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Altmäe S, Plaza-Florido A, Esteban FJ, Anguita-Ruiz A, Krjutškov K, Katayama S, Einarsdottir E, Kere J, Radom-Aizik S, Ortega FB. Effects of exercise on whole-blood transcriptome profile in children with overweight/obesity. Am J Hum Biol 2024; 36:e23983. [PMID: 37715654 DOI: 10.1002/ajhb.23983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 08/23/2023] [Accepted: 08/24/2023] [Indexed: 09/18/2023] Open
Abstract
BACKGROUND The current knowledge about the molecular mechanisms underlying the health benefits of exercise is still limited, especially in childhood. We set out to investigate the effects of a 20-week exercise intervention on whole-blood transcriptome profile (RNA-seq) in children with overweight/obesity. METHODS Twenty-four children (10.21 ± 1.33 years, 46% girls) with overweight/obesity, were randomized to either a 20-week exercise program (intervention group; n = 10), or to a no-exercise control group (n = 14). Whole-blood transcriptome profile was analyzed using RNA-seq by STRT technique with GlobinLock technology. RESULTS Following the 20-week exercise intervention program, 161 genes were differentially expressed between the exercise and the control groups among boys, and 121 genes among girls (p-value <0.05), while after multiple correction, no significant difference between exercise and control groups persisted in gene expression profiles (FDR >0.05). Genes enriched in GO processes and molecular pathways showed different immune response in boys (antigen processing and presentation, infections, and T cell receptor complex) and in girls (Fc epsilon RI signaling pathway) (FDR <0.05). CONCLUSION These results suggest that 20-week exercise intervention program alters the molecular pathways involved in immune processes in children with overweight/obesity.
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Affiliation(s)
- Signe Altmäe
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Abel Plaza-Florido
- Department of Physical Education and Sports, Faculty of Sport Sciences, Sport and Health University Research Institute (iMUDS), University of Granada Granada, Granada, Spain
- Pediatric Exercise and Genomics Research Center, Department of Pediatrics, School of Medicine, University of California at Irvine, Irvine, California, USA
| | - Francisco J Esteban
- Systems Biology Unit, Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaen, Jaen, Spain
| | - Augusto Anguita-Ruiz
- Barcelona Institute for Global Health, ISGlobal Barcelona, Barcelona, Spain
- Department of Biochemistry and Molecular Biology II, School of Pharmacy, University of Granada Granada, Granada, Spain
- Center of Biomedical Research, Institute of Nutrition and Food Technology "José Mataix", University of Granada, Granada, Spain
- CIBEROBN (CIBER Physiopathology of Obesity and Nutrition), Instituto de Salud Carlos III, Madrid, Spain
| | - Kaarel Krjutškov
- Competence Centre for Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Shintaro Katayama
- Folkhälsan Research Center, Helsinki, Finland
- Stem Cells and Metabolism Research Program, Research Programs Unit, University of Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Elisabet Einarsdottir
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Science for Life Laboratory, Department of Gene Technology, KTH-Royal Institute of Technology, Solna, Sweden
| | - Juha Kere
- Folkhälsan Research Center, Helsinki, Finland
- Stem Cells and Metabolism Research Program, Research Programs Unit, University of Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Shlomit Radom-Aizik
- Pediatric Exercise and Genomics Research Center, Department of Pediatrics, School of Medicine, University of California at Irvine, Irvine, California, USA
| | - Francisco B Ortega
- Department of Physical Education and Sports, Faculty of Sport Sciences, Sport and Health University Research Institute (iMUDS), University of Granada Granada, Granada, Spain
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Faculty of Sport and Health Sciences, University of Jyväskylä, Jyväskylä, Finland
- CIBERobn Physiopathology of Obesity and Nutrition, Granada, Spain
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2
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Boskovic N, Yazgeldi G, Ezer S, Tervaniemi MH, Inzunza J, Deligiannis SP, Yaşar B, Skoog T, Krjutškov K, Katayama S, Kere J. Optimized single-cell RNA sequencing protocol to study early genome activation in mammalian preimplantation development. STAR Protoc 2023; 4:102357. [PMID: 37314922 PMCID: PMC10277609 DOI: 10.1016/j.xpro.2023.102357] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 04/24/2023] [Accepted: 05/16/2023] [Indexed: 06/16/2023] Open
Abstract
Here, we present a modification of single-cell tagged reverse transcription protocol to study gene expression on a single-cell level or with limited RNA input. We describe different enzymes for reverse transcription and cDNA amplification, modified lysis buffer, and additional clean-up steps before cDNA amplification. We also detail an optimized single-cell RNA sequencing method for handpicked single cells, or tens to hundreds of cells, as input material to study mammalian preimplantation development. For complete details on the use and execution of this protocol, please refer to Ezer et al.1.
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Affiliation(s)
- Nina Boskovic
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183 Huddinge, Sweden; Department of Obstetrics and Gynecology, University of Helsinki, 00290 Helsinki, Finland.
| | - Gamze Yazgeldi
- Folkhälsan Research Center, 00290 Helsinki, Finland; Stem Cells and Metabolism Research Program, University of Helsinki, 00290 Helsinki, Finland
| | - Sini Ezer
- Folkhälsan Research Center, 00290 Helsinki, Finland; Stem Cells and Metabolism Research Program, University of Helsinki, 00290 Helsinki, Finland
| | - Mari H Tervaniemi
- Folkhälsan Research Center, 00290 Helsinki, Finland; Stem Cells and Metabolism Research Program, University of Helsinki, 00290 Helsinki, Finland
| | - Jose Inzunza
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183 Huddinge, Sweden
| | - Spyridon Panagiotis Deligiannis
- Department of Obstetrics and Gynecology, University of Helsinki, 00290 Helsinki, Finland; Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, 50406 Tartu, Estonia
| | - Barış Yaşar
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183 Huddinge, Sweden; Department of Biotechnology, Institute of Molecular and Cell Biology, University of Tartu, 51010 Tartu, Estonia
| | - Tiina Skoog
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183 Huddinge, Sweden
| | - Kaarel Krjutškov
- Competence Centre of Health Technologies, 50411 Tartu, Estonia; Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, 50406 Tartu, Estonia
| | - Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183 Huddinge, Sweden; Folkhälsan Research Center, 00290 Helsinki, Finland; Stem Cells and Metabolism Research Program, University of Helsinki, 00290 Helsinki, Finland.
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183 Huddinge, Sweden; Folkhälsan Research Center, 00290 Helsinki, Finland; Stem Cells and Metabolism Research Program, University of Helsinki, 00290 Helsinki, Finland.
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3
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Meltsov A, Saare M, Teder H, Paluoja P, Arffman RK, Piltonen T, Laudanski P, Wielgoś M, Gianaroli L, Koel M, Peters M, Salumets A, Krjutškov K, Palta P. Targeted gene expression profiling for accurate endometrial receptivity testing. Sci Rep 2023; 13:13959. [PMID: 37633957 PMCID: PMC10460380 DOI: 10.1038/s41598-023-40991-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 08/20/2023] [Indexed: 08/28/2023] Open
Abstract
Expressional profiling of the endometrium enables the personalised timing of the window of implantation (WOI). This study presents and evaluates a novel analytical pipeline based on a TAC-seq (Targeted Allele Counting by sequencing) method for endometrial dating. The expressional profiles were clustered, and differential expression analysis was performed on the model development group, using 63 endometrial biopsies spanning over proliferative (PE, n = 18), early-secretory (ESE, n = 18), mid-secretory (MSE, n = 17) and late-secretory (LSE, n = 10) endometrial phases of the natural cycle. A quantitative predictor model was trained on the development group and validated on sequenced samples from healthy women, consisting of 52 paired samples taken from ESE and MSE phases and five LSE phase samples from 31 individuals. Finally, the developed test was applied to 44 MSE phase samples from a study group of patients diagnosed with recurrent implantation failure (RIF). In validation samples (n = 57), we detected displaced WOI in 1.8% of the samples from fertile women. In the RIF study group, we detected a significantly higher proportion of the samples with shifted WOI than in the validation set of samples from fertile women, 15.9% and 1.8% (p = 0.012), respectively. The developed model was evaluated with an average cross-validation accuracy of 98.8% and an accuracy of 98.2% in the validation group. The developed beREADY screening model enables sensitive and dynamic detection of selected transcriptome biomarkers, providing a quantitative and accurate prediction of endometrial receptivity status.
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Affiliation(s)
- Alvin Meltsov
- Competence Centre On Health Technologies, 50411, Tartu, Estonia
- Department of Genetics and Cell Biology, GROW School for Oncology and Developmental Biology, Maastricht University, 6200 MD, Maastricht, The Netherlands
| | - Merli Saare
- Competence Centre On Health Technologies, 50411, Tartu, Estonia.
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, 50406, Tartu, Estonia.
| | - Hindrek Teder
- Competence Centre On Health Technologies, 50411, Tartu, Estonia
- Institute of Biomedicine and Translational Medicine, University of Tartu, 50411, Tartu, Estonia
| | - Priit Paluoja
- Competence Centre On Health Technologies, 50411, Tartu, Estonia
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, 50406, Tartu, Estonia
| | - Riikka K Arffman
- Department of Obstetrics and Gynecology, PEDEGO Research Unit, Medical Research Center, Oulu University Hospital, University of Oulu, FI-90014, Oulu, Finland
| | - Terhi Piltonen
- Department of Obstetrics and Gynecology, PEDEGO Research Unit, Medical Research Center, Oulu University Hospital, University of Oulu, FI-90014, Oulu, Finland
| | - Piotr Laudanski
- Oviklinika Infertility Center, 01-377, Warsaw, Poland
- Women's Health Research Institute, Calisia University, 62-800, Kalisz, Poland
- Department of Obstetrics, Gynecology and Gynaecological Oncology, Medical University of Warsaw, 02-091, Warsaw, Poland
| | | | - Luca Gianaroli
- SISMeR, Reproductive Medicine Institute, 40138, Bologna, Italy
| | - Mariann Koel
- Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Maire Peters
- Competence Centre On Health Technologies, 50411, Tartu, Estonia
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, 50406, Tartu, Estonia
| | - Andres Salumets
- Competence Centre On Health Technologies, 50411, Tartu, Estonia
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, 50406, Tartu, Estonia
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet and Karolinska University Hospital, SE-141 52, Stockholm, Sweden
| | - Kaarel Krjutškov
- Competence Centre On Health Technologies, 50411, Tartu, Estonia
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, 50406, Tartu, Estonia
| | - Priit Palta
- Competence Centre On Health Technologies, 50411, Tartu, Estonia
- Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, FI-00014, Helsinki, Finland
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4
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Koel M, Krjutškov K, Saare M, Samuel K, Lubenets D, Katayama S, Einarsdottir E, Vargas E, Sola-Leyva A, Lalitkumar PG, Gemzell-Danielsson K, Blesa D, Simon C, Lanner F, Kere J, Salumets A, Altmäe S. Human endometrial cell-type-specific RNA sequencing provides new insights into the embryo-endometrium interplay. Hum Reprod Open 2022; 2022:hoac043. [PMID: 36339249 PMCID: PMC9632455 DOI: 10.1093/hropen/hoac043] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 09/21/2022] [Indexed: 08/17/2023] Open
Abstract
STUDY QUESTION Which genes regulate receptivity in the epithelial and stromal cellular compartments of the human endometrium, and which molecules are interacting in the implantation process between the blastocyst and the endometrial cells? SUMMARY ANSWER A set of receptivity-specific genes in the endometrial epithelial and stromal cells was identified, and the role of galectins (LGALS1 and LGALS3), integrin β1 (ITGB1), basigin (BSG) and osteopontin (SPP1) in embryo-endometrium dialogue among many other protein-protein interactions were highlighted. WHAT IS KNOWN ALREADY The molecular dialogue taking place between the human embryo and the endometrium is poorly understood due to ethical and technical reasons, leaving human embryo implantation mostly uncharted. STUDY DESIGN SIZE DURATION Paired pre-receptive and receptive phase endometrial tissue samples from 16 healthy women were used for RNA sequencing. Trophectoderm RNA sequences were from blastocysts. PARTICIPANTS/MATERIALS SETTING METHODS Cell-type-specific RNA-seq analysis of freshly isolated endometrial epithelial and stromal cells using fluorescence-activated cell sorting (FACS) from 16 paired pre-receptive and receptive tissue samples was performed. Endometrial transcriptome data were further combined in silico with trophectodermal gene expression data from 466 single cells originating from 17 blastocysts to characterize the first steps of embryo implantation. We constructed a protein-protein interaction network between endometrial epithelial and embryonal trophectodermal cells, and between endometrial stromal and trophectodermal cells, thereby focusing on the very first phases of embryo implantation, and highlighting the molecules likely to be involved in the embryo apposition, attachment and invasion. MAIN RESULTS AND THE ROLE OF CHANCE In total, 499 epithelial and 581 stromal genes were up-regulated in the receptive phase endometria when compared to pre-receptive samples. The constructed protein-protein interactions identified a complex network of 558 prioritized protein-protein interactions between trophectodermal, epithelial and stromal cells, which were grouped into clusters based on the function of the involved molecules. The role of galectins (LGALS1 and LGALS3), integrin β1 (ITGB1), basigin (BSG) and osteopontin (SPP1) in the embryo implantation process were highlighted. LARGE SCALE DATA RNA-seq data are available at www.ncbi.nlm.nih.gov/geo under accession number GSE97929. LIMITATIONS REASONS FOR CAUTION Providing a static snap-shot of a dynamic process and the nature of prediction analysis is limited to the known interactions available in databases. Furthermore, the cell sorting technique used separated enriched epithelial cells and stromal cells but did not separate luminal from glandular epithelium. Also, the use of biopsies taken from non-pregnant women and using spare IVF embryos (due to ethical considerations) might miss some of the critical interactions characteristic of natural conception only. WIDER IMPLICATIONS OF THE FINDINGS The findings of our study provide new insights into the molecular embryo-endometrium interplay in the first steps of implantation process in humans. Knowledge about the endometrial cell-type-specific molecules that coordinate successful implantation is vital for understanding human reproduction and the underlying causes of implantation failure and infertility. Our study results provide a useful resource for future reproductive research, allowing the exploration of unknown mechanisms of implantation. We envision that those studies will help to improve the understanding of the complex embryo implantation process, and hopefully generate new prognostic and diagnostic biomarkers and therapeutic approaches to target both infertility and fertility, in the form of new contraceptives. STUDY FUNDING/COMPETING INTERESTS This research was funded by the Estonian Research Council (grant PRG1076); Horizon 2020 innovation grant (ERIN, grant no. EU952516); Enterprise Estonia (grant EU48695); the EU-FP7 Marie Curie Industry-Academia Partnerships and Pathways (IAPP, grant SARM, EU324509); Spanish Ministry of Economy, Industry and Competitiveness (MINECO) and European Regional Development Fund (FEDER) (grants RYC-2016-21199, ENDORE SAF2017-87526-R, and Endo-Map PID2021-127280OB-100); Programa Operativo FEDER Andalucía (B-CTS-500-UGR18; A-CTS-614-UGR20), Junta de Andalucía (PAIDI P20_00158); Margarita Salas program for the Requalification of the Spanish University system (UJAR01MS); the Knut and Alice Wallenberg Foundation (KAW 2015.0096); Swedish Research Council (2012-2844); and Sigrid Jusélius Foundation; Academy of Finland. A.S.-L. is funded by the Spanish Ministry of Science, Innovation and Universities (PRE2018-085440). K.G.-D. has received consulting fees and/or honoraria from RemovAid AS, Norway Bayer, MSD, Gedeon Richter, Mithra, Exeltis, MedinCell, Natural cycles, Exelgyn, Vifor, Organon, Campus Pharma and HRA-Pharma and NIH support to the institution; D.B. is an employee of IGENOMIX. The rest of the authors declare no conflict of interest.
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Affiliation(s)
- Mariann Koel
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Cell Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Kaarel Krjutškov
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Merli Saare
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Külli Samuel
- Competence Centre on Health Technologies, Tartu, Estonia
| | - Dmitri Lubenets
- Department of Cell Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Shintaro Katayama
- Stem Cells and Metabolism Research Program, Research Programs Unit, University of Helsinki, and Folkhälsan Research Center, Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Elisabet Einarsdottir
- Stem Cells and Metabolism Research Program, Research Programs Unit, University of Helsinki, and Folkhälsan Research Center, Helsinki, Finland
- Science for Life Laboratory, Department of Gene Technology, KTH-Royal Institute of Technology, Solna, Sweden
| | - Eva Vargas
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
- Systems Biology Unit, Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaén, Jaén, Spain
| | - Alberto Sola-Leyva
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
| | - Parameswaran Grace Lalitkumar
- Department of Women’s and Children’s Health, Division of Obstetrics and Gynecology, Karolinska Institutet, and Karolinska Univeristy Hospital, Stockholm,Sweden
| | - Kristina Gemzell-Danielsson
- Department of Women’s and Children’s Health, Division of Obstetrics and Gynecology, Karolinska Institutet, and Karolinska Univeristy Hospital, Stockholm,Sweden
| | - David Blesa
- Department of Product Development, IGENOMIX, Valencia, Spain
| | - Carlos Simon
- Department of Obstetrics and Gynecology, Valencia University and INCLIVA in Valencia, Valencia, Spain
- Department of Obstetrics and Gynecology, BIDMC, Harvard University, Boston, MA, USA
| | - Fredrik Lanner
- Department of Clinical Science, Intervention and Technology, Division of Obstetrics and Gynecology, Karolinska Institutet, Stockholm,Sweden
- Ming Wai Lau Center for Reparative Medicine, Stockholm node, Karolinska Institutet, Stockholm, Sweden
| | - Juha Kere
- Stem Cells and Metabolism Research Program, Research Programs Unit, University of Helsinki, and Folkhälsan Research Center, Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Andres Salumets
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Department of Clinical Science, Intervention and Technology, Division of Obstetrics and Gynecology, Karolinska Institutet, Stockholm,Sweden
| | - Signe Altmäe
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada, Spain
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
- Department of Clinical Science, Intervention and Technology, Division of Obstetrics and Gynecology, Karolinska Institutet, Stockholm,Sweden
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5
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Vuoristo S, Bhagat S, Hydén-Granskog C, Yoshihara M, Gawriyski L, Jouhilahti EM, Ranga V, Tamirat M, Huhtala M, Kirjanov I, Nykänen S, Krjutškov K, Damdimopoulos A, Weltner J, Hashimoto K, Recher G, Ezer S, Paluoja P, Paloviita P, Takegami Y, Kanemaru A, Lundin K, Airenne TT, Otonkoski T, Tapanainen JS, Kawaji H, Murakawa Y, Bürglin TR, Varjosalo M, Johnson MS, Tuuri T, Katayama S, Kere J. DUX4 is a multifunctional factor priming human embryonic genome activation. iScience 2022; 25:104137. [PMID: 35402882 PMCID: PMC8990217 DOI: 10.1016/j.isci.2022.104137] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 02/04/2022] [Accepted: 03/18/2022] [Indexed: 12/13/2022] Open
Abstract
Double homeobox 4 (DUX4) is expressed at the early pre-implantation stage in human embryos. Here we show that induced human DUX4 expression substantially alters the chromatin accessibility of non-coding DNA and activates thousands of newly identified transcribed enhancer-like regions, preferentially located within ERVL-MaLR repeat elements. CRISPR activation of transcribed enhancers by C-terminal DUX4 motifs results in the increased expression of target embryonic genome activation (EGA) genes ZSCAN4 and KHDC1P1. We show that DUX4 is markedly enriched in human zygotes, followed by intense nuclear DUX4 localization preceding and coinciding with minor EGA. DUX4 knockdown in human zygotes led to changes in the EGA transcriptome but did not terminate the embryos. We also show that the DUX4 protein interacts with the Mediator complex via the C-terminal KIX binding motif. Our findings contribute to the understanding of DUX4 as a regulator of the non-coding genome.
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Affiliation(s)
- Sanna Vuoristo
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177 Huddinge, Sweden.,Department of Obstetrics and Gynecology, 00014, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | - Shruti Bhagat
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177 Huddinge, Sweden.,RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Instutute for the Advanced Study of Human Biology, Kyoto University, Kyoto 606-8501, Japan
| | | | - Masahito Yoshihara
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177 Huddinge, Sweden
| | - Lisa Gawriyski
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Eeva-Mari Jouhilahti
- Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland
| | - Vipin Ranga
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
| | - Mahlet Tamirat
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
| | - Mikko Huhtala
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
| | - Ida Kirjanov
- Department of Obstetrics and Gynecology, 00014, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | - Sonja Nykänen
- Department of Obstetrics and Gynecology, 00014, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | - Kaarel Krjutškov
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177 Huddinge, Sweden.,Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland.,Competence Centre for Health Technologies, 51010 Tartu, Estonia.,University of Tartu, Department of Obstetrics and Gynecology, Institute of Clinical Medicine, 50406 Tartu, Estonia
| | | | - Jere Weltner
- Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland
| | - Kosuke Hashimoto
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan
| | - Gaëlle Recher
- Laboratoire Photonique Numérique et Nanosciences, CNRS, Institut d'Optique Graduate School, University of Bordeaux, UMR 5298, 33400 Bordeaux, France
| | - Sini Ezer
- Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland.,Folkhälsan Research Center, 00290 Helsinki, Finland
| | - Priit Paluoja
- Competence Centre for Health Technologies, 51010 Tartu, Estonia.,Institute of Clinical Medicine, University of Tartu, 50090 Tartu, Estonia.,University of Helsinki, Doctoral Program in Population Health, 00014 Helsinki, Finland
| | - Pauliina Paloviita
- Department of Obstetrics and Gynecology, 00014, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | | | | | - Karolina Lundin
- Department of Obstetrics and Gynecology, 00014, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland
| | - Tomi T Airenne
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
| | - Timo Otonkoski
- Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland.,Children's Hospital, Helsinki University Central Hospital, 00290
| | - Juha S Tapanainen
- Department of Obstetrics and Gynecology, 00014, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland.,Reproductive Medicine Unit, Helsinki University Hospital, 00290 Helsinki, Finland.,Oulu University Hospital, 90220 Oulu, Finland
| | - Hideya Kawaji
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,RIKEN Preventive Medicine and Diagnosis Innovation Program, Wako 351-0198, Japan.,Tokyo Metropolitan Institute of Medical Science, Tokyo 156-8506, Japan
| | - Yasuhiro Murakawa
- RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, Japan.,Instutute for the Advanced Study of Human Biology, Kyoto University, Kyoto 606-8501, Japan.,IFOM, The FIRC Institute of Molecular Oncology, 20139 Milan, Italy.,Department of Medical Systems Genomics, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Thomas R Bürglin
- Department of Biomedicine, University of Basel, 4031 Basel, Switzerland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, 00790 Helsinki, Finland
| | - Mark S Johnson
- Structural Bioinformatics Laboratory, Biochemistry, Faculty of Science and Engineering, Åbo Akademi University, 20520 Turku, Finland
| | - Timo Tuuri
- Department of Obstetrics and Gynecology, 00014, University of Helsinki and Helsinki University Hospital, 00290 Helsinki, Finland.,Reproductive Medicine Unit, Helsinki University Hospital, 00290 Helsinki, Finland
| | - Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177 Huddinge, Sweden.,Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland.,Folkhälsan Research Center, 00290 Helsinki, Finland
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, 17177 Huddinge, Sweden.,Stem Cells and Metabolism Research Program, University of Helsinki, 00014 Helsinki, Finland.,Folkhälsan Research Center, 00290 Helsinki, Finland
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6
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Zhytnik L, Peters M, Tilk K, Reimand T, Ilisson P, Kahre T, Murumets Ü, Ehrenberg A, Ustav EL, Tõnisson N, Mölder S, Teder H, Krjutškov K, Salumets A. Prenatal diagnosis of a 46,XY karyotype female fetus with an SRY-associated gonadal dysgenesis, conceived through an intracytoplasmic sperm injection: a case report. BMC Pregnancy Childbirth 2022; 22:105. [PMID: 35123446 PMCID: PMC8818175 DOI: 10.1186/s12884-022-04431-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 01/26/2022] [Indexed: 11/19/2022] Open
Abstract
Background Permanent progression of paternal age and development of reproductive medicine lead to increase in number of children conceived with assisted reproductive techniques (ART). Although it is uncertain if ARTs have direct influence on offspring health, advanced paternal age, associated comorbidities and reduced fertility possess significant risks of genetic disorders to the offspring. With a broad implementation of a non-invasive prenatal testing (NIPT), more cases of genetic disorders, including sex discordance are revealed. Among biological causes of sex discordance are disorders of sexual development, majority of which are associated with the SRY gene. Case presentation We report a case of a non-invasive prenatal testing and ultrasound sex discordance in a 46,XY karyotype female fetus with an SRY pathogenic variant, who was conceived through an intracytoplasmic sperm injection (ICSI) due to severe oligozoospermia of the father. Advanced mean age of ICSI patients is associated with risk of de novo mutations and monogenic disorders in the offspring. Additionally, ICSI patients have higher risk to harbour infertility-predisposing mutations, including mutations in the SRY gene. These familial and de novo genetic factors predispose ICSI-conceived children to congenital malformations and might negatively affect reproductive health of ICSI-patients’ offspring. Conclusions Oligozoospermic patients planning assisted reproduction are warranted to undergo genetic counselling and testing for possible inherited and mosaic mutations, and risk factors for de novo mutations.
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7
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Paluoja P, Teder H, Ardeshirdavani A, Bayindir B, Vermeesch J, Salumets A, Krjutškov K, Palta P. Systematic evaluation of NIPT aneuploidy detection software tools with clinically validated NIPT samples. PLoS Comput Biol 2021; 17:e1009684. [PMID: 34928946 PMCID: PMC8722721 DOI: 10.1371/journal.pcbi.1009684] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 01/03/2022] [Accepted: 11/27/2021] [Indexed: 11/18/2022] Open
Abstract
Non-invasive prenatal testing (NIPT) is a powerful screening method for fetal aneuploidy detection, relying on laboratory and computational analysis of cell-free DNA. Although several published computational NIPT analysis tools are available, no prior comprehensive, head-to-head accuracy comparison of the various tools has been published. Here, we compared the outcome accuracies obtained for clinically validated samples with five commonly used computational NIPT aneuploidy analysis tools (WisecondorX, NIPTeR, NIPTmer, RAPIDR, and GIPseq) across various sequencing depths (coverage) and fetal DNA fractions. The sample set included cases of fetal trisomy 21 (Down syndrome), trisomy 18 (Edwards syndrome), and trisomy 13 (Patau syndrome). We determined that all of the compared tools were considerably affected by lower sequencing depths, such that increasing proportions of undetected trisomy cases (false negatives) were observed as the sequencing depth decreased. We summarised our benchmarking results and highlighted the advantages and disadvantages of each computational NIPT software. To conclude, trisomy detection for lower coverage NIPT samples (e.g. 2.5M reads per sample) is technically possible but can, with some NIPT tools, produce troubling rates of inaccurate trisomy detection, especially in low-FF samples. Non-invasive prenatal testing analysis relies on computational algorithms that are used for inferring chromosomal aneuploidies, such as chromosome 21 triploidy in the case of Down syndrome. However, the performance of these algorithms has not been compared on the same clinically validated data. Here we conducted a head-to-head comparison of WGS-based NIPT aneuploidy detection tools. Our findings indicate that at and below 2.5M reads per sample, the least accurate algorithm would miss detection of almost a third of trisomy cases. Furthermore, we describe and quantify a previously undocumented aneuploidy risk uncertainty that is mainly relevant in cases of very low sequencing coverage (at and below 1.25M reads per sample) and could, in the worst-case scenario, lead to a false negative rate of 245 undetected trisomies per 1,000 trisomy cases. Our findings underscore the importance of the informed selection of NIPT software tools in combination with sequencing coverage, which directly impacts NIPT sequencing cost and accuracy.
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Affiliation(s)
- Priit Paluoja
- Doctoral Programme in Population Health, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Competence Centre for Health Technologies, Tartu, Estonia
| | - Hindrek Teder
- Competence Centre for Health Technologies, Tartu, Estonia
- Institute of Biomedicine and Translational Medicine, Department of Biomedicine, University of Tartu, Tartu, Estonia
| | | | - Baran Bayindir
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | | | - Andres Salumets
- Competence Centre for Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Division of Obstetrics and Gynecology, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Stockholm, Sweden
| | - Kaarel Krjutškov
- Competence Centre for Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Priit Palta
- Competence Centre for Health Technologies, Tartu, Estonia
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- * E-mail:
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8
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Khatun M, Meltsov A, Lavogina D, Loid M, Kask K, Arffman RK, Rossi HR, Lättekivi F, Jääger K, Krjutškov K, Rinken A, Salumets A, Piltonen TT. Decidualized endometrial stromal cells present with altered androgen response in PCOS. Sci Rep 2021; 11:16287. [PMID: 34381107 PMCID: PMC8357821 DOI: 10.1038/s41598-021-95705-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 07/23/2021] [Indexed: 01/27/2023] Open
Abstract
Hyperandrogenic women with PCOS show disrupted decidualization (DE) and placentation. Dihydrotestosterone (DHT) is reported to enhance DE in non-PCOS endometrial stromal cells (eSCCtrl); however, this has not been assessed in PCOS cells (eSCPCOS). Therefore, we studied the transcriptome profile of non-decidualized (non-DE) and DE eSCs from women with PCOS and Ctrl in response to short-term estradiol (E2) and/or progesterone (P4) exposure with/without (±) DHT. The non-DE eSCs were subjected to E2 ± DHT treatment, whereas the DE (0.5 mM 8-Br-cAMP, 96 h) eSCs were post-treated with E2 and P4 ± DHT, and RNA-sequenced. Validation was performed by immunofluorescence and immunohistochemistry. The results showed that, regardless of treatment, the PCOS and Ctrl samples clustered separately. The comparison of DE vs. non-DE eSCPCOS without DHT revealed PCOS-specific differentially expressed genes (DEGs) involved in mitochondrial function and progesterone signaling. When further adding DHT, we detected altered responses for lysophosphatidic acid (LPA), inflammation, and androgen signaling. Overall, the results highlight an underlying defect in decidualized eSCPCOS, present with or without DHT exposure, and possibly linked to the altered pregnancy outcomes. We also report novel factors which elucidate the mechanisms of endometrial dysfunction in PCOS.
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Affiliation(s)
- Masuma Khatun
- Department of Obstetrics and Gynaecology, PEDEGO Research Unit, Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Alvin Meltsov
- Competence Centre on Health Technologies, Tartu, Estonia.,Department of Computer Science, University of Tartu, Tartu, Estonia
| | - Darja Lavogina
- Competence Centre on Health Technologies, Tartu, Estonia.,Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Marina Loid
- Competence Centre on Health Technologies, Tartu, Estonia.,Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Keiu Kask
- Competence Centre on Health Technologies, Tartu, Estonia.,Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Riikka K Arffman
- Department of Obstetrics and Gynaecology, PEDEGO Research Unit, Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Henna-Riikka Rossi
- Department of Obstetrics and Gynaecology, PEDEGO Research Unit, Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Freddy Lättekivi
- Department of Pathophysiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia.,Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Kersti Jääger
- Competence Centre on Health Technologies, Tartu, Estonia
| | - Kaarel Krjutškov
- Competence Centre on Health Technologies, Tartu, Estonia.,Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Ago Rinken
- Institute of Chemistry, University of Tartu, Tartu, Estonia
| | - Andres Salumets
- Competence Centre on Health Technologies, Tartu, Estonia.,Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Division of Obstetrics and Gynaecology, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Stockholm, Sweden
| | - Terhi T Piltonen
- Department of Obstetrics and Gynaecology, PEDEGO Research Unit, Medical Research Center, Oulu University Hospital, University of Oulu, Oulu, Finland.
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9
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Zhytnik L, Peters M, Tilk K, Simm K, Tõnisson N, Reimand T, Maasalu K, Acharya G, Krjutškov K, Salumets A. From late fatherhood to prenatal screening of monogenic disorders: evidence and ethical concerns. Hum Reprod Update 2021; 27:1056-1085. [PMID: 34329448 DOI: 10.1093/humupd/dmab023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Revised: 06/27/2021] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND With the help of ART, an advanced parental age is not considered to be a serious obstacle for reproduction anymore. However, significant health risks for future offspring hide behind the success of reproductive medicine for the treatment of reduced fertility associated with late parenthood. Although an advanced maternal age is a well-known risk factor for poor reproductive outcomes, understanding the impact of an advanced paternal age on offspring is yet to be elucidated. De novo monogenic disorders (MDs) are highly associated with late fatherhood. MDs are one of the major sources of paediatric morbidity and mortality, causing significant socioeconomic and psychological burdens to society. Although individually rare, the combined prevalence of these disorders is as high as that of chromosomal aneuploidies, indicating the increasing need for prenatal screening. With the help of advanced reproductive technologies, families with late paternity have the option of non-invasive prenatal testing (NIPT) for multiple MDs (MD-NIPT), which has a sensitivity and specificity of almost 100%. OBJECTIVE AND RATIONALE The main aims of the current review were to examine the effect of late paternity on the origin and nature of MDs, to highlight the role of NIPT for the detection of a variety of paternal age-associated MDs, to describe clinical experiences and to reflect on the ethical concerns surrounding the topic of late paternity and MD-NIPT. SEARCH METHODS An extensive search of peer-reviewed publications (1980-2021) in English from the PubMed and Google Scholar databases was based on key words in different combinations: late paternity, paternal age, spermatogenesis, selfish spermatogonial selection, paternal age effect, de novo mutations (DNMs), MDs, NIPT, ethics of late fatherhood, prenatal testing and paternal rights. OUTCOMES An advanced paternal age provokes the accumulation of DNMs, which arise in continuously dividing germline cells. A subset of DNMs, owing to their effect on the rat sarcoma virus protein-mitogen-activated protein kinase signalling pathway, becomes beneficial for spermatogonia, causing selfish spermatogonial selection and outgrowth, and in some rare cases may lead to spermatocytic seminoma later in life. In the offspring, these selfish DNMs cause paternal age effect (PAE) disorders with a severe and even life-threatening phenotype. The increasing tendency for late paternity and the subsequent high risk of PAE disorders indicate an increased need for a safe and reliable detection procedure, such as MD-NIPT. The MD-NIPT approach has the capacity to provide safe screening for pregnancies at risk of PAE disorders and MDs, which constitute up to 20% of all pregnancies. The primary risks include pregnancies with a paternal age over 40 years, a previous history of an affected pregnancy/child, and/or congenital anomalies detected by routine ultrasonography. The implementation of NIPT-based screening would support the early diagnosis and management needed in cases of affected pregnancy. However, the benefits of MD-NIPT need to be balanced with the ethical challenges associated with the introduction of such an approach into routine clinical practice, namely concerns regarding reproductive autonomy, informed consent, potential disability discrimination, paternal rights and PAE-associated issues, equity and justice in accessing services, and counselling. WIDER IMPLICATIONS Considering the increasing parental age and risks of MDs, combined NIPT for chromosomal aneuploidies and microdeletion syndromes as well as tests for MDs might become a part of routine pregnancy management in the near future. Moreover, the ethical challenges associated with the introduction of MD-NIPT into routine clinical practice need to be carefully evaluated. Furthermore, more focus and attention should be directed towards the ethics of late paternity, paternal rights and paternal genetic guilt associated with pregnancies affected with PAE MDs.
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Affiliation(s)
- Lidiia Zhytnik
- Competence Centre on Health Technologies, Tartu, Estonia
| | - Maire Peters
- Competence Centre on Health Technologies, Tartu, Estonia.,Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Kadi Tilk
- Competence Centre on Health Technologies, Tartu, Estonia
| | - Kadri Simm
- Institute of Philosophy and Semiotics, Faculty of Arts and Humanities, University of Tartu, Tartu, Estonia.,Centre of Ethics, University of Tartu, Tartu, Estonia
| | - Neeme Tõnisson
- Institute of Genomics, University of Tartu, Tartu, Estonia.,Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia.,Department of Reproductive Medicine, West Tallinn Central Hospital, Tallinn, Estonia
| | - Tiia Reimand
- Department of Clinical Genetics, United Laboratories, Tartu University Hospital, Tartu, Estonia.,Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Katre Maasalu
- Clinic of Traumatology and Orthopaedics, Tartu University Hospital, Tartu, Estonia.,Department of Traumatology and Orthopaedics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Ganesh Acharya
- Division of Obstetrics and Gynaecology, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Stockholm, Sweden
| | - Kaarel Krjutškov
- Competence Centre on Health Technologies, Tartu, Estonia.,Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Andres Salumets
- Competence Centre on Health Technologies, Tartu, Estonia.,Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Institute of Genomics, University of Tartu, Tartu, Estonia.,Division of Obstetrics and Gynaecology, Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Stockholm, Sweden
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10
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Plaza-Florido A, Altmäe S, Esteban FJ, Cadenas-Sanchez C, Aguilera CM, Einarsdottir E, Katayama S, Krjutškov K, Kere J, Zaldivar F, Radom-Aizik S, Ortega FB. Distinct whole-blood transcriptome profile of children with metabolic healthy overweight/obesity compared to metabolic unhealthy overweight/obesity. Pediatr Res 2021; 89:1687-1694. [PMID: 33230195 DOI: 10.1038/s41390-020-01276-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 09/18/2020] [Accepted: 10/27/2020] [Indexed: 01/04/2023]
Abstract
BACKGROUND Youth populations with overweight/obesity (OW/OB) exhibit heterogeneity in cardiometabolic health phenotypes. The underlying mechanisms for those differences are still unclear. This study aimed to analyze the whole-blood transcriptome profile (RNA-seq) of children with metabolic healthy overweight/obesity (MHO) and metabolic unhealthy overweight/obesity (MUO) phenotypes. METHODS Twenty-seven children with OW/OB (10.1 ± 1.3 years, 59% boys) from the ActiveBrains project were included. MHO was defined as having none of the following criteria for metabolic syndrome: elevated fasting glucose, high serum triglycerides, low high-density lipoprotein-cholesterol, and high systolic or diastolic blood pressure, while MUO was defined as presenting one or more of these criteria. Inflammatory markers were additionally determined. Total blood RNA was analyzed by 5'-end RNA-sequencing. RESULTS Whole-blood transcriptome analysis revealed a distinct pattern of gene expression in children with MHO compared to MUO children. Thirty-two genes differentially expressed were linked to metabolism, mitochondrial, and immune functions. CONCLUSIONS The identified gene expression patterns related to metabolism, mitochondrial, and immune functions contribute to a better understanding of why a subset of the population remains metabolically healthy despite having overweight/obesity. IMPACT A distinct pattern of whole-blood transcriptome profile (RNA-seq) was identified in children with metabolic healthy overweight/obesity (MHO) compared to metabolic unhealthy overweight/obesity (MUO) phenotype. The most relevant genes in understanding the molecular basis underlying the MHO/MUO phenotypes in children could be: RREB1, FAM83E, SLC44A1, NRG1, TMC5, CYP3A5, TRIM11, and ADAMTSL2. The identified whole-blood transcriptome profile related to metabolism, mitochondrial, and immune functions contribute to a better understanding of why a subset of the population remains metabolically healthy despite having overweight/obesity.
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Affiliation(s)
- Abel Plaza-Florido
- PROFITH "PROmoting FITness and Health Through Physical Activity" Research Group, Sport and Health University Research Institute (iMUDS), Department of Physical and Sports Education, Faculty of Sport Sciences, University of Granada, 18011, Granada, Spain.
| | - Signe Altmäe
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada, Spain.,Competence Centre on Health Technologies, Tartu, Estonia.,Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain
| | - Francisco J Esteban
- Systems Biology Unit, Department of Experimental Biology, Faculty of Experimental Sciences, University of Jaen, Jaen, Spain
| | - Cristina Cadenas-Sanchez
- PROFITH "PROmoting FITness and Health Through Physical Activity" Research Group, Sport and Health University Research Institute (iMUDS), Department of Physical and Sports Education, Faculty of Sport Sciences, University of Granada, 18011, Granada, Spain.,Institute for Innovation & Sustainable Development in Food Chain (IS-FOOD), Public University of Navarra, Pamplona, Spain
| | - Concepción M Aguilera
- Instituto de Investigación Biosanitaria ibs.GRANADA, Granada, Spain.,Department of Biochemistry and Molecular Biology II, Institute of Nutrition and Food Technology, Centre for Biomedical Research, University of Granada, Granada, Spain.,CIBER Fisiopatología de la Obesidad y la Nutrición (CIBEROBN), Madrid, Spain
| | - Elisabet Einarsdottir
- Science for Life Laboratory, Department of Gene Technology, KTH Royal Institute of Technology, SE-171 21, Solna, Sweden
| | - Shintaro Katayama
- Stem Cells and Metabolism Research Program (STEMM), University of Helsinki, and Folkhälsan Research Center, Helsinki, Finland.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Kaarel Krjutškov
- Competence Centre on Health Technologies, Tartu, Estonia.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Institute of Clinical Medicine, Department of Obstetrics and Gynecology, University of Tartu, Tartu, Estonia
| | - Juha Kere
- Stem Cells and Metabolism Research Program (STEMM), University of Helsinki, and Folkhälsan Research Center, Helsinki, Finland.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Frank Zaldivar
- Pediatric Exercise and Genomics Research Center, UC Irvine School of Medicine, Irvine, CA, USA
| | - Shlomit Radom-Aizik
- Pediatric Exercise and Genomics Research Center, UC Irvine School of Medicine, Irvine, CA, USA
| | - Francisco B Ortega
- PROFITH "PROmoting FITness and Health Through Physical Activity" Research Group, Sport and Health University Research Institute (iMUDS), Department of Physical and Sports Education, Faculty of Sport Sciences, University of Granada, 18011, Granada, Spain.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
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11
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Käck U, Einarsdottir E, van Hage M, Asarnoj A, James A, Nopp A, Krjutškov K, Katayama S, Kere J, Lilja G, Söderhäll C, Konradsen JR. Nasal upregulation of CST1 in dog-sensitised children with severe allergic airway disease. ERJ Open Res 2021; 7:00917-2020. [PMID: 33898616 DOI: 10.1183/23120541.00917-2020] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Accepted: 01/27/2021] [Indexed: 12/27/2022] Open
Abstract
Background The clinical presentation of children sensitised to dog dander varies from asymptomatic to severe allergic airway disease, but the genetic mechanisms underlying these differences are not clear. The objective of the present study was to investigate nasal transcriptomic profiles associated with dog dander sensitisation in school children and to reveal clinical symptoms related with these profiles. Methods RNA was extracted from nasal epithelial cell brushings of children sensitised to dog dander and healthy controls. Blood sample analyses included IgE against dog dander, dog allergen molecules, other airborne and food allergens, basophil activation and white blood cell counts. Clinical history of asthma and rhinitis was recorded, and lung function was assessed (spirometry, methacholine provocation and exhaled nitric oxide fraction). Results The most overexpressed gene in children sensitised to dog dander compared to healthy controls was CST1, coding for Cystatin 1. A cluster of these children with enhanced CST1 expression showed lower forced expiratory volume in 1 s, increased bronchial hyperreactivity, pronounced eosinophilia and higher basophil allergen threshold sensitivity compared with other children sensitised to dog dander. In addition, multi-sensitisation to lipocalins was more common in this group. Conclusions Overexpression of CST1 is associated with more severe allergic airway disease in children sensitised to dog dander. CST1 is thus a possible biomarker of the severity of allergic airway disease and a possible therapeutic target for the future treatment of airborne allergy.
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Affiliation(s)
- Ulrika Käck
- Dept of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden.,Sach's Children and Youth Hospital, Södersjukhuset, Stockholm, Sweden
| | - Elisabet Einarsdottir
- Dept of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Department of Gene Technology, KTH-Royal Institute of Technology, Solna, Sweden.,Folkhälsan Research Center, Helsinki, Finland
| | - Marianne van Hage
- Dept of Medicine Solna, Division of Immunology and Allergy, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Anna Asarnoj
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden.,Dept of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Anna James
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Anna Nopp
- Dept of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden.,Sach's Children and Youth Hospital, Södersjukhuset, Stockholm, Sweden
| | - Kaarel Krjutškov
- Dept of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.,Department of Obstetrics and Gynecology, University of Tartu, Tartu, Estonia.,Competence Centre on Health Technologies, Tartu, Estonia
| | - Shintaro Katayama
- Dept of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.,Folkhälsan Research Center, Helsinki, Finland.,University of Helsinki, Stem Cells and Metabolism Research Program, Helsinki, Finland
| | - Juha Kere
- Dept of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.,Folkhälsan Research Institute, and Stem Cell and Metabolism Research Program, University of Helsinki, Helsinki, Finland
| | - Gunnar Lilja
- Dept of Clinical Science and Education, Södersjukhuset, Karolinska Institutet, Stockholm, Sweden.,Sach's Children and Youth Hospital, Södersjukhuset, Stockholm, Sweden
| | - Cilla Söderhäll
- Dept of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden.,Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden.,Dept of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.,These authors contributed equally
| | - Jon R Konradsen
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden.,Dept of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.,These authors contributed equally
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12
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Varshney MK, Yu NYL, Katayama S, Li X, Liu T, Wu WF, Töhönen V, Krjutškov K, Kere J, Fan X, Inzunza J, Gustafsson JÅ, Nalvarte I. Motor Function Deficits in the Estrogen Receptor Beta Knockout Mouse: Role on Excitatory Neurotransmission and Myelination in the Motor Cortex. Neuroendocrinology 2021; 111:27-44. [PMID: 31991411 DOI: 10.1159/000506162] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 01/25/2020] [Indexed: 11/19/2022]
Abstract
BACKGROUND Male estrogen receptor beta (ERβ) knockout (BERKO) mice display anxiety and aggression linked to, among others, altered serotonergic signaling in the basolateral amygdala and dorsal raphe, impaired cortical radial glia migration, and reduced GABAergic signaling. The effects on primary motor cortex (M1 cortex) and locomotor activity as a consequence of ERβ loss have not been investigated. OBJECTIVE The aim of this study was to determine whether locomotor activity is altered as a consequence of the changes in the M1 cortex. METHODS The locomotor activity of male wild-type (WT) and BERKO mice was evaluated using the open-field and rotarod tests. Molecular changes in the M1 cortex were analyzed by RNA sequencing, electron microscopy, electrophysiology, and immunohistological techniques. In addition, we established oligodendrocyte (OL) cultures from WT and BERKO mouse embryonic stem cells to evaluate OL function. RESULTS Locomotor profiling revealed that BERKO mice were more active than WT mice but had impaired motor coordination. Analysis of the M1 cortex pointed out differences in synapse function and myelination. There was a reduction in GABAergic signaling resulting in imbalanced excitatory and inhibitory neurotransmission as well as a defective OL differentiation accompanied by myelin defects. The effects of ERβ loss on OL differentiation were confirmed in vitro. CONCLUSION ERβ is an important regulator of GABAergic interneurons and OL differentiation, which impacts on adult M1 cortex function and may be linked to increased locomotor activity and decreased motor coordination in BERKO mice.
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Affiliation(s)
| | - Nancy Yiu-Lin Yu
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Xin Li
- Department of Developmental Neuropsychology, School of Psychology, Third Military Medical University, Chongqing, China
| | - Tianyao Liu
- Department of Developmental Neuropsychology, School of Psychology, Third Military Medical University, Chongqing, China
| | - Wan-Fu Wu
- Center for Nuclear Receptors and Cell Signaling, University of Houston, Houston, Texas, USA
| | - Virpi Töhönen
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Kaarel Krjutškov
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Competence Center on Health Technologies, Tartu, Estonia
- Folkhälsan Research Institute, Helsinki, and Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Folkhälsan Research Institute, Helsinki, and Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
| | - Xiaotang Fan
- Department of Developmental Neuropsychology, School of Psychology, Third Military Medical University, Chongqing, China
| | - José Inzunza
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Jan-Åke Gustafsson
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- Center for Nuclear Receptors and Cell Signaling, University of Houston, Houston, Texas, USA
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
| | - Ivan Nalvarte
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden,
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13
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Gordevičius J, Narmontė M, Gibas P, Kvederavičiūtė K, Tomkutė V, Paluoja P, Krjutškov K, Salumets A, Kriukienė E. Identification of fetal unmodified and 5-hydroxymethylated CG sites in maternal cell-free DNA for non-invasive prenatal testing. Clin Epigenetics 2020; 12:153. [PMID: 33081811 PMCID: PMC7574562 DOI: 10.1186/s13148-020-00938-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 09/14/2020] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Massively parallel sequencing of maternal cell-free DNA (cfDNA) is widely used to test fetal genetic abnormalities in non-invasive prenatal testing (NIPT). However, sequencing-based approaches are still of high cost. Building upon previous knowledge that placenta, the main source of fetal circulating DNA, is hypomethylated in comparison to maternal tissue counterparts of cfDNA, we propose that targeting either unmodified or 5-hydroxymethylated CG sites specifically enriches fetal genetic material and reduces numbers of required analytical sequencing reads thereby decreasing cost of a test. METHODS We employed uTOPseq and hmTOP-seq approaches which combine covalent derivatization of unmodified or hydroxymethylated CG sites, respectively, with next generation sequencing, or quantitative real-time PCR. RESULTS We detected increased 5-hydroxymethylcytosine (5hmC) levels in fetal chorionic villi (CV) tissue samples as compared with peripheral blood. Using our previously developed uTOP-seq and hmTOP-seq approaches we obtained whole-genome uCG and 5hmCG maps of 10 CV tissue and 38 cfDNA samples in total. Our results indicated that, in contrast to conventional whole genome sequencing, such epigenomic analysis highly specifically enriches fetal DNA fragments from maternal cfDNA. While both our approaches yielded 100% accuracy in detecting Down syndrome in fetuses, hmTOP-seq maintained such accuracy at ultra-low sequencing depths using only one million reads. We identified 2164 and 1589 placenta-specific differentially modified and 5-hydroxymethylated regions, respectively, in chromosome 21, as well as 3490 and 2002 Down syndrome-specific differentially modified and 5-hydroxymethylated regions, respectively, that can be used as biomarkers for identification of Down syndrome or other epigenetic diseases of a fetus. CONCLUSIONS uTOP-seq and hmTOP-seq approaches provide a cost-efficient and sensitive epigenetic analysis of fetal abnormalities in maternal cfDNA. The results demonstrated that T21 fetuses contain a perturbed epigenome and also indicated that fetal cfDNA might originate from fetal tissues other than placental chorionic villi. Robust covalent derivatization followed by targeted analysis of fetal DNA by sequencing or qPCR presents an attractive strategy that could help achieve superior sensitivity and specificity in prenatal diagnostics.
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Affiliation(s)
- Juozas Gordevičius
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, 10257, Vilnius, Lithuania
| | - Milda Narmontė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, 10257, Vilnius, Lithuania
| | - Povilas Gibas
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, 10257, Vilnius, Lithuania
| | - Kotryna Kvederavičiūtė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, 10257, Vilnius, Lithuania
| | - Vita Tomkutė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, 10257, Vilnius, Lithuania
| | - Priit Paluoja
- Competence Centre On Health Technologies, Teaduspargi 13, 50411, Tartu, Estonia.,Faculty of Medicine, University of Helsinki, 00014, Helsinki, Finland
| | - Kaarel Krjutškov
- Competence Centre On Health Technologies, Teaduspargi 13, 50411, Tartu, Estonia.,Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, L. Puusepa 8, 50406, Tartu, Estonia
| | - Andres Salumets
- Competence Centre On Health Technologies, Teaduspargi 13, 50411, Tartu, Estonia.,Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, L. Puusepa 8, 50406, Tartu, Estonia.,Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, HUS, PO Box 140, 00029, Helsinki, Finland.,Estonian Genome Center, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Edita Kriukienė
- Department of Biological DNA Modification, Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, 10257, Vilnius, Lithuania. .,Institute of Biotechnology, Vilnius University, Saulėtekio av. 7, 10257, Vilnius, Lithuania.
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14
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Veerus P, Salumets A, Naaber P, Krjutškov K, Tilk K, Laanpere M, Uusküla A. Seroprevalence of SARS-CoV-2 antibodies among pregnant women in Estonia: A call for epidemiological studies. Acta Obstet Gynecol Scand 2020; 99:1736-1737. [PMID: 32970836 PMCID: PMC7537018 DOI: 10.1111/aogs.13995] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 09/14/2020] [Accepted: 09/15/2020] [Indexed: 11/28/2022]
Affiliation(s)
- Piret Veerus
- National Institute for Health Development, Tallinn, Estonia
| | - Andres Salumets
- Competence Center on Health Technologies, Tartu, Estonia.,Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Institute of Genomics, University of Tartu, Tartu, Estonia.,Institute of Veterinary Medicine and Animal Sciences, Estonian University of Life Sciences, Tartu, Estonia
| | - Paul Naaber
- SYNLAB Estonia, Tallinn, Estonia.,Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Kaarel Krjutškov
- Competence Center on Health Technologies, Tartu, Estonia.,Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Kadi Tilk
- Competence Center on Health Technologies, Tartu, Estonia
| | - Made Laanpere
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Anneli Uusküla
- Department of Family Medicine and Public Health, University of Tartu, Tartu, Estonia
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15
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Saare M, Laisk T, Teder H, Paluoja P, Palta P, Koel M, Kirss F, Karro H, Sõritsa D, Salumets A, Krjutškov K, Peters M. A molecular tool for menstrual cycle phase dating of endometrial samples in endometriosis transcriptome studies†. Biol Reprod 2020; 101:1-3. [PMID: 31004479 DOI: 10.1093/biolre/ioz072] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 04/18/2019] [Indexed: 01/30/2023] Open
Affiliation(s)
- Merli Saare
- Competence Centre on Health Technologies; Tartu, Estonia.,Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu; Tartu, Estonia
| | - Triin Laisk
- Competence Centre on Health Technologies; Tartu, Estonia.,Estonian Genome Center Science Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Hindrek Teder
- Competence Centre on Health Technologies; Tartu, Estonia.,Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Priit Paluoja
- Competence Centre on Health Technologies; Tartu, Estonia.,Institute of Computer Science, University of Tartu, Estonia
| | - Priit Palta
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Finland
| | - Mariann Koel
- Competence Centre on Health Technologies; Tartu, Estonia.,Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Fred Kirss
- Tartu University Hospital, Women's Clinic, Tartu, Estonia
| | - Helle Karro
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu; Tartu, Estonia.,Tartu University Hospital, Women's Clinic, Tartu, Estonia
| | - Deniss Sõritsa
- Competence Centre on Health Technologies; Tartu, Estonia.,Elite Clinic, Tartu, Estonia
| | - Andres Salumets
- Competence Centre on Health Technologies; Tartu, Estonia.,Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu; Tartu, Estonia.,Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Kaarel Krjutškov
- Competence Centre on Health Technologies; Tartu, Estonia.,Research Program of Molecular Neurology, Research Programs Unit, University of Helsinki, and Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Maire Peters
- Competence Centre on Health Technologies; Tartu, Estonia.,Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu; Tartu, Estonia
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16
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Bieder A, Yoshihara M, Katayama S, Krjutškov K, Falk A, Kere J, Tapia-Páez I. Dyslexia Candidate Gene and Ciliary Gene Expression Dynamics During Human Neuronal Differentiation. Mol Neurobiol 2020; 57:2944-2958. [PMID: 32445086 PMCID: PMC7320047 DOI: 10.1007/s12035-020-01905-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 03/19/2020] [Indexed: 11/30/2022]
Abstract
Developmental dyslexia (DD) is a neurodevelopmental condition with complex genetic mechanisms. A number of candidate genes have been identified, some of which are linked to neuronal development and migration and to ciliary functions. However, expression and regulation of these genes in human brain development and neuronal differentiation remain uncharted. Here, we used human long-term self-renewing neuroepithelial stem (lt-NES, here termed NES) cells derived from human induced pluripotent stem cells to study neuronal differentiation in vitro. We characterized gene expression changes during differentiation by using RNA sequencing and validated dynamics for selected genes by qRT-PCR. Interestingly, we found that genes related to cilia were significantly enriched among upregulated genes during differentiation, including genes linked to ciliopathies with neurodevelopmental phenotypes. We confirmed the presence of primary cilia throughout neuronal differentiation. Focusing on dyslexia candidate genes, 33 out of 50 DD candidate genes were detected in NES cells by RNA sequencing, and seven candidate genes were upregulated during differentiation to neurons, including DYX1C1 (DNAAF4), a highly replicated DD candidate gene. Our results suggest a role of ciliary genes in differentiating neuronal cells and show that NES cells provide a relevant human neuronal model to study ciliary and DD candidate genes.
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Affiliation(s)
- Andrea Bieder
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 9, 141 57, Huddinge, Sweden.
| | - Masahito Yoshihara
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 9, 141 57, Huddinge, Sweden
| | - Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 9, 141 57, Huddinge, Sweden
| | - Kaarel Krjutškov
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 9, 141 57, Huddinge, Sweden.,Competence Centre on Health Technologies, Tartu, Estonia.,Research Program of Molecular Neurology, Research Programs Unit, University of Helsinki, Helsinki, Finland.,Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Anna Falk
- Department of Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Hälsovägen 9, 141 57, Huddinge, Sweden. .,Research Program of Molecular Neurology, Research Programs Unit, University of Helsinki, Helsinki, Finland. .,Folkhälsan Institute of Genetics, Helsinki, Finland. .,School of Basic and Medical Biosciences, King's College London, London, UK.
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17
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Raime K, Krjutškov K, Remm M. Method for the Identification of Plant DNA in Food Using Alignment-Free Analysis of Sequencing Reads: A Case Study on Lupin. Front Plant Sci 2020; 11:646. [PMID: 32528502 PMCID: PMC7253697 DOI: 10.3389/fpls.2020.00646] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 04/27/2020] [Indexed: 06/11/2023]
Abstract
Fast and reliable analytical methods for the identification of plants from metagenomic samples play an important role in identifying the components of complex mixtures of processed biological materials, including food, herbal products, gut contents or environmental samples. Different PCR-based methods that are commonly used for plant identification from metagenomic samples are often inapplicable due to DNA degradation, a low level of successful amplification or a lack of detection power. We introduce a method that combines metagenomic sequencing and an alignment-free k-mer based approach for the identification of plant DNA in processed metagenomic samples. Our method identifies plant DNA directly from metagenomic sequencing reads and does not require mapping or assembly of the reads. We identified more than 31,000 Lupinus-specific 32-mers from assembled chloroplast genome sequences. We demonstrate that lupin DNA can be detected from controlled mixtures of sequences from target species (different Lupinus species) and closely related non-target species (Arachis hypogaea, Glycine max, Pisum sativum, Vicia faba, Phaseolus vulgaris, Lens culinaris, and Cicer arietinum). Moreover, these 32-mers are detectable in the following processed samples: lupin flour, conserved seeds and baked cookies containing different amounts of lupin flour. Under controlled conditions, lupin-specific components are detectable in baked cookies containing a minimum of 0.05% of lupin flour in wheat flour.
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Affiliation(s)
- Kairi Raime
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | | | - Maido Remm
- Department of Bioinformatics, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
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18
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Katayama S, Stenberg Hammar K, Krjutškov K, Einarsdottir E, Hedlin G, Kere J, Söderhäll C. Acute wheeze-specific gene module shows correlation with vitamin D and asthma medication. Eur Respir J 2020; 55:13993003.01330-2019. [PMID: 31619476 DOI: 10.1183/13993003.01330-2019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Accepted: 10/07/2019] [Indexed: 12/23/2022]
Abstract
BACKGROUND Airway obstruction and wheezing in preschool children with recurrent viral infections are a major clinical problem, and are recognised as a risk factor for the development of chronic asthma. We aimed to analyse whether gene expression profiling provides evidence for pathways that delineate distinct groups of children with wheeze, and in combination with clinical information could contribute to diagnosis and prognosis of disease development. METHODS We analysed leukocyte transcriptomes from preschool children (6 months-3 years) at acute wheeze (n=107), and at a revisit 2-3 months later, comparing them to age-matched healthy controls (n=66). RNA-sequencing applying GlobinLock was used. The cases were followed clinically until age 7 years. Differential expression tests, weighted correlation network analysis and logistic regression were applied and correlations to 76 clinical traits evaluated. FINDINGS Significant enrichment of genes involved in the innate immune responses was observed in children with wheeze. We identified a unique acute wheeze-specific gene-module, which was associated with vitamin D levels (p<0.005) in infancy, and asthma medication and FEV1%/FVC (forced expiratory volume in 1 s/forced vital capacity) ratio several years later, at age 7 years (p<0.005). A model that predicts leukotriene receptor antagonist medication at 7 years of age with high accuracy was developed (area under the curve 0.815, 95% CI 0.668-0.962). INTERPRETATION Gene expression profiles in blood from preschool wheezers predict asthma symptoms at school age, and therefore serve as biomarkers. The acute wheeze-specific gene module suggests that molecular phenotyping in combination with clinical information already at an early episode of wheeze may help to distinguish children who will outgrow their wheeze from those who will develop chronic asthma.
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Affiliation(s)
- Shintaro Katayama
- Dept of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Both authors contributed equally
| | - Katarina Stenberg Hammar
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden.,Dept of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden.,Both authors contributed equally
| | - Kaarel Krjutškov
- Dept of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Competence Centre on Health Technologies, Tartu, Estonia.,Folkhälsan Institute of Genetics, and Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
| | - Elisabet Einarsdottir
- Dept of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Folkhälsan Institute of Genetics, and Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland.,SciLifeLab, Dept of Gene Technology, KTH-Royal Institute of Technology, Solna, Sweden
| | - Gunilla Hedlin
- Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden.,Dept of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Juha Kere
- Dept of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Folkhälsan Institute of Genetics, and Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland.,School of Basic and Medical Biosciences, King's College London, Guy's Hospital, London, UK
| | - Cilla Söderhäll
- Dept of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden .,Dept of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
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19
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Žilina O, Rekker K, Kaplinski L, Sauk M, Paluoja P, Teder H, Ustav EL, Tõnisson N, Reimand T, Ridnõi K, Palta P, Vermeesch JR, Krjutškov K, Kurg A, Salumets A. Creating basis for introducing non‐invasive prenatal testing in the Estonian public health setting. Prenat Diagn 2019; 39:1262-1268. [PMID: 31691324 DOI: 10.1002/pd.5578] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Revised: 06/25/2019] [Accepted: 09/29/2019] [Indexed: 12/13/2022]
Abstract
OBJECTIVE The study aimed to validate a whole-genome sequencing-based NIPT laboratory method and our recently developed NIPTmer aneuploidy detection software with the potential to integrate the pipeline into prenatal clinical care in Estonia. METHOD In total, 424 maternal blood samples were included. Analysis pipeline involved cell-free DNA extraction, library preparation and massively parallel sequencing on Illumina platform. Aneuploidies were determined with NIPTmer software, which is based on counting pre-defined per-chromosome sets of unique k-mers from sequencing raw data. SeqFF was implemented to estimate cell-free fetal DNA (cffDNA) fraction. RESULTS NIPTmer identified correctly all samples of non-mosaic trisomy 21 (T21, 15/15), T18 (9/9), T13 (4/4) and monosomy X (4/4) cases, with the 100% sensitivity. However, one mosaic T18 remained undetected. Six false-positive (FP) results were observed (FP rate of 1.5%, 6/398), including three for T18 (specificity 99.3%) and three for T13 (specificity 99.3%). The level of cffDNA of <4% was estimated in eight samples, including one sample with T13 and T18. Despite low cffDNA level, these two samples were determined as aneuploid. CONCLUSION We believe that the developed NIPT method can successfully be used as a universal primary screening test in combination with ultrasound scan for the first trimester fetal examination.
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Affiliation(s)
- Olga Žilina
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Kadri Rekker
- Competence Centre on Health Technologies, Tartu, Estonia.,Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Lauris Kaplinski
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Martin Sauk
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Priit Paluoja
- Competence Centre on Health Technologies, Tartu, Estonia
| | - Hindrek Teder
- Competence Centre on Health Technologies, Tartu, Estonia.,Institute of Bio- and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Eva-Liina Ustav
- Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Women's Clinic, Tartu University Hospital, Tartu, Estonia
| | - Neeme Tõnisson
- Institute of Genomics, University of Tartu, Tartu, Estonia.,Department of Clinical Genetics, Tartu University Hospital, Tartu, Estonia
| | - Tiia Reimand
- Institute of Bio- and Translational Medicine, University of Tartu, Tartu, Estonia.,Department of Clinical Genetics, Tartu University Hospital, Tartu, Estonia
| | - Konstantin Ridnõi
- Center for Perinatal Care, Women's Clinic, East-Tallinn Central Hospital, Tallinn, Estonia.,Department of Clinical Genetics, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Priit Palta
- Institute of Genomics, University of Tartu, Tartu, Estonia.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Joris Robert Vermeesch
- Centre for Human Genetics, University Hospital Leuven, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Kaarel Krjutškov
- Competence Centre on Health Technologies, Tartu, Estonia.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Ants Kurg
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Andres Salumets
- Competence Centre on Health Technologies, Tartu, Estonia.,Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia.,Institute of Bio- and Translational Medicine, University of Tartu, Tartu, Estonia.,Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
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20
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Saare M, Laisk T, Teder H, Paluoja P, Palta P, Koel M, Kirss F, Karro H, Sõritsa D, Salumets A, Krjutškov K, Peters M. A molecular tool for menstrual cycle phase dating of endometrial samples in endometriosis transcriptome studies†. Biol Reprod 2019; 101:868. [PMID: 31687746 DOI: 10.1093/biolre/ioz092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Merli Saare
- Competence Centre on Health Technologies; Tartu, Estonia.,Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu; Tartu, Estonia
| | - Triin Laisk
- Competence Centre on Health Technologies; Tartu, Estonia.,Estonian Genome Center Science Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Hindrek Teder
- Competence Centre on Health Technologies; Tartu, Estonia.,Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Priit Paluoja
- Competence Centre on Health Technologies; Tartu, Estonia.,Institute of Computer Science, University of Tartu, Estonia
| | - Priit Palta
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Finland
| | - Mariann Koel
- Competence Centre on Health Technologies; Tartu, Estonia.,Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Fred Kirss
- Tartu University Hospital, Women's Clinic, Tartu, Estonia
| | - Helle Karro
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu; Tartu, Estonia.,Tartu University Hospital, Women's Clinic, Tartu, Estonia
| | - Deniss Sõritsa
- Competence Centre on Health Technologies; Tartu, Estonia.,Elite Clinic, Tartu, Estonia
| | - Andres Salumets
- Competence Centre on Health Technologies; Tartu, Estonia.,Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu; Tartu, Estonia.,Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Kaarel Krjutškov
- Competence Centre on Health Technologies; Tartu, Estonia.,Research Program of Molecular Neurology, Research Programs Unit, University of Helsinki, and Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Maire Peters
- Competence Centre on Health Technologies; Tartu, Estonia.,Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu; Tartu, Estonia
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21
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Vakkilainen S, Skoog T, Einarsdottir E, Middleton A, Pekkinen M, Öhman T, Katayama S, Krjutškov K, Kovanen PE, Varjosalo M, Lindqvist A, Kere J, Mäkitie O. The human long non-coding RNA gene RMRP has pleiotropic effects and regulates cell-cycle progression at G2. Sci Rep 2019; 9:13758. [PMID: 31551465 PMCID: PMC6760211 DOI: 10.1038/s41598-019-50334-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 09/03/2019] [Indexed: 12/14/2022] Open
Abstract
RMRP was the first non-coding nuclear RNA gene implicated in a disease. Its mutations cause cartilage-hair hypoplasia (CHH), an autosomal recessive skeletal dysplasia with growth failure, immunodeficiency, and a high risk for malignancies. This study aimed to gain further insight into the role of RNA Component of Mitochondrial RNA Processing Endoribonuclease (RMRP) in cellular physiology and disease pathogenesis. We combined transcriptome analysis with single-cell analysis using fibroblasts from CHH patients and healthy controls. To directly assess cell cycle progression, we followed CHH fibroblasts by pulse-labeling and time-lapse microscopy. Transcriptome analysis identified 35 significantly upregulated and 130 downregulated genes in CHH fibroblasts. The downregulated genes were significantly connected to the cell cycle. Multiple other pathways, involving regulation of apoptosis, bone and cartilage formation, and lymphocyte function, were also affected, as well as PI3K-Akt signaling. Cell-cycle studies indicated that the CHH cells were delayed specifically in the passage from G2 phase to mitosis. Our findings expand the mechanistic understanding of CHH, indicate possible pathways for therapeutic intervention and add to the limited understanding of the functions of RMRP.
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Affiliation(s)
- Svetlana Vakkilainen
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland. .,Folkhälsan Research Center, Institute of Genetics, Helsinki, Finland.
| | - Tiina Skoog
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Elisabet Einarsdottir
- Folkhälsan Research Center, Institute of Genetics, Helsinki, Finland.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland
| | - Anna Middleton
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Minna Pekkinen
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Folkhälsan Research Center, Institute of Genetics, Helsinki, Finland
| | - Tiina Öhman
- Institute of Biotechnology, and Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Kaarel Krjutškov
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland.,Competence Centre on Health Technologies, Tartu, Estonia
| | - Panu E Kovanen
- Department of Pathology, University of Helsinki, and HUSLAB, Helsinki University Hospital, Helsinki, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, and Helsinki Institute of Life Science, University of Helsinki, Helsinki, Finland
| | - Arne Lindqvist
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Juha Kere
- Folkhälsan Research Center, Institute of Genetics, Helsinki, Finland.,Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland.,Department of Medical and Molecular Genetics, King's College, London, UK
| | - Outi Mäkitie
- Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland.,Folkhälsan Research Center, Institute of Genetics, Helsinki, Finland.,Department of Molecular Medicine and Surgery, Karolinska Institutet and Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
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22
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Stepanjuk A, Koel M, Pook M, Saare M, Jääger K, Peters M, Krjutškov K, Ingerpuu S, Salumets A. MUC20 expression marks the receptive phase of the human endometrium. Reprod Biomed Online 2019; 39:725-736. [PMID: 31519421 DOI: 10.1016/j.rbmo.2019.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 04/20/2019] [Accepted: 05/08/2019] [Indexed: 11/19/2022]
Abstract
RESEARCH QUESTION How does mucin MUC20 expression change during the menstrual cycle in different cell types of human endometrium? DESIGN Study involved examination of MUC20 expression in two previously published RNA-seq datasets in whole endometrial tissue (n = 10), sorted endometrial epithelial (n = 44) or stromal (n = 42) cell samples. RNA-Seq results were validated by quantitative reverse transcription polymerase chain reaction (qRT-PCR) in whole tissue (n = 10), sorted epithelial (n = 17) and stromal (n = 17) cell samples. MUC20 protein localization and expression were analysed in human endometrium by immunohistochemical analysis of intact endometrial tissue (n = 6) and also Western blot of cultured stromal and epithelial cells (n = 2). RESULTS MUC20 is differentially expressed in the endometrium between the pre-receptive and receptive phases. We show that MUC20 is predominantly expressed by epithelial cells of the receptive endometrium, both at the mRNA (RNA-Seq, P = 0.005; qRT-PCR, P = 0.039) and protein levels (Western blot; immunohistochemistry, P = 0.029). CONCLUSION Our results indicate MUC20 as a novel marker of mid-secretory endometrial biology. We propose a model of MUC20 function in the hepatocyte growth factor (HGF)-activated mesenchymal-epithelial transition (MET) receptor signalling specifically in the receptive phase. Further investigations should reveal the precise function of MUC20 in human endometrium and the possible connection between MUC20 and HGF-activated MET receptor signalling. MUC20 could potentially be included in the list of endometrial receptivity markers after further clinical validation.
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Affiliation(s)
- Artjom Stepanjuk
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, Tartu 51010, Estonia
| | - Mariann Koel
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, Tartu 51010, Estonia; Competence Centre on Health Technologies, Tiigi 61b, Tartu 50410, Estonia
| | - Martin Pook
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, Tartu 51010, Estonia
| | - Merli Saare
- Competence Centre on Health Technologies, Tiigi 61b, Tartu 50410, Estonia; Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, L. Puusepa 8, Tartu 50406, Estonia
| | - Kersti Jääger
- Competence Centre on Health Technologies, Tiigi 61b, Tartu 50410, Estonia
| | - Maire Peters
- Competence Centre on Health Technologies, Tiigi 61b, Tartu 50410, Estonia; Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, L. Puusepa 8, Tartu 50406, Estonia
| | - Kaarel Krjutškov
- Competence Centre on Health Technologies, Tiigi 61b, Tartu 50410, Estonia; Research Program of Molecular Neurology, Research Programs Unit, University of Helsinki, and Folkhälsan Institute of Genetics, Haartmaninkatu 8, Helsinki 00290, Finland
| | - Sulev Ingerpuu
- Institute of Molecular and Cell Biology, University of Tartu, Riia 23, Tartu 51010, Estonia
| | - Andres Salumets
- Competence Centre on Health Technologies, Tiigi 61b, Tartu 50410, Estonia; Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, L. Puusepa 8, Tartu 50406, Estonia; Department of Biomedicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Ravila 19, Tartu 50411, Estonia; Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Haartmaninkatu 2, Helsinki 00014, Finland.
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23
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Katayama S, Panelius J, Koskenmies S, Skoog T, Mähönen K, Kisand K, Bondet V, Duffy D, Krjutškov K, Kere J, Ranki A. Delineating the Healthy Human Skin UV Response and Early Induction of Interferon Pathway in Cutaneous Lupus Erythematosus. J Invest Dermatol 2019; 139:2058-2061.e4. [DOI: 10.1016/j.jid.2019.02.035] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/05/2019] [Accepted: 02/28/2019] [Indexed: 12/21/2022]
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24
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Katayama S, Skoog T, Söderhäll C, Einarsdottir E, Krjutškov K, Kere J. Guide for library design and bias correction for large-scale transcriptome studies using highly multiplexed RNAseq methods. BMC Bioinformatics 2019; 20:418. [PMID: 31409293 PMCID: PMC6693229 DOI: 10.1186/s12859-019-3017-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 07/31/2019] [Indexed: 11/10/2022] Open
Abstract
Background Standard RNAseq methods using bulk RNA and recent single-cell RNAseq methods use DNA barcodes to identify samples and cells, and the barcoded cDNAs are pooled into a library pool before high throughput sequencing. In cases of single-cell and low-input RNAseq methods, the library is further amplified by PCR after the pooling. Preparation of hundreds or more samples for a large study often requires multiple library pools. However, sometimes correlation between expression profiles among the libraries is low and batch effect biases make integration of data between library pools difficult. Results We investigated 166 technical replicates in 14 RNAseq libraries made using the STRT method. The patterns of the library biases differed by genes, and uneven library yields were associated with library biases. The former bias was corrected using the NBGLM-LBC algorithm, which we present in the current study. The latter bias could not be corrected directly, but could be solved by omitting libraries with particularly low yields. A simulation experiment suggested that the library bias correction using NBGLM-LBC requires a consistent sample layout. The NBGLM-LBC correction method was applied to an expression profile for a cohort study of childhood acute respiratory illness, and the library biases were resolved. Conclusions The R source code for the library bias correction named NBGLM-LBC is available at https://shka.github.io/NBGLM-LBC and https://shka.bitbucket.io/NBGLM-LBC. This method is applicable to correct the library biases in various studies that use highly multiplexed sequencing-based profiling methods with a consistent sample layout with samples to be compared (e.g., “cases” and “controls”) equally distributed in each library. Electronic supplementary material The online version of this article (10.1186/s12859-019-3017-9) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183, Huddinge, Sweden.
| | - Tiina Skoog
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183, Huddinge, Sweden
| | - Cilla Söderhäll
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183, Huddinge, Sweden.,Department of Women's and Children's Health, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Elisabet Einarsdottir
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183, Huddinge, Sweden.,Folkhälsan Institute of Genetics, and Molecular Neurology Research Program, University of Helsinki, 00014, Helsinki, Finland
| | - Kaarel Krjutškov
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183, Huddinge, Sweden.,Folkhälsan Institute of Genetics, and Molecular Neurology Research Program, University of Helsinki, 00014, Helsinki, Finland.,Competence Centre on Health Technologies, 50410, Tartu, Estonia
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, 14183, Huddinge, Sweden.,Folkhälsan Institute of Genetics, and Molecular Neurology Research Program, University of Helsinki, 00014, Helsinki, Finland.,School of Basic and Medical Biosciences, King's College London, Guy's Hospital, London, SE1 9RT, UK
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25
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Teder H, Paluoja P, Rekker K, Salumets A, Krjutškov K, Palta P. Computational framework for targeted high-coverage sequencing based NIPT. PLoS One 2019; 14:e0209139. [PMID: 31283802 PMCID: PMC6613673 DOI: 10.1371/journal.pone.0209139] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 06/20/2019] [Indexed: 12/16/2022] Open
Abstract
Non-invasive prenatal testing (NIPT) enables accurate detection of fetal chromosomal trisomies. The majority of publicly available computational methods for sequencing-based NIPT analyses rely on low-coverage whole-genome sequencing (WGS) data and are not applicable for targeted high-coverage sequencing data from cell-free DNA samples. Here, we present a novel computational framework for a targeted high-coverage sequencing-based NIPT analysis. The developed framework uses a hidden Markov model (HMM) in conjunction with a supplemental machine learning model, such as decision tree (DT) or support vector machine (SVM), to detect fetal trisomy and parental origin of additional fetal chromosomes. These models were developed using simulated datasets covering a wide range of biologically relevant scenarios with various chromosomal quantities, parental origins of extra chromosomes, fetal DNA fractions, and sequencing read depths. Developed models were tested on simulated and experimental targeted sequencing datasets. Consequently, we determined the functional feasibility and limitations of each proposed approach and demonstrated that read count-based HMM achieved the best overall classification accuracy of 0.89 for detecting fetal euploidies and trisomies on simulated dataset. Furthermore, we show that by using the DT and SVM on the HMM classification results, it was possible to increase the final trisomy classification accuracy to 0.98 and 0.99, respectively. We demonstrate that read count and allelic ratio-based models can achieve a high accuracy (up to 0.98) for detecting fetal trisomy even if the fetal fraction is as low as 2%. Currently, existing commercial NIPT analysis requires at least 4% of fetal fraction, which can be possibly a challenge in case of early gestational age (<10 weeks) or high maternal body mass index (>35 kg/m2). More accurate detection can be achieved at higher sequencing depth using HMM in conjunction with supplemental models, which significantly improve the trisomy detection especially in borderline scenarios (e.g., very low fetal fraction) and enables to perform NIPT even earlier than 10 weeks of pregnancy.
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Affiliation(s)
- Hindrek Teder
- Competence Centre on Health Technologies, Tartu, Estonia.,Institute of Biomedicine and Translational Medicine, Department of Biomedicine, University of Tartu, Tartu, Estonia
| | - Priit Paluoja
- Competence Centre on Health Technologies, Tartu, Estonia.,Institute of Computer Science, University of Tartu, Tartu, Estonia
| | - Kadri Rekker
- Competence Centre on Health Technologies, Tartu, Estonia.,Institute of Clinical Medicine, Department of Obstetrics and Gynecology, University of Tartu, Tartu, Estonia
| | - Andres Salumets
- Competence Centre on Health Technologies, Tartu, Estonia.,Institute of Biomedicine and Translational Medicine, Department of Biomedicine, University of Tartu, Tartu, Estonia.,Institute of Clinical Medicine, Department of Obstetrics and Gynecology, University of Tartu, Tartu, Estonia.,Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Kaarel Krjutškov
- Competence Centre on Health Technologies, Tartu, Estonia.,Research Program of Molecular Neurology, Research Programs Unit, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Priit Palta
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
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26
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Madissoon E, Damdimopoulos A, Katayama S, Krjutškov K, Einarsdottir E, Mamia K, De Groef B, Hovatta O, Kere J, Damdimopoulou P. Pleomorphic Adenoma Gene 1 Is Needed For Timely Zygotic Genome Activation and Early Embryo Development. Sci Rep 2019; 9:8411. [PMID: 31182756 PMCID: PMC6557853 DOI: 10.1038/s41598-019-44882-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 05/22/2019] [Indexed: 01/09/2023] Open
Abstract
Pleomorphic adenoma gene 1 (PLAG1) is a transcription factor involved in cancer and growth. We discovered a de novo DNA motif containing a PLAG1 binding site in the promoters of genes activated during zygotic genome activation (ZGA) in human embryos. This motif was located within an Alu element in a region that was conserved in the murine B1 element. We show that maternally provided Plag1 is needed for timely mouse preimplantation embryo development. Heterozygous mouse embryos lacking maternal Plag1 showed disrupted regulation of 1,089 genes, spent significantly longer time in the 2-cell stage, and started expressing Plag1 ectopically from the paternal allele. The de novo PLAG1 motif was enriched in the promoters of the genes whose activation was delayed in the absence of Plag1. Further, these mouse genes showed a significant overlap with genes upregulated during human ZGA that also contain the motif. By gene ontology, the mouse and human ZGA genes with de novo PLAG1 motifs were involved in ribosome biogenesis and protein synthesis. Collectively, our data suggest that PLAG1 affects embryo development in mice and humans through a conserved DNA motif within Alu/B1 elements located in the promoters of a subset of ZGA genes.
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Affiliation(s)
- Elo Madissoon
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-14186, Stockholm, Sweden.
| | - Anastasios Damdimopoulos
- Bioinformatics and Expression Analysis core facility, Department of Biosciences and Nutrition, Karolinska Institutet, SE-14186, Stockholm, Sweden
| | - Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-14186, Stockholm, Sweden
| | - Kaarel Krjutškov
- Competence Centre on Health Technologies, 50410, Tartu, Estonia.,Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, 00014, Helsinki, Finland
| | - Elisabet Einarsdottir
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-14186, Stockholm, Sweden.,Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, 00014, Helsinki, Finland
| | - Katariina Mamia
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, SE-14186, Stockholm, Sweden
| | - Bert De Groef
- Department of Physiology, Anatomy and Microbiology, La Trobe University, Bundoora, Victoria, 3086, Australia
| | - Outi Hovatta
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, SE-14186, Stockholm, Sweden
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-14186, Stockholm, Sweden. .,Research Programs Unit, Molecular Neurology, University of Helsinki, and Folkhälsan Institute of Genetics, 00014, Helsinki, Finland. .,School of Basic and Medical Biosciences, King's College London, Guy's Hospital, London, WC2R 2LS, UK.
| | - Pauliina Damdimopoulou
- Department of Biosciences and Nutrition, Karolinska Institutet, SE-14186, Stockholm, Sweden. .,Department of Clinical Science, Intervention and Technology, Karolinska Institutet, SE-14186, Stockholm, Sweden.
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27
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Einarsdottir E, Pekkinen M, Krjutškov K, Katayama S, Kere J, Mäkitie O, Viljakainen H. A preliminary transcriptome analysis suggests a transitory effect of vitamin D on mitochondrial function in obese young Finnish subjects. Endocr Connect 2019; 8:559-570. [PMID: 30965285 PMCID: PMC6499919 DOI: 10.1530/ec-18-0537] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Accepted: 04/09/2019] [Indexed: 12/14/2022]
Abstract
OBJECTIVE The effect of vitamin D at the transcriptome level is poorly understood, and furthermore, it is unclear if it differs between obese and normal-weight subjects. The objective of the study was to explore the transcriptome effects of vitamin D supplementation. DESIGN AND METHODS We analysed peripheral blood gene expression using GlobinLock oligonucleotides followed by RNA sequencing in individuals participating in a 12-week randomised double-blinded placebo-controlled vitamin D intervention study. The study involved 18 obese and 18 normal-weight subjects (of which 20 males) with mean (±s.d.) age 20.4 (±2.5) years and BMIs 36 (±10) and 23 (±4) kg/m2, respectively. The supplemental daily vitamin D dose was 50 µg (2000 IU). Data were available at baseline, 6- and 12-week time points and comparisons were performed between the vitamin D and placebo groups separately in obese and normal-weight subjects. RESULTS Significant transcriptomic changes were observed at 6 weeks, and only in the obese subjects: 1724 genes were significantly upregulated and 186 genes were downregulated in the vitamin D group compared with placebo. Further analyses showed several enriched gene categories connected to mitochondrial function and metabolism, and the most significantly enriched pathway was related to oxidative phosphorylation (adjusted P value 3.08 × 10-14). Taken together, our data suggest an effect of vitamin D supplementation on mitochondrial function in obese subjects. CONCLUSIONS Vitamin D supplementation affects gene expression in obese, but not in normal-weight subjects. The altered genes are enriched in pathways related to mitochondrial function. The present study increases the understanding of the effects of vitamin D at the transcriptome level.
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Affiliation(s)
- Elisabet Einarsdottir
- Folkhälsan Institute of Genetics, University of Helsinki, Helsinki, Finland
- Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Minna Pekkinen
- Folkhälsan Institute of Genetics, University of Helsinki, Helsinki, Finland
- Children’s Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Kaarel Krjutškov
- Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland
- Competence Centre on Health Technologies, Tartu, Estonia
| | - Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Juha Kere
- Folkhälsan Institute of Genetics, University of Helsinki, Helsinki, Finland
- Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- School of Basic and Medical Biosciences, King’s College London, Guy’s Hospital, London, United Kingdom
| | - Outi Mäkitie
- Folkhälsan Institute of Genetics, University of Helsinki, Helsinki, Finland
- Children’s Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Molecular Medicine and Surgery and Center for Molecular Medicine, Karolinska Institutet, Stockholm, Sweden
- Department of Clinical Genetics, Karolinska University Hospital, Stockholm, Sweden
| | - Heli Viljakainen
- Folkhälsan Institute of Genetics, University of Helsinki, Helsinki, Finland
- Department of Food and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Correspondence should be addressed to H Viljakainen:
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28
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Štšepetova J, Truu J, Runnel R, Nõmmela R, Saag M, Olak J, Nõlvak H, Preem JK, Oopkaup K, Krjutškov K, Honkala E, Honkala S, Mäkinen K, Mäkinen PL, Vahlberg T, Vermeiren J, Bosscher D, de Cock P, Mändar R. Impact of polyols on Oral microbiome of Estonian schoolchildren. BMC Oral Health 2019; 19:60. [PMID: 30999906 PMCID: PMC6471963 DOI: 10.1186/s12903-019-0747-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Accepted: 03/26/2019] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Oral microbiome has significant impact on both oral and general health. Polyols have been promoted as sugar substitutes in prevention of oral diseases. We aimed to reveal the effect of candies containing erythritol, xylitol or control (sorbitol) on salivary microbiome. METHODS Ninety children (11.3 ± 0.6 years) consumed candies during 3 years. Microbial communities were profiled using Illumina HiSeq 2000 sequencing and real-time PCR. RESULTS The dominant phyla in saliva were Firmicutes (39.1%), Proteobacteria (26.1%), Bacteroidetes (14.7%), Actinobacteria (12%) and Fusobacteria (6%). The microbiome of erythritol group significantly differed from that of the other groups. Both erythritol and xylitol reduced the number of observed bacterial phylotypes in comparison to the control group. The relative abundance of the genera Veillonella, Streptococcus and Fusobacterium were higher while that of Bergeyella lower after erythritol intervention when comparing with control. The lowest prevalence of caries-related mutans streptococci corresponded with the lowest clinical caries markers in the erythritol group. CONCLUSIONS Daily consumption of erythritol, xylitol or control candies has a specific influence on the salivary microbiome composition in schoolchildren. Erythritol is associated with the lowest prevalence of caries-related mutans streptococci and the lowest levels of clinical caries experience. TRIAL REGISTRATION ClinicalTrials.gov Identifier NCT01062633.
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Affiliation(s)
- Jelena Štšepetova
- Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
- Competence Centre on Health Technologies, Tartu, Estonia
| | - Jaak Truu
- Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Riina Runnel
- Institute of Dentistry, University of Tartu, Tartu, Estonia
| | - Rita Nõmmela
- Institute of Dentistry, University of Tartu, Tartu, Estonia
| | - Mare Saag
- Institute of Dentistry, University of Tartu, Tartu, Estonia
| | - Jana Olak
- Institute of Dentistry, University of Tartu, Tartu, Estonia
| | - Hiie Nõlvak
- Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Jens-Konrad Preem
- Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Kristjan Oopkaup
- Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | | | - Eino Honkala
- Institute of Clinical Dentistry, University of Tromso, Tromso, Norway
| | - Sisko Honkala
- Institute of Clinical Dentistry, University of Tromso, Tromso, Norway
| | - Kauko Mäkinen
- Institute of Dentistry, University of Turku, Turku, Finland
| | | | - Tero Vahlberg
- Faculty of Medicine, University of Turku, Turku, Finland
| | | | | | | | - Reet Mändar
- Department of Microbiology, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
- Competence Centre on Health Technologies, Tartu, Estonia
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29
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Pussila M, Törönen P, Einarsdottir E, Katayama S, Krjutškov K, Holm L, Kere J, Peltomäki P, Mäkinen MJ, Linden J, Nyström M. Mlh1 deficiency in normal mouse colon mucosa associates with chromosomally unstable colon cancer. Carcinogenesis 2019; 39:788-797. [PMID: 29701748 PMCID: PMC5973430 DOI: 10.1093/carcin/bgy056] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 04/24/2018] [Indexed: 12/18/2022] Open
Abstract
Colorectal cancer (CRC) genome is unstable and different types of instabilities, such as chromosomal instability (CIN) and microsatellite instability (MSI) are thought to reflect distinct cancer initiating mechanisms. Although 85% of sporadic CRC reveal CIN, 15% reveal mismatch repair (MMR) malfunction and MSI, the hallmarks of Lynch syndrome with inherited heterozygous germline mutations in MMR genes. Our study was designed to comprehensively follow genome-wide expression changes and their implications during colon tumorigenesis. We conducted a long-term feeding experiment in the mouse to address expression changes arising in histologically normal colonic mucosa as putative cancer preceding events, and the effect of inherited predisposition (Mlh1+/−) and Western-style diet (WD) on those. During the 21-month experiment, carcinomas developed mainly in WD-fed mice and were evenly distributed between genotypes. Unexpectedly, the heterozygote (B6.129-Mlh1tm1Rak) mice did not show MSI in their CRCs. Instead, both wildtype and heterozygote CRC mice showed a distinct mRNA expression profile and shortage of several chromosomal segregation gene-specific transcripts (Mlh1, Bub1, Mis18a, Tpx2, Rad9a, Pms2, Cenpe, Ncapd3, Odf2 and Dclre1b) in their colon mucosa, as well as an increased mitotic activity and abundant numbers of unbalanced/atypical mitoses in tumours. Our genome-wide expression profiling experiment demonstrates that cancer preceding changes are already seen in histologically normal colon mucosa and that decreased expressions of Mlh1 and other chromosomal segregation genes may form a field-defect in mucosa, which trigger MMR-proficient, chromosomally unstable CRC.
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Affiliation(s)
- Marjaana Pussila
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Biosciences Research Programme
| | - Petri Törönen
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Elisabet Einarsdottir
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Folkhälsan Institute of Genetics, Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland
| | - Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Kaarel Krjutškov
- Folkhälsan Institute of Genetics, Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland.,Competence Centre on Health Technologies, Tartu, Estonia
| | - Liisa Holm
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Biosciences Research Programme.,Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Folkhälsan Institute of Genetics, Molecular Neurology Research Program, University of Helsinki, Helsinki, Finland.,Department of Genetics and Molecular Medicine, King's College London, London, UK
| | - Päivi Peltomäki
- Medicum, Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland
| | - Markus J Mäkinen
- Cancer and Translational Medicine Research Unit, Department of Pathology, University of Oulu, Oulu, Finland.,Medical Research Center Oulu, Oulu University Hospital, University of Oulu, Oulu, Finland
| | - Jere Linden
- Department of Basic Veterinary Sciences, FCLAP, University of Helsinki, Helsinki, Finland
| | - Minna Nyström
- Faculty of Biological and Environmental Sciences, Molecular and Integrative Biosciences Research Programme
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30
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Teder H, Koel M, Paluoja P, Jatsenko T, Rekker K, Laisk-Podar T, Kukuškina V, Velthut-Meikas A, Fjodorova O, Peters M, Kere J, Salumets A, Palta P, Krjutškov K. TAC-seq: targeted DNA and RNA sequencing for precise biomarker molecule counting. NPJ Genom Med 2018; 3:34. [PMID: 30588329 PMCID: PMC6299075 DOI: 10.1038/s41525-018-0072-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Accepted: 11/26/2018] [Indexed: 12/22/2022] Open
Abstract
Targeted next-generation sequencing (NGS) methods have become essential in medical research and diagnostics. In addition to NGS sensitivity and high-throughput capacity, precise biomolecule counting based on unique molecular identifier (UMI) has potential to increase biomolecule detection accuracy. Although UMIs are widely used in basic research its introduction to clinical assays is still in progress. Here, we present a robust and cost-effective TAC-seq (Targeted Allele Counting by sequencing) method that uses UMIs to estimate the original molecule counts of mRNAs, microRNAs, and cell-free DNA. We applied TAC-seq in three different clinical applications and compared the results with standard NGS. RNA samples extracted from human endometrial biopsies were analyzed using previously described 57 mRNA-based receptivity biomarkers and 49 selected microRNAs at different expression levels. Cell-free DNA aneuploidy testing was based on cell line (47,XX, +21) genomic DNA. TAC-seq mRNA profiling showed identical clustering results to transcriptome RNA sequencing, and microRNA detection demonstrated significant reduction in amplification bias, allowing to determine minor expression changes between different samples that remained undetermined by standard NGS. The mimicking experiment for cell-free DNA fetal aneuploidy analysis showed that TAC-seq can be applied to count highly fragmented DNA, detecting significant (p = 7.6 × 10-4) excess of chromosome 21 molecules at 10% fetal fraction level. Based on three proof-of-principle applications we demonstrate that TAC-seq is an accurate and highly potential biomarker profiling method for advanced medical research and diagnostics.
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Affiliation(s)
- Hindrek Teder
- 1Competence Centre on Health Technologies, Tartu, Estonia.,2Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Mariann Koel
- 1Competence Centre on Health Technologies, Tartu, Estonia.,3Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Priit Paluoja
- 1Competence Centre on Health Technologies, Tartu, Estonia.,4Institute of Computer Science, University of Tartu, Tartu, Estonia
| | | | - Kadri Rekker
- 1Competence Centre on Health Technologies, Tartu, Estonia.,5Institute of Clinical Medicine, Department of Obstetrics and Gynaecology, University of Tartu, Tartu, Estonia
| | - Triin Laisk-Podar
- 1Competence Centre on Health Technologies, Tartu, Estonia.,5Institute of Clinical Medicine, Department of Obstetrics and Gynaecology, University of Tartu, Tartu, Estonia.,6Estonian Genome Center, University of Tartu, Tartu, Estonia
| | | | - Agne Velthut-Meikas
- 1Competence Centre on Health Technologies, Tartu, Estonia.,7Department of Chemistry and Biotechnology, School of Science, Tallinn University of Technology, Tallinn, Estonia
| | - Olga Fjodorova
- 3Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Maire Peters
- 1Competence Centre on Health Technologies, Tartu, Estonia.,5Institute of Clinical Medicine, Department of Obstetrics and Gynaecology, University of Tartu, Tartu, Estonia
| | - Juha Kere
- 8Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,9Research Program of Molecular Neurology, Research Programs Unit, University of Helsinki, and Folkhälsan Institute of Genetics, Helsinki, Finland.,10School of Basic and Medical Biosciences, Guy's Hospital, King's College London, London, UK
| | - Andres Salumets
- 1Competence Centre on Health Technologies, Tartu, Estonia.,5Institute of Clinical Medicine, Department of Obstetrics and Gynaecology, University of Tartu, Tartu, Estonia.,11Institute of Biomedicine and Translational Medicine, Department of Biomedicine, University of Tartu, Tartu, Estonia.,12Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Priit Palta
- 6Estonian Genome Center, University of Tartu, Tartu, Estonia.,13Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Kaarel Krjutškov
- 1Competence Centre on Health Technologies, Tartu, Estonia.,8Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,9Research Program of Molecular Neurology, Research Programs Unit, University of Helsinki, and Folkhälsan Institute of Genetics, Helsinki, Finland
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31
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Suhorutshenko M, Kukushkina V, Velthut-Meikas A, Altmäe S, Peters M, Mägi R, Krjutškov K, Koel M, Codoñer FM, Martinez-Blanch JF, Vilella F, Simón C, Salumets A, Laisk T. Endometrial receptivity revisited: endometrial transcriptome adjusted for tissue cellular heterogeneity. Hum Reprod 2018; 33:2074-2086. [DOI: 10.1093/humrep/dey301] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 09/26/2018] [Indexed: 12/30/2022] Open
Affiliation(s)
- Marina Suhorutshenko
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Viktorija Kukushkina
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Agne Velthut-Meikas
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Signe Altmäe
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, Granada, Spain
| | - Maire Peters
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
| | - Reedik Mägi
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Kaarel Krjutškov
- Competence Centre on Health Technologies, Tartu, Estonia
- Research Program of Molecular Neurology, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Mariann Koel
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Cell Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | | | | | | | - Carlos Simón
- Igenomix Foundation/INCLIVA, Valencia, Spain
- Research Department, Igenomix SL, Valencia, Spain
- Department of Pediatrics, Obstetrics and Gynecology, Valencia University, Valencia, Spain
| | - Andres Salumets
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
- Department of Biomedicine, Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Triin Laisk
- Competence Centre on Health Technologies, Tartu, Estonia
- Department of Obstetrics and Gynecology, Institute of Clinical Medicine, University of Tartu, Tartu, Estonia
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu, Estonia
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32
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Hakonen E, Chandra V, Fogarty CL, Yu NYL, Ustinov J, Katayama S, Galli E, Danilova T, Lindholm P, Vartiainen A, Einarsdottir E, Krjutškov K, Kere J, Saarma M, Lindahl M, Otonkoski T. MANF protects human pancreatic beta cells against stress-induced cell death. Diabetologia 2018; 61:2202-2214. [PMID: 30032427 PMCID: PMC6133171 DOI: 10.1007/s00125-018-4687-y] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/18/2018] [Accepted: 06/12/2018] [Indexed: 12/22/2022]
Abstract
AIMS/HYPOTHESIS There is a great need to identify factors that could protect pancreatic beta cells against apoptosis or stimulate their replication and thus prevent or reverse the development of diabetes. One potential candidate is mesencephalic astrocyte-derived neurotrophic factor (MANF), an endoplasmic reticulum (ER) stress inducible protein. Manf knockout mice used as a model of diabetes develop the condition because of increased apoptosis and reduced proliferation of beta cells, apparently related to ER stress. Given this novel association between MANF and beta cell death, we studied the potential of MANF to protect human beta cells against experimentally induced ER stress. METHODS Primary human islets were challenged with proinflammatory cytokines, with or without MANF. Cell viability was analysed and global transcriptomic analysis performed. Results were further validated using the human beta cell line EndoC-βH1. RESULTS There was increased expression and secretion of MANF in human beta cells in response to cytokines. Addition of recombinant human MANF reduced cytokine-induced cell death by 38% in human islets (p < 0.05). MANF knockdown in EndoC-βH1 cells led to increased ER stress after cytokine challenge. Mechanistic studies showed that the protective effect of MANF was associated with repression of the NF-κB signalling pathway and amelioration of ER stress. MANF also increased the proliferation of primary human beta cells twofold when TGF-β signalling was inhibited (p < 0.01). CONCLUSIONS/INTERPRETATION Our studies show that exogenous MANF protein can provide protection to human beta cells against death induced by inflammatory stress. The antiapoptotic and mitogenic properties of MANF make it a potential therapeutic agent for beta cell protection.
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Affiliation(s)
- Elina Hakonen
- Research Programs Unit, Molecular Neurology, Biomedicum Helsinki, University of Helsinki, PO Box 63, (Haartmaninkatu 8), 00014, Helsinki, Finland
- Children's Hospital, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Vikash Chandra
- Research Programs Unit, Molecular Neurology, Biomedicum Helsinki, University of Helsinki, PO Box 63, (Haartmaninkatu 8), 00014, Helsinki, Finland.
| | | | - Nancy Yiu-Lin Yu
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Jarkko Ustinov
- Research Programs Unit, Molecular Neurology, Biomedicum Helsinki, University of Helsinki, PO Box 63, (Haartmaninkatu 8), 00014, Helsinki, Finland
| | - Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Emilia Galli
- Research Program in Developmental Biology, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Tatiana Danilova
- Research Program in Developmental Biology, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Päivi Lindholm
- Research Program in Developmental Biology, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Aki Vartiainen
- Research Programs Unit, Molecular Neurology, Biomedicum Helsinki, University of Helsinki, PO Box 63, (Haartmaninkatu 8), 00014, Helsinki, Finland
| | - Elisabet Einarsdottir
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- The Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Kaarel Krjutškov
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- The Folkhälsan Institute of Genetics, Helsinki, Finland
- Competence Centre on Health Technologies, Tartu, Estonia
| | - Juha Kere
- Research Programs Unit, Molecular Neurology, Biomedicum Helsinki, University of Helsinki, PO Box 63, (Haartmaninkatu 8), 00014, Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
- The Folkhälsan Institute of Genetics, Helsinki, Finland
- Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Mart Saarma
- Research Program in Developmental Biology, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Maria Lindahl
- Research Program in Developmental Biology, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Timo Otonkoski
- Research Programs Unit, Molecular Neurology, Biomedicum Helsinki, University of Helsinki, PO Box 63, (Haartmaninkatu 8), 00014, Helsinki, Finland.
- Children's Hospital, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland.
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33
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Coenen-Stass AML, Sork H, Gatto S, Godfrey C, Bhomra A, Krjutškov K, Hart JR, Westholm JO, O'Donovan L, Roos A, Lochmüller H, Puri PL, El Andaloussi S, Wood MJA, Roberts TC. Comprehensive RNA-Sequencing Analysis in Serum and Muscle Reveals Novel Small RNA Signatures with Biomarker Potential for DMD. Mol Ther Nucleic Acids 2018; 13:1-15. [PMID: 30219269 PMCID: PMC6140421 DOI: 10.1016/j.omtn.2018.08.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Revised: 08/13/2018] [Accepted: 08/13/2018] [Indexed: 01/03/2023]
Abstract
Extracellular small RNAs (sRNAs), including microRNAs (miRNAs), are promising biomarkers for diseases such as Duchenne muscular dystrophy (DMD), although their biological relevance is largely unknown. To investigate the relationship between intracellular and extracellular sRNA levels on a global scale, we performed sRNA sequencing in four muscle types and serum from wild-type, dystrophic mdx, and mdx mice in which dystrophin protein expression was restored by exon skipping. Differentially abundant sRNAs were identified in serum (mapping to miRNA, small nuclear RNA [snRNA], and PIWI-interacting RNA [piRNA] loci). One novel candidate biomarker, miR-483, was increased in both mdx serum and muscle, and also elevated in DMD patient sera. Dystrophin restoration induced global shifts in miRNA (including miR-483) and snRNA-fragment abundance toward wild-type levels. Specific serum piRNA-like sRNAs also responded to exon skipping therapy. Absolute miRNA expression in muscle was positively correlated with abundance in the circulation, although multiple highly expressed miRNAs in muscle were not elevated in mdx serum, suggesting that both passive and selective release mechanisms contribute to serum miRNA levels. In conclusion, this study has revealed new insights into the sRNA biology of dystrophin deficiency and identified novel DMD biomarkers.
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Affiliation(s)
- Anna M L Coenen-Stass
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | - Helena Sork
- Department of Laboratory Medicine, Karolinska Institutet, Huddinge 141 86, Sweden
| | - Sole Gatto
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Caroline Godfrey
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | - Amarjit Bhomra
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | - Kaarel Krjutškov
- Department of Biosciences and Nutrition, Center for Innovative Medicine, Karolinska Institutet, Huddinge 141 83, Sweden; Competence Centre on Health Technologies, Tartu 50410, Estonia
| | - Jonathan R Hart
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA 92037, USA
| | - Jakub O Westholm
- Science for Life Laboratory, Department of Biochemistry and Biophysics, Stockholm University, 17121 Solna, Sweden
| | - Liz O'Donovan
- Medical Research Council, Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Andreas Roos
- The John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK; Biomedical Research Department, Leibniz-Institute für Analytische Wissenschaften-ISAS-e.V., Otto-Hahn-Strasse 6b, 44227 Dortmund, Germany
| | - Hanns Lochmüller
- The John Walton Muscular Dystrophy Research Centre, MRC Centre for Neuromuscular Diseases, Institute of Genetic Medicine, Newcastle University, Central Parkway, Newcastle upon Tyne NE1 3BZ, UK; Department of Neuropediatrics and Muscle Disorders, Medical Center-University of Freiburg, Faculty of Medicine, Freiburg, Germany; Centro Nacional de Análisis Genómico (CNAG-CRG), Center for Genomic Regulation, Barcelona Institute of Science and Technology (BIST), Barcelona, Spain
| | - Pier Lorenzo Puri
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA; IRCCS Fondazione Santa Lucia, Rome, Italy
| | - Samir El Andaloussi
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK; Department of Laboratory Medicine, Karolinska Institutet, Huddinge 141 86, Sweden
| | - Matthew J A Wood
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK.
| | - Thomas C Roberts
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK; Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
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34
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Weltner J, Balboa D, Katayama S, Bespalov M, Krjutškov K, Jouhilahti EM, Trokovic R, Kere J, Otonkoski T. Human pluripotent reprogramming with CRISPR activators. Nat Commun 2018; 9:2643. [PMID: 29980666 PMCID: PMC6035213 DOI: 10.1038/s41467-018-05067-x] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Accepted: 06/13/2018] [Indexed: 02/08/2023] Open
Abstract
CRISPR-Cas9-based gene activation (CRISPRa) is an attractive tool for cellular reprogramming applications due to its high multiplexing capacity and direct targeting of endogenous loci. Here we present the reprogramming of primary human skin fibroblasts into induced pluripotent stem cells (iPSCs) using CRISPRa, targeting endogenous OCT4, SOX2, KLF4, MYC, and LIN28A promoters. The low basal reprogramming efficiency can be improved by an order of magnitude by additionally targeting a conserved Alu-motif enriched near genes involved in embryo genome activation (EEA-motif). This effect is mediated in part by more efficient activation of NANOG and REX1. These data demonstrate that human somatic cells can be reprogrammed into iPSCs using only CRISPRa. Furthermore, the results unravel the involvement of EEA-motif-associated mechanisms in cellular reprogramming.
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Affiliation(s)
- Jere Weltner
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, Faculty of Medicine, University of Helsinki, Helsinki, 00014, Finland.
| | - Diego Balboa
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, Faculty of Medicine, University of Helsinki, Helsinki, 00014, Finland
| | - Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, 141 83, Sweden
| | - Maxim Bespalov
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, Faculty of Medicine, University of Helsinki, Helsinki, 00014, Finland
| | - Kaarel Krjutškov
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, 141 83, Sweden
- Competence Centre on Health Technologies, Tartu, 50410, Estonia
| | - Eeva-Mari Jouhilahti
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, Faculty of Medicine, University of Helsinki, Helsinki, 00014, Finland
| | - Ras Trokovic
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, Faculty of Medicine, University of Helsinki, Helsinki, 00014, Finland
| | - Juha Kere
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, Faculty of Medicine, University of Helsinki, Helsinki, 00014, Finland.
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, 141 83, Sweden.
- School of Basic and Medical Biosciences, Guy's Hospital, King's College London, London, SE1 9RT, UK.
- Folkhälsan Institute of Genetics, Helsinki, 00290, Finland.
| | - Timo Otonkoski
- Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, Faculty of Medicine, University of Helsinki, Helsinki, 00014, Finland.
- Children's Hospital, Helsinki University Central Hospital, University of Helsinki, Helsinki, 00290, Finland.
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35
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Altmäe S, Koel M, Võsa U, Adler P, Suhorutšenko M, Laisk-Podar T, Kukushkina V, Saare M, Velthut-Meikas A, Krjutškov K, Aghajanova L, Lalitkumar PG, Gemzell-Danielsson K, Giudice L, Simón C, Salumets A. Meta-signature of human endometrial receptivity: a meta-analysis and validation study of transcriptomic biomarkers. Sci Rep 2017; 7:10077. [PMID: 28855728 PMCID: PMC5577343 DOI: 10.1038/s41598-017-10098-3] [Citation(s) in RCA: 140] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Accepted: 07/28/2017] [Indexed: 12/21/2022] Open
Abstract
Previous transcriptome studies of the human endometrium have revealed hundreds of simultaneously up- and down-regulated genes that are involved in endometrial receptivity. However, the overlap between the studies is relatively small, and we are still searching for potential diagnostic biomarkers. Here we perform a meta-analysis of endometrial-receptivity associated genes on 164 endometrial samples (76 from 'pre-receptive' and 88 from mid-secretory, 'receptive' phase endometria) using a robust rank aggregation (RRA) method, followed by enrichment analysis, and regulatory microRNA prediction. We identify a meta-signature of endometrial receptivity involving 57 mRNA genes as putative receptivity markers, where 39 of these we confirm experimentally using RNA-sequencing method in two separate datasets. The meta-signature genes highlight the importance of immune responses, the complement cascade pathway and the involvement of exosomes in mid-secretory endometrial functions. Bioinformatic prediction identifies 348 microRNAs that could regulate 30 endometrial-receptivity associated genes, and we confirm experimentally the decreased expression of 19 microRNAs with 11 corresponding up-regulated meta-signature genes in our validation experiments. The 57 identified meta-signature genes and involved pathways, together with their regulatory microRNAs could serve as promising and sought-after biomarkers of endometrial receptivity, fertility and infertility.
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Affiliation(s)
- Signe Altmäe
- Department of Women's and Children's Health, Division of Obstetrics and Gynecology, Karolinska Institutet, and Karolinska University Hospital, 17176, Stockholm, Sweden.
- Competence Centre on Health Technologies, 50410, Tartu, Estonia.
- Department of Biochemistry and Molecular Biology, Faculty of Sciences, University of Granada, 18016, Granada, Spain.
| | - Mariann Koel
- Competence Centre on Health Technologies, 50410, Tartu, Estonia
- Department of Biosciences and Nutrition, and Center for Innovative Medicine, Karolinska Institutet, 14183, Huddinge, Sweden
- Department of Cell Biology, Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
| | - Urmo Võsa
- Estonian Genome Center, University of Tartu, 51010, Tartu, Estonia
| | - Priit Adler
- Institute of Computer Science, University of Tartu, Tartu, 50409, Estonia
| | - Marina Suhorutšenko
- Competence Centre on Health Technologies, 50410, Tartu, Estonia
- Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, 51014, Tartu, Estonia
| | - Triin Laisk-Podar
- Competence Centre on Health Technologies, 50410, Tartu, Estonia
- Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, 51014, Tartu, Estonia
| | | | - Merli Saare
- Competence Centre on Health Technologies, 50410, Tartu, Estonia
- Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, 51014, Tartu, Estonia
| | | | - Kaarel Krjutškov
- Competence Centre on Health Technologies, 50410, Tartu, Estonia
- Department of Biosciences and Nutrition, and Center for Innovative Medicine, Karolinska Institutet, 14183, Huddinge, Sweden
| | - Lusine Aghajanova
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, 94143-0132, CA, USA
| | - Parameswaran G Lalitkumar
- Department of Women's and Children's Health, Division of Obstetrics and Gynecology, Karolinska Institutet, and Karolinska University Hospital, 17176, Stockholm, Sweden
| | - Kristina Gemzell-Danielsson
- Department of Women's and Children's Health, Division of Obstetrics and Gynecology, Karolinska Institutet, and Karolinska University Hospital, 17176, Stockholm, Sweden
| | - Linda Giudice
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, 94143-0132, CA, USA
| | - Carlos Simón
- Department of Obstetrics and Gynaecology, Valencia University & INCLIVA, Igenomix & Fundación IVI, 46021, Valencia, Spain
| | - Andres Salumets
- Competence Centre on Health Technologies, 50410, Tartu, Estonia
- Department of Obstetrics and Gynaecology, Institute of Clinical Medicine, University of Tartu, 51014, Tartu, Estonia
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, FI-00029, HUS, Finland
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Koel M, Võsa U, Krjutškov K, Einarsdottir E, Kere J, Tapanainen J, Katayama S, Ingerpuu S, Jaks V, Stenman UH, Lundin K, Tuuri T, Salumets A. Optimizing bone morphogenic protein 4-mediated human embryonic stem cell differentiation into trophoblast-like cells using fibroblast growth factor 2 and transforming growth factor-β/activin/nodal signalling inhibition. Reprod Biomed Online 2017. [PMID: 28647356 DOI: 10.1016/j.rbmo.2017.06.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Several studies have demonstrated that human embryonic stem cells (hESC) can be differentiated into trophoblast-like cells if exposed to bone morphogenic protein 4 (BMP4) and/or inhibitors of fibroblast growth factor 2 (FGF2) and the transforming growth factor beta (TGF-β)/activin/nodal signalling pathways. The goal of this study was to investigate how the inhibitors of these pathways improve the efficiency of hESC differentiation when compared with basic BMP4 treatment. RNA sequencing was used to analyse the effects of all possible inhibitor combinations on the differentiation of hESC into trophoblast-like cells over 12 days. Genes differentially expressed compared with untreated cells were identified at seven time points. Additionally, expression of total human chorionic gonadotrophin (HCG) and its hyperglycosylated form (HCG-H) were determined by immunoassay from cell culture media. We showed that FGF2 inhibition with BMP4 activation up-regulates syncytiotrophoblast-specific genes (CGA, CGB and LGALS16), induces several molecular pathways involved in embryo implantation and triggers HCG-H production. In contrast, inhibition of the TGF-β/activin/nodal pathway decreases the ability of hESC to form trophoblast-like cells. Information about the conditions needed for hESC differentiation toward trophoblast-like cells helps us to find an optimal model for studying the early development of human trophoblasts in normal and in complicated pregnancy.
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Affiliation(s)
- Mariann Koel
- Competence Centre on Health Technologies, Tartu, Estonia; Department of Cell Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia; Department of Biosciences and Nutrition, and Centre for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden.
| | - Urmo Võsa
- Estonian Genome Center, University of Tartu, Tartu, Estonia
| | - Kaarel Krjutškov
- Competence Centre on Health Technologies, Tartu, Estonia; Department of Biosciences and Nutrition, and Centre for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden; Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Elisabet Einarsdottir
- Department of Biosciences and Nutrition, and Centre for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden; Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Juha Kere
- Department of Biosciences and Nutrition, and Centre for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden; Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Juha Tapanainen
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Shintaro Katayama
- Department of Biosciences and Nutrition, and Centre for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden
| | - Sulev Ingerpuu
- Department of Cell Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Viljar Jaks
- Department of Cell Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia; Department of Biosciences, Karolinska Institutet, Huddinge, Sweden
| | - Ulf-Hakan Stenman
- Department of Clinical Chemistry, University of Helsinki, Helsinki, Finland
| | - Karolina Lundin
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Timo Tuuri
- Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Andres Salumets
- Competence Centre on Health Technologies, Tartu, Estonia; Department of Obstetrics and Gynecology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; Department of Obstetrics and Gynaecology, University of Tartu, Tartu, Estonia; Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
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37
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Kaustio M, Haapaniemi E, Göös H, Hautala T, Park G, Syrjänen J, Einarsdottir E, Sahu B, Kilpinen S, Rounioja S, Fogarty CL, Glumoff V, Kulmala P, Katayama S, Tamene F, Trotta L, Morgunova E, Krjutškov K, Nurmi K, Eklund K, Lagerstedt A, Helminen M, Martelius T, Mustjoki S, Taipale J, Saarela J, Kere J, Varjosalo M, Seppänen M. Damaging heterozygous mutations in NFKB1 lead to diverse immunologic phenotypes. J Allergy Clin Immunol 2017; 140:782-796. [PMID: 28115215 DOI: 10.1016/j.jaci.2016.10.054] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 09/02/2016] [Accepted: 10/07/2016] [Indexed: 10/20/2022]
Abstract
BACKGROUND The nuclear factor κ light-chain enhancer of activated B cells (NF-κB) signaling pathway is a key regulator of immune responses. Accordingly, mutations in several NF-κB pathway genes cause immunodeficiency. OBJECTIVE We sought to identify the cause of disease in 3 unrelated Finnish kindreds with variable symptoms of immunodeficiency and autoinflammation. METHODS We applied genetic linkage analysis and next-generation sequencing and functional analyses of NFKB1 and its mutated alleles. RESULTS In all affected subjects we detected novel heterozygous variants in NFKB1, encoding for p50/p105. Symptoms in variant carriers differed depending on the mutation. Patients harboring a p.I553M variant presented with antibody deficiency, infection susceptibility, and multiorgan autoimmunity. Patients with a p.H67R substitution had antibody deficiency and experienced autoinflammatory episodes, including aphthae, gastrointestinal disease, febrile attacks, and small-vessel vasculitis characteristic of Behçet disease. Patients with a p.R157X stop-gain experienced hyperinflammatory responses to surgery and showed enhanced inflammasome activation. In functional analyses the p.R157X variant caused proteasome-dependent degradation of both the truncated and wild-type proteins, leading to a dramatic loss of p50/p105. The p.H67R variant reduced nuclear entry of p50 and showed decreased transcriptional activity in luciferase reporter assays. The p.I553M mutation in turn showed no change in p50 function but exhibited reduced p105 phosphorylation and stability. Affinity purification mass spectrometry also demonstrated that both missense variants led to altered protein-protein interactions. CONCLUSION Our findings broaden the scope of phenotypes caused by mutations in NFKB1 and suggest that a subset of autoinflammatory diseases, such as Behçet disease, can be caused by rare monogenic variants in genes of the NF-κB pathway.
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Affiliation(s)
- Meri Kaustio
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Emma Haapaniemi
- Folkhälsan Institute of Genetics, Helsinki, Finland; Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Helka Göös
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Timo Hautala
- Department of Internal Medicine, Oulu University Hospital, Oulu, Finland
| | - Giljun Park
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland
| | - Jaana Syrjänen
- Department of Internal Medicine, Tampere University Hospital, Tampere, Finland
| | - Elisabet Einarsdottir
- Folkhälsan Institute of Genetics, Helsinki, Finland; Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden; Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
| | - Biswajyoti Sahu
- Research Programs Unit, Genome-scale Biology Program, University of Helsinki, Helsinki, Finland
| | - Sanna Kilpinen
- Department of Internal Medicine, Jyväskylä Central Hospital, Jyväskylä, Finland
| | - Samuli Rounioja
- Fimlab Laboratories, Tampere University Hospital, Tampere, Finland; Tampere Center for Child Health Research, Tampere University Hospital, Tampere, Finland
| | - Christopher L Fogarty
- Folkhälsan Institute of Genetics, Helsinki, Finland; Abdominal Center Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | - Virpi Glumoff
- Research Unit of Biomedicine, University of Oulu, Oulu, Finland
| | - Petri Kulmala
- Research Unit of Biomedicine, University of Oulu, Oulu, Finland; Research Unit for Pediatrics, Pediatric Neurology, Pediatric Surgery, Child Psychiatry, Dermatology, Clinical Genetics, Obstetrics and Gynecology, Otorhinolaryngology and Ophthalmology (PEDEGO) and MRC Oulu, Oulu University Hospital and University of Oulu, Oulu, Finland
| | - Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Fitsum Tamene
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Luca Trotta
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Ekaterina Morgunova
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Kaarel Krjutškov
- Folkhälsan Institute of Genetics, Helsinki, Finland; Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden; Competence Centre on Health Technologies, Tartu, Estonia
| | - Katariina Nurmi
- Department of Rheumatology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Kari Eklund
- Department of Rheumatology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Anssi Lagerstedt
- Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - Merja Helminen
- Tampere Center for Child Health Research, Tampere University Hospital, Tampere, Finland
| | - Timi Martelius
- Adult Immunodeficiency Unit, Infectious Diseases, Inflammation Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Satu Mustjoki
- Hematology Research Unit Helsinki, Department of Clinical Chemistry and Hematology, University of Helsinki, Helsinki, Finland; Comprehensive Cancer Center, Helsinki University Central Hospital, Helsinki, Finland
| | - Jussi Taipale
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Janna Saarela
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Juha Kere
- Folkhälsan Institute of Genetics, Helsinki, Finland; Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden; Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland.
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Mikko Seppänen
- Adult Immunodeficiency Unit, Infectious Diseases, Inflammation Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; Rare Diseases Center, Children's Hospital, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
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38
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Haapaniemi EM, Fogarty CL, Keskitalo S, Katayama S, Vihinen H, Ilander M, Mustjoki S, Krjutškov K, Lehto M, Hautala T, Eriksson O, Jokitalo E, Velagapudi V, Varjosalo M, Seppänen M, Kere J. Combined immunodeficiency and hypoglycemia associated with mutations in hypoxia upregulated 1. J Allergy Clin Immunol 2016; 139:1391-1393.e11. [PMID: 27913302 DOI: 10.1016/j.jaci.2016.09.050] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 08/26/2016] [Accepted: 09/10/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Emma M Haapaniemi
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden; Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland; Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland.
| | - Christopher L Fogarty
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland; Abdominal Center Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | - Salla Keskitalo
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden; Center for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden; Science for Life Laboratory, Solna, Sweden
| | - Helena Vihinen
- Institute of Biotechnology, Electron Microscopy Unit, University of Helsinki, Helsinki, Finland
| | - Mette Ilander
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland; Department of Clinical Chemistry, University of Helsinki, Helsinki, Finland
| | - Satu Mustjoki
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland; Department of Clinical Chemistry, University of Helsinki, Helsinki, Finland
| | - Kaarel Krjutškov
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden; Center for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden; Competence Centre on Health Technologies, Tartu, Estonia
| | - Markku Lehto
- Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland; Abdominal Center Nephrology, University of Helsinki and Helsinki University Hospital, Helsinki, Finland; Research Programs Unit, Diabetes and Obesity, University of Helsinki, Helsinki, Finland
| | | | - Ove Eriksson
- Faculty of Medicine, Department of Biochemistry and Developmental Biology, University of Helsinki, Helsinki, Finland
| | - Eija Jokitalo
- Institute of Biotechnology, Electron Microscopy Unit, University of Helsinki, Helsinki, Finland
| | - Vidya Velagapudi
- Metabolomics Unit, Institute for Molecular Medicine Finland FIMM, University of Helsinki, Helsinki, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Mikko Seppänen
- Rare Disease Center, Children's Hospital and Adult Immunodeficiency Unit, Inflammation Center, Helsinki University and Helsinki University Hospital, Helsinki, Finland
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden; Folkhälsan Institute of Genetics, Folkhälsan Research Center, Helsinki, Finland; Research Programs Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland; Center for Innovative Medicine, Karolinska Institutet, Huddinge, Sweden
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39
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Jouhilahti EM, Madissoon E, Vesterlund L, Töhönen V, Krjutškov K, Plaza Reyes A, Petropoulos S, Månsson R, Linnarsson S, Bürglin T, Lanner F, Hovatta O, Katayama S, Kere J. The human PRD-like homeobox gene LEUTX has a central role in embryo genome activation. Development 2016; 143:3459-3469. [PMID: 27578796 PMCID: PMC5087614 DOI: 10.1242/dev.134510] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 08/12/2016] [Indexed: 12/13/2022]
Abstract
Leucine twenty homeobox (LEUTX) is a paired (PRD)-like homeobox gene that is expressed almost exclusively in human embryos during preimplantation development. We previously identified a novel transcription start site for the predicted human LEUTX gene based on the transcriptional analysis of human preimplantation embryos. The novel variant encodes a protein with a complete homeodomain. Here, we provide a detailed description of the molecular cloning of the complete homeodomain-containing LEUTX Using a human embryonic stem cell overexpression model we show that the complete homeodomain isoform is functional and sufficient to activate the transcription of a large proportion of the genes that are upregulated in human embryo genome activation (EGA), whereas the previously predicted partial homeodomain isoform is largely inactive. Another PRD-like transcription factor, DPRX, is then upregulated as a powerful repressor of transcription. We propose a two-stage model of human EGA in which LEUTX acts as a transcriptional activator at the 4-cell stage, and DPRX as a balancing repressor at the 8-cell stage. We conclude that LEUTX is a candidate regulator of human EGA.
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Affiliation(s)
- Eeva-Mari Jouhilahti
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, Huddinge 141 83, Sweden
| | - Elo Madissoon
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, Huddinge 141 83, Sweden
| | - Liselotte Vesterlund
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, Huddinge 141 83, Sweden
| | - Virpi Töhönen
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, Huddinge 141 83, Sweden
| | - Kaarel Krjutškov
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, Huddinge 141 83, Sweden Competence Centre on Health Technologies, Tartu 50410, Estonia
| | - Alvaro Plaza Reyes
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm 141 86, Sweden
| | - Sophie Petropoulos
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm 141 86, Sweden
| | - Robert Månsson
- Center for Hematology and Regenerative Medicine Huddinge, Karolinska Institute, Stockholm 14183, Sweden
| | - Sten Linnarsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Thomas Bürglin
- Department of Biomedicine, University of Basel, Basel 4058, Switzerland
| | - Fredrik Lanner
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm 141 86, Sweden
| | - Outi Hovatta
- Department of Clinical Science, Intervention and Technology, Karolinska Institutet, Karolinska University Hospital Huddinge, Stockholm 141 86, Sweden
| | - Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, Huddinge 141 83, Sweden
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Novum, Huddinge 141 83, Sweden Science for Life Laboratory, Tomtebodavägen 23 A, Solna 171 21, Sweden Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Biomedicum 1, Haartmaninkatu 8, Helsinki 00290, Finland
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40
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Krjutškov K, Koel M, Roost AM, Katayama S, Einarsdottir E, Jouhilahti EM, Söderhäll C, Jaakma Ü, Plaas M, Vesterlund L, Lohi H, Salumets A, Kere J. Globin mRNA reduction for whole-blood transcriptome sequencing. Sci Rep 2016; 6:31584. [PMID: 27515369 PMCID: PMC4981843 DOI: 10.1038/srep31584] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 07/26/2016] [Indexed: 12/15/2022] Open
Abstract
The transcriptome analysis of whole-blood RNA by sequencing holds promise for the identification and tracking of biomarkers; however, the high globin mRNA (gmRNA) content of erythrocytes hampers whole-blood and buffy coat analyses. We introduce a novel gmRNA locking assay (GlobinLock, GL) as a robust and simple gmRNA reduction tool to preserve RNA quality, save time and cost. GL consists of a pair of gmRNA-specific oligonucleotides in RNA initial denaturation buffer that is effective immediately after RNA denaturation and adds only ten minutes of incubation to the whole cDNA synthesis procedure when compared to non-blood RNA analysis. We show that GL is fully effective not only for human samples but also for mouse and rat, and so far incompletely studied cow, dog and zebrafish.
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Affiliation(s)
- Kaarel Krjutškov
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Competence Centre on Health Technologies, Tartu, Estonia.,Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Mariann Koel
- Competence Centre on Health Technologies, Tartu, Estonia.,Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | | | - Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Elisabet Einarsdottir
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Eeva-Mari Jouhilahti
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Cilla Söderhäll
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Department of Women's and Children's Health, Karolinska Institutet, Stockholm, Sweden
| | - Ülle Jaakma
- Competence Centre on Health Technologies, Tartu, Estonia.,Department of Reproductive Biology, Estonian University of Life Sciences, Tartu, Estonia
| | - Mario Plaas
- Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia
| | - Liselotte Vesterlund
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden
| | - Hannes Lohi
- Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Andres Salumets
- Competence Centre on Health Technologies, Tartu, Estonia.,Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu, Estonia.,Department of Obstetrics and Gynaecology, University of Tartu, Tartu, Estonia.,Department of Obstetrics and Gynecology, Helsinki University Hospital, Helsinki, Finland
| | - Juha Kere
- Department of Biosciences and Nutrition, Karolinska Institutet, Huddinge, Sweden.,Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki, Finland
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41
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Madissoon E, Jouhilahti EM, Vesterlund L, Töhönen V, Krjutškov K, Petropoulous S, Einarsdottir E, Linnarsson S, Lanner F, Månsson R, Hovatta O, Bürglin TR, Katayama S, Kere J. Characterization and target genes of nine human PRD-like homeobox domain genes expressed exclusively in early embryos. Sci Rep 2016; 6:28995. [PMID: 27412763 PMCID: PMC4944136 DOI: 10.1038/srep28995] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Accepted: 06/06/2016] [Indexed: 01/07/2023] Open
Abstract
PAIRED (PRD)-like homeobox genes belong to a class of predicted transcription factor genes. Several of these PRD-like homeobox genes have been predicted in silico from genomic sequence but until recently had no evidence of transcript expression. We found recently that nine PRD-like homeobox genes, ARGFX, CPHX1, CPHX2, DPRX, DUXA, DUXB, NOBOX, TPRX1 and TPRX2, were expressed in human preimplantation embryos. In the current study we characterized these PRD-like homeobox genes in depth and studied their functions as transcription factors. We cloned multiple transcript variants from human embryos and showed that the expression of these genes is specific to embryos and pluripotent stem cells. Overexpression of the genes in human embryonic stem cells confirmed their roles as transcription factors as either activators (CPHX1, CPHX2, ARGFX) or repressors (DPRX, DUXA, TPRX2) with distinct targets that could be explained by the amino acid sequence in homeodomain. Some PRD-like homeodomain transcription factors had high concordance of target genes and showed enrichment for both developmentally important gene sets and a 36 bp DNA recognition motif implicated in Embryo Genome Activation (EGA). Our data implicate a role for these previously uncharacterized PRD-like homeodomain proteins in the regulation of human embryo genome activation and preimplantation embryo development.
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Affiliation(s)
- Elo Madissoon
- Biosciences and Nutrition, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | | | | | - Virpi Töhönen
- Biosciences and Nutrition, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Kaarel Krjutškov
- Biosciences and Nutrition, Karolinska Institutet, Huddinge, Stockholm, Sweden
- Competence Centre on Health Technologies, Tartu, Estonia
| | - Sophie Petropoulous
- Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Elisabet Einarsdottir
- Biosciences and Nutrition, Karolinska Institutet, Huddinge, Stockholm, Sweden
- Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Sten Linnarsson
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Fredrik Lanner
- Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Robert Månsson
- Department of Laboratory Medicine, Division of Clinical Immunology, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Outi Hovatta
- Department of Clinical Science, Intervention and Technology (CLINTEC), Karolinska Institutet, Huddinge, Stockholm, Sweden
| | | | - Shintaro Katayama
- Biosciences and Nutrition, Karolinska Institutet, Huddinge, Stockholm, Sweden
| | - Juha Kere
- Biosciences and Nutrition, Karolinska Institutet, Huddinge, Stockholm, Sweden
- Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki, Finland
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42
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Körber I, Katayama S, Einarsdottir E, Krjutškov K, Hakala P, Kere J, Lehesjoki AE, Joensuu T. Gene-Expression Profiling Suggests Impaired Signaling via the Interferon Pathway in Cstb-/- Microglia. PLoS One 2016; 11:e0158195. [PMID: 27355630 PMCID: PMC4927094 DOI: 10.1371/journal.pone.0158195] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Accepted: 06/13/2016] [Indexed: 01/26/2023] Open
Abstract
Progressive myoclonus epilepsy of Unverricht-Lundborg type (EPM1, OMIM254800) is an autosomal recessive neurodegenerative disorder characterized by stimulus-sensitive and action-activated myoclonus, tonic-clonic epileptic seizures, and ataxia. Loss-of-function mutations in the gene encoding the cysteine protease inhibitor cystatin B (CSTB) underlie EPM1. The deficiency of CSTB in mice (Cstb-/- mice) generates a phenotype resembling the symptoms of EPM1 patients and is accompanied by microglial activation at two weeks of age and an upregulation of immune system-associated genes in the cerebellum at one month of age. To shed light on molecular pathways and processes linked to CSTB deficiency in microglia we characterized the transcriptome of cultured Cstb-/- mouse microglia using microarray hybridization and RNA sequencing (RNA-seq). The gene expression profiles obtained with these two techniques were in good accordance and not polarized to either pro- or anti-inflammatory status. In Cstb-/- microglia, altogether 184 genes were differentially expressed. Of these, 33 genes were identified by both methods. Several interferon-regulated genes were weaker expressed in Cstb-/- microglia compared to control. This was confirmed by quantitative real-time PCR of the transcripts Irf7 and Stat1. Subsequently, we explored the biological context of CSTB deficiency in microglia more deeply by functional enrichment and canonical pathway analysis. This uncovered a potential role for CSTB in chemotaxis, antigen-presentation, and in immune- and defense response-associated processes by altering JAK-STAT pathway signaling. These data support and expand the previously suggested involvement of inflammatory processes to the disease pathogenesis of EPM1 and connect CSTB deficiency in microglia to altered expression of interferon-regulated genes.
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Affiliation(s)
- Inken Körber
- Folkhälsan Institute of Genetics, Helsinki, Finland
- Research Program’s Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
- Neuroscience Center, University of Helsinki, Helsinki, Finland
| | - Shintaro Katayama
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Elisabet Einarsdottir
- Folkhälsan Institute of Genetics, Helsinki, Finland
- Research Program’s Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Kaarel Krjutškov
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
- Competence Centre on Health Technologies, Tartu, Estonia
| | - Paula Hakala
- Folkhälsan Institute of Genetics, Helsinki, Finland
- Research Program’s Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
- Neuroscience Center, University of Helsinki, Helsinki, Finland
| | - Juha Kere
- Folkhälsan Institute of Genetics, Helsinki, Finland
- Research Program’s Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
- Department of Biosciences and Nutrition, Karolinska Institutet, Stockholm, Sweden
| | - Anna-Elina Lehesjoki
- Folkhälsan Institute of Genetics, Helsinki, Finland
- Research Program’s Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
- Neuroscience Center, University of Helsinki, Helsinki, Finland
| | - Tarja Joensuu
- Folkhälsan Institute of Genetics, Helsinki, Finland
- Research Program’s Unit, Molecular Neurology, University of Helsinki, Helsinki, Finland
- Neuroscience Center, University of Helsinki, Helsinki, Finland
- * E-mail:
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Krjutškov K, Katayama S, Saare M, Vera-Rodriguez M, Lubenets D, Samuel K, Laisk-Podar T, Teder H, Einarsdottir E, Salumets A, Kere J. Single-cell transcriptome analysis of endometrial tissue. Hum Reprod 2016; 31:844-53. [PMID: 26874359 PMCID: PMC4791917 DOI: 10.1093/humrep/dew008] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 01/11/2016] [Indexed: 12/22/2022] Open
Abstract
STUDY QUESTION How can we study the full transcriptome of endometrial stromal and epithelial cells at the single-cell level? SUMMARY ANSWER By compiling and developing novel analytical tools for biopsy, tissue cryopreservation and disaggregation, single-cell sorting, library preparation, RNA sequencing (RNA-seq) and statistical data analysis. WHAT IS KNOWN ALREADY Although single-cell transcriptome analyses from various biopsied tissues have been published recently, corresponding protocols for human endometrium have not been described. STUDY DESIGN, SIZE, DURATION The frozen-thawed endometrial biopsies were fluorescence-activated cell sorted (FACS) to distinguish CD13-positive stromal and CD9-positive epithelial cells and single-cell transcriptome analysis performed from biopsied tissues without culturing the cells. We studied gene transcription, applying a modern and efficient RNA-seq protocol. In parallel, endometrial stromal cells were cultured and global expression profiles were compared with uncultured cells. PARTICIPANTS/MATERIALS, SETTING, METHODS For method validation, we used two endometrial biopsies, one from mid-secretory phase (Day 21, LH+8) and another from late-secretory phase (Day 25). The samples underwent single-cell FACS sorting, single-cell RNA-seq library preparation and Illumina sequencing. MAIN RESULTS AND THE ROLE OF CHANCE Here we present a complete pipeline for single-cell gene-expression studies, from clinical sampling to statistical data analysis. Tissue manipulation, starting from disaggregation and cell-type-specific labelling and ending with single-cell automated sorting, is managed within 90 min at low temperature to minimize changes in the gene expression profile. The single living stromal and epithelial cells were sorted using CD13- and CD9-specific antibodies, respectively. Of the 8622 detected genes, 2661 were more active in cultured stromal cells than in biopsy cells. In the comparison of biopsy versus cultured cells, 5603 commonly expressed genes were detected, with 241 significantly differentially expressed genes. Of these, 231 genes were up- and 10 down-regulated in cultured cells, respectively. In addition, we performed a gene ontology analysis of the differentially expressed genes and found that these genes are mainly related to cell cycle, translational processes and metabolism. LIMITATIONS, REASONS FOR CAUTION Although CD9-positive single epithelial cells sorting was successfully established in our laboratory, the amount of transcriptome data per individual epithelial cell was low, complicating further analysis. This step most likely failed due to the high dose of RNases that are released by the cells' natural processes, or due to rapid turnaround time or the apoptotic conditions in freezing- or single-cell solutions. Since only the cells from the late-secretory phase were subject to more focused analysis, further studies including larger sample size from the different time-points of the natural menstrual cycle are needed. The methodology also needs further optimization to examine different cell types at high quality. WIDER IMPLICATIONS OF THE FINDINGS The symbiosis between clinical biopsy and the sophisticated laboratory and bioinformatic protocols described here brings together clinical diagnostic needs and modern laboratory and bioinformatic solutions, enabling us to implement a precise analytical toolbox for studying the endometrial tissue even at the single-cell level.
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Affiliation(s)
- K Krjutškov
- Competence Centre on Health Technologies, Tartu 50410, Estonia Department of Biosciences and Nutrition, and Center for Innovative Medicine, Karolinska Institutet, Huddinge 141 83, Sweden
| | - S Katayama
- Department of Biosciences and Nutrition, and Center for Innovative Medicine, Karolinska Institutet, Huddinge 141 83, Sweden
| | - M Saare
- Competence Centre on Health Technologies, Tartu 50410, Estonia Department of Obstetrics and Gynaecology, University of Tartu, Tartu 51014, Estonia
| | | | - D Lubenets
- Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia
| | - K Samuel
- Competence Centre on Health Technologies, Tartu 50410, Estonia
| | - T Laisk-Podar
- Competence Centre on Health Technologies, Tartu 50410, Estonia Department of Obstetrics and Gynaecology, University of Tartu, Tartu 51014, Estonia
| | - H Teder
- Competence Centre on Health Technologies, Tartu 50410, Estonia
| | - E Einarsdottir
- Department of Biosciences and Nutrition, and Center for Innovative Medicine, Karolinska Institutet, Huddinge 141 83, Sweden Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki 00014, Finland
| | - A Salumets
- Competence Centre on Health Technologies, Tartu 50410, Estonia Department of Obstetrics and Gynaecology, University of Tartu, Tartu 51014, Estonia Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu 50411, Estonia
| | - J Kere
- Department of Biosciences and Nutrition, and Center for Innovative Medicine, Karolinska Institutet, Huddinge 141 83, Sweden Molecular Neurology Research Program, University of Helsinki and Folkhälsan Institute of Genetics, Helsinki 00014, Finland
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Tammiste A, Jiang T, Fischer K, Mägi R, Krjutškov K, Pettai K, Esko T, Li Y, Tansey KE, Carroll LS, Uher R, McGuffin P, Võsa U, Tšernikova N, Saria A, Ng PC, Eller T, Vasar V, Nutt DJ, Maron E, Wang J, Metspalu A. Whole-exome sequencing identifies a polymorphism in the BMP5 gene associated with SSRI treatment response in major depression. J Psychopharmacol 2013; 27:915-20. [PMID: 23926243 DOI: 10.1177/0269881113499829] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Although antidepressants are widely used in the pharmacotherapy of major depressive disorder (MDD), their efficacy is still insufficient as approximately one-third of the patients do not fully recover even after several treatment trials. Inter-individual genetic differences are thought to contribute to the variability in antidepressant response; however, current findings from pharmacogenetic studies are uncertain or not clearly replicated. Here we report the first application of full exome sequencing for the analysis of pharmacogenomics on antidepressant treatment. After 12 weeks of treatment with the selective serotonin re-uptake inhibitor escitalopram, we selected five clear responders and five clear non-responders for exome sequencing. By comparing the allele counts of previously known single nucleotide polymorphisms and novel polymorphisms we selected 38 markers for further genotyping in two independent patient samples treated with escitalopram (n=116 and n=394). The A allele, carried by approximately 30% of the patients with MDD, of rs41271330 in the bone morphogenetic protein (BMP5) gene showed strong association with worse treatment response in both sample sets (p=0.001), indicating that this is an promising pharmacogenetic marker for prediction of antidepressant therapeutic outcome.
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Affiliation(s)
- Anu Tammiste
- 1Institute of Molecular and Cell Biology, University of Tartu, Estonia
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Krjutškov K, Koltšina M, Grand K, Võsa U, Sauk M, Tõnisson N, Salumets A. Tissue-specific mitochondrial heteroplasmy at position 16,093 within the same individual. Curr Genet 2013; 60:11-6. [PMID: 23842853 PMCID: PMC3895442 DOI: 10.1007/s00294-013-0398-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 06/27/2013] [Accepted: 06/29/2013] [Indexed: 11/30/2022]
Abstract
Human mitochondrial DNA (mtDNA) research has entered a massively parallel sequencing (MPS) era, providing deep insight into mtDNA genomics and molecular diagnostics. Analysis can simultaneously include coding and control regions, many samples can be studied in parallel, and even minor heteroplasmic changes can be detected. We investigated heteroplasmy using 16 different tissues from three unrelated males aged 40–54 years at the time of death. mtDNA was enriched using two independent overlapping long-range PCR amplicons and analysed by employing illumina paired-end sequencing. Point mutation heteroplasmy at position 16,093 (m.16093T > C) in the non-coding regulatory region showed great variability among one of the studied individuals; heteroplasmy extended from 5.1 % in red bone marrow to 62.0 % in the bladder. Red (5.1 %) and yellow bone marrow (8.9 %) clustered into one group and two arteries and two aortas from different locations into another (31.2–50.9 %), giving an ontogenetic explanation for the formation of somatic mitochondrial heteroplasmy. Our results demonstrate that multi-tissue screening using MPS provides surprising data even when there is a limited number (3) of study subjects and they give reason to speculate that mtDNA heteroplasmic frequency, distribution, and even its possible role in complex diseases or phenotypes seem to be underestimated.
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Affiliation(s)
- Kaarel Krjutškov
- Competence Centre on Reproductive Medicine and Biology, Tartu, Estonia,
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Nikopensius T, Annilo T, Jagomägi T, Gilissen C, Kals M, Krjutškov K, Mägi R, Eelmets M, Gerst-Talas U, Remm M, Saag M, Hoischen A, Metspalu A. Non-syndromic Tooth Agenesis Associated with a Nonsense Mutation in Ectodysplasin-A (EDA). J Dent Res 2013; 92:507-11. [DOI: 10.1177/0022034513487210] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Mutations in the ectodysplasin-A ( EDA) gene have been generally associated with X-linked hypohidrotic ectodermal dysplasia (XLHED). Recently, missense mutations in EDA have been reported to cause familial non-syndromic tooth agenesis. In this study, we report a novel EDA mutation in an Estonian family segregating non-syndromic tooth agenesis with variable expressivity. Affected individuals had no associated defects in other ectodermal organs. Using whole-exome sequencing, we identified a heterozygous nonsense mutation c.874G>T (p.Glu292X) in the TNF homology domain of EDA in all affected female patients. This protein-altering variant arose de novo, and the potentially causative allele was transmitted to affected offspring from the affected mother. We suggest that the dental phenotype variability described in heterozygous female carriers of EDA mutation may occur because of the differential pattern of X-chromosome inactivation, which retains reduced levels of EDA-receptor signaling in tissues involved in tooth morphogenesis. This results in selective tooth agenesis rather than XLHED phenotype. The present study broadens the mutation spectrum for this locus and demonstrates that EDA mutations may result in non-syndromic tooth agenesis in heterozygous females.
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Affiliation(s)
- T. Nikopensius
- Institute of Molecular and Cell Biology, University of Tartu, Estonia
- Estonian Genome Center, University of Tartu, Estonia
| | - T. Annilo
- Institute of Molecular and Cell Biology, University of Tartu, Estonia
| | - T. Jagomägi
- Department of Stomatology, Faculty of Medicine, University of Tartu, Estonia
| | - C. Gilissen
- Department of Human Genetics, Nijmegen Center for Molecular Life Sciences, Institute for Genetic and Metabolic Disease, Radboud University Nijmegen Medical Center, Nijmegen, the Netherlands
| | - M. Kals
- Estonian Genome Center, University of Tartu, Estonia
| | - K. Krjutškov
- Institute of Molecular and Cell Biology, University of Tartu, Estonia
- Department of Biosciences and Nutrition, Karolinska Institute, Huddinge, Sweden
| | - R. Mägi
- Estonian Genome Center, University of Tartu, Estonia
| | - M. Eelmets
- Institute of Molecular and Cell Biology, University of Tartu, Estonia
| | - U. Gerst-Talas
- Institute of Molecular and Cell Biology, University of Tartu, Estonia
| | - M. Remm
- Institute of Molecular and Cell Biology, University of Tartu, Estonia
| | - M. Saag
- Department of Stomatology, Faculty of Medicine, University of Tartu, Estonia
| | - A. Hoischen
- Department of Human Genetics, Nijmegen Center for Molecular Life Sciences, Institute for Genetic and Metabolic Disease, Radboud University Nijmegen Medical Center, Nijmegen, the Netherlands
| | - A. Metspalu
- Institute of Molecular and Cell Biology, University of Tartu, Estonia
- Estonian Genome Center, University of Tartu, Estonia
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Beer B, Krjutškov K, Erb R, Viltrop T, Oberacher H. A novel amplification strategy for genotyping with liquid chromatography-electrospray ionization mass spectrometry. Analyst 2013; 137:5325-33. [PMID: 23034565 DOI: 10.1039/c2an35440c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Among numerous available genotyping techniques, mass spectrometry (MS) based methods play a major role in providing high quality genotype data at reasonable costs for research and diagnostics, e.g. for pharmacogenetic applications. Ion-pair reversed-phase liquid chromatography hyphenated to electrospray ionization time-of-flight MS (ICEMS) is, for example, a powerful instrument that allows a direct characterization of complex mixtures of polymerase chain reaction (PCR) amplified DNA fragments. Current limitations of PCR-ICEMS genotyping are mainly concerned with the multiplex PCR set-up. Assay development often requires time-consuming primer design and intensive optimization of PCR conditions. To overcome this restraint, a robust amplification strategy originally combined with arrayed primer extension genotyping was transferred and adapted to ICEMS genotyping. The modifications involved limitation of the primer length, application of two universal sequences and amplification with an appropriate DNA polymerase. To demonstrate the applicability of the novel amplification strategy for ICEMS, a 23-plex pharmacogenetic genotyping assay was developed. After slight optimization steps, an efficient and quantitatively balanced amplification of all targeted markers was achieved, resulting in a convenient characterization of the multiplexed PCR fragments with ICEMS. Expenditure of time, costs and hands-on work associated with assay design and optimization was dramatically lowered compared to previous multiplex PCR-ICEMS assays. The developed 23-plex assay was applied in a pharmacogenetic study including 284 individuals (genotype call rate 99.0%). A total of 399 SNPs were retyped by Sanger sequencing (concordance rate 99.8%). The PCR-ICEMS assay turned out to be an accurate, reliable, cost-effective and a ready-to-use tool for pharmacogenetic genotyping.
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Affiliation(s)
- Beate Beer
- Institute of Legal Medicine, Innsbruck Medical University, Muellerstrasse 44, 6020 Innsbruck, Austria
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Morris AP, Voight BF, Teslovich TM, Ferreira T, Segrè AV, Steinthorsdottir V, Strawbridge RJ, Khan H, Grallert H, Mahajan A, Prokopenko I, Kang HM, Dina C, Esko T, Fraser RM, Kanoni S, Kumar A, Lagou V, Langenberg C, Luan J, Lindgren CM, Müller-Nurasyid M, Pechlivanis S, Rayner NW, Scott LJ, Wiltshire S, Yengo L, Kinnunen L, Rossin EJ, Raychaudhuri S, Johnson AD, Dimas AS, Loos RJF, Vedantam S, Chen H, Florez JC, Fox C, Liu CT, Rybin D, Couper DJ, Kao WHL, Li M, Cornelis MC, Kraft P, Sun Q, van Dam RM, Stringham HM, Chines PS, Fischer K, Fontanillas P, Holmen OL, Hunt SE, Jackson AU, Kong A, Lawrence R, Meyer J, Perry JRB, Platou CGP, Potter S, Rehnberg E, Robertson N, Sivapalaratnam S, Stančáková A, Stirrups K, Thorleifsson G, Tikkanen E, Wood AR, Almgren P, Atalay M, Benediktsson R, Bonnycastle LL, Burtt N, Carey J, Charpentier G, Crenshaw AT, Doney ASF, Dorkhan M, Edkins S, Emilsson V, Eury E, Forsen T, Gertow K, Gigante B, Grant GB, Groves CJ, Guiducci C, Herder C, Hreidarsson AB, Hui J, James A, Jonsson A, Rathmann W, Klopp N, Kravic J, Krjutškov K, Langford C, Leander K, Lindholm E, Lobbens S, Männistö S, Mirza G, Mühleisen TW, Musk B, Parkin M, Rallidis L, Saramies J, Sennblad B, Shah S, Sigurðsson G, Silveira A, Steinbach G, Thorand B, Trakalo J, Veglia F, Wennauer R, Winckler W, Zabaneh D, Campbell H, van Duijn C, Uitterlinden AG, Hofman A, Sijbrands E, Abecasis GR, Owen KR, Zeggini E, Trip MD, Forouhi NG, Syvänen AC, Eriksson JG, Peltonen L, Nöthen MM, Balkau B, Palmer CNA, Lyssenko V, Tuomi T, Isomaa B, Hunter DJ, Qi L, Shuldiner AR, Roden M, Barroso I, Wilsgaard T, Beilby J, Hovingh K, Price JF, Wilson JF, Rauramaa R, Lakka TA, Lind L, Dedoussis G, Njølstad I, Pedersen NL, Khaw KT, Wareham NJ, Keinanen-Kiukaanniemi SM, Saaristo TE, Korpi-Hyövälti E, Saltevo J, Laakso M, Kuusisto J, Metspalu A, Collins FS, Mohlke KL, Bergman RN, Tuomilehto J, Boehm BO, Gieger C, Hveem K, Cauchi S, Froguel P, Baldassarre D, Tremoli E, Humphries SE, Saleheen D, Danesh J, Ingelsson E, Ripatti S, Salomaa V, Erbel R, Jöckel KH, Moebus S, Peters A, Illig T, de Faire U, Hamsten A, Morris AD, Donnelly PJ, Frayling TM, Hattersley AT, Boerwinkle E, Melander O, Kathiresan S, Nilsson PM, Deloukas P, Thorsteinsdottir U, Groop LC, Stefansson K, Hu F, Pankow JS, Dupuis J, Meigs JB, Altshuler D, Boehnke M, McCarthy MI. Large-scale association analysis provides insights into the genetic architecture and pathophysiology of type 2 diabetes. Nat Genet 2012; 44:981-90. [PMID: 22885922 PMCID: PMC3442244 DOI: 10.1038/ng.2383] [Citation(s) in RCA: 1413] [Impact Index Per Article: 117.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Accepted: 07/11/2012] [Indexed: 11/09/2022]
Abstract
To extend understanding of the genetic architecture and molecular basis of type 2 diabetes (T2D), we conducted a meta-analysis of genetic variants on the Metabochip, including 34,840 cases and 114,981 controls, overwhelmingly of European descent. We identified ten previously unreported T2D susceptibility loci, including two showing sex-differentiated association. Genome-wide analyses of these data are consistent with a long tail of additional common variant loci explaining much of the variation in susceptibility to T2D. Exploration of the enlarged set of susceptibility loci implicates several processes, including CREBBP-related transcription, adipocytokine signaling and cell cycle regulation, in diabetes pathogenesis.
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Affiliation(s)
- Andrew P Morris
- Wellcome Trust Centre for Human Genetics, University of Oxford, UK.
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Nikopensius T, Kempa I, Ambrozaitytė L, Jagomägi T, Saag M, Matulevičienė A, Utkus A, Krjutškov K, Tammekivi V, Piekuse L, Akota I, Barkane B, Krumina A, Klovins J, Lace B, Kučinskas V, Metspalu A. Variation in FGF1, FOXE1, and TIMP2 genes is associated with nonsyndromic cleft lip with or without cleft palate. Birth Defects Res A Clin Mol Teratol 2011; 91:218-25. [PMID: 21462296 DOI: 10.1002/bdra.20791] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2010] [Revised: 01/19/2011] [Accepted: 01/23/2011] [Indexed: 12/28/2022]
Abstract
BACKGROUND Nonsyndromic cleft lip with or without cleft palate (CL/P) is a common complex birth defect caused by the interaction between multiple genes and environmental factors. METHODS Five hundred and eighty-seven single nucleotide polymorphisms in 40 candidate genes related to orofacial clefting were tested for association with CL/P in a clefting sample composed of 300 patients and 606 controls from Estonian, Latvian, and Lithuanian populations. RESULTS In case-control comparisons, the minor alleles of FGF1 rs34010 (p = 4.56 × 10(-4) ), WNT9B rs4968282 (p = 0.0013), and FOXE1 rs7860144 (p = 0.0021) were associated with a decreased risk of CL/P. Multiple haplotypes in FGF1, FOXE1, and TIMP2 and haplotypes in WNT9B, PVRL2, and LHX8 were associated with CL/P. The strongest association was found for protective haplotype rs250092/rs34010 GT in the FGF1 gene (p = 5.01 × 10(-4) ). The strongest epistatic interaction was observed between the COL2A1 and WNT3 genes. CONCLUSIONS Our results provide for the first time evidence implicating FGF1 in the occurrence of CL/P, and support TIMP2 and WNT9B as novel loci predisposing to CL/P. We have also replicated recently reported significant associations between variants in or near FOXE1 and CL/P. It is likely that variation in FOXE1, TIMP2, and the FGF and Wnt signaling pathway genes confers susceptibility to nonsyndromic CL/P in Northeastern European populations.
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Affiliation(s)
- Tiit Nikopensius
- Institute of Molecular and Cell Biology, University of Tartu, Estonia.
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Viltrop T, Krjutškov K, Palta P, Metspalu A. Comparison of DNA extraction methods for multiplex polymerase chain reaction. Anal Biochem 2010; 398:260-2. [DOI: 10.1016/j.ab.2009.11.026] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2009] [Revised: 11/16/2009] [Accepted: 11/17/2009] [Indexed: 11/28/2022]
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