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  • 1
    In: Journal of Molecular and Cellular Cardiology, Elsevier BV, Vol. 40, No. 6 ( 2006-06), p. 1015-
    Type of Medium: Online Resource
    ISSN: 0022-2828
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2006
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  • 2
    Online Resource
    Online Resource
    Springer Science and Business Media LLC ; 2015
    In:  Nature Communications Vol. 6, No. 1 ( 2015-09-24)
    In: Nature Communications, Springer Science and Business Media LLC, Vol. 6, No. 1 ( 2015-09-24)
    Abstract: Single-cell analysis reveals aspects of cellular physiology not evident from population-based studies, particularly in the case of highly multiplexed methods such as mass cytometry (CyTOF) able to correlate the levels of multiple signalling, differentiation and cell fate markers. Immunofluorescence (IF) microscopy adds information on cell morphology and the microenvironment that are not obtained using flow-based techniques, but the multiplicity of conventional IF is limited. This has motivated development of imaging methods that require specialized instrumentation, exotic reagents or proprietary protocols that are difficult to reproduce in most laboratories. Here we report a public-domain method for achieving high multiplicity single-cell IF using cyclic immunofluorescence (CycIF), a simple and versatile procedure in which four-colour staining alternates with chemical inactivation of fluorophores to progressively build a multichannel image. Because CycIF uses standard reagents and instrumentation and is no more expensive than conventional IF, it is suitable for high-throughput assays and screening applications.
    Type of Medium: Online Resource
    ISSN: 2041-1723
    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2015
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  • 3
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2014
    In:  Cancer Research Vol. 74, No. 19_Supplement ( 2014-10-01), p. 5502-5502
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 74, No. 19_Supplement ( 2014-10-01), p. 5502-5502
    Abstract: Most analyses of cellular responses to anti-cancer drugs focus on variation in potency (e.g. GI50 or IC50) under the assumption that potency is the most important difference between effective and ineffective drugs or sensitive and resistant cells. We took a multi-parametric approach involving analysis of additional features such as maximum effect (Emax), the slope of the dose-response curve (Hill Slope; HS), and the area under the curve (AUC). We found that a subset of these parameters varies in a systematic manner with cell line and another subset with drug class. For cell cycle inhibitors, Emax generally correlates with cell proliferation rate but this is not always true: Emax ∼ 0 for S-phase specific drugs such as cisplatin, carboplatin and oxaliplatin across multiple cell lines. For drugs targeting the Akt/PI3K/mTOR pathway the slope of the dose-response curve is unusually shallow (HS & lt; & lt; 1). Classical pharmacology has no ready explanation for this phenomenon but single-cell analysis showed that it correlated with significant and heritable cell-to-cell variability in the extent of target inhibition. We conclude that parameters other than potency should be considered in the comparative analysis of drug response, particularly at clinically relevant concentrations near and above IC50. Citation Format: Mohammad Fallahi-Sichani, Saman Honarnejad, Laura M. Heiser, Joe W. Gray, Peter K. Sorger. Metrics other than potency reveal systematic variation in responses to cancer drugs. [abstract] . In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5502. doi:10.1158/1538-7445.AM2014-5502
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2014
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  • 4
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2013
    In:  Cancer Research Vol. 73, No. 8_Supplement ( 2013-04-15), p. 1810-1810
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 73, No. 8_Supplement ( 2013-04-15), p. 1810-1810
    Abstract: The most malignant central nervous system cancer, Glioblastoma Mulitforme (GBM), accounts for the majority of primary brain cancer-related deaths (Porter, McCarthy et al. 2010) and has an average post-diagnostic survival rate of just over 14 months (Behin, Hoang-Xuan et al. 2003; Stupp, Mason et al. 2005; Louis, Ohgaki et al. 2007). The epidermal growth factor receptor (EGFR) (Wong, Ruppert et al. 1992; Mukasa, Wykosky et al. 2010) has been shown to play central roles in GBM tumorigenesis and therapeutic resistance and reports have indicated that ∼50% of all GBMs display aberrant activation of EGFR and of these ∼50% also express a ligand-independent, constitutively active mutant, EGFRvIII (Nishikawa, Ji et al. 1994) that is associated with increased tumorigenecity and mortality (Heimberger, Hlatky et al. 2005; Heimberger, Suki et al. 2005). In addition, several reports have indicated that the c-Jun N-terminal kinase 2 (JNK2) is activated in the majority of GBM tumors when compared to normal brain tissue (Antonyak, Kenyon et al. 2002; Tsuiki, Tnani et al. 2003; Cui, Han et al. 2006) and JNK2 activation strongly correlates with both GBM histological grade and expression of EGFR (Li, Wang et al. 2008). Current therapies specifically targeting the EGFR have limited success and the universal resurgence of tumors post-treatment occurs due to infiltrating tumor cells that escape initial surgery and exhibit profound resistance to irradiation and current chemotherapy treatments (Claes, Idema et al. 2007). Therefore, the identification of novel tractable targets for improved therapeutics and the molecular and genetic profiling of GBMs continues to be a necessity. To this end we have compared the gene expression profiles of U87 GBM cells with cells expressing EGFRvIII (U87EGFRvIII) and specifically studied genes modulated by JNK2 using microarray analysis comparing U87EGFRvIII cells expressing either short hairpin RNA directed against JNK2 (U87EGFRvIIIshJNK2) or a non-silencing control (U87EGFRvIIIshNS). Gene expression profiles revealed 390 EGFRvIII-induced genes that were significantly associated with targeted loss of JNK2 expression by a minimum of 2 fold on comparison to non-silencing controls. JNK2 modulated gene clusters related to cell movement were revealed with Ingenuity Pathway Analysis (IPA) and included interesting genes such as HGF, MMP7, FGF10, PDGFRA and IGFBP5. Ultimately, these studies, allowed us to further understand the molecular mechanisms driving EGFRvIII-induced tumorigenesis and such knowledge will ultimately enhance our ability to develop an efficacious GBM therapy that can increase the effectiveness of clinically approved drugs. Citation Format: Vanessa Saunders, Mohammad Fallahi-Sichani, Yuan Yuan Ling, Derek Duckett. Analysis of EGFRvIII mediated responses driven by JNK2 in Glioblastoma Multiforme. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1810. doi:10.1158/1538-7445.AM2013-1810
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2013
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  • 5
    Online Resource
    Online Resource
    American Association for Cancer Research (AACR) ; 2013
    In:  Cancer Research Vol. 73, No. 8_Supplement ( 2013-04-15), p. 5213-5213
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 73, No. 8_Supplement ( 2013-04-15), p. 5213-5213
    Abstract: Melanoma is the deadliest form of skin cancer and the leading cause of death from skin disease. The BRAF(V600E) mutation is found in approximately 60% of melanomas. It causes constitutive activation of the RAF/MEK/ERK signaling pathway in these tumors leading to uncontrolled cell growth. Inhibition of BRAF(V600E) induces apoptosis in melanoma cells which has been used as the basis for molecular targeted therapy of melanoma. Small-molecule compounds such as Vemurafenib, Dabrafenib and other selective BRAF(V600E) inhibitors specifically bind BRAF(V600E), and have been shown to cause dramatic, but transient, tumor regression in vivo. The precise mechanisms of cell death following BRAF inhibition remain obscure; the literature posits a diversity of ways in which apoptosis is induced. However, it is unclear whether a single but complex network is involved or whether mechanisms differ from one cell type to the next. This is an important issue because use of BRAF(V600E) inhibitors in the treatment of melanoma is seriously challenged by the absence of durable responses; even in initially responsive patients tumors usually re-emerge within months and are observed to be drug resistant. An important challenge is thus to understand determinants of initial sensitivity to BRAF inhibition beyond V600E mutation and to determine which of these are involved in resistance. Using high throughput measurement of the abundance and state of modification of multiple proteins representing diverse signaling pathways at the basal level and over time in multiple melanoma cell lines exposed to different doses of BRAF inhibitors and data-driven mathematical modeling, we determine how the complex dynamics of signaling pathways are controlled in different cell lines and how drugs targeting BRAF(V600E) alter this signaling. Our analysis shows that the basal level of some proteins such as PTEN, pERK, pS6, pAkt, and β-catenin vary up to 100-fold among different lines prior drug treatment. Further, these cell lines show different degrees of oncogene addiction and remarkable diversity with respect to the level of ERK inhibition and apoptosis as well as activation or inhibition of other signaling cascades following BRAF inhibition. We use mathematical modeling to relate basal levels of signaling proteins and their dynamics following BRAF inhibition to pharmacological descriptors of sensitivity to multiple BRAF drugs. Thus, we identify key signaling nodes within the signaling networks of the melanoma cells which determine the differential phenotypic consequences of BRAF inhibition. This approach will be critical for predicting and ultimately improving drug sensitivity in resistant tumors (e.g. via co-treatment strategies). Citation Format: Mohammad Fallahi-Sichani, Nathan J. Moerke, Anahita Dastur, Cyril H. Benes, Peter K. Sorger. A systems biology approach to understanding differential phenotypic outcome of BRAF(V600E) inhibition in melanoma cells. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 5213. doi:10.1158/1538-7445.AM2013-5213
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2013
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  • 6
    In: Free Radical Biology and Medicine, Elsevier BV, Vol. 100 ( 2016-11), p. S84-
    Type of Medium: Online Resource
    ISSN: 0891-5849
    Language: English
    Publisher: Elsevier BV
    Publication Date: 2016
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    SSG: 12
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  • 7
    In: Molecular Systems Biology, EMBO, Vol. 11, No. 3 ( 2015-03)
    Abstract: image Adaptive responses to RAF / MEK inhibitors are analyzed systematically across a panel of BRAF V 600E melanoma lines to reveal a role for cell‐to‐cell variability induced by the JNK /c‐Jun pathway and other factors in adaptive drug resistance. Adaptive responses are profiled using a combination of multiplex measurements across time, dose, cell line and drug type, statistical modeling and single‐cell analysis. BRAF V600E melanoma lines differ in sensitivity to RAF/MEK inhibition with respect to both IC 50 and maximal effect ( E max ), reflecting cell‐to‐cell variability in drug response. Adaptive responses to RAF/MEK inhibition are diverse and involve multiple signaling pathways. The JNK/c‐Jun pathway is a common adaptive response that decreases drug maximum effect. JNK inhibition prevents induction of quiescence by RAF inhibition and promotes apoptosis.
    Type of Medium: Online Resource
    ISSN: 1744-4292 , 1744-4292
    Language: English
    Publisher: EMBO
    Publication Date: 2015
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    SSG: 12
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  • 8
    In: American Journal of Rhinology, SAGE Publications, Vol. 20, No. 6 ( 2006-11), p. 577-581
    Abstract: Different techniques in neuroimaging have been proposed for assessment of olfactory dysfunction but they are not without limitations. Recently, some studies showed the usefulness of single photon emission–computed tomography (SPECT) in evaluation of patients with posttraumatic anosmia. This study was designed to assess the possible diagnostic value of SPECT findings in patients with posttraumatic anosmia in comparison with magnetic resonance imaging (MRI)/CT imaging. Methods Sixteen patients who had head trauma and consequently anosmia, which was defined according to Cain's identification test, were included in this study. Two nonanosmic groups, traumatic patients and nontraumatic healthy individuals, were selected as control groups for this study. Qualitative and semiquantitative brain perfusion SPECT was performed by measuring the uptake ratio of the orbital frontal cortex to occipital pole in the sagittal projections (uptake index). All 16 target patients had a previous CT scan and/or MRI. Semiquantitative and qualitative brain perfusion SPECT were compared with radiological imaging. Results Semiquantitative assessment of brain perfusion SPECT revealed remarkable orbital frontal hypoperfusion as compared with two control groups. 87.5% of anosmic patients showed orbital frontal hypoperfusion (≥2 SD below the lowest level in healthy controls). In addition, the semiquantitative SPECT method detected more orbitofrontal abnormality than the qualitative method or radiological imaging (MRI and/or CT). Conclusion Findings suggest that by using SPECT, posttraumatic anosmia corresponds to the hypoperfusion in the orbital frontal cortex in a great number of patients. Because of its availability, rather low cost, technical ease, and possibility to obtain objective quantitative information, brain perfusion SPECT can be complementary to other diagnostic techniques in the evaluation of olfactory function, although additional neurophysiological and imaging studies are needed.
    Type of Medium: Online Resource
    ISSN: 1050-6586 , 1539-6290
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    Language: English
    Publisher: SAGE Publications
    Publication Date: 2006
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  • 9
    In: Cancer Research, American Association for Cancer Research (AACR), Vol. 77, No. 13_Supplement ( 2017-07-01), p. 5561-5561
    Abstract: Adaptation and fractional response of tumor cells to targeted inhibitors of oncogenic pathways creates a population of viable tumor cells from which fully resistant clones can ultimately arise. Thus, understanding transient drug adaptation is key for both improving the effectiveness of treatment and delaying/controlling acquired resistance. Despite the wealth of information available about feedback mechanisms associated with adaptive resistance, most of our knowledge in this area comes from studying drug response in bulk tumor cell populations. Furthermore, the phenotypic consequences of drug adaptation have been often studied at a few fixed time-points, when drug-adapted cells exhibit a high population-average activity in multiple pro-growth signaling cascades. It therefore remains unclear how the initial responses to drug relate to subsequent phenotypes such as cell death or adaptation. This is likely a key point for designing novel approaches to overcome fractional drug response in tumor cells and to achieve durable therapy. We use real-time live-cell imaging, single-cell analysis and molecular profiling to show that exposure of BRAFV600E melanoma cells to RAF/MEK inhibitors elicits a time-variable and heterogeneous response in which some cells die, some arrest and the remainder adapt to drug. Drug-adapted cells up-regulate markers of the neural crest (e.g. NGFR), a melanocyte precursor, and grow slowly. The drug-induced slowly-cycling NFGRHigh state is only transiently stable, reverting to the drug-naïve state within two weeks of drug withdrawal as measured by the restoration of RAF/MEK inhibitor sensitivity, accelerated rate of cell division and reduced expression of NGFR. Transcriptional and biochemical profiling of cell lines and human tumors implicates a role for the c-Jun/ECM/FAK/Src cascade in driving the de-differentiated resistance program. We identify multiple drugs targeting this cascade as well as BET bromodomain inhibitors that block this resistance program in cell lines and in a BRAFV600E melanoma xenograft model and increase sensitivity and maximal effect (Emax) of RAF/MEK inhibitors. Our study reveals directly how drug adaptation happens in individual tumor cells leading to emergence of heterogeneous cell sub-populations with reduced drug-sensitivity that may be targeted by drug combinations. Citation Format: Mohammad Fallahi-Sichani, Verena Becker, Benjamin Izar, Gregory J. Baker, Jia-Ren Lin, Sarah A. Boswell, Levi A. Garraway, Peter K. Sorger. Single-cell analysis reveals an adaptive, transiently heritable, slowly-dividing, drug-resistant state inhibitable by drug combinations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 5561. doi:10.1158/1538-7445.AM2017-5561
    Type of Medium: Online Resource
    ISSN: 0008-5472 , 1538-7445
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    Language: English
    Publisher: American Association for Cancer Research (AACR)
    Publication Date: 2017
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    detail.hit.zdb_id: 1432-1
    detail.hit.zdb_id: 410466-3
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  • 10
    Online Resource
    Online Resource
    The American Association of Immunologists ; 2004
    In:  The Journal of Immunology Vol. 173, No. 2 ( 2004-07-15), p. 1094-1102
    In: The Journal of Immunology, The American Association of Immunologists, Vol. 173, No. 2 ( 2004-07-15), p. 1094-1102
    Abstract: Postnatal T lymphocyte differentiation in the thymus is a multistage process involving serial waves of lineage specification, proliferative expansion, and survival/cell death decisions. Although these are believed to originate from signals derived from various thymic stromal cells, the ultimate consequence of these signals is to induce the transcriptional changes that are definitive of each step. To help to characterize this process, high density microarrays were used to analyze transcription factor gene expression in RNA derived from progenitors at each stage of T lymphopoietic differentiation, and the results were validated by a number of appropriate methods. We find a large number of transcription factors to be expressed in developing T lymphocytes, including many with known roles in the control of differentiation, proliferation, or cell survival/death decisions in other cell types. Some of these are expressed throughout the developmental process, whereas others change substantially at specific developmental transitions. The latter are particularly interesting, because stage-specific changes make it increasingly likely that the corresponding transcription factors may be involved in stage-specific processes. Overall, the data presented here represent a large resource for gene discovery and for confirmation of results obtained through other methods.
    Type of Medium: Online Resource
    ISSN: 0022-1767 , 1550-6606
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    Language: English
    Publisher: The American Association of Immunologists
    Publication Date: 2004
    detail.hit.zdb_id: 1475085-5
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