Harri Lempiäinen
Novartis
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Publication
Featured researches published by Harri Lempiäinen.
PLOS ONE | 2011
Harri Lempiäinen; Arne Müller; Sarah Brasa; Soon-Siong Teo; Tim-Christoph Roloff; Laurent Morawiec; Natasa Zamurovic; Axel Vicart; Enrico Funhoff; Philippe Couttet; Dirk Schübeler; Olivier Grenet; Jennifer Marlowe; Jonathan G. Moggs; Rémi Terranova
Evidence suggests that epigenetic perturbations are involved in the adverse effects associated with some drugs and toxicants, including certain classes of non-genotoxic carcinogens. Such epigenetic changes (altered DNA methylation and covalent histone modifications) may take place at the earliest stages of carcinogenesis and their identification holds great promise for biomedical research. Here, we evaluate the sensitivity and specificity of genome-wide epigenomic and transcriptomic profiling in phenobarbital (PB)-treated B6C3F1 mice, a well-characterized rodent model of non-genotoxic liver carcinogenesis. Methylated DNA Immunoprecipitation (MeDIP)-coupled microarray profiling of 17,967 promoter regions and 4,566 intergenic CpG islands was combined with genome-wide mRNA expression profiling to identify liver tissue-specific PB-mediated DNA methylation and transcriptional alterations. Only a limited number of significant anti-correlations were observed between PB-induced transcriptional and promoter-based DNA methylation perturbations. However, the constitutive androstane receptor (CAR) target gene Cyp2b10 was found to be concomitantly hypomethylated and transcriptionally activated in a liver tissue-specific manner following PB treatment. Furthermore, analysis of active and repressive histone modifications using chromatin immunoprecipitation revealed a strong PB-mediated epigenetic switch at the Cyp2b10 promoter. Our data reveal that PB-induced transcriptional perturbations are not generally associated with broad changes in the DNA methylation status at proximal promoters and suggest that the drug-inducible CAR pathway regulates an epigenetic switch from repressive to active chromatin at the target gene Cyp2b10. This study demonstrates the utility of integrated epigenomic and transcriptomic profiling for elucidating early mechanisms and biomarkers of non-genotoxic carcinogenesis.
Nucleic Acids Research | 2013
John P. Thomson; Jennifer M. Hunter; Harri Lempiäinen; Arne Müller; Rémi Terranova; Jonathan G. Moggs; Richard R. Meehan
Aberrant DNA methylation is a common feature of neoplastic lesions, and early detection of such changes may provide powerful mechanistic insights and biomarkers for carcinogenesis. Here, we investigate dynamic changes in the mouse liver DNA methylome associated with short (1 day) and prolonged (7, 28 and 91 days) exposure to the rodent liver non-genotoxic carcinogen, phenobarbital (PB). We find that the distribution of 5mC/5hmC is highly consistent between untreated individuals of a similar age; yet, changes during liver maturation in a transcriptionally dependent manner. Following drug treatment, we identify and validate a series of differentially methylated or hydroxymethylated regions: exposure results in staged transcriptional responses with distinct kinetic profiles that strongly correlate with promoter proximal region 5hmC levels. Furthermore, reciprocal changes for both 5mC and 5hmC in response to PB suggest that active demethylation may be taking place at each set of these loci via a 5hmC intermediate. Finally, we identify potential early biomarkers for non-genotoxic carcinogenesis, including several genes aberrantly expressed in liver cancer. Our work suggests that 5hmC profiling can be used as an indicator of cell states during organ maturation and drug-induced responses and provides novel epigenetic signatures for non-genotoxic carcinogen exposure.
Genome Biology | 2012
John P. Thomson; Harri Lempiäinen; James Alexander Hackett; Colm E. Nestor; Arne Müller; Federico Bolognani; Dirk Schübeler; Rémi Terranova; Diana Reinhardt; Jonathan G. Moggs; Richard R. Meehan
BackgroundInduction and promotion of liver cancer by exposure to non-genotoxic carcinogens coincides with epigenetic perturbations, including specific changes in DNA methylation. Here we investigate the genome-wide dynamics of 5-hydroxymethylcytosine (5hmC) as a likely intermediate of 5-methylcytosine (5mC) demethylation in a DNA methylation reprogramming pathway. We use a rodent model of non-genotoxic carcinogen exposure using the drug phenobarbital.ResultsExposure to phenobarbital results in dynamic and reciprocal changes to the 5mC/5hmC patterns over the promoter regions of a cohort of genes that are transcriptionally upregulated. This reprogramming of 5mC/5hmC coincides with characteristic changes in the histone marks H3K4me2, H3K27me3 and H3K36me3. Quantitative analysis of phenobarbital-induced genes that are involved in xenobiotic metabolism reveals that both DNA modifications are lost at the transcription start site, while there is a reciprocal relationship between increasing levels of 5hmC and loss of 5mC at regions immediately adjacent to core promoters.ConclusionsCollectively, these experiments support the hypothesis that 5hmC is a potential intermediate in a demethylation pathway and reveal precise perturbations of the mouse liver DNA methylome and hydroxymethylome upon exposure to a rodent hepatocarcinogen.
Toxicological Sciences | 2013
Harri Lempiäinen; Philippe Couttet; Federico Bolognani; Arne Müller; Valerie Dubost; Raphaëlle Luisier; Alberto del Rio-Espinola; Veronique Vitry; Elif B. Unterberger; John P. Thomson; Fridolin Treindl; Ute Metzger; Clemens Wrzodek; Florian Hahne; Tulipan Zollinger; Sarah Brasa; Magdalena Kalteis; M. Marcellin; Fanny Giudicelli; Albert Braeuning; Laurent Morawiec; Natasa Zamurovic; Ulrich Längle; Nico Scheer; Dirk Schübeler; Jay I. Goodman; Salah-Dine Chibout; Jennifer Marlowe; Diethilde Theil; David J. Heard
The molecular events during nongenotoxic carcinogenesis and their temporal order are poorly understood but thought to include long-lasting perturbations of gene expression. Here, we have investigated the temporal sequence of molecular and pathological perturbations at early stages of phenobarbital (PB) mediated liver tumor promotion in vivo. Molecular profiling (mRNA, microRNA [miRNA], DNA methylation, and proteins) of mouse liver during 13 weeks of PB treatment revealed progressive increases in hepatic expression of long noncoding RNAs and miRNAs originating from the Dlk1-Dio3 imprinted gene cluster, a locus that has recently been associated with stem cell pluripotency in mice and various neoplasms in humans. PB induction of the Dlk1-Dio3 cluster noncoding RNA (ncRNA) Meg3 was localized to glutamine synthetase-positive hypertrophic perivenous hepatocytes, suggesting a role for β-catenin signaling in the dysregulation of Dlk1-Dio3 ncRNAs. The carcinogenic relevance of Dlk1-Dio3 locus ncRNA induction was further supported by in vivo genetic dependence on constitutive androstane receptor and β-catenin pathways. Our data identify Dlk1-Dio3 ncRNAs as novel candidate early biomarkers for mouse liver tumor promotion and provide new opportunities for assessing the carcinogenic potential of novel compounds.
Toxicological Sciences | 2014
Raphaëlle Luisier; Harri Lempiäinen; Nina Scherbichler; Albert Braeuning; Miriam Geissler; Valerie Dubost; Arne Müller; Nico Scheer; Salah-Dine Chibout; Hisanori Hara; Frank Picard; Diethilde Theil; Philippe Couttet; Antonio Vitobello; Olivier Grenet; Bettina Grasl-Kraupp; Heidrun Ellinger-Ziegelbauer; John P. Thomson; Richard R. Meehan; Clifford R. Elcombe; Colin J. Henderson; C. Roland Wolf; Michael Schwarz; Pierre Moulin; Rémi Terranova; Jonathan G. Moggs
The constitutive androstane receptor (CAR) and the pregnane X receptor (PXR) are closely related nuclear receptors involved in drug metabolism and play important roles in the mechanism of phenobarbital (PB)-induced rodent nongenotoxic hepatocarcinogenesis. Here, we have used a humanized CAR/PXR mouse model to examine potential species differences in receptor-dependent mechanisms underlying liver tissue molecular responses to PB. Early and late transcriptomic responses to sustained PB exposure were investigated in liver tissue from double knock-out CAR and PXR (CAR(KO)-PXR(KO)), double humanized CAR and PXR (CAR(h)-PXR(h)), and wild-type C57BL/6 mice. Wild-type and CAR(h)-PXR(h) mouse livers exhibited temporally and quantitatively similar transcriptional responses during 91 days of PB exposure including the sustained induction of the xenobiotic response gene Cyp2b10, the Wnt signaling inhibitor Wisp1, and noncoding RNA biomarkers from the Dlk1-Dio3 locus. Transient induction of DNA replication (Hells, Mcm6, and Esco2) and mitotic genes (Ccnb2, Cdc20, and Cdk1) and the proliferation-related nuclear antigen Mki67 were observed with peak expression occurring between 1 and 7 days PB exposure. All these transcriptional responses were absent in CAR(KO)-PXR(KO) mouse livers and largely reversible in wild-type and CAR(h)-PXR(h) mouse livers following 91 days of PB exposure and a subsequent 4-week recovery period. Furthermore, PB-mediated upregulation of the noncoding RNA Meg3, which has recently been associated with cellular pluripotency, exhibited a similar dose response and perivenous hepatocyte-specific localization in both wild-type and CAR(h)-PXR(h) mice. Thus, mouse livers coexpressing human CAR and PXR support both the xenobiotic metabolizing and the proliferative transcriptional responses following exposure to PB.
Epigenomics | 2014
Timo Wittenberger; Sara Sleigh; Daniel Reisel; M. Zikan; Benjamin Wahl; Marianna Alunni-Fabbroni; Allison Jones; Iona Evans; Julian Koch; Tobias Paprotka; Harri Lempiäinen; Tamas Rujan; Brigitte Rack; David Cibula; Martin Widschwendter
Breast, ovarian and endometrial cancers cause significant morbidity and mortality. Despite the presence of existing screening, diagnostic and treatment modalities, they continue to pose considerable unsolved challenges. Overdiagnosis is a growing problem in breast cancer screening and neither screening nor early diagnosis of ovarian or endometrial cancer is currently possible. Moreover, treatment of the diversity of these cancers presenting in the clinic is not sufficiently personalized at present. Recent technological advances, including reduced representation bisulfite sequencing, methylation arrays, digital PCR, next-generation sequencing and advanced statistical data analysis, enable the analysis of methylation patterns in cell-free tumor DNA in serum/plasma. Ongoing work is bringing these methods together for the analysis of samples from large clinical trials, which have been collected well in advance of cancer diagnosis. These efforts pave the way for the development of a noninvasive method that would enable us to overcome existing challenges to personalized medicine.
International Journal of Cancer | 2014
Elif B. Unterberger; Johannes Eichner; Clemens Wrzodek; Harri Lempiäinen; Raphaëlle Luisier; Rémi Terranova; Ute Metzger; Simon M. Plummer; Thomas Knorpp; Albert Braeuning; Jonathan G. Moggs; Markus F. Templin; Valerie S. Honndorf; Martial Piotto; Andreas Zell; Michael Schwarz
The process of hepatocarcinogenesis in the diethylnitrosamine (DEN) initiation/phenobarbital (PB) promotion mouse model involves the selective clonal outgrowth of cells harboring oncogene mutations in Ctnnb1, while spontaneous or DEN‐only‐induced tumors are often Ha‐ras‐ or B‐raf‐mutated. The molecular mechanisms and pathways underlying these different tumor sub‐types are not well characterized. Their identification may help identify markers for xenobiotic promoted versus spontaneously occurring liver tumors. Here, we have characterized mouse liver tumors harboring either Ctnnb1 or Ha‐ras mutations via integrated molecular profiling at the transcriptional, translational and post‐translational levels. In addition, metabolites of the intermediary metabolism were quantified by high resolution 1H magic angle nuclear magnetic resonance. We have identified tumor genotype‐specific differences in mRNA and miRNA expression, protein levels, post‐translational modifications, and metabolite levels that facilitate the molecular and biochemical stratification of tumor phenotypes. Bioinformatic integration of these data at the pathway level led to novel insights into tumor genotype‐specific aberrant cell signaling and in particular to a better understanding of alterations in pathways of the cell intermediary metabolism, which are driven by the constitutive activation of the β‐Catenin and Ha‐ras oncoproteins in tumors of the two genotypes.
Scientific Reports | 2018
Harri Lempiäinen; Ingrid Brænne; Tom Michoel; Vinicius Tragante; Baiba Vilne; Tom R. Webb; Theodosios Kyriakou; Johannes Eichner; Lingyao Zeng; Christina Willenborg; Oscar Franzén; Arno Ruusalepp; Anuj Goel; Sander W. van der Laan; Claudia Biegert; Stephen E. Hamby; Husain A. Talukdar; Hassan Foroughi Asl; Martin Dichgans; Tobias Dreker; Mira Graettinger; Philip Gribbon; Thorsten Kessler; Rainer Malik; Matthias Prestel; Barbara Stiller; Christine Schofield; Gerard Pasterkamp; Hugh Watkins; Nilesh J. Samani
Genome-wide association studies (GWAS) have identified over two hundred chromosomal loci that modulate risk of coronary artery disease (CAD). The genes affected by variants at these loci are largely unknown and an untapped resource to improve our understanding of CAD pathophysiology and identify potential therapeutic targets. Here, we prioritized 68 genes as the most likely causal genes at genome-wide significant loci identified by GWAS of CAD and examined their regulatory roles in 286 metabolic and vascular tissue gene-protein sub-networks (“modules”). The modules and genes within were scored for CAD druggability potential. The scoring enriched for targets of cardiometabolic drugs currently in clinical use and in-depth analysis of the top-scoring modules validated established and revealed novel target tissues, biological processes, and druggable targets. This study provides an unprecedented resource of tissue-defined gene–protein interactions directly affected by genetic variance in CAD risk loci.
Genome Medicine | 2017
Martin Widschwendter; Iona Evans; Allison Jones; Shohreh Ghazali; Daniel Reisel; Andy Ryan; Aleksandra Gentry-Maharaj; M. Zikan; David Cibula; Johannes Eichner; Marianna Alunni-Fabbroni; Julian Koch; Wolfgang Janni; Tobias Paprotka; Timo Wittenberger; Usha Menon; Benjamin Wahl; Brigitte Rack; Harri Lempiäinen
BackgroundMonitoring treatment and early detection of fatal breast cancer (BC) remains a major unmet need. Aberrant circulating DNA methylation (DNAme) patterns are likely to provide a highly specific cancer signal. We hypothesized that cell-free DNAme markers could indicate disseminated breast cancer, even in the presence of substantial quantities of background DNA.MethodsWe used reduced representation bisulfite sequencing (RRBS) of 31 tissues and established serum assays based on ultra-high coverage bisulfite sequencing in two independent prospective serum sets (n = 110). The clinical use of one specific region, EFC#93, was validated in 419 patients (in both pre- and post-adjuvant chemotherapy samples) from SUCCESS (Simultaneous Study of Gemcitabine-Docetaxel Combination adjuvant treatment, as well as Extended Bisphosphonate and Surveillance-Trial) and 925 women (pre-diagnosis) from the UKCTOCS (UK Collaborative Trial of Ovarian Cancer Screening) population cohort, with overall survival and occurrence of incident breast cancer (which will or will not lead to death), respectively, as primary endpoints.ResultsA total of 18 BC specific DNAme patterns were discovered in tissue, of which the top six were further tested in serum. The best candidate, EFC#93, was validated for clinical use. EFC#93 was an independent poor prognostic marker in pre-chemotherapy samples (hazard ratio [HR] for death = 7.689) and superior to circulating tumor cells (CTCs) (HR for death = 5.681). More than 70% of patients with both CTCs and EFC#93 serum DNAme positivity in their pre-chemotherapy samples relapsed within five years. EFC#93-positive disseminated disease in post-chemotherapy samples seems to respond to anti-hormonal treatment. The presence of EFC#93 serum DNAme identified 42.9% and 25% of women who were diagnosed with a fatal BC within 3–6 and 6–12 months of sample donation, respectively, with a specificity of 88%. The sensitivity with respect to detecting fatal BC was ~ 4-fold higher compared to non-fatal BC.ConclusionsDetection of EFC#93 serum DNAme patterns offers a new tool for early diagnosis and management of disseminated breast cancers. Clinical trials are required to assess whether EFC#93-positive women in the absence of radiological detectable breast cancers will benefit from anti-hormonal treatment before the breast lesions become clinically apparent.
Genome Medicine | 2017
Martin Widschwendter; M. Zikan; Benjamin Wahl; Harri Lempiäinen; Tobias Paprotka; Iona Evans; Allison Jones; Shohreh Ghazali; Daniel Reisel; Johannes Eichner; Tamas Rujan; Zhen Yang; Andrew E. Teschendorff; Andy Ryan; David Cibula; Usha Menon; Timo Wittenberger