon regulatory factor (IRF) 3, an important measure of induction of type I interferon antiviral response, in primary human immune cells including in solid tissues. After tissue digestion and protocol optimization by spectral flow cytometry, cell suspension is stained for intracellular IRF3 and acquired by IFC. Image analysis is performed using an optimized nuclear mask and similarity score parameter to correlate the location of IRF3 staining and a nuclear dye. The technique measures IRF3 activation at a single cell level and can detect small changes in the percent of activated cells providing objective quantitative data for statistical analysis.
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Affiliation(s)
- Radiana T Trifonova
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA.
- Department of Pediatrics, Harvard Medical School, Boston, MA, USA.
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
| | - Natasha S Barteneva
- PCMM-Harvard Medical School, Boston Children's Hospital, Boston, MA, USA.
- Department of Biology, School of Sciences and Technology, Nazarbayev University, Astana, Kazakhstan.
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11
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Turner KA, Kalafatis M. The Case Back on the TRAIL: Death Receptors as Markers for rhTRAIL Sensitivity. J Appl Lab Med 2017; 2:176-185. [PMID: 32630980 DOI: 10.1373/jalm.2017.023408] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Accepted: 04/11/2017] [Indexed: 11/06/2022]
Abstract
BACKGROUND Personalized cancer treatments can be applied to the clinical use of recombinant human tumor necrosis factor-related apoptosis-inducing ligand (rhTRAIL). rhTRAIL holds great promise because of its selectivity for cancer cells. However, rhTRAIL clinical trials were conducted without the screening of patients' tumors for rhTRAIL-binding death receptor (DR)4 and DR5, and the unselected treatment resulted in a lack of clinical benefit. Here we propose an in vitro test to analyze tumor cells isolated from patients for the membrane expression of DRs to determine patient suitability for rhTRAIL treatment. METHODS Using a panel of malignant melanoma cell lines, the correlation between DR membrane expression and rhTRAIL sensitivity was evaluated. The membrane expression of DR4 and DR5 was examined through staining with anti-DR4 and -DR5 antibodies followed by fluorescence-activated cell sorting. rhTRAIL sensitivity was determined through Annexin-V and propidium iodide staining and Western blotting after rhTRAIL treatment. RESULTS Here we show a direct correlation between the membrane expression of DRs and rhTRAIL sensitivity. rhTRAIL-sensitive melanoma lines, on average, had nearly 4-fold more DR4 and >2-fold more DR5 than rhTRAIL-resistant lines. For a cancer cell to display rhTRAIL sensitivity, the optimum expression of DRs is essential. To overcome the apoptotic threshold, cancer cells must express DRs >2-fold higher compared with their benign counterpart. CONCLUSION These data show the potential of this flow cytometry-based assay for the analysis of isolated tumor cells for DR membrane expression. By first determining a patient's susceptibility to rhTRAIL-based treatments, they can be more appropriately placed in rhTRAIL clinical trials and improve rhTRAIL as an anticancer therapeutic.
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Affiliation(s)
- Katherine A Turner
- Department of Chemistry, Cleveland State University, Cleveland, OH.,Center for Gene Regulation in Health and Disease (GRHD), Cleveland State University, Cleveland, OH
| | - Michael Kalafatis
- Department of Chemistry, Cleveland State University, Cleveland, OH.,Center for Gene Regulation in Health and Disease (GRHD), Cleveland State University, Cleveland, OH.,Taussig Cancer Institute, Cleveland Clinic Foundation, Cleveland, OH.,Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, OH
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12
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Singh DK, Ahrens CC, Li W, Vanapalli SA. Label-free fingerprinting of tumor cells in bulk flow using inline digital holographic microscopy. BIOMEDICAL OPTICS EXPRESS 2017; 8:536-554. [PMID: 28270966 PMCID: PMC5330580 DOI: 10.1364/boe.8.000536] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 12/21/2016] [Accepted: 12/22/2016] [Indexed: 05/19/2023]
Abstract
Large-scale and label-free phenotyping of cells holds great promise in medicine, especially in cancer diagnostics and prognosis. Here, we introduce inline digital holography microscopy for volumetric imaging of cells in bulk flow and fingerprinting of flowing tumor cells based on two metrics, in-focus scattered intensity and cell diameter. Using planar distribution of immobilized particles, we identify the optimal recording distance and microscope objective magnification that minimizes the error in measurement of particle position, size and scattered intensity. Using the optimized conditions and the two metrics, we demonstrate the capacity to enumerate and fingerprint more than 100,000 cells. Finally, we highlight the power of our label-free and high throughput technology by characterizing breast tumor cell lines with different metastatic potentials and distinguishing drug resistant ovarian cancer cells from their parental cell line.
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Affiliation(s)
| | - Caroline C. Ahrens
- Department of Chemical Engineering, Texas Tech University, Lubbock, Texas, USA
| | - Wei Li
- Department of Chemical Engineering, Texas Tech University, Lubbock, Texas, USA
| | - Siva A. Vanapalli
- Department of Chemical Engineering, Texas Tech University, Lubbock, Texas, USA
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13
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Abstract
In these last few decades the great explosion of the molecular approaches has casted a little shadow on the DNA quantitative analysis. Nevertheless DNA cytochemistry represented a long piece of history in cell biology since the advent of the Feulgen reaction. This discovery was really the milestone of the emerging quantitative cytochemistry, and scientists from all over the world produced a very large literature on this subject. This first era of quantitation (histochemistry followed by cytochemistry) started by means of absorption measurements (histophotometry and cytophotometry). The successive introduction of fluorescence microscopy gave a great boost to quantitation, making easier and faster the determination of cell components by means of cytofluorometry. The development of flow cytometry further contributed to the importance of quantitative cytochemistry. At its beginning, the mission of flow cytometry was still DNA quantitation. For a decade the Feulgen reaction had been the reference methodology for both conventional and flow cytofluorometry; the advent of Shiff-type reagents contributed to expand the variety of possible fluorochromes excitable in the entire visible spectrum as well as in the ultraviolet region. The fluorescence scenario was progressively enriched by new probes among which are the intercalating dyes which made DNA quantitation simple and fast, thus spreading it worldwide. The final explosion of cytofluorometry was made possible by the availability of a large variety of probes directly binding DNA structure. In addition, immunofluorescence allowed to correlate the cell cycle-related DNA content to other cell markers. In the clinical application of flow cytometry, this promoted the introduction of multiparametric analyses aimed at describing the cytokinetic characteristics of a given cell subpopulation defined by a specific immunophenotype setting.
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Affiliation(s)
- Giuliano Mazzini
- Institute of Molecular Genetics, CNR, Via Abbiategrasso 207, 27100, Pavia, Italy. .,Department of Biology and Biotechnology "Lazzaro Spallanzani", University of Pavia, Pavia, Italy.
| | - Marco Danova
- Department of Medicine, Azienda Socio-Sanitaria Territoriale of Pavia, Pavia, Italy
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14
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Multiplexed labeling system for high-throughput cell sorting. Anal Biochem 2016; 508:124-8. [PMID: 27181032 DOI: 10.1016/j.ab.2016.05.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 04/28/2016] [Accepted: 05/04/2016] [Indexed: 11/23/2022]
Abstract
Flow cytometry and fluorescence activated cell sorting techniques were designed to realize configurable classification and separation of target cells. A number of cell phenotypes with different functionalities have recently been revealed. Before simultaneous selective capture of cells, it is desirable to label different samples with the corresponding dyes in a multiplexing manner to allow for a single analysis. However, few methods to obtain multiple fluorescent colors for various cell types have been developed. Even when restricted laser sources are employed, a small number of color codes can be expressed simultaneously. In this study, we demonstrate the ability to manifest DNA nanostructure-based multifluorescent colors formed by a complex of dyes. Highly precise self-assembly of fluorescent dye-conjugated oligonucleotides gives anisotropic DNA nanostructures, Y- and tree-shaped DNA (Y-DNA and T-DNA, respectively), which may be used as platforms for fluorescent codes. As a proof of concept, we have demonstrated seven different fluorescent codes with only two different fluorescent dyes using T-DNA. This method provides maximum efficiency for current flow cytometry. We are confident that this system will provide highly efficient multiplexed fluorescent detection for bioanalysis compared with one-to-one fluorescent correspondence for specific marker detection.
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15
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Domingues P, González-Tablas M, Otero Á, Pascual D, Miranda D, Ruiz L, Sousa P, Ciudad J, Gonçalves JM, Lopes MC, Orfao A, Tabernero MD. Tumor infiltrating immune cells in gliomas and meningiomas. Brain Behav Immun 2016. [PMID: 26216710 DOI: 10.1016/j.bbi.2015.07.019] [Citation(s) in RCA: 196] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Tumor-infiltrating immune cells are part of a complex microenvironment that promotes and/or regulates tumor development and growth. Depending on the type of cells and their functional interactions, immune cells may play a key role in suppressing the tumor or in providing support for tumor growth, with relevant effects on patient behavior. In recent years, important advances have been achieved in the characterization of immune cell infiltrates in central nervous system (CNS) tumors, but their role in tumorigenesis and patient behavior still remain poorly understood. Overall, these studies have shown significant but variable levels of infiltration of CNS tumors by macrophage/microglial cells (TAM) and to a less extent also lymphocytes (particularly T-cells and NK cells, and less frequently also B-cells). Of note, TAM infiltrate gliomas at moderate numbers where they frequently show an immune suppressive phenotype and functional behavior; in contrast, infiltration by TAM may be very pronounced in meningiomas, particularly in cases that carry isolated monosomy 22, where the immune infiltrates also contain greater numbers of cytotoxic T and NK-cells associated with an enhanced anti-tumoral immune response. In line with this, the presence of regulatory T cells, is usually limited to a small fraction of all meningiomas, while frequently found in gliomas. Despite these differences between gliomas and meningiomas, both tumors show heterogeneous levels of infiltration by immune cells with variable functionality. In this review we summarize current knowledge about tumor-infiltrating immune cells in the two most common types of CNS tumors-gliomas and meningiomas-, as well as the role that such immune cells may play in the tumor microenvironment in controlling and/or promoting tumor development, growth and control.
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Affiliation(s)
- Patrícia Domingues
- Centre for Neurosciences and Cell Biology and Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal; Centre for Cancer Research (CIC-IBMCC; CSIC/USAL; IBSAL) and Department of Medicine, University of Salamanca, Salamanca, Spain
| | - María González-Tablas
- Centre for Cancer Research (CIC-IBMCC; CSIC/USAL; IBSAL) and Department of Medicine, University of Salamanca, Salamanca, Spain
| | - Álvaro Otero
- Neurosurgery Service of the University Hospital of Salamanca, Salamanca, Spain
| | - Daniel Pascual
- Neurosurgery Service of the University Hospital of Salamanca, Salamanca, Spain
| | - David Miranda
- Neurosurgery Service of the University Hospital of Salamanca, Salamanca, Spain
| | - Laura Ruiz
- Neurosurgery Service of the University Hospital of Salamanca, Salamanca, Spain
| | - Pablo Sousa
- Neurosurgery Service of the University Hospital of Salamanca, Salamanca, Spain
| | - Juana Ciudad
- Centre for Cancer Research (CIC-IBMCC; CSIC/USAL; IBSAL) and Department of Medicine, University of Salamanca, Salamanca, Spain
| | | | - María Celeste Lopes
- Centre for Neurosciences and Cell Biology and Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - Alberto Orfao
- Centre for Cancer Research (CIC-IBMCC; CSIC/USAL; IBSAL) and Department of Medicine, University of Salamanca, Salamanca, Spain
| | - María Dolores Tabernero
- Centre for Cancer Research (CIC-IBMCC; CSIC/USAL; IBSAL) and Department of Medicine, University of Salamanca, Salamanca, Spain; Neurosurgery Service of the University Hospital of Salamanca, Salamanca, Spain; Instituto de Estudios de Ciencias de la salud de Castilla y León (IECSCYL-IBSAL) and Research Unit of the University Hospital of Salamanca, Salamanca, Spain.
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16
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Manzoni M, Comolli G, Torchio M, Mazzini G, Danova M. Circulating endothelial cells and their subpopulations: role as predictive biomarkers in antiangiogenic therapy for colorectal cancer. Clin Colorectal Cancer 2014; 14:11-7. [PMID: 25591800 DOI: 10.1016/j.clcc.2014.12.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Revised: 12/13/2014] [Accepted: 12/16/2014] [Indexed: 12/13/2022]
Abstract
Several anticancer therapies have been developed to block angiogenesis, a key mechanism in tumor growth and metastasis. The predominantly cytostatic action of these compounds makes an assessment of their clinical activities inadequate if based only on the reduction of the tumor dimensions, as this may not reflect their true biologic efficacy. Thus, it is crucial to identify biomarkers that permit the recognition of potentially responsive subjects and to spare toxicity in those who are unlikely to benefit from treatment. Circulating endothelial cells (CECs) have been recently indicated as potential surrogate biomarkers of angiogenesis in several types of cancer. The possibility of rapidly quantifying these cells represents a promising tool for monitoring the clinical outcome of tumors with the potential to assess response to various treatments. However, the identification and quantification of CECs is technically difficult and not well standardized. A variety of methods to detect CECs in patients with solid tumors have been used; these are based on different technical approaches, combinations of surface markers, sample handling, and staining protocols. With an expanding interest in the field of potential clinical applications for CECs in oncology, the development of standardized protocols for analysis is mandatory. The aim of this review was to critically summarize the available data concerning the clinical value of CECs and their subpopulations as biomarkers of antiangiogenic therapy in patients with metastatic colorectal cancer.
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Affiliation(s)
- Mariangela Manzoni
- Department of Medical Oncology, Azienda Ospedaliera "Ospedale Maggiore", Crema, Italy.
| | - Giuditta Comolli
- Laboratories of Biotechnology and Virology/Microbiology Department, Fondazione IRCCS, Pavia, Italy
| | - Martina Torchio
- Institute of Molecular Genetics, National Research Council, Pavia, Italy
| | - Giuliano Mazzini
- Department of Internal Medicine and Medical Oncology, Ospedale di Vigevano, Vigevano, Italy
| | - Marco Danova
- Institute of Molecular Genetics, National Research Council, Pavia, Italy
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17
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Robins HS, Ericson NG, Guenthoer J, O'Briant KC, Tewari M, Drescher CW, Bielas JH. Digital genomic quantification of tumor-infiltrating lymphocytes. Sci Transl Med 2014; 5:214ra169. [PMID: 24307693 DOI: 10.1126/scitranslmed.3007247] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Infiltrating T lymphocytes are frequently found in malignant tumors and are suggestive of a host cancer immune response. Multiple independent studies have documented that the presence and quantity of tumor-infiltrating lymphocytes (TILs) are strongly correlated with increased survival. However, because of methodological factors, the exact effect of TILs on prognosis has remained enigmatic, and inclusion of TILs in standard prognostic panels has been limited. For example, some reports enumerate all CD3(+) cells, some count only cytotoxic CD8(+) T cells, and the criteria used to score tumors as TIL-positive or TIL-negative are inconsistent among studies. To address this limitation, we introduce a robust digital DNA-based assay, termed QuanTILfy, to count TILs and assess T cell clonality in tissue samples, including tumors. We demonstrate the clonal specificity of this approach by the diagnosis of T cell acute lymphoblastic leukemia and the accurate, sensitive, and highly reproducible measurement of TILs in primary and metastatic ovarian cancer. Our experiments demonstrate an association between higher TIL counts and improved survival among women with ovarian cancer, and are consistent with previous observations that the immune response against ovarian cancer is a meaningful and independent prognostic factor. Surprisingly, the TIL repertoire is diverse for all tumors in the study with no notable oligoclonal expansions. Furthermore, because variability in the measurement and characterization of TILs has limited their clinical utility as biomarkers, these results highlight the significant translational potential of a robust, standardizable DNA-based assay to assess TILs in a variety of cancer types.
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Affiliation(s)
- Harlan S Robins
- Herbold Computational Biology Program, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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18
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Bjornson ZB, Nolan GP, Fantl WJ. Single-cell mass cytometry for analysis of immune system functional states. Curr Opin Immunol 2013; 25:484-94. [PMID: 23999316 DOI: 10.1016/j.coi.2013.07.004] [Citation(s) in RCA: 167] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 07/05/2013] [Accepted: 07/08/2013] [Indexed: 01/11/2023]
Abstract
Mass cytometry facilitates high-dimensional, quantitative analysis of the effects of bioactive molecules on cell populations at single-cell resolution. Datasets are generated with panels of up to 45 antibodies. Each antibody is conjugated to a polymer chelated with a stable metal isotope, usually in the lanthanide series of the periodic table. Antibody panels recognize surface markers to delineate cell types simultaneously with intracellular signaling molecules to measure biological functions, such as metabolism, survival, DNA damage, cell cycle and apoptosis, to provide an overall determination of the network state of an individual cell. This review will cover the basics of mass cytometry as well as outline assays developed for the platform that enhance the immunologist's analytical arsenal.
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Affiliation(s)
- Zach B Bjornson
- Stanford University School of Medicine, Department of Microbiology & Immunology, Baxter Laboratory for Stem Cell Biology, 269 Campus Drive, Stanford, CA 94305-5175, USA
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19
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O'Donnell EA, Ernst DN, Hingorani R. Multiparameter flow cytometry: advances in high resolution analysis. Immune Netw 2013; 13:43-54. [PMID: 23700394 PMCID: PMC3659255 DOI: 10.4110/in.2013.13.2.43] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2013] [Revised: 02/20/2013] [Accepted: 02/25/2013] [Indexed: 01/10/2023] Open
Abstract
Over the past 40 years, flow cytometry has emerged as a leading, application-rich technology that supports high-resolution characterization of individual cells which function in complex cellular networks such as the immune system. This brief overview highlights advances in multiparameter flow cytometric technologies and reagent applications for characterization and functional analysis of cells modulating the immune network. These advances significantly support high-throughput and high-content analyses and enable an integrated understanding of the cellular and molecular interactions that underlie complex biological systems.
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20
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Galbraith D. Flow cytometry and cell sorting: the next generation. Methods 2013; 57:249-50. [PMID: 22939984 DOI: 10.1016/j.ymeth.2012.08.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Accepted: 08/15/2012] [Indexed: 01/13/2023] Open
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