Daniel S Peeper

Netherlands Cancer Institute, Amsterdamo, North Holland, Netherlands

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Publications (56)787.21 Total impact

  • Daniel S Peeper
    Molecular oncology. 08/2014;
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    ABSTRACT: Expression of the BRAFV600E oncoprotein is known to cause benign lesions, for example melanocytic nevi (moles). In spite of the oncogenic function of mutant BRAF, these lesions are arrested by a cell-autonomous mechanism called Oncogene-Induced Senescence (OIS). Infrequently, nevi can progress to malignant melanoma, through mechanisms that are incompletely understood. To gain more insight into this vital tumor suppression mechanism, we performed a mass spectrometry-based screening of the proteome and phosphoproteome in cycling and senescent cells as well as cells that have abrogated senescence. Proteome analysis of senescent cells revealed the upregulation of established senescence biomarkers, including specific cytokines, but also several proteins not previously associated with senescence, including extracellular matrix-interacting. Using both general and targeted phosphopeptide enrichment by Ti4+-IMAC and phosphotyrosine antibody enrichment, we identified over 15,000 phosphorylation sites. Among the regulated phosphorylation sites we encountered components of the interleukin, BRAF/MAPK and CDK-retinoblastoma (Rb) pathways and several other factors. The extensive proteome and phosphoproteome dataset of BRAFV600E-expressing senescent cells provides molecular clues as to how OIS is initiated, maintained or evaded, serving as a comprehensive proteomic basis for functional validation.
    Molecular & cellular proteomics : MCP. 06/2014;
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    ABSTRACT: The activation of oncogenes in primary cells blocks proliferation by inducing oncogene-induced senescence (OIS), a highly potent in vivo tumor-suppressing program. A prime example is mutant BRAF, which drives OIS in melanocytic nevi. Progression to melanoma occurs only in the context of additional alteration(s) like the suppression of PTEN, which abrogates OIS. Here, we performed a near-genomewide short hairpin (sh)RNA screen for novel OIS regulators and identified by next generation sequencing and functional validation seven genes. While all but one were upregulated in OIS, their depletion abrogated BRAF(V) (600E) -induced arrest. With genome-wide DNA methylation analysis we found one of these genes, RASEF, to be hypermethylated in primary cutaneous melanomas compared to nevi. Bypass of OIS by depletion of RASEF was associated with suppression of several senescence biomarkers including senescence-associated (SA)-β-galactosidase activity, interleukins and tumor suppressor p15(INK) (4B) . Restoration of RASEF expression inhibited proliferation. These results illustrate the power of shRNA OIS bypass screens and identify a potential novel melanoma suppressor gene. This article is protected by copyright. All rights reserved.
    Pigment Cell & Melanoma Research 04/2014; · 5.84 Impact Factor
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    ABSTRACT: Dysfunctional telomeres suppress tumour progression by activating cell-intrinsic programs that lead to growth arrest. Increased levels of TRF2, a key factor in telomere protection, are observed in various human malignancies and contribute to oncogenesis. We demonstrate here that a high level of TRF2 in tumour cells decreased their ability to recruit and activate natural killer (NK) cells. Conversely, a reduced dose of TRF2 enabled tumour cells to be more easily eliminated by NK cells. Consistent with these results, a progressive upregulation of TRF2 correlated with decreased NK cell density during the early development of human colon cancer. By screening for TRF2-bound genes, we found that HS3ST4-a gene encoding for the heparan sulphate (glucosamine) 3-O-sulphotransferase 4-was regulated by TRF2 and inhibited the recruitment of NK cells in an epistatic relationship with TRF2. Overall, these results reveal a TRF2-dependent pathway that is tumour-cell extrinsic and regulates NK cell immunity.
    Nature Cell Biology 06/2013; · 20.76 Impact Factor
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    ABSTRACT: In response to tenacious stress signals, such as the unscheduled activation of oncogenes, cells can mobilize tumour suppressor networks to avert the hazard of malignant transformation. A large body of evidence indicates that oncogene-induced senescence (OIS) acts as such a break, withdrawing cells from the proliferative pool almost irreversibly, thus crafting a vital pathophysiological mechanism that protects against cancer. Despite the widespread contribution of OIS to the cessation of tumorigenic expansion in animal models and humans, we have only just begun to define the underlying mechanism and identify key players. Although deregulation of metabolism is intimately linked to the proliferative capacity of cells, and senescent cells are thought to remain metabolically active, little has been investigated in detail about the role of cellular metabolism in OIS. Here we show, by metabolic profiling and functional perturbations, that the mitochondrial gatekeeper pyruvate dehydrogenase (PDH) is a crucial mediator of senescence induced by BRAF(V600E), an oncogene commonly mutated in melanoma and other cancers. BRAF(V600E)-induced senescence was accompanied by simultaneous suppression of the PDH-inhibitory enzyme pyruvate dehydrogenase kinase 1 (PDK1) and induction of the PDH-activating enzyme pyruvate dehydrogenase phosphatase 2 (PDP2). The resulting combined activation of PDH enhanced the use of pyruvate in the tricarboxylic acid cycle, causing increased respiration and redox stress. Abrogation of OIS, a rate-limiting step towards oncogenic transformation, coincided with reversion of these processes. Further supporting a crucial role of PDH in OIS, enforced normalization of either PDK1 or PDP2 expression levels inhibited PDH and abrogated OIS, thereby licensing BRAF(V600E)-driven melanoma development. Finally, depletion of PDK1 eradicated melanoma subpopulations resistant to targeted BRAF inhibition, and caused regression of established melanomas. These results reveal a mechanistic relationship between OIS and a key metabolic signalling axis, which may be exploited therapeutically.
    Nature 05/2013; · 38.60 Impact Factor
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    ABSTRACT: The involvement of epigenetic alterations in the pathogenesis of melanoma is increasingly recognized. Here, we performed genome-wide DNA methylation analysis of primary cutaneous melanoma and benign melanocytic nevus interrogating 14 495 genes using BeadChip technology. This genome-wide view of promoter methylation in primary cutaneous melanoma revealed an array of recurrent DNA methylation alterations with potential diagnostic applications. Among 106 frequently hypermethylated genes, there were many novel methylation targets and tumor suppressor genes. Highly recurrent methylation of the HOXA9, MAPK13, CDH11, PLEKHG6, PPP1R3C, and CLDN11 genes was established. Promoter methylation of MAPK13, encoding p38δ, was present in 67% of primary and 85% of metastatic melanomas. Restoration of MAPK13 expression in melanoma cells exhibiting epigenetic silencing of this gene reduced proliferation, indicative of tumor suppressive functions. This study demonstrates that DNA methylation alterations are widespread in melanoma and suggests that epigenetic silencing of MAPK13 contributes to melanoma progression.
    Pigment Cell & Melanoma Research 03/2013; · 5.84 Impact Factor
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    ABSTRACT: Departments of a Molecular Oncology, b Pathology, d Cell Biology II, e Molecular Pathology, and f Molecular Carcinogenesis, Metastasis confronts clinicians with two major challenges: estimat-ing the patient's risk of metastasis and identifying therapeutic tar-gets. Because they are key signal integrators connecting cellular processes to clinical outcome, we aimed to identify transcriptional nodes regulating cancer cell metastasis. Using rodent xenograft models that we previously developed, we identified the transcrip-tion factor Fos-related antigen-1 (Fra-1) as a key coordinator of me-tastasis. Because Fra-1 often is overexpressed in human metastatic breast cancers and has been shown to control their invasive poten-tial in vitro, we aimed to assess the implication and prognostic sig-nificance of the Fra-1–dependent genetic program in breast cancer metastasis and to identify potential Fra-1–dependent therapeutic targets. In several in vivo assays in mice, we demonstrate that stable RNAi depletion of Fra-1 from human breast cancer cells strongly suppresses their ability to metastasize. These results support a clin-ically important role for Fra-1 and the genetic program it controls. We show that a Fra-1–dependent gene-expression signature accu-rately predicts recurrence of breast cancer. Furthermore, a synthetic lethal drug screen revealed that antagonists of the adenosine re-ceptor A 2B (ADORA2B) are preferentially toxic to breast tumor cells expressing Fra-1. Both RNAi silencing and pharmacologic blockade of ADORA2B inhibited filopodia formation and invasive activity of breast cancer cells and correspondingly reduced tumor outgrowth in the lungs. These data show that Fra-1 activity is causally involved in and is a prognostic indicator of breast cancer metastasis. They sug-gest that Fra-1 activity predicts responsiveness to inhibition of phar-macologically tractable targets, such as ADORA2B, which may be used for clinical interference of metastatic breast cancer. epithelial-mesenchymal transition | invasion
    Proceedings of the National Academy of Sciences 01/2013; · 9.81 Impact Factor
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    ABSTRACT: Human melanocytic nevi (moles) are benign lesions harboring activated oncogenes, including BRAF. Although this oncogene initially acts mitogenically, eventually, oncogene-induced senescence (OIS) ensues. Nevi can infrequently progress to melanomas, but the mechanistic relationship with OIS is unclear. We show here that PTEN depletion abrogates BRAF(V600E)-induced senescence in human fibroblasts and melanocytes. Correspondingly, in established murine BRAF(V600E)-driven nevi, acute shRNA-mediated depletion of PTEN prompted tumor progression. Furthermore, genetic analysis of laser-guided microdissected human contiguous nevus-melanoma specimens recurrently revealed identical mutations in BRAF or NRAS in adjacent benign and malignant melanocytes. The PI3K pathway was often activated through either decreased PTEN or increased AKT3 expression in melanomas relative to their adjacent nevi. Pharmacologic PI3K inhibition in melanoma cells suppressed proliferation and induced the senescence-associated tumor suppressor p15(INK4B). This treatment also eliminated subpopulations resistant to targeted BRAF(V600E) inhibition. Our findings suggest that a significant proportion of melanomas arise from nevi. Furthermore, these results demonstrate that PI3K pathway activation serves as a rate-limiting event in this setting, acting at least in part by abrogating OIS. The reactivation of senescence features and elimination of cells refractory to BRAF(V600E) inhibition by PI3K inhibition warrants further investigation into the therapeutic potential of simultaneously targeting these pathways in melanoma.
    Genes & development 05/2012; 26(10):1055-69. · 12.08 Impact Factor
  • Daniel S Peeper
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    ABSTRACT: In recent years, many groups have detected biomarkers of cellular senescence in a plethora of neoplastic lesions, in model systems, and humans. Indeed, we have come to realize that oncogene-induced senescence (OIS) acts as a potent barrier to oncogenic transformation, operating alongside cell death programs. We have begun to uncover some of its underlying principles, but many fundamental questions remain. In this perspective, some of the 'knowns' and 'unknowns' of OIS are discussed, with a focus on melanomagenesis.
    Pigment Cell & Melanoma Research 12/2011; 24(6):1107-11. · 5.84 Impact Factor
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    Daniel S Peeper
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    ABSTRACT: Age brings not just wisdom, but also, alas, many traits that to most of us are much less attractive. It now seems that, at least in mice, clearance of senescent cells delays some of the maladies associated with ageing. See Letter p.232
    Nature 11/2011; 479(7372):186-7. · 38.60 Impact Factor
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    ABSTRACT: Oncogene-induced senescence (OIS) is a growth arrest triggered by the enforced expression of cancer-promoting genes and acts as a barrier against malignant transformation in vivo. In this study, by a combination of in vitro and in vivo approaches, we investigate the role of OIS in tumours originating from the thyroid epithelium. We found that expression of different thyroid tumour-associated oncogenes in primary human thyrocytes triggers senescence, as demonstrated by the presence of OIS hallmarks: changes in cell morphology, accumulation of SA-β-Gal and senescence-associated heterochromatic foci, and upregulation of transcription of the cyclin-dependent kinase inhibitors p16(INK4a) and p21(CIP1). Furthermore, immunohistochemical analysis of a panel of thyroid tumours characterised by different aggressiveness showed that the expression of OIS markers such as p16(INK4a), p21(CIP1) and IGFBP7 is upregulated at early stages, and lost during thyroid tumour progression. Taken together, our results suggest a role of OIS in thyroid carcinogenesis.
    Endocrine Related Cancer 09/2011; 18(6):743-57. · 5.26 Impact Factor
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    Daniel S Peeper
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    ABSTRACT: A/U-rich elements (AREs) are short sequences in the 3′UTRs of genes, acting in cis to regulate mRNA decay and translation. In this issue of The EMBO Journal, Basu et al (2011) describe a new function for AREs, in the context of the C/EBPβ transcription factor. Specifically, they show that the C/EBPβ ARE is responsible for sequestering the corresponding protein from subcellular compartments in which kinases reside to derepress C/EBPβ. As a result, the transcription factor is unable to execute its cytostatic function in the face of an oncogenic insult. These results reveal a new mode of regulation of an already carefully controlled transcription factor. Given the widespread occurrence of AREs in genes, they also predict that this process, termed ‘3′UTR regulation of protein activity’ (UPA), may have a more common role in controlling protein activities.
    The EMBO Journal 09/2011; 30(18):3663-3664. · 9.82 Impact Factor
  • Patricia A Possik, Daniel S Peeper
    Pigment Cell & Melanoma Research 08/2011; 24(4):586-7. · 5.84 Impact Factor
  • M A Smit, D S Peeper
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    ABSTRACT: Anoikis (detachment-induced apoptosis) prevents the survival of cells at inappropriate sites of the body and can therefore act as a barrier to metastasis. In a function-based genome-wide screen, we have previously identified the neurotrophic tyrosine kinase receptor TrkB as a potent suppressor of anoikis. Consistently, activated TrkB oncogenically transforms non-malignant epithelial cells and causes them to invade and produce metastatic tumors in vivo. Overexpression of activated TrkB also results in morphological transformation, resembling epithelial-mesenchymal transition (EMT). E-cadherin, an important EMT regulator, and two E-cadherin repressors, Twist and Snail, are critical for these TrkB functions. As Snail has been shown to induce Zeb1, another E-cadherin repressor, we hypothesized that Zeb1 could be a TrkB target, too. We show here that Zeb1 is required for TrkB-induced EMT in epithelial cells, as RNAi-mediated knockdown of Zeb1 reverted the morphological changes induced by TrkB. Furthermore, Zeb1 is involved in TrkB-induced anoikis resistance, migration and invasion. In vivo, knockdown of Zeb1 strongly reduced TrkB-induced metastasis. Finally, epistasis experiments showed that Zeb1 acts downstream of Twist and Snail. We conclude that Zeb1 is required for several TrkB-induced effects in vitro and in vivo, including metastasis.
    Oncogene 04/2011; 30(35):3735-44. · 8.56 Impact Factor
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    ABSTRACT: Oncogene-induced cellular senescence (OIS) is an increasingly recognized tumour suppressor mechanism that confines the outgrowth of neoplastic cells in vivo. It relies on a complex signalling network, but only few components have been identified so far. Gene-expression profiling revealed a >100-fold increase in the levels of the transcription factor and putative tumour suppressor gene TGFβ-stimulated clone 22 (TSC22D1) in BRAF(E600)-induced senescence, in both human fibroblasts and melanocytes. Only the short TSC22D1 transcript was upregulated, whereas the abundance of the large protein variant was suppressed by proteasomal degradation. The TSC22D1 protein variants, in complex with their dimerization partner TSC22 homologue gene 1 (THG1), exerted opposing functions, as selective depletion of the short form, or conversely, overexpression of the large variant, resulted in abrogation of OIS. This was accompanied by the suppression of several inflammatory factors and p15(INK4B), with TSC22D1 acting as a critical effector of C/EBPβ. Our results demonstrate that the differential regulation of antagonistic TSC22D1 variants is required for the establishment of OIS and suggest distinct contributions of TSC22 family members to the progression of BRAF(E600)-driven neoplasia.
    The EMBO Journal 03/2011; 30(9):1753-65. · 9.82 Impact Factor
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    ABSTRACT: Cancer originates from cells that have acquired mutations in genes critical for controlling cell proliferation, survival and differentiation. Often, tumors continue to depend on these so-called driver mutations, providing the rationale for targeted anticancer therapies. To date, large-scale sequencing analyses have revealed hundreds of mutations in human tumors. However, without their functional validation it remains unclear which mutations correspond to driver, or rather bystander, mutations and, therefore, whether the mutated gene represents a target for therapeutic intervention. In human colorectal tumors, the neurotrophic receptor TRKB has been found mutated on two different sites in its kinase domain (TRKB(T695I) and TRKB(D751N)). Another site, in the extracellular part of TRKB, is mutated in a human lung adenocarcinoma cell line (TRKB(L138F)). Lastly, our own analysis has identified one additional TRKB point mutation proximal to the kinase domain (TRKB(P507L)) in a human melanoma cell line. The functional consequences of all these point mutations, however, have so far remained elusive. Previously, we have shown that TRKB is a potent suppressor of anoikis and that TRKB-expressing cells form highly invasive and metastatic tumors in nude mice. To assess the functional consequences of these four TRKB mutations, we determined their potential to suppress anoikis and to form tumors in nude mice. Unexpectedly, both colon cancer-derived mutants, TRKB(T695I) and TRKB(D751N), displayed reduced activity compared to that of wild-type TRKB. Consistently, upon stimulation with the TRKB ligand BDNF, these mutants were impaired in activating TRKB and its downstream effectors AKT and ERK. The two mutants derived from human tumor cell lines (TRKB(L138F) and TRKB(P507L)) were functionally indistinguishable from wild-type TRKB in both in-vitro and in-vivo assays. In conclusion, we fail to detect any gain-of-function of four cancer-derived TRKB point mutations.
    PLoS ONE 01/2011; 6(2):e16871. · 3.73 Impact Factor
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    ABSTRACT: Almost half a century after the first reports describing the limited replicative potential of primary cells in culture, there is now overwhelming evidence for the existence of "cellular senescence" in vivo. It is being recognized as a critical feature of mammalian cells to suppress tumorigenesis, acting alongside cell death programs. Here, we review the various features of cellular senescence and discuss their contribution to tumor suppression. Additionally, we highlight the power and limitations of the biomarkers currently used to identify senescent cells in vitro and in vivo.
    Genes & development 11/2010; 24(22):2463-79. · 12.08 Impact Factor
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    Marjon A Smit, Daniel S Peeper
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    ABSTRACT: The epithelial-mesenchymal transition is involved in several physiological processes. However, it is also believed to contribute to cancer progression. Conversely, cellular senescence constitutes a failsafe program against cancer progression. Interestingly, EMT and senescence seem to cross paths, with several factors playing dominant roles in both settings. Here, we describe recent observations that link these important cellular processes.
    Aging 10/2010; 2(10):735-41. · 4.70 Impact Factor
  • Daniel S Peeper
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    ABSTRACT: Senescence is increasingly recognized as a critical feature of mammalian cells to suppress tumorigenesis, acting together with cell death programs. Whether senescence, like programmed cell death, can be exploited therapeutically has been unclear. Pandolfi and coworkers now propose that PTEN-loss-induced cellular senescence (PICS) may be triggered in vivo for therapy.
    Cancer cell 03/2010; 17(3):219-20. · 25.29 Impact Factor
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    ABSTRACT: The Editorial Board of Aging reviews research papers published in 2009, which they believe have or will have significant impact on aging research. Among many others, the topics include genes that accelerate aging or in contrast promote longevity in model organisms, DNA damage responses and telomeres, molecular mechanisms of life span extension by calorie restriction and pharmacological interventions into aging. The emerging message in 2009 is that aging is not random but determined by a genetically-regulated longevity network and can be decelerated both genetically and pharmacologically.
    Aging 03/2010; 2(3):111-21. · 4.70 Impact Factor

Publication Stats

4k Citations
787.21 Total Impact Points

Institutions

  • 1997–2014
    • Netherlands Cancer Institute
      • • Division of Molecular Genetics
      • • Center for Biomedical Genetics
      • • Division of Molecular Carcinogenesis
      Amsterdamo, North Holland, Netherlands
  • 2006
    • VU University Amsterdam
      • Department of Pathology
      Amsterdam, North Holland, Netherlands
  • 2002
    • Whitehead Institute for Biomedical Research
      Cambridge, Massachusetts, United States
  • 1995–1997
    • Dana-Farber Cancer Institute
      Boston, Massachusetts, United States
  • 1992–1995
    • Leiden University
      • Molecular Cell Biology Group
      Leyden, South Holland, Netherlands