Immune cell profiling in cancer: molecular approaches to cell-specific identification
暂无分享,去创建一个
Keith A. Baggerly | K. Baggerly | A. Sood | S. Wu | W. Overwijk | Anil K. Sood | Sherry Y. Wu | Y. Lyons | Yasmin A. Lyons | Willem W. Overwijk
[1] Alan Sharpe,et al. High-Frequency Targetable EGFR Mutations in Sinonasal Squamous Cell Carcinomas Arising from Inverted Sinonasal Papilloma. , 2015, Cancer research.
[2] Silvano Sozzani,et al. Nomenclature of monocytes and dendritic cells in blood. , 2010, Blood.
[3] David E. Misek,et al. Profiling Changes in Gene Expression during Differentiation and Maturation of Monocyte-derived Dendritic Cells Using Both Oligonucleotide Microarrays and Proteomics* , 2001, The Journal of Biological Chemistry.
[4] R. Dummer,et al. Induction of Genes Mediating Interferon-dependent Extracellular Trap Formation during Neutrophil Differentiation* , 2004, Journal of Biological Chemistry.
[5] Thomas D. Schmittgen,et al. RNA isolation from mouse pancreas: a ribonuclease-rich tissue. , 2014, Journal of visualized experiments : JoVE.
[6] J. Galon,et al. [Intratumoral immune microenvironment and survival: the immunoscore]. , 2014, Medecine sciences : M/S.
[7] R. Melamed,et al. Gene expression microarrays: glimpses of the immunological genome , 2006, Nature Immunology.
[8] J Zeleznikow,et al. Molecular immunology databases and data repositories. , 2000, Journal of immunological methods.
[9] J. Galon,et al. Imaging , Diagnosis , Prognosis Prognostic and Predictive Values of the Immunoscore in Patients with Rectal Cancer , 2014 .
[10] J. Paulauskis,et al. Assessment of fixatives, fixation, and tissue processing on morphology and RNA integrity. , 2006, Experimental and molecular pathology.
[11] A. Hummon,et al. Proteomic Challenges: Sample Preparation Techniques for Microgram-Quantity Protein Analysis from Biological Samples , 2015, International journal of molecular sciences.
[12] N. Kiwanuka,et al. Characterization of Neutrophil Subsets in Healthy Human Pregnancies , 2014, PloS one.
[13] G. Mills,et al. An efficient procedure for protein extraction from formalin-fixed, paraffin-embedded tissues for reverse phase protein arrays , 2012, Proteome Science.
[14] Yudong D. He,et al. Gene expression profiling predicts clinical outcome of breast cancer , 2002, Nature.
[15] A. Nobel,et al. Supervised risk predictor of breast cancer based on intrinsic subtypes. , 2009, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.
[16] D. Sargent,et al. Validation of the Immunoscore (IM) as a prognostic marker in stage I/II/III colon cancer: Results of a worldwide consortium-based analysis of 1,336 patients. , 2016 .
[17] R. Nussenblatt,et al. Standardizing immunophenotyping for the Human Immunology Project , 2012, Nature Reviews Immunology.
[18] Wing-Cheong Wong,et al. Gene expression profiling reveals the defining features of the classical, intermediate, and nonclassical human monocyte subsets. , 2011, Blood.
[19] C. Rudin,et al. Nivolumab versus Docetaxel in Advanced Nonsquamous Non-Small-Cell Lung Cancer. , 2015, The New England journal of medicine.
[20] M. Caligiuri,et al. The biology of human natural killer-cell subsets. , 2001, Trends in immunology.
[21] Do-Hyun Nam,et al. Single-cell mRNA sequencing identifies subclonal heterogeneity in anti-cancer drug responses of lung adenocarcinoma cells , 2015, Genome Biology.
[22] Ronald W. Davis,et al. Quantitative Monitoring of Gene Expression Patterns with a Complementary DNA Microarray , 1995, Science.
[23] F. Marincola,et al. Towards the introduction of the ‘Immunoscore’ in the classification of malignant tumours , 2013, The Journal of pathology.
[24] P. Coulie,et al. From defined human tumor antigens to effective immunization? , 1995, Immunology today.
[25] S. Mallal,et al. RAS/MAPK Activation Is Associated with Reduced Tumor-Infiltrating Lymphocytes in Triple-Negative Breast Cancer: Therapeutic Cooperation Between MEK and PD-1/PD-L1 Immune Checkpoint Inhibitors , 2015, Clinical Cancer Research.
[26] Rong Fan,et al. Microchip platforms for multiplex single-cell functional proteomics with applications to immunology and cancer research , 2013, Genome Medicine.
[27] Z. Trajanoski,et al. Spatiotemporal dynamics of intratumoral immune cells reveal the immune landscape in human cancer. , 2013, Immunity.
[28] Ash A. Alizadeh,et al. Cell-type specific gene expression profiles of leukocytes in human peripheral blood , 2006, BMC Genomics.
[29] R. Bast,et al. Use of Biomarkers to Guide Decisions on Adjuvant Systemic Therapy for Women With Early-Stage Invasive Breast Cancer: American Society of Clinical Oncology Clinical Practice Guideline. , 2016, Journal of clinical oncology : official journal of the American Society of Clinical Oncology.
[30] Valentina Proserpio,et al. Single‐cell technologies to study the immune system , 2015, Immunology.
[31] L. Maltais,et al. Mouse cell surface antigens: nomenclature and immunophenotyping. , 1998, Journal of immunology.
[32] Jonathan M Irish,et al. Analysis of protein phosphorylation and cellular signaling events by flow cytometry: techniques and clinical applications. , 2004, Clinical immunology.
[33] Ping Jin,et al. Molecular signatures of maturing dendritic cells: implications for testing the quality of dendritic cell therapies , 2010, Journal of Translational Medicine.
[34] Junbo Wang,et al. Development of Microfluidic Systems Enabling High-Throughput Single-Cell Protein Characterization , 2016, Sensors.
[35] Garry P Nolan,et al. Single-cell Mass Cytometry for Analysis of Immune System Functional States This Review Comes from a Themed Issue on Host Pathogens Basic Concepts of Mass Cytometry , 2022 .
[36] David M. Simcha,et al. Tackling the widespread and critical impact of batch effects in high-throughput data , 2010, Nature Reviews Genetics.
[37] J Christopher Love,et al. On-chip activation and subsequent detection of individual antigen-specific T cells. , 2010, Analytical chemistry.
[38] R. Beelen,et al. Immature Neutrophils Mediate Tumor Cell Killing via IgA but Not IgG Fc Receptors1 , 2005, The Journal of Immunology.
[39] X. Liu,et al. Big data mining yields novel insights on cancer , 2015, Nature Genetics.
[40] D. Koller,et al. The Immunological Genome Project: networks of gene expression in immune cells , 2008, Nature Immunology.
[41] R. Germain,et al. Variability and Robustness in T Cell Activation from Regulated Heterogeneity in Protein Levels , 2008, Science.
[42] J. Castle,et al. Development of a microarray platform for FFPET profiling: application to the classification of human tumors , 2009, Journal of Translational Medicine.
[43] Jeong Eon Lee,et al. Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer , 2017, Nature Communications.
[44] C. Sautès-Fridman,et al. The immune contexture in human tumours: impact on clinical outcome , 2012, Nature Reviews Cancer.
[45] A. Brazma,et al. Reuse of public genome-wide gene expression data , 2012, Nature Reviews Genetics.
[46] J. Larkin,et al. Pembrolizumab versus Ipilimumab in Advanced Melanoma. , 2015, The New England journal of medicine.
[47] Ludmila V. Danilova,et al. Tumor immune microenvironment characterization in clear cell renal cell carcinoma identifies prognostic and immunotherapeutically relevant messenger RNA signatures , 2016, Genome Biology.
[48] M. Woodruff,et al. Immune Response , 1969, Nature.
[49] S. Goerdt,et al. Macrophage activation and polarization: nomenclature and experimental guidelines. , 2014, Immunity.
[50] Alexander D. Diehl,et al. Ontology based molecular signatures for immune cell types via gene expression analysis , 2013, BMC Bioinformatics.
[51] J. Laštovička. The Phenotypic Markers of CD4 + CD25 + T Regulatory Lymphocytes , 2013 .
[52] L. Lefrançois,et al. Endogenous naive CD8+ T cell precursor frequency regulates primary and memory responses to infection. , 2008, Immunity.
[53] RNA Extraction from Animal and Human's Cancerous Tissues: Does Tissue Matter? , 2015, International journal of molecular and cellular medicine.
[54] A. Bittner,et al. Comparison of RNA-Seq and Microarray in Transcriptome Profiling of Activated T Cells , 2014, PloS one.
[55] S. Ichiyama,et al. Flow cytometric method for enumeration and classification of reactive immature granulocyte populations. , 2000, Cytometry.
[56] Alex K. Shalek,et al. Heterogeneity in immune responses: from populations to single cells. , 2014, Trends in immunology.
[57] Charles Zegar,et al. Advantages and limitations of microarray technology in human cancer , 2003, Oncogene.
[58] L. Miller,et al. Conservation of immune gene signatures in solid tumors and prognostic implications , 2016, BMC Cancer.
[59] Susan M. Chang,et al. Comprehensive mutation analysis in NRG Oncology/RTOG 9813: A phase III trial of RT + TMZ vs RT + nu for anaplastic astrocytoma and mixed anaplastic oligoastrocytoma (Astrocytoma Dominant). , 2016 .
[60] Shibin Song,et al. ImmuCo: a database of gene co-expression in immune cells , 2014, Nucleic Acids Res..
[61] L. Staudt,et al. Signatures of the immune response. , 2001, Immunity.
[62] Ralph Weissleder,et al. Magnetic relaxation switches capable of sensing molecular interactions , 2002, Nature Biotechnology.
[63] L. D. Hall,et al. Dissection of immune gene networks in primary melanoma tumors critical for antitumor surveillance of patients with stage II-III resectable disease. , 2014, The Journal of investigative dermatology.
[64] S. Michiels,et al. Statistical controversies in clinical research: prognostic gene signatures are not (yet) useful in clinical practice , 2016, Annals of oncology : official journal of the European Society for Medical Oncology.
[65] Franck Pagès,et al. Tumor immunosurveillance in human cancers , 2011, Cancer and Metastasis Reviews.
[66] Jennifer L. Osborn,et al. Direct multiplexed measurement of gene expression with color-coded probe pairs , 2008, Nature Biotechnology.
[67] Axel Hoos,et al. Ipilimumab plus dacarbazine for previously untreated metastatic melanoma. , 2011, The New England journal of medicine.
[68] Rona S. Gertner,et al. Single-cell transcriptomics reveals bimodality in expression and splicing in immune cells , 2013, Nature.
[69] D. Klatzmann,et al. Human and Mouse CD8+CD25+FOXP3+ Regulatory T Cells at Steady State and during Interleukin-2 Therapy , 2015, Front. Immunol..
[70] Pablo Tamayo,et al. Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles , 2005, Proceedings of the National Academy of Sciences of the United States of America.
[71] M. Gerstein,et al. RNA-Seq: a revolutionary tool for transcriptomics , 2009, Nature Reviews Genetics.
[72] J Christopher Love,et al. Concurrent detection of secreted products from human lymphocytes by microengraving: cytokines and antigen-reactive antibodies. , 2008, Clinical immunology.
[73] C. Sotiriou,et al. CCR 20th Anniversary Commentary: Gene-Expression Signature in Breast Cancer—Where Did It Start and Where Are We Now? , 2015, Clinical Cancer Research.
[74] Phillip G. Popovich,et al. Novel Markers to Delineate Murine M1 and M2 Macrophages , 2015, PloS one.
[75] M. Probst-Kepper,et al. Signatures of human regulatory T cells: an encounter with old friends and new players , 2006, Genome Biology.
[76] M. Cragg,et al. Molecular markers of B-cell lymphoma. , 1999, Seminars in cancer biology.
[77] Yong‐jun Liu,et al. Mouse and human dendritic cell subtypes , 2002, Nature Reviews Immunology.
[78] J. Ferreira,et al. Comparison of Two Methods of RNA Extraction from Formalin-Fixed Paraffin-Embedded Tissue Specimens , 2014, BioMed research international.
[79] Sean Ferree,et al. Analytical validation of the PAM50-based Prosigna Breast Cancer Prognostic Gene Signature Assay and nCounter Analysis System using formalin-fixed paraffin-embedded breast tumor specimens , 2014, BMC Cancer.
[80] David Baltimore,et al. Multifunctional T-cell analyses to study response and progression in adoptive cell transfer immunotherapy. , 2013, Cancer discovery.
[81] H. Moch,et al. Tissue microarrays for rapid linking of molecular changes to clinical endpoints. , 2001, The American journal of pathology.
[82] H. Schreiber,et al. Innate and adaptive immune cells in the tumor microenvironment , 2013, Nature Immunology.
[83] Antoni Ribas,et al. Single-cell analysis tools for drug discovery and development , 2015, Nature Reviews Drug Discovery.
[84] Diego G. Silva,et al. Identification of T Cell-Restricted Genes, and Signatures for Different T Cell Responses, Using a Comprehensive Collection of Microarray Datasets1 , 2005, The Journal of Immunology.
[85] Rong Fan,et al. A Clinical Microchip for Evaluation of Single Immune Cells Reveals High Functional Heterogeneity in Phenotypically Similar T Cells Nih Public Access Author Manuscript Design Rationale and Detection Limit of the Scbc Online Methods Microchip Fabrication On-chip Secretion Profiling Supplementary Mater , 2022 .
[86] Jérôme Galon,et al. [Intratumoral immune microenvironment and survival: the immunoscore]. , 2014, Medecine sciences : M/S.
[87] Rong Fan,et al. Single-cell proteomic chip for profiling intracellular signaling pathways in single tumor cells , 2011, Proceedings of the National Academy of Sciences.
[88] Amin R. Mazloom,et al. Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages , 2012, Nature Immunology.
[89] Heath C. Thomas,et al. Protein Extraction of Formalin-fixed, Paraffin-embedded Tissue Enables Robust Proteomic Profiles by Mass Spectrometry , 2009, The journal of histochemistry and cytochemistry : official journal of the Histochemistry Society.
[90] Teresa H. Y. Meng,et al. CytoSPADE: high-performance analysis and visualization of high-dimensional cytometry data , 2012, Bioinform..
[91] A. Corthay,et al. How do Regulatory T Cells Work? , 2009, Scandinavian journal of immunology.
[92] David E. Fisher,et al. Precision medicine for cancer with next-generation functional diagnostics , 2015, Nature Reviews Cancer.
[93] H. Meinzer,et al. Techniques and clinical applications , 1999 .
[94] Silke Richter,et al. Comparison and optimization of methods for the simultaneous extraction of DNA, RNA, proteins, and metabolites. , 2016, Analytical biochemistry.
[95] Aedín C. Culhane,et al. Gene Expression Atlas update—a value-added database of microarray and sequencing-based functional genomics experiments , 2011, Nucleic Acids Res..
[96] Garry P. Nolan,et al. Simultaneous measurement of multiple active kinase states using polychromatic flow cytometry , 2002, Nature Biotechnology.
[97] John R. Haliburton,et al. Abseq: Ultrahigh-throughput single cell protein profiling with droplet microfluidic barcoding , 2017, Scientific Reports.
[98] D. Mennerich,et al. Next-generation insights into regulatory T cells: expression profiling and FoxP3 occupancy in Human , 2011, Nucleic acids research.
[99] J. Shendure. The beginning of the end for microarrays? , 2008, Nature Methods.
[100] Pedro Romero,et al. Four Functionally Distinct Populations of Human Effector-Memory CD8+ T Lymphocytes1 , 2007, The Journal of Immunology.
[101] C. Garbe,et al. RNA isolation from human skin tissues for colorimetric differential display. , 1998, Journal of biochemical and biophysical methods.
[102] Sean C. Bendall,et al. Cytometry by time-of-flight shows combinatorial cytokine expression and virus-specific cell niches within a continuum of CD8+ T cell phenotypes. , 2012, Immunity.
[103] F. M. Marincola,et al. Immunoscore and Immunoprofiling in cancer: an update from the melanoma and immunotherapy bridge 2015 , 2016, Journal of Translational Medicine.
[104] Ramnik J. Xavier,et al. Gene enrichment profiles reveal T-cell development, differentiation, and lineage-specific transcription factors including ZBTB25 as a novel NF-AT repressor. , 2010, Blood.
[105] W. C. Chan,et al. Genome wide transcriptional analysis of resting and IL2 activated human natural killer cells: gene expression signatures indicative of novel molecular signaling pathways , 2007, BMC Genomics.
[106] Shimon Sakaguchi,et al. Immuno-Navigator, a batch-corrected coexpression database, reveals cell type-specific gene networks in the immune system , 2016, Proceedings of the National Academy of Sciences.
[107] P. Febbo,et al. Immune Signatures Predict Prognosis in Localized Cancer , 2010, Cancer investigation.
[108] Mark Connors,et al. Quiescent phenotype of tumor-specific CD8+ T cells following immunization. , 2004, Blood.
[109] Maqc Consortium. The MicroArray Quality Control ( MAQC )-II study of common practices for the development and validation of microarray-based predictive models , 2012 .
[110] Ruth R. Montgomery,et al. CyTOF supports efficient detection of immune cell subsets from small samples. , 2014, Journal of immunological methods.