his.sePublications
Change search
Link to record
Permanent link

Direct link
BETA
Publications (10 of 10) Show all publications
Holmgren, G., Sartipy, P., Andersson, C. X., Lindahl, A. & Synnergren, J. (2018). Expression profiling of human pluripotent stem cell-derived cardiomyocytes exposed to doxorubicin - integration and visualization of multi omics data. Toxicological Sciences, 163(1), 182-195
Open this publication in new window or tab >>Expression profiling of human pluripotent stem cell-derived cardiomyocytes exposed to doxorubicin - integration and visualization of multi omics data
Show others...
2018 (English)In: Toxicological Sciences, ISSN 1096-6080, E-ISSN 1096-0929, Vol. 163, no 1, p. 182-195Article in journal (Refereed) Published
Abstract [en]

Anthracyclines, such as doxorubicin, are highly efficient chemotherapeutic agents against a variety of cancers. However, anthracyclines are also among the most cardiotoxic therapeutic drugs presently on the market. Chemotherapeutic-induced cardiomyopathy is one of the leading causes of disease and mortality in cancer survivors. The exact mechanisms responsible for doxorubicin-induced cardiomyopathy are not completely known, but the fact that the cardiotoxicity is dose-dependent and that there is a variation in time-to-onset of toxicity, and gender- and age differences suggests that several mechanisms may be involved.In the present study, we investigated doxorubicin-induced cardiotoxicity in human pluripotent stem cell-derived cardiomyocytes using proteomics. In addition, different sources of omics data (protein, mRNA, and microRNA) from the same experimental setup were further combined and analyzed using newly developed methods to identify differential expression in data of various origin and types. Subsequently, the results were integrated in order to generate a combined visualization of the findings.In our experimental model system, we exposed cardiomyocytes derived from human pluripotent stem cells to doxorubicin for up to two days, followed by a wash-out period of additionally 12 days. Besides an effect on the cell morphology and cardiomyocyte functionality, the data show a strong effect of doxorubicin on all molecular levels investigated. Differential expression patterns that show a linkage between the proteome, transcriptome, and the regulatory microRNA network, were identified. These findings help to increase the understanding of the mechanisms behind anthracycline-induced cardiotoxicity and suggest putative biomarkers for this condition.

Keywords
Human pluripotent stem cells, cardiomyocytes, doxorubicin, multi-omics data, proteomics, toxicity
National Category
Bioinformatics (Computational Biology)
Research subject
Bioinformatics; INF502 Biomarkers; INF501 Integration of -omics Data
Identifiers
urn:nbn:se:his:diva-14745 (URN)10.1093/toxsci/kfy012 (DOI)000432299900018 ()29385562 (PubMedID)2-s2.0-85046994085 (Scopus ID)
Available from: 2018-02-14 Created: 2018-02-14 Last updated: 2019-02-14Bibliographically approved
Sartipy, P., Holmgren, G., Synnergren, J., Andersson, C. & Lindahl, A. (2017). Visual integration of multiple omics data from human pluripotent stem cell-derived cardiomyocytes. In: : . Paper presented at International Society for Stem Cell Research (ISSCR) Annual meeting, Boston 14–17 June 2017 (pp. 13).
Open this publication in new window or tab >>Visual integration of multiple omics data from human pluripotent stem cell-derived cardiomyocytes
Show others...
2017 (English)Conference paper, Poster (with or without abstract) (Refereed)
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Research subject
Bioinformatics
Identifiers
urn:nbn:se:his:diva-14761 (URN)
Conference
International Society for Stem Cell Research (ISSCR) Annual meeting, Boston 14–17 June 2017
Available from: 2018-02-20 Created: 2018-02-20 Last updated: 2018-02-26Bibliographically approved
Pradip, A., Steel, D., Jacobsson, S., Holmgren, G., Ingelman-Sundberg, M., Sartipy, P., . . . Edsbagge, J. (2016). High Content Analysis of Human Pluripotent Stem Cell Derived Hepatocytes Reveals Drug Induced Steatosis and Phospholipidosis. Stem Cells International, 2016, Article ID 2475631.
Open this publication in new window or tab >>High Content Analysis of Human Pluripotent Stem Cell Derived Hepatocytes Reveals Drug Induced Steatosis and Phospholipidosis
Show others...
2016 (English)In: Stem Cells International, ISSN 1687-9678, Vol. 2016, article id 2475631Article in journal (Refereed) Published
Abstract [en]

Hepatotoxicity is one of the most cited reasons for withdrawal of approved drugs from the market. The use of nonclinically relevant in vitro and in vivo testing systems contributes to the high attrition rates. Recent advances in differentiating human induced pluripotent stem cells (hiPSCs) into pure cultures of hepatocyte-like cells expressing functional drug metabolizing enzymes open up possibilities for novel, more relevant human cell based toxicity models. The present study aimed to investigate the use of hiPSC derived hepatocytes for conducting mechanistic toxicity testing by image based high content analysis (HCA). The hiPSC derived hepatocytes were exposed to drugs known to cause hepatotoxicity through steatosis and phospholipidosis, measuring several endpoints representing different mechanisms involved in drug induced hepatotoxicity. The hiPSC derived hepatocytes were benchmarked to the HepG2 cell line and generated robust HCA data with low imprecision between plates and batches. The different parameters measured were detected at subcytotoxic concentrations and the order of which the compounds were categorized (as severe, moderate, mild, or nontoxic) based on the degree of injury at isomolar concentration corresponded to previously published data. Taken together, the present study shows how hiPSC derived hepatocytes can be used as a platform for screening drug induced hepatotoxicity by HCA.

Place, publisher, year, edition, pages
Hindawi Publishing Corporation, 2016
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Research subject
Bioinformatics
Identifiers
urn:nbn:se:his:diva-12039 (URN)10.1155/2016/2475631 (DOI)000371516600001 ()26880940 (PubMedID)2-s2.0-84955472147 (Scopus ID)
Available from: 2016-03-15 Created: 2016-03-15 Last updated: 2018-07-31Bibliographically approved
Holmgren, G. (2016). In vitro toxicity testing using human pluripotent stem cell derivatives. (Doctoral dissertation). University of Gothenburg
Open this publication in new window or tab >>In vitro toxicity testing using human pluripotent stem cell derivatives
2016 (English)Doctoral thesis, comprehensive summary (Other academic)
Place, publisher, year, edition, pages
University of Gothenburg, 2016. p. 82
Keywords
toxicity testing, human pluripotent stem cells, cardiomyocytes, hepatocytes, microarray, quantitative proteomics, bioinformatics, transcriptomics, microRNA
National Category
Bioinformatics and Systems Biology Cell Biology Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Research subject
Medical sciences
Identifiers
urn:nbn:se:his:diva-13340 (URN)978-91-629-0001-4 (ISBN)978-91-629-0002-1 (ISBN)
Public defence
2016-12-15, 09:00 (English)
Opponent
Supervisors
Note

I avhandlingen ingår även:

Holmgren, G., Sartipy, P., Andersson, C.X., Lindahl, A., and Synnergren, J. Expression profiling of human pluripotent stem cell-derived cardiomyocytes exposed to doxorubicin – integration and visualization of multi omics data Manuscript

Available from: 2017-11-27 Created: 2017-01-26 Last updated: 2018-07-31Bibliographically approved
Holmgren, G., Synnergren, J., Andersson, C. X., Lindahl, A. & Sartipy, P. (2016). MicroRNAs as potential biomarkers for doxorubicin-induced cardiotoxicity. Toxicology in Vitro, 34, 26-34
Open this publication in new window or tab >>MicroRNAs as potential biomarkers for doxorubicin-induced cardiotoxicity
Show others...
2016 (English)In: Toxicology in Vitro, ISSN 0887-2333, E-ISSN 1879-3177, Vol. 34, p. 26-34Article in journal (Refereed) Published
Abstract [en]

Anthracyclines, such as doxorubicin, are well-established, highly efficient anti-neoplastic drugs used for treatment of a variety of cancers, including solid tumors, leukemia, lymphomas, and breast cancer. The successful use of doxorubicin has, however, been hampered by severe cardiotoxic side-effects. In order to prevent or reverse negative side-effects of doxorubicin, it is important to find early biomarkers of heart injury and drug-induced cardiotoxicity. The high stability under extreme conditions, presence in various body fluids, and tissue-specificity, makes microRNAs very suitable as clinical biomarkers. The present study aimed towards evaluating the early and late effects of doxorubicin on the microRNA expression in cardiomyocytes derived from human pluripotent stem cells. We report on several microRNAs, including miR-34a, miR-34b, miR-187, miR-199a, miR-199b, miR-146a, miR-15b, miR-130a, miR-214, and miR-424, that are differentially expressed upon, and after, treatment with doxorubicin. Investigation of the biological relevance of the identified microRNAs revealed connections to cardiomyocyte function and cardiotoxicity, thus supporting the findings of these microRNAs as potential biomarkers for drug-induced cardiotoxicity.

Place, publisher, year, edition, pages
Elsevier, 2016
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Research subject
Bioinformatics
Identifiers
urn:nbn:se:his:diva-12339 (URN)10.1016/j.tiv.2016.03.009 (DOI)000379273800004 ()27033315 (PubMedID)2-s2.0-84962362050 (Scopus ID)
Available from: 2016-06-08 Created: 2016-06-08 Last updated: 2018-07-31Bibliographically approved
Holmgren, G., Synnergren, J., Bogestål, Y., Améen, C., Åkesson, K., Holmgren, S., . . . Sartipy, P. (2015). Identification of novel biomarkers for doxorubicin-induced toxicity in human cardiomyocytes derived from pluripotent stem cells. Toxicology, 328, 102-111
Open this publication in new window or tab >>Identification of novel biomarkers for doxorubicin-induced toxicity in human cardiomyocytes derived from pluripotent stem cells
Show others...
2015 (English)In: Toxicology, ISSN 0300-483X, E-ISSN 1879-3185, Vol. 328, p. 102-111Article in journal (Refereed) Published
Abstract [en]

Doxorubicin is a chemotherapeutic agent indicated for the treatment of a variety of cancer types, including leukaemia, lymphomas, and many solid tumours. The use of doxorubicin is, however, associated with severe cardiotoxicity, often resulting in early discontinuation of the treatment. Importantly, the toxic symptoms can occur several years after the termination of the doxorubicin administration. In this study, the toxic effects of doxorubicin exposure have been investigated in cardiomyocytes derived from human embryonic stem cells (hESC). The cells were exposed to different concentrations of doxorubicin for up to 2 days, followed by a 12 day recovery period. Notably, the cell morphology was altered during drug treatment and the cells showed a reduced contractile ability, most prominent at the highest concentration of doxorubicin at the later time points. A general cytotoxic response measured as Lactate dehydrogenase leakage was observed after 2 days' exposure compared to the vehicle control, but this response was absent during the recovery period. A similar dose-dependant pattern was observed for the release of cardiac specific troponin T (cTnT) after 1 day and 2 days of treatment with doxorubicin. Global transcriptional profiles in the cells revealed clusters of genes that were differentially expressed during doxorubicin exposure, a pattern that in some cases was sustained even throughout the recovery period, suggesting that these genes could be used as sensitive biomarkers for doxorubicin-induced toxicity in human cardiomyocytes. The results from this study show that cTnT release can be used as a measurement of acute cardiotoxicity due to doxorubicin. However, for the late onset of doxorubicin-induced cardiomyopathy, cTnT release might not be the most optimal biomarker. As an alternative, some of the genes that we identified as differentially expressed after doxorubicin exposure could serve as more relevant biomarkers, and may also help to explain the cellular mechanisms behind the late onset apoptosis associated with doxorubicin-induced cardiomyopathy.

Place, publisher, year, edition, pages
Elsevier, 2015
Keywords
Biomarkers, Cardiomyocytes, Doxorubicin, Human pluripotent stem cells, Toxicity
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Research subject
Bioinformatics
Identifiers
urn:nbn:se:his:diva-11417 (URN)10.1016/j.tox.2014.12.018 (DOI)000349881500013 ()25529476 (PubMedID)2-s2.0-84920119624 (Scopus ID)
Available from: 2015-08-25 Created: 2015-08-25 Last updated: 2018-07-31Bibliographically approved
Holmgren, G., Ghosheh, N., Zeng, X., Bogestål, Y., Sartipy, P. & Synnergren, J. (2015). Identification of stable reference genes in differentiating human pluripotent stem cells. Physiological Genomics, 47(6), 232-239
Open this publication in new window or tab >>Identification of stable reference genes in differentiating human pluripotent stem cells
Show others...
2015 (English)In: Physiological Genomics, ISSN 1094-8341, E-ISSN 1531-2267, Vol. 47, no 6, p. 232-239Article in journal (Refereed) Published
Abstract [en]

Reference genes, often referred to as housekeeping genes (HKGs), are frequently used to normalize gene expression data based on the assumption that they are expressed at a constant level in the cells. However, several studies have shown that there may be a large variability in the gene expression levels of HKGs in various cell types. In a previous study, employing human embryonic stem cells (hESCs) subjected to spontaneous differentiation, we observed that the expression of commonly used HKG varied to a degree that rendered them inappropriate to use as reference genes under those experimental settings. Here we present a substantially extended study of the HKG signature in human pluripotent stem cells (hPSC), including nine global gene expression datasets from both hESC and human induced pluripotent stem cells (hiPSCs), obtained during directed differentiation towards endoderm-, mesoderm-, and ectoderm derivatives. Sets of stably expressed genes were compiled and a handful of genes (e.g., EID2, ZNF324B, CAPN10, and RABEP2) were identified as generally applicable reference genes in hPSCs across all cell lines and experimental conditions. The stability in gene expression profiles was confirmed by quantitative PCR (RT-qPCR) analysis. Taken together, the current results suggest that differentiating hPSCs have a distinct HKG signature, which in some aspects is different from somatic cell types, and underscore the necessity to validate the stability of reference genes under the actual experimental setup used. In addition, the novel putative HKGs identified in this study can preferentially be used for normalization of gene expression data obtained from differentiating hPSCs.

Place, publisher, year, edition, pages
American Physiological Society, 2015
Keywords
Differentiation, Endogenous controls; Gene expression, Housekeeping genes, Human pluripotent stem cells, Normalization, Reference genes
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Research subject
Bioinformatics
Identifiers
urn:nbn:se:his:diva-11419 (URN)10.1152/physiolgenomics.00130.2014 (DOI)000357489400005 ()25852171 (PubMedID)2-s2.0-84930975405 (Scopus ID)
Available from: 2015-08-25 Created: 2015-08-25 Last updated: 2018-07-31Bibliographically approved
Holmgren, G., Sjögren, A.-K., Barragan, I., Sabirsh, A., Sartipy, P., Synnergren, J., . . . Edsbagge, J. (2014). Long-term chronic toxicity testing using human pluripotent stem cell-derived hepatocytes. Drug Metabolism And Disposition, 42(9), 1401-1406
Open this publication in new window or tab >>Long-term chronic toxicity testing using human pluripotent stem cell-derived hepatocytes
Show others...
2014 (English)In: Drug Metabolism And Disposition, ISSN 0090-9556, E-ISSN 1521-009X, Vol. 42, no 9, p. 1401-1406Article in journal (Refereed) Published
Abstract [en]

Human pluripotent stem cells (hPSC) have the potential to become important tools for the establishment of new models for in vitro drug testing of, for example, toxicity and pharmacological effects. Late-stage attrition in the pharmaceutical industry is to a large extent caused by selection of drug candidates using nonpredictive preclinical models that are not clinically relevant. The current hepatic in vivo and in vitro models show clear limitations, especially for studies of chronic hepatotoxicity. For these reasons, we evaluated the potential of using hPSC-derived hepatocytes for long-term exposure to toxic drugs. The differentiated hepatocytes were incubated with hepatotoxic compounds for up to 14 days, using a repeated-dose approach. The hPSC-derived hepatocytes became more sensitive to the toxic compounds after extended exposures and, in addition to conventional cytotoxicity, evidence of phospholipidosis and steatosis was also observed in the cells. This is, to the best of our knowledge, the first report of a long-term toxicity study using hPSC-derived hepatocytes, and the observations support further development and validation of hPSC-based toxicity models for evaluating novel drugs, chemicals, and cosmetics.

Place, publisher, year, edition, pages
American Society for Pharmacology and Experimental Therapeutics, 2014
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Research subject
Bioinformatics
Identifiers
urn:nbn:se:his:diva-10212 (URN)10.1124/dmd.114.059154 (DOI)000341254300005 ()24980256 (PubMedID)2-s2.0-84906846876 (Scopus ID)
Available from: 2014-11-22 Created: 2014-11-22 Last updated: 2018-07-31Bibliographically approved
Ulvestad, M., Nordell, P., Asplund, A., Rehnström, M., Jacobsson, S., Holmgren, G., . . . Andersson, T. B. (2013). Drug metabolizing enzyme and transporter protein profiles of hepatocytes derived from human embryonic and induced pluripotent stem cells. Biochemical Pharmacology, 86(5), 691-702
Open this publication in new window or tab >>Drug metabolizing enzyme and transporter protein profiles of hepatocytes derived from human embryonic and induced pluripotent stem cells
Show others...
2013 (English)In: Biochemical Pharmacology, ISSN 0006-2952, E-ISSN 1356-1839, Vol. 86, no 5, p. 691-702Article in journal (Refereed) Published
Abstract [en]

Human embryonic and induced pluripotent stem cell-derived hepatocytes (hESC-Hep and hiPSC-Hep) have the potential to provide relevant human in vitro model systems for toxicity testing and drug discovery studies. In this study, the expression and function of important drug metabolizing cytochrome P450 (CYP) enzymes and transporter proteins in hESC-Hep and hiPSC-Hep were compared to cryopreserved human primary hepatocytes (hphep) and HepG2 cells. Overall, CYP activities in hESC-Hep and hiPSC-Hep were much lower than in hphep cultured for 4 h, but CYP1A and 3A activities were comparable to levels in hphep cultured for 48 h (CYP1A: 35% and 26% of 48 h hphep, respectively; CYP3A: 80% and 440% of 48 h hphep, respectively). Importantly, in hESC-Hep and hiPSC-Hep, CYP activities were stable or increasing for at least one week in culture which was in contrast to the rapid loss of CYP activities in cultured hphep between 4 and 48 h after plating. With regard to transporters, in hESC-Hep and hiPSC-Hep, pronounced NTCP activity (17% and 29% of 4 h hphep, respectively) and moderate BSEP activity (6% and 8% of 4 h hphep, respectively) were observed. Analyses of mRNA expression and immunocytochemistry supported the observed CYP and transporter activities and showed expression of additional CYPs and transporters. In conclusion, the stable expression and function of CYPs and transporters in hESC-Hep and hiPSC-Hep for at least one week opens up the possibility to reproducibly perform long term and extensive studies, e.g. chronic toxicity testing, in a stem cell-derived hepatic system. (C) 2013 Elsevier Inc. All rights reserved.

Place, publisher, year, edition, pages
Elsevier, 2013
Keywords
Human embryonic stem cell-derived hepatocytes, Human induced pluripotent stem cell- derived hepatocytes, Cytochrome P450, Transporter proteins, Hepatocytes
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Research subject
Natural sciences
Identifiers
urn:nbn:se:his:diva-8597 (URN)10.1016/j.bcp.2013.06.029 (DOI)000323404500012 ()23856292 (PubMedID)2-s2.0-84884903479 (Scopus ID)
Available from: 2013-10-31 Created: 2013-10-30 Last updated: 2017-12-06Bibliographically approved
Doktorova, T. Y., Yildirimman, R., Vinken, M., Vilardell, M., Vanhaecke, T., Gmuender, H., . . . Rogiers, V. (2013). Transcriptomic responses generated by hepatocarcinogens in a battery of liver-based in vitro models. Carcinogenesis, 34(6), 1393-1402
Open this publication in new window or tab >>Transcriptomic responses generated by hepatocarcinogens in a battery of liver-based in vitro models
Show others...
2013 (English)In: Carcinogenesis, ISSN 0143-3334, E-ISSN 1460-2180, Vol. 34, no 6, p. 1393-1402Article in journal (Refereed) Published
Abstract [en]

As the conventional approach to assess the potential of a chemical to cause cancer in humans still includes the 2-year rodent carcinogenicity bioassay, development of alternative methodologies is needed. In the present study, the transcriptomics responses following exposure to genotoxic (GTX) and non-genotoxic (NGTX) hepatocarcinogens and non-carcinogens (NC) in five liver-based in vitro models, namely conventional and epigenetically stabilized cultures of primary rat hepatocytes, the human hepatoma-derived cell lines HepaRG and HepG2 and human embryonic stem cell-derived hepatocyte-like cells, are examined. For full characterization of the systems, several bioinformatics approaches are employed including gene-based, ConsensusPathDB-based and classification analysis. They provide convincingly similar outcomes, namely that upon exposure to carcinogens, the HepaRG generates a gene classifier (a gene classifier is defined as a selected set of characteristic gene signatures capable of distinguishing GTX, NGTX carcinogens and NC) able to discriminate the GTX carcinogens from the NGTX carcinogens and NC. The other in vitro models also yield cancer-relevant characteristic gene groups for the GTX exposure, but some genes are also deregulated by the NGTX carcinogens and NC. Irrespective of the tested in vitro model, the most uniformly expressed pathways following GTX exposure are the p53 and those that are subsequently induced. The NGTX carcinogens triggered no characteristic cancer-relevant gene profiles in all liver-based in vitro systems. In conclusion, liver-based in vitro models coupled with transcriptomics techniques, especially in the case when the HepaRG cell line is used, represent valuable tools for obtaining insight into the mechanism of action and identification of GTX carcinogens.

Place, publisher, year, edition, pages
Oxford University Press, 2013
National Category
Medical Biotechnology (with a focus on Cell Biology (including Stem Cell Biology), Molecular Biology, Microbiology, Biochemistry or Biopharmacy)
Research subject
Natural sciences
Identifiers
urn:nbn:se:his:diva-8429 (URN)10.1093/carcin/bgt054 (DOI)000320271100025 ()23393228 (PubMedID)2-s2.0-84878968809 (Scopus ID)
Available from: 2013-08-19 Created: 2013-08-19 Last updated: 2017-12-06Bibliographically approved
Organisations
Identifiers
ORCID iD: ORCID iD iconorcid.org/0000-0002-0402-1437

Search in DiVA

Show all publications