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Nielsen, Gunnlaugur

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Nielsen

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Gunnlaugur

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Nielsen, Gunnlaugur
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    Genotyping Cancer-Associated Genes in Chordoma Identifies Mutations in Oncogenes and Areas of Chromosomal Loss Involving CDKN2A, PTEN, and SMARCB1
    (Public Library of Science, 2014) Choy, Edwin; MacConaill, Laura; Cote, Gregory; Le, Long P.; Shen, Jacson K.; Nielsen, Gunnlaugur; Iafrate, Anthony; Garraway, Levi; Hornicek, Francis; Duan, Zhenfeng
    The molecular mechanisms underlying chordoma pathogenesis are unknown. We therefore sought to identify novel mutations to better understand chordoma biology and to potentially identify therapeutic targets. Given the relatively high costs of whole genome sequencing, we performed a focused genetic analysis using matrix-assisted laser desorption/ionization-time of flight mass spectrometer (Sequenom iPLEX genotyping). We tested 865 hotspot mutations in 111 oncogenes and selected tumor suppressor genes (OncoMap v. 3.0) of 45 human chordoma tumor samples. Of the analyzed samples, seven were identified with at least one mutation. Six of these were from fresh frozen samples, and one was from a paraffin embedded sample. These observations were validated using an independent platform using homogeneous mass extend MALDI-TOF (Sequenom hME Genotyping). These genetic alterations include: ALK (A877S), CTNNB1 (T41A), NRAS (Q61R), PIK3CA (E545K), PTEN (R130), CDKN2A (R58*), and SMARCB1 (R40*). This study reports on the largest comprehensive mutational analysis of chordomas performed to date. To focus on mutations that have the greatest chance of clinical relevance, we tested only oncogenes and tumor suppressor genes that have been previously implicated in the tumorigenesis of more common malignancies. We identified rare genetic changes that may have functional significance to the underlying biology and potential therapeutics for chordomas. Mutations in CDKN2A and PTEN occurred in areas of chromosomal copy loss. When this data is paired with the studies showing 18 of 21 chordoma samples displaying copy loss at the locus for CDKN2A, 17 of 21 chordoma samples displaying copy loss at PTEN, and 3 of 4 chordoma samples displaying deletion at the SMARCB1 locus, we can infer that a loss of heterozygosity at these three loci may play a significant role in chordoma pathogenesis.
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    Integrative genomic analyses of neurofibromatosis tumours identify SOX9 as a biomarker and survival gene
    (WILEY-VCH Verlag, 2009) Miller, Shyra J; Jessen, Walter J; Mehta, Tapan; Hardiman, Atira; Sites, Emily; Kaiser, Sergio; Jegga, Anil G; Upadhyaya, Meena; Giovannini, Marco; Wallace, Margaret R; Lopez, Eva; Serra, Eduard; Lazaro, Conxi; Page, Grier; Aronow, Bruce J; Ratner, Nancy; Li, Hua; Muir, David; Nielsen, Gunnlaugur; Stemmer-Rachamimov, Anat
    Understanding the biological pathways critical for common neurofibromatosis type 1 (NF1) peripheral nerve tumours is essential, as there is a lack of tumour biomarkers, prognostic factors and therapeutics. We used gene expression profiling to define transcriptional changes between primary normal Schwann cells (n = 10), NF1-derived primary benign neurofibroma Schwann cells (NFSCs) (n = 22), malignant peripheral nerve sheath tumour (MPNST) cell lines (n = 13), benign neurofibromas (NF) (n = 26) and MPNST (n = 6). Dermal and plexiform NFs were indistinguishable. A prominent theme in the analysis was aberrant differentiation. NFs repressed gene programs normally active in Schwann cell precursors and immature Schwann cells. MPNST signatures strongly differed; genes up-regulated in sarcomas were significantly enriched for genes activated in neural crest cells. We validated the differential expression of 82 genes including the neural crest transcription factor SOX9 and SOX9 predicted targets. SOX9 immunoreactivity was robust in NF and MPSNT tissue sections and targeting SOX9 – strongly expressed in NF1-related tumours – caused MPNST cell death. SOX9 is a biomarker of NF and MPNST, and possibly a therapeutic target in NF1.
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    Recurrent Chromosomal Copy Number Alterations in Sporadic Chordomas
    (Public Library of Science, 2011) Le, Long Phi; Nielsen, Gunnlaugur; Rosenberg, Andrew Eric; Thomas, Dafydd; Batten, Julie M.; Deshpande, Vikram; Schwab, Joseph; Duan, Zhenfeng; Xavier, Ramnik; Hornicek, Francis; Iafrate, Anthony
    The molecular events in chordoma pathogenesis have not been fully delineated, particularly with respect to copy number changes. Understanding copy number alterations in chordoma may reveal critical disease mechanisms that could be exploited for tumor classification and therapy. We report the copy number analysis of 21 sporadic chordomas using array comparative genomic hybridization (CGH). Recurrent copy changes were further evaluated with immunohistochemistry, methylation specific PCR, and quantitative real-time PCR. Similar to previous findings, large copy number losses, involving chromosomes 1p, 3, 4, 9, 10, 13, 14, and 18, were more common than copy number gains. Loss of CDKN2A with or without loss of CDKN2B on 9p21.3 was observed in 16/20 (80%) unique cases of which six (30%) showed homozygous deletions ranging from 76 kilobases to 4.7 megabases. One copy loss of the 10q23.31 region which encodes PTEN was found in 16/20 (80%) cases. Loss of CDKN2A and PTEN expression in the majority of cases was not attributed to promoter methylation. Our sporadic chordoma cases did not show hotspot point mutations in some common cancer gene targets. Moreover, most of these sporadic tumors are not associated with T (brachyury) duplication or amplification. Deficiency of CDKN2A and PTEN expression, although shared across many other different types of tumors, likely represents a key aspect of chordoma pathogenesis. Sporadic chordomas may rely on mechanisms other than copy number gain if they indeed exploit T/ brachyury for proliferation.
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    Intraosseous Synovial Sarcoma of the Proximal Tibia
    (Hindawi Publishing Corporation, 2011) Beck, Sarah E.; Nielsen, Gunnlaugur; Raskin, Kevin; Schwab, Joseph
    Synovial Sarcoma is a malignant mesenchymal tumor that comprises 5–10% of all soft tissue sarcomas. The mean age of onset is thirty years old. Intraosseous presentation is very rare and has only been documented a few times. We report herein a case of a 53-year-old man with synovial sarcoma arising in the left proximal tibia. The patient underwent a wide surgical resection and reconstruction, followed by adjuvant chemotherapy. Three years later, the patient developed a local recurrence that resulted in an above-the-knee amputation. Eight months later, the patient has completed chemotherapy and is without signs of recurrence. The current recommended treatment for synovial sarcoma is wide surgical resection followed by chemotherapy as well as long-term followup. Despite improved surgical techniques, long-term survival rates remain low.