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Alviggi C, Longobardi S, Papaleo E, Santi D, Alfano S, Vanni VS, Campitiello MR, De Rosa P, Strina I, Huhtaniemi I, Pursiheimo JP, D'Hooghe T, Humaidan P, Conforti A. Genetic Variants of Gonadotropins and Their Receptors Could Influence Controlled Ovarian Stimulation: IVF Data from a Prospective Multicenter Study. Genes (Basel) 2023; 14:1269. [PMID: 37372449 DOI: 10.3390/genes14061269] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Revised: 04/19/2023] [Accepted: 05/22/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Specific polymorphisms might influence controlled ovarian stimulation in women undergoing assisted reproductive technologies (ARTs). Data regarding possible interactions of these polymorphisms are still scanty. The aim of this analysis was to evaluate the effect of polymorphisms of gonadotropins and their receptors in women undergoing ART. METHODS A total of 94 normogonadotropic patients from three public ART units were enrolled. Patients underwent a gonadotropin releasing hormone (GnRH) long down-regulation protocol with a starting dose of 150 IU of recombinant follicular stimulating hormone (FSH) daily. Eight polymorphisms were genotyped. RESULTS A total of 94 women (mean age 30.71 ± 2.61) were recruited. Fewer fertilized and mature oocytes were retrieved in homozygous carriers of luteinizing hormone/choriogonadotropin receptor (LHCGR) 291 (T/T) than in heterozygous C/T carriers (p = 0.035 and p = 0.05, respectively). In FSH receptor (FSHR) rs6165 and FSHR rs6166 carriers, the ratio between total gonadotropin consumption and number of oocytes retrieved differed significantly among three genotypes (p = 0.050), and the ratio was lower in homozygous A/A carriers than in homozygous G/G and heterozygous carriers. Women who co-expressed allele G in FSHR-29 rs1394205 and FSHR rs6166 and allele C LHCGR 291 rs12470652 are characterized by an increased ratio between total FSH dosage and number of oocytes collected after ovarian stimulation (risk ratio: 5.44, CI 95%: 3.18-7.71, p < 0.001). CONCLUSIONS Our study demonstrated that specific polymorphisms affect the response to ovarian stimulation. Despite this finding, more robust studies are required to establish the clinical utility of genotype analysis before ovarian stimulation.
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Affiliation(s)
- Carlo Alviggi
- Department of Public Health, University of Naples Federico II, Via Sergio Pansini, 80131 Naples, Italy
| | | | | | - Daniele Santi
- Unit of Endocrinology, Department of Biomedical, Metabolic and Neural Sciences, University of Modena and Reggio Emilia, 41121 Modena, Italy
| | - Simona Alfano
- Department of Neuroscience, Reproductive Science and Odontostomatology, University of Naples Federico II, Via Sergio Pansini, 80131 Naples, Italy
| | | | - Maria Rosaria Campitiello
- Department of Obstetrics and Gynecology and Physiopathology of Human Reproduction, ASL Salerno, 84124 Salerno, Italy
| | - Pasquale De Rosa
- Azienda Ospedaliera Universitaria Federico II di Napoli, 80131 Naples, Italy
| | - Ida Strina
- Department of Public Health, University of Naples Federico II, Via Sergio Pansini, 80131 Naples, Italy
| | - Ilpo Huhtaniemi
- Faculty of Medicine, Department of Surgery and Cancer, London W12 0NN, UK
| | | | - Thomas D'Hooghe
- Department of Development and Regeneration, KU Leuven, 3000 Leuven, Belgium
| | - Peter Humaidan
- Fertility Clinic at Skive Regional Hospital, Faculty of Health, Aarhus University, 8000 Aarhus, Denmark
| | - Alessandro Conforti
- Department of Neuroscience, Reproductive Science and Odontostomatology, University of Naples Federico II, Via Sergio Pansini, 80131 Naples, Italy
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2
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Bourgery M, Ekholm E, Hiltunen A, Heino TJ, Pursiheimo JP, Bendre A, Yatkin E, Laitala T, Määttä J, Säämänen AM. Signature of circulating small non-coding RNAs during early fracture healing in mice. Bone Rep 2022; 17:101627. [PMID: 36304905 PMCID: PMC9593857 DOI: 10.1016/j.bonr.2022.101627] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 10/04/2022] [Accepted: 10/15/2022] [Indexed: 11/06/2022] Open
Abstract
Fracture healing is a complex process with multiple overlapping metabolic and differentiation phases. Small non-coding RNAs are involved in the regulation of fracture healing and their presence in circulation is under current interest due to their obvious value as potential biomarkers. Circulating microRNAs (miRNAs) have been characterized to some extent but the current knowledge on tRNA-derived small RNA fragments (tsRNAs) is relatively scarce, especially in circulation. In this study, the spectrum of circulating miRNAs and tsRNAs was analysed by next generation sequencing to show their differential expression during fracture healing in vivo. Analysed tsRNA fragments included stress-induced translation interfering tRNA fragments (tiRNAs or tRNA halves) and internal tRNA fragments (i-tRF), within the size range of 28–36 bp. To unveil the expression of these non-coding RNAs, genome-wide analysis was performed on two months old C57BL/6 mice on days 1, 5, 7, 10, and 14 (D1, D5, D7, D10, and D14) after a closed tibial fracture. Valine isoacceptor tRNA-derived Val-AAC 5′end and Val-CAC 5′end fragments were the major types of 5′end tiRNAs in circulation, comprising about 65 % of the total counts. Their expression was not affected by fracture. After a fracture, the levels of two 5′end tiRNAs Lys-TTT 5′ and Lys-CTT 5′ were decreased and His-GTG 5′ was increased through D1-D14. The level of miR-451a was decreased on the first post-fracture day (D1), whereas miR-328-3p, miR-133a-3p, miR-375-3p, miR-423-5p, and miR-150-5p were increased post-fracture. These data provide evidence on how fracture healing could provoke systemic metabolic effects and further pinpoint the potential of small non-coding RNAs as biomarkers for tissue regeneration.
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Affiliation(s)
- Matthieu Bourgery
- Integrative Physiology and Pharmacology Unit, Institute of Biomedicine, University of Turku, Finland
| | - Erika Ekholm
- Integrative Physiology and Pharmacology Unit, Institute of Biomedicine, University of Turku, Finland
| | | | - Terhi J. Heino
- Integrative Physiology and Pharmacology Unit, Institute of Biomedicine, University of Turku, Finland
| | - Juha-Pekka Pursiheimo
- Integrative Physiology and Pharmacology Unit, Institute of Biomedicine, University of Turku, Finland,Genomill Health, Turku, Finland
| | - Ameya Bendre
- Integrative Physiology and Pharmacology Unit, Institute of Biomedicine, University of Turku, Finland,Division of Pediatric Endocrinology and Center for Molecular Medicine, Department of Women's and Children's Health, Karolinska Institutet and University Hospital, Stockholm, Sweden
| | - Emrah Yatkin
- Central Animal Laboratory, University of Turku, Turku, Finland
| | - Tiina Laitala
- Integrative Physiology and Pharmacology Unit, Institute of Biomedicine, University of Turku, Finland
| | - Jorma Määttä
- Integrative Physiology and Pharmacology Unit, Institute of Biomedicine, University of Turku, Finland,Turku Center for Disease Modeling (TCDM), Turku, Finland
| | - Anna-Marja Säämänen
- Integrative Physiology and Pharmacology Unit, Institute of Biomedicine, University of Turku, Finland,Corresponding author at: Institute of Biomedicine, University of Turku, Finland.
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3
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Bourgery M, Ekholm E, Fagerlund K, Hiltunen A, Puolakkainen T, Pursiheimo JP, Heino T, Määttä J, Heinonen J, Yatkin E, Laitala T, Säämänen AM. Multiple targets identified with genome wide profiling of small RNA and mRNA expression are linked to fracture healing in mice. Bone Rep 2021; 15:101115. [PMID: 34458508 PMCID: PMC8379442 DOI: 10.1016/j.bonr.2021.101115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 04/01/2021] [Revised: 07/08/2021] [Accepted: 08/02/2021] [Indexed: 12/21/2022] Open
Abstract
Long-bone fracture is a common injury and its healing process at the fracture site involves several overlapping phases, including inflammation, migration of mesenchymal progenitors into the fracture site, endochondral ossification, angiogenesis and finally bone remodelling. Increasing evidence shows that small noncoding RNAs are important regulators of chondrogenesis, osteogenesis and fracture healing. MicroRNAs are small single-stranded, non-coding RNA-molecules intervening in most physiological and biological processes, including fracture healing. Angiogenin-cleaved 5' tRNA halves, also called as tiRNAs (stress-induced RNAs) have been shown to repress protein translation. In order to gain further understanding on the role of small noncoding RNAs in fracture healing, genome wide expression profiles of tiRNAs, miRNAs and mRNAs were followed up to 14 days after fracture in callus tissue of an in vivo mouse model with closed tibial fracture and, compared to intact bone and articular cartilage at 2 months of age. Total tiRNA expression level in cartilage was only approximately one third of that observed in control D0 bone. In callus tissue, 11 mature 5'end tiRNAs out of 191 tiRNAs were highly expressed, and seven of them were differentially expressed during fracture healing. When comparing the control tissues, 25 miRNAs characteristic to bone and 29 miRNAs characteristic to cartilage tissue homeostasis were identified. Further, a total of 54 out of 806 miRNAs and 5420 out of 18,700 mRNAs were differentially expressed (DE) in callus tissue during fracture healing and, in comparison to control bone. They were associated to gene ontology processes related to mesenchymal tissue development and differentiation. A total of 581 miRNA-mRNA interactions were identified for these 54 DE miRNAs by literature searches in PubMed, thereby linking by Spearman correlation analysis 14 downregulated and 28 upregulated miRNAs to 164 negatively correlating and 168 positively correlating miRNA-mRNA pairs with chondrogenic and osteogenic phases of fracture healing. These data indicated that tiRNAs and miRNAs were differentially expressed in fracture callus tissue, suggesting them important physiological functions during fracture healing. Hence, the data provided by this study may contribute to future clinical applications, such as potential use as biomarkers or as tools in the development of novel therapeutic approaches for fracture healing.
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Affiliation(s)
| | - Erika Ekholm
- Institute of Biomedicine, University of Turku, Finland
| | | | | | - Tero Puolakkainen
- Institute of Biomedicine, University of Turku, Finland
- Department of Oral and Maxillofacial Diseases, University of Helsinki and Helsinki University Hospital, Finland
| | | | - Terhi Heino
- Institute of Biomedicine, University of Turku, Finland
| | - Jorma Määttä
- Institute of Biomedicine, University of Turku, Finland
- Turku Center for Disease Modeling (TCDM), Finland
| | | | - Emrah Yatkin
- Central Animal Laboratory, University of Turku, Turku, Finland
| | - Tiina Laitala
- Institute of Biomedicine, University of Turku, Finland
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Abstract
BACKGROUND Elevated Anoctamin 7 (ANO7) expression is associated with poor survival in prostate cancer patients. OBJECTIVE The aim was to discover proteins that interact with ANO7 to understand its functions and regulatory mechanisms. METHODS The proximity-dependent biotin identification (BioID) method was utilized. ANO7 fused to biotin ligase was transiently transfected into LNCaP cells, and the biotinylated proteins were collected and analysed by mass spectrometry. Four identified proteins were stained with dual fluorescent immunostaining and visualized using Stimulated emission depletion microscopy (STED). RESULTS After bioinformatic filtering steps, 64 potentially ANO7-interacting proteins were identified and analysed with the GO enrichment analysis tool. One of the most prominently enriched cellular components was cellular vesicle. Co-localization was showed for staphylococcal nuclease and tudor domain containing 1 (SND1), heat shock protein family A (Hsp70) member 1A (HSPA1A), adaptor related protein complex 2 subunit beta 1 (AP2B1) and coatomer protein complex subunit gamma 2 (COPG2). CONCLUSIONS This is the first study in which ANO7 interacting proteins have been identified. Although further studies are needed, the findings reported here expand our understanding of the role and regulation of ANO7 in prostate cancer cells. Furthermore, these results are likely to introduce new targets for the novel cancer therapies.
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Affiliation(s)
- Elina Kaikkonen
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Aliisa Takala
- Institute of Biomedicine, University of Turku, Turku, Finland
| | | | | | - Johanna Schleutker
- Institute of Biomedicine, University of Turku, Turku, Finland.,Department of Medical Genetics, Genomics, Laboratory Division, Turku University Hospital, Turku, Finland
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5
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Kaikkonen E, Rantapero T, Zhang Q, Taimen P, Laitinen V, Kallajoki M, Jambulingam D, Ettala O, Knaapila J, Boström PJ, Wahlström G, Sipeky C, Pursiheimo JP, Tammela T, Kellokumpu-Lehtinen PL, Fey V, Maehle L, Wiklund F, Wei GH, Schleutker J. ANO7 is associated with aggressive prostate cancer. Int J Cancer 2018; 143:2479-2487. [PMID: 30157291 PMCID: PMC6589920 DOI: 10.1002/ijc.31746] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [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: 01/23/2018] [Revised: 05/09/2018] [Accepted: 06/15/2018] [Indexed: 12/29/2022]
Abstract
Prostate cancer is one of the most common and heritable human cancers. Our aim was to find germline biomarkers that can predict disease outcome. We previously detected predisposing signals at 2q37, the location of the prostate specific ANO7 gene. To investigate, in detail, the associations between the ANO7 gene and PrCa risk and disease aggressiveness, ANO7 was sequenced in castration resistant tumors together with samples from unselected PrCa patients and unaffected males. Two pathogenic variants were discovered and genotyped in 1769 patients and 1711 unaffected males. Expression of ANO7 vs. PrCa aggressiveness was investigated. Different databases along with Swedish and Norwegian cohorts were used for validation. Case–control and aggressive vs. nonaggressive association analyses were performed against risk and/or cancer aggressiveness. The ANO7 mRNA level and patient survival were analyzed using expression data from databases. Variant rs77559646 showed both risk (OR 1.40; p = 0.009, 95% CI 1.09–1.78) and association with aggressive PrCa (Genotype test p = 0.04). It was found to be an eQTL for ANO7 (Linear model p‐values for Finnish patients p = 0.009; Camcap prostate tumor p = 2.53E‐06; Stockholm prostate tumor cohort p = 1.53E‐13). rs148609049 was not associated with risk, but was related to shorter survival (HR 1.56; 95% CI 1.03–2.36). High ANO7 expression was independently linked to poor survival (HR 18.4; 95% CI 1.43–237). ANO7 genotypes correlate with expression and biochemical relapse, suggesting that ANO7 is a potential PrCa susceptibility gene and that its elevated expression correlates with disease severity and outcome. What's new? The discovery of germline biomarkers to predict outcome in prostate cancer could greatly aid disease management. One such marker of particular interest in this regard is the prostate‐specific gene ANO7, which previous studies have associated with high‐grade prostate cancer. Here, specific germline ANO7 genotypes were associated with increased prostate cancer risk. In patients, ANO7 expression correlated with disease severity, with elevated expression associated with decreased overall survival. The data suggest that ANO7 is a susceptibility marker in prostate cancer and, with further characterization, could be used to inform patient selection strategies and therapeutic approaches.
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Affiliation(s)
- Elina Kaikkonen
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Tommi Rantapero
- Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Qin Zhang
- Biocenter Oulu, University of Oulu, Oulu, Finland.,Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Pekka Taimen
- Institute of Biomedicine, University of Turku, Turku, Finland.,Department of Pathology, University of Turku and Turku University Hospital, Turku, Finland
| | | | - Markku Kallajoki
- Department of Pathology, University of Turku and Turku University Hospital, Turku, Finland
| | | | - Otto Ettala
- Department of Urology, Turku University Hospital, Turku, Finland
| | - Juha Knaapila
- Department of Urology, Turku University Hospital, Turku, Finland
| | - Peter J Boström
- Department of Urology, Turku University Hospital, Turku, Finland
| | | | - Csilla Sipeky
- Institute of Biomedicine, University of Turku, Turku, Finland
| | | | - Teuvo Tammela
- Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland.,Department of Urology, Tampere University Hospital, Tampere, Finland
| | - Pirkko-Liisa Kellokumpu-Lehtinen
- Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland.,Department of Oncology, Tampere University Hospital, Tampere, Finland
| | | | - Vidal Fey
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Lovise Maehle
- Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Fredrik Wiklund
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Gong-Hong Wei
- Biocenter Oulu, University of Oulu, Oulu, Finland.,Faculty of Biochemistry and Molecular Medicine, University of Oulu, Oulu, Finland
| | - Johanna Schleutker
- Institute of Biomedicine, University of Turku, Turku, Finland.,Department of Medical Genetics, TUCH Microbiology and Genetics, Turku University Hospital, Turku, Finland
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6
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Rintala A, Riikonen I, Toivonen A, Pietilä S, Munukka E, Pursiheimo JP, Elo LL, Arikoski P, Luopajärvi K, Schwab U, Uusitupa M, Heinonen S, Savilahti E, Eerola E, Ilonen J. Early fecal microbiota composition in children who later develop celiac disease and associated autoimmunity. Scand J Gastroenterol 2018; 53:403-409. [PMID: 29504486 DOI: 10.1080/00365521.2018.1444788] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [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: 02/08/2023]
Abstract
OBJECTIVES Several studies have reported that the intestinal microbiota composition of celiac disease (CD) patients differs from healthy individuals. The possible role of gut microbiota in the pathogenesis of the disease is, however, not known. Here, we aimed to assess the possible differences in early fecal microbiota composition between children that later developed CD and healthy controls matched for age, sex and HLA risk genotype. MATERIALS AND METHODS We used 16S rRNA gene sequencing to examine the fecal microbiota of 27 children with high genetic risk of developing CD. Nine of these children developed the disease by the age of 4 years. Stool samples were collected at the age of 9 and 12 months, before any of the children had developed CD. The fecal microbiota composition of children who later developed the disease was compared with the microbiota of the children who did not have CD or associated autoantibodies at the age of 4 years. Delivery mode, early nutrition, and use of antibiotics were taken into account in the analyses. RESULTS No statistically significant differences in the fecal microbiota composition were found between children who later developed CD (n = 9) and the control children without disease or associated autoantibodies (n = 18). CONCLUSIONS Based on our results, the fecal microbiota composition at the age of 9 and 12 months is not associated with the development of CD. Our results, however, do not exclude the possibility of duodenal microbiota changes or a later microbiota-related trigger for the disease.
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Affiliation(s)
- Anniina Rintala
- a Department of Medical Microbiology and Immunology , University of Turku , Turku , Finland.,b Department of Clinical Microbiology , Turku University Hospital , Turku , Finland
| | - Iiris Riikonen
- a Department of Medical Microbiology and Immunology , University of Turku , Turku , Finland
| | - Anne Toivonen
- c Department of Bacteriology and Immunology , University of Helsinki and Laboratory Services (HUSLAB), Division of Clinical Microbiology, Helsinki University Hospital , Helsinki , Finland.,d Department of Clinical Microbiology , Institute of Clinical Medicine, University of Eastern Finland , Kuopio , Finland
| | - Sami Pietilä
- e Turku Centre for Biotechnology , University of Turku and Åbo Akademi University , Turku , Finland
| | - Eveliina Munukka
- a Department of Medical Microbiology and Immunology , University of Turku , Turku , Finland
| | | | - Laura L Elo
- e Turku Centre for Biotechnology , University of Turku and Åbo Akademi University , Turku , Finland
| | - Pekka Arikoski
- g Department of Pediatrics , Kuopio University Hospital and University of Eastern Finland , Kuopio , Finland
| | - Kristiina Luopajärvi
- h Children's Hospital, Department of Pediatrics , Helsinki University Hospital and University of Helsinki , Helsinki , Finland
| | - Ursula Schwab
- i Institute of Public Health and Clinical Nutrition , University of Eastern Finland , Kuopio , Finland
| | - Matti Uusitupa
- i Institute of Public Health and Clinical Nutrition , University of Eastern Finland , Kuopio , Finland
| | - Seppo Heinonen
- j Department of Obstetrics and Gynecology , Helsinki University Hospital and University of Helsinki , Helsinki , Finland
| | - Erkki Savilahti
- h Children's Hospital, Department of Pediatrics , Helsinki University Hospital and University of Helsinki , Helsinki , Finland
| | - Erkki Eerola
- a Department of Medical Microbiology and Immunology , University of Turku , Turku , Finland.,b Department of Clinical Microbiology , Turku University Hospital , Turku , Finland
| | - Jorma Ilonen
- a Department of Medical Microbiology and Immunology , University of Turku , Turku , Finland.,k Immunogenetics Laboratory , Institute of Biomedicine, University of Turku , Turku , Finland
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Rintala A, Pietilä S, Munukka E, Eerola E, Pursiheimo JP, Laiho A, Pekkala S, Huovinen P. Gut Microbiota Analysis Results Are Highly Dependent on the 16S rRNA Gene Target Region, Whereas the Impact of DNA Extraction Is Minor. J Biomol Tech 2017; 28:19-30. [PMID: 28260999 DOI: 10.7171/jbt.17-2801-003] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Next-generation sequencing (NGS) is currently the method of choice for analyzing gut microbiota composition. As gut microbiota composition is a potential future target for clinical diagnostics, it is of utmost importance to enhance and optimize the NGS analysis procedures. Here, we have analyzed the impact of DNA extraction and selected 16S rDNA primers on the gut microbiota NGS results. Bacterial DNA from frozen stool specimens was extracted with 5 commercially available DNA extraction kits. Special attention was paid to the semiautomated DNA extraction methods that could expedite the analysis procedure, thus being especially suitable for clinical settings. The microbial composition was analyzed with 2 distinct protocols: 1 targeting the V3-V4 and the other targeting the V4-V5 area of the bacterial 16S rRNA gene. The overall effect of DNA extraction on the gut microbiota 16S rDNA profile was relatively small, whereas the 16S rRNA gene target region had an immense impact on the results. Furthermore, semiautomated DNA extraction methods clearly appeared suitable for NGS procedures, proposing that application of these methods could importantly reduce hands-on time and human errors without compromising the validity of results.
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Affiliation(s)
- Anniina Rintala
- Department of Medical Microbiology and Immunology, University of Turku, Turku, Finland;; Department of Clinical Microbiology and Immunology, Turku University Hospital, Turku, Finland
| | | | - Eveliina Munukka
- Department of Medical Microbiology and Immunology, University of Turku, Turku, Finland;; Department of Clinical Microbiology and Immunology, Turku University Hospital, Turku, Finland
| | - Erkki Eerola
- Department of Medical Microbiology and Immunology, University of Turku, Turku, Finland;; Department of Clinical Microbiology and Immunology, Turku University Hospital, Turku, Finland
| | | | - Asta Laiho
- Turku Centre for Biotechnology, Turku, Finland
| | - Satu Pekkala
- Unit of Health Sciences, Faculty of Sports, University of Jyväskylä, Jyväskylä, Finland
| | - Pentti Huovinen
- Department of Medical Microbiology and Immunology, University of Turku, Turku, Finland
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8
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Salomäki-Myftari H, Vähätalo LH, Ailanen L, Pietilä S, Laiho A, Hänninen A, Pursiheimo JP, Munukka E, Rintala A, Savontaus E, Pesonen U, Koulu M. Neuropeptide Y Overexpressing Female and Male Mice Show Divergent Metabolic but Not Gut Microbial Responses to Prenatal Metformin Exposure. PLoS One 2016; 11:e0163805. [PMID: 27681875 PMCID: PMC5040270 DOI: 10.1371/journal.pone.0163805] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 09/14/2016] [Indexed: 11/19/2022] Open
Abstract
Background Prenatal metformin exposure has been shown to improve the metabolic outcome in the offspring of high fat diet fed dams. However, if this is evident also in a genetic model of obesity and whether gut microbiota has a role, is not known. Methods The metabolic effects of prenatal metformin exposure were investigated in a genetic model of obesity, mice overexpressing neuropeptide Y in the sympathetic nervous system and in brain noradrenergic neurons (OE-NPYDβH). Metformin was given for 18 days to the mated female mice. Body weight, body composition, glucose tolerance and serum parameters of the offspring were investigated on regular diet from weaning and sequentially on western diet (at the age of 5–7 months). Gut microbiota composition was analysed by 16S rRNA sequencing at 10–11 weeks. Results In the male offspring, metformin exposure inhibited weight gain. Moreover, weight of white fat depots and serum insulin and lipids tended to be lower at 7 months. In contrast, in the female offspring, metformin exposure impaired glucose tolerance at 3 months, and subsequently increased body weight gain, fat mass and serum cholesterol. In the gut microbiota, a decline in Erysipelotrichaceae and Odoribacter was detected in the metformin exposed offspring. Furthermore, the abundance of Sutterella tended to be decreased and Parabacteroides increased. Gut microbiota composition of the metformin exposed male offspring correlated to their metabolic phenotype. Conclusion Prenatal metformin exposure caused divergent metabolic phenotypes in the female and male offspring. Nevertheless, gut microbiota of metformin exposed offspring was similarly modified in both genders.
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Affiliation(s)
- Henriikka Salomäki-Myftari
- Institute of Biomedicine, Department of Pharmacology, Drug Development and Therapeutics, University of Turku, Turku, Finland
- Drug Research Doctoral Programme (DRDP), University of Turku, Turku, Finland
| | - Laura H. Vähätalo
- Institute of Biomedicine, Department of Pharmacology, Drug Development and Therapeutics, University of Turku, Turku, Finland
- Drug Research Doctoral Programme (DRDP), University of Turku, Turku, Finland
| | - Liisa Ailanen
- Institute of Biomedicine, Department of Pharmacology, Drug Development and Therapeutics, University of Turku, Turku, Finland
- Drug Research Doctoral Programme (DRDP), University of Turku, Turku, Finland
| | - Sami Pietilä
- Bioinformatics Unit, Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Asta Laiho
- Bioinformatics Unit, Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Arno Hänninen
- Institute of Biomedicine, Department of Medical Microbiology and Immunology, University of Turku, Turku, Finland
| | - Juha-Pekka Pursiheimo
- Turku Clinical Sequencing Laboratory, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Eveliina Munukka
- Institute of Biomedicine, Department of Medical Microbiology and Immunology, University of Turku, Turku, Finland
| | - Anniina Rintala
- Institute of Biomedicine, Department of Medical Microbiology and Immunology, University of Turku, Turku, Finland
| | - Eriika Savontaus
- Institute of Biomedicine, Department of Pharmacology, Drug Development and Therapeutics, University of Turku, Turku, Finland
| | - Ullamari Pesonen
- Institute of Biomedicine, Department of Pharmacology, Drug Development and Therapeutics, University of Turku, Turku, Finland
| | - Markku Koulu
- Institute of Biomedicine, Department of Pharmacology, Drug Development and Therapeutics, University of Turku, Turku, Finland
- * E-mail:
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9
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Löf C, Patyra K, Kuulasmaa T, Vangipurapu J, Undeutsch H, Jaeschke H, Pajunen T, Kero A, Krude H, Biebermann H, Kleinau G, Kühnen P, Rantakari K, Miettinen P, Kirjavainen T, Pursiheimo JP, Mustila T, Jääskeläinen J, Ojaniemi M, Toppari J, Ignatius J, Laakso M, Kero J. Detection of Novel Gene Variants Associated with Congenital Hypothyroidism in a Finnish Patient Cohort. Thyroid 2016; 26:1215-24. [PMID: 27373559 PMCID: PMC5036323 DOI: 10.1089/thy.2016.0016] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
BACKGROUND Congenital hypothyroidism (CH) is defined as the lack of thyroid hormones at birth. Mutations in at least 15 different genes have been associated with this disease. While up to 20% of CH cases are hereditary, the majority of cases are sporadic with unknown etiology. Apart from a monogenic pattern of inheritance, multigenic mechanisms have been suggested to play a role in CH. The genetics of CH has not been studied in Finland so far. Therefore, multigenic sequencing of CH candidate genes was performed in a Finnish patient cohort with both familial and sporadic CH. METHODS A targeted next-generation sequencing (NGS) panel, covering all exons of the major CH genes, was applied for 15 patients with sporadic and 11 index cases with familial CH. RESULTS Among the familial cases, six pathogenic mutations were found in the TPO, PAX8, and TSHR genes. Furthermore, pathogenic NKX2.1 and TG mutations were identified from sporadic cases, together with likely pathogenic variants in the TG, NKX2.5, SLC26A4, and DUOX2 genes. All identified novel pathogenic mutations were confirmed by Sanger-sequencing and characterized in silico and/or in vitro. CONCLUSION In summary, the CH panel provides an efficient, cost-effective, and multigenic screening tool for both known and novel CH gene mutations. Hence, it may be a useful method to identify accurately the genetic etiology for dyshormogenic, familial, or syndromic forms of CH.
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Affiliation(s)
- Christoffer Löf
- Department of Physiology, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Konrad Patyra
- Department of Physiology, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Teemu Kuulasmaa
- Faculty of Health Sciences, Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Jagadish Vangipurapu
- Faculty of Health Sciences, Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Henriette Undeutsch
- Department of Physiology, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Holger Jaeschke
- Department of Physiology, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Tuulia Pajunen
- Department of Physiology, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Andreina Kero
- Department of Physiology, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Heiko Krude
- Institute of Experimental Pediatric Endocrinology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Heike Biebermann
- Institute of Experimental Pediatric Endocrinology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Gunnar Kleinau
- Institute of Experimental Pediatric Endocrinology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Peter Kühnen
- Institute of Experimental Pediatric Endocrinology, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Krista Rantakari
- Hospital for Children and Adolescents, Hospital District of Helsinki and Uusimaa, Helsinki, Finland
| | - Päivi Miettinen
- Hospital for Children and Adolescents, Hospital District of Helsinki and Uusimaa, Helsinki, Finland
| | - Turkka Kirjavainen
- Hospital for Children and Adolescents, Hospital District of Helsinki and Uusimaa, Helsinki, Finland
| | - Juha-Pekka Pursiheimo
- Turku Clinical Sequencing Laboratory, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Taina Mustila
- Department of Pediatrics, Seinäjoki Central Hospital, Seinäjoki, Finland
| | - Jarmo Jääskeläinen
- Department of Pediatrics, Seinäjoki Central Hospital, Seinäjoki, Finland
| | - Marja Ojaniemi
- Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
| | - Jorma Toppari
- Department of Physiology, Institute of Biomedicine, University of Turku, Turku, Finland
- Department of Pediatrics, Turku University Hospital, Turku, Finland
| | - Jaakko Ignatius
- Department of Clinical Genetics, Turku University Hospital, Turku, Finland
| | - Markku Laakso
- Faculty of Health Sciences, Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland, Kuopio, Finland
| | - Jukka Kero
- Department of Physiology, Institute of Biomedicine, University of Turku, Turku, Finland
- Department of Pediatrics, Turku University Hospital, Turku, Finland
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10
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Laiterä T, Kurki MI, Pursiheimo JP, Zetterberg H, Helisalmi S, Rauramaa T, Alafuzoff I, Remes AM, Soininen H, Haapasalo A, Jääskeläinen JE, Hiltunen M, Leinonen V. The Expression of Transthyretin and Amyloid-β Protein Precursor is Altered in the Brain of Idiopathic Normal Pressure Hydrocephalus Patients. J Alzheimers Dis 2016; 48:959-68. [PMID: 26444765 DOI: 10.3233/jad-150268] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [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: 01/12/2023]
Abstract
BACKGROUND Idiopathic normal pressure hydrocephalus (iNPH) is a dementing condition in which Alzheimer's disease (AD)-related amyloid-β (Aβ) plaques are frequently observed in the neocortex. iNPH patients with prominent Aβ pathology show AD-related alterations in amyloid-β protein precursor (AβPP) processing resulting from increased γ-secretase activity. OBJECTIVES Our goal was to assess potential alterations in the global gene expression profile in the brain of iNPH patients as compared to non-demented controls and to evaluate the levels of the identified targets in the cerebrospinal fluid (CSF) of iNPH patients. METHODS The genome-wide expression profile of ~35,000 probes was assessed in the RNA samples obtained from 22 iNPH patients and eight non-demented control subjects using a microarray chip. The soluble levels of sAβPPα, sAβPPβ, and transthyretin (TTR) were measured from the CSF of 102 iNPH patients using ELISA. RESULTS After correcting the results for multiple testing, significant differences in the expression of TTR and A βPP were observed between iNPH and control subjects. The mRNA levels of TTR were on average 17-fold lower in iNPH samples compared to control samples. Conversely, the expression level of A βPP was on average three times higher in iNPH samples as compared to control samples. Interestingly, the expression of α-secretase (ADAM10) was also increased in iNPH patients. In the lumbar CSF samples, soluble TTR levels showed a significant positive correlation with sAβPPα and sAβPPβ, but TTR levels did not predict the brain pathology or the shunt response. CONCLUSIONS These findings suggest differences in the expression profile of key factors involved in AD-related cellular events in the brain of iNPH patients.
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Affiliation(s)
- Tiina Laiterä
- Institute of Clinical Medicine - Neurology, University of Eastern Finland and Department of Neurology, Kuopio University Hospital, Kuopio, Finland.,Institute of Clinical Medicine - Neurosurgery, University of Eastern Finland and Neurosurgery of NeuroCenter, Kuopio University Hospital, Kuopio, Finland
| | - Mitja I Kurki
- Institute of Clinical Medicine - Neurosurgery, University of Eastern Finland and Neurosurgery of NeuroCenter, Kuopio University Hospital, Kuopio, Finland
| | | | - Henrik Zetterberg
- Clinical Neurochemistry Laboratory, Department of Psychiatry and Neurochemistry, The Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Seppo Helisalmi
- Institute of Clinical Medicine - Neurology, University of Eastern Finland and Department of Neurology, Kuopio University Hospital, Kuopio, Finland
| | - Tuomas Rauramaa
- Institute of Clinical Medicine - Pathology, University of Eastern Finland and Department of Pathology, Kuopio University Hospital, Kuopio, Finland.,Department of Pathology, Kuopio University Hospital, Kuopio, Finland
| | - Irina Alafuzoff
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Anne M Remes
- Institute of Clinical Medicine - Neurology, University of Eastern Finland and Department of Neurology, Kuopio University Hospital, Kuopio, Finland
| | - Hilkka Soininen
- Institute of Clinical Medicine - Neurology, University of Eastern Finland and Department of Neurology, Kuopio University Hospital, Kuopio, Finland
| | - Annakaisa Haapasalo
- Institute of Clinical Medicine - Neurology, University of Eastern Finland and Department of Neurology, Kuopio University Hospital, Kuopio, Finland.,Department of Neurobiology, A.I. Virtanen Institute for Molecular Sciences, Kuopio, Finland
| | - Juha E Jääskeläinen
- Institute of Clinical Medicine - Neurosurgery, University of Eastern Finland and Neurosurgery of NeuroCenter, Kuopio University Hospital, Kuopio, Finland
| | - Mikko Hiltunen
- Institute of Clinical Medicine - Neurology, University of Eastern Finland and Department of Neurology, Kuopio University Hospital, Kuopio, Finland.,Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Ville Leinonen
- Institute of Clinical Medicine - Neurosurgery, University of Eastern Finland and Neurosurgery of NeuroCenter, Kuopio University Hospital, Kuopio, Finland
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11
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Lövgren J, Pursiheimo JP, Pyykkö M, Salmi J, Lamminmäki U. Next generation sequencing of all variable loops of synthetic single framework scFv-Application in anti-HDL antibody selections. N Biotechnol 2016; 33:790-796. [PMID: 27450754 DOI: 10.1016/j.nbt.2016.07.009] [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] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 07/01/2016] [Accepted: 07/17/2016] [Indexed: 11/30/2022]
Abstract
Next generation sequencing (NGS) can be applied to monitoring antibody phage display library selection processes to follow the enrichment of each individual antibody clone. Utilising the recent development of the Illumina sequencing platform enabling sequencing up to 2×300bp, we have developed a method to deep sequence all complementarity determining regions (CDRs) in the clones obtained from a synthetic single framework antibody library. This was complemented by an in-house bioinformatics pipeline for efficient analysis of the sequencing results. The method was utilised to study antibody selections against high density lipoprotein (HDL) particles. Sequencing of the output from each selection round enabled extraction of useful information on both the total copy numbers as well as the relative enrichment rates of the clones. Ten antibody clones showing different ranking in terms of frequency were reproduced from synthetic DNA constructs and their capacity to bind HDL was verified by an immunoassay. The method thus facilitates the isolation of clones of interest, and in particular can assist retrieval of less efficiently enriched, yet interesting clones, which are unlikely to be identified by conventional, random colony picking based, screening.
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Affiliation(s)
- Janita Lövgren
- Department of Biochemistry, Division of Biotechnology, University of Turku, Turku, Finland.
| | - Juha-Pekka Pursiheimo
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Mikko Pyykkö
- Department of Biochemistry, Division of Biotechnology, University of Turku, Turku, Finland
| | - Jussi Salmi
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
| | - Urpo Lamminmäki
- Department of Biochemistry, Division of Biotechnology, University of Turku, Turku, Finland
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12
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Djakow J, Kramná L, Dušátková L, Uhlík J, Pursiheimo JP, Svobodová T, Pohunek P, Cinek O. An effective combination of sanger and next generation sequencing in diagnostics of primary ciliary dyskinesia. Pediatr Pulmonol 2016; 51:498-509. [PMID: 26228299 DOI: 10.1002/ppul.23261] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [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] [Received: 12/28/2014] [Revised: 06/15/2015] [Accepted: 06/16/2015] [Indexed: 01/07/2023]
Abstract
BACKGROUND Primary ciliary dyskinesia (PCD) is a multigenic autosomal recessive condition affecting respiratory tract and other organs where ciliary motility is required. The extent of its genetic heterogeneity is remarkable. The aim of the study was to develop a cost-effective pipeline for genetic diagnostics using a combination of Sanger and next generation sequencing (NGS). MATERIALS AND METHODS Data and samples of 33 families with 38 affected subjects with PCD diagnosed in childhood were collected over the territory of the Czech Republic. A panel of 18 PCD causative or candidate genes was implemented into an Illumina TruSeq Custom Amplicon NGS assay, and three ancestral mutations in SPAG1 were screened by conventional Sanger sequencing, which was also used for the confirmation of the NGS results and for the analysis of familial segregation. RESULTS The causative gene was DNAH5 in 11/33 (33%) probands, SPAG1 in 8/33 (24%), and DNAI1, CCDC40, LRRC6 in one family each. If the high proportion of subjects with bi-allelic ancestral mutations in SPAG1 is corroborated in other Caucasian populations, a simple Sanger sequencing test for these three mutations may serve as an effective pre-screening step, being followed by an NGS panel for other, much larger, PCD genes. CONCLUSIONS We present a combination of Sanger sequencing with an NGS panel for known and candidate PCD genes, implemented in a moderate-size national collection of patients. This strategy has proven to be cost-effective, rapid and reliable, and was able to detect the causative gene in two thirds of our PCD patients.
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Affiliation(s)
- Jana Djakow
- Department of Paediatrics, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Czech Republic
| | - Lenka Kramná
- Department of Paediatrics, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Czech Republic
| | - Lenka Dušátková
- Department of Paediatrics, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Czech Republic
| | - Jiří Uhlík
- Department of Histology and Embryology, 2nd Faculty of Medicine, Charles University in Prague, Czech Republic
| | - Juha-Pekka Pursiheimo
- Department of Medical Biochemistry and Genetics, University of Turku, Turku, Finland
| | - Tamara Svobodová
- Department of Paediatrics, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Czech Republic
| | - Petr Pohunek
- Department of Paediatrics, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Czech Republic
| | - Ondřej Cinek
- Department of Paediatrics, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Czech Republic
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13
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Natunen T, Takalo M, Kemppainen S, Leskelä S, Marttinen M, Kurkinen KMA, Pursiheimo JP, Sarajärvi T, Viswanathan J, Gabbouj S, Solje E, Tahvanainen E, Pirttimäki T, Kurki M, Paananen J, Rauramaa T, Miettinen P, Mäkinen P, Leinonen V, Soininen H, Airenne K, Tanzi RE, Tanila H, Haapasalo A, Hiltunen M. Relationship between ubiquilin-1 and BACE1 in human Alzheimer's disease and APdE9 transgenic mouse brain and cell-based models. Neurobiol Dis 2015; 85:187-205. [PMID: 26563932 DOI: 10.1016/j.nbd.2015.11.005] [Citation(s) in RCA: 25] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2015] [Revised: 09/13/2015] [Accepted: 11/07/2015] [Indexed: 11/16/2022] Open
Abstract
Accumulation of β-amyloid (Aβ) and phosphorylated tau in the brain are central events underlying Alzheimer's disease (AD) pathogenesis. Aβ is generated from amyloid precursor protein (APP) by β-site APP-cleaving enzyme 1 (BACE1) and γ-secretase-mediated cleavages. Ubiquilin-1, a ubiquitin-like protein, genetically associates with AD and affects APP trafficking, processing and degradation. Here, we have investigated ubiquilin-1 expression in human brain in relation to AD-related neurofibrillary pathology and the effects of ubiquilin-1 overexpression on BACE1, tau, neuroinflammation, and neuronal viability in vitro in co-cultures of mouse embryonic primary cortical neurons and microglial cells under acute neuroinflammation as well as neuronal cell lines, and in vivo in the brain of APdE9 transgenic mice at the early phase of the development of Aβ pathology. Ubiquilin-1 expression was decreased in human temporal cortex in relation to the early stages of AD-related neurofibrillary pathology (Braak stages 0-II vs. III-IV). There was a trend towards a positive correlation between ubiquilin-1 and BACE1 protein levels. Consistent with this, ubiquilin-1 overexpression in the neuron-microglia co-cultures with or without the induction of neuroinflammation resulted in a significant increase in endogenously expressed BACE1 levels. Sustained ubiquilin-1 overexpression in the brain of APdE9 mice resulted in a moderate, but insignificant increase in endogenous BACE1 levels and activity, coinciding with increased levels of soluble Aβ40 and Aβ42. BACE1 levels were also significantly increased in neuronal cells co-overexpressing ubiquilin-1 and BACE1. Ubiquilin-1 overexpression led to the stabilization of BACE1 protein levels, potentially through a mechanism involving decreased degradation in the lysosomal compartment. Ubiquilin-1 overexpression did not significantly affect the neuroinflammation response, but decreased neuronal viability in the neuron-microglia co-cultures under neuroinflammation. Taken together, these results suggest that ubiquilin-1 may mechanistically participate in AD molecular pathogenesis by affecting BACE1 and thereby APP processing and Aβ accumulation.
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Affiliation(s)
- Teemu Natunen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Mari Takalo
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland; Department of Neurobiology, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Susanna Kemppainen
- Department of Neurobiology, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Stina Leskelä
- Department of Neurobiology, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Mikael Marttinen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Kaisa M A Kurkinen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Juha-Pekka Pursiheimo
- Department of Medical Biochemistry and Genetics, Institute of Biomedicine, Turku, Finland
| | - Timo Sarajärvi
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Jayashree Viswanathan
- Institute of Clinical Medicine - Neurology, University of Eastern Finland, Kuopio, Finland
| | - Sami Gabbouj
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Eino Solje
- Institute of Clinical Medicine - Neurology, University of Eastern Finland, Kuopio, Finland
| | - Eveliina Tahvanainen
- Institute of Clinical Medicine - Neurology, University of Eastern Finland, Kuopio, Finland
| | - Tiina Pirttimäki
- Department of Neurobiology, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Mitja Kurki
- Neurosurgery sIA Group, Kuopio University Hospital, Kuopio, Finland
| | - Jussi Paananen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Tuomas Rauramaa
- Department of Pathology, Kuopio University Hospital, Kuopio, Finland; Institute of Clinical Medicine - Pathology, University of Eastern Finland, Kuopio, Finland
| | - Pasi Miettinen
- Department of Neurobiology, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Petra Mäkinen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Ville Leinonen
- Neurosurgery of NeuroCenter, Kuopio University Hospital, Kuopio, Finland; Neurosurgery of NeuroCenter, University of Eastern Finland, Kuopio, Finland
| | - Hilkka Soininen
- Institute of Clinical Medicine - Neurology, University of Eastern Finland, Kuopio, Finland; Department of Neurology, Kuopio University Hospital, Kuopio, Finland
| | - Kari Airenne
- The Department of Biotechnology and Molecular Medicine, University of Eastern Finland, Kuopio, Finland
| | - Rudolph E Tanzi
- Genetics and Aging Research Unit, Massachusetts General Hospital, Charlestown, Boston, MA 02129, United States; Harvard Medical School, Boston, MA 02129, United States
| | - Heikki Tanila
- Department of Neurobiology, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Annakaisa Haapasalo
- Department of Neurobiology, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland; Department of Neurology, Kuopio University Hospital, Kuopio, Finland.
| | - Mikko Hiltunen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland; Department of Neurology, Kuopio University Hospital, Kuopio, Finland.
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14
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Kramná L, Kolářová K, Oikarinen S, Pursiheimo JP, Ilonen J, Simell O, Knip M, Veijola R, Hyöty H, Cinek O. Gut virome sequencing in children with early islet autoimmunity. Diabetes Care 2015; 38:930-3. [PMID: 25678103 DOI: 10.2337/dc14-2490] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [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: 10/21/2014] [Accepted: 01/06/2015] [Indexed: 02/03/2023]
Abstract
OBJECTIVE This study used next-generation sequencing (NGS) technologies to characterize the gut virome at the onset of islet autoimmunity. RESEARCH DESIGN AND METHODS We conducted a case-control study nested within the Finnish Diabetes Prediction and Prevention (DIPP) cohort. The stool virome in 19 case children, who turned islet autoantibody positive before the age of 2 years and later developed clinical type 1 diabetes, and 19 tightly matched control subjects was analyzed using NGS performed from stool samples collected 3, 6, and 9 months before the onset of islet autoimmunity. Human virus findings were verified using real-time PCR. RESULTS One or more human viruses were present in 10.4% and bacteriophages were in 54% of the samples. The virome composition showed no association with islet autoimmunity. NGS was less sensitive and specific than real-time PCR. CONCLUSIONS The present data suggest no dramatic changes in the gut virome shortly before the emergence of islet autoimmunity and emphasize the need of verification of mass sequencing results when viral exposure is assessed in association studies.
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Affiliation(s)
- Lenka Kramná
- Department of Pediatrics, University Hospital Motol, and 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Kateřina Kolářová
- Department of Pediatrics, University Hospital Motol, and 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
| | - Sami Oikarinen
- Department of Virology, School of Medicine, University of Tampere, Tampere, Finland
| | - Juha-Pekka Pursiheimo
- Department of Medical Biochemistry and Genetics, University of Turku, Turku, Finland
| | - Jorma Ilonen
- Department of Immunogenetics, University of Turku, Turku, Finland
| | - Olli Simell
- Department of Pediatrics, Turku University Central Hospital, Turku, Finland
| | - Mikael Knip
- Children's Hospital, University of Helsinki, and Helsinki University Central Hospital, Helsinki, Finland Diabetes and Obesity Research Program, University of Helsinki, Helsinki, Finland Department of Pediatrics, Tampere University Hospital, Tampere, Finland Folklhälsan Research Center, Helsinki, Finland
| | - Riitta Veijola
- Department of Pediatrics, Oulu University Hospital, and University of Oulu, Oulu, Finland
| | - Heikki Hyöty
- Department of Virology, School of Medicine, University of Tampere, Tampere, Finland Fimlab Laboratories, Pirkanmaa Hospital District, Tampere, Finland
| | - Ondrej Cinek
- Department of Pediatrics, University Hospital Motol, and 2nd Faculty of Medicine, Charles University in Prague, Prague, Czech Republic
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15
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16
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Toivonen RK, Emani R, Munukka E, Rintala A, Laiho A, Pietilä S, Pursiheimo JP, Soidinsalo P, Linhala M, Eerola E, Huovinen P, Hänninen A. Fermentable fibres condition colon microbiota and promote diabetogenesis in NOD mice. Diabetologia 2014; 57:2183-92. [PMID: 25031069 DOI: 10.1007/s00125-014-3325-6] [Citation(s) in RCA: 28] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 06/17/2014] [Indexed: 12/16/2022]
Abstract
AIMS/HYPOTHESIS Gut microbiota (GM) and diet both appear to be important in the pathogenesis of type 1 diabetes. Fermentable fibres (FFs), of which there is an ample supply in natural, diabetes-promoting diets, are used by GM as a source of energy. Our aim was to determine whether FFs modify GM and diabetes incidence in the NOD mouse. METHODS Female NOD mice were weaned to a semisynthetic diet and the effects of FF supplementation on diabetes incidence and insulitis were evaluated. Real-time quantitative PCR was employed to determine the effects imposed to gene transcripts in the colon and lymph nodes. Changes to GM were analysed by next-generation sequencing. RESULTS NOD mice fed semisynthetic diets free from FFs were largely protected from diabetes while semisynthetic diets supplemented with the FFs pectin and xylan (PX) resulted in higher diabetes incidence. Semisynthetic diet free from FFs altered GM composition significantly; addition of PX changed the composition of the GM towards that found in natural-diet-fed mice and increased production of FF-derived short-chain fatty acid metabolites in the colon. The highly diabetogenic natural diet was associated with expression of proinflammatory and stress-related genes in the colon, while the semisynthetic diet free from FFs promoted Il4, Il22, Tgfβ and Foxp3 transcripts in the colon and/or pancreatic lymph node. PX in the same diet counteracted these effects and promoted stress-related IL-18 activation in gut epithelial cells. 16S RNA sequencing revealed each diet to give rise to its particular GM composition, with different Firmicutes to Bacteroidetes ratios, and enrichment of mucin-degrading Ruminococcaceae following diabetes-protective FF-free diet. CONCLUSIONS/INTERPRETATION FFs condition microbiota, affect colon homeostasis and are important components of natural, diabetes-promoting diets in NOD mice.
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Affiliation(s)
- Raine K Toivonen
- Department of Medical Microbiology and Immunology, University of Turku, Kiinamyllynkatu 13, 20520, Turku, Finland,
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17
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Pavicic W, Nieminen TT, Gylling A, Pursiheimo JP, Laiho A, Gyenesei A, Järvinen HJ, Peltomäki P. Promoter-specific alterations of APC are a rare cause for mutation-negative familial adenomatous polyposis. Genes Chromosomes Cancer 2014; 53:857-64. [PMID: 24946964 DOI: 10.1002/gcc.22197] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Revised: 06/04/2014] [Accepted: 06/05/2014] [Indexed: 12/30/2022] Open
Abstract
n familial adenomatous polyposis (FAP), 20% of classical and 70% of attenuated/atypical (AFAP) cases remain mutation-negative after routine testing; yet, allelic expression imbalance may suggest an APC alteration. Our aim was to determine the proportion of families attributable to genetic or epigenetic changes in the APC promoter region. We studied 51 unrelated families/cases (26 with classical FAP and 25 with AFAP) with no point mutations in the exons and exon/intron borders and no rearrangements by multiplex ligation-dependent probe amplification (MLPA, P043-B1). Promoter-specific events of APC were addressed by targeted resequencing, MLPA (P043-C1), methylation-specific MLPA, and Sanger sequencing of promoter regions. A novel 132-kb deletion encompassing the APC promoter 1B and upstream sequence occurred in a classical FAP family with allele-specific APC expression. No promoter-specific point mutations or hypermethylation were present in any family. In conclusion, promoter-specific alterations are a rare cause for mutation-negative FAP (1/51, 2%). The frequency and clinical correlations of promoter 1B deletions are poorly defined. This investigation provides frequencies of 1/26 (4%) for classical FAP, 0/25 (0%) for AFAP, and 1/7 (14%) for families with allele-specific expression of APC. Clinically, promoter 1B deletions may associate with classical FAP without extracolonic manifestations.
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Affiliation(s)
- Walter Pavicic
- Department of Medical Genetics, Haartman Institute, University of Helsinki, Helsinki, Finland; Laboratorio de Citogenética y Mutagénesis, Instituto Multidisciplinario de Biología Celular (IMBICE-CONICET-CICPBA), La Plata, Argentina
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18
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Halimaa P, Lin YF, Ahonen VH, Blande D, Clemens S, Gyenesei A, Häikiö E, Kärenlampi SO, Laiho A, Aarts MGM, Pursiheimo JP, Schat H, Schmidt H, Tuomainen MH, Tervahauta AI. Gene expression differences between Noccaea caerulescens ecotypes help to identify candidate genes for metal phytoremediation. Environ Sci Technol 2014; 48:3344-53. [PMID: 24559272 DOI: 10.1021/es4042995] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Populations of Noccaea caerulescens show tremendous differences in their capacity to hyperaccumulate and hypertolerate metals. To explore the differences that could contribute to these traits, we undertook SOLiD high-throughput sequencing of the root transcriptomes of three phenotypically well-characterized N. caerulescens accessions, i.e., Ganges, La Calamine, and Monte Prinzera. Genes with possible contribution to zinc, cadmium, and nickel hyperaccumulation and hypertolerance were predicted. The most significant differences between the accessions were related to metal ion (di-, trivalent inorganic cation) transmembrane transporter activity, iron and calcium ion binding, (inorganic) anion transmembrane transporter activity, and antioxidant activity. Analysis of correlation between the expression profile of each gene and the metal-related characteristics of the accessions disclosed both previously characterized (HMA4, HMA3) and new candidate genes (e.g., for nickel IRT1, ZIP10, and PDF2.3) as possible contributors to the hyperaccumulation/tolerance phenotype. A number of unknown Noccaea-specific transcripts also showed correlation with Zn(2+), Cd(2+), or Ni(2+) hyperaccumulation/tolerance. This study shows that N. caerulescens populations have evolved great diversity in the expression of metal-related genes, facilitating adaptation to various metalliferous soils. The information will be helpful in the development of improved plants for metal phytoremediation.
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Affiliation(s)
- Pauliina Halimaa
- Department of Biology, University of Eastern Finland , P.O. Box 1627, Kuopio, 70210, Finland
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19
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Natunen T, Martiskainen H, Sarajärvi T, Helisalmi S, Pursiheimo JP, Viswanathan J, Laitinen M, Mäkinen P, Kauppinen T, Rauramaa T, Leinonen V, Alafuzoff I, Haapasalo A, Soininen H, Hiltunen M. Effects of NR1H3 genetic variation on the expression of liver X receptor α and the progression of Alzheimer's disease. PLoS One 2013; 8:e80700. [PMID: 24278306 PMCID: PMC3835410 DOI: 10.1371/journal.pone.0080700] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [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: 09/09/2013] [Accepted: 10/16/2013] [Indexed: 01/19/2023] Open
Abstract
Alzheimer's disease (AD) has been postulated to involve defects in the clearance of amyloid-β (Aβ). Activation of liver X receptor α (LXRα) increases the expression of apolipoprotein E (ApoE) as well as cholesterol transporters ABCA1 and ABCG1, leading to augmented clearance of Aβ. We have previously shown that the C allele of rs7120118 in the NR1H3 gene encoding LXRα reduces the risk of AD. Here, we wanted to assess whether the rs7120118 variation affects the progression of AD and modulates the expression of NR1H3 and its downstream targets APOE, ABCA1 and ABCG1.We utilized tissue samples from the inferior temporal cortex of 87 subjects, which were subdivided according to Braak staging into mild, moderate and severe AD groups on the basis of AD-related neurofibrillary pathology. APOE ε4 allele increased soluble Aβ42 levels in the tissue samples in a dose-dependent manner, but did not affect the expression status of APOE. In contrast, the CC genotype of rs7120118 was underrepresented in the severe group, although this result did not reach statistical significance. Also, patients with the CC genotype of rs7120118 showed significantly decreased soluble Aβ42 levels as compared to the patients with TT genotype. Although the severity of AD did not affect NR1H3 expression, the mRNA levels of NR1H3 among the patients with CT genotype of rs7120118 were significantly increased as compared to the patients with TT genotype. These results suggest that genetic variation in NR1H3 modulates the expression of LXRα and the levels of soluble Aβ42.
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Affiliation(s)
- Teemu Natunen
- Institute of Clinical Medicine – Neurology, University of Eastern Finland and Department of Neurology, Kuopio University Hospital, Kuopio, Finland
| | - Henna Martiskainen
- Institute of Clinical Medicine – Neurology, University of Eastern Finland and Department of Neurology, Kuopio University Hospital, Kuopio, Finland
| | - Timo Sarajärvi
- Institute of Clinical Medicine – Neurology, University of Eastern Finland and Department of Neurology, Kuopio University Hospital, Kuopio, Finland
| | - Seppo Helisalmi
- Institute of Clinical Medicine – Neurology, University of Eastern Finland and Department of Neurology, Kuopio University Hospital, Kuopio, Finland
| | | | - Jayashree Viswanathan
- Institute of Clinical Medicine – Neurology, University of Eastern Finland and Department of Neurology, Kuopio University Hospital, Kuopio, Finland
| | - Marjo Laitinen
- Institute of Clinical Medicine – Neurology, University of Eastern Finland and Department of Neurology, Kuopio University Hospital, Kuopio, Finland
| | - Petra Mäkinen
- Institute of Clinical Medicine – Neurology, University of Eastern Finland and Department of Neurology, Kuopio University Hospital, Kuopio, Finland
| | - Tarja Kauppinen
- Institute of Clinical Medicine – Neurology, University of Eastern Finland and Department of Neurology, Kuopio University Hospital, Kuopio, Finland
| | - Tuomas Rauramaa
- Department of Pathology, Kuopio University Hospital, Finland and Institute of Clinical Medicine, Unit of Pathology, University of Eastern Finland, Kuopio, Finland
| | - Ville Leinonen
- Institute of Clinical Medicine – Neurosurgery, University of Eastern Finland and Neurosurgery of NeuroCenter, Kuopio University Hospital, Kuopio, Finland
| | - Irina Alafuzoff
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Annakaisa Haapasalo
- Institute of Clinical Medicine – Neurology, University of Eastern Finland and Department of Neurology, Kuopio University Hospital, Kuopio, Finland
| | - Hilkka Soininen
- Institute of Clinical Medicine – Neurology, University of Eastern Finland and Department of Neurology, Kuopio University Hospital, Kuopio, Finland
| | - Mikko Hiltunen
- Institute of Clinical Medicine – Neurology, University of Eastern Finland and Department of Neurology, Kuopio University Hospital, Kuopio, Finland
- * E-mail:
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20
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Närvä E, Pursiheimo JP, Laiho A, Rahkonen N, Emani MR, Viitala M, Laurila K, Sahla R, Lund R, Lähdesmäki H, Jaakkola P, Lahesmaa R. Continuous hypoxic culturing of human embryonic stem cells enhances SSEA-3 and MYC levels. PLoS One 2013; 8:e78847. [PMID: 24236059 PMCID: PMC3827269 DOI: 10.1371/journal.pone.0078847] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [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: 04/11/2013] [Accepted: 09/16/2013] [Indexed: 12/29/2022] Open
Abstract
Low oxygen tension (hypoxia) contributes critically to pluripotency of human embryonic stem cells (hESCs) by preventing spontaneous differentiation and supporting self-renewal. However, it is not well understood how hESCs respond to reduced oxygen availability and what are the molecular mechanisms maintaining pluripotency in these conditions. In this study we characterized the transcriptional and molecular responses of three hESC lines (H9, HS401 and HS360) on short (2 hours), intermediate (24 hours) and prolonged (7 days) exposure to low oxygen conditions (4% O2). In response to prolonged hypoxia the expression of pluripotency surface marker SSEA-3 was increased. Furthermore, the genome wide gene-expression analysis revealed that a substantial proportion (12%) of all hypoxia-regulated genes in hESCs, were directly linked to the mechanisms controlling pluripotency or differentiation. Moreover, transcription of MYC oncogene was induced in response to continuous hypoxia. At the protein level MYC was stabilized through phosphorylation already in response to a short hypoxic exposure. Total MYC protein levels remained elevated throughout all the time points studied. Further, MYC protein expression in hypoxia was affected by silencing HIF2α, but not HIF1α. Since MYC has a crucial role in regulating pluripotency we propose that induction of sustained MYC expression in hypoxia contributes to activation of transcriptional programs critical for hESC self-renewal and maintenance of enhanced pluripotent state.
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Affiliation(s)
- Elisa Närvä
- Turku Centre for Biotechnology, Turku University and Åbo Akademi University, Turku, Finland
| | - Juha-Pekka Pursiheimo
- Turku Centre for Biotechnology, Turku University and Åbo Akademi University, Turku, Finland
| | - Asta Laiho
- Turku Centre for Biotechnology, Turku University and Åbo Akademi University, Turku, Finland
| | - Nelly Rahkonen
- Turku Centre for Biotechnology, Turku University and Åbo Akademi University, Turku, Finland
| | - Maheswara Reddy Emani
- Turku Centre for Biotechnology, Turku University and Åbo Akademi University, Turku, Finland
| | - Miro Viitala
- Turku Centre for Biotechnology, Turku University and Åbo Akademi University, Turku, Finland
| | - Kirsti Laurila
- Turku Centre for Biotechnology, Turku University and Åbo Akademi University, Turku, Finland
- Department of Information and Computer Science at Aalto University School of Science, Espoo, Finland
| | - Roosa Sahla
- Turku Centre for Biotechnology, Turku University and Åbo Akademi University, Turku, Finland
- Department of Information and Computer Science at Aalto University School of Science, Espoo, Finland
| | - Riikka Lund
- Turku Centre for Biotechnology, Turku University and Åbo Akademi University, Turku, Finland
| | - Harri Lähdesmäki
- Turku Centre for Biotechnology, Turku University and Åbo Akademi University, Turku, Finland
- Department of Information and Computer Science at Aalto University School of Science, Espoo, Finland
| | - Panu Jaakkola
- Turku Centre for Biotechnology, Turku University and Åbo Akademi University, Turku, Finland
- Department of Oncology and Radiotherapy, Turku University Hospital, Turku, Finland
| | - Riitta Lahesmaa
- Turku Centre for Biotechnology, Turku University and Åbo Akademi University, Turku, Finland
- * E-mail:
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21
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Kämäläinen A, Viswanathan J, Natunen T, Helisalmi S, Kauppinen T, Pikkarainen M, Pursiheimo JP, Alafuzoff I, Kivipelto M, Haapasalo A, Soininen H, Herukka SK, Hiltunen M. GRN variant rs5848 reduces plasma and brain levels of granulin in Alzheimer's disease patients. J Alzheimers Dis 2013; 33:23-7. [PMID: 22890097 DOI: 10.3233/jad-2012-120946] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Genetic variants in the granulin (GRN) gene have been shown to increase the risk of Alzheimer's disease (AD). Here, we report that the A allele of rs5848 in GRN reduces plasma granulin levels in a dose-dependent manner in a clinically-defined AD sample cohort. Similarly, the mRNA levels of granulin were decreased with respect to A allele of rs5848 in the inferior temporal cortex of neuropathologically confirmed AD patients. Our findings suggest that the A allele of rs5848 is functionally relevant by reducing the expression of granulin.
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Affiliation(s)
- Anna Kämäläinen
- Institute of Clinical Medicine - Neurology, University of Eastern Finland, Kuopio, Finland
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22
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Natunen T, Parrado AR, Helisalmi S, Pursiheimo JP, Sarajärvi T, Mäkinen P, Kurkinen KM, Mullin K, Alafuzoff I, Haapasalo A, Bertram L, Soininen H, Tanzi RE, Hiltunen M. Elucidation of the BACE1 Regulating Factor GGA3 in Alzheimer's Disease. ACTA ACUST UNITED AC 2013; 37:217-32. [DOI: 10.3233/jad-130104] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Teemu Natunen
- Institute of Clinical Medicine-Neurology, University of Eastern Finland, Kuopio, Finland
| | - Antonio R. Parrado
- Genetics and Aging Research Unit, Massachusetts General Hospital, Charlestown, and Harvard Medical School, Boston, MA, USA
| | - Seppo Helisalmi
- Institute of Clinical Medicine-Neurology, University of Eastern Finland, Kuopio, Finland
| | | | - Timo Sarajärvi
- Institute of Clinical Medicine-Neurology, University of Eastern Finland, Kuopio, Finland
| | - Petra Mäkinen
- Institute of Clinical Medicine-Neurology, University of Eastern Finland, Kuopio, Finland
| | - Kaisa M.A. Kurkinen
- Institute of Clinical Medicine-Neurology, University of Eastern Finland, Kuopio, Finland
| | - Kristina Mullin
- Genetics and Aging Research Unit, Massachusetts General Hospital, Charlestown, and Harvard Medical School, Boston, MA, USA
| | - Irina Alafuzoff
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Annakaisa Haapasalo
- Institute of Clinical Medicine-Neurology, University of Eastern Finland, Kuopio, Finland
| | - Lars Bertram
- Neuropsychiatric Genetics Group, Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Hilkka Soininen
- Institute of Clinical Medicine-Neurology, University of Eastern Finland, Kuopio, Finland
- Department of Neurology, Kuopio University Hospital, Kuopio, Finland
| | - Rudolph E. Tanzi
- Genetics and Aging Research Unit, Massachusetts General Hospital, Charlestown, and Harvard Medical School, Boston, MA, USA
| | - Mikko Hiltunen
- Institute of Clinical Medicine-Neurology, University of Eastern Finland, Kuopio, Finland
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Rantanen K, Pursiheimo JP, Högel H, Miikkulainen P, Sundström J, Jaakkola PM. p62/SQSTM1 regulates cellular oxygen sensing by attenuating PHD3 activity through aggregate sequestration and enhanced degradation. J Cell Sci 2013; 126:1144-54. [PMID: 23345396 DOI: 10.1242/jcs.115667] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The hypoxia-inducible factor (HIF) prolyl hydroxylase PHD3 regulates cellular responses to hypoxia. In normoxia the expression of PHD3 is low and it occurs in cytosolic aggregates. SQSTM1/p62 (p62) recruits proteins into cytosolic aggregates, regulates metabolism and protein degradation and is downregulated by hypoxia. Here we show that p62 determines the localization, expression and activity of PHD3. In normoxia PHD3 interacted with p62 in cytosolic aggregates, and p62 was required for PHD3 aggregation that was lost upon transfer to hypoxia, allowing PHD3 to be expressed evenly throughout the cell. In line with this, p62 enhanced the normoxic degradation of PHD3. Depletion of p62 in normoxia led to elevated PHD3 levels, whereas forced p62 expression in hypoxia downregulated PHD3. The loss of p62 resulted in enhanced interaction of PHD3 with HIF-α and reduced HIF-α levels. The data demonstrate p62 is a critical regulator of the hypoxia response and PHD3 activity, by inducing PHD3 aggregation and degradation under normoxia.
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Affiliation(s)
- Krista Rantanen
- Turku Centre for Biotechnology, Turku University and Åbo Akademi University, Turku, Finland
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24
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Teittinen KJ, Laiho A, Uusimäki A, Pursiheimo JP, Gyenesei A, Lohi O. Expression of small nucleolar RNAs in leukemic cells. Cell Oncol (Dordr) 2012; 36:55-63. [PMID: 23229394 DOI: 10.1007/s13402-012-0113-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/05/2012] [Indexed: 11/25/2022] Open
Abstract
PURPOSE Small nucleolar RNAs (snoRNAs) direct sequence-specific modifications to ribosomal RNA. We hypothesized that the expression of snoRNAs may be altered in leukemic cells. METHODS The expression of snoRNAs was analyzed in various leukemic cell lines by massive parallel sequencing (SOLiD). Quantitative real-time PCR (RT-qPCR) was used to validate the expression profiles. RESULTS Our results show characteristic differences in the expression patterns of snoRNAs between cell lines representing the main subgroups of leukemia, AML, pre-B-ALL and T-ALL, respectively. In RT-qPCR analyses, several snoRNAs were found to be differentially expressed in T-ALL as compared to pre-B-ALL cell lines. CONCLUSIONS snoRNAs are differentially expressed in various leukemic cell lines and could, therefore, be potentially useful in the classification of leukemia subgroups.
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Affiliation(s)
- Kaisa J Teittinen
- Tampere Center for Child Health Research, University of Tampere School of Medicine and Tampere University Hospital, Biokatu, FIN, Tampere, Finland.
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25
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Närvä E, Rahkonen N, Emani MR, Lund R, Pursiheimo JP, Nästi J, Autio R, Rasool O, Denessiouk K, Lähdesmäki H, Rao A, Lahesmaa R. RNA-binding protein L1TD1 interacts with LIN28 via RNA and is required for human embryonic stem cell self-renewal and cancer cell proliferation. Stem Cells 2012; 30:452-60. [PMID: 22162396 DOI: 10.1002/stem.1013] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Human embryonic stem cells (hESC) have a unique capacity to self-renew and differentiate into all the cell types found in human body. Although the transcriptional regulators of pluripotency are well studied, the role of cytoplasmic regulators is still poorly characterized. Here, we report a new stem cell-specific RNA-binding protein L1TD1 (ECAT11, FLJ10884) required for hESC self-renewal and cancer cell proliferation. Depletion of L1TD1 results in immediate downregulation of OCT4 and NANOG. Furthermore, we demonstrate that OCT4, SOX2, and NANOG all bind to the promoter of L1TD1. Moreover, L1TD1 is highly expressed in seminomas, and depletion of L1TD1 in these cancer cells influences self-renewal and proliferation. We show that L1TD1 colocalizes and interacts with LIN28 via RNA and directly with RNA helicase A (RHA). LIN28 has been reported to regulate translation of OCT4 in complex with RHA. Thus, we hypothesize that L1TD1 is part of the L1TD1-RHA-LIN28 complex that could influence levels of OCT4. Our results strongly suggest that L1TD1 has an important role in the regulation of stemness.
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Affiliation(s)
- Elisa Närvä
- Turku Centre for Biotechnology, University of Turku and Åbo Akademi University, Turku, Finland
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26
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Pursiheimo JP, Saari J, Jalkanen M, Salmivirta M. Cooperation of protein kinase A and Ras/ERK signaling pathways is required for AP-1-mediated activation of fibroblast growth factor-inducible response element (FiRE). J Biol Chem 2002; 277:25344-55. [PMID: 12004054 DOI: 10.1074/jbc.m112381200] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Recent studies suggest a crucial role for protein kinase A (PKA) in the regulation of growth factor signaling. However, the effect of PKA on the transcription of growth factor-responsive genes has drawn far less attention. Here we have investigated the signaling mechanisms involved in the activation of an activator protein-1 (AP-1)-driven, growth factor-specific enhancer element, fibroblast growth factor-inducible response element (FiRE). The activation was found to be mediated by three phorbol 12-O-tetradecanoate-13-acetate-response element-related DNA elements of FiRE, including motif 4 and two distinct elements of motif 5 (referred to as M5-1 and M5-2). All three elements were required for full FiRE activity. Stimulation of cells with fibroblast growth factor-2 (FGF-2) induced the binding of AP-1 to motif 4 and M5-2, whereas M5-1 did not show detectable binding. The FGF-2-induced FiRE activation appeared to require cooperational function of the Ras/ERK and PKA pathways. Inhibition of either of the pathways abolished the binding of AP-1 complexes to motif 4 and motif 5 and the subsequent FiRE activation. By contrast, costimulation of cells with FGF-2 and the PKA activator 8-bromo-cyclic AMP increased the binding of AP-1 to FiRE and potentiated the level of transcriptional activity. The cooperational function of these two pathways was confirmed by experiments with cell lines stably expressing 4-hydroxytamoxifen-inducible oncogenic Raf-1 (DeltaRaf-1:ER[DD]). Noticeably, the induction systems showed variations with respect to regulation of AP-1-driven activation of FiRE. These differences were likely to originate from the ability of these two systems to induce the differential activation pattern of the Ras/ERK pathway.
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27
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Abstract
Protein kinase A (PKA) has been proposed to regulate the signal transduction through the Ras/extracellular-regulated kinase (ERK) pathway. Here we demonstrate that when the PKA activity was inhibited prior to growth factor stimulus the signal flow through the Ras/ERK pathway was significantly increased. Furthermore, the data indicated that this PKA-mediated regulation was simultaneously targeted to the upstream kinase Raf-1 and to the ERK-specific phosphatase mitogen-activated protein kinase phosphatase-1 (MKP-1). Moreover, our data suggested that the level of PKA activity determined the transcription rate of mkp-1 gene, whereas the Ras/ERK signal was required to protect the MKP-1 protein against degradation. These results point to a tight regulatory relationship between PKA and the growth factor signaling, and further suggest an important role for basal PKA activity in such regulation. We propose that PKA adjusts the activity of the Ras/ERK pathway and maintains it within a physiologically appropriate level.
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Affiliation(s)
- Juha-Pekka Pursiheimo
- Turku Centre for Biotechnology, University of Turku, and Abo Akademi University, Tykistökatu 6B, BioCity, 20520 Turku, Finland.
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28
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Pursiheimo JP, Jalkanen M, Taskén K, Jaakkola P. Involvement of protein kinase A in fibroblast growth factor-2-activated transcription. Proc Natl Acad Sci U S A 2000; 97:168-73. [PMID: 10618389 PMCID: PMC26634 DOI: 10.1073/pnas.97.1.168] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [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] [Indexed: 11/18/2022] Open
Abstract
Polypeptide growth factors activate common signal transduction pathways, yet they can induce transcription of different target genes. The mechanisms that control this specificity are not completely understood. Recently, we have described a fibroblast growth factor (FGF)-inducible response element, FiRE, on the syndecan-1 gene. In NIH 3T3 cells, the FiRE is activated by FGF-2 but not by several other growth factors, such as platelet-derived growth factor or epidermal growth factor, suggesting that FGF-2 activates signaling pathways that diverge from pathways activated by other growth factors. In this paper, we report that the activation of FiRE by FGF-2 requires protein kinase A (PKA) in NIH 3T3 cells. The PKA-specific inhibitor H-89 (N-[2-(p-bromocinnamylamino)ethyl]-5-isoquinolinesulfonamide) blocked the FGF-2-induced activation of FiRE, the transcription of the syndecan-1 gene, and cell proliferation. Also, expression of a dominant-negative form of PKA inhibited the FGF-2-induced FiRE activation and the transcription of the syndecan-1 gene. The binding of activator protein-1 transcription-factor complexes, required for the activation of FiRE, was blocked by inhibition of PKA activity before FGF-2 treatment. In accordance with the growth factor specificity of FiRE, the activity of PKA was stimulated by FGF-2 but not by platelet-derived growth factor or epidermal growth factor. Furthermore, a portion of the PKA catalytic subunit pool was translocated to the nucleus by FGF-2. Noticeably, the total cellular cAMP concentration was not affected by FGF-2 stimulus. We propose that the FGF-2-selective transcriptional activation through FiRE is caused by the ability of FGF-2 to control PKA activity.
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Affiliation(s)
- J P Pursiheimo
- Turku Centre for Biotechnology, University of Turku, Tykistökatu 6B, BioCity, FIN-20520 Turku, Finland
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