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  • 1
    Publication Date: 2015-07-15
    Description: Immune cells function in an interacting hierarchy that coordinates the activities of various cell types according to genetic and environmental contexts. We developed graphical approaches to construct an extensible immune reference map from mass cytometry data of cells from different organs, incorporating landmark cell populations as flags on the map to compare cells from distinct samples. The maps recapitulated canonical cellular phenotypes and revealed reproducible, tissue-specific deviations. The approach revealed influences of genetic variation and circadian rhythms on immune system structure, enabled direct comparisons of murine and human blood cell phenotypes, and even enabled archival fluorescence-based flow cytometry data to be mapped onto the reference framework. This foundational reference map provides a working definition of systemic immune organization to which new data can be integrated to reveal deviations driven by genetics, environment, or pathology.〈br /〉〈br /〉〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4537647/" target="_blank"〉〈img src="https://static.pubmed.gov/portal/portal3rc.fcgi/4089621/img/3977009" border="0"〉〈/a〉   〈a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4537647/" target="_blank"〉This paper as free author manuscript - peer-reviewed and accepted for publication〈/a〉〈br /〉〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Spitzer, Matthew H -- Gherardini, Pier Federico -- Fragiadakis, Gabriela K -- Bhattacharya, Nupur -- Yuan, Robert T -- Hotson, Andrew N -- Finck, Rachel -- Carmi, Yaron -- Zunder, Eli R -- Fantl, Wendy J -- Bendall, Sean C -- Engleman, Edgar G -- Nolan, Garry P -- 1R01CA130826/CA/NCI NIH HHS/ -- 1R01GM109836/GM/NIGMS NIH HHS/ -- 1R01NS089533/NS/NINDS NIH HHS/ -- 1U19AI100627/AI/NIAID NIH HHS/ -- 201303028/PHS HHS/ -- 5-24927/PHS HHS/ -- 5R01AI073724/AI/NIAID NIH HHS/ -- 5U54CA143907/CA/NCI NIH HHS/ -- 7500108142/PHS HHS/ -- F31 CA189331/CA/NCI NIH HHS/ -- F31CA189331/CA/NCI NIH HHS/ -- F32 GM093508/GM/NIGMS NIH HHS/ -- F32 GM093508-01/GM/NIGMS NIH HHS/ -- HHSF223201210194C/PHS HHS/ -- HHSN268201000034C/HV/NHLBI NIH HHS/ -- HHSN272200700038C/AI/NIAID NIH HHS/ -- HHSN272200700038C/PHS HHS/ -- HHSN272201200028C/PHS HHS/ -- K99 GM104148/GM/NIGMS NIH HHS/ -- K99GM104148-01/GM/NIGMS NIH HHS/ -- N01-HV-00242/HV/NHLBI NIH HHS/ -- P01 CA034233/CA/NCI NIH HHS/ -- P01 CA034233-22A1/CA/NCI NIH HHS/ -- PN2 EY018228/EY/NEI NIH HHS/ -- PN2EY018228 0158 G KB065/EY/NEI NIH HHS/ -- R01 AI073724/AI/NIAID NIH HHS/ -- R01 CA130826/CA/NCI NIH HHS/ -- R01 CA184968/CA/NCI NIH HHS/ -- R01 GM109836/GM/NIGMS NIH HHS/ -- R01 NS089533/NS/NINDS NIH HHS/ -- R01CA184968/CA/NCI NIH HHS/ -- R33 CA183654/CA/NCI NIH HHS/ -- R33 CA183692/CA/NCI NIH HHS/ -- RFA CA 09-009/CA/NCI NIH HHS/ -- RFA CA 09-011/CA/NCI NIH HHS/ -- T32 GM007276/GM/NIGMS NIH HHS/ -- T32GM007276/GM/NIGMS NIH HHS/ -- U19 AI057229/AI/NIAID NIH HHS/ -- U19 AI100627/AI/NIAID NIH HHS/ -- U54 CA149145/CA/NCI NIH HHS/ -- U54CA149145/CA/NCI NIH HHS/ -- Howard Hughes Medical Institute/ -- New York, N.Y. -- Science. 2015 Jul 10;349(6244):1259425. doi: 10.1126/science.1259425.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA. Department of Pathology, Stanford University, Stanford, CA 94305, USA. Program in Immunology, Stanford University, Stanford, CA 94305, USA. gnolan@stanford.edu matthew.spitzer@stanford.edu. ; Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA. ; Department of Pathology, Stanford University, Stanford, CA 94305, USA. ; Department of Pathology, Stanford University, Stanford, CA 94305, USA. Program in Immunology, Stanford University, Stanford, CA 94305, USA. ; Department of Obstetrics and Gynecology, Division of Gynecologic Oncology, Stanford University, Stanford, CA 94305, USA. ; Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Stanford, CA 94305, USA. Program in Immunology, Stanford University, Stanford, CA 94305, USA. gnolan@stanford.edu matthew.spitzer@stanford.edu.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/26160952" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Bone Marrow/immunology ; Circadian Rhythm/immunology ; Flow Cytometry ; Genetic Variation ; Humans ; Immune System/*cytology/*immunology ; Mice ; Mice, Inbred C57BL ; Models, Biological ; Phenotype ; Reference Standards
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 2
    Publication Date: 2015-04-30
    Description: Whereas cancers grow within host tissues and evade host immunity through immune-editing and immunosuppression, tumours are rarely transmissible between individuals. Much like transplanted allogeneic organs, allogeneic tumours are reliably rejected by host T cells, even when the tumour and host share the same major histocompatibility complex alleles, the most potent determinants of transplant rejection. How such tumour-eradicating immunity is initiated remains unknown, although elucidating this process could provide the basis for inducing similar responses against naturally arising tumours. Here we find that allogeneic tumour rejection is initiated in mice by naturally occurring tumour-binding IgG antibodies, which enable dendritic cells (DCs) to internalize tumour antigens and subsequently activate tumour-reactive T cells. We exploited this mechanism to treat autologous and autochthonous tumours successfully. Either systemic administration of DCs loaded with allogeneic-IgG-coated tumour cells or intratumoral injection of allogeneic IgG in combination with DC stimuli induced potent T-cell-mediated antitumour immune responses, resulting in tumour eradication in mouse models of melanoma, pancreas, lung and breast cancer. Moreover, this strategy led to eradication of distant tumours and metastases, as well as the injected primary tumours. To assess the clinical relevance of these findings, we studied antibodies and cells from patients with lung cancer. T cells from these patients responded vigorously to autologous tumour antigens after culture with allogeneic-IgG-loaded DCs, recapitulating our findings in mice. These results reveal that tumour-binding allogeneic IgG can induce powerful antitumour immunity that can be exploited for cancer immunotherapy.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Carmi, Yaron -- Spitzer, Matthew H -- Linde, Ian L -- Burt, Bryan M -- Prestwood, Tyler R -- Perlman, Nicola -- Davidson, Matthew G -- Kenkel, Justin A -- Segal, Ehud -- Pusapati, Ganesh V -- Bhattacharya, Nupur -- Engleman, Edgar G -- 5T32AI007290-27/AI/NIAID NIH HHS/ -- F31 CA189331/CA/NCI NIH HHS/ -- F31CA189331/CA/NCI NIH HHS/ -- P30 CA124435/CA/NCI NIH HHS/ -- T32 AI007290/AI/NIAID NIH HHS/ -- U01 CA141468/CA/NCI NIH HHS/ -- England -- Nature. 2015 May 7;521(7550):99-104. doi: 10.1038/nature14424. Epub 2015 Apr 29.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉School of Medicine, Department of Pathology, Stanford University, Palo Alto, California 94305, USA. ; 1] School of Medicine, Department of Pathology, Stanford University, Palo Alto, California 94305, USA [2] School of Medicine, Baxter Laboratory in Stem Cell Biology, Department of Microbiology and Immunology, Stanford University, Palo Alto, California 94305, USA. ; School of Medicine, Department of Cardiothoracic Surgery, Stanford University, Palo Alto, California 94305, USA. ; School of Medicine, Department of Biochemistry, Stanford University, Palo Alto, California 94305, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25924063" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
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  • 3
    Keywords: APOPTOSIS ; CANCER ; CELLS ; GROWTH ; CELL ; Germany ; PATHWAY ; PATHWAYS ; NETWORK ; NETWORKS ; SYSTEM ; DISEASE ; PROTEIN ; PROTEINS ; transcription ; ACTIVATION ; FAMILY ; TRANSCRIPTION FACTOR ; CONTRAST ; ALPHA ; TRANSCRIPTION FACTORS ; SUBUNIT ; ASSAY ; NUMBER ; SIGNALING PATHWAY ; SIGNALING PATHWAYS ; TNF ; signaling ; ELISA ; ONCOLOGY ; RESOURCE ; high throughput ; HIGH-THROUGHPUT ; TIMES ; IMMUNE ; Cellular signaling ; SHIFT ; B ACTIVITY ; chemiluminescent ; NF kappa B ; NF-kappaB ; NFkB
    Abstract: Contemporary research on cellular signaling has undergone a shift of focus from qualitative measurements of single signaling pathways to high-throughput quantitation of comprehensive signaling networks. Notably, nuclear factor-kappaB (NF kappa B) is a family of transcription factors involved in immune and inflammatory responses, developmental processes, cellular growth and apoptosis and is deregulated in a number of disease states. We have established a chemiluminescent oligonucleotide-based enzyme-linked immunosorbent assay (co-ELISA) that is simple and quantitative. In contrast to currently used assays, it allows quantitation of all NF kappa B components (i.e., RelA, p50, p52, RelB and c-Rel). In addition, it can make use of whole extract and does not require cumbersome nuclear/cytosolic fractionation, saving time and resources. Co-ELISA has a 3.5- to 43-fold higher signal-over-noise ratio than currently available assays, whereas the percent relative standard deviation is 3- to 6-fold lower. Furthermore, the novel method is faster than electrophoretic mobility shift assay, not restricted to transfectable cells as is the case for luciferase reporter assays and 10 times more cost efficient than commercially available ELISA assays. Co-ELISA is a sensitive, fast and cost-efficient quantitation method for all DNA-binding NF kappa B proteins that can be used in high-throughput experimentation
    Type of Publication: Journal article published
    PubMed ID: 19924814
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  • 4
    Keywords: APOPTOSIS ; EXPRESSION ; IN-VITRO ; SURVIVAL ; BLOOD ; GENES ; T-CELLS ; SIGNAL ; B-CELLS ; antigen processing ; CHRONIC LYMPHOCYTIC-LEUKEMIA ; FEATURES ; INDUCE ; chronic lymphocytic leukaemia ; immunocompetence ; lysozyme ; nurse-like cells
    Abstract: Chronic lymphocytic leukaemia (CLL) cells convert CD14(+) cells from patients into 'nurse-like' cells (NLCs). CLL cells can also convert CD14(+) peripheral blood mononuclear cells (PBMCs) from healthy donors into cells with morphological similarities to NLCs (CD14(CLL)-cells). However it is unclear whether only CLL cells induce this conversion process. This study showed that CD14(+) PBMCs from healthy donors could also be converted into differentiated cells (CD14(B)-cells) by non-malignant B-cells. In order to identify changes specifically induced by CLL cells, we compared gene expression profiles of NLCs, CD14(CLL)-cells and CD14(B)-cells. CD14(+) cells cultured with CLL cells were more similar to NLCs than those cultured with non-malignant B-cells. The most significant changes induced by CLL cells were deregulation of the antigen presentation pathway and of genes related to immunity. NLCs had reduced levels of lysozyme activity, CD74 and HLA-DR in-vitro while expression of inhibitory FCGR2B was increased. These findings suggest an impaired immunocompetence of NLCs which, if found in-vivo, could contribute to the immunodeficiency in CLL patients
    Type of Publication: Journal article published
    PubMed ID: 21615384
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  • 5
    Keywords: DNA methylation ; FACTOR-KAPPA-B ; CHRONIC LYMPHOCYTIC-LEUKEMIA ; DISEASE PROGRESSION ; CHROMOSOME 13Q14 ; TUMOR-SUPPRESSOR LOCUS ; LONG NONCODING RNAS ; PROMOTER CPG METHYLATION ; PI3K/NF-KAPPA-B PATHWAY ; ANTISENSE TRANSCRIPTS
    Abstract: Non-coding RNAs are much more common than previously thought. However, for the vast majority of non-coding RNAs, the cellular function remains enigmatic. The two long non-coding RNA (lncRNA) genes DLEU1 and DLEU2 map to a critical region at chromosomal band 13q14.3 that is recurrently deleted in solid tumors and hematopoietic malignancies like chronic lymphocytic leukemia (CLL). While no point mutations have been found in the protein coding candidate genes at 13q14.3, they are deregulated in malignant cells, suggesting an epigenetic tumor suppressor mechanism. We therefore characterized the epigenetic makeup of 13q14.3 in CLL cells and found histone modifications by chromatin-immunoprecipitation (ChIP) that are associated with activated transcription and significant DNA-demethylation at the transcriptional start sites of DLEU1 and DLEU2 using 5 different semi-quantitative and quantitative methods (aPRIMES, BioCOBRA, MCIp, MassARRAY, and bisulfite sequencing). These epigenetic aberrations were correlated with transcriptional deregulation of the neighboring candidate tumor suppressor genes, suggesting a coregulation in cis of this gene cluster. We found that the 13q14.3 genes in addition to their previously known functions regulate NF-kB activity, which we could show after overexpression, siRNA-mediated knockdown, and dominant-negative mutant genes by using Western blots with previously undescribed antibodies, by a customized ELISA as well as by reporter assays. In addition, we performed an unbiased screen of 810 human miRNAs and identified the miR-15/16 family of genes at 13q14.3 as the strongest inducers of NF-kB activity. In summary, the tumor suppressor mechanism at 13q14.3 is a cluster of genes controlled by two lncRNA genes that are regulated by DNA-methylation and histone modifications and whose members all regulate NF-kB. Therefore, the tumor suppressor mechanism in 13q14.3 underlines the role both of epigenetic aberrations and of lncRNA genes in human tumorigenesis and is an example of colocalization of a functionally related gene cluster.
    Type of Publication: Journal article published
    PubMed ID: 23593011
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  • 6
    Keywords: APOPTOSIS ; EXPRESSION ; SURVIVAL ; ACTIVATION ; T-CELLS ; ALPHA ; INHIBITORS ; INDUCED TNF RECEPTOR ; CYTOKINE MODULATION
    Abstract: BACKGROUND: Thalidomide may represent a novel therapeutic strategy in the treatment of chronic lymphocytic leukemia (CLL). Since the activation of nuclear factor kappa B (NF-kappaB) causes not only malignant transformation and tumor progression, but also allows tumor cells to evade immune surveillance, NF-kappaB signaling components might constitute a potential target for future therapy in CLL. OBJECTIVES: The current study is an attempt to characterize proteins regulated by thalidomide. Thalidomide's influence on NF-kappaB proteins and on regulatory T cells (Treg) in CLL was investigated. MATERIAL AND METHODS: A total of 15 patients with CLL were treated with a combined thalidomide/fludarabine regimen. Peripheral blood mononuclear cells were separated by Ficoll density gradient centrifugation. To evaluate glucocorticoidinduced tumour-necrosis-factor-receptor-related protein (GITR) expression in regulatory T cells, cells incubated with anti-CD3, ani-CD4 and anti-CD25 were permeabilized and then stained with anti-FOXP3 and analyzed using flow cytometry. Human TNF enzyme-linked immunosorbent assay (ELISA) was used to determine the tumor necrosis factor (TNF) levels in the serum. To evaluate NF-kappaB activity, chemiluminescent oligonucleotide-based ELISA was performed. RESULTS: It was found that thalidomide regulates NF-kappaB activity differentially, and the activity of certain NF-kappaB components correlated with TNF levels and T regulatory cell (CD4 + CD25 high GITR + ). CONCLUSIONS: These results might indicate that thalidomide not only regulates TNF but also directly interferes with NF-kappaB components.
    Type of Publication: Journal article published
    PubMed ID: 24596000
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  • 7
  • 8
    Keywords: RECEPTOR ; IN-VITRO ; proliferation ; SURVIVAL ; LIGAND ; KAPPA-B ; CHRONIC LYMPHOCYTIC-LEUKEMIA ; SIGNALING MECHANISMS ; NORMAL B-CELLS ; SPONTANEOUS APOPTOSIS
    Abstract: Chronic lymphocytic leukemia (CLL) cells fail to enter apoptosis in vivo as opposed to their non-malignant B-lymphocyte counterparts. The ability of CLL cells to escape apoptosis is highly dependent on their microenvironment. Compared to nonmalignant B cells, CLL cells are more responsive to complex stimuli that can be reproduced in vitro by the addition of cytokines. To understand the molecular mechanism of the environment-dependent anti-apoptotic signaling circuitry of CLL cells, we quantified the effect of the SDF-1, BAFF, APRIL, anti-IgM, interleukin-4 (IL4) and secreted CD40L (sCD40L) on the survival of in vitro cultured CLL cells and found IL4 and sCD40L to be most efficient in rescuing CLL cells from apoptosis. In quantitative dose-response experiments using cell survival as readout, the binding affinity of IL4 to its receptor was similar between malignant and non-malignant cells. However, the downstream signaling in terms of the amount of STAT6 and its degree of phosphorylation was highly stimulated in CLL cells. In contrast, the response to sCD40L showed a loss of cooperative binding in CLL cells but displayed a largely increased ligand binding affinity. Although a high-throughput microscopy analysis did not reveal a significant difference in the spatial CD40 receptor organization, the downstream signaling showed an enhanced activation of the NF-kB pathway in the malignant cells. Thus, we propose that the anti-apoptotic phenotype of CLL involves a sensitized response for IL4 dependent STAT6 phosphorylation, and an activation of NF-kB signaling due to an increased affinity of sCD40L to its receptor.
    Type of Publication: Journal article published
    PubMed ID: 24828787
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  • 9
    Keywords: CELLS ; CELL ; Germany ; PATIENT ; T cells ; T-CELL ; T-CELLS ; leukaemia ; regulatory T cells ; HELPER-CELLS
    Type of Publication: Journal article published
    PubMed ID: 19961483
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  • 10
    Keywords: T-CELLS ; NECROSIS-FACTOR-ALPHA ; REFRACTORY MULTIPLE-MYELOMA ; CHRONIC LYMPHOCYTIC-LEUKEMIA ; MYELODYSPLASTIC SYNDROMES ; NATURAL-KILLER-CELL ; LENALIDOMIDE PLUS DEXAMETHASONE ; DEPENDENT CELLULAR CYTOTOXICITY ; CHROMOSOME 5Q DELETION ; THALIDOMIDE ANALOGS
    Abstract: Immune modulatory drugs have been successfully used to treat patients with multiple myeloma (MM), myelodysplastic syndromes displaying loss of 5q (del5q MDS) and chronic lymphocytic leukemia (CLL). Immune modulatory drugs are used in first-line therapy in combination with functionally complementary compounds, but have also shown efficacy in refractory disease. However, their exact mode of action remains unclear. Here we describe the clinical impact of these compounds on MM, del5q MDS and CLL, discuss their mode of action with respect to intracellular targets, focus on the phenotypic changes that immune modulatory compounds induce in the tumor microenvironment and how they modulate the immune response.
    Type of Publication: Journal article published
    PubMed ID: 21645972
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