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  • 101. Alvarado, C
    et al.
    Alarcon-Riquelme, Marta E.
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Fernández, C
    Participation of Bcl-2 and fas molecules in the apoptosis induced by hyperthermia, dexamethasone and gamma irradiation in splenic B lymphocytes1997In: Rev Invest Clin, Vol. 49, p. 171-Article in journal (Refereed)
  • 102. Alvarez, V
    et al.
    Parussini, F
    Aslund, L
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Cazzulo, JJ
    Expression in insect cells of active mature cruzipain from Trypanosomacruzi, containing its C-terminal domain.2002In: Protein Expr Purif, Vol. 26, p. 467-Article in journal (Refereed)
  • 103. Alvarsson, M
    et al.
    Sundkvist, G
    Lager, I
    Henricsson, M
    Berntorp, K
    Fernqvist-Forbes, E
    Steen, L
    Westermark, G
    Westermark, P
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Örn, T
    Grill, V
    Beneficial effects of insulin versus sulphonylurea on insulin secretion and metabolic control in recently diagnosed type 2 diabetic patients2003In: Diabetes Care, Vol. 26, p. 2231-Article in journal (Refereed)
  • 104. Amarzguioui, M
    et al.
    Mucchiano, G
    Haggqvist, B
    Westermark, P
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Kavlie, A
    Sletten, K
    Prydz, H
    Extensive intimal apolipoprotein A1-derived amyloid deposits in a patient with an apolipoprotein A1 mutation.1998In: Biochem Biophys Res Commun, Vol. 242, p. 534-Article in journal (Refereed)
  • 105. Amberla, Kaarina
    et al.
    Wäljas, Minna
    Tuominen, Susanna
    Almkvist, Ove
    Pöyhönen, Minna
    Tuisku, Seppo
    Kalimo, Hannu
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology. Patologi/neuropatologi.
    Viitanen, Matti
    Insidious cognitive decline in CADASIL.2004In: Stroke, ISSN 1524-4628, Vol. 35, no 7, p. 1598-602Article in journal (Refereed)
  • 106.
    Ameur, Adam
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
    Rada-Iglesias, Alvaro
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
    Komorowski, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
    Wadelius, Claes
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Identification of candidate regulatory SNPs by combination of transcription-factor-binding site prediction, SNP genotyping and haploChIP2009In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 37, no 12, p. e85-Article in journal (Refereed)
    Abstract [en]

    Disease-associated SNPs detected in large-scale association studies are   frequently located in non-coding genomic regions, suggesting that they may be involved in transcriptional regulation. Here we describe a new strategy for detecting regulatory SNPs (rSNPs), by combining   computational and experimental approaches. Whole genome ChIP-chip data   for USF1 was analyzed using a novel motif finding algorithm called   BCRANK. 1754 binding sites were identified and 140 candidate rSNPs were   found in the predicted sites. For validating their regulatory function,   seven SNPs found to be heterozygous in at least one of four human cell   samples were investigated by ChIP and sequence analysis (haploChIP). In   four of five cases where the SNP was predicted to affect binding, USF1   was preferentially bound to the allele containing the consensus motif.   Allelic differences in binding for other proteins and histone marks   further reinforced the SNPs regulatory potential. Moreover, for one of   these SNPs, H3K36me3 and POLR2A levels at neighboring heterozygous SNPs   indicated effects on transcription. Our strategy, which is entirely   based on in vivo data for both the prediction and validation steps, can   identify individual binding sites at base pair resolution and predict   rSNPs. Overall, this approach can help to pinpoint the causative SNPs   in complex disorders where the associated haplotypes are located in regulatory regions. Availability: BCRANK is available from Bioconductor  (http://www.bioconductor.org).

  • 107.
    Ameur, Adam
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology, Genomics.
    Wetterbom, Anna
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Feuk, Lars
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology, Genomics.
    Gyllensten, Ulf
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Global and unbiased detection of splice junctions from RNA-seq data2010In: Genome Biology, ISSN 1474-760X, Vol. 11, no 3, p. R34-Article in journal (Refereed)
    Abstract [en]

    We have developed a new strategy for de novo prediction of splice junctions in short-read RNA-seq data, suitable for detection of novel splicing events and chimeric transcripts. When tested on mouse RNA-seq data, > 31,000 splice events were predicted, of which 88% bridged between two regions separated by <= 100 kb, and 74% connected two exons of the same RefSeq gene. Our method also reports genomic rearrangements such as insertions and deletions.

  • 108.
    Amini, Hashem
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health, Obstetrics and Gynaecology.
    Antonsson, Per
    Papadogiannakis, Nikos
    Ericson, Katharina
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Pilo, Christina
    Eriksson, Lars
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Westgren, Magnus
    Axelsson, Ove
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health, Obstetrics and Gynaecology.
    Comparison of ultrasound and autopsy findings in pregnancies terminated due to fetal anomalies2006In: Acta Obstetricia et Gynecologica Scandinavica, ISSN 0001-6349, E-ISSN 1600-0412, Vol. 85, no 10, p. 1208-1216Article in journal (Refereed)
    Abstract [en]

    Objective. To compare antenatal diagnoses with autopsy findings in pregnancies terminated after ultrasound detection of fetal anomalies. A second aim was to study the quality of antenatal fetal diagnosis over time. Design. Retrospective, multicenter study over two consecutive six-year periods in Uppsala and Stockholm. Setting. Cases were identified through fetal autopsy reports. Subjects. Three hundred and twenty-eight fetuses from pregnancies terminated between 1992 and 2003 because of ultrasonographically diagnosed anomalies. Main outcome measures. The findings at the last ultrasound examination were compared with the autopsy reports. Results. In 299 cases (91.2%) ultrasound findings either exactly matched or were essentially similar to the autopsy findings. In 23 cases (7%) ultrasound findings were not confirmed at autopsy, but the postnatal findings were at least as severe as the antenatal ones. In six cases (1.8%) termination was performed for an anomaly which proved to be less severe than was predicted by ultrasound. The number of such cases was the same in both six-year periods, while the total number of cases increased from 113 in the first to 215 in the second period. Fetal examination provided further diagnostic information in 47% of the cases. In 10% a syndrome was disclosed. Conclusion. Termination of pregnancy was not always based on a correct antenatal diagnosis. All fetuses but one from terminated pregnancies had evident anomalies. In six cases (1.8%) the decision to terminate was based on suboptimal prognostic and diagnostic information. Fetal autopsy by an experienced perinatal pathologist is essential to provide a definitive diagnosis.

  • 109.
    Amini, Hashem
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health.
    Axelsson, Ove
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Women's and Children's Health.
    Ollars, Birgitta
    Swedish Birth Defects Registry, National Board of Health and Welfare, Stockholm, Sweden.
    Annerén, Göran
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    The Swedish Birth Defects Registry: ascertainment and incidence of spina bifida and cleft lip/palate2009In: Acta Obstetricia et Gynecologica Scandinavica, ISSN 0001-6349, E-ISSN 1600-0412, Vol. 88, no 6, p. 654-659Article in journal (Refereed)
    Abstract [en]

    OBJECTIVES: To assess the ascertainment of spina bifida and cleft lip/palate (CLP) in newborns and in fetuses from terminated pregnancies (ToPs) in the Swedish Birth Defects Registry (BDR) and to estimate the true incidences of these two anomalies. DESIGN: Retrospective register study. SETTING: Center for Epidemiology at the Swedish National Board of Health and Welfare, and Uppsala University Hospital. POPULATION: Newborns and fetuses from ToPs with spina bifida (1999-2004) and CLP (1999-2002) in Sweden. METHODS: Data from four registries/sources were used to estimate ascertainment in BDR and incidences of spina bifida and CLP. Main outcome measure: Ascertainment, under-ascertainment, and true incidence. RESULTS: For newborns, under-ascertainment of spina bifida and CLP were 6 and 13%, respectively, in BDR after record linkage with the Medical Birth Registry. Ascertainment of cleft palate increased when accompanied by cleft lip. The under-ascertainment of spina bifida in ToPs after 18 gestational weeks was 27%. Ascertainment of CLP in all ToPs and of spina bifida in ToPs before the 18th gestational week could not be estimated. The majority (109/155, 70%) of ToPs with spina bifida occurred before the 18th week. The estimated incidence of spina bifida per 10,000 births was 6.1 (2.4 newborns and 3.7 ToPs) and of CLP 20.1 (18.9 newborns and 1.2 ToPs). CONCLUSION: The ascertainments are relatively high for newborns in BDR, but lower or unknown for ToPs, which has an impact on the surveillance of spina bifida in view of the high proportion of ToPs.

  • 110.
    Amini, RM
    et al.
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Enblad, G
    Department of Oncology, Radiology and Clinical Immunology.
    Engstrom, P
    Christensson, B
    Glimelius, B
    Department of Oncology, Radiology and Clinical Immunology.
    Sundstrom, C
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Relapsed Hodgkin's lymphoma: immunostaining patterns in relation tosurvival.2002In: Leuk Lymphoma, Vol. 43, p. 1253-Article in journal (Refereed)
  • 111.
    Amini, R-M
    et al.
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Oncology, Radiology and Clinical Immunology.
    Enblad, G
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Oncology, Radiology and Clinical Immunology.
    Sundstrom, C
    Department of Genetics and Pathology.
    Glimelis, B
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Oncology, Radiology and Clinical Immunology.
    Patients suffering from both Hodgkin´s disease (HD) and non-Hodgkin lymphomas (NHL). A clinico-pathological and immunohistochemical populatio-based study of 32 patients.1997In: Int J Cancer, Vol. 71, p. 510-Article in journal (Refereed)
  • 112. Amini, RM
    et al.
    Enblad, G
    Sundstrom, C
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Glimelius, B
    Patients suffereing from both Hodgkin's disease and non-Hodgkin's lymphoma: a clinico-pathological and immuno-histchemical population-based study of 32 patients.1997In: Int J Cancer, Vol. 71, p. 10-Article in journal (Refereed)
  • 113.
    Amini, RM
    et al.
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Enblad, Gunilla
    Department of Oncology, Radiology and Clinical Immunology.
    Relationship between Hodgkin's and non-Hodgkin's lymphomas.2003In: Med Oncol, Vol. 20, p. 211-Article in journal (Refereed)
  • 114.
    Amini, Rose-Marie
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Aaltonen, Kirsimari
    Nevanlinna, Heli
    Carvalho, Ricardo
    Salonen, Laura
    Heikkilä, Päivi
    Blomqvist, Carl
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Oncology, Radiology and Clinical Immunology.
    Mast cells and eosinophils in invasive breast carcinoma2007In: BMC Cancer, ISSN 1471-2407, E-ISSN 1471-2407, Vol. 7, p. 165-Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Inflammatory cells in the tumour stroma has gained increasing interest recently. Thus, we aimed to study the frequency and prognostic impact of stromal mast cells and tumour infiltrating eosinophils in invasive breast carcinomas. METHODS: Tissue microarrays containing 234 cases of invasive breast cancer were prepared and analysed for the presence of stromal mast cells and eosinophils. Tumour infiltrating eosinophils were counted on hematoxylin-eosin slides. Immunostaining for tryptase was done and the total number of mast cells were counted and correlated to the proliferation marker Ki 67, positivity for estrogen and progesterone receptors, clinical parameters and clinical outcome. RESULTS: Stromal mast cells were found to correlate to low grade tumours and estrogen receptor positivity. There was a total lack of eosinophils in breast cancer tumours. CONCLUSION: A high number of mast cells in the tumours correlated to low-grade tumours and estrogen receptor positivity. Eosinophils are not tumour infiltrating in breast cancers.

  • 115.
    Amini, Rose-Marie
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Oncology, Radiology and Clinical Immunology.
    Berglund, Mattias
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Oncology, Radiology and Clinical Immunology.
    Rosenquist, Richard
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Oncology, Radiology and Clinical Immunology.
    von Heideman, Anne
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Oncology, Radiology and Clinical Immunology.
    Lagercrantz, Svetlana
    Thunberg, Ulf
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Oncology, Radiology and Clinical Immunology.
    Bergh, Jonas
    Sundström, Christer
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Glimelius, Bengt
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Oncology, Radiology and Clinical Immunology.
    Enblad, Gunilla
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Oncology, Radiology and Clinical Immunology.
    A novel B-cell line (U-2932) established from a patient with a diffuse large B-cell lymphoma following Hodgkin lymphoma2002In: Leukemia and Lymphoma, ISSN 1042-8194, E-ISSN 1029-2403, Vol. 43, no 11, p. 2179-2189Article in journal (Refereed)
    Abstract [en]

    Little is known about mechanisms leading to secondary non-Hodgkin lymphomas (NHL) in patients treated for Hodgkin lymphoma (HL). Our aim was to characterise in detail a cell line derived from a diffuse large B-cell lymphoma (DLBCL) that had developed in a patient with relapsing HL. The cell line U-2932 was established from ascites in a patient suffering from DLBCL previously treated for HL with multiple chemotherapy regimens. Characterisation was based on morphology, immunophenotype, Epstein-Barr virus (EBV)-status, IgH gene rearrangement status, tumourigenicity, p53 sequencing, and immunohistochemical expression of p53, BCL-2 and BCL-6. The karyotype was investigated using G-banding, comparative genomic hybridisation (CGH) and spectral karyotype (SKY) analysis. This cell line shows typical morphological features of a DLBCL and grows as colonies in nude mice. It expresses a B-cell phenotype with a somatically hypermutated V(H)4-39 gene and is negative for EBV. The origin of U-2932 was confirmed by demonstrating an identical V(H)4 rearrangement in ascites from the patient. A point mutation of the tumour-suppressor gene p53 was detected in amino acid position 176 and immunohistochemical over-expression of the p53 protein was also demonstrated. U-2932 carries a complex karyotype including high-level amplifications of the chromosomal bands 18q21 and 3q27 and expresses aberrant BCL-2 and BCL-6 immunohistochemically. We were unable to investigate the clonal relationship between the original HL and U-2932. In conclusion, U-2932 is a unique B cell line established from a patient suffering from HL followed by NHL. Overexpression of BCL-2, BCL-6 and p53 may play a role in the tumourigenesis and drug resistance. This cell line may become a useful tool to better understand the mechanisms responsible for development of secondary NHL in patients treated for HL.

  • 116.
    Amini, Rose-Marie
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Oncology, Radiology and Clinical Immunology.
    Enblad, Gunilla
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Oncology, Radiology and Clinical Immunology.
    Engström, Peter
    Christensson, Birger
    Glimelius, Bengt
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Oncology, Radiology and Clinical Immunology.
    Sundström, Christer
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Relapsed Hodgkin's lymphoma: immunostaining patterns in relation to survival2002In: Leukemia and Lymphoma, ISSN 1042-8194, E-ISSN 1029-2403, Vol. 43, no 6, p. 1253-1260Article in journal (Refereed)
    Abstract [en]

    Patients with relapsing Hodgkin's lymphoma (HL) have a rather poor prognosis and mechanisms that lead to resistance to therapy are poorly understood. Our aims were to investigate the immunohistochemical staining patterns of Rb (retinoblastoma protein) and the p53 tumour suppressor protein in HL at initial presentation and at relapse in order to elucidate a possible role in disease progression and resistance to therapy. Further to evaluate the presence and prognostic importance of Epstein-Barr virus (EBV) and anaplastic lymphoma kinase (ALK). Eighty-one cases of relapsing HL were reexamined histopathologically and immunostained for the expression of p53, Rb, ALK and CD30. EBV was detected with LMP-1 stainings and in situ hybridisation for EBER. Clinical data were extracted from the Swedish National Health Care Programme for HL. Median follow-up time was six years (range 0-12) from the date of relapse. The majority of cases were positive for p53 and Rb both at presentation and at relapse, though to a different extent. Both an increase and a decrease in the proportion of stained tumour cells were observed. None of our cases was ALK-positive and 44% were EBV-positive. No specific staining pattern was directly correlated to survival. In 12 patients a switch in HL subtype from diagnosis to relapse was observed and the five-year Hodgkin-specific survival (HLS) was statistically significantly inferior, 37 vs 81% (p = 0.002), in those patients. We found a significant relation between the expression of p53 and EBV at diagnosis and relapse, indicating a clonal relationship. We were unable to find any specific staining pattern of p53 or Rb, affecting survival.

  • 117. Ammerlaan, Anneke C J
    et al.
    De Bustos, Cecilia
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Ararou, Abdelhay
    Buckley, Patrick G
    Mantripragada, Kiran K
    Verstegen, Marco J
    Hulsebos, Theo J M
    Dumanski, Jan P
    Localization of a putative low-penetrance ependymoma susceptibility locus to 22q11 using a chromosome 22 tiling-path genomic microarray2005In: Genes, chromosomes & cancer, ISSN 1045-2257, Vol. 43, no 4, p. 329-38Article in journal (Refereed)
  • 118. Ammerlaan, Anneke C J
    et al.
    de Bustos, Cecilia
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Ararou, Abdelhay
    Buckley, Patrick G
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Mantripragada, Kiran K
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Verstegen, Marco J
    Hulsebos, Theo J M
    Dumanski, Jan P
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Localization of a putative low-penetrance ependymoma susceptibility locus to 22q11 using a chromosome 22 tiling-path genomic microarray.2005In: Genes Chromosomes Cancer, ISSN 1045-2257, Vol. 43, no 4, p. 329-38Article in journal (Refereed)
  • 119. Anderlid, BM
    et al.
    Schoumans, J
    Anneren, G
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Tapia-Paez, I
    Dumanski, J
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Blennow, E
    Nordenskjold, M
    FISH-mapping of a 100-kb terminal 22q13 deletion.2002In: Hum Genet, Vol. 110, p. 439-Article in journal (Refereed)
  • 120. Anderlid, Britt-Marie
    et al.
    Annerén, Göran
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Blennow, Elisabeth
    Nordenskjöld, Magnus
    Subtelomeric rearrangements detected by FISH in patients with idiopatic mental retardation1999In: Am J Hum Genet, Vol. 65, p. A67-Article, book review (Other scientific)
  • 121.
    Andersson, Ann-Catrin
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Studies on Human Endogenous Retroviruses (HERVs) with Special Focus on ERV32002Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Human endogenous retroviruses (HERVs) represent approximately 7% of the human genome. This investigation was focused on one particular HERV, ERV3, with the main purpose of characterising its gene expression patterns and genomic distribution of ERV3-like sequences. Furthermore, this careful expression study should provide insights into the biological role of HERVs. The impact of HERVs in health and disease is not yet clarified. ERV3 is expressed as three envelope (env) transcripts, of which two also contain a cellular gene, H-plk (human proviral linked Krüppel). ERV3 env expression was mainly investigated at the RNA level. The gene expression of two other HERVs, HERV-K and HERV-E was analysed and compared with ERV3 activity.

    Real-time PCRs were developed and in combination with in situ hybridisation, it was found that ERV3 is expressed in a tissue- and cell-specific way. High levels of ERV3 mRNA (up to six times over Histone3.3) were demonstrated in placenta, sebaceous glands, foetal and adult adrenal glands, brown adipose tissue, corpus luteum, pituitary gland, thymus and testis. In monocytic cells including both normal monocytes and malignant U-937 cells, elevated mRNA levels were observed after retinoic acid (RA)-induced differentiation. ERV3-encoded Env protein was detected in selected cases, one following RA-treatment. In addition, several new ERV3-like sequences were discovered in the human genome.

    ERV3 was found to have conserved open reading frames in contrast to other ERV3-like sequences in the human genome. This suggests that ERV3 may be involved in important cellular processes such as differentiation, cell fusion, immunomodulation and protection against infectious retroviruses. The developed techniques and obtained results will allow further studies of HERV expression to better correlate HERV activity to both normal development and disease.

    List of papers
    1. Elevated levels of the human endogenous retrovirus ERV3 in human sebaceous glands
    Open this publication in new window or tab >>Elevated levels of the human endogenous retrovirus ERV3 in human sebaceous glands
    Show others...
    1996 (English)In: Journal of Investigative Dermatology, ISSN 0022-202X, E-ISSN 1523-1747, Vol. 106, no 1, p. 125-128Article in journal (Refereed) Published
    Abstract [en]

    ERV3 (HERV-R) is a complete human endogenous retrovirus located on the long arm of chromosome 7. Long terminal repeat-envelope (env) gene spliced mRNAs of 9 and 3.5 kb are widely expressed in human tissues and cells, but gag-pol mRNAs have not been found. Furthermore, the env gp70 gene contains an open reading frame throughout its length. The highest expression of ERV3 mRNA detected so far is in placenta and the lowest in choriocarcinoma cell lines. We have previously shown that the human monoblastic cell line U-937 and some normal and neoplastic tissues also express high levels of ERV3 env message by Northern blot analysis; however, this method does not distinguish between mRNA expression in different cell types in tissues. In this report, we have studied the ERV3 mRNA expression in specific cell types of human skin by in situ hybridization. We found high levels expression of ERV3 env mRNA in human sebaceous glands in normal skin and dermoid cysts of the ovary. In all glands, the expression is maximal in the periphery of the lobule and ceases towards the center in the region of characteristic holocrine secretion. Since it is known that the regulation of sebaceous glands is primarily via steroid hormones, particularly androgens, it is possible that expression of ERV3 is hormone dependent.

    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:uu:diva-89897 (URN)10.1111/1523-1747.ep12329612 (DOI)8592062 (PubMedID)
    Available from: 2002-05-10 Created: 2002-05-10 Last updated: 2017-12-14Bibliographically approved
    2. Expression of the endogenous retrovirus ERV3 (HERV-R) during induced monocytic differentiation in the U-937 cell line
    Open this publication in new window or tab >>Expression of the endogenous retrovirus ERV3 (HERV-R) during induced monocytic differentiation in the U-937 cell line
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    1996 (English)In: International Journal of Cancer, ISSN 0020-7136, E-ISSN 1097-0215, Vol. 67, no 3, p. 451-456Article in journal (Refereed) Published
    Abstract [en]

    ERV3 (HERV-R) is a complete human endogenous retrovirus located on the long arm of chromosome 7. LTR-env-gene-spliced mRNA of 9 and 3.5 Kb is widely expressed in human tissues and cells, but gag-pol mRNA has not been found. Further, the env gp70 gene contains an open reading frame throughout its length and its expression has recently been detected as a full-length protein. The highest expression of ERV3 detected so far is in placenta and the lowest in cytotrophoblasts and choriocarcinoma cell lines. In this report we have studied ERV3 mRNA and protein expression in the human monoblastic cell line U-937 during differentiation into monocytes/macrophages. Differentiation of U-937 cells was induced by 1,25a-dihydroxyvitamin D3 (vitD3), retinoic acid (RA), gamma interferon (IFN-gamma) and phorbol-myristate-acetate (PMA-TPA). The expression of ERV3 env mRNA was found to be differentiation-associated, with high expression detected in the late stages of monocytic development. Using TPA, the expression of ERV3 env was detected as 9- and 3.5-kb transcripts by Northern blotting, as mRNA by in situ hybridization and as a cytoplasmic 65-kDa protein by immunofluorescence and Western blots. Low levels of basal expression were found, with up-regulation of both message and protein at 24 to 48 hr after addition of TPA. Induction with vitD3, IFN-gamma and RA produced higher levels of mRNA at earlier time points. It is concluded that the U-937 cell line represents an excellent model system for further studies to study the relationship between ERV3 expression and cellular differentiation.

    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:uu:diva-89898 (URN)10.1002/(SICI)1097-0215(19960729)67:3<451::AID-IJC23>3.0.CO;2-9 (DOI)8707424 (PubMedID)
    Available from: 2002-05-10 Created: 2002-05-10 Last updated: 2017-12-14Bibliographically approved
    3. Developmnental expression of HERV-R (ERV3) and HERV-K in human tissue
    Open this publication in new window or tab >>Developmnental expression of HERV-R (ERV3) and HERV-K in human tissue
    Show others...
    2002 (English)In: Virology, ISSN 0042-6822, E-ISSN 1096-0341, Vol. 297, no 2, p. 220-225Article in journal (Refereed) Published
    Abstract [en]

    The human endogenous retroviruses (HERVs), ERV3 (HERV-R) and HERV-K, are both known to be transcriptionally active in human placenta. In the case of ERV3 there is also indirect evidence for its participation in cellular differentiation. In this study we examined the expression of ERV3 (HERV-R) and HERV-K in human normal fetal tissues by in situ hybridization. The highest level of ERV3 env expression was detected in primitive adrenal cortex. Elevated levels of expression were also found in the following developing tissues: kidneys (tubules), tongue, heart, liver, and central nervous system. Tissue-specific expression was found for HERV-K rec (former cORF) but not for pol/int transcripts. The highest rec expression was found in placenta and levels slightly higher than sense control were found in the rest of the tissues examined. Pol/Int was not possible to quantitate. It appears that ERV3 is expressed in an organ-specific way during embryogenesis and might suggest a possible role in the development and differentiation of human tissues.

    National Category
    Medical and Health Sciences
    Identifiers
    urn:nbn:se:uu:diva-89899 (URN)10.1006/viro.2002.1428 (DOI)12083821 (PubMedID)
    Available from: 2002-05-10 Created: 2002-05-10 Last updated: 2017-12-14Bibliographically approved
    4. ERV3 and related sequences in humans; studies of RNA expression by real-time PCR and in situ hybridisation
    Open this publication in new window or tab >>ERV3 and related sequences in humans; studies of RNA expression by real-time PCR and in situ hybridisation
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-89900 (URN)
    Available from: 2002-05-10 Created: 2002-05-10 Last updated: 2010-01-13Bibliographically approved
    5. ERV3 in relation to cell differentiation in normal and neoplastic monocytes
    Open this publication in new window or tab >>ERV3 in relation to cell differentiation in normal and neoplastic monocytes
    Show others...
    Manuscript (Other academic)
    Identifiers
    urn:nbn:se:uu:diva-89901 (URN)
    Available from: 2002-05-10 Created: 2002-05-10 Last updated: 2010-01-13Bibliographically approved
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  • 122.
    Andersson, Ann-Catrin
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Strömberg, Sara
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Bäckvall, Helena
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Kampf, Caroline
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Uhlén, Mathias
    Wester, Kenneth
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Pontén, Fredrik
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Analysis of protein expression in cell microarrays: A tool for antibody-based proteomics2006In: Journal of Histochemistry and Cytochemistry, ISSN 0022-1554, E-ISSN 1551-5044, Vol. 54, no 12, p. 1413-1423Article in journal (Refereed)
    Abstract [en]

    Tissue microarray (TMA) technology provides a possibility to explore protein expression patterns in a multitude of normal and disease tissues in a high-throughput setting. Although TMAs have been used for analysis of tissue samples, robust methods for studying in vitro cultured cell lines and cell aspirates in a TMA format have been lacking. We have adopted a technique to homogeneously distribute cells in an agarose gel matrix, creating an artificial tissue. This enables simultaneous profiling of protein expression in suspension- and adherent-grown cell samples assembled in a microarray. In addition, the present study provides an optimized strategy for the basic laboratory steps to efficiently produce TMAs. Presented modifications resulted in an improved quality of specimens and a higher section yield compared with standard TMA production protocols. Sections from the generated cell TMAs were tested for immunohistochemical staining properties using 20 well-characterized antibodies. Comparison of immunoreactivity in cultured dispersed cells and corresponding cells in tissue samples showed congruent results for all tested antibodies. We conclude that a modified TIVIA technique, including cell samples, provides a valuable tool for high-throughput analysis of protein expression, and that this technique can be used for global approaches to explore the human proteome.

  • 123.
    Andersson, Ann-Catrin
    et al.
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Svensson, Ann-Catrin
    Rolny, Charlotte
    Andersson, Göran
    Larsson, Erik
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Expression of an endogenous retrovirus ERV (HERV-R) mRNA in normal and neoplastic tissues1998In: Int J of Oncology, Vol. 12, p. 309-Article in journal (Refereed)
  • 124.
    Andersson, Ann-Catrin
    et al.
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Venables, Patrick J W
    Tönjes, Ralf R
    Scherer, Jürgen
    Eriksson, Lars
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Larsson, Erik
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Developmental expression of HERV-R (ERV3) and HERV-K in human tissue.2002In: Virology, ISSN 0042-6822, Vol. 297, no 2, p. 220-5Article in journal (Refereed)
  • 125.
    Andersson, Ann-Catrin
    et al.
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Yun, Zhihong
    Larsson, Erik
    Blomberg, Jonas
    ERV3 and related sequences in humans; studies of RNA expression by real-time PCR and in situ hybridisationManuscript (Other academic)
  • 126.
    Andersson, Ann-Catrin
    et al.
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Yun, Zhihong
    Department of Medical Sciences.
    Sperber, Göran
    Department of Neuroscience.
    Larsson, Erik
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Blomberg, Jonas
    Department of Medical Sciences.
    ERV3 and related sequences in humans: structure and RNA expression.2005In: J Virol, ISSN 0022-538X, Vol. 79, no 14, p. 9270-84Article in journal (Refereed)
  • 127.
    Andersson, Ann-Catrin
    et al.
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Öberg, Fredrik
    Dimberg, Anna
    Blomberg, Jonas
    Larsson, Erik
    ERV3 in relation to cell differentiation in normal and neoplastic monocytesManuscript (Other academic)
  • 128.
    Andersson, Arne
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Cell Biology.
    Bohman, Sara
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Cell Biology.
    Borg, L. A. Håkan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Cell Biology.
    Paulsson, Johan F.
    Schultz, Sebastian W.
    Westermark, Gunilla T.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Cell Biology.
    Westermark, Per
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Amyloid deposition in transplanted human pancreatic islets: a conceivable cause of their long-term failure2008In: Experimental diabetes research, ISSN 1687-5214, Vol. 2008, p. 562985-Article, review/survey (Refereed)
    Abstract [en]

    Following the encouraging report of the Edmonton group, there was a rejuvenation of the islet transplantation field. After that, more pessimistic views spread when long-term results of the clinical outcome were published. A progressive loss of the beta-cell function meant that almost all patients were back on insulin therapy after 5 years. More than 10 years ago, we demonstrated that amyloid deposits rapidly formed in human islets and in mouse islets transgenic for human IAPP when grafted into nude mice. It is, therefore, conceivable to consider amyloid formation as one potential candidate for the long-term failure. The present paper reviews attempts in our laboratories to elucidate the dynamics of and mechanisms behind the formation of amyloid in transplanted islets with special emphasis on the impact of long-term hyperglycemia.

  • 129.
    Andersson, Björn
    et al.
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Lu, Fei
    Muzny, Donna
    Warren, Stephen
    Gibbs, Richard
    Complete sequence of a 38.4-kb human cosmid insert containing the polymorphic marker DXS455 from Xq281995In: DNA Sequence, Vol. 5, p. 219-Article in journal (Refereed)
  • 130.
    Andersson, Björn
    et al.
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Lu, Jing
    Edwards, Kimberly
    Muzny, Donna
    Gibbs, Richard
    A method for 96-well M13 DNA template preparations for large scale DNA sequencing1996In: BioTechniques, Vol. 20, p. 1022-Article in journal (Refereed)
  • 131.
    Andersson, Björn
    et al.
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Lu, Jing
    Shen, Ying
    Wentland, Meredith
    Gibbs, Richard
    Simultaneous shotgun sequencing of multiple cDNA clones1997In: DNA Sequence, Vol. 7, p. 63-Article in journal (Refereed)
  • 132.
    Andersson, Björn
    et al.
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Wentland, Meredith
    Ricafrente, Jennifer
    Liu, Wen
    Gibbs, Richard
    A "double adaptor" method for improved shotgun library construction1996In: Anal. Biochem., Vol. 236, p. 107-Article in journal (Refereed)
  • 133.
    Andersson, Björn
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Åslund, Lena
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Tammi, Martti
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Tran, Ahn-Nhi
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Hoheisel, Jörg D.
    Pettersson, Ulf
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Complete sequence of a 93.4 kb contig from chromosome 3 of Trypanosoma cruzi containing a strand switch region1998In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 8, no 8, p. 809-816Article in journal (Refereed)
    Abstract [en]

    We have initiated large-scale sequencing of the third smallest chromosome of the CL Brener strain of Trypanosoma cruzi and we report here the complete sequence of a contig consisting of three cosmids. This contig covers 93.4 kb and has been found to contain 20-30 novel genes and several repeat elements, including a novel chromosome 3-specific 400-bp repeat sequence. The intergenic sequences were found to be rich in di- and trinucleotide repeats of varying lengths and also contained several known T. cruzi repeat elements. The sequence contains 29 open reading frames (ORFs) longer than 700 bp, the longest being 5157 bp, and a large number of shorter ORFs. Of the long ORFs, seven show homology to known genes in parasites and other organisms, whereas four ORFs were confirmed by sequencing of cDNA clones. Two shorter ORFs were confirmed by a database homology and a cDNA clone, respectively, and one RNA gene was identified. The identified genes include two copies of the gene for alanine-aminotransferase as well as genes for glucose-6-phosphate isomerase, protein kinases and phosphatases, and an ATP synthase subunit. An interesting feature of the sequence was that the genes appear to be organized in two long clusters containing multiple genes on the same strand. The two clusters are transcribed in opposite directions and they are separated by an approximately 20-kb long, relatively GC-rich sequence, that contains two large repetitive elements as well as a pseudogene for cruzipain and a gene for U2snRNA. It is likely that this strand switch region contains one or more regulatory and promoter regions. The reported sequence provides the first insight into the genome organization of T. cruzi and shows the potential of this approach for rapid identification of novel genes. [The sequence data described in this paper have been submitted to the GenBank data library under accession nos. AF052831-AF052833.]

  • 134. Andersson, Cecilia
    et al.
    Henriksson, Sara
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Nilsson, Mats
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy.
    Mirazimi, Ali
    Different localization of CCHFV vRNA compared cRNA during infection as determined by in situ padlock probe detectionManuscript (preprint) (Other academic)
  • 135.
    Andersson, Claes R.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Pharmacology.
    Fryknäs, Mårten
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Pharmacology. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Rickardson, Linda
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Pharmacology.
    Larsson, Rolf
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Pharmacology.
    Isaksson, Anders
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Pharmacology.
    Gustafsson, Mats G.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Pharmacology. Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Signals and Systems Group.
    In vitro drug sensitivity-gene expression correlations involve a tissue of origin dependency2007In: Journal of chemical information and modeling, ISSN 1549-9596, Vol. 47, no 1, p. 239-248Article in journal (Refereed)
    Abstract [en]

    A major concern of chemogenomics is to associate drug activity with biological variables. Several reports have clustered cell line drug activity profiles as well as drug activity-gene expression correlation profiles and noted that the resulting groupings differ but still reflect mechanism of action. The present paper shows that these discrepancies can be viewed as a weighting of drug-drug distances, the weights depending on which cell lines the two drugs differ in.

  • 136.
    Andersson, Claes R.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
    Isaksson, Anders
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Gustafsson, Mats G.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology. Uppsala University, Disciplinary Domain of Science and Technology, Technology, Department of Engineering Sciences, Signal Processing.
    Bayesian detection of periodic mRNA time profiles withouth use of training examples2006In: BMC Bioinformatics, ISSN 1471-2105, E-ISSN 1471-2105, Vol. 7, p. 63-Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Detection of periodically expressed genes from microarray data without use of known periodic and non-periodic training examples is an important problem, e.g. for identifying genes regulated by the cell-cycle in poorly characterised organisms. Commonly the investigator is only interested in genes expressed at a particular frequency that characterizes the process under study but this frequency is seldom exactly known. Previously proposed detector designs require access to labelled training examples and do not allow systematic incorporation of diffuse prior knowledge available about the period time. RESULTS: A learning-free Bayesian detector that does not rely on labelled training examples and allows incorporation of prior knowledge about the period time is introduced. It is shown to outperform two recently proposed alternative learning-free detectors on simulated data generated with models that are different from the one used for detector design. Results from applying the detector to mRNA expression time profiles from S. cerevisiae showsthat the genes detected as periodically expressed only contain a small fraction of the cell-cycle genes inferred from mutant phenotype. For example, when the probability of false alarm was equal to 7%, only 12% of the cell-cycle genes were detected. The genes detected as periodically expressed were found to have a statistically significant overrepresentation of known cell-cycle regulated sequence motifs. One known sequence motif and 18 putative motifs, previously not associated with periodic expression, were also over represented. CONCLUSION: In comparison with recently proposed alternative learning-free detectors for periodic gene expression, Bayesian inference allows systematic incorporation of diffuse a priori knowledge about, e.g. the period time. This results in relative performance improvements due to increased robustness against errors in the underlying assumptions. Results from applying the detector to mRNA expression time profiles from S. cerevisiae include several new findings that deserve further experimental studies.

  • 137. Andersson, L.
    et al.
    Gustavson, K.-H.
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Att klona eller inte klona.1997In: Läkartidningen, Vol. 94, p. 2071-Article in journal (Other scientific)
  • 138.
    Andersson, Robin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
    Bruder, Carl E G
    Piotrowski, Arkadiusz
    Menzel, Uwe
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Nord, Helena
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Sandgren, Johanna
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Surgical Sciences.
    Hvidsten, Torgeir R
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
    de Ståhl, Teresita Diaz
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Dumanski, Jan P
    Komorowski, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
    A Segmental Maximum A Posteriori Approach to Genome-wide Copy Number Profiling2008In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 24, no 6, p. 751-758Article in journal (Other academic)
    Abstract [en]

    MOTIVATION: Copy number profiling methods aim at assigning DNA copy numbers to chromosomal regions using measurements from microarray-based comparative genomic hybridizations. Among the proposed methods to this end, Hidden Markov Model (HMM)-based approaches seem promising since DNA copy number transitions are naturally captured in the model. Current discrete-index HMM-based approaches do not, however, take into account heterogeneous information regarding the genomic overlap between clones. Moreover, the majority of existing methods are restricted to chromosome-wise analysis. RESULTS: We introduce a novel Segmental Maximum A Posteriori approach, SMAP, for DNA copy number profiling. Our method is based on discrete-index Hidden Markov Modeling and incorporates genomic distance and overlap between clones. We exploit a priori information through user-controllable parameterization that enables the identification of copy number deviations of various lengths and amplitudes. The model parameters may be inferred at a genome-wide scale to avoid overfitting of model parameters often resulting from chromosome-wise model inference. We report superior performances of SMAP on synthetic data when compared with two recent methods. When applied on our new experimental data, SMAP readily recognizes already known genetic aberrations including both large-scale regions with aberrant DNA copy number and changes affecting only single features on the array. We highlight the differences between the prediction of SMAP and the compared methods and show that SMAP accurately determines copy number changes and benefits from overlap consideration.

  • 139.
    Andersson, Robin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
    Enroth, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
    Barbacioru, Catalin
    Reddy Bysani, Madhu Sudhan
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Wallerman, Ola
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Tuch, Brian
    Lee, Clarence
    Peckham, Heather
    McKernan, Kevin
    de la Vega, Francisco
    Komorowski, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
    Wadelius, Claes
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Strand-based mixture modeling of nucleosome positioning in HepG2 cells and their regulatory dynamics in response to TGF-beta treatmentManuscript (preprint) (Other academic)
  • 140.
    Andersson, Robin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
    Enroth, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
    Rada-Iglesias, Alvaro
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
    Wadelius, Claes
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Komorowski, Jan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
    Nucleosomes are well positioned in exons and carry characteristic histone modifications2009In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 19, no 10, p. 1732-1741Article in journal (Refereed)
    Abstract [en]

    The genomes of higher organisms are packaged in nucleosomes with functional histone modifications. Until now, genome-wide nucleosome and histone modification studies have focused on transcription start sites (TSSs) where nucleosomes in RNA polymerase II (RNAPII) occupied genes are well positioned and have histone modifications that are characteristic of expression status. Using public data, we here show that there is a higher nucleosome-positioning signal in internal human exons and that this positioning is independent of expression. We observed a similarly strong nucleosome-positioning signal in internal exons of C. elegans. Among the 38 histone modifications analyzed in man, H3K36me3, H3K79me1, H2BK5me1, H3K27me1, H3K27me2 and H3K27me3 had evidently higher signal in internal exons than in the following introns and were clearly related to exon expression. These observations are suggestive of roles in splicing. Thus, exons are not only characterized by their coding capacity but also by their nucleosome organization, which seems evolutionary conserved since it is present in both primates and nematodes.

  • 141. Andersson, S
    et al.
    Alemi, M
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Rylander, E
    Strand, A
    Larsson, B
    Sallstrom, J
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Wilander, E
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Uneven distribution of HPV 16 E6 prototype and variant (L83V) oncoprotein in cervical neoplastic lesions2000In: Brit J Cancer, Vol. 83, p. 307-Article in journal (Refereed)
  • 142. Andersson, S
    et al.
    Hellström, A-C
    Ren, Zhi-Ping
    Wilander, Erik
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology. Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    The carcinogenic role of oncogenic HPV and p53 gene mutation in cervical adenocarcinomas.2006In: Med Oncol, ISSN 1357-0560, Vol. 23, no 1, p. 113-9Article in journal (Refereed)
  • 143. Andersson, S
    et al.
    Rylander, E
    Larsson, B
    Strand , A
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Medical Sciences.
    Silfversvärd, C
    Department of Surgical Sciences.
    Wilander, E
    Department of Genetics and Pathology.
    The role of human papillomavirus in cervical adenocarcinoma carcinogenesis.2001In: Eur J Cancer , Vol. 37, p. 246-Article in journal (Refereed)
  • 144. Andersson, S
    et al.
    Safari, H
    Mints, M
    Lewensohn-Fuchs, I
    Gyllensten, U
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Johansson, B
    Type distribution, viral load and integration status of high-risk human papillomaviruses in pre-stages of cervical cancer (CIN).2005In: Br J Cancer, ISSN 0007-0920, Vol. 92, no 12, p. 2195-200Article in journal (Refereed)
  • 145. Andersson, Sonia
    et al.
    Mints, Miriam
    Sallstrom, Jan
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology. Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Wilander, Erik
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology. Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    The relative distribution of oncogenic types of human papillomavirus in benign, pre-malignant and malignant cervical biopsies. A study with human papillomavirus deoxyribonucleic acid sequence analysis.2005In: Cancer Detect Prev, ISSN 0361-090X, Vol. 29, no 1, p. 37-41Article in journal (Refereed)
  • 146.
    Andersson, T
    et al.
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Medical Sciences.
    Johansson, AG
    Westermark, P
    Department of Genetics and Pathology.
    Lundmark, K
    Vanlig svamp gav ovanlig hudinfektion1999In: Läkartidningen, Vol. 96, p. 4926-Article in journal (Other scientific)
  • 147. Ando, Y
    et al.
    Gustavsson, Å
    Suhr, O
    Ohlsson, P-I
    Terazaki, H
    Obayashi, K
    Yamashita, T
    Ando, E
    Negi, A
    Ando, M
    Westermark, P
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Impact of cysteine (Cys)-conjugation and pH on amyloid formation of wild type and Met30 transthyretin (TTR)1999In: Amyloid and Amyloidosis 1998, Parthenon, New York , 1999, p. 44-Chapter in book (Other scientific)
  • 148.
    Andrae, J
    et al.
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Hansson, I
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Afink, GB
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Nister, M
    Uppsala University, Medicinska vetenskapsområdet, Faculty of Medicine, Department of Genetics and Pathology.
    Platelet-derived growth factor receptor-alpha in ventricular zone cellsand in developing neurons.2001In: Mol Cell Neurosci, Vol. 17, p. 1001-Article in journal (Refereed)
  • 149.
    Andrae, Johanna
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Bongcam-Rudloff, Erik
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Hansson, Inga
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Lendahl, Urban
    Westermark, Bengt
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Nister, Monica
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    A 1.8kb GFAP-promoter fragment is active in specific regions of theembryonic CNS2001In: Mechanisms of Development, ISSN 0925-4773, E-ISSN 1872-6356, Vol. 107, no 1-2, p. 181-5Article in journal (Refereed)
    Abstract [en]

    The intermediate filament glial fibrillary acidic protein (GFAP) constitutes the major cytoskeletal protein in astrocytes (J. Neuroimmunol. 8 (1985) 203) and is traditionally referred to as a specific marker for astrocytes. To identify early glial precursors, we created GFAPpromoter-lacZ transgenic mice, using a 1.8kb 5' fragment of human GFAP. The expression of the transgene was first detected in the neuroepithelium at embryonic day 9.5. It was further found in the ventricular zone of the developing telencephalon, in the cerebellar primordium, trigeminal ganglia, and radial glia. Later, scattered beta-gal+ cells were seen in pons, brain stem and glia limitans. The results indicate that GFAP activity is regulated in a region-specific manner during central nervous system (CNS) development and that the gene is turned on in different cell types independently.

  • 150.
    Andrae, Johanna
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Molander, Catrin
    Smits, Anja
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience, Neurology.
    Funa, Keiko
    Nistér, Monica
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Genetics and Pathology.
    Platelet-derived growth factor-B and -C and active α-receptors in medulloblastoma cells2002In: Biochemical and Biophysical Research Communications - BBRC, ISSN 0006-291X, E-ISSN 1090-2104, Vol. 296, no 3, p. 604-611Article in journal (Refereed)
    Abstract [en]

    The malignant childhood brain tumor medulloblastoma belongs to the group of primitive neuroectodermal tumours (PNETs). Medulloblastomas are thought to arise from remnants of the transient external germinal layer in the cerebellum. Proliferation, differentiation, and motility of cells in the central nervous system are regulated by growth factors, e.g., platelet-derived growth factor (PDGF). Recently, it was shown that higher level of PDGF α-receptor expression is characteristic of metastatic medulloblastomas. We have investigated five medulloblastoma/PNET cell lines and found that the PDGF α-receptor is actively signalling in most of them, an activity most likely driven by endogenously produced PDGF-C. PDGF-C is normally present in cells of the developing external germinal layer and our results are consistent with the idea that medulloblastomas are derived from such cells undergoing early neuronal differentiation. Moreover, the expression of PDGF and its receptors was associated with neuronal characteristics, but not with high levels of c-myc expression in the medullablastoma cells.

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