Immune cell profiling in cancer: molecular approaches to cell-specific identification

[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.