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Backman S, Botling J, Nord H, Ghosal S, Stålberg P, Juhlin CC, Almlöf J, Sundin A, Zhang L, Moens L, Eriksson B, Welin S, Hellman P, Skogseid B, Pacak K, Mollazadegan K, Åkerström T, Crona J. The Evolutionary History of Metastatic Pancreatic Neuroendocrine Tumours Reveals a Therapy Driven Route to High-Grade Transformation. medRxiv 2024:2024.01.08.24300723. [PMID: 38313278 PMCID: PMC10836126 DOI: 10.1101/2024.01.08.24300723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Tumour evolution with acquisition of more aggressive disease characteristics is a hallmark of disseminated cancer. Metastatic pancreatic neuroendocrine tumours (PanNETs) in particular, show frequent progression from a low/intermediate to a high-grade disease. To understand the molecular mechanisms underlying this phenomenon, we performed multi-omics analysis of 32 longitudinal samples from six metastatic PanNET patients. Following MEN1 inactivation, PanNETs exhibit genetic heterogeneity on both spatial and temporal dimensions with parallel and convergent tumuor evolution involving the ATRX/DAXX and mTOR pathways. Following alkylating chemotherapy treatment, some PanNETs develop mismatch repair deficiency and acquire a hypermutator phenotype. This DNA hypermutation phenotype was only found in cases that also showed transformation into a high-grade PanNET. Overall, our findings contribute to broaden the understanding of metastatic PanNET, and suggests that therapy driven disease evolution is an important hallmark of this disease.
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Tsakonas G, Lewensohn R, Botling J, Ortiz-Villalon C, Micke P, Friesland S, Nord H, Lindskog M, Sandelin M, Hydbring P, Ekman S. An immune gene expression signature distinguishes central nervous system metastases from primary tumours in non-small-cell lung cancer. Eur J Cancer 2020; 132:24-34. [PMID: 32325417 DOI: 10.1016/j.ejca.2020.03.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Revised: 03/08/2020] [Accepted: 03/18/2020] [Indexed: 01/09/2023]
Abstract
BACKGROUND Dissemination of non-small-cell lung cancer (NSCLC) in the central nervous system is a frequent and challenging clinical problem. Systemic or local therapies rarely prolong survival and have modest activity regarding local control. Alterations in gene expression in brain metastasis versus primary tumour may increase aggressiveness and impair therapeutic efforts. METHODS We identified 25 patients with surgically removed NSCLC brain metastases in two different patient cohorts. For 13 of these patients, primary tumour samples were available. Gene expression analysis using the nCounter® PanCancer Immune Profiling gene expression panel (nanoString technologies Inc.) was performed in brain metastases and primary tumour samples. Identification of differentially expressed genes was conducted on normalized data using the nSolver analysis software. RESULTS We compared gene expression patterns in brain metastases with primary tumours. Brain metastasis samples displayed a distinct clustering pattern compared to primary tumour samples with a statistically significant downregulation of genes related to immune response and immune cell activation. Results from KEGG term analysis on differentially expressed genes revealed a concomitant enrichment of multiple KEGG terms associated with the immune system. We identified a 12-gene immune signature that clearly separated brain metastases from primary tumours. CONCLUSIONS We identified a unique gene downregulation pattern in brain metastases compared with primary tumours. This finding may explain the lower intracranial efficacy of systemic therapy, especially immunotherapy, in brain metastasis of patients with NSCLC.
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MESH Headings
- Adenocarcinoma of Lung/genetics
- Adenocarcinoma of Lung/pathology
- Adenocarcinoma of Lung/therapy
- Biomarkers, Tumor/genetics
- Brain Neoplasms/genetics
- Brain Neoplasms/secondary
- Brain Neoplasms/therapy
- Carcinoma, Large Cell/genetics
- Carcinoma, Large Cell/pathology
- Carcinoma, Large Cell/therapy
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/pathology
- Carcinoma, Non-Small-Cell Lung/therapy
- Carcinoma, Squamous Cell/genetics
- Carcinoma, Squamous Cell/pathology
- Carcinoma, Squamous Cell/therapy
- Combined Modality Therapy
- Female
- Follow-Up Studies
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Humans
- Lung Neoplasms/genetics
- Lung Neoplasms/pathology
- Lung Neoplasms/therapy
- Lymphatic Metastasis
- Male
- Middle Aged
- Prognosis
- Small Cell Lung Carcinoma/genetics
- Small Cell Lung Carcinoma/pathology
- Small Cell Lung Carcinoma/therapy
- Transcriptome
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Affiliation(s)
- Georgios Tsakonas
- Thoracic Oncology Center, Karolinska University Hospital, Stockholm, Sweden; Department of Oncology and Pathology, Karolinska Institutet, Visionsgatan 4, 17164 Stockholm, Sweden
| | - Rolf Lewensohn
- Thoracic Oncology Center, Karolinska University Hospital, Stockholm, Sweden; Department of Oncology and Pathology, Karolinska Institutet, Visionsgatan 4, 17164 Stockholm, Sweden
| | - Johan Botling
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala Sweden
| | - Cristian Ortiz-Villalon
- Department of Oncology and Pathology, Karolinska Institutet, Visionsgatan 4, 17164 Stockholm, Sweden
| | - Patrick Micke
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala Sweden
| | - Signe Friesland
- Thoracic Oncology Center, Karolinska University Hospital, Stockholm, Sweden; Department of Oncology and Pathology, Karolinska Institutet, Visionsgatan 4, 17164 Stockholm, Sweden
| | - Helena Nord
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Magnus Lindskog
- Department of Immunology, Genetics and Pathology, Uppsala University/Department of Oncology, Uppsala University Hospital, Sweden
| | - Martin Sandelin
- Department of Medical Sciences, Uppsala University/ Department of Oncology, Uppsala University Hospital, Sweden
| | - Per Hydbring
- Department of Oncology and Pathology, Karolinska Institutet, Visionsgatan 4, 17164 Stockholm, Sweden
| | - Simon Ekman
- Thoracic Oncology Center, Karolinska University Hospital, Stockholm, Sweden; Department of Oncology and Pathology, Karolinska Institutet, Visionsgatan 4, 17164 Stockholm, Sweden.
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Botling J, Nord H, Soderberg A, Micke P, Isaksson J, Smeds P, Moens L. P2.04-67 Comparative Analysis of TMB and Mutations by Comprehensive Genomic Profiling (TSO500) in FFPE NSCLC Samples. J Thorac Oncol 2019. [DOI: 10.1016/j.jtho.2019.08.1572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Cavalli M, Pan G, Nord H, Wallén Arzt E, Wallerman O, Wadelius C. Genetic prevention of hepatitis C virus-induced liver fibrosis by allele-specific downregulation of MERTK. Hepatol Res 2017; 47:826-830. [PMID: 27577861 DOI: 10.1111/hepr.12810] [Citation(s) in RCA: 18] [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: 07/07/2016] [Revised: 08/24/2016] [Accepted: 08/28/2016] [Indexed: 01/02/2023]
Abstract
AIM Infection by hepatitis C virus (HCV) can result in the development of liver fibrosis and may eventually progress into cirrhosis and hepatocellular carcinoma. However, the molecular mechanisms for this process are not fully known. Several genome-wide association studies have been carried out to pinpoint causative variants in HCV-infected patient cohorts, but these variants are usually not the functional ones. The aim of this study was to identify the regulatory single nucleotide polymorphism associated with the risk of HCV-induced liver fibrosis and elucidate its molecular mechanism. METHODS We utilized a bioinformatics approach to identify a non-coding regulatory variant, located in an intron of the MERTK gene, based on differential transcription factor binding between the alleles. We validated the results using expression reporter assays and electrophoresis mobility shift assays. RESULTS Chromatin immunoprecipitation sequencing indicated that transcription factor(s) bind stronger to the A allele of rs6726639. Electrophoresis mobility shift assays supported these findings and suggested that the transcription factor is interferon regulatory factor 1 (IRF1). Luciferase report assays showed lower enhancer activity from the A allele and that IRF1 may act as a repressor. CONCLUSIONS Treatment of hepatitis C with interferon-α results in increased IRF1 levels and our data suggest that this leads to an allele-specific downregulation of MERTK mediated by an allelic effect on the regulatory element containing the functional rs6726639. This variant also shows the hallmarks for being the driver of the genome-wide association studies for reduced risk of liver fibrosis and non-alcoholic fatty liver disease at MERTK.
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Affiliation(s)
- Marco Cavalli
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Gang Pan
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Helena Nord
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Emelie Wallén Arzt
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.,Department of Biosciences and Nutrition, Center for Biosciences, Karolinska Institute, Huddinge, Sweden
| | - Ola Wallerman
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Claes Wadelius
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
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Pan G, Ameur A, Enroth S, Bysani M, Nord H, Cavalli M, Essand M, Gyllensten U, Wadelius C. PATZ1 down-regulates FADS1 by binding to rs174557 and is opposed by SP1/SREBP1c. Nucleic Acids Res 2017; 45:2408-2422. [PMID: 27932482 PMCID: PMC5389558 DOI: 10.1093/nar/gkw1186] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [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: 09/20/2016] [Revised: 11/02/2016] [Accepted: 11/24/2016] [Indexed: 11/14/2022] Open
Abstract
The FADS1 and FADS2 genes in the FADS cluster encode the rate-limiting enzymes in the synthesis of long-chain polyunsaturated fatty acids (LC-PUFAs). Genetic variation in this region has been associated with a large number of diseases and traits many of them correlated to differences in metabolism of PUFAs. However, the causative variants leading to these associations have not been identified. Here we find that the multiallelic rs174557 located in an AluYe5 element in intron 1 of FADS1 is functional and lies within a PATZ1 binding site. The derived allele of rs174557, which is the common variant in most populations, diminishes binding of PATZ1, a transcription factor conferring allele-specific downregulation of FADS1. The PATZ1 binding site overlaps with a SP1 site. The competitive binding between the suppressive PATZ1 and the activating complex of SP1 and SREBP1c determines the enhancer activity of this region, which regulates expression of FADS1.
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Affiliation(s)
- Gang Pan
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 75237, Sweden
| | - Adam Ameur
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 75237, Sweden
| | - Stefan Enroth
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 75237, Sweden
| | - Madhusudhan Bysani
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 75237, Sweden
| | - Helena Nord
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 75237, Sweden
| | - Marco Cavalli
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 75237, Sweden
| | - Magnus Essand
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 75237, Sweden
| | - Ulf Gyllensten
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 75237, Sweden
| | - Claes Wadelius
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala 75237, Sweden
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Cavalli M, Pan G, Nord H, Wallén Arzt E, Wallerman O, Wadelius C. Allele-specific transcription factor binding in liver and cervix cells unveils many likely drivers of GWAS signals. Genomics 2016; 107:248-54. [PMID: 27126307 DOI: 10.1016/j.ygeno.2016.04.006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [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] [Received: 03/22/2016] [Revised: 04/18/2016] [Accepted: 04/24/2016] [Indexed: 12/31/2022]
Abstract
Genome-wide association studies (GWAS) point to regions with associated genetic variants but rarely to a specific gene and therefore detailed knowledge regarding the genes contributing to complex traits and diseases remains elusive. The functional role of GWAS-SNPs is also affected by linkage disequilibrium with many variants on the same haplotype and sometimes in the same regulatory element almost equally likely to mediate the effect. Using ChIP-seq data on many transcription factors, we pinpointed genetic variants in HepG2 and HeLa-S3 cell lines which show a genome-wide significant difference in binding between alleles. We identified a collection of 3713 candidate functional regulatory variants many of which are likely drivers of GWAS signals or genetic difference in expression. A recent study investigated many variants before finding the functional ones at the GALNT2 locus, which we found in our genome-wide screen in HepG2. This illustrates the efficiency of our approach.
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Affiliation(s)
- Marco Cavalli
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Gang Pan
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Helena Nord
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Emelie Wallén Arzt
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Ola Wallerman
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden; Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Claes Wadelius
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
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Cavalli M, Pan G, Nord H, Eriksson N, Wadelius C, Wadelius M. Novel regulatory variant detected on the VKORC1 haplotype that is associated with warfarin dose. Pharmacogenomics 2016; 17:1305-14. [PMID: 26847243 DOI: 10.2217/pgs-2015-0013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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: 02/06/2023] Open
Abstract
AIM Warfarin dose requirement is associated with VKORC1 rs9923231, and we studied whether it is a functional variant. MATERIALS & METHODS We selected variants in linkage disequilibrium with rs9923231 that bind transcription factors in an allele-specific way. Representative haplotypes were cloned or constructed, nuclear protein binding and transcriptional activity were evaluated. RESULTS rs56314408C>T and rs2032915C>T were detected in a liver enhancer in linkage disequilibrium with rs9923231. The rs56314408-rs2032915 C-C haplotype preferentially bound nuclear proteins and had higher transcriptional activity than T-T and the African-specific T-C. A motif for TFAP2A/C was disrupted by rs56314408T. No difference in transcriptional activity was detected for rs9923231G>A. CONCLUSION Our results supported an activating role for rs56314408C, while rs9923231G>A had no evidence of being functional.
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Affiliation(s)
- Marco Cavalli
- Department of Immunology, Genetics & Pathology, & Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Gang Pan
- Department of Immunology, Genetics & Pathology, & Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Helena Nord
- Department of Immunology, Genetics & Pathology, & Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Niclas Eriksson
- Uppsala Clinical Research Center & Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Claes Wadelius
- Department of Immunology, Genetics & Pathology, & Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Mia Wadelius
- Department of Medical Sciences & Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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Cavalli M, Pan G, Nord H, Wadelius C. Looking beyond GWAS: allele-specific transcription factor binding drives the association of GALNT2 to HDL-C plasma levels. Lipids Health Dis 2016; 15:18. [PMID: 26817450 PMCID: PMC4728761 DOI: 10.1186/s12944-016-0183-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 01/15/2016] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Plasma levels of high-density lipoprotein cholesterol (HDL-C) have been associated to cardiovascular disease. The high heritability of HDL-C plasma levels has been an incentive for several genome wide association studies (GWASs) which identified, among others, variants in the first intron of the GALNT2 gene strongly associated to HDL-C levels. However, the lead GWAS SNP associated to HDL-C levels in this genomic region, rs4846914, is located outside of transcription factor (TF) binding sites defined by chromatin immunoprecipitation followed by DNA sequencing (ChIP-seq) experiments in the ENCODE project and is therefore unlikely to be functional. In this study we apply a bioinformatics approach which rely on the premise that ChIP-seq reads can identify allele specific binding of a TF at cell specific regulatory elements harboring allele specific SNPs (AS-SNPs). EMSA and luciferase assays were used to validate the allele specific binding and to test the enhancer activity of the regulatory element harboring the AS-SNP rs4846913 as well as the neighboring rs2144300 which are in high LD with rs4846914. FINDINGS Using luciferase assays we found that rs4846913 and the neighboring rs2144300 displayed allele specific enhancer activity. We propose that an inhibitor binds preferentially to the rs4846913-C allele with an inhibitory boost from the synergistic binding of other TFs at the neighboring SNP rs2144300. These events influence the transcription level of GALNT2. CONCLUSIONS The results suggest that rs4846913 and rs2144300 drive the association to HDL-C plasma levels through an inhibitory regulation of GALNT2 rather than the reported lead GWAS SNP rs4846914.
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Affiliation(s)
- Marco Cavalli
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
| | - Gang Pan
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Helena Nord
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Claes Wadelius
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden.
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Abstract
BACKGROUND ChIP-seq is the method of choice for genome-wide studies of protein-DNA interactions. We describe a new method for ChIP-seq sample preparation, termed lobChIP, where the library reactions are performed on cross-linked ChIP fragments captured on beads. RESULTS The lobChIP method was found both to reduce time and cost and to simplify the processing of many samples in parallel. lobChIP has an early incorporation of barcoded sequencing adaptors that minimizes the risk of sample cross-contamination and can lead to reduced amount of adaptor dimers in the sequencing libraries, while allowing for direct decross-linking and amplification of the sample. CONCLUSIONS With results for histone modifications and transcription factors, we show that lobChIP performs equal to or better than standard protocols and that it makes it possible to go from cells to sequencing ready libraries within a single day.
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Affiliation(s)
- Ola Wallerman
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, BMC, Uppsala University, Box 815, 75108 Uppsala, Sweden ; Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Helena Nord
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, BMC, Uppsala University, Box 815, 75108 Uppsala, Sweden
| | - Madhusudhan Bysani
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, BMC, Uppsala University, Box 815, 75108 Uppsala, Sweden ; Department of Clinical Sciences, CRC, Lund University Diabetes Center, Malmö, Sweden
| | - Lisa Borghini
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, BMC, Uppsala University, Box 815, 75108 Uppsala, Sweden ; Human Genetics, Genome Institute of Singapore, Singapore, Singapore
| | - Claes Wadelius
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, BMC, Uppsala University, Box 815, 75108 Uppsala, Sweden
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Burguière AC, Nord H, von Hofsten J. Alkali-like myosin light chain-1 (myl1) is an early marker for differentiating fast muscle cells in zebrafish. Dev Dyn 2011; 240:1856-63. [PMID: 21674687 DOI: 10.1002/dvdy.22677] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
During myogenesis, muscle precursors become divided into either fast- or slow-twitch fibres, which in the zebrafish occupy distinct domains in the embryo. Genes encoding sarcomeric proteins specific for fast or slow fibres are frequently used as lineage markers. In an attempt to identify and evaluate early definitive markers for cells in the fast-twitch pathway, we analysed genes encoding proteins contributing to the fast sarcomeric structures. The previously uncharacterized zebrafish alkali-like myosin light chain gene (myl1) was found to be expressed exclusively in cells in the fast-twitch pathway initiated at an early stage of fast fibre differentiation. Myl1 was expressed earlier, and in a more fibre type restricted manner, than any of the previously described and frequently used fast myosin light and heavy chain and troponin muscle markers mylz2, mylz3, tnni2, tnnt3a, fMyHC1.3. In summary, this study introduces a novel marker for early differentiating fast muscle cells.
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Affiliation(s)
- A C Burguière
- Umeå Centre for Molecular Medicine, UCMM, Umeå University, Umeå, Sweden
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Sandgren J, Diaz de Ståhl T, Andersson R, Menzel U, Piotrowski A, Nord H, Bäckdahl M, Kiss NB, Brauckhoff M, Komorowski J, Dralle H, Hessman O, Larsson C, Akerström G, Bruder C, Dumanski JP, Westin G. Recurrent genomic alterations in benign and malignant pheochromocytomas and paragangliomas revealed by whole-genome array comparative genomic hybridization analysis. Endocr Relat Cancer 2010; 17:561-79. [PMID: 20410162 DOI: 10.1677/erc-09-0310] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [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] [Indexed: 11/27/2022]
Abstract
Pheochromocytomas and abdominal paragangliomas are adrenal and extra-adrenal catecholamine-producing tumours. They arise due to heritable cancer syndromes, or more frequently occur sporadically due to an unknown genetic cause. The majority of cases are benign, but malignant tumours are observed. Previous comparative genomic hybridization (CGH) and loss of heterozygosity studies have shown frequent deletions of chromosome arms 1p, 3q and 22q in pheochromocytomas. We applied high-resolution whole-genome array CGH on 53 benign and malignant pheochromocytomas and paragangliomas to narrow down candidate regions as well as to identify chromosomal alterations more specific to malignant tumours. Minimal overlapping regions (MORs) were identified on 16 chromosomes, with the most frequent MORs of deletion (> or = 32%) occurring on chromosome arms 1p, 3q, 11p/q, 17p and 22q, while the chromosome arms 1q, 7p, 12q and 19p harboured the most common MORs of gain (> or = 14%). The most frequent MORs (61-75%) in the pheochromocytomas were identified at 1p, and the four regions of common losses encompassed 1p36, 1p32-31, 1p22-21 and 1p13. Tumours that did not show 1p loss generally demonstrated aberrations on chromosome 11. Gain of chromosomal material was significantly more frequent among the malignant cases. Moreover, gain at 19q, trisomy 12 and loss at 11q were positively associated with malignant pheochromocytomas, while 1q gain was commonly observed in the malignant paragangliomas. Our study revealed novel and narrow recurrent chromosomal regions of loss and gain at several autosomes, a prerequisite for identifying candidate tumour suppressor genes and oncogenes involved in the development of adrenal and extra-adrenal catecholamine-producing tumours.
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Affiliation(s)
- Johanna Sandgren
- Department of Surgical Sciences, Uppsala University Hospital Rudbeck Laboratory, Uppsala University, SE-751 85 Uppsala, Sweden.
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Nord H, Segersten U, Sandgren J, Wester K, Busch C, Menzel U, Komorowski J, Dumanski JP, Malmström PU, Díaz de Ståhl T. Focal amplifications are associated with high grade and recurrences in stage Ta bladder carcinoma. Int J Cancer 2010; 126:1390-402. [PMID: 19821490 DOI: 10.1002/ijc.24954] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Urinary bladder cancer is a heterogeneous disease with tumors ranging from papillary noninvasive (stage Ta) to solid muscle infiltrating tumors (stage T2+). The risk of progression and death for the most frequent diagnosed type, Ta, is low, but the high incidence of recurrences has a significant effect on the patients' quality of life and poses substantial costs for health care systems. Consequently, the purpose of this study was to search for predictive factors of recurrence on the basis of genetic profiling. A clinically well characterized cohort of Ta bladder carcinomas, selected by the presence or absence of recurrences, was evaluated by an integrated analysis of DNA copy number changes and gene expression (clone-based 32K, respectively, U133Plus2.0 arrays). Only a few chromosomal aberrations have previously been defined in superficial bladder cancer. Surprisingly, the profiling of Ta tumors with a high-resolution array showed that DNA copy alterations are relatively common in this tumor type. Furthermore, we observed an overrepresentation of focal amplifications within high-grade and recurrent cases. Known (FGFR3, CCND1, MYC, MDM2) and novel candidate genes were identified within the loci. For example, MYBL2, a nuclear transcription factor involved in cell-cycle progression; YWHAB, an antiapoptotic protein; and SDC4, an important component of focal adhesions represent interesting candidates detected within two amplicons on chromosome 20, for which DNA amplification correlated with transcript up-regulation. The observed overrepresentation of amplicons within high-grade and recurrent cases may be clinically useful for the identification of patients who will benefit from a more aggressive therapy.
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Affiliation(s)
- Helena Nord
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-75185 Uppsala, Sweden
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Nord H, Hartmann C, Andersson R, Menzel U, Pfeifer S, Piotrowski A, Bogdan A, Kloc W, Sandgren J, Olofsson T, Hesselager G, Blomquist E, Komorowski J, von Deimling A, Bruder CEG, Dumanski JP, Díaz de Ståhl T. Characterization of novel and complex genomic aberrations in glioblastoma using a 32K BAC array. Neuro Oncol 2010; 11:803-18. [PMID: 19304958 DOI: 10.1215/15228517-2009-013] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Glioblastomas (GBs) are malignant CNS tumors often associated with devastating symptoms. Patients with GB have a very poor prognosis, and despite treatment, most of them die within 12 months from diagnosis. Several pathways, such as the RAS, tumor protein 53 (TP53), and phosphoinositide kinase 3 (PIK3) pathways, as well as the cell cycle control pathway, have been identified to be disrupted in this tumor. However, emerging data suggest that these aberrations represent only a fraction of the genetic changes involved in gliomagenesis. In this study, we have applied a 32K clone-based genomic array, covering 99% of the current assembly of the human genome, to the detailed genetic profiling of a set of 78 GBs. Complex patterns of aberrations, including high and narrow copy number amplicons, as well as a number of homozygously deleted loci, were identified. Amplicons that varied both in number (three on average) and in size (1.4 Mb on average) were frequently detected (81% of the samples). The loci encompassed not only previously reported oncogenes (EGFR, PDGFRA, MDM2, and CDK4) but also numerous novel oncogenes as GRB10, MKLN1, PPARGC1A, HGF, NAV3, CNTN1, SYT1, and ADAMTSL3. BNC2, PTPLAD2, and PTPRE, on the other hand, represent novel candidate tumor suppressor genes encompassed within homozygously deleted loci. Many of these genes are already linked to several forms of cancer; others represent new candidate genes that may serve as prognostic markers or even as therapeutic targets in the future. The large individual variation observed between the samples demonstrates the underlying complexity of the disease and strengthens the demand for an individualized therapy based on the genetic profile of the patient.
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Affiliation(s)
- Helena Nord
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, SE-75185 Uppsala, Sweden
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Díaz de Ståhl T, Sandgren J, Piotrowski A, Nord H, Andersson R, Menzel U, Bogdan A, Thuresson AC, Poplawski A, von Tell D, Hansson CM, Elshafie AI, Elghazali G, Imreh S, Nordenskjöld M, Upadhyaya M, Komorowski J, Bruder CEG, Dumanski JP. Profiling of copy number variations (CNVs) in healthy individuals from three ethnic groups using a human genome 32 K BAC-clone-based array. Hum Mutat 2008; 29:398-408. [PMID: 18058796 DOI: 10.1002/humu.20659] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Teresita Díaz de Ståhl
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
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Andersson R, Bruder CEG, Piotrowski A, Menzel U, Nord H, Sandgren J, Hvidsten TR, Diaz de Ståhl T, Dumanski JP, Komorowski J. A segmental maximum a posteriori approach to genome-wide copy number profiling. ACTA ACUST UNITED AC 2008; 24:751-8. [PMID: 18204059 DOI: 10.1093/bioinformatics/btn003] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [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
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.
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Affiliation(s)
- Robin Andersson
- The Linnaeus Centre for Bioinformatics, Uppsala University, 751 24 Uppsala, Sweden
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Nord H, Foverskov CE, Nielsen GB, Halvarson H, Nilsson L. The Anodic Dissolution of Iron. II. Passivation of Iron in Neutral Acetic Acid-Sodium Acetate Solutions. ACTA ACUST UNITED AC 1964. [DOI: 10.3891/acta.chem.scand.18-0681] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Lundblad G, Kierkegaard P, Magnéli A, Nielsen GB, Nord H, Jart A. Gel Filtration Chromatography in the Separation of Human Serum. ACTA ACUST UNITED AC 1961. [DOI: 10.3891/acta.chem.scand.15-0212] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Granath KA, Kinell PO, Sparrman B, Nielsen GB, Nord H, Jart A. Structural Changes Induced in Solid Dextran by Irradiation with Gamma Rays. ACTA ACUST UNITED AC 1961. [DOI: 10.3891/acta.chem.scand.15-0141] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Lagercrantz C, Hartmann S, Sparrman B, Nielsen GB, Nord H, Jart A. Formation of Free Radicals from Some Phenothiazine Derivatives as Studied by Electron Spin Resonance. ACTA ACUST UNITED AC 1961. [DOI: 10.3891/acta.chem.scand.15-1545] [Citation(s) in RCA: 32] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Bjellerup L, Virtanen AI, Sparrman B, Nielsen GB, Nord H, Jart A. On the Accuracy of Heat of Combustion Data Obtained with a Precision Moving-Bomb Calorimetric Method for Organic Bromine Compounds. ACTA ACUST UNITED AC 1961. [DOI: 10.3891/acta.chem.scand.15-0121] [Citation(s) in RCA: 49] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Haight, Jr. GP, Frankenberg CV, Sparrman B, Nielsen GB, Nord H, Jart A. The Molybdenum Catalyzed Reduction of Hydroxylamine with Stannous Chloride. ACTA ACUST UNITED AC 1961. [DOI: 10.3891/acta.chem.scand.15-2026] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Kjekshus A, Kierkegaard P, Magnéli A, Nielsen GB, Nord H, Jart A. On the Reaction between Platinum and Sulfur, Selenium, or Tellurium. I. Preparation of PtS, PtSe(0.80), and PtTe. ACTA ACUST UNITED AC 1961. [DOI: 10.3891/acta.chem.scand.15-0159] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Augustinsson KB, Jonsson G, Sparrman B, Nielsen GB, Nord H, Jart A. Effects of Ionizing Radiation on Arylesterase and Cholinesterase. ACTA ACUST UNITED AC 1961. [DOI: 10.3891/acta.chem.scand.15-0011] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Werner PE, Kierkegaard P, Magnéli A, Nielsen GB, Nord H, Jart A. Note on the Thermal Expansion of the Wolfram Bronzes of Potassium, Rubidium and Cesium. ACTA ACUST UNITED AC 1961. [DOI: 10.3891/acta.chem.scand.15-0427] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Bouveng HO, Høeg H, Michelsen K, Nielsen GB, Nord H, Jart A. Phenylisocyanate Derivatives of Carbohydrates. II. Location of the O-Acetyl Groups in Birch Xylan. ACTA ACUST UNITED AC 1961. [DOI: 10.3891/acta.chem.scand.15-0096] [Citation(s) in RCA: 44] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Nilsson M, Høeg H, Michelsen K, Nielsen GB, Nord H, Jart A. Dihydrochalcones from the Fronds of Pityrogramma chrysophylla var. marginata, Domin. ACTA ACUST UNITED AC 1961. [DOI: 10.3891/acta.chem.scand.15-0154] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Honkanen E, Virtanen AI, Sparrman B, Nielsen GB, Nord H, Jart A. On the Reaction of 2,4-Dihydroxy-1,4-benzoxazin-3-one to 2(3)-Benzoxazolinone. ACTA ACUST UNITED AC 1961. [DOI: 10.3891/acta.chem.scand.15-0221] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Baltscheffsky M, Lundquist K, Sparrman B, Nielsen GB, Nord H, Jart A. On Light-Induced Phosphorylation and Oxidation of Reduced Diphosphopyridine Nucleotide in Rhodospirillum rubrum. ACTA ACUST UNITED AC 1961. [DOI: 10.3891/acta.chem.scand.15-0215] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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