Publications by authors named "Sumit Deswal"

13 Publications

  • Page 1 of 1

Apelin inhibition prevents resistance and metastasis associated with anti-angiogenic therapy.

EMBO Mol Med 2019 08 24;11(8):e9266. Epub 2019 Jun 24.

Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna BioCenter, Vienna, Austria.

Angiogenesis is a hallmark of cancer, promoting growth and metastasis. Anti-angiogenic treatment has limited efficacy due to therapy-induced blood vessel alterations, often followed by local hypoxia, tumor adaptation, progression, and metastasis. It is therefore paramount to overcome therapy-induced resistance. We show that Apelin inhibition potently remodels the tumor microenvironment, reducing angiogenesis, and effectively blunting tumor growth. Functionally, targeting Apelin improves vessel function and reduces polymorphonuclear myeloid-derived suppressor cell infiltration. Importantly, in mammary and lung cancer, Apelin prevents resistance to anti-angiogenic receptor tyrosine kinase (RTK) inhibitor therapy, reducing growth and angiogenesis in lung and breast cancer models without increased hypoxia in the tumor microenvironment. Apelin blockage also prevents RTK inhibitor-induced metastases, and high Apelin levels correlate with poor prognosis of anti-angiogenic therapy patients. These data identify a druggable anti-angiogenic drug target that reduces tumor blood vessel densities and normalizes the tumor vasculature to decrease metastases.
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http://dx.doi.org/10.15252/emmm.201809266DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6685079PMC
August 2019

BET-Bromodomain Inhibitors Engage the Host Immune System and Regulate Expression of the Immune Checkpoint Ligand PD-L1.

Cell Rep 2017 02;18(9):2162-2174

Peter MacCallum Cancer Centre, Melbourne, VIC 3000, Australia; Sir Peter MacCallum Department of Oncology, The University of Melbourne, Parkville, VIC 3010, Australia. Electronic address:

BET inhibitors (BETi) target bromodomain-containing proteins and are currently being evaluated as anti-cancer agents. We find that maximal therapeutic effects of BETi in a Myc-driven B cell lymphoma model required an intact host immune system. Genome-wide analysis of the BETi-induced transcriptional response identified the immune checkpoint ligand Cd274 (Pd-l1) as a Myc-independent, BETi target-gene. BETi directly repressed constitutively expressed and interferon-gamma (IFN-γ) induced CD274 expression across different human and mouse tumor cell lines and primary patient samples. Mechanistically, BETi decreased Brd4 occupancy at the Cd274 locus without any change in Myc occupancy, resulting in transcriptional pausing and rapid loss of Cd274 mRNA production. Finally, targeted inhibition of the PD-1/PD-L1 axis by combining anti-PD-1 antibodies and the BETi JQ1 caused synergistic responses in mice bearing Myc-driven lymphomas. Our data uncover an interaction between BETi and the PD-1/PD-L1 immune-checkpoint and provide mechanistic insight into the transcriptional regulation of CD274.
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http://dx.doi.org/10.1016/j.celrep.2017.02.011DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5340981PMC
February 2017

SWI/SNF regulates a transcriptional program that induces senescence to prevent liver cancer.

Genes Dev 2016 Oct 13;30(19):2187-2198. Epub 2016 Oct 13.

MRC Clinical Sciences Centre (CSC), London W12 0NN, United Kingdom.

Oncogene-induced senescence (OIS) is a potent tumor suppressor mechanism. To identify senescence regulators relevant to cancer, we screened an shRNA library targeting genes deleted in hepatocellular carcinoma (HCC). Here, we describe how knockdown of the SWI/SNF component ARID1B prevents OIS and cooperates with RAS to induce liver tumors. ARID1B controls p16 and p21 transcription but also regulates DNA damage, oxidative stress, and p53 induction, suggesting that SWI/SNF uses additional mechanisms to regulate senescence. To systematically identify SWI/SNF targets regulating senescence, we carried out a focused shRNA screen. We discovered several new senescence regulators, including ENTPD7, an enzyme that hydrolyses nucleotides. ENTPD7 affects oxidative stress, DNA damage, and senescence. Importantly, expression of ENTPD7 or inhibition of nucleotide synthesis in ARID1B-depleted cells results in re-establishment of senescence. Our results identify novel mechanisms by which epigenetic regulators can affect tumor progression and suggest that prosenescence therapies could be employed against SWI/SNF-mutated cancers.
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http://dx.doi.org/10.1101/gad.286112.116DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5088567PMC
October 2016

Transcriptional plasticity promotes primary and acquired resistance to BET inhibition.

Nature 2015 Sep 14;525(7570):543-547. Epub 2015 Sep 14.

Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), 1030 Vienna, Austria.

Following the discovery of BRD4 as a non-oncogene addiction target in acute myeloid leukaemia (AML), bromodomain and extra terminal protein (BET) inhibitors are being explored as a promising therapeutic avenue in numerous cancers. While clinical trials have reported single-agent activity in advanced haematological malignancies, mechanisms determining the response to BET inhibition remain poorly understood. To identify factors involved in primary and acquired BET resistance in leukaemia, here we perform a chromatin-focused RNAi screen in a sensitive MLL-AF9;Nras(G12D)-driven AML mouse model, and investigate dynamic transcriptional profiles in sensitive and resistant mouse and human leukaemias. Our screen shows that suppression of the PRC2 complex, contrary to effects in other contexts, promotes BET inhibitor resistance in AML. PRC2 suppression does not directly affect the regulation of Brd4-dependent transcripts, but facilitates the remodelling of regulatory pathways that restore the transcription of key targets such as Myc. Similarly, while BET inhibition triggers acute MYC repression in human leukaemias regardless of their sensitivity, resistant leukaemias are uniformly characterized by their ability to rapidly restore MYC transcription. This process involves the activation and recruitment of WNT signalling components, which compensate for the loss of BRD4 and drive resistance in various cancer models. Dynamic chromatin immunoprecipitation sequencing and self-transcribing active regulatory region sequencing of enhancer profiles reveal that BET-resistant states are characterized by remodelled regulatory landscapes, involving the activation of a focal MYC enhancer that recruits WNT machinery in response to BET inhibition. Together, our results identify and validate WNT signalling as a driver and candidate biomarker of primary and acquired BET resistance in leukaemia, and implicate the rewiring of transcriptional programs as an important mechanism promoting resistance to BET inhibitors and, potentially, other chromatin-targeted therapies.
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http://dx.doi.org/10.1038/nature14898DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4921058PMC
September 2015

Kidins220/ARMS associates with B-Raf and the TCR, promoting sustained Erk signaling in T cells.

J Immunol 2013 Mar 28;190(5):1927-35. Epub 2013 Jan 28.

Department of Molecular Immunology, Institute of Biology III, Faculty of Biology, University of Freiburg and Max Planck-Institute of Immunobiology and Epigenetics, Freiburg, Germany.

The activation kinetics of MAPK Erk are critical for T cell development and activation. In particular, sustained Erk signaling is required for T cell activation and effector functions, such as IL-2 production. Although Raf-1 triggers transient Erk activation, B-Raf is implicated in sustained Erk signaling after TCR stimulation. In this study, we show that B-Raf is dephosphorylated on its inhibitory serine 365 upon TCR triggering. However, it is unknown how B-Raf activation is coupled to the TCR. Using mass spectrometry, we identified protein kinase D-interacting substrate of 220 kDa (Kidins220)/ankyrin repeat-rich membrane spanning protein, mammalian target of rapamycin, Rictor, Dock2, and GM130 as novel B-Raf interaction partners. We focused on Kidins220, a protein that has been studied in neuronal cells and found that it associated with the pre-TCR, αβTCR, and γδTCR. Upon prolonged TCR stimulation, the Kidins220-TCR interaction was reduced, as demonstrated by immunoprecipitation and proximity ligation assays. We show that Kidins220 is required for TCR-induced sustained, but not transient, Erk activation. Consequently, induction of the immediate early gene products and transcription factors c-Fos and Erg-1 was blocked, and upregulation of the activation markers CD69, IL-2, and IFN-γ was reduced. Further, Kidins220 was required for optimal calcium signaling. In conclusion, we describe Kidins220 as a novel TCR-interacting protein that couples B-Raf to the TCR. Kidins220 is mandatory for sustained Erk signaling; thus, it is crucial for TCR-mediated T cell activation.
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http://dx.doi.org/10.4049/jimmunol.1200653DOI Listing
March 2013

Semi-automatic determination of cell surface areas used in systems biology.

Front Biosci (Elite Ed) 2013 Jan 1;5:533-45. Epub 2013 Jan 1.

BIOSS Centre for Biological Signaling Studies, University of Freiburg, Germany.

Quantitative biology requires high precision measurement of cellular parameters such as surface areas or volumes. Here, we have developed an integrated approach in which the data from 3D confocal microscopy and 2D high-resolution transmission electron microscopy were combined. The volumes and diameters of the cells within one population were automatically measured from the confocal data sets. The perimeter of the cell slices was measured in the TEM images using a semi-automated segmentation into background, cytoplasm and nucleus. These data in conjunction with approaches from stereology allowed for an unbiased estimate of surface areas with high accuracy. We have determined the volumes and surface areas of the cells and nuclei of six different immune cell types. In mast cells for example, the resulting cell surface was 3.5 times larger than the theoretical surface assuming the cell was a sphere with the same volume. Thus, our accurate data can now serve as inputs in modeling approaches in systems immunology.
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http://dx.doi.org/10.2741/e635DOI Listing
January 2013

Quantitative analysis of protein phosphorylations and interactions by multi-colour IP-FCM as an input for kinetic modelling of signalling networks.

PLoS One 2011 29;6(7):e22928. Epub 2011 Jul 29.

Max Planck Institute of Immunobiology and Epigenetics, and Faculty of Biology, Biology III, University of Freiburg, Freiburg, Germany.

Background: To understand complex biological signalling mechanisms, mathematical modelling of signal transduction pathways has been applied successfully in last few years. However, precise quantitative measurements of signal transduction events such as activation-dependent phosphorylation of proteins, remains one bottleneck to this success.

Methodology/principal Findings: We use multi-colour immunoprecipitation measured by flow cytometry (IP-FCM) for studying signal transduction events to unrivalled precision. In this method, antibody-coupled latex beads capture the protein of interest from cellular lysates and are then stained with differently fluorescent-labelled antibodies to quantify the amount of the immunoprecipitated protein, of an interaction partner and of phosphorylation sites. The fluorescence signals are measured by FCM. Combining this procedure with beads containing defined amounts of a fluorophore allows retrieving absolute numbers of stained proteins, and not only relative values. Using IP-FCM we derived multidimensional data on the membrane-proximal T-cell antigen receptor (TCR-CD3) signalling network, including the recruitment of the kinase ZAP70 to the TCR-CD3 and subsequent ZAP70 activation by phosphorylation in the murine T-cell hybridoma and primary murine T cells. Counter-intuitively, these data showed that cell stimulation by pervanadate led to a transient decrease of the phospho-ZAP70/ZAP70 ratio at the TCR. A mechanistic mathematical model of the underlying processes demonstrated that an initial massive recruitment of non-phosphorylated ZAP70 was responsible for this behaviour. Further, the model predicted a temporal order of multisite phosphorylation of ZAP70 (with Y319 phosphorylation preceding phosphorylation at Y493) that we subsequently verified experimentally.

Conclusions/significance: The quantitative data sets generated by IP-FCM are one order of magnitude more precise than Western blot data. This accuracy allowed us to gain unequalled insight into the dynamics of the TCR-CD3-ZAP70 signalling network.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0022928PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3146539PMC
December 2011

Calorie restriction up-regulates iron and copper transport genes in Saccharomyces cerevisiae.

Mol Biosyst 2011 Feb 28;7(2):394-402. Epub 2010 Oct 28.

Department of Biotechnology, National Institute of Pharmaceutical Education and Research, Sector 67, S A S Nagar, Punjab, 160062, India.

Calorie restriction (CR) is a non genetic intervention, known to confer longevity benefits across the various phyla from unicellular yeast to mammals. CR also invokes homeostatic responses similar to stress, however the sequence of molecular events leading to longevity is still illusive. In this study, we analysed the whole genome gene expression profile in response to CR, mutations mimicking CR, heat shock and H(2)O(2) from a gene ontology perspective. Our analysis revealed that mitochondrion is a common hub in the gene expression programme under these conditions and the electron transport chain (ETC) is a major player. Consequently the genes involved in the metal ion transport were also significantly up-regulated. We confirmed the results of the in silico analysis using quantitative real time PCR which showed up-regulation of genes involved in respiration and transport of iron and copper. The promoter activity of one of the representative genes, FET3, was also found to be higher upon calorie restriction. Altogether, our results indicate that upon calorie restriction the levels of iron and copper fall in cells, which elicits a transcriptional response up-regulating the genes involved in their uptake to maintain cellular homeostasis.
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http://dx.doi.org/10.1039/c0mb00084aDOI Listing
February 2011

Pre-clustered TCR complexes.

FEBS Lett 2010 Dec 7;584(24):4832-7. Epub 2010 Sep 7.

Department of Molecular Immunology, Max Planck-Institute of Immunobiology and Institute of Biology III, Faculty of Biology, University of Freiburg, Freiburg, Germany.

The T-cell antigen receptor (TCR) is a multisubunit transmembrane complex that mediates the antigen-specific activation of T cells. Using a variety of techniques, several research groups have shown that TCRs are at least partially pre-clustered before antigen binding. These new findings are contradictory to the "classical" view, according to which TCRs are randomly distributed on the cell surface and only associate upon antigen binding. In this review we try to answer the following questions: What are the experimental evidences for the existence of pre-clustered TCRs? How can the TCR pre-clusters be activated upon antigen binding? Which functional consequences for T-cell activation arise from the pre-clustering of TCRs.
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http://dx.doi.org/10.1016/j.febslet.2010.09.004DOI Listing
December 2010

Detection of phosphorylated T and B cell antigen receptor species by Phos-tag SDS- and Blue Native-PAGE.

Immunol Lett 2010 May 22;130(1-2):51-6. Epub 2009 Dec 22.

Department for Molecular Immunology, Max Planck-Institute for Immunobiology, Freiburg, Germany.

Detection of phospho-proteins and differently phosphorylated forms of the same protein are important in understanding cell behaviour. One novel method is Phos-tag SDS-PAGE. A dinuclear Mn(2+) complex that binds to phosphate groups (the Phos-tag) is covalently attached to the polyacrylamide gel matrix. Thus, phosphorylated proteins are retarded in their migration and can be distinguished from their non-phosphorylated counterparts. We applied Phos-tag SDS-PAGE to the analysis of the zeta, CD3epsilon and CD3delta subunits of the T cell antigen receptor (TCR-CD3). Pervanadate stimulation generated six different phospho-zeta and each two different CD3epsilon and CD3delta forms. This corresponds to the phosphorylatable tyrosines on their cytoplasmic tails. The phosphorylation pattern was compatible with random phosphorylation events. Further, we showed that the Phos-tag technology can be applied to Blue Native (BN)-PAGE. This extends the applicability to the analysis of native protein complexes. Upon pervanadate stimulation the TCR-CD3 complex was predominantly detected as two distinct phospho-complexes. In contrast, the B cell antigen receptor (BCR) appeared as one phospho-form. Thus, Phos-tag BN-PAGE is useful for the analysis of different phosphorylation states of multiprotein complexes.
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http://dx.doi.org/10.1016/j.imlet.2009.12.012DOI Listing
May 2010

Models of antigen receptor activation in the design of vaccines.

Curr Pharm Des 2009 ;15(28):3237-48

Max Planck-Institute for Immunobiology and University of Freiburg, Stübeweg 51, 79108 Freiburg, Germany.

Vaccination techniques have developed rapidly over the last several decades from the immunization with live attenuated pathogens to the use of peptide and DNA subunit vaccines, from the use of classical adjuvants to cell-directed delivery. Vaccination techiques are also under investigation for the treatment of tumors and autoimmune diseases. However, profound knowledge of activation mechanisms of the immune cells on a molecular level is prerequisite for a better understanding of the immune response, and for the development of effective immunomodulatory tools. In this review we discuss the models of BCR and TCR activation, and using the example of some vacciantion technologies, we show, how the understanding of these models could help in the design of a new generation of vaccines.
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http://dx.doi.org/10.2174/138161209789105216DOI Listing
January 2010

A novel range based QSAR study of human neuropeptide Y (NPY) Y5 receptor inhibitors.

Eur J Med Chem 2007 Apr 2;42(4):463-70. Epub 2006 Nov 2.

Pharmacoinformatics Division, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Punjab 160062, India.

A conventional QSAR study has been carried out using thermodynamic and other descriptors, on a set of arylsulfonamidomethylcyclohexyl derivatives as antagonists of potential obesity drug target human neuropeptide Y Y5 receptor. In addition, a novel range based method was applied to obtain a QSAR model so that the information contained in the compounds for which an approximate value instead of exact value of inhibitory activity was available could be included in the model. Analysis of models suggests that range based model is better in screening biologically active compounds from chemical library. The conventional model is able to predict activity accurately only for active compounds whereas the range based method is better in discriminating active and inactive compounds.
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http://dx.doi.org/10.1016/j.ejmech.2006.09.011DOI Listing
April 2007

Quantitative structure activity relationship studies of aryl heterocycle-based thrombin inhibitors.

Eur J Med Chem 2006 Nov 1;41(11):1339-46. Epub 2006 Aug 1.

Pharmacoinformatics division National Institute of Pharmaceutical Education and Research, Sector 67, Phase X, 160062 SAS Nagar, Punjab, India.

A quantitative structure activity relationship (QSAR) analysis has been performed on a data set of 42 aryl heterocycle-based thrombin inhibitors. Several types of descriptors including topological, spatial, thermodynamic, information content and E-state indices were used to derive a quantitative relationship between the anti thrombin activity and structural properties. Genetic algorithm based genetic function approximation method of variable selection was used to generate the model. Best model was developed when number of descriptors in the equation was set to five. Highly statistically significant model was obtained with atom type logP descriptors, logP and Shadow_YZ. The model is not only able to predict the activity of new compounds but also explained the important regions in the molecules in a quantitative manner.
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http://dx.doi.org/10.1016/j.ejmech.2006.07.001DOI Listing
November 2006